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  • Title: Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch.
    Author: Morelli MJ, Allen RJ, Tănase-Nicola S, ten Wolde PR.
    Journal: J Chem Phys; 2008 Jan 28; 128(4):045105. PubMed ID: 18248012.
    Abstract:
    In many stochastic simulations of biochemical reaction networks, it is desirable to "coarse grain" the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network that is particularly sensitive to dynamical fluctuations: a bistable genetic switch. We remove protein-DNA and/or protein-protein association-dissociation reactions from the reaction set using various coarse-graining strategies. We determine the effects on the steady-state probability distribution function and on the rate of fluctuation-driven switch flipping transitions. We find that protein-protein interactions may be safely eliminated from the reaction set, but protein-DNA interactions may not. We also find that it is important to use the chemical master equation rather than macroscopic rate equations to compute effective propensity functions for the coarse-grained reactions.
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