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Stochastic simulation of chemically reacting systems using multi-core processors

Lookup NU author(s): Dr Colin Gillespie

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Abstract

In recent years, computer simulations have become increasingly useful when trying to understand the complex dynamics of biochemical networks, particularly in stochastic systems. In such situations stochastic simulation is vital in gaining an understanding of the inherent stochasticity present, as these models are rarely analytically tractable. However, a stochastic approach can be computationally prohibitive for many models. A number of approximations have been proposed that aim to speed up stochastic simulations. However, the majority of these approaches are fundamentally serial in terms of central processing unit (CPU) usage. In this paper, we propose a novel simulation algorithm that utilises the potential of multi-core machines. This algorithm partitions the model into smaller sub-models. These sub-models are then simulated, in parallel, on separate CPUs. We demonstrate that this method is accurate and can speed-up the simulation by a factor proportional to the number of processors available. (C) 2012 American Institute of Physics. [doi: 10.1063/1.3670416]


Publication metadata

Author(s): Gillespie CS

Publication type: Article

Publication status: Published

Journal: Journal of Chemical Physics

Year: 2012

Volume: 136

Issue: 1

Print publication date: 03/01/2012

ISSN (print): 0021-9606

ISSN (electronic): 1089-7690

Publisher: American Institute of Physics

URL: http://dx.doi.org/10.1063/1.3670416

DOI: 10.1063/1.3670416


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