Structural simplification of chemical reaction networks in partial steady states

Guillaume Madelaine (1) , Cédric Lhoussaine (2) , Joachim Niehren (3) , Elisa Tonello (4)

1 BioComputing
2 Université de Lille
3 LINKS - Linking Dynamic Data
4 UON - University of Nottingham, UK

We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate interme- diate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten’s simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rule repeatedly and applied it to reaction networks from systems biology. Keywords: bioinformatics;systemsbiology;reactionnetwork;contextualequivalence.

Mots clés: deterministic semantics; equivalence; system biology; chemical reaction network; structural simplification

Domaines: Bio-informatique [q-bio.QM]; Chimie théorique et/ou physique

Guillaume Madelaine, Cédric Lhoussaine, Joachim Niehren, Elisa Tonello. Structural simplification of chemical reaction networks in partial steady states. BioSystems, 2016, Special Issue of CMSB'2015, 149, pp.34--49. ⟨10.1016/j.biosystems.2016.08.003⟩. ⟨hal-01350517⟩