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Journal of Chemical Physics / Volume 136 / Issue 1 / ARTICLES / Theoretical Methods and Algorithms

J. Chem. Phys. 136, 014101 (2012); http://dx.doi.org/10.1063/1.3670416 (8 pages)

Stochastic simulation of chemically reacting systems using multi-core processors

Colin S. Gillespie

School of Mathematics & Statistics, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom

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(Received 19 July 2011; accepted 28 November 2011; published online 3 January 2012)

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.

© 2012 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. APPROACH
    1. The MIDIA algorithm
    2. Illustrative example: The molecular chaperone model
    3. Adaptive time steps
    4. Results
  3. MCCOLLUM’S GENE REGULATION NETWORK
    1. Accuracy
    2. Speed-up
  4. ERROR ANALYSIS
  5. DISCUSSION

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KEYWORDS and PACS

Keywords

chemistry computing, multiprocessing systems, program processors, reaction kinetics theory, stochastic processes

PACS

  • 82.20.Wt

    Computational modeling; simulation

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3670416

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

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