Stochastic thermodynamics of chemical reaction networks

Journal of Chemical Physics

Volumn 126, Issue 4, 2007, Pages

  Schmiedl, Tim ^a   Seifert, Udo ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ENERGY BALANCE; ENTROPY; STOCHASTIC CONTROL SYSTEMS; THEOREM PROVING; THERMODYNAMICS;

CYCLIC REACTION NETWORK; ENTROPY PRODUCTION; INTEGRAL FLUCTUATION THEOREM; INTERNAL ENERGY;

REACTION KINETICS;

EID: 33847717110     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2428297     Document Type: Article

References (61)

1. N. G. van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 1981).
2. C. W. Gardiner, Handbook of Stochastic Methods, 3rd ed. (Springer-Verlag, Berlin, 2004).
3. G. Nicolis and I. Prigogine, Self-Organization in Nonequilibrium Systems: From Dissipative Structures to Order through Fluctuations (Wiley, New York, 1977).
4. J. Schnakenberg, Rev. Mod. Phys. 48, 571 (1976).
5. C. Y. Mou, J. li Luo, and G. Nicolis, J. Chem. Phys. 84, 7011 (1986).
6. P. Gaspard, J. Chem. Phys. 120, 8898 (2004).
7. D. Andrieux and P. Gaspard, J. Chem. Phys. 121, 6167 (2004).
8. H. H. McAdams and A. Arkin, Proc. Natl. Acad. Sci. U.S.A. 94, 814 (1997).
9. T. B. Kepler and T. C. Elston, Biophys. J. 81, 3116 (2001).
10. J. Paulsson, Nature (London) 427, 415 (2004).
11. T. Shibata and K. Fujimoto, Proc. Natl. Acad. Sci. U.S.A. 102, 331 (2005).
12. A. Parmeggiani, F. Jülicher, A. Ajdari, and J. Prost, Phys. Rev. E 60, 2127 (1999).
13. M. E. Fisher and A. B. Kolomeisky, Proc. Natl. Acad. Sci. U.S.A. 96, 6597 (1999).
14. R. Lipowsky, Phys. Rev. Lett. 85, 4401 (2000).
15. C. Maes and M. H. van Wieren, J. Stat. Phys. 112, 329 (2003).
16. J. E. Baker, J. Theor. Biol. 228, 467 (2004).
17. C. Bustamante, J. Liphardt, and F. Ritort, Phys. Today 58 (7), 43 (2005).
18. K. Sekimoto, Prog. Theor. Phys. Suppl. 130, 17 (1998).
19. T. Shibata and K. Sekimoto, J. Phys. Soc. Jpn. 69, 2455 (2000).
20. C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997).
21. C. Jarzynski, Phys. Rev. E 56, 5018 (1997).
22. G. E. Crooks, Phys. Rev. E 60, 2721 (1999).
23. G. E. Crooks, Phys. Rev. E 61, 2361 (2000).
24. D. J. Evans and D. J. Searles, Phys. Rev. E 50, 1645 (1994).
25. G. Gallavotti and E. G. D. Cohen, Phys. Rev. Lett. 74, 2694 (1995).
26. J. Kurchan, J. Phys. A 31, 3719 (1998).
27. J. L. Lebowitz and H. Spohn, J. Stat. Phys. 95, 333 (1999).
28. C. Maes, Śm. Poincaŕ 2, 29 (2003).
29. C. Maes and K. Netocny, J. Stat. Phys. 110, 269 (2003).
30. T. Hatano and S. Sasa, Phys. Rev. Lett. 86, 3463 (2001).
31. U. Seifert, Phys. Rev. Lett. 95, 040602 (2005).
32. G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. 98, 3658 (2001).
33. J. Liphardt, S. Dumont, S. B. Smith, I. Tinoco, Jr., and C. Bustamante, Science 296, 1832 (2002).
34. S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004).
35. O. Braun, A. Hanke, and U. Seifert, Phys. Rev. Lett. 93, 158105 (2004).
36. D. Collin, F. Ritort, C. Jarzynski, S. Smith, I. Tinoco, and C. Bustamante, Nature (London) 437, 231 (2005).
37. T. Speck and U. Seifert, Eur. Phys. J. B 43, 543 (2005).
38. G. M. Wang, E. M. Sevick, E. Mittag, D. J. Searles, and D. J. Evans, Phys. Rev. Lett. 89, 050601 (2002).
39. D. M. Carberry, J. C. Reid, G. M. Wang, E. M. Sevick, D. J. Searles, and D. J. Evans, Phys. Rev. Lett. 92, 140601 (2004).
40. E. H. Trepagnier, C. Jarzynski, F. Ritort, G. E. Crooks, C. J. Bustamante, and J. Liphardt, Proc. Natl. Acad. Sci. U.S.A. 101, 15038 (2004).
41. V. Blickle, T. Speck, L. Helden, U. Seifert, and C. Bechinger, Phys. Rev. Lett. 96, 070603 (2006).
42. D. Andrieux and P. Gaspard, J. Stat. Mech.: Theory Exp. 01, P01001 (2006).
43. U. Seifert, J. Phys. A 37, L517 (2004).
44. H. Qian, Phys. Rev. E 64, 022101 (2001).
45. H. Qian and D. A. Beard, Biophys. Chem. 114, 213 (2005).
46. H. Qian, J. Phys.: Condens. Matter 17, S3783 (2005).
47. W. J. Heuett and H. Qian, J. Chem. Phys. 124, 044110 (2006).
48. T. L. Hill, Free Energy Transduction and Biochemical Cycle Kinetics, 2nd ed. (Dover, New York, 1989).
49. T. Shibata, e-print cond-mat/0012404.
50. T. Schmiedl, T. Speck, and U. Seifert, J. Stat. Phys. (in press).
51. Y. Oono and M. Paniconi, Prog. Theor. Phys. Suppl. 130, 29 (1998).
52. D. A. McQuarrie, Statistical Mechanics (University Science Books, Sausalito, 2000).
53. T. L. Hill, Statistical Thermodynamics (Dover, New York, 1986).
54. U. Seifert, Europhys. Lett. 70, 36 (2005).
55. C. Jarzynski, J. Stat. Phys. 96, 415 (1999).
56. T. Speck and U. Seifert, J. Phys. A 38, L581 (2005).
57. T. Schmiedl, Diploma thesis, Universität Stuttgart, 2006.
58. W. Min, L. Jiang, J. Yu, S. C. Kou, H. Qian, and X. S. Xie, Nano Lett. 5, 2372 (2005).
59. S. Schuler, T. Speck, C. Tietz, J. Wrachtrup, and U. Seifert, Phys. Rev. Lett. 94, 180602 (2005).
60. C. Tietz, S. Schuler, T. Speck, U. Seifert, and J. Wrachtrup, Phys. Rev. Lett. 97, 050602 (2006).
61. F. Schwabl, Statistical Mechanics, 1st ed. (Springer, New York, 2002).