Thermodynamics of a conformational change using a random walk in energy-reaction coordinate space: Application to methane dimer hydrophobic interactions

Journal of Chemical Physics

Volumn 130, Issue 7, 2009, Pages

  Morozov, A N ^a,b,c   Lin, S H ^a,b  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^b INSTITUTE OF ATOMIC AND MOLECULAR SCIENCES   (Taiwan)

^c INSTITUTE OF SURFACE CHEMISTRY   (Ukraine)

Author keywords

[No Author keywords available]

Indexed keywords

CONVERGENCE OF NUMERICAL METHODS; ENTROPY; LEARNING ALGORITHMS; METAL RECOVERY; METHANE; MOLECULAR DYNAMICS; STATISTICAL MECHANICS; THERMODYNAMICS;

CONFORMATIONAL CHANGES; DENSITY OF STATES DISTRIBUTIONS; ENERGY ENTROPIES; FINITE-DIFFERENCE APPROXIMATIONS; FIRST-PRINCIPLES; FREE ENERGY POTENTIALS; HEAT CAPACITIES; HYDROPHOBIC INTERACTIONS; MOLECULAR DYNAMIC SIMULATIONS; OPTIMAL CONVERGENCES; RANDOM WALKS; REACTION COORDINATES; RELATIVE ENERGIES; SAMPLING ALGORITHMS; TEMPERATURE DEPENDENCES; THERMODYNAMIC QUANTITIES;

HYDROPHOBICITY;

EID: 60749120298     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3077658     Document Type: Article

References (52)

1. S. H. Northrup, M. R. Pear, C. Y. Lee, J. A. McCammon, and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.79.13.4035 79, 4035 (1982).
2. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 0021-9991 10.1016/0021-9991(77)90121-8 23, 187 (1977).
3. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.61.2635 61, 2635 (1988).
4. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.63.1195 63, 1195 (1989).
5. J. Lee, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.71.211 71, 211 (1993).
6. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, J. Comput. Chem. 0192-8651 10.1002/jcc.540130812 13, 1011 (1992).
7. R. W. W. Hooft, B. P. van Eijck, and J. Kroon, J. Chem. Phys. 0021-9606 10.1063/1.463947 97, 6690 (1992).
8. D. E. Smith and A. D. J. Haymet, J. Chem. Phys. 0021-9606 10.1063/1.464809 98, 6445 (1993).
9. C. L. Brooks III, J. Phys. Chem. 0022-3654 10.1021/j100283a017 90, 6680 (1986).
10. D. E. Smith, L. Zhang, and A. D. J. Haymet, J. Am. Chem. Soc. 0002-7863 10.1021/ja00040a068 114, 5875 (1992).
11. D. J. Tobias and C. L. Brooks III, J. Chem. Phys. 0021-9606 10.1063/1.457951 92, 2582 (1990).
12. S. W. Rick and B. J. Berne, J. Phys. Chem. B 1089-5647 10.1021/jp971579z 101, 10488 (1997).
13. E. Gallicchio, M. M. Kubo, and R. M. Levy, J. Phys. Chem. B 1089-5647 10.1021/jp0006274 104, 6271 (2000).
14. N. Matubayasi and M. Nakahara, J. Phys. Chem. B 1089-5647 10.1021/jp002105u 104, 10352 (2000).
15. T. Ghosh, A. E. Garcia, and S. Garde, J. Chem. Phys. 0021-9606 10.1063/1.1431582 116, 2480 (2002).
16. D. Paschek, J. Chem. Phys. 0021-9606 10.1063/1.1652015 120, 6674 (2004).
17. N. Choudhury and B. M. Pettitt, J. Phys. Chem. B 1089-5647 10.1021/jp056909r 110, 8459 (2006).
18. M. V. Athawale, S. Sarupria, and S. Garde, J. Phys. Chem. B 1089-5647 10.1021/jp073485n 112, 5661 (2008).
19. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, Phys. Rev. E 1063-651X 10.1103/PhysRevE.66.056703 66, 056703 (2002).
20. Q. Yan, R. Faller, and J. J. de Pablo, J. Chem. Phys. 0021-9606 10.1063/1.1463055 116, 8745 (2002).
21. Q. Yan and J. J. de Pablo, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.90.035701 90, 035701 (2003).
22. D. P. Landau, S. H. Tsai, and M. Exler, Am. J. Phys. 0002-9505 10.1119/1.1707017 72, 1294 (2004).
23. E. A. Mastny and J. J. de Pablo, J. Chem. Phys. 0021-9606 10.1063/1.1874792 122, 124109 (2005).
24. P. Poulain, F. Calvo, R. Antoine, M. Broyer, and P. Dugourd, Phys. Rev. E 1063-651X 10.1103/PhysRevE.73.056704 73, 056704 (2006).
25. C. G. Zhou, T. C. Schulthess, S. Torbrugge, and D. P. Landau, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.96.120201 96, 120201 (2006).
26. S. H. Tsai, F. G. Wang, and D. P. Landau, Braz. J. Phys. 0103-9733 10.1590/S0103-97332008000100003 38, 6 (2008).
27. F. Wang and D. P. Landau, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett. 86.2050 86, 2050 (2001).
28. F. Wang and D. P. Landau, Phys. Rev. E 1063-651X 10.1103/PhysRevE.64. 056101 64, 056101 (2001).
29. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 0021-9606 10.1063/1.1699114 21, 1087 (1953).
30. R. E. Belardinelli and V. D. Pereyra, J. Chem. Phys. 0021-9606 10.1063/1.2803061 127, 184105 (2007).
31. A. N. Morozov and S. H. Lin, Phys. Rev. E 1063-651X 10.1103/PhysRevE.76. 026701 76, 026701 (2007).
32. C. G. Zhou and R. N. Bhatt, Phys. Rev. E 1063-651X 10.1103/PhysRevE.72. 025701 72, 025701 (R) (2005).
33. B. Widom, P. Bhimalapuram, and K. Koga, Phys. Chem. Chem. Phys. 1463-9076 10.1039/b304038k 5, 3085 (2003).
34. C. L. Brooks III, M. Karplus, and B. M. Pettit, Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics (Wiley, New York, 1987).
35. A. N. Morozov and S. H. Lin, J. Phys. Chem. B 110, 20555 (2006). 1520-6106
36. K. A. Dill, Biochemistry 0006-2960 10.1021/bi00483a001 29, 7133 (1990).
37. H. J. Dyson, P. E. Wright, and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.0605504103 103, 13057 (2006).
38. A. N. Morozov, Y. J. Shiu, C. T. Liang, M. Y. Tsai, and S. H. Lin, J. Biol. Phys. 0092-0606 10.1007/s10867-008-9062-7 33, 255 (2007).
39. C. Pangali, M. Rao, and B. J. Berne, J. Chem. Phys. 0021-9606 10.1063/1.438702 71, 2982 (1979).
40. S. Ludemann, H. Schreiber, R. Abseher, and O. Steinhauser, J. Chem. Phys. 0021-9606 10.1063/1.470899 104, 286 (1996).
41. W. S. Young and C. L. Brooks III, J. Chem. Phys. 0021-9606 10.1063/1.474027 106, 9265 (1997).
42. E. Sobolewski, M. Makowski, C. Czaplewski, A. Liwo, S. Oldziej, and H. A. Scheraga, J. Phys. Chem. B 111, 10765 (2007). 1520-6106
43. A. Troster and C. Dellago, Phys. Rev. E 1063-651X 10.1103/PhysRevE.71. 066705 71, 066705 (2005).
44. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 0021-9606 10.1063/1.445869 79, 926 (1983).
45. W. L. Jorgensen, J. D. Madura, and C. J. Swenson, J. Am. Chem. Soc. 0002-7863 10.1021/ja00334a030 106, 6638 (1984).
46. M. P. Allen and D. G. Tidesley, Computer Simulation of Liquids (Oxford University Press, New York, 1987), Chap., p. 21.
47. M. Neumann, J. Chem. Phys. 0021-9606 10.1063/1.448553 82, 5663 (1985).
48. G. Lamoureux, J. A. D. MacKerell, and B. Roux, J. Chem. Phys. 0021-9606 10.1063/1.1598191 119, 5185 (2003).
49. S. Shimizu and H. S. Chan, J. Am. Chem. Soc. 0002-7863 10.1021/ja0034390 123, 2083 (2001).
50. S. W. Rick, J. Phys. Chem. B 1089-5647 10.1021/jp034725b 107, 9853 (2003).
51. D. Paschek, J. Chem. Phys. 0021-9606 10.1063/1.1737294 120, 10605 (2004).
52. M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 0021-9606 10.1063/1.481505 112, 8910 (2000).