Journal of Mathematical Chemistry

, Volume 53, Issue 8, pp 1657–1686 | Cite as

Reaction network realizations of rational biochemical systems and their structural properties

  • Attila Gábor
  • Katalin M. Hangos
  • Julio R. Banga
  • Gábor Szederkényi
Original Paper

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.

Keywords

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

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Attila Gábor
    • 1
  • Katalin M. Hangos
    • 2
    • 3
  • Julio R. Banga
    • 1
  • Gábor Szederkényi
    • 2
    • 4
  1. 1.BioProcess Engineering Group, Instituto de Investigaciones MarinasCSICVigoSpain
  2. 2.Process Control Research GroupComputer and Automation Research InstituteBudapestHungary
  3. 3.Department of Electrical Engineering and Information SystemsUniversity of PannoniaVeszprémHungary
  4. 4.Faculty of Information Technology and BionicsPázmány Péter Catholic UniversityBudapestHungary

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