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

Confinement by biased velocity jumps: aggregation of Escherichia coli

We investigate a linear kinetic equation derived from a velocity jump process modelling bacterial chemotaxis in the presence of an external chemical signal centered at the origin. We prove the existence of a positive equilibrium distribution with an exponential decay at infinity. We deduce a hypocoercivity result, namely: the solution of the Cauchy problem converges exponentially fast towards the stationary state. The strategy follows [J. Dolbeault, C. Mouhot, and C. Schmeiser, Hypocoercivity for linear kinetic equations conserving mass, Trans. AMS 2014]. The novelty here is that the equilibrium does not belong to the null spaces of the collision operator and of the transport operator. From a modelling viewpoint it is related to the observation that exponential confinement is generated by a spatially inhomogeneous bias in the velocity jump process.Comment: 15 page

Well-balanced and asymptotic preserving schemes for kinetic models

In this paper, we propose a general framework for designing numerical schemes that have both well-balanced (WB) and asymptotic preserving (AP) properties, for various kinds of kinetic models. We are interested in two different parameter regimes, 1) When the ratio between the mean free path and the characteristic macroscopic length $\epsilon$ tends to zero, the density can be described by (advection) diffusion type (linear or nonlinear) macroscopic models; 2) When $\epsilon$ = O(1), the models behave like hyperbolic equations with source terms and we are interested in their steady states. We apply the framework to three different kinetic models: neutron transport equation and its diffusion limit, the transport equation for chemotaxis and its Keller-Segel limit, and grey radiative transfer equation and its nonlinear diffusion limit. Numerical examples are given to demonstrate the properties of the schemes

A High Order Stochastic Asymptotic Preserving Scheme for Chemotaxis Kinetic Models with Random Inputs

In this paper, we develop a stochastic Asymptotic-Preserving (sAP) scheme for the kinetic chemotaxis system with random inputs, which will converge to the modified Keller-Segel model with random inputs in the diffusive regime. Based on the generalized Polynomial Chaos (gPC) approach, we design a high order stochastic Galerkin method using implicit-explicit (IMEX) Runge-Kutta (RK) time discretization with a macroscopic penalty term. The new schemes improve the parabolic CFL condition to a hyperbolic type when the mean free path is small, which shows significant efficiency especially in uncertainty quantification (UQ) with multi-scale problems. The stochastic Asymptotic-Preserving property will be shown asymptotically and verified numerically in several tests. Many other numerical tests are conducted to explore the effect of the randomness in the kinetic system, in the aim of providing more intuitions for the theoretic study of the chemotaxis models

Mathematical description of bacterial traveling pulses

The Keller-Segel system has been widely proposed as a model for bacterial waves driven by chemotactic processes. Current experiments on {\em E. coli} have shown precise structure of traveling pulses. We present here an alternative mathematical description of traveling pulses at a macroscopic scale. This modeling task is complemented with numerical simulations in accordance with the experimental observations. Our model is derived from an accurate kinetic description of the mesoscopic run-and-tumble process performed by bacteria. This model can account for recent experimental observations with {\em E. coli}. Qualitative agreements include the asymmetry of the pulse and transition in the collective behaviour (clustered motion versus dispersion). In addition we can capture quantitatively the main characteristics of the pulse such as the speed and the relative size of tails. This work opens several experimental and theoretical perspectives. Coefficients at the macroscopic level are derived from considerations at the cellular scale. For instance the stiffness of the signal integration process turns out to have a strong effect on collective motion. Furthermore the bottom-up scaling allows to perform preliminary mathematical analysis and write efficient numerical schemes. This model is intended as a predictive tool for the investigation of bacterial collective motion

Numerical methods for one-dimensional aggregation equations

We focus in this work on the numerical discretization of the one dimensional aggregation equation \pa_t\rho + \pa_x (v\rho)=0, $v=a(W'*\rho)$, in the attractive case. Finite time blow up of smooth initial data occurs for potential $W$ having a Lipschitz singularity at the origin. A numerical discretization is proposed for which the convergence towards duality solutions of the aggregation equation is proved. It relies on a careful choice of the discretized macroscopic velocity $v$ in order to give a sense to the product $v \rho$. Moreover, using the same idea, we propose an asymptotic preserving scheme for a kinetic system in hyperbolic scaling converging towards the aggregation equation in hydrodynamical limit. Finally numerical simulations are provided to illustrate the results