Transition path sampling: Throwing ropes over rough mountain passes, in the dark

Annual Review of Physical Chemistry

Volumn 53, Issue , 2002, Pages 291-318

  Bolhuis, Peter G ^a   Chandler, David ^b   Dellago, Christoph ^c   Geissler, Phillip L ^d  

^a Department of Chemical Engineering ^*  (Netherlands)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF ROCHESTER   (United States)

^d HARVARD UNIVERSITY   (United States)

Author keywords

Basins of attraction; Complex systems; Kinetics; Potential surfaces; Rare events; Trajectories; Transition states

Indexed keywords

EID: 0036424048     PISSN: 0066426X     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.physchem.53.082301.113146     Document Type: Article

References (73)

1. Dellago C, Bolhuis PG, Csajka FS, Chandler D. 1998. J. Chem. Phys. 108:1964-77
2. Dellago C, Bolhuis PG, Chandler D. 1998. J. Chem. Phys. 108:9236-45
3. Bolhuis PG, Dellago C, Chandler D. 1998. Faraday Discuss. 110:421-36
4. Dellago C, Bolhuis PG, Chandler D. 1999. J. Chem. Phys. 110:6617-25
5. Geissler PL, Dellago C, Chandler D. 1999. Phys. Chem. Chem. Phys. 1:1317-22
6. Geissler PL, Dellago C, Chandler D. 1999. J. Phys. Chem. B 103:3706-10
7. Crooks GE. 1999. Excursions in statistical dynamics. PhD thesis. Univ. Calif., Berkeley. 107 pp.
8. Bolhuis PG, Chandler D. 2000. J. Chem. Phys. 113:8154-60
9. Bolhuis PG, Dellago C, Chandler D. 2000. Proc. Natl. Acad. Sci. USA 97:5877-82
10. Vlugt TJH, Dellago C, Smit B. 2000. J. Chem. Phys. 113:8791-99
11. Geissler PL, Dellago C, Chandler D, Hutter J, Parrinello M. 2000. Chem. Phys. Lett. 321:225-30
12. Geissler PL, Chandler D. 2000. J. Chem. Phys. 113:9759-65
13. Geissler PL, Dellago C, Chandler D, Hutter J, Parrinello M. 2001. Science 291: 2121-24
14. Crooks GE, Chandler D. 2001. Phys. Rev. E 64:026109
15. Anderson JB. 1973. J. Chem. Phys. 58: 4684-92
16. Bennett CH. 1977. In Algorithms for Chemical Computations, ed. RE Christoffersen, pp. 63-97. Washington, DC: Am. Chem. Soc.
17. Chandler D. 1978. J. Chem. Phys. 68:2959-70
18. Anderson JB. 1995. Adv. Chem. Phys. 91:381-431
19. Chandler D. 1998. In Classical and Quantum Dynamics in Condensed Phase Simulations, ed. BJ Berne, G Ciccotti, DF Coker, pp. 3-23. Singapore: World Sci. In this book version of this article, the numbering of equations does not match that of the text. A corrected version can be obtained as a PDF file at http://gold.cchem.berkeley.edu/ bibliography.html.
20. Frenkel D, Smit B. 1996. Understanding Molecular Simulation: From Algorithms to Applications, San Diego, CA: Academic
21. Chandler D. 1987. Introduction to Modern Statistical Mechanics. New York: Oxford Univ. Press
22. Cerjan CJ, Miller WH. 1981. J. Chem. Phys. 75:2800-6
23. Wales D, Miller MA, Walsh TR. 1998. Nature 394:758-60
24. Binder K, Heermann DW. 1992. Monte Carlo Methods in Statistical Physics: An Introduction. New York: Springer-Verlag
25. Newman MEJ, Barkema GT. 1999. Monte Carlo Methods in Statistical Physics. New York: Oxford Univ. Press
26. Pratt LR. 1986. J. Chem. Phys. 85:5045-48
27. Toda M, Kubo R, Saito N. 1995. Statistical Physics I. New York: Springer. 2nd. ed.
28. Zwanzig R. 2001. Nonequilibrium Statistical Mechanics. New York: Oxford Univ. Press
29. Elber R, Karplus M. 1987. Chem. Phys. Lett. 139:375-80
30. Elber R, Meller J, Olender R. 1999. J. Phys. Chem. B 103:899-911
31. Henkelman G, Johannesson G, Jonsson H. 2000. In Progress on Theoretical Chemistry and Physics, ed. SD Schwartz. Dordrecht, Netherlands: Kluwer
32. Voter AF. 1997. Phys. Rev. Lett. 78:3908-11
33. Grubmüller H. 1995. Phys. Rev. E 52:2893-906
34. Gillilan RE, Wilson KR. 1996. J. Chem. Phys. 105:9299-315
35. Gillilan RE. 1992. J. Chem. Phys. 97:1757-72
36. Sevick EM, Bell AT, Theodorou DN. 1993. J. Chem. Phys. 98:3196-212
37. Eastman P, Grönbech-Jensen N, Doniach S. 2001. J. Chem. Phys. 114:3823-41
38. Zuckerman DM, Woolf TB. 1999 J. Chem. Phys. 111:9475-84
39. Marx D, Tuckerman ME, Hutter J, Parrinello M. 1999. Nature 397:601-4
40. Schmitt UW, Voth GA. 1999. J. Chem. Phys. 111:9361-81
41. Day TJF, Schmitt UW, Voth GA. 2000. J. Am. Chem. Soc. 122:12027-28
42. Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich EI. 1998. J. Chem. Phys. 108:334-50
43. Bryant Z, Pande VS, Rokhsar DS. 2000. Biophys. J. 108:584-89
44. Klosek MM, Matkowsky BJ, Schuss Z. 1991. Ber. Bunsenges. Phys. Chem. 95: 331-37
45. Belch AC, Berkowitz M, McCammon JA. 1986. J. Am. Chem. Soc. 108:1755-61
46. Guardia E, Rey R, Padró JA. 1991. Chem Phys. 155:187-95
47. Karim OA, McCammon JA. 1986. J. Am. Chem. Soc. 108:1762-66
48. Rey R, Guardia E. 1992. J. Phys. Chem. 96:4712-18
49. Truhlar DG, Garrett BC. 2000. J. Phys. Chem. B 104:1069-72
50. Gasser U, Weeks ER, Schofield A, Pusey PN, Weitz DA. 2000. Science 292:258-62
51. Geissler PL, Van Voorhis T, Dellago C. 2000. Chem. Phys. Lett. 324:149-55
52. Car R, Parrinello M. 1985. Phys. Rev. Lett. 55:2471-74
53. Parrinello M. 1997. Solid State Commun. 102:107-20
54. Rice OK, Ramsperger HC. 1927. J. Am. Chem. Soc. 49:1617-29
55. Rice OK, Ramsperger HC. 1928. J. Am. Chem. Soc. 50:617-20
56. Kassel LS. 1928. J. Phys. Chem. 32:225-42
57. Marcus R, Rice OK. 1951. J. Phys. Colloid Chem. 55:894-908
58. Laria D, Rodriguez J, Dellago C, Chandler D. 2001. J. Phys. Chem. A 105:2646-51
59. Frantz DD, Freeman DL, Doll JD. 1990. J. Chem. Phys. 93:2769-84
60. Berg BA, Neuhaus T. 1992. Phys. Rev. Lett. 68:9-12
61. Geyer CJ. 1995. J. Am. Stat. Assoc. 80:909-20
62. Vlugt TJH, Smit B. 2001. Phys. Chem. Commun. 2:1-7
63. Pande VS, Grosberg AYu, Rokhsar DS, Tanaka T. 1998. Curr. Opin. Struct. Biol. 8:68-79
64. Karplus M. 2000. J. Phys. Chem. B 104:11-27
65. Eigen M, de Maeyer L. 1955. Z. Elektrochem. 59:986-93
66. Eigen M. 1964. Angew. Chem. Int. Edit. 3:1-19
67. Tuckerman M, Laasonen K, Sprik M, Parrinello M. 1995. J. Chem. Phys. 103: 150-61
68. Agmon N. 1999. Isr. J. Chem. 39:493-502
69. Bagchi B, Oxtoby DW, Fleming GR. 1984. Chem. Phys. 86:257-67
70. Mardia KV, Kent JT, Bibby JM. 1979. Multivariate Analysis. London: Academic
71. Tenenbaum JB, de Silva V, Langford JC. 2000. Science 290:2319-23
72. Roweis ST, Saul LK. 2000. Science 290: 2323-26
73. Miller WH. 1998. Faraday Discuss. 110:1-21