A differential fluctuation theorem

Journal of Physical Chemistry B

Volumn 112, Issue 19, 2008, Pages 6168-6174

  Maragakis, Paul ^a,c   Spichty, Martin ^b   Karplus, Martin ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITÉ LOUIS PASTEUR   (France)

^c D E SHAW RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICS; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY; RISK ASSESSMENT; THERMODYNAMICS;

ALANINE DIPEPTIDE; CONFORMATIONAL FREE-ENERGY; FLUCTUATION THEOREM; FREE-ENERGY DIFFERENCE; GENERALIZED COORDINATES; LABORATORY EXPERIMENTS; MODEL SYSTEMS; MOLECULAR DYNAMICS SIMULATIONS; NON-EQUILIBRIUM; NON-EQUILIBRIUM THERMODYNAMICS; NONEQUILIBRIUM WORK;

FREE ENERGY;

ALANINE; DIPEPTIDE;

ARTICLE; BAYES THEOREM; CHEMISTRY; COMPUTER SIMULATION; THERMODYNAMICS;

ALANINE; BAYES THEOREM; COMPUTER SIMULATION; DIPEPTIDES; THERMODYNAMICS;

EID: 44949159733     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp077037r     Document Type: Article

References (64)

1. Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690-2693.
2. Jarzynski, C. Phys. Rev. E 1997, 56, 5018-5035.
3. Crooks, G. E. J. Stat. Phys. 1998, 90, 1481-1487.
4. Crooks, G. E. Phys. Rev. E 1999, 60, 2721-2726.
5. Crooks, G. E. Phys. Rev. E 2000, 67, 2361-2366.
6. Jarzynski, C. J. Stat. Phys. 2000, 98, 77-102.
7. Evans, D.; Cohen, E.; Morriss, G. Phys. Rev. Lett. 1993, 71, 2401-2404.
8. Evans, D. J.; Searles, D. J. Phys. Rev. E 1994, 50, 1645-1648.
9. Galavotti, G. J. Stat. Phys. 1995, 78, 1571-1589.
10. Leff, H.; Rex, A. Maxwell's Demon: Entropy, Information, Computing; Princeton University Press: Princeton, NJ, 1990.
11. Loschmidt, J. Sitzungsber. Kais. Akad. Wiss. Wien, Math.-Naturwiss. Kl. 1876, 73, 128-142.
12. Jarzynski, C. J. Stat. Phys. 1999, 96, 415-427.
13. Prigogine, I. Science 1978, 201, 777-785.
14. Hummer, G.; Szabo, A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 3658-3661.
15. Hummer, G.; Szabo, A. Acc. Chem. Res. 2005, 38, 504-513.
16. Liphardt, J.; Dumont, S.; Smith, S. B.; Tinoco, I.; Bustamante, C. Science 2002, 296, 1832-1835.
17. Collin, D.; Ritort, F.; Jarzynski, C.; Smith, S. B.; Tinoco, I.; Bustamante, C. Nature 2005, 437, 231-234.
18. Bennett, C. H. J. Comput. Phys. 1976, 22, 245-268.
19. Shirts, M. R.; Bair, E.; Hooker, G.; Pande, V. S. Phys. Rev. Lett. 2003, 91, 140601.
20. Maragakis, P.; Spichty, M.; Karplus, M. Phys. Rev. Lett. 2006, 96, 100602.
21. Maragakis, P.; Ritort, F.; Bustamante, C.; Karplus, M.; Crooks, G. E. ArXiv e-prints 2007, 707, http://arxiv.org/pdf/0707.0089.
22. Rossky, P. J.; Karplus, M. J. Am. Chem. Soc. 1979, 101, 1913-1937.
23. Brady, J.; Karplus, M. J. Am. Chem. Soc. 1985, 107, 6103-6105.
24. Pettitt, B. M.; Karplus, M. Chem. Phys. Lett. 1985, 121, 194-201.
25. Mezei, M. J. Comput. Phys. 1987, 68, 237-248.
26. Anderson, A. G.; Hermans, J. Proteins 1988, 3, 262-265.
27. Tobias, D.; Brooks, C., III. J. Phys. Chem. 1992, 96, 3864-3870.
28. Olender, R.; Elber, R. J. Chem. Phys. 1996, 105, 9299-9315.
29. Bartels, C.; Karplus, M. J. Comput. Chem. 1997, 18, 1450-1462.
30. MacKerell, A. D., Jr.; Bashford, D.; Bellott, R. L.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
31. Apostolakis, J.; Ferrara, P.; Caflisch, A. J. Chem. Phys. 1999, 110, 2099-2108.
32. Smith, P. E. J. Chem. Phys. 1999, 111, 5568-5579.
33. Wang, J. M.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
34. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. J. Phys. Chem. B 2001, 105, 6474-6487.
35. Ren, P. Y.; Ponder, J. W. J. Comput. Chem. 2002, 23, 1497-1506.
36. Hu, H.; Eistner, M.; Hermans, J. Proteins 2003, 50, 451-463.
37. MacKerell, A. D.; Feig, M.; Brooks, C. L. J. Comput. Chem. 2004, 25, 1400-1415.
38. Ren, W.; Vanden-Eijnden, E.; Maragakis, P.; Weinan, E. J. Chem. Phys. 2005, 123, 134109.
39. Rosso, L.; Abrams, J. B.; Tuckerman, M. E. J. Phys. Chem. B 2005, 109, 4162-4167.
40. Ensing, B.; De Vivo, M.; Liu, Z.; Moore, P.; Klein, M. L. Acc. Chem. Res. 2006, 39, 73-81.
41. van der Vaart, A.; Karplus, M. J. Chem. Phys. 2007, 126, 164106.
42. Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103.
43. Jaynes, E. T. Probability Theory: The Logic of Science; Cambridge University Press: New York, 2003.
44. Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300-313.
45. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562-12566.
46. Earl, D. J.; Deem, M. W. Phys. Chem. Chem. Phys. 2005, 7, 3910-3916.
47. Geyer, C. J. Markov chain Monte Carlo maximum likelihood. In Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface; Keramidas, E. M., Ed.; Interface Foundation: Fairfax Station, 1991.
48. Yamada, T.; Kawasaki, K. Prog. Theor. Phys. 1967, 38, 1031-1051.
49. Morriss, G.; Evans, D. Phys. Rev. A 1988, 37, 3605-3608.
50. Adib, A. B. J. Chem. Phys. 2006, 124, 144111.
51. Paramore, S.; Ayton, G. S.; Voth, G. A. J. Chem. Phys. 2007, 126, 051102.
52. Ferrenberg, A.; Swendsen, R. Phys. Rev. Lett. 1989, 63, 1195-1198.
53. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
54. Reiher, W., III. Theoretical studies of hydrogen bonding. Ph.D. Thesis, Department of Chemistry, Harvard University, 1985.
55. Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902-1921.
56. Schaefer, M.; Karplus, M. J. Phys. Chem. 1996, 100, 1578-1599.
57. Dellago, C.; Bolhuis, P. G.; Geissler, P. L. Adv. Chem. Phys. 2002, 123, 1-78.
58. Sun, S. X. J. Chem. Phys. 2003, 118, 5769-5775.
59. Ytreberg, F. M.; Zuckerman, D. M. J. Chem. Phys. 2004, 120, 10876-10879.
60. Atilgan, E.; Sun, S. X. J. Chem. Phys. 2004, 121, 10392-10400.
61. Ritort, F. J. Phys.: Condens. Matter 2006, 18, R531-R583.
62. Ernst, R.; G., B.; A, W. Principles of Nuclear Magnetic Resonances in One and Two Dimensions; Clarendon: Oxford, 1987.
63. Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14190-14196.
64. Although, in principle, the term "identity" would be appropriate for both our and the Crooks fluctuation theorem, we use the term "theorem" in anticipation of the close connection between these two relations.