Computational identification of irreducible state-spaces for stochastic reaction networks

DOI10.1137/17M1134299MaRDI QIDQ3176263zbMATHOpenAlexWikidataFDO

Authors Ankit Gupta, Mustafa Khammash

Publication date 19 July 2018

Published in SIAM Journal on Applied Dynamical Systems (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1505.06594

zbMATH Keywords

ergodicitystationaritystochastic reaction networksstate-space analysisclosed communication classesirreducible state-spaces

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Monte Carlo methods (65C05) Computational methods for stochastic equations (aspects of stochastic analysis) (60H35) Continuous-time Markov processes on discrete state spaces (60J27)

Abstract: Stochastic models of reaction networks are becoming increasingly important in Systems Biology. In these models, the dynamics is generally represented by a continuous-time Markov chain whose states denote the copy-numbers of the constituent species. The state-space on which this process resides is a subset of non-negative integer lattice and for many examples of interest, this state-space is countably infinite. This causes numerous problems in analyzing the Markov chain and understanding its long-term behavior. These problems are further confounded by the presence of conservation relations among species which constrain the dynamics in complicated ways. In this paper we provide a linear-algebraic procedure to disentangle these conservation relations and represent the state-space in a special decomposed form, based on the copy-number ranges of various species and dependencies among them. This decomposed form is advantageous for analyzing the stochastic model and for a large class of networks we demonstrate how this form can be used for finding all the closed communication classes for the Markov chain within the infinite state-space. Such communication classes are irreducible state-spaces for the dynamics and they support all the extremal stationary distributions for the Markov chain. Hence our results provide important insights into the long-term behavior and stability properties of stochastic models of reaction networks. We discuss how the knowledge of these irreducible state-spaces can be used in many ways such as speeding-up stochastic simulations of multiscale networks or in identifying the stationary distributions of complex-balanced networks. We illustrate our results with several examples of gene-expression networks from Systems Biology.

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Cited in

(10)

• Some network conditions for positive recurrence of stochastically modeled reaction networks
• Ergodicity analysis and antithetic integral control of a class of stochastic reaction networks with delays
• Structural classification of continuous time Markov chains with applications
• Stationary distributions of continuous-time Markov chains: a review of theory and truncation-based approximations
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