Solitary waves in twist-opening models of DNA dynamics

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

Volumn 78, Issue 1, 2008, Pages

  Gaeta, Giuseppe ^a   Venier, Laura ^a  

^a UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ASYMPTOTIC ANALYSIS; DIFFERENCE EQUATIONS; DIFFERENTIAL EQUATIONS; DIFFERENTIATION (CALCULUS); DNA; DYNAMICS; GENES; LIQUID WAVES; MODELS; NUCLEIC ACIDS; ORDINARY DIFFERENTIAL EQUATIONS; ORGANIC ACIDS;

AMERICAN PHYSICAL SOCIETY (APS); ASYMPTOTIC BEHAVIORS; DEGREES OF FREEDOM; DNA DYNAMICS; DNA MODELING; FIRST ORDERS; PHYSICAL PARAMETERS; SOLITARY WAVE SOLUTIONS; SOLITARY WAVES; TRAVELING SOLITARY WAVE SOLUTIONS;

WAVES;

EID: 47249101079     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.78.011901     Document Type: Article

References (74)

1. W. Saenger, Principles of Nucleic Acid Structure (Springer, Berlin, 1984).
2. C. Calladine, H. Drew, B. Luisi, and A. Travers, Understanding DNA, 3rd ed. (Academic Press, London, 2004).
3. S. W. Englander, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.77.12.7222 77, 7222 (1980).
4. M. Peyrard, Nonlinearity NONLE5 0951-7715 10.1088/0951-7715/17/2/R01 17, R1 (2004).
5. M. Peyrard and Th. Dauxois, Physique de Solitons (Editions CNRS, Paris, 2004)
6. M. Peyrard and Th. Dauxois, [Physics of Solitons (Academic Press, London, 2006)].
7. M. Peyrard, Nat. Phys. ZZZZZZ 1745-2473 2, 13 (2006).
8. G. Gaeta, C. Reiss, M. Peyrard, and Th. Dauxois, Riv. Nuovo Cimento RNUCAC 0035-5917 10.1007/BF02506678 17, 1 (1994).
9. L. V. Yakushevich, Nonlinear Physics of DNA, 2nd ed. (Wiley, Chichester, U.K., 2004).
10. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.62.2755 62, 2755 (1989).
11. Th. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.47.R44 47, R44 (1993).
12. L. V. Yakushevich, Phys. Lett. A PYLAAG 0375-9601 10.1016/0375-9601(89) 90425-8 136, 413 (1989).
13. L. V. Yakushevich, Physica D PDNPDT 0167-2789 10.1016/0167-2789(94)90038- 8 79, 77 (1994).
14. M. Barbi, S. Cocco, and M. Peyrard, Phys. Lett. A PYLAAG 0375-9601 10.1016/S0375-9601(99)00059-6 253, 358 (1999).
15. S. Cocco, M. Barbi, and M. Peyrard, Phys. Lett. A PYLAAG 0375-9601 10.1016/S0375-9601(99)00058-4 253, 161 (1999).
16. M. Barbi, S. Cocco, M. Peyrard, and S. Ruffo, J. Biol. Phys. JBPHBZ 0092-0606 10.1023/A:1005139326775 24, 97 (1999).
17. D. Poland and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1727785 45, 1456 (1966)
18. D. Poland and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1727786 45, 1464 (1966)
19. D. Poland and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1727893 45, 2071 (1966).
20. Y. Kafri, D. Mukamel, and L. Peliti, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.85.4988 85, 4988 (2000).
21. D. Hennig, J. F. R. Archilla, and J. M. Romero, J. R. Soc., Interface JRSICU 1742-5689 10.1098/rsif.2004.0024 2, 89 (2005).
22. M. Kohandel and B. Y. Ha, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.73.011905 73, 011905 (2006).
23. N.A. Kovaleva, Polym. Sci., Ser. A Ser. B PSSBEG 48, 278 (2006).
24. W. Lim, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.75.031918 75, 031918 (2007).
25. G. Weber, Nat. Phys. ZZZZZZ 1745-2473 2, 55 (2006).
26. A. Bar, Y. Kafri, and D. Mukamel, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.038103 98, 038103 (2007).
27. R. Everaers, S. Kumar, and C. Simm, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.75.041918 75, 041918 (2007).
28. A. Hanke, M. G. Ochoa and R. Metzler, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.018106 100, 018106 (2008).
29. S. Cocco and R. Monasson, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.83.5178 83, 5178 (1999)
30. S. Cocco and R. Monasson, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.481646 112, 10017 (2000).
31. G. Gaeta and L. Venier, J. Nonlin. Math. Phys. (to be published)
32. see also L. Venier, M.Sc. thesis, Università di Milano, 2007.
33. S. Zdravković and M. V. Satarić, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.77.031906 77, 031906 (2008).
34. M. Cadoni, R. De Leo, and G. Gaeta, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.75.021919 75, 021919 (2007).
35. M. Cadoni, R. De Leo, and G. Gaeta, J. Nonlinear Math. Phys. ZZZZZZ 1402-9251 14, 128 (2007)
36. M. Cadoni, R. De Leo, and G. Gaeta, J. Phys. A JPHAC5 0305-4470 10.1088/1751-8113/40/29/022 40, 8517 (2007)
37. M. Cadoni, R. De Leo, and G. Gaeta, J. Phys. A JPHAC5 0305-4470 10.1088/1751-8113/40/43/006 40, 12917 (2007).
38. M. Cadoni, e-print arXiv:0710.4475, Int. J. Non-Linear Mech. (to be published).
39. R. De Leo and S. Demelio, e-print arXiv:0711.1069, Int. J. Non-Linear Mech. (to be published).
40. Nonlinear Excitations in Biomolecules, edited by, M. Peyrard, Proceedings of a Workshop, Les Houches, 1994 (Springer, Berlin/ Les Editions de Physique, Paris, 1995).
41. N. Bruant, Biophys. J. 77, 2366 (1999). 0006-3495
42. S. Cuesta-Lopez, J. Errami, and M. Peyrard, J. Biol. Phys. JBPHBZ 0092-0606 10.1007/s10867-005-3244-3 31, 273 (2005)
43. M. Peyrard, S. Cuesta-López, and G. James, Nonlinearity NONLE5 0951-7715 10.1088/0951-7715/21/6/T02 21, T91 (2008).
44. S. B. Smith, L. Finzi, and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.1439819 258, 1122 (1992).
45. R. Lavery, J. Phys. C 14, R383 (2002). 0022-3719
46. C. Bustamante, Z. Bryant, and S. B. Smith, Nature (London) NATUAS 0028-0836 10.1038/nature01405 421, 423 (2003).
47. F. Ritort, J. Phys. C 18, R531 (2006). 0022-3719
48. D. Bensimon, A. J. Simon, V. Croquette, and A. Bensimon, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.74.4754 74, 4754 (1995).
49. B. Essevaz-Roulet, U. Bockelmann, and F. Heslot, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.94.22.11935 94, 11935 (1997).
50. U. Bockelmann, B. Essevaz-Roulet, and F. Heslot, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.79.4489 79, 4489 (1997)
51. U. Bockelmann, B. Essevaz-Roulet, and F. Heslot, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.58.2386 58, 2386 (1998).
52. W. Reisner, K. J. Morton, R. Riehn, Y. M. Yang, Z. Yu, M. Rosen, J. C. Sturm, S. Y. Chou, E. Frey, and R. H. Austin, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.196101 94, 196101 (2005).
53. V. Baldazzi, S. Cocco, E. Marinari, and R. Monasson, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.128102 96, 128102 (2006).
54. A. K. Chattopadhyay and D. Marenduzzo, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.088101 98, 088101 (2007).
55. A. Crut, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0700333104 104, 11957 (2007).
56. C. Ke, M. Humeniuk, H. S-Gracz, and P. E. Marszalek, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.99.018302 99, 018302 (2007).
57. W. J. Greenleaf, M. T. Woodside, and S. M. Block, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.36.101106.101451 36, 171 (2007).
58. K. C. Neuman, T. Lionnet, and J. F. Allemand, Annu. Rev. Mater. Res. ARMRCU 1531-7331 10.1146/annurev.matsci.37.052506.084336 37, 33 (2007).
59. P. Cluzel, Science SCIEAS 0036-8075 10.1126/science.271.5250.792 271, 792 (1996).
60. S. B. Smith, Y. Cui, and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.274.5288.795 271, 795 (1996).
61. J. F. Allemand, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.95.24.14152 95, 14152 (1998).
62. J. F. Leger, G. Romano, A. Sarkar, J. Robert, L. Bourdieu, D. Chatenay, and J. F. Marko, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.83.1066 83, 1066 (1999).
63. T. R. Strick, Rep. Prog. Phys. RPPHAG 0034-4885 10.1088/0034-4885/66/1/ 201 66, 1 (2003).
64. E. W. Prohofsky, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.38.1538 38, 1538 (1988).
65. V. I. Arnold, Mathematical Methods of Classical Mechanics (Springer, Berlin, 1983).
66. L. D. Landau and I. M. Lifshitz, Mechanics, Theoretical Physics Vol. 1 (Pergamon, London, 1955).
67. S. Zdravković and M. V. Satarić, Europhys. Lett. EULEEJ 0295-5075 10.1209/0295-5075/78/38004 78, 38004 (2007).
68. G. Saccomandi and I. Sgura, J. R. Soc. Interface 3, 655 (2006). 1742-5689
69. G. Saccomandi, Int. J. Non-Linear Mech. IJNMAG 0020-7462 10.1016/S0020-7462(02)00192-0 39, 331 (2004).
70. M. Destrade and G. Saccomandi, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.73.065604 73, 065604 (R) (2006).
71. G. Gaeta, Europhys. Lett. EULEEJ 0295-5075 10.1209/0295-5075/79/20003 79, 20003 (2007).
72. G. Gaeta, T. Gramchev, and S. Walcher, J. Phys. A JPHAC5 0305-4470 10.1088/1751-8113/40/17/007 40, 4493 (2007).
73. A. Dubrovin, S. P. Novikov, and A. Fomenko, Modern Geometry (Springer, Berlin, 1984).
74. L. V. Yakushevich, A. V. Savin, and L. I. Manevitch, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.66.016614 66, 016614 (2002).