Literature DB >> 18266441

Incorporating postleap checks in tau-leaping.

David F Anderson1.   

Abstract

By explicitly representing the reaction times of discrete chemical systems as the firing times of independent, unit rate Poisson processes, we develop a new adaptive tau-leaping procedure. The procedure developed is novel in that accuracy is guaranteed by performing postleap checks. Because the representation we use separates the randomness of the model from the state of the system, we are able to perform the postleap checks in such a way that the statistics of the sample paths generated will not be biased by the rejections of leaps. Further, since any leap condition is ensured with a probability of one, the simulation method naturally avoids negative population values.

Year:  2008        PMID: 18266441     DOI: 10.1063/1.2819665

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  10 in total

1.  Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle.

Authors:  Zhen Liu; Yang Pu; Fei Li; Clifford A Shaffer; Stefan Hoops; John J Tyson; Yang Cao
Journal:  J Chem Phys       Date:  2012-01-21       Impact factor: 3.488

2.  Accurate stochastic simulation via the step anticipation tau-leaping (SAL) algorithm.

Authors:  Mary Sehl; Alexander V Alekseyenko; Kenneth L Lange
Journal:  J Comput Biol       Date:  2009-09       Impact factor: 1.479

3.  An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping.

Authors:  Wonryull Koh; Kim T Blackwell
Journal:  J Chem Phys       Date:  2011-04-21       Impact factor: 3.488

4.  Lazy Updating of hubs can enable more realistic models by speeding up stochastic simulations.

Authors:  Kurt Ehlert; Laurence Loewe
Journal:  J Chem Phys       Date:  2014-11-28       Impact factor: 3.488

Review 5.  Stochastic chemical kinetics : A review of the modelling and simulation approaches.

Authors:  Paola Lecca
Journal:  Biophys Rev       Date:  2013-07-30

6.  Perspective: Stochastic algorithms for chemical kinetics.

Authors:  Daniel T Gillespie; Andreas Hellander; Linda R Petzold
Journal:  J Chem Phys       Date:  2013-05-07       Impact factor: 3.488

7.  Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species-species modelling.

Authors:  J D Brunner; N Chia
Journal:  J R Soc Interface       Date:  2019-10-23       Impact factor: 4.118

8.  New "Tau-Leap" Strategy for Accelerated Stochastic Simulation.

Authors:  Doraiswami Ramkrishna; Che-Chi Shu; Vu Tran
Journal:  Ind Eng Chem Res       Date:  2014-09-22       Impact factor: 3.720

9.  A Comparison of Deterministic and Stochastic Modeling Approaches for Biochemical Reaction Systems: On Fixed Points, Means, and Modes.

Authors:  Sayuri K Hahl; Andreas Kremling
Journal:  Front Genet       Date:  2016-08-31       Impact factor: 4.599

10.  Quasi-Monte Carlo Methods Applied to Tau-Leaping in Stochastic Biological Systems.

Authors:  Casper H L Beentjes; Ruth E Baker
Journal:  Bull Math Biol       Date:  2018-05-25       Impact factor: 1.758

  10 in total

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