Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics

J.S. van Zon, P.R. ten Wolde

    Research output: Contribution to JournalArticleAcademicpeer-review

    Abstract

    We present a technique, called Green's function reaction dynamics (GFRD), for particle-based simulations of reaction-diffusion systems. GFRD uses a maximum time step such that only single particles or pairs of particles have to be considered. For these particles, the Smoluchowski equations are solved analytically using Green's functions, which are used to set up an event-driven algorithm. We apply the technique to a model of gene expression. Under biologically relevant conditions, GFRD is up to 5 orders of magnitude faster than conventional particle-based schemes. © 2005 The American Physical Society.
    Original languageEnglish
    JournalPhysical Review Letters
    Volume94
    Issue number12
    DOIs
    Publication statusPublished - 2005

    Bibliographical note

    Simulating biochemical networks at the particle level and in time and space: Green's function reaction dynamics

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