Parallel replica dynamics method for bistable stochastic reaction networks: simulation and sensitivity analysis

DOI10.1063/1.5017955arXiv1705.06807WikidataQ47572001 ScholiaQ47572001MaRDI QIDQ6286864FDOQ6286864

Publication date: 18 May 2017

Abstract: Stochastic reaction networks that exhibit bistability are common in many fields such as systems biology and materials science. Sampling of the stationary distribution is crucial for understanding and characterizing the long term dynamics of bistable stochastic dynamical systems. However, this is normally hindered by the insufficient sampling of the rare transitions between the two metastable regions. In this paper, we apply the parallel replica (ParRep) method for continuous time Markov chain to accelerate the stationary distribution sampling of bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions and it is very easy to implement. We combine ParRep with the path space information bounds for parametric sensitivity analysis. We demonstrate the efficiency and accuracy of the method by studying the Schl"{o}gl model and the genetic switches network.

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Monte Carlo methods (65C05) Applications to the sciences (65Z05) Classical flows, reactions, etc. in chemistry (92E20) Stochastic methods applied to problems in equilibrium statistical mechanics (82B31)

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