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On Parallel Stochastic Simulation of Diffusive Systems

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Computational Methods in Systems Biology (CMSB 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5307))

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Abstract

The parallel simulation of biochemical reactions is a very interesting problem: biochemical systems are inherently parallel, yet the majority of the algorithms to simulate them, including the well-known and widespread Gillespie SSA, are strictly sequential. Here we investigate, in a general way, how to characterize the simulation of biochemical systems in terms of Discrete Event Simulation. We dissect their inherent parallelism in order both to exploit the work done in this area and to speed-up their simulation. We study the peculiar characteristics of discrete biological simulations in order to select the parallelization technique which provides the greater benefits, as well as to touch its limits. We then focus on reaction-diffusion systems: we design and implement an efficient parallel algorithm for simulating such systems that include both reactions between entities and movements throughout the space.

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Author information

Authors and Affiliations

  1. The Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Piazza Manci, 17, 38100, Povo (TN), Italy

    Lorenzo Dematté & Tommaso Mazza

  2. Department of Information Engineering and Computer Science (DISI), University of Trento, Italy

    Lorenzo Dematté

Authors
  1. Lorenzo Dematté
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  2. Tommaso Mazza
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Brandenburg University of Technology, Postbox 10 13 44, 03013, Cottbus, Germany

    Monika Heiner

  2. University of Rostock, Albert-Einstein-Str. 21, D-18059, Rostock, Germany

    Adelinde M. Uhrmacher

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Dematté, L., Mazza, T. (2008). On Parallel Stochastic Simulation of Diffusive Systems. In: Heiner, M., Uhrmacher, A.M. (eds) Computational Methods in Systems Biology. CMSB 2008. Lecture Notes in Computer Science(), vol 5307. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88562-7_16

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  • DOI: https://doi.org/10.1007/978-3-540-88562-7_16

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-88561-0

  • Online ISBN: 978-3-540-88562-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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