DNA denaturation bubbles at criticality

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

Volumn 77, Issue 3, 2008, Pages

  Theodorakopoulos, Nikos ^a,b  

^a THEORETICAL AND PHYSICAL CHEMISTRY INSTITUTE   (Greece)

^b UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BUBBLES (IN FLUIDS); DENATURATION; FREE ENERGY; STATISTICAL MECHANICS;

DNA DENATURATION BUBBLES; NONLINEAR BASE-STACKING INTERACTIONS;

DNA;

EID: 41549144880     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.77.031919     Document Type: Article

References (21)

1. Cf. M. Peyrard, Nonlinearity NONLE5 0951-7715 10.1088/0951-7715/17/2/R01 17, R1 (2004) and references cited therein.
2. C. H. Choi, G. Kalosakas, K. O. Rasmussen, M. Hiromura, A. R. Bishop, and A. Usheva, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkh335 32, 1584 (2004).
3. G. Kalosakas, K. O. Rasmussen, M. Hiromura, A. R. Bishop, C. H. Choi, and A. Usheva, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i2004-10167-8 68, 127 (2004).
4. T. S. van Erp, S. Cuesta-Lopez, J.-G. Hagmann, and M. Peyrard, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.95.218104 95, 218104 (2005).
5. C. H. Choi, A. Usheva, G. Kalosakas, K. O. Rasmussen, and A. R. Bishop, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.239801 96, 239801 (2006).
6. T. S. van Erp, S. Cuesta-Lopez, J.-G. Hagmann, and M. Peyrard, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.239802 96, 239802 (2006).
7. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.62.2755 62, 2755 (1989)
8. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.47.R44 47, R44 (1993).
9. N. Theodorakopoulos, T. Dauxois, and M. Peyrard, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.85.6 85, 6 (2000).
10. T. Dauxois, N. Theodorakopoulos, and M. Peyrard, J. Stat. Phys. JSTPBS 0022-4715 10.1023/A:1014546415934 107, 869 (2002).
11. N. Theodorakopoulos, Physica D 216, 185 (2006). 0167-2789
12. W. Sung and J.-H. Jeon, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.69.031902 69, 031902 (2004).
13. S. Ares and G. Kalosakas, Nano Lett. NALEFD 1530-6984 10.1021/nl062304a 7, 307 (2007).
14. The authors of Ref. analyze some preliminary data in terms of a product of an exponential function and a power law with a characteristic exponent which in the case of pure G-C chains approaches a value slightly below 2 at the critical temperature. The latter result is somewhat problematical; it implies-contrary to the known thermodynamic behavior of the model under consideration-a continuous transition and a concomitant proliferation of large-size bubbles, such that the average bubble size would diverge (cf. the results reported here and the discussion in Sec. 3).
15. D. Cule and T. Hwa, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.79.2375 79, 2375 (1997).
16. Handbook of Mathematical Functions, edited by, M. Abramowitz, and, I. A. Stegun, (Dover, New York, 1965), p. 886.
17. The astute reader will note that the probability of small-bubble formation is higher at lower temperatures. This apparently counterintuitive property is due to the definition of a bubble, which demands that the two ends be bound. Pn is a probability of a configuration of an n+2 site group; it reflects the competition between holding the ends bound (higher probability at lower temperatures) and softening the bonds of the n interior sites (higher probability at higher temperatures).
18. The form 9 has been derived in the context of the Poland-Scheraga model, with the exponent c associated with the entropy of loops (bubbles) modeled as self-avoiding polymer chains. There is no a priori reason why the result of such a geometrically based description-which mainly reflects the dimensionality of space-should correspond to any feature of the one-dimensional nonlinear lattice dynamics of the PBD model (cf., however, below for some general arguments and a more detailed description of the meaning of the exponent c in the PBD context).
19. D. Poland and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1727786 45, 1464 (1966).
20. N. Theodorakopoulos, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.68. 026109 68, 026109 (2003).
21. Cf. S. Aubry, Physica D PDNPDT 0167-2789 10.1016/j.physd.2005.12.020 216, 1 (2006) and references therein.