Multiscale simulation of stochastic reaction-diffusion networks

Abstract

The most commonly employed spatial stochastic simulation methods for biochemical systems in molecular systems biology are reviewed from a multiscale perspective. Three levels of approximation are distinguished: macroscopic, mesoscopic, and microscopic levels. The relation between the levels of approximation is discussed for both reactions between molecules and transport of the molecules through a solvent. Computational methods are described for each level separately and for hybrid methods involving two levels. Free software implementing these methods in space and time is surveyed.