Reaction-diffusion master equation in the microscopic limit

Abstract

Stochastic modeling of reaction-diffusion kinetics has emerged as a powerful theoretical tool in the study of biochemical reaction networks. Two frequently employed models are the particle-tracking Smoluchowski framework and the on-lattice reaction-diffusion master equation (RDME) framework. As the mesh size goes from coarse to fine, the RDME initially becomes more accurate. However, recent developments have shown that it will become increasingly inaccurate compared to the Smoluchowski model as the lattice spacing becomes very fine. Here we give a general and simple argument for why the RDME breaks down. Our analysis reveals a hard limit on the voxel size for which no local RDME can agree with the Smoluchowski model and lets us quantify this limit in two and three dimensions. In this light we review and discuss recent work in which the RDME has been modified in different ways in order to better agree with the microscale model for very small voxel sizes.