Free-energy landscapes from adaptively biased methods: Application to quantum systems

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 82, Issue 4, 2010, Pages

  Calvo, F ^a  

^a UNIVERSITÉ DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; QUANTUM OPTICS; REACTION KINETICS;

ADAPTIVE BIASING; CLASSICAL STATISTICS; ENERGY PATHWAY; FREE ENERGY LANDSCAPE; FUNNEL LANDSCAPES; LENNARD-JONES CLUSTER; QUANTUM SUPERPOSITIONS; REACTION COORDINATES;

FREE ENERGY;

EID: 78651341878     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.82.046703     Document Type: Article

References (55)

1. J. G. Kirkwood, J. Chem. Phys. 3, 300 (1935). 10.1063/1.1749657
2. R. W. Zwanzig, J. Chem. Phys. 22, 1420 (1954). 10.1063/1.1740409
3. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. 53, 291 (2002). 10.1146/annurev.physchem.53.082301.113146
4. T. S. van Erp, D. Moroni, and P. G. Bolhuis, J. Chem. Phys. 118, 7762 (2003) 10.1063/1.1562614
5. D. J. Wales, Mol. Phys. 100, 3285 (2002) 10.1080/00268970210162691
6. R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 124, 024102 (2006). 10.1063/1.2140273
7. G. M. Torrie and J.-P. Valleau, J. Comput. Phys. 23, 187 (1977). 10.1016/0021-9991(77)90121-8
8. B. A. Berg and T. Neuhaus, Phys. Rev. Lett. 68, 9 (1992). 10.1103/PhysRevLett.68.9
9. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, J. Comput. Chem. 16, 1339 (1995) 10.1002/jcc.540161104
10. D. L. Minh and J. D. Chodera, J. Chem. Phys. 131, 134110 (2009). 10.1063/1.3242285
11. L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006). 10.1016/j.cplett.2006.05.062
12. F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001). 10.1103/PhysRevLett.86.2050
13. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002). 10.1073/pnas.202427399
14. S. Marsili, A. Barducci, R. Chelli, P. Procacci, and V. Schettino, J. Phys. Chem. B 110, 14011 (2006). 10.1021/jp062755j
15. E. Darve and J. Pohorille, J. Chem. Phys. 115, 9169 (2001). 10.1063/1.1410978
16. G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. 98, 3658 (2001). 10.1073/pnas.071034098
17. M. Athènes, Eur. Phys. J. B 38, 651 (2004). 10.1140/epjb/e2004- 00159-0
18. C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997). 10.1103/PhysRevLett.78. 2690
19. G. E. Crooks, J. Stat. Phys. 90, 1481 (1998). 10.1023/A:1023208217925
20. M. P. Allen and D. J. Tildesley, Computer Simulations of Liquids (Oxford University Press, Oxford, 1987).
21. M. Esposito and S. Mukamel, Phys. Rev. E 73, 046129 (2006). 10.1103/PhysRevE.73.046129
22. W. De Roeck and C. Maes, Phys. Rev. E 69, 026115 (2004). 10.1103/PhysRevE.69.026115
23. P. Talkner, E. Lutz, and P. Hänggi, Phys. Rev. E 75, 050102 (R) (2007) 10.1103/PhysRevE.75.050102
24. S. Deffner and E. Lutz, Phys. Rev. E 77, 021128 (2008). 10.1103/PhysRevE.77.021128
25. R. van Zon, L. Hernández de la Peña, G. H. Peslherbe, and J. Schofield, Phys. Rev. E 78, 041103 (2008) 10.1103/PhysRevE.78.041103
26. R. van Zon, L. Hernández de la Peña, G. H. Peslherbe, and J. Schofield, Phys. Rev. E 78, 041104 (2008). 10.1103/PhysRevE.78.041104
27. L. Hernández de la Peña and G. H. Peslherbe, J. Phys. Chem. B 114, 5404 (2010). 10.1021/jp908742n
28. P. Raiteri, A. Laio, F. Luigi Gervasio, C. Micheletti, and M. Parrinello, J. Phys. Chem. B 110, 3533 (2006). 10.1021/jp054359r
29. V. Babin, C. Roland, and C. Sagui, J. Chem. Phys. 128, 134101 (2008). 10.1063/1.2844595
30. T. Lelièvre, M. Rousset, and G. Stoltz, J. Chem. Phys. 126, 134111 (2007). 10.1063/1.2711185
31. J. P. K. Doye, M. A. Miller, and D. J. Wales, J. Chem. Phys. 110, 6896 (1999). 10.1063/1.478595
32. F. Calvo, J. P. K. Doye, and D. J. Wales, J. Chem. Phys. 114, 7312 (2001). 10.1063/1.1359768
33. C. Predescu, P. A. Frantsuzov, and V. A. Mandelshtam, J. Chem. Phys. 122, 154305 (2005). 10.1063/1.1860331
34. P. Poulain, F. Calvo, R. Antoine, M. Broyer, and Ph. Dugourd, Phys. Rev. E 73, 056704 (2006). 10.1103/PhysRevE.73.056704
35. G. Adjanor, M. Athènes, and F. Calvo, Eur. Phys. J. B 53, 47 (2006). 10.1140/epjb/e2006-00353-0
36. F. J. Pinski and A. M. Stuart, J. Chem. Phys. 132, 184104 (2010). 10.1063/1.3391160
37. P. J. Steinhardt, D. R. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983). 10.1103/PhysRevB.28.784
38. V. A. Mandelshtam and P. A. Frantsuzov, J. Chem. Phys. 124, 204511 (2006). 10.1063/1.2202312
39. D. J. Wales, Mol. Phys. 78, 151 (1993). 10.1080/00268979300100141
40. J. P. K. Doye, D. J. Wales, and M. A. Miller, J. Chem. Phys. 109, 8143 (1998). 10.1063/1.477477
41. J. P. Neirotti, F. Calvo, D. L. Freeman, and J. D. Doll, J. Chem. Phys. 112, 10340 (2000) 10.1063/1.481671
42. F. Calvo, J. P. Neirotti, D. L. Freeman, and J. D. Doll, J. Chem. Phys. 112, 10350 (2000). 10.1063/1.481672
43. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989). 10.1103/PhysRevLett.63.1195
44. M. Athènes and F. Calvo, ChemPhysChem 9, 2332 (2008). 10.1002/cphc.200800427
45. I. Coluzza and D. Frenkel, ChemPhysChem 6, 1779 (2005). 10.1002/cphc.200400629
46. B. Strodel and D. J. Wales, Chem. Phys. Lett. 466, 105 (2008). 10.1016/j.cplett.2008.10.085
47. F. Calvo, Mol. Phys. 100, 3421 (2002) 10.1080/00268970210158632
48. Q. Yan, R. Faller, and J. J. de Pablo, J. Chem. Phys. 116, 8745 (2002). 10.1063/1.1463055
49. L. Zhan, Comput. Phys. Commun. 179, 339 (2008) 10.1016/j.cpc.2008.04.002
50. G. Brown, T. C. Schulthess, W. R. Elwasif, and D. E. Bernoldt, Oak Ridge National Laboratory Technical Report No. ORNL/TM-2005/1, 2005 (unpublished).
51. G. J. Martyna, D. J. Tobias, and M. L. Klein, J. Chem. Phys. 101, 4177 (1994). 10.1063/1.467468
52. A. Pérez, M. E. Tuckerman, and M. H. Müser, J. Chem. Phys. 130, 184105 (2009). 10.1063/1.3126950
53. M. E. Tuckerman, B. J. Berne, G. J. Martyna, and M. L. Klein, J. Chem. Phys. 99, 2796 (1993). 10.1063/1.465188
54. I. R. Craig and D. E. Manolopoulos, J. Chem. Phys. 121, 3368 (2004). 10.1063/1.1777575
55. J. Deckman, P. A. Frantsuzov, and V. A. Mandelshtam, Phys. Rev. E 77, 052102 (2008). 10.1103/PhysRevE.77.052102