Stochastic dynamics and denaturation of thermalized DNA

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

Volumn 77, Issue 2, 2008, Pages

  Deng, Mao Lin ^a   Zhu, Wei Qiu ^a,b  

^a ZHEJIANG UNIVERSITY   (China)

^b RESEARCH CENTER FOR APPLIED SCIENCES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

DENATURATION; DIFFERENTIAL EQUATIONS; MONTE CARLO METHODS; PROBABILITY DENSITY FUNCTION; RANDOM PROCESSES;

FRICTION COEFFICIENT; HAMILTONIAN SYSTEMS; LANGEVIN EQUATIONS; STOCHASTIC DYNAMICS;

DNA;

EID: 40849092611     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.77.021918     Document Type: Article

References (26)

1. J. Santalucia, Jr., Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.95.4.1460 95, 1460 (1998).
2. T. Hwa, E. Marinari, K. Sneppen, and L.-H. Tang, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0736291100 100, 4411 (2003).
3. G. Altan-Bonnet, A. Libchaber, and O. Krichevsky, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.90.138101 90, 138101 (2003).
4. M. Guéron and J. L. Leroy, Methods Enzymol. MENZAU 0076-6879 10.1016/S0076-6879(95)61018-9 261, 383 (1995).
5. D. Poland and H. A. Scheraga, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1727785 45, 1456 (1966).
6. M. Peyrard and A. R. Bishop, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.62.2755 62, 2755 (1989).
7. T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.47.R44 47, R44 (1993).
8. D. J. Bicout and E. Kats, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.70.010902 70, 010902 (R) (2004).
9. A. Bar, Y. Kafri, and D. Mukamel, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.038103 98, 038103 (2007).
10. A. Hanke and R. Metzler, J. Phys. A JPHAC5 0305-4470 10.1088/0305-4470/ 36/36/101 36, L473 (2003).
11. H. C. Fogedby and R. Metzler, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.98.070601 98, 070601 (2007).
12. N. Theodorakopoulos, M. Peyrard, and R. S. MacKay, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.258101 93, 258101 (2004).
13. A. Campa and A. Giansanti, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.58.3585 58, 3585 (1998).
14. 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).
15. G. Kalosakas, K. Ø. Rasmussen, A. R. Bishop, C. H. Choi, and A. Usheva, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i2004-10167-8 68, 127 (2004).
16. T. Novotný, J. N. Pedersen, T. Ambjörnsson, M. S. Hansen, and R. Metzler, Europhys. Lett. EULEEJ 0295-5075 10.1209/0295-5075/77/48001 77, 48001 (2007).
17. T. Ambjörnsson, S. K. Banik, O. Krichevsky, and R. Metzler, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.97.128105 97, 128105 (2006).
18. W. Q. Zhu, Appl. Mech. Rev. AMREAD 0003-6900 10.1115/1.2193137 59, 230 (2006).
19. W. Q. Zhu, Nonlinear Stochastic Dynamics and Control-Hamiltonian Theoretical Framework (Science Press, Beijing, 2003) (in Chinese).
20. W. Q. Zhu and Y. Q. Yang, J. Appl. Mech. JAMCAV 0021-8936 10.1115/1.2787267 64, 157 (1997).
21. W. Q. Zhu, Z. L. Huang, and Y. Q. Yang, J. Appl. Mech. 64, 975 (1997). 0021-8936
22. W. Q. Zhu, Z. L. Huang, and Y. Suzuki, Int. J. Non-Linear Mech. IJNMAG 0020-7462 10.1016/S0020-7462(01)00018-X 37, 419 (2002).
23. M. Peyrard, Nonlinearity NONLE5 0951-7715 10.1088/0951-7715/17/2/R01 17, R1 (2004).
24. W. Saenger, Principles of Nucleic Acid Structure (Springer, Berlin, 1984).
25. W. Ebeling, L. Schimansky-Geier, and Y. M. Romanovsky, Stochastic Dynamics of Reacting Biomolecules (World Scientific, Singapore, 2002).
26. R. Z. Khasminskii, Kibernetika 4, 260 (1968) (in Russian).