A computational approach to extinction events in chemical reaction networks with discrete state spaces

DOI10.1016/J.MBS.2017.10.003zbMATH Open1382.92144arXiv1701.02014OpenAlexW2573359569WikidataQ47653104 ScholiaQ47653104MaRDI QIDQ680446FDOQ680446

Matthew D. Johnston

Publication date: 23 January 2018

Published in: Mathematical Biosciences (Search for Journal in Brave)

Abstract: Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist of a series of systems of equalities and inequalities on the edges of a modified reaction network called a domination-expanded reaction network. In this paper, we present a computational implementation of these conditions written in Python and apply the program on examples drawn from the biochemical literature, including a model of polyamine metabolism in mammals and a model of the pentose phosphate pathway in Trypanosoma brucei. We also run the program on 458 models from the European Bioinformatics Institute's BioModels Database and report our results.

Full work available at URL: https://arxiv.org/abs/1701.02014

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zbMATH Keywords

algorithmslinear programmingstochastic processreaction networkdiscrete extinction

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Computational methods for problems pertaining to biology (92-08)

Cites Work

• A computational approach to persistence, permanence, and endotacticity of biochemical reaction systems
• A Petri net approach to the study of persistence in chemical reaction networks
• Introduction to stochastic processes.
• Chemical mechanism structure and the coincidence of the stoichiometric and kinetie subspaces
• Stochastic Analysis of Biochemical Systems
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• Title not available (Why is that?)
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• Conditions for extinction events in chemical reaction networks with discrete state spaces
• Dynamical properties of discrete reaction networks
• Dominance and T-Invariants for Petri Nets and Chemical Reaction Networks

Cited In (5)

• Reachability analysis of low-order discrete state reaction networks obeying conservation laws
• Conditions for extinction events in chemical reaction networks with discrete state spaces
• Polynomial time coverability analysis in discrete state chemical reaction network subclasses
• Discrepancies between extinction events and boundary equilibria in reaction networks
• Polynomial Time Reachability Analysis in Discrete State Chemical Reaction Networks Obeying Conservation Laws

Uses Software

• BioModels
• Python
• crnpy
• GitHub

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