K -leap method for accelerating stochastic simulation of coupled chemical reactions

Xiaodong Cai, Zhouyi Xu

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34 Scopus citations

Abstract

Leap methods are very promising for accelerating stochastic simulation of a well stirred chemically reacting system, while providing acceptable simulation accuracy. In Gillespie's τ -leap method [D. Gillespie, J. Phys. Chem. 115, 1716 (2001)], the number of firings of each reaction channel during a leap is a Poisson random variable, whose sample values are unbounded. This may cause large changes in the populations of certain molecular species during a leap, thereby violating the leap condition. In this paper, we develop an alternative leap method called the K -leap method, in which we constrain the total number of reactions occurring during a leap to be a number K calculated from the leap condition. As the number of firings of each reaction channel during a leap is upper bounded by a properly chosen number, our K -leap method can better satisfy the leap condition, thereby improving simulation accuracy. Since the exact stochastic simulation algorithm (SSA) is a special case of our K -leap method when K=1, our K -leap method can naturally change from the exact SSA to an approximate leap method during simulation, whenever the leap condition allows to do so.

Original languageEnglish (US)
Article number074102
JournalJournal of Chemical Physics
Volume126
Issue number7
DOIs
StatePublished - Feb 28 2007

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ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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