Erban, R. and Chapman, S. J.
(2009)
Stochastic modelling of reactiondiffusion processes:
algorithms for bimolecular reactions.
Not specified
.
(Submitted)

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Abstract
Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling reactiondiffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an onlattice model described by the reactiondiffusion master equation. The second SSA is an offlattice 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).
Item Type:  Article 

Subjects:  D  G > General 
Research Groups:  Oxford Centre for Collaborative Applied Mathematics 
ID Code:  835 
Deposited By:  Dr M. Stoll 
Deposited On:  08 Oct 2009 16:22 
Last Modified:  29 May 2015 18:31 
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