A computational approach to extinction events in chemical reaction networks with discrete state spaces
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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.
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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
- Polynomial time reachability analysis in discrete state chemical reaction networks obeying conservation laws
- Discrepancies between extinction events and boundary equilibria in reaction networks
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