Literature DB >> 29335680

Flows, scaling, and the control of moment hierarchies for stochastic chemical reaction networks.

Eric Smith1, Supriya Krishnamurthy2.   

Abstract

Stochastic chemical reaction networks (CRNs) are complex systems that combine the features of concurrent transformation of multiple variables in each elementary reaction event and nonlinear relations between states and their rates of change. Most general results concerning CRNs are limited to restricted cases where a topological characteristic known as deficiency takes a value 0 or 1, implying uniqueness and positivity of steady states and surprising, low-information forms for their associated probability distributions. Here we derive equations of motion for fluctuation moments at all orders for stochastic CRNs at general deficiency. We show, for the standard base case of proportional sampling without replacement (which underlies the mass-action rate law), that the generator of the stochastic process acts on the hierarchy of factorial moments with a finite representation. Whereas simulation of high-order moments for many-particle systems is costly, this representation reduces the solution of moment hierarchies to a complexity comparable to solving a heat equation. At steady states, moment hierarchies for finite CRNs interpolate between low-order and high-order scaling regimes, which may be approximated separately by distributions similar to those for deficiency-zero networks and connected through matched asymptotic expansions. In CRNs with multiple stable or metastable steady states, boundedness of high-order moments provides the starting condition for recursive solution downward to low-order moments, reversing the order usually used to solve moment hierarchies. A basis for a subset of network flows defined by having the same mean-regressing property as the flows in deficiency-zero networks gives the leading contribution to low-order moments in CRNs at general deficiency, in a 1/n expansion in large particle numbers. Our results give a physical picture of the different informational roles of mean-regressing and non-mean-regressing flows and clarify the dynamical meaning of deficiency not only for first-moment conditions but for all orders in fluctuations.

Year:  2017        PMID: 29335680      PMCID: PMC5765883          DOI: 10.1103/PhysRevE.96.062102

Source DB:  PubMed          Journal:  Phys Rev E        ISSN: 2470-0045            Impact factor:   2.529


  10 in total

1.  Detecting autocatalytic, self-sustaining sets in chemical reaction systems.

Authors:  Wim Hordijk; Mike Steel
Journal:  J Theor Biol       Date:  2004-04-21       Impact factor: 2.691

2.  Nonequilibrium phase transitions in biomolecular signal transduction.

Authors:  Eric Smith; Supriya Krishnamurthy; Walter Fontana; David Krakauer
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2011-11-23

3.  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

4.  Intrinsic information carriers in combinatorial dynamical systems.

Authors:  Russ Harmer; Vincent Danos; Jérôme Feret; Jean Krivine; Walter Fontana
Journal:  Chaos       Date:  2010-09       Impact factor: 3.642

5.  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

6.  Comparison of different moment-closure approximations for stochastic chemical kinetics.

Authors:  David Schnoerr; Guido Sanguinetti; Ramon Grima
Journal:  J Chem Phys       Date:  2015-11-14       Impact factor: 3.488

7.  Understanding bistability in complex enzyme-driven reaction networks.

Authors:  Gheorghe Craciun; Yangzhong Tang; Martin Feinberg
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-30       Impact factor: 11.205

Review 8.  Stochastic thermodynamics, fluctuation theorems and molecular machines.

Authors:  Udo Seifert
Journal:  Rep Prog Phys       Date:  2012-11-20

9.  Generic strategies for chemical space exploration.

Authors:  Jakob L Andersen; Christoph Flamm; Daniel Merkle; Peter F Stadler
Journal:  Int J Comput Biol Drug Des       Date:  2014-05-28

10.  The stochastic behavior of a molecular switching circuit with feedback.

Authors:  Supriya Krishnamurthy; Eric Smith; David Krakauer; Walter Fontana
Journal:  Biol Direct       Date:  2007-05-31       Impact factor: 4.540

  10 in total
  1 in total

1.  Intrinsic and Extrinsic Thermodynamics for Stochastic Population Processes with Multi-Level Large-Deviation Structure.

Authors:  Eric Smith
Journal:  Entropy (Basel)       Date:  2020-10-07       Impact factor: 2.524

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.