Universal properties of mechanisms from two-state trajectories

Journal of Chemical Physics

Volumn 128, Issue 11, 2008, Pages

  Flomenbom, O ^a   Silbey, R J ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA REDUCTION; PROBABILITY DENSITY FUNCTION; STATISTICAL METHODS;

KINETIC SCHEMES; STATISTICAL PROPERTIES;

CRYSTAL SYMMETRY;

PROTEIN;

ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; KINETICS; MATHEMATICS; METABOLISM;

COMPUTER SIMULATION; KINETICS; MATHEMATICS; MODELS, BIOLOGICAL; PROTEINS;

EID: 41049100515     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2825613     Document Type: Article

References (77)

1. W. E. Moerner and M. Orrit, Science SCIEAS 0036-8075 10.1126/science.283. 5408.1670 283, 1670 (1999).
2. S. Weiss, Science SCIEAS 0036-8075 10.1126/science.283.5408.1676 283, 1676 (1999).
3. E. Neher and B. Sakmanm, Nature (London) NATUAS 0028-0836 10.1038/260799a0 260, 799 (1976).
4. D. D. Boehr, H. J. Dyson, and P. E. Wright, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr050312q 106, 3055 (2006).
5. R. D. Smiley and G. G. Hammes, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr0502955 106, 3080 (2006).
6. X. Michalet, S. Weiss, and M. Jager, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr0404343 106, 1785 (2006).
7. C. G. Nichols, Nature (London) NATUAS 0028-0836 10.1038/nature04711 440, 470 (2006).
8. A. Mitra, R. Tascione, A. Auerbach, and S. Licht, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.068783 89, 3071 (2005).
9. J. J. Kasianowicz, E. Brandin, D. Branton, and D. W. Deamer, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.93.24.13770 93, 13770 (1996).
10. L. Kullman, P. A. Gurnev, M. Winterhalter, and S. M. Bezrukov, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.038101 96, 038101 (2006).
11. B. Schuler, E. A. Lipman, and W. A. Eaton, Nature (London) NATUAS 0028-0836 10.1038/nature01060 419, 743 (2002).
12. H. Yang, G. Luo, P. Karnchanaphanurach, T. Louie, I. Rech, S. Cova, L. Xun, and X. S. Xie, Science SCIEAS 0036-8075 10.1126/science.1086911 302, 262 (2003).
13. W. Min, G. Lou, B. J. Cherayil, S. C. Kou, and X. S. Xie, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.198302 94, 198302 (2005).
14. E. Rhoades, E. Gussakovsky, and G. Haran, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.2628068100 100, 3197 (2003).
15. X. Zhuang, H. Kim, M. J. B. Pereira, H. P. Babcock, N. G. Walter, and S. Chu, Science SCIEAS 0036-8075 10.1126/science.1069013 296, 1473 (2002).
16. T. Ha, A. Y. Ting, J. Liang, W. B. Caldwell, A. A. Deniz, D. S. Chemla, P. G. Schultz, and S. Weiss, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.3.893 96, 893 (1999).
17. H. Lu, L. Xun, and X. S. Xie, Science SCIEAS 0036-8075 10.1126/science.282.5395.1877 282, 1877 (1998).
18. L. Edman, Z. Földes-Papp, S. Wennmalm, and R. Rigler, Chem. Phys. CMPHC2 0301-0104 10.1016/S0301-0104(99)00098-1 247, 11 (1999).
19. K. Velonia, O. Flomenbom, D. Loos, Angew. Chem., Int. Ed. ACIEF5 1433-7851 10.1002/anie.200460625 44, 560 (2005).
20. B. P. English, W. Min, A. M. van Oijen, K. T. Lee, G. Luo, H. Sun, B. J. Cherayil, S. C. Kou, and X. S. Xie, Nat. Chem. Biol. NCBABT 1552-4450 10.1038/nchembio759 2, 87 (2006).
21. S. Nie, D. T. Chiu, and R. N. Zare, Science SCIEAS 0036-8075 10.1126/science.7973650 266, 1018 (1994).
22. R. Shusterman, S. Alon, T. Gavrinyov, and O. Krichevsky, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.92.048303 92, 048303 (2004).
23. G. Zumofen, J. Hohlbein, and C. G. Hübner, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.260601 93, 260601 (2004).
24. A. E. Cohen and W. E. Moerner, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0509976103 103, 4362 (2006).
25. M. Orrit and J. Bernard, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.65.2716 65, 2716 (1990).
26. R. M. Dickson, A. B. Cubitt, R. Y. Tsien, and W. E. Moerner, Nature (London) NATUAS 0028-0836 10.1038/41048 388, 355 (1997).
27. I. Chung and M. G. Bawendi, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.70.165304 70, 165304 (2004).
28. R. J. Davenport, G. J. L. Wuite, R. Landick, and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.287.5462.2497 287, 2497 (2000).
29. N. R. Forde, D. Izhaky, G. R. Woodcock, G. J. L. Wuite, and C. Bustamante, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas. 142417799 99, 11682 (2002).
30. K. Adelman, A. La Porta, T. J. Santangelo, J. T. Lis, J. W. Roberts, and M. D. Wang, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas. 212358999 99, 13538 (2002).
31. F. Ritort, J. Phys.: Condens. Matter JCOMEL 0953-8984 10.1088/0953-8984/18/32/R01 18, R531 (2006).
32. Y. Levy, A. Caflisch, J. N. Onuchic, and P. G. Wolynes, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2004.04.028 340, 67 (2004).
33. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.53.082301.113146 53, 291 (2002).
34. D. Colquhoun and A. G. Hawkes, Philos. Trans. R. Soc. London, Ser. B PTRBAE 0962-8436 10.1098/rstb.1982.0156 300, 1 (1982).
35. D. R. Fredkin and J. A. Rice, J. Appl. Probab. JPRBAM 0021-9002 10.2307/3214130 23, 208 (1986).
36. J. Cao, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(00)00809-5 327, 38 (2000).
37. P. Kienker, Proc. R. Soc. London, Ser. B PRLBA4 0962-8452 236, 269 (1989).
38. R. J. Bauer, B. F. Bowman, and J. L. Kenyon, Biophys. J. BIOJAU 0006-3495 52, 961 (1987).
39. O. Flomenbom, J. Klafter, and A. Szabo, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.104.055905 88, 3780 (2005).
40. O. Flomenbom and J. Klafter, Acta Phys. Pol. B APOBBB 0587-4254 36, 1527 (2005).
41. J. B. Witkoskie and J. Cao, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1785783 121, 6361 (2004).
42. W. J. Bruno, J. Yang, and J. Pearson, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0409110102 102, 6326 (2005).
43. O. Flomenbom and R. J. Silbey, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0604546103 103, 10907 (2006).
44. L. Song and K. L. Magleby, Biophys. J. BIOJAU 0006-3495 67, 91 (1994).
45. N. G. Van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 1992).
46. J. Yang, W. J. Bruno, W. S. Hlavacek, and J. E. Pearson, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.071852 91, 1136 (2006).
47. D. Colquhoun, K. A. Dowsland, M. Beato, and A. J. Plested, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.103.038679 86, 3510 (2004).
48. H. Yang and X. S. Xie, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1521154 117, 10965 (2002).
49. F. L. H. Brown, Acc. Chem. Res. ACHRE4 0001-4842 10.1021/ar050028l 39, 363 (2006).
50. E. Barkai, Y. Jung, and R. Silbey, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.55.111803.143246 55, 457 (2004).
51. F. Qin, A. Auerbach, and F. Sachs, Biophys. J. BIOJAU 0006-3495 70, 264 (1996).
52. J. Wang and P. Wolynes, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.74.4317 74, 4317 (1995).
53. E. Geva and J. L. Skinner, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(98)00322-4 288, 225 (1998).
54. S. Yang and J. Cao, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1521155 117, 10996 (2002).
55. O. Flomenbom and J. Klafter, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1979489 123, 064903 (2005).
56. J. Y. Sung and R. J. Silbey, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2005.08.057 415, 10 (2005).
57. J. W. Shaevitz, S. M. Block, and M. J. Schnitzer, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.064295 89, 2277 (2005).
58. O. Flomenbom, J. Hofkens, K. Velonia, F. C. de Schryver, A. E. Rowan, R. J. M. Nolte, J. Klafter, and R. J. Silbey, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2006.10.060 432, 371 (2006).
59. B. Hille, Ion Channels of Excitable Membranes (Sinauer, Sunderland, MA, 2001).
60. I. Goychuk and P. Hänggi, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.70.051915 70, 051915 (2004).
61. G. L. Millhauser, E. E. Salpeter, and R. E. Oswald, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.85.5.1503 85, 1503 (1988).
62. N. Agmon, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp0012911 104, 7830 (2000).
63. O. Flomenbom, K. Velonia, D. Loos, S. Masuo, M. Cotlet, Y. Engelborghs, J. Hofkens, A. E. Rowan, R. J. M. Nolte, M. Van der Auweraer, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0409039102 102, 2368 (2005).
64. I. V. Gopich and A. Szabo, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2180770 124, 154712 (2006).
65. H. Qian and E. L. Elson, Biophys. Chem. BICIAZ 0301-4622 10.1016/S0301-4622(02)00145-X 101, 565 (2002).
66. S. C. Kou, B. J. Cherayil, W. Min, B. P. English, and X. S. Xie, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp051490q 109, 19068 (2005).
67. S. Bianco, P. Grigolini, and P. Paradisi, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2087427 123, 174704 (2005).
68. Y. Kafri, D. K. Lubensky, and D. R. Nelson, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.103.036152 86, 3373 (2004).
69. M. E. Fisher and A. B. Kolomeisky, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.12.6597 96, 6597 (1999).
70. A. B. Kolomeisky and M. E. Fisher, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1326912 113, 10867 (2000).
71. U. Seifert, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i2005-10003-9 70, 36 (2005).
72. M. O. Vlad, F. Moran, F. W. Schneider, and J. Ross, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.192439099 99, 12548 (2002).
73. P. Allegrini, G. Aquino, P. Grigolini, L. Palatella, and A. Rosa, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.68.056123 68, 056123 (2003).
74. O. Flomenborn and J. Klafter, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.95.098105 95, 098105 (2005); O. Flomenbom, J. Klafter, and R. J. Silbey, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.97.178901 97, 178901 (2006).
75. O. Flomenbom and R. J. Silbey, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2749518 127, 034102 (2007).
76. J. Tang and R. A. Marcus, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2128409 123, 204511 (2005).
77. G. Bel, Y. J. Zheng, and F. L. H. Brown, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp062345v 110, 19066 (2006).