Interbasin motion approach to dynamics of conformationally constrained peptides

Journal of Chemical Physics

Volumn 118, Issue 12, 2003, Pages 5673-5682

  Despa, Florin ^a   Fernández, Ariel ^a   Berry, R Stephen ^a   Levy, Yaakov ^b   Jortner, Joshua ^b  

^a THE UNIVERSITY OF CHICAGO   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; FRICTION; MOLECULAR DYNAMICS; PHASE TRANSITIONS; PROBABILITY DENSITY FUNCTION; RELAXATION PROCESSES; THERMODYNAMIC PROPERTIES;

INTERBASIN MOTION APPROACH; MARKOVIAN LIMIT; THERMAL BATH; TRANSITION STATE THEORY;

POLYPEPTIDES;

EID: 0344951101     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1554393     Document Type: Article

References (39)

1. Y. Levy and O. M. Becker, Phys. Rev. Lett. 81, 1126 (1998).
2. O. M. Becker, Y. Levy, and O. Ravitz, J. Phys. Chem. B 104, 2123 (2000).
3. Y. Levy and O. M. Becker, J. Chem. Phys. 114, 993 (2001).
4. Y. Levy, J. Jortner, and O. M. Becker, Proc. Natl. Acad. Sci. U.S.A. 98, 2188 (2001).
5. Y. Levy, J. Jortner, and O. M. Becker, J. Chem. Phys. 115, 10533 (2001).
6. J. C. Light, J. Chem. Phys. 40, 3221 (1995).
7. P. M. Rodger and M. G. Sceats, J. Chem. Phys. 83, 3358 (1985)
8. M. G. Sceats, Adv. Chem. Phys. 70, 357 (1988).
9. A. Nitzan, Adv. Chem. Phys. 70, 489 (1988).
10. (a) R. S. Berry and R. E. Kunz, Phys. Rev. Lett. 74, 3951 (1995)
11. (b) R. E. Kunz and R. S. Berry, J. Chem. Phys. 103, 1904 (1995)
12. (c) K. D. Ball, R. S. Berry, R. E. Kunz, F.-Y. Li, A. Proykova, and D. J. Wales, Science 271, 963 (1996).
13. R. E. Kunz, The Dynamics of First-Order Phase Transitions. In Mesoscopic and Macroscopic Equilibrium and Nonequilibrium Systems (Harri Deutsch, Frankfurt/M, 1995).
14. O. M. Becker and M. Karplus, J. Chem. Phys. 106, 1495 (1997).
15. D. J. Wales, M. A. Miller, and T. Walsh, Nature (London) 394, 758 (1998)
16. M. A. Miller and D. J. Wales, J. Chem. Phys. 111, 6610 (1999).
17. F. Despa and R. S. Berry, Eur. Phys. J. D 16, 55 (2001).
18. F. Despa and R. S. Berry, J. Chem. Phys. 115, 8274 (2001).
19. Y. Levy, J. Jortner, and R. S. Berry, Phys. Chem. Chem. Phys. 4, 5052 (2002).
20. F. Despa and R. S. Berry, in Proceedings of the 11th International Symposium on Small Particles and Inorganic Clusters, Strasbourg, 9-13 Sept. 2002
21. F. Despa and R. S. Berry, Eur. Phys. J. D (to be published).
22. E. I. Shakhnovich, Phys. Rev. Lett. 72, 3907 (1994).
23. P. G. Wolynes, J. N. Onuchic, and D. Thirumalai, Science 267, 1619 (1995).
24. R. S. Berry and R. E. Kunz, Phys. Rev. Lett. 74, 3951 (1995).
25. O. M. Becker, Proteins 27, 213 (1997).
26. G. H. Weiss, Adv. Chem. Phys. 13, 1 (1966).
27. T. Komatsuzaki and M. Nagaoka, J. Chem. Phys. 105, 10838 (1996)
28. T. Komatsuzaki and M. Nagaoka, Chem. Phys. Lett. 265, 91 (1997)
29. T. Komatsuzaki and R. S. Berry, J. Chem. Phys. 110, 9160 (1999)
30. T. Komatsuzaki and R. S. Berry, J. Mol. Struct. 506, 55 (2000)
31. T. Komatsuzaki and R. S. Berry, Phys. Chem. Chem. Phys. 1, 1387 (2000).
32. We have shown that, if we drop the assumption that the thermal bath responds instantly at the frequency of the reactive mode, at least inside the region with a rapid variation of the potential (the transition zone), then the memory effects change the barrier with [F. Despa and R. S. Berry (unpublished)]: R. S. Berry, J. Chem. Phys. 112, 5223 (2000).
33. G. R. Fleming, Chemical Applications of Ultrafast Spectroscopy (Oxford University Press, Oxford, 1986).
34. R. Golestanian and M. Kardar, Phys. Rev. Lett. 78, 3421 (1997).
35. L. Pollak, M. W. Tate, A. C. Finnefrock et al., Phys. Rev. Lett. 86, 4962 (2001).
36. A. Fernández and G. Appignanesi, Phys. Rev. Lett. 78, 2668 (1997)
37. A. Fernández, K. S. Kostov, and R. S. Berry, J. Chem. Phys. 112, 5223 (2000).
38. A. Fernández, J. Chem. Phys. 114, 2489 (2001).
39. A. Fernández, A. Colubri, and R. S. Berry, Physica A 307, 235 (2002).