Titre :

Simplification of Reaction Networks, Confluence and Elementary Modes

Auteur(s) :

Madelaine, Guillaume [Auteur]
BioComputing
Tonello, Elisa [Auteur]
University of Nottingham, UK [UON]
Lhoussaine, Cedric [Auteur]
BioComputing
Niehren, Joachim [Auteur]
Linking Dynamic Data [LINKS]
BioComputing

Titre de la revue :

Computation
Multiscale and Hybrid Modeling of the Living Systems

Éditeur :

MDPI

Date de publication :

2017-02-28

ISSN :

2079-3197

Mot(s)-clé(s) en anglais :

Deterministic semantics
Ordinary differential equations
Rewrite systems
System biology
Structural simplification
Elementary modes
Chemical reaction networks
Confluence

Discipline(s) HAL :

Informatique [cs]/Bio-informatique [q-bio.QM]
Chimie/Chimie théorique et/ou physique

Résumé en anglais : [en]

Reaction networks can be simplified by eliminating linear intermediate species in partialsteady states. In this paper, we study the question whether this rewrite procedure is confluent, sothat for any given reaction network ...
Lire la suite >Reaction networks can be simplified by eliminating linear intermediate species in partialsteady states. In this paper, we study the question whether this rewrite procedure is confluent, sothat for any given reaction network with kinetic constraints, a unique normal form will be obtainedindependently of the elimination order. We first show that confluence fails for the elimination ofintermediates even without kinetics, if “dependent reactions” introduced by the simplification arenot removed. This leads us to revising the simplification algorithm into a variant of the doubledescription 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 simplificationalgorithm 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, andprovide a biological example where two different simplified networks can be obtained. Finally, wegive a criterion on the structure of the initial network that is sufficient to guarantee the confluenceof both the structure and the kinetic rates.Lire moins >

Langue :

Anglais

Comité de lecture :

Oui

Audience :

Internationale

Vulgarisation :

Non

Projet ANR :

Des modèles de population aux populations de modèles: observation, modélisation et contrôle de l'expression génique au niveau de la cellule unique

Commentaire :

Extended version of a conference paper at CMSB'2016

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL