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Structural simplification of chemical reaction networks preserving deterministic semantics

Guillaume Madelaine 1, 2 Cédric Lhoussaine 1, 2 Joachim Niehren 2, 3
2 BioComputing
CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189
3 LINKS - Linking Dynamic Data
CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189, Inria Lille - Nord Europe
Abstract : We study the structural simplification of chemical reaction networks preserving the deterministic kinetics. We aim at finding simplification rules that can eliminate intermediate molecules while preserving the dynamics of all others. The rules should be valid even though the network is plugged into a bigger context. An example is Michaelis-Menten's simplification rule for enzymatic reactions. In this paper, we present a large class of structural simplification rules for reaction networks that can eliminate intermediate molecules at equilibrium, without assuming that all molecules are at equilibrium, i.e. in a steady state. We prove the correctness of our simplification rules for all contexts that preserve the equilibrium of the eliminated molecules. Finally, we illustrate at a concrete example network from systems biology that our simplification rules may allow to drastically reduce the size of reaction networks in practice.
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Submitted on : Thursday, June 25, 2015 - 11:01:06 AM
Last modification on : Thursday, January 20, 2022 - 4:17:13 PM
Long-term archiving on: : Wednesday, September 16, 2015 - 12:15:37 AM

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  • HAL Id : hal-01168038, version 1

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Guillaume Madelaine, Cédric Lhoussaine, Joachim Niehren. Structural simplification of chemical reaction networks preserving deterministic semantics. Computational Methods in Systems Biology (CMSB), Jérémie BOURDON; Olivier ROUX, Sep 2015, Nantes, France. pp.133-144. ⟨hal-01168038⟩

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