Hummer and szabo-like potential of mean force estimator for bidirectional nonequilibrium pulling experiments/simulations

Journal of Physical Chemistry B

Volumn 114, Issue 29, 2010, Pages 9546-9554

  Nicolini, Paolo ^a   Procacci, Piero ^a,c   Chelli, Riccardo ^a,b  

^a UNIVERSITY OF FLORENCE   (Italy)

^b UNIVERSITY OF FLORENCE   (Italy)

^c Centro Interdipartimentale per Lo Studio Delle Dinamiche Complesse (CSDC)   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ESTIMATION; EXPERIMENTS; HAMILTONIANS; OPTICAL TWEEZERS;

ATOMIC FORCE MICROSCOPES; BENNETT ACCEPTANCE RATIO; COMPARATIVE ANALYSIS; CROOKS FLUCTUATION THEOREM; DYNAMICS SIMULATION; EFFECTIVE POTENTIALS; EQUILIBRIUM DISTRIBUTIONS; EXTENDED SYSTEMS; EXTERNAL PERTURBATIONS; EXTERNAL POTENTIAL; FREE ENERGY SURFACE; FREE-ENERGY DIFFERENCE; JARZYNSKI EQUALITY; NON EQUILIBRIUM; NONEQUILIBRIUM WORK; OUT OF EQUILIBRIUM; POTENTIAL OF MEAN FORCE; SINGLE-MOLECULE; TIME-DEPENDENT; UNPERTURBED SYSTEMS;

FREE ENERGY;

EID: 77954905784     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp102263y     Document Type: Article

References (38)

1. Bustamante, C.; Smith, S. B.; Liphardt, J.; Smith, D. Curr. Opin. Struct. Biol. 2000, 10, 279-285
2. Liphardt, J.; Dumont, S.; Smith, S. B.; Tinoco, I., Jr.; Bustamante, C. Science 2002, 296, 1832-1835
3. Collin, D.; Ritort, F.; Jarzynski, C.; Smith, S. B.; Tinoco, I.; Bustamante, C. Nature 2005, 437, 231-234
4. Bornschlögl, T.; Woehlke, G.; Rief, M. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 6992-6997
5. Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690-2693
6. Crooks, G. E. J. Stat. Phys. 1998, 90, 1481-1487
7. Chipot, C.; Pohorille, A., Eds.; Free Energy Calculations: Theory and Applications in Chemistry and Biology; Springer, Berlin: 2007; Vol. 86, p 188.
8. Ritort, F. J. Phys.: Condens. Matter 2006, 18, R531-R583
9. Ritort, F. Adv. Chem. Phys. 2008, 137, 31-123
10. Often referred to as forward and backward directions of the process
11. Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300-313
12. Park, S.; Schulten, K. J. Chem. Phys. 2004, 120, 5946-5961
13. Procacci, P.; Marsili, S.; Barducci, A.; Signorini, G. F.; Chelli, R. J. Chem. Phys. 2006, 125, 164101
14. Chatelain, C. J. Stat. Mech.: Theory Exp. 2007, P04011
15. Nummela, J.; Yassin, F.; Andricioaei, I. J. Chem. Phys. 2008, 128 024104
16. The equality F (z = a) =( = a), valid for large k values, is commonly known as the stiff spring approximation
17. Hummer, G.; Szabo, A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 3658-3661
18. Minh, D. D. L.; Adib, A. B. Phys. Rev. Lett. 2008, 100, 180602
19. Chelli, R.; Procacci, P. Phys. Chem. Chem. Phys. 2009, 11, 1152-1158
20. McQuarrie, D. A. Statistical Mechanics; HarperCollinsPublishers: New York, 1976.
21. Mossa, A.; Huguet, J. M.; Ritort, F. Physica E 2010, 42, 666-671
22. In eqs 5 and 6 we use the subscript HS, instead of the most appropriate J (where J stands for Jarzynski), to stress that HS [ F ]() and HS [ B ]() are the -dependent analogs of F HS [ F ](z) and F HS [ B ](z), respectively.
23. b, respectively.
24. Bennett, C. H. J. Comput. Phys. 1976, 22, 245-268
25. Shirts, M. R.; Bair, E.; Hooker, G.; Pande, V. S. Phys. Rev. Lett. 2003, 91, 140601
26. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon Press, Oxford: 1987.
27. Marsili, S.; Procacci, P. J. Phys. Chem. B 2010, 114, 2509-2516
28. Kosztin, I.; Barz, B.; Janosi, L. J. Chem. Phys. 2006, 124 064106
29. Calderon, C. P.; Chelli, R. J. Chem. Phys. 2008, 128, 145103
30. MacKerell, A.; Bashford, D.; Bellot, M.; Dunbrack, R.; Evanseck, J.; Field, M.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D. J. Phys. Chem. B 1998, 102, 3586-3616
31. Hoover, W. G. Phys. Rev. A 1985, 31, 1695-1697
32. Hoover, W. G. Phys. Rev. A 1986, 34, 2499-2500
33. Marsili, S.; Signorini, G. F.; Chelli, R.; Marchi, M.; Procacci, P. J. Comput. Chem. 2010, 31, 1106-1116
34. Crooks, G. E. Phys. Rev. E 2000, 61, 2361-2366
35. Gore, J.; Ritort, F.; Bustamante, C. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12564-12569
36. Feng, E. H.; Crooks, G. E. Phys. Rev. Lett. 2008, 101 090602
37. Henin, J.; Chipot, C. J. Chem. Phys. 2004, 121, 2904-2914
38. Hummer, G.; Szabo, A. Acc. Chem. Res. 2005, 38, 504-513