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Published Online: 30 January 2006
Accepted: November 2005

Efficient step size selection for the tau-leaping simulation method

J. Chem. Phys. 124, 044109 (2006); https://doi.org/10.1063/1.2159468
Yang Caoa)
  • Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061
    • Daniel T. Gillespie
  • Dan T. Gillespie Consulting, 30504 Cordoba Place, Castaic, California 91384
    • Linda R. Petzold
  • Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California 93106
    • more...View Affiliations
    ABSTRACT
    The tau-leaping method of simulating the stochastic time evolution of a well-stirred chemically reacting system uses a Poisson approximation to take time steps that leap over many reaction events. Theory implies that tau leaping should be accurate so long as no propensity function changes its value “significantly” during any time step τ. Presented here is an improved procedure for estimating the largest value for τ that is consistent with this condition. This new τ-selection procedure is more accurate, easier to code, and faster to execute than the currently used procedure. The speedup in execution will be especially pronounced in systems that have many reaction channels.

    ACKNOWLEDGMENTS

    This work was supported in part by the California Institute of Technology under DARPA Award No. F30602-01-2-0558, by the U.S. Department of Energy under DOE Award No. DE-FG02-04ER25621, by the National Science Foundation under NSF Award Nos. CCF-0326576 and ACI00-86061, by the Institute for Collaborative Biotechnologies through Grant No. DAAD19-03-D-0004 from the U.S. Army Research Office, and by the Molecular Sciences Institute under Contract No. 244725 with Sandia National Laboratories and the Department of Energy’s “Genomes to Life” program.

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