Equilibrium time correlation functions from irreversible transformations in trajectory space

Journal of Physical Chemistry B

Volumn 108, Issue 21, 2004, Pages 6667-6672

  Geissler, Phillip L ^a,c   Dellago, Christoph ^b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF VIENNA   (Austria)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CORRELATION METHODS; FREE ENERGY; FUNCTIONS; ISOMERIZATION; MATHEMATICAL TRANSFORMATIONS; PHASE TRANSITIONS; POTENTIAL ENERGY; PROBABILITY; RATE CONSTANTS; REACTION KINETICS; STATISTICAL MECHANICS; THERMODYNAMICS;

EQUILIBRIUM FLUCTUATIONS; IRREVERSIBLE TRANSFORMATIONS; TIME CORRELATION FUNCTIONS; TRANSITION PATH;

TRAJECTORIES;

EID: 2942562278     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp037211l     Document Type: Article

References (35)

1. Anderson, J. B. J. Chem. Phys. 1973, 58, 4684. Bennett, C. H. In Algorithms for Chemical Computations; Christoffersen R. E., Ed.: American Chemical Society: Washington, DC, 1977; pp 63-97. Chandler, D. J. Chem. Phys. 1978, 68, 2959.
2. Anderson, J. B. J. Chem. Phys. 1973, 58, 4684. Bennett, C. H. In Algorithms for Chemical Computations; Christoffersen R. E., Ed.: American Chemical Society: Washington, DC, 1977; pp 63-97. Chandler, D. J. Chem. Phys. 1978, 68, 2959.
3. Anderson, J. B. J. Chem. Phys. 1973, 58, 4684. Bennett, C. H. In Algorithms for Chemical Computations; Christoffersen R. E., Ed.: American Chemical Society: Washington, DC, 1977; pp 63-97. Chandler, D. J. Chem. Phys. 1978, 68, 2959.
4. Doye, J. P. K.; Wales, D. J. Z. Phys. D 1997, 40, 194.
5. Elber, R.; Karplus, M. Chem. Phys. Lett. 1987, 139, 375. Elber, R.; Meller, J.; Olender, R. J. Phys. Chem. B 1999, 103, 899.
6. Elber, R.; Karplus, M. Chem. Phys. Lett. 1987, 139, 375. Elber, R.; Meller, J.; Olender, R. J. Phys. Chem. B 1999, 103, 899.
7. Henkelman, G.; Johannesson, G.; Jónsson, H. In Progress on Theoretical Chemistry and Physics; Schwartz, S. D., Ed.; Kluwer Academic Publishers: Dordrecht, The Netherlands. 2000.
8. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562.
9. Voter, A. F.; Montalenti, F.; German, T. C. Annu. Rev. Mater. Res. 2002, 32, 321.
10. Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. J. Chem. Phys. 1998, 108, 1964.
11. Ren, W.; E, W.; Vanden-Eijnden, E. Phys. Rev. B 2002, 66, 052301.
12. Corcelli, S. A.; Rahman, J. A.; Tully, J. C. J. Chem. Phys. 2003, 118, 1085.
13. Chandler, D. Introduction to Modern Statistical Mechanics; Oxford University Press: Oxford, U.K., 1987.
14. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Annu. Rev. Phys. Chem. 2002, 53, 291.
15. Dellago, C.; Bolhuis, P. G.; Geissler, P. L. Adv. Chem. Phys. 2002, 123, 1.
16. Geissler, P. L.; Dellago, C.; Chandler, D.; Hutter, J.; Parrinello, M. Science 2001, 291, 2121.
17. Bolhuis, P. G.; Dellago, C.; Chandler, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5877.
18. Ensing, B.; Baerends, E. J. J. Phys. Chem. 2002, 106, 7902.
19. Rodriguez, J.; Moreina, G.; Laria, D. Chem. Phys. Lett. 2002, 356, 147.
20. Dellago, C.; Bolhuis, P. G.; Chandler, D. J. Chem. Phys. 1999, 110, 6617.
21. Vlugt, T. J. H.; Smit, B. Phys. Chem. Commun. 2001, 2, 11.
22. Dellago, C.; Geissler, P. L. Proceedings of "The Monte Carlo Method in the Physical Sciences: Celebrating the 50th anniversary of the Metropolis algorithm"; AIP Conference Proceedings; AIP: Melville, NY, 2003; Vol. 690, p 192.
23. Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690.
24. Crooks, G. E. J. Stat. Phys. 1998, 90, 1481.
25. The cancellation of partition functions leading to eq 14 is made possible by defining an energy function that preserves the form of a canonical distribution. A formally analogous cancellation has been described for kinetic Monte Carlo trajectories biased in such a way that only the endpoint probabilities are modified [Cai, W.; Kalos, M. H.; de Koning, M.; Bulatov, V. V. Phys. Rev. E 2002, 66, 046703].
26. Straub, J. E.; Borkovec, M.; Berne, B. J. J. Chem. Phys. 1988, 89, 4833.
27. Metropolis, N.; Metropolis, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1953, 21, 1087.
28. Dellago, C.; Bolhuis, P. G.; Chandler, D. J. Chem. Phys. 1999, 110, 6617.
29. Dellago, C.; Geissler, P. L. Proceedings of "The Monte Carlo Method in the Physical Sciences: Celebrating the 50th anniversary of the Metropolis algorithm"; AIP Conference Proceedings; AIP: Melville, NY, 2003; Vol. 690.
30. Hummer, G.; Szabo, A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 3658; Liphardt, J.; Dumont, S.; Smith, S. B.; Tinoco, I.; Bustamante, C. Science 2002, 296, 1832.
31. Hummer, G.; Szabo, A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 3658; Liphardt, J.; Dumont, S.; Smith, S. B.; Tinoco, I.; Bustamante, C. Science 2002, 296, 1832.
32. Hendrix, D. A.; Jarzynski, C. J. Chem. Phys. 2001, 114, 5974.
33. Hummer, G. J. Chem. Phys. 2001, 114, 7330.
34. Gore, J.; Ritort, F.; Bustamante, C. Proc. Natl. Acad. Sci. 2003, 100, 12564.
35. Sun, S. X. J. Chem. Phys. 2003, 118, 5769.