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A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks

Alexander Slepoy, Aidan P. Thompson, Steven J. Plimpton
The time evolution of species concentrations in biochemical reaction networks is often modeled using the stochastic simulation algorithm (SSA) Phys. Chem. 81, 2340 (1977)?. The computational cost of the original SSA scaled linearly with the number of reactions in the network. Gibson and Bruck developed a logarithmic scaling version of the SSA which uses a priority queue or binary tree for more efficient reaction selection Phys. Chem. A 104, 1876 (2000)?. More generally, this problem is one of dynamic discrete random variate generation which finds many uses in kinetic Monte Carlo and discrete event simulation. We present here a constant-time algorithm, whose cost is independent of the number of reactions, enabled by a slightly more complex underlying data structure. While applicable to kinetic Monte Carlo simulations in general, we describe the algorithm in the context of biochemical simulations and demonstrate its competitive performance on small- and medium-size networks, as well as its superior constant-time performance on very large networks, which are becoming necessary to represent the increasing complexity of biochemical data for pathways that mediate cell function.
Keywords: constant-time, gillespie
The Journal of Chemical Physics 128(20), pages 205101+, 2008, AIP
@article{SlepoyJPC2008,
    abstract = {The time evolution of species concentrations in biochemical reaction networks is often modeled using the stochastic simulation algorithm (SSA) [
Gillespie, J. Phys. Chem. 81, 2340 (1977)
]. The computational cost of the original SSA scaled linearly with the number of reactions in the network. Gibson and Bruck developed a logarithmic scaling version of the SSA which uses a priority queue or binary tree for more efficient reaction selection [
Gibson and Bruck, J. Phys. Chem. A 104, 1876 (2000)
]. More generally, this problem is one of dynamic discrete random variate generation which finds many uses in kinetic Monte Carlo and discrete event simulation. We present here a constant-time algorithm, whose cost is independent of the number of reactions, enabled by a slightly more complex underlying data structure. While applicable to kinetic Monte Carlo simulations in general, we describe the algorithm in the context of biochemical simulations and demonstrate its competitive performance on small- and medium-size networks, as well as its superior constant-time performance on very large networks, which are becoming necessary to represent the increasing complexity of biochemical data for pathways that mediate cell function.},
    author = {Slepoy, Alexander and Thompson, Aidan P. and Plimpton, Steven J.},
    citeulike-article-id = {5909892},
    citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=JCPSA6000128000020205101000001\&idtype=cvips\&gifs=yes},
    citeulike-linkout-1 = {http://link.aip.org/link/?JCP/128/205101},
    citeulike-linkout-2 = {http://dx.doi.org/10.1063/1.2919546},
    doi = {10.1063/1.2919546},
    journal = {The Journal of Chemical Physics},
    keywords = {constant-time, gillespie},
    number = {20},
    pages = {205101+},
    posted-at = {2010-07-31 15:46:19},
    priority = {2},
    publisher = {AIP},
    title = {A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks},
    url = {http://dx.doi.org/10.1063/1.2919546},
    volume = {128},
    year = {2008}
}