Symbolic dynamics of biochemical pathways as finite states machines

Olivier F. Roux und Jérémie Bourdon (Editoren)
Ovidiu Radulescu, Satya Samal, Aurélien Naldi, Dima Grigoriev und Andreas Weber
In proceedings of Computational Methods in Systems Biology - 13th International Conference (CMSB 2015), Nantes, France, pages 104-120, Springer, 2015
 

Abstract

We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that symbolic dynamics of monomolecular reaction networks with separated rate constants can be described by deterministic, acyclic automata with a number of states that is inferior to the number of biochemical species. For nonlinear pathways, we propose a general approach to approximate their dynamics by finite state machines working on the metastable states of the network (long life states where the system has slow dynamics). For networks with polynomial rate functions we propose to compute metastable states as solutions of the tropical equilibration problem. Tropical equilibrations are defined by the equality of at least two dominant monomials of opposite signs in the differential equations of each dynamic variable. In algebraic geometry, tropical equilibrations are tantamount to tropical prevarieties, that are finite intersections of tropical hypersurfaces.

Bibtex

@INPROCEEDINGS{RadulescuEtAl2015a,
     author = {Radulescu, Ovidiu and Samal, Satya and Naldi, Aur{\'e}lien and Grigoriev, Dima and Weber, Andreas},
     editor = {Roux, Olivier F. and Bourdon, J{\'e}r{\'e}mie},
      pages = {104--120},
      title = {Symbolic dynamics of biochemical pathways as finite states machines},
  booktitle = {Computational Methods in Systems Biology - 13th International Conference (CMSB 2015)},
     series = {Lecture Notes in Computer Science},
     volume = {9308},
       year = {2015},
  publisher = {Springer},
   location = {Nantes, France},
   abstract = {We discuss the symbolic dynamics of biochemical networks with separate timescales. We show that
               symbolic dynamics of monomolecular reaction networks with separated rate constants can be described
               by deterministic, acyclic automata with a number of states that is inferior to the number of
               biochemical species. For nonlinear pathways, we propose a general approach to approximate their
               dynamics by finite state machines working on the metastable states of the network (long life states
               where the system has slow dynamics). For networks with polynomial rate functions we propose to
               compute metastable states as solutions of the tropical equilibration problem. Tropical
               equilibrations are defined by the equality of at least two dominant monomials of opposite signs in
               the differential equations of each dynamic variable. In algebraic geometry, tropical equilibrations
               are tantamount to tropical prevarieties, that are finite intersections of tropical hypersurfaces.},
        doi = {10.1007/978-3-319-23401-4_10}
}