Dynamics of chain closure: Approximate treatment of nonlocal interactions

Journal of Chemical Physics

Volumn 120, Issue 5, 2004, Pages 2482-2489

  Debnath, Pallavi ^a   Cherayil, Binny J ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; COMPUTER SIMULATION; CONFORMATIONS; CORRELATION METHODS; DIFFUSION; DIMERS; ERROR ANALYSIS; HAMILTONIANS; HYDRODYNAMICS; MATHEMATICAL MODELS; MOLECULAR WEIGHT; MONOMERS; POLYPEPTIDES; PROTEINS; SOLVENTS;

COLLAPSED POLYMERS; CYCLIZATION; EDWARDS MODELS; NONLOCAL INTERACTIONS;

MACROMOLECULES;

BIOPOLYMER;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; MACROMOLECULE; MOTION; STATISTICAL MODEL;

BIOPOLYMERS; CHEMISTRY; COMPUTER SIMULATION; MACROMOLECULAR SUBSTANCES; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; MOTION;

EID: 1442281485     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1637574     Document Type: Review

References (49)

1. D. Thirumalai, J. Phys. Chem. B 103, 608 (1999); Z. Guo and D. Thirumalai, Biopolymers 36, 83 (1995).
2. D. Thirumalai, J. Phys. Chem. B 103, 608 (1999); Z. Guo and D. Thirumalai, Biopolymers 36, 83 (1995).
3. P. Flory, Statistical Mechanics of Chain Molecules (Hanser, Munich, 1989); D. Poland and H. A. Scheraga, Theory of Helix-Coil Transitions in Biopolymers (Academic, New York, 1970).
4. P. Flory, Statistical Mechanics of Chain Molecules (Hanser, Munich, 1989); D. Poland and H. A. Scheraga, Theory of Helix-Coil Transitions in Biopolymers (Academic, New York, 1970).
5. A. Dua and B. J. Cherayil, J. Chem. Phys. 116, 399 (2002).
6. A. Dua and B. J. Cherayil, J. Chem. Phys. 117, 7765 (2002).
7. W. J. Wedemeyer and H. A. Scheraga, Encyclopedia of Life Sciences 15, 334 (2002).
8. S. F. Edwards, Proc. Phys. Soc. London 85, 613 (1965).
9. B. J. Cherayil and P. Biswas, J. Chem. Phys. 99, 9230 (1993).
10. G. Wilemski and M. Fixman, J. Chem. Phys. 58, 4009 (1973); 60, 866 (1974); 60, 878 (1974).
11. G. Wilemski and M. Fixman, J. Chem. Phys. 58, 4009 (1973); 60, 866 (1974); 60, 878 (1974).
12. G. Wilemski and M. Fixman, J. Chem. Phys. 58, 4009 (1973); 60, 866 (1974); 60, 878 (1974).
13. R. W. Pastor, R. Zwanzig, and A. Szabo, J. Chem. Phys. 105, 3878 (1996).
14. P. Debnath and B. J. Cherayil (unpublished).
15. M. Doi, Chem. Phys. 9, 455 (1975).
16. K. F. Freed, Adv. Chem. Phys. 22, 1 (1972); K. F. Freed, Renormalization Group Theory of Macromolecules (Wiley, N.Y., 1987).
17. K. F. Freed, Adv. Chem. Phys. 22, 1 (1972); K. F. Freed, Renormalization Group Theory of Macromolecules (Wiley, N.Y., 1987).
18. P. J. Flory, J. Chem. Phys. 17, 303 (1949); P. J. Flory and T. G. Fox, J. Am. Chem. Soc. 73, 1904 (1951); M. E. Fisher, J. Phys. Soc. Jpn. 26, 44 (1968).
19. P. J. Flory, J. Chem. Phys. 17, 303 (1949); P. J. Flory and T. G. Fox, J. Am. Chem. Soc. 73, 1904 (1951); M. E. Fisher, J. Phys. Soc. Jpn. 26, 44 (1968).
20. P. J. Flory, J. Chem. Phys. 17, 303 (1949); P. J. Flory and T. G. Fox, J. Am. Chem. Soc. 73, 1904 (1951); M. E. Fisher, J. Phys. Soc. Jpn. 26, 44 (1968).
21. P.-G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, 1979.)
22. T. G. Dewey, J. Chem. Phys. 98, 2250 (1993).
23. P. Biswas and B. J. Cherayil, J. Chem. Phys. 100, 4665 (1994).
24. P. Biswas and B. J. Cherayil, J. Phys. Chem. 99, 816 (1995).
25. P. Biswas, A. Paramekanti, and B. J. Cherayil, J. Chem. Phys. 104, 3360 (1996).
26. C. Maccone, Nuovo Cimento B61, 229 (1981); B65, 259 (1981).
27. C. Maccone, Nuovo Cimento B61, 229 (1981); B65, 259 (1981).
28. I. S. Gradshteyn and I. M. Ryzhik, Tables of Integrals, Series and Products (Academic, San Diego, 1980.)
29. M. Doi and S. F. Edwards, Theory of Polymer Dynamics (Clarendon, Oxford, 1986.)
30. M. Sakata and M. Doi, Polym. J. 8, 409 (1976).
31. A. Perico and C. Cuniberti, J. Polym. Sci., Polym. Phys. Ed. 15, 1435 (1977).
32. M. G. Brereton and A. Rusli, Polymer 17, 395 (1976).
33. P. J. Flory, U. W. Suter, and M. Mutter, J. Am. Chem. Soc. 98, 5740 (1976); U. W. Suter, M. Mutter, and P. J. Flory, ibid. 98, 5745 (1976).
34. P. J. Flory, U. W. Suter, and M. Mutter, J. Am. Chem. Soc. 98, 5740 (1976); U. W. Suter, M. Mutter, and P. J. Flory, ibid. 98, 5745 (1976).
35. A. Szabo, K. Schulten, and Z. Schulten, J. Chem. Phys. 72, 4350 (1980).
36. O. Bieri, J. Wirz, B. Hollrung, M. Schutkowski. M. Drewello, and T. Keifhaber. Proc. Natl. Acad. Sci. U.S.A. 96, 9597 (1999).
37. R. R. Hudgins, F. Huang, G. Gramlich, and W. M. Nau, J. Am. Chem. Soc. 124, 556 (2002).
38. L. J. Lapidus, W. A. Eaton, and J. Hofrichter, Proc. Natl. Acad. Sci. U.S.A. 97, 7720 (2000).
39. L. J. Lapidus. P. J. Steinbach, W. A. Eaton, A. Szabo, and J. Hofrichter, J. Phys. Chem. B 106, 11628 (2002); M. Buscaglia, B. Schuler, L. Lapidus, W. A. Eaton, and J. Hofrichter, J. Mol. Biol. 332, 9 (2003).
40. L. J. Lapidus. P. J. Steinbach, W. A. Eaton, A. Szabo, and J. Hofrichter, J. Phys. Chem. B 106, 11628 (2002); M. Buscaglia, B. Schuler, L. Lapidus, W. A. Eaton, and J. Hofrichter, J. Mol. Biol. 332, 9 (2003).
41. J. J. Portman, J. Chem. Phys. 118, 2381 (2003).
42. S. Jun, J. Bechhoefer, and B.-Y. Ha, Europhys. Lett. (to be published).
43. Z. Wang and D. E. Makarov, J. Chem. Phys. 117, 4591 (2002).
44. B. Friedman and B. O'Shaughnessy, Phys. Rev. A 40, 5950 (1989); B. Friedman and B. O'Shaughnessy, Macromolecules 26, 4888 (1993).
45. B. Friedman and B. O'Shaughnessy, Phys. Rev. A 40, 5950 (1989); B. Friedman and B. O'Shaughnessy, Macromolecules 26, 4888 (1993).
46. A. Rey and J. J. Freire, Macromolecules 24, 4673 (1991); A. Podtelezhnikov and A. Vologodskii, ibid. 30, 6668 (1997).
47. A. Rey and J. J. Freire, Macromolecules 24, 4673 (1991); A. Podtelezhnikov and A. Vologodskii, ibid. 30, 6668 (1997).
48. W. A. Winnik, in Cyclic Polymers, edited by J. A. Semlyen (Elsevier, New York, 1986).
49. I. S. Millet, S. Doniach, and K. W. Plaxco, Adv. Protein Chem. 62, 241 (2002).