Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation

Authors

  • Elijah Roberts,

    1. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
    2. Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
    Current affiliation:
    1. Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218
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  • John E. Stone,

    1. Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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  • Zaida Luthey-Schulten

    Corresponding author
    1. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
    2. Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
    3. Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
    • Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

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    • Fax: 217-244-3186


Abstract

Spatial stochastic simulation is a valuable technique for studying reactions in biological systems. With the availability of high-performance computing (HPC), the method is poised to allow integration of data from structural, single-molecule and biochemical studies into coherent computational models of cells. Here, we introduce the Lattice Microbes software package for simulating such cell models on HPC systems. The software performs either well-stirred or spatially resolved stochastic simulations with approximated cytoplasmic crowding in a fast and efficient manner. Our new algorithm efficiently samples the reaction-diffusion master equation using NVIDIA graphics processing units and is shown to be two orders of magnitude faster than exact sampling for large systems while maintaining an accuracy of 0.1%. Display of cell models and animation of reaction trajectories involving millions of molecules is facilitated using a plug-in to the popular VMD visualization platform. The Lattice Microbes software is open source and available for download at http://www.scs.illinois.edu/schulten/lm © 2012 Wiley Periodicals, Inc.

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