Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation

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

Volumn 72, Issue 5, 2005, Pages

  Joyeux, Marc ^a   Buyukdagli, Sahin ^a  

^a LIPHY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMICAL MODEL; FINITE STACKING ENTHALPIES; THERMAL DENATURATION;

ENTHALPY; INTEGRAL EQUATIONS; MATHEMATICAL MODELS; MELTING; MOLECULAR DYNAMICS; THERMODYNAMICS;

DNA;

DNA;

ANISOTROPY; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DNA DENATURATION; DNA SEQUENCE; ENTROPY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; STATISTICAL MODEL; STRUCTURE ACTIVITY RELATION; TEMPERATURE; THERMODYNAMICS;

ANISOTROPY; BASE SEQUENCE; COMPUTER SIMULATION; DNA; ENTROPY; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; SEQUENCE ANALYSIS, DNA; STRUCTURE-ACTIVITY RELATIONSHIP; TEMPERATURE; THERMODYNAMICS;

EID: 28844449314     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.72.051902     Document Type: Article

References (18)

1. D. Poland and H. A. Scheraga, Theory of Helix-coil Transitions in Biopolymers (Academic Press, New York, 1970).
2. R. M. Wartell and A. S. Benight, Phys. Rep. PRPLCM 0370-1573 10.1016/0370-1573(85)90060-2 126, 67 (1985).
3. O. Gotoh, Adv. Biophys. ADVBAT 0065-227X 16, 3 (1983).
4. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.62.2755 62, 2755 (1989).
5. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.47.R44 47, R44 (1993).
6. N. Theodorakopoulos, T. Dauxois, and M. Peyrard, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.85.6 85, 6 (2000).
7. D. Poland and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1727785 45, 1456 (1966);
8. D. Poland and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1727786 45, 1464 (1966).
9. Y. Kafri, D. Mukamel, and L. Peliti, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.85.4988 85, 4988 (2000).
10. J. SantaLucia, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.95.4.1460 95, 1460 (1998).
11. R. D. Blake, J. W. Bizzaro, J. D. Blake, G. R. Day, S. G. Delcourt, J. Knowles, K. A. Marx, and J. SantaLucia, Bioinformatics BOINFP 1367-4803 10.1093/bioinformatics/15.5.370 15, 370 (1999).
12. Y.-L. Zhang, W.-M. Zheng, J. X. Liu, and Y. Z. Chen, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.56.7100 56, 7100 (1997).
13. M. Peyrard, Nonlinearity NONLE5 0951-7715 10.1088/0951-7715/17/2/R01 17, R1 (2004).
14. T. Shimomura, K. Denda, A. Kitamura, T. Kawaguchi, M. Kito, J. Kondo, S. Kagaya, L. Qin, H. Takata, K. Miyazawa, and N. Kitamura, J. Biol. Chem. JBCHA3 0021-9258 272, 6370 (1997).
15. E. Carlon, M. L. Malki, and R. Blossey, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.178101 94, 178101 (2005).
16. A. Campa and A. Giansanti, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.58.3585 58, 3585 (1998).
17. T. Schneider and E. Stoll, Phys. Rev. B PRBMDO 0163-1829 10.1103/PhysRevB.22.5317 22, 5317 (1980).
18. A. Brünger, C. B. Brooks, and M. Karplus, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(84)80098-6 105, 495 (1984).