Format

Send to

Choose Destination
See comment in PubMed Commons below
J Chem Phys. 2010 Jan 28;132(4):044102. doi: 10.1063/1.3297948.

A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks.

Author information

1
Institute of Theoretical Computer Science and Swiss Institute of Bioinformatics, ETH Zurich, CH-8092 Z├╝rich, Switzerland. rajeshr@ethz.ch

Abstract

We present the partial-propensity stochastic simulation algorithm with composition-rejection sampling (PSSA-CR). It is an exact formulation of the stochastic simulation algorithm (SSA) for well-stirred systems of coupled chemical reactions. The new formulation is a partial-propensity variant [R. Ramaswamy, N. Gonzalez-Segredo, and I. F. Sbalzarini, J. Chem. Phys. 130, 244104 (2009)] of the composition- rejection SSA [A. Slepoy, A. P. Thompson, and S. J. Plimpton, J. Chem. Phys. 128, 205101 (2008)]. The computational cost of this new formulation is bounded by a constant for weakly coupled reaction networks, and it increases at most linearly with the number of chemical species for strongly coupled reaction networks. PSSA-CR thus combines the advantages of partial-propensity methods and the composition-rejection SSA, providing favorable scaling of the computational cost for all classes of reaction networks.

PMID:
20113014
DOI:
10.1063/1.3297948
[Indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for American Institute of Physics
    Loading ...
    Support Center