Equilibrium and kinetic phenomena in a stiff homopolymer and possible applications to DNA

Journal of Chemical Physics

Volumn 105, Issue 16, 1996, Pages 7116-7134

  Kuznetsov, Yu A ^a,b   Timoshenko, E G ^a   Dawson, K A ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b INSTITUTE OF THEORETICAL AND EXPERIMENTAL BIOPHYSICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0039797153     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.472514     Document Type: Article

References (52)

1. P. G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, 1988).
2. J. des Cloizeaux and G. Jannink, Polymers in Solution (Clarendon, Oxford, 1990).
3. M. Doi and S. F. Edwards, The Theory of Polymer Dynamics (Oxford Science, New York, 1989).
4. A. Yu. Grosberg and A. R. Khokhlov, Statistical Physics of Macromolecules (AIP, New York, 1994).
5. B. Ostrovsky and Y. Bar-Yam, Comput. Polym. Sci. 3, 9 (1993);
6. M. A. Smith, Y. Bar-Yam, Y. Rabin, B. Ostrovski, C. A. Bennett, N. Margolus, and T. Toffoli, Comput. Polymer Sci. 2, 165 (1992).
7. Yu. A. Kuznetsov, E. G. Timoshenko, and K. A. Dawson, J. Chem. Phys. 103, 4807 (1995);
8. 104, 336 (1996).
9. A. Byrne, P. Kieman, D. Green, and K. A. Dawson, J. Chem. Phys. 102, 573 (1995).
10. T. A. Kavassalis and P. R. Sundrarajan, Macromolecules 26,4144 (1993);
11. G. Tanaka and W. L. Mattice, ibid. 28, 1049 (1995).
12. P. G. de Gennes, J. Phys. Lett. 46, L639 (1985).
13. E. G. Timoshenko, Yu. A. Kuznetsov, and K. A. Dawson, J. Chem. Phys. 102, 1816 (1995);
14. K. A. Dawson, E. G. Timoshenko, and P. Kiernan, Nuovo Cimento D 16, 675 (1994).
15. Yu. A. Kuznetsov, E. G. Timoshenko, and K. A. Dawson, J. Chem. Phys. 104, 3338 (1996).
16. G. Allegra and F. Ganazzoli, J. Chem. Phys. 83, 397 (1985).
17. F. Ganazzoli, R. La Ferla, and G. Allegra, Macromolecules 28, 5285 (1995).
18. 3.
19. b is the bare mobility of monomers. Henceforth we shall disregard the hydrodynamic interaction, which could be easily incorporated into our scheme and discussed in detail in Ref. 11.
20. E. G. Timoshenko, Yu. A. Kuznetsov, and K. A. Dawson, Phys. Rev. E 53, 3886 (1996); ibid, (in press).
21. V. A. Bloomfield, Biopolymers 31, 1471 (1991);
22. J. Ubbink and T. Odijk, Biophys. J. 68, 54 (1995);
23. Europhys. Lett. 33, 353 (1996);
24. N. V. Hud, K. H. Downing, and R. Balhorn, Proc. Natl. Acad. Sci. USA 92, 3581 (1995).
25. L. S. Lerman, Proc. Natl. Acad. Sci. USA 68, 1886 (1971);
26. U. K. Laemmli, ibid. 72, 4288 (1975);
27. Yu. M. Evdokimov et al., Nucl. Acids Res. 3, 2353 (1976);
28. G. E. Plum, P. G. Arscott, and V. A. Bloomfield, Biopolymers 30, 631 (1990);
29. V. V. Vasilevskaya, A. R. Khokhlov, Y. Matsuzawa, and K. Yoshikawa, J. Chem. Phys. 102, 6595 (1995).
30. A. Yu. Grosberg, Biophysics 24, 30 (1979);
31. A. Yu. Grosberg and A. R. Khokhlov, Adv. Polym. Sci. 41, 53 (1981).
32. O. Kratky and G. Porod, Rec. Trav. Chim. 68, 1106 (1949);
33. H. Yamakawa, Annu. Rev. Phys. Chem. 35, 23 (1984).
34. R. A. Harris and J. E. Hearst, J. Chem. Phys. 44, 2595 (1966).
35. B. H. Zimm, J. Chem. Phys. 24, 269 (1956);
36. M. V. Volkenstein, Configurational Statistics of Polymeric Chains (Interscience, New York, 1963);
37. P. J. Flory, Statistical Mechanics of Chain Molecules (Interscience, New York, 1969);
38. M. Bixon and R. Zwanzig, J. Chem. Phys. 68, 1896 (1978);
39. A. Perico, S. Bisio and C. Cuniberti, Macromolecules 17, 2686 (1984).
40. Formulas for an open polymer may be found in Ref. 11.
41. Note that the Gaussian trial Hamiltonian has the flaw that the extended coil has an incorrect (Reiss) swelling exponent v=2/3, unless one makes a specific cut-off (Ref. 35).
42. min one can, strictly speaking, say that it is connected to the mean squared intrinsic diameter only up to some multiplicative factor, depending on many details of the local interaction.
43. Since for a finite size system this continuous transition occurs in a region of width ∼1/N, the transition line is not so well defined. Practically, curve I has been obtained as the point of the most rapid decrease of the radius of gyration.
44. 3.
45. V. V. Vasilevskaya, A. R. Khokhlov, S. Kidoaki, and K. Yoshikawa (unpublished).
46. E. G. Timoshenko and K. A. Dawson, Phys. Rev. E 51 (1), 492 (1995).
47. H. Isambert, A. C. Maggs, Macromolecules 29, 1036 (1996).
48. S. Kidoaki and K. Yoshikawa et al. (unpublished).
49. H. E. Stanley et al., Nuovo Cimento D 16, 1339 (1994).
50. A. Yu. Grosberg, Yu. A. Kuznetsov, E. G. Timoshenko, and K. A. Dawson (unpublished).
51. A. Yu. Grosberg and D. V. Kuznetsov, Macromolecules 26, 4249 (1993).
52. D. Bratko and K. A. Dawson, J. Chem. Phys. 99, 5352 (1993).