Stochastic reaction-diffusion simulation with MesoRD

被引：244

作者：

Hattne, J ^{[1
]}

Fange, D ^{[1
]}

Elf, J ^{[1
]}

机构：

[1] Uppsala Univ, Dept Cell & Mol Biol, BMC, S-75124 Uppsala, Sweden

来源：

BIOINFORMATICS | 2005年 / 21卷 / 12期

关键词：

D O I：

10.1093/bioinformatics/bti431

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

MesoRD is a tool for stochastic simulation of chemical reactions and diffusion. In particular, it is an implementation of the next subvolume method, which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation.

引用

页码：2923 / 2924

页数：2

共 14 条

[1]

Ander M., 2004, Systems Biology, V1, P129, DOI 10.1049/sb:20045017

[2] Stochastic simulation of chemical reactions with spatial resolution and single molecule detail [J].

Andrews, SS ;

Bray, D .

PHYSICAL BIOLOGY, 2004, 1 (03) :137-151

[3] MICROSCOPIC SIMULATIONS OF CHEMICAL INSTABILITIES [J].

Baras, F. ;

Mansour, M. Malek .

ADVANCES IN CHEMICAL PHYSICS <D>, 1997, 100 :393-474

[4]

ELF J, 2004, SYST BIOL, V2, P230, DOI DOI 10.1049/SB:20045021

[5] Efficient exact stochastic simulation of chemical systems with many species and many channels [J].

Gibson, MA ;

Bruck, J .

JOURNAL OF PHYSICAL CHEMISTRY A, 2000, 104 (09) :1876-1889

[6] GENERAL METHOD FOR NUMERICALLY SIMULATING STOCHASTIC TIME EVOLUTION OF COUPLED CHEMICAL-REACTIONS [J].

GILLESPIE, DT .

JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (04) :403-434

[7] Dynamic structures in Escherichia coli: Spontaneous formation of MinE rings and MinD polar zones [J].

Huang, KC ;

Meir, Y ;

Wingreen, NS .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (22) :12724-12728

[8] The systems biology markup language (SBML):: a medium for representation and exchange of biochemical network models [J].

Hucka, M ;

Finney, A ;

Sauro, HM ;

Bolouri, H ;

Doyle, JC ;

Kitano, H ;

Arkin, AP ;

Bornstein, BJ ;

Bray, D ;

Cornish-Bowden, A ;

Cuellar, AA ;

Dronov, S ;

Gilles, ED ;

Ginkel, M ;

Gor, V ;

Goryanin, II ;

Hedley, WJ ;

Hodgman, TC ;

Hofmeyr, JH ;

Hunter, PJ ;

Juty, NS ;

Kasberger, JL ;

Kremling, A ;

Kummer, U ;

Le Novère, N ;

Loew, LM ;

Lucio, D ;

Mendes, P ;

Minch, E ;

Mjolsness, ED ;

Nakayama, Y ;

Nelson, MR ;

Nielsen, PF ;

Sakurada, T ;

Schaff, JC ;

Shapiro, BE ;

Shimizu, TS ;

Spence, HD ;

Stelling, J ;

Takahashi, K ;

Tomita, M ;

Wagner, J ;

Wang, J .

BIOINFORMATICS, 2003, 19 (04) :524-531

[9] EFFECTS OF DIFFUSION ON FLUCTUATIONS IN OPEN CHEMICAL SYSTEMS [J].

KURAMOTO, Y .

PROGRESS OF THEORETICAL PHYSICS, 1974, 52 (02) :711-713

[10] RENORMALIZATION-GROUP STUDY OF THE A+B-]PHI DIFFUSION-LIMITED REACTION [J].

LEE, BP ;

CARDY, J .

JOURNAL OF STATISTICAL PHYSICS, 1995, 80 (5-6) :971-1007

← 1 2 →