Stability analysis and simulations of coupled bulk-surface reaction–diffusion systems

In 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

Heterogeneity and strong competition in ecology

We study a competition-diffusion model while performing simultaneous homogenization and strong competition limits. The limit problem is shown to be a Stefan type evolution equation with effective coefficients. We also perform some numerical simulations in one and two spatial dimensions that suggest that oscillations in motilities are detrimental to invasion behaviour of a species

Quasi-equilibrium optical nonlinearities in spin-polarized GaAs

Semiconductor Bloch equations, which microscopically describe the dynamics of a Coulomb interacting, spin-unpolarized electron-hole plasma, can be solved in two limits: the coherent and the quasi-equilibrium regime. These equations have been recently extended to include the spin degree of freedom, and used to explain spin dynamics in the coherent regime. In the quasi-equilibrium limit, one solves the Bethe-Salpeter equation in a two-band model to describe how optical absorption is affected by Coulomb interactions within a spin-unpolarized plasma of arbitrary density. In this work, we modified the solution of the Bethe-Salpeter equation to include spin-polarization and light holes in a three-band model, which allowed us to account for spin-polarized versions of many-body effects in absorption. The calculated absorption reproduced the spin-dependent, density-dependent and spectral trends observed in bulk GaAs at room temperature, in a recent pump-probe experiment with circularly polarized light. Hence our results may be useful in the microscopic modelling of density-dependent optical nonlinearities in spin-polarized semiconductors.Comment: 7 pages, 6 figure

A Generative-Discriminative Basis Learning Framework to Predict Clinical Severity from Resting State Functional MRI Data

We propose a matrix factorization technique that decomposes the resting state fMRI (rs-fMRI) correlation matrices for a patient population into a sparse set of representative subnetworks, as modeled by rank one outer products. The subnetworks are combined using patient specific non-negative coefficients; these coefficients are also used to model, and subsequently predict the clinical severity of a given patient via a linear regression. Our generative-discriminative framework is able to exploit the structure of rs-fMRI correlation matrices to capture group level effects, while simultaneously accounting for patient variability. We employ ten fold cross validation to demonstrate the predictive power of our model on a cohort of fifty eight patients diagnosed with Autism Spectrum Disorder. Our method outperforms classical semi-supervised frameworks, which perform dimensionality reduction on the correlation features followed by non-linear regression to predict the clinical scores

Amine-Gold Linked Single-Molecule Junctions: Experiment and Theory

The measured conductance distribution for single molecule benzenediamine-gold junctions, based on 59,000 individual conductance traces recorded while breaking a gold point contact in solution, has a clear peak at 0.0064 G$_{0}$ with a width of $\pm$ 40%. Conductance calculations based on density functional theory (DFT) for 15 distinct junction geometries show a similar spread. Differences in local structure have a limited influence on conductance because the amine-Au bonding motif is well-defined and flexible. The average calculated conductance (0.046 G$_{0}$) is seven times larger than experiment, suggesting the importance of many-electron corrections beyond DFT

Near-IR studies of recurrent nova V745 Scorpii during its 2014 outburst

The recurrent nova (RN) V745 Scorpii underwent its third known outburst on 2014 February 6. Infrared monitoring of the eruption on an almost daily basis, starting from 1.3d after discovery, shows the emergence of a powerful blast wave generated by the high velocity nova ejecta exceeding 4000 kms$^{-1}$ plowing into its surrounding environment. The temperature of the shocked gas is raised to a high value exceeding 10$^{8}$K immediately after outburst commencement. The energetics of the outburst clearly surpass those of similar symbiotic systems like RS Oph and V407 Cyg which have giant secondaries. The shock does not show a free-expansion stage but rather shows a decelerative Sedov-Taylor phase from the beginning. Such strong shockfronts are known to be sites for $\gamma$ ray generation. V745 Sco is the latest nova, apart from five other known novae, to show $\gamma$ ray emission. It may be an important testbed to resolve the crucial question whether all novae are generically $\gamma$ ray emitters by virtue of having a circumbinary reservoir of material that is shocked by the ejecta rather than $\gamma$ ray generation being restricted to only symbiotic systems with a shocked red giant (RG) wind. The lack of a free-expansion stage favors V745 Sco to have a density enhancement around the white dwarf (WD), above that contributed by a RG wind. Our analysis also suggests that the WD in V745 Sco is very massive and a potential progenitor for a future SN Ia explosion.Comment: To appear in ApJ (Letters

Modelling cell motility and chemotaxis with evolving surface finite elements

We present a mathematical and a computational framework for the modelling of cell motility. The cell membrane is represented by an evolving surface, with the movement of the cell determined by the interaction of various forces that act normal to the surface. We consider external forces such as those that may arise owing to inhomogeneities in the medium and a pressure that constrains the enclosed volume, as well as internal forces that arise from the reaction of the cells' surface to stretching and bending. We also consider a protrusive force associated with a reaction-diffusion system (RDS) posed on the cell membrane, with cell polarization modelled by this surface RDS. The computational method is based on an evolving surface finite-element method. The general method can account for the large deformations that arise in cell motility and allows the simulation of cell migration in three dimensions. We illustrate applications of the proposed modelling framework and numerical method by reporting on numerical simulations of a model for eukaryotic chemotaxis and a model for the persistent movement of keratocytes in two and three space dimensions. Movies of the simulated cells can be obtained from http://homepages.warwick.ac.uk/maskae/CV_Warwick/Chemotaxis.html