There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.
Abstract
Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling
reaction-diffusion processes in cellular and molecular biology. In this paper, two
commonly used SSAs are 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.
In both cases, it is shown that the commonly used implementation of bimolecular reactions
(i.e. the reactions of the form A + B -> C, or A + A -> C) might lead to incorrect
results. Improvements of both SSAs are suggested which overcome the difficulties highlighted.
In particular, a formula is presented for the smallest possible compartment size (lattice
spacing) which can be correctly implemented in the first model. This implementation
uses a new formula for the rate of bimolecular reactions per compartment (lattice
site).