title: A computational approach to persistence, permanence, and endotacticity of biochemical reaction systems.
abstract: 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.
authors.affiliation: Department of Mathematics, University of Wisconsin-Madison, Madison, WI, 53706, USA. mjohnston3@wisc.edu.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Johnston
authors.affiliation: Department of Mathematics, West Virginia University, Morgantown, WV, 26506, USA.
authors.forename: Casian
authors.initials: C
authors.lastname: Pantea
authors.affiliation: Department of Mathematics, University of Portsmouth, Portsmouth, PO1 3HF, UK.
authors.forename: Pete
authors.initials: P
authors.lastname: Donnell
mesh_terms: D000465:Algorithms; D000818:Animals; D001669:Biochemical Phenomena; D057906:Circadian Clocks; D007700:Kinetics; D055641:Mathematical Concepts; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D010766:Phosphorylation; D011382:Programming, Linear; D049490:Systems Biology
keywords: Chemical kinetics; Chemical reaction network; Endotactic; Permanence; Persistence