Remarks on the chemical Fokker-Planck and Langevin equations: Nonphysical currents at equilibrium

被引:19
作者
Ceccato, Alessandro [1 ]
Frezzato, Diego [1 ]
机构
[1] Univ Padua, Dept Chem Sci, Via Marzolo 1, I-35131 Padua, Italy
关键词
STOCHASTIC SIMULATION; KINETICS; SYSTEMS;
D O I
10.1063/1.5016158
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The chemical Langevin equation and the associated chemical Fokker-Planck equation are wellknown continuous approximations of the discrete stochastic evolution of reaction networks. In this work, we show that these approximations suffer from a physical inconsistency, namely, the presence of nonphysical probability currents at the thermal equilibrium even for closed and fully detailedbalanced kinetic schemes. An illustration is given for a model case. Published by AIP Publishing.
引用
收藏
页数:8
相关论文
共 26 条
[1]   Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks [J].
Adalsteinsson, D ;
McMillen, D ;
Elston, TC .
BMC BIOINFORMATICS, 2004, 5 (1)
[2]  
[Anonymous], MATH PROGRAMMING STU
[3]   Efficient step size selection for the tau-leaping simulation method [J].
Cao, Y ;
Gillespie, DT ;
Petzold, LR .
JOURNAL OF CHEMICAL PHYSICS, 2006, 124 (04)
[4]   DIFFUSION MAPS, REDUCTION COORDINATES, AND LOW DIMENSIONAL REPRESENTATION OF STOCHASTIC SYSTEMS [J].
Coifman, R. R. ;
Kevrekidis, I. G. ;
Lafon, S. ;
Maggioni, M. ;
Nadler, B. .
MULTISCALE MODELING & SIMULATION, 2008, 7 (02) :842-864
[5]   Finite state projection based bounds to compare chemical master equation models using single-cell data [J].
Fox, Zachary ;
Neuert, Gregor ;
Munsky, Brian .
JOURNAL OF CHEMICAL PHYSICS, 2016, 145 (07)
[6]  
Gardiner C. W., 1990, HDB STOCHASTIC METHO
[7]   Stochastic simulation of chemical kinetics [J].
Gillespie, Daniel T. .
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, 2007, 58 (35-55) :35-55
[8]   Perspective: Stochastic algorithms for chemical kinetics [J].
Gillespie, Daniel T. ;
Hellander, Andreas ;
Petzold, Linda R. .
JOURNAL OF CHEMICAL PHYSICS, 2013, 138 (17)
[9]   Deterministic Limit of Stochastic Chemical Kinetics [J].
Gillespie, Daniel T. .
JOURNAL OF PHYSICAL CHEMISTRY B, 2009, 113 (06) :1640-1644
[10]   The chemical Langevin and Fokker-Planck equations for the reversible isomerization reaction [J].
Gillespie, DT .
JOURNAL OF PHYSICAL CHEMISTRY A, 2002, 106 (20) :5063-5071