Thermally activated processes in polymer dynamics

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

Volumn 68, Issue 6 1, 2003, Pages 611111-6111112

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

^a INFM   (Italy)

^b UNIVERSITY OF FLORENCE   (Italy)

^c ISTITUTO NAZIONALE DI OTTICA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHEMICAL ACTIVATION; COMPUTER SIMULATION; ELECTRON ENERGY LEVELS; ENTROPY; GLASS TRANSITION; HAMILTONIANS; HOMOPOLYMERIZATION; MOLECULAR DYNAMICS; MONTE CARLO METHODS; RANDOM PROCESSES; THERMAL EFFECTS;

HETEROPOLYMERS; THERMALLY ACTIVATED PROCESSES;

POLYMERS;

EID: 1442281231     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (27)

1. P.G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, NY, 1979).
2. I.E. Creighton, Proteins: Structures and Molecular Properties (Freeman, New York, 1993).
3. F.H. Stillinger and T.A. Weber, Science 225, 983 (1984).
4. R.S. Berry, N. Elmaci, J.P. Rose, and B. Vekhter, Proc. Natl. Acad. Sci. U.S.A. 94, 9520 (1997).
5. S.V. Krivov and M. Karplus, J. Chem. Phys. 117, 10894 (2002).
6. D.A. Evans and D.J. Wales, J. Chem. Phys. 118, 3891 (2003).
7. J.S. Langer, Ann. Phys. (N.Y.) 54, 258 (1969).
8. F.H. Stillinger, T.H. Gordon, and C.L. Hirshfeld, Phys. Rev. E 48, 1469 (1993).
9. A. Torcini, R. Livi, and A. Politi, J. Biol. Phys. 27, 181 (2001).
10. For the sake of simplicity, all variables are expressed in adimensional units. The harmonic term turns out to be stiff because α=20 is much larger than the constants corresponding to the two other interaction processes included in the model.
11. A. Irbäck and F. Potthast, J. Chem. Phys. 103, 10298 (1995).
12. A. Irbäck, C. Peterson, and F. Potthast, Phys. Rev. E 55, 860 (1997).
13. E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992).
14. S. Nosé, J. Chem. Phys. 81, 511 (1984); W.G. Hoover, Phys. Rev. A 31, 1695 (1985).
15. S. Nosé, J. Chem. Phys. 81, 511 (1984); W.G. Hoover, Phys. Rev. A 31, 1695 (1985).
16. H.A. Kramers, Physica (Amsterdam) 7, 284 (1940).
17. J.S. Langer, Ann. Phys. (N.Y.) 41, 108 (1967).
18. The original formula differs by a factor of 2 since we are here referring to the first passage time at the boundary, rather than to the neighboring minimum.
19. L. Angelani, G. Parisi, G. Ruocco, and G. Viliani, Phys. Rev. Lett. 81, 4648 (1998); Phys. Rev. E 61, 1681 (2000).
20. L. Angelani, G. Parisi, G. Ruocco, and G. Viliani, Phys. Rev. Lett. 81, 4648 (1998); Phys. Rev. E 61, 1681 (2000).
21. G. Daldoss, O. Pilla, G. Viliani, C. Brangian, and G. Ruocco, Phys. Rev. B 60, 3200 (1999).
22. R.E. Kunz and R.S. Berry, J. Chem. Phys. 103, 1904 (1995).
23. P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. 62, 251 (1990).
24. l≤1.06 for S4.
25. T. Veitshans, D. Klimov, and D. Thirumalai, Folding Des. 2, 1 (1997).
26. Notice that the first three beads of S4 are all polar and are thus repelled by the vast majority of the remaining hydrophobic ones.
27. A. Tiberio, Laurea thesis, Università di Firenze, Firenze, 2000.