Milestoning with transition memory

Journal of Chemical Physics

Volumn 135, Issue 22, 2011, Pages

  Hawk, Alexander T ^a   Makarov, Dmitrii E ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRUTE FORCE; FIRST PASSAGE TIME; HYPER-SURFACES; INDEPENDENT TRANSITIONS; KINETICS AND THERMODYNAMICS; LANGEVIN DYNAMICS; MARKOV RENEWAL PROCESS; MD SIMULATION; MEAN FIRST PASSAGE TIME; MOLECULAR PROCESS; POLYMER CHAINS; REACTION COORDINATES; TIME-SCALES; TOY MODELS; TRANSITION PROBABILITIES; TRANSITION TIME;

DYNAMICS; MOLECULAR DYNAMICS; PROBABILITY DISTRIBUTIONS; REACTION KINETICS; THERMODYNAMICS;

TRAJECTORIES;

POLYMER;

ARTICLE; CHEMISTRY; CONFORMATION; KINETICS; MOLECULAR DYNAMICS; THERMODYNAMICS;

KINETICS; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; POLYMERS; THERMODYNAMICS;

EID: 83755206870     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3666840     Document Type: Article

References (40)

1. A. E. Cardenas and R. Elber, Proteins: Struct., Funct., Genet. 51 (2), 245 (2003). 10.1002/prot.10349 (Pubitemid 36397757)
2. X. W. Fang, P. Thiyagarajan, T. R. Sosnick, and T. Pan, Proc. Natl. Acad. Sci. U.S.A. 99 (13), 8518 (2002). 10.1073/pnas.142288399 (Pubitemid 34693594)
3. D. E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R. O. Dror, M. P. Eastwood, J. A. Bank, J. M. Jumper, J. K. Salmon, Y. B. Shan, and W. Wriggers, Science 330 (6002), 341 (2010). 10.1126/science.1187409
4. 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 (Pubitemid 35336255)
5. D. Moroni, T. S. van Erp, and P. G. Bolhuis, Physica A 340 (1-3), 395 (2004). 10.1016/j.physa.2004.04.033
6. T. S. van Erp and P. G. Bolhuis, J. Comput. Phys. 205 (1), 157 (2005). 10.1016/j.jcp.2004.11.003
7. C. Valeriani, R. J. Allen, M. J. Morelli, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 127 (11), 114109 (2007). 10.1063/1.2767625 (Pubitemid 47469588)
8. R. J. Allen, D. Frenkel, and P. R. ten Wolde, J. Chem. Phys. 124 (19), 024102 (2006). 10.1063/1.2140273 (Pubitemid 43100174)
9. N. S. Hinrichs and V. S. Pande, J. Chem. Phys. 126 (24), 244101 (2007). 10.1063/1.2740261 (Pubitemid 47141397)
10. N. V. Buchete and G. Hummer, J. Phys. Chem. B 112 (19), 6057 (2008). 10.1021/jp0761665
11. M. Sarich, F. Noe, and C. Schutte, Multiscale Model. Simul. 8 (4), 1154 (2010). 10.1137/090764049
12. D. Moroni, P. G. Bolhuis, and T. S. van Erp, J. Chem. Phys. 120 (9), 4055 (2004). 10.1063/1.1644537
13. A. K. Faradjian and R. Elber, J. Chem. Phys. 120 (23), 10880 (2004). 10.1063/1.1738640
14. D. Shalloway and A. K. Faradjian, J. Chem. Phys. 124 (5), 054112 (2006). 10.1063/1.2161211 (Pubitemid 43202674)
15. R. Elber, Biophys. J. 92 (9), L85 (2007). 10.1529/biophysj.106.101899 (Pubitemid 46691100)
16. E. Vanden-Eijnden, M. Venturoli, G. Ciccotti, and R. Elber, J. Chem. Phys. 129 (17), 174102 (2008). 10.1063/1.2996509
17. K. Kuczera, G. S. Jas, and R. Elber, J. Phys. Chem. A 113 (26), 7461 (2009). 10.1021/jp900407w
18. E. Vanden-Eijnden and M. Venturoli, J. Chem. Phys. 130 (19), 194101 (2009). 10.1063/1.3129843
19. L. Maragliano, E. Vanden-Eijnden, and B. Roux, J. Chem. Theory Comput. 5 (10), 2589 (2009). 10.1021/ct900279z
20. R. Elber and A. West, Proc. Natl. Acad. Sci. U.S.A. 107 (11), 5001 (2010). 10.1073/pnas.0909636107
21. P. Majek and R. Elber, J. Chem. Theory Comput. 6 (6), 1805 (2010). 10.1021/ct100114j
22. S. Kirmizialtin and R. Elber, J. Phys. Chem. A 115, 6137 (2011). 10.1021/jp111093c
23. R. Pyke, Ann. Math. Stat. 32 (4), 1231 (1961). 10.1214/aoms/1177704863
24. A. M. A. West, R. Elber, and D. Shalloway, J. Chem. Phys. 126 (14), 145104 (2007). 10.1063/1.2716389 (Pubitemid 46610034)
25. M. Doi, Chem. Phys. 9 (3), 455 (1975). 10.1016/0301-0104(75)80083-8
26. I. M. Sokolov, Phys. Rev. Lett. 90 (8), 080601 (2003). 10.1103/PhysRevLett.90.080601
27. G. Wilemski and M. Fixman, J. Chem. Phys. 60 (3), 866 (1974). 10.1063/1.1681162
28. B. Friedman and B. Oshaughnessy, Macromolecules 26 (18), 4888 (1993). 10.1021/ma00070a025
29. A. Szabo, K. Schulten, and Z. Schulten, J. Chem. Phys. 72 (8), 4350 (1980). 10.1063/1.439715
30. N. M. Toan, G. Morrison, C. Hyeon, and D. Thirumalai, J. Phys. Chem. B 112 (19), 6094 (2008). 10.1021/jp076510y
31. J. Z. Y. Chen, H. K. Tsao, and Y. J. Sheng, Phys. Rev. E 72 (3), 031804 (2005). 10.1103/PhysRevE.72.031804 (Pubitemid 41778102)
32. P. Debnath and B. J. Cherayil, J. Chem. Phys. 120 (5), 2482 (2004). 10.1063/1.1637574
33. L. J. Lapidus, P. J. Steinbach, W. A. Eaton, A. Szabo, and J. Hofrichter, J. Phys. Chem. B 106 (44), 11628 (2002). 10.1021/jp020829v (Pubitemid 35361136)
34. R. W. Pastor, R. Zwanzig, and A. Szabo, J. Chem. Phys. 105 (9), 3878 (1996). 10.1063/1.472208
35. A. Podtelezhnikov and A. Vologodskii, Macromolecules 30 (21), 6668 (1997). 10.1021/ma970391a
36. J. J. Portman, J. Chem. Phys. 118 (5), 2381 (2003). 10.1063/1.1532728
37. R. R. Cheng, T. Uzawa, K. W. Plaxco, and D. E. Makarov, J. Phys. Chem. B 113 (42), 14026 (2009). 10.1021/jp902291n
38. T. Uzawa, R. R. Cheng, K. J. Cash, D. E. Makarov, and K. W. Plaxco, Biophys. J. 97 (1), 205 (2009). 10.1016/j.bpj.2009.04.036
39. M. Doi and S. F. Edwards, The Theory of Polymer Dynamics (ClarendonOxford University Press, OxfordNew York, 1986).
40. P. G. De Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, NY, 1979).