ANALYSIS OF BROWNIAN DYNAMICS SIMULATIONS OF REVERSIBLE BIMOLECULAR REACTIONS

被引：58

作者：

Lipkova, Jana ^{[1
]}

Zygalakis, Konstantinos C. ^{[2
]}

Chapman, S. Jonathan ^{[2
]}

Erban, Radek ^{[2
]}

机构：

[1] Charles Univ Prague, Fac Math & Phys, Prague 18675 8, Czech Republic

[2] Univ Oxford, Inst Math, Oxford OX1 3LB, England

来源：

SIAM JOURNAL ON APPLIED MATHEMATICS | 2011年 / 71卷 / 03期

基金：

欧洲研究理事会;

关键词：

Brownian dynamics; stochastic simulation algorithms; reaction-diffusion problems; reversible bimolecular reactions; STOCHASTIC SIMULATION; DIFFUSION; MOLECULE; KINETICS;

D O I：

10.1137/100794213

中图分类号：

O29 [应用数学];

学科分类号：

070104 ;

摘要：

A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the lambda-(rho) over bar model for irreversible bimolecular reactions which was introduced in [R. Erban and S. J. Chapman, Phys. Biol., 6 (2009), 046001]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated.

引用

页码：714 / 730

页数：17

共 50 条

[41] Brownian Dynamics Simulations of the Reactions of Hydrated Electrons with Components of DNAs and a DNA Double-Helix
Journal of Computational Chemistry, 18 (07):
[42] Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double-helix
Soirat, AJA
Wong, CF
Osman, R
Weinstein, H
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1997, 18 (07) : 888 - 901
[43] Brownian dynamics simulations of fluorescence fluctuation spectroscopy
Marisa Huertas de la Torre
Riccardo Forni
Giuseppe Chirico
European Biophysics Journal, 2001, 30 : 129 - 139
[44] Self-phoretic Brownian dynamics simulations
Roca-Bonet, Sergi
Ripoll, Marisol
EUROPEAN PHYSICAL JOURNAL E, 2022, 45 (03):
[45] Brownian dynamics simulations of filled particle gels
Wijmans, CM
Dickinson, E
JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS, 1998, 94 (01): : 129 - 137
[46] Brownian dynamics simulations of dilute polystyrene solutions
Li, L
Larson, RG
Sridhar, T
JOURNAL OF RHEOLOGY, 2000, 44 (02) : 291 - 322
[47] Brownian dynamics simulations of polyalanine in salt solutions
Yu, WB
Wong, CF
Zhang, J
JOURNAL OF PHYSICAL CHEMISTRY, 1996, 100 (37): : 15280 - 15289
[48] Brownian dynamics simulations of associating diblock copolymers
Cass, M. J.
Heyes, D. M.
English, R. J.
LANGMUIR, 2007, 23 (12) : 6576 - 6587
[49] Brownian dynamics simulations of attractive polymers in solution
Xiao, C
Heyes, DM
JOURNAL OF CHEMICAL PHYSICS, 2002, 117 (05): : 2377 - 2388
[50] Brownian dynamics simulations of fluorescence fluctuation spectroscopy
de la Torre, MH
Forni, R
Chirico, G
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2001, 30 (02): : 129 - 139

← 1 2 3 4 5 →