Radek Erban and S Jonathan Chapman 2009 Phys. Biol. 6 046001 doi:10.1088/1478-3975/6/4/046001
Stochastic modelling of reaction–diffusion processes: algorithms for bimolecular reactions
Radek Erban and S Jonathan Chapman
Show affiliationsSeveral stochastic simulation algorithms (SSAs) have recently been 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).
- PACS
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87.15.R- Reactions and kinetics
- Subjects
- Dates
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Issue 4 (December 2009)
Received 6 March 2009, accepted for publication 3 July 2009
Published 21 August 2009
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Stochastic modelling of reaction–diffusion processes: algorithms for bimolecular reactions
Radek Erban and S Jonathan Chapman 2009 Phys. Biol. 6 046001
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