Cycle kinetics, steady state thermodynamics and motors - A paradigm for living matter physics

Journal of Physics Condensed Matter

Volumn 17, Issue 47, 2005, Pages

  Qian, Hong ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; ISOTHERMS; MATHEMATICAL MODELS; OPEN SYSTEMS; PROTEINS; REACTION KINETICS; THERMODYNAMICS;

CYCLE KINETICS; MOLECULAR MOTORS; MOTOR PROTEINS; NONEQUILIBRIUM STEADY STATE THEORY;

MOLECULAR PHYSICS;

EID: 27744481288     PISSN: 09538984     EISSN: None     Source Type: Journal    
DOI: 10.1088/0953-8984/17/47/010     Document Type: Article

References (105)

1. Edsall J T and Wyman J 1958 Biophysical Chemistry (New York: Academic)
2. Tanford C 1961 Physical Chemistry of Macromolecules (New York: Wiley)
3. Cantor C R and Schimmel P R 1980 Biophysical Chemistry (San Francisco, CA: Freeman)
4. Eisenberg H 2002 Biophys. Chem. 98 3-13
5. Eisenberg H 2002 Biophys. Chem. 100 33-48
6. Eisenberg H 2002 Biophys. Chem. 101 15-27
7. Hill T L 1960 An Introduction to Statistical Thermodynamics (New York: Dover)
8. Nicolis G and Prigogine I 1977 Self-Organization in Nonequilibrium Systems (New York: Wiley-Interscience)
9. Westerhoff H V and Palsson B Ø 2004 Nat. Biotechnol. 22 1249-52
10. Hill T L 1977 Free Energy Transduction in Biology: the Steady-State Kinetic and Thermodynamic Formalism (New York: Academic)
11. Huxley A F 1957 Prog. Biophys. Biophys. Chem. 7 257-314
12. Hill T L 1974 Prog. Biophys. Mol. Biol. 28 267-340
13. Hill T L 1975 Prog. Biophys. Mol. Biol. 29 105-59
14. Hill T L 1995 Free Energy Transduction and Biochemical Cycle Kinetics (New York: Springer)
15. Sheetz M P and Spudich J A 1983 Nature 303 31-5
16. Vale R D, Schnapp B J, Reese T S and Sheetz M P 1985 Cell 40 449-54
17. Tolman R C 1924 Phys. Rev. 23 693-709
18. Lewis G N 1925 Proc. Natl Acad. Sci. USA 11 179-83
19. Qian H 2001 Proc. R. Soc. A 457 1645-55
20. Schnakenberg J 1976 Rev. Mod. Phys. 48 571-85
21. Qian H and Beard D A 2005 Biophys. Chem. 114 213-20
22. Fermi E 1956 Thermodynamics (New York: Dover)
23. Jarzynski C 1997 Phys. Rev. Lett. 78 2690-3
24. Xie X S 2002 personal communication
25. Hummer G and Szabo A 2001 Proc. Natl Acad. Sci. USA 98 3658-61
26. Liphardt J, Dumont S, Smith S B, Tinoco I and Bustamante C 2002 Science 296 1832-5
27. Wyman J and Gill S J 1990 Binding and Linkage: Functional Chemistry of Biological Macromolecules (Mill Valley, CA: Univ. Sci. Books)
28. Hatano T and Sasa S 2001 Phys. Rev. Lett. 86 3463-6
29. Trepagnier E H, Jarzynski C, Ritort F, Crooke G E, Bustamante C J and Liphardt J 2004 Proc. Natl Acad. Sci. USA 101 15038-41
30. Qian H, Yu J and Xie X S 2004 in preparation
31. Lebowitz J L and Spohn H 2001 J. Stat. Phys. 95 333-65
32. Qian H 1997 Biophys. Chem. 67 263-7
33. Qian H 2000 Biophys. Chem. 83 35-43
34. Fisher M E and Kolomeisky A B 1999 Proc. Natl Acad. Sci. USA 96 6597-602
35. Fisher M E and Kolomeisky A B 1999 Physica A 274 241-66
36. Fisher M E and Kolomeisky A B 2001 Proc. Natl Acad. Sci. USA 98 7748-53
37. Kolomeisky A B and Fisher M E 2003 Biophys. J. 84 1642-50
38. Betterton M D and Jülicher F 2003 Phys. Rev. Lett. 91 258103
39. Stukalin E B, Phillips H and Kolomeisky A B 2005 Phys. Rev. Lett. 94 238101
40. Delagoutte E and von Hippel P H 2003 Q. Rev. Biophys. 36 1-69
41. Qian H 2004 Phys. Rev. E 69 012901
42. Oosawa F and Nakaoka Y 1977 J. Theor. Biol. 66 747-61
43. Oosawa F, Tsuchiya M and Kubori T 1987 Stochastic Models in Biology ed M Kimura, G Kallianpur and T Hida (New York: Springer) pp 158-70
44. Vale R D and Oosawa F 1990 Adv. Biophys. 26 97-134
45. Astumian R D, Chock P B, Tsong T Y, Chen Y-d and Westerhoff H V 1987 Proc. Natl Acad. Sci. USA 84 434-8
46. Chen Y-d 1987 Proc. Natl Acad. Sci. USA 84 729-33
47. Tsong T Y and Astumian R D 1987 Prog. Biophys. Mol. Biol. 50 1-45
48. Tsong T Y 1990 Ann. Rev. Biophys. Biophys. Chem. 19 83-106
49. Ajdari A and Prost J 1992 Acad. Sci. Paris 315 1635-9
50. Leibler S and Huse D A 1993 J. Cell Biol. 121 1357-68
51. Peskin C S, Odell G M and Oster G F 1993 Biophys. J. 65 316-24
52. Astumian R D and Bier M 1994 Phys. Rev. Lett. 72 1766-9
53. Magnasco M O 1994 Phys. Rev. Lett. 72 2656-9
54. Doering C R, Horsthemke W and Riordan J 1994 Phys. Rev. Lett. 72 2984-7
55. Astumian R D 1997 Science 276 917-22
56. Jülicher F, Ajdari A and Prost J 1997 Rev. Mod. Phys. 69 1269-81
57. Bustamante C, Keller D and Oster G 2001 Acc. Chem. Res. 34 412-20
58. Astumian R D and Hänggi P 2002 Phys. Today 55 33-9
59. Reimann P 2002 Phys. Rep. 361 57-265
60. Parrondo J M R and de Cisneros B J 2002 Appl. Phys. A 75 179-91
61. Qian H 2002 J. Phys. Chem. B 106 2065-73
62. Epstein M and Herzog W 1998 Theoretical Models of Skeletal Muscle: Biological and Mathematical Considerations (New York: Wiley)
63. Oster G and Wang H 2003 Trends Cell Biol. 13 114-21
64. Baker J E 2004 J. Theor. Biol. 228 467-76
65. Qian H 1998 Phys. Rev. Lett. 81 3063-6
66. Keller D and Bustamante C 2000 Biophys. J. 78 541-56
67. Zhou H-X and Chen Y-d 1996 Phys. Rev. Lett. 77 194-7
68. Lipowsky R 2000 Phys. Rev. Lett. 85 4401-4
69. Qian H 2001 Phys. Rev. E 64 022101
70. Sasai M and Wolynes P G 2003 Proc. Natl Acad. Sci. USA 100 2374-9
71. Qian H, Qian M and Tang X 2002 J. Stat. Phys. 107 1129-41
72. Jiang D-q, Qian M and Qian M-P 2004 Mathematical Theory of Nonequilibrium Steady-State (LNM vol 1833) (New York: Springer)
73. Chen Y-d 1978 Biophys. J. 21 279-85
74. Oosawa F and Masai J 1982 Biophys. Chem. 16 33-40
75. Qian M, Qian M-P and Zhang X-J 2003 Phys. Lett. A 309 371-6
76. Berdichevsky V and Gitterman M 1998 Physica A 249 88-95
77. Qian H and Qian M 2000 Phys. Rev. Lett. 84 2271-4
78. Hänggi P 2002 Chem. Phys. Chem. 3 285-90
79. Qian H, Beard D A and Liang S-D 2003 Eur. J. Biochem. 270 415-21
80. Qian H, Saffarian S and Elson E L 2002 Proc. Natl Acad. Sci. USA 99 10376-81
81. Qian H 2002 Phys. Rev. E 65 021111
82. Graham R 1989 Noise in Nonlinear Dynamical Systems ed F Moss and P V E McClintock pp 225-78
83. Bak P, Tang C and Wiesenfeld K 1988 Phys. Rev. A 38 364-74
84. Qian H 2003 Biophys. Chem. 105 585-93
85. Qian H and Reluga T C 2005 Phys. Rev. Lett. 94 028101
86. de Groot S R and Mazur P 1984 Nonequilibrium Thermodynamics (New York: Dover)
87. Pérez-Madrid A, Rubí J M and Mazur P 1994 Physica A 212 231-8
88. Reguera D, Rubí J M and Villa J M G 2005 J. Phys. Chem. B at press
89. Villa J M G and Rubí J M 2001 Proc. Natl Acad. Sci. USA 98 11081-4
90. Kjelstrup S, Rubí J M and Bedeaus D 2005 J. Theor. Biol. 234 7-12
91. Kwon C, Ao P and Thouless D J 2005 Proc. Natl Acad. Sci. USA at press
92. Zhu X-M, Yin L, Hood L and Ao P 2004 J. Bioinf. Comput. Biol. 2 785-817
93. Dorfman J R 1999 An Introduction to Chaos in Nonequilibrium Statistical Mechanics (Cambridge: Cambridge University Press)
94. Derrida B, Lebowitz J L and Speer E R 2002 Phys. Rev. Lett. 89 030601
95. Ruelle D P 2003 Proc. Natl Acad. Sci. USA 100 3054-8
96. Evans D J, Cohen E G D and Morriss G P 1993 Phys. Rev. Lett. 71 2401-4
97. Khinchin A I 1960 Mathematical Foundations of Statistical Mechanics (New York: Dover)
98. Blanchard P, Cessac B and Krüger T 2000 J. Stat. Phys. 98 375-404
99. Cessac B, Blanchard P, Krüger T and Meunier J L 2004 J. Stat. Phys. 115 1283-326
100. Carlson J M, Chayes J T, Grannan E R and Swindle G H 1990 Phys. Rev. Lett. 65 2547-50
101. Reed W J and Hughes B D 2002 Phys. Rev. E 66 067103
102. Seifert U 2005 Europhys. Lett. 70 36-41
103. Seifert U 2005 Phys. Rev. Lett. 95 040602
104. Qian H 2005 Preprint cond-mat/0507659
105. Qian H 2005 Preprint cond-mat/0508013