Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories

Rory M. Donovan, Andrew J. Sedgewick, James R. Faeder, Daniel Zuckerman

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

We apply the "weighted ensemble" (WE) simulation strategy, previously employed in the context of molecular dynamics simulations, to a series of systems-biology models that range in complexity from a one-dimensional system to a system with 354 species and 3680 reactions. WE is relatively easy to implement, does not require extensive hand-tuning of parameters, does not depend on the details of the simulation algorithm, and can facilitate the simulation of extremely rare events. For the coupled stochastic reaction systems we study,WE is able to produce accurate and efficient approximations of the joint probability distribution for all chemical species for all time t. WE is also able to efficiently extract mean first passage times for the systems, via the construction of a steady-state condition with feedback. In all cases studied here, WE results agree with independent "brute-force" calculations, but significantly enhance the precision with which rare or slow processes can be characterized. Speedups over "brute-force" in sampling rare events via the Gillespie direct Stochastic Simulation Algorithm range from ∼10 12 to ∼1018 for characterizing rare states in a distribution, and ∼102 to ∼104 for finding mean first passage times.

Original languageEnglish (US)
Article number115105
JournalJournal of Chemical Physics
Volume139
Issue number11
DOIs
StatePublished - Sep 21 2013
Externally publishedYes

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Reaction kinetics
reaction kinetics
Trajectories
trajectories
Probability distributions
Molecular dynamics
simulation
Tuning
Sampling
Feedback
Computer simulation
biology
sampling
tuning
molecular dynamics
approximation
Systems Biology

ASJC Scopus subject areas

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

Cite this

Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories. / Donovan, Rory M.; Sedgewick, Andrew J.; Faeder, James R.; Zuckerman, Daniel.

In: Journal of Chemical Physics, Vol. 139, No. 11, 115105, 21.09.2013.

Research output: Contribution to journalArticle

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