Extracting kinetic and stationary distribution information from short MD trajectories via a collection of surrogate diffusion models

Journal of Chemical Theory and Computation

Volumn 5, Issue 1, 2009, Pages 47-58

  Calderon, Christopher P ^a   Arora, Karunesh ^b  

^a Rice University   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 61549123002     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct800282a     Document Type: Article

References (78)

1. Bustamante, C.; Bryant, Z.; Smith, S. Nature 2003, 421, 423.
2. Carrion-Vazquez, M.; Oberhauser, A.; Fisher, T.; Marszalek, P.; Li, H.; Fernandez, J. Prog. Biophys. Mol. Bio. 2000, 74, 63.
3. Stock, G.; Ghosh, K.; Dill, K. J. Chem. Phys. 2008, 128, 194102.
4. Collin, D.; Ritort, F.; Jarzynski, C.; Smith, S.; Tinoco, I., Jr.; Bustamante, C. Nature 2005, 437, 231.
5. Min, W.; Gopich, I.; English, B.; Kou, S.; Xie, X.; Szabo, A. J. Phys. Chem. B 2006, 110, 20093.
6. Smith, S.; Cui, Y.; Bustamante, C. Science 1996, 271, 795.
7. Rief, M.; Clausen-Schaumann, H.; Gaub, H. Nat. Struct. Biol. 1999, 6, 346.
8. Clausen-Schaumann, H.; Rief, M.; Tolksdorf, C.; Gaub, H. Biophys. J. 2000, 78, 1997.
9. Albrecht, C.; Neuert, G.; Lugmaier, R.; Gaub, H. Biophys. J. 2008, 94, 4766.
10. Lee, G.; Rabbi, M.; Marszalek, R. C. P. Small 2007, 5, 809.
11. (l 1) Ke, C.; Humeniuk, M.; S-Gracz, H.; Marszalek, P. Phys. Rev. Lett. 2007, 99, 018302.
12. Harris, N. C.; Song, Y.; Klang, C.-H. Phys. Rev. Lett. 2007, 99, 068101.
13. Dixit, S.; Singh-Zocchi, M.; Hanne, J.; Zocchi, G. Phy. Rev. Lett. 2005, 94, 118101.
14. Vendruscolo, M.; Dobson, C. Science 2006, 313, 1586.
15. Liu, S.; Bokinsky, G.; Walter, N.; Zhuang, X. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 12634.
16. Greenleaf, W.; Frieda, K.; Foster, D.; Woodside, M.; Block, S. Science 2008, 319, 630.
17. Schlick, T.; Skeel, R. D.; Brunger, A. T.; Kale, L. V.; Board, J. A.; Hermans, J.; Schulten, K. J. Comput. Phys. 1999, 151, 9.
18. Zwanzig, R. Brownian motion and Langevin equations. In Nonequilibrium Statistical Mechanics, 1st ed.; Oxford University Press: New York, 2001; pp 3, 24, 143.
19. Chorin, A. J.; Kupferman, A. K. R. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 4094.
20. Kopelevich, D.; Panagiotopoulos, A.; Kevrekidis, I. J. Chem. Phys. 2005, 122, 044908.
21. Givon, D.; Kupferman, R.; Stuart, A. Nonlinearity 2004, 17, R55.
22. E. W.; Liu, D.; Vanden-Eijnden, E. Commun. Pur. Appl. Math. 2005, 58, 1544.
23. Borgia, A.; Williams, P.; Clarke, J. Annu. Rev. Biochem. 2008, 77, 101.
24. Schlick, T. Molecular dynamics: Basics. In Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd ed.; Marsden, J., Sirovich, L., Wiggins, S., Antman, S., Eds.; Springer-Verlag: New York, 2002; pp 394-406.
25. Sotomayor, M.; Schulten, K. Science 2007, 316, 1144.
26. Simms, A.; Toofanny, R.; Kehl, C.; Benson, N.; Daggett, V. Protein. Eng. Des. Sel. 2008, 21, 369.
27. Maragakis, P.; Lindorff-Larsen, K.; Eastwood, M.; Dror, R.; Klepeis, J.; Arkin, I.; Jensen, M.; Xu, H.; Trbovic, N.; Friesner, R.; Palmer, A.; Shaw, D. J. Phys. Chem. B 2008, 112, 6155.
28. Moffitt, J.; Chemla, Y.; Smith, S.; Bustamante, C. Annu. Rev. Biochem. 2008, 77, 19-1.
29. Calderon, C. J. Chem. Phys. 2007, 126, 084106.
30. Calderon, C.; Chelli, R. J. Chem. Phys. 2008, 128, 145103.
31. Calderon, C.; Chen, W.; Harris, N.; Lin, K.; Kiang, C. J. Phys.: Condens. Matter 2008, in press.
32. Calderon, C.; Harris, N.; Kiang, C.-H.; Cox, D. J. Phys. Chem. B 2008, in press.
33. Hummer, G. New J. Phys. 2005, 7, 1.
34. Calderon, C. Multiscale Model. Simul. 2007, 6, 656.
35. Chahine, J.; Oliveira, R.; Leite, V.; Wang, J. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14646.
36. Snow, C.; Rhee, Y.; Pande, V. S. Biophys. J. 2006, 95, 078102.
37. Sigg, D.; Qian, H.; Bezanilla, F. Biophys. J. 1999, 76, 782.
38. Park, S.; Schulten, K. J. Chem. Phys. 2004, 120, 5946.
39. Khatri, B. S.; Byrne, K.; Kawakami, M.; Brockwell, D.; Smith, D.; Radford, S.; McLeish, T. Faraday Discuss 2008, 139, 35.
40. Aït-Sahalia, Y. Econometrica 2002, 70, 223.
41. Jimenez, J.; Ozaki, T. J Time Ser. Anal. 2005, 27, 77.
42. Hong, Y.; Li, H. Rev. Finance Stud. 2005, 18, 37-84.
43. Chen, S.; C. Y., T. submitted to J. Econometrics. http://www.stat.iastate.edu/preprint/articles/2006-21.pdf (accessed Oct 1, 2008).
44. Chen, S.; Tang, C. Ann. Stat. 2008, 36, 167.
45. Walther, K.; Brujic, J.; Li, H.; Fernandez, J. Biophys. J. 2006, 90, 3806.
46. Minh, D.; Bui, J.; Chang, C.; Jain, T.; Swanson, J.; McCammon, J. Biophys. J. Lett. 2005, 72 (89), L25.
47. Procacci, P. S., M.; Barducci, A.; Signorini, G.; Chelli, R. J. Chem. Phys. 2006, 125, 164101.
48. Paramore, S.; Ayton, G.; Voth, G. J. Chem. Phys. 2007, 14, 105105.
49. Henzler-Wildman, K.; et al. Nature 2007, 450, 06410.
50. Muller, C. W.; Schulz, G. E. J. Mol. Biol. 1992, 224 (1), 159.
51. Arora, K.; Brooks, C., III Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18496.
52. Socci, N. D.; Onuchic, J. N.; Wolynes, P. G. J. Chem. Phys. 1996, 104, 5860.
53. Frenkel, D.; Smit, B. Molecular dynamics simulations. In Understanding Molecular Simulation: From Algorithms to Applications, 1st ed.; Academic Press: San Diego, CA, 1996; pp 75-88, 377.
54. Beck, D.; Daggett, V. Biophys. J. 2007, 93, 3382.
55. Kevrekidis, I.; Gear, C.; Hummer, G. AIChE J. 2004, 50, 474.
56. Givon, D.; Kevrekidis, I.; Kupferman, R. Commun. Math. Sci. 2006, 4, 707.
57. Horenko, I.; Hartmann, C.; Schütte, C. Phys. Rev. E 2007, 76, 016706.
58. Evensen, G.; van Leeuwen, P. Mon. Weather. Rev. 2000, 128, 1852.
59. Vanden-Eijnden, E. Commun. Pur. Appl. Math 2003, 1, 385.
60. Zhang, L.; Mykland, P.; Ait-Sahalia, Y. J. Am. Stat. Assoc. 2005, 100, 1394.
61. Calderon, C.; Martinez, J.; Carroll, R.; Sorensen, D. submitted 2008.
62. Calderon, C.; Janosi, L.; Kosztin, I. Technical Report, TR08-24; CAAM Dept.: Rice University, 2008.
63. Kou, S.; Xie, X. Phys. Rev. Lett. 2004, 93, 18.
64. Ait-Sahalia, Y.; Fan, J.; Peng, H. Social Science Research Network. http://www.stat.iastate.edu/preprint/articles/2006-21.pdf (accessed Oct 1, 2008).
65. Kloeden, P.; Platen, E. Introductions Numerical Solution of Stochastic Differential Equations, 1st ed.; Springer-Verlag: Berlin, 1999; p 37.
66. Chandrasekhar, S. Rev. Mod. Phys. 1943, 15, 1.
67. El-Ansary, M.; Khalil, H. SIAM J. Control Optim. 1986, 24, 83.
68. Skorokhod, A. V. Asymptotic behavior of systems of stochastic equations containing a small parameter. In Asymptotic Methods in the Theory of Stochastic Differential Equations, 1st ed.; Amer Mathematical Society: Providence, RI, 1989; p 77.
69. Krishnan, J.; Runborg, O.; Kevrekidis, I. Comput. Chem. Eng. 2004, 28, 557.
70. Erban, R.; Frewen, T.; Wang, X.; Elston, T.; Coifman, R.; Nadler, B.; Kevrekidis, I. J. Chem. Phys. 2007, 126, 155103.
71. Pavliotis, G. A.; Stuart, A. M. J. Stat. Phys. 2007, 127, 741.
72. Kutoyants, Y. Diffusion processes and statistical problems. In Statistical Inference for Ergodic Diffusion Processes, 1st ed.; Springer: New York, 2004; p50.
73. Risken, H. Fokker-Planck equation for one variable. In The Fokker-Planck Equation, 2nd ed.; Springer-Verlag: Berlin, 1996; p 98.
74. Chodera, J.; Swope, W.; Pitera, J.; Seok, C.; Dill, K. J. Chem. Theory Comput. 2007, 3, 26.
75. Chu, J.-W.; Trout, B. L.; Brooks, B. R. J. Chem. Phys. 2003, 119 (24), 12708.
76. Michael, S.; Salsbury, F., Jr.; Brooks, C., III J. Chem. Phys. 2002, 116 (24), 10606.
77. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
78. Marsili, S.; Barducci, A.; Chelli, R.; Procacci, P.; Schettino, V. J. Phys. Chem. B 2006, 110, 14011.