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A computational approach to persistence, permanence, and endotacticity of biochemical reaction systems

Research output: Contribution to journalArticlepeer-review

  • Matthew D. Johnston
  • Casian Pantea
  • Pete Donnell

We introduce a mixed-integer linear programming (MILP) framework capable of determining whether a chemical reaction network possesses the property of being endotactic or strongly endotactic. The network property of being strongly endotactic is known to lead to persistence and permanence of chemical species under genetic kinetic assumptions, while the same result is conjectured but as yet unproved for general endotactic networks. The algorithms we present are the first capable of verifying endotacticity of chemical reaction networks for systems with greater than two constituent species. We implement the algorithms in the open-source online package CoNtRol and apply them to a large sample of networks from the European Bioinformatics Institute’s BioModels Database. We use strong endotacticity to establish for the first time the permanence of a well-studied circadian clock mechanism.

Original languageEnglish
Pages (from-to)467-498
Number of pages32
JournalJournal of Mathematical Biology
Volume72
Issue number1-2
Early online date19 May 2015
DOIs
Publication statusPublished - 1 Jan 2016

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    Rights statement: The final publication is available at Springer via http://dx.doi.org/10.1007%2Fs00285-015-0892-1.

    Accepted author manuscript (Post-print), 586 KB, PDF document

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