Efficient exact and K -skip methods for stochastic simulation of coupled chemical reactions

Xiaodong Cai, Ji Wen

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8 Scopus citations

Abstract

Gillespie's direct method (DM) [D. Gillespie, J. Chem. Phys. 81, 2340 (1977)] for exact stochastic simulation of chemical reaction systems has been widely adopted. It is easy to implement but requires large computation for relatively large systems. Recently, two more efficient methods, next reaction method (NRM) [M. A. Gibson and J. Bruck, J. Phys. Chem. A 105, 1876 (2000)] and optimized DM (ODM) [Y. Cao, J. Chem. Phys. 121, 4059 (2004)], have been developed to improve simulation speed. It has been demonstrated that the ODM is the state-of-the-art most efficient method for exact stochastic simulation of most practical reaction systems. In this paper, we first develop an exact stochastic simulation algorithm named ODMK that is more efficient than the ODM. We then develop an approximate method named K -skip method to further accelerate simulation. Using two chemical reaction systems, we demonstrate that our ODMK and K -skip method can save 20%-30% and 70%-80% simulation time, respectively, comparing to the ODM. We also show that our ODMK and K -skip method provide almost the same simulation accuracy as the ODM.

Original languageEnglish (US)
Article number064108
JournalJournal of Chemical Physics
Volume131
Issue number6
DOIs
StatePublished - Aug 28 2009

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ASJC Scopus subject areas

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

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