Literature DB >> 31230146

Discrepancies between extinction events and boundary equilibria in reaction networks.

David F Anderson1, Daniele Cappelletti2,3.   

Abstract

Reaction networks are mathematical models of interacting chemical species that are primarily used in biochemistry. There are two modeling regimes that are typically used, one of which is deterministic and one that is stochastic. In particular, the deterministic model consists of an autonomous system of differential equations, whereas the stochastic system is a continuous-time Markov chain. Connections between the two modeling regimes have been studied since the seminal paper by Kurtz (J Chem Phys 57(7):2976-2978, 1972), where the deterministic model is shown to be a limit of a properly rescaled stochastic model over compact time intervals. Further, more recent studies have connected the long-term behaviors of the two models when the reaction network satisfies certain graphical properties, such as weak reversibility and a deficiency of zero. These connections have led some to conjecture a link between the long-term behavior of the two models exists, in some sense. In particular, one is tempted to believe that positive recurrence of all states for the stochastic model implies the existence of positive equilibria in the deterministic setting, and that boundary equilibria of the deterministic model imply the occurrence of an extinction event in the stochastic setting. We prove in this paper that these implications do not hold in general, even if restricting the analysis to networks that are bimolecular and that conserve the total mass. In particular, we disprove the implications in the special case of models that have absolute concentration robustness, thus answering in the negative a conjecture stated in the literature in 2014.

Keywords:  Absolute concentration robustness; Absorbing states; Continuous time Markov chains; Limit behaviour; Ordinary differential equations; Reaction networks

Year:  2019        PMID: 31230146     DOI: 10.1007/s00285-019-01394-9

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.  Lyapunov Functions, Stationary Distributions, and Non-equilibrium Potential for Reaction Networks.

Authors:  David F Anderson; Gheorghe Craciun; Manoj Gopalkrishnan; Carsten Wiuf
Journal:  Bull Math Biol       Date:  2015-09-16       Impact factor: 1.758

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.  Quasi-Steady-State Approximations Derived from the Stochastic Model of Enzyme Kinetics.

Authors:  Hye-Won Kang; Wasiur R KhudaBukhsh; Heinz Koeppl; Grzegorz A Rempała
Journal:  Bull Math Biol       Date:  2019-02-12       Impact factor: 1.758

5.  Non-explosivity of Stochastically Modeled Reaction Networks that are Complex Balanced.

Authors:  David F Anderson; Daniele Cappelletti; Masanori Koyama; Thomas G Kurtz
Journal:  Bull Math Biol       Date:  2018-08-16       Impact factor: 1.758

6.  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

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

Authors:  Matthew D Johnston; David F Anderson; Gheorghe Craciun; Robert Brijder
Journal:  J Math Biol       Date:  2017-09-26       Impact factor: 2.259

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.  Product-Form Stationary Distributions for Deficiency Zero Networks with Non-mass Action Kinetics.

Authors:  David F Anderson; Simon L Cotter
Journal:  Bull Math Biol       Date:  2016-10-27       Impact factor: 1.758

  9 in total
  2 in total

1.  A hidden integral structure endows absolute concentration robust systems with resilience to dynamical concentration disturbances.

Authors:  Daniele Cappelletti; Ankit Gupta; Mustafa Khammash
Journal:  J R Soc Interface       Date:  2020-10-28       Impact factor: 4.118

2.  Slack reactants: A state-space truncation framework to estimate quantitative behavior of the chemical master equation.

Authors:  Jinsu Kim; Jason Dark; German Enciso; Suzanne Sindi
Journal:  J Chem Phys       Date:  2020-08-07       Impact factor: 3.488

  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.