Reaction network realizations of rational biochemical systems and their structural properties

Attila Gábor, Katalin M. Hangos, Julio R. Banga, Gábor Szederkényi

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

In this paper, a frequently used representation of mass-action type reaction networks is extended to a more general system class where the reaction rates are in rational function form. An algorithm is given to compute a possible reaction graph from the kinetic differential equations. However, this structure is generally non-unique, as it is illustrated through the phenomenon of dynamical equivalence, when different reaction network structures correspond to exactly the same dynamics. It is shown that under some technical assumptions, the so-called dense realization containing the maximal number of reactions, forms a super-structure in the sense that the reaction graph of any dynamically equivalent reaction network is the sub-graph of the dense realization. Additionally, optimization based methods are given to find dynamically equivalent realizations with preferred properties, such as dense realizations or sparse realizations. The introduced concepts are illustrated by examples.

Original languageEnglish
Pages (from-to)1657-1686
Number of pages30
JournalJournal of Mathematical Chemistry
Volume53
Issue number8
DOIs
Publication statusPublished - Sep 13 2015

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Keywords

  • Biochemical reaction graph
  • Dynamic equivalence
  • Dynamic models
  • Parameter-free model analysis

ASJC Scopus subject areas

  • Chemistry(all)
  • Applied Mathematics

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