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An efficient and exact stochastic simulation method to analyze rare events in biochemical systems.

Publication ,  Journal Article
Kuwahara, H; Mura, I
Published in: The Journal of chemical physics
October 2008

In robust biological systems, wide deviations from highly controlled normal behavior may be rare, yet they may result in catastrophic complications. While in silico analysis has gained an appreciation as a tool to offer insights into system-level properties of biological systems, analysis of such rare events provides a particularly challenging computational problem. This paper proposes an efficient stochastic simulation method to analyze rare events in biochemical systems. Our new approach can substantially increase the frequency of the rare events of interest by appropriately manipulating the underlying probability measure of the system, allowing high-precision results to be obtained with substantially fewer simulation runs than the conventional direct Monte Carlo simulation. Here, we show the algorithm of our new approach, and we apply it to the analysis of rare deviant transitions of two systems, resulting in several orders of magnitude speedup in generating high-precision estimates compared with the conventional Monte Carlo simulation.

Published In

The Journal of chemical physics

DOI

EISSN

1089-7690

ISSN

0021-9606

Publication Date

October 2008

Volume

129

Issue

16

Start / End Page

165101

Related Subject Headings

  • Stochastic Processes
  • Monte Carlo Method
  • Models, Chemical
  • Models, Biological
  • Likelihood Functions
  • Kinetics
  • Enzymes
  • Chemical Physics
  • Algorithms
  • 51 Physical sciences
 

Citation

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Kuwahara, H., & Mura, I. (2008). An efficient and exact stochastic simulation method to analyze rare events in biochemical systems. The Journal of Chemical Physics, 129(16), 165101. https://doi.org/10.1063/1.2987701
Kuwahara, Hiroyuki, and Ivan Mura. “An efficient and exact stochastic simulation method to analyze rare events in biochemical systems.The Journal of Chemical Physics 129, no. 16 (October 2008): 165101. https://doi.org/10.1063/1.2987701.
Kuwahara H, Mura I. An efficient and exact stochastic simulation method to analyze rare events in biochemical systems. The Journal of chemical physics. 2008 Oct;129(16):165101.
Kuwahara, Hiroyuki, and Ivan Mura. “An efficient and exact stochastic simulation method to analyze rare events in biochemical systems.The Journal of Chemical Physics, vol. 129, no. 16, Oct. 2008, p. 165101. Epmc, doi:10.1063/1.2987701.
Kuwahara H, Mura I. An efficient and exact stochastic simulation method to analyze rare events in biochemical systems. The Journal of chemical physics. 2008 Oct;129(16):165101.

Published In

The Journal of chemical physics

DOI

EISSN

1089-7690

ISSN

0021-9606

Publication Date

October 2008

Volume

129

Issue

16

Start / End Page

165101

Related Subject Headings

  • Stochastic Processes
  • Monte Carlo Method
  • Models, Chemical
  • Models, Biological
  • Likelihood Functions
  • Kinetics
  • Enzymes
  • Chemical Physics
  • Algorithms
  • 51 Physical sciences