Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/american-physical-society-aps/path-summation-formulation-of-the-master-equation-wsx7VDpqZf
References (13)
-
S. Ozkan, S. Ozkan, K. Dill, I. Bahar, I. Bahar (2003)
Computing the transition state populations in simple protein models.Biopolymers, 68 1
-
D. Gillespie (1977)
Exact Stochastic Simulation of Coupled Chemical ReactionsThe Journal of Physical Chemistry, 81
-
D. Evans, D. Searles (2002)
The Fluctuation TheoremAdvances in Physics, 51
-
G. Fredrickson, H. Andersen (1985)
Facilitated kinetic Ising models and the glass transitionJournal of Chemical Physics, 83
-
P. Gaspard (2004)
Fluctuation theorem for nonequilibrium reactions.The Journal of chemical physics, 120 19
-
G. Crooks (1999)
Path-ensemble averages in systems driven far from equilibriumPhysical Review E, 61
-
A. Bortz, M. Kalos, J. Lebowitz (1975)
A new algorithm for Monte Carlo simulation of Ising spin systemsJournal of Computational Physics, 17
-
A. Kolomeisky, M. Fisher (2000)
Periodic sequential kinetic models with jumping, branching and deathsPhysica A-statistical Mechanics and Its Applications, 279
-
H. Stehfest (1970)
Algorithm 368: Numerical inversion of Laplace transforms [D5]Commun. ACM, 13
-
J. Lebowitz, H. Spohn (1998)
A Gallavotti–Cohen-Type Symmetry in the Large Deviation Functional for Stochastic DynamicsJournal of Statistical Physics, 95
-
C. Gardiner (1986)
Handbook of stochastic methods - for physics, chemistry and the natural sciences, Second Edition -
P. Bolhuis, D. Chandler, C. Dellago, P. Geissler (2002)
Transition path sampling: throwing ropes over rough mountain passes, in the dark.Annual review of physical chemistry, 53
-
R. Allen, P. Warren, P. Wolde (2004)
Sampling rare switching events in biochemical networks.Physical review letters, 94 1
- Publisher
- American Physical Society (APS)
- Copyright
- Copyright © 2006 The American Physical Society
- ISSN
- 1079-7114
- DOI
- 10.1103/PhysRevLett.96.210602
- pmid
- 16803224
- Publisher site
- See Article on Publisher Site
Abstract
Markovian dynamics, modeled by the kinetic master equation, has wide ranging applications in chemistry, physics, and biology. We derive an exact expression for the probability of a Markovian path in discrete state space for an arbitrary number of states and path length. The total probability of paths repeatedly visiting a set of states can be explicitly summed. The transition probability between states can be expressed as a sum over all possible paths connecting the states. The derived path probabilities satisfy the fluctuation theorem. The paths can be the starting point for a path space Monte Carlo procedure which can serve as an alternative algorithm to analyze pathways in a complex reaction network.
Journal
Physical Review Letters – American Physical Society (APS)
Published: Jun 2, 2006