We describe an exact approach for calculating transition probabilities and waiting times in finite-state discrete-time Markov processes. All the states and the rules for transitions between them must be known in advance. We can then calculate averages over a given ensemble of paths for both additive and multiplicative properties in a nonstochastic and noniterative fashion. In particular, we can calculate the mean first-passage time between arbitrary groups of stationary points for discrete path sampling databases, and hence extract phenomenological rate constants. We present a number of examples to demonstrate the efficiency and robustness of this approach.
REFERENCES
1.
G.
Bolch
, S.
Greiner
, H.
de Meer
, and K. S.
Trivedi
, Queueing Networks and Markov Chains
(Wiley
, New York
, 1998
).2.
G. R.
Grimmett
and D. R.
Stirzaker
, Probability and Random Processes
(Oxford University Press
, Oxford
, 2005
).3.
G. R.
Grimmett
and D. R.
Stirzaker
, One Thousand Exercises in Probability
(Oxford University Press
, Oxford
, 2005
).4.
D. J.
Wales
, Energy Landscapes: Applications to Clusters, Biomolecules and Glasses
(Cambridge University Press
, Cambridge
, 2003
).5.
D. J.
Wales
, Mol. Phys.
100
, 3285
(2002
).6.
N. G.
van Kampen
, Stochastic Processes in Physics and Chemistry
(Elsevier
, Amsterdam
, 1981
).7.
A. B.
Bortz
, M. H.
Kalos
, and J. L.
Lebowitz
, J. Comput. Phys.
17
, 10
(1975
).8.
K. A.
Fichthorn
and W. H.
Weinberg
, J. Chem. Phys.
95
, 1090
(1991
).9.
M. A.
Miller
, Ph.D. thesis Energy Landscapes and Dynamics of Model Clusters, University of Cambridge
, March 1999
.10.
M.
Block
, R.
Kunert
, E.
Schöll
, T.
Boeck
, and T.
Teubner
, New J. Phys.
6
, 166
(2004
).11.
D.
Mukherjee
, C. G.
Sonwane
, and M. R.
Zachariah
, J. Chem. Phys.
119
, 3391
(2003
).12.
F. M.
Bulnes
, V. D.
Pereyra
, and J. L.
Riccardo
, Phys. Rev. E
58
, 86
(1998
).13.
14.
D. J.
Wales
, Mol. Phys.
102
, 883
(2004
).15.
D. A.
Evans
and D. J.
Wales
, J. Chem. Phys.
121
, 1080
(2004
).16.
D. A.
Evans
and D. J.
Wales
, J. Chem. Phys.
119
, 9947
(2003
).17.
M. S.
Apaydin
, D. L.
Brutlag
, C.
Guestrin
, D.
Hsu
, and J.-C.
Latombe
, in RECOMB ’02: Proceedings of the Sixth Annual International Conference on Computational Biology
(ACM
, New York, NY
, 2002
), pp. 12
–21
.18.
M. S.
Apaydin
, C. E.
Guestrin
, C.
Varma
, D. L.
Brutlag
, and J.-C.
Latombe
, Bioinformatics
18
, S18
(2002
).19.
N.
Singhal
, C. D.
Snow
, and V. S.
Pande
, J. Chem. Phys.
121
, 415
(2004
).20.
21.
T. H.
Cormen
, C. E.
Leiserson
, R. L.
Rivest
, and C.
Stein
, Introduction to Algorithms
, 2nd ed. (MIT
, Cambridge, MA
, 2001
).22.
NIST,
Dictionary of Algorithms and Data Structures
, http://www.nist.gov/dads/23.
Wikipedia, the Free Encyclopedia, http://www.wikipedia.org/
24.
A.
Bar-Haim
and J.
Klafter
, J. Chem. Phys.
109
, 5187
(1998
).25.
M. A.
Novotny
, Phys. Rev. Lett.
74
, 1
(1995
).26.
27.
B. E.
Trumbo
, Relationship Between the Poisson and Exponential Distributions
, http://www.sci.csuhayward.edu/statistics/Resources/Essays/PoisExp.htm28.
T. F.
Middleton
, Ph.D. thesis, Energy Landscapes of Model Glasses, University of Cambridge
, March 2003
.29.
D. A.
Reed
and G.
Ehrlich
, Surf. Sci.
105
, 603
(1981
).30.
31.
M.
Raykin
, J. Phys. A
26
, 449
(1992
).32.
K. P. N.
Murthy
and K. W.
Kehr
, Phys. Rev. A
40
, 2082
(1989
).33.
S. A.
Trygubenko
, Ph.D. thesis, University of Cambridge
, January 2006
.34.
35.
I.
Goldhirsch
and Y.
Gefen
, Phys. Rev. A
33
, 2583
(1986
).36.
I.
Goldhirsch
and Y.
Gefen
, Phys. Rev. A
35
, 1317
(1987
).37.
E. W.
Weisstein
, Complete Graph
, MathWorld—A Wolfram Web Resource
, http://mathworld.wolfram.com/CompleteGraph.html38.
39.
40.
D.
Zheng
, Y.
Liu
, and Z. D.
Wang
, J. Phys. A
28
, L409
(1995
).41.
42.
P. C.
Bressloff
, V. M.
Dwyer
, and M. J.
Kearney
, J. Phys. A
29
, 1881
(1996
).43.
S.
Revathi
, V.
Balakrishnan
, S.
Lakshmibala
, and K. P. N.
Murthy
, Phys. Rev. E
54
, 2298
(1996
).44.
K.
Kim
, J. S.
Choi
, and Y. S.
Kong
, J. Phys. Soc. Jpn.
67
, 1583
(1998
).45.
K.
Kim
, G. H.
Kim
, and Y. S.
Kong
, Fractals
8
, 181
(2000
).46.
J.
Asikainen
, J.
Heinonen
, and T.
Ala-Nissila
, Phys. Rev. E
66
, 066706
(2002
).47.
P. A.
Pury
and M. O.
Cáceres
, J. Phys. A
36
, 2695
(2003
).48.
M.
Slutsky
, M.
Kardar
, and L. A.
Mirny
, Phys. Rev. E
69
, 061903
(2004
).49.
M.
Slutsky
and L. A.
Mirny
, Biophys. J.
87
, 4021
(2004
).50.
D.
ben Avraham
, S.
Redner
, and Z.
Cheng
, J. Stat. Phys.
56
, 437
(1989
).51.
52.
O.
Matan
and S.
Havlin
, Phys. Rev. A
40
, 6573
(1989
).53.
H.
Haucke
, S.
Washburn
, A. D.
Benoit
, C. P.
Umbach
, and R. A.
Webb
, Phys. Rev. B
41
, 12454
(1990
).54.
55.
S. H.
Noskowicz
and I.
Goldhirsch
, Phys. Rev. A
42
, 2047
(1990
).56.
S.
Revathi
and V.
Balakrishnan
, Phys. Rev. E
47
, 916
(1993
).57.
V.
Balakrishnan
and C.
Vandenbroeck
, Physica A
217
, 1
(1995
).58.
A. R.
Kerstein
and R. B.
Pandey
, Phys. Rev. A
35
, 3575
(1987
).59.
Y.
Gefen
and I.
Goldhirsch
, Phys. Rev. B
35
, 8639
(1987
).60.
61.
J. W.
Haus
and K. W.
Kehr
, Phys. Rep.
150
, 263
(1987
).62.
I. G. S. H.
Noskowicz
, J. Stat. Phys.
48
, 255
(1987
).63.
R.
Landauer
and M.
Buttiker
, Phys. Rev. B
36
, 6255
(1987
).64.
65.
J.
Koplik
, S.
Redner
, and D.
Wilkinson
, Phys. Rev. A
37
, 2619
(1988
).66.
67.
68.
A. E.
Conway
and N. D.
Georganas
, Queueing Networks: Exact Computational Algorithms
(MIT
, Cambridge, MA
, 1989
).69.
D.
Eppstein
, Z.
Galil
, and G. F.
Italiano
, in Algorithms and Theory of Computation Handbook
, edited by M. J.
Atallah
(CRC
, Boca Raton, FL
, 1999
), Chap. 8.70.
B. V.
Cherkassky
, A. V.
Goldberg
, and T.
Radzik
, in SODA ’94: Proceedings of the Fifth Annual ACM-SIAM Symposium on Discrete Algorithms
(Society for Industrial and Applied Mathematics
, Philadelphia, PA
, 1994
), pp. 516
–525
.71.
G.
Ramalingam
and T.
Reps
, J. Algorithms
21
, 267
(1996
).72.
73.
GNU General Public License
, http://www.gnu.org/copyleft/gpl.html74.
75.
DEBIAN—The Universal Operating System
, http://www.debian.org/76.
S. A.
Trygubenko
and D. J.
Wales
, J. Chem. Phys.
120
, 2082
(2004
).77.
78.
P.
Labastie
and R. L.
Whetten
, Phys. Rev. Lett.
65
, 1567
(1990
).79.
R. S.
Berry
, T. L.
Beck
, H. L.
Davis
, and J.
Jellinek
, Adv. Chem. Phys.
70B
, 75
(1988
).80.
J. P. K.
Doye
and C. P.
Massen
, J. Chem. Phys.
122
, 084105
(2005
).81.
© 2006 American Institute of Physics.
2006
American Institute of Physics
You do not currently have access to this content.