DOI: 10.1063/1.1824902. The slow-scale stochastic simulation algorithm

The slow-scale stochastic simulation algorithm

10.1063/1.1824902

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

Reactions in real chemical systems often take place on vastly different time scales, with “fast” reaction channels firing very much more frequently than “slow” ones. These firings will be interdependent if, as is usually the case, the fast and slow reactions involve some of the same species. An exact stochastic simulation of such a system will necessarily spend most of its time simulating the more numerous fast reaction events. This is a frustratingly inefficient allocation of computational effort when dynamical stiffness is present, since in that case a fast reaction event will be of much less importance to the system’s evolution than will a slow reaction event. For such situations, this paper develops a systematic approximate theory that allows one to stochastically advance the system in time by simulating the firings of only the slow reaction events. Developing an effective strategy to implement this theory poses some challenges, but as is illustrated here for two simple systems, when those challenges can be overcome, very substantial increases in simulation speed can be realized.

Bibliography

Cao, Y., Gillespie, D. T., & Petzold, L. R. (2004). The slow-scale stochastic simulation algorithm. The Journal of Chemical Physics, 122(1).

Authors 3

Yang Cao (first)
Daniel T. Gillespie (additional)
Linda R. Petzold (additional)

References 14 Referenced 360

10.1016/0021-9991(76)90041-3 / J. Comput. Phys. (1976)
10.1021/j100540a008 / J. Phys. Chem. (1977)
10.1016/0378-4371(92)90283-V / Physica A (1992)
10.1063/1.1505860 / J. Chem. Phys. (2002)
10.1063/1.1545446 / J. Chem. Phys. (2003)
10.1063/1.1627296 / J. Chem. Phys. (2003)
10.1063/1.1378322 / J. Chem. Phys. (2001)
10.1063/1.1613254 / J. Chem. Phys. (2003)
10.1093/genetics/149.4.1633 / Genetics (1998)
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10.1063/1.1378791 / Chaos (2001)
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Dates

Type	When
Created	20 years, 7 months ago (Jan. 15, 2005, 10:50 a.m.)
Deposited	2 years, 2 months ago (June 25, 2023, 11:54 p.m.)
Indexed	3 weeks ago (Aug. 6, 2025, 8:53 a.m.)
Issued	20 years, 8 months ago (Dec. 15, 2004)
Published	20 years, 8 months ago (Dec. 15, 2004)
Published Online	20 years, 8 months ago (Dec. 15, 2004)
Published Print	20 years, 7 months ago (Jan. 1, 2005)

Funders 0

None

BibTeX

@article{Cao_2004, title={The slow-scale stochastic simulation algorithm}, volume={122}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.1824902}, DOI={10.1063/1.1824902}, number={1}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Cao, Yang and Gillespie, Daniel T. and Petzold, Linda R.}, year={2004}, month=dec }

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