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Simplification of Reaction Networks, Confluence and Elementary Modes

Guillaume Madelaine 1 Elisa Tonello 2 Cédric Lhoussaine 1 Joachim Niehren 1, 3
1 BioComputing
CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189
3 LINKS - Linking Dynamic Data
Inria Lille - Nord Europe, CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189
Abstract : Reaction networks can be simplified by eliminating linear intermediate species in partial steady states. In this paper, we study the question whether this rewrite procedure is confluent, so that for any given reaction network with kinetic constraints, a unique normal form will be obtained independently of the elimination order. We first show that confluence fails for the elimination of intermediates even without kinetics, if “dependent reactions” introduced by the simplification are not removed. This leads us to revising the simplification algorithm into a variant of the double description method for computing elementary modes, so that it keeps track of kinetic information. Folklore results on elementary modes then imply the confluence of the revised simplification algorithm with respect to the network structure, i.e., the structure of fully simplified networks is unique. We show however that the kinetic rates assigned to the reactions may not be unique, and provide a biological example where two different simplified networks can be obtained. Finally, we give a criterion on the structure of the initial network that is sufficient to guarantee the confluence of both the structure and the kinetic rates.
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Submitted on : Thursday, February 23, 2017 - 3:08:34 PM
Last modification on : Friday, January 7, 2022 - 3:44:02 AM
Long-term archiving on: : Wednesday, May 24, 2017 - 2:50:18 PM

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Guillaume Madelaine, Elisa Tonello, Cédric Lhoussaine, Joachim Niehren. Simplification of Reaction Networks, Confluence and Elementary Modes. Computation, MDPI, 2017, Multiscale and Hybrid Modeling of the Living Systems. ⟨hal-01471074⟩

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