Nonlinear analysis of the dynamics of DNA breathing

Journal of Biological Physics

Volumn 35, Issue 1, 2009, Pages 73-89

  Peyrard, M ^a   Cuesta Lopez S ^a   James, G ^b  

^a UNIVERSITÉ DE LYON   (France)

^b UNIV GRENOBLE ALPES   (France)

Author keywords

Base pair; DNA breathing; Nonlinear dynamics

Indexed keywords

DNA;

ARTICLE; BASE PAIRING; COVALENT BOND; DNA BREATHING; DNA DENATURATION; DNA HELIX; DNA STRUCTURE; ENERGY; GENETIC CODE; HYDROGEN BOND; MOLECULAR DYNAMICS; NONLINEAR SYSTEM; PRIORITY JOURNAL; SIMULATION; TEMPERATURE; THEORETICAL MODEL;

EID: 63149177111     PISSN: 00920606     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10867-009-9127-2     Document Type: Article

References (23)

1. J.D. Watson F.H.C. Crick 1953 Molecular structure of nucleic acids Nature 171 737 738
2. J.L. Leroy M. Kochoyan T. Huynh-Dinh M. Guéron 1988 Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton J. Mol. Biol. 200 223 238
3. R.M. Wartell A.S. Benight 1985 Thermal denaturation of DNA molecules: a comparison of theory with experiments Phys. Rep. 126 67
4. J.G. Duguid V.A. Bloomfield J.M. Benevides G.J. Thomas 1996 DNA melting investigated by differential scanning calorimetry and Raman spectroscopy Biophys. J. 71 3350
5. A. Cupane C. Bologna O. Rizzo E. Vitrano L. Cordone 1997 Local dynamics of DNA probed with optical absorption spectroscopy of bound ethidium bromide Biophys. J. 73 959
6. H.M. Sobell 1985 Actinomycin and DNA transcription Proc. Natl. Acad. Sci. U. S. A. 82 5328 5331
7. G. Altan-Bonnet A. Libchaber O. Krichevsky 2003 Bubble dynamics in double-stranded DNA Phys. Rev. Lett. 90 138101
8. A. Spassky D. Angelov 2002 Temperature-dependence of UV laser one-electron oxidative guanine modifications as a probe of local stacking fluctuations and conformational transitions J. Mol. Biol. 323 9 15
9. M. Peyrard S. Cuesta López D. Angelov 2009 J. Phys. Condensed Matter 21 034103-1-13
10. M. Peyrard 2004 Nonlinear dynamics and statistical physics of DNA Nonlinearity 17 R1 R40
11. N. Theodorakopoulos T. Dauxois M. Peyrard 2000 Order of the phase transition in models of DNA thermal denaturation Phys. Rev. Lett. 85 6 9
12. T. Dauxois M. Peyrard A.R. Bishop 1993 Entropy driven DNA denaturation Phys. Rev. E 47 R44 R47
13. R.S. MacKay S. Aubry 1994 Proof of existence of breathers for time-reversible or Hamiltonian networks of weakly coupled oscillators Nonlinearity 7 1623 1643
14. S. Flach C.R. Willis 1998 Discrete breathers Phys. Rep. 295 181 264
15. J.-A. Sepulchre R.S. MacKay 1997 Localized oscillations in conservative or dissipative networks of weakly coupled autonomous oscillators Nonlinearity 10 679 713
16. G. James B. Sánchez-Rey J. Cuevas 2009 Breathers in inhomogeneous nonlinear lattices: an analysis via center manifold reduction Rev. Math. Phys. 21 1 1 58
17. M. Peyrard J. Farago 2000 Nonlinear localization in thermalized lattices: application to DNA Physica A 288 199 217
18. M. Guéron E. Charretier J. Hagerhorst M. Kochoyan J.L. Leroy A. Moraillon 1990
19. A. Campa A. Giansanti 1998 Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains Phys. Rev. E 58 3585 3588
20. E. Giudice P. Várnai R. Lavery 2003 Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations Nucleic Acids Res. 31 1434 1443
21. S. Aubry G. Abramovici 1990 Chaotic trajectories in the standard map. The concept of anti-integrability Physica D 43 199 219
22. S. Aubry 1995 Anti-integrability in dynamical and variational problems Physica D 86 284 296
23. G.L. Alfimov V.A. Brazhnyi V.V. Konotop 2004 On classification of intrinsic localized modes for the discrete nonlinear Schrödinger equation Physica D 194 127 150