A multiple time interval finite state projection algorithm for the solution to the chemical master equation

DOI10.1016/J.JCP.2007.05.016MaRDI QIDQ2456722zbMATH OpenOpenAlexFDO

Authors Brian Munsky, Mustafa Khammash

Publication date 19 October 2007

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jcp.2007.05.016

zbMATH Keywords

chemical master equationMarkov processesstochastic gene regulatory networks

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Genetics and epigenetics (92D10)

Review text

This paper is concentrated to one computational difficulty that arises when system trajectories slowly drift over regions of the configuration space during long time intervals. A new approach for choosing and expanding the projection for the original finite state projection algorithm is presented. The authors introduce an approach to automatically choosing and expanding the projection necessary to achieve a desired accuracy and then illustrate this algorithm on a simplified model from the field of systems biology.

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Cites work

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• Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems
• Stochastic approach to chemical kinetics
• Stochastic modelling of gene regulatory networks
• Stochastic processes in physics and chemistry.

Cited in

(56)

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• Structure-preserving discretization of the chemical master equation
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