Biology – Quantitative Biology – Quantitative Methods
Scientific paper
2008-04-25
Biology
Quantitative Biology
Quantitative Methods
25 pages, 7 figures, submitted to Journal of Chemical Physics
Scientific paper
10.1063/1.2958287
Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In these models, components move by diffusion, and can react with one another upon contact. However, when reactions are incorporated into a Brownian Dynamics algorithm, attention must be paid to avoid violations of the detailed-balance rule, and therefore introducing systematic errors in the simulation. We present a Brownian Dynamics algorithm for reaction-diffusion systems that rigorously obeys detailed balance for equilibrium reactions. By comparing the simulation results to exact analytical results for a bimolecular reaction, we show that the algorithm correctly reproduces both equilibrium and dynamical quantities. We apply our scheme to a ``push-pull'' network in which two antagonistic enzymes covalently modify a substrate. Our results highlight that the diffusive behaviour of the reacting species can reduce the gain of the response curve of this network.
Morelli Marco J.
ten Wolde Pieter Rein
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