Conditions for extinction events in chemical reaction networks with discrete state spaces

J Math Biol. 2018 May;76(6):1535-1558. doi: 10.1007/s00285-017-1182-x. Epub 2017 Sep 26.

Abstract

We study chemical reaction networks with discrete state spaces and present sufficient conditions on the structure of the network that guarantee the system exhibits an extinction event. The conditions we derive involve creating a modified chemical reaction network called a domination-expanded reaction network and then checking properties of this network. Unlike previous results, our analysis allows algorithmic implementation via systems of equalities and inequalities and suggests sequences of reactions which may lead to extinction events. We apply the results to several networks including an EnvZ-OmpR signaling pathway in Escherichia coli.

Keywords: Extinction; Petri net; Reaction graph; Reaction network; Stochastic process.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Outer Membrane Proteins / metabolism
  • Bacterial Proteins / metabolism
  • Biochemical Phenomena
  • Computational Biology
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / metabolism
  • Kinetics
  • Mathematical Concepts
  • Metabolic Networks and Pathways*
  • Models, Biological*
  • Multienzyme Complexes / metabolism
  • Signal Transduction
  • Stochastic Processes
  • Trans-Activators / metabolism

Substances

  • Bacterial Outer Membrane Proteins
  • Bacterial Proteins
  • Escherichia coli Proteins
  • Multienzyme Complexes
  • Trans-Activators
  • osmolarity response regulator proteins
  • envZ protein, E coli