Stochastic dynamics of model proteins on a directed graph

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 79, Issue 6, 2009, Pages

  Bongini, Lorenzo ^a,b   Casetti, Lapo ^a,b,c   Livi, Roberto ^a,b,c   Politi, Antonio ^b,d   Torcini, Alessandro ^b,c,d  

^a UNIVERSITY OF FLORENCE   (Italy)

^b Centro Interdipartimentale per Lo Studio Delle Dinamiche Complesse   (Italy)

^c INFN SEZIONE DI FIRENZE   (Italy)

^d ISTITUTO DEI SISTEMI COMPLESSI   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CONSTANT TEMPERATURE; DIRECTED GRAPHS; DYNAMICAL PROPERTIES; ENERGY LANDSCAPE; EQUILIBRATION PROCESS; EQUILIBRATION TIME; GRAPH REPRESENTATION; GRAPH STRUCTURES; HETEROPOLYMERS; HOMOPOLYMER; KINETIC PROPERTIES; MODEL PROTEINS; MOLECULAR DYNAMICS SIMULATIONS; NATIVE CONFIGURATION; ORDERS OF MAGNITUDE; POTENTIAL ENERGY LANDSCAPES; RENORMALIZATION; SPATIAL HOMOGENEITY; STOCHASTIC DYNAMICS; TEMPERATURE DEPENDENT; TIME-SCALE; TOPOLOGICAL PROPERTIES;

GRAPH THEORY; GRAPHIC METHODS; MARKOV PROCESSES; MOLECULAR DYNAMICS; POTENTIAL ENERGY; STOCHASTIC MODELS;

DYNAMICS;

EID: 67650490684     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.79.061925     Document Type: Article

References (34)

1. R. Schilling, in Collective Dynamics of Nonlinear and Disordered Systems, edited by, G. Radons, W. Just, and, P. Häussler, (Springer, Berlin, 2005).
2. M. Dobson, A. Sali, and M. Karplus, Angew. Chem., Int. Ed. 37, 868 (1998). 10.1002/(SICI)1521-3773(19980420)37:7<868::AID-ANIE868>3.0.CO;2-H
3. R. Kubo, M. Toda, and N. Hashitsume, Statistical Physics II: Nonequilibrium Statistical Mechanics (Springer, Berlin, 2008).
4. U. Balucani and M. Zoppi, Dynamics of the Liquid State (Clarendon, Oxford, 1994).
5. D. J. Wales, Energy Landscapes (Cambridge University Press, Cambridge, 2003).
6. P. E. Leopold, M. Montal, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 89, 8721 (1992). 10.1073/pnas.89.18.8721
7. F. H. Stillinger and T. A. Weber, Science 225, 983 (1984). 10.1126/science.225.4666.983
8. S. Sastry, P. G. Debenedetti, and F. H. Stillinger, Nature (London) 393, 554 (1998). 10.1038/31146
9. P. N. Mortenson and D. J. Wales, J. Chem. Phys. 114, 6443 (2001). 10.1063/1.1343486
10. J. S. Langer, Ann. Phys. 54, 258 (1969). 10.1016/0003-4916(69)90153-5
11. P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. 62, 251 (1990). 10.1103/RevModPhys.62.251
12. L. Bongini, R. Livi, A. Politi, and A. Torcini, Phys. Rev. E 68, 061111 (2003). 10.1103/PhysRevE.68.061111
13. L. Bongini, R. Livi, A. Politi, and A. Torcini, Phys. Rev. E 72, 051929 (2005). 10.1103/PhysRevE.72.051929
14. L. A. Mirny and E. I. Shakhnovich, J. Mol. Biol. 264, 1164 (1996). 10.1006/jmbi.1996.0704
15. A. Torcini, R. Livi, and A. Politi, J. Biol. Phys. 27, 181 (2001). 10.1023/A:1013104123892
16. F. H. Stillinger, T. Head-Gordon, and C. L. Hirshfeld, Phys. Rev. E 48, 1469 (1993). 10.1103/PhysRevE.48.1469
17. A. Irbäck, C. Peterson, and F. Potthast, Phys. Rev. E 55, 860 (1997). 10.1103/PhysRevE.55.860
18. Y. Jabri, The Mountain Pass Theorem: Encyclopedia of Mathematics and its Applications (Cambridge University Press, Cambridge, 2003).
19. D. Moroni, T. S. van Erp, and P. G. Bolhuis, Physica A 340, 395 (2004). 10.1016/j.physa.2004.04.033
20. J. P. K. Doye and D. J. Wales, Z. Phys. D: At., Mol. Clusters 40, 194 (1997). 10.1007/s004600050192
21. L. J. Lewis and N. Mousseau, Comput. Mater. Sci. 20, 285 (2001). 10.1016/S0927-0256(00)00184-1
22. The procedure can be accelerated by applying quasi-Newtonian algorithms.
23. S. Gerschgorin, Izv. Akad. Nauk USSR Otd. Fiz.-, Mat. Nauk 7, 749 (1931).
24. N. G. Van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 1981).
25. R. Burioni and D. Cassi, Phys. Rev. Lett. 76, 1091 (1996). 10.1103/PhysRevLett.76.1091
26. M. A. Miller and D. J. Wales, J. Chem. Phys. 111, 6610 (1999). 10.1063/1.480011
27. S. V. Krivov and M. Karplus, J. Chem. Phys. 117, 10894 (2002); 10.1063/1.1517606
28. D. A. Evans and D. J. Wales, J. Chem. Phys. 118, 3891 (2003). 10.1063/1.1540099
29. F. Rao and A. Calfisch, J. Mol. Biol. 342, 299 (2004). 10.1016/j.jmb.2004.06.063
30. Notice that the low-frequency component of the spectrum corresponds to collective modes as in the case of network elements connected by harmonic interactions. In the case of a regular network, d coincides with the lattice dimension d.
31. D. C. Sorensen, Institute for Computer Applications in Science and Engineering (ICASE) Technical Report TR-96-40, 1996 (unpublished).
32. M. Baiesi, L. Bongini, L. Casetti, and L. Tattini, Phys. Rev. E (to be published).
33. C. H. Q. Ding, X. He, and H. Zha, Proceedings of the ACM International Conference on Knowledge Discovery and Data Mining, 2001 (unpublished), p. 275.
34. E. K. P. Chong and S. H. Zak, An Introduction to Optimization, 2nd ed. (Wiley, New York, 2001).