On the assumptions underlying milestoning

Journal of Chemical Physics

Volumn 129, Issue 17, 2008, Pages

  Vanden Eijnden, Eric ^a   Venturoli, Maddalena ^a   Ciccotti, Giovanni ^b   Elber, Ron ^c  

^a NEW YORK UNIVERSITY   (United States)

^b UNIVERSITÀ DI ROMA LA SAPIENZA   (Italy)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICS; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY; REACTION KINETICS; SURFACE REACTIONS; TRAJECTORIES;

BARRIER CROSSINGS; CLOSED FORMS; DIFFUSIVE TRANSITIONS; ISOCOMMITTOR SURFACES; KINETIC INFORMATIONS; MARKOV STATE MODELS; MD TRAJECTORIES; MEAN FIRST PASSAGE TIMES; PRACTICAL IMPLICATIONS; SUCCESSIVE TRANSITIONS; TIME EVOLUTIONS; TIME LAGS; TRANSITION PATHS;

PROBABILITY DISTRIBUTIONS;

ARTICLE; CHEMICAL MODEL; KINETICS; REPRODUCIBILITY; SURFACE PROPERTY; TIME;

KINETICS; MODELS, CHEMICAL; REPRODUCIBILITY OF RESULTS; SURFACE PROPERTIES; TIME FACTORS;

EID: 55949099868     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2996509     Document Type: Article

References (30)

1. A. K. Faradjian and R. Elber, J. Chem. Phys. 120, 10880 (2004).
2. D. Shalloway and A. K. Faradijan, J. Chem. Phys. 124, 054112 (2006).
3. A. M. A. West, R. Elber, and D. Shalloway, J. Chem. Phys. 126, 145104 (2007).
4. R. Elber, Biophys. J. 92, L85 (2007).
5. E. Vanden-Eijnden, M. Venturoli, and R. Elber, " Markovian milestoning with Voronoi tessellations.," J. Chem. Phys. (2008) (in preparation).
6. W. E and E. Vanden-Eijnden, J. Stat. Phys. 123, 503 (2006).
7. E. Vanden-Eijnden, in Computer Simulations in Condensed Matter: From Materials to Chemical Biology, edited by, M. Ferrario, G. Ciccotti, and, K. Binder, (Springer, Berlin, 2006), Vol. 1, pp. 439-478.
8. P. Metzner, C. Schütte, and E. Vanden-Eijnden, J. Chem. Phys. 125, 084110 (2006).
9. W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002).
10. W. E, W. Ren, and E. Vanden-Eijnden, Chem. Phys. Lett. 413, 242 (2005).
11. W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005).
12. W. E, E. Vanden-Eijnden, and P. Maragakis, J. Chem. Phys. 123, 134109 (2005).
13. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. 125, 024106 (2006).
14. E. Vanden-Eijnden and M. Venturoli, " Revisiting the Finite Temperature String Method for the Calculation of Reaction Tubes and Free Energies.," J. Chem. Phys. (to be published).
15. D. Shalloway, J. Chem. Phys. 105, 9986 (1996).
16. A. Ulitsky and D. Shalloway, J. Chem. Phys. 109, 1670 (1998).
17. G. Hummer and I. Kevrekidis, J. Chem. Phys. 118, 10762 (2003).
18. W. Swope, J. Pitera, and F. Suits, J. Phys. Chem. B 108, 6571 (2004).
19. W. C. Swope, J. W. Pitera, F. Suits, M. C. Pitman, M. Eleftheriou, B. G. Fitch, R. S. Germain, A. Rayshubski, T. J. C. Ward, Y. Zhestkov, and R. J. Zhou, J. Phys. Chem. B 108, 6582 (2004).
20. S. Krivov and M. Karplus, J. Chem. Phys. 117, 10894 (2004).
21. F. Noe, I. Horenko, C. Schütte, and J. Smith, J. Chem. Phys. 126, 155102 (2007).
22. N. Buchete and G. Hummer, J. Phys. Chem. B 112, 6057 (2008).
23. J. Chodera, N. Singhal, W. C. Swope, V. S. Pande, and K. A. Dill, J. Chem. Phys. 126, 155101 (2007).
24. D. Moroni, T. S. van Erp, and P. G. Bolhuis, Physica A 340, 395 (2004).
25. D. Moroni, P. G. Bolhuis, and T. S. van Erp, J. Chem. Phys. 120, 4055 (2004).
26. R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 124, 024102 (2006).
27. A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005).
28. B. Peters and B. L. Trout, J. Chem. Phys. 125, 054108 (2006).
29. S. Huo and J. E. Straub, J. Chem. Phys. 107, 5000 (1997).
30. I. Karatzas and S. E. Shreve, Brownian Motion and Stochastic Calculus, Graduate Texts in Mathematics Vol. 113, 2nd ed. (Springer-Verlag, New York, 1991).