Computational identification of irreducible state-spaces for stochastic reaction networks

DOI10.1137/17M1134299zbMATH Open1393.60079arXiv1505.06594OpenAlexW2964216632WikidataQ129955544 ScholiaQ129955544MaRDI QIDQ3176263FDOQ3176263

Authors: Ankit Gupta, Mustafa Khammash 

Publication date: 19 July 2018

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

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.

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

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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)

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Cited In (8)

• State-estimators for chemical reaction networks of Feinberg-Horn-Jackson zero deficiency type
• Steady-State Sensitivity Analysis of Continuous Time Markov Chains
• An algebraic method to calculate parameter regions for constrained steady-state distribution in stochastic reaction networks
• Title not available (Why is that?)
• Ergodicity Analysis and Antithetic Integral Control of a Class of Stochastic Reaction Networks with Delays
• Computational Translation Framework Identifies Biochemical Reaction Networks with Special Topologies and Their Long-Term Dynamics
• Structural classification of continuous time Markov chains with applications
• Stationary Distributions of Continuous-Time Markov Chains: A Review of Theory and Truncation-Based Approximations

Uses Software

• CERENA

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