Literature DB >> 28951955

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

Matthew D Johnston1, David F Anderson2, Gheorghe Craciun2,3, Robert Brijder4.   

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.

Entities:  

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

Mesh:

Substances:

Year:  2017        PMID: 28951955     DOI: 10.1007/s00285-017-1182-x

Source DB:  PubMed          Journal:  J Math Biol        ISSN: 0303-6812            Impact factor:   2.259


  9 in total

1.  Product-form stationary distributions for deficiency zero chemical reaction networks.

Authors:  David F Anderson; Gheorghe Craciun; Thomas G Kurtz
Journal:  Bull Math Biol       Date:  2010-03-20       Impact factor: 1.758

2.  A modified next reaction method for simulating chemical systems with time dependent propensities and delays.

Authors:  David F Anderson
Journal:  J Chem Phys       Date:  2007-12-07       Impact factor: 3.488

3.  Structural sources of robustness in biochemical reaction networks.

Authors:  Guy Shinar; Martin Feinberg
Journal:  Science       Date:  2010-03-12       Impact factor: 47.728

4.  A computational approach to persistence, permanence, and endotacticity of biochemical reaction systems.

Authors:  Matthew D Johnston; Casian Pantea; Pete Donnell
Journal:  J Math Biol       Date:  2015-05-19       Impact factor: 2.259

5.  Stochastic analysis of biochemical reaction networks with absolute concentration robustness.

Authors:  David F Anderson; Germán A Enciso; Matthew D Johnston
Journal:  J R Soc Interface       Date:  2014-02-12       Impact factor: 4.118

6.  Transient absolute robustness in stochastic biochemical networks.

Authors:  German A Enciso
Journal:  J R Soc Interface       Date:  2016-08       Impact factor: 4.118

7.  Translated chemical reaction networks.

Authors:  Matthew D Johnston
Journal:  Bull Math Biol       Date:  2014-03-08       Impact factor: 1.758

8.  A computational approach to extinction events in chemical reaction networks with discrete state spaces.

Authors:  Matthew D Johnston
Journal:  Math Biosci       Date:  2017-10-10       Impact factor: 2.144

9.  Dynamical properties of Discrete Reaction Networks.

Authors:  Loïc Paulevé; Gheorghe Craciun; Heinz Koeppl
Journal:  J Math Biol       Date:  2013-05-31       Impact factor: 2.259

  9 in total
  2 in total

1.  Discrepancies between extinction events and boundary equilibria in reaction networks.

Authors:  David F Anderson; Daniele Cappelletti
Journal:  J Math Biol       Date:  2019-06-22       Impact factor: 2.259

2.  Derivation of stationary distributions of biochemical reaction networks via structure transformation.

Authors:  Hyukpyo Hong; Jinsu Kim; M Ali Al-Radhawi; Eduardo D Sontag; Jae Kyoung Kim
Journal:  Commun Biol       Date:  2021-05-24
  2 in total

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