Denaturation patterns in heterogeneous DNA

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

Volumn 81, Issue 5, 2010, Pages

  Zoli, Marco ^a  

^a UNIVERSITY OF CAMERINO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE-THYMINE; BASE PAIRS; BASE-PAIR FLUCTUATIONS; COMPLEMENTARY STRAND; CONFIGURATION SPACE; COOPERATIVITY; DNA FRAGMENT; DOUBLE STRANDS; HEAT PEAK; MODEL POTENTIAL; MULTI-STEP; NON-LINEAR MODEL; PARTITION FUNCTIONS; PATH INTEGRAL METHOD; PATH-INTEGRAL; RELATIVE DISPLACEMENT; SECOND LAW OF THERMODYNAMICS; THERMODYNAMICAL PROPERTIES; TIME-DEPENDENT;

DENATURATION; DNA; GENES; HYDROGEN BONDS; MOLECULAR VIBRATIONS; SPECIFIC HEAT;

DNA SEQUENCES;

EID: 77952407106     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.81.051910     Document Type: Article

References (66)

1. R. M. Wartell and A. S. Benight, Phys. Rep. 126, 67 (1985). 10.1016/0370-1573(85)90060-2
2. J. Yan and J. F. Marko, Phys. Rev. Lett. 93, 108108 (2004). 10.1103/PhysRevLett.93.108108
3. E. W. Prohofsky, Phys. Rev. A 38, 1538 (1988). 10.1103/PhysRevA.38.1538
4. P. L. Felgner, T. R. Gadek, M. Holm, R. Roman, H. W. Chan, M. Wenz, J. P. Northrop, G. M. Ringold, and M. Danielsen, Proc. Natl. Acad. Sci. U.S.A. 84, 7413 (1987). 10.1073/pnas.84.21.7413
5. J. O. Rädler, I. Koltover, T. Salditt, and C. R. Safinya, Science 275, 810 (1997). 10.1126/science.275.5301.810
6. R. B. Inman and R. L. Baldwin, J. Mol. Biol. 8, 452 (1964). 10.1016/S0022-2836(64)80003-6
7. R. D. Blake and S. G. Delcourt, Nucleic Acids Res. 26, 3323 (1998). 10.1093/nar/26.14.3323
8. R. Blossey and E. Carlon, Phys. Rev. E 68, 061911 (2003). 10.1103/PhysRevE.68.061911
9. Y. Zeng, A. Montrichok, and G. Zocchi, Phys. Rev. Lett. 91, 148101 (2003). 10.1103/PhysRevLett.91.148101
10. A. Krueger, E. Protozanova, and M. D. Frank-Kamenetskii, Biophys. J. 90, 3091 (2006). 10.1529/biophysj.105.078774
11. S. Buyukdagli and M. Joyeux, Phys. Rev. E 77, 031903 (2008). 10.1103/PhysRevE.77.031903
12. P. Yakovchuk, E. Protozanova, and M. D. Frank-Kamenetskii, Nucleic Acids Res. 34, 564 (2006). 10.1093/nar/gkj454
13. D. Poland and H. Scheraga, J. Chem. Phys. 45, 1456 (1966) 10.1063/1.1727785
14. D. Poland and H. Scheraga, J. Chem. Phys. 45, 1464 (1966). 10.1063/1.1727786
15. M. Ya. Azbel', J. Chem. Phys. 62, 3635 (1975). 10.1063/1.430960
16. M. E. Fisher, J. Chem. Phys. 45, 1469 (1966). 10.1063/1.1727787
17. C. Richard and A. J. Guttmann, J. Stat. Phys. 115, 925 (2004). 10.1023/B:JOSS.0000022370.48118.8b
18. A. Wada, H. Tachibana, S. Ueno, Y. Husimi, and Y. Machida, Nature (London) 269, 352 (1977). 10.1038/269352a0
19. M. Y. Azbel, Phys. Rev. A 20, 1671 (1979). 10.1103/PhysRevA.20.1671
20. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. 62, 2755 (1989). 10.1103/PhysRevLett.62.2755
21. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E 47, R44 (1993). 10.1103/PhysRevE.47.R44
22. N. Theodorakopoulos, T. Dauxois, and M. Peyrard, Phys. Rev. Lett. 85, 6 (2000). 10.1103/PhysRevLett.85.6
23. Y. Kafri, D. Mukamel, and L. Peliti, Phys. Rev. Lett. 85, 4988 (2000). 10.1103/PhysRevLett.85.4988
24. M. S. Causo, B. Coluzzi, and P. Grassberger, Phys. Rev. E 62, 3958 (2000). 10.1103/PhysRevE.62.3958
25. E. Carlon, E. Orlandini, and A. L. Stella, Phys. Rev. Lett. 88, 198101 (2002). 10.1103/PhysRevLett.88.198101
26. A. Hanke and R. Metzler, Phys. Rev. Lett. 90, 159801 (2003). 10.1103/PhysRevLett.90.159801
27. A. Bar, Y. Kafri, and D. Mukamel, Phys. Rev. Lett. 98, 038103 (2007). 10.1103/PhysRevLett.98.038103
28. J. Rudnick and T. Kuriabova, Phys. Rev. E 77, 051903 (2008). 10.1103/PhysRevE.77.051903
29. J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. 99, 088103 (2007). 10.1103/PhysRevLett.99.088103
30. A. Hanke, M. G. Ochoa, and R. Metzler, Phys. Rev. Lett. 100, 018106 (2008). 10.1103/PhysRevLett.100.018106
31. F. de los Santos, O. Al Hammal, and M. A. Muñoz, Phys. Rev. E 77, 032901 (2008). 10.1103/PhysRevE.77.032901
32. D. Cule and T. Hwa, Phys. Rev. Lett. 79, 2375 (1997). 10.1103/PhysRevLett.79.2375
33. C. H. Choi, G. Kalosakas, K. Ø. Rasmussen, M. Hiromura, A. R. Bishop, and A. Usheva, Nucleic Acids Res. 32, 1584 (2004). 10.1093/nar/gkh335
34. T. S. van Erp, S. Cuesta-López, and M. Peyrard, Eur. Phys. J. E 20, 421 (2006). 10.1140/epje/i2006-10032-2
35. A. Montrichok, G. Gruner, and G. Zocchi, Europhys. Lett. 62, 452 (2003). 10.1209/epl/i2003-00417-3
36. Y. Zeng, A. Montrichok, and G. Zocchi, J. Mol. Biol. 339, 67 (2004). 10.1016/j.jmb.2004.02.072
37. K. Drukker and G. C. Schatz, J. Phys. Chem. B 104, 6108 (2000). 10.1021/jp000550j
38. M. Joyeux and S. Buyukdagli, Phys. Rev. E 72, 051902 (2005). 10.1103/PhysRevE.72.051902
39. M. Sales-Pardo, R. Guimerà, A. A. Moreira, J. Widom, and L. A. N. Amaral, Phys. Rev. E 71, 051902 (2005). 10.1103/PhysRevE.71.051902
40. T. A. Knotts, N. Rathore, D. C. Schwartz, and J. J. de Pablo, J. Chem. Phys. 126, 084901 (2007). 10.1063/1.2431804
41. E. J. Sambriski, D. C. Schwartz, and J. J. de Pablo, Biophys. J. 96, 1675 (2009). 10.1016/j.bpj.2008.09.061
42. M. Zoli, Phys. Rev. E 79, 041927 (2009). 10.1103/PhysRevE.79.041927
43. R. P. Feynman and A. R. Hibbs, Quantum Mechanics and Path Integrals (McGraw-Hill, New York, 1965).
44. R. P. Feynman, Rev. Mod. Phys. 20, 367 (1948). 10.1103/RevModPhys.20.367
45. J. B. Fiche, A. Buhot, R. Calemczuk, and T. Livache, Biophys. J. 92, 935 (2007). 10.1529/biophysj.106.097790
46. J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. E 77, 011913 (2008). 10.1103/PhysRevE.77.011913
47. G. Altan-Bonnet, A. Libchaber, and O. Krichevsky, Phys. Rev. Lett. 90, 138101 (2003). 10.1103/PhysRevLett.90.138101
48. S. Buyukdagli and M. Joyeux, Phys. Rev. E 73, 051910 (2006). 10.1103/PhysRevE.73.051910
49. Y. Kim, K. V. Devi-Prasad, and E. W. Prohofsky, Phys. Rev. B 32, 5185 (1985). 10.1103/PhysRevB.32.5185
50. Y. Kim and E. W. Prohofsky, Phys. Rev. B 35, 2399 (1987). 10.1103/PhysRevB.35.2399
51. M. E. Tuckerman, D. Marx, M. L. Klein, and M. Parrinello, Science 275, 817 (1997). 10.1126/science.275.5301.817
52. M. Peyrard, Nonlinearity 17, R1 (2004). 10.1088/0951-7715/17/2/R01
53. A. Campa and A. Giansanti, Phys. Rev. E 58, 3585 (1998). 10.1103/PhysRevE.58.3585
54. Due to the on site potential with unbounded transverse stretching y n, a thermodynamic phase transition is possible also in the harmonic (ρ = 0) Peyrard-Bishop Hamiltonian. Thus there is no contradiction with general theorems regarding the impossibility of phase transitions in one-dimensional systems.
55. L. van Hove, Physica 16, 137 (1950). 10.1016/0031-8914(50)90072-3
56. A. E. Allahverdyan, Zh. S. Gevorkian, Chin-Kun Hu, and Th. M. Nieuwenhuizen, Phys. Rev. E 79, 031903 (2009). 10.1103/PhysRevE.79.031903
57. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E 47, 684 (1993). 10.1103/PhysRevE.47.684
58. S. Ares, N. K. Voulgarakis, K. Ø. Rasmussen, and A. R. Bishop, Phys. Rev. Lett. 94, 035504 (2005). 10.1103/PhysRevLett.94.035504
59. D. J. Scalapino, M. Sears, and R. A. Ferrel, Phys. Rev. B 6, 3409 (1972). 10.1103/PhysRevB.6.3409
60. Y. L. Zhang, W. M. Zheng, J. X. Liu, and Y. Z. Chen, Phys. Rev. E 56, 7100 (1997). 10.1103/PhysRevE.56.7100
61. H. Kleinert, Path Integrals in Quantum Mechanics, Statistics, Polymer Physics, and Financial Markets (World Scientific, Singapore, 2004).
62. M. Zoli, Phys. Rev. B 71, 205111 (2005). 10.1103/PhysRevB.71.205111
63. M. Zoli, Phys. Rev. B 72, 214302 (2005). 10.1103/PhysRevB.72.214302
64. F. Xu, A. M. Pellino, and W. Knoll, Thin Solid Films 516, 8634 (2008). 10.1016/j.tsf.2008.06.067
65. S. Cuesta-López, D. Angelov, and M. Peyrard, EPL 87, 48009 (2009). 10.1209/0295-5075/87/48009
66. Z. Rapti, A. Smerzi, K. Ø. Rassmussen, A. R. Bishop, C. H. Choi, and A. Usheva, Phys. Rev. E 73, 051902 (2006). 10.1103/PhysRevE.73.051902