Stochastic simulation algorithms for reaction-diffusion systems

27 January 2011
Radek Erban
Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this talk, two commonly used SSAs will be studied. The first SSA is an on-lattice model described by the reaction-diffusion master equation. The second SSA is an off-lattice model based on the simulation of Brownian motion of individual molecules and their reactive collisions. The connections between SSAs and the deterministic models (based on reaction-diffusion PDEs) will be presented. I will consider chemical reactions both at a surface and in the bulk. I will show how the "microscopic" parameters should be chosen to achieve the correct "macroscopic" reaction rate. This choice is found to depend on which SSA is used. I will also present multiscale algorithms which use models with a different level of detail in different parts of the computational domain.
  • Differential Equations and Applications Seminar