Maximum Caliber: A variational approach applied to two-state dynamics

Journal of Chemical Physics

Volumn 128, Issue 19, 2008, Pages

  Stock, Gerhard ^a   Ghosh, Kingshuk ^b   Dill, Ken A ^b  

^a GOETHE UNIVERSITY   (Germany)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICAL SYSTEMS; FUNCTION EVALUATION; PHASE EQUILIBRIA; STATISTICAL MECHANICS; VARIATIONAL TECHNIQUES;

DYNAMICAL PARTITION FUNCTION; DYNAMICAL PROPERTIES; MICROSTATES; TWO-STATE DYNAMICS;

MOLECULAR VIBRATIONS;

ALGORITHM; ARTICLE; COMPUTER SIMULATION; ENTROPY; METHODOLOGY; NORMAL DISTRIBUTION; PHYSICAL CHEMISTRY; STATISTICAL MODEL; THEORETICAL MODEL; TIME;

ALGORITHMS; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; ENTROPY; MODELS, STATISTICAL; MODELS, THEORETICAL; NORMAL DISTRIBUTION; TIME FACTORS;

EID: 44349108866     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2918345     Document Type: Article

References (27)

1. H. B. Callen, Thermodynamics and an Introduction to Thermostatistics (Wiley, New York, 1985).
2. N. G. Van Kampen, Stochastic Processes in Physics and Chemistry (Elsevier, Amsterdam, 1997).
3. R. Zwanzig, Nonequilibrium Statistical Mechanics (Oxford University Press, Oxford, 2001).
4. R. M. Mazo, Brownian Motion (Clarendon, Oxford, 2002).
5. E. T. Jaynes, Annu. Rev. Phys. Chem. 0066-426X 10.1146/annurev.pc.31. 100180.003051 31, 579 (1980).
6. R. Blossey, Computational Biology: A Statistical Mechanics Perspective (Chapman & Hall/CRC, New York, 2006).
7. D. A. Beard and H. Qian, Chemical Biophysics: Quantitative Analysis of Cellular Systems (Cambridge University Press, Cambridge, 2008).
8. E. T. Jaynes, Phys. Rev. 0031-899X 10.1103/PhysRev.106.620 106, 620 (1957).
9. See http://bayes.wustl.edu/ for numerous helpful references on the Maximum Entropy formulation.
10. K. Dill and S. Bromberg, Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology (Garland Science, New York, 2003).
11. E. T. Jaynes, in The Maximum Entropy Formalism, edited by, R. D. Levine, and, M. Tribus, (MIT, Cambridge, MA, 1978), p. 15.
12. E. T. Jaynes, in Complex Systems-Operational Approaches, edited by, H. Haken, (Springer, Berlin, 1985), pp. 254-269.
13. L. S. Schulman, Techniques and Applications of Path Integration (Wiley, New York, 1981).
14. J. P. Dougherty, Philos. Trans. R. Soc. London, Ser. A 0962-8428 10.1098/rsta.1994.0022 346, 259 (1994).
15. R. C. Dewar, J. Phys. A 0305-4470 10.1088/0305-4470/38/21/L01 38, L371 (2005).
16. K. Ghosh, K. Dill, M. M. Inamdar, E. Seitaridou, and R. Phillips, Am. J. Phys. 0002-9505 10.1119/1.2142789 74, 123 (2006).
17. E. Seitaridou, M. Inamdar, R. Phillips, K. Ghosh, and K. Dill, J. Phys. Chem. 111, 2288 (2007). 0022-3654
18. D. Wu, K. Ghosh, M. Inamdar, H. Lee, S. Fraser, K. Dill, and R. Phillips (to be published) (2008).
19. D. J. Evans, E. G. D. Cohen, and G. P. Morriss, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.71.2401 71, 2401 (1993).
20. G. M. Wang, E. M. Sevick, E. Mittag, D. J. Searles, and D. J. Evans, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.89.050601 89, 050601 (2002).
21. D. T. Gillespie, J. Phys. Chem. 0022-3654 10.1021/j100540a008 81, 2340 (1977).
22. M. A. Gibson and J. Bruck, J. Phys. Chem. A 1089-5639 10.1021/jp993732q 104, 1876 (2000).
23. D. T. Gillespie, Annu. Rev. Phys. Chem. 0066-426X 10.1146/annurev. physchem.58.032806.104637 58, 35 (2007).
24. R. Zwanzig, J. Phys. Chem. B 1089-5647 10.1021/jp0034630 105, 6472 (2001).
25. P. K. Purohit, J. Kondev, and R. Phillips, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.0737893100 100, 3173 (2003).
26. V. B. P. Leite, J. N. Onuchic, G. Stell, and J. Wang, Biophys. J. 0006-3495 10.1529/biophysj.104.046243 87, 3633 (2004).
27. R. K. Pathria, Statistical Mechanics (Butterworth-Heinemann, Oxford, 1996).