Mean exit time in irregularly-shaped annular and composite disc domains

Calculating the mean exit time (MET) for models of diffusion is a classical problem in statistical physics, with various applications in biophysics, economics and heat and mass transfer. While many exact results for MET are known for diffusion in simple geometries involving homogeneous materials, calculating MET for diffusion in realistic geometries involving heterogeneous materials is typically limited to repeated stochastic simulations or numerical solutions of the associated boundary value problem (BVP). In this work we derive exact solutions for the MET in irregular annular domains, including some applications where diffusion occurs in heterogenous media. These solutions are obtained by taking the exact results for MET in an annulus, and then constructing various perturbation solutions to account for the irregular geometries involved. These solutions, with a range of boundary conditions, are implemented symbolically and compare very well with averaged data from repeated stochastic simulations and with numerical solutions of the associated BVP. Software to implement the exact solutions is available on \href{https://github.com/ProfMJSimpson/Exit_time}{GitHub}.

Stochastic simulations reveal that dendritic spine morphology regulates synaptic plasticity in a deterministic manner

Dendritic spines act as computational units and must adapt their responses according to their activation history. Calcium influx acts as the first signaling step during postsynaptic activation and is a determinant of synaptic weight change. Dendritic spines also come in a variety of sizes and shapes. To probe the relationship between calcium dynamics and spine morphology, we used a stochastic reaction-diffusion model of calcium dynamics in idealized and realistic geometries. We show that despite the stochastic nature of the various calcium channels, receptors, and pumps, spine size and shape can separately modulate calcium dynamics and subsequently synaptic weight updates in a deterministic manner. The relationships between calcium dynamics and spine morphology identified in idealized geometries also hold in realistic geometries suggesting that there are geometrically determined deterministic relationships that may modulate synaptic weight change.

2D thermo-mechanical-chemical coupled numerical models of interactions between a cooling magma chamber and a visco-elastic host rock

<div> <p>A recent focus of studies in geodynamic modeling and magmatic petrology is to understand the coupled behavior between deformation and magmatic processes. Here, we present a 2D numerical model of an upper crustal magma (or mush) chamber in a visco-elastic host rock, with coupled thermal, mechanical and chemical processes, accounting for thermodynamically consistent material parameters. The magma chamber is isolated from deeper sources of magma (at least periodically) and it is cooling, and thus shrinking. We quantify the changes of pressure and stress around a cooling magma chamber and a warming host rock, using a compressible visco-elastic formulation, considering both simplified idealized and more complex and realistic geometries of the magma chamber.</p> </div><div> <p>We present solutions based on a self-consistent system of the conservation equations for coupled thermo-mechanical-chemical processes, under the assumptions of slow (negligible inertial forces), visco-elastic deformation and constant chemical bulk composition. The thermodynamic melting/crystallization model is based on a pelitic melting model calculated with Perple_X, assuming a granitic composition and is incorporated as a look-up table. We will discuss the numerical implementation, show the results of systematic numerical simulations, and illustrate the effect of volume changes due to temperature changes (including the possibility melting and crystallization) on stress and pressure evolution in magmatic systems.</p> </div>

On the speed and numerical stability of ice-dynamics approximations

<p>The Stokes solution to ice dynamics is computationally expensive, and in many cases unnecessary. Many approximations have been developed that reduce the complexity of the problem and thus reduce computational cost. Most approximations can generally be tuned to give reasonable solutions to ice-dynamics problems, depending on the domain and scale being simulated. However, the inherent numerical stability of time-stepping with different solvers has not been studied in detail. Here we investigate how different approximations lead to limits on the maximum timestep in mass conservation calculations for both idealized and realistic geometries. The ice-sheet models Yelmo and CISM are used to compare the following approximations: the shallow-ice approximation (SIA), the shallow-shelf approximation (SSA), the SIA+SSA approximation (Hybrid) and two variants of the L1L2 solver, namely one that reduces to SIA in the case of no-sliding (dubbed L1L2-SIA here) and the so-called depth-integrated viscosity approximation (DIVA). We find that these approaches vary significantly with respect to numerical stability. The extreme dependence on the local surface gradient of the SIA-based approximations (SIA, Hybrid, L1L2-SIA) leads to an amplified local velocity response and greater potential for instability, especially as grid resolution increases. In contrast, the SSA and DIVA approximations allow for longer time steps, because numerical oscillations in ice thickness are damped with increasing resolution. Given its high fidelity to the Stokes solution and its favorable stability properties, we demonstrate the strong case for using the DIVA approximation in many contexts.</p>

Control of helical navigation by three-dimensional flagellar beating

Helical swimming is a ubiquitous strategy for motile cells to generate self-gradients for environmental sensing. The model biflagellate Chlamydomonas reinhardtii rotates at a constant 1 – 2 Hz as it swims, but the mechanism is unclear. Here, we show unequivocally that the rolling motion derives from a persistent, non-planar flagellar beat pattern. This is revealed by high-speed imaging and micromanipulation of live cells. We construct a fully-3D model to relate flagellar beating directly to the free-swimming trajectories. For realistic geometries, the model reproduces both the sense and magnitude of the axial rotation of live cells. We show that helical swimming requires further symmetry-breaking between the two flagella. These functional differences underlie all tactic responses, particularly phototaxis. We propose a control strategy by which cells steer towards or away from light by modulating the sign of biflagellar dominance.

Landau levels in wrinkled and rippled graphene sheets

We study the discrete energy spectrum of curved graphene sheets in the presence of a magnetic field. The shifting of the Landau levels is determined for complex and realistic geometries of curved graphene sheets. The energy levels follow a similar square root dependence on the energy quantum number as for rippled and flat graphene sheets. The Landau levels are shifted towards lower energies proportionally to the average deformation and the effect is larger compared to a simple uni-axially rippled geometry. Furthermore, the resistivity of wrinkled graphene sheets is calculated for different average space curvatures and shown to obey a linear relation. The study is carried out with a quantum lattice Boltzmann method, solving the Dirac equation on curved manifolds.

Chebyshev multidomain pseudospectral method to solve cardiac wave equations with rotational anisotropy

The implementation of numerical methods to solve and study equations for cardiac wave propagation in realistic geometries is very costly, in terms of computational resources. The aim of this work is to show the improvement that can be obtained with Chebyshev polynomials-based methods over the classical finite difference schemes to obtain numerical solutions of cardiac models. To this end, we present a Chebyshev multidomain (CMD) Pseudospectral method to solve a simple two variable cardiac models on three-dimensional anisotropic media and we show the usefulness of the method over the traditional finite differences scheme widely used in the literature.