Applied Mathematics Researchhttp://hdl.handle.net/10023/962018-03-24T04:06:18Z2018-03-24T04:06:18ZModelling the effects of bacterial cell state and spatial location on tuberculosis treatment : insights from a hybrid multiscale cellular automaton modelBowness, RuthChaplain, Mark A.J.Powathil, Gibin G.Gillespie, Stephen H.http://hdl.handle.net/10023/129832018-03-24T02:30:12Z2018-06-07T00:00:00ZIf improvements are to be made in tuberculosis (TB) treatment, an increased understanding of disease in the lung is needed. Studies have shown that bacteria in a less metabolically active state, associated with the presence of lipid bodies, are less susceptible to antibiotics, and recent results have highlighted the disparity in concentration of different compounds into lesions. Treatment success therefore depends critically on the responses of the individual bacteria that constitute the infection. We propose a hybrid, individual-based approach that analyses spatio-temporal dynamics at the cellular level, linking the behaviour of individual bacteria and host cells with the macroscopic behaviour of the microenvironment. The individual elements (bacteria, macrophages and T cells) are modelled using cellular automaton (CA) rules, and the evolution of oxygen, drugs and chemokine dynamics are incorporated in order to study the effects of the microenvironment in the pathological lesion. We allow bacteria to switch states depending on oxygen concentration, which affects how they respond to treatment. This is the first multiscale model of its type to consider both oxygen-driven phenotypic switching of the Mycobacterium tuberculosis and antibiotic treatment. Using this model, we investigate the role of bacterial cell state and of initial bacterial location on treatment outcome. We demonstrate that when bacteria are located further away from blood vessels, less favourable outcomes are more likely, i.e. longer time before infection is contained/cleared, treatment failure or later relapse. We also show that in cases where bacteria remain at the end of simulations, the organisms tend to be slower-growing and are often located within granulomas, surrounded by caseous material.
This work was supported by the Medical Research Council [grant number MR/P014704/1] and the PreDiCT-TB consortium (IMI Joint undertaking grant agreement number 115337, resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013) and EFPIA companies’ in kind contribution.
2018-06-07T00:00:00ZBowness, RuthChaplain, Mark A.J.Powathil, Gibin G.Gillespie, Stephen H.If improvements are to be made in tuberculosis (TB) treatment, an increased understanding of disease in the lung is needed. Studies have shown that bacteria in a less metabolically active state, associated with the presence of lipid bodies, are less susceptible to antibiotics, and recent results have highlighted the disparity in concentration of different compounds into lesions. Treatment success therefore depends critically on the responses of the individual bacteria that constitute the infection. We propose a hybrid, individual-based approach that analyses spatio-temporal dynamics at the cellular level, linking the behaviour of individual bacteria and host cells with the macroscopic behaviour of the microenvironment. The individual elements (bacteria, macrophages and T cells) are modelled using cellular automaton (CA) rules, and the evolution of oxygen, drugs and chemokine dynamics are incorporated in order to study the effects of the microenvironment in the pathological lesion. We allow bacteria to switch states depending on oxygen concentration, which affects how they respond to treatment. This is the first multiscale model of its type to consider both oxygen-driven phenotypic switching of the Mycobacterium tuberculosis and antibiotic treatment. Using this model, we investigate the role of bacterial cell state and of initial bacterial location on treatment outcome. We demonstrate that when bacteria are located further away from blood vessels, less favourable outcomes are more likely, i.e. longer time before infection is contained/cleared, treatment failure or later relapse. We also show that in cases where bacteria remain at the end of simulations, the organisms tend to be slower-growing and are often located within granulomas, surrounded by caseous material.Photospheric observations of surface and body modes in solar magnetic poresKeys, Peter H.Morton, Richard J.Jess, David B.Verth, GaryGrant, Samuel D.T.Mathioudakis, MihalisMackay, Duncan HendryDoyle, John G.Christian, Damian J.Keenan, Francis P.Erdélyi, Robertushttp://hdl.handle.net/10023/129012018-03-13T00:16:25Z2018-03-05T00:00:00ZOver the past number of years, great strides have been made in identifying the various low-order magnetohydrodynamic wave modes observable in a number of magnetic structures found within the solar atmosphere. However, one aspect of these modes that has remained elusive, until now, is their designation as either surface or body modes. This property has significant implications on how these modes transfer energy from the waveguide to the surrounding plasma. Here, for the first time to our knowledge, we present conclusive, direct evidence of these wave characteristics in numerous pores which were observed to support sausage modes. As well as outlining methods to detect these modes in observations, we make estimates of the energies associated with each mode. We find surface modes more frequently in the data, and also that surface modes appear to carry more energy than those displaying signatures of body modes. We find frequencies in the range of ~2 to 12 mHz with body modes as high as 11 mHz, but we do not find surface modes above 10 mHz. It is expected that the techniques we have applied will help researchers search for surface and body signatures in other modes and in differing structures to those presented here.
2018-03-05T00:00:00ZKeys, Peter H.Morton, Richard J.Jess, David B.Verth, GaryGrant, Samuel D.T.Mathioudakis, MihalisMackay, Duncan HendryDoyle, John G.Christian, Damian J.Keenan, Francis P.Erdélyi, RobertusOver the past number of years, great strides have been made in identifying the various low-order magnetohydrodynamic wave modes observable in a number of magnetic structures found within the solar atmosphere. However, one aspect of these modes that has remained elusive, until now, is their designation as either surface or body modes. This property has significant implications on how these modes transfer energy from the waveguide to the surrounding plasma. Here, for the first time to our knowledge, we present conclusive, direct evidence of these wave characteristics in numerous pores which were observed to support sausage modes. As well as outlining methods to detect these modes in observations, we make estimates of the energies associated with each mode. We find surface modes more frequently in the data, and also that surface modes appear to carry more energy than those displaying signatures of body modes. We find frequencies in the range of ~2 to 12 mHz with body modes as high as 11 mHz, but we do not find surface modes above 10 mHz. It is expected that the techniques we have applied will help researchers search for surface and body signatures in other modes and in differing structures to those presented here.Transverse Wave Induced Kelvin-Helmholtz rolls in spiculesAntolin, PatrickSchmit, DonPereira, Tiago M. D.De Pontieu, BartDe Moortel, Inekehttp://hdl.handle.net/10023/128802018-03-11T00:33:38Z2018-03-01T00:00:00ZIn addition to their jet-like dynamic behaviour, spicules usually exhibit strong transverse speeds, multi-stranded structure and heating from chromospheric to transition region temperatures. In this work we first analyse Hinode & IRIS observations of spicules and find different behaviours in terms of their Doppler velocity evolution and collective motion of their sub-structure. Somehave a Doppler shift sign change that is rather fixed along the spicule axis, and lack coherence in the oscillatory motion of strand-like structure, matching rotation models or long wavelength torsional Alfvén waves. Others exhibit a Doppler shift sign change at maximum displacement and coherent motion of their strands, suggesting acollective MHD wave. By comparing with an idealised 3-D MHD simulation combined with radiative transfer modelling, we analyse the role of transverse MHD waves and associated instabilities in spicule-like features. We find that Transverse Wave Induced Kelvin-Helmholtz (TWIKH) rolls lead to coherence of strand-like structure in imaging and spectral maps, as seen in some observations. The rapid transverse dynamics and the density and temperature gradients at the spicule boundary lead toring-shaped Mg II k and Ca II H source functions in the transverse cross-section, potentially allowing IRIS to capture the KHI dynamics. Twists and currents propagate along the spicule at Alfvénic speeds, and the temperature variations within TWIKH rolls produce sudden appearance / disappearance of strands seen in Doppler velocity and in Ca II H intensity. However, only a mild intensity increase in higher temperature lines is obtained, suggesting there is an additional heating mechanism at work in spicules.
This research has received funding from the UK Science and Technology Facilities Council (Consolidated Grant ST/K000950/1) and the European Union Horizon 2020 research and innovation programme (grant agreement No. 647214).
2018-03-01T00:00:00ZAntolin, PatrickSchmit, DonPereira, Tiago M. D.De Pontieu, BartDe Moortel, InekeIn addition to their jet-like dynamic behaviour, spicules usually exhibit strong transverse speeds, multi-stranded structure and heating from chromospheric to transition region temperatures. In this work we first analyse Hinode & IRIS observations of spicules and find different behaviours in terms of their Doppler velocity evolution and collective motion of their sub-structure. Somehave a Doppler shift sign change that is rather fixed along the spicule axis, and lack coherence in the oscillatory motion of strand-like structure, matching rotation models or long wavelength torsional Alfvén waves. Others exhibit a Doppler shift sign change at maximum displacement and coherent motion of their strands, suggesting acollective MHD wave. By comparing with an idealised 3-D MHD simulation combined with radiative transfer modelling, we analyse the role of transverse MHD waves and associated instabilities in spicule-like features. We find that Transverse Wave Induced Kelvin-Helmholtz (TWIKH) rolls lead to coherence of strand-like structure in imaging and spectral maps, as seen in some observations. The rapid transverse dynamics and the density and temperature gradients at the spicule boundary lead toring-shaped Mg II k and Ca II H source functions in the transverse cross-section, potentially allowing IRIS to capture the KHI dynamics. Twists and currents propagate along the spicule at Alfvénic speeds, and the temperature variations within TWIKH rolls produce sudden appearance / disappearance of strands seen in Doppler velocity and in Ca II H intensity. However, only a mild intensity increase in higher temperature lines is obtained, suggesting there is an additional heating mechanism at work in spicules.Examining the role of individual movement in promoting coexistence in a spatially explicit prisoner's dilemmaBurgess, Andrew E. F.Lorenzi, TommasoSchofield, Pietà G.Hubbard, Stephen F.Chaplain, Mark A. J.http://hdl.handle.net/10023/128132018-03-01T00:15:25Z2017-04-21T00:00:00ZThe emergence of cooperation is a major conundrum of evolutionary biology. To unravel this evolutionary riddle, several models have been developed within the theoretical framework of spatial game theory, focussing on the interactions between two general classes of player, "cooperators" and "defectors". Generally, explicit movement in the spatial domain is not considered in these models, with strategies moving via imitation or through colonisation of neighbouring sites. We present here a spatially explicit stochastic individual-based model in which pure cooperators and defectors undergo random motion via diffusion and also chemotaxis guided by the gradient of a semiochemical. Individual movement rules are derived from an underlying system of reaction-diffusion-taxis partial differential equations which describes the dynamics of the local number of individuals and the concentration of the semiochemical. Local interactions are governed by the payoff matrix of the classical prisoner's dilemma, and accumulated payoffs are translated into offspring. We investigate the cases of both synchronous and non-synchronous generations. Focussing on an ecological scenario where defectors are parasitic on cooperators, we find that random motion and semiochemical sensing bring about self-generated patterns in which resident cooperators and parasitic defectors can coexist in proportions that fluctuate about non-zero values. Remarkably, coexistence emerges as a genuine consequence of the natural tendency of cooperators to aggregate into clusters, without the need for them to find physical shelter or outrun the parasitic defectors. This provides further evidence that spatial clustering enhances the benefits of mutual cooperation and plays a crucial role in preserving cooperative behaviours.
AEFB gratefully acknowledges the support of an EPSRC CASE PhD studentship.
2017-04-21T00:00:00ZBurgess, Andrew E. F.Lorenzi, TommasoSchofield, Pietà G.Hubbard, Stephen F.Chaplain, Mark A. J.The emergence of cooperation is a major conundrum of evolutionary biology. To unravel this evolutionary riddle, several models have been developed within the theoretical framework of spatial game theory, focussing on the interactions between two general classes of player, "cooperators" and "defectors". Generally, explicit movement in the spatial domain is not considered in these models, with strategies moving via imitation or through colonisation of neighbouring sites. We present here a spatially explicit stochastic individual-based model in which pure cooperators and defectors undergo random motion via diffusion and also chemotaxis guided by the gradient of a semiochemical. Individual movement rules are derived from an underlying system of reaction-diffusion-taxis partial differential equations which describes the dynamics of the local number of individuals and the concentration of the semiochemical. Local interactions are governed by the payoff matrix of the classical prisoner's dilemma, and accumulated payoffs are translated into offspring. We investigate the cases of both synchronous and non-synchronous generations. Focussing on an ecological scenario where defectors are parasitic on cooperators, we find that random motion and semiochemical sensing bring about self-generated patterns in which resident cooperators and parasitic defectors can coexist in proportions that fluctuate about non-zero values. Remarkably, coexistence emerges as a genuine consequence of the natural tendency of cooperators to aggregate into clusters, without the need for them to find physical shelter or outrun the parasitic defectors. This provides further evidence that spatial clustering enhances the benefits of mutual cooperation and plays a crucial role in preserving cooperative behaviours.The coronal monsoon : thermal nonequilibrium revealed by periodic coronal rainAuchère, FrédéricFroment, ClaraSoubrié, ElieAntolin, PatrickOliver, RamonPelouze, Gabrielhttp://hdl.handle.net/10023/127612018-02-25T01:33:25Z2018-02-05T00:00:00ZWe report on the discovery of periodic coronal rain in an off-limb sequence of Solar Dynamics Observatory/Atmospheric Imaging Assembly images. The showers are co-spatial and in phase with periodic (6.6 hr) intensity pulsations of coronal loops of the sort described by Auchère et al. and Froment et al. These new observations make possible a unified description of both phenomena. Coronal rain and periodic intensity pulsations of loops are two manifestations of the same physical process: evaporation/condensation cycles resulting from a state of thermal nonequilibrium. The fluctuations around coronal temperatures produce the intensity pulsations of loops, and rain falls along their legs if thermal runaway cools the periodic condensations down and below transition-region temperatures. This scenario is in line with the predictions of numerical models of quasi-steadily and footpoint heated loops. The presence of coronal rain—albeit non-periodic—in several other structures within the studied field of view implies that this type of heating is at play on a large scale.
P.A. has received funding from the UK Science and Technology Facilities Council (Consolidated Grant ST/K000950/1) and the European Union Horizon 2020 research and innovation programme (grant agreement No. 647214).
2018-02-05T00:00:00ZAuchère, FrédéricFroment, ClaraSoubrié, ElieAntolin, PatrickOliver, RamonPelouze, GabrielWe report on the discovery of periodic coronal rain in an off-limb sequence of Solar Dynamics Observatory/Atmospheric Imaging Assembly images. The showers are co-spatial and in phase with periodic (6.6 hr) intensity pulsations of coronal loops of the sort described by Auchère et al. and Froment et al. These new observations make possible a unified description of both phenomena. Coronal rain and periodic intensity pulsations of loops are two manifestations of the same physical process: evaporation/condensation cycles resulting from a state of thermal nonequilibrium. The fluctuations around coronal temperatures produce the intensity pulsations of loops, and rain falls along their legs if thermal runaway cools the periodic condensations down and below transition-region temperatures. This scenario is in line with the predictions of numerical models of quasi-steadily and footpoint heated loops. The presence of coronal rain—albeit non-periodic—in several other structures within the studied field of view implies that this type of heating is at play on a large scale.A multiscale mathematical model of tumour invasive growthPeng, LuTrucu, DumitruLin, PingThompson, AlastairChaplain, Mark A. J.http://hdl.handle.net/10023/127392018-02-18T00:16:15Z2017-03-01T00:00:00ZKnown as one of the hallmarks of cancer (Hanahan and Weinberg in Cell 100:57–70, 2000) cancer cell invasion of human body tissue is a complicated spatio-temporal multiscale process which enables a localised solid tumour to transform into a systemic, metastatic and fatal disease. This process explores and takes advantage of the reciprocal relation that solid tumours establish with the extracellular matrix (ECM) components and other multiple distinct cell types from the surrounding microenvironment. Through the secretion of various proteolytic enzymes such as matrix metalloproteinases or the urokinase plasminogen activator (uPA), the cancer cell population alters the configuration of the surrounding ECM composition and overcomes the physical barriers to ultimately achieve local cancer spread into the surrounding tissue. The active interplay between the tissue-scale tumour dynamics and the molecular mechanics of the involved proteolytic enzymes at the cell scale underlines the biologically multiscale character of invasion and raises the challenge of modelling this process with an appropriate multiscale approach. In this paper, we present a new two-scale moving boundary model of cancer invasion that explores the tissue-scale tumour dynamics in conjunction with the molecular dynamics of the urokinase plasminogen activation system. Building on the multiscale moving boundary method proposed in Trucu et al. (Multiscale Model Simul 11(1):309–335, 2013), the modelling that we propose here allows us to study the changes in tissue-scale tumour morphology caused by the cell-scale uPA microdynamics occurring along the invasive edge of the tumour. Our computational simulation results demonstrate a range of heterogeneous dynamics which are qualitatively similar to the invasive growth patterns observed in a number of different types of cancer, such as the tumour infiltrative growth patterns discussed in Ito et al. (J Gastroenterol 47:1279–1289, 2012).
2017-03-01T00:00:00ZPeng, LuTrucu, DumitruLin, PingThompson, AlastairChaplain, Mark A. J.Known as one of the hallmarks of cancer (Hanahan and Weinberg in Cell 100:57–70, 2000) cancer cell invasion of human body tissue is a complicated spatio-temporal multiscale process which enables a localised solid tumour to transform into a systemic, metastatic and fatal disease. This process explores and takes advantage of the reciprocal relation that solid tumours establish with the extracellular matrix (ECM) components and other multiple distinct cell types from the surrounding microenvironment. Through the secretion of various proteolytic enzymes such as matrix metalloproteinases or the urokinase plasminogen activator (uPA), the cancer cell population alters the configuration of the surrounding ECM composition and overcomes the physical barriers to ultimately achieve local cancer spread into the surrounding tissue. The active interplay between the tissue-scale tumour dynamics and the molecular mechanics of the involved proteolytic enzymes at the cell scale underlines the biologically multiscale character of invasion and raises the challenge of modelling this process with an appropriate multiscale approach. In this paper, we present a new two-scale moving boundary model of cancer invasion that explores the tissue-scale tumour dynamics in conjunction with the molecular dynamics of the urokinase plasminogen activation system. Building on the multiscale moving boundary method proposed in Trucu et al. (Multiscale Model Simul 11(1):309–335, 2013), the modelling that we propose here allows us to study the changes in tissue-scale tumour morphology caused by the cell-scale uPA microdynamics occurring along the invasive edge of the tumour. Our computational simulation results demonstrate a range of heterogeneous dynamics which are qualitatively similar to the invasive growth patterns observed in a number of different types of cancer, such as the tumour infiltrative growth patterns discussed in Ito et al. (J Gastroenterol 47:1279–1289, 2012).Penalized nonparametric scalar-on-function regression via principal coordinatesReiss, Philip T.Miller, David L.Wu, Pei ShienHua, Wen Yuhttp://hdl.handle.net/10023/126632018-02-04T00:16:01Z2017-01-01T00:00:00ZA number of classical approaches to nonparametric regression have recently been extended to the case of functional predictors. This article introduces a new method of this type, which extends intermediate-rank penalized smoothing to scalar-on-function regression. In the proposed method, which we call principal coordinate ridge regression, one regresses the response on leading principal coordinates defined by a relevant distance among the functional predictors, while applying a ridge penalty. Our publicly available implementation, based on generalized additive modeling software, allows for fast optimal tuning parameter selection and for extensions to multiple functional predictors, exponential family-valued responses, and mixed-effects models. In an application to signature verification data, principal coordinate ridge regression, with dynamic time warping distance used to define the principal coordinates, is shown to outperform a functional generalized linear model. Supplementary materials for this article are available online.
Philip Reiss, Pei-Shien Wu, and Wen-Yu Hua gratefully acknowledge the support of the U.S. National Institute of Mental Health (grant 1R01MH095836-01A1).
2017-01-01T00:00:00ZReiss, Philip T.Miller, David L.Wu, Pei ShienHua, Wen YuA number of classical approaches to nonparametric regression have recently been extended to the case of functional predictors. This article introduces a new method of this type, which extends intermediate-rank penalized smoothing to scalar-on-function regression. In the proposed method, which we call principal coordinate ridge regression, one regresses the response on leading principal coordinates defined by a relevant distance among the functional predictors, while applying a ridge penalty. Our publicly available implementation, based on generalized additive modeling software, allows for fast optimal tuning parameter selection and for extensions to multiple functional predictors, exponential family-valued responses, and mixed-effects models. In an application to signature verification data, principal coordinate ridge regression, with dynamic time warping distance used to define the principal coordinates, is shown to outperform a functional generalized linear model. Supplementary materials for this article are available online.Module theory : an approach to linear algebraBlyth, Thomas Scotthttp://hdl.handle.net/10023/126432018-02-11T00:33:00Z2018-01-01T00:00:00ZOriginally published in 1977 by Oxford University Press, with a second edition published in 1990. This is a revised version of the second edition published for the first time in electronic form. This electronic edition is published by the University of St Andrews.
2018-01-01T00:00:00ZBlyth, Thomas ScottFlare particle acceleration in the interaction of twisted coronal flux ropesThrelfall, J.Hood, A. W.Browning, P. K.http://hdl.handle.net/10023/126272018-01-30T00:16:22Z2017-12-22T00:00:00ZAims. The aim of this work is to investigate and characterise non-thermal particle behaviour in a three-dimensional (3D) magnetohydrodynamical (MHD) model of unstable multi-threaded flaring coronal loops. Methods. We have used a numerical scheme which solves the relativistic guiding centre approximation to study the motion of electrons and protons. The scheme uses snapshots from high resolution numerical MHD simulations of coronal loops containing two threads, where a single thread becomes unstable and (in one case) destabilises and merges with an additional thread. Results. The particle responses to the reconnection and fragmentation in MHD simulations of two loop threads are examined in detail. We illustrate the role played by uniform background resistivity and distinguish this from the role of anomalous resistivity using orbits in an MHD simulation where only one thread becomes unstable without destabilising further loop threads. We examine the (scalable) orbit energy gains and final positions recovered at different stages of a second MHD simulation wherein a secondary loop thread is destabilised by (and merges with) the first thread. We compare these results with other theoretical particle acceleration models in the context of observed energetic particle populations during solar flares.
The authors gratefully acknowledge the support of the U.K. Science and Technology Facilities Council. JT and AWH acknowledge the financial support of STFC through the Consolidated grant, ST/N000609/1, to the University of St Andrews. PKB acknowledges STFC support through ST/P000428/1 at the University of Manchester.
2017-12-22T00:00:00ZThrelfall, J.Hood, A. W.Browning, P. K.Aims. The aim of this work is to investigate and characterise non-thermal particle behaviour in a three-dimensional (3D) magnetohydrodynamical (MHD) model of unstable multi-threaded flaring coronal loops. Methods. We have used a numerical scheme which solves the relativistic guiding centre approximation to study the motion of electrons and protons. The scheme uses snapshots from high resolution numerical MHD simulations of coronal loops containing two threads, where a single thread becomes unstable and (in one case) destabilises and merges with an additional thread. Results. The particle responses to the reconnection and fragmentation in MHD simulations of two loop threads are examined in detail. We illustrate the role played by uniform background resistivity and distinguish this from the role of anomalous resistivity using orbits in an MHD simulation where only one thread becomes unstable without destabilising further loop threads. We examine the (scalable) orbit energy gains and final positions recovered at different stages of a second MHD simulation wherein a secondary loop thread is destabilised by (and merges with) the first thread. We compare these results with other theoretical particle acceleration models in the context of observed energetic particle populations during solar flares.Aggregation and travelling wave dynamics in a two-population model of cancer cell growth and invasionBitsouni, VasilikiTrucu, DumitruChaplain, Mark Andrew JosephEftimie, Ralucahttp://hdl.handle.net/10023/125952018-01-24T11:30:08Z2018-01-15T00:00:00ZCells adhere to each other and to the extracellular matrix (ECM) through protein molecules on the surface of the cells. The breaking and forming of adhesive bonds, a process critical in cancer invasion and metas- tasis, can be influenced by the mutation of cancer cells. In this paper, we develop a nonlocal mathematical model describing cancer cell invasion and movement as a result of integrin-controlled cell-cell adhesion and cell-matrix adhesion, for two cancer cell populations with different levels of mutation. The partial differential equations for cell dynamics are coupled with ordinary differential equations describing the extracellular matrix (ECM) degradation and the production and decay of integrins. We use this model to investigate the role of cancer mutation on the possibility of cancer clonal competition with alternating dominance, or even competitive exclusion (phenomena observed experimentally). We discuss different possible cell aggregation patterns, as well as travelling wave patterns. In regard to the travelling waves, we investigate the effect of cancer mutation rate on the speed of cancer invasion.
Funding: Engineering and Physical Sciences Research Council (UK) grant numbers EP/L504932/1 (VB), EP/K033689/1 (RE).
2018-01-15T00:00:00ZBitsouni, VasilikiTrucu, DumitruChaplain, Mark Andrew JosephEftimie, RalucaCells adhere to each other and to the extracellular matrix (ECM) through protein molecules on the surface of the cells. The breaking and forming of adhesive bonds, a process critical in cancer invasion and metas- tasis, can be influenced by the mutation of cancer cells. In this paper, we develop a nonlocal mathematical model describing cancer cell invasion and movement as a result of integrin-controlled cell-cell adhesion and cell-matrix adhesion, for two cancer cell populations with different levels of mutation. The partial differential equations for cell dynamics are coupled with ordinary differential equations describing the extracellular matrix (ECM) degradation and the production and decay of integrins. We use this model to investigate the role of cancer mutation on the possibility of cancer clonal competition with alternating dominance, or even competitive exclusion (phenomena observed experimentally). We discuss different possible cell aggregation patterns, as well as travelling wave patterns. In regard to the travelling waves, we investigate the effect of cancer mutation rate on the speed of cancer invasion.Combining radiation with hyperthermia : a multiscale model informed by in vitro experimentsBrüningk, SarahPowathil, GibinZiegenhein, PeterIjaz, JannatRivens, IanNill, S.Chaplain, Mark Andrew JosephOelfke, Uweter Haar, Gailhttp://hdl.handle.net/10023/125902018-02-18T00:33:12Z2018-01-01T00:00:00ZCombined radiotherapy and hyperthermia offer great potential for the successful treatment of radio-resistant tumours through thermo-radiosensitization. Tumour response heterogeneity, due to intrinsic, or micro-environmentally induced factors, may greatly influence treatment outcome, but is difficult to account for using traditional treatment planning approaches. Systems oncology simulation, using mathematical models designed to predict tumour growth and treatment response, provides a powerful tool for analysis and optimization of combined treatments. We present a framework that simulates such combination treatments on a cellular level. This multiscale hybrid cellular automaton simulates large cell populations (up to 107 cells) in vitro, while allowing individual cell-cycle progression, and treatment response by modelling radiation-induced mitotic cell death, and immediate cell kill in response to heating. Based on a calibration using a number of experimental growth, cell cycle and survival datasets for HCT116 cells, model predictions agreed well (R2 > 0.95) with experimental data within the range of (thermal and radiation) doses tested (0–40 CEM43, 0–5 Gy). The proposed framework offers flexibility for modelling multimodality treatment combinations in different scenarios. It may therefore provide an important step towards the modelling of personalized therapies using a virtual patient tumour.
Funding: Cancer Research UK. Research at The Institute of Cancer Research is supported by Cancer Research UK under Programme C33589/A19727. Peter Ziegenhein is supported by Cancer Research UK under Programme C33589/A19908.
2018-01-01T00:00:00ZBrüningk, SarahPowathil, GibinZiegenhein, PeterIjaz, JannatRivens, IanNill, S.Chaplain, Mark Andrew JosephOelfke, Uweter Haar, GailCombined radiotherapy and hyperthermia offer great potential for the successful treatment of radio-resistant tumours through thermo-radiosensitization. Tumour response heterogeneity, due to intrinsic, or micro-environmentally induced factors, may greatly influence treatment outcome, but is difficult to account for using traditional treatment planning approaches. Systems oncology simulation, using mathematical models designed to predict tumour growth and treatment response, provides a powerful tool for analysis and optimization of combined treatments. We present a framework that simulates such combination treatments on a cellular level. This multiscale hybrid cellular automaton simulates large cell populations (up to 107 cells) in vitro, while allowing individual cell-cycle progression, and treatment response by modelling radiation-induced mitotic cell death, and immediate cell kill in response to heating. Based on a calibration using a number of experimental growth, cell cycle and survival datasets for HCT116 cells, model predictions agreed well (R2 > 0.95) with experimental data within the range of (thermal and radiation) doses tested (0–40 CEM43, 0–5 Gy). The proposed framework offers flexibility for modelling multimodality treatment combinations in different scenarios. It may therefore provide an important step towards the modelling of personalized therapies using a virtual patient tumour.Quiescent prominences in the era of ALMA. II. Kinetic temperature diagnosticsGunár, StanislavHeinzel, PetrAnzer, UlrichMackay, Duncan Hendryhttp://hdl.handle.net/10023/125572018-02-25T01:33:21Z2018-01-20T00:00:00ZWe provide the theoretical background for diagnostics of the thermal properties of solar prominences observed by the Atacama Large Millimeter/submillimeter Array (ALMA). To do this, we employ the 3D Whole-Prominence Fine Structure (WPFS) model that produces synthetic ALMA-like observations of a complex simulated prominence. We use synthetic observations derived at two different submillimeter/millimeter (SMM) wavelengths—one at a wavelength at which the simulated prominence is completely optically thin and another at a wavelength at which a significant portion of the simulated prominence is optically thick—as if these were the actual ALMA observations. This allows us to develop a technique for an analysis of the prominence plasma thermal properties from such a pair of simultaneous high-resolution ALMA observations. The 3D WPFS model also provides detailed information about the distribution of the kinetic temperature and the optical thickness along any line of sight. We can thus assess whether the measure of the kinetic temperature derived from observations accurately represents the actual kinetic temperature properties of the observed plasma. We demonstrate here that in a given pixel the optical thickness at the wavelength at which the prominence plasma is optically thick needs to be above unity or even larger to achieve a sufficient accuracy of the derived information about the kinetic temperature of the analyzed plasma. Information about the optical thickness cannot be directly discerned from observations at the SMM wavelengths alone. However, we show that a criterion that can identify those pixels in which the derived kinetic temperature values correspond well to the actual thermal properties in which the observed prominence can be established.
Funding: UK STFC, the Leverhulme Trust, and NASA (D.H.M.)
2018-01-20T00:00:00ZGunár, StanislavHeinzel, PetrAnzer, UlrichMackay, Duncan HendryWe provide the theoretical background for diagnostics of the thermal properties of solar prominences observed by the Atacama Large Millimeter/submillimeter Array (ALMA). To do this, we employ the 3D Whole-Prominence Fine Structure (WPFS) model that produces synthetic ALMA-like observations of a complex simulated prominence. We use synthetic observations derived at two different submillimeter/millimeter (SMM) wavelengths—one at a wavelength at which the simulated prominence is completely optically thin and another at a wavelength at which a significant portion of the simulated prominence is optically thick—as if these were the actual ALMA observations. This allows us to develop a technique for an analysis of the prominence plasma thermal properties from such a pair of simultaneous high-resolution ALMA observations. The 3D WPFS model also provides detailed information about the distribution of the kinetic temperature and the optical thickness along any line of sight. We can thus assess whether the measure of the kinetic temperature derived from observations accurately represents the actual kinetic temperature properties of the observed plasma. We demonstrate here that in a given pixel the optical thickness at the wavelength at which the prominence plasma is optically thick needs to be above unity or even larger to achieve a sufficient accuracy of the derived information about the kinetic temperature of the analyzed plasma. Information about the optical thickness cannot be directly discerned from observations at the SMM wavelengths alone. However, we show that a criterion that can identify those pixels in which the derived kinetic temperature values correspond well to the actual thermal properties in which the observed prominence can be established.Comparison of methods for modelling coronal magnetic fieldsGoldstraw, E. E.Hood, A. W.Browning, P. K.Cargill, P. J.http://hdl.handle.net/10023/124382018-03-20T15:30:05Z2018-02-26T00:00:00ZAims. Four different approximate approaches used to model the stressing of coronal magnetic fields due to an imposed photospheric motion are compared with each other and the results from a full time-dependent magnetohydrodynamic (MHD) code. The assumptions used for each of the approximate methods are tested by considering large photospheric footpoint displacements. Methods. We consider a simple model problem, comparing the full nonlinear magnetohydrodynamic evolution, determined with the Lare2D numerical code, with four approximate approaches. Two of these,magneto-frictional relaxation and a quasi-1D Grad-Shafranov approach, assume sequences of equilibria, whilst the other two methods, a second-order linearisation of the MHD equations and Reduced MHD, are time-dependent. Results. The relaxation method is very accurate compared to full MHD for force-free equilibria for all footpoint displacements but has significant errors when the plasma β0 is of order unity. The 1D approach gives an extremely accurate description of the equilibria away from the photospheric boundary layers, and agrees well with Lare2D for all parameter values tested. The linearised MHD equations correctly predict the existence of photospheric boundary layers that are present in the full MHD results. As soon as the footpoint displacement becomes a significant fraction of the loop length, the RMHD method fails to model the sequences of equilibria correctly. The full numerical solution is interesting in its own right, and care must be taken for low β0 plasmas if the viscosity is too high.
Funding: STFC through the Consolidated grant ST/N000609/1 (AWH); STFC studentship, ST/I505999/1 (EEG).
2018-02-26T00:00:00ZGoldstraw, E. E.Hood, A. W.Browning, P. K.Cargill, P. J.Aims. Four different approximate approaches used to model the stressing of coronal magnetic fields due to an imposed photospheric motion are compared with each other and the results from a full time-dependent magnetohydrodynamic (MHD) code. The assumptions used for each of the approximate methods are tested by considering large photospheric footpoint displacements. Methods. We consider a simple model problem, comparing the full nonlinear magnetohydrodynamic evolution, determined with the Lare2D numerical code, with four approximate approaches. Two of these,magneto-frictional relaxation and a quasi-1D Grad-Shafranov approach, assume sequences of equilibria, whilst the other two methods, a second-order linearisation of the MHD equations and Reduced MHD, are time-dependent. Results. The relaxation method is very accurate compared to full MHD for force-free equilibria for all footpoint displacements but has significant errors when the plasma β0 is of order unity. The 1D approach gives an extremely accurate description of the equilibria away from the photospheric boundary layers, and agrees well with Lare2D for all parameter values tested. The linearised MHD equations correctly predict the existence of photospheric boundary layers that are present in the full MHD results. As soon as the footpoint displacement becomes a significant fraction of the loop length, the RMHD method fails to model the sequences of equilibria correctly. The full numerical solution is interesting in its own right, and care must be taken for low β0 plasmas if the viscosity is too high.Piecewise uniform potential vorticity pancake shielded vorticesReinaud, Jean Noelhttp://hdl.handle.net/10023/124192018-01-07T03:54:15Z2017-01-01T00:00:00ZShielded vortices consist of a core of potential vorticity of a given sign surrounded (or shielded) by a layer of opposite-signed potential vorticity. Such vortices have specific properties and have been the focus of numerous studies, first in two dimensional geometries (where potential vorticity is just the vertical component of the vorticity vector) and in geophysical applications (mostly in layered models). The present paper focuses on three-dimensional, spheroidal shielded vortices. In particular, we focus on vortical structures whose overall volume-integrated potential vorticity is zero. We restrict attention to vortices of piecewise uniform potential vorticity in the present research. We first revisit the problem within the quasi-geostrophic model, then we extend the results to the non-hydrostatic regime. We show that the stability of the structure depends on the ratio of potential vorticity between the inner core and the outer shield. In particular it depends on the polarity of the core and of the wavenumber of the azimuthal mode perturbed.
2017-01-01T00:00:00ZReinaud, Jean NoelShielded vortices consist of a core of potential vorticity of a given sign surrounded (or shielded) by a layer of opposite-signed potential vorticity. Such vortices have specific properties and have been the focus of numerous studies, first in two dimensional geometries (where potential vorticity is just the vertical component of the vorticity vector) and in geophysical applications (mostly in layered models). The present paper focuses on three-dimensional, spheroidal shielded vortices. In particular, we focus on vortical structures whose overall volume-integrated potential vorticity is zero. We restrict attention to vortices of piecewise uniform potential vorticity in the present research. We first revisit the problem within the quasi-geostrophic model, then we extend the results to the non-hydrostatic regime. We show that the stability of the structure depends on the ratio of potential vorticity between the inner core and the outer shield. In particular it depends on the polarity of the core and of the wavenumber of the azimuthal mode perturbed.JPEG2000 image compression on solar EUV imagesFischer, CatherineMueller, DanielDe Moortel, Inekehttp://hdl.handle.net/10023/123672018-01-07T03:53:09Z2017-01-01T00:00:00ZFor future solar missions as well as ground-based telescopes, efficient ways to return and process data has become increasingly important. Solar Or-biter, e.g., the next ESA/NASA mission to explore the Sun and the heliosphere,is a deep-space mission, which implies a limited telemetry rate that makes efficient onboard data compression a necessity to achieve the mission science goals.Missions like the Solar Dynamics Observatory (SDO) and future ground-based telescopes such as the Daniel K. Inouye Solar Telescope, on the other hand,face the challenge of making petabyte-sized solar data archives accessible to the solar community. New image compression standards address these challenges by implementing efficient and flexible compression algorithms that can be tailored to user requirements. We analyse solar images from the Atmospheric Imaging Assembly (AIA) instrument onboard SDO to study the effect of lossy JPEG2000(from the Joint Photographic Experts Group 2000) image compression at different bit rates. To assess the quality of compressed images, we use the mean structural similarity (MSSIM) index as well as the widely used peak signal-to noise ratio (PSNR) as metrics and compare the two in the context of solar EUV images. In addition, we perform tests to validate the scientific use of the lossily compressed images by analysing examples of an on-disk and off-limb coronal loop oscillation time series observed by AIA/SDO.
2017-01-01T00:00:00ZFischer, CatherineMueller, DanielDe Moortel, InekeFor future solar missions as well as ground-based telescopes, efficient ways to return and process data has become increasingly important. Solar Or-biter, e.g., the next ESA/NASA mission to explore the Sun and the heliosphere,is a deep-space mission, which implies a limited telemetry rate that makes efficient onboard data compression a necessity to achieve the mission science goals.Missions like the Solar Dynamics Observatory (SDO) and future ground-based telescopes such as the Daniel K. Inouye Solar Telescope, on the other hand,face the challenge of making petabyte-sized solar data archives accessible to the solar community. New image compression standards address these challenges by implementing efficient and flexible compression algorithms that can be tailored to user requirements. We analyse solar images from the Atmospheric Imaging Assembly (AIA) instrument onboard SDO to study the effect of lossy JPEG2000(from the Joint Photographic Experts Group 2000) image compression at different bit rates. To assess the quality of compressed images, we use the mean structural similarity (MSSIM) index as well as the widely used peak signal-to noise ratio (PSNR) as metrics and compare the two in the context of solar EUV images. In addition, we perform tests to validate the scientific use of the lossily compressed images by analysing examples of an on-disk and off-limb coronal loop oscillation time series observed by AIA/SDO.Energy release in driven twisted coronal loopsBareford, Michael RGordovskyy, MykolaBrowning, PhilippaHood, Alan Williamhttp://hdl.handle.net/10023/123052018-01-07T03:10:31Z2016-01-01T00:00:00ZMagnetic reconnection in twisted magnetic flux tubes, representing coronal loops, is investigated. The main goal is to establish the influence of the field geometry and various thermodynamic effects on the stability of twisted flux tubes and on the size and distribution of heated regions. In particular, we aim to investigate to what extent the earlier idealised models, based on the initially cylindrically symmetric flux tubes, are different from more realistic models, including the large-scale curvature, atmospheric stratification, thermal conduction and other effects. In addition, we compare the roles of Ohmic heating and shock heating in energy conversion during magnetic reconnection in twisted loops. The models with straight flux tubes show similar distribution of heated plasma during the reconnection: it initially forms a helical shape, which subsequently becomes very fragmented. The heating in these models is rather uniformly distributed along flux tubes. At the same time, the hot plasma regions in curved loops are asymmetric, and concentrate close to the loop tops. Large-scale curvature has a destabilising in influence: lower twist is needed for instability. Footpoint convergence normally delays instability slightly, although, in some cases converging flux tubes can be less stable. Finally, introducing a stratified atmosphere gives rise to decaying wave propagation, which has destabilising effect.
This work is funded by Science and Technology Facilities Council (UK). This equipment was funded by a BIS National E-Infrastructure capital grant ST/K00042X/1, DiRAC Operations grant ST/K003267/1 and Durham University.
2016-01-01T00:00:00ZBareford, Michael RGordovskyy, MykolaBrowning, PhilippaHood, Alan WilliamMagnetic reconnection in twisted magnetic flux tubes, representing coronal loops, is investigated. The main goal is to establish the influence of the field geometry and various thermodynamic effects on the stability of twisted flux tubes and on the size and distribution of heated regions. In particular, we aim to investigate to what extent the earlier idealised models, based on the initially cylindrically symmetric flux tubes, are different from more realistic models, including the large-scale curvature, atmospheric stratification, thermal conduction and other effects. In addition, we compare the roles of Ohmic heating and shock heating in energy conversion during magnetic reconnection in twisted loops. The models with straight flux tubes show similar distribution of heated plasma during the reconnection: it initially forms a helical shape, which subsequently becomes very fragmented. The heating in these models is rather uniformly distributed along flux tubes. At the same time, the hot plasma regions in curved loops are asymmetric, and concentrate close to the loop tops. Large-scale curvature has a destabilising in influence: lower twist is needed for instability. Footpoint convergence normally delays instability slightly, although, in some cases converging flux tubes can be less stable. Finally, introducing a stratified atmosphere gives rise to decaying wave propagation, which has destabilising effect.Study on the tumor-induced angiogenesis using mathematical modelsSuzuki, TakashiMinerva, DhisaNishiyama, KoichiKoshikawa, NaohikoChaplain, Mark Andrew Josephhttp://hdl.handle.net/10023/122562018-01-23T15:30:07Z2018-01-01T00:00:00ZWe studied angiogenesis using mathematical models describing the dynamics of tip cells. We reviewed the basic ideas of angiogenesis models and its numerical simulation technique to produce realistic computer graphics images of sprouting angiogenesis. We examined the classical model of Anderson-Chaplain using fundamental concepts of mass transport and chemical reaction with ECM degradation included. We then constructed two types of numerical schemes, model-faithful and model-driven ones, where new techniques of numerical simulation are introduced, such as transient probability, particle velocity, and Boolean variables.
This work was supported by JSPS KAKENHI 16H06576 and JSPS Core-to-Core Project International Research Network.
2018-01-01T00:00:00ZSuzuki, TakashiMinerva, DhisaNishiyama, KoichiKoshikawa, NaohikoChaplain, Mark Andrew JosephWe studied angiogenesis using mathematical models describing the dynamics of tip cells. We reviewed the basic ideas of angiogenesis models and its numerical simulation technique to produce realistic computer graphics images of sprouting angiogenesis. We examined the classical model of Anderson-Chaplain using fundamental concepts of mass transport and chemical reaction with ECM degradation included. We then constructed two types of numerical schemes, model-faithful and model-driven ones, where new techniques of numerical simulation are introduced, such as transient probability, particle velocity, and Boolean variables.Special subgroups of regular semigroupsBlyth, T. S.Almeida Santos, M. H.http://hdl.handle.net/10023/122312018-01-07T03:53:19Z2017-10-03T00:00:00ZExtending the notions of inverse transversal and associate subgroup, we consider a regular semigroup S with the property that there exists a subsemigroup T which contains, for each x∈S, a unique y such that both xy and yx are idempotent. Such a subsemigroup is necessarily a group which we call a special subgroup. Here we investigate regular semigroups with this property. In particular, we determine when the subset of perfect elements is a subsemigroup and describe its structure in naturally arising situations.
This work was partially supported by the Portuguese Foundation for Science and Technology through the grant UID/MAT/00297/2013 (CMA).
2017-10-03T00:00:00ZBlyth, T. S.Almeida Santos, M. H.Extending the notions of inverse transversal and associate subgroup, we consider a regular semigroup S with the property that there exists a subsemigroup T which contains, for each x∈S, a unique y such that both xy and yx are idempotent. Such a subsemigroup is necessarily a group which we call a special subgroup. Here we investigate regular semigroups with this property. In particular, we determine when the subset of perfect elements is a subsemigroup and describe its structure in naturally arising situations.Regularity of Navier--Stokes flows with bounds for the pressureTran, Chuong V.Yu, Xinweihttp://hdl.handle.net/10023/122302018-01-07T03:50:56Z2017-05-01T00:00:00ZThis study derives regularity criteria for solutions of the Navier–Stokes equations. Let Ω(t) := {x : |u(x, t)| > c ||u||Lr(R3) }, for some r ≥ 3 and constant c independent of t, with measure |Ω|. It is shown that if ||p + P||L3/2(Ω) becomes sufficiently small as |Ω| decreases, then||u||L(r+6)/3(R3) decays and regularity is secured. Here p is the physical pressure and P is a pressure moderator of relatively broad forms. The implications of the results are discussed and regularity criteria in terms of bounds for |p + P| within Ω are deduced.
This paper was presented at the Warwick EPSRC Symposium on PDEs in Fluid Mechanics, September 2016. Part of this research was carried out when CVT was visiting the University of Alberta, whose hospitality is gratefully acknowledged. XY was partially supported by NSERC Discovery grant RES0020476
2017-05-01T00:00:00ZTran, Chuong V.Yu, XinweiThis study derives regularity criteria for solutions of the Navier–Stokes equations. Let Ω(t) := {x : |u(x, t)| > c ||u||Lr(R3) }, for some r ≥ 3 and constant c independent of t, with measure |Ω|. It is shown that if ||p + P||L3/2(Ω) becomes sufficiently small as |Ω| decreases, then||u||L(r+6)/3(R3) decays and regularity is secured. Here p is the physical pressure and P is a pressure moderator of relatively broad forms. The implications of the results are discussed and regularity criteria in terms of bounds for |p + P| within Ω are deduced.Simulating the coronal evolution of AR 11437 using SDO/HMI magnetogramsYardley, Stephanie L.Mackay, Duncan H.Green, Lucie M.http://hdl.handle.net/10023/122262018-02-13T16:30:08Z2018-01-10T00:00:00ZThe coronal magnetic field evolution of AR 11437 is simulated by applying the magnetofrictional relaxation technique of Mackay et al. (2011). A sequence of photospheric line-of-sight magnetograms produced by SDO/HMI are used todrive the simulation and continuously evolve the coronal magnetic field of the active region through a series of nonlinear force-free equilibria. The simulation is started during the first stages of the active region emergence so that its full evolution from emergence to decay can be simulated. A comparison of the simulation results with SDO/AIA observations show that many aspects of the active region's observed coronal evolution are reproduced. In particular,it shows the presence of a flux rope, which forms at the same location as sheared coronal loops in the observations. The observations show that eruptions occur on 2012 March 17 at 05:09 UT and 10:45 UT and on 2012 March 20 at14:31 UT. The simulation reproduces the first and third eruption, with the simulated flux rope erupting roughly 1 and10 hours before the observed ejections, respectively. A parameter study is conducted where the boundary and initial conditions are varied along with the physical effects of Ohmic diffusion, hyperdiffusion and an additional injection of helicity. When comparing the simulations, the evolution of the magnetic field, free magnetic energy, relative helicity and flux rope eruption timings do not change significantly. This indicates that the key element in reproducing the coronal evolution of AR 11437 is the use of line-of-sight magnetograms to drive the evolution of the coronal magnetic field.
Funding: STFC via the Consolidated Grant SMC1/YST025 (SLY), STFC and the Levehulme Trust (DHM).
2018-01-10T00:00:00ZYardley, Stephanie L.Mackay, Duncan H.Green, Lucie M.The coronal magnetic field evolution of AR 11437 is simulated by applying the magnetofrictional relaxation technique of Mackay et al. (2011). A sequence of photospheric line-of-sight magnetograms produced by SDO/HMI are used todrive the simulation and continuously evolve the coronal magnetic field of the active region through a series of nonlinear force-free equilibria. The simulation is started during the first stages of the active region emergence so that its full evolution from emergence to decay can be simulated. A comparison of the simulation results with SDO/AIA observations show that many aspects of the active region's observed coronal evolution are reproduced. In particular,it shows the presence of a flux rope, which forms at the same location as sheared coronal loops in the observations. The observations show that eruptions occur on 2012 March 17 at 05:09 UT and 10:45 UT and on 2012 March 20 at14:31 UT. The simulation reproduces the first and third eruption, with the simulated flux rope erupting roughly 1 and10 hours before the observed ejections, respectively. A parameter study is conducted where the boundary and initial conditions are varied along with the physical effects of Ohmic diffusion, hyperdiffusion and an additional injection of helicity. When comparing the simulations, the evolution of the magnetic field, free magnetic energy, relative helicity and flux rope eruption timings do not change significantly. This indicates that the key element in reproducing the coronal evolution of AR 11437 is the use of line-of-sight magnetograms to drive the evolution of the coronal magnetic field.Lumped finite elements for reaction-cross-diffusion systems on stationary surfacesFrittelli, MassimoMadzvamuse, AnotidaSgura, IvonneVenkataraman, Chandrasekharhttp://hdl.handle.net/10023/121822018-01-07T04:04:17Z2017-12-15T00:00:00ZWe consider a lumped surface finite element method (LSFEM) for the spatial approximation of reaction-diffusion equations on closed compact surfaces in R3 in the presence of cross-diffusion. We provide a fully-discrete scheme by applying the implicit-explicit (IMEX) Euler method. We provide sufficient conditions for the existence of polytopal invariant regions for the numerical solution after spatial and full discretisations. Furthermore, we prove optimal error bounds for the semi- and fully-discrete methods, that is the convergence rates are quadratic in the meshsize and linear in the timestep. To support our theoretical findings, we provide two numerical tests. The first test confirms that in the absence of lumping numerical solutions violate the invariant region leading to blow-up due to the nature of the kinetics. The second experiment is an example of Turing pattern formation in the presence of cross-diffusion on the sphere.
All the authors (AM, IS, CV, MF) thank the Isaac Newton Institute for Mathematical Sciences for its hospitality during the programme (Coupling Geometric PDEs with Physics for Cell Morphology, Motility and Pattern Formation; EPSRC EP/K032208/1). This work (AM) has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642866. AM and CV acknowledge support from the Engineering and Physical Sciences Research Council (EP/J016780/1) on Modelling, analysis and simulation of spatial patterning on evolving biological surfaces and the Leverhulme Trust Research Project Grant (RPG-2014-149) on Unravelling new mathematics for 3D cell migration. AM was partially supported by a fellowship from the Simons Foundation. AM is a Royal Society Wolfson Research Merit Award Holder, generously funded by the Wolfson Foundation.
2017-12-15T00:00:00ZFrittelli, MassimoMadzvamuse, AnotidaSgura, IvonneVenkataraman, ChandrasekharWe consider a lumped surface finite element method (LSFEM) for the spatial approximation of reaction-diffusion equations on closed compact surfaces in R3 in the presence of cross-diffusion. We provide a fully-discrete scheme by applying the implicit-explicit (IMEX) Euler method. We provide sufficient conditions for the existence of polytopal invariant regions for the numerical solution after spatial and full discretisations. Furthermore, we prove optimal error bounds for the semi- and fully-discrete methods, that is the convergence rates are quadratic in the meshsize and linear in the timestep. To support our theoretical findings, we provide two numerical tests. The first test confirms that in the absence of lumping numerical solutions violate the invariant region leading to blow-up due to the nature of the kinetics. The second experiment is an example of Turing pattern formation in the presence of cross-diffusion on the sphere.Above the noise : the search for periodicities in the inner heliosphereThrelfall, James WilliamDe Moortel, InekeConlon, Thomas Michaelhttp://hdl.handle.net/10023/120542018-02-25T01:33:17Z2017-11-01T00:00:00ZRemote sensing of coronal and heliospheric periodicities can provide vital insight into the local conditions and dynamics of the solar atmosphere. We seek to trace long (one hour or longer) periodic oscillatory signatures (previously identified above the limb in the corona by, e.g., Telloni et al., 2013, Astrophys. J., 767, 138) from their origin at the solar surface out into the heliosphere. To do this, we combine on-disk measurements taken by the Atmospheric Imaging Assembly (AIA) onboard the Solar Dynamics Observatory (SDO) and concurrent extreme ultra-violet (EUV) and coronagraph data from one of the Solar Terrestrial Relations Observatory (STEREO) spacecraft to study the evolution of two active regions in the vicinity of an equatorial coronal hole over several days in early 2011. Fourier and wavelet analysis of signals are performed. Applying white-noise-based confidence levels to the power spectra associated with detrended intensity time series yields detections of oscillatory signatures with periods from 6 − 13 hours in both AIA and STEREO data. As was found by Telloni et al. (2013), these signatures are aligned with local magnetic structures. However, typical spectral power densities all vary substantially as a function of period, indicating spectra dominated by red (rather than white) noise. Contrary to the white-noise-based results, applying global confidence levels based on a generic background noise model (allowing a combination of white noise, red noise, and transients following Auch`ere et al., 2016, Astrophys. J., 825, 110) without detrending the time series, uncovers only sporadic, spatially uncorrelated evidence of periodic signatures in either instrument. Automating this method to individual pixels in the STEREO/COR coronagraph field of view is non-trivial.
2017-11-01T00:00:00ZThrelfall, James WilliamDe Moortel, InekeConlon, Thomas MichaelRemote sensing of coronal and heliospheric periodicities can provide vital insight into the local conditions and dynamics of the solar atmosphere. We seek to trace long (one hour or longer) periodic oscillatory signatures (previously identified above the limb in the corona by, e.g., Telloni et al., 2013, Astrophys. J., 767, 138) from their origin at the solar surface out into the heliosphere. To do this, we combine on-disk measurements taken by the Atmospheric Imaging Assembly (AIA) onboard the Solar Dynamics Observatory (SDO) and concurrent extreme ultra-violet (EUV) and coronagraph data from one of the Solar Terrestrial Relations Observatory (STEREO) spacecraft to study the evolution of two active regions in the vicinity of an equatorial coronal hole over several days in early 2011. Fourier and wavelet analysis of signals are performed. Applying white-noise-based confidence levels to the power spectra associated with detrended intensity time series yields detections of oscillatory signatures with periods from 6 − 13 hours in both AIA and STEREO data. As was found by Telloni et al. (2013), these signatures are aligned with local magnetic structures. However, typical spectral power densities all vary substantially as a function of period, indicating spectra dominated by red (rather than white) noise. Contrary to the white-noise-based results, applying global confidence levels based on a generic background noise model (allowing a combination of white noise, red noise, and transients following Auch`ere et al., 2016, Astrophys. J., 825, 110) without detrending the time series, uncovers only sporadic, spatially uncorrelated evidence of periodic signatures in either instrument. Automating this method to individual pixels in the STEREO/COR coronagraph field of view is non-trivial.Vortex scaling ranges in two-dimensional turbulenceBurgess, B. H.Dritschel, D. G.Scott, R. K.http://hdl.handle.net/10023/120292018-01-07T04:03:49Z2017-11-01T00:00:00ZWe survey the role of coherent vortices in two-dimensional turbulence, including formation mechanisms, implications for classical similarity and inertial range theories, and characteristics of the vortex populations. We review early work on the spatial and temporal scaling properties of vortices in freely evolving turbulence and more recent developments, including a spatiotemporal scaling theory for vortices in the forced inverse energy cascade. We emphasize that Kraichnan-Batchelor similarity theories and vortex scaling theories are best viewed as complementary and together provide a more complete description of two-dimensional turbulence. In particular, similarity theory has a continued role in describing the weak filamentary sea between the vortices. Moreover, we locate both classical inertial and vortex scaling ranges within the broader framework of scaling in far-from-equilibrium systems, which generically exhibit multiple fixed point solutions with distinct scaling behaviour. We describe how stationary transport in a range of scales comoving with the dilatation of flow features, as measured by the growth in vortex area, constrains the vortex number density in both freely evolving and forced two-dimensional turbulence. The new theories for coherent vortices reveal previously hidden nontrivial scaling, point to new dynamical understanding, and provide a novel exciting window into two-dimensional turbulence.
2017-11-01T00:00:00ZBurgess, B. H.Dritschel, D. G.Scott, R. K.We survey the role of coherent vortices in two-dimensional turbulence, including formation mechanisms, implications for classical similarity and inertial range theories, and characteristics of the vortex populations. We review early work on the spatial and temporal scaling properties of vortices in freely evolving turbulence and more recent developments, including a spatiotemporal scaling theory for vortices in the forced inverse energy cascade. We emphasize that Kraichnan-Batchelor similarity theories and vortex scaling theories are best viewed as complementary and together provide a more complete description of two-dimensional turbulence. In particular, similarity theory has a continued role in describing the weak filamentary sea between the vortices. Moreover, we locate both classical inertial and vortex scaling ranges within the broader framework of scaling in far-from-equilibrium systems, which generically exhibit multiple fixed point solutions with distinct scaling behaviour. We describe how stationary transport in a range of scales comoving with the dilatation of flow features, as measured by the growth in vortex area, constrains the vortex number density in both freely evolving and forced two-dimensional turbulence. The new theories for coherent vortices reveal previously hidden nontrivial scaling, point to new dynamical understanding, and provide a novel exciting window into two-dimensional turbulence.Preserving invariance properties of reaction-diffusion systems on stationary surfacesFrittelli, MassimoMadzvamuse, AnotideSgura, IvonneVenkataraman, Chandrasekharhttp://hdl.handle.net/10023/120212018-02-01T14:30:23Z2017-10-27T00:00:00ZWe propose and analyse a lumped surface finite element method for the numerical approximation of reaction–diffusion systems on stationary compact surfaces in ℝ3. The proposed method preserves the invariant regions of the continuous problem under discretization and, in the special case of scalar equations, it preserves the maximum principle. On the application of a fully discrete scheme using the implicit–explicit Euler method in time, we prove that invariant regions of the continuous problem are preserved (i) at the spatially discrete level with no restriction on the meshsize and (ii) at the fully discrete level under a timestep restriction. We further prove optimal error bounds for the semidiscrete and fully discrete methods, that is, the convergence rates are quadratic in the meshsize and linear in the timestep. Numerical experiments are provided to support the theoretical findings. We provide examples in which, in the absence of lumping, the numerical solution violates the invariant region leading to blow-up.
This work (AM, CV) is partly supported by the EPSRC grant number EP/J016780/1 and the Leverhulme Trust Research Project Grant (RPG-2014-149). The authors (MF, AM, IS CV) would like to thank the Isaac Newton Institute for Mathematical Sciences for its hospitality during the programme [Coupling Geometric PDEs with Physics for Cell Morphology, Motility and Pattern Formation] supported by EPSRC Grant Number EP/K032208/1. AM acknowledges funding from the European Union Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642866 and was partially supported by a grant from the Simons Foundation. AM is a Royal Society Wolfson Research Merit Award Holder funded generously by the Wolfson Foundation.
2017-10-27T00:00:00ZFrittelli, MassimoMadzvamuse, AnotideSgura, IvonneVenkataraman, ChandrasekharWe propose and analyse a lumped surface finite element method for the numerical approximation of reaction–diffusion systems on stationary compact surfaces in ℝ3. The proposed method preserves the invariant regions of the continuous problem under discretization and, in the special case of scalar equations, it preserves the maximum principle. On the application of a fully discrete scheme using the implicit–explicit Euler method in time, we prove that invariant regions of the continuous problem are preserved (i) at the spatially discrete level with no restriction on the meshsize and (ii) at the fully discrete level under a timestep restriction. We further prove optimal error bounds for the semidiscrete and fully discrete methods, that is, the convergence rates are quadratic in the meshsize and linear in the timestep. Numerical experiments are provided to support the theoretical findings. We provide examples in which, in the absence of lumping, the numerical solution violates the invariant region leading to blow-up.Bifurcations and chaotic dynamics in a tumour-immune-virus systemEftimie, R.Macnamara, C. K.Dushoff, JonathanBramson, J. L.Earn, D. J. D.http://hdl.handle.net/10023/119992018-01-07T03:54:34Z2016-12-07T00:00:00ZDespite mounting evidence that oncolytic viruses can be effective in treating cancer, understanding the details of the interactions between tumour cells, oncolytic viruses and immune cells that could lead to tumour control or tumour escape is still an open problem. Mathematical modelling of cancer oncolytic therapies has been used to investigate the biological mechanisms behind the observed temporal patterns of tumour growth. However, many models exhibit very complex dynamics, which renders them difficult to investigate. In this case, bifurcation diagrams could enable the visualisation of model dynamics by identifying (in the parameter space) the particular transition points between different behaviours. Here, we describe and investigate two simple mathematical models for oncolytic virus cancer therapy, with constant and immunity-dependent carrying capacity. While both models can exhibit complex dynamics, namely fixed points, periodic orbits and chaotic behaviours, only the model with immunity-dependent carrying capacity can exhibit them for biologically realistic situations, i.e., before the tumour grows too large and the experiment is terminated. Moreover, with the help of the bifurcation diagrams we uncover two unexpected behaviours in virus-tumour dynamics: (i) for short virus half-life, the tumour size seems to be too small to be detected, while for long virus half-life the tumour grows to larger sizes that can be detected; (ii) some model parameters have opposite effects on the transient and asymptotic dynamics of the tumour.
2016-12-07T00:00:00ZEftimie, R.Macnamara, C. K.Dushoff, JonathanBramson, J. L.Earn, D. J. D.Despite mounting evidence that oncolytic viruses can be effective in treating cancer, understanding the details of the interactions between tumour cells, oncolytic viruses and immune cells that could lead to tumour control or tumour escape is still an open problem. Mathematical modelling of cancer oncolytic therapies has been used to investigate the biological mechanisms behind the observed temporal patterns of tumour growth. However, many models exhibit very complex dynamics, which renders them difficult to investigate. In this case, bifurcation diagrams could enable the visualisation of model dynamics by identifying (in the parameter space) the particular transition points between different behaviours. Here, we describe and investigate two simple mathematical models for oncolytic virus cancer therapy, with constant and immunity-dependent carrying capacity. While both models can exhibit complex dynamics, namely fixed points, periodic orbits and chaotic behaviours, only the model with immunity-dependent carrying capacity can exhibit them for biologically realistic situations, i.e., before the tumour grows too large and the experiment is terminated. Moreover, with the help of the bifurcation diagrams we uncover two unexpected behaviours in virus-tumour dynamics: (i) for short virus half-life, the tumour size seems to be too small to be detected, while for long virus half-life the tumour grows to larger sizes that can be detected; (ii) some model parameters have opposite effects on the transient and asymptotic dynamics of the tumour.On interfaces between cell populations with different mobilitiesLorenzi, TommasoLorz, AlexanderPerthame, Benoithttp://hdl.handle.net/10023/119802018-01-07T03:41:44Z2017-03-01T00:00:00ZPartial differential equations describing the dynamics of cell population densities from a fluid mechanical perspective can model the growth of avascular tumours. In this framework, we consider a system of equations that describes the interaction between a population of dividing cells and a population of non-dividing cells. The two cell populations are characterised by different mobilities. We present the results of numerical simulations displaying two-dimensional spherical waves with sharp interfaces between dividing and non-dividing cells. Furthermore, we numerically observe how different ratios between the mobilities change the morphology of the interfaces, and lead to the emergence of finger-like patterns of invasion above a threshold. Motivated by these simulations, we study the existence of one-dimensional travelling wave solutions.
2017-03-01T00:00:00ZLorenzi, TommasoLorz, AlexanderPerthame, BenoitPartial differential equations describing the dynamics of cell population densities from a fluid mechanical perspective can model the growth of avascular tumours. In this framework, we consider a system of equations that describes the interaction between a population of dividing cells and a population of non-dividing cells. The two cell populations are characterised by different mobilities. We present the results of numerical simulations displaying two-dimensional spherical waves with sharp interfaces between dividing and non-dividing cells. Furthermore, we numerically observe how different ratios between the mobilities change the morphology of the interfaces, and lead to the emergence of finger-like patterns of invasion above a threshold. Motivated by these simulations, we study the existence of one-dimensional travelling wave solutions.The interaction of two surface vortices near a topographic slope in a stratified oceande Marez, CharlyCarton, XavierMorvan, MathieuReinaud, Jean Noelhttp://hdl.handle.net/10023/119722017-12-24T00:32:20Z2017-12-01T00:00:00ZWe study the influence of bottom topography on the interaction of two identical vortices in a two-layer, quasi-geostrophic model. The two vortices have piecewise-uniform potential vorticity, and are lying in the upper layer of the model. The topography is a smooth bottom slope. For two cyclones, topography modifies the merger critical distance and the merger efficiency: the topographic wave and vortices can advect the two cyclones along the shelf when they are initially far from it, or towards the shelf when they are initially closer to it. They can also advect the two cyclones towards each other, and thus favour merger. The topographic wave and vortices exert a deformation on these cyclones, which filament. Regimes of partial vortex merger or of vortex splitting are then observed. The interaction of the vorticity poles in the two layers are analysed to explain the evolution of the two upper layer cyclones. For taller topography, two new regimes appear: vortex drift and splitting, and filamentation and asymmetric merger. They are due to the hetonic coupling of lower layer vorticity with the upper vortices, or to the strong shear that the former exert on the latter. The interaction of two anticyclones shows regimes of co-rotation or merger, but specifically, it leads to the drift of the two vortices away from the slope, via a hetonic coupling with opposite signed vorticity in the lower layer. This vorticity originates in the breaking of the topographic wave. The analysis of passive tracer evolution confirms the inshore or offshore drift of the fluid, the formation of tracer fronts along filaments and its mixing in regions of vortex merger. The trajectories of particles indicates how the fluid initially in the vortices is finally partitioned.
2017-12-01T00:00:00Zde Marez, CharlyCarton, XavierMorvan, MathieuReinaud, Jean NoelWe study the influence of bottom topography on the interaction of two identical vortices in a two-layer, quasi-geostrophic model. The two vortices have piecewise-uniform potential vorticity, and are lying in the upper layer of the model. The topography is a smooth bottom slope. For two cyclones, topography modifies the merger critical distance and the merger efficiency: the topographic wave and vortices can advect the two cyclones along the shelf when they are initially far from it, or towards the shelf when they are initially closer to it. They can also advect the two cyclones towards each other, and thus favour merger. The topographic wave and vortices exert a deformation on these cyclones, which filament. Regimes of partial vortex merger or of vortex splitting are then observed. The interaction of the vorticity poles in the two layers are analysed to explain the evolution of the two upper layer cyclones. For taller topography, two new regimes appear: vortex drift and splitting, and filamentation and asymmetric merger. They are due to the hetonic coupling of lower layer vorticity with the upper vortices, or to the strong shear that the former exert on the latter. The interaction of two anticyclones shows regimes of co-rotation or merger, but specifically, it leads to the drift of the two vortices away from the slope, via a hetonic coupling with opposite signed vorticity in the lower layer. This vorticity originates in the breaking of the topographic wave. The analysis of passive tracer evolution confirms the inshore or offshore drift of the fluid, the formation of tracer fronts along filaments and its mixing in regions of vortex merger. The trajectories of particles indicates how the fluid initially in the vortices is finally partitioned.Can substorm particle acceleration be applied to solar flares?Birn, JoachimBattaglia, MarinaFletcher, LyndsayHesse, MichaelNeukirch, Thomashttp://hdl.handle.net/10023/119122018-01-07T04:05:56Z2017-10-20T00:00:00ZUsing test particle studies in the electromagnetic fields of three-dimensional magnetohydrodynamic (MHD) simulations of magnetic reconnection, we study the energization of charged particles in the context of the standard two-ribbon flare picture in analogy to the standard magnetospheric substorm paradigm. In particular, we investigate the effects of the collapsing field ("collapsing magnetic trap") below a reconnection site, which has been demonstrated to be the major acceleration mechanism that causes energetic particle acceleration and injections observed in Earth's magnetotail associated with substorms and other impulsive events. We contrast an initially force-free, high-shear field (low beta) with low and moderate shear, finite-pressure (high-beta) arcade structures, where beta represents the ratio between gas (plasma) and magnetic pressure. We demonstrate that the energization affects large numbers of particles, but the acceleration is modest in the presence of a significant shear field. Without incorporating loss mechanisms, the effect on particles at different energies is similar, akin to adiabatic heating, and thus is not a likely mechanism to generate a power-law tail onto a (heated or not heated) Maxwellian velocity distribution.
2017-10-20T00:00:00ZBirn, JoachimBattaglia, MarinaFletcher, LyndsayHesse, MichaelNeukirch, ThomasUsing test particle studies in the electromagnetic fields of three-dimensional magnetohydrodynamic (MHD) simulations of magnetic reconnection, we study the energization of charged particles in the context of the standard two-ribbon flare picture in analogy to the standard magnetospheric substorm paradigm. In particular, we investigate the effects of the collapsing field ("collapsing magnetic trap") below a reconnection site, which has been demonstrated to be the major acceleration mechanism that causes energetic particle acceleration and injections observed in Earth's magnetotail associated with substorms and other impulsive events. We contrast an initially force-free, high-shear field (low beta) with low and moderate shear, finite-pressure (high-beta) arcade structures, where beta represents the ratio between gas (plasma) and magnetic pressure. We demonstrate that the energization affects large numbers of particles, but the acceleration is modest in the presence of a significant shear field. Without incorporating loss mechanisms, the effect on particles at different energies is similar, akin to adiabatic heating, and thus is not a likely mechanism to generate a power-law tail onto a (heated or not heated) Maxwellian velocity distribution.Collisionless current sheet equilibriaNeukirch, ThomasWilson, FionaAllanson, Oliver Douglashttp://hdl.handle.net/10023/118902018-02-11T01:35:57Z2018-01-01T00:00:00ZCurrent sheets are important for the structure and dynamics of many plasma systems. In space and astrophysical plasmas they play a crucial role in activity processes, for example by facilitating the release of magnetic energy via processes such as magnetic reconnection. In this contribution we will focus on collisionless plasma systems. A sensible first step in any investigation of physical processes involving current sheets is to find appropriate equilibrium solutions. The theory of collisionless plasma equilibria is well established, but over the past few years there has been a renewed interest in finding equilibrium distribution functions for collisionless current sheets with particular properties, for example for cases where the current density is parallel to the magnetic field (force-free current sheets). This interest is due to a combination of scientific curiosity and potential applications to space and astrophysical plasmas. In this paper we will give an overview of some of the recent developments, discuss their potential applications and address a number of open questions.
The authors acknowledge financial support by the UK Science and Technology Facilities Council Consolidated Grants ST/K000950/1 and and ST/N000609/1, as well as Doctoral Training Grant ST/K502327/1. OA also acknowledges support by the UK Natural Environment Research Council Grant NE/P017274/1.
2018-01-01T00:00:00ZNeukirch, ThomasWilson, FionaAllanson, Oliver DouglasCurrent sheets are important for the structure and dynamics of many plasma systems. In space and astrophysical plasmas they play a crucial role in activity processes, for example by facilitating the release of magnetic energy via processes such as magnetic reconnection. In this contribution we will focus on collisionless plasma systems. A sensible first step in any investigation of physical processes involving current sheets is to find appropriate equilibrium solutions. The theory of collisionless plasma equilibria is well established, but over the past few years there has been a renewed interest in finding equilibrium distribution functions for collisionless current sheets with particular properties, for example for cases where the current density is parallel to the magnetic field (force-free current sheets). This interest is due to a combination of scientific curiosity and potential applications to space and astrophysical plasmas. In this paper we will give an overview of some of the recent developments, discuss their potential applications and address a number of open questions.Vertical structure of tropospheric winds on gas giantsScott, R. K.Dunkerton, T. J.http://hdl.handle.net/10023/118502018-03-04T01:40:48Z2017-04-16T00:00:00ZZonal mean zonal velocity profiles from cloud-tracking observations on Jupiter and Saturn are used to infer latitudinal variations of potential temperature consistent with a shear stable potential vorticity distribution. Immediately below the cloud tops, density stratification is weaker on the poleward and stronger on the equatorward flanks of midlatitude jets, while at greater depth the opposite relation holds. Thermal wind balance then yields the associated vertical shears of midlatitude jets in an altitude range bounded above by the cloud-tops and bounded below by the level where the latitudinal gradient of static stability changes sign. The inferred vertical shear below the cloud tops is consistent with existing thermal profiling of the upper troposphere.The sense of the associated mean meridional circulation in the upper troposphere is discussed and expected magnitudes are given based on existing estimates of the radiative timescale on each planet.
Support for this work was generously provided by the National Science Foundation.
2017-04-16T00:00:00ZScott, R. K.Dunkerton, T. J.Zonal mean zonal velocity profiles from cloud-tracking observations on Jupiter and Saturn are used to infer latitudinal variations of potential temperature consistent with a shear stable potential vorticity distribution. Immediately below the cloud tops, density stratification is weaker on the poleward and stronger on the equatorward flanks of midlatitude jets, while at greater depth the opposite relation holds. Thermal wind balance then yields the associated vertical shears of midlatitude jets in an altitude range bounded above by the cloud-tops and bounded below by the level where the latitudinal gradient of static stability changes sign. The inferred vertical shear below the cloud tops is consistent with existing thermal profiling of the upper troposphere.The sense of the associated mean meridional circulation in the upper troposphere is discussed and expected magnitudes are given based on existing estimates of the radiative timescale on each planet.Vortex merger near a topographic slope in a homogeneous rotating fluidCarton, XavierMorvan, MathieuReinaud, Jean NoelSokolovskiy, MikhailL'Hégaret, PierreVic, Clémenthttp://hdl.handle.net/10023/117792018-01-07T04:05:29Z2017-10-01T00:00:00ZThe effect of a bottom slope on the merger of two identical Rankine vortices is investigated in a two dimensional, quasi-geostrophic, incompressible fluid. When two cyclones initially lie parallel to the slope, and more than two vortex diameters away from the slope, the critical merger distance is unchanged. When the cyclones are closer to the slope, they can merge at larger distances, but they lose more mass into filaments, thus weakening the efficiency of merger. Several effects account for this: the topographic Rossby wave advects the cyclones, reduces their mutual distance and deforms them. This along shelf wave breaks into filaments and into secondary vortices which shear out the initial cyclones. The global motion of fluid towards the shallow domain and the erosion of the two cyclones are confirmed by the evolution of particles seeded both in the cyclone sand near the topographic slope. The addition of tracer to the flow indicates that diffusion is ballistic at early times. For two anticyclones, merger is also facilitated because one vortex is ejected offshore towards the other, via coupling with a topographic cyclone. Again two anticyclones can merge at large distance but they are eroded in the process. Finally, for taller topographies, the critical merger distance is again increased and the topographic influence can scatter or completely erode one of the two initial cyclones. Conclusions are drawn on possible improvements of the model configuration for an application to the ocean.
This work is a contribution to the PHYSINDIEN research program. It was supported by CNRS-RFBR contract PRC 1069/16-55-150001.
2017-10-01T00:00:00ZCarton, XavierMorvan, MathieuReinaud, Jean NoelSokolovskiy, MikhailL'Hégaret, PierreVic, ClémentThe effect of a bottom slope on the merger of two identical Rankine vortices is investigated in a two dimensional, quasi-geostrophic, incompressible fluid. When two cyclones initially lie parallel to the slope, and more than two vortex diameters away from the slope, the critical merger distance is unchanged. When the cyclones are closer to the slope, they can merge at larger distances, but they lose more mass into filaments, thus weakening the efficiency of merger. Several effects account for this: the topographic Rossby wave advects the cyclones, reduces their mutual distance and deforms them. This along shelf wave breaks into filaments and into secondary vortices which shear out the initial cyclones. The global motion of fluid towards the shallow domain and the erosion of the two cyclones are confirmed by the evolution of particles seeded both in the cyclone sand near the topographic slope. The addition of tracer to the flow indicates that diffusion is ballistic at early times. For two anticyclones, merger is also facilitated because one vortex is ejected offshore towards the other, via coupling with a topographic cyclone. Again two anticyclones can merge at large distance but they are eroded in the process. Finally, for taller topographies, the critical merger distance is again increased and the topographic influence can scatter or completely erode one of the two initial cyclones. Conclusions are drawn on possible improvements of the model configuration for an application to the ocean.Emergence of spatial patterns in a mathematical model for the co-culture dynamics of epithelial-like and mesenchymal-like cellsDelitala, MarcelloLorenzi, Tommasohttp://hdl.handle.net/10023/117752018-01-07T03:43:54Z2017-02-01T00:00:00ZAccumulating evidence indicates that the interaction between epithelial and mesenchymal cells plays a pivotal role in cancer development and metastasis formation. Here we propose an integro-differential model for the co-culture dynamics of epithelial-like and mesenchymal-like cells. Our model takes into account the effects of chemotaxis, adhesive interactions between epithelial-like cells, proliferation and competition for nutrients. We present a sample of numerical results which display the emergence of spots, stripes and honeycomb patterns, depending on parameters and initial data. These simulations also suggest that epithelial-like and mesenchymal-like cells can segregate when there is little competition for nutrients. Furthermore, our computational results provide a possible explanation for how the concerted action between epithelial-cell adhesion and mesenchymal-cell spreading can precipitate the formation of ring-like structures, which resemble the fibrous capsules frequently observed in hepatic tumours.
2017-02-01T00:00:00ZDelitala, MarcelloLorenzi, TommasoAccumulating evidence indicates that the interaction between epithelial and mesenchymal cells plays a pivotal role in cancer development and metastasis formation. Here we propose an integro-differential model for the co-culture dynamics of epithelial-like and mesenchymal-like cells. Our model takes into account the effects of chemotaxis, adhesive interactions between epithelial-like cells, proliferation and competition for nutrients. We present a sample of numerical results which display the emergence of spots, stripes and honeycomb patterns, depending on parameters and initial data. These simulations also suggest that epithelial-like and mesenchymal-like cells can segregate when there is little competition for nutrients. Furthermore, our computational results provide a possible explanation for how the concerted action between epithelial-cell adhesion and mesenchymal-cell spreading can precipitate the formation of ring-like structures, which resemble the fibrous capsules frequently observed in hepatic tumours.Spatio-temporal models of synthetic genetic oscillatorsMacnamara, Cicely K.Chaplain, Mark A. J.http://hdl.handle.net/10023/117742018-01-07T03:40:19Z2017-02-01T00:00:00ZSignal transduction pathways play a major role in many important aspects of cellular function e.g. cell division, apoptosis. One important class of signal transduction pathways is gene regulatory networks (GRNs). In many GRNs, proteins bind to gene sites in the nucleus thereby altering the transcription rate. Such proteins are known as transcription factors. If the binding reduces the transcription rate there is a negative feedback leading to oscillatory behaviour in mRNA and protein levels, both spatially (e.g. by observing fluorescently labelled molecules in single cells) and temporally (e.g. by observing protein/mRNA levels over time). Recent computational modelling has demonstrated that spatial movement of the molecules is a vital component of GRNs and may cause the oscillations. These numerical findings have subsequently been proved rigorously i.e. the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf bifurcation. In this paper we first present a model of the canonical GRN (the Hes1 protein) and show the effect of varying the spatial location of gene and protein production sites on the oscillations. We then extend the approach to examine spatio-temporal models of synthetic gene regulatory networks e.g. n-gene repressilators and activator-repressor systems.
2017-02-01T00:00:00ZMacnamara, Cicely K.Chaplain, Mark A. J.Signal transduction pathways play a major role in many important aspects of cellular function e.g. cell division, apoptosis. One important class of signal transduction pathways is gene regulatory networks (GRNs). In many GRNs, proteins bind to gene sites in the nucleus thereby altering the transcription rate. Such proteins are known as transcription factors. If the binding reduces the transcription rate there is a negative feedback leading to oscillatory behaviour in mRNA and protein levels, both spatially (e.g. by observing fluorescently labelled molecules in single cells) and temporally (e.g. by observing protein/mRNA levels over time). Recent computational modelling has demonstrated that spatial movement of the molecules is a vital component of GRNs and may cause the oscillations. These numerical findings have subsequently been proved rigorously i.e. the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf bifurcation. In this paper we first present a model of the canonical GRN (the Hes1 protein) and show the effect of varying the spatial location of gene and protein production sites on the oscillations. We then extend the approach to examine spatio-temporal models of synthetic gene regulatory networks e.g. n-gene repressilators and activator-repressor systems.The eruption of a small-scale emerging flux rope as the driver of an M-class flare and of a coronal mass ejectionYan, X. L.Jiang, C. W.Xue, Z. K.Wang, J. C.Priest, E. R.Yang, L. H.Kong, D. F.Cao, W. D.Ji, H. S.http://hdl.handle.net/10023/117612018-03-04T02:30:37Z2017-08-10T00:00:00ZSolar flares and coronal mass ejections are the most powerful explosions in the Sun. They are major sources of potentially destructive space weather conditions. However, the possible causes of their initiation remain controversial. Using high-resolution data observed by the New Solar Telescope of Big Bear Solar Observatory, supplemented by Solar Dynamics Observatory observations, we present unusual observations of a small-scale emerging flux rope near a large sunspot, whose eruption produced an M-class flare and a coronal mass ejection. The presence of the small-scale flux rope was indicated by static nonlinear force-free field extrapolation as well as data-driven magnetohydrodynamics modeling of the dynamic evolution of the coronal three-dimensional magnetic field. During the emergence of the flux rope, rotation of satellite sunspots at the footpoints of the flux rope was observed. Meanwhile, the Lorentz force, magnetic energy, vertical current, and transverse fields were increasing during this phase. The free energy from the magnetic flux emergence and twisting magnetic fields is sufficient to power the M-class flare. These observations present, for the first time, the complete process, from the emergence of the small-scale flux rope, to the production of solar eruptions.
This work is sponsored by the National Science Foundation of China (NSFC) under the grant numbers 11373066, 11603071, 11503080, 11633008, 11533008, by the Key Laboratory of Solar Activity of CAS under numbers KLSA201603, KLSA201508, by the Yunnan Science Foundation of China under number 2013FB086, CAS "Light of West China" Program, by the Youth Innovation Promotion Association CAS (No.2011056), and the national basic research program of China (973 program, 2011CB811400). The BBSO operation is supported by NJIT, US NSF AGS-1250818, and NASA NNX13AG14G grants, and the NST operation is partly supported by the Korea Astronomy and Space Science Institute and Seoul National University and by the strategic priority research program of CAS with Grant No. XDB09000000.
2017-08-10T00:00:00ZYan, X. L.Jiang, C. W.Xue, Z. K.Wang, J. C.Priest, E. R.Yang, L. H.Kong, D. F.Cao, W. D.Ji, H. S.Solar flares and coronal mass ejections are the most powerful explosions in the Sun. They are major sources of potentially destructive space weather conditions. However, the possible causes of their initiation remain controversial. Using high-resolution data observed by the New Solar Telescope of Big Bear Solar Observatory, supplemented by Solar Dynamics Observatory observations, we present unusual observations of a small-scale emerging flux rope near a large sunspot, whose eruption produced an M-class flare and a coronal mass ejection. The presence of the small-scale flux rope was indicated by static nonlinear force-free field extrapolation as well as data-driven magnetohydrodynamics modeling of the dynamic evolution of the coronal three-dimensional magnetic field. During the emergence of the flux rope, rotation of satellite sunspots at the footpoints of the flux rope was observed. Meanwhile, the Lorentz force, magnetic energy, vertical current, and transverse fields were increasing during this phase. The free energy from the magnetic flux emergence and twisting magnetic fields is sufficient to power the M-class flare. These observations present, for the first time, the complete process, from the emergence of the small-scale flux rope, to the production of solar eruptions.Interaction between a surface quasi-geostrophic buoyancy filament and an internal vortexReinaud, Jean NoelDritschel, David GerardCarton, Xavierhttp://hdl.handle.net/10023/117272018-01-07T03:46:44Z2016-09-23T00:00:00ZThis paper focuses on the nonlinear interaction between a surface quasi-geostrophic buoyancy filament and an internal vortex. We first revisit the stability of an isolated buoyancy filament. The buoyancy profile considered is continuous and leads to a continuous velocity field, albeit one with infinite shear just outside its edge. The stability properties of an isolated filament help to interpret the unsteady interaction with a sub-surface (internal) vortex studied next. We find that, in all cases, the filament breaks into billows, analogous in form to those occurring in Kelvin-Helmholtz shear instability. For intense buoyancy filaments, the vortex itself may undergo strong deformations, including being split into several pieces. Generally, the nonlinear interaction causes both the filament and the vortex to lose their respective ‘self’-energies to the energy of interaction. The flow evolution depends sensitively on whether the vertical vorticity of the filament and the vortex have the same or opposite signs — termed “cooperative” and “adverse” shear respectively. In cooperative shear, the filament rolls up into a coherent surface eddy above a vortex initially placed below it, whereas in adverse shear, buoyancy is expelled above the vortex. Although sufficiently great shear induced by the buoyancy filament may split the vortex in both cases, adverse shear is significantly more destructive.
2016-09-23T00:00:00ZReinaud, Jean NoelDritschel, David GerardCarton, XavierThis paper focuses on the nonlinear interaction between a surface quasi-geostrophic buoyancy filament and an internal vortex. We first revisit the stability of an isolated buoyancy filament. The buoyancy profile considered is continuous and leads to a continuous velocity field, albeit one with infinite shear just outside its edge. The stability properties of an isolated filament help to interpret the unsteady interaction with a sub-surface (internal) vortex studied next. We find that, in all cases, the filament breaks into billows, analogous in form to those occurring in Kelvin-Helmholtz shear instability. For intense buoyancy filaments, the vortex itself may undergo strong deformations, including being split into several pieces. Generally, the nonlinear interaction causes both the filament and the vortex to lose their respective ‘self’-energies to the energy of interaction. The flow evolution depends sensitively on whether the vertical vorticity of the filament and the vortex have the same or opposite signs — termed “cooperative” and “adverse” shear respectively. In cooperative shear, the filament rolls up into a coherent surface eddy above a vortex initially placed below it, whereas in adverse shear, buoyancy is expelled above the vortex. Although sufficiently great shear induced by the buoyancy filament may split the vortex in both cases, adverse shear is significantly more destructive.Particle acceleration with anomalous pitch angle scattering in 2D magnetohydrodynamic reconnection simulationsBorissov, AlexeiKontar, EduardThrelfall, James WilliamNeukirch, Thomashttp://hdl.handle.net/10023/117142018-01-07T04:03:59Z2017-09-01T00:00:00ZThe conversion of magnetic energy into other forms (such as plasma heating, bulk plasma flows, and non-thermal particles) during solar flares is one of the outstanding open problems in solar physics. It is generally accepted that magnetic reconnection plays a crucialrole in these conversion processes. In order to achieve the rapid energy release required in solar flares, an anomalous resistivity, which is orders of magnitude higher than the Spitzer resistivity, is often used in magnetohydrodynamic (MHD) simulations of reconnection in the corona. The origin of Spitzer resistivity is based on Coulomb scattering, which becomes negligible at the high energies achieved by accelerated particles. As a result, simulations of particle acceleration in reconnection events are often performed in the absence of any interaction between accelerated particles and any background plasma. This need not be the case for scattering associated with anomalous resistivity caused by turbulence within solar flares, as the higher resistivity implies an elevated scattering rate. We present results of test particle calculations, with and without pitch angle scattering, subject to fields derived from MHD simulations of two-dimensional (2D) X-point reconnection. Scattering rates proportional to the ratio of the anomalous resistivity to the local Spitzer resistivity, as well as at fixed values, are considered. Pitch angle scattering, which is independent of the anomalous resistivity, causes higher maximum energies in comparison to those obtained without scattering. Scattering rates which are dependent on the local anomalous resistivity tend to produce fewer highly energised particles due to weaker scattering in the separatrices, even though scattering in the current sheet may be stronger when compared to resistivity-independent scattering. Strong scattering also causes an increase in the number of particles exiting the computational box in the reconnection outflow region, as opposed to along the separatrices as is the case in the absence of scattering.
A.B. would like to thank the University of St Andrews for financial support from the 7th Century Scholarship and the Scottish Government for support from the Saltire Scholarship. E.P.K.’s work is partially supported by a STFC consolidated grant ST/L000741/1. J.T. and T.N. gratefully acknowledge the support of the UK STFC (consolidated grant SN/N000609/1).
2017-09-01T00:00:00ZBorissov, AlexeiKontar, EduardThrelfall, James WilliamNeukirch, ThomasThe conversion of magnetic energy into other forms (such as plasma heating, bulk plasma flows, and non-thermal particles) during solar flares is one of the outstanding open problems in solar physics. It is generally accepted that magnetic reconnection plays a crucialrole in these conversion processes. In order to achieve the rapid energy release required in solar flares, an anomalous resistivity, which is orders of magnitude higher than the Spitzer resistivity, is often used in magnetohydrodynamic (MHD) simulations of reconnection in the corona. The origin of Spitzer resistivity is based on Coulomb scattering, which becomes negligible at the high energies achieved by accelerated particles. As a result, simulations of particle acceleration in reconnection events are often performed in the absence of any interaction between accelerated particles and any background plasma. This need not be the case for scattering associated with anomalous resistivity caused by turbulence within solar flares, as the higher resistivity implies an elevated scattering rate. We present results of test particle calculations, with and without pitch angle scattering, subject to fields derived from MHD simulations of two-dimensional (2D) X-point reconnection. Scattering rates proportional to the ratio of the anomalous resistivity to the local Spitzer resistivity, as well as at fixed values, are considered. Pitch angle scattering, which is independent of the anomalous resistivity, causes higher maximum energies in comparison to those obtained without scattering. Scattering rates which are dependent on the local anomalous resistivity tend to produce fewer highly energised particles due to weaker scattering in the separatrices, even though scattering in the current sheet may be stronger when compared to resistivity-independent scattering. Strong scattering also causes an increase in the number of particles exiting the computational box in the reconnection outflow region, as opposed to along the separatrices as is the case in the absence of scattering.The theoretical foundation of 3D Alfvén resonances : time dependent solutionsElsden, T.Wright, A. N.http://hdl.handle.net/10023/117062018-03-04T01:40:48Z2017-03-01T00:00:00ZWe present results from a 3D numerical simulation which investigates the coupling of fast and Alfvén magnetohydrodynamic (MHD) waves in a nonuniform dipole equilibrium. This represents the time dependent extension of the normal mode (∝ exp(−iωt)) analysis of Wright and Elsden [2016], and provides a theoretical basis for understanding 3D Alfvén resonances. Wright and Elsden [2016] show that these are fundamentally different to resonances in 1D and 2D. We demonstrate the temporal behaviour of the Alfvén resonance, which is formed within the ‘Resonant Zone’; a channel of the domain where a family of solutions exists such that the natural Alfvén frequency matches the fast mode frequency. At early times, phase mixing leads to the production of prominent ridges in the energy density, whose shape is determined by the Alfvén speed profile and the chosen background magnetic field geometry. These off resonant ridges decay in time, leaving only a main 3D resonant sheet in the steady state. We show that the width of the 3D resonance in time and in space can be accurately estimated by adapting previous analytical estimates from 1D theory. We further provide an analytical estimate for the resonance amplitude in 3D, based upon extending 2D theory.
Both authors were funded in part by STFC (through Consolidated Grant ST/N000609/1) and The Leverhulme Trust (through Research Grant RPG-2016-071).
2017-03-01T00:00:00ZElsden, T.Wright, A. N.We present results from a 3D numerical simulation which investigates the coupling of fast and Alfvén magnetohydrodynamic (MHD) waves in a nonuniform dipole equilibrium. This represents the time dependent extension of the normal mode (∝ exp(−iωt)) analysis of Wright and Elsden [2016], and provides a theoretical basis for understanding 3D Alfvén resonances. Wright and Elsden [2016] show that these are fundamentally different to resonances in 1D and 2D. We demonstrate the temporal behaviour of the Alfvén resonance, which is formed within the ‘Resonant Zone’; a channel of the domain where a family of solutions exists such that the natural Alfvén frequency matches the fast mode frequency. At early times, phase mixing leads to the production of prominent ridges in the energy density, whose shape is determined by the Alfvén speed profile and the chosen background magnetic field geometry. These off resonant ridges decay in time, leaving only a main 3D resonant sheet in the steady state. We show that the width of the 3D resonance in time and in space can be accurately estimated by adapting previous analytical estimates from 1D theory. We further provide an analytical estimate for the resonance amplitude in 3D, based upon extending 2D theory.Wave of chaos in a spatial eco-epidemiological system : generating realistic patterns of patchiness in rabbit-lynx dynamicsUpadhyay, RanjitRoy, ParimitaVenkataraman, C.Madzvamuse, Anotidahttp://hdl.handle.net/10023/116662018-01-07T03:47:54Z2016-11-01T00:00:00ZIn the present paper, we propose and analyse an eco-epidemiological model with diffusion to study the dynamics of rabbit populations which are consumed by lynx populations. Existence, boundedness, stability and bifurcation analyses of solutions for the proposed rabbit-lynx model are performed. Results show that in the presence of diffusion the model has the potential of exhibiting Turing instability. Numerical results (finite difference and finite element methods) reveal the existence of the wave of chaos and this appears to be a dominant mode of disease dispersal. We also show the mechanism of spatiotemporal pattern formation resulting from the Hopf bifurcation analysis, which can be a potential candidate for understanding the complex spatiotemporal dynamics of eco-epidemiological systems. Implications of the asymptotic transmission rate on disease eradication among rabbit population which in turn enhances the survival of Iberian lynx are discussed.
AM and CV would like to acknowledge support from the Engineering and Physical Sciences Research Council grant (EP/J016780/1) and the Leverhulme Trust Research Project Grant (RPG-2014-149).
2016-11-01T00:00:00ZUpadhyay, RanjitRoy, ParimitaVenkataraman, C.Madzvamuse, AnotidaIn the present paper, we propose and analyse an eco-epidemiological model with diffusion to study the dynamics of rabbit populations which are consumed by lynx populations. Existence, boundedness, stability and bifurcation analyses of solutions for the proposed rabbit-lynx model are performed. Results show that in the presence of diffusion the model has the potential of exhibiting Turing instability. Numerical results (finite difference and finite element methods) reveal the existence of the wave of chaos and this appears to be a dominant mode of disease dispersal. We also show the mechanism of spatiotemporal pattern formation resulting from the Hopf bifurcation analysis, which can be a potential candidate for understanding the complex spatiotemporal dynamics of eco-epidemiological systems. Implications of the asymptotic transmission rate on disease eradication among rabbit population which in turn enhances the survival of Iberian lynx are discussed.On the energetics of a two-layer baroclinic flowJougla, ThibaultDritschel, David Gerardhttp://hdl.handle.net/10023/116372018-01-07T03:56:59Z2017-04-01T00:00:00ZThe formation, evolution and co-existence of jets and vortices in turbulent planetary atmospheres is examined using a two-layer quasi-geostrophic β -channel shallow-water model. The study in particular focuses on the vertical structure of jets. Following Panetta & Held (J. Atmos. Sci., vol. 45 (22), 1988, pp. 3354–3365), a vertical shear arising from latitudinal heating variations is imposed on the flow and maintained by thermal damping. Idealised convection between the upper and lower layers is implemented by adding cyclonic/anti-cyclonic pairs, called hetons, to the flow, though the qualitative flow evolution is evidently not sensitive to this or other small-scale stochastic forcing. A very wide range of simulations have been conducted. A characteristic simulation which exhibits alternation between two different phases, quiescent and turbulent, is examined in detail. We study the energy transfers between different components and modes, and find the classical picture of barotropic/baroclinic energy transfers to be too simplistic. We also discuss the dependence on thermal damping and on the imposed vertical shear. Both have a strong influence on the flow evolution. Thermal damping is a major factor affecting the stability of the flow while vertical shear controls the number of jets in the domain, qualitatively through the Rhines scale LRh = √U/β.
2017-04-01T00:00:00ZJougla, ThibaultDritschel, David GerardThe formation, evolution and co-existence of jets and vortices in turbulent planetary atmospheres is examined using a two-layer quasi-geostrophic β -channel shallow-water model. The study in particular focuses on the vertical structure of jets. Following Panetta & Held (J. Atmos. Sci., vol. 45 (22), 1988, pp. 3354–3365), a vertical shear arising from latitudinal heating variations is imposed on the flow and maintained by thermal damping. Idealised convection between the upper and lower layers is implemented by adding cyclonic/anti-cyclonic pairs, called hetons, to the flow, though the qualitative flow evolution is evidently not sensitive to this or other small-scale stochastic forcing. A very wide range of simulations have been conducted. A characteristic simulation which exhibits alternation between two different phases, quiescent and turbulent, is examined in detail. We study the energy transfers between different components and modes, and find the classical picture of barotropic/baroclinic energy transfers to be too simplistic. We also discuss the dependence on thermal damping and on the imposed vertical shear. Both have a strong influence on the flow evolution. Thermal damping is a major factor affecting the stability of the flow while vertical shear controls the number of jets in the domain, qualitatively through the Rhines scale LRh = √U/β.Exact Vlasov-Maxwell equilibria for asymmetric current sheetsAllanson, O.Wilson, F.Neukirch, T.Liu, Yi-HsinHodgson, J. D. B.http://hdl.handle.net/10023/116262018-01-07T04:04:19Z2017-09-16T00:00:00ZThe NASA Magnetospheric Multiscale mission has made in-situ diffusion region and kinetic-scale resolution measurements of asymmetric magnetic reconnection for the first time [Burch et al., 2016], in the Earth’s magnetopause. The principal theoretical tool currently used to model collisionless asymmetric reconnection is particle-in-cell simulations. Many particle-in-cell simulations of asymmetric collisionless reconnection start from an asymmetric Harris-type magnetic field, but with distribution functions that are not exact equilibrium solutions of the Vlasov equation. We present new and exact equilibrium solutions of the Vlasov-Maxwell system that are self-consistent with one-dimensional asymmetric current sheets, with an asymmetric Harris-type magnetic field profile, plus a constant non-zero guide field. The distribution functions can be represented as a combination of four shifted Maxwellian distribution functions. This equilibrium describes a magnetic field configuration with more freedom than the previously known exact solution [Alpers, 1969], and has different bulk flow properties.
Funding: Science and Technology Facilities Council Consolidated Grant Nos. ST/K000950/1 and ST/N000609/1 (O.A., T.N., J.D.B.H.and F.W.), the Science and Technology Facilities Council Doctoral Training Grant No. ST/K502327/1 (O.A. and J.D.B.H), the Natural Environment Research Council Grant No. NE/P017274/1 (Rad-Sat) (O.A.)
2017-09-16T00:00:00ZAllanson, O.Wilson, F.Neukirch, T.Liu, Yi-HsinHodgson, J. D. B.The NASA Magnetospheric Multiscale mission has made in-situ diffusion region and kinetic-scale resolution measurements of asymmetric magnetic reconnection for the first time [Burch et al., 2016], in the Earth’s magnetopause. The principal theoretical tool currently used to model collisionless asymmetric reconnection is particle-in-cell simulations. Many particle-in-cell simulations of asymmetric collisionless reconnection start from an asymmetric Harris-type magnetic field, but with distribution functions that are not exact equilibrium solutions of the Vlasov equation. We present new and exact equilibrium solutions of the Vlasov-Maxwell system that are self-consistent with one-dimensional asymmetric current sheets, with an asymmetric Harris-type magnetic field profile, plus a constant non-zero guide field. The distribution functions can be represented as a combination of four shifted Maxwellian distribution functions. This equilibrium describes a magnetic field configuration with more freedom than the previously known exact solution [Alpers, 1969], and has different bulk flow properties.Spatial variation in boundary conditions can govern selection and location of eyespots in butterfly wingsVenkataraman, ChandrasekharSekimura, Toshiohttp://hdl.handle.net/10023/116182018-02-11T01:36:19Z2017-01-01T00:00:00ZDespite being the subject of widespread study, many aspects of the development of eyespot patterns in butterfly wings remain poorly understood. In this work, we examine, through numerical simulations, a mathematical model for eyespot focus point formation in which a reaction-diffusion system is assumed to play the role of the patterning mechanism. In the model, changes in the boundary conditions at the veins at the proximal boundary alone are capable of determining whether or not an eyespot focus forms in a given wing cell and the eventual position of focus points within the wing cell. Furthermore, an auxiliary surface reaction diffusion system posed along the entire proximal boundary of the wing cells is proposed as the mechanism that generates the necessary changes in the proximal boundary profiles. In order to illustrate the robustness of the model, we perform simulations on a curved wing geometry that is somewhat closer to a biological realistic domain than the rectangular wing cells previously considered, and we also illustrate the ability of the model to reproduce experimental results on artificial selection of eyespots.
2017-01-01T00:00:00ZVenkataraman, ChandrasekharSekimura, ToshioDespite being the subject of widespread study, many aspects of the development of eyespot patterns in butterfly wings remain poorly understood. In this work, we examine, through numerical simulations, a mathematical model for eyespot focus point formation in which a reaction-diffusion system is assumed to play the role of the patterning mechanism. In the model, changes in the boundary conditions at the veins at the proximal boundary alone are capable of determining whether or not an eyespot focus forms in a given wing cell and the eventual position of focus points within the wing cell. Furthermore, an auxiliary surface reaction diffusion system posed along the entire proximal boundary of the wing cells is proposed as the mechanism that generates the necessary changes in the proximal boundary profiles. In order to illustrate the robustness of the model, we perform simulations on a curved wing geometry that is somewhat closer to a biological realistic domain than the rectangular wing cells previously considered, and we also illustrate the ability of the model to reproduce experimental results on artificial selection of eyespots.Force-free collisionless current sheet models with non-uniform temperature and density profilesWilson, FionaNeukirch, ThomasAllanson, Oliver Douglashttp://hdl.handle.net/10023/116142018-01-07T04:04:03Z2017-08-17T00:00:00ZWe present a class of one-dimensional, strictly neutral, Vlasov-Maxwell equilibrium distribution functions for force-free current sheets, with magnetic fields defined in terms of Jacobian elliptic functions, extending the results of Abraham-Shrauner48 to allow for non-uniform density and temperature pro les. To achieve this, we use an approach previously applied to the force-free Harris sheet by Kolotkov et al.49. In one limit of the parameters, we recover the model of Kolotkov et al.49, while another limit gives a linear force-free field. We discuss conditions on the parameters such that the distribution functions are always positive, and give expressions for the pressure, density, temperature and bulk- ow velocities of the equilibrium, discussing differences from previous models. We also present some illustrative plots of the distribution function in velocity space.
The authors acknowledge the support of the Science and Technology Facilities Council via the consolidated grants ST/K000950/1 and ST/N000609/1 and the doctoral training grant ST/K502327/1 (O. A.), and the Natural Environment Research Council via grant no. NE/P017274/1 (Rad-Sat) (O. A.). F. W. and T. N. would also like to thank the University of St Andrews for general financial support
2017-08-17T00:00:00ZWilson, FionaNeukirch, ThomasAllanson, Oliver DouglasWe present a class of one-dimensional, strictly neutral, Vlasov-Maxwell equilibrium distribution functions for force-free current sheets, with magnetic fields defined in terms of Jacobian elliptic functions, extending the results of Abraham-Shrauner48 to allow for non-uniform density and temperature pro les. To achieve this, we use an approach previously applied to the force-free Harris sheet by Kolotkov et al.49. In one limit of the parameters, we recover the model of Kolotkov et al.49, while another limit gives a linear force-free field. We discuss conditions on the parameters such that the distribution functions are always positive, and give expressions for the pressure, density, temperature and bulk- ow velocities of the equilibrium, discussing differences from previous models. We also present some illustrative plots of the distribution function in velocity space.Erwin Schrödinger and quantum wave mechanicsO'Connor, John J.Robertson, Edmund F.http://hdl.handle.net/10023/115432018-01-07T04:05:04Z2017-08-22T00:00:00ZThe fathers of matrix quantum mechanics believed that the quantum particles are unanschaulich (unvisualizable) and that quantum particles pop into existence only when we measure them. Challenging the orthodoxy, in 1926 Erwin Schrödinger developed his wave equation that describes the quantum particles as a packet of quantum probability amplitudes evolving in space and time. Thus, Schrödinger visualized the unvisualizable and lifted the veil that has been obscuring the wonders of the quantum world.
2017-08-22T00:00:00ZO'Connor, John J.Robertson, Edmund F.The fathers of matrix quantum mechanics believed that the quantum particles are unanschaulich (unvisualizable) and that quantum particles pop into existence only when we measure them. Challenging the orthodoxy, in 1926 Erwin Schrödinger developed his wave equation that describes the quantum particles as a packet of quantum probability amplitudes evolving in space and time. Thus, Schrödinger visualized the unvisualizable and lifted the veil that has been obscuring the wonders of the quantum world.The stability of Mars' annular polar vortexSeviour, WilliamWaugh, DarrynScott, Richard Kirknesshttp://hdl.handle.net/10023/115412018-02-11T01:35:06Z2017-05-01T00:00:00ZThe Martian polar atmosphere is known to have a persistent local minimum in potential vorticity (PV) near the winter pole, with a region of high PV encircling it. This finding is surprising since an isolated band of PV is barotropically unstable, a result going back to Rayleigh. Here we investigate the stability of a Mars-like annular vortex using numerical integrations of the rotating shallow water equations. We show how the mode of instability and its growth rate depends upon the latitude and width of the annulus. By introducing thermal relaxation towards an annular equilibrium profile with a time scale similar to that of the instability, we are able to simulate a persistent annular vortex with similar characteristics as that observed in the Martian atmosphere. This time scale, typically 0.5-2 sols, is similar to radiative relaxation time scales for Mars’ polar atmosphere. We also demonstrate that the persistence of an annular vortex is robust to topographic forcing, as long as it is below a certain amplitude. We hence propose that the persistence of this barotropically unstable annular vortex is permitted due to the combination of short radiative relaxation time scales and relatively weak topographic forcing in the Martian polar atmosphere.
This research was partially supported by a NASA grant from the Mars Fundamental Research Program (NNX14AG53G).
2017-05-01T00:00:00ZSeviour, WilliamWaugh, DarrynScott, Richard KirknessThe Martian polar atmosphere is known to have a persistent local minimum in potential vorticity (PV) near the winter pole, with a region of high PV encircling it. This finding is surprising since an isolated band of PV is barotropically unstable, a result going back to Rayleigh. Here we investigate the stability of a Mars-like annular vortex using numerical integrations of the rotating shallow water equations. We show how the mode of instability and its growth rate depends upon the latitude and width of the annulus. By introducing thermal relaxation towards an annular equilibrium profile with a time scale similar to that of the instability, we are able to simulate a persistent annular vortex with similar characteristics as that observed in the Martian atmosphere. This time scale, typically 0.5-2 sols, is similar to radiative relaxation time scales for Mars’ polar atmosphere. We also demonstrate that the persistence of an annular vortex is robust to topographic forcing, as long as it is below a certain amplitude. We hence propose that the persistence of this barotropically unstable annular vortex is permitted due to the combination of short radiative relaxation time scales and relatively weak topographic forcing in the Martian polar atmosphere.Multimodality imaging and mathematical modelling of drug delivery to glioblastomasBoujelben, AhmedWatson, MichaelMcDougall, StevenYen, Yi-FenGerstner, ElizabethCatana, CiprianDeisboeck, ThomasBatchelor, TracyBoas, DavidRosen, BruceKalpathy-Cramer, JayashreeChaplain, Mark Andrew Josephhttp://hdl.handle.net/10023/115132018-01-07T03:45:09Z2016-10-06T00:00:00ZPatients diagnosed with glioblastoma, an aggressive brain tumour, have a poor prognosis, with a median overall survival of less than 15 months. Vasculature within these tumours is typically abnormal, with increased tortuosity, dilation and disorganization and they typically exhibit a disrupted blood brain barrier. Although it has been hypothesized that the “normalization” of the vasculature resulting from anti-angiogenic therapies could improve drug delivery through improved blood flow, there is also evidence that suggests that the restoration of blood brain barrier integrity might limit the delivery of therapeutic agents and hence their effectiveness. In this paper we apply mathematical models of blood flow, vascular permeability and diffusion within the tumour microenvironment to investigate the effect of these competing factors on drug delivery. Preliminary results from the modelling indicate that all three physiological parameters investigated – flow rate, vessel permeability, and tissue diffusion coefficient – interact nonlinearly to produce the observed average drug concentration in the microenvironment.
MAJC would like to thank the Isaac Newton Institute for Mathematical Sciences for its hospitality during the programme “Coupling Geometric PDEs with Physics for Cell Morphology, Motility and Pattern Formation” supported by EPSRC Grant Number EP/K032208/1.
2016-10-06T00:00:00ZBoujelben, AhmedWatson, MichaelMcDougall, StevenYen, Yi-FenGerstner, ElizabethCatana, CiprianDeisboeck, ThomasBatchelor, TracyBoas, DavidRosen, BruceKalpathy-Cramer, JayashreeChaplain, Mark Andrew JosephPatients diagnosed with glioblastoma, an aggressive brain tumour, have a poor prognosis, with a median overall survival of less than 15 months. Vasculature within these tumours is typically abnormal, with increased tortuosity, dilation and disorganization and they typically exhibit a disrupted blood brain barrier. Although it has been hypothesized that the “normalization” of the vasculature resulting from anti-angiogenic therapies could improve drug delivery through improved blood flow, there is also evidence that suggests that the restoration of blood brain barrier integrity might limit the delivery of therapeutic agents and hence their effectiveness. In this paper we apply mathematical models of blood flow, vascular permeability and diffusion within the tumour microenvironment to investigate the effect of these competing factors on drug delivery. Preliminary results from the modelling indicate that all three physiological parameters investigated – flow rate, vessel permeability, and tissue diffusion coefficient – interact nonlinearly to produce the observed average drug concentration in the microenvironment.Pressure moderation and effective pressure in Navier-Stokes flowsTran, Chuong VanYu, Xinweihttp://hdl.handle.net/10023/114992018-01-07T03:45:48Z2016-08-17T00:00:00ZWe study the Cauchy problem of the Navier–Stokes equations by both semi-analytic and classical energy methods. The former approach provides a physical picture of how viscous effects may or may not be able to suppress singularity development. In the latter approach, we examine the pressure term that drives the dynamics of the velocity norms ||u||Lq , for q ≥ 3. A key idea behind this investigation is due to the fact that the pressure p in this term is determined upto a function of both space and |u|, say Ƥ(x, |u|), which may assume relatively broad forms. This allows us to use Ƥ as a pressure moderator in the evolution equation for ||u||Lq , whereby optimal regularity criteria can be sought by varying Ƥ within its admissible classes. New regularity criteria are derived with and without making use of the moderator. The results obtained in the absence of the moderator feature some improvement over existing criteria in the literature. Several criteria are derived in terms of the moderated (effective) pressure p+Ƥ. A simple moderation scheme and the plausibility of the present approach to the problem of Navier–Stokes regularity are discussed.
2016-08-17T00:00:00ZTran, Chuong VanYu, XinweiWe study the Cauchy problem of the Navier–Stokes equations by both semi-analytic and classical energy methods. The former approach provides a physical picture of how viscous effects may or may not be able to suppress singularity development. In the latter approach, we examine the pressure term that drives the dynamics of the velocity norms ||u||Lq , for q ≥ 3. A key idea behind this investigation is due to the fact that the pressure p in this term is determined upto a function of both space and |u|, say Ƥ(x, |u|), which may assume relatively broad forms. This allows us to use Ƥ as a pressure moderator in the evolution equation for ||u||Lq , whereby optimal regularity criteria can be sought by varying Ƥ within its admissible classes. New regularity criteria are derived with and without making use of the moderator. The results obtained in the absence of the moderator feature some improvement over existing criteria in the literature. Several criteria are derived in terms of the moderated (effective) pressure p+Ƥ. A simple moderation scheme and the plausibility of the present approach to the problem of Navier–Stokes regularity are discussed.Energetics of the Kelvin-Helmholtz instability induced by transverse waves in twisted coronal loopsHowson, T. A.De Moortel, I.Antolin, P.http://hdl.handle.net/10023/114442018-02-11T01:36:01Z2017-11-16T00:00:00ZAims. We quantify the effects of twisted magnetic fields on the development of the magnetic Kelvin-Helmholtz instability (KHI) in transversely oscillating coronal loops. Methods. We modelled a fundamental standing kink mode in a straight, density-enhanced magnetic flux tube using the magnetohydrodynamics code, Lare3d. In order to evaluate the impact of an azimuthal component of the magnetic field, various degrees of twist were included within the flux tube’s magnetic field. Results. The process of resonant absorption is only weakly affected by the presence of a twisted magnetic field. However, the subsequent evolution of the KHI is sensitive to the strength of the azimuthal component of the field. Increased twist values inhibit the deformation of the loop’s density profile, which is associated with the growth of the instability. Despite this, much smaller scales in the magnetic field are generated when there is a non-zero azimuthal component present. Hence, the instability is more energetic in cases with (even weakly) twisted fields. Field aligned flows at the loop apex are established in a twisted regime once the instability has formed. Further, in the straight field case, there is no net vertical component of vorticity when integrated across the loop. However, the inclusion of azimuthal magnetic field generates a preferred direction for the vorticity which oscillates during the kink mode. Conclusions. The KHI may have implications for wave heating in the solar atmosphere due to the creation of small length scales and the generation of a turbulent regime. Whilst magnetic twist does suppress the development of the vortices associated with the instability, the formation of the KHI in a twisted regime will be accompanied by greater Ohmic dissipation due to the larger currents that are produced, even if only weak twist is present. The presence of magnetic twist will likely make the instability more difficult to detect in the corona, but will enhance its contribution to heating the solar atmosphere. Further, the development of velocities along the loop may have observational applications for inferring the presence of magnetic twist within coronal structures.
The research leading to these results has received funding from the UK Science and Technology Facilities Council (consolidated grant ST/N000609/1) and the European Union Horizon 2020 research and innovation programme (grant agreement No. 647214).
2017-11-16T00:00:00ZHowson, T. A.De Moortel, I.Antolin, P.Aims. We quantify the effects of twisted magnetic fields on the development of the magnetic Kelvin-Helmholtz instability (KHI) in transversely oscillating coronal loops. Methods. We modelled a fundamental standing kink mode in a straight, density-enhanced magnetic flux tube using the magnetohydrodynamics code, Lare3d. In order to evaluate the impact of an azimuthal component of the magnetic field, various degrees of twist were included within the flux tube’s magnetic field. Results. The process of resonant absorption is only weakly affected by the presence of a twisted magnetic field. However, the subsequent evolution of the KHI is sensitive to the strength of the azimuthal component of the field. Increased twist values inhibit the deformation of the loop’s density profile, which is associated with the growth of the instability. Despite this, much smaller scales in the magnetic field are generated when there is a non-zero azimuthal component present. Hence, the instability is more energetic in cases with (even weakly) twisted fields. Field aligned flows at the loop apex are established in a twisted regime once the instability has formed. Further, in the straight field case, there is no net vertical component of vorticity when integrated across the loop. However, the inclusion of azimuthal magnetic field generates a preferred direction for the vorticity which oscillates during the kink mode. Conclusions. The KHI may have implications for wave heating in the solar atmosphere due to the creation of small length scales and the generation of a turbulent regime. Whilst magnetic twist does suppress the development of the vortices associated with the instability, the formation of the KHI in a twisted regime will be accompanied by greater Ohmic dissipation due to the larger currents that are produced, even if only weak twist is present. The presence of magnetic twist will likely make the instability more difficult to detect in the corona, but will enhance its contribution to heating the solar atmosphere. Further, the development of velocities along the loop may have observational applications for inferring the presence of magnetic twist within coronal structures.A new approach for modelling chromospheric evaporation in response to enhanced coronal heating : II. Non-uniform heatingJohnston, C. D.Hood, A. W.Cargill, P. J.De Moortel, I.http://hdl.handle.net/10023/114272018-02-25T01:33:13Z2017-09-01T00:00:00ZWe proposed that the use of an approximate “jump condition” at the solar transition region permits fast and accurate numerical solutions of the one dimensional hydrodynamic equations when the corona undergoes impulsive heating. In particular, it eliminates the need for the very short timesteps imposed by a highly resolved numerical grid. This paper presents further examples of the applicability of the method for cases of non-uniform heating, in particular, nanoflare trains (uniform in space but non-uniform in time) and spatially localised impulsive heating, including at the loop apex and base of the transition region. In all cases the overall behaviour of the coronal density and temperature shows good agreement with a fully resolved one dimensional model and is significantly better than the equivalent results from a 1D code run without using the jump condition but with the same coarse grid. A detailed assessment of the errors introduced by the jump condition is presented showing that the causes of discrepancy with the fully resolved code are (i) the neglect of the terms corresponding to the rate of change of total energy in the unresolved atmosphere; (ii) mass motions at the base of the transition region and (iii) for some cases with footpoint heating, an over-estimation of the radiative losses in the transition region.
This project has received funding from the Science and Technology Facilities Council (UK) through the consolidated grant ST/N000609/1 and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 647214).
2017-09-01T00:00:00ZJohnston, C. D.Hood, A. W.Cargill, P. J.De Moortel, I.We proposed that the use of an approximate “jump condition” at the solar transition region permits fast and accurate numerical solutions of the one dimensional hydrodynamic equations when the corona undergoes impulsive heating. In particular, it eliminates the need for the very short timesteps imposed by a highly resolved numerical grid. This paper presents further examples of the applicability of the method for cases of non-uniform heating, in particular, nanoflare trains (uniform in space but non-uniform in time) and spatially localised impulsive heating, including at the loop apex and base of the transition region. In all cases the overall behaviour of the coronal density and temperature shows good agreement with a fully resolved one dimensional model and is significantly better than the equivalent results from a 1D code run without using the jump condition but with the same coarse grid. A detailed assessment of the errors introduced by the jump condition is presented showing that the causes of discrepancy with the fully resolved code are (i) the neglect of the terms corresponding to the rate of change of total energy in the unresolved atmosphere; (ii) mass motions at the base of the transition region and (iii) for some cases with footpoint heating, an over-estimation of the radiative losses in the transition region.N-body dynamics on closed surfaces : the axioms of mechanicsBoatto, StefanellaDritschel, David GerardSchaefer, Rodrigo Ghttp://hdl.handle.net/10023/114262018-01-07T03:46:39Z2016-08-01T00:00:00ZA major challenge for our understanding of the mathematical basis of particle dynamics is the formulation of N-body and N-vortex dynamics on Riemann surfaces. In this paper, we show how the two problems are, in fact, closely related when considering the role played by the intrinsic geometry of the surface. This enables a straightforward deduction of the dynamics of point masses, using recently derived results for point vortices on general closed differentiable surfaces M endowed with a metric g. We find, generally, that Kepler's Laws do not hold. What is more, even Newton's First Law (the law of inertia) fails on closed surfaces with variable curvature (e.g. the ellipsoid).
D.G.D. gratefully acknowledges support for this research from CNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico ) and FINEP (Inovação e Pesquisa) in Brazil, and from the UK Engineering and Physical Sciences Research Council (grant no. EP/H001794/1)
2016-08-01T00:00:00ZBoatto, StefanellaDritschel, David GerardSchaefer, Rodrigo GA major challenge for our understanding of the mathematical basis of particle dynamics is the formulation of N-body and N-vortex dynamics on Riemann surfaces. In this paper, we show how the two problems are, in fact, closely related when considering the role played by the intrinsic geometry of the surface. This enables a straightforward deduction of the dynamics of point masses, using recently derived results for point vortices on general closed differentiable surfaces M endowed with a metric g. We find, generally, that Kepler's Laws do not hold. What is more, even Newton's First Law (the law of inertia) fails on closed surfaces with variable curvature (e.g. the ellipsoid).Interaction of a mode-2 internal solitary wave with narrow isolated topographyDeepwell, DavidStastna, MarekCarr, MagdaDavies, Peter A.http://hdl.handle.net/10023/114062018-01-07T04:02:48Z2017-07-31T00:00:00ZNumerical and experimental studies of the transit of a mode-2 internal solitary wave over an isolated ridge are presented. All studies used a quasi-two-layer fluid with a pycnocline centred at the mid-depth. The wave amplitude and total fluid depth were both varied, while the topography remained fixed. The strength of the interaction between the internal solitary waves and the hill was found to be characterized by three regimes: weak, moderate, and strong interactions. The weak interaction exhibited negligible wave modulation and bottom surface stress. The moderate interaction generated weak and persistent vorticity in the lower layer, in addition to negligible wave modulation. The strong interaction clearly showed material from the trapped core of the mode-2 wave extracted in the form of a thin filament while generating a strong vortex at the hill. A criterion for the strength of the interaction was found by non-dimensionalizing the wave amplitude by the lower layer depth, a/ℓ. A passive tracer was used to measure the conditions for resuspension of boundary material due to the interaction. The speed and prevalence of cross boundary layer transport increased with a/ℓ.
This research was supported by the Natural Sciences and Engineering Research Council of Canada through a Discovery Grant (MS), and the Government of Ontario through a Queen Elizabeth II Graduate Scholarship in Science and Technology (DD). The experimental work was conducted at The University of Dundee by DD and MC with the aid of grants provided by The University of Dundee, the University of St Andrews, and the University of Waterloo.
2017-07-31T00:00:00ZDeepwell, DavidStastna, MarekCarr, MagdaDavies, Peter A.Numerical and experimental studies of the transit of a mode-2 internal solitary wave over an isolated ridge are presented. All studies used a quasi-two-layer fluid with a pycnocline centred at the mid-depth. The wave amplitude and total fluid depth were both varied, while the topography remained fixed. The strength of the interaction between the internal solitary waves and the hill was found to be characterized by three regimes: weak, moderate, and strong interactions. The weak interaction exhibited negligible wave modulation and bottom surface stress. The moderate interaction generated weak and persistent vorticity in the lower layer, in addition to negligible wave modulation. The strong interaction clearly showed material from the trapped core of the mode-2 wave extracted in the form of a thin filament while generating a strong vortex at the hill. A criterion for the strength of the interaction was found by non-dimensionalizing the wave amplitude by the lower layer depth, a/ℓ. A passive tracer was used to measure the conditions for resuspension of boundary material due to the interaction. The speed and prevalence of cross boundary layer transport increased with a/ℓ.Interaction between a surface quasi-geostrophic buoyancy anomaly jet and internal vorticesReinaud, Jean NoelDritschel, David GerardCarton, Xavierhttp://hdl.handle.net/10023/114042018-01-07T04:04:12Z2017-08-01T00:00:00ZThis paper addresses the dynamical coupling of the ocean's surface and the ocean's interior. In particular, we investigate the dynamics of an oceanic surface jet, and its interaction with vortices at depth. The jet is induced by buoyancy (density) anomalies at the surface. We first focus on the jet alone. The linear stability indicates there are two modes of instability: the sinuous and the varicose modes. When a vortex in present below the jet, it interacts with it. The velocity field induced by the vortex perturbs the jet and triggers its destabilisation. The jet also influences the vortex by pushing it under a region of co-operative shear. Strong jets may also partially shear out the vortex. We also investigate the interaction between a surface jet and a vortex dipole in the interior. Again, strong jets may partially shear out the vortex structure. The jet also modifies the trajectory of the dipole. Dipoles travelling towards the jet at shallow incidence angles may be reflected by the jet. Vortices travelling at moderate incidence angles normally cross below the jet. This is related to the displacement of the two vortices of the dipole by the shear induced by the jet. Intense jets may also destabilise early and form streets of billows. These billows can pair with the vortices and separate the dipole.
2017-08-01T00:00:00ZReinaud, Jean NoelDritschel, David GerardCarton, XavierThis paper addresses the dynamical coupling of the ocean's surface and the ocean's interior. In particular, we investigate the dynamics of an oceanic surface jet, and its interaction with vortices at depth. The jet is induced by buoyancy (density) anomalies at the surface. We first focus on the jet alone. The linear stability indicates there are two modes of instability: the sinuous and the varicose modes. When a vortex in present below the jet, it interacts with it. The velocity field induced by the vortex perturbs the jet and triggers its destabilisation. The jet also influences the vortex by pushing it under a region of co-operative shear. Strong jets may also partially shear out the vortex. We also investigate the interaction between a surface jet and a vortex dipole in the interior. Again, strong jets may partially shear out the vortex structure. The jet also modifies the trajectory of the dipole. Dipoles travelling towards the jet at shallow incidence angles may be reflected by the jet. Vortices travelling at moderate incidence angles normally cross below the jet. This is related to the displacement of the two vortices of the dipole by the shear induced by the jet. Intense jets may also destabilise early and form streets of billows. These billows can pair with the vortices and separate the dipole.Observations and numerical models of coronal heating associated with spiculesDe Pontieu, BartDe Moortel, InekeMartinez-Sykora, JuanMcIntosh, Scotthttp://hdl.handle.net/10023/113582018-02-25T01:33:15Z2017-08-20T00:00:00ZSpicules have been proposed as significant contributors to the mass and energy balance of the corona. While previous observations have provided a glimpse of short-lived transient brightenings in the corona that are associated with spicules,these observations have been contested and are the subject of a vigorous debate both on the modeling and the observational side. Therefore, it remains unclear whether plasma is heated to coronal temperatures in association with spicules.We use high-resolution observations of the chromosphere and transition region with the Interface Region Imaging Spectrograph (IRIS) and of the corona with the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO) to show evidence of the formation of coronal structures associated with spicular mass ejections and heating of plasma to transition region and coronal temperatures. Our observations suggest that a significant fraction of the highly dynamic loop fan environment associated with plage regions may be the result of the formation of such new coronal strands, a process that previously had been interpreted as the propagation of transient propagating coronal disturbances (PCD)s. Our observations are supported by 2.5D radiative MHD simulations that show heating to coronal temperatures in association with spicules. Our results suggest that heating and strong flows play an important role in maintaining the substructure of loop fans, in addition to the waves that permeate this low coronal environment.
2017-08-20T00:00:00ZDe Pontieu, BartDe Moortel, InekeMartinez-Sykora, JuanMcIntosh, ScottSpicules have been proposed as significant contributors to the mass and energy balance of the corona. While previous observations have provided a glimpse of short-lived transient brightenings in the corona that are associated with spicules,these observations have been contested and are the subject of a vigorous debate both on the modeling and the observational side. Therefore, it remains unclear whether plasma is heated to coronal temperatures in association with spicules.We use high-resolution observations of the chromosphere and transition region with the Interface Region Imaging Spectrograph (IRIS) and of the corona with the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory (SDO) to show evidence of the formation of coronal structures associated with spicular mass ejections and heating of plasma to transition region and coronal temperatures. Our observations suggest that a significant fraction of the highly dynamic loop fan environment associated with plage regions may be the result of the formation of such new coronal strands, a process that previously had been interpreted as the propagation of transient propagating coronal disturbances (PCD)s. Our observations are supported by 2.5D radiative MHD simulations that show heating to coronal temperatures in association with spicules. Our results suggest that heating and strong flows play an important role in maintaining the substructure of loop fans, in addition to the waves that permeate this low coronal environment.Evolutionary dynamics of phenotype-structured populations : from individual-level mechanisms to population-level consequencesChisholm, Rebecca H.Lorenzi, TommasoDesvillettes, LaurentHughes, Barry D.http://hdl.handle.net/10023/113282018-01-07T03:44:35Z2016-08-01T00:00:00ZEpigenetic mechanisms are increasingly recognised as integral to the adaptation of species that face environmental changes. In particular, empirical work has provided important insights into the contribution of epigenetic mechanisms to the persistence of clonal species, from which a number of verbal explanations have emerged that are suited to logical testing by proof-of-concept mathematical models. Here, we present a stochastic agent-based model and a related deterministic integrodifferential equation model for the evolution of a phenotype-structured population composed of asexually-reproducing and competing organisms which are exposed to novel environmental conditions. This setting has relevance to the study of biological systems where colonising asexual populations must survive and rapidly adapt to hostile environments, like pathogenesis, invasion and tumour metastasis. We explore how evolution might proceed when epigenetic variation in gene expression can change the reproductive capacity of individuals within the population in the new environment. Simulations and analyses of our models clarify the conditions under which certain evolutionary paths are possible, and illustrate that whilst epigenetic mechanisms may facilitate adaptation in asexual species faced with environmental change, they can also lead to a type of “epigenetic load” and contribute to extinction. Moreover, our results offer a formal basis for the claim that constant environments favour individuals with low rates of stochastic phenotypic variation. Finally, our model provides a “proof of concept” of the verbal hypothesis that phenotypic stability is a key driver in rescuing the adaptive potential of an asexual lineage, and supports the notion that intense selection pressure can, to an extent, offset the deleterious effects of high phenotypic instability and biased epimutations, and steer an asexual population back from the brink of an evolutionary dead end.
This research was supported in part by the Australian Research Council (DP140100339) and by the French National Research Agency through the ANR blanche project Kibord [ANR-13-BS01-0004] and the “ANR JC” project Modevol [ANR-13-JS01-0009]. TL was also supported in part by the Hadamard Mathematics Labex, backed by the Fondation Mathématique Jacques Hadamard, through a grant overseen by the French National Research Agency [ANR-11-LABX-0056-LMH]. LD was also supported in part by Université Sorbonne Paris Cité “Investissements d’Avenir”[ANR-11-IDEX-0005].
2016-08-01T00:00:00ZChisholm, Rebecca H.Lorenzi, TommasoDesvillettes, LaurentHughes, Barry D.Epigenetic mechanisms are increasingly recognised as integral to the adaptation of species that face environmental changes. In particular, empirical work has provided important insights into the contribution of epigenetic mechanisms to the persistence of clonal species, from which a number of verbal explanations have emerged that are suited to logical testing by proof-of-concept mathematical models. Here, we present a stochastic agent-based model and a related deterministic integrodifferential equation model for the evolution of a phenotype-structured population composed of asexually-reproducing and competing organisms which are exposed to novel environmental conditions. This setting has relevance to the study of biological systems where colonising asexual populations must survive and rapidly adapt to hostile environments, like pathogenesis, invasion and tumour metastasis. We explore how evolution might proceed when epigenetic variation in gene expression can change the reproductive capacity of individuals within the population in the new environment. Simulations and analyses of our models clarify the conditions under which certain evolutionary paths are possible, and illustrate that whilst epigenetic mechanisms may facilitate adaptation in asexual species faced with environmental change, they can also lead to a type of “epigenetic load” and contribute to extinction. Moreover, our results offer a formal basis for the claim that constant environments favour individuals with low rates of stochastic phenotypic variation. Finally, our model provides a “proof of concept” of the verbal hypothesis that phenotypic stability is a key driver in rescuing the adaptive potential of an asexual lineage, and supports the notion that intense selection pressure can, to an extent, offset the deleterious effects of high phenotypic instability and biased epimutations, and steer an asexual population back from the brink of an evolutionary dead end.Our dynamic sun : 2017 Hannes Alfvén Medal lecture at the EGUPriest, Erichttp://hdl.handle.net/10023/113202018-01-07T04:03:52Z2017-07-14T00:00:00ZThis lecture summarises how our understanding of many aspects of the Sun has been revolutionised over the past few years by new observations and models. Much of the dynamic behaviour of the Sun is driven by the magnetic field since, in the outer atmosphere, it represents the largest source of energy by far. The interior of the Sun possesses a strong shear layer at the base of the convection zone, where sunspot magnetic fields are generated. A small-scale dynamo may also be operating near the surface of the Sun, generating magnetic fields that thread the lowest layer of the solar atmosphere, the turbulent photosphere. Above the photosphere lies the highly dynamic fine-scale chromosphere, and beyond that is the rare corona at high temperatures exceeding 1 million degrees K. Possible magnetic mechanisms for heating the corona and driving the solar wind (two intriguing and unsolved puzzles) are described. Other puzzles include the structure of giant flux ropes, known as prominences, which have complex fine structure. Occasionally, they erupt and produce huge ejections of mass and magnetic fields (coronal mass ejections), which can disrupt the space environment of the Earth. When such eruptions originate in active regions around sunspots, they are also associated with solar flares, in which magnetic energy is converted to kinetic energy, heat and fast-particle energy. A new theory will be presented for the origin of the twist that is observed in erupting prominences and for the nature of reconnection in the rise phase of an eruptive flare or coronal mass ejection.
2017-07-14T00:00:00ZPriest, EricThis lecture summarises how our understanding of many aspects of the Sun has been revolutionised over the past few years by new observations and models. Much of the dynamic behaviour of the Sun is driven by the magnetic field since, in the outer atmosphere, it represents the largest source of energy by far. The interior of the Sun possesses a strong shear layer at the base of the convection zone, where sunspot magnetic fields are generated. A small-scale dynamo may also be operating near the surface of the Sun, generating magnetic fields that thread the lowest layer of the solar atmosphere, the turbulent photosphere. Above the photosphere lies the highly dynamic fine-scale chromosphere, and beyond that is the rare corona at high temperatures exceeding 1 million degrees K. Possible magnetic mechanisms for heating the corona and driving the solar wind (two intriguing and unsolved puzzles) are described. Other puzzles include the structure of giant flux ropes, known as prominences, which have complex fine structure. Occasionally, they erupt and produce huge ejections of mass and magnetic fields (coronal mass ejections), which can disrupt the space environment of the Earth. When such eruptions originate in active regions around sunspots, they are also associated with solar flares, in which magnetic energy is converted to kinetic energy, heat and fast-particle energy. A new theory will be presented for the origin of the twist that is observed in erupting prominences and for the nature of reconnection in the rise phase of an eruptive flare or coronal mass ejection.Diffusion driven oscillations in gene regulatory networksMacnamara, Cicely KrystynaChaplain, Mark Andrew Josephhttp://hdl.handle.net/10023/112582018-03-04T01:38:44Z2016-10-21T00:00:00ZGene regulatory networks (GRNs) play an important role in maintaining cellular function by correctly timing key processes such as cell division and apoptosis. GRNs are known to contain similar structural components, which describe how genes and proteins within a network interact - typically by feedback. In many GRNs, proteins bind to gene-sites in the nucleus thereby altering the transcription rate. If the binding reduces the transcription rate there is a negative feedback leading to oscillatory behaviour in mRNA and protein levels, both spatially (e.g. by observing fluorescently labelled molecules in single cells) and temporally (e.g. by observing protein/mRNA levels over time). Mathematical modelling of GRNs has focussed on such oscillatory behaviour. Recent computational modelling has demonstrated that spatial movement of the molecules is a vital component of GRNs, while it has been proved rigorously that the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf-bifurcation. In this paper we consider the spatial aspect further by considering the specific location of gene and protein production, showing that there is an optimum range for the distance between an mRNA gene-site and a protein production site in order to achieve oscillations. We first present a model of a well-known GRN, the Hes1 system, and then extend the approach to examine spatio-temporal models of synthetic GRNs e.g. n-gene repressilator and activator-repressor systems. By incorporating the idea of production sites into such models we show that the spatial component is vital to fully understand GRN dynamics.
2016-10-21T00:00:00ZMacnamara, Cicely KrystynaChaplain, Mark Andrew JosephGene regulatory networks (GRNs) play an important role in maintaining cellular function by correctly timing key processes such as cell division and apoptosis. GRNs are known to contain similar structural components, which describe how genes and proteins within a network interact - typically by feedback. In many GRNs, proteins bind to gene-sites in the nucleus thereby altering the transcription rate. If the binding reduces the transcription rate there is a negative feedback leading to oscillatory behaviour in mRNA and protein levels, both spatially (e.g. by observing fluorescently labelled molecules in single cells) and temporally (e.g. by observing protein/mRNA levels over time). Mathematical modelling of GRNs has focussed on such oscillatory behaviour. Recent computational modelling has demonstrated that spatial movement of the molecules is a vital component of GRNs, while it has been proved rigorously that the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf-bifurcation. In this paper we consider the spatial aspect further by considering the specific location of gene and protein production, showing that there is an optimum range for the distance between an mRNA gene-site and a protein production site in order to achieve oscillations. We first present a model of a well-known GRN, the Hes1 system, and then extend the approach to examine spatio-temporal models of synthetic GRNs e.g. n-gene repressilator and activator-repressor systems. By incorporating the idea of production sites into such models we show that the spatial component is vital to fully understand GRN dynamics.MapMySmoke : feasibility of a new quit cigarette smoking mobile phone application using integrated geo-positioning technology, and motivational messaging within a primary care settingSchick, Robert S.Kelsey, Thomas W.Marston, JohnSampson, KayHumphris, Gerald M.http://hdl.handle.net/10023/112052017-12-31T00:37:24Z2017-07-14T00:00:00ZBackground: Approximately 11,000 people die in Scotland each year as a result of smoking-related causes. Quitting smoking is relatively easy; maintaining a quit attempt is a very difficult task with success rates for unaided quit attempts stubbornly remaining in the single digits. Pharmaceutical treatment can improve these rates by lowering the overall reward factor of nicotine. However, these and related nicotine replacement therapies do not operate on, or address, the spatial and contextual aspects of smoking behaviour. With the ubiquity of smartphones that can log spatial, quantitative and qualitative data related to smoking behaviour, there exists a person-centred clinical opportunity to support smokers attempting to quit by first understanding their smoking behaviour and subsequently sending them dynamic messages to encourage health behaviour change within a situational context. Methods: We have built a smartphone app—MapMySmoke—that works on Android and iOS platforms. The deployment of this app within a clinical National Health Service (NHS) setting has two distinct phases: (1) a 2-week logging phase where pre-quit patients log all of their smoking and craving events; and (2) a post-quit phase where users receive dynamic support messages and can continue to log craving events, and should they occur, relapse events. Following the initial logging phase, patients consult with their general practitioner (GP) or healthcare provider to review their smoking patterns and to outline a precise, individualised quit attempt plan. Our feasibility study consists of assessment of an initial app version during and after use by eight patients recruited from an NHS Fife GP practice. In addition to evaluation of the app as a potential smoking cessation aid, we have assessed the user experience, technological requirements and security of the data flow. Results: In an initial feasibility study, we have deployed the app for a small number of patients within one GP practice in NHS Fife. We recruited eight patients within one surgery, four of whom actively logged information about their smoking behaviour. Initial feedback was very positive, and users indicated a willingness to log their craving and smoking events. In addition, two out of three patients who completed follow-up interviews noted that the app helped them reduce the number of cigarettes they smoked per day, while the third indicated that it had helped them quit. The study highlighted the use of pushed notifications as a potential technology for maintaining quit attempts, and the security of collection of data was audited. These initial results influenced the design of a planned second larger study, comprised of 100 patients, the primary objectives of which are to use statistical modelling to identify times and places of probable switches into smoking states, and to target these times with dynamic health behaviour messaging. Conclusions: While the health benefits of quitting smoking are unequivocal, such behaviour change is very difficult to achieve. Many factors are likely to contribute to maintaining smoking behaviour, yet the precise role of cues derived from the spatial environment remains unclear. The rise of smartphones, therefore, allows clinicians the opportunity to better understand the spatial aspects of smoking behaviour and affords them the opportunity to push targeted individualised health support messages at vulnerable times and places.
This work was funded in part by an NHS Fife Research and Development Bursary Award to all authors. In addition, we have received funding from the University of St Andrews’ EPSRC Impact Acceleration Account. In 2013, Schick received a LEADERS award from the Scottish Universities Life Sciences Alliance that started this project.
2017-07-14T00:00:00ZSchick, Robert S.Kelsey, Thomas W.Marston, JohnSampson, KayHumphris, Gerald M.Background: Approximately 11,000 people die in Scotland each year as a result of smoking-related causes. Quitting smoking is relatively easy; maintaining a quit attempt is a very difficult task with success rates for unaided quit attempts stubbornly remaining in the single digits. Pharmaceutical treatment can improve these rates by lowering the overall reward factor of nicotine. However, these and related nicotine replacement therapies do not operate on, or address, the spatial and contextual aspects of smoking behaviour. With the ubiquity of smartphones that can log spatial, quantitative and qualitative data related to smoking behaviour, there exists a person-centred clinical opportunity to support smokers attempting to quit by first understanding their smoking behaviour and subsequently sending them dynamic messages to encourage health behaviour change within a situational context. Methods: We have built a smartphone app—MapMySmoke—that works on Android and iOS platforms. The deployment of this app within a clinical National Health Service (NHS) setting has two distinct phases: (1) a 2-week logging phase where pre-quit patients log all of their smoking and craving events; and (2) a post-quit phase where users receive dynamic support messages and can continue to log craving events, and should they occur, relapse events. Following the initial logging phase, patients consult with their general practitioner (GP) or healthcare provider to review their smoking patterns and to outline a precise, individualised quit attempt plan. Our feasibility study consists of assessment of an initial app version during and after use by eight patients recruited from an NHS Fife GP practice. In addition to evaluation of the app as a potential smoking cessation aid, we have assessed the user experience, technological requirements and security of the data flow. Results: In an initial feasibility study, we have deployed the app for a small number of patients within one GP practice in NHS Fife. We recruited eight patients within one surgery, four of whom actively logged information about their smoking behaviour. Initial feedback was very positive, and users indicated a willingness to log their craving and smoking events. In addition, two out of three patients who completed follow-up interviews noted that the app helped them reduce the number of cigarettes they smoked per day, while the third indicated that it had helped them quit. The study highlighted the use of pushed notifications as a potential technology for maintaining quit attempts, and the security of collection of data was audited. These initial results influenced the design of a planned second larger study, comprised of 100 patients, the primary objectives of which are to use statistical modelling to identify times and places of probable switches into smoking states, and to target these times with dynamic health behaviour messaging. Conclusions: While the health benefits of quitting smoking are unequivocal, such behaviour change is very difficult to achieve. Many factors are likely to contribute to maintaining smoking behaviour, yet the precise role of cues derived from the spatial environment remains unclear. The rise of smartphones, therefore, allows clinicians the opportunity to better understand the spatial aspects of smoking behaviour and affords them the opportunity to push targeted individualised health support messages at vulnerable times and places.Mathematical modelling of cancer invasion : the multiple roles of TGF-β pathway on tumour proliferation and cell adhesionBitsouni, VasilikiChaplain, Mark Andrew JosephEftimie, Ralucahttp://hdl.handle.net/10023/111622018-01-08T15:30:12Z2017-09-01T00:00:00ZIn this paper, we develop a non-local mathematical model describing cancer cell invasion and movement as a result of integrin-controlled cell–cell adhesion and cell–matrix adhesion, and transforming growth factor-beta (TGF-β) effect on cell proliferation and adhesion, for two cancer cell populations with different levels of mutation. The model consists of partial integro-differential equations describing the dynamics of two cancer cell populations, coupled with ordinary differential equations describing the extracellular matrix (ECM) degradation and the production and decay of integrins, and with a parabolic PDE governing the evolution of TGF-β concentration. We prove the global existence of weak solutions to the model. We then use our model to explore numerically the role of TGF-β in cell aggregation and movement.
VB acknowledges support from an Engineering and Physical Sciences Research Council (UK) grant number EP/L504932/1. RE was partially supported by an Engineering and Physical Sciences Research Council (UK) grant number EP/K033689/1.
2017-09-01T00:00:00ZBitsouni, VasilikiChaplain, Mark Andrew JosephEftimie, RalucaIn this paper, we develop a non-local mathematical model describing cancer cell invasion and movement as a result of integrin-controlled cell–cell adhesion and cell–matrix adhesion, and transforming growth factor-beta (TGF-β) effect on cell proliferation and adhesion, for two cancer cell populations with different levels of mutation. The model consists of partial integro-differential equations describing the dynamics of two cancer cell populations, coupled with ordinary differential equations describing the extracellular matrix (ECM) degradation and the production and decay of integrins, and with a parabolic PDE governing the evolution of TGF-β concentration. We prove the global existence of weak solutions to the model. We then use our model to explore numerically the role of TGF-β in cell aggregation and movement.The characteristics of billows generated by internal solitary wavesCarr, MagdaFranklin, JamesKing, Stuart EdwardDavies, PeterGrue, JohnDritschel, David Gerardhttp://hdl.handle.net/10023/111562018-03-04T01:40:42Z2017-02-01T00:00:00ZThe spatial and temporal development of shear-induced overturning billows associated with breaking internal solitary waves is studied by means of a combined laboratory and numerical investigation. The waves are generated in the laboratory by a lock exchange mechanism and they are simulated numerically via a contour-advective semi-Lagrangian method. The properties of individual billows (maximum height attained, time of collapse, growth rate, speed, wavelength, Thorpe scale) are determined in each case, and the billow interaction processes are studied and classified. For broad flat waves, similar characteristics are seen to those in parallel shear flow, but, for waves not at the conjugate flow limit, billow characteristics are affected by the spatially varying wave-induced shear flow. Wave steepness and wave amplitude are shown to have a crucial influence on determining the type of interaction that occurs between billows and whether billow overturning can be arrested. Examples are given in which billows (i) evolve independently of one another, (ii) pair with one another, (iii) engulf/entrain one another and (iv) fail to completely overturn. It is shown that the vertical extent a billow can attain (and the associated Thorpe scale of the billow) is dependent on wave amplitude but that its value saturates once a given amplitude is reached. It is interesting to note that this amplitude is less than the conjugate flow limit amplitude. The number of billows that form on a wave is shown to be dependent on wavelength; shorter waves support fewer but larger billows than their long-wave counterparts for a given stratification.
2017-02-01T00:00:00ZCarr, MagdaFranklin, JamesKing, Stuart EdwardDavies, PeterGrue, JohnDritschel, David GerardThe spatial and temporal development of shear-induced overturning billows associated with breaking internal solitary waves is studied by means of a combined laboratory and numerical investigation. The waves are generated in the laboratory by a lock exchange mechanism and they are simulated numerically via a contour-advective semi-Lagrangian method. The properties of individual billows (maximum height attained, time of collapse, growth rate, speed, wavelength, Thorpe scale) are determined in each case, and the billow interaction processes are studied and classified. For broad flat waves, similar characteristics are seen to those in parallel shear flow, but, for waves not at the conjugate flow limit, billow characteristics are affected by the spatially varying wave-induced shear flow. Wave steepness and wave amplitude are shown to have a crucial influence on determining the type of interaction that occurs between billows and whether billow overturning can be arrested. Examples are given in which billows (i) evolve independently of one another, (ii) pair with one another, (iii) engulf/entrain one another and (iv) fail to completely overturn. It is shown that the vertical extent a billow can attain (and the associated Thorpe scale of the billow) is dependent on wave amplitude but that its value saturates once a given amplitude is reached. It is interesting to note that this amplitude is less than the conjugate flow limit amplitude. The number of billows that form on a wave is shown to be dependent on wavelength; shorter waves support fewer but larger billows than their long-wave counterparts for a given stratification.Solar coronal jets : observations, theory, and modelingRaouafi, N. E.Patsourakos, S.Pariat, E.Young, P. R.Sterling, A. C.Savcheva, A.Shimojo, M.Moreno-Insertis, F.DeVore, C. R.Archontis, V.Török, T.Mason, H.Curdt, W.Meyer, K.Dalmasse, K.Matsui, Y.http://hdl.handle.net/10023/111482018-03-11T01:35:30Z2016-11-01T00:00:00ZCoronal jets represent important manifestations of ubiquitous solar transients, which may be the source of significant mass and energy input to the upper solar atmosphere and the solar wind. While the energy involved in a jet-like event is smaller than that of “nominal” solar flares and coronal mass ejections (CMEs), jets share many common properties with these phenomena, in particular, the explosive magnetically driven dynamics. Studies of jets could, therefore, provide critical insight for understanding the larger, more complex drivers of the solar activity. On the other side of the size-spectrum, the study of jets could also supply important clues on the physics of transients close or at the limit of the current spatial resolution such as spicules. Furthermore, jet phenomena may hint to basic process for heating the corona and accelerating the solar wind; consequently their study gives us the opportunity to attack a broad range of solar-heliospheric problems.
S. Patsourakos acknowledges support from an FP7 Marie Curie Grant (FP7-PEOPLE-2010-RG/268288) as well as European Union (European Social Fund—ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF)—Research Funding Program: Thales. A.C. Sterling was supported by funding from the Heliophysics Division of NASA’s Science Mission Directorate through the Living With a Star Targeted Research and Technology Program, and by funding from the Hinode Project Office at NASA/MSFC. P.R. Young acknowledges funding from National Science Foundation grant AGS-1159353. T. Török was supported by NASA’s HSR and LWS programs. K. Dalmasse acknowledges support from the Computational and Information Systems Laboratory and from the HAO, as well as support from the AFOSR under award FA9550-15-1-0030.
2016-11-01T00:00:00ZRaouafi, N. E.Patsourakos, S.Pariat, E.Young, P. R.Sterling, A. C.Savcheva, A.Shimojo, M.Moreno-Insertis, F.DeVore, C. R.Archontis, V.Török, T.Mason, H.Curdt, W.Meyer, K.Dalmasse, K.Matsui, Y.Coronal jets represent important manifestations of ubiquitous solar transients, which may be the source of significant mass and energy input to the upper solar atmosphere and the solar wind. While the energy involved in a jet-like event is smaller than that of “nominal” solar flares and coronal mass ejections (CMEs), jets share many common properties with these phenomena, in particular, the explosive magnetically driven dynamics. Studies of jets could, therefore, provide critical insight for understanding the larger, more complex drivers of the solar activity. On the other side of the size-spectrum, the study of jets could also supply important clues on the physics of transients close or at the limit of the current spatial resolution such as spicules. Furthermore, jet phenomena may hint to basic process for heating the corona and accelerating the solar wind; consequently their study gives us the opportunity to attack a broad range of solar-heliospheric problems.Interaction between a quasi-geostrophic buoyancy filament and a hetonReinaud, Jean NoelCarton, XavierDritschel, David Gerardhttp://hdl.handle.net/10023/111382017-12-31T00:37:22Z2017-09-01T00:00:00ZWe investigate the interaction between a heton and a current generated by a filament of buoyancy anomaly at the surface. Hetons are baroclinic dipoles consisting of a pair of vortices of opposite sign lying at different depths. Such structures have a self-induced motion whenever the pair of vortices are offset horizontally. A surface buoyancy filament generates a shear flow since the density perturbation modifies locally the pressure field. The vertical shear induced by the filament offsets the vortices of the heton if vertically aligned initially. Moreover, if the vortex nearer the surface is in adverse horizontal shear with the buoyancy filament the heton tends to move towards the filament. Conversely, if the upper vortex is in cooperative horizontal shear with the buoyancy filament, the heton moves away from it. The filament is also naturally unstable and eventually breaks into a series of billows as it is perturbed by the heton. Moderate to large intensity surface buoyancy distributions separate the vortices of the heton, limiting its advection as a baroclinic dipole. Instead, the vortices of the heton start to interact strongly with surface billows. Additionally, the vortices of the heton can be partially destroyed by the filament if the shear it induces is sufficiently large.
2017-09-01T00:00:00ZReinaud, Jean NoelCarton, XavierDritschel, David GerardWe investigate the interaction between a heton and a current generated by a filament of buoyancy anomaly at the surface. Hetons are baroclinic dipoles consisting of a pair of vortices of opposite sign lying at different depths. Such structures have a self-induced motion whenever the pair of vortices are offset horizontally. A surface buoyancy filament generates a shear flow since the density perturbation modifies locally the pressure field. The vertical shear induced by the filament offsets the vortices of the heton if vertically aligned initially. Moreover, if the vortex nearer the surface is in adverse horizontal shear with the buoyancy filament the heton tends to move towards the filament. Conversely, if the upper vortex is in cooperative horizontal shear with the buoyancy filament, the heton moves away from it. The filament is also naturally unstable and eventually breaks into a series of billows as it is perturbed by the heton. Moderate to large intensity surface buoyancy distributions separate the vortices of the heton, limiting its advection as a baroclinic dipole. Instead, the vortices of the heton start to interact strongly with surface billows. Additionally, the vortices of the heton can be partially destroyed by the filament if the shear it induces is sufficiently large.Heating by transverse waves in simulated coronal loopsKarampelas, K.Van Doorsselaere, T.Antolin, P.http://hdl.handle.net/10023/111222018-03-11T01:37:24Z2017-08-25T00:00:00ZContext. Recent numerical studies of oscillating flux tubes have established the significance of resonant absorption in the damping of propagating transverse oscillations in coronal loops. The nonlinear nature of the mechanism has been examined alongside the Kelvin-Helmholtz instability,which is expected to manifest in the resonant layers at the edges of the flux tubes. While these two processes have been hypothesized to heat coronal loops through the dissipation of wave energy into smaller scales, the occurring mixing with the hotter surroundings can potentially hide this effect. Aims. We aim to study the effects of wave heating from driven and standing kink waves in a coronal loop. Methods. Using the MPI-AMRVAC code, we perform ideal, three dimensional magnetohydrodynamic (MHD) simulations of both (a) footpoint driven and (b) free standing oscillations in a straight coronal flux tube, in the presence of numerical resistivity. Results. We have observed the development of Kelvin-Helmholtz eddies at the loop boundary layer of all three models considered here, as well as an increase of the volume averaged temperature inside the loop. The main heating mechanism in our setups was Ohmic dissipation, as indicated by the higher values for the temperatures and current densities located near the footpoints. The introduction of a temperature gradient between the inner tube and the surrounding plasma, suggests that the mixing of the two regions, in the case of hotter environment, greatly increases the temperature of the tube at the site of the strongest turbulence, beyond the contribution of the aforementioned wave heating mechanism.
K.K. was funded by GOA-2015-014 (KU Leuven). T.V.D was supported by the IAP P7/08 CHARM (Belspo) and the GOA-2015-014 (KU Leuven). P.A. acknowledges funding from the UK Science and Technology Facilities Council and the European Union Horizon 2020 research and innovation programme (grant agreement No. 647214).
2017-08-25T00:00:00ZKarampelas, K.Van Doorsselaere, T.Antolin, P.Context. Recent numerical studies of oscillating flux tubes have established the significance of resonant absorption in the damping of propagating transverse oscillations in coronal loops. The nonlinear nature of the mechanism has been examined alongside the Kelvin-Helmholtz instability,which is expected to manifest in the resonant layers at the edges of the flux tubes. While these two processes have been hypothesized to heat coronal loops through the dissipation of wave energy into smaller scales, the occurring mixing with the hotter surroundings can potentially hide this effect. Aims. We aim to study the effects of wave heating from driven and standing kink waves in a coronal loop. Methods. Using the MPI-AMRVAC code, we perform ideal, three dimensional magnetohydrodynamic (MHD) simulations of both (a) footpoint driven and (b) free standing oscillations in a straight coronal flux tube, in the presence of numerical resistivity. Results. We have observed the development of Kelvin-Helmholtz eddies at the loop boundary layer of all three models considered here, as well as an increase of the volume averaged temperature inside the loop. The main heating mechanism in our setups was Ohmic dissipation, as indicated by the higher values for the temperatures and current densities located near the footpoints. The introduction of a temperature gradient between the inner tube and the surrounding plasma, suggests that the mixing of the two regions, in the case of hotter environment, greatly increases the temperature of the tube at the site of the strongest turbulence, beyond the contribution of the aforementioned wave heating mechanism.Comparison of variational balance models for the rotating shallow water equationsDritschel, David GerardGottwald, GeorgOliver, Marcelhttp://hdl.handle.net/10023/111002018-01-07T04:02:34Z2017-07-01T00:00:00ZWe present an extensive numerical comparison of a family of balance models appropriate to the semi-geostrophic limit of the rotating shallow water equations, and derived by variational asymptotics in Oliver (J. Fluid Mech., vol. 551, 2006, pp. 197–234) for small Rossby numbers Ro . This family of generalized large-scale semi-geostrophic (GLSG) models contains the L 1-model introduced by Simon (J. Fluid. Mech., vol. 132, pp. 431-444) as a special case. We use these models to produce balanced initial states for the full shallow water equations. We then numerically investigate how well these models capture the dynamics of an initially balanced shallow water flow. It is shown that, whereas the L 1-member of the GLSG family is able to reproduce the balanced dynamics of the full shallow water equations on time scales of O ( 1/Ro ) very well, all other members develop significant unphysical high wave number contributions in the ageostrophic vorticity which spoil the dynamics.
Funding through the TRR 181 is gratefully acknowledged. GAG’s initial work was funded by the Australian Research Council grant DP0452147. All three authors received support for this research from the UK Engineering and Physical Sciences Research Council (grant number EP/H001794/1).
2017-07-01T00:00:00ZDritschel, David GerardGottwald, GeorgOliver, MarcelWe present an extensive numerical comparison of a family of balance models appropriate to the semi-geostrophic limit of the rotating shallow water equations, and derived by variational asymptotics in Oliver (J. Fluid Mech., vol. 551, 2006, pp. 197–234) for small Rossby numbers Ro . This family of generalized large-scale semi-geostrophic (GLSG) models contains the L 1-model introduced by Simon (J. Fluid. Mech., vol. 132, pp. 431-444) as a special case. We use these models to produce balanced initial states for the full shallow water equations. We then numerically investigate how well these models capture the dynamics of an initially balanced shallow water flow. It is shown that, whereas the L 1-member of the GLSG family is able to reproduce the balanced dynamics of the full shallow water equations on time scales of O ( 1/Ro ) very well, all other members develop significant unphysical high wave number contributions in the ageostrophic vorticity which spoil the dynamics.3D pic simulations of collisionless shocks at lunar magnetic anomalies and their role in forming lunar swirlsBamford, R. A.Alves, E. P.Cruz, F.Kellett, B. J.Fonsesca, R. A.Silva, L. O.Trines, R. M. G. M.Halekas, J. S.Kamer, G.Harnett, E.Cairns, Robert AlanBingham, R.http://hdl.handle.net/10023/110672018-01-07T04:02:21Z2016-10-18T00:00:00ZInvestigation of the lunar crustal magnetic anomalies offers a comprehensive long-term data set of observations of small-scale magnetic fields and their interaction with the solar wind. In this paper a review of the observations of lunar mini-magnetospheres is compared quantifiably with theoretical kinetic-scale plasma physics and 3D particle-in-cell simulations. The aim of this paper is to provide a complete picture of all the aspects of the phenomena and to show how the observations from all the different and international missions interrelate. The analysis shows that the simulations are consistent with the formation of miniature (smaller than the ion Larmor orbit) collisionless shocks and miniature magnetospheric cavities, which has not been demonstrated previously. The simulations reproduce the finesse and form of the differential proton patterns that are believed to be responsible for the creation of both the "lunar swirls" and "dark lanes." Using a mature plasma physics code like OSIRIS allows us, for the first time, to make a side-by-side comparison between model and space observations. This is shown for all of the key plasma parameters observed to date by spacecraft, including the spectral imaging data of the lunar swirls. The analysis of miniature magnetic structures offers insight into multi-scale mechanisms and kinetic-scale aspects of planetary magnetospheres.
The authors would like to thank the Science and Technology Facilities Council for fundamental physics and computing resources that were provided by funding from STFC’s Scientific Computing Department, and would like to thank the European Research Council (ERC 2010 AdG Grant 267841) and FCT (Portugal) grants SFRH/BD/75558/2010 for support.
2016-10-18T00:00:00ZBamford, R. A.Alves, E. P.Cruz, F.Kellett, B. J.Fonsesca, R. A.Silva, L. O.Trines, R. M. G. M.Halekas, J. S.Kamer, G.Harnett, E.Cairns, Robert AlanBingham, R.Investigation of the lunar crustal magnetic anomalies offers a comprehensive long-term data set of observations of small-scale magnetic fields and their interaction with the solar wind. In this paper a review of the observations of lunar mini-magnetospheres is compared quantifiably with theoretical kinetic-scale plasma physics and 3D particle-in-cell simulations. The aim of this paper is to provide a complete picture of all the aspects of the phenomena and to show how the observations from all the different and international missions interrelate. The analysis shows that the simulations are consistent with the formation of miniature (smaller than the ion Larmor orbit) collisionless shocks and miniature magnetospheric cavities, which has not been demonstrated previously. The simulations reproduce the finesse and form of the differential proton patterns that are believed to be responsible for the creation of both the "lunar swirls" and "dark lanes." Using a mature plasma physics code like OSIRIS allows us, for the first time, to make a side-by-side comparison between model and space observations. This is shown for all of the key plasma parameters observed to date by spacecraft, including the spectral imaging data of the lunar swirls. The analysis of miniature magnetic structures offers insight into multi-scale mechanisms and kinetic-scale aspects of planetary magnetospheres.Cell population heterogeneity and evolution towards drug resistance in cancer : biological and mathematical assessment, theoretical treatment optimisationChisholm, Rebecca H.Lorenzi, TommasoClairambault, Jeanhttp://hdl.handle.net/10023/110362018-01-07T03:43:52Z2016-11-01T00:00:00ZBackground. Drug-induced drug resistance in cancer has been attributed to diverse biological mechanisms at the individual cell or cell population scale, relying on stochastically or epigenetically varying expression of phenotypes at the single cell level, and on the adaptability of tumours at the cell population level. Scope of review. We focus on intra-tumour heterogeneity, namely between-cell variability within cancer cell populations, to account for drug resistance. To shed light on such heterogeneity, we review evolutionary mechanisms that encompass the great evolution that has designed multicellular organisms, as well as smaller windows of evolution on the time scale of human disease. We also present mathematical models used to predict drug resistance in cancer and optimal control methods that can circumvent it in combined therapeutic strategies. Major conclusions. Plasticity in cancer cells, i.e., partial reversal to a stem-like status in individual cells and resulting adaptability of cancer cell populations, may be viewed as backward evolution making cancer cell populations resistant to drug insult. This reversible plasticity is captured by mathematical models that incorporate between-cell heterogeneity through continuous phenotypic variables. Such models have the benefit of being compatible with optimal control methods for the design of optimised therapeutic protocols involving combinations of cytotoxic and cytostatic treatments with epigenetic drugs and immunotherapies. General significance. Gathering knowledge from cancer and evolutionary biology with physiologically based mathematical models of cell population dynamics should provide oncologists with a rationale to design optimised therapeutic strategies to circumvent drug resistance, that still remains a major pitfall of cancer therapeutics. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
2016-11-01T00:00:00ZChisholm, Rebecca H.Lorenzi, TommasoClairambault, JeanBackground. Drug-induced drug resistance in cancer has been attributed to diverse biological mechanisms at the individual cell or cell population scale, relying on stochastically or epigenetically varying expression of phenotypes at the single cell level, and on the adaptability of tumours at the cell population level. Scope of review. We focus on intra-tumour heterogeneity, namely between-cell variability within cancer cell populations, to account for drug resistance. To shed light on such heterogeneity, we review evolutionary mechanisms that encompass the great evolution that has designed multicellular organisms, as well as smaller windows of evolution on the time scale of human disease. We also present mathematical models used to predict drug resistance in cancer and optimal control methods that can circumvent it in combined therapeutic strategies. Major conclusions. Plasticity in cancer cells, i.e., partial reversal to a stem-like status in individual cells and resulting adaptability of cancer cell populations, may be viewed as backward evolution making cancer cell populations resistant to drug insult. This reversible plasticity is captured by mathematical models that incorporate between-cell heterogeneity through continuous phenotypic variables. Such models have the benefit of being compatible with optimal control methods for the design of optimised therapeutic protocols involving combinations of cytotoxic and cytostatic treatments with epigenetic drugs and immunotherapies. General significance. Gathering knowledge from cancer and evolutionary biology with physiologically based mathematical models of cell population dynamics should provide oncologists with a rationale to design optimised therapeutic strategies to circumvent drug resistance, that still remains a major pitfall of cancer therapeutics. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.Scaling theory for vortices in the two-dimensional inverse energy cascadeBurgess, B. H.Scott, R. K.http://hdl.handle.net/10023/110142017-10-17T18:30:10Z2017-01-01T00:00:00ZWe propose a new similarity theory for the two-dimensional inverse energy cascade and the coherent vortex population it contains when forced at intermediate scales. Similarity arguments taking into account enstrophy conservation and a prescribed constant energy injection rate such that E∼t yield three length scales, lω, lE and lψ, associated with the vorticity field, energy peak and streamfunction, and predictions for their temporal evolutions, t1/2, t and t3/2, respectively. We thus predict that vortex areas grow linearly in time, A∼l2ω∼t, while the spectral peak wavenumber kE ≡ 2πl−1E ∼ t−1. We construct a theoretical framework involving a three-part, time-evolving vortex number density distribution, n(A) ∼ tαiA−ri, i ∈ 1,2,3. Just above the forcing scale (i =1) there is a forcing-equilibrated scaling range in which the number of vortices at fixed A is constant and vortex ‘self-energy’ Evcm = (2D)−1∫ωv2A2n(A) dA is conserved in A-space intervals [μA0(t), A0(t)] comoving with the growth in vortex area, A0(t) ∼ t. In this range, α1 = 0 and n(A) ∼ A−3. At intermediate scales (i = 2) sufficiently far from the forcing and the largest vortex, there is a range with a scale-invariant vortex size distribution. We predict that in this range the vortex enstrophy Zvcm = (2D)−1∫ ωv2An(A)dA is conserved and n(A) ∼ t−1A−1. The final range (i = 3), which extends over the largest vortex-containing scales, conserves σvcm = (2D)−1∫ ωv2n(A)dA. If ωv2 is constant in time, this is equivalent to conservation of vortex number Nvcm =∫ n(A)dA. This regime represents a ‘front’ of sparse vortices, which are effectively point-like; in this range we predict n(A) ∼ tr3−1A−r3. Allowing for time-varying ωv2 results in a small but significant correction to these temporal dependences. High-resolution numerical simulations verify the predicted vortex and spectral peak growth rates, as well as the theoretical picture of the three scaling ranges in the vortex population. Vortices steepen the energy spectrum E(k) past the classical k−5/3 scaling in the range k ∈ [kf , kv], where kv is the wavenumber associated with the largest vortex, while at larger scales the slope approaches −5/3. Though vortices disrupt the classical scaling, their number density distribution and evolution reveal deeper and more complex scale invariance, and suggest an effective theory of the inverse cascade in terms of vortex interactions.
B.H.B. is supported by the Natural Environment Research Council grant NE/M014983/1.
2017-01-01T00:00:00ZBurgess, B. H.Scott, R. K.We propose a new similarity theory for the two-dimensional inverse energy cascade and the coherent vortex population it contains when forced at intermediate scales. Similarity arguments taking into account enstrophy conservation and a prescribed constant energy injection rate such that E∼t yield three length scales, lω, lE and lψ, associated with the vorticity field, energy peak and streamfunction, and predictions for their temporal evolutions, t1/2, t and t3/2, respectively. We thus predict that vortex areas grow linearly in time, A∼l2ω∼t, while the spectral peak wavenumber kE ≡ 2πl−1E ∼ t−1. We construct a theoretical framework involving a three-part, time-evolving vortex number density distribution, n(A) ∼ tαiA−ri, i ∈ 1,2,3. Just above the forcing scale (i =1) there is a forcing-equilibrated scaling range in which the number of vortices at fixed A is constant and vortex ‘self-energy’ Evcm = (2D)−1∫ωv2A2n(A) dA is conserved in A-space intervals [μA0(t), A0(t)] comoving with the growth in vortex area, A0(t) ∼ t. In this range, α1 = 0 and n(A) ∼ A−3. At intermediate scales (i = 2) sufficiently far from the forcing and the largest vortex, there is a range with a scale-invariant vortex size distribution. We predict that in this range the vortex enstrophy Zvcm = (2D)−1∫ ωv2An(A)dA is conserved and n(A) ∼ t−1A−1. The final range (i = 3), which extends over the largest vortex-containing scales, conserves σvcm = (2D)−1∫ ωv2n(A)dA. If ωv2 is constant in time, this is equivalent to conservation of vortex number Nvcm =∫ n(A)dA. This regime represents a ‘front’ of sparse vortices, which are effectively point-like; in this range we predict n(A) ∼ tr3−1A−r3. Allowing for time-varying ωv2 results in a small but significant correction to these temporal dependences. High-resolution numerical simulations verify the predicted vortex and spectral peak growth rates, as well as the theoretical picture of the three scaling ranges in the vortex population. Vortices steepen the energy spectrum E(k) past the classical k−5/3 scaling in the range k ∈ [kf , kv], where kv is the wavenumber associated with the largest vortex, while at larger scales the slope approaches −5/3. Though vortices disrupt the classical scaling, their number density distribution and evolution reveal deeper and more complex scale invariance, and suggest an effective theory of the inverse cascade in terms of vortex interactions.A robust and efficient adaptive multigrid solver for the optimal control of phase field formulations of geometric evolution lawsYang, Feng WeiVenkataraman, ChandrasekharStyles, VanessaMadzvamuse, Anotidahttp://hdl.handle.net/10023/109092018-01-07T03:45:59Z2017-01-01T00:00:00ZWe propose and investigate a novel solution strategy to efficiently and accurately compute approximate solutions to semilinear optimal control problems, focusing on the optimal control of phase field formulations of geometric evolution laws. The optimal control of geometric evolution laws arises in a number of applications in fields including material science, image processing, tumour growth and cell motility. Despite this, many open problems remain in the analysis and approximation of such problems. In the current work we focus on a phase field formulation of the optimal control problem, hence exploiting the well developed mathematical theory for the optimal control of semilinear parabolic partial differential equations. Approximation of the resulting optimal control problem is computationally challenging, requiring massive amounts of computational time and memory storage. The main focus of this work is to propose, derive, implement and test an efficient solution method for such problems. The solver for the discretised partial differential equations is based upon a geometric multigrid method incorporating advanced techniques to deal with the nonlinearities in the problem and utilising adaptive mesh refinement. An in-house two grid solution strategy for the forward and adjoint problems, that significantly reduces memory requirements and CPU time, is proposed and investigated computationally. Furthermore, parallelisation as well as an adaptive-step gradient update for the control are employed to further improve efficiency. Along with a detailed description of our proposed solution method together with its implementation we present a number of computational results that demonstrate and evaluate our algorithms with respect to accuracy and efficiency. A highlight of the present work is simulation results on the optimal control of phase field formulations of geometric evolution laws in 3-D which would be computationally infeasible without the solution strategies proposed in the present work.
All authors acknowledge support from the Leverhulme Trust Research Project Grant (RPG-2014-149). The work of CV, VS and AMwas partially supported by the Engineering and Physical Sciences Research Council, UK grant (EP/J016780/1). This work (AM) has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642866. The work of CV is partially supported by an EPSRC Impact Accelerator Account award. The authors (FWY, CV, VS, AM) thank the Isaac Newton Institute for Mathematical Sciences for its hospitality during the programme (Coupling Geometric PDEs with Physics for Cell Morphology, Motility and Pattern Formation; EPSRC EP/K032208/1). AM was partially supported by Fellowships from the Simons Foundation.
2017-01-01T00:00:00ZYang, Feng WeiVenkataraman, ChandrasekharStyles, VanessaMadzvamuse, AnotidaWe propose and investigate a novel solution strategy to efficiently and accurately compute approximate solutions to semilinear optimal control problems, focusing on the optimal control of phase field formulations of geometric evolution laws. The optimal control of geometric evolution laws arises in a number of applications in fields including material science, image processing, tumour growth and cell motility. Despite this, many open problems remain in the analysis and approximation of such problems. In the current work we focus on a phase field formulation of the optimal control problem, hence exploiting the well developed mathematical theory for the optimal control of semilinear parabolic partial differential equations. Approximation of the resulting optimal control problem is computationally challenging, requiring massive amounts of computational time and memory storage. The main focus of this work is to propose, derive, implement and test an efficient solution method for such problems. The solver for the discretised partial differential equations is based upon a geometric multigrid method incorporating advanced techniques to deal with the nonlinearities in the problem and utilising adaptive mesh refinement. An in-house two grid solution strategy for the forward and adjoint problems, that significantly reduces memory requirements and CPU time, is proposed and investigated computationally. Furthermore, parallelisation as well as an adaptive-step gradient update for the control are employed to further improve efficiency. Along with a detailed description of our proposed solution method together with its implementation we present a number of computational results that demonstrate and evaluate our algorithms with respect to accuracy and efficiency. A highlight of the present work is simulation results on the optimal control of phase field formulations of geometric evolution laws in 3-D which would be computationally infeasible without the solution strategies proposed in the present work.Particle acceleration in collapsing magnetic traps with a braking plasma jetBorissov, AlexeiNeukirch, ThomasThrelfall, James Williamhttp://hdl.handle.net/10023/108962018-01-07T03:42:18Z2016-01-01T00:00:00ZCollapsing magnetic traps (CMTs) are one proposed mechanism for generating non-thermal particle populations in solar flares. CMTs occur if an initially stretched magnetic field structure relaxes rapidly into a lower-energy configuration, which is believed to happen as a by-product of magnetic reconnection. A similar mechanism for energising particles has also been found to operate in the Earth's magnetotail. One particular feature proposed to be of importance for particle acceleration in the magnetotail is that of a braking plasma jet, i.e. a localised region of strong flow encountering stronger magnetic field which causes the jet to slow down and stop. Such a feature has not been included in previously proposed analytical models of CMTs for solar flares. In this work we incorporate a braking plasma jet into a well studied CMT model for the first time. We present results of test particle calculations in this new CMT model. We observe and characterise new types of particle behaviour caused by the magnetic structure of the jet braking region, which allows electrons to be trapped both in the braking jet region and the loop legs. We compare and contrast the behaviour of particle orbits for various parameter regimes of the underlying trap by examining particle trajectories, energy gains and the frequency with which different types of particle orbit are found for each parameter regime.
2016-01-01T00:00:00ZBorissov, AlexeiNeukirch, ThomasThrelfall, James WilliamCollapsing magnetic traps (CMTs) are one proposed mechanism for generating non-thermal particle populations in solar flares. CMTs occur if an initially stretched magnetic field structure relaxes rapidly into a lower-energy configuration, which is believed to happen as a by-product of magnetic reconnection. A similar mechanism for energising particles has also been found to operate in the Earth's magnetotail. One particular feature proposed to be of importance for particle acceleration in the magnetotail is that of a braking plasma jet, i.e. a localised region of strong flow encountering stronger magnetic field which causes the jet to slow down and stop. Such a feature has not been included in previously proposed analytical models of CMTs for solar flares. In this work we incorporate a braking plasma jet into a well studied CMT model for the first time. We present results of test particle calculations in this new CMT model. We observe and characterise new types of particle behaviour caused by the magnetic structure of the jet braking region, which allows electrons to be trapped both in the braking jet region and the loop legs. We compare and contrast the behaviour of particle orbits for various parameter regimes of the underlying trap by examining particle trajectories, energy gains and the frequency with which different types of particle orbit are found for each parameter regime.A complex solar coronal jet with two phasesChen, JieSu, JiangtaoDeng, YuanyongPriest, E. R.http://hdl.handle.net/10023/108932018-01-07T04:01:49Z2017-05-04T00:00:00ZJets often occur repeatedly from almost the same location. In this paper, a complex solar jet was observed with two phases to the west of NOAA AR 11513 on 2012 July 2. If it had been observed at only moderate resolution, the two phases and their points of origin would have been regarded as identical. However, at high resolution we find that the two phases merge into one another and the accompanying footpoint brightenings occur at different locations. The phases originate from different magnetic patches rather than being one phase originating from the same patch. Photospheric line of sight (LOS) magnetograms show that the bases of the two phases lie in two different patches of magnetic flux that decrease in size during the occurrence of the two phases. Based on these observations, we suggest that the driving mechanism of the two successive phases is magnetic cancellation of two separate magnetic fragments with an opposite-polarity fragment between them.
This work was partly supported by National Natural Science Foundation of China (grant Nos. 11303048, 11673033, 11373040, 11427901). This work was also partly supported by an International Exchanges cost share award with NSFC for overseas travel between collaborators in the UK and China, and State Key Laboratory for Space Weather, Center for Space Science and Applied Research, Chinese Academy of Sciences.
2017-05-04T00:00:00ZChen, JieSu, JiangtaoDeng, YuanyongPriest, E. R.Jets often occur repeatedly from almost the same location. In this paper, a complex solar jet was observed with two phases to the west of NOAA AR 11513 on 2012 July 2. If it had been observed at only moderate resolution, the two phases and their points of origin would have been regarded as identical. However, at high resolution we find that the two phases merge into one another and the accompanying footpoint brightenings occur at different locations. The phases originate from different magnetic patches rather than being one phase originating from the same patch. Photospheric line of sight (LOS) magnetograms show that the bases of the two phases lie in two different patches of magnetic flux that decrease in size during the occurrence of the two phases. Based on these observations, we suggest that the driving mechanism of the two successive phases is magnetic cancellation of two separate magnetic fragments with an opposite-polarity fragment between them.A new class of vacillations of the stratospheric polar vortexScott, Richard Kirknesshttp://hdl.handle.net/10023/108872018-03-04T01:37:42Z2016-07-01T00:00:00ZA new class of persistent vacillations of the winter polar vortex, under the action of topographic wave forcing and radiative cooling, is identified in numerical integrations of the rotating shallow water equations. The vacillations are obtained provided only that care is taken to prevent the unconstrained growth of tropical easterlies that otherwise develop as the result of persistent angular momentum deposition at low latitudes. The vacillation cycle involves purely barotropic dynamics and is characterized by a dynamically controlled rapid splitting and rapid reformation of the vortex followed by a more gradual period of vortex intensification under the influence of radiative relaxation. The onset of the splitting occurs when the frequency of the free mode of the vortex approaches that of the forcing and resembles a resonant excitation. Experiments with an alternative basic state suggest that the vacillations are a robust feature of the topographically forced and radiatively relaxed vortex. In contrast to the behavior found in models with vertical structure, the period of the vacillation cycles here increases with increasing forcing amplitude. A wide range of forcing amplitude exists over which the vortex exhibits distinct regime transitions between a strong, vacillating state and a state in which the vortex is weak and the zonal mean polar flow nearly zero. Comparison with observational reanalysis suggest that the vacillation cycles obtained here may be relevant to the dynamics of some sudden warming events and that the onset of a radiatively dominated regime may be usefully linked to the loss of vortex area following such an event.
2016-07-01T00:00:00ZScott, Richard KirknessA new class of persistent vacillations of the winter polar vortex, under the action of topographic wave forcing and radiative cooling, is identified in numerical integrations of the rotating shallow water equations. The vacillations are obtained provided only that care is taken to prevent the unconstrained growth of tropical easterlies that otherwise develop as the result of persistent angular momentum deposition at low latitudes. The vacillation cycle involves purely barotropic dynamics and is characterized by a dynamically controlled rapid splitting and rapid reformation of the vortex followed by a more gradual period of vortex intensification under the influence of radiative relaxation. The onset of the splitting occurs when the frequency of the free mode of the vortex approaches that of the forcing and resembles a resonant excitation. Experiments with an alternative basic state suggest that the vacillations are a robust feature of the topographically forced and radiatively relaxed vortex. In contrast to the behavior found in models with vertical structure, the period of the vacillation cycles here increases with increasing forcing amplitude. A wide range of forcing amplitude exists over which the vortex exhibits distinct regime transitions between a strong, vacillating state and a state in which the vortex is weak and the zonal mean polar flow nearly zero. Comparison with observational reanalysis suggest that the vacillation cycles obtained here may be relevant to the dynamics of some sudden warming events and that the onset of a radiatively dominated regime may be usefully linked to the loss of vortex area following such an event.Bombs and flares at the surface and lower atmosphere of the SunHansteen, V. H.Archontis, V.Pereira, T. M. D.Carlsson, M.Rouppe van der Voort, L.Leenaarts, J.http://hdl.handle.net/10023/107412017-10-17T17:30:05Z2017-04-10T00:00:00ZA spectacular manifestation of solar activity is the appearance of transient brightenings in the far wings of the Hα line, known as Ellerman bombs (EBs). Recent observations obtained by the Interface Region Imaging Spectrograph have revealed another type of plasma "bombs" (UV bursts) with high temperatures of perhaps up to 8 ×104 K within the cooler lower solar atmosphere. Realistic numerical modeling showing such events is needed to explain their nature. Here, we report on 3D radiative magnetohydrodynamic simulations of magnetic flux emergence in the solar atmosphere. We find that ubiquitous reconnection between emerging bipolar magnetic fields can trigger EBs in the photosphere, UV bursts in the mid/low chromosphere and small (nano-/micro-) flares (106 K) in the upper chromosphere. These results provide new insights into the emergence and build up of the coronal magnetic field and the dynamics and heating of the solar surface and lower atmosphere.
This research was supported by the Research Council of Norway and by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007–2013)/ERC Grant agreement no. 291058.
2017-04-10T00:00:00ZHansteen, V. H.Archontis, V.Pereira, T. M. D.Carlsson, M.Rouppe van der Voort, L.Leenaarts, J.A spectacular manifestation of solar activity is the appearance of transient brightenings in the far wings of the Hα line, known as Ellerman bombs (EBs). Recent observations obtained by the Interface Region Imaging Spectrograph have revealed another type of plasma "bombs" (UV bursts) with high temperatures of perhaps up to 8 ×104 K within the cooler lower solar atmosphere. Realistic numerical modeling showing such events is needed to explain their nature. Here, we report on 3D radiative magnetohydrodynamic simulations of magnetic flux emergence in the solar atmosphere. We find that ubiquitous reconnection between emerging bipolar magnetic fields can trigger EBs in the photosphere, UV bursts in the mid/low chromosphere and small (nano-/micro-) flares (106 K) in the upper chromosphere. These results provide new insights into the emergence and build up of the coronal magnetic field and the dynamics and heating of the solar surface and lower atmosphere.Elongation of flare ribbonsQiu, JiongLongcope, Dana W.Cassak, Paul A.Priest, Eric R.http://hdl.handle.net/10023/106862018-02-04T01:41:03Z2017-03-20T00:00:00ZWe present an analysis of the apparent elongation motion of flare ribbons along the polarity inversion line (PIL), as well as the shear of flare loops in several two-ribbon flares. Flare ribbons and loops spread along the PIL at a speed ranging from a few to a hundred km s-1. The shear measured from conjugate footpoints is consistent with the measurement from flare loops, and both show the decrease of shear toward a potential field as a flare evolves and ribbons and loops spread along the PIL. Flares exhibiting fast bidirectional elongation appear to have a strong shear, which may indicate a large magnetic guide field relative to the reconnection field in the coronal current sheet. We discuss how the analysis of ribbon motion could help infer properties in the corona where reconnection takes place.
J.Q., D.W.L., and P.A.C. gratefully acknowledge support by NSF SHINE collaborative grant AGS-1460059.
2017-03-20T00:00:00ZQiu, JiongLongcope, Dana W.Cassak, Paul A.Priest, Eric R.We present an analysis of the apparent elongation motion of flare ribbons along the polarity inversion line (PIL), as well as the shear of flare loops in several two-ribbon flares. Flare ribbons and loops spread along the PIL at a speed ranging from a few to a hundred km s-1. The shear measured from conjugate footpoints is consistent with the measurement from flare loops, and both show the decrease of shear toward a potential field as a flare evolves and ribbons and loops spread along the PIL. Flares exhibiting fast bidirectional elongation appear to have a strong shear, which may indicate a large magnetic guide field relative to the reconnection field in the coronal current sheet. We discuss how the analysis of ribbon motion could help infer properties in the corona where reconnection takes place.The role of spatial variations of abiotic factors in mediating intratumour phenotypic heterogeneityLorenzi, TommasoVenkataraman, ChandrasekharLorz, AlexanderChaplain, Mark A. J.http://hdl.handle.net/10023/106852018-01-21T00:32:53Z2017-04-20T00:00:00ZA growing body of evidence indicates that the progression of cancer can be viewed as an eco-evolutionary process. Under this perspective, we present here a space- and phenotype-structured model of selection dynamics between cancer cells within a solid tumour. In the framework of this model, we combine formal analyses with numerical simulations to investigate in silico the role played by the spatial distribution of abiotic components of the tumour microenvironment in mediating phenotypic selection of cancer cells. Numerical simulations are performed both on the 3D geometry of an in silico multicellular tumour spheroid and on the 3D geometry of an in vivo human hepatic tumour, which was imaged using computerised tomography. The results obtained show that inhomogeneities in the spatial distribution of oxygen, currently observed in solid tumours, can promote the creation of distinct local niches and lead to the selection of different phenotypic variants within the same tumour. This process fosters the emergence of stable phenotypic heterogeneity and supports the presence of hypoxic cells resistant to cytotoxic therapy prior to treatment. Our theoretical results demonstrate the importance of integrating spatial data with ecological principles when evaluating the therapeutic response of solid tumours.
CV wishes to acknowledge partial support from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642866. AL was supported by King Abdullah University of Science and Technology (KAUST) baseline and start-up funds (BAS/1/1648-01-01 and BAS/1/1648-01-02). MAJC gratefully acknowledge support of EPSRC grant no. EP/N014642/1.
2017-04-20T00:00:00ZLorenzi, TommasoVenkataraman, ChandrasekharLorz, AlexanderChaplain, Mark A. J.A growing body of evidence indicates that the progression of cancer can be viewed as an eco-evolutionary process. Under this perspective, we present here a space- and phenotype-structured model of selection dynamics between cancer cells within a solid tumour. In the framework of this model, we combine formal analyses with numerical simulations to investigate in silico the role played by the spatial distribution of abiotic components of the tumour microenvironment in mediating phenotypic selection of cancer cells. Numerical simulations are performed both on the 3D geometry of an in silico multicellular tumour spheroid and on the 3D geometry of an in vivo human hepatic tumour, which was imaged using computerised tomography. The results obtained show that inhomogeneities in the spatial distribution of oxygen, currently observed in solid tumours, can promote the creation of distinct local niches and lead to the selection of different phenotypic variants within the same tumour. This process fosters the emergence of stable phenotypic heterogeneity and supports the presence of hypoxic cells resistant to cytotoxic therapy prior to treatment. Our theoretical results demonstrate the importance of integrating spatial data with ecological principles when evaluating the therapeutic response of solid tumours.Extrapolating cetacean densities to quantitatively assess human impacts on populations in the high seasMannocci, LauraRoberts, Jason J.Miller, David L.Halpin, Patrick N.http://hdl.handle.net/10023/106822018-03-11T01:36:19Z2017-06-01T00:00:00ZAs human activities expand beyond national jurisdictions to the high seas, there is an increasing need to consider anthropogenic impacts to species inhabiting these waters. The current scarcity of scientific observations of cetaceans in the high seas impedes the assessment of population-level impacts of these activities. We developed plausible density estimates to facilitate a quantitative assessment of anthropogenic impacts on cetacean populations in these waters. Our study region extended from a well-surveyed region within the U.S. Exclusive Economic Zone into a large region of the western North Atlantic sparsely surveyed for cetaceans. We modeled densities of 15 cetacean taxa with available line transect survey data and habitat covariates and extrapolated predictions to sparsely surveyed regions. We formulated models to reduce the extent of extrapolation beyond covariate ranges, and constrained them to model simple and generalizable relationships. To evaluate confidence in the predictions, we mapped where predictions were made outside sampled covariate ranges, examined alternate models, and compared predicted densities with maps of sightings from sources that could not be integrated into our models. Confidence levels in model results depended on the taxon and geographic area and highlighted the need for additional surveying in environmentally distinct areas. With application of necessary caution, our density estimates can inform management needs in the high seas, such as the quantification of potential cetacean interactions with military training exercises, shipping, fisheries, and deep-sea mining and be used to delineate areas of special biological significance in international waters. Our approach is generally applicable to other marine taxa and geographic regions for which management will be implemented but data are sparse.
Funding for this study came from the U.S. Fleet Forces Command (Cooperative Agreement N62470-13-2-8008), NASA (NNX08AK73G) and NOAA/NMFS (EE-133F-14-SE-3558).
2017-06-01T00:00:00ZMannocci, LauraRoberts, Jason J.Miller, David L.Halpin, Patrick N.As human activities expand beyond national jurisdictions to the high seas, there is an increasing need to consider anthropogenic impacts to species inhabiting these waters. The current scarcity of scientific observations of cetaceans in the high seas impedes the assessment of population-level impacts of these activities. We developed plausible density estimates to facilitate a quantitative assessment of anthropogenic impacts on cetacean populations in these waters. Our study region extended from a well-surveyed region within the U.S. Exclusive Economic Zone into a large region of the western North Atlantic sparsely surveyed for cetaceans. We modeled densities of 15 cetacean taxa with available line transect survey data and habitat covariates and extrapolated predictions to sparsely surveyed regions. We formulated models to reduce the extent of extrapolation beyond covariate ranges, and constrained them to model simple and generalizable relationships. To evaluate confidence in the predictions, we mapped where predictions were made outside sampled covariate ranges, examined alternate models, and compared predicted densities with maps of sightings from sources that could not be integrated into our models. Confidence levels in model results depended on the taxon and geographic area and highlighted the need for additional surveying in environmentally distinct areas. With application of necessary caution, our density estimates can inform management needs in the high seas, such as the quantification of potential cetacean interactions with military training exercises, shipping, fisheries, and deep-sea mining and be used to delineate areas of special biological significance in international waters. Our approach is generally applicable to other marine taxa and geographic regions for which management will be implemented but data are sparse.Bystander effects and their implications for clinical radiation therapy : insights from multiscale in silico experimentsPowathil, GibinMunro, Alastair JohnChaplain, Mark Andrew JosephSwat, Maciejhttp://hdl.handle.net/10023/106152018-03-18T01:37:18Z2016-07-21T00:00:00ZRadiotherapy is a commonly used treatment for cancer and is usually given in varying doses. At low radiation doses relatively few cells die as a direct response to radiation but secondary radiation effects, such as DNA mutation or bystander phenomena, may affect many cells. Consequently it is at low radiation levels where an understanding of bystander effects is essential in designing novel therapies with superior clinical outcomes. In this article, we use a hybrid multiscale mathematical model to study the direct effects of radiation as well as radiation-induced bystander effects on both tumour cells and normal cells. We show that bystander responses play a major role in mediating radiation damage to cells at low-doses of radiotherapy, doing more damage than that due to direct radiation. The survival curves derived from our computational simulations showed an area of hyper-radiosensitivity at low-doses that are not obtained using a traditional radiobiological model.
GGP and MAJC thank University of Dundee, where this research was carried out. The authors gratefully acknowledge the support of the ERC Advanced Investigator Grant 227619, M5CGS - From Mutations to Metastases: Multiscale Mathematical Modelling of Cancer Growth and Spread. AJM Acknowledges support from EU BIOMICS Project DG-CNECT Contract 318202.
2016-07-21T00:00:00ZPowathil, GibinMunro, Alastair JohnChaplain, Mark Andrew JosephSwat, MaciejRadiotherapy is a commonly used treatment for cancer and is usually given in varying doses. At low radiation doses relatively few cells die as a direct response to radiation but secondary radiation effects, such as DNA mutation or bystander phenomena, may affect many cells. Consequently it is at low radiation levels where an understanding of bystander effects is essential in designing novel therapies with superior clinical outcomes. In this article, we use a hybrid multiscale mathematical model to study the direct effects of radiation as well as radiation-induced bystander effects on both tumour cells and normal cells. We show that bystander responses play a major role in mediating radiation damage to cells at low-doses of radiotherapy, doing more damage than that due to direct radiation. The survival curves derived from our computational simulations showed an area of hyper-radiosensitivity at low-doses that are not obtained using a traditional radiobiological model.Particle acceleration due to coronal non-null magnetic reconnectionThrelfall, James WilliamNeukirch, ThomasParnell, Clare Elizabethhttp://hdl.handle.net/10023/105512018-01-07T03:57:16Z2017-03-01T00:00:00ZVarious topological features, for example magnetic null-points and separators, have been inferred as likely sites of magnetic reconnection and particle acceleration in the solar atmosphere. In fact, magnetic reconnection is not constrained to solely take place at or near such topological features and may also take place in the absence of such features. Studies of particle acceleration using non-topological reconnection experiments embedded in the solar atmosphere are uncommon. We aim to investigate and characterise particle behaviour in a model of magnetic reconnection which causes an arcade of solar coronal magnetic field to twist and form an erupting flux rope, crucially in the absence of any common topological features where reconnection is often thought to occur. We use a numerical scheme which evolves the gyro-averaged orbit equations of single electrons and protons in time and space, and simulate the gyromotion of particles in a fully analytical global field model. We observe and discuss how the magnetic and electric fields of the model and the initial conditions of each orbit may lead to acceleration of protons and electrons up to 2 MeV in energy (depending on model parameters). We describe the morphology of time-dependent acceleration and impact sites for each particle species and compare our findings to those recovered by topologically based studies of three-dimensional (3D) reconnection and particle acceleration. We also broadly compare aspects of our findings to general observational features typically seen during two-ribbon flare events.
2017-03-01T00:00:00ZThrelfall, James WilliamNeukirch, ThomasParnell, Clare ElizabethVarious topological features, for example magnetic null-points and separators, have been inferred as likely sites of magnetic reconnection and particle acceleration in the solar atmosphere. In fact, magnetic reconnection is not constrained to solely take place at or near such topological features and may also take place in the absence of such features. Studies of particle acceleration using non-topological reconnection experiments embedded in the solar atmosphere are uncommon. We aim to investigate and characterise particle behaviour in a model of magnetic reconnection which causes an arcade of solar coronal magnetic field to twist and form an erupting flux rope, crucially in the absence of any common topological features where reconnection is often thought to occur. We use a numerical scheme which evolves the gyro-averaged orbit equations of single electrons and protons in time and space, and simulate the gyromotion of particles in a fully analytical global field model. We observe and discuss how the magnetic and electric fields of the model and the initial conditions of each orbit may lead to acceleration of protons and electrons up to 2 MeV in energy (depending on model parameters). We describe the morphology of time-dependent acceleration and impact sites for each particle species and compare our findings to those recovered by topologically based studies of three-dimensional (3D) reconnection and particle acceleration. We also broadly compare aspects of our findings to general observational features typically seen during two-ribbon flare events.Blockage of saline intrusions in restricted, two-layer exchange flows across a submerged sill obstructionCuthbertson, AlanLaanearu, JanekCarr, MagdaSommeria, JoelViboud, Samuelhttp://hdl.handle.net/10023/105432018-02-16T15:30:04Z2018-02-01T00:00:00ZResults are presented from a series of large-scale experiments investigating the internal and near-bed dynamics of bi-directional stratified flows with a net-barotropic component across a submerged, trapezoidal, sill obstruction. High-resolution velocity and density profiles are obtained in the vicinity of the obstruction to observe internal-flow dynamics under a range of parametric forcing conditions (i.e. variable saline and fresh water volume fluxes; density differences; sill obstruction submergence depths). Detailed synoptic velocity fields are measured across the sill crest using 2D particle image velocimetry, while the density structure of the two-layer exchange flows is measured using micro-conductivity probes at several sill locations. These measurements are designed to aid qualitative and quantitative interpretation of the internal-flow processes associated with the lower saline intrusion layer blockage conditions, and indicate that the primary mechanism for this blockage is mass exchange from the saline intrusion layer due to significant interfacial mixing and entrainment under dominant, net-barotropic, flow conditions in the upper freshwater layer. This interfacial mixing is quantified by considering both the isopycnal separation of vertically-sorted density profiles across the sill, as well as calculation of corresponding Thorpe overturning length scales. Analysis of the synoptic velocity fields and density profiles also indicates that the net exchange flow conditions remain subcritical (G < 1) across the sill for all parametric conditions tested. An analytical two-layer exchange flow model is then developed to include frictional and entrainment effects, both of which are needed to account for turbulent stresses and saline entrainment into the upper freshwater layer. The experimental results are used to validate two key model parameters: (1) the internal-flow head loss associated with boundary friction and interfacial shear; and (2) the mass exchange from the lower saline layer into the upper fresh layer due to entrainment.
The work has been supported by European Community’s Seventh Framework Programme through the grant to the budget of the Integrating Activity HYDRALAB IV within the Transnational Access Activities, Contract No. 261520.
2018-02-01T00:00:00ZCuthbertson, AlanLaanearu, JanekCarr, MagdaSommeria, JoelViboud, SamuelResults are presented from a series of large-scale experiments investigating the internal and near-bed dynamics of bi-directional stratified flows with a net-barotropic component across a submerged, trapezoidal, sill obstruction. High-resolution velocity and density profiles are obtained in the vicinity of the obstruction to observe internal-flow dynamics under a range of parametric forcing conditions (i.e. variable saline and fresh water volume fluxes; density differences; sill obstruction submergence depths). Detailed synoptic velocity fields are measured across the sill crest using 2D particle image velocimetry, while the density structure of the two-layer exchange flows is measured using micro-conductivity probes at several sill locations. These measurements are designed to aid qualitative and quantitative interpretation of the internal-flow processes associated with the lower saline intrusion layer blockage conditions, and indicate that the primary mechanism for this blockage is mass exchange from the saline intrusion layer due to significant interfacial mixing and entrainment under dominant, net-barotropic, flow conditions in the upper freshwater layer. This interfacial mixing is quantified by considering both the isopycnal separation of vertically-sorted density profiles across the sill, as well as calculation of corresponding Thorpe overturning length scales. Analysis of the synoptic velocity fields and density profiles also indicates that the net exchange flow conditions remain subcritical (G < 1) across the sill for all parametric conditions tested. An analytical two-layer exchange flow model is then developed to include frictional and entrainment effects, both of which are needed to account for turbulent stresses and saline entrainment into the upper freshwater layer. The experimental results are used to validate two key model parameters: (1) the internal-flow head loss associated with boundary friction and interfacial shear; and (2) the mass exchange from the lower saline layer into the upper fresh layer due to entrainment.Contribution of mode-coupling and phase-mixing of Alfvén waves to coronal heatingPagano, P.De Moortel, I.http://hdl.handle.net/10023/105172018-03-11T01:37:02Z2017-05-12T00:00:00ZContext. Phase-mixing of Alfvén waves in the solar corona has been identified as one possible candidate to explain coronal heating. While this scenario is supported by observations of ubiquitous oscillations in the corona carrying sufficient wave energy and by theoretical models that have described the concentration of energy in small-scale structures, it is still unclear whether this wave energy can be converted into thermal energy in order to maintain the million-degree hot solar corona. Aims. The aim of this work is to assess how much energy can be converted into thermal energy by a phase-mixing process triggered by the propagation of Alfvénic waves in a cylindric coronal structure, such as a coronal loop, and to estimate the impact of this conversion on the coronal heating and thermal structure of the solar corona. Methods. To this end, we ran 3D MHD simulations of a magnetised cylinder where the Alfvén speed varies through a boundary shell, and a footpoint driver is set to trigger kink modes that mode couple to torsional Alfvén modes in the boundary shell. These Alfvén waves are expected to phase-mix, and the system allows us to study the subsequent thermal energy deposition. We ran a reference simulation to explain the main process and then we varied the simulation parameters, such as the size of the boundary shell, its structure, and the persistence of the driver. Results. When we take high values of magnetic resistivity and strong footpoint drivers into consideration, we find that i) phase-mixing leads to a temperature increase of the order of 105 K or less, depending on the structure of the boundary shell, ii) this energy is able to balance the radiative losses only in the localised region involved in the heating, and iii) we can determine the influence of the boundary layer and the persistence of the driver on the thermal structure of the system. Conclusions. Our conclusion is that as a result of the extreme physical parameters we adopted and the moderate impact on the heating of the system, it is unlikely that phase-mixing can contribute on a global scale to the heating of the solar corona.
This research has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 647214) and from the UK Science and Technology Facilities Council. This work used the DiRAC Data Centric system at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk. This equipment was funded by a BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/K00087X/1, DiRAC Operations grant ST/K003267/1 and Durham University.
2017-05-12T00:00:00ZPagano, P.De Moortel, I.Context. Phase-mixing of Alfvén waves in the solar corona has been identified as one possible candidate to explain coronal heating. While this scenario is supported by observations of ubiquitous oscillations in the corona carrying sufficient wave energy and by theoretical models that have described the concentration of energy in small-scale structures, it is still unclear whether this wave energy can be converted into thermal energy in order to maintain the million-degree hot solar corona. Aims. The aim of this work is to assess how much energy can be converted into thermal energy by a phase-mixing process triggered by the propagation of Alfvénic waves in a cylindric coronal structure, such as a coronal loop, and to estimate the impact of this conversion on the coronal heating and thermal structure of the solar corona. Methods. To this end, we ran 3D MHD simulations of a magnetised cylinder where the Alfvén speed varies through a boundary shell, and a footpoint driver is set to trigger kink modes that mode couple to torsional Alfvén modes in the boundary shell. These Alfvén waves are expected to phase-mix, and the system allows us to study the subsequent thermal energy deposition. We ran a reference simulation to explain the main process and then we varied the simulation parameters, such as the size of the boundary shell, its structure, and the persistence of the driver. Results. When we take high values of magnetic resistivity and strong footpoint drivers into consideration, we find that i) phase-mixing leads to a temperature increase of the order of 105 K or less, depending on the structure of the boundary shell, ii) this energy is able to balance the radiative losses only in the localised region involved in the heating, and iii) we can determine the influence of the boundary layer and the persistence of the driver on the thermal structure of the system. Conclusions. Our conclusion is that as a result of the extreme physical parameters we adopted and the moderate impact on the heating of the system, it is unlikely that phase-mixing can contribute on a global scale to the heating of the solar corona.Imaging observations of magnetic reconnection in a solar eruptive flareLi, Y.Sun, X.Ding, M. D.Qiu, J.Priest, E. R.http://hdl.handle.net/10023/104862018-03-04T01:40:54Z2017-01-31T00:00:00ZSolar flares are among the most energetic events in the solar atmosphere. It is widely accepted that flares are powered by magnetic reconnection in the corona. An eruptive flare is usually accompanied by a coronal mass ejection, both of which are probably driven by the eruption of a magnetic flux rope (MFR). Here we report an eruptive flare on 2016 March 23 observed by the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory. The extreme-ultraviolet imaging observations exhibit the clear rise and eruption of an MFR. In particular, the observations reveal solid evidence of magnetic reconnection from both the corona and chromosphere during the flare. Moreover, weak reconnection is observed before the start of the flare. We find that the preflare weak reconnection is of tether-cutting type and helps the MFR to rise slowly. Induced by a further rise of the MFR, strong reconnection occurs in the rise phases of the flare, which is temporally related to the MFR eruption. We also find that the magnetic reconnection is more of 3D-type in the early phase, as manifested in a strong-to-weak shear transition in flare loops, and becomes more 2D-like in the later phase, as shown by the apparent rising motion of an arcade of flare loops.
2017-01-31T00:00:00ZLi, Y.Sun, X.Ding, M. D.Qiu, J.Priest, E. R.Solar flares are among the most energetic events in the solar atmosphere. It is widely accepted that flares are powered by magnetic reconnection in the corona. An eruptive flare is usually accompanied by a coronal mass ejection, both of which are probably driven by the eruption of a magnetic flux rope (MFR). Here we report an eruptive flare on 2016 March 23 observed by the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory. The extreme-ultraviolet imaging observations exhibit the clear rise and eruption of an MFR. In particular, the observations reveal solid evidence of magnetic reconnection from both the corona and chromosphere during the flare. Moreover, weak reconnection is observed before the start of the flare. We find that the preflare weak reconnection is of tether-cutting type and helps the MFR to rise slowly. Induced by a further rise of the MFR, strong reconnection occurs in the rise phases of the flare, which is temporally related to the MFR eruption. We also find that the magnetic reconnection is more of 3D-type in the early phase, as manifested in a strong-to-weak shear transition in flare loops, and becomes more 2D-like in the later phase, as shown by the apparent rising motion of an arcade of flare loops.The effects of resistivity and viscosity on the Kelvin-Helmholtz instability in oscillating coronal loopsHowson, T. A.De Moortel, I.Antolin, P.http://hdl.handle.net/10023/104502018-03-11T01:36:52Z2017-06-16T00:00:00ZAims. Investigate the effects of resistivity and viscosity on the onset and growth of the Kelvin-Helmholtz instability (KHI) in an oscillating coronal loop. Methods. We modelled a standing kink wave in a density-enhanced loop with the three dimensional (3-D), resistive magnetohydrodynamics code, Lare3d. We conducted a parameter study on the viscosity and resistivity coefficients to examine the effects of dissipation on the KHI. Results. Enhancing the viscosity (ν) and resistivity (η) acts to suppress the KHI. Larger values of ν and η delay the formation of the instability and, in some cases, prevent the onset completely. This leads to the earlier onset of heating for smaller values of the transport coefficients. We note that viscosity has a greater effect on the development of the KHI than resistivity. Furthermore, when using anomalous resistivity, the Ohmic heating rate associated with the KHI may be greater than that associated with the phase mixing that occurs in an instability-suppressed regime (using uniform resistivity). Conclusions. From our study, it is clear that the heating rate crucially depends on the formation of small length scales (influenced by the numerical resolution) as well as the values of resistivity and viscosity. As larger values of the transport coefficients suppress the KHI, the onset of heating is delayed but the heating rate is larger. As increased numerical resolution allows smaller length scales to develop, the heating rate will be higher even for the same values of η and ν.
The research leading to these results has received funding from the UK Science and Technology Facilities Council and the European Union Horizon 2020 research and innovation programme (grant agreement No. 647214).
2017-06-16T00:00:00ZHowson, T. A.De Moortel, I.Antolin, P.Aims. Investigate the effects of resistivity and viscosity on the onset and growth of the Kelvin-Helmholtz instability (KHI) in an oscillating coronal loop. Methods. We modelled a standing kink wave in a density-enhanced loop with the three dimensional (3-D), resistive magnetohydrodynamics code, Lare3d. We conducted a parameter study on the viscosity and resistivity coefficients to examine the effects of dissipation on the KHI. Results. Enhancing the viscosity (ν) and resistivity (η) acts to suppress the KHI. Larger values of ν and η delay the formation of the instability and, in some cases, prevent the onset completely. This leads to the earlier onset of heating for smaller values of the transport coefficients. We note that viscosity has a greater effect on the development of the KHI than resistivity. Furthermore, when using anomalous resistivity, the Ohmic heating rate associated with the KHI may be greater than that associated with the phase mixing that occurs in an instability-suppressed regime (using uniform resistivity). Conclusions. From our study, it is clear that the heating rate crucially depends on the formation of small length scales (influenced by the numerical resolution) as well as the values of resistivity and viscosity. As larger values of the transport coefficients suppress the KHI, the onset of heating is delayed but the heating rate is larger. As increased numerical resolution allows smaller length scales to develop, the heating rate will be higher even for the same values of η and ν.Geostrophic tripolar vortices in a two-layer fluid : linear stability and nonlinear evolution of equilibriaReinaud, Jean NoelSokolovskiy, MikhailCarton, Xavierhttp://hdl.handle.net/10023/104112018-01-07T03:58:11Z2017-03-01T00:00:00ZWe investgate equilibrium solutions for tripolar vortices in a two-layer quasi-geostrophic flow. Two of the vortices are like-signed and lie in one layer. An opposite-signed vortex lies in the other layer. The families of equilibria can be spanned by the distance (called separation) between the two like-signed vortices. Two equilibrium configurations are possible when the opposite-signed vortex lies between the two other vortices. In the first configuration (called ordinary roundabout), the opposite signed vortex is equidistant to the two other vortices. In the second configuration (eccentric roundabouts), the distances are unequal. We determine the equilibria numerically and describe their characteristics for various internal deformation radii. The two branches of equilibria can co-exist and intersect for small deformation radii. Then, the eccentric roundabouts are stable while unstable ordinary roundabouts can be found. Indeed, ordinary roundabouts exist at smaller separations than eccentric roundabouts do, thus inducing stronger vortex interactions. However, for larger deformation radii, eccentric roundabouts can also be unstable. Then, the two branches of equilibria do not cross. The branch of eccentric roundabouts only exists for large separations. Near the end of the branch of eccentric roundabouts (at the smallest separation), one of the like-signed vortices exhibits a sharp inner corner where instabilities can be triggered. Finally, we investigate of the nonlinear evolution of a few selected cases of tripoles.
2017-03-01T00:00:00ZReinaud, Jean NoelSokolovskiy, MikhailCarton, XavierWe investgate equilibrium solutions for tripolar vortices in a two-layer quasi-geostrophic flow. Two of the vortices are like-signed and lie in one layer. An opposite-signed vortex lies in the other layer. The families of equilibria can be spanned by the distance (called separation) between the two like-signed vortices. Two equilibrium configurations are possible when the opposite-signed vortex lies between the two other vortices. In the first configuration (called ordinary roundabout), the opposite signed vortex is equidistant to the two other vortices. In the second configuration (eccentric roundabouts), the distances are unequal. We determine the equilibria numerically and describe their characteristics for various internal deformation radii. The two branches of equilibria can co-exist and intersect for small deformation radii. Then, the eccentric roundabouts are stable while unstable ordinary roundabouts can be found. Indeed, ordinary roundabouts exist at smaller separations than eccentric roundabouts do, thus inducing stronger vortex interactions. However, for larger deformation radii, eccentric roundabouts can also be unstable. Then, the two branches of equilibria do not cross. The branch of eccentric roundabouts only exists for large separations. Near the end of the branch of eccentric roundabouts (at the smallest separation), one of the like-signed vortices exhibits a sharp inner corner where instabilities can be triggered. Finally, we investigate of the nonlinear evolution of a few selected cases of tripoles.A general setting for symmetric distributions and their relationship to general distributionsJupp, P.E.Regoli, G.Azzalini, A.http://hdl.handle.net/10023/103702018-01-07T03:36:21Z2016-06-01T00:00:00ZA standard method of obtaining non-symmetrical distributions is that of modulating symmetrical distributions by multiplying the densities by a perturbation factor. This has been considered mainly for central symmetry of a Euclidean space in the origin. This paper enlarges the concept of modulation to the general setting of symmetry under the action of a compact topological group on the sample space. The main structural result relates the density of an arbitrary distribution to the density of the corresponding symmetrised distribution. Some general methods for constructing modulating functions are considered. The effect that transformations of the sample space have on symmetry of distributions is investigated. The results are illustrated by general examples, many of them in the setting of directional statistics.
2016-06-01T00:00:00ZJupp, P.E.Regoli, G.Azzalini, A.A standard method of obtaining non-symmetrical distributions is that of modulating symmetrical distributions by multiplying the densities by a perturbation factor. This has been considered mainly for central symmetry of a Euclidean space in the origin. This paper enlarges the concept of modulation to the general setting of symmetry under the action of a compact topological group on the sample space. The main structural result relates the density of an arbitrary distribution to the density of the corresponding symmetrised distribution. Some general methods for constructing modulating functions are considered. The effect that transformations of the sample space have on symmetry of distributions is investigated. The results are illustrated by general examples, many of them in the setting of directional statistics.Logarithmic improvement of regularity criteria for the Navier-Stokes equations in terms of pressureTran, Chuong VanYu, Xinweihttp://hdl.handle.net/10023/103192018-02-18T01:36:21Z2016-08-01T00:00:00ZIn this article we prove a logarithmic improvement of regularity criteria in the multiplier spaces for the Cauchy problem of the incompressible Navier-Stokes equations in terms of pressure. This improves the main result in [S. Benbernou, A note on the regularity criterion in terms of pressure for the Navier-Stokes equations, Applied Mathematics Letters 22 (2009) 1438–1443].
XY is partially supported by a grant from NSERC.
2016-08-01T00:00:00ZTran, Chuong VanYu, XinweiIn this article we prove a logarithmic improvement of regularity criteria in the multiplier spaces for the Cauchy problem of the incompressible Navier-Stokes equations in terms of pressure. This improves the main result in [S. Benbernou, A note on the regularity criterion in terms of pressure for the Navier-Stokes equations, Applied Mathematics Letters 22 (2009) 1438–1443].A combined theory for magnetohydrodynamic equilibria with anisotropic pressure and magnetic shearHodgson, Jonathan David BrockieNeukirch, Thomashttp://hdl.handle.net/10023/103052018-01-07T03:53:54Z2017-03-10T00:00:00ZWe present a new approach to the theory of magnetohydrodynamic equilibria with anisotropic pressure, magnetic shear and translational/rotational invariance. This approach involves combining two existing formalisms in order to eliminate their individual weaknesses. The theoretical aspects of the method are explored in detail along with numerical solutions which make use of the method. Eventually, this method could be applied to model various plasma systems, such as planetary magnetospheres.
Grant numbers: Science and Technology Facilities Council via Doctoral Training Grant [ST/K502327/1], Consolidated Grant [ST/K000950/1] and Consolidated Grant [ST/N000609/1].
2017-03-10T00:00:00ZHodgson, Jonathan David BrockieNeukirch, ThomasWe present a new approach to the theory of magnetohydrodynamic equilibria with anisotropic pressure, magnetic shear and translational/rotational invariance. This approach involves combining two existing formalisms in order to eliminate their individual weaknesses. The theoretical aspects of the method are explored in detail along with numerical solutions which make use of the method. Eventually, this method could be applied to model various plasma systems, such as planetary magnetospheres.Observations and modelling of the pre-flare period of the 29 March 2014 X1 flareWoods, M. M.Harra, L. K.Matthews, S. A.Mackay, D. H.Dacie, S.Long, D. M.http://hdl.handle.net/10023/102982018-03-04T01:40:40Z2017-02-01T00:00:00ZOn the 29 March 2014 NOAA active region (AR) 12017 produced an X1 flare which was simultaneously observed by an unprecedented number of observatories. We have investigated the pre-flare period of this flare from 14:00 UT until 19:00 UT using joint observations made by the Interface Region Imaging Spectrometer (IRIS) and the Hinode Extreme Ultraviolet Imaging Spectrometer (EIS). Spectral lines providing coverage of the solar atmosphere from chromosphere to the corona were analysed to investigate pre-flare activity within the AR. The results of the investigation have revealed evidence of strongly blue-shifted plasma flows, with velocities up to 200 km-1, being observed 40 minutes prior to flaring. These flows are located along the filament present in the active region and are both spatially discrete and transient. In order to constrain the possible explanations for this activity, we undertake non-potential magnetic field modelling of the active region. This modelling indicates the existence of a weakly twisted flux rope along the polarity inversion line in the region where a filament and the strong pre-flare flows are observed. We then discuss how these observations relate to the current models of flare triggering. We conclude that the most likely drivers of the observed activity are internal reconnection in the flux rope, early onset of the flare reconnection, or tether cutting reconnection along the filament.
MMW and SD acknowledge STFC for support via their PhD Studentships. DML is an Early-Career Fellow, funded by the Leverhulme Trust.
2017-02-01T00:00:00ZWoods, M. M.Harra, L. K.Matthews, S. A.Mackay, D. H.Dacie, S.Long, D. M.On the 29 March 2014 NOAA active region (AR) 12017 produced an X1 flare which was simultaneously observed by an unprecedented number of observatories. We have investigated the pre-flare period of this flare from 14:00 UT until 19:00 UT using joint observations made by the Interface Region Imaging Spectrometer (IRIS) and the Hinode Extreme Ultraviolet Imaging Spectrometer (EIS). Spectral lines providing coverage of the solar atmosphere from chromosphere to the corona were analysed to investigate pre-flare activity within the AR. The results of the investigation have revealed evidence of strongly blue-shifted plasma flows, with velocities up to 200 km-1, being observed 40 minutes prior to flaring. These flows are located along the filament present in the active region and are both spatially discrete and transient. In order to constrain the possible explanations for this activity, we undertake non-potential magnetic field modelling of the active region. This modelling indicates the existence of a weakly twisted flux rope along the polarity inversion line in the region where a filament and the strong pre-flare flows are observed. We then discuss how these observations relate to the current models of flare triggering. We conclude that the most likely drivers of the observed activity are internal reconnection in the flux rope, early onset of the flare reconnection, or tether cutting reconnection along the filament.Forward modeling of standing slow modes in flaring coronal loopsYuan, D.Van Doorsselaere, T.Banerjee, D.Antolin, P.http://hdl.handle.net/10023/102952018-01-07T03:56:01Z2015-07-02T00:00:00ZStanding slow-mode waves in hot flaring loops are exclusively observed in spectrometers and are used to diagnose the magnetic field strength and temperature of the loop structure. Owing to the lack of spatial information, the longitudinal mode cannot be effectively identified. In this study, we simulate standing slow-mode waves in flaring loops and compare the synthesized line emission properties with Solar Ultraviolet Measurements of Emitted Radiation spectrographic and Solar Dynamics Observatory/Atmospheric Imaging Assembly imaging observations. We find that the emission intensity and line width oscillations are a quarter period out of phase with Doppler shift velocity in both time and spatial domain, which can be used to identify a standing slow-mode wave from spectroscopic observations. However, the longitudinal overtones could only be measured with the assistance of imagers. We find emission intensity asymmetry in the positive and negative modulations; this is because the contribution function pertaining to the atomic emission process responds differently to positive and negative temperature variations. One may detect half periodicity close to the loop apex, where emission intensity modulation is relatively small. The line-of-sight projection affects the observation of Doppler shift significantly. A more accurate estimate of the amplitude of velocity perturbation is obtained by de-projecting the Doppler shift by a factor of 1–2θ/π rather than the traditionally used cosθ. If a loop is heated to the hotter wing, the intensity modulation could be overwhelmed by background emission, while the Doppler shift velocity could still be detected to a certain extent.
2015-07-02T00:00:00ZYuan, D.Van Doorsselaere, T.Banerjee, D.Antolin, P.Standing slow-mode waves in hot flaring loops are exclusively observed in spectrometers and are used to diagnose the magnetic field strength and temperature of the loop structure. Owing to the lack of spatial information, the longitudinal mode cannot be effectively identified. In this study, we simulate standing slow-mode waves in flaring loops and compare the synthesized line emission properties with Solar Ultraviolet Measurements of Emitted Radiation spectrographic and Solar Dynamics Observatory/Atmospheric Imaging Assembly imaging observations. We find that the emission intensity and line width oscillations are a quarter period out of phase with Doppler shift velocity in both time and spatial domain, which can be used to identify a standing slow-mode wave from spectroscopic observations. However, the longitudinal overtones could only be measured with the assistance of imagers. We find emission intensity asymmetry in the positive and negative modulations; this is because the contribution function pertaining to the atomic emission process responds differently to positive and negative temperature variations. One may detect half periodicity close to the loop apex, where emission intensity modulation is relatively small. The line-of-sight projection affects the observation of Doppler shift significantly. A more accurate estimate of the amplitude of velocity perturbation is obtained by de-projecting the Doppler shift by a factor of 1–2θ/π rather than the traditionally used cosθ. If a loop is heated to the hotter wing, the intensity modulation could be overwhelmed by background emission, while the Doppler shift velocity could still be detected to a certain extent.Resonant absorption of transverse oscillations and associated heating in a solar prominence. I. Observational aspectsOkamoto, Takenori J.Antolin, PatrickDe Pontieu, BartUitenbroek, HanVan Doorsselaere, TomYokoyama, Takaakihttp://hdl.handle.net/10023/102942018-02-11T01:34:57Z2015-08-11T00:00:00ZTransverse magnetohydrodynamic waves have been shown to be ubiquitous in the solar atmosphere and can, in principle, carry sufficient energy to generate and maintain the Sun's million-degree outer atmosphere or corona. However, direct evidence of the dissipation process of these waves and subsequent heating has not yet been directly observed. Here we report on high spatial, temporal, and spectral resolution observations of a solar prominence that show a compelling signature of so-called resonant absorption, a long hypothesized mechanism to efficiently convert and dissipate transverse wave energy into heat. Aside from coherence in the transverse direction, our observations show telltale phase differences around 180° between transverse motions in the plane-of-sky and line-of-sight velocities of the oscillating fine structures or threads, and also suggest significant heating from chromospheric to higher temperatures. Comparison with advanced numerical simulations support a scenario in which transverse oscillations trigger a Kelvin–Helmholtz instability (KHI) at the boundaries of oscillating threads via resonant absorption. This instability leads to numerous thin current sheets in which wave energy is dissipated and plasma is heated. Our results provide direct evidence for wave-related heating in action, one of the candidate coronal heating mechanisms.
2015-08-11T00:00:00ZOkamoto, Takenori J.Antolin, PatrickDe Pontieu, BartUitenbroek, HanVan Doorsselaere, TomYokoyama, TakaakiTransverse magnetohydrodynamic waves have been shown to be ubiquitous in the solar atmosphere and can, in principle, carry sufficient energy to generate and maintain the Sun's million-degree outer atmosphere or corona. However, direct evidence of the dissipation process of these waves and subsequent heating has not yet been directly observed. Here we report on high spatial, temporal, and spectral resolution observations of a solar prominence that show a compelling signature of so-called resonant absorption, a long hypothesized mechanism to efficiently convert and dissipate transverse wave energy into heat. Aside from coherence in the transverse direction, our observations show telltale phase differences around 180° between transverse motions in the plane-of-sky and line-of-sight velocities of the oscillating fine structures or threads, and also suggest significant heating from chromospheric to higher temperatures. Comparison with advanced numerical simulations support a scenario in which transverse oscillations trigger a Kelvin–Helmholtz instability (KHI) at the boundaries of oscillating threads via resonant absorption. This instability leads to numerous thin current sheets in which wave energy is dissipated and plasma is heated. Our results provide direct evidence for wave-related heating in action, one of the candidate coronal heating mechanisms.Resonant absorption of transverse oscillations and associated heating in a solar prominence. II. Numerical aspectsAntolin, P.Okamoto, T. J.De Pontieu, B.Uitenbroek, H.Van Doorsselaere, T.Yokoyama, T.http://hdl.handle.net/10023/102932018-02-11T01:34:56Z2015-08-11T00:00:00ZTransverse magnetohydrodynamic (MHD) waves are ubiquitous in the solar atmosphere and may be responsible for generating the Sun's million-degree outer atmosphere. However, direct evidence of the dissipation process and heating from these waves remains elusive. Through advanced numerical simulations combined with appropriate forward modeling of a prominence flux tube, we provide the observational signatures of transverse MHD waves in prominence plasmas. We show that these signatures are characterized by a thread-like substructure, strong transverse dynamical coherence, an out-of-phase difference between plane-of-the-sky motions and line-of-sight velocities, and enhanced line broadening and heating around most of the flux tube. A complex combination between resonant absorption and Kelvin–Helmholtz instabilities (KHIs) takes place in which the KHI extracts the energy from the resonant layer and dissipates it through vortices and current sheets, which rapidly degenerate into turbulence. An inward enlargement of the boundary is produced in which the turbulent flows conserve the characteristic dynamics from the resonance, therefore guaranteeing detectability of the resonance imprints. We show that the features described in the accompanying paper through coordinated Hinode and Interface Region Imaging Spectrograph observations match the numerical results well.
2015-08-11T00:00:00ZAntolin, P.Okamoto, T. J.De Pontieu, B.Uitenbroek, H.Van Doorsselaere, T.Yokoyama, T.Transverse magnetohydrodynamic (MHD) waves are ubiquitous in the solar atmosphere and may be responsible for generating the Sun's million-degree outer atmosphere. However, direct evidence of the dissipation process and heating from these waves remains elusive. Through advanced numerical simulations combined with appropriate forward modeling of a prominence flux tube, we provide the observational signatures of transverse MHD waves in prominence plasmas. We show that these signatures are characterized by a thread-like substructure, strong transverse dynamical coherence, an out-of-phase difference between plane-of-the-sky motions and line-of-sight velocities, and enhanced line broadening and heating around most of the flux tube. A complex combination between resonant absorption and Kelvin–Helmholtz instabilities (KHIs) takes place in which the KHI extracts the energy from the resonant layer and dissipates it through vortices and current sheets, which rapidly degenerate into turbulence. An inward enlargement of the boundary is produced in which the turbulent flows conserve the characteristic dynamics from the resonance, therefore guaranteeing detectability of the resonance imprints. We show that the features described in the accompanying paper through coordinated Hinode and Interface Region Imaging Spectrograph observations match the numerical results well.Hα and EUV observations of a partial CMEChristian, Damian J.Jess, David B.Antolin, PatrickMathioudakis, Mihalishttp://hdl.handle.net/10023/102912018-01-07T03:56:04Z2015-05-12T00:00:00ZWe have obtained Hα high spatial and time resolution observations of the upper solar chromosphere and supplemented these with multi-wavelength observations from the Solar Dynamics Observatory (SDO) and the Hinode Extreme-ultraviolet Imaging Spectrometer. The Hα observations were conducted on 2012 February 11 with the Hydrogen-Alpha Rapid Dynamics Camera instrument at the National Solar Observatory's Dunn Solar Telescope. Our Hα observations found large downflows of chromospheric material returning from coronal heights following a failed prominence eruption. We have detected several large condensations ("blobs") returning to the solar surface at velocities of ≈200 km s−1 in both Hα and several SDO Atmospheric Imaging Assembly band passes. The average derived size of these "blobs" in Hα is 500 by 3000 km2 in the directions perpendicular and parallel to the direction of travel, respectively. A comparison of our "blob" widths to those found from coronal rain, indicate that there are additional, smaller, unresolved "blobs" in agreement with previous studies and recent numerical simulations. Our observed velocities and decelerations of the "blobs" in both Hα and SDO bands are less than those expected for gravitational free-fall and imply additional magnetic or gas pressure impeding the flow. We derived a kinetic energy of ≈2 orders of magnitude lower for the main eruption than a typical coronal mass ejection, which may explain its partial nature.
2015-05-12T00:00:00ZChristian, Damian J.Jess, David B.Antolin, PatrickMathioudakis, MihalisWe have obtained Hα high spatial and time resolution observations of the upper solar chromosphere and supplemented these with multi-wavelength observations from the Solar Dynamics Observatory (SDO) and the Hinode Extreme-ultraviolet Imaging Spectrometer. The Hα observations were conducted on 2012 February 11 with the Hydrogen-Alpha Rapid Dynamics Camera instrument at the National Solar Observatory's Dunn Solar Telescope. Our Hα observations found large downflows of chromospheric material returning from coronal heights following a failed prominence eruption. We have detected several large condensations ("blobs") returning to the solar surface at velocities of ≈200 km s−1 in both Hα and several SDO Atmospheric Imaging Assembly band passes. The average derived size of these "blobs" in Hα is 500 by 3000 km2 in the directions perpendicular and parallel to the direction of travel, respectively. A comparison of our "blob" widths to those found from coronal rain, indicate that there are additional, smaller, unresolved "blobs" in agreement with previous studies and recent numerical simulations. Our observed velocities and decelerations of the "blobs" in both Hα and SDO bands are less than those expected for gravitational free-fall and imply additional magnetic or gas pressure impeding the flow. We derived a kinetic energy of ≈2 orders of magnitude lower for the main eruption than a typical coronal mass ejection, which may explain its partial nature.The multi-thermal and multi-stranded nature of coronal rainAntolin, P.Vissers, G.Pereira, T. M. D.Rouppe van der Voort, L.Scullion, E.http://hdl.handle.net/10023/102902018-02-25T01:33:08Z2015-06-09T00:00:00ZWe analyze coordinated observations of coronal rain in loops, spanning chromospheric, transition region (TR), and coronal temperatures with sub-arcsecond spatial resolution. Coronal rain is found to be a highly multithermal phenomenon with a high degree of co-spatiality in the multi-wavelength emission. EUV darkening and quasi-periodic intensity variations are found to be strongly correlated with coronal rain showers. Progressive cooling of coronal rain is observed, leading to a height dependence of the emission. A fast-slow two-step catastrophic cooling progression is found, which may reflect the transition to optically thick plasma states. The intermittent and clumpy appearance of coronal rain at coronal heights becomes more continuous and persistent at chromospheric heights just before impact, mainly due to a funnel effect from the observed expansion of the magnetic field. Strong density inhomogeneities of 0.″2-0.″5 are found, in which a transition from temperatures of 105 to 104 K occurs. The 0.″2-0.″8 width of the distribution of coronal rain is found to be independent of temperature. The sharp increase in the number of clumps at the coolest temperatures, especially at higher resolution, suggests that the bulk distribution of the rain remains undetected. Rain clumps appear organized in strands in both chromospheric and TR temperatures. We further find structure reminiscent of the magnetohydrodynamic (MHD) thermal mode (also known as entropy mode), thereby suggesting an important role of thermal instability in shaping the basic loop substructure. Rain core densities are estimated to vary between 2 × 1010 and 2.5 × 1011cm−3, leading to significant downward mass fluxes per loop of 1–5 × 109 g s−1, thus suggesting a major role in the chromosphere-corona mass cycle.
2015-06-09T00:00:00ZAntolin, P.Vissers, G.Pereira, T. M. D.Rouppe van der Voort, L.Scullion, E.We analyze coordinated observations of coronal rain in loops, spanning chromospheric, transition region (TR), and coronal temperatures with sub-arcsecond spatial resolution. Coronal rain is found to be a highly multithermal phenomenon with a high degree of co-spatiality in the multi-wavelength emission. EUV darkening and quasi-periodic intensity variations are found to be strongly correlated with coronal rain showers. Progressive cooling of coronal rain is observed, leading to a height dependence of the emission. A fast-slow two-step catastrophic cooling progression is found, which may reflect the transition to optically thick plasma states. The intermittent and clumpy appearance of coronal rain at coronal heights becomes more continuous and persistent at chromospheric heights just before impact, mainly due to a funnel effect from the observed expansion of the magnetic field. Strong density inhomogeneities of 0.″2-0.″5 are found, in which a transition from temperatures of 105 to 104 K occurs. The 0.″2-0.″8 width of the distribution of coronal rain is found to be independent of temperature. The sharp increase in the number of clumps at the coolest temperatures, especially at higher resolution, suggests that the bulk distribution of the rain remains undetected. Rain clumps appear organized in strands in both chromospheric and TR temperatures. We further find structure reminiscent of the magnetohydrodynamic (MHD) thermal mode (also known as entropy mode), thereby suggesting an important role of thermal instability in shaping the basic loop substructure. Rain core densities are estimated to vary between 2 × 1010 and 2.5 × 1011cm−3, leading to significant downward mass fluxes per loop of 1–5 × 109 g s−1, thus suggesting a major role in the chromosphere-corona mass cycle.Unresolved fine-scale structure in solar coronal loop-topsScullion, E.Rouppe van der Voort, L.Wedemeyer, S.Antolin, P.http://hdl.handle.net/10023/102882018-03-18T01:39:06Z2014-11-24T00:00:00ZNew and advanced space-based observing facilities continue to lower the resolution limit and detect solar coronal loops in greater detail. We continue to discover even finer substructures within coronal loop cross-sections, in order to understand the nature of the solar corona. Here, we push this lower limit further to search for the finest coronal loop substructures, through taking advantage of the resolving power of the Swedish 1 m Solar Telescope/CRisp Imaging Spectro-Polarimeter (CRISP), together with co-observations from the Solar Dynamics Observatory/Atmospheric Image Assembly (AIA). High-resolution imaging of the chromospheric Hα 656.28 nm spectral line core and wings can, under certain circumstances, allow one to deduce the topology of the local magnetic environment of the solar atmosphere where its observed. Here, we study post-flare coronal loops, which become filled with evaporated chromosphere that rapidly condenses into chromospheric clumps of plasma (detectable in Hα) known as a coronal rain, to investigate their fine-scale structure. We identify, through analysis of three data sets, large-scale catastrophic cooling in coronal loop-tops and the existence of multi-thermal, multi-stranded substructures. Many cool strands even extend fully intact from loop-top to footpoint. We discover that coronal loop fine-scale strands can appear bunched with as many as eight parallel strands within an AIA coronal loop cross-section. The strand number density versus cross-sectional width distribution, as detected by CRISP within AIA-defined coronal loops, most likely peaks at well below 100 km, and currently, 69% of the substructure strands are statistically unresolved in AIA coronal loops.
2014-11-24T00:00:00ZScullion, E.Rouppe van der Voort, L.Wedemeyer, S.Antolin, P.New and advanced space-based observing facilities continue to lower the resolution limit and detect solar coronal loops in greater detail. We continue to discover even finer substructures within coronal loop cross-sections, in order to understand the nature of the solar corona. Here, we push this lower limit further to search for the finest coronal loop substructures, through taking advantage of the resolving power of the Swedish 1 m Solar Telescope/CRisp Imaging Spectro-Polarimeter (CRISP), together with co-observations from the Solar Dynamics Observatory/Atmospheric Image Assembly (AIA). High-resolution imaging of the chromospheric Hα 656.28 nm spectral line core and wings can, under certain circumstances, allow one to deduce the topology of the local magnetic environment of the solar atmosphere where its observed. Here, we study post-flare coronal loops, which become filled with evaporated chromosphere that rapidly condenses into chromospheric clumps of plasma (detectable in Hα) known as a coronal rain, to investigate their fine-scale structure. We identify, through analysis of three data sets, large-scale catastrophic cooling in coronal loop-tops and the existence of multi-thermal, multi-stranded substructures. Many cool strands even extend fully intact from loop-top to footpoint. We discover that coronal loop fine-scale strands can appear bunched with as many as eight parallel strands within an AIA coronal loop cross-section. The strand number density versus cross-sectional width distribution, as detected by CRISP within AIA-defined coronal loops, most likely peaks at well below 100 km, and currently, 69% of the substructure strands are statistically unresolved in AIA coronal loops.First high-resolution spectroscopic observations of an erupting prominence within a coronal mass ejection by the Interface Region Imaging Spectrograph (IRIS)Liu, WeiDe Pontieu, BartVial, Jean-ClaudeTitle, Alan M.Carlsson, MatsUitenbroek, HanOkamoto, Takenori J.Berger, Thomas E.Antolin, Patrickhttp://hdl.handle.net/10023/102872018-01-07T03:56:05Z2015-04-21T00:00:00ZSpectroscopic observations of prominence eruptions associated with coronal mass ejections (CMEs), although relatively rare, can provide valuable plasma and three-dimensional geometry diagnostics. We report the first observations by the Interface Region Imaging Spectrograph mission of a spectacular fast CME/prominence eruption associated with an equivalent X1.6 flare on 2014 May 9. The maximum plane-of-sky and Doppler velocities of the eruption are 1200 and 460 km s−1, respectively. There are two eruption components separated by ~200 km s−1 in Doppler velocity: a primary, bright component and a secondary, faint component, suggesting a hollow, rather than solid, cone-shaped distribution of material. The eruption involves a left-handed helical structure undergoing counterclockwise (viewed top-down) unwinding motion. There is a temporal evolution from upward eruption to downward fallback with less-than-free-fall speeds and decreasing nonthermal line widths. We find a wide range of Mg ii k/h line intensity ratios (less than ~2 expected for optically-thin thermal emission): the lowest ever reported median value of 1.17 found in the fallback material, a comparably high value of 1.63 in nearby coronal rain, and intermediate values of 1.53 and 1.41 in the two eruption components. The fallback material exhibits a strong (>5α ) linear correlation between the k/h ratio and the Doppler velocity as well as the line intensity. We demonstrate that Doppler dimming of scattered chromospheric emission by the erupted material can potentially explain such characteristics.
2015-04-21T00:00:00ZLiu, WeiDe Pontieu, BartVial, Jean-ClaudeTitle, Alan M.Carlsson, MatsUitenbroek, HanOkamoto, Takenori J.Berger, Thomas E.Antolin, PatrickSpectroscopic observations of prominence eruptions associated with coronal mass ejections (CMEs), although relatively rare, can provide valuable plasma and three-dimensional geometry diagnostics. We report the first observations by the Interface Region Imaging Spectrograph mission of a spectacular fast CME/prominence eruption associated with an equivalent X1.6 flare on 2014 May 9. The maximum plane-of-sky and Doppler velocities of the eruption are 1200 and 460 km s−1, respectively. There are two eruption components separated by ~200 km s−1 in Doppler velocity: a primary, bright component and a secondary, faint component, suggesting a hollow, rather than solid, cone-shaped distribution of material. The eruption involves a left-handed helical structure undergoing counterclockwise (viewed top-down) unwinding motion. There is a temporal evolution from upward eruption to downward fallback with less-than-free-fall speeds and decreasing nonthermal line widths. We find a wide range of Mg ii k/h line intensity ratios (less than ~2 expected for optically-thin thermal emission): the lowest ever reported median value of 1.17 found in the fallback material, a comparably high value of 1.63 in nearby coronal rain, and intermediate values of 1.53 and 1.41 in the two eruption components. The fallback material exhibits a strong (>5α ) linear correlation between the k/h ratio and the Doppler velocity as well as the line intensity. We demonstrate that Doppler dimming of scattered chromospheric emission by the erupted material can potentially explain such characteristics.Simulating the in situ condensation process of solar prominencesXia, C.Keppens, R.Antolin, P.Porth, O.http://hdl.handle.net/10023/102852018-03-11T01:36:38Z2014-08-27T00:00:00ZProminences in the solar corona are a hundredfold cooler and denser than their surroundings, with a total mass of 1013 up to 1015 g. Here, we report on the first comprehensive simulations of three-dimensional, thermally and gravitationally stratified magnetic flux ropes where in situ condensation to a prominence occurs due to radiative losses. After a gradual thermodynamic adjustment, we witness a phase where runaway cooling occurs while counter-streaming shearing flows drain off mass along helical field lines. After this drainage, a prominence-like condensation resides in concave upward field regions, and this prominence retains its overall characteristics for more than two hours. While condensing, the prominence establishes a prominence-corona transition region where magnetic field-aligned thermal conduction is operative during the runaway cooling. The prominence structure represents a force-balanced state in a helical flux rope. The simulated condensation demonstrates a right-bearing barb, as a remnant of the drainage. Synthetic images at extreme ultraviolet wavelengths follow the onset of the condensation, and confirm the appearance of horns and a three-part structure for the stable prominence state, as often seen in erupting prominences. This naturally explains recent Solar Dynamics Observatory views with the Atmospheric Imaging Assembly on prominences in coronal cavities demonstrating horns.
2014-08-27T00:00:00ZXia, C.Keppens, R.Antolin, P.Porth, O.Prominences in the solar corona are a hundredfold cooler and denser than their surroundings, with a total mass of 1013 up to 1015 g. Here, we report on the first comprehensive simulations of three-dimensional, thermally and gravitationally stratified magnetic flux ropes where in situ condensation to a prominence occurs due to radiative losses. After a gradual thermodynamic adjustment, we witness a phase where runaway cooling occurs while counter-streaming shearing flows drain off mass along helical field lines. After this drainage, a prominence-like condensation resides in concave upward field regions, and this prominence retains its overall characteristics for more than two hours. While condensing, the prominence establishes a prominence-corona transition region where magnetic field-aligned thermal conduction is operative during the runaway cooling. The prominence structure represents a force-balanced state in a helical flux rope. The simulated condensation demonstrates a right-bearing barb, as a remnant of the drainage. Synthetic images at extreme ultraviolet wavelengths follow the onset of the condensation, and confirm the appearance of horns and a three-part structure for the stable prominence state, as often seen in erupting prominences. This naturally explains recent Solar Dynamics Observatory views with the Atmospheric Imaging Assembly on prominences in coronal cavities demonstrating horns.Detection of supersonic downflows and associated heating events in the transition region above sunspotsKleint, L.Antolin, P.Tian, H.Judge, P.Testa, P.De Pontieu, B.Martínez-Sykora, J.Reeves, K. K.Wuelser, J. P.McKillop, S.Saar, S.Carlsson, M.Boerner, P.Hurlburt, N.Lemen, J.Tarbell, T. D.Title, A.Golub, L.Hansteen, V.Jaeggli, S.Kankelborg, C.http://hdl.handle.net/10023/102822018-02-18T01:38:00Z2014-06-27T00:00:00ZInterface Region Imaging Spectrograph data allow us to study the solar transition region (TR) with an unprecedented spatial resolution of 0″33. On 2013 August 30, we observed bursts of high Doppler shifts suggesting strong supersonic downflows of up to 200 km s–1 and weaker, slightly slower upflows in the spectral lines Mg II h and k, C II 1336, Si IV 1394 Å, and 1403 Å, that are correlated with brightenings in the slitjaw images (SJIs). The bursty behavior lasts throughout the 2 hr observation, with average burst durations of about 20 s. The locations of these short-lived events appear to be the umbral and penumbral footpoints of EUV loops. Fast apparent downflows are observed along these loops in the SJIs and in the Atmospheric Imaging Assembly, suggesting that the loops are thermally unstable. We interpret the observations as cool material falling from coronal heights, and especially coronal rain produced along the thermally unstable loops, which leads to an increase of intensity at the loop footpoints, probably indicating an increase of density and temperature in the TR. The rain speeds are on the higher end of previously reported speeds for this phenomenon, and possibly higher than the free-fall velocity along the loops. On other observing days, similar bright dots are sometimes aligned into ribbons, resembling small flare ribbons. These observations provide a first insight into small-scale heating events in sunspots in the TR.
2014-06-27T00:00:00ZKleint, L.Antolin, P.Tian, H.Judge, P.Testa, P.De Pontieu, B.Martínez-Sykora, J.Reeves, K. K.Wuelser, J. P.McKillop, S.Saar, S.Carlsson, M.Boerner, P.Hurlburt, N.Lemen, J.Tarbell, T. D.Title, A.Golub, L.Hansteen, V.Jaeggli, S.Kankelborg, C.Interface Region Imaging Spectrograph data allow us to study the solar transition region (TR) with an unprecedented spatial resolution of 0″33. On 2013 August 30, we observed bursts of high Doppler shifts suggesting strong supersonic downflows of up to 200 km s–1 and weaker, slightly slower upflows in the spectral lines Mg II h and k, C II 1336, Si IV 1394 Å, and 1403 Å, that are correlated with brightenings in the slitjaw images (SJIs). The bursty behavior lasts throughout the 2 hr observation, with average burst durations of about 20 s. The locations of these short-lived events appear to be the umbral and penumbral footpoints of EUV loops. Fast apparent downflows are observed along these loops in the SJIs and in the Atmospheric Imaging Assembly, suggesting that the loops are thermally unstable. We interpret the observations as cool material falling from coronal heights, and especially coronal rain produced along the thermally unstable loops, which leads to an increase of intensity at the loop footpoints, probably indicating an increase of density and temperature in the TR. The rain speeds are on the higher end of previously reported speeds for this phenomenon, and possibly higher than the free-fall velocity along the loops. On other observing days, similar bright dots are sometimes aligned into ribbons, resembling small flare ribbons. These observations provide a first insight into small-scale heating events in sunspots in the TR.Forward modeling of gyrosynchrotron intensity perturbations by sausage modesReznikova, V. E.Antolin, P.Van Doorsselaere, T.http://hdl.handle.net/10023/102802018-01-07T03:56:12Z2014-03-28T00:00:00ZTo determine the observable radio signatures of the fast sausagestanding wave, we examine gyrosynchrotron (GS) emission modulation usinga linear three-dimensional magnetohydrodynamic model of a plasmacylinder. Effects of the line-of-sight angle and instrumental resolutionon perturbations of the GS intensity are analyzed for two models: a basemodel with strong Razin suppression and a low-density model in which theRazin effect was unimportant. Our finding contradicts previouspredictions made with simpler models: an in-phase variation of intensitybetween low (f <fpeak) and high (f > fpeak) frequencies is found for the low-density model and ananti-phase variation for the base model in the case of a viewing angleof 45°. The spatially inhomogeneous character of the oscillatingemission source and the spatial resolution of the model are found tohave a significant effect on the resulting intensity.
2014-03-28T00:00:00ZReznikova, V. E.Antolin, P.Van Doorsselaere, T.To determine the observable radio signatures of the fast sausagestanding wave, we examine gyrosynchrotron (GS) emission modulation usinga linear three-dimensional magnetohydrodynamic model of a plasmacylinder. Effects of the line-of-sight angle and instrumental resolutionon perturbations of the GS intensity are analyzed for two models: a basemodel with strong Razin suppression and a low-density model in which theRazin effect was unimportant. Our finding contradicts previouspredictions made with simpler models: an in-phase variation of intensitybetween low (f <fpeak) and high (f > fpeak) frequencies is found for the low-density model and ananti-phase variation for the base model in the case of a viewing angleof 45°. The spatially inhomogeneous character of the oscillatingemission source and the spatial resolution of the model are found tohave a significant effect on the resulting intensity.Fine strand-like structure in the solar corona from magnetohydrodynamic transverse oscillationsAntolin, P.Yokoyama, T.Van Doorsselaere, T.http://hdl.handle.net/10023/102792018-03-11T01:36:40Z2014-05-13T00:00:00ZCurrent analytical and numerical modeling suggest the existence of ubiquitous thin current sheets in the corona that could explain the observed heating requirements. On the other hand, new high resolution observations of the corona indicate that its magnetic field may tend to organize itself in fine strand-like structures of few hundred kilometers widths. The link between small structure in models and the observed widths of strand-like structure several orders of magnitude larger is still not clear. A popular theoretical scenario is the nanoflare model, in which each strand is the product of an ensemble of heating events. Here, we suggest an alternative mechanism for strand generation. Through forward modeling of three-dimensional MHD simulations we show that small amplitude transverse MHD waves can lead in a few periods time to strand-like structure in loops in EUV intensity images. Our model is based on previous numerical work showing that transverse MHD oscillations can lead to Kelvin-Helmholtz instabilities that deform the cross-sectional area of loops. While previous work has focused on large amplitude oscillations, here we show that the instability can occur even for low wave amplitudes for long and thin loops, matching those presently observed in the corona. We show that the vortices generated from the instability are velocity sheared regions with enhanced emissivity hosting current sheets. Strands result as a complex combination of the vortices and the line-of-sight angle, last for timescales of a period, and can be observed for spatial resolutions of a tenth of loop radius.
2014-05-13T00:00:00ZAntolin, P.Yokoyama, T.Van Doorsselaere, T.Current analytical and numerical modeling suggest the existence of ubiquitous thin current sheets in the corona that could explain the observed heating requirements. On the other hand, new high resolution observations of the corona indicate that its magnetic field may tend to organize itself in fine strand-like structures of few hundred kilometers widths. The link between small structure in models and the observed widths of strand-like structure several orders of magnitude larger is still not clear. A popular theoretical scenario is the nanoflare model, in which each strand is the product of an ensemble of heating events. Here, we suggest an alternative mechanism for strand generation. Through forward modeling of three-dimensional MHD simulations we show that small amplitude transverse MHD waves can lead in a few periods time to strand-like structure in loops in EUV intensity images. Our model is based on previous numerical work showing that transverse MHD oscillations can lead to Kelvin-Helmholtz instabilities that deform the cross-sectional area of loops. While previous work has focused on large amplitude oscillations, here we show that the instability can occur even for low wave amplitudes for long and thin loops, matching those presently observed in the corona. We show that the vortices generated from the instability are velocity sheared regions with enhanced emissivity hosting current sheets. Strands result as a complex combination of the vortices and the line-of-sight angle, last for timescales of a period, and can be observed for spatial resolutions of a tenth of loop radius.Forward modeling of EUV and gyrosynchrotron emission from coronal plasmas with FoMoVan Doorsselaere, TomAntolin, PatrickYuan, DingReznikova, VeronikaMagyar, Norberthttp://hdl.handle.net/10023/102752018-01-21T00:31:43Z2016-02-26T00:00:00ZThe FOMO code was developed to calculate the EUV and UV emission from optically thin coronal plasmas. The input data for FOMO consists of the plasma density, temperature and velocity on a 3D grid. This is translated to emissivity on the 3D grid, using CHIANTI data. Then, the emissivity is integrated along the line-of-sight (LOS) to calculate the emergent spectral line for synthetic spectrometer observations. The code also generates the emission channels for synthetic AIA imaging observations. Moreover, the code has been extended to model also the gyrosynchrotron emission from plasmas with a population of non-thermal particles. In this case, also optically thick plasmas may be modeled. The radio spectrum is calculated over a large wavelength range, allowing for the comparison with data from a wide range of radio telescopes.
Odysseus funding (FWO-Vlaanderen), IAPP7/08CHARM (Belspo), GOA-2015-014 (KULeuven), NAOJ Visiting Fellows Program. N Misa PhD student of the FWO-Vlaanderen.
2016-02-26T00:00:00ZVan Doorsselaere, TomAntolin, PatrickYuan, DingReznikova, VeronikaMagyar, NorbertThe FOMO code was developed to calculate the EUV and UV emission from optically thin coronal plasmas. The input data for FOMO consists of the plasma density, temperature and velocity on a 3D grid. This is translated to emissivity on the 3D grid, using CHIANTI data. Then, the emissivity is integrated along the line-of-sight (LOS) to calculate the emergent spectral line for synthetic spectrometer observations. The code also generates the emission channels for synthetic AIA imaging observations. Moreover, the code has been extended to model also the gyrosynchrotron emission from plasmas with a population of non-thermal particles. In this case, also optically thick plasmas may be modeled. The radio spectrum is calculated over a large wavelength range, allowing for the comparison with data from a wide range of radio telescopes.Observational signatures of transverse magnetohydrodynamic waves and associated dynamic instabilities in coronal flux tubesAntolin, PatrickMoortel, Ineke DeDoorsselaere, Tom VanYokoyama, Takaakihttp://hdl.handle.net/10023/102562018-03-11T01:36:47Z2017-02-22T00:00:00ZMHD waves permeate the solar atmosphere and constitute potential coronal heating agents. Yet, the waves detected so far may be but a small subset of the true existing wave power. Detection is limited by instrumental constraints, but also by wave processes that localise the wave power in undetectable spatial scales. In this study we conduct 3D MHD simulations and forward modelling of standing transverse MHD waves in coronal loops with uniform and non-uniform temperature variation in the perpendicular cross-section. The observed signatures are largely dominated by the combination of the Kelvin-Helmholtz instability (KHI), resonant absorption and phase mixing. In the presence of a cross-loop temperature gradient we find that emission lines sensitive to the loop core catch different signatures than those more sensitive to the loop boundary and the surrounding corona, leading to an out-of-phase intensity modulation produced by the KHI mixing. Common signatures to all considered models include an intensity and loop width modulation at half the kink period, fine strand-like structure, a characteristic arrow-shaped structure in the Doppler maps, overall line broadening in time but particularly at the loop edges. For our model, most of these features can be captured with a spatial resolution of 0.33″ and spectral resolution of 25 km s-1, although severe over-estimation of the line width is obtained. Resonant absorption leads to a significant decrease of the observed kinetic energy from Doppler motions over time, which is not recovered by a corresponding increase in the line width from phase mixing and the KHI motions. We estimate this hidden wave energy to be a factor of 5-10 of the observed value.
This research has received funding from the UK Science and Technology Facilities Council and the European Union Horizon 2020 research and innovation programme (grant agreement No. 647214), and also from JSPS KAKENHI Grant Numbers 25220703 (PI: S. Tsuneta) and 15H03640 (PI: T. Yokoyama). T.V.D. was supported by FWO Vlaanderen’s Odysseus programme, GOA-2015-014 (KU Leuven) and the IAP P7/08 CHARM (Belspo).
2017-02-22T00:00:00ZAntolin, PatrickMoortel, Ineke DeDoorsselaere, Tom VanYokoyama, TakaakiMHD waves permeate the solar atmosphere and constitute potential coronal heating agents. Yet, the waves detected so far may be but a small subset of the true existing wave power. Detection is limited by instrumental constraints, but also by wave processes that localise the wave power in undetectable spatial scales. In this study we conduct 3D MHD simulations and forward modelling of standing transverse MHD waves in coronal loops with uniform and non-uniform temperature variation in the perpendicular cross-section. The observed signatures are largely dominated by the combination of the Kelvin-Helmholtz instability (KHI), resonant absorption and phase mixing. In the presence of a cross-loop temperature gradient we find that emission lines sensitive to the loop core catch different signatures than those more sensitive to the loop boundary and the surrounding corona, leading to an out-of-phase intensity modulation produced by the KHI mixing. Common signatures to all considered models include an intensity and loop width modulation at half the kink period, fine strand-like structure, a characteristic arrow-shaped structure in the Doppler maps, overall line broadening in time but particularly at the loop edges. For our model, most of these features can be captured with a spatial resolution of 0.33″ and spectral resolution of 25 km s-1, although severe over-estimation of the line width is obtained. Resonant absorption leads to a significant decrease of the observed kinetic energy from Doppler motions over time, which is not recovered by a corresponding increase in the line width from phase mixing and the KHI motions. We estimate this hidden wave energy to be a factor of 5-10 of the observed value.Balanced solutions for an ellipsoidal vortex in a rotating stratified flowMckiver, William J.Dritschel, David G.http://hdl.handle.net/10023/102272017-11-07T21:30:39Z2016-09-01T00:00:00ZWe consider the motion of a single ellipsoidal vortex with uniform potential vorticity in a rotating stratified fluid at finite Rossby number . Building on previous solutions obtained under the quasi-geostrophic approximation (at first order in ), we obtain analytical solutions for the balanced part of the flow at . These solutions capture important ageostrophic effects giving rise to an asymmetry in the evolution of cyclonic and anticyclonic vortices. Previous work has shown that, if the velocity field induced by an ellipsoidal vortex only depends linearly on spatial coordinates inside the vortex, i.e. , then the dynamics reduces markedly to a simple matrix equation. The instantaneous vortex shape and orientation are encapsulated in a symmetric matrix , which is acted upon by the flow matrix to provide the vortex evolution. Under the quasi-geostrophic approximation, the flow matrix is determined by inverting the potential vorticity to obtain the streamfunction via Poisson's equation, which has a known analytical solution depending on elliptic integrals. Here we show that higher-order balanced solutions, up to second order in the Rossby number, can also be calculated analytically. However, in this case there is a vector potential that requires the solution of three Poisson equations for each of its components. The source terms for these equations are independent of spatial coordinates within the ellipsoid, depending only on the elliptic integrals solved at the leading, quasi-geostrophic order. Unlike the quasi-geostrophic case, these source terms do not in general vanish outside the ellipsoid and have an inordinately complicated dependence on spatial coordinates. In the special case of an ellipsoid whose axes are aligned with the coordinate axes, we are able to derive these source terms and obtain the full analytical solution to the three Poisson equations. However, if one considers the homogeneous case, whereby the outer source terms are neglected, one can obtain an approximate solution having a compact matrix form analogous to the leading-order quasi-geostrophic case. This approximate solution proves to be highly accurate for the general case of an arbitrarily oriented ellipsoid, as verified through comparisons of the solutions with solutions obtained from numerical simulations of an ellipsoid using an accurate nonlinear balance model, even at moderate Rossby numbers.
Support for this research has come from the UK Engineering and Physical Sciences Research Council (grant number EP/H001794/1).
2016-09-01T00:00:00ZMckiver, William J.Dritschel, David G.We consider the motion of a single ellipsoidal vortex with uniform potential vorticity in a rotating stratified fluid at finite Rossby number . Building on previous solutions obtained under the quasi-geostrophic approximation (at first order in ), we obtain analytical solutions for the balanced part of the flow at . These solutions capture important ageostrophic effects giving rise to an asymmetry in the evolution of cyclonic and anticyclonic vortices. Previous work has shown that, if the velocity field induced by an ellipsoidal vortex only depends linearly on spatial coordinates inside the vortex, i.e. , then the dynamics reduces markedly to a simple matrix equation. The instantaneous vortex shape and orientation are encapsulated in a symmetric matrix , which is acted upon by the flow matrix to provide the vortex evolution. Under the quasi-geostrophic approximation, the flow matrix is determined by inverting the potential vorticity to obtain the streamfunction via Poisson's equation, which has a known analytical solution depending on elliptic integrals. Here we show that higher-order balanced solutions, up to second order in the Rossby number, can also be calculated analytically. However, in this case there is a vector potential that requires the solution of three Poisson equations for each of its components. The source terms for these equations are independent of spatial coordinates within the ellipsoid, depending only on the elliptic integrals solved at the leading, quasi-geostrophic order. Unlike the quasi-geostrophic case, these source terms do not in general vanish outside the ellipsoid and have an inordinately complicated dependence on spatial coordinates. In the special case of an ellipsoid whose axes are aligned with the coordinate axes, we are able to derive these source terms and obtain the full analytical solution to the three Poisson equations. However, if one considers the homogeneous case, whereby the outer source terms are neglected, one can obtain an approximate solution having a compact matrix form analogous to the leading-order quasi-geostrophic case. This approximate solution proves to be highly accurate for the general case of an arbitrarily oriented ellipsoid, as verified through comparisons of the solutions with solutions obtained from numerical simulations of an ellipsoid using an accurate nonlinear balance model, even at moderate Rossby numbers.High Gaussicity feedhorns for sub-/ millimeter wave applicationsRobertson, Duncan A.McKay, Johannes E.Hunter, Robert I.Speirs, Peter J.Smith, Graham M.http://hdl.handle.net/10023/101712018-01-07T03:13:42Z2016-11-28T00:00:00ZIn feedhorn design, the power coupling to the fundamental free-space LG00 mode, or Gaussicity, is a good proxy for high performance, particularly the sidelobe and cross-polar levels and the near-field behavior. Gaussicity can be maximized by ensuring that the first few horn modes reach the aperture with the appropriate phase and amplitude relationship. We present two feedhorn designs for which the Gaussicity was maximized in order to achieve high performance. The first is a 94 GHz corrugated horn with a tanh-linear profile, manufactured by electroforming, which achieves a Gaussicity of 99.92% at band center and sidelobes at the -60 dB level. The second is a 340 GHz smooth-walled spline horn which achieves a Gaussicity of >99.2% over a 10% bandwidth, sidelobes below -30 dB and excellent near-field behavior. This design has been successfully fabricated in E-plane split block suitable for low volume manufacture, for example for imaging arrays.
2016-11-28T00:00:00ZRobertson, Duncan A.McKay, Johannes E.Hunter, Robert I.Speirs, Peter J.Smith, Graham M.In feedhorn design, the power coupling to the fundamental free-space LG00 mode, or Gaussicity, is a good proxy for high performance, particularly the sidelobe and cross-polar levels and the near-field behavior. Gaussicity can be maximized by ensuring that the first few horn modes reach the aperture with the appropriate phase and amplitude relationship. We present two feedhorn designs for which the Gaussicity was maximized in order to achieve high performance. The first is a 94 GHz corrugated horn with a tanh-linear profile, manufactured by electroforming, which achieves a Gaussicity of 99.92% at band center and sidelobes at the -60 dB level. The second is a 340 GHz smooth-walled spline horn which achieves a Gaussicity of >99.2% over a 10% bandwidth, sidelobes below -30 dB and excellent near-field behavior. This design has been successfully fabricated in E-plane split block suitable for low volume manufacture, for example for imaging arrays.Solar science with the Atacama Large Millimeter/Submillimeter Array — a new view of our sunWedemeyer, S.Bastian, T.Brajša, R.Hudson, H.Fleishman, G.Loukitcheva, M.Fleck, B.Kontar, E. P.De Pontieu, B.Yagoubov, P.Tiwari, S. K.Soler, R.Black, J. H.Antolin, P.Scullion, E.Gunár, S.Labrosse, N.Ludwig, H.-G.Benz, A. O.White, S. M.Hauschildt, P.Doyle, J. G.Nakariakov, V. M.Ayres, T.Heinzel, P.Karlicky, M.Van Doorsselaere, T.Gary, D.Alissandrakis, C. E.Nindos, A.Solanki, S. K.Rouppe van der Voort, L.Shimojo, M.Kato, Y.Zaqarashvili, T.Perez, E.Selhorst, C. L.Barta, M.http://hdl.handle.net/10023/101562018-01-07T03:55:57Z2016-04-01T00:00:00ZThe Atacama Large Millimeter/submillimeter Array (ALMA) is a new powerful tool for observing the Sun at high spatial, temporal, and spectral resolution. These capabilities can address a broad range of fundamental scientific questions in solar physics. The radiation observed by ALMA originates mostly from the chromosphere—a complex and dynamic region between the photosphere and corona, which plays a crucial role in the transport of energy and matter and, ultimately, the heating of the outer layers of the solar atmosphere. Based on first solar test observations, strategies for regular solar campaigns are currently being developed. State-of-the-art numerical simulations of the solar atmosphere and modeling of instrumental effects can help constrain and optimize future observing modes for ALMA. Here we present a short technical description of ALMA and an overview of past efforts and future possibilities for solar observations at submillimeter and millimeter wavelengths. In addition, selected numerical simulations and observations at other wavelengths demonstrate ALMA's scientific potential for studying the Sun for a large range of science cases.
2016-04-01T00:00:00ZWedemeyer, S.Bastian, T.Brajša, R.Hudson, H.Fleishman, G.Loukitcheva, M.Fleck, B.Kontar, E. P.De Pontieu, B.Yagoubov, P.Tiwari, S. K.Soler, R.Black, J. H.Antolin, P.Scullion, E.Gunár, S.Labrosse, N.Ludwig, H.-G.Benz, A. O.White, S. M.Hauschildt, P.Doyle, J. G.Nakariakov, V. M.Ayres, T.Heinzel, P.Karlicky, M.Van Doorsselaere, T.Gary, D.Alissandrakis, C. E.Nindos, A.Solanki, S. K.Rouppe van der Voort, L.Shimojo, M.Kato, Y.Zaqarashvili, T.Perez, E.Selhorst, C. L.Barta, M.The Atacama Large Millimeter/submillimeter Array (ALMA) is a new powerful tool for observing the Sun at high spatial, temporal, and spectral resolution. These capabilities can address a broad range of fundamental scientific questions in solar physics. The radiation observed by ALMA originates mostly from the chromosphere—a complex and dynamic region between the photosphere and corona, which plays a crucial role in the transport of energy and matter and, ultimately, the heating of the outer layers of the solar atmosphere. Based on first solar test observations, strategies for regular solar campaigns are currently being developed. State-of-the-art numerical simulations of the solar atmosphere and modeling of instrumental effects can help constrain and optimize future observing modes for ALMA. Here we present a short technical description of ALMA and an overview of past efforts and future possibilities for solar observations at submillimeter and millimeter wavelengths. In addition, selected numerical simulations and observations at other wavelengths demonstrate ALMA's scientific potential for studying the Sun for a large range of science cases.Global sausage oscillation of solar flare loops detected by the Interface Region Imaging SpectrographTian, HuiYoung, Peter R.Reeves, Katharine K.Wang, TongjiangAntolin, PatrickChen, BinHe, Jiansenhttp://hdl.handle.net/10023/101402018-03-04T01:40:39Z2016-05-20T00:00:00ZAn observation from the Interface Region Imaging Spectrograph reveals coherent oscillations in the loops of an M1.6 flare on 2015 March 12. Both the intensity and Doppler shift of Fe xxi 1354.08 Å show clear oscillations with a period of ˜25 s. Remarkably similar oscillations were also detected in the soft X-ray flux recorded by the Geostationary Operational Environmental Satellites (GOES). With an estimated phase speed of ˜2420 km s-1 and a derived electron density of at least 5.4 × 1010cm-3, the observed short-period oscillation is most likely the global fast sausage mode of a hot flare loop. We find a phase shift of ˜π/2 (1/4 period) between the Doppler shift oscillation and the intensity/GOES oscillations, which is consistent with a recent forward modeling study of the sausage mode. The observed oscillation requires a density contrast between the flare loop and coronal background of a factor ≥42. The estimated phase speed of the global mode provides a lower limit of the Alfvén speed outside the flare loop. We also find an increase of the oscillation period,which might be caused by the separation of the loop footpoints with time.
2016-05-20T00:00:00ZTian, HuiYoung, Peter R.Reeves, Katharine K.Wang, TongjiangAntolin, PatrickChen, BinHe, JiansenAn observation from the Interface Region Imaging Spectrograph reveals coherent oscillations in the loops of an M1.6 flare on 2015 March 12. Both the intensity and Doppler shift of Fe xxi 1354.08 Å show clear oscillations with a period of ˜25 s. Remarkably similar oscillations were also detected in the soft X-ray flux recorded by the Geostationary Operational Environmental Satellites (GOES). With an estimated phase speed of ˜2420 km s-1 and a derived electron density of at least 5.4 × 1010cm-3, the observed short-period oscillation is most likely the global fast sausage mode of a hot flare loop. We find a phase shift of ˜π/2 (1/4 period) between the Doppler shift oscillation and the intensity/GOES oscillations, which is consistent with a recent forward modeling study of the sausage mode. The observed oscillation requires a density contrast between the flare loop and coronal background of a factor ≥42. The estimated phase speed of the global mode provides a lower limit of the Alfvén speed outside the flare loop. We also find an increase of the oscillation period,which might be caused by the separation of the loop footpoints with time.Flux-rope twist in eruptive flares and CMEs : due to zipper and main-phase reconnectionPriest, Eric RonaldLongcope, D.W.http://hdl.handle.net/10023/101142018-01-07T03:54:52Z2017-01-01T00:00:00ZThe nature of three-dimensional reconnection when a twisted flux tube erupts during an eruptive flare or coronal mass ejection is considered. The reconnection has two phases: first of all, 3D “zipper reconnection” propagates along the initial coronal arcade, parallel to the polarity inversion line (PIL); then subsequent quasi-2D “main phase reconnection” in the low corona around a flux rope during its eruption produces coronal loops and chromospheric ribbons that propagate away from the PIL in a direction normal to it. One scenario starts with a sheared arcade: the zipper reconnection creates a twisted flux rope of roughly one turn (2π radians of twist), and then main phase reconnection builds up the bulk of the erupting flux rope with a relatively uniform twist of a few turns. A second scenario starts with a pre-existing flux rope under the arcade. Here the zipper phase can create a core with many turns that depend on the ratio of the magnetic fluxes in the newly formed flare ribbons and the new flux rope. Main phase reconnection then adds a layer of roughly uniform twist to the twisted central core. Both phases and scenarios are modeled in a simple way that assumes the initial magnetic flux is fragmented along the PIL. The model uses conservation of magnetic helicity and flux, together with equipartition of magnetic helicity, to deduce the twist of the erupting flux rope in terms the geometry of the initial configuration. Interplanetary observations show some flux ropes have a fairly uniform twist, which could be produced when the zipper phase and any pre-existing flux rope possess small or moderate twist (up to one or two turns). Other interplanetary flux ropes have highly twisted cores (up to five turns), which could be produced when there is a pre-existing flux rope and an active zipper phase that creates substantial extra twist.
Funding: UK Science and Technology Facilities Council
2017-01-01T00:00:00ZPriest, Eric RonaldLongcope, D.W.The nature of three-dimensional reconnection when a twisted flux tube erupts during an eruptive flare or coronal mass ejection is considered. The reconnection has two phases: first of all, 3D “zipper reconnection” propagates along the initial coronal arcade, parallel to the polarity inversion line (PIL); then subsequent quasi-2D “main phase reconnection” in the low corona around a flux rope during its eruption produces coronal loops and chromospheric ribbons that propagate away from the PIL in a direction normal to it. One scenario starts with a sheared arcade: the zipper reconnection creates a twisted flux rope of roughly one turn (2π radians of twist), and then main phase reconnection builds up the bulk of the erupting flux rope with a relatively uniform twist of a few turns. A second scenario starts with a pre-existing flux rope under the arcade. Here the zipper phase can create a core with many turns that depend on the ratio of the magnetic fluxes in the newly formed flare ribbons and the new flux rope. Main phase reconnection then adds a layer of roughly uniform twist to the twisted central core. Both phases and scenarios are modeled in a simple way that assumes the initial magnetic flux is fragmented along the PIL. The model uses conservation of magnetic helicity and flux, together with equipartition of magnetic helicity, to deduce the twist of the erupting flux rope in terms the geometry of the initial configuration. Interplanetary observations show some flux ropes have a fairly uniform twist, which could be produced when the zipper phase and any pre-existing flux rope possess small or moderate twist (up to one or two turns). Other interplanetary flux ropes have highly twisted cores (up to five turns), which could be produced when there is a pre-existing flux rope and an active zipper phase that creates substantial extra twist.On the stability of homogeneous steady states of a chemotaxis system with logistic growth termChaplain, Mark Andrew JosephTello, J. I.http://hdl.handle.net/10023/100872018-03-18T01:36:40Z2016-07-01T00:00:00ZWe consider a nonlinear PDEs system of Parabolic-Elliptic type with chemotactic terms. The system models the movement of a population “n” towards a higher concentration of a chemical “c” in a bounded domain Ω. We consider constant chemotactic sensitivity χ and an elliptic equation to describe the distribution of the chemicalnt − dnΔn = −χdiv(n∇c) + μn(1−n), −dcΔc + c = h(n) for a monotone increasing and lipschitz function h. We study the asymptotic behavior of solutions under the assumption of 2χ∣h′∣ < μ. As a result of the asymptotic stability we obtain the uniqueness of the strictly positive steady states.
2016-07-01T00:00:00ZChaplain, Mark Andrew JosephTello, J. I.We consider a nonlinear PDEs system of Parabolic-Elliptic type with chemotactic terms. The system models the movement of a population “n” towards a higher concentration of a chemical “c” in a bounded domain Ω. We consider constant chemotactic sensitivity χ and an elliptic equation to describe the distribution of the chemicalnt − dnΔn = −χdiv(n∇c) + μn(1−n), −dcΔc + c = h(n) for a monotone increasing and lipschitz function h. We study the asymptotic behavior of solutions under the assumption of 2χ∣h′∣ < μ. As a result of the asymptotic stability we obtain the uniqueness of the strictly positive steady states.Magneto-static modeling from SUNRISE/IMaX : application to an active region observed with SUNRISE IIWiegelmann, T.Neukirch, ThomasNickeler, D. H.Solanki, S. K.Barthol, P.Gandorfer, A.Gizon, L.Hirzberger, J.Riethmüller, T. L.Noort, M. vanRodríguez, J. BlancoDel Toro Iniesta, J. C.Suárez, D. OrozcoSchmidt, W.Pillet, V. MartínezKnölker, M.http://hdl.handle.net/10023/100832018-01-07T03:55:20Z2017-03-22T00:00:00ZMagneto-static models may overcome some of the issues facing force-free magnetic field extrapolations. So far they have seen limited use and have faced problems when applied to quiet-Sun data. Here we present a first application to an active region. We use solar vector magnetic field measurements gathered by the IMaX polarimeter during the flight of the \sunrise{} balloon-borne solar observatory in June 2013 as boundary condition for a magneto-static model of the higher solar atmosphere above an active region. The IMaX data are embedded in active region vector magnetograms observed with SDO/HMI. This work continues our magneto-static extrapolation approach, which has been applied earlier ({\it Paper I}) to a quiet Sun region observed with \sunrise{} I. In an active region the signal-to-noise-ratio in the measured Stokes parameters is considerably higher than in the quiet Sun and consequently the IMaX measurements of the horizontal photospheric magnetic field allow us to specify the free parameters of the model in a special class of linear magneto-static equilibria. The high spatial resolution of IMaX (110-130 km, pixel size 40 km) enables us to model the non-force-free layer between the photosphere and the mid chromosphere vertically by about 50 grid points. In our approach we can incorporate some aspects of the mixed beta layer of photosphere and chromosphere, e.g., taking a finite Lorentz force into account, which was not possible with lower resolution photospheric measurements in the past. The linear model does not, however, permit to model intrinsic nonlinear structures like strongly localized electric currents.
2017-03-22T00:00:00ZWiegelmann, T.Neukirch, ThomasNickeler, D. H.Solanki, S. K.Barthol, P.Gandorfer, A.Gizon, L.Hirzberger, J.Riethmüller, T. L.Noort, M. vanRodríguez, J. BlancoDel Toro Iniesta, J. C.Suárez, D. OrozcoSchmidt, W.Pillet, V. MartínezKnölker, M.Magneto-static models may overcome some of the issues facing force-free magnetic field extrapolations. So far they have seen limited use and have faced problems when applied to quiet-Sun data. Here we present a first application to an active region. We use solar vector magnetic field measurements gathered by the IMaX polarimeter during the flight of the \sunrise{} balloon-borne solar observatory in June 2013 as boundary condition for a magneto-static model of the higher solar atmosphere above an active region. The IMaX data are embedded in active region vector magnetograms observed with SDO/HMI. This work continues our magneto-static extrapolation approach, which has been applied earlier ({\it Paper I}) to a quiet Sun region observed with \sunrise{} I. In an active region the signal-to-noise-ratio in the measured Stokes parameters is considerably higher than in the quiet Sun and consequently the IMaX measurements of the horizontal photospheric magnetic field allow us to specify the free parameters of the model in a special class of linear magneto-static equilibria. The high spatial resolution of IMaX (110-130 km, pixel size 40 km) enables us to model the non-force-free layer between the photosphere and the mid chromosphere vertically by about 50 grid points. In our approach we can incorporate some aspects of the mixed beta layer of photosphere and chromosphere, e.g., taking a finite Lorentz force into account, which was not possible with lower resolution photospheric measurements in the past. The linear model does not, however, permit to model intrinsic nonlinear structures like strongly localized electric currents.A relaxation model of coronal heating in multiple interacting flux ropesHussain, A. S.Browning, P. K.Hood, A. W.http://hdl.handle.net/10023/100702018-01-07T03:54:57Z2017-04-01T00:00:00ZContext: Heating the solar corona requires dissipation of stored magnetic energy, which may occur in twisted magnetic fields. Recently published numerical simulations show that the ideal kink instability in a twisted magnetic thread may trigger energy release in stable twisted neighbours, and demonstrate an avalanche of heating events. Aims: We aim to construct a Taylor relaxation model for the energy release from two flux ropes and compare this with the outcomes of the simulations. We then aim to extend the model to large numbers of flux ropes, allowing the possibility of modelling a heating avalanche, and calculation of the energy release for ensembles of twisted threads with varying twist profiles. Methods: The final state is calculated by assuming a helicity-conserving relaxation to a minimum energy state. Multiple scenarios are examined, which include kink-unstable flux ropes relaxing on their own, as well as stable and unstable flux ropes merging into a single rope as a result of magnetic reconnection. We consider alternative constraints that determine the spatial extent of the final relaxed state. Results: Good agreement is found between the relaxation model and the magnetohydrodynamic simulations, both for interactions of two twisted threads and for a multi-thread avalanche. The model can predict the energy release for flux ropes of varying degrees of twist, which relax individually or which merge through reconnection into a single flux rope. It is found that the energy output of merging flux ropes is dominated by the energy of the most strongly twisted rope. Conclusions: The relaxation approach provides a very good estimate of the energy release in an ensemble of twisted threads of which one is kink-unstable.
The authors wish to recognise funding from EPSRC through the Fusion Centre for Doctoral Training (Fusion-CDT - grant code: EP/K504178/1) through which this project is possible. Support from STFC for PKB and AWH is also acknowledged (grant numbers ST/L000768/1 and ST/N000609/1).
2017-04-01T00:00:00ZHussain, A. S.Browning, P. K.Hood, A. W.Context: Heating the solar corona requires dissipation of stored magnetic energy, which may occur in twisted magnetic fields. Recently published numerical simulations show that the ideal kink instability in a twisted magnetic thread may trigger energy release in stable twisted neighbours, and demonstrate an avalanche of heating events. Aims: We aim to construct a Taylor relaxation model for the energy release from two flux ropes and compare this with the outcomes of the simulations. We then aim to extend the model to large numbers of flux ropes, allowing the possibility of modelling a heating avalanche, and calculation of the energy release for ensembles of twisted threads with varying twist profiles. Methods: The final state is calculated by assuming a helicity-conserving relaxation to a minimum energy state. Multiple scenarios are examined, which include kink-unstable flux ropes relaxing on their own, as well as stable and unstable flux ropes merging into a single rope as a result of magnetic reconnection. We consider alternative constraints that determine the spatial extent of the final relaxed state. Results: Good agreement is found between the relaxation model and the magnetohydrodynamic simulations, both for interactions of two twisted threads and for a multi-thread avalanche. The model can predict the energy release for flux ropes of varying degrees of twist, which relax individually or which merge through reconnection into a single flux rope. It is found that the energy output of merging flux ropes is dominated by the energy of the most strongly twisted rope. Conclusions: The relaxation approach provides a very good estimate of the energy release in an ensemble of twisted threads of which one is kink-unstable.A new approach for modelling chromospheric evaporation in response to enhanced coronal heating. I. The methodJohnston, Craig DavidHood, Alan WilliamCargill, PeterDe Moortel, Inekehttp://hdl.handle.net/10023/100632018-02-25T01:32:57Z2017-01-01T00:00:00ZWe present a new computational approach that addresses the difficulty of obtaining the correct interaction between the solar corona and the transition region in response to rapid heating events. In the coupled corona, transition region and chromosphere system, an enhanced downward conductive flux results in an upflow (chromospheric evaporation).However, obtaining the correct upflow generally requires high spatial resolution in order to resolve the transition region. With an unresolved transition region, artificially low coronal densities are obtained because the downward heat flux ‘jumps’ across the unresolved region to the chromosphere, underestimating the upflows. Here, we treat the lower transition region as a discontinuity that responds to changing coronal conditions through the imposition of a jump condition that is derived from an integrated form of energy conservation. To illustrate and benchmark this approach against a fully resolved one-dimensional model, we present field-aligned simulations of coronal loops in response to a range of impulsive (spatially uniform) heating events. We show that our approach leads to a significant improvement in the coronal density evolution than just when using coarse spatial resolutions insufficient to resolve the lower transition region. Our approach compensates for the jumping of the heat flux by imposing a velocity correction that ensures that the energy from the heat flux goes into driving the transition region dynamics, rather than being lost through radiation. Hence, it is possible to obtain improved coronal densities. The advantages of using this approach in both one-dimensional hydrodynamic and three-dimensional magnetohydrodynamic simulations are discussed.
C.D.J. acknowledges the financial support of the Carnegie Trust for the Universities of Scotland. This project has received funding from the Science and Technology Facilities Council (UK) through the consolidated grant ST/N000609/1 and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 647214).
2017-01-01T00:00:00ZJohnston, Craig DavidHood, Alan WilliamCargill, PeterDe Moortel, InekeWe present a new computational approach that addresses the difficulty of obtaining the correct interaction between the solar corona and the transition region in response to rapid heating events. In the coupled corona, transition region and chromosphere system, an enhanced downward conductive flux results in an upflow (chromospheric evaporation).However, obtaining the correct upflow generally requires high spatial resolution in order to resolve the transition region. With an unresolved transition region, artificially low coronal densities are obtained because the downward heat flux ‘jumps’ across the unresolved region to the chromosphere, underestimating the upflows. Here, we treat the lower transition region as a discontinuity that responds to changing coronal conditions through the imposition of a jump condition that is derived from an integrated form of energy conservation. To illustrate and benchmark this approach against a fully resolved one-dimensional model, we present field-aligned simulations of coronal loops in response to a range of impulsive (spatially uniform) heating events. We show that our approach leads to a significant improvement in the coronal density evolution than just when using coarse spatial resolutions insufficient to resolve the lower transition region. Our approach compensates for the jumping of the heat flux by imposing a velocity correction that ensures that the energy from the heat flux goes into driving the transition region dynamics, rather than being lost through radiation. Hence, it is possible to obtain improved coronal densities. The advantages of using this approach in both one-dimensional hydrodynamic and three-dimensional magnetohydrodynamic simulations are discussed.Spectral non-locality, absolute equilibria and Kraichnan-Leith-Batchelor phenomenology in two-dimensional turbulent energy cascadesBurgess, B. H.Shepherd, T. G.http://hdl.handle.net/10023/100622018-01-07T03:55:17Z2013-06-01T00:00:00ZWe study the degree to which Kraichnan-Leith-Batchelor (KLB) phenomenology describes two-dimensional energy cascades in alpha turbulence, governed by δθ/δt + J(ψ, θ) = ν ∇2θ + f, where θ = (-Δ)α/2ψ is generalized vorticity, and ψ over bar (k)= k-α θ over bar (k) in Fourier space. These models differ in spectral non-locality, and include surface quasigeostrophic flow (alpha = 1), regular two-dimensional flow (α = 2) and rotating shallow flow (α = 3), which is the isotropic limit of a mantle convection model. We re-examine arguments for dual inverse energy and direct enstrophy cascades, including Fjørtoft analysis, which we extend to general α, and point out their limitations. Using an α-dependent eddy-damped quasinormal Markovian (EDQNM) closure, we seek self-similar inertial range solutions and study their characteristics. Our present focus is not on coherent structures, which the EDQNM filters out, but on any self-similar and approximately Gaussian turbulent component that may exist in the flow and be described by KLB phenomenology. For this, the EDQNM is an appropriate tool. Non-local triads contribute increasingly to the energy flux as α increases. More importantly, the energy cascade is downscale in the self-similar inertial range for 2.5 <α <10. At α = 2.5 and α = 10, the KLB spectra correspond, respectively, to enstrophy and energy equipartition, and the triad energy transfers and flux vanish identically. Eddy turnover time and strain rate arguments suggest the inverse energy cascade should obey KLB phenomenology and be self-similar for α <4. However, downscale energy flux in the EDQNM self-similar inertial range for α > 2.5 leads us to predict that any inverse cascade for α ≥ 2.5 will not exhibit KLB phenomenology, and specifically the KLB energy spectrum. Numerical simulations confirm this: the inverse cascade energy spectrum for α ≥ 2.5 is significantly steeper than the KLB prediction, while for α <2.5 we obtain the KLB spectrum.
2013-06-01T00:00:00ZBurgess, B. H.Shepherd, T. G.We study the degree to which Kraichnan-Leith-Batchelor (KLB) phenomenology describes two-dimensional energy cascades in alpha turbulence, governed by δθ/δt + J(ψ, θ) = ν ∇2θ + f, where θ = (-Δ)α/2ψ is generalized vorticity, and ψ over bar (k)= k-α θ over bar (k) in Fourier space. These models differ in spectral non-locality, and include surface quasigeostrophic flow (alpha = 1), regular two-dimensional flow (α = 2) and rotating shallow flow (α = 3), which is the isotropic limit of a mantle convection model. We re-examine arguments for dual inverse energy and direct enstrophy cascades, including Fjørtoft analysis, which we extend to general α, and point out their limitations. Using an α-dependent eddy-damped quasinormal Markovian (EDQNM) closure, we seek self-similar inertial range solutions and study their characteristics. Our present focus is not on coherent structures, which the EDQNM filters out, but on any self-similar and approximately Gaussian turbulent component that may exist in the flow and be described by KLB phenomenology. For this, the EDQNM is an appropriate tool. Non-local triads contribute increasingly to the energy flux as α increases. More importantly, the energy cascade is downscale in the self-similar inertial range for 2.5 <α <10. At α = 2.5 and α = 10, the KLB spectra correspond, respectively, to enstrophy and energy equipartition, and the triad energy transfers and flux vanish identically. Eddy turnover time and strain rate arguments suggest the inverse energy cascade should obey KLB phenomenology and be self-similar for α <4. However, downscale energy flux in the EDQNM self-similar inertial range for α > 2.5 leads us to predict that any inverse cascade for α ≥ 2.5 will not exhibit KLB phenomenology, and specifically the KLB energy spectrum. Numerical simulations confirm this: the inverse cascade energy spectrum for α ≥ 2.5 is significantly steeper than the KLB prediction, while for α <2.5 we obtain the KLB spectrum.Note on Prodi-Serrin-Ladyzhenskaya type regularity criteria for the Navier-Stokes equationsTran, Chuong VanYu, Xinweihttp://hdl.handle.net/10023/100482018-01-07T03:54:41Z2017-01-18T00:00:00ZIn this article we prove new regularity criteria of the Prodi-Serrin-Ladyzhenskaya type for the Cauchy problem of the three-dimensional Navier-Stokes equations. Our results improve the classical Lr(0,T;Ls) regularity criteria for both velocity and pressure by factors of certain nagative powers of the scaling invariant norm ||u||L3 and ||u||H1/2.
X.Y. is partially supported by the Discovery Grant No. RES0020476 from NSERC.
2017-01-18T00:00:00ZTran, Chuong VanYu, XinweiIn this article we prove new regularity criteria of the Prodi-Serrin-Ladyzhenskaya type for the Cauchy problem of the three-dimensional Navier-Stokes equations. Our results improve the classical Lr(0,T;Ls) regularity criteria for both velocity and pressure by factors of certain nagative powers of the scaling invariant norm ||u||L3 and ||u||H1/2.Vortex merger in surface quasi-geostrophyCarton, XavierCiani, DanieleVerron, JacquesReinaud, Jean NoelSokolovskiy, Mikhailhttp://hdl.handle.net/10023/100162018-01-07T03:08:37Z2016-01-01T00:00:00ZThe merger of two identical surface temperature vortices is studied in the surface quasi- geostrophic model. The motivation for this study is the observation of the merger of sub- mesoscale vortices in the ocean. Firstly, the interaction between two point vortices, in the absence or in the presence of an external deformation field, is investigated. The rotation rate of the vortices, their stationary positions and the stability of these positions are determined. Then, a numerical model provides the steady states of two finite-area, constant-temperature, vortices. Such states are less deformed than their counterparts in two-dimensional incom- pressible flows. Finally, numerical simulations of the nonlinear surface quasi-geostrophic equations are used to investigate the finite-time evolution of initially identical and sym- metric, constant temperature vortices. The critical merger distance is obtained and the deformation of the vortices before or after merger is determined. The addition of external deformation is shown to favor or to oppose merger depending on the orientation of the vor- tex pair with respect to the strain axes. An explanation for this observation is proposed. Conclusions are drawn towards an application of this study to oceanic vortices.
2016-01-01T00:00:00ZCarton, XavierCiani, DanieleVerron, JacquesReinaud, Jean NoelSokolovskiy, MikhailThe merger of two identical surface temperature vortices is studied in the surface quasi- geostrophic model. The motivation for this study is the observation of the merger of sub- mesoscale vortices in the ocean. Firstly, the interaction between two point vortices, in the absence or in the presence of an external deformation field, is investigated. The rotation rate of the vortices, their stationary positions and the stability of these positions are determined. Then, a numerical model provides the steady states of two finite-area, constant-temperature, vortices. Such states are less deformed than their counterparts in two-dimensional incom- pressible flows. Finally, numerical simulations of the nonlinear surface quasi-geostrophic equations are used to investigate the finite-time evolution of initially identical and sym- metric, constant temperature vortices. The critical merger distance is obtained and the deformation of the vortices before or after merger is determined. The addition of external deformation is shown to favor or to oppose merger depending on the orientation of the vor- tex pair with respect to the strain axes. An explanation for this observation is proposed. Conclusions are drawn towards an application of this study to oceanic vortices.Observing the formation of flare-driven coronal rainScullion, E.Rouppe Van Der Voort, L.Antolin, P.Wedemeyer, S.Vissers, G.Kontar, E. P.Gallagher, P.http://hdl.handle.net/10023/100012018-02-25T01:33:06Z2016-12-20T00:00:00ZFlare-driven coronal rain can manifest from rapidly cooled plasma condensations near coronal loop-tops in thermally unstable post-flare arcades. We detect 5 phases that characterise the post-flare decay:heating, evaporation, conductive cooling dominance for ~120 s, radiative/ enthalpy cooling dominance for ~4700 s and finally catastrophic cooling occurring within 35-124 s leading to rain strands with s periodicity of 55-70 s. We find an excellent agreement between the observations and model predictions of the dominant cooling timescales and the onset of catastrophic cooling. At the rain formation site we detect co-moving, multi-thermal rain clumps that undergo catastrophic cooling from ~1 MK to ~22000 K. During catastrophic cooling the plasma cools at a maximum rate of 22700 K s-1 in multiple loop-top sources. We calculated the density of the EUV plasma from the DEM of the multi-thermal source employing regularised inversion. Assuming a pressure balance, we estimate the density of the chromospheric component of rain to be 9.21x1011 ±1.76x1011 cm-3 which is comparable with quiescent coronal rain densities. With up to 8 parallel strands in the EUV loop cross section, we calculate the mass loss rate from the post-flare arcade to be as much as 1.98x1012 ± 4.95x1011 g s-1. Finally, we reveal a close proximity between the model predictions of 105.8 K and the observed properties between 105.9 K and 106.2 K, that defines the temperature onset of catastrophic cooling. The close correspondence between the observations and numerical models suggests that indeed acoustic waves (with a sound travel time of 68 s) could play an important role in redistributing energy and sustaining the enthalpy-based radiative cooling.
PA. GV are funded by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement nr. 291058
2016-12-20T00:00:00ZScullion, E.Rouppe Van Der Voort, L.Antolin, P.Wedemeyer, S.Vissers, G.Kontar, E. P.Gallagher, P.Flare-driven coronal rain can manifest from rapidly cooled plasma condensations near coronal loop-tops in thermally unstable post-flare arcades. We detect 5 phases that characterise the post-flare decay:heating, evaporation, conductive cooling dominance for ~120 s, radiative/ enthalpy cooling dominance for ~4700 s and finally catastrophic cooling occurring within 35-124 s leading to rain strands with s periodicity of 55-70 s. We find an excellent agreement between the observations and model predictions of the dominant cooling timescales and the onset of catastrophic cooling. At the rain formation site we detect co-moving, multi-thermal rain clumps that undergo catastrophic cooling from ~1 MK to ~22000 K. During catastrophic cooling the plasma cools at a maximum rate of 22700 K s-1 in multiple loop-top sources. We calculated the density of the EUV plasma from the DEM of the multi-thermal source employing regularised inversion. Assuming a pressure balance, we estimate the density of the chromospheric component of rain to be 9.21x1011 ±1.76x1011 cm-3 which is comparable with quiescent coronal rain densities. With up to 8 parallel strands in the EUV loop cross section, we calculate the mass loss rate from the post-flare arcade to be as much as 1.98x1012 ± 4.95x1011 g s-1. Finally, we reveal a close proximity between the model predictions of 105.8 K and the observed properties between 105.9 K and 106.2 K, that defines the temperature onset of catastrophic cooling. The close correspondence between the observations and numerical models suggests that indeed acoustic waves (with a sound travel time of 68 s) could play an important role in redistributing energy and sustaining the enthalpy-based radiative cooling.Toward a PV-based algorithm for the dynamical core of hydrostatic global modelsMohebalhojeh, Ali R.Joghataei, MohammadDritschel, David G.http://hdl.handle.net/10023/99572018-01-07T03:47:09Z2016-06-01T00:00:00ZThe diabatic contour-advective semi-Lagrangian (DCASL) algorithms previously constructed for the shallow-water and multilayer Boussinesq primitive equations are extended to multilayer non-Boussinesq equations on the sphere using a hybrid terrain-following-isentropic (sigma-) vertical coordinate. It is shown that the DCASL algorithms face challenges beyond more conventional algorithms in that various types of damping, filtering, and regularization are required for computational stability, and the nonlinearity of the hydrostatic equation in the sigma- coordinate causes convergence problems with setting up a semi-implicit time-stepping scheme to reduce computational cost. The prognostic variables are an approximation to the Rossby-Ertel potential vorticity Q, a scaled pressure thickness, the horizontal divergence, and the surface potential temperature. Results from the DCASL algorithm in two formulations of the sigma- coordinate, differing only in the rate at which the vertical coordinate tends to with increasing height, are assessed using the baroclinic instability test case introduced by Jablonowski and Williamson in 2006. The assessment is based on comparisons with available reference solutions as well as results from two other algorithms derived from the DCASL algorithm: one with a semi-Lagrangian solution for Q and another with an Eulerian grid-based solution procedure with relative vorticity replacing Q as the prognostic variable. It is shown that at intermediate resolutions, results comparable to the reference solutions can be obtained.
2016-06-01T00:00:00ZMohebalhojeh, Ali R.Joghataei, MohammadDritschel, David G.The diabatic contour-advective semi-Lagrangian (DCASL) algorithms previously constructed for the shallow-water and multilayer Boussinesq primitive equations are extended to multilayer non-Boussinesq equations on the sphere using a hybrid terrain-following-isentropic (sigma-) vertical coordinate. It is shown that the DCASL algorithms face challenges beyond more conventional algorithms in that various types of damping, filtering, and regularization are required for computational stability, and the nonlinearity of the hydrostatic equation in the sigma- coordinate causes convergence problems with setting up a semi-implicit time-stepping scheme to reduce computational cost. The prognostic variables are an approximation to the Rossby-Ertel potential vorticity Q, a scaled pressure thickness, the horizontal divergence, and the surface potential temperature. Results from the DCASL algorithm in two formulations of the sigma- coordinate, differing only in the rate at which the vertical coordinate tends to with increasing height, are assessed using the baroclinic instability test case introduced by Jablonowski and Williamson in 2006. The assessment is based on comparisons with available reference solutions as well as results from two other algorithms derived from the DCASL algorithm: one with a semi-Lagrangian solution for Q and another with an Eulerian grid-based solution procedure with relative vorticity replacing Q as the prognostic variable. It is shown that at intermediate resolutions, results comparable to the reference solutions can be obtained.A comparison of global magnetic field skeletons and active-region upflowsEdwards, S. J.Parnell, C. E.Harra, L. K.Culhane, J. L.Brooks, D. H.http://hdl.handle.net/10023/98752018-01-07T03:43:56Z2016-01-01T00:00:00ZPlasma upflows have been detected in active regions using Doppler velocity maps. The origin and nature of these upflows is not well known with many of their characteristics determined from the examination of single events. In particular, some studies suggest these upflows occur along open field lines and, hence, are linked to sources of the solar wind. To investigate the relationship these upflows may have with the solar wind, and to probe what may be driving them, this paper considers seven active regions observed on the solar disc using the Extreme ultraviolet Imaging Spectrometer aboard Hinode between August 2011 and September 2012. Plasma upflows are observed in all these active regions. The locations of these upflows are compared to the global potential magnetic field extrapolated from the Solar Dynamics Observatory, Helioseismic and Magnetic Imager daily synoptic magnetogram taken on the day the upflows were observed. The structure of the magnetic field is determined by constructing its magnetic skeleton in order to help identify open-field regions and also sites where magnetic reconnection at global features is likely to occur. As a further comparison, measurements of the temperature, density and composition of the plasma are taken from regions with active-region upflows. In most cases the locations of the upflows in the active regions do not correspond to areas of open field, as predicted by a global coronal potential-field model, and therefore these upflows are not always sources of the slow solar wind. The locations of the upflows are, in general, intersected by separatrix surfaces associated with null points located high in the corona; these could be important sites of reconnection with global consequences.
2016-01-01T00:00:00ZEdwards, S. J.Parnell, C. E.Harra, L. K.Culhane, J. L.Brooks, D. H.Plasma upflows have been detected in active regions using Doppler velocity maps. The origin and nature of these upflows is not well known with many of their characteristics determined from the examination of single events. In particular, some studies suggest these upflows occur along open field lines and, hence, are linked to sources of the solar wind. To investigate the relationship these upflows may have with the solar wind, and to probe what may be driving them, this paper considers seven active regions observed on the solar disc using the Extreme ultraviolet Imaging Spectrometer aboard Hinode between August 2011 and September 2012. Plasma upflows are observed in all these active regions. The locations of these upflows are compared to the global potential magnetic field extrapolated from the Solar Dynamics Observatory, Helioseismic and Magnetic Imager daily synoptic magnetogram taken on the day the upflows were observed. The structure of the magnetic field is determined by constructing its magnetic skeleton in order to help identify open-field regions and also sites where magnetic reconnection at global features is likely to occur. As a further comparison, measurements of the temperature, density and composition of the plasma are taken from regions with active-region upflows. In most cases the locations of the upflows in the active regions do not correspond to areas of open field, as predicted by a global coronal potential-field model, and therefore these upflows are not always sources of the slow solar wind. The locations of the upflows are, in general, intersected by separatrix surfaces associated with null points located high in the corona; these could be important sites of reconnection with global consequences.The energy budget of stellar magnetic fields : comparing non-potential simulations and observationsLehmann, L. T.Jardine, M. M.Vidotto, A. A.Mackay, D. H.See, V.Donati, J.-F.Folsom, C. P.Jeffers, S. V.Marsden, S. C.Morin, J.Petit, P.http://hdl.handle.net/10023/98692018-01-08T11:30:18Z2017-03-21T00:00:00ZThe magnetic geometry of the surface magnetic fields of more than 55 cool stars have now been mapped using spectropolarimetry. In order to better understand these observations, we compare the magnetic fieldt opology at different surface scale sizes of observed and simulated cool stars. For ease of comparison between the high-resolution non-potential magnetofrictional simulations and the relatively low-resolution observations, we filter out the small-scale field in the simulations using a spherical harmonics decomposition. We show that the large-scalefield topologies of the solar-based simulations produce values of poloidal/toroidal fields and fractions of energy in axisymmetric modes that are similar to the observations. These global non-potential evolution model simulations capture key magnetic features of the observed solar-like stars through the processes of surface flux transport and magnetic flux emergence. They do not, however, reproduce the magnetic field of M-dwarfs or stars with dominantly toroidal field.Furthermore, we analyse the magnetic field topologies of individual spherical harmonics for the simulations and discover that the dipole is predominately poloidal, while the quadrupole shows the highest fraction of toroidal fields. Magnetic field structures smaller than a quadrupole display a fixed ratio between the poloidal and toroidal magnetic energies.
LTL acknowledges support from the Scottish Universities Physics Alliance (SUPA) prize studentship and the University of St Andrews Higgs studentship. MMJ and VS acknowledge a Science & Technology Facilities Council (STFC) postdoctoral fellowship.
2017-03-21T00:00:00ZLehmann, L. T.Jardine, M. M.Vidotto, A. A.Mackay, D. H.See, V.Donati, J.-F.Folsom, C. P.Jeffers, S. V.Marsden, S. C.Morin, J.Petit, P.The magnetic geometry of the surface magnetic fields of more than 55 cool stars have now been mapped using spectropolarimetry. In order to better understand these observations, we compare the magnetic fieldt opology at different surface scale sizes of observed and simulated cool stars. For ease of comparison between the high-resolution non-potential magnetofrictional simulations and the relatively low-resolution observations, we filter out the small-scale field in the simulations using a spherical harmonics decomposition. We show that the large-scalefield topologies of the solar-based simulations produce values of poloidal/toroidal fields and fractions of energy in axisymmetric modes that are similar to the observations. These global non-potential evolution model simulations capture key magnetic features of the observed solar-like stars through the processes of surface flux transport and magnetic flux emergence. They do not, however, reproduce the magnetic field of M-dwarfs or stars with dominantly toroidal field.Furthermore, we analyse the magnetic field topologies of individual spherical harmonics for the simulations and discover that the dipole is predominately poloidal, while the quadrupole shows the highest fraction of toroidal fields. Magnetic field structures smaller than a quadrupole display a fixed ratio between the poloidal and toroidal magnetic energies.Theoretical foundation of 3D Alfvén resonances : normal modesWright, Andrew NicholasElsden, Thomas Williamhttp://hdl.handle.net/10023/98472018-03-04T01:40:01Z2016-12-20T00:00:00ZWe consider the resonant coupling of fast and Alfvén magnetohydrodynamic (MHD) waves in a 3D equilibrium. Numerical solutions to normal modes (∝ exp(−iωt)) are presented along with a theoretical framework to interpret them. The solutions we find are fundamentally different to those in 1D and 2D. In 3D there exists an infinite number of possible resonant solutions within a “Resonant Zone", and we show how boundary conditions and locally 2D regions can favour particular solutions. A unique feature of the resonance in 3D is switching between different permissible solutions when the boundary of the Resonant Zone is encountered. The theoretical foundation we develop relies upon recognising that in 3D the orientation of the resonant surface will not align in a simple fashion with an equilibrium coordinate. We present a method for generating the Alfvén wave natural frequencies for an arbitrarily oriented Alfvén wave, which requires a careful treatment of scale factors describing the background magnetic field geometry.
2016-12-20T00:00:00ZWright, Andrew NicholasElsden, Thomas WilliamWe consider the resonant coupling of fast and Alfvén magnetohydrodynamic (MHD) waves in a 3D equilibrium. Numerical solutions to normal modes (∝ exp(−iωt)) are presented along with a theoretical framework to interpret them. The solutions we find are fundamentally different to those in 1D and 2D. In 3D there exists an infinite number of possible resonant solutions within a “Resonant Zone", and we show how boundary conditions and locally 2D regions can favour particular solutions. A unique feature of the resonance in 3D is switching between different permissible solutions when the boundary of the Resonant Zone is encountered. The theoretical foundation we develop relies upon recognising that in 3D the orientation of the resonant surface will not align in a simple fashion with an equilibrium coordinate. We present a method for generating the Alfvén wave natural frequencies for an arbitrarily oriented Alfvén wave, which requires a careful treatment of scale factors describing the background magnetic field geometry.Coupled bulk-surface free boundary problems arising from a mathematical model of receptor-ligand dynamicsElliot, Charles M.Ranner, ThomasVenkataraman, Chandrasekharhttp://hdl.handle.net/10023/97792018-01-07T03:51:56Z2017-02-08T00:00:00ZWe consider a coupled bulk-surface system of partial differential equations with nonlinear coupling modelling receptor-ligand dynamics. The model arises as a simplification of a mathematical model for the reaction between cell surface resident receptors and ligands present in the extra-cellular medium. We prove the existence and uniqueness of solutions. We also consider a number of biologically relevant asymptotic limits of the model. We prove convergence to limiting problems which take the form of free boundary problems posed on the cell surface. We also report on numerical simulations illustrating convergence to one of the limiting problems as well as the spatio-temporal distributions of the receptors and ligands in a realistic geometry.
This work was started whilst the authors were participants in the Isaac Newton Institute programme: “Free Boundary Problems and Related Topics” and finalised whilst the authors were participants in the Isaac Newton Institute programme: “Coupling Geometric PDEs with Physics for Cell Morphology, Motility and Pattern Formation” supported by EPSRC Grant Number EP/K032208/1. The work of CV received support from the Leverhulme Trust Research Project Grant (RPG-2014-149).
2017-02-08T00:00:00ZElliot, Charles M.Ranner, ThomasVenkataraman, ChandrasekharWe consider a coupled bulk-surface system of partial differential equations with nonlinear coupling modelling receptor-ligand dynamics. The model arises as a simplification of a mathematical model for the reaction between cell surface resident receptors and ligands present in the extra-cellular medium. We prove the existence and uniqueness of solutions. We also consider a number of biologically relevant asymptotic limits of the model. We prove convergence to limiting problems which take the form of free boundary problems posed on the cell surface. We also report on numerical simulations illustrating convergence to one of the limiting problems as well as the spatio-temporal distributions of the receptors and ligands in a realistic geometry.Kinematics of coronal rain in a transversely oscillating loop : ponderomotive force and rain-excited oscillationsVerwichte, E.Antolin, P.Rowlands, G.Kohutova, P.Neukirch, T.http://hdl.handle.net/10023/97772018-02-25T01:33:05Z2017-02-01T00:00:00ZContext. Coronal rain are cool dense blobs that form in solar coronal loops and are a manifestation of catastrophic cooling linked to thermal instability. Once formed, rain falls towards the solar surface at sub-ballistic speeds, which is not well-understood. Pressure forces seem to be the prime candidate to explain this. In many observations rain is accompanied by transverse oscillations and the interaction between the two needs to be explored. Aims. Therefore, an alternative kinematic model for coronal rain kinematics in transversely oscillating loops is developed to understand the physical nature of the observed sub-ballistic falling motion of rain. It explicitly explores the role of the ponderomotive force arising from the transverse oscillation on the rain motion as well as the capacity of rain to excite wave motion. Methods. An analytical model is presented that describes a rain blob guided by the coronal magnetic field supporting a one dimensional shear Alfvén wave as a point mass on an oscillating string. The model includes gravity and the ponderomotive force from the oscillation acting on the mass, as well as the inertia of the mass acting on the oscillation. Results. The kinematics of rain in the limit of negligible rain mass are explored and falling and trapped regimes are found, depending on wave amplitude. In the trapped regime for the fundamental mode, the rain blob bounces back and forth around the loop top at a long period inversely proportional to the oscillation amplitude. The model is compared with several observational rain studies, including one in-depth comparison with an observation that shows rain with up-and down bobbing motion. The role of rain inertia in exciting transverse oscillations is explored in inclined loops. Conclusions. It is found that the model requires displacement amplitudes of the transverse oscillation that are typically an order of magnitude larger than observed to explain the measured sub-ballistic motion of the rain. Therefore, it is concluded that the ponderomotive force is not the primary reason for understanding sub-ballistic motion, but it plays a role in cases of large loop oscillations.The appearance of rain causes the excitation of small-amplitude transverse oscillations that may explain observed events and provide a seismological tool to measure rain mass.
E.V. acknowledges support from the Warwick STFC Consolidated Grant ST/L000733/I. P.A. acknowledges support from the EU Horizon 2020 Research and Innovation programme (grant agreement No. 647214). P.K. acknowledges support from a UK STFC PhD studentship. T.N. acknowledges support from the St Andrews STFC Consolidated Grant SN/N000609/1.
2017-02-01T00:00:00ZVerwichte, E.Antolin, P.Rowlands, G.Kohutova, P.Neukirch, T.Context. Coronal rain are cool dense blobs that form in solar coronal loops and are a manifestation of catastrophic cooling linked to thermal instability. Once formed, rain falls towards the solar surface at sub-ballistic speeds, which is not well-understood. Pressure forces seem to be the prime candidate to explain this. In many observations rain is accompanied by transverse oscillations and the interaction between the two needs to be explored. Aims. Therefore, an alternative kinematic model for coronal rain kinematics in transversely oscillating loops is developed to understand the physical nature of the observed sub-ballistic falling motion of rain. It explicitly explores the role of the ponderomotive force arising from the transverse oscillation on the rain motion as well as the capacity of rain to excite wave motion. Methods. An analytical model is presented that describes a rain blob guided by the coronal magnetic field supporting a one dimensional shear Alfvén wave as a point mass on an oscillating string. The model includes gravity and the ponderomotive force from the oscillation acting on the mass, as well as the inertia of the mass acting on the oscillation. Results. The kinematics of rain in the limit of negligible rain mass are explored and falling and trapped regimes are found, depending on wave amplitude. In the trapped regime for the fundamental mode, the rain blob bounces back and forth around the loop top at a long period inversely proportional to the oscillation amplitude. The model is compared with several observational rain studies, including one in-depth comparison with an observation that shows rain with up-and down bobbing motion. The role of rain inertia in exciting transverse oscillations is explored in inclined loops. Conclusions. It is found that the model requires displacement amplitudes of the transverse oscillation that are typically an order of magnitude larger than observed to explain the measured sub-ballistic motion of the rain. Therefore, it is concluded that the ponderomotive force is not the primary reason for understanding sub-ballistic motion, but it plays a role in cases of large loop oscillations.The appearance of rain causes the excitation of small-amplitude transverse oscillations that may explain observed events and provide a seismological tool to measure rain mass.A test case for the inviscid shallow-water equations on the sphereScott, R. K.Harris, L. M.Polvani, L. M.http://hdl.handle.net/10023/97612018-01-07T03:36:15Z2016-01-01T00:00:00ZA numerically converged solution to the inviscid global shallow-water equations for a predefined time interval is documented to provide a convenient benchmark for model validation. The solution is based on the same initial conditions as a previously documented solution for the viscous equations. The solution is computed using two independent numerical schemes, one a pseudospectral scheme based on an expansion in spherical harmonics and the other a finite-volume scheme on a cubed-sphere grid. Flow fields and various integral norms are documented to facilitate model comparison and validation. Attention is drawn to the utility of the potential vorticity supremum as a convenient and sensitive test of numerical convergence, in which the exact value is known a priori over the entire time interval.
Partial support for this work was provided through the National Science Foundation award AGS-1333029.
2016-01-01T00:00:00ZScott, R. K.Harris, L. M.Polvani, L. M.A numerically converged solution to the inviscid global shallow-water equations for a predefined time interval is documented to provide a convenient benchmark for model validation. The solution is based on the same initial conditions as a previously documented solution for the viscous equations. The solution is computed using two independent numerical schemes, one a pseudospectral scheme based on an expansion in spherical harmonics and the other a finite-volume scheme on a cubed-sphere grid. Flow fields and various integral norms are documented to facilitate model comparison and validation. Attention is drawn to the utility of the potential vorticity supremum as a convenient and sensitive test of numerical convergence, in which the exact value is known a priori over the entire time interval.Models of interacting pairs of thin, quasi-geostrophic vortices: steady-state solutions and nonlinear stabilityBersanelli, MatteoDritschel, David G.Lancellotti, CarloPoje, Andrew C.http://hdl.handle.net/10023/97442018-01-07T03:51:05Z2016-01-01T00:00:00ZWe study pairwise interactions of elliptical quasi-geostrophic vortices as the limiting case of vanishingly thin uniform potential vorticity ellipsoids. In this limit, the product of the vertical extent of the ellipsoid and the potential vorticity within it is held fixed to a finite non-zero constant. Such elliptical 'lenses' inherit the property that, in isolation, they steadily rotate without changing shape. Here, we use this property to extend both standard moment models and Hamiltonian ellipsoidal models to approximate the dynamical interaction of such elliptical lenses. By neglecting non-elliptical deformations, the simplified models reduce the dynamics to just four degrees of freedom per vortex. For simplicity, we focus on pairwise interactions between identical elliptical vortices initially separated in both the horizontal and vertical directions. The dynamics of the simplified models are compared with the full quasi-geostrophic (QG) dynamics of the system, and show good agreement as expected for sufficiently distant lenses. The results reveal the existence of families of steadily rotating equilibria in the initial horizontal and vertical separation parameter space. For sufficiently large vertical separations, equilibria with varying shape exist for all horizontal separations. Below a critical vertical separation (stretched by the constant ratio of buoyancy to Coriolis frequencies N/f), comparable to the mean radius of either vortex, a gap opens in horizontal separation where no equilibria are possible. Solutions near the edge of this gap are unstable. In the full QG system, equilibria at the edge of the gap exhibit corners (infinite curvature) along their boundaries. Comparisons of the model results with the full nonlinear QG evolution show that the early stages of the instability are captured by the Hamiltonian elliptical model but not by the moment model that inaccurately estimates shorter-range interactions.
This work was supported by the Office of Naval Research under Grant N00014-11- 1-0087; the National Science Foundation under Grant 1107307; and the UK Engineering and Physical Sciences Research Council under grant EP/H001794/1.
2016-01-01T00:00:00ZBersanelli, MatteoDritschel, David G.Lancellotti, CarloPoje, Andrew C.We study pairwise interactions of elliptical quasi-geostrophic vortices as the limiting case of vanishingly thin uniform potential vorticity ellipsoids. In this limit, the product of the vertical extent of the ellipsoid and the potential vorticity within it is held fixed to a finite non-zero constant. Such elliptical 'lenses' inherit the property that, in isolation, they steadily rotate without changing shape. Here, we use this property to extend both standard moment models and Hamiltonian ellipsoidal models to approximate the dynamical interaction of such elliptical lenses. By neglecting non-elliptical deformations, the simplified models reduce the dynamics to just four degrees of freedom per vortex. For simplicity, we focus on pairwise interactions between identical elliptical vortices initially separated in both the horizontal and vertical directions. The dynamics of the simplified models are compared with the full quasi-geostrophic (QG) dynamics of the system, and show good agreement as expected for sufficiently distant lenses. The results reveal the existence of families of steadily rotating equilibria in the initial horizontal and vertical separation parameter space. For sufficiently large vertical separations, equilibria with varying shape exist for all horizontal separations. Below a critical vertical separation (stretched by the constant ratio of buoyancy to Coriolis frequencies N/f), comparable to the mean radius of either vortex, a gap opens in horizontal separation where no equilibria are possible. Solutions near the edge of this gap are unstable. In the full QG system, equilibria at the edge of the gap exhibit corners (infinite curvature) along their boundaries. Comparisons of the model results with the full nonlinear QG evolution show that the early stages of the instability are captured by the Hamiltonian elliptical model but not by the moment model that inaccurately estimates shorter-range interactions.The energy budget of stellar magnetic fields : comparing non-potential simulations and observationsLehmann, L. T.Jardine, M. M.Vidotto, A. A.Mackay, D. H.See, Wyke Chun VictorDonati, J. -F.Folsom, C. P.Jeffers, S. V.Marsden, SteveMorin, J.Petit, P.http://hdl.handle.net/10023/97422018-02-10T02:30:08Z2017-03-21T00:00:00ZThe magnetic geometry of the surface magnetic fields of more than 55 cool stars have now been mapped using spectropolarimetry. In order to better understand these observations, we compare the magnetic field topology at different surface scale sizes of observed and simulated cool stars. For ease of comparison between the high-resolution non-potential magnetofrictional simulations and the relatively low-resolution observations, we filter out the small-scale field in the simulations using a spherical harmonics decomposition. We show that the large-scale field topologies of the solar-based simulations produce values of poloidal/toroidal fields and fractions of energy in axisymmetric modes that are similar to the observations. These global non-potential evolution model simulations capture key magnetic features of the observed solar-like stars through the processes of surface flux transport and magnetic flux emergence. They do not, however, reproduce the magnetic field of M-dwarfs or stars with dominantly toroidal field. Furthermore, we analyse the magnetic field topologies of individual spherical harmonics for the simulations and discover that the dipole is predominately poloidal, while the quadrupole shows the highest fraction of toroidal fields. Magnetic field structures smaller than a quadrupole display a fixed ratio between the poloidal and toroidal magnetic energies.
LTL acknowledges support from the Scottish Universities Physics Alliance (SUPA) prize studentship and the University of St Andrews Higgs studentship. MMJ and VS acknowledge a Science & Technology Facilities Council (STFC) postdoctoral fellowship.
2017-03-21T00:00:00ZLehmann, L. T.Jardine, M. M.Vidotto, A. A.Mackay, D. H.See, Wyke Chun VictorDonati, J. -F.Folsom, C. P.Jeffers, S. V.Marsden, SteveMorin, J.Petit, P.The magnetic geometry of the surface magnetic fields of more than 55 cool stars have now been mapped using spectropolarimetry. In order to better understand these observations, we compare the magnetic field topology at different surface scale sizes of observed and simulated cool stars. For ease of comparison between the high-resolution non-potential magnetofrictional simulations and the relatively low-resolution observations, we filter out the small-scale field in the simulations using a spherical harmonics decomposition. We show that the large-scale field topologies of the solar-based simulations produce values of poloidal/toroidal fields and fractions of energy in axisymmetric modes that are similar to the observations. These global non-potential evolution model simulations capture key magnetic features of the observed solar-like stars through the processes of surface flux transport and magnetic flux emergence. They do not, however, reproduce the magnetic field of M-dwarfs or stars with dominantly toroidal field. Furthermore, we analyse the magnetic field topologies of individual spherical harmonics for the simulations and discover that the dipole is predominately poloidal, while the quadrupole shows the highest fraction of toroidal fields. Magnetic field structures smaller than a quadrupole display a fixed ratio between the poloidal and toroidal magnetic energies.Influence of non-potential coronal magnetic topology on solar wind modelsEdwards, Sarah JaneYeates, Anthony RobinsonBocquet, FrancoisMackay, Duncan Hendryhttp://hdl.handle.net/10023/97292018-01-07T03:09:33Z2015-10-01T00:00:00ZBy comparing a magneto-frictional model of the low coronal magnetic field to a potential field source surface model, we investigate the possible impact of non-potential magnetic structure on empirical solar wind models. These empirical models (such as Wang-Sheeley-Arge) estimate the distribution of solar wind speed solely from the magnetic field structure in the low corona. Our models are computed in a domain between the solar surface and 2.5 solar radii, and are extended to 0.1 AU using a Schatten current sheet model. The non-potential field has a more complex magnetic skeleton and quasi-separatrix structures than the potential field, leading to different sub-structure in the solar wind speed proxies. It contains twisted magnetic structures which can perturb the separatrix surfaces traced down from the base of the heliospheric current sheet. A significant difference between the models is the greater amount of open magnetic flux in the non-potential model. Using existing empirical formulae this leads to higher predicted wind speeds for two reasons: partly because magnetic flux tubes expand less rapidly with height, but more importantly because more open field lines are further from coronal hole boundaries.
2015-10-01T00:00:00ZEdwards, Sarah JaneYeates, Anthony RobinsonBocquet, FrancoisMackay, Duncan HendryBy comparing a magneto-frictional model of the low coronal magnetic field to a potential field source surface model, we investigate the possible impact of non-potential magnetic structure on empirical solar wind models. These empirical models (such as Wang-Sheeley-Arge) estimate the distribution of solar wind speed solely from the magnetic field structure in the low corona. Our models are computed in a domain between the solar surface and 2.5 solar radii, and are extended to 0.1 AU using a Schatten current sheet model. The non-potential field has a more complex magnetic skeleton and quasi-separatrix structures than the potential field, leading to different sub-structure in the solar wind speed proxies. It contains twisted magnetic structures which can perturb the separatrix surfaces traced down from the base of the heliospheric current sheet. A significant difference between the models is the greater amount of open magnetic flux in the non-potential model. Using existing empirical formulae this leads to higher predicted wind speeds for two reasons: partly because magnetic flux tubes expand less rapidly with height, but more importantly because more open field lines are further from coronal hole boundaries.Quiescent prominences in the era of ALMA : simulated observations using 3D whole-prominence fine structure modelGunar, StanislavHeinzel, PetrMackay, Duncan HendryAnzer, Ulrichhttp://hdl.handle.net/10023/97102018-02-11T01:34:33Z2016-12-20T00:00:00ZWe use the detailed 3D whole-prominence fine structure model to produce the first simulated high-resolution ALMA observations of a modeled quiescent solar prominence. The synthetic brightness temperature and optical thickness maps shown in the present paper are produced using a visualization method for the sub-millimeter/millimeter radio continua synthesis. We have obtained the simulated observations of both the prominence at the limb and the filament on the disk at wavelengths covering a broad range which encompasses the full potential of ALMA.We demonstrate here to what extent the small-scale and large-scale prominence and filament structures will be visible in the ALMA observations spanning both the optically thin and thick regimes. We analyze the relationship between the brightness and kinetic temperature of the prominence plasma. We also illustrate the opportunities ALMA will provide for studying the thermal structure of the prominence plasma from the cool prominence fine structure cores to the prominence-corona transition region. In addition, we show that the detailed 3D modeling of entire prominences with their numerous fine structures will be important for the correct interpretation of future ALMA prominence observations.
2016-12-20T00:00:00ZGunar, StanislavHeinzel, PetrMackay, Duncan HendryAnzer, UlrichWe use the detailed 3D whole-prominence fine structure model to produce the first simulated high-resolution ALMA observations of a modeled quiescent solar prominence. The synthetic brightness temperature and optical thickness maps shown in the present paper are produced using a visualization method for the sub-millimeter/millimeter radio continua synthesis. We have obtained the simulated observations of both the prominence at the limb and the filament on the disk at wavelengths covering a broad range which encompasses the full potential of ALMA.We demonstrate here to what extent the small-scale and large-scale prominence and filament structures will be visible in the ALMA observations spanning both the optically thin and thick regimes. We analyze the relationship between the brightness and kinetic temperature of the prominence plasma. We also illustrate the opportunities ALMA will provide for studying the thermal structure of the prominence plasma from the cool prominence fine structure cores to the prominence-corona transition region. In addition, we show that the detailed 3D modeling of entire prominences with their numerous fine structures will be important for the correct interpretation of future ALMA prominence observations.Deciphering satellite observations of compressional ULF waveguide modesElsden, TomWright, Andrew NicholasHartinger, Michaelhttp://hdl.handle.net/10023/97022018-01-07T03:37:29Z2016-04-01T00:00:00ZWe present an analytical method for determining incident and reflection co- efficients for flank ULF compressional waveguide modes in Earth’s magnetosphere. In the flank magnetosphere, compressional waves propagate azimuthally, but exhibit a mixed standing/propagating nature radially. Understanding this radial dependence will yield information on the energy absorption and transport of these waves. We provide a step by step method that can be applied to observations of flank ULF waves, which separates these fluctuations into incident and reflected parts. As a means of testing, we apply the method to data from a numerical waveguide simulation, which shows the effect on the reflection coefficient when energy is absorbed at a field line resonance.
T. Elsden would like to thank STFC for financial support for a doctoral training grant, number AMC3 STFC12. A.N. Wright was supported by STFC grant ST/N000609/1.
2016-04-01T00:00:00ZElsden, TomWright, Andrew NicholasHartinger, MichaelWe present an analytical method for determining incident and reflection co- efficients for flank ULF compressional waveguide modes in Earth’s magnetosphere. In the flank magnetosphere, compressional waves propagate azimuthally, but exhibit a mixed standing/propagating nature radially. Understanding this radial dependence will yield information on the energy absorption and transport of these waves. We provide a step by step method that can be applied to observations of flank ULF waves, which separates these fluctuations into incident and reflected parts. As a means of testing, we apply the method to data from a numerical waveguide simulation, which shows the effect on the reflection coefficient when energy is absorbed at a field line resonance.Transverse, propagating velocity perturbations in solar coronal loopsDe Moortel, InekePascoe, David JamesWright, Andrew NicholasHood, Alan Williamhttp://hdl.handle.net/10023/96842018-01-07T03:08:57Z2016-01-01T00:00:00ZAs waves and oscillations carry both energy and information, they have enormous potential as a plasma heating mechanism and, through seismology, to provide estimates of local plasma properties which are hard to obtain from direct measurements. Being sufficiently near to allow high-resolution observations, the atmosphere of the Sun forms a natural plasma laboratory. Recent observations have revealed that an abundance of waves and oscillations is present in the solar atmosphere, leading to a renewed interest in wave heating mechanisms. This short review paper gives an overview of recently observed transverse, propagating velocity perturbations in coronal loops. These ubiquitous perturbations are observed to undergo strong damping as they propagate. Using 3D numerical simulations of footpoint-driven transverse waves propagating in a coronal plasma with a cylindrical density structure, in combination with analytical modelling, it is demonstrated that the observed velocity perturbations can be understood in terms of coupling of different wave modes in the inhomogeneous boundaries of the loops. Mode coupling in the inhomogeneous boundary layers of the loops leads to the coupling of the transversal (kink) mode to the azimuthal (Alfven) mode, observed as the decay of the transverse kink oscillations. Both the numerical and analytical results show the spatial profile of the damped wave has a Gaussian shape to begin with, before switching to exponential decay at large heights. In addition, recent analysis of CoMP (Coronal Multi-channel Polarimeter) Doppler shift observations of large, off-limb, trans-equatorial loops shows that Fourier power at the apex appears to be higher in the high-frequency part of the spectrum than expected from theoretical models. This excess high-frequency FFT power could be tentative evidence for the onset of a cascade of the low-to-mid frequency waves into (Alfvenic) turbulence.
2016-01-01T00:00:00ZDe Moortel, InekePascoe, David JamesWright, Andrew NicholasHood, Alan WilliamAs waves and oscillations carry both energy and information, they have enormous potential as a plasma heating mechanism and, through seismology, to provide estimates of local plasma properties which are hard to obtain from direct measurements. Being sufficiently near to allow high-resolution observations, the atmosphere of the Sun forms a natural plasma laboratory. Recent observations have revealed that an abundance of waves and oscillations is present in the solar atmosphere, leading to a renewed interest in wave heating mechanisms. This short review paper gives an overview of recently observed transverse, propagating velocity perturbations in coronal loops. These ubiquitous perturbations are observed to undergo strong damping as they propagate. Using 3D numerical simulations of footpoint-driven transverse waves propagating in a coronal plasma with a cylindrical density structure, in combination with analytical modelling, it is demonstrated that the observed velocity perturbations can be understood in terms of coupling of different wave modes in the inhomogeneous boundaries of the loops. Mode coupling in the inhomogeneous boundary layers of the loops leads to the coupling of the transversal (kink) mode to the azimuthal (Alfven) mode, observed as the decay of the transverse kink oscillations. Both the numerical and analytical results show the spatial profile of the damped wave has a Gaussian shape to begin with, before switching to exponential decay at large heights. In addition, recent analysis of CoMP (Coronal Multi-channel Polarimeter) Doppler shift observations of large, off-limb, trans-equatorial loops shows that Fourier power at the apex appears to be higher in the high-frequency part of the spectrum than expected from theoretical models. This excess high-frequency FFT power could be tentative evidence for the onset of a cascade of the low-to-mid frequency waves into (Alfvenic) turbulence.Dynamical patterns of coexisting strategies in a hybrid discrete-continuum spatial evolutionary game modelBurgess, A. E. FSchofield, P. G.Hubbard, S. F.Chaplain, Mark A. J.Lorenzi, T.http://hdl.handle.net/10023/96252018-01-07T03:49:51Z2016-12-07T00:00:00ZWe present a novel hybrid modelling framework that takes into account two aspects which have been largely neglected in previous models of spatial evolutionary games: random motion and chemotaxis. A stochastic individual-based model is used to describe the player dynamics,whereas the evolution of the chemoattractant is governed by a reaction-diffusion equation. The two models are coupled by deriving individual movement rules via the discretisation of a taxis-diffusion equation which describes the evolution of the local number of players. In this framework, individuals occupying the same position can engage in a two-player game, and are awarded a payoff, interms of reproductive fitness, according to their strategy. As an example, we let individuals play the Hawk-Dove game. Numerical simulations illustrate how random motion and chemotactic response can bring about self-generated dynamical patterns that create favourable conditions for the coexistence of hawks and doves in situations in which the two strategies cannot coexist otherwise.In this sense, our work offers a new perspective of research on spatial evolutionary games, and provides a general formalism to study the dynamics of spatially-structured populations in biological and social contexts where individual motion is likely to affect natural selection of behavioural traits.
2016-12-07T00:00:00ZBurgess, A. E. FSchofield, P. G.Hubbard, S. F.Chaplain, Mark A. J.Lorenzi, T.We present a novel hybrid modelling framework that takes into account two aspects which have been largely neglected in previous models of spatial evolutionary games: random motion and chemotaxis. A stochastic individual-based model is used to describe the player dynamics,whereas the evolution of the chemoattractant is governed by a reaction-diffusion equation. The two models are coupled by deriving individual movement rules via the discretisation of a taxis-diffusion equation which describes the evolution of the local number of players. In this framework, individuals occupying the same position can engage in a two-player game, and are awarded a payoff, interms of reproductive fitness, according to their strategy. As an example, we let individuals play the Hawk-Dove game. Numerical simulations illustrate how random motion and chemotactic response can bring about self-generated dynamical patterns that create favourable conditions for the coexistence of hawks and doves in situations in which the two strategies cannot coexist otherwise.In this sense, our work offers a new perspective of research on spatial evolutionary games, and provides a general formalism to study the dynamics of spatially-structured populations in biological and social contexts where individual motion is likely to affect natural selection of behavioural traits.The usage of a three-compartment model to investigate the metabolic differences between hepatic reductase null and wild-type miceHill, LydiaChaplain, Mark Andrew JosephWolf, RolandKapelyukh, Yuryhttp://hdl.handle.net/10023/96112018-01-07T03:33:47Z2015-10-05T00:00:00ZThe Cytochrome P450 (CYP) system is involved in 90% of the human body’s interactions with xenobiotics and due to this, it has become an area of avid research including the creation of transgenic mice. This paper proposes a three-compartment model which is used to explain the drug metabolism in the Hepatic Reductase Null (HRN) mouse developed by the University of Dundee (Henderson, C. J., Otto, D. M. E., Carrie, D., Magnuson, M. A., McLaren, A. W., Rosewell, I. and Wolf, C. R. (2003) Inactivation of the hepatic cytochrome p450 system by conditional deletion of hepatic cytochrome p450 reductase. J. Biol. Chem. 278, 13480–13486). The model is compared with a two-compartment model using experimental data from studies using wild-type and HRN mice. This comparison allowed for metabolic differences between the two types of mice to be isolated. The three sets of drug data (Gefitinib, Midazolam and Thalidomide) showed that the transgenic mouse has a decreased rate of metabolism.
L.H. is currently funded by the Research Foundation Flanders (FWO) and the Belgian Science Policy Office under Grant No. IAP-VI/10.
2015-10-05T00:00:00ZHill, LydiaChaplain, Mark Andrew JosephWolf, RolandKapelyukh, YuryThe Cytochrome P450 (CYP) system is involved in 90% of the human body’s interactions with xenobiotics and due to this, it has become an area of avid research including the creation of transgenic mice. This paper proposes a three-compartment model which is used to explain the drug metabolism in the Hepatic Reductase Null (HRN) mouse developed by the University of Dundee (Henderson, C. J., Otto, D. M. E., Carrie, D., Magnuson, M. A., McLaren, A. W., Rosewell, I. and Wolf, C. R. (2003) Inactivation of the hepatic cytochrome p450 system by conditional deletion of hepatic cytochrome p450 reductase. J. Biol. Chem. 278, 13480–13486). The model is compared with a two-compartment model using experimental data from studies using wild-type and HRN mice. This comparison allowed for metabolic differences between the two types of mice to be isolated. The three sets of drug data (Gefitinib, Midazolam and Thalidomide) showed that the transgenic mouse has a decreased rate of metabolism.On the connection between propagating solar coronal disturbances and chromospheric footpointsBryans, PaulMcIntosh, Scott W.De Moortel, InekeDe Pontieu, Barthttp://hdl.handle.net/10023/96002018-02-25T01:32:59Z2016-09-01T00:00:00ZThe Interface Region Imaging Spectrograph (IRIS) provides an unparalleled opportunity to explore the (thermal) interface between the chromosphere, transition region, and the coronal plasma observed by the Atmospheric Imaging Assembly (AIA) of the Solar Dynamics Observatory (SDO). The SDO/AIA observations of coronal loop footpoints show strong recurring upward propagating signals—“propagating coronal disturbances” (PCDs) with apparent speeds of the order of 100–120 km/s-1. That signal has a clear signature in the slit-jaw images of IRIS in addition to identifiable spectral signatures and diagnostics in the Mg IIh (2803 Å) line. In analyzing the Mg IIh line, we are able to observe the presence of magnetoacoustic shock waves that are also present in the vicinity of the coronal loop footpoints. We see there is enough of a correspondence between the shock propagation in Mg IIh, the evolution of the Si IV line profiles, and the PCD evolution to indicate that these waves are an important ingredient for PCDs. In addition, the strong flows in the jet-like features in the IRIS Si IV slit-jaw images are also associated with PCDs, such that waves and flows both appear to be contributing to the signals observed at the footpoints of PCDs.
2016-09-01T00:00:00ZBryans, PaulMcIntosh, Scott W.De Moortel, InekeDe Pontieu, BartThe Interface Region Imaging Spectrograph (IRIS) provides an unparalleled opportunity to explore the (thermal) interface between the chromosphere, transition region, and the coronal plasma observed by the Atmospheric Imaging Assembly (AIA) of the Solar Dynamics Observatory (SDO). The SDO/AIA observations of coronal loop footpoints show strong recurring upward propagating signals—“propagating coronal disturbances” (PCDs) with apparent speeds of the order of 100–120 km/s-1. That signal has a clear signature in the slit-jaw images of IRIS in addition to identifiable spectral signatures and diagnostics in the Mg IIh (2803 Å) line. In analyzing the Mg IIh line, we are able to observe the presence of magnetoacoustic shock waves that are also present in the vicinity of the coronal loop footpoints. We see there is enough of a correspondence between the shock propagation in Mg IIh, the evolution of the Si IV line profiles, and the PCD evolution to indicate that these waves are an important ingredient for PCDs. In addition, the strong flows in the jet-like features in the IRIS Si IV slit-jaw images are also associated with PCDs, such that waves and flows both appear to be contributing to the signals observed at the footpoints of PCDs.The interaction between two oppositely travelling, horizontally offset, antisymmetric quasi-geostrophic hetonsReinaud, Jean NoelCarton, Xavierhttp://hdl.handle.net/10023/95932018-01-07T03:36:24Z2016-05-01T00:00:00ZWe investigate numerically the nonlinear interactions between hetons. Hetons are baroclinic structures consisting of two vortices of opposite sign lying at different depths. Hetons are long-lived. They most often translate (they can sometimes rotate) and therefore they can noticeably contribute to the transport of scalar properties in the oceans. Heton interactions can interrupt this translation and thus this transport, by inducing a reconfiguration of interacting hetons into more complex baroclinic multipoles. More specifically, we study here the general case of two hetons, which collide with an offset between their translation axes. For this purpose, we use the point vortex theory, the ellipsoidal vortex model and direct simulations in the three-dimensional quasi-geostrophic, contour surgery model. More specifically, this paper shows that there are in general three regimes for the interaction. For small horizontal offsets between the hetons, their vortices recombine as same-depth dipoles which escape at an angle. The angle depends in particular on the horizontal offset. It is a right angle for no offset, and the angle is shallower for small but finite offsets. The second limiting regime is for large horizontal offsets where the two hetons remain the same hetonic structures but are deflected by the weaker mutual interaction. Finally the intermediate regime is for moderate offsets. This is the regime where the formation of a meta-stable quadrupole is possible. The formation of this quadrupole greatly restrains transport. Indeed, it constrains the vortices to reside in a closed area. It is shown that the formation of such structures is enhanced by the quasi periodic deformation of the vortices. Indeed, these structures are nearly unobtainable for singular vortices (point vortices) but may be obtained using deformable, finite-core vortices.
2016-05-01T00:00:00ZReinaud, Jean NoelCarton, XavierWe investigate numerically the nonlinear interactions between hetons. Hetons are baroclinic structures consisting of two vortices of opposite sign lying at different depths. Hetons are long-lived. They most often translate (they can sometimes rotate) and therefore they can noticeably contribute to the transport of scalar properties in the oceans. Heton interactions can interrupt this translation and thus this transport, by inducing a reconfiguration of interacting hetons into more complex baroclinic multipoles. More specifically, we study here the general case of two hetons, which collide with an offset between their translation axes. For this purpose, we use the point vortex theory, the ellipsoidal vortex model and direct simulations in the three-dimensional quasi-geostrophic, contour surgery model. More specifically, this paper shows that there are in general three regimes for the interaction. For small horizontal offsets between the hetons, their vortices recombine as same-depth dipoles which escape at an angle. The angle depends in particular on the horizontal offset. It is a right angle for no offset, and the angle is shallower for small but finite offsets. The second limiting regime is for large horizontal offsets where the two hetons remain the same hetonic structures but are deflected by the weaker mutual interaction. Finally the intermediate regime is for moderate offsets. This is the regime where the formation of a meta-stable quadrupole is possible. The formation of this quadrupole greatly restrains transport. Indeed, it constrains the vortices to reside in a closed area. It is shown that the formation of such structures is enhanced by the quasi periodic deformation of the vortices. Indeed, these structures are nearly unobtainable for singular vortices (point vortices) but may be obtained using deformable, finite-core vortices.Modeling observed decay-less oscillations as resonantly enhanced Kelvin-Helmholtz vortices from transverse MHD waves and their seismological applicationAntolin, P.De Moortel, InekeVan Doorsselaere, T.Yokoyama, T.http://hdl.handle.net/10023/95772018-03-11T01:35:57Z2016-10-12T00:00:00ZIn the highly structured solar corona, resonant absorption is an unavoidable mechanism of energy transfer from global transverse MHD waves to local azimuthal Alfvén waves. Due to its localised nature, a direct detection of this mechanism is extremely difficult. Yet, it is the leading theory explaining the observed fast damping of the global transverse waves. However, at odds with this theoretical prediction, recent observations indicate that in the low amplitude regime such transverse MHD waves can also appear decay-less, a yet unsolved phenomenon. Recent numerical work has shown that Kelvin-Helmholtz instabilities (KHI) often accompany transverse MHD waves. In this work, we combine 3D MHD simulations and forward modelling to show that for currently achieved spatial resolution and observed small amplitudes, an apparent decay-less oscillation is obtained. This effect results from the combination of periodic brightenings produced by the KHI and the coherent motion of the KHI vortices amplified by resonant absorption. Such effect is especially clear in emission lines forming at temperatures that capture the boundary dynamics rather than the core, and reflects the low damping character of the local azimuthal Alfvén waves resonantly coupled to the kink mode. Due to phase mixing, the detected period can vary depending on the emission line, with those sensitive to the boundary having shorter periods than those sensitive to the loop core. This allows to estimate the density contrast at the boundary.
2016-10-12T00:00:00ZAntolin, P.De Moortel, InekeVan Doorsselaere, T.Yokoyama, T.In the highly structured solar corona, resonant absorption is an unavoidable mechanism of energy transfer from global transverse MHD waves to local azimuthal Alfvén waves. Due to its localised nature, a direct detection of this mechanism is extremely difficult. Yet, it is the leading theory explaining the observed fast damping of the global transverse waves. However, at odds with this theoretical prediction, recent observations indicate that in the low amplitude regime such transverse MHD waves can also appear decay-less, a yet unsolved phenomenon. Recent numerical work has shown that Kelvin-Helmholtz instabilities (KHI) often accompany transverse MHD waves. In this work, we combine 3D MHD simulations and forward modelling to show that for currently achieved spatial resolution and observed small amplitudes, an apparent decay-less oscillation is obtained. This effect results from the combination of periodic brightenings produced by the KHI and the coherent motion of the KHI vortices amplified by resonant absorption. Such effect is especially clear in emission lines forming at temperatures that capture the boundary dynamics rather than the core, and reflects the low damping character of the local azimuthal Alfvén waves resonantly coupled to the kink mode. Due to phase mixing, the detected period can vary depending on the emission line, with those sensitive to the boundary having shorter periods than those sensitive to the loop core. This allows to estimate the density contrast at the boundary.Neutral and non-neutral collisionless plasma equilibria for twisted flux tubes : the Gold-Hoyle model in a background fieldAllanson, Oliver DouglasWilson, FionaNeukirch, Thomashttp://hdl.handle.net/10023/95392018-02-11T01:34:18Z2016-09-01T00:00:00ZWe calculate exact one-dimensional collisionless plasma equilibria for a continuum of flux tube models, for which the total magnetic field is made up of the `force-free' Gold-Hoyle magnetic flux tube embedded in a uniform and anti-parallel background magnetic field. For a sufficiently weak background magnetic field, the axial component of the total magnetic field reverses at some finite radius. The presence of the background magnetic field means that the total system is not exactly force-free, but by reducing its magnitude the departure from force-free can be made as small as desired. The distribution function for each species is a function of the three constants of motion; namely the Hamiltonian and the canonical momenta in the axial and azimuthal directions. Poisson's Equation and Amp ere's Law are solved exactly, and the solution allows either electrically neutral or non-neutral configurations, depending on the values of the bulk ion and electron flows. These equilibria have possible applications in various solar, space and astrophysical contexts, as well as in the laboratory.
The authors gratefully acknowledge the support of the Science and Technology Facilities Council Consolidated Grants ST/K000950/1 and ST/N000609/1, as well as Doctoral Training Grant ST/K502327/1. We also gratefully acknowledge funding from Leverhulme Trust Research Project Grant F/00268/BB.
2016-09-01T00:00:00ZAllanson, Oliver DouglasWilson, FionaNeukirch, ThomasWe calculate exact one-dimensional collisionless plasma equilibria for a continuum of flux tube models, for which the total magnetic field is made up of the `force-free' Gold-Hoyle magnetic flux tube embedded in a uniform and anti-parallel background magnetic field. For a sufficiently weak background magnetic field, the axial component of the total magnetic field reverses at some finite radius. The presence of the background magnetic field means that the total system is not exactly force-free, but by reducing its magnitude the departure from force-free can be made as small as desired. The distribution function for each species is a function of the three constants of motion; namely the Hamiltonian and the canonical momenta in the axial and azimuthal directions. Poisson's Equation and Amp ere's Law are solved exactly, and the solution allows either electrically neutral or non-neutral configurations, depending on the values of the bulk ion and electron flows. These equilibria have possible applications in various solar, space and astrophysical contexts, as well as in the laboratory.The role of planetary waves in the tropospheric jet response to stratospheric coolingSmith, Karen L.Scott, Richard K.http://hdl.handle.net/10023/95282017-11-07T20:30:23Z2016-03-28T00:00:00ZAn idealized general circulation model is used to assess the importance of planetary-scale waves in determining the position of the tropospheric jet, specifically its tendency to shift poleward as winter stratospheric cooling is increased. Full model integrations are compared against integrations in which planetary waves are truncated in the zonal direction, and only synoptic-scale waves are retained. Two series of truncated integrations are considered, using (i) a modified radiative equilibrium temperature or (ii) a nudged-bias correction technique. Both produce tropospheric climatologies that are similar to the full model when stratospheric cooling is weak. When stratospheric cooling is increased, the results indicate that the interaction between planetary- and synoptic-scale waves plays an important role in determining the structure of the tropospheric mean flow and rule out the possibility that the jet shift occurs purely as a response to changes in the planetary- or synoptic-scale wave fields alone.
K.L.S. is funded in part by a Natural Sciences and Engineering Council of Canada Postdoctoral Fellowship. R.K.S. acknowledges support from the National Science Foundation.
2016-03-28T00:00:00ZSmith, Karen L.Scott, Richard K.An idealized general circulation model is used to assess the importance of planetary-scale waves in determining the position of the tropospheric jet, specifically its tendency to shift poleward as winter stratospheric cooling is increased. Full model integrations are compared against integrations in which planetary waves are truncated in the zonal direction, and only synoptic-scale waves are retained. Two series of truncated integrations are considered, using (i) a modified radiative equilibrium temperature or (ii) a nudged-bias correction technique. Both produce tropospheric climatologies that are similar to the full model when stratospheric cooling is weak. When stratospheric cooling is increased, the results indicate that the interaction between planetary- and synoptic-scale waves plays an important role in determining the structure of the tropospheric mean flow and rule out the possibility that the jet shift occurs purely as a response to changes in the planetary- or synoptic-scale wave fields alone.Modeling the sun's small-scale global photospheric magnetic fieldMeyer, Karen AlisonMackay, Duncan Hendryhttp://hdl.handle.net/10023/95112018-01-07T03:45:24Z2016-10-19T00:00:00ZWe present a new model for the Sun's global photospheric magnetic field during a deep minimum of activity, in which no active regions emerge. The emergence and subsequent evolution of small-scale magnetic features across the full solar surface is simulated, subject to the influence of a global supergranular flow pattern. Visually, the resulting simulated magnetograms reproduce the typical structure and scale observed in quiet Sun magnetograms. Quantitatively, the simulation quickly reaches a steady state, resulting in a mean field and flux distribution that are in good agreement with those determined from observations. A potential coronal magnetic field is extrapolated from the simulated full Sun magnetograms to consider the implications of such a quiet photospheric magnetic field on the corona and inner heliosphere. The bulk of the coronal magnetic field closes very low down, in short connections between small-scale features in the simulated magnetic network. Just 0.1% of the photospheric magnetic flux is found to be open at 2.5 R⊙, around 10–100 times less than that determined for typical Helioseismic and Magnetic Imager synoptic map observations. If such conditions were to exist on the Sun, this would lead to a significantly weaker interplanetary magnetic field than is currently observed, and hence a much higher cosmic ray flux at Earth.
2016-10-19T00:00:00ZMeyer, Karen AlisonMackay, Duncan HendryWe present a new model for the Sun's global photospheric magnetic field during a deep minimum of activity, in which no active regions emerge. The emergence and subsequent evolution of small-scale magnetic features across the full solar surface is simulated, subject to the influence of a global supergranular flow pattern. Visually, the resulting simulated magnetograms reproduce the typical structure and scale observed in quiet Sun magnetograms. Quantitatively, the simulation quickly reaches a steady state, resulting in a mean field and flux distribution that are in good agreement with those determined from observations. A potential coronal magnetic field is extrapolated from the simulated full Sun magnetograms to consider the implications of such a quiet photospheric magnetic field on the corona and inner heliosphere. The bulk of the coronal magnetic field closes very low down, in short connections between small-scale features in the simulated magnetic network. Just 0.1% of the photospheric magnetic flux is found to be open at 2.5 R⊙, around 10–100 times less than that determined for typical Helioseismic and Magnetic Imager synoptic map observations. If such conditions were to exist on the Sun, this would lead to a significantly weaker interplanetary magnetic field than is currently observed, and hence a much higher cosmic ray flux at Earth.The possible impact of L5 magnetograms on non-potential solar coronal magnetic field simulationsWeinzierl, MarionMackay, Duncan HendryYeates, Anthony RobinsonPevtsov, Alexeihttp://hdl.handle.net/10023/94802018-01-07T03:45:04Z2016-09-10T00:00:00ZThe proposed Carrington-L5 mission would bring instruments to the L5 Lagrange point to provide us with crucial data for space weather prediction. To assess the importance of including a magnetograph, we consider the possible differences in non-potential solar coronal magnetic field simulations when magnetograph observations are available from the L5 point, compared to an L1-based field of view. A time series of synoptic radial magnetic field maps is constructed to capture the emergence of two active regions from the L5 field of view. These regions are initially absent in the L1 magnetic field maps, but are included once they rotate into the L1 field of view. Non-potential simulations for the two sets of input data are compared in detail. Within the bipolar active regions themselves, differences in the magnetic field structure can exist between the two simulations once the active regions are included in both. These differences tend to reduce within 5 days of the active region being included in L1. The delayed emergence in L1 can however lead to significant persistent differences in long range connectivity between the active regions and the surrounding fields, and also in the global magnetic energy. In particular, the open magnetic flux, and the location of open magnetic foot points, are sensitive to capturing the real time of emergence. These results suggest that a magnetograph at L5 could significantly improve predictions of the non-potential corona, interplanetary magnetic field and of solar wind source regions on the Sun.
2016-09-10T00:00:00ZWeinzierl, MarionMackay, Duncan HendryYeates, Anthony RobinsonPevtsov, AlexeiThe proposed Carrington-L5 mission would bring instruments to the L5 Lagrange point to provide us with crucial data for space weather prediction. To assess the importance of including a magnetograph, we consider the possible differences in non-potential solar coronal magnetic field simulations when magnetograph observations are available from the L5 point, compared to an L1-based field of view. A time series of synoptic radial magnetic field maps is constructed to capture the emergence of two active regions from the L5 field of view. These regions are initially absent in the L1 magnetic field maps, but are included once they rotate into the L1 field of view. Non-potential simulations for the two sets of input data are compared in detail. Within the bipolar active regions themselves, differences in the magnetic field structure can exist between the two simulations once the active regions are included in both. These differences tend to reduce within 5 days of the active region being included in L1. The delayed emergence in L1 can however lead to significant persistent differences in long range connectivity between the active regions and the surrounding fields, and also in the global magnetic energy. In particular, the open magnetic flux, and the location of open magnetic foot points, are sensitive to capturing the real time of emergence. These results suggest that a magnetograph at L5 could significantly improve predictions of the non-potential corona, interplanetary magnetic field and of solar wind source regions on the Sun.3D MHD modeling of twisted coronal loopsReale, F.Orlando, S.Guarrasi, M.Mignone, A.Peres, G.Hood, A. W.Priest, E. R.http://hdl.handle.net/10023/94752018-01-07T03:46:01Z2016-10-10T00:00:00ZWe perform MHD modeling of a single bright coronal loop to include the interaction with a non-uniform magnetic field. The field is stressed by random footpoint rotation in the central region and its energy is dissipated into heating by growing currents through anomalous magnetic diffusivity that switches on in the corona above a current density threshold. We model an entire single magnetic flux tube, in the solar atmosphere extending from the high-beta chromosphere to the low-betacorona through the steep transition region. The magnetic field expands from the chromosphere to the corona. The maximum resolution is ~30 km. We obtain an overall evolution typical of loop models and realistic loop emission in the EUV and X-ray bands. The plasma confined in the fluxtube is heated to active region temperatures (~3 MK) after ~2/3 hr. Upflows from the chromosphere up to ~100 km/s fill the core of the fluxtube to densities above 109 cm-3. More heating is released in the low corona than the high corona and is finely structured both in space and time.
2016-10-10T00:00:00ZReale, F.Orlando, S.Guarrasi, M.Mignone, A.Peres, G.Hood, A. W.Priest, E. R.We perform MHD modeling of a single bright coronal loop to include the interaction with a non-uniform magnetic field. The field is stressed by random footpoint rotation in the central region and its energy is dissipated into heating by growing currents through anomalous magnetic diffusivity that switches on in the corona above a current density threshold. We model an entire single magnetic flux tube, in the solar atmosphere extending from the high-beta chromosphere to the low-betacorona through the steep transition region. The magnetic field expands from the chromosphere to the corona. The maximum resolution is ~30 km. We obtain an overall evolution typical of loop models and realistic loop emission in the EUV and X-ray bands. The plasma confined in the fluxtube is heated to active region temperatures (~3 MK) after ~2/3 hr. Upflows from the chromosphere up to ~100 km/s fill the core of the fluxtube to densities above 109 cm-3. More heating is released in the low corona than the high corona and is finely structured both in space and time.Three-dimensional forced-damped dynamical systems with rich dynamics : bifurcations, chaos and unbounded solutionsMiyaji, TomoyukiOkamoto, HisashiCraik, Alexander Duncan Davidsonhttp://hdl.handle.net/10023/94682018-01-07T03:08:08Z2015-01-01T00:00:00ZWe consider certain autonomous three-dimensional dynamical systems that can arise in mechanical and fluid-dynamical contexts. Extending a previous study in Craik and Okamoto (2002), to include linear forcing and damping, we find that the four-leaf structure discovered in that paper, and unbounded orbits, persist, but may now be accompanied by three distinct period-doubling cascades to chaos, and by orbits that approach stable equilibrium points. This rich structure is investigated both analytically and numerically, distinguishing three main cases determined by the damping and forcing parameter values.
T.M. is supported by the Grant-in-Aid for JSPS Fellow No. 24·5312. H.O. is partially supported by JSPS KAKENHI 24244007.
2015-01-01T00:00:00ZMiyaji, TomoyukiOkamoto, HisashiCraik, Alexander Duncan DavidsonWe consider certain autonomous three-dimensional dynamical systems that can arise in mechanical and fluid-dynamical contexts. Extending a previous study in Craik and Okamoto (2002), to include linear forcing and damping, we find that the four-leaf structure discovered in that paper, and unbounded orbits, persist, but may now be accompanied by three distinct period-doubling cascades to chaos, and by orbits that approach stable equilibrium points. This rich structure is investigated both analytically and numerically, distinguishing three main cases determined by the damping and forcing parameter values.Sunspot rotation : II. Effects of varying the field strength and twist of an emerging flux tubeSturrock, ZoeHood, Alan Williamhttp://hdl.handle.net/10023/94422018-01-07T03:42:25Z2016-09-01T00:00:00ZContext. Observations of flux emergence indicate that rotational velocities may develop within sunspots. However, the dependence of this rotation on sub-photospheric field strength and twist remains largely unknown. Aims. We investigate the effects of varying the initial field strength and twist of an emerging sub-photospheric magnetic flux tube onthe rotation of the sunspots at the photosphere. Methods. We consider a simple model of a stratified domain with a sub-photospheric interior layer and three overlying atmospheric layers. A twisted arched flux tube is inserted in the interior and is allowed to rise into the atmosphere. To achieve this, the MHD equations are solved using the Lagrangian-remap code, Lare3d. We perform a parameter study by independently varying the sub-photospheric magnetic field strength and twist. Results. Altering the initial magnetic field strength and twist of the flux tube significantly affects the tube’s evolution and the rotational motions that develop at the photosphere. The rotation angle, vorticity, and current show a direct dependence on the initial field strength. We find that an increase in field strength increases the angle through which the fieldlines rotate, the length of the fieldlines extending into the atmosphere, and the magnetic energy transported to the atmosphere. This also affects the amount of residual twist in the interior. The length of the fieldlines is crucial as we predict the twist per unit length equilibrates to a lower value on longer fieldlines. No such direct dependence is found when we modify the twist of the magnetic field owing to the complex effect this has on the tension force acting on the tube. However, there is still a clear ordering in quantities such as the rotation angle, helicity, and free energy with higher initial twist cases being related to sunspots that rotate more rapidly, transporting more helicity and magnetic energy to the atmosphere.
ZS acknowledges the financial support of the Carnegie Trust for Scotland. This work used the DIRAC 1, UKMHD Consortium machine at the University of St Andrews and the DiRAC Data Centric system at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/H008519/1, and STFC DiRAC Operations grant ST/K003267/1 and Durham University. DiRAC is part of the National E-Infrastructure.
2016-09-01T00:00:00ZSturrock, ZoeHood, Alan WilliamContext. Observations of flux emergence indicate that rotational velocities may develop within sunspots. However, the dependence of this rotation on sub-photospheric field strength and twist remains largely unknown. Aims. We investigate the effects of varying the initial field strength and twist of an emerging sub-photospheric magnetic flux tube onthe rotation of the sunspots at the photosphere. Methods. We consider a simple model of a stratified domain with a sub-photospheric interior layer and three overlying atmospheric layers. A twisted arched flux tube is inserted in the interior and is allowed to rise into the atmosphere. To achieve this, the MHD equations are solved using the Lagrangian-remap code, Lare3d. We perform a parameter study by independently varying the sub-photospheric magnetic field strength and twist. Results. Altering the initial magnetic field strength and twist of the flux tube significantly affects the tube’s evolution and the rotational motions that develop at the photosphere. The rotation angle, vorticity, and current show a direct dependence on the initial field strength. We find that an increase in field strength increases the angle through which the fieldlines rotate, the length of the fieldlines extending into the atmosphere, and the magnetic energy transported to the atmosphere. This also affects the amount of residual twist in the interior. The length of the fieldlines is crucial as we predict the twist per unit length equilibrates to a lower value on longer fieldlines. No such direct dependence is found when we modify the twist of the magnetic field owing to the complex effect this has on the tension force acting on the tube. However, there is still a clear ordering in quantities such as the rotation angle, helicity, and free energy with higher initial twist cases being related to sunspots that rotate more rapidly, transporting more helicity and magnetic energy to the atmosphere.Uncovering the birth of a coronal mass ejection from two-viewpoint SECCHI observationsVourlidas, A.Syntelis, P.Tsinganos, K.http://hdl.handle.net/10023/94282018-01-07T03:47:36Z2012-10-01T00:00:00ZWe investigate the initiation and formation of Coronal Mass Ejections (CMEs) via a detailed two-viewpoint analysis of low corona observations of a relatively fast CME acquired by the SECCHI instruments aboard the STEREO mission. The event which occurred on 2 January 2008, was chosen because of several unique characteristics. It shows upward motions for at least four hours before the flare peak. Its speed and acceleration profiles exhibit a number of inflections which seem to have a direct counterpart in the GOES light curves. We detect and measure, in 3D, loops that collapse toward the erupting channel while the CME is increasing in size and accelerates. We suggest that these collapsing loops are our first evidence of magnetic evacuation behind the forming CME flux rope. We report the detection of a hot structure which becomes the core of the white light CME. We observe and measure unidirectional flows along the erupting filament channel which may be associated with the eruption process. Finally, we compare these observations to the predictions from the standard flare-CME model and find a very satisfactory agreement. We conclude that the standard flare-CME concept is a reliable representation of the initial stages of CMEs and that multi-viewpoint, high cadence EUV observations can be extremely useful in understanding the formation of CMEs.
2012-10-01T00:00:00ZVourlidas, A.Syntelis, P.Tsinganos, K.We investigate the initiation and formation of Coronal Mass Ejections (CMEs) via a detailed two-viewpoint analysis of low corona observations of a relatively fast CME acquired by the SECCHI instruments aboard the STEREO mission. The event which occurred on 2 January 2008, was chosen because of several unique characteristics. It shows upward motions for at least four hours before the flare peak. Its speed and acceleration profiles exhibit a number of inflections which seem to have a direct counterpart in the GOES light curves. We detect and measure, in 3D, loops that collapse toward the erupting channel while the CME is increasing in size and accelerates. We suggest that these collapsing loops are our first evidence of magnetic evacuation behind the forming CME flux rope. We report the detection of a hot structure which becomes the core of the white light CME. We observe and measure unidirectional flows along the erupting filament channel which may be associated with the eruption process. Finally, we compare these observations to the predictions from the standard flare-CME model and find a very satisfactory agreement. We conclude that the standard flare-CME concept is a reliable representation of the initial stages of CMEs and that multi-viewpoint, high cadence EUV observations can be extremely useful in understanding the formation of CMEs.Study of the three-dimensional shape and dynamics of coronal loops observed by Hinode/EISSyntelis, P.Gontikakis, C.Georgoulis, M. K.Alissandrakis, C. E.Tsinganos, K.http://hdl.handle.net/10023/94262018-01-07T03:47:37Z2012-10-01T00:00:00ZWe study plasma flows along selected coronal loops in NOAA Active Region 10926, observed on 3 December 2006 with Hinode’sEUVImaging Spectrograph (EIS). From the shape of the loops traced on intensity images and the Doppler shifts measured along their length we compute their three-dimensional (3D) shape and plasma flow velocity using a simple geometrical model. This calculation was performed for loops visible in the Fe viii 185 Å, Fe x 184 Å, Fe xii 195 Å, Fe xiii202 Å, and Fe xv 284 Å spectral lines. In most cases the flow is unidirectional from one footpoint to the other but there are also cases of draining motions from the top of the loops to their footpoints. Our results indicate that the same loop may show different flow patterns when observed in different spectral lines, suggesting a dynamically complex rather than a monolithic structure. We have also carried out magnetic extrapolations in the linear force-free field approximation using SOHO/MDI magnetograms, aiming toward a first-order identification of extrapolated magnetic field lines corresponding to the reconstructed loops. In all cases, the best-fit extrapolated lines exhibit left-handed twist (α<0), in agreement with the dominant twist of the region.
2012-10-01T00:00:00ZSyntelis, P.Gontikakis, C.Georgoulis, M. K.Alissandrakis, C. E.Tsinganos, K.We study plasma flows along selected coronal loops in NOAA Active Region 10926, observed on 3 December 2006 with Hinode’sEUVImaging Spectrograph (EIS). From the shape of the loops traced on intensity images and the Doppler shifts measured along their length we compute their three-dimensional (3D) shape and plasma flow velocity using a simple geometrical model. This calculation was performed for loops visible in the Fe viii 185 Å, Fe x 184 Å, Fe xii 195 Å, Fe xiii202 Å, and Fe xv 284 Å spectral lines. In most cases the flow is unidirectional from one footpoint to the other but there are also cases of draining motions from the top of the loops to their footpoints. Our results indicate that the same loop may show different flow patterns when observed in different spectral lines, suggesting a dynamically complex rather than a monolithic structure. We have also carried out magnetic extrapolations in the linear force-free field approximation using SOHO/MDI magnetograms, aiming toward a first-order identification of extrapolated magnetic field lines corresponding to the reconstructed loops. In all cases, the best-fit extrapolated lines exhibit left-handed twist (α<0), in agreement with the dominant twist of the region.The spectroscopic imprint of the pre-eruptive configuration resulting into two major coronal mass ejectionsSyntelis, P.Gontikakis, C.Patsourakos, S.Tsinganos, K.http://hdl.handle.net/10023/94252018-02-25T01:32:54Z2016-04-01T00:00:00ZAims: We present a spectroscopic analysis of the pre-eruptive configuration of active region NOAA 11429, prior to two very fast coronal mass ejections (CMEs) on March 7, 2012 that are associated with this active region. We study the thermal components and the dynamics associated with the ejected flux ropes. Methods: Using differential emission measure (DEM) analysis of Hinode/EIS and SDO/AIA observations, we identify the emission components of both the flux rope and the host active region. We then follow the time evolution of the flux rope emission components by using AIA observations. The plasma density and the Doppler and non-thermal velocities associated with the flux ropes are also calculated from the EIS data. Results: The eastern and western parts of the active region, in which the two different fast CMEs originated during two X-class flares, were studied separately. In both regions we identified an emission component in the temperature range of log T = 6.8-7.1 associated with the presence of flux ropes. The time evolution of the eastern region showed an increase in the mean DEM in this temperature range by an order of magnitude, 5 h prior to the first CME. This was associated with a gradual rise and heating of the flux rope as manifested by blue-shifts and increased non-thermal velocities in Ca xv 200.97 Å, respectively. An overall upward motion of the flux ropes was measured (relative blue-shifts of ~12 km s-1). The measured electron density was found to be 4× 109-2 × 1010 cm-3 (using the ratio of Ca xv 181.90 Å over Ca xv 200.97 Å). We compare our findings with other works on the same AR to provide a unified picture of its evolution.
P.S acknowledges financial support from the programme Aristotelis/SIEMENS at the NOA.
2016-04-01T00:00:00ZSyntelis, P.Gontikakis, C.Patsourakos, S.Tsinganos, K.Aims: We present a spectroscopic analysis of the pre-eruptive configuration of active region NOAA 11429, prior to two very fast coronal mass ejections (CMEs) on March 7, 2012 that are associated with this active region. We study the thermal components and the dynamics associated with the ejected flux ropes. Methods: Using differential emission measure (DEM) analysis of Hinode/EIS and SDO/AIA observations, we identify the emission components of both the flux rope and the host active region. We then follow the time evolution of the flux rope emission components by using AIA observations. The plasma density and the Doppler and non-thermal velocities associated with the flux ropes are also calculated from the EIS data. Results: The eastern and western parts of the active region, in which the two different fast CMEs originated during two X-class flares, were studied separately. In both regions we identified an emission component in the temperature range of log T = 6.8-7.1 associated with the presence of flux ropes. The time evolution of the eastern region showed an increase in the mean DEM in this temperature range by an order of magnitude, 5 h prior to the first CME. This was associated with a gradual rise and heating of the flux rope as manifested by blue-shifts and increased non-thermal velocities in Ca xv 200.97 Å, respectively. An overall upward motion of the flux ropes was measured (relative blue-shifts of ~12 km s-1). The measured electron density was found to be 4× 109-2 × 1010 cm-3 (using the ratio of Ca xv 181.90 Å over Ca xv 200.97 Å). We compare our findings with other works on the same AR to provide a unified picture of its evolution.The major geoeffective solar eruptions of 2012 March 7: comprehensive Sun-to-Earth analysisPatsourakos, S.Georgoulis, M. K.Vourlidas, A.Nindos, A.Sarris, T.Anagnostopoulos, G.Anastasiadis, A.Chintzoglou, G.Daglis, I. A.Gontikakis, C.Hatzigeorgiu, N.Iliopoulos, A. C.Katsavrias, C.Kouloumvakos, A.Moraitis, K.Nieves-Chinchilla, T.Pavlos, G.Sarafopoulos, D.Syntelis, P.Tsironis, C.Tziotziou, K.Vogiatzis, I. I.Balasis, G.Georgiou, M.Karakatsanis, L. P.Malandraki, O. E.Papadimitriou, C.Odstrčil, D.Pavlos, E. G.Podlachikova, O.Sandberg, I.Turner, D. L.Xenakis, M. N.Sarris, E.Tsinganos, K.Vlahos, L.http://hdl.handle.net/10023/94212018-03-18T01:38:14Z2016-01-19T00:00:00ZDuring the interval 2012 March 7-11 the geospace experienced a barrage of intense space weather phenomena including the second largest geomagnetic storm of solar cycle 24 so far. Significant ultra-low-frequency wave enhancements and relativistic-electron dropouts in the radiation belts, as well as strong energetic-electron injection events in the magnetosphere were observed. These phenomena were ultimately associated with two ultra-fast (>2000 kms-1) coronal mass ejections (CMEs), linked to two X-class flares launched on early 2012 March 7. Given that both powerful events originated from solar active region NOAA 11429 and their onsets were separated by less than an hour, the analysis of the two events and the determination of solar causes and geospace effects are rather challenging. Using satellite data from a flotilla of solar, heliospheric and magnetospheric missions a synergistic Sun-to-Earth study of diverse observational solar, interplanetary and magnetospheric data sets was performed. It was found that only the second CME was Earth-directed. Using a novel method, we estimated its near-Sun magnetic field at 13R⊙ to be in the range [0.01, 0.16] G. Steep radial fall-offs of the near-Sun CME magnetic field are required to match the magnetic fields of the corresponding interplanetary CME (ICME) at 1 AU. Perturbed upstream solar-wind conditions, as resulting from the shock associated with the Earth-directed CME, offer a decent description of its kinematics. The magnetospheric compression caused by the arrival at 1 AU of the shock associated with the ICME was a key factor for radiation-belt dynamics.
2016-01-19T00:00:00ZPatsourakos, S.Georgoulis, M. K.Vourlidas, A.Nindos, A.Sarris, T.Anagnostopoulos, G.Anastasiadis, A.Chintzoglou, G.Daglis, I. A.Gontikakis, C.Hatzigeorgiu, N.Iliopoulos, A. C.Katsavrias, C.Kouloumvakos, A.Moraitis, K.Nieves-Chinchilla, T.Pavlos, G.Sarafopoulos, D.Syntelis, P.Tsironis, C.Tziotziou, K.Vogiatzis, I. I.Balasis, G.Georgiou, M.Karakatsanis, L. P.Malandraki, O. E.Papadimitriou, C.Odstrčil, D.Pavlos, E. G.Podlachikova, O.Sandberg, I.Turner, D. L.Xenakis, M. N.Sarris, E.Tsinganos, K.Vlahos, L.During the interval 2012 March 7-11 the geospace experienced a barrage of intense space weather phenomena including the second largest geomagnetic storm of solar cycle 24 so far. Significant ultra-low-frequency wave enhancements and relativistic-electron dropouts in the radiation belts, as well as strong energetic-electron injection events in the magnetosphere were observed. These phenomena were ultimately associated with two ultra-fast (>2000 kms-1) coronal mass ejections (CMEs), linked to two X-class flares launched on early 2012 March 7. Given that both powerful events originated from solar active region NOAA 11429 and their onsets were separated by less than an hour, the analysis of the two events and the determination of solar causes and geospace effects are rather challenging. Using satellite data from a flotilla of solar, heliospheric and magnetospheric missions a synergistic Sun-to-Earth study of diverse observational solar, interplanetary and magnetospheric data sets was performed. It was found that only the second CME was Earth-directed. Using a novel method, we estimated its near-Sun magnetic field at 13R⊙ to be in the range [0.01, 0.16] G. Steep radial fall-offs of the near-Sun CME magnetic field are required to match the magnetic fields of the corresponding interplanetary CME (ICME) at 1 AU. Perturbed upstream solar-wind conditions, as resulting from the shock associated with the Earth-directed CME, offer a decent description of its kinematics. The magnetospheric compression caused by the arrival at 1 AU of the shock associated with the ICME was a key factor for radiation-belt dynamics.Tracking the evolution of cancer cell populations through the mathematical lens of phenotype-structured equationsLorenzi, TommasoChisholm, Rebecca H.Clairambault, Jeanhttp://hdl.handle.net/10023/93632018-01-07T03:45:20Z2016-08-23T00:00:00ZBackground: A thorough understanding of the ecological and evolutionary mechanisms that drive the phenotypic evolution of neoplastic cells is a timely and key challenge for the cancer research community. In this respect, mathematical modelling can complement experimental cancer research by offering alternative means of understanding the results of in vitro and in vivo experiments, and by allowing for a quick and easy exploration of a variety of biological scenarios through in silico studies. Results: To elucidate the roles of phenotypic plasticity and selection pressures in tumour relapse, we present here a phenotype-structured model of evolutionary dynamics in a cancer cell population which is exposed to the action of a cytotoxic drug. The analytical tractability of our model allows us to investigate how the phenotype distribution, the level of phenotypic heterogeneity, and the size of the cell population are shaped by the strength of natural selection, the rate of random epimutations, the intensity of the competition for limited resources between cells, and the drug dose in use. Conclusions: Our analytical results clarify the conditions for the successful adaptation of cancer cells faced with environmental changes. Furthermore, the results of our analyses demonstrate that the same cell population exposed to different concentrations of the same cytotoxic drug can take different evolutionary trajectories, which culminate in the selection of phenotypic variants characterised by different levels of drug tolerance. This suggests that the response of cancer cells to cytotoxic agents is more complex than a simple binary outcome, i.e., extinction of sensitive cells and selection of highly resistant cells. Also, our mathematical results formalise the idea that the use of cytotoxic agents at high doses can act as a double-edged sword by promoting the outgrowth of drug resistant cellular clones. Overall, our theoretical work offers a formal basis for the development of anti-cancer therapeutic protocols that go beyond the ‘maximum-tolerated-dose paradigm’, as they may be more effective than traditional protocols at keeping the size of cancer cell populations under control while avoiding the expansion of drug tolerant clones.
This work was supported in part by the French National Research Agency through the “ANR blanche” project Kibord [ANR-13-BS01-0004].
2016-08-23T00:00:00ZLorenzi, TommasoChisholm, Rebecca H.Clairambault, JeanBackground: A thorough understanding of the ecological and evolutionary mechanisms that drive the phenotypic evolution of neoplastic cells is a timely and key challenge for the cancer research community. In this respect, mathematical modelling can complement experimental cancer research by offering alternative means of understanding the results of in vitro and in vivo experiments, and by allowing for a quick and easy exploration of a variety of biological scenarios through in silico studies. Results: To elucidate the roles of phenotypic plasticity and selection pressures in tumour relapse, we present here a phenotype-structured model of evolutionary dynamics in a cancer cell population which is exposed to the action of a cytotoxic drug. The analytical tractability of our model allows us to investigate how the phenotype distribution, the level of phenotypic heterogeneity, and the size of the cell population are shaped by the strength of natural selection, the rate of random epimutations, the intensity of the competition for limited resources between cells, and the drug dose in use. Conclusions: Our analytical results clarify the conditions for the successful adaptation of cancer cells faced with environmental changes. Furthermore, the results of our analyses demonstrate that the same cell population exposed to different concentrations of the same cytotoxic drug can take different evolutionary trajectories, which culminate in the selection of phenotypic variants characterised by different levels of drug tolerance. This suggests that the response of cancer cells to cytotoxic agents is more complex than a simple binary outcome, i.e., extinction of sensitive cells and selection of highly resistant cells. Also, our mathematical results formalise the idea that the use of cytotoxic agents at high doses can act as a double-edged sword by promoting the outgrowth of drug resistant cellular clones. Overall, our theoretical work offers a formal basis for the development of anti-cancer therapeutic protocols that go beyond the ‘maximum-tolerated-dose paradigm’, as they may be more effective than traditional protocols at keeping the size of cancer cell populations under control while avoiding the expansion of drug tolerant clones.Evolution of magnetic helicity during eruptive flares and coronal mass ejectionsPriest, Eric RonaldLongcope, D WJanvier, Mhttp://hdl.handle.net/10023/93202018-01-07T03:46:14Z2016-08-01T00:00:00ZDuring eruptive solar flares and coronal mass ejections, a non-potential magnetic arcade with much excess magnetic energy goes unstable and reconnects. It produces a twisted erupting flux rope and leaves behind a sheared arcade of hot coronal loops. We suggest that: the twist of the erupting flux rope can be determined from conservation of magnetic flux and magnetic helicity and equipartition of magnetic helicity. It depends on the geometry of the initial preeruptive structure. Two cases are considered, in the first of which a flux rope is not present initially but is created during the eruption by the reconnection. In the second case, a flux rope is present under the arcade in the pre-eruptive state,and the e.ect of the eruption and reconnection is to add an amount of magnetic helicity that depends on the fluxes of the rope and arcade and the geometry.
Funding: UK STFC, High Altitude Observatory and Montana State University.
2016-08-01T00:00:00ZPriest, Eric RonaldLongcope, D WJanvier, MDuring eruptive solar flares and coronal mass ejections, a non-potential magnetic arcade with much excess magnetic energy goes unstable and reconnects. It produces a twisted erupting flux rope and leaves behind a sheared arcade of hot coronal loops. We suggest that: the twist of the erupting flux rope can be determined from conservation of magnetic flux and magnetic helicity and equipartition of magnetic helicity. It depends on the geometry of the initial preeruptive structure. Two cases are considered, in the first of which a flux rope is not present initially but is created during the eruption by the reconnection. In the second case, a flux rope is present under the arcade in the pre-eruptive state,and the e.ect of the eruption and reconnection is to add an amount of magnetic helicity that depends on the fluxes of the rope and arcade and the geometry.Properties of the prominence magnetic field and plasma distributions as obtained from 3D whole-prominence fine structure modelingGunar, StanislavMackay, Duncan Hendryhttp://hdl.handle.net/10023/92032018-02-11T01:33:43Z2016-08-01T00:00:00ZAims. We analyze distributions of the magnetic field strength and prominence plasma (temperature, pressure, plasma beta, and mass) using the 3D whole-prominence fine structure model. Methods. The model combines a 3D magnetic field configuration of an entire prominence, obtained from non-linear force-free field simulations, with a detailed semi-empirically derived description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Results. We show that in the modeled prominence, the variations of the magnetic field strength and its orientation are insignificant on scales comparable to the smallest dimensions of the observed prominence fine structures. We also show the ability of the 3D whole-prominence fine structure model to reveal the distribution of the prominence plasma, with respect to its temperature within the prominence volume. This provides new insights into the composition of the prominence-corona transition region. We further demonstrate that the values of the plasma beta are small throughout the majority of the modeled prominence when realistic photospheric magnetic flux distributions and prominence plasma parameters are assumed. While this is generally true, we also find that in the region with the deepest magnetic dips, the plasma beta may increase towards unity. Finally, we show that the mass of the modeled prominence plasma is in good agreement with the mass of observed non-eruptive prominences.
2016-08-01T00:00:00ZGunar, StanislavMackay, Duncan HendryAims. We analyze distributions of the magnetic field strength and prominence plasma (temperature, pressure, plasma beta, and mass) using the 3D whole-prominence fine structure model. Methods. The model combines a 3D magnetic field configuration of an entire prominence, obtained from non-linear force-free field simulations, with a detailed semi-empirically derived description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Results. We show that in the modeled prominence, the variations of the magnetic field strength and its orientation are insignificant on scales comparable to the smallest dimensions of the observed prominence fine structures. We also show the ability of the 3D whole-prominence fine structure model to reveal the distribution of the prominence plasma, with respect to its temperature within the prominence volume. This provides new insights into the composition of the prominence-corona transition region. We further demonstrate that the values of the plasma beta are small throughout the majority of the modeled prominence when realistic photospheric magnetic flux distributions and prominence plasma parameters are assumed. While this is generally true, we also find that in the region with the deepest magnetic dips, the plasma beta may increase towards unity. Finally, we show that the mass of the modeled prominence plasma is in good agreement with the mass of observed non-eruptive prominences.Motives and tensions in the release of open educational resources : the UKOER programFalconer, Isobel JessieLittlejohn, AllisonMcGill, LouBeetham, Helenhttp://hdl.handle.net/10023/91662018-01-07T03:42:12Z2016-01-01T00:00:00ZOpen educational resources (OER) have been promoted as a path to universal education, supporting economic development and intercultural dialogue. However, to realise these benefits requires greater understanding of the factors that influence both OER supply and use. This paper examines an aspect of the supply side of the OER lifecycle – the motives prompting release – and the resultant tensions in the release process. It draws evidence from a major program of OER release projects (UKOER) funded by the UK government. The paper sets the UKOER program within the global context of OER initiatives. It uses grounded theory to identify five candidate motive types. Then, by mapping the actions evident in the UKOER program against an organisational framework derived from an activity system, it examines tensions or contradictions encountered by the projects, revealing unstated motives. The findings will be of interest to funders, institutions and educators releasing OER as they reveal potential limitations and barriers to realising the benefits of OER
It gives us pleasure to acknowledge the support of the UK Joint Information Systems Committee and Higher Education Academy, who funded the UKOER projects upon which this paper is based.
2016-01-01T00:00:00ZFalconer, Isobel JessieLittlejohn, AllisonMcGill, LouBeetham, HelenOpen educational resources (OER) have been promoted as a path to universal education, supporting economic development and intercultural dialogue. However, to realise these benefits requires greater understanding of the factors that influence both OER supply and use. This paper examines an aspect of the supply side of the OER lifecycle – the motives prompting release – and the resultant tensions in the release process. It draws evidence from a major program of OER release projects (UKOER) funded by the UK government. The paper sets the UKOER program within the global context of OER initiatives. It uses grounded theory to identify five candidate motive types. Then, by mapping the actions evident in the UKOER program against an organisational framework derived from an activity system, it examines tensions or contradictions encountered by the projects, revealing unstated motives. The findings will be of interest to funders, institutions and educators releasing OER as they reveal potential limitations and barriers to realising the benefits of OERImpact of an L5 magnetograph on nonpotential solar global magnetic field modelingMackay, Duncan HendryYeates, Anthony RobinsonBocquet, Francois-Xavierhttp://hdl.handle.net/10023/91542018-01-07T03:42:02Z2016-07-12T00:00:00ZWe present the first theoretical study to consider what improvement could be obtained in global non-potential modeling of the solar corona if magnetograph data were available from the L5 Lagrange point, in addition to from the direction of Earth. To consider this, we first carry out a "reference Sun'' simulation over two solar cycles. An important property of this simulation is that random bipole emergences are allowed across the entire solar surface at any given time (such as can occur on the Sun). Next we construct two "limited data'' simulations, where bipoles are only included when they could be seen from (i) an Earth-based magnetograph and (ii) either Earth or L5 based magnetographs. The improvement in reproducing the reference Sun simulation when an L5 view is available is quantified through considering global quantities in the limited data simulations. These include surface and polar flux, total magnetic energy, volume electric current, open flux and the number of flux ropes. Results show that when an L5 observational viewpoint is included, the accuracy of the global quantities in the limited data simulations can increase by 26-40%. This clearly shows that a magnetograph at the L5 point could significantly increase the accuracy of global non-potential modeling and with this the accuracy of future space weather forecasts.
2016-07-12T00:00:00ZMackay, Duncan HendryYeates, Anthony RobinsonBocquet, Francois-XavierWe present the first theoretical study to consider what improvement could be obtained in global non-potential modeling of the solar corona if magnetograph data were available from the L5 Lagrange point, in addition to from the direction of Earth. To consider this, we first carry out a "reference Sun'' simulation over two solar cycles. An important property of this simulation is that random bipole emergences are allowed across the entire solar surface at any given time (such as can occur on the Sun). Next we construct two "limited data'' simulations, where bipoles are only included when they could be seen from (i) an Earth-based magnetograph and (ii) either Earth or L5 based magnetographs. The improvement in reproducing the reference Sun simulation when an L5 view is available is quantified through considering global quantities in the limited data simulations. These include surface and polar flux, total magnetic energy, volume electric current, open flux and the number of flux ropes. Results show that when an L5 observational viewpoint is included, the accuracy of the global quantities in the limited data simulations can increase by 26-40%. This clearly shows that a magnetograph at the L5 point could significantly increase the accuracy of global non-potential modeling and with this the accuracy of future space weather forecasts.Explosive fragmentation of liquids in spherical geometryMilne, Alexander MitchellLongbottom, Aaron WilliamFrost, DavidLoiseau, JasonGoroshin, SamuelPetel, Orenhttp://hdl.handle.net/10023/91162018-01-07T03:43:42Z2017-05-01T00:00:00ZRapid acceleration of a spherical shell of liquid following detonation of a high explosive causes the liquid to form fine jets that are similar in appearance to the particle jets that are formed during explosive dispersal of a packed layer of solid particles. Of particular interest is determining the dependence of the scale of the jet-like structures on the physical parameters of the system, including the fluid properties (e.g., density, viscosity, surface tension) and the ratio of the mass of the liquid to that of the explosive. The present paper presents computational results from a multi-material hydrocode describing the dynamics of the explosive dispersal process. The computations are used to track the overall features of the dispersal of the liquid layer, including the wave dynamics, and motion of the spall and accretion layers. The results are compared with experimental results of spherical charges surrounded by a variety of different fluids, including water, glycerol, ethanol, and vegetable oil, which together encompass a significant range of fluid properties. The results show that the number of jet structures is not sensitive to the fluid properties, but primarily dependent on the mass ratio. Above a certain mass ratio of liquid fill to explosive burster (F/B), the number of jets is approximately constant and consistent with an empirical model based on the maximum thickness of the accretion layer. For small values of F/B, the number of liquid jets is reduced, in contrast with explosive powder dispersal, where small F/B yields a larger number of particle jets. A hypothetical explanation of these features based on nucleation of cavitation is explored numerically.
2017-05-01T00:00:00ZMilne, Alexander MitchellLongbottom, Aaron WilliamFrost, DavidLoiseau, JasonGoroshin, SamuelPetel, OrenRapid acceleration of a spherical shell of liquid following detonation of a high explosive causes the liquid to form fine jets that are similar in appearance to the particle jets that are formed during explosive dispersal of a packed layer of solid particles. Of particular interest is determining the dependence of the scale of the jet-like structures on the physical parameters of the system, including the fluid properties (e.g., density, viscosity, surface tension) and the ratio of the mass of the liquid to that of the explosive. The present paper presents computational results from a multi-material hydrocode describing the dynamics of the explosive dispersal process. The computations are used to track the overall features of the dispersal of the liquid layer, including the wave dynamics, and motion of the spall and accretion layers. The results are compared with experimental results of spherical charges surrounded by a variety of different fluids, including water, glycerol, ethanol, and vegetable oil, which together encompass a significant range of fluid properties. The results show that the number of jet structures is not sensitive to the fluid properties, but primarily dependent on the mass ratio. Above a certain mass ratio of liquid fill to explosive burster (F/B), the number of jets is approximately constant and consistent with an empirical model based on the maximum thickness of the accretion layer. For small values of F/B, the number of liquid jets is reduced, in contrast with explosive powder dispersal, where small F/B yields a larger number of particle jets. A hypothetical explanation of these features based on nucleation of cavitation is explored numerically.Impact of flux distribution on elementary heating eventsO'Hara, Jennifer PatriciaDe Moortel, Inekehttp://hdl.handle.net/10023/91092018-01-07T03:44:36Z2016-10-01T00:00:00ZContext. The complex magnetic field on the solar surface has been shown to contain a range of sizes and distributions of magnetic flux structures. The dynamic evolution of this magnetic carpet by photospheric flows provides a continual source of free magnetic energy into the solar atmosphere, that can subsequently be released by magnetic reconnection. Aims. We investigate how the distribution and number of magnetic flux sources impact the energy release and locations of heating through magnetic reconnection driven by slow footpoint motions. Methods. 3D MHD simulations using Lare3D are carried out, where flux-tubes are formed between positive and negative sources placed symmetrically on the lower and upper boundaries of the domain, respectively. The flux-tubes are subjected to rotational driving velocities on the boundaries and are forced to interact and reconnect. Results. Initially, simple flux distributions with two and four sources are compared. In both cases, central current concentrations are formed between the flux-tubes and Ohmic heating occurs. The reconnection and subsequent energy release is delayed in the four source case and is shown to produce more locations of heating, but with smaller magnitudes. Increasing the values of background field between the flux-tubes is shown to delay the onset of reconnection and increases the efficiency of heating in both the two and four source cases. The two flux-tube cases are always more energetic than the corresponding four flux-tube case, however the addition of the background field makes this disparity less significant. A final experiment with a larger number of smaller flux sources is considered and the field evolution and energetics are shown to be remarkably similar to the two source case, indicating the importance of the size and separation of the flux sources relative to the spatial scales of the velocity driver.
This work used the COSMA Data Centric system at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk. This equipment was funded by a BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/K00087X/1, DiRAC Operations grant ST/K003267/1 and Durham University. DiRAC is part of the National E-Infrastructure. I.D.M was funded by the Science and Technology Facilities Council (UK). The research leading to these results has also received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation programme (grant agreement No. 647214). J.O was funded by the Science and Technology Facilities Council (UK) by Doctoral Grant [ST/K502327/1].
2016-10-01T00:00:00ZO'Hara, Jennifer PatriciaDe Moortel, InekeContext. The complex magnetic field on the solar surface has been shown to contain a range of sizes and distributions of magnetic flux structures. The dynamic evolution of this magnetic carpet by photospheric flows provides a continual source of free magnetic energy into the solar atmosphere, that can subsequently be released by magnetic reconnection. Aims. We investigate how the distribution and number of magnetic flux sources impact the energy release and locations of heating through magnetic reconnection driven by slow footpoint motions. Methods. 3D MHD simulations using Lare3D are carried out, where flux-tubes are formed between positive and negative sources placed symmetrically on the lower and upper boundaries of the domain, respectively. The flux-tubes are subjected to rotational driving velocities on the boundaries and are forced to interact and reconnect. Results. Initially, simple flux distributions with two and four sources are compared. In both cases, central current concentrations are formed between the flux-tubes and Ohmic heating occurs. The reconnection and subsequent energy release is delayed in the four source case and is shown to produce more locations of heating, but with smaller magnitudes. Increasing the values of background field between the flux-tubes is shown to delay the onset of reconnection and increases the efficiency of heating in both the two and four source cases. The two flux-tube cases are always more energetic than the corresponding four flux-tube case, however the addition of the background field makes this disparity less significant. A final experiment with a larger number of smaller flux sources is considered and the field evolution and energetics are shown to be remarkably similar to the two source case, indicating the importance of the size and separation of the flux sources relative to the spatial scales of the velocity driver.Null point distribution in global coronal potential field extrapolationsEdwards, S.J.Parnell, C.E.http://hdl.handle.net/10023/90632018-01-07T03:07:36Z2015-07-18T00:00:00ZMagnetic null points are points in space where the magnetic field is zero. Thus, they can be important sites for magnetic reconnection by virtue of the fact that they are weak points in the magnetic field and also because they are associated with topological structures, such as separators, which lie on the boundary between four topologically distinct flux domains and therefore are also locations where reconnection occurs. The number and distribution of nulls in a magnetic field acts as a measure of the complexity of the field. In this article, the numbers and distributions of null points in global potential field extrapolations from high-resolution synoptic magnetograms are examined. Extrapolations from magnetograms obtained with the Michelson Doppler Imager (MDI) are studied in depth and compared with those from high-resolution SOlar Long-time Investigations of the Sun (SOLIS) and Heliospheric Magnetic Imager (HMI). The fall-off in the density of null points with height is found to follow a power law with a slope that differs depending on whether the data are from solar maximum or solar minimum. The distribution of null points with latitude also varies with the cycle as null points form predominantly over quiet-Sun regions and avoid active-region fields. The exception to this rule are the null points that form high in the solar atmosphere, and these null points tend to form over large areas of strong flux in active regions. From case studies of data acquired with the MDI, SOLIS, and HMI, it is found that the distribution of null points is very similar between data sets, except, of course, that there are far fewer nulls observed in the SOLIS data than in the cases from MDI and HMI due to its lower resolution.
SJE would like to thank the Isle of Man Government for support during her PhD and also for the financial support of the STFC.
2015-07-18T00:00:00ZEdwards, S.J.Parnell, C.E.Magnetic null points are points in space where the magnetic field is zero. Thus, they can be important sites for magnetic reconnection by virtue of the fact that they are weak points in the magnetic field and also because they are associated with topological structures, such as separators, which lie on the boundary between four topologically distinct flux domains and therefore are also locations where reconnection occurs. The number and distribution of nulls in a magnetic field acts as a measure of the complexity of the field. In this article, the numbers and distributions of null points in global potential field extrapolations from high-resolution synoptic magnetograms are examined. Extrapolations from magnetograms obtained with the Michelson Doppler Imager (MDI) are studied in depth and compared with those from high-resolution SOlar Long-time Investigations of the Sun (SOLIS) and Heliospheric Magnetic Imager (HMI). The fall-off in the density of null points with height is found to follow a power law with a slope that differs depending on whether the data are from solar maximum or solar minimum. The distribution of null points with latitude also varies with the cycle as null points form predominantly over quiet-Sun regions and avoid active-region fields. The exception to this rule are the null points that form high in the solar atmosphere, and these null points tend to form over large areas of strong flux in active regions. From case studies of data acquired with the MDI, SOLIS, and HMI, it is found that the distribution of null points is very similar between data sets, except, of course, that there are far fewer nulls observed in the SOLIS data than in the cases from MDI and HMI due to its lower resolution.The dependence of coronal loop heating on the characteristics of slow photospheric motionsRitchie, M. L.Wilmot-Smith, A. L.Hornig, G.http://hdl.handle.net/10023/90442018-01-07T03:44:05Z2016-06-06T00:00:00ZThe Parker hypothesis assumes that heating of coronal loops occurs due to reconnection, induced when photospheric motions braid field lines to the point of current sheet formation. In this contribution we address the question of how the nature of photospheric motions affects the heating of braided coronal loops. We design a series of boundary drivers and quantify their properties in terms of complexity and helicity injection. We examine a series of long-duration full resistive MHD simulations in which a simulated coronal loop, consisting of initially uniform field lines, is subject to these photospheric flows. Braiding of the loop is continually driven until differences in behavior induced by the drivers can be characterized. It is shown that heating is crucially dependent on the nature of the photospheric driver—coherent motions typically lead to fewer large energy release events, while more complex motions result in more frequent but less energetic heating events.
2016-06-06T00:00:00ZRitchie, M. L.Wilmot-Smith, A. L.Hornig, G.The Parker hypothesis assumes that heating of coronal loops occurs due to reconnection, induced when photospheric motions braid field lines to the point of current sheet formation. In this contribution we address the question of how the nature of photospheric motions affects the heating of braided coronal loops. We design a series of boundary drivers and quantify their properties in terms of complexity and helicity injection. We examine a series of long-duration full resistive MHD simulations in which a simulated coronal loop, consisting of initially uniform field lines, is subject to these photospheric flows. Braiding of the loop is continually driven until differences in behavior induced by the drivers can be characterized. It is shown that heating is crucially dependent on the nature of the photospheric driver—coherent motions typically lead to fewer large energy release events, while more complex motions result in more frequent but less energetic heating events.A new technique for the photospheric driving of non-potential solar coronal magnetic field simulationsWeinzierl, MarionYeates, AnthonyMackay, Duncan HendryHenney, CarlArge, C. Nickhttp://hdl.handle.net/10023/90432018-01-07T03:39:17Z2016-05-23T00:00:00ZIn this paper, we develop a new technique for driving global non-potential simulations of the Sun's coronal magnetic field solely from sequences of radial magnetic maps of the solar photosphere. A primary challenge to driving such global simulations is that the required horizontal electric field cannot be uniquely determined from such maps. We show that an "inductive" electric field solution similar to that used by previous authors successfully reproduces specific features of the coronal field evolution in both single and multiple bipole simulations. For these cases, the true solution is known because the electric field was generated from a surface flux-transport model. The match for these cases is further improved by including the non-inductive electric field contribution from surface differential rotation. Then, using this reconstruction method for the electric field, we show that a coronal non-potential simulation can be successfully driven from a sequence of ADAPT maps of the photospheric radial field, without including additional physical observations which are not routinely available.
2016-05-23T00:00:00ZWeinzierl, MarionYeates, AnthonyMackay, Duncan HendryHenney, CarlArge, C. NickIn this paper, we develop a new technique for driving global non-potential simulations of the Sun's coronal magnetic field solely from sequences of radial magnetic maps of the solar photosphere. A primary challenge to driving such global simulations is that the required horizontal electric field cannot be uniquely determined from such maps. We show that an "inductive" electric field solution similar to that used by previous authors successfully reproduces specific features of the coronal field evolution in both single and multiple bipole simulations. For these cases, the true solution is known because the electric field was generated from a surface flux-transport model. The match for these cases is further improved by including the non-inductive electric field contribution from surface differential rotation. Then, using this reconstruction method for the electric field, we show that a coronal non-potential simulation can be successfully driven from a sequence of ADAPT maps of the photospheric radial field, without including additional physical observations which are not routinely available.Solar cycle variation of magnetic flux ropes in a quasi-static coronal evolution modelYeates, A. R.Constable, J. A.Martens, P. C. H.http://hdl.handle.net/10023/90372018-01-07T03:43:57Z2010-05-01T00:00:00ZThe structure of electric current and magnetic helicity in the solar corona is closely linked to solar activity over the 11-year cycle, yet is poorly understood. As an alternative to traditional current-free "potential field" extrapolations, we investigate a model for the global coronal magnetic field which is non-potential and time-dependent, following the build-up and transport of magnetic helicity due to flux emergence and large-scale photospheric motions. This helicity concentrates into twisted magnetic flux ropes, which may lose equilibrium and be ejected. Here, we consider how the magnetic structure predicted by this model-in particular the flux ropes-varies over the solar activity cycle, based on photospheric input data from six periods of cycle 23. The number of flux ropes doubles from minimum to maximum, following the total length of photospheric polarity inversion lines. However, the number of flux rope ejections increases by a factor of eight, following the emergence rate of active regions. This is broadly consistent with the observed cycle modulation of coronal mass ejections, although the actual rate of ejections in the simulation is about a fifth of the rate of observed events. The model predicts that, even at minimum, differential rotation will produce sheared, non-potential, magnetic structure at all latitudes.
2010-05-01T00:00:00ZYeates, A. R.Constable, J. A.Martens, P. C. H.The structure of electric current and magnetic helicity in the solar corona is closely linked to solar activity over the 11-year cycle, yet is poorly understood. As an alternative to traditional current-free "potential field" extrapolations, we investigate a model for the global coronal magnetic field which is non-potential and time-dependent, following the build-up and transport of magnetic helicity due to flux emergence and large-scale photospheric motions. This helicity concentrates into twisted magnetic flux ropes, which may lose equilibrium and be ejected. Here, we consider how the magnetic structure predicted by this model-in particular the flux ropes-varies over the solar activity cycle, based on photospheric input data from six periods of cycle 23. The number of flux ropes doubles from minimum to maximum, following the total length of photospheric polarity inversion lines. However, the number of flux rope ejections increases by a factor of eight, following the emergence rate of active regions. This is broadly consistent with the observed cycle modulation of coronal mass ejections, although the actual rate of ejections in the simulation is about a fifth of the rate of observed events. The model predicts that, even at minimum, differential rotation will produce sheared, non-potential, magnetic structure at all latitudes.Coronal density structure and its role in wave damping in loopsCargill, PeterDe Moortel, InekeKiddie, Greghttp://hdl.handle.net/10023/90202018-03-11T01:34:50Z2016-05-19T00:00:00ZIt has long been established that gradients in the Alfvén speed, and in particular the plasma density, are an essential part of the damping of waves in the magnetically closed solar corona by mechanisms such as resonant absorption or phase mixing. While models of wave damping often assume a fixed density gradient, in this paper the self-consistency of such calculations is assessed by examining the temporal evolution of the coronal density. It is shown conceptually that for some coronal structures, density gradients can evolve in a way that the wave damping processes are inhibited. For the case of phase mixing we argue that: (a) wave heating cannot sustain the assumed density structure and (b) inclusion of feedback of the heating on the density gradient can lead to a highly structured density, although on long timescales. In addition, transport coefficients well in excess of classical are required to maintain the observed coronal density. Hence, the heating of closed coronal structures by global oscillations may face problems arising from the assumption of a fixed density gradient and the rapid damping of oscillations may have to be accompanied by a separate (non-wave based) heating mechanism to sustain the required density structuring.
This project has received funding from the Science and Technology Facilities Council (UK) and the European Research Council (ERC) under the European Unionʼs Horizon 2020 research and innovation program (grant agreement No 647214). The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/2007-2013) under the grant agreement SOLSPANET (project No. 269299, www.solspanet.eu/about).
2016-05-19T00:00:00ZCargill, PeterDe Moortel, InekeKiddie, GregIt has long been established that gradients in the Alfvén speed, and in particular the plasma density, are an essential part of the damping of waves in the magnetically closed solar corona by mechanisms such as resonant absorption or phase mixing. While models of wave damping often assume a fixed density gradient, in this paper the self-consistency of such calculations is assessed by examining the temporal evolution of the coronal density. It is shown conceptually that for some coronal structures, density gradients can evolve in a way that the wave damping processes are inhibited. For the case of phase mixing we argue that: (a) wave heating cannot sustain the assumed density structure and (b) inclusion of feedback of the heating on the density gradient can lead to a highly structured density, although on long timescales. In addition, transport coefficients well in excess of classical are required to maintain the observed coronal density. Hence, the heating of closed coronal structures by global oscillations may face problems arising from the assumption of a fixed density gradient and the rapid damping of oscillations may have to be accompanied by a separate (non-wave based) heating mechanism to sustain the required density structuring.From one-dimensional fields to Vlasov equilibria : Theory and application of Hermite PolynomialsAllanson, Oliver DouglasNeukirch, ThomasTroscheit, SaschaWilson, Fionahttp://hdl.handle.net/10023/89922018-01-28T01:33:49Z2016-06-01T00:00:00ZWe consider the theory and application of a solution method for the inverse problem in collisionless equilibria, namely that of calculating a Vlasov-Maxwell equilibrium for a given macroscopic (fluid) equilibrium. Using Jeans' Theorem, the equilibria are expressed as functions of the constants of motion, in the form of a Maxwellian multiplied by an unknown function of the canonical momenta. In this case it is possible to reduce the inverse problem to inverting Weierstrass transforms, which we achieve by using expansions over Hermite Polynomials. Sufficient conditions are found which guarantee the convergence,boundedness and non-negativity of the candidate solution, when satisfied. These conditions are obtained by elementary means, and it is clear how to put them into practice. Illustrative examples of the use of this method with both force-free and non force-free macroscopic equilibria are presented, including the full verification of a recently derived distribution function for the Force-Free Harris Sheet (Allanson et al. (2015)). In the effort to model equilibria with lower values of the plasma beta, solutions for the same macroscopic equilibrium in a new gauge are calculated, with numerical results presented for βpl = 0:05.
2016-06-01T00:00:00ZAllanson, Oliver DouglasNeukirch, ThomasTroscheit, SaschaWilson, FionaWe consider the theory and application of a solution method for the inverse problem in collisionless equilibria, namely that of calculating a Vlasov-Maxwell equilibrium for a given macroscopic (fluid) equilibrium. Using Jeans' Theorem, the equilibria are expressed as functions of the constants of motion, in the form of a Maxwellian multiplied by an unknown function of the canonical momenta. In this case it is possible to reduce the inverse problem to inverting Weierstrass transforms, which we achieve by using expansions over Hermite Polynomials. Sufficient conditions are found which guarantee the convergence,boundedness and non-negativity of the candidate solution, when satisfied. These conditions are obtained by elementary means, and it is clear how to put them into practice. Illustrative examples of the use of this method with both force-free and non force-free macroscopic equilibria are presented, including the full verification of a recently derived distribution function for the Force-Free Harris Sheet (Allanson et al. (2015)). In the effort to model equilibria with lower values of the plasma beta, solutions for the same macroscopic equilibrium in a new gauge are calculated, with numerical results presented for βpl = 0:05.Emergence of non-twisted magnetic fields in the Sun : jets and atmospheric responseSyntelis, P.Archontis, V.Gontikakis, C.Tsinganos, K.http://hdl.handle.net/10023/89902018-01-07T03:43:33Z2015-12-01T00:00:00ZAims. We study the emergence of a non-twisted flux tube from the solar interior into the solar atmosphere. We investigate whether the length of the buoyant part of the flux tube (i.e. λ) affects the emergence of the field and the dynamics of the evolving magnetic flux system. Methods. We perform three-dimensional (3D), time-dependent, resistive, compressible magnetohydrodynamic (MHD) simulations using the Lare3D code. Results. We find that there are considerable differences in the dynamics of the emergence of a magnetic flux tube when λ is varied. In the solar interior, for larger values of λ, the rising magnetic field emerges faster and expands more due to its lower magnetic tension. As a result, its field strength decreases and its emergence above the photosphere occurs later than in the smaller λ case. However, in both cases, the emerging field at the photosphere becomes unstable in two places, forming two magnetic bipoles that interact dynamically during the evolution of the system. Most of the dynamic phenomena occur at the current layer, which is formed at the interface between the interacting bipoles. We find the formation and ejection of plasmoids, the onset of successive jets from the interface, and the impulsive heating of the plasma in the solar atmosphere. We discuss the triggering mechanism of the jets and the atmospheric response to the emergence of magnetic flux in the two cases.
The authors acknowledge support by the EU (IEF-272549 grant) and the Royal Society. The present research has been co-financed by the European Union (European Social Fund-ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF) – Research Funding Program: Thales. Investing in knowledge society through the European Social Fund. This research has also been carried out in the frame of the research program of the RCAAM of the Academy of Athens and has been co-financed by the Program “IKY Scholarships” of the Greek national funds through the Operational Program Education and Lifelong Learning of the NSRF through the European Social Fund of ESPA 2007-2013. Finally, the work reported in this article was additionally supported by the SOLARNET project, funded by the European Commisions FP7 Capacities Program, under the Grant Agreement 312495. The simulations were performed on the STFC and SRIF funded UKMHD cluster, at the University of St Andrews.
2015-12-01T00:00:00ZSyntelis, P.Archontis, V.Gontikakis, C.Tsinganos, K.Aims. We study the emergence of a non-twisted flux tube from the solar interior into the solar atmosphere. We investigate whether the length of the buoyant part of the flux tube (i.e. λ) affects the emergence of the field and the dynamics of the evolving magnetic flux system. Methods. We perform three-dimensional (3D), time-dependent, resistive, compressible magnetohydrodynamic (MHD) simulations using the Lare3D code. Results. We find that there are considerable differences in the dynamics of the emergence of a magnetic flux tube when λ is varied. In the solar interior, for larger values of λ, the rising magnetic field emerges faster and expands more due to its lower magnetic tension. As a result, its field strength decreases and its emergence above the photosphere occurs later than in the smaller λ case. However, in both cases, the emerging field at the photosphere becomes unstable in two places, forming two magnetic bipoles that interact dynamically during the evolution of the system. Most of the dynamic phenomena occur at the current layer, which is formed at the interface between the interacting bipoles. We find the formation and ejection of plasmoids, the onset of successive jets from the interface, and the impulsive heating of the plasma in the solar atmosphere. We discuss the triggering mechanism of the jets and the atmospheric response to the emergence of magnetic flux in the two cases.Spontaneous reconnection at a separator current layer : 2. Nature of the waves and flowsE. H. Stevenson, JulieE. Parnell, Clarehttp://hdl.handle.net/10023/89602018-01-07T03:09:54Z2015-12-01T00:00:00ZSudden destabilisations of the magnetic field, such as those caused by spontaneous reconnection, will produce waves and/or flows. Here, we investigate the nature of the plasma motions resulting from spontaneous reconnection at a 3D separator. In order to clearly see the perturbations generated by the reconnection, we start from a magnetohydrostatic equilibrium containing two oppositely-signed null points joined by a generic separator along which lies a twisted current layer. The nature of the magnetic reconnection initiated in this equilibrium as a result of an anomalous resistivity is discussed in detail in \cite{Stevenson15_jgra}. The resulting sudden loss of force balance inevitably generates waves that propagate away from the diffusion region carrying the dissipated current. In their wake a twisting stagnation-flow, in planes perpendicular to the separator, feeds flux back into the original diffusion site (the separator) in order to try to regain equilibrium. This flow drives a phase of slow weak impulsive-bursty reconnection that follows on after the initial fast-reconnection phase.
JEHS would like to thank STFC for financial support during her Ph.D and continued support after on the St Andrews SMTG’s STFC consortium grant. CEP also acknowledges support from this same grant.
2015-12-01T00:00:00ZE. H. Stevenson, JulieE. Parnell, ClareSudden destabilisations of the magnetic field, such as those caused by spontaneous reconnection, will produce waves and/or flows. Here, we investigate the nature of the plasma motions resulting from spontaneous reconnection at a 3D separator. In order to clearly see the perturbations generated by the reconnection, we start from a magnetohydrostatic equilibrium containing two oppositely-signed null points joined by a generic separator along which lies a twisted current layer. The nature of the magnetic reconnection initiated in this equilibrium as a result of an anomalous resistivity is discussed in detail in \cite{Stevenson15_jgra}. The resulting sudden loss of force balance inevitably generates waves that propagate away from the diffusion region carrying the dissipated current. In their wake a twisting stagnation-flow, in planes perpendicular to the separator, feeds flux back into the original diffusion site (the separator) in order to try to regain equilibrium. This flow drives a phase of slow weak impulsive-bursty reconnection that follows on after the initial fast-reconnection phase.Spontaneous reconnection at a separator current layer : I. Nature of the reconnectionE. H. Stevenson, JulieE. Parnell, Clarehttp://hdl.handle.net/10023/89592018-01-07T03:09:53Z2016-01-27T00:00:00ZMagnetic separators, which lie on the boundary between four topologically-distinct flux domains, are prime locations in three-dimensional magnetic fields for reconnection, especially in the magnetosphere between the planetary and interplanetary magnetic field and also in the solar atmosphere. Little is known about the details of separator reconnection and so the aim of this paper, which is the first of two, is to study the properties of magnetic reconnection at a single separator. Three-dimensional, resistive magnetohydrodynamic numerical experiments are run to study separator reconnection starting from a magnetohydrostatic equilibrium which contains a twisted current layer along a single separator linking a pair of opposite-polarity null points. The resulting reconnection occurs in two phases. The first is short involving rapid-reconnection in which the current at the separator is reduced by a factor of around 2.3. Most ($75\%$) of the magnetic energy is converted during this phase, via Ohmic dissipation, directly into internal energy, with just $0.1\%$ going into kinetic energy. During this phase the reconnection occurs along most of the separator away from its ends (the nulls), but in an asymmetric manner which changes both spatially and temporally over time. The second phase is much longer and involves slow impulsive-bursty reconnection. Again Ohmic heating dominates over viscous damping. Here, the reconnection occurs in small localised bursts at random anywhere along the separator.
2016-01-27T00:00:00ZE. H. Stevenson, JulieE. Parnell, ClareMagnetic separators, which lie on the boundary between four topologically-distinct flux domains, are prime locations in three-dimensional magnetic fields for reconnection, especially in the magnetosphere between the planetary and interplanetary magnetic field and also in the solar atmosphere. Little is known about the details of separator reconnection and so the aim of this paper, which is the first of two, is to study the properties of magnetic reconnection at a single separator. Three-dimensional, resistive magnetohydrodynamic numerical experiments are run to study separator reconnection starting from a magnetohydrostatic equilibrium which contains a twisted current layer along a single separator linking a pair of opposite-polarity null points. The resulting reconnection occurs in two phases. The first is short involving rapid-reconnection in which the current at the separator is reduced by a factor of around 2.3. Most ($75\%$) of the magnetic energy is converted during this phase, via Ohmic dissipation, directly into internal energy, with just $0.1\%$ going into kinetic energy. During this phase the reconnection occurs along most of the separator away from its ends (the nulls), but in an asymmetric manner which changes both spatially and temporally over time. The second phase is much longer and involves slow impulsive-bursty reconnection. Again Ohmic heating dominates over viscous damping. Here, the reconnection occurs in small localised bursts at random anywhere along the separator.SSALMON - the Solar Simulations for the Atacama Large Millimeter Observatory NetworkWedemeyer, S.Bastian, T.Brajša, R.Barta, M.Hudson, H.Fleishman, G.Loukitcheva, M.Fleck, B.Kontar, E.De Pontieu, B.Tiwari, S.Kato, Y.Soler, R.Yagoubov, P.Black, J. H.Antolin, P.Gunár, S.Labrosse, N.Benz, A. O.Nindos, A.Steffen, M.Scullion, E.Doyle, J. G.Zaqarashvili, T.Hanslmeier, A.Nakariakov, V. M.Heinzel, P.Ayres, T.Karlicky, M.http://hdl.handle.net/10023/88742018-01-07T03:02:02Z2015-12-01T00:00:00ZThe Solar Simulations for the Atacama Large Millimeter Observatory Network (SSALMON) was initiated in 2014 in connection with two ALMA development studies. The Atacama Large Millimeter/submillimeter Array (ALMA) is a powerful new tool, which can also observe the Sun at high spatial, temporal, and spectral resolution. The international SSALMONetwork aims at co-ordinating the further development of solar observing modes for ALMA and at promoting scientific opportunities for solar physics with particular focus on numerical simulations, which can provide important constraints for the observing modes and can aid the interpretation of future observations. The radiation detected by ALMA originates mostly in the solar chromosphere – a complex and dynamic layer between the photosphere and corona, which plays an important role in the transport of energy and matter and the heating of the outer layers of the solar atmosphere. Potential targets include active regions, prominences, quiet Sun regions, flares. Here, we give a brief overview over the network and potential science cases for future solar observations with ALMA.
2015-12-01T00:00:00ZWedemeyer, S.Bastian, T.Brajša, R.Barta, M.Hudson, H.Fleishman, G.Loukitcheva, M.Fleck, B.Kontar, E.De Pontieu, B.Tiwari, S.Kato, Y.Soler, R.Yagoubov, P.Black, J. H.Antolin, P.Gunár, S.Labrosse, N.Benz, A. O.Nindos, A.Steffen, M.Scullion, E.Doyle, J. G.Zaqarashvili, T.Hanslmeier, A.Nakariakov, V. M.Heinzel, P.Ayres, T.Karlicky, M.The Solar Simulations for the Atacama Large Millimeter Observatory Network (SSALMON) was initiated in 2014 in connection with two ALMA development studies. The Atacama Large Millimeter/submillimeter Array (ALMA) is a powerful new tool, which can also observe the Sun at high spatial, temporal, and spectral resolution. The international SSALMONetwork aims at co-ordinating the further development of solar observing modes for ALMA and at promoting scientific opportunities for solar physics with particular focus on numerical simulations, which can provide important constraints for the observing modes and can aid the interpretation of future observations. The radiation detected by ALMA originates mostly in the solar chromosphere – a complex and dynamic layer between the photosphere and corona, which plays an important role in the transport of energy and matter and the heating of the outer layers of the solar atmosphere. Potential targets include active regions, prominences, quiet Sun regions, flares. Here, we give a brief overview over the network and potential science cases for future solar observations with ALMA.A computational framework for particle and whole cell tracking applied to a real biological datasetYang, Feng WeiVenkataraman, ChandrasekharStyles, VanessaKuttenberger, VerenaHorn, Eliasvon Guttenberg, ZenoMadzvamuse, Anotidahttp://hdl.handle.net/10023/87832017-11-07T20:30:18Z2016-05-24T00:00:00ZCell tracking is becoming increasingly important in cell biology as it provides a valuable tool for analysing experimental data and hence furthering our understanding of dynamic cellular phenomena. The advent of high-throughput, high-resolution microscopy and imaging techniques means that a wealth of large data is routinely generated in many laboratories. Due to the sheer magnitude of the data involved manual tracking is often cumbersome and the development of computer algorithms for automated cell tracking is thus highly desirable. In this work, we describe two approaches for automated cell tracking. Firstly, we consider particle tracking. We propose a few segmentation techniques for the detection of cells migrating in a non-uniform background, centroids of the segmented cells are then calculated and linked from frame to frame via a nearest-neighbour approach. Secondly, we consider the problem of whole cell tracking in which one wishes to reconstruct in time whole cell morphologies. Our approach is based on fitting a mathematical model to the experimental imaging data with the goal being that the physics encoded in the model is rejected in the reconstructed data. The resulting mathematical problem involves the optimal control of a phase-field formulation of a geometric evolution law. Efficient approximation of this challenging optimal control problem is achieved via advanced numerical methods for the solution of semilinear parabolic partial differential equations (PDEs) coupled with parallelisation and adaptive resolution techniques. Along with a detailed description of our algorithms, a number of simulation results are reported on. We focus on illustrating the effectivity of our approaches by applying the algorithms to the tracking of migrating cells in a dataset which reflects many of the challenges typically encountered in microscopy data.
FY, CV, VS and AM acknowledge support from the Leverhulme Trust Research Project Grant (RPG-2014-149). The work of CV, VS and AM was partially supported by the Engineering and Physical Sciences Research Council, UK grant (EP/J016780/1). This work (AM, ZG, EH, RZ) has also received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642866. The work of CV is partially supported by an EPSRC Impact Accelerator Account award.
2016-05-24T00:00:00ZYang, Feng WeiVenkataraman, ChandrasekharStyles, VanessaKuttenberger, VerenaHorn, Eliasvon Guttenberg, ZenoMadzvamuse, AnotidaCell tracking is becoming increasingly important in cell biology as it provides a valuable tool for analysing experimental data and hence furthering our understanding of dynamic cellular phenomena. The advent of high-throughput, high-resolution microscopy and imaging techniques means that a wealth of large data is routinely generated in many laboratories. Due to the sheer magnitude of the data involved manual tracking is often cumbersome and the development of computer algorithms for automated cell tracking is thus highly desirable. In this work, we describe two approaches for automated cell tracking. Firstly, we consider particle tracking. We propose a few segmentation techniques for the detection of cells migrating in a non-uniform background, centroids of the segmented cells are then calculated and linked from frame to frame via a nearest-neighbour approach. Secondly, we consider the problem of whole cell tracking in which one wishes to reconstruct in time whole cell morphologies. Our approach is based on fitting a mathematical model to the experimental imaging data with the goal being that the physics encoded in the model is rejected in the reconstructed data. The resulting mathematical problem involves the optimal control of a phase-field formulation of a geometric evolution law. Efficient approximation of this challenging optimal control problem is achieved via advanced numerical methods for the solution of semilinear parabolic partial differential equations (PDEs) coupled with parallelisation and adaptive resolution techniques. Along with a detailed description of our algorithms, a number of simulation results are reported on. We focus on illustrating the effectivity of our approaches by applying the algorithms to the tracking of migrating cells in a dataset which reflects many of the challenges typically encountered in microscopy data.Existence, stability and formation of baroclinic triples in quasi-geostrophic flowsReinaud, Jean NoelCarton, Xavierhttp://hdl.handle.net/10023/87702018-01-07T03:09:42Z2015-12-01T00:00:00ZHetons are baroclinic vortices able to transport tracers or species, and which have been observed at sea. This paper studies the offset collision of two identical hetons, often resulting in the formation of a baroclinic tripole, in a continuously stratified quasi-geostrophic model. This process is of interest since it (temporarily or definitely) stops the transport of tracers contained in the hetons. Firstly, the structure, stationarity and nonlinear stability of baroclinic tripoles composed of an upper core and of two lower (symmetric) satellites are studied analytically for point vortices and numerically for finite-area vortices. The condition for stationarity of the point vortices is obtained and it is proven that the baroclinic point tripoles are neutral. Finite-volume stationary tripoles exist with marginal states having very elongated (figure-8) upper core. In the case of vertically distant upper and lower cores, these latter can nearly joint near the center of the plane. These steady states are compared with their two-layer counterparts. Then, the nonlinear evolution of the steady states shows when they are often neutral (showing an oscillatory evolution); when they are unstable, they can either split into two hetons (by breaking of the upper core) or form a single heton (by merger of the lower satellites). These evolutions reflect the linearly unstable modes which can grow on the vorticity poles. Very tall tripoles can break up vertically due to the vertical shear mutually induced by the poles. Finally, the formation of such baroclinic tripoles from the offset collision of two identical hetons is investigated numerically. This formation occurs for hetons offset by less than the internal separation between their poles. The velocity shear during the interaction can lead to substantial filamentation by the upper core, thus forming small, upper satellites, vertically aligned with the lower ones. Finally, in the case of close and flat poles, this shear (or the baroclinic instability of the tripole) can be strong enough that the formed baroclinic tripole is short-lived and that hetons eventually emerge from the collision and drift away.
2015-12-01T00:00:00ZReinaud, Jean NoelCarton, XavierHetons are baroclinic vortices able to transport tracers or species, and which have been observed at sea. This paper studies the offset collision of two identical hetons, often resulting in the formation of a baroclinic tripole, in a continuously stratified quasi-geostrophic model. This process is of interest since it (temporarily or definitely) stops the transport of tracers contained in the hetons. Firstly, the structure, stationarity and nonlinear stability of baroclinic tripoles composed of an upper core and of two lower (symmetric) satellites are studied analytically for point vortices and numerically for finite-area vortices. The condition for stationarity of the point vortices is obtained and it is proven that the baroclinic point tripoles are neutral. Finite-volume stationary tripoles exist with marginal states having very elongated (figure-8) upper core. In the case of vertically distant upper and lower cores, these latter can nearly joint near the center of the plane. These steady states are compared with their two-layer counterparts. Then, the nonlinear evolution of the steady states shows when they are often neutral (showing an oscillatory evolution); when they are unstable, they can either split into two hetons (by breaking of the upper core) or form a single heton (by merger of the lower satellites). These evolutions reflect the linearly unstable modes which can grow on the vorticity poles. Very tall tripoles can break up vertically due to the vertical shear mutually induced by the poles. Finally, the formation of such baroclinic tripoles from the offset collision of two identical hetons is investigated numerically. This formation occurs for hetons offset by less than the internal separation between their poles. The velocity shear during the interaction can lead to substantial filamentation by the upper core, thus forming small, upper satellites, vertically aligned with the lower ones. Finally, in the case of close and flat poles, this shear (or the baroclinic instability of the tripole) can be strong enough that the formed baroclinic tripole is short-lived and that hetons eventually emerge from the collision and drift away.On the stability of continuously stratified quasi-geostrophic hetonsReinaud, Jean Noelhttp://hdl.handle.net/10023/87092018-01-07T02:59:28Z2015-04-30T00:00:00ZIn this paper we examine the stability of quasi-geostrophic hetons in a stably, continuously stratified fluid. To this purpose we first determinate numerically equilibrium states. Equilibrium hetons consist of two vortices of equal and opposite strength lying at different depths that are steadily translating without deforming. The situation is studied through a parameter space comprising the vertical offset between the vortices, their horizontal separation distance and their aspect ratio. The study first shows that the equilibrium vortices are not only strongly deformed in the vertical but that their instability modes are also varying within the height of the structures. The main purpose of the present contribution is to study families of equilibria which stem from the case of two vertically aligned cylindrical vortices. It is however shown that other branches of solutions exist with different properties. The paper concludes that hetons may be sensitive to baroclinic instabilities provided the separation distance between the poles of the hetons is moderate both in the horizontal and in the vertical directions. The hetons become stable and efficient ways to transport properties as fas as the poles are distant from one another. The critical separation distance in a non-trivial function of the radius-to-height aspect ratio of the poles.
2015-04-30T00:00:00ZReinaud, Jean NoelIn this paper we examine the stability of quasi-geostrophic hetons in a stably, continuously stratified fluid. To this purpose we first determinate numerically equilibrium states. Equilibrium hetons consist of two vortices of equal and opposite strength lying at different depths that are steadily translating without deforming. The situation is studied through a parameter space comprising the vertical offset between the vortices, their horizontal separation distance and their aspect ratio. The study first shows that the equilibrium vortices are not only strongly deformed in the vertical but that their instability modes are also varying within the height of the structures. The main purpose of the present contribution is to study families of equilibria which stem from the case of two vertically aligned cylindrical vortices. It is however shown that other branches of solutions exist with different properties. The paper concludes that hetons may be sensitive to baroclinic instabilities provided the separation distance between the poles of the hetons is moderate both in the horizontal and in the vertical directions. The hetons become stable and efficient ways to transport properties as fas as the poles are distant from one another. The critical separation distance in a non-trivial function of the radius-to-height aspect ratio of the poles.Solar prominences embedded in flux ropes : morphological features and dynamics from 3D MHD simulationsTerradas, J.Soler, R.Luna, M.Oliver, R.Ballester, J. L.Wright, Andrew Nicholashttp://hdl.handle.net/10023/87022018-03-04T01:37:37Z2016-03-30T00:00:00ZThe temporal evolution of a solar prominence inserted in a three-dimensional magnetic flux rope is investigated numerically. Using the model of Titov & Démoulin (1999) under the regime of weak twist, the cold and dense prominence counteracts gravity by modifying the initially force-free magnetic configuration. In some cases a quasi-stationary situation is achieved after the relaxation phase, characterized by the excitation of standing vertical oscillations. These oscillations show a strong attenuation with time produced by the mechanism of continuum damping due to the in homogeneous transition between the prominence and solar corona. The characteristic period of the vertical oscillations does not depend strongly on the twist of the flux rope. Nonlinearity is the responsible for triggering the Kelvin-Helmholtz instability associated to the vertical oscillations and that eventually produces horizontal structures. Contrary to other configurations in which the longitudinal axis of the prominence is permeated by a perpendicular magnetic field, like in unsheared arcades, the orientation of the prominence along the flux rope axis prevents the development of Rayleigh-Taylor instabilities and therefore the appearance of vertical structuring along this axis.
J.T. and R.S. acknowledge support from MINECO and UIB through a Ramón y Cajal grant. The authors acknowledge support by the Spanish MINECO and FEDER funds through project AYA2014-54485-P. M.L. acknowledges the support by the Spanish Ministry of Economy and Competitiveness through projects AYA2011-24808, AYA2010-18029, and AYA2014-55078-P. This work contributes to the deliverables identified in FP7 European Research Council grant agreement 277829, “Magnetic Connectivity through the Solar Partially Ionized Atmosphere” (PI: E. Khomenko). M.L., J.T., and J.L.B. also acknowledge support from the International Space Science Institute (ISSI) to the Team 314 on “Large-Amplitude Oscillation in prominences” led by M. Luna.
2016-03-30T00:00:00ZTerradas, J.Soler, R.Luna, M.Oliver, R.Ballester, J. L.Wright, Andrew NicholasThe temporal evolution of a solar prominence inserted in a three-dimensional magnetic flux rope is investigated numerically. Using the model of Titov & Démoulin (1999) under the regime of weak twist, the cold and dense prominence counteracts gravity by modifying the initially force-free magnetic configuration. In some cases a quasi-stationary situation is achieved after the relaxation phase, characterized by the excitation of standing vertical oscillations. These oscillations show a strong attenuation with time produced by the mechanism of continuum damping due to the in homogeneous transition between the prominence and solar corona. The characteristic period of the vertical oscillations does not depend strongly on the twist of the flux rope. Nonlinearity is the responsible for triggering the Kelvin-Helmholtz instability associated to the vertical oscillations and that eventually produces horizontal structures. Contrary to other configurations in which the longitudinal axis of the prominence is permeated by a perpendicular magnetic field, like in unsheared arcades, the orientation of the prominence along the flux rope axis prevents the development of Rayleigh-Taylor instabilities and therefore the appearance of vertical structuring along this axis.Copulae on products of compact Riemannian manifoldsJupp, P.E.http://hdl.handle.net/10023/86722018-01-07T03:01:06Z2015-09-01T00:00:00ZAbstract One standard way of considering a probability distribution on the unit n -cube, [0 , 1]n , due to Sklar (1959), is to decompose it into its marginal distributions and a copula, i.e. a probability distribution on [0 , 1]n with uniform marginals. The definition of copula was extended by Jones et al. (2014) to probability distributions on products of circles. This paper defines a copula as a probability distribution on a product of compact Riemannian manifolds that has uniform marginals. Basic properties of such copulae are established. Two fairly general constructions of copulae on products of compact homogeneous manifolds are given; one is based on convolution in the isometry group, the other using equivariant functions from compact Riemannian manifolds to their spaces of square integrable functions. Examples illustrate the use of copulae to analyse bivariate spherical data and bivariate rotational data.
2015-09-01T00:00:00ZJupp, P.E.Abstract One standard way of considering a probability distribution on the unit n -cube, [0 , 1]n , due to Sklar (1959), is to decompose it into its marginal distributions and a copula, i.e. a probability distribution on [0 , 1]n with uniform marginals. The definition of copula was extended by Jones et al. (2014) to probability distributions on products of circles. This paper defines a copula as a probability distribution on a product of compact Riemannian manifolds that has uniform marginals. Basic properties of such copulae are established. Two fairly general constructions of copulae on products of compact homogeneous manifolds are given; one is based on convolution in the isometry group, the other using equivariant functions from compact Riemannian manifolds to their spaces of square integrable functions. Examples illustrate the use of copulae to analyse bivariate spherical data and bivariate rotational data.The effect of interstitial pressure on therapeutic agent transport : coupling with the tumor blood and lymphatic vascular systemsWu, MinFrieboes, Hermann B.Chaplain, Mark A. J.McDougall, Steven R.Cristini, VittorioLowengrub, John S.http://hdl.handle.net/10023/86482018-03-18T01:35:52Z2014-08-21T00:00:00ZVascularized tumor growth is characterized by both abnormal interstitial fluid flow and the associated interstitial fluid pressure (IFP). Here, we study the effect that these conditions have on the transport of therapeutic agents during chemotherapy. We apply our recently developed vascular tumor growth model which couples a continuous growth component with a discrete angiogenesis model to show that hypertensive IFP is a physical barrier that may hinder vascular extravasation of agents through transvascular fluid flux convection, which drives the agents away from the tumor. This result is consistent with previous work using simpler models without blood flow or lymphatic drainage. We consider the vascular/interstitial/lymphatic fluid dynamics to show that tumors with larger lymphatic resistance increase the agent concentration more rapidly while also experiencing faster washout. In contrast, tumors with smaller lymphatic resistance accumulate less agents but are able to retain them for a longer time. The agent availability (area-under-the curve, or AUC) increases for less permeable agents as lymphatic resistance increases, and correspondingly decreases for more permeable agents. We also investigate the effect of vascular pathologies on agent transport. We show that elevated vascular hydraulic conductivity contributes to the highest AUC when the agent is less permeable, but to lower AUC when the agent is more permeable. We find that elevated interstitial hydraulic conductivity contributes to low AUC in general regardless of the transvascular agent transport capability. We also couple the agent transport with the tumor dynamics to simulate chemotherapy with the same vascularized tumor under different vascular pathologies. We show that tumors with an elevated interstitial hydraulic conductivity alone require the strongest dosage to shrink. We further show that tumors with elevated vascular hydraulic conductivity are more hypoxic during therapy and that the response slows down as the tumor shrinks due to the heterogeneity and low concentration of agents in the tumor interior compared with the cases where other pathological effects may combine to flatten the IFP and thus reduce the heterogeneity. We conclude that dual normalizations of the micronevironment ? both the vasculature and the interstitium ? are needed to maximize the effects of chemotherapy, while normalization of only one of these may be insufficient to overcome the physical resistance and may thus lead to sub-optimal outcomes.
2014-08-21T00:00:00ZWu, MinFrieboes, Hermann B.Chaplain, Mark A. J.McDougall, Steven R.Cristini, VittorioLowengrub, John S.Vascularized tumor growth is characterized by both abnormal interstitial fluid flow and the associated interstitial fluid pressure (IFP). Here, we study the effect that these conditions have on the transport of therapeutic agents during chemotherapy. We apply our recently developed vascular tumor growth model which couples a continuous growth component with a discrete angiogenesis model to show that hypertensive IFP is a physical barrier that may hinder vascular extravasation of agents through transvascular fluid flux convection, which drives the agents away from the tumor. This result is consistent with previous work using simpler models without blood flow or lymphatic drainage. We consider the vascular/interstitial/lymphatic fluid dynamics to show that tumors with larger lymphatic resistance increase the agent concentration more rapidly while also experiencing faster washout. In contrast, tumors with smaller lymphatic resistance accumulate less agents but are able to retain them for a longer time. The agent availability (area-under-the curve, or AUC) increases for less permeable agents as lymphatic resistance increases, and correspondingly decreases for more permeable agents. We also investigate the effect of vascular pathologies on agent transport. We show that elevated vascular hydraulic conductivity contributes to the highest AUC when the agent is less permeable, but to lower AUC when the agent is more permeable. We find that elevated interstitial hydraulic conductivity contributes to low AUC in general regardless of the transvascular agent transport capability. We also couple the agent transport with the tumor dynamics to simulate chemotherapy with the same vascularized tumor under different vascular pathologies. We show that tumors with an elevated interstitial hydraulic conductivity alone require the strongest dosage to shrink. We further show that tumors with elevated vascular hydraulic conductivity are more hypoxic during therapy and that the response slows down as the tumor shrinks due to the heterogeneity and low concentration of agents in the tumor interior compared with the cases where other pathological effects may combine to flatten the IFP and thus reduce the heterogeneity. We conclude that dual normalizations of the micronevironment ? both the vasculature and the interstitium ? are needed to maximize the effects of chemotherapy, while normalization of only one of these may be insufficient to overcome the physical resistance and may thus lead to sub-optimal outcomes.Recent advances in coronal heatingDe Moortel, I.Browning, P.http://hdl.handle.net/10023/86432018-03-18T01:35:39Z2015-05-28T00:00:00ZThe solar corona, the tenuous outer atmosphere of the Sun, is orders of magnitude hotter than the solar surface. This 'coronal heating problem' requires the identification of a heat source to balance losses due to thermal conduction, radiation and (in some locations) convection. The review papers in this Theo Murphy meeting issue present an overview of recent observational findings, large- and small-scale numerical modelling of physical processes occurring in the solar atmosphere and other aspects which may affect our understanding of the proposed heating mechanisms. At the same time, they also set out the directions and challenges which must be tackled by future research. In this brief introduction, we summarize some of the issues and themes which reoccur throughout this issue.
2015-05-28T00:00:00ZDe Moortel, I.Browning, P.The solar corona, the tenuous outer atmosphere of the Sun, is orders of magnitude hotter than the solar surface. This 'coronal heating problem' requires the identification of a heat source to balance losses due to thermal conduction, radiation and (in some locations) convection. The review papers in this Theo Murphy meeting issue present an overview of recent observational findings, large- and small-scale numerical modelling of physical processes occurring in the solar atmosphere and other aspects which may affect our understanding of the proposed heating mechanisms. At the same time, they also set out the directions and challenges which must be tackled by future research. In this brief introduction, we summarize some of the issues and themes which reoccur throughout this issue.Is magnetic topology important for heating the solar atmosphere?E. Parnell, C.E. H. Stevenson, J.Threlfall, J.J. Edwards, S.http://hdl.handle.net/10023/86422018-01-07T03:01:38Z2015-05-21T00:00:00ZMagnetic fields permeate the entire solar atmosphere weaving an extremely complex pattern on both local and global scales. In order to understand the nature of this tangled web of magnetic fields, its magnetic skeleton, which forms the boundaries between topologically distinct flux domains, may be determined. The magnetic skeleton consists of null points, separatrix surfaces, spines and separators. The skeleton is often used to clearly visualize key elements of the magnetic configuration, but parts of the skeleton are also locations where currents and waves may collect and dissipate. In this review, the nature of the magnetic skeleton on both global and local scales, over solar cycle time scales, is explained. The behaviour of wave pulses in the vicinity of both nulls and separators is discussed and so too is the formation of current layers and reconnection at the same features. Each of these processes leads to heating of the solar atmosphere, but collectively do they provide enough heat, spread over a wide enough area, to explain the energy losses throughout the solar atmosphere? Here, we consider this question for the three different solar regions: active regions, open-field regions and the quiet Sun. We find that the heating of active regions and open-field regions is highly unlikely to be due to reconnection or wave dissipation at topological features, but it is possible that these may play a role in the heating of the quiet Sun. In active regions, the absence of a complex topology may play an important role in allowing large energies to build up and then, subsequently, be explosively released in the form of a solar flare. Additionally, knowledge of the intricate boundaries of open-field regions (which the magnetic skeleton provides) could be very important in determining the main acceleration mechanism(s) of the solar wind.
CEP and JT acknowledge the support of STFC through the St Andrew’s SMTG consolidated grant. JEHS is supported by STFC as a PhD student. SJE is supported STFC through the Durham University Impact Acceleration Account.
2015-05-21T00:00:00ZE. Parnell, C.E. H. Stevenson, J.Threlfall, J.J. Edwards, S.Magnetic fields permeate the entire solar atmosphere weaving an extremely complex pattern on both local and global scales. In order to understand the nature of this tangled web of magnetic fields, its magnetic skeleton, which forms the boundaries between topologically distinct flux domains, may be determined. The magnetic skeleton consists of null points, separatrix surfaces, spines and separators. The skeleton is often used to clearly visualize key elements of the magnetic configuration, but parts of the skeleton are also locations where currents and waves may collect and dissipate. In this review, the nature of the magnetic skeleton on both global and local scales, over solar cycle time scales, is explained. The behaviour of wave pulses in the vicinity of both nulls and separators is discussed and so too is the formation of current layers and reconnection at the same features. Each of these processes leads to heating of the solar atmosphere, but collectively do they provide enough heat, spread over a wide enough area, to explain the energy losses throughout the solar atmosphere? Here, we consider this question for the three different solar regions: active regions, open-field regions and the quiet Sun. We find that the heating of active regions and open-field regions is highly unlikely to be due to reconnection or wave dissipation at topological features, but it is possible that these may play a role in the heating of the quiet Sun. In active regions, the absence of a complex topology may play an important role in allowing large energies to build up and then, subsequently, be explosively released in the form of a solar flare. Additionally, knowledge of the intricate boundaries of open-field regions (which the magnetic skeleton provides) could be very important in determining the main acceleration mechanism(s) of the solar wind.Depletion of nonlinearity in the pressure force driving Navier-Stokes flows : nonlinear depletion in NS flowsTran, Chuong VanYu, Xinweihttp://hdl.handle.net/10023/86202018-01-07T02:58:20Z2015-04-17T00:00:00ZThe dynamics of the velocity norms ||u||Lq for q ≥ 3, in Navier-Stokes flows is studied. The pressure term that drives this dynamics has a high degree of nonlinear depletion, which owes its origin to a genuine negative correlation between |u| and |∇|u||, among other things. Under viscous effects, such depletion may give rise to mild growth of ||u||Lq. We explore the possibility of non-singular growth of ||u||Lq.
2015-04-17T00:00:00ZTran, Chuong VanYu, XinweiThe dynamics of the velocity norms ||u||Lq for q ≥ 3, in Navier-Stokes flows is studied. The pressure term that drives this dynamics has a high degree of nonlinear depletion, which owes its origin to a genuine negative correlation between |u| and |∇|u||, among other things. Under viscous effects, such depletion may give rise to mild growth of ||u||Lq. We explore the possibility of non-singular growth of ||u||Lq.Memory versus effector immune responses in oncolytic virotherapiesMacnamara, Cicely KrystynaEftimie, Ralucahttp://hdl.handle.net/10023/86042018-01-07T03:32:46Z2015-07-21T00:00:00ZThe main priority when designing cancer immuno-therapies has been to seek viable biological mechanisms that lead to permanent cancer eradication or cancer control. Understanding the delicate balance between the role of effector and memory cells on eliminating cancer cells remains an elusive problem in immunology. Here we make an initial investigation into this problem with the help of a mathematical model for oncolytic virotherapy; although the model can in fact be made general enough to be applied also to other immunological problems. Our results show that long-term cancer control is associated with a large number of persistent effector cells (irrespective of the initial peak in effector cell numbers). However, this large number of persistent effector cells is sustained by a relatively large number of memory cells. Moreover, we show that cancer control from a dormant state cannot be predicted by the size of the memory population.
R.E. acknowledges support from an Engineering and Physical Sciences Research Council (UK) First Grant number EP/K033689/1
2015-07-21T00:00:00ZMacnamara, Cicely KrystynaEftimie, RalucaThe main priority when designing cancer immuno-therapies has been to seek viable biological mechanisms that lead to permanent cancer eradication or cancer control. Understanding the delicate balance between the role of effector and memory cells on eliminating cancer cells remains an elusive problem in immunology. Here we make an initial investigation into this problem with the help of a mathematical model for oncolytic virotherapy; although the model can in fact be made general enough to be applied also to other immunological problems. Our results show that long-term cancer control is associated with a large number of persistent effector cells (irrespective of the initial peak in effector cell numbers). However, this large number of persistent effector cells is sustained by a relatively large number of memory cells. Moreover, we show that cancer control from a dormant state cannot be predicted by the size of the memory population.On the late-time behaviour of a bounded, inviscid two-dimensional flowDritschel, David GerardQi, WanmingMarston, J.B.http://hdl.handle.net/10023/86032018-01-07T03:08:14Z2015-11-01T00:00:00ZUsing complementary numerical approaches at high resolution, we study the late-time behaviour of an inviscid incompressible two-dimensional flow on the surface of a sphere. Starting from a random initial vorticity field comprised of a small set of intermediate-wavenumber spherical harmonics, we find that, contrary to the predictions of equilibrium statistical mechanics, the flow does not evolve into a large-scale steady state. Instead, significant unsteadiness persists, characterised by a population of persistent small-scale vortices interacting with a large-scale oscillating quadrupolar vorticity field. Moreover, the vorticity develops a stepped, staircase distribution, consisting of nearly homogeneous regions separated by sharp gradients. The persistence of unsteadiness is explained by a simple point-vortex model characterising the interactions between the four main vortices which emerge.
We thank the Kavli Institute for Theoretical Physics for supporting our participation in the 2014 Program “Wave-Flow Interaction in Geophysics, Climate, Astrophysics, and Plasmas” where this work was initiated. The KITP is supported in part by the NSF Grant No. NSF PHY11-25915. This work was also supported in part by the NSF under grant Nos. DMR-1306806 and CCF-1048701 (JBM and WQ).
2015-11-01T00:00:00ZDritschel, David GerardQi, WanmingMarston, J.B.Using complementary numerical approaches at high resolution, we study the late-time behaviour of an inviscid incompressible two-dimensional flow on the surface of a sphere. Starting from a random initial vorticity field comprised of a small set of intermediate-wavenumber spherical harmonics, we find that, contrary to the predictions of equilibrium statistical mechanics, the flow does not evolve into a large-scale steady state. Instead, significant unsteadiness persists, characterised by a population of persistent small-scale vortices interacting with a large-scale oscillating quadrupolar vorticity field. Moreover, the vorticity develops a stepped, staircase distribution, consisting of nearly homogeneous regions separated by sharp gradients. The persistence of unsteadiness is explained by a simple point-vortex model characterising the interactions between the four main vortices which emerge.Whole cell tracking through the optimal control of geometric evolution lawsBlazakis, Konstantinos N.Madzvamuse, AnotidaReyes-Aldasoro, Constantino CarlosStyles, VanessaVenkataraman, Chandrasekharhttp://hdl.handle.net/10023/85822018-01-07T03:33:31Z2015-09-15T00:00:00ZCell tracking algorithms which automate and systematise the analysis of time lapse image data sets of cells are an indispensable tool in the modelling and understanding of cellular phenomena. In this study we present a theoretical framework and an algorithm for whole cell tracking. Within this work we consider that "tracking" is equivalent to a dynamic reconstruction of the whole cell data (morphologies) from static image data sets. The novelty of our work is that the tracking algorithm is driven by a model for the motion of the cell. This model may be regarded as a simplification of a recently developed physically meaningful model for cell motility. The resulting problem is the optimal control of a geometric evolution law and we discuss the formulation and numerical approximation of the optimal control problem. The overall goal of this work is to design a framework for cell tracking within which the recovered data reflects the physics of the forward model. A number of numerical simulations are presented that illustrate the applicability of our approach.
This work (A.M., V.S. and C.V.) is supported by the Engineering and Physical Sciences Research Council, UK grant (EP/J016780/1) and the Leverhulme Trust Research Project Grant (RPG-2014-149). K.B. was partially supported by the Embirikion Foundation Grant (2011-2014) – Greece.
2015-09-15T00:00:00ZBlazakis, Konstantinos N.Madzvamuse, AnotidaReyes-Aldasoro, Constantino CarlosStyles, VanessaVenkataraman, ChandrasekharCell tracking algorithms which automate and systematise the analysis of time lapse image data sets of cells are an indispensable tool in the modelling and understanding of cellular phenomena. In this study we present a theoretical framework and an algorithm for whole cell tracking. Within this work we consider that "tracking" is equivalent to a dynamic reconstruction of the whole cell data (morphologies) from static image data sets. The novelty of our work is that the tracking algorithm is driven by a model for the motion of the cell. This model may be regarded as a simplification of a recently developed physically meaningful model for cell motility. The resulting problem is the optimal control of a geometric evolution law and we discuss the formulation and numerical approximation of the optimal control problem. The overall goal of this work is to design a framework for cell tracking within which the recovered data reflects the physics of the forward model. A number of numerical simulations are presented that illustrate the applicability of our approach.Solar coronal electron heating by short-wavelength dispersive shear Alfvén wavesBingham, R.Shukla, P. K.Eliasson, B.Cairns, A.Cairns, R Alanhttp://hdl.handle.net/10023/85812018-01-07T03:30:27Z2015-09-15T00:00:00ZThe electron heating of the solar coronal plasma has remained one of the most important problems in solar physics. An explanation of the electron heating rests on the identification of the energy source and appropriate physical mechanisms via which the energy can be channelled to the electrons. Our objective here is to present an estimate for the electron heating rate in the presence of finite amplitude short-wavelength (in comparison with the ion gyroradius) dispersive shear Alfven (SWDSA) waves that propagate obliquely to the ambient magnetic field direction in the solar corona. Specifically, it is demonstrated that SWDSA waves can significantly contribute to the solar coronal electron heating via collisionless heating involving SWDSA wave-electron interactions.
This work was partially supported by the STFC through the Centre for Fundamental Physics (CfFP) at Rutherford Appleton Laboratory, Chilton, Didcot, UK. BE acknowledges support by the Engineering and Physical Sciences Research Council (EPSRC), UK, Grant no EP/M009386/1.
2015-09-15T00:00:00ZBingham, R.Shukla, P. K.Eliasson, B.Cairns, A.Cairns, R AlanThe electron heating of the solar coronal plasma has remained one of the most important problems in solar physics. An explanation of the electron heating rests on the identification of the energy source and appropriate physical mechanisms via which the energy can be channelled to the electrons. Our objective here is to present an estimate for the electron heating rate in the presence of finite amplitude short-wavelength (in comparison with the ion gyroradius) dispersive shear Alfven (SWDSA) waves that propagate obliquely to the ambient magnetic field direction in the solar corona. Specifically, it is demonstrated that SWDSA waves can significantly contribute to the solar coronal electron heating via collisionless heating involving SWDSA wave-electron interactions.The role of dimerisation and nuclear transport in the Hes1 gene regulatory networkSturrock, MarcHellander, AndreasAldakheel, SaharPetzold, LindaChaplain, Mark A. J.http://hdl.handle.net/10023/84582018-01-14T01:34:02Z2014-04-01T00:00:00ZHes1 is a member of the family of basic helix-loop-helix transcription factors and the Hes1 gene regulatory network (GRN) may be described as the canonical example of transcriptional control in eukaryotic cells, since it involves only the Hes1 protein and its own mRNA. Recently, the Hes1 protein has been established as an excellent target for an anti-cancer drug treatment, with the design of a small molecule Hes1 dimerisation inhibitor representing a promising if challenging approach to therapy. In this paper, we extend a previous spatial stochastic model of the Hes1 GRN to include nuclear transport and dimerisation of Hes1 monomers. Initially, we assume that dimerisation occurs only in the cytoplasm, with only dimers being imported into the nucleus. Stochastic simulations of this novel model using the URDME software show that oscillatory dynamics in agreement with experimental studies are retained. Furthermore, we find that our model is robust to changes in the nuclear transport and dimerisation parameters. However, since the precise dynamics of the nuclear import of Hes1 and the localisation of the dimerisation reaction are not known, we consider a second modelling scenario in which we allow for both Hes1 monomers and dimers to be imported into the nucleus, and we allow dimerisation of Hes1 to occur everywhere in the cell. Once again, computational solutions of this second model produce oscillatory dynamics in agreement with experimental studies. We also explore sensitivity of the numerical solutions to nuclear transport and dimerisation parameters. Finally, we compare and contrast the two different modelling scenarios using numerical experiments that simulate dimer disruption, and suggest a biological experiment that could distinguish which model more faithfully captures the Hes1 GRN.
2014-04-01T00:00:00ZSturrock, MarcHellander, AndreasAldakheel, SaharPetzold, LindaChaplain, Mark A. J.Hes1 is a member of the family of basic helix-loop-helix transcription factors and the Hes1 gene regulatory network (GRN) may be described as the canonical example of transcriptional control in eukaryotic cells, since it involves only the Hes1 protein and its own mRNA. Recently, the Hes1 protein has been established as an excellent target for an anti-cancer drug treatment, with the design of a small molecule Hes1 dimerisation inhibitor representing a promising if challenging approach to therapy. In this paper, we extend a previous spatial stochastic model of the Hes1 GRN to include nuclear transport and dimerisation of Hes1 monomers. Initially, we assume that dimerisation occurs only in the cytoplasm, with only dimers being imported into the nucleus. Stochastic simulations of this novel model using the URDME software show that oscillatory dynamics in agreement with experimental studies are retained. Furthermore, we find that our model is robust to changes in the nuclear transport and dimerisation parameters. However, since the precise dynamics of the nuclear import of Hes1 and the localisation of the dimerisation reaction are not known, we consider a second modelling scenario in which we allow for both Hes1 monomers and dimers to be imported into the nucleus, and we allow dimerisation of Hes1 to occur everywhere in the cell. Once again, computational solutions of this second model produce oscillatory dynamics in agreement with experimental studies. We also explore sensitivity of the numerical solutions to nuclear transport and dimerisation parameters. Finally, we compare and contrast the two different modelling scenarios using numerical experiments that simulate dimer disruption, and suggest a biological experiment that could distinguish which model more faithfully captures the Hes1 GRN.Effects of thermal conduction and compressive viscosity on the period ratio of the slow modeMacnamara, Cicely KrystynaRoberts, Bernardhttp://hdl.handle.net/10023/84232018-01-07T03:37:23Z2010-06-01T00:00:00ZAims: Increasing observational evidence of wave modes brings us to a closer understanding of the solar corona. Coronal seismology allows us to combine wave observations and theory to determine otherwise unknown parameters. The period ratio, P1/2P2, between the period P1 of the fundamental mode and the period P2 of its first overtone, is one such tool of coronal seismology and its departure from unity provides information about the structure of the corona. Methods: We consider analytically the effects of thermal conduction and compressive viscosity on the period ratio for a longitudinally propagating sound wave. Results: For coronal values of thermal conduction the effect on the period ratio is negligible. For compressive viscosity the effect on the period ratio may become important for some short hot loops. Conclusions: Damping typically has a small effect on the period ratio, suggesting that longitudinal structuring remains the most significant effect.
C.K.M. acknowledges financial support from the CarnegieTrust. Discussions with Dr. I. De Moortel and Prof. A. W. Hood are gratefully acknowledged
2010-06-01T00:00:00ZMacnamara, Cicely KrystynaRoberts, BernardAims: Increasing observational evidence of wave modes brings us to a closer understanding of the solar corona. Coronal seismology allows us to combine wave observations and theory to determine otherwise unknown parameters. The period ratio, P1/2P2, between the period P1 of the fundamental mode and the period P2 of its first overtone, is one such tool of coronal seismology and its departure from unity provides information about the structure of the corona. Methods: We consider analytically the effects of thermal conduction and compressive viscosity on the period ratio for a longitudinally propagating sound wave. Results: For coronal values of thermal conduction the effect on the period ratio is negligible. For compressive viscosity the effect on the period ratio may become important for some short hot loops. Conclusions: Damping typically has a small effect on the period ratio, suggesting that longitudinal structuring remains the most significant effect.Particle-in-cell simulations of collisionless magnetic reconnection with a non-uniform guide fieldWilson, FionaNeukirch, ThomasHesse, MichaelHarrison, Michael G.Stark, Craig R.http://hdl.handle.net/10023/83862018-01-07T03:33:55Z2016-03-01T00:00:00ZResults are presented of a first study of collisionless magnetic reconnection starting from a recently found exact nonlinear force-free Vlasov-Maxwell equilibrium. The initial state has a Harris sheet magnetic field profile in one direction and a non-uniform guide field in a second direction, resulting in a spatially constant magnetic field strength as well as a constant initial plasma density and plasma pressure. It is found that the reconnection process initially resembles guide field reconnection, but that a gradual transition to anti-parallel reconnection happens as the system evolves. The time evolution of a number of plasma parameters is investigated, and the results are compared with simulations starting from a Harris sheet equilibrium and a Harris sheet plus constant guide field equilibrium.
2016-03-01T00:00:00ZWilson, FionaNeukirch, ThomasHesse, MichaelHarrison, Michael G.Stark, Craig R.Results are presented of a first study of collisionless magnetic reconnection starting from a recently found exact nonlinear force-free Vlasov-Maxwell equilibrium. The initial state has a Harris sheet magnetic field profile in one direction and a non-uniform guide field in a second direction, resulting in a spatially constant magnetic field strength as well as a constant initial plasma density and plasma pressure. It is found that the reconnection process initially resembles guide field reconnection, but that a gradual transition to anti-parallel reconnection happens as the system evolves. The time evolution of a number of plasma parameters is investigated, and the results are compared with simulations starting from a Harris sheet equilibrium and a Harris sheet plus constant guide field equilibrium.Apparent cross-field superslow propagation of magnetohydrodynamic waves in solar plasmasKaneko, TGoossens, MarcelSoler, RobertoTerradas, JaumeVan Doorsselaere, TomYokoyama, TWright, Andrew Nicholashttp://hdl.handle.net/10023/83772018-03-04T01:36:38Z2015-10-15T00:00:00ZIn this paper we show that the phase mixing of continuum Alfvén waves and/or continuum slow waves in magnetic structures of the solar atmosphere as, e.g., coronal arcades, can create the illusion of wave propagation across the magnetic eld. This phenomenon could be erroneously interpreted as fast mag- netosonic waves. The cross-field propagation due to phase mixing of continuum waves is apparent because there is no real propagation of energy across the magnetic surfaces. We investigate the continuous Alfvén and slow spectra in 2D Cartesian equilibrium models with a purely poloidal magnetic field. We show that apparent superslow propagation across the magnetic surfaces in solar coronal structures is a consequence of the existence of continuum Alfvén waves and continuum slow waves that naturally live on those structures and phase mix as time evolves. The apparent cross-field phase velocity is related to the spatial variation of the local Alfvén/slow frequency across the magnetic surfaces and is slower than the Alfvén/sound velocities for typical coronal conditions. Understanding the nature of the apparent cross-field propagation is important for the correct analysis of numerical simulations and the correct interpretation of observations.
TK was supported by the Program for Leading Graduate School, MEXT, Japan. This work was supported by JSPS KAKENHI Grant Number 15H03640. RS acknowledges support from MINECO through project AYA2014-54485-P and from FEDER funds. RS also acknowledges support from MINECO through a ‘Juan de la Cierva’ grant, from MECD through project CEF11-0012, and from the ‘Vicerectorat d’Investigació Postgrau’ of the UIB. JT acknowledges support from the Spanish Ministerio de Educación y Ciencia through a Ramón y Cajal grant. JT acknowledges support from MINECO through project AYA2014-54485-P and from FEDER funds. MG was supported by IAP P7/08 CHARM (Belspo) and the GOA-2015-014 (KU Leuven). TVD was supported by an Odysseus grant of the FWO Vlaanderen, the IAP P7/08 CHARM (Belspo) and the GOA-2015-014 (KU Leuven)
2015-10-15T00:00:00ZKaneko, TGoossens, MarcelSoler, RobertoTerradas, JaumeVan Doorsselaere, TomYokoyama, TWright, Andrew NicholasIn this paper we show that the phase mixing of continuum Alfvén waves and/or continuum slow waves in magnetic structures of the solar atmosphere as, e.g., coronal arcades, can create the illusion of wave propagation across the magnetic eld. This phenomenon could be erroneously interpreted as fast mag- netosonic waves. The cross-field propagation due to phase mixing of continuum waves is apparent because there is no real propagation of energy across the magnetic surfaces. We investigate the continuous Alfvén and slow spectra in 2D Cartesian equilibrium models with a purely poloidal magnetic field. We show that apparent superslow propagation across the magnetic surfaces in solar coronal structures is a consequence of the existence of continuum Alfvén waves and continuum slow waves that naturally live on those structures and phase mix as time evolves. The apparent cross-field phase velocity is related to the spatial variation of the local Alfvén/slow frequency across the magnetic surfaces and is slower than the Alfvén/sound velocities for typical coronal conditions. Understanding the nature of the apparent cross-field propagation is important for the correct analysis of numerical simulations and the correct interpretation of observations.Stability analysis and simulations of coupled bulk-surface reaction-diffusion systemsMadzvamuse, AnotidaChung, Andy H. W.Venkataraman, Chandrasekharhttp://hdl.handle.net/10023/83492018-01-14T01:34:48Z2015-03-08T00:00:00ZIn this article, we formulate new models for coupled systems of bulk-surface reaction-diffusion equations on stationary volumes. The bulk reaction-diffusion equations are coupled to the surface reaction-diffusion equations through linear Robin-type boundary conditions. We then state and prove the necessary conditions for diffusion-driven instability for the coupled system. Owing to the nature of the coupling between bulk and surface dynamics, we are able to decouple the stability analysis of the bulk and surface dynamics. Under a suitable choice of model parameter values, the bulk reaction-diffusion system can induce patterning on the surface independent of whether the surface reaction-diffusion system produces or not, patterning. On the other hand, the surface reaction-diffusion system cannot generate patterns everywhere in the bulk in the absence of patterning from the bulk reaction-diffusion system. For this case, patterns can be induced only in regions close to the surface membrane. Various numerical experiments are presented to support our theoretical findings. Our most revealing numerical result is that, Robin-type boundary conditions seem to introduce a boundary layer coupling the bulk and surface dynamics.
2015-03-08T00:00:00ZMadzvamuse, AnotidaChung, Andy H. W.Venkataraman, ChandrasekharIn this article, we formulate new models for coupled systems of bulk-surface reaction-diffusion equations on stationary volumes. The bulk reaction-diffusion equations are coupled to the surface reaction-diffusion equations through linear Robin-type boundary conditions. We then state and prove the necessary conditions for diffusion-driven instability for the coupled system. Owing to the nature of the coupling between bulk and surface dynamics, we are able to decouple the stability analysis of the bulk and surface dynamics. Under a suitable choice of model parameter values, the bulk reaction-diffusion system can induce patterning on the surface independent of whether the surface reaction-diffusion system produces or not, patterning. On the other hand, the surface reaction-diffusion system cannot generate patterns everywhere in the bulk in the absence of patterning from the bulk reaction-diffusion system. For this case, patterns can be induced only in regions close to the surface membrane. Various numerical experiments are presented to support our theoretical findings. Our most revealing numerical result is that, Robin-type boundary conditions seem to introduce a boundary layer coupling the bulk and surface dynamics.Stellar coronal response to differential rotation and flux emergenceGibb, Gordon Peter SamuelMackay, Duncan HendryJardine, Moira MaryYeates, A. R.http://hdl.handle.net/10023/82982018-01-08T10:30:13Z2016-03-11T00:00:00ZWe perform a numerical parameter study to determine what effect varying differential rotation and flux emergence has on a star's non-potential coronal magnetic field. In particular we consider the effects on the star's surface magnetic flux, open magnetic flux, mean azimuthal field strength, coronal free magnetic energy, coronal heating and flux rope eruptions. To do this, we apply a magnetic flux transport model to describe the photospheric evolution, and couple this to the non-potential coronal evolution using a magnetofrictional technique. A flux emergence model is applied to add new magnetic flux on to the photosphere and into the corona. The parameters of this flux emergence model are derived from the solar flux emergence profile, however the rate of emergence can be increased to represent higher flux emergence rates than the Sun's. Overall we find that flux emergence has a greater effect on the non-potential coronal properties compared to differential rotation, with all the aforementioned properties increasing with increasing flux emergence rate. Although differential rotation has a lesser effect on the overall coronal properties compared to flux emergence, varying differential rotation does alter the coronal structure. As the differential rotation rate increases, the corona becomes more open, and more non-potential.
GPSG would like to thank the STFC for financial support. DHM would like to thank the STFC and the Leverhulme Trust for financial support. Simulations were carried out on a STFC/SRIF funded UKMHD cluster at St Andrews.
2016-03-11T00:00:00ZGibb, Gordon Peter SamuelMackay, Duncan HendryJardine, Moira MaryYeates, A. R.We perform a numerical parameter study to determine what effect varying differential rotation and flux emergence has on a star's non-potential coronal magnetic field. In particular we consider the effects on the star's surface magnetic flux, open magnetic flux, mean azimuthal field strength, coronal free magnetic energy, coronal heating and flux rope eruptions. To do this, we apply a magnetic flux transport model to describe the photospheric evolution, and couple this to the non-potential coronal evolution using a magnetofrictional technique. A flux emergence model is applied to add new magnetic flux on to the photosphere and into the corona. The parameters of this flux emergence model are derived from the solar flux emergence profile, however the rate of emergence can be increased to represent higher flux emergence rates than the Sun's. Overall we find that flux emergence has a greater effect on the non-potential coronal properties compared to differential rotation, with all the aforementioned properties increasing with increasing flux emergence rate. Although differential rotation has a lesser effect on the overall coronal properties compared to flux emergence, varying differential rotation does alter the coronal structure. As the differential rotation rate increases, the corona becomes more open, and more non-potential.Head on collisions between two quasi-geostrophic hetons in a continuously stratified fluidReinaud, Jean NoelCarton, Xavierhttp://hdl.handle.net/10023/82192018-01-07T03:05:01Z2015-09-01T00:00:00ZWe examine the interactions between two three-dimensional quasi-geostrophic hetons. The hetons are initially translating towards one another. We address the effect of the vertical distance between the two poles (vortices) constituting each heton, on the interaction. We also examine the influence of the horizontal separation between the poles within each heton. In this investigation, the two hetons are facing each other. Two configurations are possible depending on the respective location of the like-signed poles of the hetons. When they lie at the same depth, we refer to the configuration as symmetric; the anti-symmetric configuration corresponds to opposite-signed poles at the same depth. The first step in the investigation uses point vortices to represent the poles of the hetons. This approach allows to rapidly browse the parameter space and to estimate the possible heton trajectories. For a symmetric pair, hetons either reverse their trajectory or recombine and escape perpendicularly depending of their horizontal and vertical offsets. On the other hand, anti-symmetric hetons recombine and escape perpendicularly as same-depth dipoles. In a second part, we focus on finite core hetons (with finite volume poles). These hetons can deform and may be sensitive to horizontal shear induced deformations, or to baroclinic instability. These destabilisations depend on the vertical and horizontal offsets between the various poles, as well as on their width-to-height aspect ratios. They can modify the volume of the poles via vortex merger, breaking and/or shearing out; they compete with the advective evolution observed for singular (point) vortices. Importantly, hetons can break down or re-configure before they can drift away as expected from a point vortex approach. Thus a large variety of behaviours is observed in the parameter space. Finally, we briefly illustrate the behaviour of tall hetons which can be unstable to an azimuthal mode l=1 when many vertical modes of deformation are present on the heton.
Date of Acceptance : 21/07/2015
2015-09-01T00:00:00ZReinaud, Jean NoelCarton, XavierWe examine the interactions between two three-dimensional quasi-geostrophic hetons. The hetons are initially translating towards one another. We address the effect of the vertical distance between the two poles (vortices) constituting each heton, on the interaction. We also examine the influence of the horizontal separation between the poles within each heton. In this investigation, the two hetons are facing each other. Two configurations are possible depending on the respective location of the like-signed poles of the hetons. When they lie at the same depth, we refer to the configuration as symmetric; the anti-symmetric configuration corresponds to opposite-signed poles at the same depth. The first step in the investigation uses point vortices to represent the poles of the hetons. This approach allows to rapidly browse the parameter space and to estimate the possible heton trajectories. For a symmetric pair, hetons either reverse their trajectory or recombine and escape perpendicularly depending of their horizontal and vertical offsets. On the other hand, anti-symmetric hetons recombine and escape perpendicularly as same-depth dipoles. In a second part, we focus on finite core hetons (with finite volume poles). These hetons can deform and may be sensitive to horizontal shear induced deformations, or to baroclinic instability. These destabilisations depend on the vertical and horizontal offsets between the various poles, as well as on their width-to-height aspect ratios. They can modify the volume of the poles via vortex merger, breaking and/or shearing out; they compete with the advective evolution observed for singular (point) vortices. Importantly, hetons can break down or re-configure before they can drift away as expected from a point vortex approach. Thus a large variety of behaviours is observed in the parameter space. Finally, we briefly illustrate the behaviour of tall hetons which can be unstable to an azimuthal mode l=1 when many vertical modes of deformation are present on the heton.Particle dynamics in a non-flaring solar active region modelThrelfall, J.-A. Bourdin, Ph.Neukirch, T.E. Parnell, C.http://hdl.handle.net/10023/82032018-01-07T03:09:55Z2016-03-01T00:00:00ZThe aim of this work is to investigate and characterise particle behaviour in a (observationally-driven) 3D MHD model of the solar atmosphere above a slowly evolving, non-flaring active region. We use a relativistic guiding-centre particle code to investigate particle acceleration in a single snapshot of the 3D MHD simulation. Despite the lack of flare-like behaviour in the active region, direct acceleration of electrons and protons to non-thermal energies (≲ 42 MeV) was found, yielding spectra with high-energy tails which conform to a power law. Examples of particle dynamics, including particle trapping caused by local electric rather than magnetic field effects, are observed and discussed, together with implications for future experiments which simulate non-flaring active region heating and reconnection.
2016-03-01T00:00:00ZThrelfall, J.-A. Bourdin, Ph.Neukirch, T.E. Parnell, C.The aim of this work is to investigate and characterise particle behaviour in a (observationally-driven) 3D MHD model of the solar atmosphere above a slowly evolving, non-flaring active region. We use a relativistic guiding-centre particle code to investigate particle acceleration in a single snapshot of the 3D MHD simulation. Despite the lack of flare-like behaviour in the active region, direct acceleration of electrons and protons to non-thermal energies (≲ 42 MeV) was found, yielding spectra with high-energy tails which conform to a power law. Examples of particle dynamics, including particle trapping caused by local electric rather than magnetic field effects, are observed and discussed, together with implications for future experiments which simulate non-flaring active region heating and reconnection.Magnetohydrostatic modelling of stellar coronaeMacTaggart, DavidGregory, ScottNeukirch, ThomasDonati, Jean-Francoishttp://hdl.handle.net/10023/80672018-01-07T03:30:42Z2016-02-11T00:00:00ZWe introduce to the stellar physics community a method of modelling stellar coronae that can be considered to be an extension of the potential field. In this approach, the magnetic field is coupled to the background atmosphere. The model is magnetohydrostatic and is a balance between the Lorentz force, the pressure gradient and gravity. Analytical solutions are possible and we consider a particular class of equilibria in this paper. The model contains two free parameters and the effects of these on both the geometry and topology of the coronal magnetic field are investigated. A demonstration of the approach is given using a magnetogram derived from Zeeman–Doppler imaging of the 0.75 M⊙ M-dwarf star GJ 182.
2016-02-11T00:00:00ZMacTaggart, DavidGregory, ScottNeukirch, ThomasDonati, Jean-FrancoisWe introduce to the stellar physics community a method of modelling stellar coronae that can be considered to be an extension of the potential field. In this approach, the magnetic field is coupled to the background atmosphere. The model is magnetohydrostatic and is a balance between the Lorentz force, the pressure gradient and gravity. Analytical solutions are possible and we consider a particular class of equilibria in this paper. The model contains two free parameters and the effects of these on both the geometry and topology of the coronal magnetic field are investigated. A demonstration of the approach is given using a magnetogram derived from Zeeman–Doppler imaging of the 0.75 M⊙ M-dwarf star GJ 182.Particle acceleration at reconnecting separator current layersThrelfall, J.E. H. Stevenson, J.E. Parnell, C.Neukirch, T.http://hdl.handle.net/10023/80012018-01-07T03:09:56Z2016-01-01T00:00:00ZThe aim of this work is to investigate and characterise particle behaviour in a 3D MHD model of a reconnecting magnetic separator. We use a relativistic guiding-centre test-particle code to investigate electron and proton acceleration in snapshots from 3D MHD separator reconnection experiments, and compare the results with findings from an analytical separator reconnection model studied in a previous investigation. The behaviour (and acceleration) of large distributions of particles are examined in detail for both analytical and numerical separator reconnection models. Differences in acceleration sites are recovered and discussed, together with the dependence of final particle energy ranges upon the dimensions of the models and the stage of the (time-dependent) MHD reconnection event. We discuss the implications of these results for observed magnetic separators in the solar corona.
2016-01-01T00:00:00ZThrelfall, J.E. H. Stevenson, J.E. Parnell, C.Neukirch, T.The aim of this work is to investigate and characterise particle behaviour in a 3D MHD model of a reconnecting magnetic separator. We use a relativistic guiding-centre test-particle code to investigate electron and proton acceleration in snapshots from 3D MHD separator reconnection experiments, and compare the results with findings from an analytical separator reconnection model studied in a previous investigation. The behaviour (and acceleration) of large distributions of particles are examined in detail for both analytical and numerical separator reconnection models. Differences in acceleration sites are recovered and discussed, together with the dependence of final particle energy ranges upon the dimensions of the models and the stage of the (time-dependent) MHD reconnection event. We discuss the implications of these results for observed magnetic separators in the solar corona.A model for selection of eyespots on butterfly wingsSekimura, ToshioVenkataraman, ChandrasekharMadzvamuse, Anotidahttp://hdl.handle.net/10023/79042018-01-07T03:31:44Z2015-11-04T00:00:00ZUnsolved Problem The development of eyespots on the wing surface of butterflies of the family Nympalidae is one of the most studied examples of biological pattern formation. However, little is known about the mechanism that determines the number and precise locations of eyespots on the wing. Eyespots develop around signaling centers, called foci, that are located equidistant from wing veins along the midline of a wing cell (an area bounded by veins). A fundamental question that remains unsolved is, why a certain wing cell develops an eyespot, while other wing cells do not. Key Idea and Model We illustrate that the key to understanding focus point selection may be in the venation system of the wing disc. Our main hypothesis is that changes in morphogen concentration along the proximal boundary veins of wing cells govern focus point selection. Based on previous studies, we focus on a spatially two-dimensional reaction-diffusion system model posed in the interior of each wing cell that describes the formation of focus points. Using finite element based numerical simulations, we demonstrate that variation in the proximal boundary condition is sufficient to robustly select whether an eyespot focus point forms in otherwise identical wing cells. We also illustrate that this behavior is robust to small perturbations in the parameters and geometry and moderate levels of noise. Hence, we suggest that an anterior-posterior pattern of morphogen concentration along the proximal vein may be the main determinant of the distribution of focus points on the wing surface. In order to complete our model, we propose a two stage reaction-diffusion system model, in which an one-dimensional surface reaction-diffusion system, posed on the proximal vein, generates the morphogen concentrations that act as non-homogeneous Dirichlet (i.e., fixed) boundary conditions for the two-dimensional reaction-diffusion model posed in the wing cells. The two-stage model appears capable of generating focus point distributions observed in nature. Result We therefore conclude that changes in the proximal boundary conditions are sufficient to explain the empirically observed distribution of eyespot focus points on the entire wing surface. The model predicts, subject to experimental verification, that the source strength of the activator at the proximal boundary should be lower in wing cells in which focus points form than in those that lack focus points. The model suggests that the number and locations of eyespot foci on the wing disc could be largely controlled by two kinds of gradients along two different directions, that is, the first one is the gradient in spatially varying parameters such as the reaction rate along the anterior-posterior direction on the proximal boundary of the wing cells, and the second one is the gradient in source values of the activator along the veins in the proximal-distal direction of the wing cell.
The authors acknowledge financial support from the EPSRC grant EP/J016780/1. AM and CV acknowledge financial support from the Leverhulme Trust Research Project Grant (RPG-2014-149). This research was started while CV was visiting Japan as a 2013 Japanese Society for the Promotion of Science (JSPS) Summer Fellow (http://www.jsps.go.jp/). This research was finalized whilst TS, CV and AM were participants in the Isaac Newton Institute Program, Coupling Geometric PDEs with Physics for Cell Morphology, Motility and Pattern Formation. This work (AM) has received funding from the European Union Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 642866. AM was partially supported by a grant from the Simons Foundation.
2015-11-04T00:00:00ZSekimura, ToshioVenkataraman, ChandrasekharMadzvamuse, AnotidaUnsolved Problem The development of eyespots on the wing surface of butterflies of the family Nympalidae is one of the most studied examples of biological pattern formation. However, little is known about the mechanism that determines the number and precise locations of eyespots on the wing. Eyespots develop around signaling centers, called foci, that are located equidistant from wing veins along the midline of a wing cell (an area bounded by veins). A fundamental question that remains unsolved is, why a certain wing cell develops an eyespot, while other wing cells do not. Key Idea and Model We illustrate that the key to understanding focus point selection may be in the venation system of the wing disc. Our main hypothesis is that changes in morphogen concentration along the proximal boundary veins of wing cells govern focus point selection. Based on previous studies, we focus on a spatially two-dimensional reaction-diffusion system model posed in the interior of each wing cell that describes the formation of focus points. Using finite element based numerical simulations, we demonstrate that variation in the proximal boundary condition is sufficient to robustly select whether an eyespot focus point forms in otherwise identical wing cells. We also illustrate that this behavior is robust to small perturbations in the parameters and geometry and moderate levels of noise. Hence, we suggest that an anterior-posterior pattern of morphogen concentration along the proximal vein may be the main determinant of the distribution of focus points on the wing surface. In order to complete our model, we propose a two stage reaction-diffusion system model, in which an one-dimensional surface reaction-diffusion system, posed on the proximal vein, generates the morphogen concentrations that act as non-homogeneous Dirichlet (i.e., fixed) boundary conditions for the two-dimensional reaction-diffusion model posed in the wing cells. The two-stage model appears capable of generating focus point distributions observed in nature. Result We therefore conclude that changes in the proximal boundary conditions are sufficient to explain the empirically observed distribution of eyespot focus points on the entire wing surface. The model predicts, subject to experimental verification, that the source strength of the activator at the proximal boundary should be lower in wing cells in which focus points form than in those that lack focus points. The model suggests that the number and locations of eyespot foci on the wing disc could be largely controlled by two kinds of gradients along two different directions, that is, the first one is the gradient in spatially varying parameters such as the reaction rate along the anterior-posterior direction on the proximal boundary of the wing cells, and the second one is the gradient in source values of the activator along the veins in the proximal-distal direction of the wing cell.Magneto-static modeling of the mixed plasma Beta solar atmosphere based on SUNRISE/IMaX dataWiegelmann, ThomasNeukirch, ThomasNickeler, DieterSolanki, SamiMartinez Pillet, ValentinBorrero, Juan Manulehttp://hdl.handle.net/10023/78872018-01-07T03:09:59Z2015-12-01T00:00:00ZOur aim is to model the 3D magnetic field structure of the upper solar atmosphere, including regions of non-negligible plasma beta. We use high-resolution photospheric magnetic field measurements from SUNRISE/IMaX as boundary condition for a magneto-static magnetic field model. The high resolution of IMaX allows us to resolve the interface region between photosphere and corona, but modelling this region is challenging for the following reasons. While the coronal magnetic field is thought to be force-free (the Lorentz-force vanishes), this is not the case in the mixed plasma β environment in the photosphere and lower chromosphere. In our model, pressure gradients and gravity forces are taken self-consistently into account and compensate the non-vanishing Lorentz-force. Above a certain height (about 2 Mm) the non-magnetic forces become very weak and consequently the magnetic field becomes almost force-free. Here we apply a linear approach, where the electric current density consists of a superposition of a field-line parallel current and a current perpendicular to the Sun’s gravity field. We illustrate the prospects and limitations of this approach and give an outlook for an extension towards a non-linear model.
TN acknowledges support by the U.K.’s Science and Technology Facilities Council and would like to thank the MPS for its hospitality during a visit in December 2014.
2015-12-01T00:00:00ZWiegelmann, ThomasNeukirch, ThomasNickeler, DieterSolanki, SamiMartinez Pillet, ValentinBorrero, Juan ManuleOur aim is to model the 3D magnetic field structure of the upper solar atmosphere, including regions of non-negligible plasma beta. We use high-resolution photospheric magnetic field measurements from SUNRISE/IMaX as boundary condition for a magneto-static magnetic field model. The high resolution of IMaX allows us to resolve the interface region between photosphere and corona, but modelling this region is challenging for the following reasons. While the coronal magnetic field is thought to be force-free (the Lorentz-force vanishes), this is not the case in the mixed plasma β environment in the photosphere and lower chromosphere. In our model, pressure gradients and gravity forces are taken self-consistently into account and compensate the non-vanishing Lorentz-force. Above a certain height (about 2 Mm) the non-magnetic forces become very weak and consequently the magnetic field becomes almost force-free. Here we apply a linear approach, where the electric current density consists of a superposition of a field-line parallel current and a current perpendicular to the Sun’s gravity field. We illustrate the prospects and limitations of this approach and give an outlook for an extension towards a non-linear model.The appearance, motion, and disappearance of three-dimensional magnetic null pointsA. Murphy, NicholasParnell, Clare ElizabethHaynes, Andrew Lewishttp://hdl.handle.net/10023/78682018-01-07T03:08:47Z2015-10-30T00:00:00ZWhile theoretical models and simulations of magnetic reconnection often assume symmetry such that the magnetic null point when present is co-located with a flow stagnation point, the introduction of asymmetry typically leads to non-ideal flows across the null point. To understand this behavior, we present exact expressions for the motion of three-dimensional linear null points. The most general expression shows that linear null points move in the direction along which the magnetic field and its time derivative are antiparallel. Null point motion in resistive magnetohydrodynamics results from advection by the bulk plasma flow and resistive diffusion of the magnetic field, which allows non-ideal flows across topological boundaries. Null point motion is described intrinsically by parameters evaluated locally; however, global dynamics help set the local conditions at the null point. During a bifurcation of a degenerate null point into a null-null pair or the reverse, the instantaneous velocity of separation or convergence of the null-null pair will typically be infinite along the null space of the Jacobian matrix of the magnetic field, but with finite components in the directions orthogonal to the null space. Not all bifurcating null-null pairs are connected by a separator. Furthermore, except under special circumstances, there will not exist a straight line separator connecting a bifurcating null-null pair. The motion of separators cannot be described using solely local parameters because the identification of a particular field line as a separator may change as a result of non-ideal behavior elsewhere along the field line.
N.A.M. acknowledges support from NASA grants NNX11AB61G, NNX12AB25G, and NNX15AF43G; NASA contract NNM07AB07C; and NSF SHINE grants AGS-1156076 and AGS-1358342 to SAO. C.E.P. acknowledges support from the St Andrews 2013 STFC Consolidated grant.
2015-10-30T00:00:00ZA. Murphy, NicholasParnell, Clare ElizabethHaynes, Andrew LewisWhile theoretical models and simulations of magnetic reconnection often assume symmetry such that the magnetic null point when present is co-located with a flow stagnation point, the introduction of asymmetry typically leads to non-ideal flows across the null point. To understand this behavior, we present exact expressions for the motion of three-dimensional linear null points. The most general expression shows that linear null points move in the direction along which the magnetic field and its time derivative are antiparallel. Null point motion in resistive magnetohydrodynamics results from advection by the bulk plasma flow and resistive diffusion of the magnetic field, which allows non-ideal flows across topological boundaries. Null point motion is described intrinsically by parameters evaluated locally; however, global dynamics help set the local conditions at the null point. During a bifurcation of a degenerate null point into a null-null pair or the reverse, the instantaneous velocity of separation or convergence of the null-null pair will typically be infinite along the null space of the Jacobian matrix of the magnetic field, but with finite components in the directions orthogonal to the null space. Not all bifurcating null-null pairs are connected by a separator. Furthermore, except under special circumstances, there will not exist a straight line separator connecting a bifurcating null-null pair. The motion of separators cannot be described using solely local parameters because the identification of a particular field line as a separator may change as a result of non-ideal behavior elsewhere along the field line.Near-threshold electron injection in the laser-plasma wakefield accelerator leading to femtosecond bunchesIslam, M.R.Brunetti, E.Shanks, R.P.Ersfeld, B.Issac, R.C.Cipiccia, S.Anania, M.P.Welsh, G.H.Wiggins, S.M.Noble, A.Cairns, R AlanRaj, G.Jaroszynski, D.A.http://hdl.handle.net/10023/77502018-01-07T03:10:41Z2015-09-17T00:00:00ZThe laser-plasma wakefield accelerator is a compact source of high brightness, ultra-short duration electron bunches. Self-injection occurs when electrons from the background plasma gain sufficient momentum at the back of the bubble-shaped accelerating structure to experience sustained acceleration. The shortest duration and highest brightness electron bunches result from self-injection close to the threshold for injection. Here we show that in this case injection is due to the localized charge density build-up in the sheath crossing region at the rear of the bubble, which has the effect of increasing the accelerating potential to above a critical value. Bunch duration is determined by the dwell time above this critical value, which explains why single or multiple ultra-short electron bunches with little dark current are formed in the first bubble. We confirm experimentally, using coherent optical transition radiation measurements, that single or multiple bunches with femtosecond duration and peak currents of several kiloAmpere, and femtosecond intervals between bunches, emerge from the accelerator.
We gratefully acknowledge the support of the UK EPSRC (grant no. EP/J018171/1), the EU FP7 programmes: the Extreme Light Infrastructure (ELI) project, the Laserlab-Europe (no. 284464), and the EUCARD-2 project (no. 312453).
2015-09-17T00:00:00ZIslam, M.R.Brunetti, E.Shanks, R.P.Ersfeld, B.Issac, R.C.Cipiccia, S.Anania, M.P.Welsh, G.H.Wiggins, S.M.Noble, A.Cairns, R AlanRaj, G.Jaroszynski, D.A.The laser-plasma wakefield accelerator is a compact source of high brightness, ultra-short duration electron bunches. Self-injection occurs when electrons from the background plasma gain sufficient momentum at the back of the bubble-shaped accelerating structure to experience sustained acceleration. The shortest duration and highest brightness electron bunches result from self-injection close to the threshold for injection. Here we show that in this case injection is due to the localized charge density build-up in the sheath crossing region at the rear of the bubble, which has the effect of increasing the accelerating potential to above a critical value. Bunch duration is determined by the dwell time above this critical value, which explains why single or multiple ultra-short electron bunches with little dark current are formed in the first bubble. We confirm experimentally, using coherent optical transition radiation measurements, that single or multiple bunches with femtosecond duration and peak currents of several kiloAmpere, and femtosecond intervals between bunches, emerge from the accelerator.Future capabilities of CME polarimetric 3D reconstructions with the METIS instrument : a numerical testPagano, PaoloBemporad, AMackay, Duncan Hendryhttp://hdl.handle.net/10023/77482018-01-07T03:09:32Z2015-10-01T00:00:00ZContext. Understanding the 3D structure of coronal mass ejections (CMEs) is crucial for understanding the nature and origin of solar eruptions. However, owing to the optical thinness of the solar corona we can only observe the line of sight integrated emission. As a consequence the resulting projection effects hide the true 3D structure of CMEs. To derive information on the 3D structure of CMEs from white-light (total and polarized brightness) images, the polarization ratio technique is widely used. The soon-to-be-launched METIS coronagraph on board Solar Orbiter will use this technique to produce new polarimetric images. Aims. This work considers the application of the polarization ratio technique to synthetic CME observations from METIS. In particular we determine the accuracy at which the position of the centre of mass, direction and speed of propagation, and the column density of the CME can be determined along the line of sight. Methods. We perform a 3D MHD simulation of a flux rope ejection where a CME is produced. From the simulation we (i) synthesize the corresponding METIS white-light (total and polarized brightness) images and (ii) apply the polarization ratio technique to these synthesized images and compare the results with the known density distribution from the MHD simulation. In addition, we use recent results that consider how the position of a single blob of plasma is measured depending on its projected position in the plane of the sky. From this we can interpret the results of the polarization ratio technique and give an estimation of the error associated with derived parameters. Results. We find that the polarization ratio technique reproduces with high accuracy the position of the centre of mass along the line of sight. However, some errors are inherently associated with this determination. The polarization ratio technique also allows information to be derived on the real 3D direction of propagation of the CME. The determination of this is of fundamental importance for future space weather forecasting. In addition, we find that the column density derived from white-light images is accurate and we propose an improved technique where the combined use of the polarization ratio technique and white-light images minimizes the error in the estimation of column densities. Moreover, by applying the comparison to a set of snapshots of the simulation we can also assess the errors related to the trajectory and the expansion of the CME. Conclusions. Our method allows us to thoroughly test the performance of the polarization ratio technique and allows a determination of the errors associated with it, which means that it can be used to quantify the results from the analysis of the forthcoming METIS observations in white light (total and polarized brightness). Finally, we describe a satellite observing configuration relative to the Earth that can allow the technique to be efficiently used for space weather predictions.
D.H.M. would like to thank STFC and the Leverhulme Trust for their financial support. P.P. would like to thank STFC and the Leverhulme Trust. The computational work for this paper was carried out on the joint STFC and SFC (SRIF) funded cluster at the University of St Andrews (Scotland, UK).
2015-10-01T00:00:00ZPagano, PaoloBemporad, AMackay, Duncan HendryContext. Understanding the 3D structure of coronal mass ejections (CMEs) is crucial for understanding the nature and origin of solar eruptions. However, owing to the optical thinness of the solar corona we can only observe the line of sight integrated emission. As a consequence the resulting projection effects hide the true 3D structure of CMEs. To derive information on the 3D structure of CMEs from white-light (total and polarized brightness) images, the polarization ratio technique is widely used. The soon-to-be-launched METIS coronagraph on board Solar Orbiter will use this technique to produce new polarimetric images. Aims. This work considers the application of the polarization ratio technique to synthetic CME observations from METIS. In particular we determine the accuracy at which the position of the centre of mass, direction and speed of propagation, and the column density of the CME can be determined along the line of sight. Methods. We perform a 3D MHD simulation of a flux rope ejection where a CME is produced. From the simulation we (i) synthesize the corresponding METIS white-light (total and polarized brightness) images and (ii) apply the polarization ratio technique to these synthesized images and compare the results with the known density distribution from the MHD simulation. In addition, we use recent results that consider how the position of a single blob of plasma is measured depending on its projected position in the plane of the sky. From this we can interpret the results of the polarization ratio technique and give an estimation of the error associated with derived parameters. Results. We find that the polarization ratio technique reproduces with high accuracy the position of the centre of mass along the line of sight. However, some errors are inherently associated with this determination. The polarization ratio technique also allows information to be derived on the real 3D direction of propagation of the CME. The determination of this is of fundamental importance for future space weather forecasting. In addition, we find that the column density derived from white-light images is accurate and we propose an improved technique where the combined use of the polarization ratio technique and white-light images minimizes the error in the estimation of column densities. Moreover, by applying the comparison to a set of snapshots of the simulation we can also assess the errors related to the trajectory and the expansion of the CME. Conclusions. Our method allows us to thoroughly test the performance of the polarization ratio technique and allows a determination of the errors associated with it, which means that it can be used to quantify the results from the analysis of the forthcoming METIS observations in white light (total and polarized brightness). Finally, we describe a satellite observing configuration relative to the Earth that can allow the technique to be efficiently used for space weather predictions.Corotating interaction regions as seen by the STEREO Heliospheric Imagers 2007 – 2010Conlon, Thomas MichaelMilan, S.E.Davies, J.A.Williams, A.O.http://hdl.handle.net/10023/77462018-02-11T01:32:53Z2015-08-01T00:00:00ZNASA’s Solar Terrestrial Relations Observatory (STEREO) mission has coincided with a pronounced solar minimum. This allowed for easier detection of corotating interaction regions (CIRs). CIRs are formed by the interaction between fast and slow solar-wind streams ejected from source regions on the solar surface that rotate with the Sun. High-density plasma blobs that have become entrained at the stream interface can be tracked out to large elongations in data from the Heliospheric Imager (HI) instruments onboard STEREO. These blobs act as tracers of the CIR itself such that their HI signatures can be used to estimate CIR source location and radial speed. We estimate the kinematic properties of solar-wind transients associated with 40 CIRs detected by the HI instrument onboard the STEREO-A spacecraft between 2007 and 2010. We identify in-situ signatures of these transients at L1 using the Advanced Composition Explorer (ACE) and compare the in-situ parameters with the HI results. We note that solar-wind transients associated with CIRs appear to travel at or close to the slow solar-wind speed preceding the event as measured in situ. We also highlight limitations in the commonly used analysis techniques of solar-wind transients by considering variability in the solar wind.
T.M. Conlon and A.O. Williams were supported by an STFC, UK studentship and S.E. Milan was supported by STFC grant ST/K001000/1. Date of Acceptance: 08/08/2015
2015-08-01T00:00:00ZConlon, Thomas MichaelMilan, S.E.Davies, J.A.Williams, A.O.NASA’s Solar Terrestrial Relations Observatory (STEREO) mission has coincided with a pronounced solar minimum. This allowed for easier detection of corotating interaction regions (CIRs). CIRs are formed by the interaction between fast and slow solar-wind streams ejected from source regions on the solar surface that rotate with the Sun. High-density plasma blobs that have become entrained at the stream interface can be tracked out to large elongations in data from the Heliospheric Imager (HI) instruments onboard STEREO. These blobs act as tracers of the CIR itself such that their HI signatures can be used to estimate CIR source location and radial speed. We estimate the kinematic properties of solar-wind transients associated with 40 CIRs detected by the HI instrument onboard the STEREO-A spacecraft between 2007 and 2010. We identify in-situ signatures of these transients at L1 using the Advanced Composition Explorer (ACE) and compare the in-situ parameters with the HI results. We note that solar-wind transients associated with CIRs appear to travel at or close to the slow solar-wind speed preceding the event as measured in situ. We also highlight limitations in the commonly used analysis techniques of solar-wind transients by considering variability in the solar wind.Observational signatures of waves and flows in the solar coronaDe Moortel, I.Antolin, PatrickVan Doorsselaere, T.http://hdl.handle.net/10023/77222018-01-07T02:56:15Z2015-02-01T00:00:00ZPropagating perturbations have been observed in extended coronal loop structures for a number of years, but the interpretation in terms of slow (propagating) magneto-acoustic waves and/or as quasi-periodic upflows remains unresolved. We used forward-modelling to construct observational signatures associated with a simple slow magneto-acoustic wave or periodic flow model. Observational signatures were computed for the 171 Å Fe ix and the 193 Å Fe xii spectral lines. Although there are many differences between the flow and wave models, we did not find any clear, robust observational characteristics that can be used in isolation (i.e. that do not rely on a comparison between the models). For the waves model, a relatively rapid change of the average line widths as a function of (shallow) line-of-sight angles was found, whereas the ratio of the line width amplitudes to the Doppler velocity amplitudes is relatively high for the flow model. The most robust observational signature found is that the ratio of the mean to the amplitudes of the Doppler velocity is always higher than one for the flow model. This ratio is substantially higher for flows than for waves, and for the flows model used in the study is exactly the same in the 171 Å Fe ix and the 193 Å Fe xii spectral lines. However, these potential observational signatures need to be treated cautiously because they are likely to be model-dependent.
DM acknowledges support of a Royal Society University Research Fellowship and a KU Leuven Research Council senior research fellowship (SF/12/008). The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/2007-2013) under the grant agreement SOLSPANET (project No. 269299, www.solspanet.eu/solspanet ). TVD has been sponsored by an Odysseus grant of the FWO Vlaanderen. The research was performed in the context of the IAP P7/08 CHARM (Belspo) and the GOA-2015-014 (KU Leuven). TVD acknowledges the funding from the FP7 ERG grant with number 276808.
2015-02-01T00:00:00ZDe Moortel, I.Antolin, PatrickVan Doorsselaere, T.Propagating perturbations have been observed in extended coronal loop structures for a number of years, but the interpretation in terms of slow (propagating) magneto-acoustic waves and/or as quasi-periodic upflows remains unresolved. We used forward-modelling to construct observational signatures associated with a simple slow magneto-acoustic wave or periodic flow model. Observational signatures were computed for the 171 Å Fe ix and the 193 Å Fe xii spectral lines. Although there are many differences between the flow and wave models, we did not find any clear, robust observational characteristics that can be used in isolation (i.e. that do not rely on a comparison between the models). For the waves model, a relatively rapid change of the average line widths as a function of (shallow) line-of-sight angles was found, whereas the ratio of the line width amplitudes to the Doppler velocity amplitudes is relatively high for the flow model. The most robust observational signature found is that the ratio of the mean to the amplitudes of the Doppler velocity is always higher than one for the flow model. This ratio is substantially higher for flows than for waves, and for the flows model used in the study is exactly the same in the 171 Å Fe ix and the 193 Å Fe xii spectral lines. However, these potential observational signatures need to be treated cautiously because they are likely to be model-dependent.Multiscale modelling of cancer progression and treatment control : the role of intracellular heterogeneities in chemotherapy treatmentChaplain, Mark Andrew JosephPowathil, Gibinhttp://hdl.handle.net/10023/77142018-01-07T03:07:28Z2015-06-01T00:00:00ZCancer is a complex, multiscale process involving interactions at intracellular, intercellular and tissue scales that are in turn susceptible to microenvironmental changes. Each individual cancer cell within a cancer cell mass is unique, with its own internal cellular pathways and biochemical interactions. These interactions contribute to the functional changes at the cellular and tissue scale, creating a heterogenous cancer cell population. Anticancer drugs are effective in controlling cancer growth by inflicting damage to various target molecules and thereby triggering multiple cellular and intracellular pathways, leading to cell death or cell-cycle arrest. One of the major impediments in the chemotherapy treatment of cancer is drug resistance driven by multiple mechanisms, including multi-drug and cell-cycle mediated resistance to chemotherapy drugs. In this article, we discuss two hybrid multiscale modelling approaches, incorporating multiple interactions involved in the sub-cellular, cellular and microenvironmental levels to study the effects of cell-cycle, phase-specific chemotherapy on the growth and progression of cancer cells.
2015-06-01T00:00:00ZChaplain, Mark Andrew JosephPowathil, GibinCancer is a complex, multiscale process involving interactions at intracellular, intercellular and tissue scales that are in turn susceptible to microenvironmental changes. Each individual cancer cell within a cancer cell mass is unique, with its own internal cellular pathways and biochemical interactions. These interactions contribute to the functional changes at the cellular and tissue scale, creating a heterogenous cancer cell population. Anticancer drugs are effective in controlling cancer growth by inflicting damage to various target molecules and thereby triggering multiple cellular and intracellular pathways, leading to cell death or cell-cycle arrest. One of the major impediments in the chemotherapy treatment of cancer is drug resistance driven by multiple mechanisms, including multi-drug and cell-cycle mediated resistance to chemotherapy drugs. In this article, we discuss two hybrid multiscale modelling approaches, incorporating multiple interactions involved in the sub-cellular, cellular and microenvironmental levels to study the effects of cell-cycle, phase-specific chemotherapy on the growth and progression of cancer cells.Systems oncology : towards patient-specific treatment regimes informed by multiscale mathematical modellingPowathil, Gibin G.Swat, MaciejChaplain, Mark A. J.http://hdl.handle.net/10023/77132018-03-18T01:35:52Z2015-02-01T00:00:00ZThe multiscale complexity of cancer as a disease necessitates a corresponding multiscale modelling approach to produce truly predictive mathematical models capable of improving existing treatment protocols. To capture all the dynamics of solid tumour growth and its progression, mathematical modellers need to couple biological processes occurring at various spatial and temporal scales (from genes to tissues). Because effectiveness of cancer therapy is considerably affected by intracellular and extracellular heterogeneities as well as by the dynamical changes in the tissue microenvironment, any model attempt to optimise existing protocols must consider these factors ultimately leading to improved multimodal treatment regimes. By improving existing and building new mathematical models of cancer, modellers can play important role in preventing the use of potentially sub-optimal treatment combinations. In this paper, we analyse a multiscale computational mathematical model for cancer growth and spread, incorporating the multiple effects of radiation therapy and chemotherapy in the patient survival probability and implement the model using two different cell based modelling techniques. We show that the insights provided by such multiscale modelling approaches can ultimately help in designing optimal patient-specific multi-modality treatment protocols that may increase patients quality of life.
2015-02-01T00:00:00ZPowathil, Gibin G.Swat, MaciejChaplain, Mark A. J.The multiscale complexity of cancer as a disease necessitates a corresponding multiscale modelling approach to produce truly predictive mathematical models capable of improving existing treatment protocols. To capture all the dynamics of solid tumour growth and its progression, mathematical modellers need to couple biological processes occurring at various spatial and temporal scales (from genes to tissues). Because effectiveness of cancer therapy is considerably affected by intracellular and extracellular heterogeneities as well as by the dynamical changes in the tissue microenvironment, any model attempt to optimise existing protocols must consider these factors ultimately leading to improved multimodal treatment regimes. By improving existing and building new mathematical models of cancer, modellers can play important role in preventing the use of potentially sub-optimal treatment combinations. In this paper, we analyse a multiscale computational mathematical model for cancer growth and spread, incorporating the multiple effects of radiation therapy and chemotherapy in the patient survival probability and implement the model using two different cell based modelling techniques. We show that the insights provided by such multiscale modelling approaches can ultimately help in designing optimal patient-specific multi-modality treatment protocols that may increase patients quality of life.Mathematical modelling of cancer invasion : implications of cell adhesion variability for tumour infiltrative growth patternsDomschke, PiaTrucu, DumitruGerisch, AlfChaplain, Mark A. J.http://hdl.handle.net/10023/77122018-03-18T01:35:51Z2014-11-21T00:00:00ZCancer invasion, recognised as one of the hallmarks of cancer, is a complex, multiscale phenomenon involving many inter-related genetic, biochemical, cellular and tissue processes at different spatial and temporal scales. Central to invasion is the ability of cancer cells to alter and degrade an extracellular matrix. Combined with abnormal excessive proliferation and migration which is enabled and enhanced by altered cell-cell and cell-matrix adhesion, the cancerous mass can invade the neighbouring tissue. Along with tumour-induced angiogenesis, invasion is a key component of metastatic spread, ultimately leading to the formation of secondary tumours in other parts of the host body. In this paper we explore the spatio-temporal dynamics of a model of cancer invasion, where cell-cell and cell-matrix adhesion is accounted for through non-local interaction terms in a system of partial integro-differential equations. The change of adhesion properties during cancer growth and development is investigated here through time-dependent adhesion characteristics within the cell population as well as those between the cells and the components of the extracellular matrix. Our computational simulation results demonstrate a range of heterogeneous dynamics which are qualitatively similar to the invasive growth patterns observed in a number of different types of cancer, such as tumour infiltrative growth patterns (INF).
2014-11-21T00:00:00ZDomschke, PiaTrucu, DumitruGerisch, AlfChaplain, Mark A. J.Cancer invasion, recognised as one of the hallmarks of cancer, is a complex, multiscale phenomenon involving many inter-related genetic, biochemical, cellular and tissue processes at different spatial and temporal scales. Central to invasion is the ability of cancer cells to alter and degrade an extracellular matrix. Combined with abnormal excessive proliferation and migration which is enabled and enhanced by altered cell-cell and cell-matrix adhesion, the cancerous mass can invade the neighbouring tissue. Along with tumour-induced angiogenesis, invasion is a key component of metastatic spread, ultimately leading to the formation of secondary tumours in other parts of the host body. In this paper we explore the spatio-temporal dynamics of a model of cancer invasion, where cell-cell and cell-matrix adhesion is accounted for through non-local interaction terms in a system of partial integro-differential equations. The change of adhesion properties during cancer growth and development is investigated here through time-dependent adhesion characteristics within the cell population as well as those between the cells and the components of the extracellular matrix. Our computational simulation results demonstrate a range of heterogeneous dynamics which are qualitatively similar to the invasive growth patterns observed in a number of different types of cancer, such as tumour infiltrative growth patterns (INF).Stochastic modelling of chromosomal segregation : errors can introduce correctionMatzavinos, AnastasiosRoitershtein, AlexanderShtylla, BlertaVoller, ZacharyLiu, SijiaChaplain, Mark A.J.http://hdl.handle.net/10023/77112018-01-07T03:06:05Z2014-07-01T00:00:00ZCell division is a complex process requiring the cell to have many internal checks so that division may proceed and be completed correctly. Failure to divide correctly can have serious consequences, including progression to cancer. During mitosis, chromosomal segregation is one such process that is crucial for successful progression. Accurate segregation of chromosomes during mitosis requires regulation of the interactions between chromosomes and spindle microtubules. If left uncorrected, chromosome attachment errors can cause chromosome segregation defects which have serious effects on cell fates. In early prometaphase, where kinetochores are exposed to multiple microtubules originating from the two poles, there are frequent errors in kinetochore-microtubule attachment. Erroneous attachments are classified into two categories, syntelic and merotelic. In this paper, we consider a stochastic model for a possible function of syntelic and merotelic kinetochores, and we provide theoretical evidence that merotely can contribute to lessening the stochastic noise in the time for completion of the mitotic process in eukaryotic cells.
2014-07-01T00:00:00ZMatzavinos, AnastasiosRoitershtein, AlexanderShtylla, BlertaVoller, ZacharyLiu, SijiaChaplain, Mark A.J.Cell division is a complex process requiring the cell to have many internal checks so that division may proceed and be completed correctly. Failure to divide correctly can have serious consequences, including progression to cancer. During mitosis, chromosomal segregation is one such process that is crucial for successful progression. Accurate segregation of chromosomes during mitosis requires regulation of the interactions between chromosomes and spindle microtubules. If left uncorrected, chromosome attachment errors can cause chromosome segregation defects which have serious effects on cell fates. In early prometaphase, where kinetochores are exposed to multiple microtubules originating from the two poles, there are frequent errors in kinetochore-microtubule attachment. Erroneous attachments are classified into two categories, syntelic and merotelic. In this paper, we consider a stochastic model for a possible function of syntelic and merotelic kinetochores, and we provide theoretical evidence that merotely can contribute to lessening the stochastic noise in the time for completion of the mitotic process in eukaryotic cells.Mathematical modeling of tumor growth and treatmentEnderling, HeikoChaplain, Mark A. J.http://hdl.handle.net/10023/77102018-02-25T01:31:57Z2014-01-01T00:00:00ZUsing mathematical models to simulate dynamic biological processes has a long history. Over the past couple of decades or so, quantitative approaches have also made their way into cancer research. An increasing number of mathematical, physical, computational and engineering techniques have been applied to various aspects of tumor growth, with the ultimate goal of understanding the response of the cancer population to clinical intervention. So-called in silico trials that predict patient-specific response to various dose schedules or treatment combinations and sequencing are on the way to becoming an invaluable tool to optimize patient care. Herein we describe fundamentals of mathematical modeling of tumor growth and tumor-host interactions, and summarize some of the seminal and most prominent approaches.
2014-01-01T00:00:00ZEnderling, HeikoChaplain, Mark A. J.Using mathematical models to simulate dynamic biological processes has a long history. Over the past couple of decades or so, quantitative approaches have also made their way into cancer research. An increasing number of mathematical, physical, computational and engineering techniques have been applied to various aspects of tumor growth, with the ultimate goal of understanding the response of the cancer population to clinical intervention. So-called in silico trials that predict patient-specific response to various dose schedules or treatment combinations and sequencing are on the way to becoming an invaluable tool to optimize patient care. Herein we describe fundamentals of mathematical modeling of tumor growth and tumor-host interactions, and summarize some of the seminal and most prominent approaches.Mean field analysis of a spatial stochastic model of a gene regulatory networkSturrock, M.Murray, P. J.Matzavinos, A.Chaplain, M. A. J.http://hdl.handle.net/10023/77092018-01-07T03:06:04Z2015-10-01T00:00:00ZA gene regulatory network may be defined as a collection of DNA segments which interact with each other indirectly through their RNA and protein products. Such a network is said to contain a negative feedback loop if its products inhibit gene transcription, and a positive feedback loop if a gene product promotes its own production. Negative feedback loops can create oscillations in mRNA and protein levels while positive feedback loops are primarily responsible for signal amplification. It is often the case in real biological systems that both negative and positive feedback loops operate in parameter regimes that result in low copy numbers of gene products. In this paper we investigate the spatio-temporal dynamics of a single feedback loop in a eukaryotic cell. We first develop a simplified spatial stochastic model of a canonical feedback system (either positive or negative). Using a Gillespie's algorithm, we compute sample trajectories and analyse their corresponding statistics. We then derive a system of equations that describe the spatio-temporal evolution of the stochastic means. Subsequently, we examine the spatially homogeneous case and compare the results of numerical simulations with the spatially explicit case. Finally, using a combination of steady-state analysis and data clustering techniques, we explore model behaviour across a subregion of the parameter space that is difficult to access experimentally and compare the parameter landscape of our spatio-temporal and spatially-homogeneous models.
2015-10-01T00:00:00ZSturrock, M.Murray, P. J.Matzavinos, A.Chaplain, M. A. J.A gene regulatory network may be defined as a collection of DNA segments which interact with each other indirectly through their RNA and protein products. Such a network is said to contain a negative feedback loop if its products inhibit gene transcription, and a positive feedback loop if a gene product promotes its own production. Negative feedback loops can create oscillations in mRNA and protein levels while positive feedback loops are primarily responsible for signal amplification. It is often the case in real biological systems that both negative and positive feedback loops operate in parameter regimes that result in low copy numbers of gene products. In this paper we investigate the spatio-temporal dynamics of a single feedback loop in a eukaryotic cell. We first develop a simplified spatial stochastic model of a canonical feedback system (either positive or negative). Using a Gillespie's algorithm, we compute sample trajectories and analyse their corresponding statistics. We then derive a system of equations that describe the spatio-temporal evolution of the stochastic means. Subsequently, we examine the spatially homogeneous case and compare the results of numerical simulations with the spatially explicit case. Finally, using a combination of steady-state analysis and data clustering techniques, we explore model behaviour across a subregion of the parameter space that is difficult to access experimentally and compare the parameter landscape of our spatio-temporal and spatially-homogeneous models.An exact collisionless equilibrium for the Force-Free Harris Sheet with low plasma betaAllanson, Oliver DouglasNeukirch, ThomasWilson, FionaTroscheit, Saschahttp://hdl.handle.net/10023/76912018-03-18T01:36:16Z2015-10-01T00:00:00ZWe present a first discussion and analysis of the physical properties of a new exact collisionless equilibrium for a one-dimensional nonlinear force-free magnetic field, namely, the force-free Harris sheet. The solution allows any value of the plasma beta, and crucially below unity, which previous nonlinear force-free collisionless equilibria could not. The distribution function involves infinite series of Hermite polynomials in the canonical momenta, of which the important mathematical properties of convergence and non-negativity have recently been proven. Plots of the distribution function are presented for the plasma beta modestly below unity, and we compare the shape of the distribution function in two of the velocity directions to a Maxwellian distribution.
Funding: STFC Consolidated Grant [ST/K000950/1] (OA, TN & FW) and a Doctoral Training Grant [ST/K502327/1] (OA). EPSRC Doctoral Training Grant [EP/K503162/1] (ST).
2015-10-01T00:00:00ZAllanson, Oliver DouglasNeukirch, ThomasWilson, FionaTroscheit, SaschaWe present a first discussion and analysis of the physical properties of a new exact collisionless equilibrium for a one-dimensional nonlinear force-free magnetic field, namely, the force-free Harris sheet. The solution allows any value of the plasma beta, and crucially below unity, which previous nonlinear force-free collisionless equilibria could not. The distribution function involves infinite series of Hermite polynomials in the canonical momenta, of which the important mathematical properties of convergence and non-negativity have recently been proven. Plots of the distribution function are presented for the plasma beta modestly below unity, and we compare the shape of the distribution function in two of the velocity directions to a Maxwellian distribution.3D whole-prominence fine structure modeling. II. Prominence evolutionGunar, StanislavMackay, Duncan Hendryhttp://hdl.handle.net/10023/76832018-02-11T01:32:49Z2015-10-20T00:00:00ZWe use the new three-dimensional (3D) whole-prominence fine structure model to study the evolution of prominences and their fine structures in response to changes in the underlying photospheric magnetic flux distribution. The applied model combines a detailed 3D prominence magnetic field configuration with a realistic description of the prominence plasma distributed along multiple fine structures. In addition, we utilize an approximate Hα visualization technique to study the evolution of the visible cool prominence plasma both in emission (prominence) and absorption (filament). We show that the initial magnetic field configuration of the modeled prominence is significantly disturbed by the changing position of a single polarity of a magnetic bipole as the bipole is advected toward the main body of the filament. This leads to the creation of a barb, which becomes the dominant feature visible in the synthetic Hα images of both the prominence and filament views. The evolution of the bipole also creates conditions that lead to the disappearance and reappearance of large portions of the main body. We also show that an arch-like region containing a dark void (a bubble) can be naturally produced in the synthetic prominence Hα images. While not visible in terms of the magnetic field lines, it is due to a lack of Hα emission from low-pressure, low-density plasma located in shallow magnetic dips lying along the lines of sight intersecting the dark void. In addition, a quasi-vertical small-scale feature consisting of short and deep dips, piled one above the other, is produced.
2015-10-20T00:00:00ZGunar, StanislavMackay, Duncan HendryWe use the new three-dimensional (3D) whole-prominence fine structure model to study the evolution of prominences and their fine structures in response to changes in the underlying photospheric magnetic flux distribution. The applied model combines a detailed 3D prominence magnetic field configuration with a realistic description of the prominence plasma distributed along multiple fine structures. In addition, we utilize an approximate Hα visualization technique to study the evolution of the visible cool prominence plasma both in emission (prominence) and absorption (filament). We show that the initial magnetic field configuration of the modeled prominence is significantly disturbed by the changing position of a single polarity of a magnetic bipole as the bipole is advected toward the main body of the filament. This leads to the creation of a barb, which becomes the dominant feature visible in the synthetic Hα images of both the prominence and filament views. The evolution of the bipole also creates conditions that lead to the disappearance and reappearance of large portions of the main body. We also show that an arch-like region containing a dark void (a bubble) can be naturally produced in the synthetic prominence Hα images. While not visible in terms of the magnetic field lines, it is due to a lack of Hα emission from low-pressure, low-density plasma located in shallow magnetic dips lying along the lines of sight intersecting the dark void. In addition, a quasi-vertical small-scale feature consisting of short and deep dips, piled one above the other, is produced.Formation and large-scale patterns of filament channels and filamentsMackay, Duncan Hendryhttp://hdl.handle.net/10023/76732017-12-31T00:39:23Z2015-01-01T00:00:00ZThe properties and large-scale patterns of filament channels and filaments are considered. Initially, the global formation locations of filament channels and filaments are discussed, along with their hemispheric pattern. Next, observations of the formation of filament channels and filaments are described where two opposing views are considered. Finally, the wide range of models that have been constructed to consider the formation of filament channels and filaments over long time-scales are described, along with the origin of the hemispheric pattern of filaments.
2015ASSL..415..355M
2015-01-01T00:00:00ZMackay, Duncan HendryThe properties and large-scale patterns of filament channels and filaments are considered. Initially, the global formation locations of filament channels and filaments are discussed, along with their hemispheric pattern. Next, observations of the formation of filament channels and filaments are described where two opposing views are considered. Finally, the wide range of models that have been constructed to consider the formation of filament channels and filaments over long time-scales are described, along with the origin of the hemispheric pattern of filaments.Particle energisation in a collapsing magnetic trap model : the relativistic regimeEradat Oskoui, S.Neukirch, T.http://hdl.handle.net/10023/76032018-01-07T03:08:56Z2014-07-01T00:00:00ZContext. In solar flares, a large number of charged particles is accelerated to high energies. By which physical processes this is achieved is one of the main open problems in solar physics. It has been suggested that during a flare, regions of the rapidly relaxing magnetic field can form a collapsing magnetic trap (CMT) and that this trap may contribute to particle energisation. Aims. In this Research Note we focus on a particular analytical CMT model based on kinematic magnetohydrodynamics. Previous investigations of particle acceleration for this CMT model focused on the non-relativistic energy regime. It is the specific aim of this Research Note to extend the previous work to relativistic particle energies. Methods. Particle orbits were calculated numerically using the relativistic guiding centre equations. We also calculated particle orbits using the non-relativistic guiding centre equations for comparison. Results. For mildly relativistic energies the relativistic and non-relativistic particle orbits mainly agree well, but clear deviations are seen for higher energies. In particular, the final particle energies obtained from the relativistic calculations are systematically lower than the energies reached from the corresponding non-relativistic calculations, and the mirror points of the relativistic orbits are systematically higher than for the corresponding non-relativistic orbits. Conclusions. While the overall behaviour of particle orbits in CMTs does not differ qualitatively when using the relativistic guiding centre equations, there are a few systematic quantitative differences between relativistic and non-relativistic particle dynamics.
The authors acknowledge financial support by the UK’s Science and Technology Facilities Council through a Doctoral Training Grant (SEO) and Consolidated Grant ST/K000950/1 (SEO and TN).
2014-07-01T00:00:00ZEradat Oskoui, S.Neukirch, T.Context. In solar flares, a large number of charged particles is accelerated to high energies. By which physical processes this is achieved is one of the main open problems in solar physics. It has been suggested that during a flare, regions of the rapidly relaxing magnetic field can form a collapsing magnetic trap (CMT) and that this trap may contribute to particle energisation. Aims. In this Research Note we focus on a particular analytical CMT model based on kinematic magnetohydrodynamics. Previous investigations of particle acceleration for this CMT model focused on the non-relativistic energy regime. It is the specific aim of this Research Note to extend the previous work to relativistic particle energies. Methods. Particle orbits were calculated numerically using the relativistic guiding centre equations. We also calculated particle orbits using the non-relativistic guiding centre equations for comparison. Results. For mildly relativistic energies the relativistic and non-relativistic particle orbits mainly agree well, but clear deviations are seen for higher energies. In particular, the final particle energies obtained from the relativistic calculations are systematically lower than the energies reached from the corresponding non-relativistic calculations, and the mirror points of the relativistic orbits are systematically higher than for the corresponding non-relativistic orbits. Conclusions. While the overall behaviour of particle orbits in CMTs does not differ qualitatively when using the relativistic guiding centre equations, there are a few systematic quantitative differences between relativistic and non-relativistic particle dynamics.Multi-scale modelling of the dynamics of cell colonies : insights into cell-adhesion forces and cancer invasion from in silico simulationsSchluter, Daniela K.Ramis-Conde, IgnacioChaplain, Mark A. J.http://hdl.handle.net/10023/75712017-10-23T10:30:09Z2015-02-01T00:00:00ZStudying the biophysical interactions between cells is crucial to understanding how normal tissue develops, how it is structured and also when malfunctions occur. Traditional experiments try to infer events at the tissue level after observing the behaviour of and interactions between individual cells. This approach assumes that cells behave in the same biophysical manner in isolated experiments as they do within colonies and tissues. In this paper, we develop a multi-scale multi-compartment mathematical model that accounts for the principal biophysical interactions and adhesion pathways not only at a cell?cell level but also at the level of cell colonies (in contrast to the traditional approach). Our results suggest that adhesion/separation forces between cells may be lower in cell colonies than traditional isolated single-cell experiments infer. As a consequence, isolated single-cell experiments may be insufficient to deduce important biological processes such as single-cell invasion after detachment from a solid tumour. The simulations further show that kinetic rates and cell biophysical characteristics such as pressure-related cell-cycle arrest have a major influence on cell colony patterns and can allow for the development of protrusive cellular structures as seen in invasive cancer cell lines independent of expression levels of pro-invasion molecules.
2015-02-01T00:00:00ZSchluter, Daniela K.Ramis-Conde, IgnacioChaplain, Mark A. J.Studying the biophysical interactions between cells is crucial to understanding how normal tissue develops, how it is structured and also when malfunctions occur. Traditional experiments try to infer events at the tissue level after observing the behaviour of and interactions between individual cells. This approach assumes that cells behave in the same biophysical manner in isolated experiments as they do within colonies and tissues. In this paper, we develop a multi-scale multi-compartment mathematical model that accounts for the principal biophysical interactions and adhesion pathways not only at a cell?cell level but also at the level of cell colonies (in contrast to the traditional approach). Our results suggest that adhesion/separation forces between cells may be lower in cell colonies than traditional isolated single-cell experiments infer. As a consequence, isolated single-cell experiments may be insufficient to deduce important biological processes such as single-cell invasion after detachment from a solid tumour. The simulations further show that kinetic rates and cell biophysical characteristics such as pressure-related cell-cycle arrest have a major influence on cell colony patterns and can allow for the development of protrusive cellular structures as seen in invasive cancer cell lines independent of expression levels of pro-invasion molecules.Hopf bifurcation in a gene regulatory network model : molecular movement causes oscillationsChaplain, MarkPtashnyk, MariyaSturrock, Marchttp://hdl.handle.net/10023/75642018-01-07T03:06:02Z2015-06-15T00:00:00ZGene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper, we analyze a mathematical model of a canonical gene regulatory network consisting of a single negative feedback loop between a protein and its mRNA (e.g. the Hes1 transcription factor system). The model consists of two partial differential equations describing the spatio-temporal inter- actions between the protein and its mRNA in a 1-dimensional domain. Such intracellular negative feedback systems are known to exhibit oscillatory behavior and this is the case for our model, shown initially via computational simulations. In order to investigate this behavior more deeply, we undertake a linearized stability analysis of the steady states of the model. Our results show that the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf bifurcation. This shows that the spatial movement of the mRNA and protein molecules alone is sufficient to cause the oscillations. Our result has implications for transcription factors such as p53, NF-κB and heat shock proteins which are involved in regulating important cellular processes such as inflammation, meiosis, apoptosis and the heat shock response, and are linked to diseases such as arthritis and cancer.
M.A.J.C. and M.S. gratefully acknowledge the support of the ERC Advanced Investigator Grant 227619, “M5CGS — From Mutations to Metastases: Multiscale Mathematical Modelling of Cancer Growth and Spread”. M.S. would also like to thank the support from the Mathematical Biosciences Institute at the Ohio State University and NSF Grant DMS0931642.
2015-06-15T00:00:00ZChaplain, MarkPtashnyk, MariyaSturrock, MarcGene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper, we analyze a mathematical model of a canonical gene regulatory network consisting of a single negative feedback loop between a protein and its mRNA (e.g. the Hes1 transcription factor system). The model consists of two partial differential equations describing the spatio-temporal inter- actions between the protein and its mRNA in a 1-dimensional domain. Such intracellular negative feedback systems are known to exhibit oscillatory behavior and this is the case for our model, shown initially via computational simulations. In order to investigate this behavior more deeply, we undertake a linearized stability analysis of the steady states of the model. Our results show that the diffusion coefficient of the protein/mRNA acts as a bifurcation parameter and gives rise to a Hopf bifurcation. This shows that the spatial movement of the mRNA and protein molecules alone is sufficient to cause the oscillations. Our result has implications for transcription factors such as p53, NF-κB and heat shock proteins which are involved in regulating important cellular processes such as inflammation, meiosis, apoptosis and the heat shock response, and are linked to diseases such as arthritis and cancer.Magnetospheric signatures of ionospheric density cavities observed by ClusterRussell, Alexander John BarkwayKarlsson, TomasWright, Andrew Nicholashttp://hdl.handle.net/10023/75092018-01-10T19:30:04Z2015-03-01T00:00:00ZWe present Cluster measurements of large amplitude electric fields corre- lated with intense downward field-aligned currents, observed during a nightside crossing of the auroral zone. The data are reproduced by a simple model of magnetosphere-ionosphere coupling which, under different conditions, can also produce a divergent electric field signature in the downward current region, or correlation between the electric and perturbed magnetic fields. We conclude that strong electric field associated with intense downward field-aligned current, such as this observation, is a signature of ionospheric plasma depletion caused by the downward current. It is also shown that the electric field in the downward current region correlates with downward current density if a background field is present, e.g. due to magnetospheric convection.
AJBR ackowledges support from STFC under consolidated grant ST/K000993/1.
2015-03-01T00:00:00ZRussell, Alexander John BarkwayKarlsson, TomasWright, Andrew NicholasWe present Cluster measurements of large amplitude electric fields corre- lated with intense downward field-aligned currents, observed during a nightside crossing of the auroral zone. The data are reproduced by a simple model of magnetosphere-ionosphere coupling which, under different conditions, can also produce a divergent electric field signature in the downward current region, or correlation between the electric and perturbed magnetic fields. We conclude that strong electric field associated with intense downward field-aligned current, such as this observation, is a signature of ionospheric plasma depletion caused by the downward current. It is also shown that the electric field in the downward current region correlates with downward current density if a background field is present, e.g. due to magnetospheric convection.Strategies of eradicating glioma cells : a multi-scale mathematical model with miR-451-AMPK-mTOR controlKim, YangjinPowathil, GibinKang, HyunjiTrucu, DumitruKim, HyeongiLawler, SeanChaplain, Markhttp://hdl.handle.net/10023/75032018-01-07T03:06:05Z2015-01-28T00:00:00ZThe cellular dispersion and therapeutic control of glioblastoma, the most aggressive type of primary brain cancer, depends critically on the migration patterns after surgery and intracellular responses of the individual cancer cells in response to external biochemical and biomechanical cues in the microenvironment. Recent studies have shown that a particular microRNA, miR-451, regulates downstream molecules including AMPK and mTOR to determine the balance between rapid proliferation and invasion in response to metabolic stress in the harsh tumor microenvironment. Surgical removal of main tumor is inevitably followed by recurrence of the tumor due to inaccessibility of dispersed tumor cells in normal brain tissue. In order to address this multi-scale nature of glioblastoma proliferation and invasion and its response to conventional treatment, we propose a hybrid model of glioblastoma that analyses spatio-temporal dynamics at the cellular level, linking individual tumor cells with the macroscopic behaviour of cell organization and the microenvironment, and with the intracellular dynamics of miR-451-AMPK-mTOR signaling within a tumour cell. The model identifies a key mechanism underlying the molecular switches between proliferative phase and migratory phase in response to metabolic stress and biophysical interaction between cells in response to fluctuating glucose levels in the presence of blood vessels (BVs). The model predicts that cell migration, therefore efficacy of the treatment, not only depends on oxygen and glucose availability but also on the relative balance between random motility and strength of chemoattractants. Effective control of growing cells near BV sites in addition to relocalization of invisible migratory cells back to the resection site was suggested as a way of eradicating these migratory cells.
2015-01-28T00:00:00ZKim, YangjinPowathil, GibinKang, HyunjiTrucu, DumitruKim, HyeongiLawler, SeanChaplain, MarkThe cellular dispersion and therapeutic control of glioblastoma, the most aggressive type of primary brain cancer, depends critically on the migration patterns after surgery and intracellular responses of the individual cancer cells in response to external biochemical and biomechanical cues in the microenvironment. Recent studies have shown that a particular microRNA, miR-451, regulates downstream molecules including AMPK and mTOR to determine the balance between rapid proliferation and invasion in response to metabolic stress in the harsh tumor microenvironment. Surgical removal of main tumor is inevitably followed by recurrence of the tumor due to inaccessibility of dispersed tumor cells in normal brain tissue. In order to address this multi-scale nature of glioblastoma proliferation and invasion and its response to conventional treatment, we propose a hybrid model of glioblastoma that analyses spatio-temporal dynamics at the cellular level, linking individual tumor cells with the macroscopic behaviour of cell organization and the microenvironment, and with the intracellular dynamics of miR-451-AMPK-mTOR signaling within a tumour cell. The model identifies a key mechanism underlying the molecular switches between proliferative phase and migratory phase in response to metabolic stress and biophysical interaction between cells in response to fluctuating glucose levels in the presence of blood vessels (BVs). The model predicts that cell migration, therefore efficacy of the treatment, not only depends on oxygen and glucose availability but also on the relative balance between random motility and strength of chemoattractants. Effective control of growing cells near BV sites in addition to relocalization of invisible migratory cells back to the resection site was suggested as a way of eradicating these migratory cells.Sunspot rotation. I : A consequence of flux emergenceSturrock, ZoeHood, Alan WilliamArchontis, VasilisMcNeill, Craighttp://hdl.handle.net/10023/74972018-01-07T03:06:57Z2015-10-12T00:00:00ZContext. Solar eruptions and high flare activity often accompany the rapid rotation of sunspots. The study of sunspot rotation and the mechanisms driving this motion are therefore key to our understanding of how the solar atmosphere attains the conditions necessary for large energy release. Aims. We aim to demonstrate and investigate the rotation of sunspots in a 3D numerical experiment of the emergence of a magnetic flux tube as it rises through the solar interior and emerges into the atmosphere. Furthermore, we seek to show that the sub-photospheric twist stored in the interior is injected into the solar atmosphere by means of a definitive rotation of the sunspots. Methods. A numerical experiment is performed to solve the 3D resistive magnetohydrodynamic (MHD) equations using a Lagrangian-Remap code. We track the emergence of a toroidal flux tube as it rises through the solar interior and emerges into the atmosphere investigating various quantities related to both the magnetic field and plasma. Results. Through detailed analysis of the numerical experiment, we find clear evidence that the photospheric footprints or sunspots of the flux tube undergo a rotation. Significant vertical vortical motions are found to develop within the two polarity sources after the field emerges. These rotational motions are found to leave the interior portion of the field untwisted and twist up the atmospheric portion of the field. This is shown by our analysis of the relative magnetic helicity as a significant portion of the interior helicity is transported to the atmosphere. In addition, there is a substantial transport of magnetic energy to the atmosphere. Rotation angles are also calculated by tracing selected fieldlines; the fieldlines threading through the sunspot are found to rotate through angles of up to 353º over the course of the experiment. We explain the rotation by an unbalanced torque produced by the magnetic tension force, rather than an apparent effect.
ZS acknowledges the financial support of the Carnegie Trust for Scotland and CMM the support of the Royal Society of Edinburgh. This work used the DIRAC 1, UKMHD Consortium machine at the University of St Andrews and the DiRAC Data Centric system at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk). This equipment was funded by BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/H008519/1, and STFC DiRAC Operations grant ST/K003267/1 and Durham University. DiRAC is part of the National E-Infrastructure.
2015-10-12T00:00:00ZSturrock, ZoeHood, Alan WilliamArchontis, VasilisMcNeill, CraigContext. Solar eruptions and high flare activity often accompany the rapid rotation of sunspots. The study of sunspot rotation and the mechanisms driving this motion are therefore key to our understanding of how the solar atmosphere attains the conditions necessary for large energy release. Aims. We aim to demonstrate and investigate the rotation of sunspots in a 3D numerical experiment of the emergence of a magnetic flux tube as it rises through the solar interior and emerges into the atmosphere. Furthermore, we seek to show that the sub-photospheric twist stored in the interior is injected into the solar atmosphere by means of a definitive rotation of the sunspots. Methods. A numerical experiment is performed to solve the 3D resistive magnetohydrodynamic (MHD) equations using a Lagrangian-Remap code. We track the emergence of a toroidal flux tube as it rises through the solar interior and emerges into the atmosphere investigating various quantities related to both the magnetic field and plasma. Results. Through detailed analysis of the numerical experiment, we find clear evidence that the photospheric footprints or sunspots of the flux tube undergo a rotation. Significant vertical vortical motions are found to develop within the two polarity sources after the field emerges. These rotational motions are found to leave the interior portion of the field untwisted and twist up the atmospheric portion of the field. This is shown by our analysis of the relative magnetic helicity as a significant portion of the interior helicity is transported to the atmosphere. In addition, there is a substantial transport of magnetic energy to the atmosphere. Rotation angles are also calculated by tracing selected fieldlines; the fieldlines threading through the sunspot are found to rotate through angles of up to 353º over the course of the experiment. We explain the rotation by an unbalanced torque produced by the magnetic tension force, rather than an apparent effect.Evolution of field line helicity during magnetic reconnectionRussell, A. J. B.Yeates, A. R.Hornig, G.Wilmot-Smith, A. L.http://hdl.handle.net/10023/74852018-03-11T01:33:57Z2015-03-01T00:00:00ZWe investigate the evolution of field line helicity for magnetic fields that connect two boundaries without null points, with emphasis on localized finite-B magnetic reconnection. Total ( relative) magnetic helicity is already recognized as an important topological constraint on magnetohydrodynamic processes. Field line helicity offers further advantages because it preserves all topological information and can distinguish between different magnetic fields with the same total helicity. Magnetic reconnection changes field connectivity and field line helicity reflects these changes; the goal of this paper is to characterize that evolution. We start by deriving the evolution equation for field line helicity and examining its terms, also obtaining a simplified form for cases where dynamics are localized within the domain. The main result, which we support using kinematic examples, is that during localized reconnection in a complex magnetic field, the evolution of field line helicity is dominated by a work-like term that is evaluated at the field line endpoints, namely, the scalar product of the generalized field line velocity and the vector potential. Furthermore, the flux integral of this term over certain areas is very small compared to the integral of the unsigned quantity, which indicates that changes of field line helicity happen in a well-organized pairwise manner. It follows that reconnection is very efficient at redistributing helicity in complex magnetic fields despite having little effect on the total helicity.
This work was supported by the Science and Technology Facilities Council (UK) through consortium Grant Nos. ST/K000993/1 and ST/K001043 to the University of Dundee and Durham University.
2015-03-01T00:00:00ZRussell, A. J. B.Yeates, A. R.Hornig, G.Wilmot-Smith, A. L.We investigate the evolution of field line helicity for magnetic fields that connect two boundaries without null points, with emphasis on localized finite-B magnetic reconnection. Total ( relative) magnetic helicity is already recognized as an important topological constraint on magnetohydrodynamic processes. Field line helicity offers further advantages because it preserves all topological information and can distinguish between different magnetic fields with the same total helicity. Magnetic reconnection changes field connectivity and field line helicity reflects these changes; the goal of this paper is to characterize that evolution. We start by deriving the evolution equation for field line helicity and examining its terms, also obtaining a simplified form for cases where dynamics are localized within the domain. The main result, which we support using kinematic examples, is that during localized reconnection in a complex magnetic field, the evolution of field line helicity is dominated by a work-like term that is evaluated at the field line endpoints, namely, the scalar product of the generalized field line velocity and the vector potential. Furthermore, the flux integral of this term over certain areas is very small compared to the integral of the unsigned quantity, which indicates that changes of field line helicity happen in a well-organized pairwise manner. It follows that reconnection is very efficient at redistributing helicity in complex magnetic fields despite having little effect on the total helicity.On the theory of translationally invariant magnetohydrodynamic equilibria with anisotropic pressure and magnetic shearHodgson, Jonathan David BrockieNeukirch, Thomashttp://hdl.handle.net/10023/74842018-01-07T03:06:21Z2015-01-01T00:00:00ZWe present an improved formalism for translationally invariant magnetohydrodynamic equilibria with anisotropic pressure and currents with a field aligned component. The derivation of a Grad-Shafranov type equation is given along with a constraint which links the shear field to the parallel pressure. The difficulties of the formalism are discussed and various methods of circumventing these difficulties are given. A simple example is then used to highlight the methods and difficulties involved.
Funding: STFC Doctoral Training Grant ST/K502327/1 (Jonathan Hodgson) and STFC Consolidated Grant ST/K000950/1 (Thomas Neukirch)
2015-01-01T00:00:00ZHodgson, Jonathan David BrockieNeukirch, ThomasWe present an improved formalism for translationally invariant magnetohydrodynamic equilibria with anisotropic pressure and currents with a field aligned component. The derivation of a Grad-Shafranov type equation is given along with a constraint which links the shear field to the parallel pressure. The difficulties of the formalism are discussed and various methods of circumventing these difficulties are given. A simple example is then used to highlight the methods and difficulties involved.Coronal heating in multiple magnetic threadsTam, Kuan VaiHood, Alan WilliamBrowning, PhilippaCargill, Peterhttp://hdl.handle.net/10023/72592018-01-07T03:04:16Z2015-08-01T00:00:00ZContext. Heating the solar corona to several million degrees requires the conversion of magnetic energy into thermal energy. In this paper, we investigate whether an unstable magnetic thread within a coronal loop can destabilise a neighbouring magnetic thread. Aims. By running a series of simulations, we aim to understand under what conditions the destabilisation of a single magnetic thread can also trigger a release of energy in a nearby thread. Methods. The 3D magnetohydrodynamics code, Lare3d, is used to simulate the temporal evolution of coronal magnetic fields during a kink instability and the subsequent relaxation process. We assume that a coronal magnetic loop consists of non-potential magnetic threads that are initially in an equilibrium state. Results. The non-linear kink instability in one magnetic thread forms a helical current sheet and initiates magnetic reconnection. The current sheet fragments, and magnetic energy is released throughout that thread. We find that, under certain conditions, this event can destabilise a nearby thread, which is a necessary requirement for starting an avalanche of energy release in magnetic threads. Conclusions. It is possible to initiate an energy release in a nearby, non-potential magnetic thread, because the energy released from one unstable magnetic thread can trigger energy release in nearby threads, provided that the nearby structures are close to marginal stability.
We acknowledge the financial support of STFC through the Consolidated grant to the University of St Andrews.
2015-08-01T00:00:00ZTam, Kuan VaiHood, Alan WilliamBrowning, PhilippaCargill, PeterContext. Heating the solar corona to several million degrees requires the conversion of magnetic energy into thermal energy. In this paper, we investigate whether an unstable magnetic thread within a coronal loop can destabilise a neighbouring magnetic thread. Aims. By running a series of simulations, we aim to understand under what conditions the destabilisation of a single magnetic thread can also trigger a release of energy in a nearby thread. Methods. The 3D magnetohydrodynamics code, Lare3d, is used to simulate the temporal evolution of coronal magnetic fields during a kink instability and the subsequent relaxation process. We assume that a coronal magnetic loop consists of non-potential magnetic threads that are initially in an equilibrium state. Results. The non-linear kink instability in one magnetic thread forms a helical current sheet and initiates magnetic reconnection. The current sheet fragments, and magnetic energy is released throughout that thread. We find that, under certain conditions, this event can destabilise a nearby thread, which is a necessary requirement for starting an avalanche of energy release in magnetic threads. Conclusions. It is possible to initiate an energy release in a nearby, non-potential magnetic thread, because the energy released from one unstable magnetic thread can trigger energy release in nearby threads, provided that the nearby structures are close to marginal stability.Are tornado-like magnetic structures able to support solar prominence plasma?Luna, M.Moreno-Insertis, F.Priest, E.http://hdl.handle.net/10023/72022018-01-28T01:32:49Z2015-07-20T00:00:00ZRecent high-resolution and high-cadence observations have surprisingly suggested that prominence barbs exhibit apparent rotating motions suggestive of a tornado-like structure. Additional evidence has been provided by Doppler measurements. The observations reveal opposite velocities for both hot and cool plasma on the two sides of a prominence barb. This motion is persistent for several hours and has been interpreted in terms of rotational motion of prominence feet. Several authors suggest that such barb motions are rotating helical structures around a vertical axis similar to tornadoes on Earth. One of the difficulties of such a proposal is how to support cool prominence plasma in almost-vertical structures against gravity. In this work we model analytically a tornado-like structure and try to determine possible mechanisms to support the prominence plasma. We have found that the Lorentz force can indeed support the barb plasma provided the magnetic structure is sufficiently twisted and/or significant poloidal flows are present.
M. Luna and F. Moreno-Insertis acknowledge support by the Spanish Ministry of Economy and Competitiveness through projects AYA2011-24808 and AYA2014-55078-P. M.L. is also grateful to ERC-2011-StG 277829-SPIA. E.R.P. is grateful to the UK STFC and the Leverhulme Trust for financial support.
2015-07-20T00:00:00ZLuna, M.Moreno-Insertis, F.Priest, E.Recent high-resolution and high-cadence observations have surprisingly suggested that prominence barbs exhibit apparent rotating motions suggestive of a tornado-like structure. Additional evidence has been provided by Doppler measurements. The observations reveal opposite velocities for both hot and cool plasma on the two sides of a prominence barb. This motion is persistent for several hours and has been interpreted in terms of rotational motion of prominence feet. Several authors suggest that such barb motions are rotating helical structures around a vertical axis similar to tornadoes on Earth. One of the difficulties of such a proposal is how to support cool prominence plasma in almost-vertical structures against gravity. In this work we model analytically a tornado-like structure and try to determine possible mechanisms to support the prominence plasma. We have found that the Lorentz force can indeed support the barb plasma provided the magnetic structure is sufficiently twisted and/or significant poloidal flows are present.Effect of Prandtl's ration on balance in geophysical turbulenceDritschel, David GerardMcKiver, William Josephhttp://hdl.handle.net/10023/72012018-01-07T03:03:53Z2015-07-21T00:00:00ZThe fluid dynamics of the atmosphere and oceans are to a large extent controlled by the slow evolution of a scalar field called ‘potential vorticity’, with relatively fast motions such as inertia-gravity waves playing only a minor role. This state of affairs is commonly referred to as ‘balance’. Potential vorticity (PV) is a special scalar field which is materially conserved in the absence of diabatic effects and dissipation, effects which are generally weak in the atmosphere and oceans. Moreover, in a balanced flow, PV induces the entire fluid motion and its thermodynamic structure (Hoskins et al. 1985). While exact balance is generally not achievable, it is now well established that balance holds to a high degree of accuracy in rapidly rotating and strongly stratified flows. Such flows are characterised by both a small Rossby number, Ro ≡ |ζ|max/f, and a small Froude number, Fr ≡ |.h|max/N, where ζ and .h are the relative vertical and horizontal vorticity components, while f and N are the Coriolis and buoyancy frequencies. In fact, balance can even be a good approximation when Fr < ∼ Ro ∼ O(1). In this study, we examine how balance depends specifically on Prandtl’s ratio, f/N, in unforced freely-evolving turbulence. We examine a wide variety of turbulent flows, at a mature and complex stage of their evolution, making use of the fully non-hydrostatic equations under the Boussinesq and incompressible approximations. We perform numerical simulations at exceptionally high resolution in order to carefully assess the degree to which balance holds, and to determine when it breaks down. For this purpose, it proves most useful to employ an invariant, PV-based Rossby number ε, together with f/N. For a given ε, our key finding is that — for at least tens of characteristic vortex rotation periods — the flow is insensitive to f/N for all values for which the flow remains statically stable (typically f/N < ∼1). Only the vertical velocity varies in proportion to f/N, in line with quasi-geostrophic scaling for which Fr2 ≪ Ro ≪ 1. We also find that as ε increases toward unity, the maximum f/N attainable decreases toward 0. No statically stable flows occur for ε > ∼ 1. For all stable flows, balance is found to hold to a remarkably high degree: as measured by an energy norm, imbalance never exceeds more than a few percent of the balance, even in flows where Ro > 1. The vertical velocity w remains a tiny fraction of the horizontal velocity uh, even when w is dominantly balanced. Finally, typical vertical to horizontal scale ratios H/L remain close to f/N, as found previously in quasi-geostrophic turbulence for which Fr ∼ Ro ≪ 1.
Support for this research has come from the UK Engineering and Physical Sciences Research Council (grant no. EP/H001794/1).
2015-07-21T00:00:00ZDritschel, David GerardMcKiver, William JosephThe fluid dynamics of the atmosphere and oceans are to a large extent controlled by the slow evolution of a scalar field called ‘potential vorticity’, with relatively fast motions such as inertia-gravity waves playing only a minor role. This state of affairs is commonly referred to as ‘balance’. Potential vorticity (PV) is a special scalar field which is materially conserved in the absence of diabatic effects and dissipation, effects which are generally weak in the atmosphere and oceans. Moreover, in a balanced flow, PV induces the entire fluid motion and its thermodynamic structure (Hoskins et al. 1985). While exact balance is generally not achievable, it is now well established that balance holds to a high degree of accuracy in rapidly rotating and strongly stratified flows. Such flows are characterised by both a small Rossby number, Ro ≡ |ζ|max/f, and a small Froude number, Fr ≡ |.h|max/N, where ζ and .h are the relative vertical and horizontal vorticity components, while f and N are the Coriolis and buoyancy frequencies. In fact, balance can even be a good approximation when Fr < ∼ Ro ∼ O(1). In this study, we examine how balance depends specifically on Prandtl’s ratio, f/N, in unforced freely-evolving turbulence. We examine a wide variety of turbulent flows, at a mature and complex stage of their evolution, making use of the fully non-hydrostatic equations under the Boussinesq and incompressible approximations. We perform numerical simulations at exceptionally high resolution in order to carefully assess the degree to which balance holds, and to determine when it breaks down. For this purpose, it proves most useful to employ an invariant, PV-based Rossby number ε, together with f/N. For a given ε, our key finding is that — for at least tens of characteristic vortex rotation periods — the flow is insensitive to f/N for all values for which the flow remains statically stable (typically f/N < ∼1). Only the vertical velocity varies in proportion to f/N, in line with quasi-geostrophic scaling for which Fr2 ≪ Ro ≪ 1. We also find that as ε increases toward unity, the maximum f/N attainable decreases toward 0. No statically stable flows occur for ε > ∼ 1. For all stable flows, balance is found to hold to a remarkably high degree: as measured by an energy norm, imbalance never exceeds more than a few percent of the balance, even in flows where Ro > 1. The vertical velocity w remains a tiny fraction of the horizontal velocity uh, even when w is dominantly balanced. Finally, typical vertical to horizontal scale ratios H/L remain close to f/N, as found previously in quasi-geostrophic turbulence for which Fr ∼ Ro ≪ 1.On the parallel and perpendicular propagating motions visible in polar plumes : an incubator for (fast) solar wind acceleration?Liu, JiajiaMcIntosh, Scott W.De Moortel, InekeWang, Yuminghttp://hdl.handle.net/10023/71902018-01-07T03:06:36Z2015-06-20T00:00:00ZWe combine observations of the Coronal Multi-channel Polarimeter and the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory to study the characteristic properties of (propagating) Alfvenic motions and quasi-periodic intensity disturbances in polar plumes. This unique combination of instruments highlights the physical richness of the processes taking place at the base of the (fast) solar wind. The (parallel) intensity perturbations with intensity enhancements around 1% have an apparent speed of 120 km s(-1) (in both the 171 and 193 angstrom passbands) and a periodicity of 15 minutes, while the (perpendicular) Alfvenic wave motions have a velocity amplitude of 0.5 km s(-1), a phase speed of 830 km s(-1), and a shorter period of 5 minutes on the same structures. These observations illustrate a scenario where the excited Alfvenic motions are propagating along an inhomogeneously loaded magnetic field structure such that the combination could be a potential progenitor of the magnetohydrodynamic turbulence required to accelerate the fast solar wind.
J.L. was a student visitor at HAO. J.L. acknowledges the financial support for his visit to HAO from the Chinese Scholarship Council (CSC). The authors acknowledge support from NSFC 41131065, 41121003, 973 Key Project 2011CB811403, and CAS Key Research Program KZZD-EW-01-4. We also acknowledge support from NASA contracts NNX08BA99G, NNX11AN98G, NNM12AB40P, NNG09FA40C (IRIS), and NNM07AA01C (Hinode). The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/ 2007-2013) under the grant agreement SOLSPANET (project No. 269299, www.solspanet.eu/solspanet) Date of Acceptance: 25/05/2015
2015-06-20T00:00:00ZLiu, JiajiaMcIntosh, Scott W.De Moortel, InekeWang, YumingWe combine observations of the Coronal Multi-channel Polarimeter and the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory to study the characteristic properties of (propagating) Alfvenic motions and quasi-periodic intensity disturbances in polar plumes. This unique combination of instruments highlights the physical richness of the processes taking place at the base of the (fast) solar wind. The (parallel) intensity perturbations with intensity enhancements around 1% have an apparent speed of 120 km s(-1) (in both the 171 and 193 angstrom passbands) and a periodicity of 15 minutes, while the (perpendicular) Alfvenic wave motions have a velocity amplitude of 0.5 km s(-1), a phase speed of 830 km s(-1), and a shorter period of 5 minutes on the same structures. These observations illustrate a scenario where the excited Alfvenic motions are propagating along an inhomogeneously loaded magnetic field structure such that the combination could be a potential progenitor of the magnetohydrodynamic turbulence required to accelerate the fast solar wind.Uncertainties in polarimetric 3D reconstructions of coronal mass ejectionsBemporad, A.Pagano, P.http://hdl.handle.net/10023/71782018-01-07T03:06:35Z2015-04-06T00:00:00ZAims. The aim of this work is to quantify the uncertainties in the three-dimensional (3D) reconstruction of the location of coronal mass ejections (CMEs) obtained with the so-called polarization ratio technique. The method takes advantage of the different distributions along the line of sight of total (tB) and polarized (pB) brightnesses emitted by Thomson scattering to estimate the average location of the emitting plasma. This is particularly important to correctly identify of CME propagation angles and unprojected velocities, thus allowing better capabilities for space weather forecastings. Methods. To this end, we assumed two simple electron density distributions along the line of sight (a constant density and Gaussian density profiles) for a plasma blob and synthesized the expected tB and pB for different distances z of the blob from the plane of the sky and different projected altitudes.. Reconstructed locations of the blob along the line of sight were thus compared with the real ones, allowing a precise determination of uncertainties in the method. Results. Results show that, independently of the analytical density profile, when the blob is centered at a small distance from the plane of the sky (i. e. for limb CMEs) the distance from the plane of the sky starts to be significantly overestimated. Polarization ratio technique provides the line-of-sight position of the center of mass of what we call folded density distribution, given by reflecting and summing in front of the plane of the sky the fraction of density profile located behind that plane. On the other hand, when the blob is far from the plane of the sky, but with very small projected altitudes (i. e. for halo CMEs, rho< 1.4 R-circle dot), the inferred distance from that plane is significantly underestimated. Better determination of the real blob position along the line of sight is given for intermediate locations, and in particular when the blob is centered at an angle of 20 degrees from the plane of the sky. Conclusions. These result have important consequences not only for future 3D reconstruction of CMEs with polarization ratio technique, but also for the design of future coronagraphs aimed at providing a continuous monitoring of halo-CMEs for space weather prediction purposes.
P.P. acknowledges STFC for financial support. Date of Acceptance: 21/01/2015
2015-04-06T00:00:00ZBemporad, A.Pagano, P.Aims. The aim of this work is to quantify the uncertainties in the three-dimensional (3D) reconstruction of the location of coronal mass ejections (CMEs) obtained with the so-called polarization ratio technique. The method takes advantage of the different distributions along the line of sight of total (tB) and polarized (pB) brightnesses emitted by Thomson scattering to estimate the average location of the emitting plasma. This is particularly important to correctly identify of CME propagation angles and unprojected velocities, thus allowing better capabilities for space weather forecastings. Methods. To this end, we assumed two simple electron density distributions along the line of sight (a constant density and Gaussian density profiles) for a plasma blob and synthesized the expected tB and pB for different distances z of the blob from the plane of the sky and different projected altitudes.. Reconstructed locations of the blob along the line of sight were thus compared with the real ones, allowing a precise determination of uncertainties in the method. Results. Results show that, independently of the analytical density profile, when the blob is centered at a small distance from the plane of the sky (i. e. for limb CMEs) the distance from the plane of the sky starts to be significantly overestimated. Polarization ratio technique provides the line-of-sight position of the center of mass of what we call folded density distribution, given by reflecting and summing in front of the plane of the sky the fraction of density profile located behind that plane. On the other hand, when the blob is far from the plane of the sky, but with very small projected altitudes (i. e. for halo CMEs, rho< 1.4 R-circle dot), the inferred distance from that plane is significantly underestimated. Better determination of the real blob position along the line of sight is given for intermediate locations, and in particular when the blob is centered at an angle of 20 degrees from the plane of the sky. Conclusions. These result have important consequences not only for future 3D reconstruction of CMEs with polarization ratio technique, but also for the design of future coronagraphs aimed at providing a continuous monitoring of halo-CMEs for space weather prediction purposes.Non-LTE modelling of prominence fine structures using hydrogen Lyman-line profilesSchwartz, P.Gunar, S.Curdt, W.http://hdl.handle.net/10023/71772018-01-07T03:06:34Z2015-05-08T00:00:00ZAims. We perform a detailed statistical analysis of the spectral Lyman-line observations of the quiescent prominence observed on May 18, 2005. Methods. We used a profile-to-profile comparison of the synthetic Lyman spectra obtained by 2D single-thread prominence fine-structure model as a starting point for a full statistical analysis of the observed Lyman spectra. We employed 2D multi-thread fine-structure models with random positions and line-of-sight velocities of each thread to obtain a statistically significant set of synthetic Lyman-line profiles. We used for the first time multi-thread models composed of non-identical threads and viewed at line-of-sight angles different from perpendicular to the magnetic field. Results. We investigated the plasma properties of the prominence observed with the SoHO/SUMER spectrograph on May 18, 2005 by comparing the histograms of three statistical parameters characterizing the properties of the synthetic and observed line profiles. In this way, the integrated intensity, Lyman decrement ratio, and the ratio of intensity at the central reversal to the average intensity of peaks provided insight into the column mass and the central temperature of the prominence fine structures.
Date of Acceptance: 10/03/2015
2015-05-08T00:00:00ZSchwartz, P.Gunar, S.Curdt, W.Aims. We perform a detailed statistical analysis of the spectral Lyman-line observations of the quiescent prominence observed on May 18, 2005. Methods. We used a profile-to-profile comparison of the synthetic Lyman spectra obtained by 2D single-thread prominence fine-structure model as a starting point for a full statistical analysis of the observed Lyman spectra. We employed 2D multi-thread fine-structure models with random positions and line-of-sight velocities of each thread to obtain a statistically significant set of synthetic Lyman-line profiles. We used for the first time multi-thread models composed of non-identical threads and viewed at line-of-sight angles different from perpendicular to the magnetic field. Results. We investigated the plasma properties of the prominence observed with the SoHO/SUMER spectrograph on May 18, 2005 by comparing the histograms of three statistical parameters characterizing the properties of the synthetic and observed line profiles. In this way, the integrated intensity, Lyman decrement ratio, and the ratio of intensity at the central reversal to the average intensity of peaks provided insight into the column mass and the central temperature of the prominence fine structures.Extreme ultraviolet imaging of three-dimensional magnetic reconnection in a solar eruptionSun, J.Q.Cheng, X.Ding, M.D.Guo, Y.Priest, E.R.Parnell, C.E.Edwards, S.J.Zhang, J.Chen, P.F.Fang, C.http://hdl.handle.net/10023/70252018-03-11T01:33:44Z2015-06-26T00:00:00ZMagnetic reconnection, a change of magnetic field connectivity, is a fundamental physical process in which magnetic energy is released explosively, and it is responsible for various eruptive phenomena in the universe. However, this process is difficult to observe directly. Here, the magnetic topology associated with a solar reconnection event is studied in three dimensions using the combined perspectives of two spacecraft. The sequence of extreme ultraviolet images clearly shows that two groups of oppositely directed and non-coplanar magnetic loops gradually approach each other, forming a separator or quasi-separator and then reconnecting. The plasma near the reconnection site is subsequently heated from ∼ 1 to ≥ 5MK. Shortly afterwards, warm flare loops (∼3MK) appear underneath the hot plasma. Other observational signatures of reconnection, including plasma inflows and downflows, are unambiguously revealed and quantitatively measured. These observations provide direct evidence of magnetic reconnection in a three-dimensional configuration and reveal its origin.
X.C., J.Q.S., M.D.D., Y.G., P.F.C. and C.F. are supported by NSFC through grants 11303016, 11373023, 11203014 and 11025314, and by NKBRSF through grants 2011CB811402 and 2014CB744203. C.E.P. and S.J.E. are supported by the UK STFC. J.Z. is supported by US NSF AGS-1249270 and AGS-1156120.
2015-06-26T00:00:00ZSun, J.Q.Cheng, X.Ding, M.D.Guo, Y.Priest, E.R.Parnell, C.E.Edwards, S.J.Zhang, J.Chen, P.F.Fang, C.Magnetic reconnection, a change of magnetic field connectivity, is a fundamental physical process in which magnetic energy is released explosively, and it is responsible for various eruptive phenomena in the universe. However, this process is difficult to observe directly. Here, the magnetic topology associated with a solar reconnection event is studied in three dimensions using the combined perspectives of two spacecraft. The sequence of extreme ultraviolet images clearly shows that two groups of oppositely directed and non-coplanar magnetic loops gradually approach each other, forming a separator or quasi-separator and then reconnecting. The plasma near the reconnection site is subsequently heated from ∼ 1 to ≥ 5MK. Shortly afterwards, warm flare loops (∼3MK) appear underneath the hot plasma. Other observational signatures of reconnection, including plasma inflows and downflows, are unambiguously revealed and quantitatively measured. These observations provide direct evidence of magnetic reconnection in a three-dimensional configuration and reveal its origin.Ergodicity and spectral cascades in point vortex flows on the sphereDritschel, D.G.Lucia, M.Poje, A.C.http://hdl.handle.net/10023/70242018-01-07T03:05:22Z2015-06-29T00:00:00ZWe present results for the equilibrium statistics and dynamic evolution of moderately large [n=O(102-103)] numbers of interacting point vortices on the sphere under the constraint of zero mean angular momentum. For systems with equal numbers of positive and negative identical circulations, the density of rescaled energies, p(E), converges rapidly with n to a function with a single maximum with maximum entropy. Ensemble-averaged wave-number spectra of the nonsingular velocity field induced by the vortices exhibit the expected k-1 behavior at small scales for all energies. Spectra at the largest scales vary continuously with the inverse temperature of the system. For positive temperatures, spectra peak at finite intermediate wave numbers; for negative temperatures, spectra decrease everywhere. Comparisons of time and ensemble averages, over a large range of energies, strongly support ergodicity in the dynamics even for highly atypical initial vortex configurations. Crucially, rapid relaxation of spectra toward the microcanonical average implies that the direction of any spectral cascade process depends only on the relative difference between the initial spectrum and the ensemble mean spectrum at that energy, not on the energy, or temperature, of the system.
A.C.P. was supported under DOD (MURI) Grant No. N000141110087 ONR. The computations were supported by the CUNY HPCC under NSF Grants No. CNS-0855217 and No. CNS-0958379.
2015-06-29T00:00:00ZDritschel, D.G.Lucia, M.Poje, A.C.We present results for the equilibrium statistics and dynamic evolution of moderately large [n=O(102-103)] numbers of interacting point vortices on the sphere under the constraint of zero mean angular momentum. For systems with equal numbers of positive and negative identical circulations, the density of rescaled energies, p(E), converges rapidly with n to a function with a single maximum with maximum entropy. Ensemble-averaged wave-number spectra of the nonsingular velocity field induced by the vortices exhibit the expected k-1 behavior at small scales for all energies. Spectra at the largest scales vary continuously with the inverse temperature of the system. For positive temperatures, spectra peak at finite intermediate wave numbers; for negative temperatures, spectra decrease everywhere. Comparisons of time and ensemble averages, over a large range of energies, strongly support ergodicity in the dynamics even for highly atypical initial vortex configurations. Crucially, rapid relaxation of spectra toward the microcanonical average implies that the direction of any spectral cascade process depends only on the relative difference between the initial spectrum and the ensemble mean spectrum at that energy, not on the energy, or temperature, of the system.Fast approximate radiative transfer method for visualizing the fine structure of prominences in the hydrogen Hα lineHeinzel, P.Gunár, S.Anzer, U.http://hdl.handle.net/10023/70202018-01-07T03:05:19Z2015-07-01T00:00:00ZAims. We present a novel approximate radiative transfer method developed to visualize 3D whole-prominence models with multiple fine structures using the hydrogen Hα spectral line. Methods. This method employs a fast line-of-sight synthesis of the Hα line profiles through the whole 3D prominence volume and realistically reflects the basic properties of the Hα line formation in the cool and low-density prominence medium. The method can be applied both to prominences seen above the limb and filaments seen against the disk. Results. We provide recipes for the use of this method for visualizing the prominence or filament models that have multiple fine structures. We also perform tests of the method that demonstrate its accuracy under prominence conditions. Conclusions. We demonstrate that this fast approximate radiative transfer method provides realistic synthetic Hα intensities useful for a reliable visualization of prominences and filaments. Such synthetic high-resolution images of modeled prominences/filaments can be used for a direct comparison with high-resolution observations.
P.H. acknowledges the support from grant 209/12/0906 of the Grant Agency of the Czech Republic. S.G. acknowledges support from the European Commission via the Marie Curie Actions – Intra-European Fellowships Project No. 328138. P.H. and S.G. acknowledge support from project RVO:67985815 of the Astronomical Institute of the Czech Academy of Sciences and from the MPA Garching. U.A. thanks for the support from the Astronomical Institute of the Czech Academy of Sciences.
2015-07-01T00:00:00ZHeinzel, P.Gunár, S.Anzer, U.Aims. We present a novel approximate radiative transfer method developed to visualize 3D whole-prominence models with multiple fine structures using the hydrogen Hα spectral line. Methods. This method employs a fast line-of-sight synthesis of the Hα line profiles through the whole 3D prominence volume and realistically reflects the basic properties of the Hα line formation in the cool and low-density prominence medium. The method can be applied both to prominences seen above the limb and filaments seen against the disk. Results. We provide recipes for the use of this method for visualizing the prominence or filament models that have multiple fine structures. We also perform tests of the method that demonstrate its accuracy under prominence conditions. Conclusions. We demonstrate that this fast approximate radiative transfer method provides realistic synthetic Hα intensities useful for a reliable visualization of prominences and filaments. Such synthetic high-resolution images of modeled prominences/filaments can be used for a direct comparison with high-resolution observations.The use of the Poynting vector in interpreting ULF waves in magnetospheric waveguidesElsden, TomWright, Andrew Nicholashttp://hdl.handle.net/10023/69762017-11-07T15:30:11Z2015-01-01T00:00:00ZWe numerically model ultralow frequency (ULF) waves in the magnetosphere assuming an ideal, low-beta inhomogeneous plasma waveguide. The waveguide is based on the hydromagnetic box model. We develop a novel boundary condition that drives the magnetospheric boundary by pressure perturbations, in order to simulate solar wind dynamic pressure uctuations disturbing the magnetopause. The model is applied to observations from Cluster and THEMIS. Our model is able to reproduce similar wave signatures to those in the data, such as a unidirectional azimuthal Poynting vector, by interpreting the observations in terms of fast waveguide modes. Despite the simplicity of the model, we can shed light on the nature of these modes and the location of the energy source relative to the spacecraft. This is achieved by demonstrating that important information, such as phase shifts between components of the electric and magnetic fields and the balance of radial to azimuthal propagation of energy, may be extracted from a careful analysis of the components of the Poynting vector.
T.E. would like to thank STFC for financial support for a doctoral training grant. Date of Acceptance: 04/12/2014
2015-01-01T00:00:00ZElsden, TomWright, Andrew NicholasWe numerically model ultralow frequency (ULF) waves in the magnetosphere assuming an ideal, low-beta inhomogeneous plasma waveguide. The waveguide is based on the hydromagnetic box model. We develop a novel boundary condition that drives the magnetospheric boundary by pressure perturbations, in order to simulate solar wind dynamic pressure uctuations disturbing the magnetopause. The model is applied to observations from Cluster and THEMIS. Our model is able to reproduce similar wave signatures to those in the data, such as a unidirectional azimuthal Poynting vector, by interpreting the observations in terms of fast waveguide modes. Despite the simplicity of the model, we can shed light on the nature of these modes and the location of the energy source relative to the spacecraft. This is achieved by demonstrating that important information, such as phase shifts between components of the electric and magnetic fields and the balance of radial to azimuthal propagation of energy, may be extracted from a careful analysis of the components of the Poynting vector.Ellipsoidal vortices in rotating stratified fluids : beyond the quasi-geostrophic approximationTsang, Yue-KinDritschel, David G.http://hdl.handle.net/10023/68892018-01-07T02:55:03Z2015-01-01T00:00:00ZWe examine the basic properties and stability of isolated vortices having uniform potential vorticity (PV) in a non-hydrostatic rotating stratified fluid, under the Boussinesq approximation. For simplicity, we consider a uniform background rotation and a linear basic-state stratification for which both the Coriolis and buoyancy frequencies, f and N, are constant. Moreover, we take ƒ/N≪1, as typically observed in the Earth’s atmosphere and oceans. In the small Rossby number ‘quasi-geostrophic’ (QG) limit, when the flow is weak compared to the background rotation, there exist exact solutions for steadily rotating ellipsoidal volumes of uniform PV in an unbounded flow (Zhmur & Shchepetkin, Izv. Akad. Nauk SSSR Atmos. Ocean. Phys., vol. 27, 1991, pp. 492–503; Meacham, Dyn. Atmos. Oceans, vol. 16, 1992, pp. 189–223). Furthermore, a wide range of these solutions are stable as long as the horizontal and vertical aspect ratios λ and μ do not depart greatly from unity (Dritschel et al.,J. Fluid Mech., vol. 536, 2005, pp. 401–421). In the present study, we examine the behaviour of ellipsoidal vortices at Rossby numbers up to near unity in magnitude. We find that there is a monotonic increase in stability as one varies the Rossby number from nearly −1 (anticyclone) to nearly +1 (cyclone). That is, QG vortices are more stable than anticyclones at finite negative Rossby number, and generally less stable than cyclones at finite positive Rossby number. Ageostrophic effects strengthen both the rotation and the stratification within a cyclone, enhancing its stability. The converse is true for an anticyclone. For all Rossby numbers, stability is reinforced by increasing λ towards unity or decreasing μ. An unstable vortex often restabilises by developing a near-circular cross-section, typically resulting in a roughly ellipsoidal vortex, but occasionally a binary system is formed. Throughout the nonlinear evolution of a vortex, the emission of inertia–gravity waves (IGWs) is negligible across the entire parameter space investigated. Thus, vortices at small to moderate Rossby numbers, and any associated instabilities, are (ageostrophically) balanced. A manifestation of this balance is that, at finite Rossby number, an anticyclone rotates faster than a cyclone.
Support for this research has come from the UK Engineering and Physical Sciences Research Council (grant number EP/H001794/1).
2015-01-01T00:00:00ZTsang, Yue-KinDritschel, David G.We examine the basic properties and stability of isolated vortices having uniform potential vorticity (PV) in a non-hydrostatic rotating stratified fluid, under the Boussinesq approximation. For simplicity, we consider a uniform background rotation and a linear basic-state stratification for which both the Coriolis and buoyancy frequencies, f and N, are constant. Moreover, we take ƒ/N≪1, as typically observed in the Earth’s atmosphere and oceans. In the small Rossby number ‘quasi-geostrophic’ (QG) limit, when the flow is weak compared to the background rotation, there exist exact solutions for steadily rotating ellipsoidal volumes of uniform PV in an unbounded flow (Zhmur & Shchepetkin, Izv. Akad. Nauk SSSR Atmos. Ocean. Phys., vol. 27, 1991, pp. 492–503; Meacham, Dyn. Atmos. Oceans, vol. 16, 1992, pp. 189–223). Furthermore, a wide range of these solutions are stable as long as the horizontal and vertical aspect ratios λ and μ do not depart greatly from unity (Dritschel et al.,J. Fluid Mech., vol. 536, 2005, pp. 401–421). In the present study, we examine the behaviour of ellipsoidal vortices at Rossby numbers up to near unity in magnitude. We find that there is a monotonic increase in stability as one varies the Rossby number from nearly −1 (anticyclone) to nearly +1 (cyclone). That is, QG vortices are more stable than anticyclones at finite negative Rossby number, and generally less stable than cyclones at finite positive Rossby number. Ageostrophic effects strengthen both the rotation and the stratification within a cyclone, enhancing its stability. The converse is true for an anticyclone. For all Rossby numbers, stability is reinforced by increasing λ towards unity or decreasing μ. An unstable vortex often restabilises by developing a near-circular cross-section, typically resulting in a roughly ellipsoidal vortex, but occasionally a binary system is formed. Throughout the nonlinear evolution of a vortex, the emission of inertia–gravity waves (IGWs) is negligible across the entire parameter space investigated. Thus, vortices at small to moderate Rossby numbers, and any associated instabilities, are (ageostrophically) balanced. A manifestation of this balance is that, at finite Rossby number, an anticyclone rotates faster than a cyclone.Excitation and damping of broadband kink waves in the solar coronaPascoe, David JamesWright, Andrew NicholasDe Moortel, InekeHood, Alan Williamhttp://hdl.handle.net/10023/68392018-01-07T03:03:35Z2015-06-01T00:00:00ZContext. Observations such as those by the Coronal Multi-Channel Polarimeter (CoMP) have revealed that broadband kink oscillations are ubiquitous in the solar corona. Aims. We consider footpoint-driven kink waves propagating in a low β coronal plasma with a cylindrical density structure. We investigate the excitation and damping of propagating kink waves by a broadband driver, including the effects of different spatial profiles for the driver. Methods. We employ a general spatial damping profile in which the initial stage of the damping envelope is approximated by a Gaussian profile and the asymptotic state by an exponential one. We develop a method of accounting for the presence of these different damping regimes and test it using data from numerical simulations. Results. Strongly damped oscillations in low density coronal loops are more accurately described by a Gaussian spatial damping profile than an exponential profile. The consequences for coronal seismology are investigated and applied to observational data for the ubiquitous broadband waves observed by CoMP. Current data cannot distinguish between the exponential and Gaussian profiles because of the levels of noise. We demonstrate the importance of the spatial profile of the driver on the resulting damping profile. Furthermore, we show that a small-scale turbulent driver is inefficient at exciting propagating kink waves
D.J.P. acknowledges financial support from STFC. I.D.M. acknowledges support of a Royal Society University Research Fellowship. The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/ 2007−2013) under the grant agreement SOLSPANET (project No. 269299, www.solspanet.eu/solspanet).
2015-06-01T00:00:00ZPascoe, David JamesWright, Andrew NicholasDe Moortel, InekeHood, Alan WilliamContext. Observations such as those by the Coronal Multi-Channel Polarimeter (CoMP) have revealed that broadband kink oscillations are ubiquitous in the solar corona. Aims. We consider footpoint-driven kink waves propagating in a low β coronal plasma with a cylindrical density structure. We investigate the excitation and damping of propagating kink waves by a broadband driver, including the effects of different spatial profiles for the driver. Methods. We employ a general spatial damping profile in which the initial stage of the damping envelope is approximated by a Gaussian profile and the asymptotic state by an exponential one. We develop a method of accounting for the presence of these different damping regimes and test it using data from numerical simulations. Results. Strongly damped oscillations in low density coronal loops are more accurately described by a Gaussian spatial damping profile than an exponential profile. The consequences for coronal seismology are investigated and applied to observational data for the ubiquitous broadband waves observed by CoMP. Current data cannot distinguish between the exponential and Gaussian profiles because of the levels of noise. We demonstrate the importance of the spatial profile of the driver on the resulting damping profile. Furthermore, we show that a small-scale turbulent driver is inefficient at exciting propagating kink wavesCALIFA, the Calar Alto Legacy Integral Field Area survey : III. Second public data releaseGarcía-Benito, R.Zibetti, S.Sánchez, S. F.Husemann, B.de Amorim, A. L.Castillo-Morales, A.Cid Fernandes, R.Ellis, S. C.Falcón-Barroso, J.Galbany, L.Gil de Paz, A.González Delgado, R. M.Lacerda, E. A. D.López-Fernandez, R.de Lorenzo-Cáceres, A.Lyubenova, M.Marino, R. A.Mast, D.Mendoza, M. A.Pérez, E.Vale Asari, N.Aguerri, J. A. L.Ascasibar, Y.Bekerait*error*ė, S.Bland-Hawthorn, J.Barrera-Ballesteros, J. K.Bomans, D. J.Cano-Díaz, M.Catalán-Torrecilla, C.Cortijo, C.Delgado-Inglada, G.Demleitner, M.Dettmar, R.-J.Díaz, A. I.Florido, E.Gallazzi, A.García-Lorenzo, B.Gomes, J. M.Holmes, L.Iglesias-Páramo, J.Jahnke, K.Kalinova, V.Kehrig, C.Kennicutt, R. C.López-Sánchez, Á. R.Márquez, I.Masegosa, J.Meidt, S. E.Mendez-Abreu, J.Mollá, M.Monreal-Ibero, A.Morisset, C.del Olmo, A.Papaderos, P.Pérez, I.Quirrenbach, A.Rosales-Ortega, F. F.Roth, M. M.Ruiz-Lara, T.Sánchez-Blázquez, P.Sánchez-Menguiano, L.Singh, R.Spekkens, K.Stanishev, V.Torres-Papaqui, J. P.van de Ven, G.Vilchez, J. M.Walcher, C. J.Wild, V.Wisotzki, L.Ziegler, B.Alves, J.Barrado, D.Quintana, J. M.Aceituno, J.http://hdl.handle.net/10023/66642018-03-11T01:33:28Z2015-04-01T00:00:00ZThis paper describes the Second Public Data Release (DR2) of the Calar Alto Legacy Integral Field Area (CALIFA) survey. The data for 200 objects are made public, including the 100 galaxies of the First Public Data Release (DR1). Data were obtained with the integral-field spectrograph PMAS/PPak mounted on the 3.5 m telescope at the Calar Alto observatory. Two different spectral setups are available for each galaxy, (i) a low-resolution V500 setup covering the wavelength range 3745-7500 Å with a spectral resolution of 6.0 Å (FWHM); and (ii) a medium-resolution V1200 setup covering the wavelength range 3650-4840 Å with a spectral resolution of 2.3 Å (FWHM). The sample covers a redshift range between 0.005 and 0.03, with a wide range of properties in the color-magnitude diagram, stellar mass, ionization conditions, and morphological types. All the cubes in the data release were reduced with the latest pipeline, which includes improvedspectrophotometric calibration, spatial registration, and spatial resolution. The spectrophotometric calibration is better than 6% and the median spatial resolution is 2.4. In total, the second data release contains over 1.5 million spectra.
J.M.A. acknowledges support from the European Research Council Starting Grant (SEDmorph; P.I. V. Wild). V.W. acknowledges support from the European Research Council Starting Grant (SEDMorph P.I. V. Wild) and European Career Re-integration Grant (Phiz-Ev P.I. V. Wild).
2015-04-01T00:00:00ZGarcía-Benito, R.Zibetti, S.Sánchez, S. F.Husemann, B.de Amorim, A. L.Castillo-Morales, A.Cid Fernandes, R.Ellis, S. C.Falcón-Barroso, J.Galbany, L.Gil de Paz, A.González Delgado, R. M.Lacerda, E. A. D.López-Fernandez, R.de Lorenzo-Cáceres, A.Lyubenova, M.Marino, R. A.Mast, D.Mendoza, M. A.Pérez, E.Vale Asari, N.Aguerri, J. A. L.Ascasibar, Y.Bekerait*error*ė, S.Bland-Hawthorn, J.Barrera-Ballesteros, J. K.Bomans, D. J.Cano-Díaz, M.Catalán-Torrecilla, C.Cortijo, C.Delgado-Inglada, G.Demleitner, M.Dettmar, R.-J.Díaz, A. I.Florido, E.Gallazzi, A.García-Lorenzo, B.Gomes, J. M.Holmes, L.Iglesias-Páramo, J.Jahnke, K.Kalinova, V.Kehrig, C.Kennicutt, R. C.López-Sánchez, Á. R.Márquez, I.Masegosa, J.Meidt, S. E.Mendez-Abreu, J.Mollá, M.Monreal-Ibero, A.Morisset, C.del Olmo, A.Papaderos, P.Pérez, I.Quirrenbach, A.Rosales-Ortega, F. F.Roth, M. M.Ruiz-Lara, T.Sánchez-Blázquez, P.Sánchez-Menguiano, L.Singh, R.Spekkens, K.Stanishev, V.Torres-Papaqui, J. P.van de Ven, G.Vilchez, J. M.Walcher, C. J.Wild, V.Wisotzki, L.Ziegler, B.Alves, J.Barrado, D.Quintana, J. M.Aceituno, J.This paper describes the Second Public Data Release (DR2) of the Calar Alto Legacy Integral Field Area (CALIFA) survey. The data for 200 objects are made public, including the 100 galaxies of the First Public Data Release (DR1). Data were obtained with the integral-field spectrograph PMAS/PPak mounted on the 3.5 m telescope at the Calar Alto observatory. Two different spectral setups are available for each galaxy, (i) a low-resolution V500 setup covering the wavelength range 3745-7500 Å with a spectral resolution of 6.0 Å (FWHM); and (ii) a medium-resolution V1200 setup covering the wavelength range 3650-4840 Å with a spectral resolution of 2.3 Å (FWHM). The sample covers a redshift range between 0.005 and 0.03, with a wide range of properties in the color-magnitude diagram, stellar mass, ionization conditions, and morphological types. All the cubes in the data release were reduced with the latest pipeline, which includes improvedspectrophotometric calibration, spatial registration, and spatial resolution. The spectrophotometric calibration is better than 6% and the median spatial resolution is 2.4. In total, the second data release contains over 1.5 million spectra.Numerical simulations of a flux rope ejectionPagano, P.Mackay, D.H.Poedts, S.http://hdl.handle.net/10023/66502017-11-07T16:30:12Z2015-03-01T00:00:00ZCoronal mass ejections (CMEs) are the most violent phenomena observed on the Sun. One of the most successful models to explain CMEs is the flux rope ejection model, where a magnetic flux rope is expelled from the solar corona after a long phase along which the flux rope stays in equilibrium while magnetic energy is being accumulated. However, still many questions are outstanding on the detailed mechanism of the ejection and observations continuously provide new data to interpret and put in the context. Currently, extreme ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamic Observatory (SDO) are providing new insights into the early phase of CME evolution. In particular, observations show the ejection of magnetic flux ropes from the solar corona and how they evolve into CMEs. However, these observations are difficult to interpret in terms of basic physical mechanisms and quantities, thus, we need to compare equivalent quantities to test and improve our models. In our work, we intend to bridge the gap between models and observations with our model of flux rope ejection where we consistently describe the full life span of a flux rope from its formation to ejection. This is done by coupling the global non-linear force-free model (GNLFFF) built to describe the slow low- β formation phase, with a full MHD simulation run with the software MPI-AMRVAC, suitable to describe the fast MHD evolution of the flux rope ejection that happens in a heterogeneous β regime. We also explore the parameter space to identify the conditions upon which the ejection is favoured (gravity stratification and magnetic field intensity) and we produce synthesised AIA observations (171 Å and 211 Å). To carry this out, we run 3D MHD simulation in spherical coordinates where we include the role of thermal conduction and radiative losses, both of which are important for determining the temperature distribution of the solar corona during a CME. Our model of flux rope ejection is successful in realistically describing the entire life span of a flux rope and we also set some conditions for the backgroud solar corona to favour the escape of the flux rope, so that it turns into a CME. Furthermore, our MHD simulation reproduces many of the features found in the AIA observations.
2015-03-01T00:00:00ZPagano, P.Mackay, D.H.Poedts, S.Coronal mass ejections (CMEs) are the most violent phenomena observed on the Sun. One of the most successful models to explain CMEs is the flux rope ejection model, where a magnetic flux rope is expelled from the solar corona after a long phase along which the flux rope stays in equilibrium while magnetic energy is being accumulated. However, still many questions are outstanding on the detailed mechanism of the ejection and observations continuously provide new data to interpret and put in the context. Currently, extreme ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamic Observatory (SDO) are providing new insights into the early phase of CME evolution. In particular, observations show the ejection of magnetic flux ropes from the solar corona and how they evolve into CMEs. However, these observations are difficult to interpret in terms of basic physical mechanisms and quantities, thus, we need to compare equivalent quantities to test and improve our models. In our work, we intend to bridge the gap between models and observations with our model of flux rope ejection where we consistently describe the full life span of a flux rope from its formation to ejection. This is done by coupling the global non-linear force-free model (GNLFFF) built to describe the slow low- β formation phase, with a full MHD simulation run with the software MPI-AMRVAC, suitable to describe the fast MHD evolution of the flux rope ejection that happens in a heterogeneous β regime. We also explore the parameter space to identify the conditions upon which the ejection is favoured (gravity stratification and magnetic field intensity) and we produce synthesised AIA observations (171 Å and 211 Å). To carry this out, we run 3D MHD simulation in spherical coordinates where we include the role of thermal conduction and radiative losses, both of which are important for determining the temperature distribution of the solar corona during a CME. Our model of flux rope ejection is successful in realistically describing the entire life span of a flux rope and we also set some conditions for the backgroud solar corona to favour the escape of the flux rope, so that it turns into a CME. Furthermore, our MHD simulation reproduces many of the features found in the AIA observations.3D whole-prominence fine structure modelingGunar, StanislavMackay, Duncan Hendryhttp://hdl.handle.net/10023/65412018-03-18T01:35:31Z2015-04-20T00:00:00ZWe present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Halpha line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique to consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.
2015-04-20T00:00:00ZGunar, StanislavMackay, Duncan HendryWe present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Halpha line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique to consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.Experiments on the structure and stability of mode-2 internal solitary-like waves propagating on an offset pycnoclineCarr, MagdaDavies, PeterHoebers, Ruudhttp://hdl.handle.net/10023/65192018-01-07T03:00:37Z2015-01-01T00:00:00ZThe structure and stability of mode-2 internal solitary-like waves is investigated experimentally. A rank-ordered train of mode-2 internal solitary waves is generated using a lock release configuration. The pycnocline is centred either on the mid-depth of the water column (the 0% offset case) or it is offset in the positive vertical direction by a fraction of 5%, 10% or 20% of the total fluid depth. It is found that offsetting the pycnocline has little effect on the basic wave properties (e.g wave speed, wave amplitude and wave length) but it does significantly affect wave stability. Instability takes the form of small K-H-like billows in the rear of the wave and small scale overturning in the core of the wave. In the 0% offset case, instability occurs on both the upper and lower interfaces of the pycnocline and is similar in extent and vigour over the two interfaces. As the offset percentage is increased, however, instability is more pronounced on the lower interface with little or no evidence of instability being observed on the upper interface. In the 20% offset case a mode-1 tail is associated with the wave and the wave characteristics resemble qualitatively the recent field observations of Shroyer et al [E. L. Shroyer, J. N. Moum and J. D. Nash, J. Geophys. Res. 115, C07001 (2010)].
2015-01-01T00:00:00ZCarr, MagdaDavies, PeterHoebers, RuudThe structure and stability of mode-2 internal solitary-like waves is investigated experimentally. A rank-ordered train of mode-2 internal solitary waves is generated using a lock release configuration. The pycnocline is centred either on the mid-depth of the water column (the 0% offset case) or it is offset in the positive vertical direction by a fraction of 5%, 10% or 20% of the total fluid depth. It is found that offsetting the pycnocline has little effect on the basic wave properties (e.g wave speed, wave amplitude and wave length) but it does significantly affect wave stability. Instability takes the form of small K-H-like billows in the rear of the wave and small scale overturning in the core of the wave. In the 0% offset case, instability occurs on both the upper and lower interfaces of the pycnocline and is similar in extent and vigour over the two interfaces. As the offset percentage is increased, however, instability is more pronounced on the lower interface with little or no evidence of instability being observed on the upper interface. In the 20% offset case a mode-1 tail is associated with the wave and the wave characteristics resemble qualitatively the recent field observations of Shroyer et al [E. L. Shroyer, J. N. Moum and J. D. Nash, J. Geophys. Res. 115, C07001 (2010)].The motion of point vortices on closed surfacesDritschel, David GerardBoatto, Shttp://hdl.handle.net/10023/62972018-01-07T02:56:43Z2015-02-25T00:00:00ZWe develop a mathematical framework for the dynamics of a set of point vortices on a class of differentiable surfaces conformal to the unit sphere. When the sum of the vortex circulations is non-zero, a compensating uniform vorticity field is required to satisfy the Gauss condition (that the integral of the Laplace-Beltrami operator must vanish). On variable Gaussian curvature surfaces, this results in self-induced vortex motion, a feature entirely absent on the plane, the sphere or the hyperboloid.We derive explicit equations of motion for vortices on surfaces of revolution and compute their solutions for a variety of surfaces. We also apply these equations to study the linear stability of a ring of vortices on any surface of revolution. On an ellipsoid of revolution, as few as 2 vortices can be unstable on oblate surfaces or sufficiently prolate ones. This extends known results for the plane, where 7 vortices are marginally unstable [1,2], and the sphere, where 4 vortices may be unstable if sufficiently close to the equator [3].
Date of Acceptance: 29/01/2015
2015-02-25T00:00:00ZDritschel, David GerardBoatto, SWe develop a mathematical framework for the dynamics of a set of point vortices on a class of differentiable surfaces conformal to the unit sphere. When the sum of the vortex circulations is non-zero, a compensating uniform vorticity field is required to satisfy the Gauss condition (that the integral of the Laplace-Beltrami operator must vanish). On variable Gaussian curvature surfaces, this results in self-induced vortex motion, a feature entirely absent on the plane, the sphere or the hyperboloid.We derive explicit equations of motion for vortices on surfaces of revolution and compute their solutions for a variety of surfaces. We also apply these equations to study the linear stability of a ring of vortices on any surface of revolution. On an ellipsoid of revolution, as few as 2 vortices can be unstable on oblate surfaces or sufficiently prolate ones. This extends known results for the plane, where 7 vortices are marginally unstable [1,2], and the sphere, where 4 vortices may be unstable if sufficiently close to the equator [3].Understanding the Mg II and Hα spectra in a highly dynamical solar prominenceHeinzel, P.Schmieder, B.Mein, N.Gunar, S.http://hdl.handle.net/10023/61902017-12-31T00:34:23Z2015-02-10T00:00:00ZMg ii h and k and Hα spectra in a dynamical prominence have been obtained along the slit of the Interface Region Imaging Spectrograph (IRIS) and with the Meudon Multi-channel Subtractive Double Pass spectrograph on 2013 September 24, respectively. Single Mg ii line profiles are not much reversed, while at some positions along the IRIS slit the profiles show several discrete peaks that are Doppler-shifted. The intensity of these peaks is generally decreasing with their increasing Doppler shift. We interpret this unusual behavior as being due to the Doppler dimming effect. We discuss the possibility to interpret the unreversed single profiles by using a two-dimensional (2D) model of the entire prominence body with specific radiative boundary conditions. We have performed new 2D isothermal–isobaric modeling of both Hα and Mg ii lines and show the ability of such models to account for the line profile variations as observed. However, the Mg ii line-center intensities require the model with a temperature increase toward the prominence boundary. We show that even simple one-dimensional (1D) models with a prominence-to-corona transition region (PCTR) fit the observed Mg ii and Hα lines quite well, while the isothermal–isobaric models (1D or 2D) are inconsistent with simultaneous observations in the Mg ii h and k and Hα lines, meaning that the Hα line provides a strong additional constraint on the modeling. IRIS far-UV detection of the C ii lines in this prominence seems to provide a direct constraint on the PCTR part of the model.
Date of Acceptance: 08/01/2015
2015-02-10T00:00:00ZHeinzel, P.Schmieder, B.Mein, N.Gunar, S.Mg ii h and k and Hα spectra in a dynamical prominence have been obtained along the slit of the Interface Region Imaging Spectrograph (IRIS) and with the Meudon Multi-channel Subtractive Double Pass spectrograph on 2013 September 24, respectively. Single Mg ii line profiles are not much reversed, while at some positions along the IRIS slit the profiles show several discrete peaks that are Doppler-shifted. The intensity of these peaks is generally decreasing with their increasing Doppler shift. We interpret this unusual behavior as being due to the Doppler dimming effect. We discuss the possibility to interpret the unreversed single profiles by using a two-dimensional (2D) model of the entire prominence body with specific radiative boundary conditions. We have performed new 2D isothermal–isobaric modeling of both Hα and Mg ii lines and show the ability of such models to account for the line profile variations as observed. However, the Mg ii line-center intensities require the model with a temperature increase toward the prominence boundary. We show that even simple one-dimensional (1D) models with a prominence-to-corona transition region (PCTR) fit the observed Mg ii and Hα lines quite well, while the isothermal–isobaric models (1D or 2D) are inconsistent with simultaneous observations in the Mg ii h and k and Hα lines, meaning that the Hα line provides a strong additional constraint on the modeling. IRIS far-UV detection of the C ii lines in this prominence seems to provide a direct constraint on the PCTR part of the model.Simply-connected vortex-patch shallow-water quasi-equilibriaPlotka, HannaDritschel, David Gerardhttp://hdl.handle.net/10023/61792018-01-07T02:43:12Z2014-03-05T00:00:00ZWe examine the form, properties, stability and evolution of simply-connected vortex-patch relative quasi-equilibria in the single-layer ƒ-plane shallow-water model of geophysical fluid dynamics. We examine the effects of the size, shape and strength of vortices in this system, represented by three distinct parameters completely describing the families of the quasi-equilibria. Namely, these are the ratio γ=L/LD between the horizontal size of the vortices and the Rossby deformation length; the aspect ratio λ between the minor to major axes of the vortex; and a potential vorticity (PV)-based Rossby number Ro=q′/ƒ, the ratio of the PV anomaly q′ within the vortex to the Coriolis frequency ƒ. By defining an appropriate steadiness parameter, we find that the quasi-equilibria remain steady for long times, enabling us to determine the boundary of stability λc=λc(γ, Ro), for 0.25≤γ≤6 and |Ro|≤1. By calling two states which share γ,|Ro| and λ ‘equivalent’, we find a clear asymmetry in the stability of cyclonic (Ro>0) and anticyclonic (Ro<0) equilibria, with cyclones being able to sustain greater deformations than anticyclones before experiencing an instability. We find that ageostrophic motions stabilise cyclones and destabilise anticyclones. Both types of vortices undergo the same main types of unstable evolution, albeit in different ranges of the parameter space, (a) vacillations for large-γ, large-Ro states, (b) filamentation for small-γ states and (c) vortex splitting, asymmetric for intermediate-γ and symmetric for large-γ states.
This work is supported by a UK Natural Environment Research Council studentship
2014-03-05T00:00:00ZPlotka, HannaDritschel, David GerardWe examine the form, properties, stability and evolution of simply-connected vortex-patch relative quasi-equilibria in the single-layer ƒ-plane shallow-water model of geophysical fluid dynamics. We examine the effects of the size, shape and strength of vortices in this system, represented by three distinct parameters completely describing the families of the quasi-equilibria. Namely, these are the ratio γ=L/LD between the horizontal size of the vortices and the Rossby deformation length; the aspect ratio λ between the minor to major axes of the vortex; and a potential vorticity (PV)-based Rossby number Ro=q′/ƒ, the ratio of the PV anomaly q′ within the vortex to the Coriolis frequency ƒ. By defining an appropriate steadiness parameter, we find that the quasi-equilibria remain steady for long times, enabling us to determine the boundary of stability λc=λc(γ, Ro), for 0.25≤γ≤6 and |Ro|≤1. By calling two states which share γ,|Ro| and λ ‘equivalent’, we find a clear asymmetry in the stability of cyclonic (Ro>0) and anticyclonic (Ro<0) equilibria, with cyclones being able to sustain greater deformations than anticyclones before experiencing an instability. We find that ageostrophic motions stabilise cyclones and destabilise anticyclones. Both types of vortices undergo the same main types of unstable evolution, albeit in different ranges of the parameter space, (a) vacillations for large-γ, large-Ro states, (b) filamentation for small-γ states and (c) vortex splitting, asymmetric for intermediate-γ and symmetric for large-γ states.The formation and stability of Petschek reconnectionBaty, H.Forbes, T.G.Priest, E.R.http://hdl.handle.net/10023/61002018-01-07T02:54:06Z2014-11-01T00:00:00ZA combined analytical and numerical study of magnetic reconnection in two-dimensional resistive magnetohydrodynamics is carried out by using different explicit spatial variations of the resistivity. A special emphasis on the existence of stable/unstable Petschek's solutions is taken, comparing with the recent analytical model given by Forbes et al. [Phys. Plasmas 20, 052902 (2013)]. Our results show good quantitative agreement between the analytical theory and the numerical solutions for a Petschek-type solution to within an accuracy of about 10% or better. Our simulations also show that if the resistivity profile is relatively flat near the X-point, one of two possible asymmetric solutions will occur. Which solution occurs depends on small random perturbations of the initial conditions. The existence of two possible asymmetric solutions, in a system which is otherwise symmetric, constitutes an example of spontaneous symmetry breaking.
E. R. Priest is grateful to the Leverhulme Trust. T. G. Forbes received support from NASA grant NNX-10AC04G to the University of New Hampshire. H. Baty acknowledges support by French National Research Agency (ANR) through Grant ANR-13-JS05-0003-01 (Project EMPERE).
2014-11-01T00:00:00ZBaty, H.Forbes, T.G.Priest, E.R.A combined analytical and numerical study of magnetic reconnection in two-dimensional resistive magnetohydrodynamics is carried out by using different explicit spatial variations of the resistivity. A special emphasis on the existence of stable/unstable Petschek's solutions is taken, comparing with the recent analytical model given by Forbes et al. [Phys. Plasmas 20, 052902 (2013)]. Our results show good quantitative agreement between the analytical theory and the numerical solutions for a Petschek-type solution to within an accuracy of about 10% or better. Our simulations also show that if the resistivity profile is relatively flat near the X-point, one of two possible asymmetric solutions will occur. Which solution occurs depends on small random perturbations of the initial conditions. The existence of two possible asymmetric solutions, in a system which is otherwise symmetric, constitutes an example of spontaneous symmetry breaking.Helical blowout jets in the sun : untwisting and propagation of wavesLee, E.J.Archontis, V.Hood, A.W.http://hdl.handle.net/10023/60972018-01-28T01:32:10Z2015-01-01T00:00:00ZWe report on a numerical experiment of the recurrent onset of helical "blowout" jets in an emerging flux region. We find that these jets are running with velocities of ∼100-250 km s-1 and they transfer a vast amount of heavy plasma into the outer solar atmosphere. During their emission, they undergo an untwisting motion as a result of reconnection between the twisted emerging and the non-twisted pre-existing magnetic field in the solar atmosphere. For the first time in the context of blowout jets, we provide direct evidence that their untwisting motion is associated with the propagation of torsional Alfvén waves in the corona.
2015-01-01T00:00:00ZLee, E.J.Archontis, V.Hood, A.W.We report on a numerical experiment of the recurrent onset of helical "blowout" jets in an emerging flux region. We find that these jets are running with velocities of ∼100-250 km s-1 and they transfer a vast amount of heavy plasma into the outer solar atmosphere. During their emission, they undergo an untwisting motion as a result of reconnection between the twisted emerging and the non-twisted pre-existing magnetic field in the solar atmosphere. For the first time in the context of blowout jets, we provide direct evidence that their untwisting motion is associated with the propagation of torsional Alfvén waves in the corona.Statistical evidence for the existence of Alfvénic turbulence in solar coronal loopsLiu, J.Mcintosh, S.W.De Moortel, I.Threlfall, J.Bethge, C.http://hdl.handle.net/10023/59872018-01-07T02:54:51Z2014-12-10T00:00:00ZRecent observations have demonstrated that waves capable of carrying large amounts of energy are ubiquitous throughout the solar corona. However, the question of how this wave energy is dissipated (on which timescales and length scales) and released into the plasma remains largely unanswered. Both analytic and numerical models have previously shown that Alfvénic turbulence may play a key role not only in the generation of the fast solar wind, but in the heating of coronal loops. In an effort to bridge the gap between theory and observations, we expand on a recent study by analyzing 37 clearly isolated coronal loops using data from the Coronal Multi-channel Polarimeter instrument.We observe Alfvénic perturbations with phase speeds which range from 250 to 750 km s-1 and periods from 140 to 270 s for the chosen loops. While excesses of high-frequency wave power are observed near the apex of some loops (tentatively supporting the onset of Alfvénic turbulence), we show that this excess depends on loop length and the wavelength of the observed oscillations. In deriving a proportional relationship between the loop length/wavelength ratio and the enhanced wave power at the loop apex, and from the analysis of the line widths associated with these loops, our findings are supportive of the existence of Alfvénic turbulence in coronal loops.
The authors acknowledge support from NASA contracts NNX08BA99G, NNX11AN98G, NNM12AB40P, NNG09FA40C (IRIS), and NNM07AA01C (Hinode). The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/ 2007-2013) under the grant agreement SOLSPANET (project No. 269299, www.solspanet.eu/solspanet).
2014-12-10T00:00:00ZLiu, J.Mcintosh, S.W.De Moortel, I.Threlfall, J.Bethge, C.Recent observations have demonstrated that waves capable of carrying large amounts of energy are ubiquitous throughout the solar corona. However, the question of how this wave energy is dissipated (on which timescales and length scales) and released into the plasma remains largely unanswered. Both analytic and numerical models have previously shown that Alfvénic turbulence may play a key role not only in the generation of the fast solar wind, but in the heating of coronal loops. In an effort to bridge the gap between theory and observations, we expand on a recent study by analyzing 37 clearly isolated coronal loops using data from the Coronal Multi-channel Polarimeter instrument.We observe Alfvénic perturbations with phase speeds which range from 250 to 750 km s-1 and periods from 140 to 270 s for the chosen loops. While excesses of high-frequency wave power are observed near the apex of some loops (tentatively supporting the onset of Alfvénic turbulence), we show that this excess depends on loop length and the wavelength of the observed oscillations. In deriving a proportional relationship between the loop length/wavelength ratio and the enhanced wave power at the loop apex, and from the analysis of the line widths associated with these loops, our findings are supportive of the existence of Alfvénic turbulence in coronal loops.Validation of the magnetic energy vs. helicity scaling in solar magnetic structuresTziotziou, K.Moraitis, K.Georgoulis, M.K.Archontis, V.http://hdl.handle.net/10023/58722017-11-22T09:34:07Z2014-10-01T00:00:00ZAims. We assess the validity of the free magnetic energy - relative magnetic helicity diagram for solar magnetic structures. Methods. We used two different methods of calculating the free magnetic energy and the relative magnetic helicity budgets: a classical, volume-calculation nonlinear force-free (NLFF) method applied to finite coronal magnetic structures and a surface-calculation NLFF derivation that relies on a single photospheric or chromospheric vector magnetogram. Both methods were applied to two different data sets, namely synthetic active-region cases obtained by three-dimensional magneto-hydrodynamic (MHD) simulations and observed active-region cases, which include both eruptive and noneruptive magnetic structures. Results. The derived energy-helicity diagram shows a consistent monotonic scaling between relative helicity and free energy with a scaling index 0.84 ± 0.05 for both data sets and calculation methods. It also confirms the segregation between noneruptive and eruptive active regions and the existence of thresholds in both free energy and relative helicity for active regions to enter eruptive territory. Conclusions. We consider the previously reported energy-helicity diagram of solar magnetic structures as adequately validated and envision a significant role of the uncovered scaling in future studies of solar magnetism.
V.A. acknowledges support by the Royal Society. This work was supported from the EU’s Seventh Framework Program under grant agreement n° PIRG07-GA-2010-268245. It has been also cofinanced by the European Union (European Social Fund – ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF) – Research Funding Program: Thales.
2014-10-01T00:00:00ZTziotziou, K.Moraitis, K.Georgoulis, M.K.Archontis, V.Aims. We assess the validity of the free magnetic energy - relative magnetic helicity diagram for solar magnetic structures. Methods. We used two different methods of calculating the free magnetic energy and the relative magnetic helicity budgets: a classical, volume-calculation nonlinear force-free (NLFF) method applied to finite coronal magnetic structures and a surface-calculation NLFF derivation that relies on a single photospheric or chromospheric vector magnetogram. Both methods were applied to two different data sets, namely synthetic active-region cases obtained by three-dimensional magneto-hydrodynamic (MHD) simulations and observed active-region cases, which include both eruptive and noneruptive magnetic structures. Results. The derived energy-helicity diagram shows a consistent monotonic scaling between relative helicity and free energy with a scaling index 0.84 ± 0.05 for both data sets and calculation methods. It also confirms the segregation between noneruptive and eruptive active regions and the existence of thresholds in both free energy and relative helicity for active regions to enter eruptive territory. Conclusions. We consider the previously reported energy-helicity diagram of solar magnetic structures as adequately validated and envision a significant role of the uncovered scaling in future studies of solar magnetism.Simulating AIA observations of a flux rope ejectionPagano, PaoloMackay, Duncan HendryPoedts, Stephanhttp://hdl.handle.net/10023/58212018-01-07T02:53:07Z2014-08-01T00:00:00ZContext. Coronal mass ejections (CMEs) are the most violent phenomena observed on the Sun. Currently, extreme ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamic Observatory (SDO) are providing new insights into the early phase of CME evolution. In particular, observations now show the ejection of magnetic flux ropes from the solar corona and how they evolve into CMEs. While this is the case, these observations are difficult to interpret in terms of basic physical mechanisms and quantities. To fully understand CMEs we need to compare equivalent quantities derived from both observations and theoretical models. This will aid in bridging the gap between observations and models. Aims: To this end, we aim to produce synthesised AIA observations from simulations of a flux rope ejection. To carry this out we include the role of thermal conduction and radiative losses, both of which are important for determining the temperature distribution of the solar corona during a CME. Methods: We perform a simulation where a flux rope is ejected from the solar corona. From the density and temperature of the plasma in the simulation we synthesise AIA observations. The emission is then integrated along the line of sight using the instrumental response function of AIA. Results: We sythesise observations of AIA in the channels at 304 Å, 171 Å, 335 Å, and 94 Å. The synthesised observations show a number of features similar to actual observations and in particular reproduce the general development of CMEs in the low corona as observed by AIA. In particular we reproduce an erupting and expanding arcade in the 304 Å and 171 Å channels with a high density core. Conclusions: The ejection of a flux rope reproduces many of the features found in the AIA observations. This work is therefore a step forward in bridging the gap between observations and models, and can lead to more direct interpretations of EUV observations in terms of flux rope ejections. We plan to improve the model in future studies in order to perform a more quantitative comparison. Movies associated with Figs. 3, 9, and 10 are available in electronic form at http://www.aanda.org
D.H.M. would like to thank STFC, the Leverhulme Trust and the European Commission’s Seventh Framework Programme (FP7/2007-2013) for their financial support. P.P. would like to thank the European Commission’s Seventh Framework Programme (FP7/2007-2013) under grant agreement SWIFF (project 263340, http://www.swiff.eu) and STFC for financial support. These results were obtained in the framework of the projects GOA/2009-009 (KU Leuven), G.0729.11 (FWO-Vlaanderen) and C 90347 (ESA Prodex 9). The research leading to these results has also received funding from the European Commission’s Seventh Framework Programme (FP7/2007-2013) under the grant agreements SOLSPANET (project No. 269299, http:// www.solspanet.eu), SPACECAST (project No. 262468, fp7-spacecast.eu), eHeroes (project n 284461, http://www.eheroes.eu). The computational work for this paper was carried out on the joint STFC and SFC (SRIF) funded cluster at the University of St Andrews (Scotland, UK).
2014-08-01T00:00:00ZPagano, PaoloMackay, Duncan HendryPoedts, StephanContext. Coronal mass ejections (CMEs) are the most violent phenomena observed on the Sun. Currently, extreme ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamic Observatory (SDO) are providing new insights into the early phase of CME evolution. In particular, observations now show the ejection of magnetic flux ropes from the solar corona and how they evolve into CMEs. While this is the case, these observations are difficult to interpret in terms of basic physical mechanisms and quantities. To fully understand CMEs we need to compare equivalent quantities derived from both observations and theoretical models. This will aid in bridging the gap between observations and models. Aims: To this end, we aim to produce synthesised AIA observations from simulations of a flux rope ejection. To carry this out we include the role of thermal conduction and radiative losses, both of which are important for determining the temperature distribution of the solar corona during a CME. Methods: We perform a simulation where a flux rope is ejected from the solar corona. From the density and temperature of the plasma in the simulation we synthesise AIA observations. The emission is then integrated along the line of sight using the instrumental response function of AIA. Results: We sythesise observations of AIA in the channels at 304 Å, 171 Å, 335 Å, and 94 Å. The synthesised observations show a number of features similar to actual observations and in particular reproduce the general development of CMEs in the low corona as observed by AIA. In particular we reproduce an erupting and expanding arcade in the 304 Å and 171 Å channels with a high density core. Conclusions: The ejection of a flux rope reproduces many of the features found in the AIA observations. This work is therefore a step forward in bridging the gap between observations and models, and can lead to more direct interpretations of EUV observations in terms of flux rope ejections. We plan to improve the model in future studies in order to perform a more quantitative comparison. Movies associated with Figs. 3, 9, and 10 are available in electronic form at http://www.aanda.orgStellar differential rotation and coronal time-scalesGibb, Gordon Peter SamuelJardine, Moira MaryMackay, Duncan Hendryhttp://hdl.handle.net/10023/58202018-01-07T02:53:06Z2014-10-01T00:00:00ZWe investigate the time-scales of evolution of stellar coronae in response to surface differential rotation and diffusion. To quantify this, we study both the formation time and lifetime of a magnetic flux rope in a decaying bipolar active region. We apply a magnetic flux transport model to prescribe the evolution of the stellar photospheric field, and use this to drive the evolution of the coronal magnetic field via a magnetofrictional technique. Increasing the differential rotation (i.e. decreasing the equator-pole lap time) decreases the flux rope formation time. We find that the formation time is dependent upon the lap time and the surface diffusion time-scale through the relation tau_Form ∝ &surd;{tau_Laptau_Diff}. In contrast, the lifetimes of flux ropes are proportional to the lap time (tauLife∝tauLap). With this, flux ropes on stars with a differential rotation of more than eight times the solar value have a lifetime of less than 2 d. As a consequence, we propose that features such as solar-like quiescent prominences may not be easily observable on such stars, as the lifetimes of the flux ropes which host the cool plasma are very short. We conclude that such high differential rotation stars may have very dynamical coronae.
GPSG would like to thank the STFC for financial support. DHM would like to thank the STFC and the Leverhulme Trust for financial support.
2014-10-01T00:00:00ZGibb, Gordon Peter SamuelJardine, Moira MaryMackay, Duncan HendryWe investigate the time-scales of evolution of stellar coronae in response to surface differential rotation and diffusion. To quantify this, we study both the formation time and lifetime of a magnetic flux rope in a decaying bipolar active region. We apply a magnetic flux transport model to prescribe the evolution of the stellar photospheric field, and use this to drive the evolution of the coronal magnetic field via a magnetofrictional technique. Increasing the differential rotation (i.e. decreasing the equator-pole lap time) decreases the flux rope formation time. We find that the formation time is dependent upon the lap time and the surface diffusion time-scale through the relation tau_Form ∝ &surd;{tau_Laptau_Diff}. In contrast, the lifetimes of flux ropes are proportional to the lap time (tauLife∝tauLap). With this, flux ropes on stars with a differential rotation of more than eight times the solar value have a lifetime of less than 2 d. As a consequence, we propose that features such as solar-like quiescent prominences may not be easily observable on such stars, as the lifetimes of the flux ropes which host the cool plasma are very short. We conclude that such high differential rotation stars may have very dynamical coronae.Backward wave cyclotron-maser emission in the auroral magnetosphereSpeirs, D. C.Bingham, R.Cairns, R. A.Vorgul, I.Kellett, B. J.Phelps, A. D. R.Ronald, K.http://hdl.handle.net/10023/58022018-01-07T02:53:02Z2014-10-07T00:00:00ZIn this Letter, we present theory and particle-in-cell simulations describing cyclotron radio emission from Earth's auroral region and similar phenomena in other astrophysical environments. In particular, we find that the radiation, generated by a down-going electron horseshoe distribution is due to a backward wave cyclotron-maser emission process. The backward wave nature of the radiation contributes to upward refraction of the radiation that is also enhanced by a density inhomogeneity. We also show that the radiation is preferentially amplified along the auroral oval rather than transversely. The results are in agreement with recent Cluster observations.
This work was supported by EPSRC Grant No. EP/G04239X/1.
2014-10-07T00:00:00ZSpeirs, D. C.Bingham, R.Cairns, R. A.Vorgul, I.Kellett, B. J.Phelps, A. D. R.Ronald, K.In this Letter, we present theory and particle-in-cell simulations describing cyclotron radio emission from Earth's auroral region and similar phenomena in other astrophysical environments. In particular, we find that the radiation, generated by a down-going electron horseshoe distribution is due to a backward wave cyclotron-maser emission process. The backward wave nature of the radiation contributes to upward refraction of the radiation that is also enhanced by a density inhomogeneity. We also show that the radiation is preferentially amplified along the auroral oval rather than transversely. The results are in agreement with recent Cluster observations.The nature of separator current layers in MHS equilibria I. Current parallel to the separatorStevenson, Julie Elizabeth HelenParnell, Clare ElizabethPriest, Eric RonaldHaynes, Andrew Lewishttp://hdl.handle.net/10023/57852018-01-07T02:52:00Z2015-01-01T00:00:00ZSeparators, which are in many ways the three-dimensional equivalent to two-dimensional nulls, are important sites for magnetic reconnection. Magnetic reconnection occurs in strong current layers which have very short length scales. The aim of this work is to explore the nature of current layers around separators. A separator is a special field line which lies along the intersection of two separatrix surfaces and forms the boundary between four topologically distinct flux domains. In particular, here the current layer about a separator that joins two 3D nulls and lies along the intersection of their separatrix surfaces is investigated. A magnetic configuration containing a single separator embedded in a uniform plasma with a uniform electric current parallel to the separator is considered. This initial magnetic setup, which is not in equilibrium, relaxes in a non-resistive manner to form an equilibrium. The relaxation is achieved using the 3D MHD code, Lare3d, with resistivity set to zero. A series of experiments with varying initial current are run to investigate the characteristics of the resulting current layers present in the final (quasi-) equilibrium states. In each experiment, the separator collapses and a current layer forms along it. The dimensions and strength of the current layer increase with initial current. It is found that separator current layers formed from current parallel to the separator are twisted. Also the collapse of the separator is a process that evolves like an infinite-time singularity where the length, width and peak current in the layer grow slowly whilst the depth of the current layer decreases.
JEHS would like to thank STFC for financial support during her Ph.D and CEP acknowledges support from the STFC consolidated grant.
2015-01-01T00:00:00ZStevenson, Julie Elizabeth HelenParnell, Clare ElizabethPriest, Eric RonaldHaynes, Andrew LewisSeparators, which are in many ways the three-dimensional equivalent to two-dimensional nulls, are important sites for magnetic reconnection. Magnetic reconnection occurs in strong current layers which have very short length scales. The aim of this work is to explore the nature of current layers around separators. A separator is a special field line which lies along the intersection of two separatrix surfaces and forms the boundary between four topologically distinct flux domains. In particular, here the current layer about a separator that joins two 3D nulls and lies along the intersection of their separatrix surfaces is investigated. A magnetic configuration containing a single separator embedded in a uniform plasma with a uniform electric current parallel to the separator is considered. This initial magnetic setup, which is not in equilibrium, relaxes in a non-resistive manner to form an equilibrium. The relaxation is achieved using the 3D MHD code, Lare3d, with resistivity set to zero. A series of experiments with varying initial current are run to investigate the characteristics of the resulting current layers present in the final (quasi-) equilibrium states. In each experiment, the separator collapses and a current layer forms along it. The dimensions and strength of the current layer increase with initial current. It is found that separator current layers formed from current parallel to the separator are twisted. Also the collapse of the separator is a process that evolves like an infinite-time singularity where the length, width and peak current in the layer grow slowly whilst the depth of the current layer decreases.Particle acceleration at a reconnecting magnetic separatorThrelfall, J.Neukirch, T.Parnell, Clare ElizabethEradat Oskoui, S.http://hdl.handle.net/10023/57822018-01-07T02:51:59Z2015-02-01T00:00:00ZWhile the exact acceleration mechanism of energetic particles during solar flares is (as yet) unknown, magnetic reconnection plays a key role both in the release of stored magnetic energy of the solar corona and the magnetic restructuring during a flare. Recent work has shown that special field lines, called separators, are common sites of reconnection in 3D numerical experiments. To date, 3D separator reconnection sites have received little attention as particle accelerators. We investigate the effectiveness of separator reconnection as a particle acceleration mechanism for electrons and protons. We study the particle acceleration using a relativistic guiding-centre particle code in a time-dependent kinematic model of magnetic reconnection at a separator. The effect upon particle behaviour of initial position, pitch angle and initial kinetic energy are examined in detail, both for specific (single) particle examples and for large distributions of initial conditions. The separator reconnection model contains several free parameters and we study the effect of changing these parameters upon particle acceleration, in particular in view of the final particle energy ranges which agree with observed energy spectra.
2015-02-01T00:00:00ZThrelfall, J.Neukirch, T.Parnell, Clare ElizabethEradat Oskoui, S.While the exact acceleration mechanism of energetic particles during solar flares is (as yet) unknown, magnetic reconnection plays a key role both in the release of stored magnetic energy of the solar corona and the magnetic restructuring during a flare. Recent work has shown that special field lines, called separators, are common sites of reconnection in 3D numerical experiments. To date, 3D separator reconnection sites have received little attention as particle accelerators. We investigate the effectiveness of separator reconnection as a particle acceleration mechanism for electrons and protons. We study the particle acceleration using a relativistic guiding-centre particle code in a time-dependent kinematic model of magnetic reconnection at a separator. The effect upon particle behaviour of initial position, pitch angle and initial kinetic energy are examined in detail, both for specific (single) particle examples and for large distributions of initial conditions. The separator reconnection model contains several free parameters and we study the effect of changing these parameters upon particle acceleration, in particular in view of the final particle energy ranges which agree with observed energy spectra.Alfvén wave boundary condition for responsive magnetosphere- ionosphere couplingWright, A.N.Russell, A.J.B.http://hdl.handle.net/10023/56602018-01-07T02:48:33Z2014-05-01T00:00:00ZThe solution of electric fields and currents in a height-resolved ionosphere is traditionally solved as an elliptic equation with Dirichlet or Neumann boundary condition in which the magnetosphere is represented as an unresponsive (prescribed) voltage generator or current source. In this paper we derive an alternative boundary condition based upon Alfvén waves in which only the Alfvén wave from the magnetosphere that is incident upon the ionosphere (E) is prescribed. For a uniform magnetosphere the new boundary condition reduces to ∂φ/∂z=(∂2φ/ ∂x2+2∂Exi/∂x)/(μ0VAσ≥) and is evaluated at the magnetosphere-ionosphere interface. The resulting solution is interpreted as a responsive magnetosphere and establishes a key stage in the full self-consistent and nonlinear coupling of the magnetosphere and ionosphere.
A.J.B.R. thanks STFC for present support through consolidated grant ST/K000993/1 and gratefully acknowledges a Royal Commission for the Exhibition of 1851 Research Fellowship that also assisted this work.
2014-05-01T00:00:00ZWright, A.N.Russell, A.J.B.The solution of electric fields and currents in a height-resolved ionosphere is traditionally solved as an elliptic equation with Dirichlet or Neumann boundary condition in which the magnetosphere is represented as an unresponsive (prescribed) voltage generator or current source. In this paper we derive an alternative boundary condition based upon Alfvén waves in which only the Alfvén wave from the magnetosphere that is incident upon the ionosphere (E) is prescribed. For a uniform magnetosphere the new boundary condition reduces to ∂φ/∂z=(∂2φ/ ∂x2+2∂Exi/∂x)/(μ0VAσ≥) and is evaluated at the magnetosphere-ionosphere interface. The resulting solution is interpreted as a responsive magnetosphere and establishes a key stage in the full self-consistent and nonlinear coupling of the magnetosphere and ionosphere.Ultraviolet and extreme-ultraviolet emissions at the flare footpoints observed by atmosphere imaging assemblyQiu, J.Sturrock, Z.Longcope, D.W.Klimchuk, J.A.Liu, W.-J.http://hdl.handle.net/10023/54992018-01-07T02:50:54Z2013-09-01T00:00:00ZA solar flare is composed of impulsive energy release events by magnetic reconnection, which forms and heats flare loops. Recent studies have revealed a two-phase evolution pattern of UV 1600 Å emission at the feet of these loops: a rapid pulse lasting for a few seconds to a few minutes, followed by a gradual decay on timescales of a few tens of minutes. Multiple band EUV observations by the Atmosphere Imaging Assembly further reveal very similar signatures. These two phases represent different but related signatures of an impulsive energy release in the corona. The rapid pulse is an immediate response of the lower atmosphere to an intense thermal conduction flux resulting from the sudden heating of the corona to high temperatures (we rule out energetic particles due to a lack of significant hard X-ray emission). The gradual phase is associated with the cooling of hot plasma that has been evaporated into the corona. The observed footpoint emission is again powered by thermal conduction (and enthalpy), but now during a period when approximate steady-state conditions are established in the loop. UV and EUV light curves of individual pixels may therefore be separated into contributions from two distinct physical mechanisms to shed light on the nature of energy transport in a flare. We demonstrate this technique using coordinated, spatially resolved observations of UV and EUV emissions from the footpoints of a C3.2 thermal flare.
2013-09-01T00:00:00ZQiu, J.Sturrock, Z.Longcope, D.W.Klimchuk, J.A.Liu, W.-J.A solar flare is composed of impulsive energy release events by magnetic reconnection, which forms and heats flare loops. Recent studies have revealed a two-phase evolution pattern of UV 1600 Å emission at the feet of these loops: a rapid pulse lasting for a few seconds to a few minutes, followed by a gradual decay on timescales of a few tens of minutes. Multiple band EUV observations by the Atmosphere Imaging Assembly further reveal very similar signatures. These two phases represent different but related signatures of an impulsive energy release in the corona. The rapid pulse is an immediate response of the lower atmosphere to an intense thermal conduction flux resulting from the sudden heating of the corona to high temperatures (we rule out energetic particles due to a lack of significant hard X-ray emission). The gradual phase is associated with the cooling of hot plasma that has been evaporated into the corona. The observed footpoint emission is again powered by thermal conduction (and enthalpy), but now during a period when approximate steady-state conditions are established in the loop. UV and EUV light curves of individual pixels may therefore be separated into contributions from two distinct physical mechanisms to shed light on the nature of energy transport in a flare. We demonstrate this technique using coordinated, spatially resolved observations of UV and EUV emissions from the footpoints of a C3.2 thermal flare.Non-linear force-free magnetic dip models of quiescent prominence fine structuresGunar, StanislavMackay, Duncan HendryAnzer, UHeinzel, Petrhttp://hdl.handle.net/10023/54762018-02-11T01:30:56Z2013-03-01T00:00:00ZAims. We use 3D non-linear force-free magnetic field modeling of prominence/filament magnetic fields to develop the first 2D models of individual prominence fine structures based on the 3D configuration of the magnetic field of the whole prominence. Methods. We use an iterative technique to fill the magnetic dips produced by the 3D modeling with realistic prominence plasma in hydrostatic equilibrium and with a temperature structure that contains the prominence-corona transition region. With this well-defined plasma structure the radiative transfer can be treated in detail in 2D and the resulting synthetic emission can be compared with prominence/filament observations. Results. Newly developed non-linear force-free magnetic dip models are able to produce synthetic hydrogen Lyman spectra in a qualitative agreement with a range of quiescent prominence observations. Moreover, the plasma structure of these models agrees with the gravity induced prominence fine structure models which have already been shown to produce synthetic spectra in good qualitative agreement with several observed prominences. Conclusions. We describe in detail the iterative technique which can be used to produce realistic plasma models of prominence fine structures located in prominence magnetic field configurations containing dips, obtained using any kind of magnetic field modeling.
S.G. and P.H. acknowledge the support from grant 209/12/0906 of the Grant Agency of the Czech Republic. P.H. acknowledges the support from grant P209/10/1680 of the Grant Agency of the Czech Republic. S.G. and P.H. acknowledge the support from the MPA Garching; U.A. thanks for support from the Ondřejov Observatory. S.G. acknowledges the support from St Andrews University. Work of S.G. and P.H. was supported by the project RVO: 67985815. DHM acknowledges financial support from the STFC and the Leverhulme Trust. In addition research leading to these results has received funding from the European Commission’s Seventh Framework Programme (FP7/2007-2013) under the grant agreement SWIFF (project N° 263340, http://www.swiff.eu).
2013-03-01T00:00:00ZGunar, StanislavMackay, Duncan HendryAnzer, UHeinzel, PetrAims. We use 3D non-linear force-free magnetic field modeling of prominence/filament magnetic fields to develop the first 2D models of individual prominence fine structures based on the 3D configuration of the magnetic field of the whole prominence. Methods. We use an iterative technique to fill the magnetic dips produced by the 3D modeling with realistic prominence plasma in hydrostatic equilibrium and with a temperature structure that contains the prominence-corona transition region. With this well-defined plasma structure the radiative transfer can be treated in detail in 2D and the resulting synthetic emission can be compared with prominence/filament observations. Results. Newly developed non-linear force-free magnetic dip models are able to produce synthetic hydrogen Lyman spectra in a qualitative agreement with a range of quiescent prominence observations. Moreover, the plasma structure of these models agrees with the gravity induced prominence fine structure models which have already been shown to produce synthetic spectra in good qualitative agreement with several observed prominences. Conclusions. We describe in detail the iterative technique which can be used to produce realistic plasma models of prominence fine structures located in prominence magnetic field configurations containing dips, obtained using any kind of magnetic field modeling.Effects of M dwarf magnetic fields on potentially habitable planetsVidotto, A.A.Jardine, M.Morin, J.Donati, J.-F.Lang, P.Russell, A.J.B.http://hdl.handle.net/10023/54622018-03-18T01:33:44Z2013-09-02T00:00:00ZWe investigate the effect of the magnetic fields of M dwarf (dM) stars on potentially habitable Earth-like planets. These fields can reduce the size of planetary magnetospheres to such an extent that a significant fraction of the planet’s atmosphere may be exposed to erosion by the stellar wind. We used a sample of 15 active dM stars, for which surface magnetic-field maps were reconstructed, to determine the magnetic pressure at the planet orbit and hence the largest size of its magnetosphere, which would only be decreased by considering the stellar wind. Our method provides a fast means to assess which planets are most affected by the stellar magnetic field, which can be used as a first study to be followed by more sophisticated models. We show that hypothetical Earth-like planets with similar terrestrial magnetisation (~1 G) orbiting at the inner (outer) edge of the habitable zone of these stars would present magnetospheres that extend at most up to 6 (11.7) planetary radii. To be able to sustain an Earth-sized magnetosphere, with the exception of only a few cases, the terrestrial planet would either (1) need to orbit significantly farther out than the traditional limits of the habitable zone; or else, (2) if it were orbiting within the habitable zone, it would require at least a magnetic field ranging from a few G to up to a few thousand G. By assuming a magnetospheric size that is more appropriate for the young-Earth (3.4 Gyr ago), the required planetary magnetic fields are one order of magnitude weaker. However, in this case, the polar-cap area of the planet, which is unprotected from transport of particles to/from interplanetary space, is twice as large. At present, we do not know how small the smallest area of the planetary surface is that could be exposed and would still not affect the potential for formation and development of life in a planet. As the star becomes older and, therefore, its rotation rate and magnetic field reduce, the interplanetary magnetic pressure decreases and the magnetosphere of planets probably expands. Using an empirically derived rotation-activity/magnetism relation, we provide an analytical expression for estimating the shortest stellar rotation period for which an Earth-analogue in the habitable zone could sustain an Earth-sized magnetosphere. We find that the required rotation rate of the early- and mid-dM stars (with periods ≳37–202 days) is slower than the solar one, and even slower for the late-dM stars (≳63–263 days). Planets orbiting in the habitable zone of dM stars that rotate faster than this have smaller magnetospheric sizes than that of the Earth magnetosphere. Because many late-dM stars are fast rotators, conditions for terrestrial planets to harbour Earth-sized magnetospheres are more easily achieved for planets orbiting slowly rotating early- and mid-dM stars.
A.A.V. acknowledges support from the Royal Astronomical Society through a post-doctoral fellowship. J.M. acknowledges support from a fellowship of the Alexander von Humboldt foundation. P.L. acknowledges funding from a STFC scholarship. AJBR is a Research Fellow of the Royal Commission for the Exhibition of 1851.
2013-09-02T00:00:00ZVidotto, A.A.Jardine, M.Morin, J.Donati, J.-F.Lang, P.Russell, A.J.B.We investigate the effect of the magnetic fields of M dwarf (dM) stars on potentially habitable Earth-like planets. These fields can reduce the size of planetary magnetospheres to such an extent that a significant fraction of the planet’s atmosphere may be exposed to erosion by the stellar wind. We used a sample of 15 active dM stars, for which surface magnetic-field maps were reconstructed, to determine the magnetic pressure at the planet orbit and hence the largest size of its magnetosphere, which would only be decreased by considering the stellar wind. Our method provides a fast means to assess which planets are most affected by the stellar magnetic field, which can be used as a first study to be followed by more sophisticated models. We show that hypothetical Earth-like planets with similar terrestrial magnetisation (~1 G) orbiting at the inner (outer) edge of the habitable zone of these stars would present magnetospheres that extend at most up to 6 (11.7) planetary radii. To be able to sustain an Earth-sized magnetosphere, with the exception of only a few cases, the terrestrial planet would either (1) need to orbit significantly farther out than the traditional limits of the habitable zone; or else, (2) if it were orbiting within the habitable zone, it would require at least a magnetic field ranging from a few G to up to a few thousand G. By assuming a magnetospheric size that is more appropriate for the young-Earth (3.4 Gyr ago), the required planetary magnetic fields are one order of magnitude weaker. However, in this case, the polar-cap area of the planet, which is unprotected from transport of particles to/from interplanetary space, is twice as large. At present, we do not know how small the smallest area of the planetary surface is that could be exposed and would still not affect the potential for formation and development of life in a planet. As the star becomes older and, therefore, its rotation rate and magnetic field reduce, the interplanetary magnetic pressure decreases and the magnetosphere of planets probably expands. Using an empirically derived rotation-activity/magnetism relation, we provide an analytical expression for estimating the shortest stellar rotation period for which an Earth-analogue in the habitable zone could sustain an Earth-sized magnetosphere. We find that the required rotation rate of the early- and mid-dM stars (with periods ≳37–202 days) is slower than the solar one, and even slower for the late-dM stars (≳63–263 days). Planets orbiting in the habitable zone of dM stars that rotate faster than this have smaller magnetospheric sizes than that of the Earth magnetosphere. Because many late-dM stars are fast rotators, conditions for terrestrial planets to harbour Earth-sized magnetospheres are more easily achieved for planets orbiting slowly rotating early- and mid-dM stars.Numerical simulation of a self-similar cascade of filament instabilities in the surface quasigeostrophic systemScott, R. K.Dritschel, D. G.http://hdl.handle.net/10023/54362018-01-07T02:50:25Z2014-04-11T00:00:00ZWe provide numerical evidence for the existence of a cascade of filament instabilities in the surface quasigeostrophic system for rotating, stratified flow near a horizontal boundary. The cascade involves geometrically shrinking spatial and temporal scales and implies the singular collapse of the filament width to zero in a finite time. The numerical method is both spatially and temporally adaptive, permitting the accurate simulation of the evolution over an unprecedented range of spatial scales spanning over ten orders of magnitude. It provides the first convincing demonstration of the cascade, in which the large separation of scales between subsequent instabilities has made previous numerical simulation difficult.
2014-04-11T00:00:00ZScott, R. K.Dritschel, D. G.We provide numerical evidence for the existence of a cascade of filament instabilities in the surface quasigeostrophic system for rotating, stratified flow near a horizontal boundary. The cascade involves geometrically shrinking spatial and temporal scales and implies the singular collapse of the filament width to zero in a finite time. The numerical method is both spatially and temporally adaptive, permitting the accurate simulation of the evolution over an unprecedented range of spatial scales spanning over ten orders of magnitude. It provides the first convincing demonstration of the cascade, in which the large separation of scales between subsequent instabilities has made previous numerical simulation difficult.Inertial-range dynamics and scaling laws of two-dimensional magnetic turbulence in the weak-field regimeBlackbourn, Luke Austen KazimierzTran, Chuong Vanhttp://hdl.handle.net/10023/53582017-08-16T23:48:09Z2014-08-21T00:00:00ZWe study inertial-range dynamics and scaling laws in unforced two-dimensional magnetohydrodynamic turbulence in the regime of moderately small and small initial magnetic-to-kinetic energy ratio $r_0$, with an emphasis on the latter. The regime of small $r_0$ corresponds to a relatively weak field and strong magnetic stretching, whereby the turbulence is characterized by an intense conversion of kinetic into magnetic energy (dynamo action in the three-dimensional context). This conversion is an inertial-range phenomenon and, upon becoming quasi-saturated, deposits the converted energy within the inertial range rather than transferring it to the small scales. As a result, the magnetic energy spectrum $E_\b(k)$ in the inertial range can become quite shallow and may not be adequately explained or understood in terms of conventional cascade theories. It is demonstrated by numerical simulations at high Reynolds numbers (and unity magnetic Prandtl number) that the energetics and inertial-range scaling depend strongly on $r_0$. In particular, for fully developed turbulence with $r_0$ in the range $[1/4,1/4096]$, $E_\b(k)$ is found to scale as $k^{\alpha}$, where $\alpha\gtrsim-1$, including $\alpha>0$. The extent of such a shallow spectrum is limited, becoming broader as $r_0$ is decreased. The slope $\alpha$ increases as $r_0$ is decreased, appearing to tend to $+1$ in the limit of small $r_0$. This implies equipartition of magnetic energy among the Fourier modes of the inertial range and the scaling $k^{-1}$ of the magnetic potential variance, whose flux is direct rather than inverse. This behavior of the potential resembles that of a passive scalar. However, unlike a passive scalar whose variance dissipation rate slowly vanishes in the diffusionless limit, the dissipation rate of the magnetic potential variance scales linearly with the diffusivity in that limit. Meanwhile, the kinetic energy spectrum is relatively steep, followed by a much shallower tail due to strong anti-dynamo excitation. This gives rise to a total energy spectrum poorly obeying a power-law scaling.
The work reported here was partially supported by an EPSRC postgraduate studentship to L.A.K.B. L.A.K.B. was further supported by an EPSRC doctoral prize.
2014-08-21T00:00:00ZBlackbourn, Luke Austen KazimierzTran, Chuong VanWe study inertial-range dynamics and scaling laws in unforced two-dimensional magnetohydrodynamic turbulence in the regime of moderately small and small initial magnetic-to-kinetic energy ratio $r_0$, with an emphasis on the latter. The regime of small $r_0$ corresponds to a relatively weak field and strong magnetic stretching, whereby the turbulence is characterized by an intense conversion of kinetic into magnetic energy (dynamo action in the three-dimensional context). This conversion is an inertial-range phenomenon and, upon becoming quasi-saturated, deposits the converted energy within the inertial range rather than transferring it to the small scales. As a result, the magnetic energy spectrum $E_\b(k)$ in the inertial range can become quite shallow and may not be adequately explained or understood in terms of conventional cascade theories. It is demonstrated by numerical simulations at high Reynolds numbers (and unity magnetic Prandtl number) that the energetics and inertial-range scaling depend strongly on $r_0$. In particular, for fully developed turbulence with $r_0$ in the range $[1/4,1/4096]$, $E_\b(k)$ is found to scale as $k^{\alpha}$, where $\alpha\gtrsim-1$, including $\alpha>0$. The extent of such a shallow spectrum is limited, becoming broader as $r_0$ is decreased. The slope $\alpha$ increases as $r_0$ is decreased, appearing to tend to $+1$ in the limit of small $r_0$. This implies equipartition of magnetic energy among the Fourier modes of the inertial range and the scaling $k^{-1}$ of the magnetic potential variance, whose flux is direct rather than inverse. This behavior of the potential resembles that of a passive scalar. However, unlike a passive scalar whose variance dissipation rate slowly vanishes in the diffusionless limit, the dissipation rate of the magnetic potential variance scales linearly with the diffusivity in that limit. Meanwhile, the kinetic energy spectrum is relatively steep, followed by a much shallower tail due to strong anti-dynamo excitation. This gives rise to a total energy spectrum poorly obeying a power-law scaling.Distribution of electric currents in solar active regionsTörök, T.Leake, J.E.Titov, V.S.Archontis, V.Mikić, Z.Linton, M.G.Dalmasse, K.Aulanier, G.Kliem, B.http://hdl.handle.net/10023/53222018-02-18T01:32:55Z2014-02-10T00:00:00ZThere has been a long-standing debate on the question of whether or not electric currents in solar active regions are neutralized. That is, whether or not the main (or direct) coronal currents connecting the active region polarities are surrounded by shielding (or return) currents of equal total value and opposite direction. Both theory and observations are not yet fully conclusive regarding this question, and numerical simulations have, surprisingly, barely been used to address it. Here we quantify the evolution of electric currents during the formation of a bipolar active region by considering a three-dimensional magnetohydrodynamic simulation of the emergence of a sub-photospheric, current-neutralized magnetic flux rope into the solar atmosphere. We find that a strong deviation from current neutralization develops simultaneously with the onset of significant flux emergence into the corona, accompanied by the development of substantial magnetic shear along the active region's polarity inversion line. After the region has formed and flux emergence has ceased, the strong magnetic fields in the region's center are connected solely by direct currents, and the total direct current is several times larger than the total return current. These results suggest that active regions, the main sources of coronal mass ejections and flares, are born with substantial net currents, in agreement with recent observations. Furthermore, they support eruption models that employ pre-eruption magnetic fields containing such currents.
The contributions of T.T., V.S.T., and Z.M. were supported by NASA's HTP, LWS, and SR&T programs. J.E.L and M.G.L. were supported by NASA/LWS. M.G.L. received support also from the ONR 6.1 program. The simulation was performed under grant of computer time from the D.o.D. HPC Program. B.K. was supported by the DFG. V.A. acknowledges support through the IEF-272549 grant.
2014-02-10T00:00:00ZTörök, T.Leake, J.E.Titov, V.S.Archontis, V.Mikić, Z.Linton, M.G.Dalmasse, K.Aulanier, G.Kliem, B.There has been a long-standing debate on the question of whether or not electric currents in solar active regions are neutralized. That is, whether or not the main (or direct) coronal currents connecting the active region polarities are surrounded by shielding (or return) currents of equal total value and opposite direction. Both theory and observations are not yet fully conclusive regarding this question, and numerical simulations have, surprisingly, barely been used to address it. Here we quantify the evolution of electric currents during the formation of a bipolar active region by considering a three-dimensional magnetohydrodynamic simulation of the emergence of a sub-photospheric, current-neutralized magnetic flux rope into the solar atmosphere. We find that a strong deviation from current neutralization develops simultaneously with the onset of significant flux emergence into the corona, accompanied by the development of substantial magnetic shear along the active region's polarity inversion line. After the region has formed and flux emergence has ceased, the strong magnetic fields in the region's center are connected solely by direct currents, and the total direct current is several times larger than the total return current. These results suggest that active regions, the main sources of coronal mass ejections and flares, are born with substantial net currents, in agreement with recent observations. Furthermore, they support eruption models that employ pre-eruption magnetic fields containing such currents.Recurrent explosive eruptions and the "sigmoid-to-arcade" transformation in the Sun driven by dynamical magnetic flux emergenceArchontis, V.Hood, A.W.Tsinganos, K.http://hdl.handle.net/10023/53192018-01-07T02:49:48Z2014-05-10T00:00:00ZWe report on three-dimensional MHD simulations of recurrent mini coronal mass ejection (CME)-like eruptions in a small active region (AR), which is formed by the dynamical emergence of a twisted (not kink unstable) flux tube from the solar interior. The eruptions develop as a result of the repeated formation and expulsion of new flux ropes due to continuous emergence and reconnection of sheared field lines along the polarity inversion line of the AR. The acceleration of the eruptions is triggered by tether-cutting reconnection at the current sheet underneath the erupting field. We find that each explosive eruption is followed by reformation of a sigmoidal structure and a subsequent "sigmoid-to-flare arcade" transformation in the AR. These results might have implications for recurrent CMEs and eruptive sigmoids/flares observations and theoretical studies.
The authors acknowledge support by EU (IEF-272549 grant) and the Royal Society.
2014-05-10T00:00:00ZArchontis, V.Hood, A.W.Tsinganos, K.We report on three-dimensional MHD simulations of recurrent mini coronal mass ejection (CME)-like eruptions in a small active region (AR), which is formed by the dynamical emergence of a twisted (not kink unstable) flux tube from the solar interior. The eruptions develop as a result of the repeated formation and expulsion of new flux ropes due to continuous emergence and reconnection of sheared field lines along the polarity inversion line of the AR. The acceleration of the eruptions is triggered by tether-cutting reconnection at the current sheet underneath the erupting field. We find that each explosive eruption is followed by reformation of a sigmoidal structure and a subsequent "sigmoid-to-flare arcade" transformation in the AR. These results might have implications for recurrent CMEs and eruptive sigmoids/flares observations and theoretical studies.Observations of a hybrid double-streamer/pseudostreamer in the solar coronaRachmeler, L.A.Platten, S.J.Bethge, C.Seaton, D.B.Yeates, A.R.http://hdl.handle.net/10023/53182018-01-07T02:49:47Z2014-05-20T00:00:00ZWe report on the first observation of a single hybrid magnetic structure that contains both a pseudostreamer and a double streamer. This structure was originally observed by the SWAP instrument on board the PROBA2 satellite between 2013 May 5 and 10. It consists of a pair of filament channels near the south pole of the Sun. On the western edge of the structure, the magnetic morphology above the filaments is that of a side-by-side double streamer, with open field between the two channels. On the eastern edge, the magnetic morphology is that of a coronal pseudostreamer without the central open field. We investigated this structure with multiple observations and modeling techniques. We describe the topology and dynamic consequences of such a unified structure.
D.B.S. and L.A.R. acknowledge support from the Belgian Federal Science Policy Office (BELSPO) through the ESA-PRODEX program, grant No. 4000103240. S.J.P. acknowledges the financial support of the Isle of Man Government.
2014-05-20T00:00:00ZRachmeler, L.A.Platten, S.J.Bethge, C.Seaton, D.B.Yeates, A.R.We report on the first observation of a single hybrid magnetic structure that contains both a pseudostreamer and a double streamer. This structure was originally observed by the SWAP instrument on board the PROBA2 satellite between 2013 May 5 and 10. It consists of a pair of filament channels near the south pole of the Sun. On the western edge of the structure, the magnetic morphology above the filaments is that of a side-by-side double streamer, with open field between the two channels. On the eastern edge, the magnetic morphology is that of a coronal pseudostreamer without the central open field. We investigated this structure with multiple observations and modeling techniques. We describe the topology and dynamic consequences of such a unified structure.Clusters of small eruptive flares produced by magnetic reconnection in the SunArchontis, V.Hansteen, V.http://hdl.handle.net/10023/53162018-01-07T02:49:46Z2014-06-10T00:00:00ZWe report on the formation of small solar flares produced by patchy magnetic reconnection between interacting magnetic loops. A three-dimensional (3D) magnetohydrodynamic (MHD) numerical experiment was performed, where a uniform magnetic flux sheet was injected into a fully developed convective layer. The gradual emergence of the field into the solar atmosphere results in a network of magnetic loops, which interact dynamically forming current layers at their interfaces. The formation and ejection of plasmoids out of the current layers leads to patchy reconnection and the spontaneous formation of several small (size ≈1-2 Mm) flares. We find that these flares are short-lived (30 s-3 minutes) bursts of energy in the range O(1025-1027) erg, which is basically the nanoflare-microflare range. Their persistent formation and co-operative action and evolution leads to recurrent emission of fast EUV/X-ray jets and considerable plasma heating in the active corona.
This research was supported by the Research Council of Norway through the grant "Solar Atmospheric Modelling" and through grants of computing time from the Programme for Supercomputing, by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement No. 291058 and by computing project s1061 from the High End Computing Division of NASA. The authors acknowledge support by the EU (IEF-272549 grant) and the Royal Society.
2014-06-10T00:00:00ZArchontis, V.Hansteen, V.We report on the formation of small solar flares produced by patchy magnetic reconnection between interacting magnetic loops. A three-dimensional (3D) magnetohydrodynamic (MHD) numerical experiment was performed, where a uniform magnetic flux sheet was injected into a fully developed convective layer. The gradual emergence of the field into the solar atmosphere results in a network of magnetic loops, which interact dynamically forming current layers at their interfaces. The formation and ejection of plasmoids out of the current layers leads to patchy reconnection and the spontaneous formation of several small (size ≈1-2 Mm) flares. We find that these flares are short-lived (30 s-3 minutes) bursts of energy in the range O(1025-1027) erg, which is basically the nanoflare-microflare range. Their persistent formation and co-operative action and evolution leads to recurrent emission of fast EUV/X-ray jets and considerable plasma heating in the active corona.Loss cone evolution and particle escape in collapsing magnetic trap models in solar flaresEradat Oskoui, SolmazNeukirch, ThomasGrady, Keith Jameshttp://hdl.handle.net/10023/52752018-01-07T02:43:49Z2014-03-01T00:00:00ZContext. Collapsing magnetic traps (CMTs) have been suggested as one possible mechanism responsible for the acceleration of high-energy particles during solar flares. An important question regarding the CMT acceleration mechanism is which particle orbits escape and which are trapped during the time evolution of a CMT. While some models predict the escape of the majority of particle orbits, other more sophisticated CMT models show that, in particular, the highest-energy particles remain trapped at all times. The exact prediction is not straightforward because both the loss cone angle and the particle orbit pitch angle evolve in time in a CMT. Aims. Our aim is to gain a better understanding of the conditions leading to either particle orbit escape or trapping in CMTs. Methods. We present a detailed investigation of the time evolution of particle orbit pitch angles in the CMT model of Giuliani and collaborators and compare this with the time evolution of the loss cone angle. The non-relativistic guiding centre approximation is used to calculate the particle orbits. We also use simplified models to corroborate the findings of the particle orbit calculations. Results. We find that there is a critical initial pitch angle for each field line of a CMT that divides trapped and escaping particle orbits. This critical initial pitch angle is greater than the initial loss cone angle, but smaller than the asymptotic (final) loss cone angle for that field line. As the final loss cone angle in CMTs is larger than the initial loss cone angle, particle orbits with pitch angles that cross into the loss cone during their time evolution will escape whereas all other particle orbits are trapped. We find that in realistic CMT models, Fermi acceleration will only dominate in the initial phase of the CMT evolution and, in this case, can reduce the pitch angle, but that betatron acceleration will dominate for later stages of the CMT evolution leading to a systematic increase of the pitch angle. Whether a particle escapes or remains trapped depends critically on the relative importance of the two acceleration mechanisms, which cannot be decoupled in more sophisticated CMT models.
This work was financially supported by the UK’s Science and Technology Facilities Council.
2014-03-01T00:00:00ZEradat Oskoui, SolmazNeukirch, ThomasGrady, Keith JamesContext. Collapsing magnetic traps (CMTs) have been suggested as one possible mechanism responsible for the acceleration of high-energy particles during solar flares. An important question regarding the CMT acceleration mechanism is which particle orbits escape and which are trapped during the time evolution of a CMT. While some models predict the escape of the majority of particle orbits, other more sophisticated CMT models show that, in particular, the highest-energy particles remain trapped at all times. The exact prediction is not straightforward because both the loss cone angle and the particle orbit pitch angle evolve in time in a CMT. Aims. Our aim is to gain a better understanding of the conditions leading to either particle orbit escape or trapping in CMTs. Methods. We present a detailed investigation of the time evolution of particle orbit pitch angles in the CMT model of Giuliani and collaborators and compare this with the time evolution of the loss cone angle. The non-relativistic guiding centre approximation is used to calculate the particle orbits. We also use simplified models to corroborate the findings of the particle orbit calculations. Results. We find that there is a critical initial pitch angle for each field line of a CMT that divides trapped and escaping particle orbits. This critical initial pitch angle is greater than the initial loss cone angle, but smaller than the asymptotic (final) loss cone angle for that field line. As the final loss cone angle in CMTs is larger than the initial loss cone angle, particle orbits with pitch angles that cross into the loss cone during their time evolution will escape whereas all other particle orbits are trapped. We find that in realistic CMT models, Fermi acceleration will only dominate in the initial phase of the CMT evolution and, in this case, can reduce the pitch angle, but that betatron acceleration will dominate for later stages of the CMT evolution leading to a systematic increase of the pitch angle. Whether a particle escapes or remains trapped depends critically on the relative importance of the two acceleration mechanisms, which cannot be decoupled in more sophisticated CMT models.The solar cycle variation of topological structures in the global solar coronaPlatten, S.J.Parnell, C.E.Haynes, A.L.Priest, E.R.MacKay, D.H.http://hdl.handle.net/10023/52712018-01-28T01:31:43Z2014-05-01T00:00:00ZContext. The complicated distribution of magnetic flux across the solar photosphere results in a complex web of coronal magnetic field structures. To understand this complexity, the magnetic skeleton of the coronal field can be calculated. The skeleton highlights the (separatrix) surfaces that divide the field into topologically distinct regions, allowing open-field regions on the solar surface to be located. Furthermore, separatrix surfaces and their intersections with other separatrix surfaces (i.e., separators) are important likely energy release sites. Aims. The aim of this paper is to investigate, throughout the solar cycle, the nature of coronal magnetic-field topologies that arise under the potential-field source-surface approximation. In particular, we characterise the typical global fields at solar maximum and minimum. Methods. Global magnetic fields are extrapolated from observed Kitt Peak and SOLIS synoptic magnetograms, from Carrington rotations 1645 to 2144, using the potential-field source-surface model. This allows the variations in the coronal skeleton to be studied over three solar cycles. Results. The main building blocks which make up magnetic fields are identified and classified according to the nature of their separatrix surfaces. The magnetic skeleton reveals that, at solar maximum, the global coronal field involves a multitude of topological structures at all latitudes criss-crossing throughout the atmosphere. Many open-field regions exist originating anywhere on the photosphere. At solar minimum, the coronal topology is heavily influenced by the solar magnetic dipole. A strong dipole results in a simple large-scale structure involving just two large polar open-field regions, but, at short radial distances between ± 60° latitude, the small-scale topology is complex. If the solar magnetic dipole if weak, as in the recent minimum, then the low-latitude quiet-sun magnetic fields may be globally significant enough to create many disconnected open-field regions between ± 60° latitude, in addition to the two polar open-field regions.
S.J.P. acknowledges financial support from the Isle of Man Government. E.R.P. is grateful to the Leverhulme Trust for his emeritus fellowship. The research leading to these results has received funding from the European Commission’s Seventh Framework Programme (FP7/2007-2013) under the grant agreement SWIFF (project No. 263340, www.swiff.eu).
2014-05-01T00:00:00ZPlatten, S.J.Parnell, C.E.Haynes, A.L.Priest, E.R.MacKay, D.H.Context. The complicated distribution of magnetic flux across the solar photosphere results in a complex web of coronal magnetic field structures. To understand this complexity, the magnetic skeleton of the coronal field can be calculated. The skeleton highlights the (separatrix) surfaces that divide the field into topologically distinct regions, allowing open-field regions on the solar surface to be located. Furthermore, separatrix surfaces and their intersections with other separatrix surfaces (i.e., separators) are important likely energy release sites. Aims. The aim of this paper is to investigate, throughout the solar cycle, the nature of coronal magnetic-field topologies that arise under the potential-field source-surface approximation. In particular, we characterise the typical global fields at solar maximum and minimum. Methods. Global magnetic fields are extrapolated from observed Kitt Peak and SOLIS synoptic magnetograms, from Carrington rotations 1645 to 2144, using the potential-field source-surface model. This allows the variations in the coronal skeleton to be studied over three solar cycles. Results. The main building blocks which make up magnetic fields are identified and classified according to the nature of their separatrix surfaces. The magnetic skeleton reveals that, at solar maximum, the global coronal field involves a multitude of topological structures at all latitudes criss-crossing throughout the atmosphere. Many open-field regions exist originating anywhere on the photosphere. At solar minimum, the coronal topology is heavily influenced by the solar magnetic dipole. A strong dipole results in a simple large-scale structure involving just two large polar open-field regions, but, at short radial distances between ± 60° latitude, the small-scale topology is complex. If the solar magnetic dipole if weak, as in the recent minimum, then the low-latitude quiet-sun magnetic fields may be globally significant enough to create many disconnected open-field regions between ± 60° latitude, in addition to the two polar open-field regions.Dynamic properties of bright points in an active regionKeys, P.H.Mathioudakis, M.Jess, D.B.MacKay, D.H.Keenan, F.P.http://hdl.handle.net/10023/52642018-01-07T02:48:57Z2014-06-20T00:00:00ZContext. Bright points (BPs) are small-scale, magnetic features ubiquitous across the solar surface. Previously, we have observed and noted their properties for quiet Sun regions. Here, we determine the dynamic properties of BPs using simultaneous quiet Sun and active region data. Aims. The aim of this paper is to compare the properties of BPs in both active and quiet Sun regions and to determine any difference in the dynamics and general properties of BPs as a result of the varying magnetic activity within these two regions. Methods. High spatial and temporal resolution G-band observations of active region AR11372 were obtained with the Rapid Oscillations in the Solar Atmosphere instrument at the Dunn Solar Telescope. Three subfields of varying polarity and magnetic flux density were selected with the aid of magnetograms obtained from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory. Bright points within these subfields were subsequently tracked and analysed. Results. It is found that BPs within active regions display attenuated velocity distributions with an average horizontal velocity of ∼0.6 km s-1, compared to the quiet region which had an average velocity of 0.9 km s-1. Active region BPs are also ∼21% larger than quiet region BPs and have longer average lifetimes (∼132 s) than their quiet region counterparts (88 s). No preferential flow directions are observed within the active region subfields. The diffusion index (γ) is estimated at ∼1.2 for the three regions. Conclusions. We confirm that the dynamic properties of BPs arise predominately from convective motions. The presence of stronger field strengths within active regions is the likely reason behind the varying properties observed. We believe that larger amounts of magnetic flux will attenuate BP velocities by a combination of restricting motion within the intergranular lanes and by increasing the number of stagnation points produced by inhibited convection. Larger BPs are found in regions of higher magnetic flux density and we believe that lifetimes increase in active regions as the magnetic flux stabilises the BPs.
This work has been supported by the UK Science and Technology Facilities Council (STFC). Observations were obtained at the National Solar Observatory, operated by the Association of Universities for Research in Astronomy, Inc. (AURA), under cooperative agreement with the National Science Foundation. D.B.J. would like to thank the STFC for an Ernest Rutherford Fellowship. We are also grateful for support sponsored by the Air Force Office of Scientific Research, Air Force Material Command, USAF under grant number FA8655-09-13085.
2014-06-20T00:00:00ZKeys, P.H.Mathioudakis, M.Jess, D.B.MacKay, D.H.Keenan, F.P.Context. Bright points (BPs) are small-scale, magnetic features ubiquitous across the solar surface. Previously, we have observed and noted their properties for quiet Sun regions. Here, we determine the dynamic properties of BPs using simultaneous quiet Sun and active region data. Aims. The aim of this paper is to compare the properties of BPs in both active and quiet Sun regions and to determine any difference in the dynamics and general properties of BPs as a result of the varying magnetic activity within these two regions. Methods. High spatial and temporal resolution G-band observations of active region AR11372 were obtained with the Rapid Oscillations in the Solar Atmosphere instrument at the Dunn Solar Telescope. Three subfields of varying polarity and magnetic flux density were selected with the aid of magnetograms obtained from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory. Bright points within these subfields were subsequently tracked and analysed. Results. It is found that BPs within active regions display attenuated velocity distributions with an average horizontal velocity of ∼0.6 km s-1, compared to the quiet region which had an average velocity of 0.9 km s-1. Active region BPs are also ∼21% larger than quiet region BPs and have longer average lifetimes (∼132 s) than their quiet region counterparts (88 s). No preferential flow directions are observed within the active region subfields. The diffusion index (γ) is estimated at ∼1.2 for the three regions. Conclusions. We confirm that the dynamic properties of BPs arise predominately from convective motions. The presence of stronger field strengths within active regions is the likely reason behind the varying properties observed. We believe that larger amounts of magnetic flux will attenuate BP velocities by a combination of restricting motion within the intergranular lanes and by increasing the number of stagnation points produced by inhibited convection. Larger BPs are found in regions of higher magnetic flux density and we believe that lifetimes increase in active regions as the magnetic flux stabilises the BPs.Vortical control of forced two-dimensional turbulenceFontane, Jerome Jacob LouisDritschel, David GerardScott, Richard Kirknesshttp://hdl.handle.net/10023/52362018-01-07T02:42:32Z2013-01-14T00:00:00ZA new numerical technique for the simulation of forced two-dimensional turbulence[D. Dritschel and J. Fontane, “The combined Lagrangian advection method,” J. Comput. Phys.229, 5408–5417 (Year: 2010)10.1016/j.jcp.2010.03.048] is used to examine the validity of Kraichnan-Batchelor scaling laws at higher Reynolds number than previously accessible with classical pseudo-spectral methods, making use of large simulation ensembles to allow a detailed consideration of the inverse cascade in a quasi-steady state. Our results support the recent finding of Scott [R. Scott, “Nonrobustness of the two-dimensional turbulent inverse cascade,” Phys. Rev. E75, 046301 (Year: 2007)10.1103/PhysRevE.75.046301], namely that when a direct enstrophy cascading range is well-represented numerically, a steeper energy spectrum proportional to k−2 is obtained in place of the classical k −5/3 prediction. It is further shown that this steep spectrum is associated with a faster growth of energy at large scales, scaling like t −1 rather than Kraichnan's prediction of t −3/2. The deviation from Kraichnan's theory is related to the emergence of a population of vortices that dominate the distribution of energy across scales, and whose number density and vorticity distribution with respect to vortex area are related to the shape of the enstrophy spectrum. An analytical model is proposed which closely matches the numerical spectra between the large scales and the forcing scale.
Jérôme Fontane is supported by the European Community in the framework of the CONVECT project under Grant No. PIEF-GA-2008-221003.
2013-01-14T00:00:00ZFontane, Jerome Jacob LouisDritschel, David GerardScott, Richard KirknessA new numerical technique for the simulation of forced two-dimensional turbulence[D. Dritschel and J. Fontane, “The combined Lagrangian advection method,” J. Comput. Phys.229, 5408–5417 (Year: 2010)10.1016/j.jcp.2010.03.048] is used to examine the validity of Kraichnan-Batchelor scaling laws at higher Reynolds number than previously accessible with classical pseudo-spectral methods, making use of large simulation ensembles to allow a detailed consideration of the inverse cascade in a quasi-steady state. Our results support the recent finding of Scott [R. Scott, “Nonrobustness of the two-dimensional turbulent inverse cascade,” Phys. Rev. E75, 046301 (Year: 2007)10.1103/PhysRevE.75.046301], namely that when a direct enstrophy cascading range is well-represented numerically, a steeper energy spectrum proportional to k−2 is obtained in place of the classical k −5/3 prediction. It is further shown that this steep spectrum is associated with a faster growth of energy at large scales, scaling like t −1 rather than Kraichnan's prediction of t −3/2. The deviation from Kraichnan's theory is related to the emergence of a population of vortices that dominate the distribution of energy across scales, and whose number density and vorticity distribution with respect to vortex area are related to the shape of the enstrophy spectrum. An analytical model is proposed which closely matches the numerical spectra between the large scales and the forcing scale.Resistive magnetohydrodynamic reconnection : resolving long-term, chaotic dynamicsKeppens, R.Porth, O.Galsgaard, K.Frederiksen, J.T.Restante, A.L.Lapenta, G.Parnell, C.http://hdl.handle.net/10023/52332018-01-07T02:48:36Z2013-09-13T00:00:00ZIn this paper, we address the long-term evolution of an idealised double current system entering reconnection regimes where chaotic behavior plays a prominent role. Our aim is to quantify the energetics in high magnetic Reynolds number evolutions, enriched by secondary tearing events, multiple magnetic island coalescence, and compressive versus resistive heating scenarios. Our study will pay particular attention to the required numerical resolutions achievable by modern (grid-adaptive) computations, and comment on the challenge associated with resolving chaotic island formation and interaction. We will use shock-capturing, conservative, grid-adaptive simulations for investigating trends dominated by both physical (resistivity) and numerical (resolution) parameters, and confront them with (visco-)resistive magnetohydrodynamic simulations performed with very different, but equally widely used discretization schemes. This will allow us to comment on the obtained evolutions in a manner irrespective of the adopted discretization strategy. Our findings demonstrate that all schemes used (finite volume based shock-capturing, high order finite differences, and particle in cell-like methods) qualitatively agree on the various evolutionary stages, and that resistivity values of order 0.001 already can lead to chaotic island appearance. However, none of the methods exploited demonstrates convergence in the strong sense in these chaotic regimes. At the same time, nonperturbed tests for showing convergence over long time scales in ideal to resistive regimes are provided as well, where all methods are shown to agree. Both the advantages and disadvantages of specific discretizations as applied to this challenging problem are discussed.
We acknowledge financial support from the EC FP7/2007-2013 Grant Agreement SWIFF (No. 263340) and from project GOA/2009/009 (KU Leuven). This research has been funded by the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office (IAP P7/08 CHARM). Part of the simulations used the infrastructure of the VSC-Flemish Supercomputer Center, funded by the Hercules Foundation and the Flemish Government-Department EWI. Another part of the simulations was done at the former Danish Center for Scientific Computing at Copenhagen University which is now part of DeIC Danish e-Infrastructure Cooperation.
2013-09-13T00:00:00ZKeppens, R.Porth, O.Galsgaard, K.Frederiksen, J.T.Restante, A.L.Lapenta, G.Parnell, C.In this paper, we address the long-term evolution of an idealised double current system entering reconnection regimes where chaotic behavior plays a prominent role. Our aim is to quantify the energetics in high magnetic Reynolds number evolutions, enriched by secondary tearing events, multiple magnetic island coalescence, and compressive versus resistive heating scenarios. Our study will pay particular attention to the required numerical resolutions achievable by modern (grid-adaptive) computations, and comment on the challenge associated with resolving chaotic island formation and interaction. We will use shock-capturing, conservative, grid-adaptive simulations for investigating trends dominated by both physical (resistivity) and numerical (resolution) parameters, and confront them with (visco-)resistive magnetohydrodynamic simulations performed with very different, but equally widely used discretization schemes. This will allow us to comment on the obtained evolutions in a manner irrespective of the adopted discretization strategy. Our findings demonstrate that all schemes used (finite volume based shock-capturing, high order finite differences, and particle in cell-like methods) qualitatively agree on the various evolutionary stages, and that resistivity values of order 0.001 already can lead to chaotic island appearance. However, none of the methods exploited demonstrates convergence in the strong sense in these chaotic regimes. At the same time, nonperturbed tests for showing convergence over long time scales in ideal to resistive regimes are provided as well, where all methods are shown to agree. Both the advantages and disadvantages of specific discretizations as applied to this challenging problem are discussed.The effect of slip length on vortex rebound from a rigid boundarySutherland, D.Macaskill, C.Dritschel, D.G.http://hdl.handle.net/10023/52322018-01-07T02:48:36Z2013-09-23T00:00:00ZThe problem of a dipole incident normally on a rigid boundary, for moderate to large Reynolds numbers, has recently been treated numerically using a volume penalisation method by Nguyen van yen, Farge, and Schneider [Phys. Rev. Lett.106, 184502 (2011)]. Their results indicate that energy dissipating structures persist in the inviscid limit. They found that the use of penalisation methods intrinsically introduces some slip at the boundary wall, where the slip approaches zero as the Reynolds number goes to infinity, so reducing to the no-slip case in this limit. We study the same problem, for both no-slip and partial slip cases, using compact differences on a Chebyshev grid in the direction normal to the wall and Fourier methods in the direction along the wall. We find that for the no-slip case there is no indication of the persistence of energy dissipating structures in the limit as viscosity approaches zero and that this also holds for any fixed slip length. However, when the slip length is taken to vary inversely with Reynolds number then the results of Nguyen van yen et al. are regained. It therefore appears that the prediction that energy dissipating structures persist in the inviscid limit follows from the two limits of wall slip length going to zero, and viscosity going to zero, not being treated independently in their use of the volume penalisation method.
2013-09-23T00:00:00ZSutherland, D.Macaskill, C.Dritschel, D.G.The problem of a dipole incident normally on a rigid boundary, for moderate to large Reynolds numbers, has recently been treated numerically using a volume penalisation method by Nguyen van yen, Farge, and Schneider [Phys. Rev. Lett.106, 184502 (2011)]. Their results indicate that energy dissipating structures persist in the inviscid limit. They found that the use of penalisation methods intrinsically introduces some slip at the boundary wall, where the slip approaches zero as the Reynolds number goes to infinity, so reducing to the no-slip case in this limit. We study the same problem, for both no-slip and partial slip cases, using compact differences on a Chebyshev grid in the direction normal to the wall and Fourier methods in the direction along the wall. We find that for the no-slip case there is no indication of the persistence of energy dissipating structures in the limit as viscosity approaches zero and that this also holds for any fixed slip length. However, when the slip length is taken to vary inversely with Reynolds number then the results of Nguyen van yen et al. are regained. It therefore appears that the prediction that energy dissipating structures persist in the inviscid limit follows from the two limits of wall slip length going to zero, and viscosity going to zero, not being treated independently in their use of the volume penalisation method.Progress towards numerical and experimental simulations of fusion relevant beam instabilitiesKing, M.Bryson, R.Ronald, K.Cairns, R. A.McConville, S. L.Speirs, D. C.Phelps, A. D. R.Bingham, R.Gillespie, K. M.Cross, A. W.Vorgul, I.Trines, R.http://hdl.handle.net/10023/51862018-01-07T03:11:45Z2014-05-07T00:00:00ZIn certain plasmas, non-thermal electron distributions can produce instabilities. These instabilities may be useful or potentially disruptive. Therefore the study of these instabilities is of importance in a variety of fields including fusion science and astrophysics. Following on from previous work conducted at the University of Strathclyde on the cyclotron resonance maser instability that was relevant to astrophysical radiowave generation, further instabilities are being investigated. Particular instabilities of interest are the anomalous Doppler instability which can occur in magnetic confinement fusion plasmas and the two-stream instability that is of importance in fast-ignition inertial confinement fusion. To this end, computational simulations have been undertaken to investigate the behaviour of both the anomalous Doppler and two-stream instabilities with the goal of designing an experiment to observe these behaviours in a laboratory.
2014-05-07T00:00:00ZKing, M.Bryson, R.Ronald, K.Cairns, R. A.McConville, S. L.Speirs, D. C.Phelps, A. D. R.Bingham, R.Gillespie, K. M.Cross, A. W.Vorgul, I.Trines, R.In certain plasmas, non-thermal electron distributions can produce instabilities. These instabilities may be useful or potentially disruptive. Therefore the study of these instabilities is of importance in a variety of fields including fusion science and astrophysics. Following on from previous work conducted at the University of Strathclyde on the cyclotron resonance maser instability that was relevant to astrophysical radiowave generation, further instabilities are being investigated. Particular instabilities of interest are the anomalous Doppler instability which can occur in magnetic confinement fusion plasmas and the two-stream instability that is of importance in fast-ignition inertial confinement fusion. To this end, computational simulations have been undertaken to investigate the behaviour of both the anomalous Doppler and two-stream instabilities with the goal of designing an experiment to observe these behaviours in a laboratory.Scaled Experiment to Investigate Auroral Kilometric Radiation Mechanisms in the Presence of Background ElectronsMcConville, S. L.Ronald, K.Speirs, D. C.Gillespie, K. M.Phelps, A. D. R.Cross, A. W.Bingham, R.Robertson, C. W.Whyte, C. G.He, W.King, M.Bryson, R.Vorgul, I.Cairns, R. A.Kellett, B. J.http://hdl.handle.net/10023/51852018-01-07T03:11:44Z2014-05-07T00:00:00ZAuroral Kilometric Radiation (AKR) emissions occur at frequencies similar to 300kHz polarised in the X-mode with efficiencies similar to 1-2% [1,2] in the auroral density cavity in the polar regions of the Earth's magnetosphere, a region of low density plasma similar to 3200km above the Earth's surface, where electrons are accelerated down towards the Earth whilst undergoing magnetic compression. As a result of this magnetic compression the electrons acquire a horseshoe distribution function in velocity space. Previous theoretical studies have predicted that this distribution is capable of driving the cyclotron maser instability. To test this theory a scaled laboratory experiment was constructed to replicate this phenomenon in a controlled environment, [3-5] whilst 2D and 3D simulations are also being conducted to predict the experimental radiation power and mode, [6-9]. The experiment operates in the microwave frequency regime and incorporates a region of increasing magnetic field as found at the Earth's pole using magnet solenoids to encase the cylindrical interaction waveguide through which an initially rectilinear electron beam (12A) was accelerated by a 75keV pulse. Experimental results showed evidence of the formation of the horseshoe distribution function. The radiation was produced in the near cut-off TE01 mode, comparable with X-mode characteristics, at 4.42GHz. Peak microwave output power was measured similar to 35kW and peak efficiency of emission similar to 2%, [3]. A Penning trap was constructed and inserted into the interaction waveguide to enable generation of a background plasma which would lead to closer comparisons with the magnetospheric conditions. Initial design and measurements are presented showing the principle features of the new geometry.
2014-05-07T00:00:00ZMcConville, S. L.Ronald, K.Speirs, D. C.Gillespie, K. M.Phelps, A. D. R.Cross, A. W.Bingham, R.Robertson, C. W.Whyte, C. G.He, W.King, M.Bryson, R.Vorgul, I.Cairns, R. A.Kellett, B. J.Auroral Kilometric Radiation (AKR) emissions occur at frequencies similar to 300kHz polarised in the X-mode with efficiencies similar to 1-2% [1,2] in the auroral density cavity in the polar regions of the Earth's magnetosphere, a region of low density plasma similar to 3200km above the Earth's surface, where electrons are accelerated down towards the Earth whilst undergoing magnetic compression. As a result of this magnetic compression the electrons acquire a horseshoe distribution function in velocity space. Previous theoretical studies have predicted that this distribution is capable of driving the cyclotron maser instability. To test this theory a scaled laboratory experiment was constructed to replicate this phenomenon in a controlled environment, [3-5] whilst 2D and 3D simulations are also being conducted to predict the experimental radiation power and mode, [6-9]. The experiment operates in the microwave frequency regime and incorporates a region of increasing magnetic field as found at the Earth's pole using magnet solenoids to encase the cylindrical interaction waveguide through which an initially rectilinear electron beam (12A) was accelerated by a 75keV pulse. Experimental results showed evidence of the formation of the horseshoe distribution function. The radiation was produced in the near cut-off TE01 mode, comparable with X-mode characteristics, at 4.42GHz. Peak microwave output power was measured similar to 35kW and peak efficiency of emission similar to 2%, [3]. A Penning trap was constructed and inserted into the interaction waveguide to enable generation of a background plasma which would lead to closer comparisons with the magnetospheric conditions. Initial design and measurements are presented showing the principle features of the new geometry.3D PiC code investigations of Auroral Kilometric Radiation mechanismsGillespie, K. M.McConville, S. L.Speirs, D. C.Ronald, K.Phelps, A. D. R.Bingham, R.Cross, A. W.Robertson, C. W.Whyte, C. G.He, W.Vorgul, I.Cairns, R. A.Kellett, B. J.http://hdl.handle.net/10023/51842018-01-07T03:11:45Z2014-01-01T00:00:00ZEfficient (similar to 1%) electron cyclotron radio emissions are known to originate in the X mode from regions of locally depleted plasma in the Earths polar magnetosphere. These emissions are commonly referred to as the Auroral Kilometric Radiation (AKR). AKR occurs naturally in these polar regions where electrons are accelerated by electric fields into the increasing planetary magnetic dipole. Here conservation of the magnetic moment converts axial to rotational momentum forming a horseshoe distribution in velocity phase space. This distribution is unstable to cyclotron emission with radiation emitted in the X-mode. Initial studies were conducted in the form of 2D PiC code simulations [1] and a scaled laboratory experiment that was constructed to reproduce the mechanism of AKR. As studies progressed, 3D PiC code simulations were conducted to enable complete investigation of the complex interaction dimensions. A maximum efficiency of 1.25% is predicted from these simulations in the same mode and frequency as measured in the experiment. This is also consistent with geophysical observations and the predictions of theory.
2014-01-01T00:00:00ZGillespie, K. M.McConville, S. L.Speirs, D. C.Ronald, K.Phelps, A. D. R.Bingham, R.Cross, A. W.Robertson, C. W.Whyte, C. G.He, W.Vorgul, I.Cairns, R. A.Kellett, B. J.Efficient (similar to 1%) electron cyclotron radio emissions are known to originate in the X mode from regions of locally depleted plasma in the Earths polar magnetosphere. These emissions are commonly referred to as the Auroral Kilometric Radiation (AKR). AKR occurs naturally in these polar regions where electrons are accelerated by electric fields into the increasing planetary magnetic dipole. Here conservation of the magnetic moment converts axial to rotational momentum forming a horseshoe distribution in velocity phase space. This distribution is unstable to cyclotron emission with radiation emitted in the X-mode. Initial studies were conducted in the form of 2D PiC code simulations [1] and a scaled laboratory experiment that was constructed to reproduce the mechanism of AKR. As studies progressed, 3D PiC code simulations were conducted to enable complete investigation of the complex interaction dimensions. A maximum efficiency of 1.25% is predicted from these simulations in the same mode and frequency as measured in the experiment. This is also consistent with geophysical observations and the predictions of theory.Numerical simulation of unconstrained cyclotron resonant maser emissionSpeirs, D. C.Gillespie, K. M.Ronald, K.McConville, S. L.Phelps, A. D. R.Cross, A. W.Bingham, R.Kellett, B. J.Cairns, R. A.Vorgul, I.http://hdl.handle.net/10023/51832018-01-07T03:11:44Z2014-05-07T00:00:00ZWhen a mainly rectilinear electron beam is subject to significant magnetic compression, conservation of magnetic moment results in the formation of a horseshoe shaped velocity distribution. It has been shown that such a distribution is unstable to cyclotron emission and may be responsible for the generation of Auroral Kilometric Radiation (AKR) an intense rf emission sourced at high altitudes in the terrestrial auroral magnetosphere. PiC code simulations have been undertaken to investigate the dynamics of the cyclotron emission process in the absence of cavity boundaries with particular consideration of the spatial growth rate, spectral output and rf conversion efficiency. Computations reveal that a well-defined cyclotron emission process occurs albeit with a low spatial growth rate compared to waveguide bounded simulations. The rf output is near perpendicular to the electron beam with a slight backward-wave character reflected in the spectral output with a well defined peak at 2.68GHz, just below the relativistic electron cyclotron frequency. The corresponding rf conversion efficiency of 1.1% is comparable to waveguide bounded simulations and consistent with the predictions of kinetic theory that suggest efficient, spectrally well defined radiation emission can be obtained from an electron horseshoe distribution in the absence of radiation boundaries.
2014-05-07T00:00:00ZSpeirs, D. C.Gillespie, K. M.Ronald, K.McConville, S. L.Phelps, A. D. R.Cross, A. W.Bingham, R.Kellett, B. J.Cairns, R. A.Vorgul, I.When a mainly rectilinear electron beam is subject to significant magnetic compression, conservation of magnetic moment results in the formation of a horseshoe shaped velocity distribution. It has been shown that such a distribution is unstable to cyclotron emission and may be responsible for the generation of Auroral Kilometric Radiation (AKR) an intense rf emission sourced at high altitudes in the terrestrial auroral magnetosphere. PiC code simulations have been undertaken to investigate the dynamics of the cyclotron emission process in the absence of cavity boundaries with particular consideration of the spatial growth rate, spectral output and rf conversion efficiency. Computations reveal that a well-defined cyclotron emission process occurs albeit with a low spatial growth rate compared to waveguide bounded simulations. The rf output is near perpendicular to the electron beam with a slight backward-wave character reflected in the spectral output with a well defined peak at 2.68GHz, just below the relativistic electron cyclotron frequency. The corresponding rf conversion efficiency of 1.1% is comparable to waveguide bounded simulations and consistent with the predictions of kinetic theory that suggest efficient, spectrally well defined radiation emission can be obtained from an electron horseshoe distribution in the absence of radiation boundaries.Laminar shocks in high power laser plasma interactionsCairns, R. A.Bingham, R.Norreys, P.Trines, R.http://hdl.handle.net/10023/51802018-03-18T01:33:26Z2014-02-01T00:00:00ZWe propose a theory to describe laminar ion sound structures in a collisionless plasma. Reflection of a small fraction of the upstream ions converts the well known ion acoustic soliton into a structure with a steep potential gradient upstream and with downstream oscillations. The theory provides a simple interpretation of results dating back more than forty years but, more importantly, is shown to provide an explanation for recent observations on laser produced plasmas relevant to inertial fusion and to ion acceleration. (C) 2014 AIP Publishing LLC.
2014-02-01T00:00:00ZCairns, R. A.Bingham, R.Norreys, P.Trines, R.We propose a theory to describe laminar ion sound structures in a collisionless plasma. Reflection of a small fraction of the upstream ions converts the well known ion acoustic soliton into a structure with a steep potential gradient upstream and with downstream oscillations. The theory provides a simple interpretation of results dating back more than forty years but, more importantly, is shown to provide an explanation for recent observations on laser produced plasmas relevant to inertial fusion and to ion acceleration. (C) 2014 AIP Publishing LLC.Effect of collisions on amplification of laser beams by Brillouin scattering in plasmasHumphrey, K. A.Trines, R. M. G. M.Fiuza, F.Speirs, D. C.Norreys, P.Cairns, R. A.Silva, L. O.Bingham, R.http://hdl.handle.net/10023/51732018-03-18T01:32:45Z2013-10-01T00:00:00ZWe report on particle in cell simulations of energy transfer between a laser pump beam and a counter-propagating seed beam using the Brillouin scattering process in uniform plasma including collisions. The results presented show that the ion acoustic waves excited through naturally occurring Brillouin scattering of the pump field are preferentially damped without affecting the driven Brillouin scattering process resulting from the beating of the pump and seed fields together. We find that collisions, including the effects of Landau damping, allow for a more efficient transfer of energy between the laser beams, and a significant reduction in the amount of seed pre-pulse produced.
Authors KH, RT, DCS, RAC, RB were supported by EPSRC grant EP/G04239X/1.
2013-10-01T00:00:00ZHumphrey, K. A.Trines, R. M. G. M.Fiuza, F.Speirs, D. C.Norreys, P.Cairns, R. A.Silva, L. O.Bingham, R.We report on particle in cell simulations of energy transfer between a laser pump beam and a counter-propagating seed beam using the Brillouin scattering process in uniform plasma including collisions. The results presented show that the ion acoustic waves excited through naturally occurring Brillouin scattering of the pump field are preferentially damped without affecting the driven Brillouin scattering process resulting from the beating of the pump and seed fields together. We find that collisions, including the effects of Landau damping, allow for a more efficient transfer of energy between the laser beams, and a significant reduction in the amount of seed pre-pulse produced.Quasi-geostrophic shallow-water doubly-connected vortex equilibria and their stabilityPlotka, HannaDritschel, David Gerardhttp://hdl.handle.net/10023/51722018-01-07T02:39:23Z2013-05-01T00:00:00ZWe examine the form, properties, stability and evolution of doubly-connected (two-vortex) relative equilibria in the single-layer ƒ-plane quasi-geostrophic shallow-water model of geophysical fluid dynamics. Three parameters completely describe families of equilibria in this system: the ratio γ =L/LD between the horizontal size of the vortices and the Rossby deformation length; the area ratio α of the smaller to the larger vortex; and the minimum distance δ between the two vortices. We vary 0 < γ ≤ 10 and 0.1 ≤ α ≤ 1.0, determining the boundary of stability δ = δC(γ,α). We also examine the nonlinear development of the instabilities and the transitions to other near-equilibrium configurations. Two modes of instability occur when δ < δC: a small -γ asymmetric (wave 3) mode, which is absent for α ≳ 0.6; and a large -γ mode. In general, major structural changes take place during the nonlinear evolution of the vortices, which near δC may be classified as follows: (i) vacillations about equilibrium for γ ≳ 2.5; (ii) partial straining out, associated with the small -γ mode, where either one or both of the vortices get smaller for γ ≲ 2.5 and α ≲ 0.6; (iii) partial merger, occurring at the transition region between the two modes of instability, where one of the vortices gets bigger, and (iv) complete merger, associated with the large-γ mode. We also find that although conservative inviscid transitions to equilibria with the same energy, angular momentum and circulation are possible, they are not the preferred evolutionary path.
H.P. acknowledges the support of a NERC studentship. D.G.D. received support for this research from the UK Engineering and Physical Sciences Research Council (grant EP/H001794/1).
2013-05-01T00:00:00ZPlotka, HannaDritschel, David GerardWe examine the form, properties, stability and evolution of doubly-connected (two-vortex) relative equilibria in the single-layer ƒ-plane quasi-geostrophic shallow-water model of geophysical fluid dynamics. Three parameters completely describe families of equilibria in this system: the ratio γ =L/LD between the horizontal size of the vortices and the Rossby deformation length; the area ratio α of the smaller to the larger vortex; and the minimum distance δ between the two vortices. We vary 0 < γ ≤ 10 and 0.1 ≤ α ≤ 1.0, determining the boundary of stability δ = δC(γ,α). We also examine the nonlinear development of the instabilities and the transitions to other near-equilibrium configurations. Two modes of instability occur when δ < δC: a small -γ asymmetric (wave 3) mode, which is absent for α ≳ 0.6; and a large -γ mode. In general, major structural changes take place during the nonlinear evolution of the vortices, which near δC may be classified as follows: (i) vacillations about equilibrium for γ ≳ 2.5; (ii) partial straining out, associated with the small -γ mode, where either one or both of the vortices get smaller for γ ≲ 2.5 and α ≲ 0.6; (iii) partial merger, occurring at the transition region between the two modes of instability, where one of the vortices gets bigger, and (iv) complete merger, associated with the large-γ mode. We also find that although conservative inviscid transitions to equilibria with the same energy, angular momentum and circulation are possible, they are not the preferred evolutionary path.The influence of the magnetic field on running penumbral waves in the solar chromosphereJess, DavidReznikova, VVan Doorsselaere, TomMackay, Duncan HendryKeys, Peterhttp://hdl.handle.net/10023/51552018-03-11T01:31:35Z2013-12-03T00:00:00ZWe use images of high spatial and temporal resolution, obtained using both ground- and space-based instrumentation, to investigate the role magnetic field inclination angles play in the propagation characteristics of running penumbral waves in the solar chromosphere. Analysis of a near-circular sunspot, close to the center of the solar disk, reveals a smooth rise in oscillatory period as a function of distance from the umbral barycenter. However, in one directional quadrant, corresponding to the north direction, a pronounced kink in the period-distance diagram is found. Utilizing a combination of the inversion of magnetic Stokes vectors and force-free field extrapolations, we attribute this behavior to the cut-off frequency imposed by the magnetic field geometry in this location. A rapid, localized inclination of the magnetic field lines in the north direction results in a faster increase in the dominant periodicity due to an accelerated reduction in the cut-off frequency. For the first time, we reveal how the spatial distribution of dominant wave periods, obtained with one of the highest resolution solar instruments currently available, directly reflects the magnetic geometry of the underlying sunspot, thus opening up a wealth of possibilities in future magnetohydrodynamic seismology studies. In addition, the intrinsic relationships we find between the underlying magnetic field geometries connecting the photosphere to the chromosphere, and the characteristics of running penumbral waves observed in the upper chromosphere, directly supports the interpretation that running penumbral wave phenomena are the chromospheric signature of upwardly propagating magneto-acoustic waves generated in the photosphere.
D.B.J. acknowledges the European Commission and the Fonds Wetenschappelijk Onderzoek (FWO) for the award of a Marie Curie Pegasus Fellowship during which this work was initiated, in addition to the UK Science and Technology Facilities Council (STFC) for the award of an Ernest Rutherford Fellowship which allowed the completion of this project. The research carried out by V.E.R. is partly supported by grant MC FP7-PEOPLE-2011-IRSES-295272. T.V.D. acknowledges funding from the Odysseus Programme of the FWO Vlaanderen and from the EU's 7th Framework Programme as an ERG with grant number 276808. P.H.K. and D.H.M. are grateful to STFC for research support. This research has been funded by the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office (IAP P7/08 CHARM).
2013-12-03T00:00:00ZJess, DavidReznikova, VVan Doorsselaere, TomMackay, Duncan HendryKeys, PeterWe use images of high spatial and temporal resolution, obtained using both ground- and space-based instrumentation, to investigate the role magnetic field inclination angles play in the propagation characteristics of running penumbral waves in the solar chromosphere. Analysis of a near-circular sunspot, close to the center of the solar disk, reveals a smooth rise in oscillatory period as a function of distance from the umbral barycenter. However, in one directional quadrant, corresponding to the north direction, a pronounced kink in the period-distance diagram is found. Utilizing a combination of the inversion of magnetic Stokes vectors and force-free field extrapolations, we attribute this behavior to the cut-off frequency imposed by the magnetic field geometry in this location. A rapid, localized inclination of the magnetic field lines in the north direction results in a faster increase in the dominant periodicity due to an accelerated reduction in the cut-off frequency. For the first time, we reveal how the spatial distribution of dominant wave periods, obtained with one of the highest resolution solar instruments currently available, directly reflects the magnetic geometry of the underlying sunspot, thus opening up a wealth of possibilities in future magnetohydrodynamic seismology studies. In addition, the intrinsic relationships we find between the underlying magnetic field geometries connecting the photosphere to the chromosphere, and the characteristics of running penumbral waves observed in the upper chromosphere, directly supports the interpretation that running penumbral wave phenomena are the chromospheric signature of upwardly propagating magneto-acoustic waves generated in the photosphere.Simulating the formation of a sigmoidal flux rope in AR10977 from SOHO/MDI magnetogramsGibb, Gordon Peter SamuelMackay, Duncan HendryGreen, LucieMeyer, Karen Alisonhttp://hdl.handle.net/10023/51542018-02-18T01:32:08Z2014-02-20T00:00:00ZThe modeling technique of Mackay et al. is applied to simulate the coronal magnetic field of NOAA active region AR10977 over a seven day period (2007 December 2-10). The simulation is driven with a sequence of line-of-sight component magnetograms from SOHO/MDI and evolves the coronal magnetic field though a continuous series of non-linear force-free states. Upon comparison with Hinode/XRT observations, results show that the simulation reproduces many features of the active region's evolution. In particular, it describes the formation of a flux rope across the polarity inversion line during flux cancellation. The flux rope forms at the same location as an observed X-ray sigmoid. After five days of evolution, the free magnetic energy contained within the flux rope was found to be 3.9 × 1030 erg. This value is more than sufficient to account for the B1.4 GOES flare observed from the active region on 2007 December 7. At the time of the observed eruption, the flux rope was found to contain 20% of the active region flux. We conclude that the modeling technique proposed in Mackay et al.—which directly uses observed magnetograms to energize the coronal field—is a viable method to simulate the evolution of the coronal magnetic field.
G.P.S.G. acknowledges STFC for financial support. D.H.M. acknowledges the STFC, the Leverhulme Trust, and the EU FP7 funded project "SWIFF" (263340) for financial support. L.M.G. acknowledges to the Royal Society for a University Research Fellowship. K.A.M. acknowledges the Leverhulme Trust for financial support. Simulations were carried out on a STFC/SRIF funded UKMHD cluster at St Andrews.
2014-02-20T00:00:00ZGibb, Gordon Peter SamuelMackay, Duncan HendryGreen, LucieMeyer, Karen AlisonThe modeling technique of Mackay et al. is applied to simulate the coronal magnetic field of NOAA active region AR10977 over a seven day period (2007 December 2-10). The simulation is driven with a sequence of line-of-sight component magnetograms from SOHO/MDI and evolves the coronal magnetic field though a continuous series of non-linear force-free states. Upon comparison with Hinode/XRT observations, results show that the simulation reproduces many features of the active region's evolution. In particular, it describes the formation of a flux rope across the polarity inversion line during flux cancellation. The flux rope forms at the same location as an observed X-ray sigmoid. After five days of evolution, the free magnetic energy contained within the flux rope was found to be 3.9 × 1030 erg. This value is more than sufficient to account for the B1.4 GOES flare observed from the active region on 2007 December 7. At the time of the observed eruption, the flux rope was found to contain 20% of the active region flux. We conclude that the modeling technique proposed in Mackay et al.—which directly uses observed magnetograms to energize the coronal field—is a viable method to simulate the evolution of the coronal magnetic field.First comparison of wave observations from CoMP and AIA/SDOThrelfall, James WilliamDe Moortel, InekeMcIntosh, ScottBethge, Christianhttp://hdl.handle.net/10023/51532018-01-07T02:43:13Z2013-08-01T00:00:00ZContext. Waves have long been thought to contribute to the heating of the solar corona and the generation of the solar wind. Recent observations have demonstrated evidence of quasi-periodic longitudinal disturbances and ubiquitous transverse wave propagation in many different coronal environments. Aims. This paper investigates signatures of different types of oscillatory behaviour, both above the solar limb and on-disk, by comparing findings from the Coronal Multi-channel Polarimeter (CoMP) and the Atmospheric Imaging Assembly (AIA) on-board the Solar Dynamics Observatory (SDO) for the same active region. Methods. We study both transverse and longitudinal motion by comparing and contrasting time-distance images of parallel and perpendicular cuts along/across active region fan loops. Comparisons between parallel space-time diagram features in CoMP Doppler velocity and transverse oscillations in AIA images are made, together with space-time analysis of propagating quasi-periodic intensity features seen near the base of loops in AIA. Results. Signatures of transverse motions are observed along the same magnetic structure using CoMP Doppler velocity (vphase = 600 → 750 km s-1, P = 3 → 6 min) and in AIA/SDO above the limb (P = 3 → 8 min). Quasi-periodic intensity features (vphase = 100 → 200 km s-1, P = 6 → 11 min) also travel along the base of the same structure. On the disk, signatures of both transverse and longitudinal intensity features were observed by AIA, and both show similar properties to signatures found along structures anchored in the same active region three days earlier above the limb. Correlated features are recovered by space-time analysis of neighbouring tracks over perpendicular distances of ≲2.6 Mm.
I.D.M. acknowledges support of a Royal Society University Research Fellowship. The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/2007-2013) under the grant agreements SOLSPANET (project No. 269299, www.solspanet.eu/solspanet).
2013-08-01T00:00:00ZThrelfall, James WilliamDe Moortel, InekeMcIntosh, ScottBethge, ChristianContext. Waves have long been thought to contribute to the heating of the solar corona and the generation of the solar wind. Recent observations have demonstrated evidence of quasi-periodic longitudinal disturbances and ubiquitous transverse wave propagation in many different coronal environments. Aims. This paper investigates signatures of different types of oscillatory behaviour, both above the solar limb and on-disk, by comparing findings from the Coronal Multi-channel Polarimeter (CoMP) and the Atmospheric Imaging Assembly (AIA) on-board the Solar Dynamics Observatory (SDO) for the same active region. Methods. We study both transverse and longitudinal motion by comparing and contrasting time-distance images of parallel and perpendicular cuts along/across active region fan loops. Comparisons between parallel space-time diagram features in CoMP Doppler velocity and transverse oscillations in AIA images are made, together with space-time analysis of propagating quasi-periodic intensity features seen near the base of loops in AIA. Results. Signatures of transverse motions are observed along the same magnetic structure using CoMP Doppler velocity (vphase = 600 → 750 km s-1, P = 3 → 6 min) and in AIA/SDO above the limb (P = 3 → 8 min). Quasi-periodic intensity features (vphase = 100 → 200 km s-1, P = 6 → 11 min) also travel along the base of the same structure. On the disk, signatures of both transverse and longitudinal intensity features were observed by AIA, and both show similar properties to signatures found along structures anchored in the same active region three days earlier above the limb. Correlated features are recovered by space-time analysis of neighbouring tracks over perpendicular distances of ≲2.6 Mm.Erratum : "a numerical model of standard to blowout jets" (2013, ApJL, 769, L21)Archontis, VasilisHood, Alan Williamhttp://hdl.handle.net/10023/51522018-01-07T02:43:11Z2013-06-10T00:00:00Z2013-06-10T00:00:00ZArchontis, VasilisHood, Alan WilliamThe emergence of weakly twisted magnetic fields in the SunArchontis, VasilisHood, Alan WilliamTsinganos, Khttp://hdl.handle.net/10023/51512018-01-21T01:31:05Z2013-11-01T00:00:00ZWe have studied the emergence of a weakly twisted magnetic flux tube from the upper convection zone into the solar atmosphere. It is found that the rising magnetized plasma does not undergo the classical, single Ω-shaped loop emergence, but it becomes unstable in two places, forming two magnetic lobes that are anchored in small-scale bipolar structures at the photosphere, between the two main flux concentrations. The two magnetic lobes rise and expand into the corona, forming an overall undulating magnetic flux system. The dynamical interaction of the lobes results in the triggering of high-speed and hot jets and the formation of successive cool and hot loops that coexist in the emerging flux region. Although the initial emerging field is weakly twisted, a highly twisted magnetic flux rope is formed at the low atmosphere, due to shearing and reconnection. The new flux rope (hereafter post-emergence flux rope) does not erupt. It remains confined by the overlying field. Although there is no ejective eruption of the post-emergence rope, it is found that a considerable amount of axial and azimuthal flux is transferred into the solar atmosphere during the emergence of the magnetic field.
The simulations were performed on the STFC and SRIF funded UKMHD cluster, at the University of St Andrews. K.T. and V.A. acknowledge EU support (IEF-272549 grant).
2013-11-01T00:00:00ZArchontis, VasilisHood, Alan WilliamTsinganos, KWe have studied the emergence of a weakly twisted magnetic flux tube from the upper convection zone into the solar atmosphere. It is found that the rising magnetized plasma does not undergo the classical, single Ω-shaped loop emergence, but it becomes unstable in two places, forming two magnetic lobes that are anchored in small-scale bipolar structures at the photosphere, between the two main flux concentrations. The two magnetic lobes rise and expand into the corona, forming an overall undulating magnetic flux system. The dynamical interaction of the lobes results in the triggering of high-speed and hot jets and the formation of successive cool and hot loops that coexist in the emerging flux region. Although the initial emerging field is weakly twisted, a highly twisted magnetic flux rope is formed at the low atmosphere, due to shearing and reconnection. The new flux rope (hereafter post-emergence flux rope) does not erupt. It remains confined by the overlying field. Although there is no ejective eruption of the post-emergence rope, it is found that a considerable amount of axial and azimuthal flux is transferred into the solar atmosphere during the emergence of the magnetic field.Production of small-scale Alfvén waves by ionospheric depletion, nonlinear magnetosphere-ionosphere coupling and phase mixingRussell, A. J. B.Wright, Andrew NicholasStreltsov, A. V.http://hdl.handle.net/10023/51502018-01-07T02:42:10Z2013-04-03T00:00:00ZRockets and satellites have previously observed small-scale Alfven waves inside large-scale downward field-aligned currents, and numerical simulations have associated their formation with self-consistent magnetosphere-ionosphere coupling. The origin of these waves was previously attributed to ionospheric feedback instability; however, we show that they arise in numerical experiments in which the instability is excluded. A new interpretation is proposed in which strong ionospheric depletion and associated current broadening (a nonlinear steepening/wave-breaking process) form magnetosphereionosphere waves inside a downward current region and these oscillations drive upgoing inertial Alfven waves in the overlying plasma. The resulting waves are governed by characteristic periods, which are a good match to previously observed periods for reasonable assumed conditions. Meanwhile, wavelengths perpendicular to the magnetic field initially map to an ionospheric scale comparable to the electron inertial length for the low-altitude magnetosphere, but become shorter with time due to frequency-based phase mixing of boundary waves (a new manifestation of phase mixing). Under suitable conditions, these could act as seeds for the ionospheric feedback instability.
The authors acknowledge the International Space Science Institute (Switzerland) for funding the program that inspired this work. AJBR is grateful to the Royal Commission for the Exhibition of 1851 for present support and acknowledges an STFC studentship that funded part of this work.
2013-04-03T00:00:00ZRussell, A. J. B.Wright, Andrew NicholasStreltsov, A. V.Rockets and satellites have previously observed small-scale Alfven waves inside large-scale downward field-aligned currents, and numerical simulations have associated their formation with self-consistent magnetosphere-ionosphere coupling. The origin of these waves was previously attributed to ionospheric feedback instability; however, we show that they arise in numerical experiments in which the instability is excluded. A new interpretation is proposed in which strong ionospheric depletion and associated current broadening (a nonlinear steepening/wave-breaking process) form magnetosphereionosphere waves inside a downward current region and these oscillations drive upgoing inertial Alfven waves in the overlying plasma. The resulting waves are governed by characteristic periods, which are a good match to previously observed periods for reasonable assumed conditions. Meanwhile, wavelengths perpendicular to the magnetic field initially map to an ionospheric scale comparable to the electron inertial length for the low-altitude magnetosphere, but become shorter with time due to frequency-based phase mixing of boundary waves (a new manifestation of phase mixing). Under suitable conditions, these could act as seeds for the ionospheric feedback instability.A numerical model of standard to blowout jetsArchontis, VasilisHood, A. W.http://hdl.handle.net/10023/51402018-01-28T01:31:09Z2013-05-09T00:00:00ZWe report on three-dimensional (3D) MHD simulations of the formation of jets produced during the emergence and eruption of solar magnetic fields. The interaction between an emerging and an ambient magnetic field in the solar atmosphere leads to (external) reconnection and the formation of "standard" jets with an inverse Y-shaped configuration. Eventually, low-atmosphere (internal) reconnection of sheared fieldlines in the emerging flux region produces an erupting magnetic flux rope and a reconnection jet underneath it. The erupting plasma blows out the ambient field and, moreover, it unwinds as it is ejected into the outer solar atmosphere. The fast emission of the cool material that erupts together with the hot outflows due to external/internal reconnection form a wider "blowout" jet. We show the transition from "standard" to "blowout" jets and report on their 3D structure. The physical plasma properties of the jets are consistent with observational studies.
2013-05-09T00:00:00ZArchontis, VasilisHood, A. W.We report on three-dimensional (3D) MHD simulations of the formation of jets produced during the emergence and eruption of solar magnetic fields. The interaction between an emerging and an ambient magnetic field in the solar atmosphere leads to (external) reconnection and the formation of "standard" jets with an inverse Y-shaped configuration. Eventually, low-atmosphere (internal) reconnection of sheared fieldlines in the emerging flux region produces an erupting magnetic flux rope and a reconnection jet underneath it. The erupting plasma blows out the ambient field and, moreover, it unwinds as it is ejected into the outer solar atmosphere. The fast emission of the cool material that erupts together with the hot outflows due to external/internal reconnection form a wider "blowout" jet. We show the transition from "standard" to "blowout" jets and report on their 3D structure. The physical plasma properties of the jets are consistent with observational studies.SWIFF : space weather integrated forecasting frameworkLapenta, GiovanniPierrard, VivianeKeppens, RonyMarkidis, StefanoPoedts, StefaanŠebek, OndřejTrávníček, Pavel MHenri, PierreCalifano, FrancescoPegoraro, FrancescoFaganello, MatteoOlshevsky, VyacheslavRestante, Anna LisaNordlund, ÅkeTrier Frederiksen, JacobMackay, Duncan HendryParnell, Clare ElizabethBemporad, AlessandroSusino, RobertoBorremans, Krishttp://hdl.handle.net/10023/50492018-01-07T02:40:40Z2013-02-18T00:00:00ZSWIFF is a project funded by the Seventh Framework Programme of the European Commission to study the mathematical-physics models that form the basis for space weather forecasting. The phenomena of space weather span a tremendous scale of densities and temperature with scales ranging 10 orders of magnitude in space and time. Additionally even in local regions there are concurrent processes developing at the electron, ion and global scales strongly interacting with each other. The fundamental challenge in modelling space weather is the need to address multiple physics and multiple scales. Here we present our approach to take existing expertise in fluid and kinetic models to produce an integrated mathematical approach and software infrastructure that allows fluid and kinetic processes to be modelled together. SWIFF aims also at using this new infrastructure to model specific coupled processes at the Solar Corona, in the interplanetary space and in the interaction at the Earth magnetosphere.
This research has received funding from the European Commission’s FP7 Program with the grant agreement SWIFF (Project No. 2633430, swiff.eu). The KU Leuven simulations were conducted on the computational resources provided by the PRACE Tier-0 Project No. 2011050747 (Curie supercomputer) and by the Flemish Supercomputer Center (VIC3). Additional computational support is provided at KU Leuven by the NASA NCCS (Discover) and NAS (Pleiades) Divisons, as part of the support to the NASA MMS Mission. UNIPI acknowledges the HPC resources of CINECA made available within the Distributed European Computing Initiative by the PRACE-2IP, receiving funding from the European Community’s Seventh Framework Programme (FP7/ 2007-2013) under Grant Agreement No. nRI-283493. Work at UNIPI was supported by the Italian Supercomputing Center – CINECA under the ISCRA initiative. Work at UNIPI was supported by the HPC-EUROPA2 project (Project No. 228398) with the support of the European Commission – Capacities Area – Research Infrastructures. Work performed at IAP, ASCR was supported also by the Project RVO: 68378289.
2013-02-18T00:00:00ZLapenta, GiovanniPierrard, VivianeKeppens, RonyMarkidis, StefanoPoedts, StefaanŠebek, OndřejTrávníček, Pavel MHenri, PierreCalifano, FrancescoPegoraro, FrancescoFaganello, MatteoOlshevsky, VyacheslavRestante, Anna LisaNordlund, ÅkeTrier Frederiksen, JacobMackay, Duncan HendryParnell, Clare ElizabethBemporad, AlessandroSusino, RobertoBorremans, KrisSWIFF is a project funded by the Seventh Framework Programme of the European Commission to study the mathematical-physics models that form the basis for space weather forecasting. The phenomena of space weather span a tremendous scale of densities and temperature with scales ranging 10 orders of magnitude in space and time. Additionally even in local regions there are concurrent processes developing at the electron, ion and global scales strongly interacting with each other. The fundamental challenge in modelling space weather is the need to address multiple physics and multiple scales. Here we present our approach to take existing expertise in fluid and kinetic models to produce an integrated mathematical approach and software infrastructure that allows fluid and kinetic processes to be modelled together. SWIFF aims also at using this new infrastructure to model specific coupled processes at the Solar Corona, in the interplanetary space and in the interaction at the Earth magnetosphere.Frequency of behavior witnessed and conformity in an everyday social contextClaidière, N.Bowler, M.Brookes, S.Brown, R.Whiten, A.http://hdl.handle.net/10023/50242018-01-07T02:47:00Z2014-06-20T00:00:00ZConformity is thought to be an important force in human evolution because it has the potential to stabilize cultural homogeneity within groups and cultural diversity between groups. However, the effects of such conformity on cultural and biological evolution will depend much on the particular way in which individuals are influenced by the frequency of alternative behavioral options they witness. In a previous study we found that in a natural situation people displayed a tendency to be 'linear-conformist'. When visitors to a Zoo exhibit were invited to write or draw answers to questions on cards to win a small prize and we manipulated the proportion of text versus drawings on display, we found a strong and significant effect of the proportion of text displayed on the proportion of text in the answers, a conformist effect that was largely linear with a small non-linear component. However, although this overall effect is important to understand cultural evolution, it might mask a greater diversity of behavioral responses shaped by variables such as age, sex, social environment and attention of the participants. Accordingly we performed a further study explicitly to analyze the effects of these variables, together with the quality of the information participants' responses made available to further visitors. Results again showed a largely linear conformity effect that varied little with the variables analyzed.
2014-06-20T00:00:00ZClaidière, N.Bowler, M.Brookes, S.Brown, R.Whiten, A.Conformity is thought to be an important force in human evolution because it has the potential to stabilize cultural homogeneity within groups and cultural diversity between groups. However, the effects of such conformity on cultural and biological evolution will depend much on the particular way in which individuals are influenced by the frequency of alternative behavioral options they witness. In a previous study we found that in a natural situation people displayed a tendency to be 'linear-conformist'. When visitors to a Zoo exhibit were invited to write or draw answers to questions on cards to win a small prize and we manipulated the proportion of text versus drawings on display, we found a strong and significant effect of the proportion of text displayed on the proportion of text in the answers, a conformist effect that was largely linear with a small non-linear component. However, although this overall effect is important to understand cultural evolution, it might mask a greater diversity of behavioral responses shaped by variables such as age, sex, social environment and attention of the participants. Accordingly we performed a further study explicitly to analyze the effects of these variables, together with the quality of the information participants' responses made available to further visitors. Results again showed a largely linear conformity effect that varied little with the variables analyzed.The transterminator ion flow at Venus at solar minimumWood, A. G.Pryse, S. E.Grande, M.Whittaker, I. C.Coates, A. J.Husband, K.Baumjohann, W.Zhang, T. L.Mazelle, C.Kallio, E.Fraenz, M.McKenna-Lawlor, S.Wurz, P.http://hdl.handle.net/10023/47952018-01-07T02:45:24Z2012-12-01T00:00:00ZThe transterminator ion flow in the Venusian ionosphere is observed at solar minimum for the first time. Such a flow, which transports ions from the day to the nightside, has been observed previously around solar maximum. At solar minimum this transport process is severely inhibited by the lower altitude of the ionopause. The observations presented were those made of the Venusian ionospheric plasma by the ASPERA-4 experiment onboard the Venus Express spacecraft, and which constitute the first extensive in-situ measurements of the plasma near solar minimum. Observations near the terminator of the energies of ions of ionospheric origin showed asymmetry between the noon and midnight sectors, which indicated an antisunward ion flow with a velocity of (2.5 +/- 1.5) km s(-1). It is suggested that this ion flow contributes to maintaining the nightside ionosphere near the terminator region at solar minimum. The interpretation of the result was reinforced by observed asymmetries in the ion number counts. The observed dawn-dusk asymmetry was consistent with a nightward transport of ions while the noon-midnight observations indicated that the flow was highly variable but could contribute to the maintenance of the nightside ionosphere.
Financial support for this paper was provided by the UK Science and Technology Facilities Council under grant PP/E001157/1.
2012-12-01T00:00:00ZWood, A. G.Pryse, S. E.Grande, M.Whittaker, I. C.Coates, A. J.Husband, K.Baumjohann, W.Zhang, T. L.Mazelle, C.Kallio, E.Fraenz, M.McKenna-Lawlor, S.Wurz, P.The transterminator ion flow in the Venusian ionosphere is observed at solar minimum for the first time. Such a flow, which transports ions from the day to the nightside, has been observed previously around solar maximum. At solar minimum this transport process is severely inhibited by the lower altitude of the ionopause. The observations presented were those made of the Venusian ionospheric plasma by the ASPERA-4 experiment onboard the Venus Express spacecraft, and which constitute the first extensive in-situ measurements of the plasma near solar minimum. Observations near the terminator of the energies of ions of ionospheric origin showed asymmetry between the noon and midnight sectors, which indicated an antisunward ion flow with a velocity of (2.5 +/- 1.5) km s(-1). It is suggested that this ion flow contributes to maintaining the nightside ionosphere near the terminator region at solar minimum. The interpretation of the result was reinforced by observed asymmetries in the ion number counts. The observed dawn-dusk asymmetry was consistent with a nightward transport of ions while the noon-midnight observations indicated that the flow was highly variable but could contribute to the maintenance of the nightside ionosphere.Shallow-water vortex equilibria and their stabilityPłotka, H.Dritschel, D.G.http://hdl.handle.net/10023/47622018-01-07T02:45:09Z2011-01-01T00:00:00ZWe first describe the equilibrium form and stability of steadily-rotating simply-connected vortex patches in the single-layer quasi-geostrophic model of geophysical fluid dynamics. This model, valid for rotating shallow-water flow in the limit of small Rossby and Froude numbers, has an intrinsic length scale L called the "Rossby deformation length" relating the strength of stratification to that of the background rotation rate. Specifically, L = c/f where c = √gH is a characteristic gravity-wave speed, g is gravity (or "reduced" gravity in a two-layer context where one layer is infinitely deep), H is the mean active layer depth, and f is the Coriolis frequency (here constant). We next introduce ageostrophic effects by using the full shallow-water model to generate what we call "quasi-equilibria". These equilibria are not strictly steady, but radiate such weak gravity waves that they are steady for all practical purposes. Through an artificial ramping procedure, we ramp up the potential vorticity anomaly of the fluid particles in our quasi-geostrophic equilibria to obtain shallow-water quasi-equilibria at finite Rossby number. We show a few examples of these states in this paper.
2011-01-01T00:00:00ZPłotka, H.Dritschel, D.G.We first describe the equilibrium form and stability of steadily-rotating simply-connected vortex patches in the single-layer quasi-geostrophic model of geophysical fluid dynamics. This model, valid for rotating shallow-water flow in the limit of small Rossby and Froude numbers, has an intrinsic length scale L called the "Rossby deformation length" relating the strength of stratification to that of the background rotation rate. Specifically, L = c/f where c = √gH is a characteristic gravity-wave speed, g is gravity (or "reduced" gravity in a two-layer context where one layer is infinitely deep), H is the mean active layer depth, and f is the Coriolis frequency (here constant). We next introduce ageostrophic effects by using the full shallow-water model to generate what we call "quasi-equilibria". These equilibria are not strictly steady, but radiate such weak gravity waves that they are steady for all practical purposes. Through an artificial ramping procedure, we ramp up the potential vorticity anomaly of the fluid particles in our quasi-geostrophic equilibria to obtain shallow-water quasi-equilibria at finite Rossby number. We show a few examples of these states in this paper.Propagating coupled Alfvén and kink oscillations in an arbitrary inhomogeneous coronaPascoe, David JamesWright, Andrew NicholasDe Moortel, Inekehttp://hdl.handle.net/10023/47552018-01-07T02:34:57Z2011-04-10T00:00:00ZObservations have revealed ubiquitous transverse velocity perturbation waves propagating in the solar corona. We perform three-dimensional numerical simulations of footpoint-driven transverse waves propagating in a low β plasma. We consider the cases of distorted cylindrical flux tubes and a randomly generated inhomogeneous medium. When density structuring is present, mode coupling in inhomogeneous regions leads to the coupling of the kink mode to the Alfvén mode. The decay of the propagating kink wave is observed as energy is transferred to the local Alfvén mode. In all cases considered, modest changes in density were capable of efficiently converting energy from the driving footpoint motion to localized Alfv´en modes. We have demonstrated that mode coupling efficiently couples propagating kink perturbations to Alfvén modes in an arbitrary inhomogeneous medium. This has the consequence that transverse footpoint motions at the base of the corona will deposit energy to Alfvén modes in the corona.
D.J.P. acknowledges financial support from STFC. I.D.M. acknowledges support of a Royal Society University Research Fellowship.
2011-04-10T00:00:00ZPascoe, David JamesWright, Andrew NicholasDe Moortel, InekeObservations have revealed ubiquitous transverse velocity perturbation waves propagating in the solar corona. We perform three-dimensional numerical simulations of footpoint-driven transverse waves propagating in a low β plasma. We consider the cases of distorted cylindrical flux tubes and a randomly generated inhomogeneous medium. When density structuring is present, mode coupling in inhomogeneous regions leads to the coupling of the kink mode to the Alfvén mode. The decay of the propagating kink wave is observed as energy is transferred to the local Alfvén mode. In all cases considered, modest changes in density were capable of efficiently converting energy from the driving footpoint motion to localized Alfv´en modes. We have demonstrated that mode coupling efficiently couples propagating kink perturbations to Alfvén modes in an arbitrary inhomogeneous medium. This has the consequence that transverse footpoint motions at the base of the corona will deposit energy to Alfvén modes in the corona.Modeling the dispersal of an active region : quantifying energy input into the coronaMackay, Duncan HendryGreen, Lucievan Ballegooijen, Aadhttp://hdl.handle.net/10023/47542018-02-18T01:30:35Z2011-03-10T00:00:00ZIn this paper, a new technique for modeling nonlinear force-free fields directly from line-of-sight magnetogram observations is presented. The technique uses sequences of magnetograms directly as lower boundary conditions to drive the evolution of coronal magnetic fields between successive force-free equilibria over long periods of time. It is illustrated by applying it to SOHO: MDI observations of a decaying active region, NOAA AR 8005. The active region is modeled during a four-day period around its central meridian passage. Over this time, the dispersal of the active region is dominated by random motions due to small-scale convective cells. Through studying the buildup of magnetic energy in the model, it is found that such small-scale motions may inject anywhere from (2.5-3) × 1025 erg s-1 of free magnetic energy into the coronal field. Most of this energy is stored within the center of the active region in the low corona, below 30 Mm. After four days, the buildup of free energy is 10% that of the corresponding potential field. This energy buildup is sufficient to explain the radiative losses at coronal temperatures within the active region. Small-scale convective motions therefore play an integral part in the energy balance of the corona. This new technique has wide ranging applications with the new high-resolution, high-cadence observations from the SDO:HMI and SDO:AIA instruments.
Funding: UK STFC. Royal Society Research Grants Scheme.
2011-03-10T00:00:00ZMackay, Duncan HendryGreen, Lucievan Ballegooijen, AadIn this paper, a new technique for modeling nonlinear force-free fields directly from line-of-sight magnetogram observations is presented. The technique uses sequences of magnetograms directly as lower boundary conditions to drive the evolution of coronal magnetic fields between successive force-free equilibria over long periods of time. It is illustrated by applying it to SOHO: MDI observations of a decaying active region, NOAA AR 8005. The active region is modeled during a four-day period around its central meridian passage. Over this time, the dispersal of the active region is dominated by random motions due to small-scale convective cells. Through studying the buildup of magnetic energy in the model, it is found that such small-scale motions may inject anywhere from (2.5-3) × 1025 erg s-1 of free magnetic energy into the coronal field. Most of this energy is stored within the center of the active region in the low corona, below 30 Mm. After four days, the buildup of free energy is 10% that of the corresponding potential field. This energy buildup is sufficient to explain the radiative losses at coronal temperatures within the active region. Small-scale convective motions therefore play an integral part in the energy balance of the corona. This new technique has wide ranging applications with the new high-resolution, high-cadence observations from the SDO:HMI and SDO:AIA instruments.The effects of line-of-sight integration on multistrand coronal loop oscillationsDe Moortel, InekePascoe, David Jameshttp://hdl.handle.net/10023/47522018-03-04T01:31:14Z2012-02-10T00:00:00ZIDM acknowledges support of a Royal Society University Research Fellowship.
2012-02-10T00:00:00ZDe Moortel, InekePascoe, David JamesStanding kink modes in three-dimensional coronal loopsDe Moortel, InekePascoe, David Jameshttp://hdl.handle.net/10023/47452018-01-07T02:43:21Z2014-03-11T00:00:00ZSo far, the straight flux tube model proposed by Edwin & Roberts is the most commonly used tool in practical coronal seismology, in particular, to infer values of the (coronal) magnetic field from observed, standing kink mode oscillations. In this paper, we compare the period predicted by this basic model with three-dimensional (3D) numerical simulations of standing kink mode oscillations, as the period is a crucial parameter in the seismological inversion to determine the magnetic field. We perform numerical simulations of standing kink modes in both straight and curved 3D coronal loops and consider excitation by internal and external drivers. The period of oscillation for the displacement of dense coronal loops is determined by the loop length and the kink speed, in agreement with the estimate based on analytical theory for straight flux tubes. For curved coronal loops embedded in a magnetic arcade and excited by an external driver, a secondary mode with a period determined by the loop length and external Alfvén speed is also present. When a low number of oscillations is considered, these two periods can result in a single, non-resolved (broad) peak in the power spectrum, particularly for low values of the density contrast for which the two periods will be relatively similar. In that case (and for this particular geometry), the presence of this additional mode would lead to ambiguous seismological estimates of the magnetic field strength.
I.D.M. acknowledges support from a Royal Society University Research Fellowship. The computational work for this paper was carried out at the joint STFC and SFC (SRIF)-fundedclusterattheUniversityofStAndrews(UK). The research leading to these results has also received funding from the European Commissions Seventh Framework Programme (FP7/2007-2013) under the grant agreement SOLSPANET (project No. 269299;www.solspanet.eu/solspanet).
2014-03-11T00:00:00ZDe Moortel, InekePascoe, David JamesSo far, the straight flux tube model proposed by Edwin & Roberts is the most commonly used tool in practical coronal seismology, in particular, to infer values of the (coronal) magnetic field from observed, standing kink mode oscillations. In this paper, we compare the period predicted by this basic model with three-dimensional (3D) numerical simulations of standing kink mode oscillations, as the period is a crucial parameter in the seismological inversion to determine the magnetic field. We perform numerical simulations of standing kink modes in both straight and curved 3D coronal loops and consider excitation by internal and external drivers. The period of oscillation for the displacement of dense coronal loops is determined by the loop length and the kink speed, in agreement with the estimate based on analytical theory for straight flux tubes. For curved coronal loops embedded in a magnetic arcade and excited by an external driver, a secondary mode with a period determined by the loop length and external Alfvén speed is also present. When a low number of oscillations is considered, these two periods can result in a single, non-resolved (broad) peak in the power spectrum, particularly for low values of the density contrast for which the two periods will be relatively similar. In that case (and for this particular geometry), the presence of this additional mode would lead to ambiguous seismological estimates of the magnetic field strength.Simulating the "Sliding Doors" Effect Through Magnetic Flux EmergenceMacTaggart, DavidHood, Alan Williamhttp://hdl.handle.net/10023/47422018-01-07T02:31:15Z2010-06-04T00:00:00ZRecent Hinode photospheric vector magnetogram observations have shown that the opposite polarities of a long arcade structure move apart and then come together. In addition to this "sliding doors" effect, orientations of horizontal magnetic fields along the polarity inversion line on the photosphere evolve from a normal-polarity configuration to an inverse one. To explain this behavior, a simple model by Okamoto et al. suggested that it is the result of the emergence of a twisted flux rope. Here, we model this scenario using a three-dimensional megnatohydrodynamic simulation of a twisted flux rope emerging into a pre-existing overlying arcade. We construct magnetograms from the simulation and compare them with the observations. The model produces the two signatures mentioned above. However, the cause of the "sliding doors" effect differs from the previous model.
D.M. acknowledges financial assistance from STFC. The computational work for this Letter was carried out on the joint STFC and SFC (SRIF) funded cluster at the University of St. Andrews. D.M. and A.W.H. acknowledge financial support form the European Commission through the SOLAIRE Network (MTRN-CT-2006-035484).
2010-06-04T00:00:00ZMacTaggart, DavidHood, Alan WilliamRecent Hinode photospheric vector magnetogram observations have shown that the opposite polarities of a long arcade structure move apart and then come together. In addition to this "sliding doors" effect, orientations of horizontal magnetic fields along the polarity inversion line on the photosphere evolve from a normal-polarity configuration to an inverse one. To explain this behavior, a simple model by Okamoto et al. suggested that it is the result of the emergence of a twisted flux rope. Here, we model this scenario using a three-dimensional megnatohydrodynamic simulation of a twisted flux rope emerging into a pre-existing overlying arcade. We construct magnetograms from the simulation and compare them with the observations. The model produces the two signatures mentioned above. However, the cause of the "sliding doors" effect differs from the previous model.The storage and dissipation of magnetic energy in the quiet sun corona determined from SDO/HMI magnetogramsMeyer, Karen AlisonSabol, JurajMackay, Duncan Hendryvan Ballegooijen, Aadhttp://hdl.handle.net/10023/47412018-01-07T02:43:19Z2013-05-30T00:00:00ZIn recent years, higher cadence, higher resolution observations have revealed the quiet-Sun photosphere to be complex and rapidly evolving. Since magnetic fields anchored in the photosphere extend up into the solar corona, it is expected that the small-scale coronal magnetic field exhibits similar complexity. For the first time, the quiet-Sun coronal magnetic field is continuously evolved through a series of non-potential, quasi-static equilibria, deduced from magnetograms observed by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, where the photospheric boundary condition which drives the coronal evolution exactly reproduces the observed magnetograms. The build-up, storage, and dissipation of magnetic energy within the simulations is studied. We find that the free magnetic energy built up and stored within the field is sufficient to explain small-scale, impulsive events such as nanoflares. On comparing with coronal images of the same region, the energy storage and dissipation visually reproduces many of the observed features. The results indicate that the complex small-scale magnetic evolution of a large number of magnetic features is a key element in explaining the nature of the solar corona.
2013ApJ...770L..18M
2013-05-30T00:00:00ZMeyer, Karen AlisonSabol, JurajMackay, Duncan Hendryvan Ballegooijen, AadIn recent years, higher cadence, higher resolution observations have revealed the quiet-Sun photosphere to be complex and rapidly evolving. Since magnetic fields anchored in the photosphere extend up into the solar corona, it is expected that the small-scale coronal magnetic field exhibits similar complexity. For the first time, the quiet-Sun coronal magnetic field is continuously evolved through a series of non-potential, quasi-static equilibria, deduced from magnetograms observed by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, where the photospheric boundary condition which drives the coronal evolution exactly reproduces the observed magnetograms. The build-up, storage, and dissipation of magnetic energy within the simulations is studied. We find that the free magnetic energy built up and stored within the field is sufficient to explain small-scale, impulsive events such as nanoflares. On comparing with coronal images of the same region, the energy storage and dissipation visually reproduces many of the observed features. The results indicate that the complex small-scale magnetic evolution of a large number of magnetic features is a key element in explaining the nature of the solar corona.Potential Evidence for the Onset of Alfvénic Turbulence in Trans-equatorial Coronal LoopsDe Moortel, InekeMcIntosh, ScottThrelfall, James WilliamBethge, ChristianLiu, Jhttp://hdl.handle.net/10023/47402018-01-07T02:43:13Z2014-02-10T00:00:00ZThis study investigates Coronal Multi-channel Polarimeter Doppler-shift observations of a large, off-limb, trans-equatorial loop system observed on 2012 April 10-11. Doppler-shift oscillations with a broad range of frequencies are found to propagate along the loop with a speed of about 500 km s–1. The power spectrum of perturbations travelling up from both loop footpoints is remarkably symmetric, probably due to the almost perfect north-south alignment of the loop system. Compared to the power spectrum at the footpoints of the loop, the Fourier power at the apex appears to be higher in the high-frequency part of the spectrum than expected from theoretical models. We suggest this excess high-frequency power could be tentative evidence for the onset of a cascade of the low-to-mid frequency waves into (Alfvénic) turbulence.
2014-02-10T00:00:00ZDe Moortel, InekeMcIntosh, ScottThrelfall, James WilliamBethge, ChristianLiu, JThis study investigates Coronal Multi-channel Polarimeter Doppler-shift observations of a large, off-limb, trans-equatorial loop system observed on 2012 April 10-11. Doppler-shift oscillations with a broad range of frequencies are found to propagate along the loop with a speed of about 500 km s–1. The power spectrum of perturbations travelling up from both loop footpoints is remarkably symmetric, probably due to the almost perfect north-south alignment of the loop system. Compared to the power spectrum at the footpoints of the loop, the Fourier power at the apex appears to be higher in the high-frequency part of the spectrum than expected from theoretical models. We suggest this excess high-frequency power could be tentative evidence for the onset of a cascade of the low-to-mid frequency waves into (Alfvénic) turbulence.The detection of numerous magnetic separators in a three-dimensional magnetohydrodynamic model of solar emerging fluxParnell, Clare ElizabethMaclean, Rhona ClaireHaynes, Andrew Lewishttp://hdl.handle.net/10023/47392018-01-07T02:31:52Z2010-12-20T00:00:00ZMagnetic separators in three-dimensional (3D) magnetic fields are believed to be often associated with locations of magnetic reconnection. In this preliminary study, we investigate this relationship using data from a numerical resistive 3D MHD experiment of a solar flux emergence event. For the first time separators are detected in complex magnetic fields resulting from a 3D resistive MHD model of flux emergence. Two snapshots of the model, taken from different stages of its evolution, are analyzed. Numerous separators are found in both snapshots, and their properties, including their geometry, length, relationship to the magnetic null points, and integrated parallel electric field are studied. The separators reside at the junctions between the emerging flux, the overlying field, and two other flux domains that are newly formed by reconnection. The long separators, which connect clusters of nulls that lie either side of the emerging flux, pass through spatially localized regions of high parallel electric field and correspond to local maxima in integrated parallel electric field. These factors indicate that strong magnetic reconnection takes place along many of the separators, and that separators play a key role during the interaction of emerging and overlying flux.
2010-12-20T00:00:00ZParnell, Clare ElizabethMaclean, Rhona ClaireHaynes, Andrew LewisMagnetic separators in three-dimensional (3D) magnetic fields are believed to be often associated with locations of magnetic reconnection. In this preliminary study, we investigate this relationship using data from a numerical resistive 3D MHD experiment of a solar flux emergence event. For the first time separators are detected in complex magnetic fields resulting from a 3D resistive MHD model of flux emergence. Two snapshots of the model, taken from different stages of its evolution, are analyzed. Numerous separators are found in both snapshots, and their properties, including their geometry, length, relationship to the magnetic null points, and integrated parallel electric field are studied. The separators reside at the junctions between the emerging flux, the overlying field, and two other flux domains that are newly formed by reconnection. The long separators, which connect clusters of nulls that lie either side of the emerging flux, pass through spatially localized regions of high parallel electric field and correspond to local maxima in integrated parallel electric field. These factors indicate that strong magnetic reconnection takes place along many of the separators, and that separators play a key role during the interaction of emerging and overlying flux.Global-scale consequences of magnetic-helicity injection and condensation on the sunMackay, Duncan HendryDeVore, RickAntiochos, Spirohttp://hdl.handle.net/10023/47352018-01-28T01:30:33Z2014-04-01T00:00:00ZIn the recent paper of Antiochos, a new concept for the injection of magnetic helicity into the solar corona by small-scale convective motions and its condensation onto polarity inversion lines (PILs) has been developed. We investigate this concept through global simulations of the Sun’s photospheric and coronal magnetic fields, and compare the results with the hemispheric pattern of solar filaments. Assuming that the vorticity of the cells is predominately counter-clockwise/clockwise in the northern/southern hemisphere, the convective motions inject negative/positive helicity into each hemisphere. The simulations show that: (1) on a north–south oriented PIL, both differential rotation and convective motions inject the same sign of helicity, which matches that required to reproduce the hemispheric pattern of filaments. (2) On a high-latitude east–west oriented polar crown or subpolar crown PIL, the vorticity of the cells has to be approximately 2–3 times greater than the local differential-rotation gradient in order to overcome the incorrect sign of helicity injection from differential rotation. (3) In the declining phase of the cycle, as a bipole interacts with the polar field, in some cases, helicity condensation can reverse the effect of differential rotation along the east–west lead arm but not in all cases. The results show that this newly developed concept of magnetic helicity injection and condensation, in conjunction with the mechanisms used in Yeates et al., is a viable explanation for the hemispheric pattern of filaments. Future observational studies should focus on examining the vorticity component within convective motions to determine both its magnitude and latitudinal variation relative to the differential-rotation gradient on the Sun.
2014-04-01T00:00:00ZMackay, Duncan HendryDeVore, RickAntiochos, SpiroIn the recent paper of Antiochos, a new concept for the injection of magnetic helicity into the solar corona by small-scale convective motions and its condensation onto polarity inversion lines (PILs) has been developed. We investigate this concept through global simulations of the Sun’s photospheric and coronal magnetic fields, and compare the results with the hemispheric pattern of solar filaments. Assuming that the vorticity of the cells is predominately counter-clockwise/clockwise in the northern/southern hemisphere, the convective motions inject negative/positive helicity into each hemisphere. The simulations show that: (1) on a north–south oriented PIL, both differential rotation and convective motions inject the same sign of helicity, which matches that required to reproduce the hemispheric pattern of filaments. (2) On a high-latitude east–west oriented polar crown or subpolar crown PIL, the vorticity of the cells has to be approximately 2–3 times greater than the local differential-rotation gradient in order to overcome the incorrect sign of helicity injection from differential rotation. (3) In the declining phase of the cycle, as a bipole interacts with the polar field, in some cases, helicity condensation can reverse the effect of differential rotation along the east–west lead arm but not in all cases. The results show that this newly developed concept of magnetic helicity injection and condensation, in conjunction with the mechanisms used in Yeates et al., is a viable explanation for the hemispheric pattern of filaments. Future observational studies should focus on examining the vorticity component within convective motions to determine both its magnitude and latitudinal variation relative to the differential-rotation gradient on the Sun.The Sun's global photospheric and coronal magnetic fields : observations and modelsMackay, Duncan HendryYeates, Anthony Robinsonhttp://hdl.handle.net/10023/47142017-12-31T00:31:28Z2012-11-01T00:00:00ZIn this review, our present day understanding of the Sun's global photospheric and coronal magnetic fields is discussed from both observational and theoretical viewpoints. Firstly, the large-scale properties of photospheric magnetic fields are described, along with recent advances in photospheric magnetic flux transport models. Following this, the wide variety of theoretical models used to simulate global coronal magnetic fields are described. From this, the combined application of both magnetic flux transport simulations and coronal modeling techniques to describe the phenomena of coronal holes, the Sun's open magnetic flux and the hemispheric pattern of solar filaments is discussed. Finally, recent advances in non-eruptive global MHD models are described. While the review focuses mainly on solar magnetic fields, recent advances in measuring and modeling stellar magnetic fields are described where appropriate. In the final section key areas of future research are identified.
2012LRSP....9....6M Funding: STFC, the Leverhulme Trust and European Commission’s Seventh Framework Programme (FP7/2007-2013) under the grant agreement SWIFF (project no. 263340, http://www.swiff.eu).
2012-11-01T00:00:00ZMackay, Duncan HendryYeates, Anthony RobinsonIn this review, our present day understanding of the Sun's global photospheric and coronal magnetic fields is discussed from both observational and theoretical viewpoints. Firstly, the large-scale properties of photospheric magnetic fields are described, along with recent advances in photospheric magnetic flux transport models. Following this, the wide variety of theoretical models used to simulate global coronal magnetic fields are described. From this, the combined application of both magnetic flux transport simulations and coronal modeling techniques to describe the phenomena of coronal holes, the Sun's open magnetic flux and the hemispheric pattern of solar filaments is discussed. Finally, recent advances in non-eruptive global MHD models are described. While the review focuses mainly on solar magnetic fields, recent advances in measuring and modeling stellar magnetic fields are described where appropriate. In the final section key areas of future research are identified.Laboratory astrophysics : investigation of planetary and astrophysical maser emissionSpeirs, DavidCairns, R AlanKellett, BarryVorgul, IrenaMcConville, SandraCross, AdrianPhelps, AlanRonald, KevinBingham, Roberthttp://hdl.handle.net/10023/44942018-03-18T01:32:26Z2013-01-01T00:00:00ZThis paper describes a model for cyclotron maser emission applicable to planetary auroral radio emission, the stars UV Ceti and CU Virginus, blazar jets and astrophysical shocks. These emissions may be attributed to energetic electrons moving into convergent magnetic fields that are typically found in association with dipole like planetary magnetospheres or shocks. It is found that magnetic compression leads to the formation of a velocity distribution having a horseshoe shape as a result of conservation of the electron magnetic moment. Under certain plasma conditions where the local electron plasma frequency ωpe is much less than the cyclotron frequency ωce the distribution is found to be unstable to maser type radiation emission. We have established a laboratory-based facility that has verified many of the details of our original theoretical description and agrees well with numerical simulations. The experiment has demonstrated that the horseshoe distribution produces cyclotron emission at a frequency just below the local electron cyclotron frequency, with polarisation close to X-mode and propagating nearly perpendicularly to the electron beam motion. We discuss recent developments in the theory and simulation of the instability including addressing radiation escape problems, and relate these to the laboratory, space, and astrophysical observations. The experiments showed strong narrow band EM emissions at frequencies just below the cold-plasma cyclotron frequency as predicted by the theory. Measurements of the conversion efficiency, mode and spectral content were in close agreement with the predictions of numerical simulations undertaken using a particle-in-cell code and also with satellite observations confirming the horseshoe maser as an important emission mechanism in geophysical/astrophysical plasmas. In each case we address how the radiation can escape the plasma without suffering strong absorption at the second harmonic layer.
2013-01-01T00:00:00ZSpeirs, DavidCairns, R AlanKellett, BarryVorgul, IrenaMcConville, SandraCross, AdrianPhelps, AlanRonald, KevinBingham, RobertThis paper describes a model for cyclotron maser emission applicable to planetary auroral radio emission, the stars UV Ceti and CU Virginus, blazar jets and astrophysical shocks. These emissions may be attributed to energetic electrons moving into convergent magnetic fields that are typically found in association with dipole like planetary magnetospheres or shocks. It is found that magnetic compression leads to the formation of a velocity distribution having a horseshoe shape as a result of conservation of the electron magnetic moment. Under certain plasma conditions where the local electron plasma frequency ωpe is much less than the cyclotron frequency ωce the distribution is found to be unstable to maser type radiation emission. We have established a laboratory-based facility that has verified many of the details of our original theoretical description and agrees well with numerical simulations. The experiment has demonstrated that the horseshoe distribution produces cyclotron emission at a frequency just below the local electron cyclotron frequency, with polarisation close to X-mode and propagating nearly perpendicularly to the electron beam motion. We discuss recent developments in the theory and simulation of the instability including addressing radiation escape problems, and relate these to the laboratory, space, and astrophysical observations. The experiments showed strong narrow band EM emissions at frequencies just below the cold-plasma cyclotron frequency as predicted by the theory. Measurements of the conversion efficiency, mode and spectral content were in close agreement with the predictions of numerical simulations undertaken using a particle-in-cell code and also with satellite observations confirming the horseshoe maser as an important emission mechanism in geophysical/astrophysical plasmas. In each case we address how the radiation can escape the plasma without suffering strong absorption at the second harmonic layer.Magnetohydrodynamics dynamical relaxation of coronal magnetic fields : I. Parallel untwisted magnetic fields in 2DFuentes Fernandez, JorgeParnell, Clare ElizabethHood, Alan Williamhttp://hdl.handle.net/10023/43782018-01-07T02:31:53Z2010-05-01T00:00:00ZContext. For the last thirty years, most of the studies on the relaxation of stressed magnetic fields in the solar environment have only considered the Lorentz force, neglecting plasma contributions, and therefore, limiting every equilibrium to that of a force-free field. Aims: Here we begin a study of the non-resistive evolution of finite beta plasmas and their relaxation to magnetohydrostatic states, where magnetic forces are balanced by plasma-pressure gradients, by using a simple 2D scenario involving a hydromagnetic disturbance to a uniform magnetic field. The final equilibrium state is predicted as a function of the initial disturbances, with aims to demonstrate what happens to the plasma during the relaxation process and to see what effects it has on the final equilibrium state. Methods: A set of numerical experiments are run using a full MHD code, with the relaxation driven by magnetoacoustic waves damped by viscous effects. The numerical results are compared with analytical calculations made within the linear regime, in which the whole process must remain adiabatic. Particular attention is paid to the thermodynamic behaviour of the plasma during the relaxation. Results: The analytical predictions for the final non force-free equilibrium depend only on the initial perturbations and the total pressure of the system. It is found that these predictions hold surprisingly well even for amplitudes of the perturbation far outside the linear regime. Conclusions: Including the effects of a finite plasma beta in relaxation experiments leads to significant differences from the force-free case.
2010-05-01T00:00:00ZFuentes Fernandez, JorgeParnell, Clare ElizabethHood, Alan WilliamContext. For the last thirty years, most of the studies on the relaxation of stressed magnetic fields in the solar environment have only considered the Lorentz force, neglecting plasma contributions, and therefore, limiting every equilibrium to that of a force-free field. Aims: Here we begin a study of the non-resistive evolution of finite beta plasmas and their relaxation to magnetohydrostatic states, where magnetic forces are balanced by plasma-pressure gradients, by using a simple 2D scenario involving a hydromagnetic disturbance to a uniform magnetic field. The final equilibrium state is predicted as a function of the initial disturbances, with aims to demonstrate what happens to the plasma during the relaxation process and to see what effects it has on the final equilibrium state. Methods: A set of numerical experiments are run using a full MHD code, with the relaxation driven by magnetoacoustic waves damped by viscous effects. The numerical results are compared with analytical calculations made within the linear regime, in which the whole process must remain adiabatic. Particular attention is paid to the thermodynamic behaviour of the plasma during the relaxation. Results: The analytical predictions for the final non force-free equilibrium depend only on the initial perturbations and the total pressure of the system. It is found that these predictions hold surprisingly well even for amplitudes of the perturbation far outside the linear regime. Conclusions: Including the effects of a finite plasma beta in relaxation experiments leads to significant differences from the force-free case.Flux emergence and coronal eruptionArchontis, VasilisHood, Alan Williamhttp://hdl.handle.net/10023/43762018-01-07T01:32:15Z2010-05-01T00:00:00ZAims. Our aim is to study the photospheric flux distribution of a twisted flux tube that emerges from the solar interior. We also report on the eruption of a new flux rope when the emerging tube rises into a pre-existing magnetic field in the corona. Methods. To study the evolution, we use 3D numerical simulations by solving the time-dependent and resistive MHD equations. We qualitatively compare our numerical results with MDI magnetograms of emerging flux at the solar surface. Results. We find that the photospheric magnetic flux distribution consists of two regions of opposite polarities and elongated magnetic tails on the two sides of the polarity inversion line (PIL), depending on the azimuthal nature of the emerging field lines and the initial field strength of the rising tube. Their shape is progressively deformed due to plasma motions towards the PIL. Our results are in qualitative agreement with observational studies of magnetic flux emergence in active regions (ARs). Moreover, if the initial twist of the emerging tube is small, the photospheric magnetic field develops an undulating shape and does not possess tails. In all cases, we find that a new flux rope is formed above the original axis of the emerging tube that may erupt into the corona, depending on the strength of the ambient field.
2010-05-01T00:00:00ZArchontis, VasilisHood, Alan WilliamAims. Our aim is to study the photospheric flux distribution of a twisted flux tube that emerges from the solar interior. We also report on the eruption of a new flux rope when the emerging tube rises into a pre-existing magnetic field in the corona. Methods. To study the evolution, we use 3D numerical simulations by solving the time-dependent and resistive MHD equations. We qualitatively compare our numerical results with MDI magnetograms of emerging flux at the solar surface. Results. We find that the photospheric magnetic flux distribution consists of two regions of opposite polarities and elongated magnetic tails on the two sides of the polarity inversion line (PIL), depending on the azimuthal nature of the emerging field lines and the initial field strength of the rising tube. Their shape is progressively deformed due to plasma motions towards the PIL. Our results are in qualitative agreement with observational studies of magnetic flux emergence in active regions (ARs). Moreover, if the initial twist of the emerging tube is small, the photospheric magnetic field develops an undulating shape and does not possess tails. In all cases, we find that a new flux rope is formed above the original axis of the emerging tube that may erupt into the corona, depending on the strength of the ambient field.Magnetohydrodynamic kink waves in two-dimensional non-uniform prominence threadsArregui, ISoler, RBallester, J.Wright, Andrew Nicholashttp://hdl.handle.net/10023/43742018-01-07T02:35:40Z2011-09-01T00:00:00ZAims. We analyse the oscillatory properties of resonantly damped transverse kink oscillations in two-dimensional prominence threads. Methods. The fine structures are modelled as cylindrically symmetric magnetic flux tubes with a dense central part with prominence plasma properties and an evacuated part, both surrounded by coronal plasma. The equilibrium density is allowed to vary non-uniformly in both the transverse and the longitudinal directions. We examine the influence of longitudinal density structuring on periods, damping times, and damping rates for transverse kink modes computed by numerically solving the linear resistive magnetohydrodynamic (MHD) equations. Results. The relevant parameters are the length of the thread and the density in the evacuated part of the tube, two quantities that are difficult to directly estimate from observations. We find that both of them strongly influence the oscillatory periods and damping times, and to a lesser extent the damping ratios. The analysis of the spatial distribution of perturbations and of the energy flux into the resonances allows us to explain the obtained damping times. Conclusions. Implications for prominence seismology, the physics of resonantly damped kink modes in two-dimensional magnetic flux tubes, and the heating of prominence plasmas are discussed.
2011-09-01T00:00:00ZArregui, ISoler, RBallester, J.Wright, Andrew NicholasAims. We analyse the oscillatory properties of resonantly damped transverse kink oscillations in two-dimensional prominence threads. Methods. The fine structures are modelled as cylindrically symmetric magnetic flux tubes with a dense central part with prominence plasma properties and an evacuated part, both surrounded by coronal plasma. The equilibrium density is allowed to vary non-uniformly in both the transverse and the longitudinal directions. We examine the influence of longitudinal density structuring on periods, damping times, and damping rates for transverse kink modes computed by numerically solving the linear resistive magnetohydrodynamic (MHD) equations. Results. The relevant parameters are the length of the thread and the density in the evacuated part of the tube, two quantities that are difficult to directly estimate from observations. We find that both of them strongly influence the oscillatory periods and damping times, and to a lesser extent the damping ratios. The analysis of the spatial distribution of perturbations and of the energy flux into the resonances allows us to explain the obtained damping times. Conclusions. Implications for prominence seismology, the physics of resonantly damped kink modes in two-dimensional magnetic flux tubes, and the heating of prominence plasmas are discussed.Thermal conduction effects on the kink instability in coronal loopsBotha, G. J. J.Arber, T. D.Hood, A. W.http://hdl.handle.net/10023/43732018-01-07T02:32:35Z2011-01-01T00:00:00ZContext. Heating of the solar corona by nanoflares, which are small transient events in which stored magnetic energy is dissipated by magnetic reconnection, may occur as the result of the nonlinear phase of the kink instability (Hood et al. 2009). Because of the high temperatures reached through these reconnection events, thermal conduction cannot be ignored in the evolution of the kink instability. Aims. To study the effect of thermal conduction on the nonlinear evolution of the kink instability of a coronal loop. To assess the efficiency of loop heating and the role of thermal conduction, both during the kink instability and for the long time evolution of the loop. Methods. Numerically solve the 3D nonlinear magnetohydrodynamic equations to simulate the evolution of a coronal loop that is initially in an unstable equilibrium. The initial state has zero net current. A comparison is made of the time evolution of the loop with thermal conduction and without thermal conduction. Results. Thermal conduction along magnetic field lines reduces the local temperature. This leads to temperatures that are an order of magnitude lower than those obtained in the absence of thermal conductivity. Consequently, different spectral lines are activated with and without the inclusion of thermal conduction, which have consequences for observations of solar corona loops. The conduction process is also important on the timescale of the fast magnetohydrodynamic phenomena. It reduces the kinetic energy released by an order of magnitude. Conclusions. Thermal conduction plays an essential role in the kink instability of coronal loops and cannot be ignored in the forward modelling of such loops.
2011-01-01T00:00:00ZBotha, G. J. J.Arber, T. D.Hood, A. W.Context. Heating of the solar corona by nanoflares, which are small transient events in which stored magnetic energy is dissipated by magnetic reconnection, may occur as the result of the nonlinear phase of the kink instability (Hood et al. 2009). Because of the high temperatures reached through these reconnection events, thermal conduction cannot be ignored in the evolution of the kink instability. Aims. To study the effect of thermal conduction on the nonlinear evolution of the kink instability of a coronal loop. To assess the efficiency of loop heating and the role of thermal conduction, both during the kink instability and for the long time evolution of the loop. Methods. Numerically solve the 3D nonlinear magnetohydrodynamic equations to simulate the evolution of a coronal loop that is initially in an unstable equilibrium. The initial state has zero net current. A comparison is made of the time evolution of the loop with thermal conduction and without thermal conduction. Results. Thermal conduction along magnetic field lines reduces the local temperature. This leads to temperatures that are an order of magnitude lower than those obtained in the absence of thermal conductivity. Consequently, different spectral lines are activated with and without the inclusion of thermal conduction, which have consequences for observations of solar corona loops. The conduction process is also important on the timescale of the fast magnetohydrodynamic phenomena. It reduces the kinetic energy released by an order of magnitude. Conclusions. Thermal conduction plays an essential role in the kink instability of coronal loops and cannot be ignored in the forward modelling of such loops.Alfven wave phase-mixing and damping in the ion cyclotron range of frequenciesThrelfall, J.McClements, K. G.De Moortel, I.http://hdl.handle.net/10023/43722018-01-07T02:32:35Z2011-01-01T00:00:00ZAims. We determine the effect of the Hall term in the generalised Ohm's law on the damping and phase mixing of Alfven waves in the ion cyclotron range of frequencies in uniform and non-uniform equilibrium plasmas. Methods. Wave damping in a uniform plasma is treated analytically, whilst a Lagrangian remap code (Lare2d) is used to study Hall effects on damping and phase mixing in the presence of an equilibrium density gradient. Results. The magnetic energy associated with an initially Gaussian field perturbation in a uniform resistive plasma is shown to decay algebraically at a rate that is unaffected by the Hall term to leading order in k(2)delta(2)(i) where k is wavenumber and delta(i) is ion skin depth. A similar algebraic decay law applies to whistler perturbations in the limit k(2)delta(2)(i) >> 1. In a non-uniform plasma it is found that the spatially-integrated damping rate due to phase mixing is lower in Hall MHD than it is in MHD, but the reduction in the damping rate, which can be attributed to the effects of wave dispersion, tends to zero in both the weak and strong phase mixing limits.
2011-01-01T00:00:00ZThrelfall, J.McClements, K. G.De Moortel, I.Aims. We determine the effect of the Hall term in the generalised Ohm's law on the damping and phase mixing of Alfven waves in the ion cyclotron range of frequencies in uniform and non-uniform equilibrium plasmas. Methods. Wave damping in a uniform plasma is treated analytically, whilst a Lagrangian remap code (Lare2d) is used to study Hall effects on damping and phase mixing in the presence of an equilibrium density gradient. Results. The magnetic energy associated with an initially Gaussian field perturbation in a uniform resistive plasma is shown to decay algebraically at a rate that is unaffected by the Hall term to leading order in k(2)delta(2)(i) where k is wavenumber and delta(i) is ion skin depth. A similar algebraic decay law applies to whistler perturbations in the limit k(2)delta(2)(i) >> 1. In a non-uniform plasma it is found that the spatially-integrated damping rate due to phase mixing is lower in Hall MHD than it is in MHD, but the reduction in the damping rate, which can be attributed to the effects of wave dispersion, tends to zero in both the weak and strong phase mixing limits.Nonlinear wave propagation and reconnection at magnetic X-points in the Hall MHD regimeThrelfall, James WilliamParnell, Clare ElizabethDe Moortel, InekeMcClements, KenArber, Tony D.http://hdl.handle.net/10023/43682018-02-18T01:31:12Z2012-07-01T00:00:00ZContext: The highly dynamical, complex nature of the solar atmosphere naturally implies the presence of waves in a topologically varied magnetic environment. Here, the interaction of waves with topological features such as null points is inevitable and potentially important for energetics. The low resistivity of the solar coronal plasma implies that non-magnetohydrodynamic (MHD) effects should be considered in studies of magnetic energy release in this environment. Aims: This paper investigates the role of the Hall term in the propagation and dissipation of waves, their interaction with 2D magnetic X-points and the nature of the resulting reconnection. Methods: A Lagrangian remap shock-capturing code (Lare2d) was used to study the evolution of an initial fast magnetoacoustic wave annulus for a range of values of the ion skin depth (δi) in resistive Hall MHD. A magnetic null-point finding algorithm was also used to locate and track the evolution of the multiple null-points that are formed in the system. Results: Depending on the ratio of ion skin depth to system size, our model demonstrates that Hall effects can play a key role in the wave-null interaction. In particular, the initial fast-wave pulse now consists of whistler and ion-cyclotron components; the dispersive nature of the whistler wave leads to (i) earlier interaction with the null; (ii) the creation of multiple additional, transient nulls and, hence, an increased number of energy release sites. In the Hall regime, the relevant timescales (such as the onset of reconnection and the period of the oscillatory relaxation) of the system are reduced significantly, and the reconnection rate is enhanced.
2012-07-01T00:00:00ZThrelfall, James WilliamParnell, Clare ElizabethDe Moortel, InekeMcClements, KenArber, Tony D.Context: The highly dynamical, complex nature of the solar atmosphere naturally implies the presence of waves in a topologically varied magnetic environment. Here, the interaction of waves with topological features such as null points is inevitable and potentially important for energetics. The low resistivity of the solar coronal plasma implies that non-magnetohydrodynamic (MHD) effects should be considered in studies of magnetic energy release in this environment. Aims: This paper investigates the role of the Hall term in the propagation and dissipation of waves, their interaction with 2D magnetic X-points and the nature of the resulting reconnection. Methods: A Lagrangian remap shock-capturing code (Lare2d) was used to study the evolution of an initial fast magnetoacoustic wave annulus for a range of values of the ion skin depth (δi) in resistive Hall MHD. A magnetic null-point finding algorithm was also used to locate and track the evolution of the multiple null-points that are formed in the system. Results: Depending on the ratio of ion skin depth to system size, our model demonstrates that Hall effects can play a key role in the wave-null interaction. In particular, the initial fast-wave pulse now consists of whistler and ion-cyclotron components; the dispersive nature of the whistler wave leads to (i) earlier interaction with the null; (ii) the creation of multiple additional, transient nulls and, hence, an increased number of energy release sites. In the Hall regime, the relevant timescales (such as the onset of reconnection and the period of the oscillatory relaxation) of the system are reduced significantly, and the reconnection rate is enhanced.Phase mixing of nonlinear visco-resistive Alfvén waves