Building Markov state models along pathways to determine free energies and rates of transitions

Journal of Chemical Physics

Volumn 129, Issue 6, 2008, Pages

  Pan, Albert C ^a   Roux, Benòt ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORINE COMPOUNDS; MINE FLOODING; RATE CONSTANTS; RELAXATION PROCESSES; TRAJECTORIES;

COLLECTIVE VARIABLES; COMPLEX SYSTEMS; DISCRETE STATES; EFFICIENT METHODS; MARKOV MODELLING; MARKOV STATE MODELS; MODEL SYSTEMS; REACTION PATHWAYS; SLOW RELAXATIONS; STABLE STATES; STATE-TO-STATE TRANSITION;

MARKOV PROCESSES;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER SIMULATION; KINETICS; PROBABILITY; THERMODYNAMICS; TIME;

COMPUTER SIMULATION; KINETICS; MARKOV CHAINS; MODELS, MOLECULAR; THERMODYNAMICS; TIME FACTORS;

EID: 49849097184     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2959573     Document Type: Article

References (36)

1. B. Hille, Ion Channels of Excitable Membranes, 3rd ed. (Sinauer, Sunderland, MA, 2001).
2. B. F. Volkman, D. Lipson, D. E. Wemmer, and D. Kern, Science 0036-8075 10.1126/science.291.5512.2429 291, 2429 (2001).
3. D. Chandler, J. Chem. Phys. 0021-9606 10.1063/1.436049 68, 2959 (1978).
4. A. F. Voter, Phys. Rev. B 0163-1829 10.1103/PhysRevB.57.R13985 57, R13985 (1998).
5. T. S. van Erp, D. Moroni, and P. G. Bolhuis, J. Chem. Phys. 0021-9606 10.1063/1.1562614 118, 7762 (2003).
6. G. Hummer and I. G. Kevrekidis, J. Chem. Phys. 0021-9606 10.1063/1.1574777 118, 10762 (2003).
7. W. C. Swope, J. W. Pitera, and F. Suits, J. Phys. Chem. B 1089-5647 10.1021/jp037421y 108, 6571 (2004).
8. W. C. Swope, J. W. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. G. Fitch, R. S. Germain, A. Rayshubski, T. J. C. Ward, Y. Zhestkov, and R. Zhou, J. Phys. Chem. B 1089-5647 10.1021/jp037422q 108, 6582 (2004).
9. N. Singhal, C. D. Snow, and V. S. Pande, J. Chem. Phys. 0021-9606 10.1063/1.1738647 121, 415 (2004).
10. A. K. Faradjian and R. Elber, J. Chem. Phys. 0021-9606 10.1063/1.1738640 120, 10880 (2004).
11. N. -V. Buchete and G. Hummer, Phys. Rev. E 1063-651X 10.1103/PhysRevE.77. 030902 77, 030902 (2008).
12. G. Jayachandran, V. Vishal, and V. S. Pande, J. Chem. Phys. 0021-9606 10.1063/1.2171194 124, 164902 (2006).
13. S. Sriraman, I. Kevrekidis, and G. Hummer, J. Phys. Chem. B 1089-5647 10.1021/jp046448u 109, 6479 (2005).
14. P. M. Kasson and V. S. Pande, PLOS Comput. Biol. 3, e220 (2007). 1553-734X
15. D. Sezer, J. Freed, and B. Roux, J. Phys. Chem. B 112, 5755 (2008).
16. S. P. Elmer, S. Park, and V. S. Pande, J. Chem. Phys. 0021-9606 10.1063/1.2001648 123, 114902 (2005).
17. S. P. Elmer, S. Park, and V. S. Pande, J. Chem. Phys. 0021-9606 10.1063/1.2008230 123, 114903 (2005).
18. R. Du, V. S. Pande, A. Y. Grosberg, T. Tanaka, and E. S. Shakhnovich, J. Chem. Phys. 0021-9606 10.1063/1.475393 108, 334 (1998).
19. P. Geissler, C. Dellago, and D. Chandler, J. Phys. Chem. B 1089-5647 10.1021/jp984837g 103, 3706 (1999).
20. P. G. Bolhuis, C. Dellago, D. Chandler, and P. Geissler, Annu. Rev. Phys. Chem. 0066-426X 10.1146/annurev.physchem.53.082301.113146 53, 291 (2002).
21. A. Pan, D. Sezer, and B. Roux, J. Phys. Chem. B 1089-5647 10.1021/jp0777059 112, 3432 (2008).
22. W. Ren, E. Vanden-Eijnden, P. Maragakis, and W. E., J. Chem. Phys. 0021-9606 10.1063/1.2013256 123, 134109 (2005).
23. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. 0021-9606 10.1063/1.2212942 125, 024106 (2006).
24. N. Singhal and V. S. Pande, J. Chem. Phys. 0021-9606 10.1063/1.2116947 123, 204909 (2005).
25. N. S. Hinrichs and V. S. Pande, J. Chem. Phys. 0021-9606 10.1063/1.2740261 126, 244101 (2007).
26. E. Vanden-Eijnden, Transition Path Theory, Computer Simulations in Condensed Matter: From Materials to Chemical Biology Vol. 2 (Springer, New York, 2006), p. 439.
27. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, New York, 1987).
28. See http://www.science.uva.nl/~bolhuis/tps/content/exercise.pdf for more information about this potential energy surface.
29. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 0192-8651 10.1002/jcc.540040211 4, 187 (1983).
30. J. D. Chodera, N. Singhal, V. S. Pande, K. A. Dill, and W. C. Swope, J. Chem. Phys. 0021-9606 10.1063/1.2714538 126, 155101 (2007).
31. W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 1089-5647 10.1021/jp0455430 109, 6688 (2005).
32. W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 0163-1829 10.1103/PhysRevB.66.052301 66, 052301 (2002).
33. D. Moroni, P. G. Bolhuis, and T. S. van Erp, J. Chem. Phys. 0021-9606 10.1063/1.1644537 120, 4055 (2004).
34. S. Park, T. E. Klein, and V. S. Pande, Biophys. J. 93, 4108 (2007). 0006-3495
35. J. D. Chodera, W. C. Swope, J. W. Pitera, and K. A. Dill, Multiscale Model. Simul. 1540-3459 10.1137/06065146X 5, 1214 (2006).
36. M. Galassi, J. Davies, J. Theiler, B. Gough, G. Jungman, M. Booth, and F. Rossi, GNU Scientific Library Reference Manual, 2nd ed. (Network Theory, Bristol, UK, 2006), http://www.gnu.org/software/gsl/.