Reconstructing Free Energy Profiles from Nonequilibrium Relaxation Trajectories

Journal of Statistical Physics

Volumn 144, Issue 2, 2011, Pages 344-366

  Zhang, Qi ^a   Brujić, Jasna ^b,c   Vanden Eijnden, Eric ^a,c  

^a NEW YORK UNIVERSITY   (United States)

^b POLYTECHNIC UNIVERSITY   (United States)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Bayesian sampling; Free energy calculation; Maximum likelihood; Nonequilibrium sampling

Indexed keywords

EID: 79960978673     PISSN: 00224715     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10955-011-0242-7     Document Type: Article

References (33)

1. Kollman, P.: Chem. Rev. 93(7), 2395 (1993).
2. Dobson, C., Karplus, M.: Curr. Opin. Struct. Biol. 9(1), 92 (1999).
3. Frauenfelder, H., Wolynes, P., Austin, R.: Rev. Mod. Phys. 71(2), S419 (1999).
4. Dill, K., Bromberg, S.: Molecular Driving Forces. Garland Science, New York (2003).
5. Onuchic, J. N., Wolynes, P. G.: Curr. Opin. Struct. Biol. 14, 70 (2004).
6. Frenkel, D., Smit, B.: Understanding Molecular Simulation: From Algorithms to Applications. Academic Press, New York (2002).
7. Fatt, P., Katz, B.: J. Physiol. 117(1), 109 (1952).
8. Woodside, M. T., Behnke-Parks, W. M., Larizadeh, K., Travers, K., Herschlag, D., Block, S. M.: Proc. Natl. Acad. Sci. USA 103(16), 6190 (2006).
9. Gebhardt, J., Bornschlögl, T., Rief, M.: Proc. Natl. Acad. Sci. USA 107(5), 2013 (2010).
10. Finkelstein, A. V., Ptitsyn, O. B.: Protein Physics: A Course of Lectures. Academic Press, Amsterdam (2002).
11. Roux, B.: Comput. Phys. Commun. 91, 275 (1995).
12. Jarzynski, C.: Phys. Rev. Lett. 78, 2690 (1997).
13. Jarzynski, C.: Phys. Rev. E 56, 5018 (1997).
14. Crooks, G.: J. Stat. Phys. 90(5), 1481 (1998).
15. Crooks, G. E.: Phys. Rev. E 60, 2721 (1999).
16. Hummer, G., Szabo, A.: Proc. Natl. Acad. Sci. USA 98(7), 3658 (2001).
17. Liphardt, J., Dumont, S., Smith, S. B., Tinoco Jr., I., Bustamante, C.: Science 296(5574), 1832 (2002).
18. Collin, D., Ritort, F., Jarzynski, C., Smith, S. B., Tinoco Jr., I., Bustamante, C.: Nature 437(7056), 231 (2005).
19. Minh, D. D. L., Adib, A. B.: Phys. Rev. Lett. 100(18), 180602 (2008).
20. Hummer, G.: J. Chem. Phys. 14(17), 7330 (2001).
21. Oberhofer, H., Dellago, C., Geissler, P. L.: J. Phys. Chem. B 109(14), 6902 (2005).
22. Oberhofer, H., Dellago, C.: J. Comput. Chem. 30(11), 1726 (2009).
23. Minh, D. D. L., Chodera, J. D.: J. Chem. Phys. 131(13), 134110 (2009).
24. Hamill, O. P., Marty, A., Neher, E., Sakmann, B., Sigworth, F. J.: Pflügers Arch. 391, 85 (1981).
25. Fernandez, J. M., Li, H.: Science 303(5664), 1674 (2004).
26. Walther, K. A., Grater, F., Dougan, L., Badilla, C. L., Berne, B. J., Fernandez, J. M.: Proc. Natl. Acad. Sci. USA 104, 7916 (2007).
27. Berkovich, R., Garcia-Manyes, S., Urbakh, M., Klafter, J., Fernandez, J. M.: Biophys. J. 98, 2692 (2010).
28. Ball, G., Chou, T.: Inverse Probl. 40(4), 1053 (2004).
29. Best, R. B., Hummer, G.: Proc. Natl. Acad. Sci. USA 107(3), 1088 (2010).
30. Stuart, A. M.: Acta Numer. 19, 451 (2010).
31. Pokern, Y., Stuart, A., Vanden-Eijnden, E.: Multiscale Model. Simul. 8, 69 (2009).
32. Durrett, R.: Stochastic Calculus. CRC Press, Boca Raton (1996).
33. Ikeda, N., Watanabe, S.: Stochastic Differential Equations and Diffusion Processes. North-Holland Mathematical Library, vol. 24. North-Holland, Amsterdam (1981).