Literature DB >> 25569862

Multi-scale approach for simulating time-delay biochemical reaction systems.

Yuanling Niu1, Kevin Burrage2, Chengjian Zhang3.   

Abstract

This study presents a multi-scale approach for simulating time-delay biochemical reaction systems when there are wide ranges of molecular numbers. The authors construct a new efficient approach based on partitioning into slow and fast subsets in conjunction with predictor-corrector methods. This multi-scale approach is shown to be much more efficient than existing methods such as the delay stochastic simulation algorithm and the modified next reaction method. Numerical testing on several important problems in systems biology confirms the accuracy and computational efficiency of this approach.

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Year:  2015        PMID: 25569862      PMCID: PMC8687155          DOI: 10.1049/iet-syb.2013.0023

Source DB:  PubMed          Journal:  IET Syst Biol        ISSN: 1751-8849            Impact factor:   1.615


  17 in total

1.  Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays.

Authors:  Nicholas A M Monk
Journal:  Curr Biol       Date:  2003-08-19       Impact factor: 10.834

2.  Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator.

Authors:  Julian Lewis
Journal:  Curr Biol       Date:  2003-08-19       Impact factor: 10.834

3.  A multi-scaled approach for simulating chemical reaction systems.

Authors:  Kevin Burrage; Tianhai Tian; Pamela Burrage
Journal:  Prog Biophys Mol Biol       Date:  2004 Jun-Jul       Impact factor: 3.667

4.  Noise-induced cooperative behavior in a multicell system.

Authors:  Luonan Chen; Ruiqi Wang; Tianshou Zhou; Kazuyuki Aihara
Journal:  Bioinformatics       Date:  2005-03-17       Impact factor: 6.937

5.  Delay-induced stochastic oscillations in gene regulation.

Authors:  Dmitri Bratsun; Dmitri Volfson; Lev S Tsimring; Jeff Hasty
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

6.  Chemical models of genetic toggle switches.

Authors:  Patrick B Warren; Pieter Rein ten Wolde
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

7.  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

8.  Exact stochastic simulation of coupled chemical reactions with delays.

Authors:  Xiaodong Cai
Journal:  J Chem Phys       Date:  2007-03-28       Impact factor: 3.488

9.  A tunable synthetic mammalian oscillator.

Authors:  Marcel Tigges; Tatiana T Marquez-Lago; Jörg Stelling; Martin Fussenegger
Journal:  Nature       Date:  2009-01-15       Impact factor: 49.962

10.  Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop.

Authors:  Hiromi Hirata; Shigeki Yoshiura; Toshiyuki Ohtsuka; Yasumasa Bessho; Takahiro Harada; Kenichi Yoshikawa; Ryoichiro Kageyama
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

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