Exact stochastic simulation of coupled chemical reactions with delays

Research output: Contribution to journalArticle

89 Citations (Scopus)

Abstract

Gillespie's exact stochastic simulation algorithm (SSA) [J. Phys. Chem. 81, 2350 (1977)] has been widely used to simulate the stochastic dynamics of chemically reacting systems. In this algorithm, it is assumed that all reactions occur instantly. While this is true in many cases, it is also possible that some chemical reactions, such as gene transcription and translation in living cells, take certain time to finish after they are initiated. Thus, the product of such reactions will emerge after certain delays. Apparently, Gillespie's SSA is not an exact algorithm for chemical reaction systems with delays. In this paper, the author develops an exact SSA for chemical reaction systems with delays, based upon the same fundamental premise of stochastic kinetics used by Gillespie in the development of his SSA. He then shows that an algorithm modified from Gillespie's SSA by Barrio et al. [PLOS Comput. Biol. 2, 1017 (2006)] is also an exact SSA for chemical reaction systems with delays, but it needs to generate more random variables than the author's algorithm.

Original languageEnglish
Article number124108
JournalJournal of Chemical Physics
Volume126
Issue number12
DOIs
StatePublished - Apr 8 2007

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Chemical reactions
chemical reactions
simulation
random variables
Transcription
Random variables
genes
Genes
Cells
Kinetics
kinetics
products

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Exact stochastic simulation of coupled chemical reactions with delays. / Cai, Xiaodong.

In: Journal of Chemical Physics, Vol. 126, No. 12, 124108, 08.04.2007.

Research output: Contribution to journalArticle

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