Literature DB >> 25215268

Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks.

Patrick Smadbeck1, Yiannis N Kaznessis1.   

Abstract

Stochasticity in the dynamics of small reacting systems requires discrete-probabilistic models of reaction kinetics instead of traditional continuous-deterministic ones. The master probability equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks. With the first solution of chemical master equations, a wide range of experimental observations of small-system interactions may be mathematically conceptualized.

Entities:  

Keywords:  Chemical Master Equation; Closure Scheme; Stochastic Reaction Networks

Year:  2014        PMID: 25215268      PMCID: PMC4157358          DOI: 10.1016/j.coche.2014.07.001

Source DB:  PubMed          Journal:  Curr Opin Chem Eng        ISSN: 2211-3398            Impact factor:   5.163


  23 in total

1.  Binomial leap methods for simulating stochastic chemical kinetics.

Authors:  Tianhai Tian; Kevin Burrage
Journal:  J Chem Phys       Date:  2004-12-01       Impact factor: 3.488

2.  Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method.

Authors:  Abhijit Chatterjee; Kapil Mayawala; Jeremy S Edwards; Dionisios G Vlachos
Journal:  Bioinformatics       Date:  2005-02-04       Impact factor: 6.937

3.  Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates.

Authors:  Weinan E; Di Liu; Eric Vanden-Eijnden
Journal:  J Chem Phys       Date:  2005-11-15       Impact factor: 3.488

4.  The finite state projection algorithm for the solution of the chemical master equation.

Authors:  Brian Munsky; Mustafa Khammash
Journal:  J Chem Phys       Date:  2006-01-28       Impact factor: 3.488

5.  Moment-closure approximations for mass-action models.

Authors:  C S Gillespie
Journal:  IET Syst Biol       Date:  2009-01       Impact factor: 1.615

6.  proTeOn and proTeOff, new protein devices that inducibly activate bacterial gene expression.

Authors:  Katherine Volzing; Konstantinos Biliouris; Yiannis N Kaznessis
Journal:  ACS Chem Biol       Date:  2011-08-18       Impact factor: 5.100

7.  Model reduction of multiscale chemical langevin equations: a numerical case study.

Authors:  Vassilios Sotiropoulos; Marie-Nathalie Contou-Carrere; Prodromos Daoutidis; Yiannis N Kaznessis
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2009 Jul-Sep       Impact factor: 3.710

8.  SynBioSS: the synthetic biology modeling suite.

Authors:  Anthony D Hill; Jonathan R Tomshine; Emma M B Weeding; Vassilios Sotiropoulos; Yiannis N Kaznessis
Journal:  Bioinformatics       Date:  2008-08-30       Impact factor: 6.937

9.  Stochastic model reduction using a modified Hill-type kinetic rate law.

Authors:  Patrick Smadbeck; Yiannis Kaznessis
Journal:  J Chem Phys       Date:  2012-12-21       Impact factor: 3.488

10.  Multiscale Hy3S: hybrid stochastic simulation for supercomputers.

Authors:  Howard Salis; Vassilios Sotiropoulos; Yiannis N Kaznessis
Journal:  BMC Bioinformatics       Date:  2006-02-24       Impact factor: 3.169

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