A hybrid method for micro-mesoscopic stochastic simulation of reaction-diffusion systems.

The present paper introduces a new micro-meso hybrid algorithm based on the Ghost Cell Method concept in which the microscopic subdomain is governed by the Reactive Multi-Particle Collision (RMPC) dynamics. The mesoscopic subdomain is modeled using the Reaction-Diffusion Master Equation (RDME). The RDME is solved by means of the Inhomogeneous Stochastic Simulation Algorithm.

Reactive multi-particle collision dynamics with reactive boundary conditions.

In the present study, an off-lattice particle-based method called the reactive multi-particle collision (RMPC) dynamics is extended to model reaction-diffusion systems with reactive boundary conditions in which the a priori diffusion coefficient of the particles needs to be maintained throughout the simulation. To this end, the authors have made use of the so-called bath particles whose purpose is only to ensure proper diffusion of the main particles in the system. In order to model partial adsorption by a reactive boundary in the RMPC, the probability of a particle being adsorbed, once it hits the boundary, is calculated by drawing an analogy between the RMPC and Brownian Dynamics.

Steady flow through a constricted cylinder by multiparticle collision dynamics.

The flow characterization of blood through healthy and diseased flow geometries is of interest to researchers and clinicians alike, as it may allow for early detection, and monitoring, of cardiovascular disease. In this paper, we use a numerically efficient particle-based flow model called multiparticle collision dynamics (MPC for short) to study the effect of compressibility and slip of flow of a Newtonian fluid through a cylinder with a local constriction. We use a cumulative averaging method to compare our MPC results to the finite-element solution of the incompressible no-slip Navier-Stokes equations in the same geometry.

Spiral wave dynamics in excitable media with spherical geometries.

We describe the spatial and temporal organization of spiral and scroll waves in spherical shells of different sizes and solid spheres. We present simulation results for the evolution of the dynamics and clustering of spiral waves as a function of the excitability of the medium. The excitability, topology, and size of the domain places restrictions on how single and multiarmed spiral waves are organized in space.