Bubble generation in a twisted and bent DNA-like model

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

Volumn 70, Issue 3 2, 2004, Pages

  Larsen, P V ^a   Christiansen, P L ^a   Bang, O ^a   Archilla, J F R ^b   Gaididei, Yu B ^c  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b UNIVERSITY OF SEVILLE   (Spain)

^c BOGOLYUBOV INSTITUTE FOR THEORETICAL PHYSICS   (Ukraine)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DNA; HYDROGEN BONDS; MATHEMATICAL MODELS; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE; POLYPEPTIDES; PROTEINS; RANDOM PROCESSES; TEMPERATURE DISTRIBUTION;

BUBBLE GENERATION; DNA MOLECULES; MOLECULAR SITES; PROTEIN STRUCTURES;

BUBBLE FORMATION;

EID: 42749102019     PISSN: 15393755     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.70.036609     Document Type: Article

References (51)

1. J. D. Watson and F. H. C. Crick, Nature (London) 171, 737 (1953).
2. C. R. Calladine and H. R. Drew, Understanding DNA (Academic, London, 2002).
3. W. Saenger, Principles of Nucleic Acid Structure (Springer, New York, 1984).
4. L. V. Yakushevich, Nonlinear Physics of DNA (Wiley, New York, 1998).
5. C. Reiss, in Nonlinear Excitations in Biomolecules, edited by M. Peyrard (Springer, Les Ulis, 1994).
6. J. J.-L. Ting and M. Peyrard, Phys. Rev. E 53, 1011 (1996).
7. M. Techera, L. L. Daemen, and E. W. Prohofsky, Phys. Rev. A 40, 6636 (1989).
8. J. Cuevas, F. Palmero, J. F. R. Archilla, and F. R. Romero, J. Phys. A 35, 10 519 (2002).
9. K. Forinash, T. Cretegny, and M. Peyrard, Phys. Rev. E 55, 4740 (1997).
10. V. Muto, A. C. Scott, and P. L. Christiansen, Phys. Lett. A 136, 33 (1989); Physica D 44, 75 (1990); V. Muto, Nanobiology 1, 325 (1992).
11. V. Muto, A. C. Scott, and P. L. Christiansen, Phys. Lett. A 136, 33 (1989); Physica D 44, 75 (1990); V. Muto, Nanobiology 1, 325 (1992).
12. V. Muto, A. C. Scott, and P. L. Christiansen, Phys. Lett. A 136, 33 (1989); Physica D 44, 75 (1990); V. Muto, Nanobiology 1, 325 (1992).
13. I. Bena, A. Saxena, G. P. Tsironis, M. Ibañes, and J. M. Sancho, Phys. Rev. E 67, 037601 (2003).
14. K. Forinash, M. Peyrard, and B. Malomed, Phys. Rev. E 49, 3400 (1994).
15. S. F. Mingaleev, P. L. Christiansen, Yu. B. Gaididei, M. Johansson, and K. Ø. Rasmussen, J. Biol. Phys. 25, 41 (1999).
16. O. Bang and M. Peyrard, Physica D 81, 9 (1995); Phys. Rev. E 53, 4 (1996); 53, 4143 (1996).
17. O. Bang and M. Peyrard, Physica D 81, 9 (1995); Phys. Rev. E 53, 4 (1996); 53, 4143 (1996).
18. O. Bang and M. Peyrard, Physica D 81, 9 (1995); Phys. Rev. E 53, 4 (1996); 53, 4143 (1996).
19. H. Feddersen, Phys. Lett. A 154, 391 (1991).
20. T. Dauxois and M. Peyrard, Phys. Rev. Lett. 70, 3935 (1993).
21. F. Zhang, M. A. Collins, and Yu. S. Kivshar, Phys. Rev. E 51, 3774 (1995).
22. M. Techera, L. L. Daemen, and E. W. Prohofsky, Phys. Rev. A 42, 1008 (1990).
23. M. Salerno, Phys. Rev. A 44, 5292 (1991).
24. T. Hwa, E. Marinari, K. Sneppen, and L.-h. Tang, Proc. Natl. Acad. Sci. U.S.A. 100, 4411 (2003).
25. G. Altan-Bonnet, A. Libchaber, and O. Krichevsky, Phys. Rev. Lett. 90, 138101 (2003).
26. C. H. Choi, G. Kalosakas, K. Ø. Rasmussen, M. Hiromura, A. R. Bishop, and A. Usheva, Nucleic Acids Res. 32, 1584 (2004).
27. J. Cuevas, J. F. R. Archilla, Yu. B. Gaididei, and F. R. Romero, Physica D 163, 106 (2002).
28. L. Cruzeiro-Hansson, Phys. Lett. A 249, 465 (1998).
29. M. Barbi, S. Cocco, and M. Peyrard, Phys. Lett. A 253, 358 (1999).
30. M. Barbi, S. Cocco, M. Peyrard, and S. Ruffo, J. Biol. Phys. 24, 97 (1999).
31. P. L. Christiansen, Yu. B. Gaididei, and S. F. Mingaleev, J. Phys.: Condens. Matter 13, 1181 (2001).
32. S. F. M. Mingaleev, Yu. B. Gaididei, P. L. Christiansen, and Yu. S. Kivshar, Europhys. Lett. 59, 403 (2002).
33. R. Reigada, J. M. Sancho, M. I. Ibañes, and G. P. Tsironis, J. Phys. A 34, 8465 (2001).
34. J. Cuevas, F. Palmero, J. F. R. Archilla, and F. R. Romero, Phys. Lett. A 299, 221 (2002).
35. B. Sánchez-Rey, J. F. R. Archilla, F. Palmero, and F. R. Romero, Phys. Rev. E 66, 017601 (2002).
36. J. F. R. Archilla, Yu. B. Gaididei, P. L. Christiansen, and J. Cuevas, J. Phys. A 35, 8885 (2002).
37. J. F.R. Archilla, P. L. Christiansen, S. F. Mingaleev, and Yu. B. Gaididei, J. Phys. A 34, 6363 (2001).
38. Yu. B. Gaididei, S. F. Mingaleev, and P. L. Christiansen, Phys. Rev. E 62, R53 (2000).
39. A. Campa, Phys. Rev. E 63, 021901 (2001).
40. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E 47, 684 (1993).
41. G. P. Tsironis, A. R. Bishop, A. V. Savin, and A. V. Zolotaryuk, Phys. Rev. E 60, 6610 (1999).
42. M. Peyrard, Physica D 119, 184 (1998).
43. T. Dauxois, M. Peyrard, and C. R. Willis, Physica D 57, 267 (1992).
44. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. 62, 2755 (1989).
45. P. V. Larsen, P. L. Christiansen, O. Bang, J. F. R. Archilla, and Yu. B. Gaididei, Phys. Rev. E 69, 026603 (2004).
46. L. D. Landau and E. M. Lifshitz, The Classical Theory of Fields, revised 2nd ed. (Pergamon, Warsaw, 1962), p. 115.
47. M. V. Salarić, Physica D 126, 60 (1999).
48. J. Pranata, S. G. Wierschke, and W. L. Jorgensen, J. Am. Chem. Soc. 113, 2810 (1991).
49. This is also the case for a nonrigid chain [28].
50. Recent calculations by J. Cuevas, J. F. R. Archilla, E. B. Starikov, and D. Hennig indicate a value of q about 10 times smaller.
51. N-1 and the legs are not complete symmetric in order to use the same initial conditions for both cases.