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Article overview
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A computational approach to persistence, permanence, and endotacticity of biochemical reaction systems | | Matthew D. Johnston
; Casian Pantea
; Pete Donnell
; | | Date: |
15 Dec 2014 | | 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 several
well-studied biochemical examples, including the general $n$-site
phosphorylation / dephosphorylation networks and a circadian clock mechanism. | | Source: | arXiv, 1412.4662 | | Services: | Forum | Review | PDF | Favorites | |
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