A derivation of the master equation from path entropy maximization

Journal of Chemical Physics

Volumn 137, Issue 7, 2012, Pages

  Lee, Julian ^a   Pressé, Steve ^b  

^a Soongsil University   (South Korea)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COARSE GRAINING; ENTROPY MAXIMIZATION; MASTER EQUATIONS; MAXIMUM ENTROPY;

ENTROPY; INVERSE PROBLEMS; STOCHASTIC MODELS;

MARKOV PROCESSES;

ARTICLE; ENTROPY; PROBABILITY; SOLUTION AND SOLUBILITY; STATISTICS;

ENTROPY; MARKOV CHAINS; SOLUTIONS; STOCHASTIC PROCESSES;

EID: 84865517782     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4743955     Document Type: Article

References (33)

1. N. G. van Kampen, Stochastic Processes in Chemistry and Physics (North-Holland, Amsterdam, 1981).
2. K. L. Chung, Lectures from Markov Processes to Brownian Motion (Springer-Verlag, New York, 1982).
3. I. Gopich and A. Szabo, J. Chem. Phys. 118, 454 (2003). 10.1063/1.1523896
4. J. Cao and R. J. Silbey, J. Phys. Chem. B 112, 12867 (2008). 10.1021/jp803347m
5. A. M. Berezhkovskii, A. Szabo, and G. H. Weiss, J. Chem. Phys. 110, 9145 (1999). 10.1063/1.478836
6. X.-J. Zhang, H. Qian, and M. Qian, Phys. Rep. 510, 1 (2012). 10.1016/j.physrep.2011.09.002
7. H. Ge, H. Qian, and M. Qian, Phys. Rep. 510, 87 (2012). 10.1016/j.physrep.2011.09.001
8. F. L. H. Brown, Acc. Chem. Res. 39, 363 (2006). 10.1021/ar050028l
9. H. D. Feng and J. Wang, Chem. Phys. Lett. 501, 562 (2011). 10.1016/j.cplett.2010.11.017
10. S. R. de Groot and P. Mazur, Non-Equilibrium Thermodynamics (Dover, New York, 1983).
11. J.-H. Prinz, J. D. Chodera, V. S. Pande, W. C. Swope, J. C. Smith, and F. Noé, J. Chem. Phys. 134, 244108 (2011). 10.1063/1.3592153
12. V. S. Pande, K. Beauchamp, and G. R. Bowman, Methods 52, 99 (2010). 10.1016/j.ymeth.2010.06.002
13. P. Kasson and V. S. Pande, Pac. Symp. Biocomput. 15, 260 (2010).
14. A. A. Filyukov and V. Y. Karpov, J. Eng. Phys. Thermophys. 13, 326 (1967); 10.1007/BF00832348
15. A. A. Filyukov and V. Y. Karpov, J. Eng. Phys. Thermophys. 13, 416 (1967); 10.1007/BF00828961
16. A. A. Filyukov, J. Eng. Phys. Thermophys. 14, 429 (1968). 10.1007/BF00828058
17. E. T. Jaynes, Macroscopic prediction., in Complex Systems Operational Approaches in Neurobiology, Physics, and Computers, edited by, H. Haken, (Springer-Verlag, Berlin, 1985).
18. J. E. Shore and R. W. Johnson, IEEE Trans. Inf. Theory 26, 26 (1980). 10.1109/TIT.1980.1056144
19. E. T. Jaynes, Phys. Rev. 106, 620 (1957); 10.1103/PhysRev.106.620
20. E. T. Jaynes, Phys. Rev. 108, 171 (1957). 10.1103/PhysRev.108.171
21. S. F. Gull and G. J. Daniell, Nature (London) 272, 686 (1978). 10.1038/272686a0
22. P. J. Steinbach, K. Chu, H. Frauenfelder, J. B. Johnson, D. C. Lamb, G. U. Nienhaus, T. B. Sauke, and R. D. Young, Biophys. J. 61, 235 (1992). 10.1016/S0006-3495(92)81830-1
23. E. T. Jaynes, Probability Theory: The Logic of Science (Cambridge University Press, London, 2003).
24. G. Stock, K. Ghosh, and K. A. Dill, J. Chem. Phys. 128, 194102 (2008). 10.1063/1.2918345 (Pubitemid 351733964)
25. K. Ghosh, K. A. Dill, M. M. Inamdar, E. Seitaridou, and R. Phillips, Am. J. Phys. 74, 123 (2006). 10.1119/1.2142789 (Pubitemid 43258528)
26. R. Zwanzig, Nonequilibrium Statistical Mechanics (Oxford University Press, New York, 2001).
27. D. T. Gillespie, J. Phys. Chem. 81, 2340 (1977). 10.1021/j100540a008
28. H. Ge, S. Pressé, K. Ghosh, and K. A. Dill, J. Chem. Phys. 136, 064108 (2012). 10.1063/1.3681941
29. A. Berman and R. J. Plemmons, Nonnegative Matrices in the Mathematical Sciences (SIAM, 1994).
30. S. P. Meyn and R. L. Tweedie, Markov Chains and Stochastic Stability (Springer-Verlag, London, 1993).
31. E. Seneta, Non-Negative Matrices and Markov Chains (Springer, 1981).
32. D. L. Isaacson and I. Madsen, Markov Chains: Theory and Applications (Wiley, 1976).
33. C. J. Monthus, J. Stat. Mech.: Theory Exp. 2011, P03008. 10.1088/1742-5468/2011/03/P03008