Analyzing milestoning networks for molecular kinetics: Definitions, algorithms, and examples

Journal of Chemical Physics

Volumn 139, Issue 17, 2013, Pages

  Viswanath, Shruthi ^a,b   Kreuzer, Steven M ^c   Cardenas, Alfredo E ^b   Elber, Ron ^b,d  

^a University of Texas at Austin   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c The University of Texas at Austin   (United States)

^d The University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASYMPTOTIC EFFICIENCY; DIJKSTRA'S ALGORITHMS; KINETIC INFORMATION; MARKOV STATE MODELS; MEMBRANE PERMEATION; MOLECULAR DYNAMICS SIMULATIONS; NETWORK REPRESENTATION; TRANSITION PATH THEORIES;

ALGORITHMS; DATA VISUALIZATION; INTEGRAL EQUATIONS; KINETICS; MOLECULAR DYNAMICS; PHASE SPACE METHODS; SPACE FLIGHT;

COMPLEX NETWORKS;

ALGORITHM; ARTICLE; KINETICS; MOLECULAR DYNAMICS;

ALGORITHMS; KINETICS; MOLECULAR DYNAMICS SIMULATION;

EID: 84887579015     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4827495     Document Type: Article

References (47)

1. P. Metzner, C. Schutte, and E. Vanden-Eijnden, Multiscale Model. Simul. 7 (3), 1192-1219 (2009). 10.1137/070699500
2. A. Berezhkovskii, G. Hummer, and A. Szabo, J. Chem. Phys. 130 (20), 205102 (2009). 10.1063/1.3139063
3. P. Majek and R. Elber, J. Chem. Theory Comput. 6 (6), 1805-1817 (2010). 10.1021/ct100114j
4. J. D. Chodera, N. Singhal, V. S. Pande, K. A. Dill, and W. C. Swope, J. Chem. Phys. 126 (15), 155101 (2007). 10.1063/1.2714538
5. C. Schutte, F. Noe, J. F. Lu, M. Sarich, and E. Vanden-Eijnden, J. Chem. Phys. 134 (20), 204105 (2011). 10.1063/1.3590108
6. S. Kirmizialtin and R. Elber, J. Phys. Chem. A 115 (23), 6137-6148 (2011). 10.1021/jp111093c
7. G. S. Jas, W. A. Hegefeld, P. Majek, K. Kuczera, and R. Elber, J. Phys. Chem. B 116 (23), 6598-6610 (2012). 10.1021/jp211645s
8. S. Kreuzer, T. J. Moon, and R. Elber, J. Chem. Phys. 139 (12), 121902 (2013). 10.1063/1.4811366
9. S. Kreuzer and R. Elber, Biophys. J. 105 (4), 951-961 (2013). 10.1016/j.bpj.2013.05.064
10. S. M. Kreuzer, R. Elber, and T. J. Moon, J. Phys. Chem. B 116 (29), 8662-8691 (2012). 10.1021/jp300788e
11. A. F. Voter, Phys. Rev. Lett. 78 (20), 3908-3911 (1997). 10.1103/PhysRevLett.78.3908
12. R. Czerminski and R. Elber, Int. J. Quantum Chem. 38, 167-186 (1990). 10.1002/qua.560382419
13. A. Ulitsky and R. Elber, J. Chem. Phys. 92 (2), 1510-1511 (1990). 10.1063/1.458112
14. H. Jonsson, G. Mills, and K. W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by, B. J. Berne, G. Ciccotti, and, D. F. Coker, (World Scientific, Singapore, 1998), pp. 385-403.
15. R. Olender and R. Elber, J. Mol. Struct.: THEOCHEM 398-399, 63-71 (1997). 10.1016/S0166-1280(97)00038-9
16. R. Elber and D. Shalloway, J. Chem. Phys. 112 (13), 5539-5545 (2000). 10.1063/1.481131
17. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. 125 (2), 024106 (2006). 10.1063/1.2212942
18. E. Weinan, W. Q. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109 (14), 6688-6693 (2005). 10.1021/jp0455430
19. E. Weinan, W. Q. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66 (5), 052301 (2002). 10.1103/PhysRevB.66.052301
20. S. A. Beccara, T. Skrbic, R. Covino, and P. Faccioli, Proc. Natl. Acad. Sci. U.S.A. 109 (7), 2330-2335 (2012). 10.1073/pnas.1111796109
21. P. Faccioli, M. Sega, F. Pederiva, and H. Orland, Phys. Rev. Lett. 97 (10), 108101 (2006). 10.1103/PhysRevLett.97.108101
22. R. Czerminski and R. Elber, J. Chem. Phys. 92 (9), 5580-5601 (1990). 10.1063/1.458491
23. D. Wales, Energy Landscapes with Applications to Clusters, Biomolecules and Glasses (Cambridge University Press, Cambridge, 2003).
24. D. G. Truhlar, B. C. Garrett, and S. J. Klippenstein, J. Phys. Chem. 100 (31), 12771-12800 (1996). 10.1021/jp953748q
25. A. Onufriev, D. Bashford, and D. A. Case, Proteins: Struct., Funct., Bioinf. 55 (2), 383-394 (2004). 10.1002/prot.20033
26. R. Czerminski and R. Elber, Proc. Natl. Acad. Sci. U.S.A. 86 (18), 6963-6967 (1989). 10.1073/pnas.86.18.6963
27. S. Thomas, X. Y. Tang, L. Tapia, and N. M. Amato, J. Comput. Biol. 14 (6), 839-855 (2007). 10.1089/cmb.2007.R019
28. E. Weinan and E. Vanden-Eijnden, Annu. Rev. Phys. Chem. 61, 391-420 (2010). 10.1146/annurev.physchem.040808.090412
29. M. Berkowitz, J. D. Morgan, J. A. McCammon, and S. H. Northrup, J. Chem. Phys. 79 (11), 5563-5565 (1983). 10.1063/1.445675
30. S. H. Huo and J. E. Straub, J. Chem. Phys. 107 (13), 5000-5006 (1997). 10.1063/1.474863
31. R. J. Zhao, J. F. Shen, and R. D. Skeel, J. Chem. Theory Comput. 6 (8), 2411-2423 (2010). 10.1021/ct900689m
32. A. K. Faradjian and R. Elber, J. Chem. Phys. 120 (23), 10880-10889 (2004). 10.1063/1.1738640
33. A. M. A. West, R. Elber, and D. Shalloway, J. Chem. Phys. 126 (14), 145104 (2007). 10.1063/1.2716389
34. D. Shalloway and A. K. Faradjian, J. Chem. Phys. 124 (5), 054112 (2006). 10.1063/1.2161211
35. T. C. Hu, Oper. Res. 9 (6), 898-900 (1961). 10.1287/opre.9.6.898
36. M. Pollack, Oper Res 8 (5), 733-736 (1960). 10.1287/opre.8.5.733
37. V. Vassilevska, in Proceedings of the Nineteenth Annual Acm-Siam Symposium on Discrete Algorithms (ACM, San Francisco, CA, 2008), pp. 465-472.
38. V. Vassilevska, R. Williams, and R. Yuster, " All-pairs bottleneck paths for general graphs in truly sub-cubic time.," in Proceedings of the thirty-ninth annual ACM symposium on theory of computing (ACM, New York, NY, 2007), pp. 585-589. 10.1145/1250790.1250876
39. E. W. Dijkstra, Numer. Math. 1 (1), 269 (1959). 10.1007/BF01386390
40. T. Cormen, C. Leiserson, R. Rivest, and C. Stein, Introduction to Algorithms, 3rd ed. (MIT Press, Boston, 2009).
41. M. L. Fredman and R. E. Tarjan, J. ACM 34 (3), 596-615 (1987). 10.1145/28869.28874
42. F. Noe, C. Schutte, E. Vanden-Eijnden, L. Reich, and T. R. Weikl, Proc. Natl. Acad. Sci. U.S.A. 106 (45), 19011-19016 (2009). 10.1073/pnas.0905466106
43. V. Batagelj and A. Mrvar, Connections 21 (2), 47-57 (1998).
44. A. Cardenas and R. Elber, Mol. Phys. (in press).
45. A. E. Cardenas, G. S. Jas, K. Y. DeLeon, W. A. Hegefeld, K. Kuczera, and R. Elber, J. Phys. Chem. B 116 (9), 2739-2750 (2012). 10.1021/jp2102447
46. M. Bastian, S. Heymann, and M. Jacomy, in International AAAI Conference on Weblogs and Social Media (Association for Advancement of Artificial Intelligence, 2009).
47. R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Y. Li, G. Verkhivker, C. Keasar, J. Zhang, and A. Ulitsky, Comput. Phys. Commun. 91 (1-3), 159-189 (1995). 10.1016/0010-4655(95)00047-J