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A new approximate method for the stochastic simulation of chemical systems: The representative reaction approach

Authors

  • Shantanu Kadam,

    1. Physical Chemistry Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411 008, India
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  • Kumar Vanka

    Corresponding author
    1. Physical Chemistry Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411 008, India
    • Physical Chemistry Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411 008, India
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Abstract

We have developed two new approximate methods for stochastically simulating chemical systems. The methods are based on the idea of representing all the reactions in the chemical system by a single reaction, i.e., by the “representative reaction approach” (RRA). Discussed in the article are the concepts underlying the new methods along with flowchart with all the steps required for their implementation. It is shown that the two RRA methods {with the reaction equation image as the representative reaction (RR)} perform creditably with regard to accuracy and computational efficiency, in comparison to the exact stochastic simulation algorithm (SSA) developed by Gillespie and are able to successfully reproduce at least the first two moments of the probability distribution of each species in the systems studied. As such, the RRA methods represent a promising new approach for stochastically simulating chemical systems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012

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