J. D. Watson and F. H. Crick, MOLECULAR STRUCTURE OF NUCLEIC ACIDS, JAMA, vol.269, issue.15, pp.737-738, 1953.
DOI : 10.1001/jama.1993.03500150078030

S. W. Englander, N. R. Kallenbach, A. J. Heeger, J. A. Krumhansl, and S. Litwin, Nature of the open state in long polynucleotide double helices: possibility of soliton excitations., Proc. Nat. Acad. Sci. (USA), p.7222, 1980.
DOI : 10.1073/pnas.77.12.7222

D. Poland and H. A. Scheraga, Phase Transitions in One Dimension and the Helix???Coil Transition in Polyamino Acids, The Journal of Chemical Physics, vol.45, issue.5, pp.1456-1463, 1966.
DOI : 10.1063/1.1727785

D. Poland and H. A. Scheraga, Occurrence of a Phase Transition in Nucleic Acid Models, The Journal of Chemical Physics, vol.45, issue.5, pp.1464-1469, 1966.
DOI : 10.1063/1.1727786

M. Peyrard, Nonlinear dynamics and statistical physics of DNA, Nonlinearity, vol.17, issue.2, pp.1-40, 2004.
DOI : 10.1088/0951-7715/17/2/R01

N. Theodorakopoulos, M. Peyrard, and R. S. Mackay, Nonlinear Structures and Thermodynamic Instabilities in a One-Dimensional Lattice System, Physical Review Letters, vol.93, issue.25, pp.258101-258102, 2004.
DOI : 10.1103/PhysRevLett.93.258101

R. S. Mackay and S. Aubry, Proof of existence of breathers for time-reversible or Hamiltonian networks of weakly coupled oscillators, Nonlinearity, vol.7, issue.6, pp.1623-1643, 1994.
DOI : 10.1088/0951-7715/7/6/006

J. Maddox, Towards the calculation of DNA Nature339, 1989.

R. B. Inman and R. L. Baldwin, Helix-random coil transitions in DNA homopolymer pairs, Journal of Molecular Biology, vol.8, issue.4, pp.452-469, 1964.
DOI : 10.1016/S0022-2836(64)80003-6

N. Theodorakopoulos, T. Dauxois, and M. Peyrard, Order of the Phase Transition in Models of DNA Thermal Denaturation, Physical Review Letters, vol.85, issue.1, pp.6-9, 2000.
DOI : 10.1103/PhysRevLett.85.6

Y. Kafri, D. Mukamel, and L. Peliti, Why is the DNA Denaturation Transition First Order?, Physical Review Letters, vol.85, issue.23, pp.4988-4991, 2000.
DOI : 10.1103/PhysRevLett.85.4988

J. L. Leroy, M. Kochoyan, T. Huynh-dinh, and M. Guéron, Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton, Journal of Molecular Biology, vol.200, issue.2, pp.223-238, 1988.
DOI : 10.1016/0022-2836(88)90236-7

M. Guéron, E. Charretier, J. Hagerhorst, M. Kochoyan, J. L. Leroy et al., Application of Imino Proton Exchange to Nucleic Acid Kinetics and Structures in Structure and Methods, 1990.

E. Giuice, P. Várnai, and R. Lavery, Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations, Nucleic Acids Research, vol.31, issue.5, pp.1434-1443, 2003.
DOI : 10.1093/nar/gkg239

M. Peyrard, S. Cuesta-lópez, and G. James, Nonlinear Analysis of the Dynamics of DNA Breathing, Journal of Biological Physics, vol.194, issue.1
DOI : 10.1007/s10867-009-9127-2

URL : https://hal.archives-ouvertes.fr/hal-00389844

A. Wada, S. Yabuki, and Y. , Husimi Fine structure in the thermal denaturation of DNA: high temperature resolution spectrometric studies, CRC Critical Reviews in Biochemistry, pp.87-144, 1980.

C. H. Choi, G. Kalosakas, K. O. Rasmussen, M. Hiromura, A. R. Bishop et al., DNA dynamically directs its own transcription initiation Nucleic Acid Research, pp.1584-1590, 2004.

T. S. Van-erp, S. Cuesta-lópez, J. Hagmann, and M. Peyrard, Can One Predict DNA Transcription Start Sites by Studying Bubbles?, Physical Review Letters, vol.95, issue.21, p.218104, 2005.
DOI : 10.1103/PhysRevLett.95.218104

A. Montrichok, G. Gruner, and G. Zocchi, Trapping intermediates in the melting transition of DNA oligomers, Europhysics Letters (EPL), vol.62, issue.3, pp.452-458, 2003.
DOI : 10.1209/epl/i2003-00417-3

Y. Zeng, A. Montrichok, and G. Zocchi, Bubble Nucleation and Cooperativity in DNA Melting, Journal of Molecular Biology, vol.339, issue.1, pp.67-75, 2004.
DOI : 10.1016/j.jmb.2004.02.072

A. Spassky and D. Angelov, Temperature-dependence of UV Laser One-electron Oxidative Guanine Modifications as a Probe of Local Stacking Fluctuations and Conformational Transitions, Journal of Molecular Biology, vol.323, issue.1, pp.9-15, 2002.
DOI : 10.1016/S0022-2836(02)00878-1

S. For-instance-the-dinamelt-server-http, DINAMelt web server for nucleic acid melting prediction. Nucleic Acid Research, pp.33-577, 2005.

A. Campa and A. Giansanti, Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains, Physical Review E, vol.58, issue.3, pp.3585-3588, 1998.
DOI : 10.1103/PhysRevE.58.3585

V. Ivanov, D. Piontkovski, and G. Zocchi, Local cooperativity mechanism in the DNA melting transition Phys, Rev. E, vol.71, p.41909, 2005.

M. Barbi, S. Cocco, and M. Peyrard, Helicoidal model for DNA opening, Physics Letters A, vol.253, issue.5-6, pp.358-369, 1999.
DOI : 10.1016/S0375-9601(99)00059-6

M. Barbi, S. Lepri, M. Peyrard, and N. Theodorakopoulos, Thermal denaturation of a helicoidal DNA model, Physical Review E, vol.68, issue.6, pp.61909-61910, 2003.
DOI : 10.1103/PhysRevE.68.061909

J. Errami, M. Peyrard, and N. Theodorakopoulos, Modeling DNA beacons at the mesoscopic scale, The European Physical Journal E, vol.88, issue.4, pp.397-411, 2007.
DOI : 10.1140/epje/i2007-10200-x

URL : https://hal.archives-ouvertes.fr/ensl-00517615

A. A. Samoletov, C. P. Dettmann, and M. A. Chaplain, Thermostats for ???Slow??? Configurational Modes, Journal of Statistical Physics, vol.61, issue.6, pp.1321-1336, 2007.
DOI : 10.1007/s10955-007-9365-2