J. D. Watson and F. H. Crick, MOLECULAR STRUCTURE OF NUCLEIC ACIDS, JAMA, vol.269, issue.15, pp.171-737, 1953.
DOI : 10.1001/jama.1993.03500150078030

F. H. Crick and J. D. Watson, The Complementary Structure of Deoxyribonucleic Acid, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.223, issue.1152, p.223, 1954.
DOI : 10.1098/rspa.1954.0101

R. E. Franklin and R. G. Gosling, Molecular configuration in sodium thymonucleate, Nature, pp.171-740, 1953.

R. Wing, Crystal structure analysis of a complete turn of B-DNA, Nature, vol.73, issue.5784, pp.287-755, 1980.
DOI : 10.1038/287755a0

C. O. Pabo and R. T. Sauer, Protein-DNA Recognition, Annual Review of Biochemistry, vol.53, issue.1, 1984.
DOI : 10.1146/annurev.bi.53.070184.001453

Z. Kudritskaya and V. Danilov, Quantum mechanical study of bases interactions in various associates in atomic dipole approximation, Journal of Theoretical Biology, vol.59, issue.2, p.59, 1976.
DOI : 10.1016/0022-5193(76)90172-7

V. R. Cooper, Stacking Interactions and the Twist of DNA, Journal of the American Chemical Society, vol.130, issue.4, pp.130-1304, 2008.
DOI : 10.1021/ja0761941

C. Bouchiat, Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements, Biophysical Journal, vol.76, issue.1, p.76, 1999.
DOI : 10.1016/S0006-3495(99)77207-3

C. Bustamante, Entropic elasticity of lambda-phage DNA, Science, vol.265, issue.5178, p.1599, 1994.
DOI : 10.1126/science.8079175

R. M. Wartell and A. S. Benight, Thermal denaturation of DNA molecules: A comparison of theory with experiment, Physics Reports, vol.126, issue.2, p.126, 1985.
DOI : 10.1016/0370-1573(85)90060-2

G. Altan-bonnet, Bubble Dynamics in Double-Stranded DNA, Physical Review Letters, vol.90, issue.13, p.90, 2003.
DOI : 10.1103/PhysRevLett.90.138101

S. Tyagi and F. R. Kramer, Molecular Beacons: Probes that Fluoresce upon Hybridization, Nature Biotechnology, vol.13, issue.3, 1996.
DOI : 10.1073/pnas.93.18.9881

O. Gotoh, Prediction of melting profiles and local Helix stability for sequenced DNA, Advances in Biophysics, vol.16, p.16, 1983.
DOI : 10.1016/0065-227X(83)90007-2

B. S. Alexandrov, A nonlinear dynamic model of DNA with a sequence-dependent stacking term, Nucleic Acids Research, vol.37, issue.7, p.2405, 2009.
DOI : 10.1093/nar/gkp016

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.45-1464, 1966.
DOI : 10.1063/1.1727786

D. Poland and H. A. Scheraga, Phase transitions in one dimension and the HelixCoil transition in polyamino acids, The Journal of Chemical Physics, pp.45-1456, 1966.

M. E. Fisher, Effect of Excluded Volume on Phase Transitions in Biopolymers, The Journal of Chemical Physics, vol.45, issue.5, pp.45-1469, 1966.
DOI : 10.1063/1.1727787

M. E. Fisher, Walks, walls, wetting, and melting, Journal of Statistical Physics, vol.32, issue.50, 1984.
DOI : 10.1007/BF01009436

Y. Kafri, Why is the DNA denaturation transition first order? Physical Review Letters, p.4988, 2000.

Y. Kafri, Melting and unzipping of DNA, The European Physical Journal B - Condensed Matter, vol.27, issue.1, 2002.
DOI : 10.1140/epjb/e20020138

H. C. Fogedby and R. Metzler, DNA Bubble Dynamics as a Quantum Coulomb Problem, Physical Review Letters, vol.98, issue.7, pp.98-070601, 2007.
DOI : 10.1103/PhysRevLett.98.070601

T. Ambjrnsson, Sequence Sensitivity of Breathing Dynamics in Heteropolymer DNA, Physical Review Letters, vol.97, issue.12, pp.97-128105, 2006.
DOI : 10.1103/PhysRevLett.97.128105

K. P. Murthy and G. M. Schtz, Mean bubble formation time in DNA denaturation, EPL (Europhysics Letters), vol.96, issue.6, p.96, 2011.
DOI : 10.1209/0295-5075/96/68003

A. Bar, Loop Dynamics in DNA Denaturation, Physical Review Letters, vol.98, issue.3, pp.98-038103, 2007.
DOI : 10.1103/PhysRevLett.98.038103

J. Palmeri, Thermal Denaturation of Fluctuating DNA Driven by Bending Entropy, Physical Review Letters, vol.99, issue.8, pp.99-088103, 2007.
DOI : 10.1103/PhysRevLett.99.088103

URL : https://hal.archives-ouvertes.fr/hal-00123812

J. Palmeri, Thermal denaturation of fluctuating finite DNA chains: The role of bending rigidity in bubble nucleation, Physical Review E, vol.77, issue.1, pp.77-011913, 2008.
DOI : 10.1103/PhysRevE.77.011913

URL : https://hal.archives-ouvertes.fr/hal-00173154

M. Manghi, Coupling between denaturation and chain conformations in DNA: stretching, bending, torsion and finite size effects, Journal of Physics: Condensed Matter, vol.21, issue.3, p.34104, 2009.
DOI : 10.1088/0953-8984/21/3/034104

URL : https://hal.archives-ouvertes.fr/hal-00316382

A. K. Dasanna, Strand diffusion-limited closure of denaturation bubbles in DNA, EPL (Europhysics Letters), vol.98, issue.3, p.98, 2012.
DOI : 10.1209/0295-5075/98/38002

URL : https://hal.archives-ouvertes.fr/hal-00702529

M. Peyrard and A. R. Bishop, Statistical mechanics of a nonlinear model for DNA denaturation, Physical Review Letters, vol.62, issue.23, pp.62-2755, 1989.
DOI : 10.1103/PhysRevLett.62.2755

T. Dauxois, Entropy-driven DNA denaturation, Physical Review E, vol.47, issue.1, pp.47-91, 1993.
DOI : 10.1103/PhysRevE.47.R44

T. Dauxois, Dynamics and thermodynamics of a nonlinear model for DNA denaturation, Physical Review E, vol.47, issue.1, p.47, 1993.
DOI : 10.1103/PhysRevE.47.684

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

M. Peyrard, Nonlinear Analysis of the Dynamics of DNA Breathing, Journal of Biological Physics, vol.194, issue.1, p.73, 2009.
DOI : 10.1007/s10867-009-9127-2

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

T. Dauxois, Thermodynamic instabilities in one dimension: Correlations, scaling and solitons, Journal of Statistical Physics, vol.107, issue.869, 2002.
URL : https://hal.archives-ouvertes.fr/hal-01140180

T. Dauxois, Localized breather-like solution in a discrete Klein-Gordon model and application to DNA, Physica D: Nonlinear Phenomena, vol.57, issue.3-4, p.57, 1992.
DOI : 10.1016/0167-2789(92)90003-6

G. J. Martyna, Nos[e-acute]?hoover chains: The canonical ensemble via continuous dynamics, The Journal of Chemical Physics, pp.97-2635, 1992.

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.58-3585, 1998.
DOI : 10.1103/PhysRevE.58.3585

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

S. Cocco and R. Monasson, Statistical Mechanics of Torque Induced Denaturation of DNA, Physical Review Letters, vol.83, issue.24, 1999.
DOI : 10.1103/PhysRevLett.83.5178

M. Barbi, A twist opening model for dna, Journal of Biological Physics, vol.24, issue.97, 1999.

S. Zdravkovi´czdravkovi´c, HELICOIDAL PEYRARD???BISHOP MODEL OF DNA DYNAMICS, Journal of Nonlinear Mathematical Physics, vol.18, issue.sup2, p.463, 2011.
DOI : 10.1142/9789812799203

A. Campa, Bubble propagation in a helicoidal molecular chain, Physical Review E, vol.63, issue.2, 2001.
DOI : 10.1103/PhysRevE.63.021901

J. Jeon, A semiflexible chain model of local denaturation in double-stranded DNA, The Journal of Chemical Physics, vol.124, issue.16, pp.124-164905, 2006.
DOI : 10.1063/1.2192774

J. Kim, A breathing wormlike chain model on DNA denaturation and bubble: Effects of stacking interactions, The Journal of Chemical Physics, vol.128, issue.5, pp.128-055101, 2008.
DOI : 10.1063/1.2827471

O. Lee, How double-stranded DNA breathing enhances its flexibility and instability on short length scales, Physical Review E, vol.81, issue.2, pp.81-021906, 2010.
DOI : 10.1103/PhysRevE.81.021906

A. Hanke and R. Metzler, Bubble dynamics in DNA, Journal of Physics A: Mathematical and General, vol.36, issue.36, p.473, 2003.
DOI : 10.1088/0305-4470/36/36/101

D. T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, Journal of Computational Physics, vol.22, issue.4, pp.22-403, 1976.
DOI : 10.1016/0021-9991(76)90041-3

D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions, The Journal of Physical Chemistry, vol.81, issue.25, pp.81-2340, 1977.
DOI : 10.1021/j100540a008

S. K. Banik, Stochastic approach to DNA breathing dynamics, Europhysics Letters (EPL), vol.71, issue.5, p.71, 2005.
DOI : 10.1209/epl/i2005-10144-9

T. Ambjörnsson, Breathing Dynamics in Heteropolymer DNA, Biophysical Journal, vol.92, issue.8, 2007.
DOI : 10.1529/biophysj.106.095935

T. Ambjörnsson, Master equation approach to DNA breathing in heteropolymer DNA, Physical Review E, vol.75, issue.2, pp.75-021908, 2007.
DOI : 10.1103/PhysRevE.75.021908

S. Wärmländer, Imino proton exchange in DNA catalyzed by ammonia and trimethylamine: evidence for a secondary Long-Lived open state of the base pair, Biochemistry, vol.607, p.39, 1999.

M. Bishop, Molecular dynamics of polymeric systems, The Journal of Chemical Physics, vol.70, issue.3, p.1299, 1979.
DOI : 10.1063/1.437567

J. Baschnagel, Monte carlo simulation of polymers: Coarsegrained models, in computational soft matter: From synthetic polymers to proteins edited by n, 2004.

P. M. Morse, Diatomic Molecules According to the Wave Mechanics. II. Vibrational Levels, Physical Review, vol.34, issue.1, 1929.
DOI : 10.1103/PhysRev.34.57

T. A. Knotts, A coarse grain model for DNA, The Journal of Chemical Physics, vol.126, issue.8, p.84901, 2007.
DOI : 10.1063/1.2431804

M. Manghi, Probing DNA conformational changes with high temporal resolution by tethered particle motion, Physical Biology, vol.7, issue.4, p.46003, 2010.
DOI : 10.1088/1478-3975/7/4/046003

URL : https://hal.archives-ouvertes.fr/hal-00557866

F. Zhang and M. A. Collins, Model simulations of DNA dynamics, Physical Review E, vol.52, issue.4, pp.52-4217, 1995.
DOI : 10.1103/PhysRevE.52.4217

S. Nos, A unified formulation of the constant temperature molecular dynamics methods, The Journal of Chemical Physics, vol.81, issue.1, pp.81-511, 1984.
DOI : 10.1063/1.447334

W. G. Hoover, Canonical dynamics: Equilibrium phase-space distributions, Physical Review A, vol.31, issue.3, pp.31-1695, 1985.
DOI : 10.1103/PhysRevA.31.1695

D. J. Evans and B. L. Holian, The Nose???Hoover thermostat, The Journal of Chemical Physics, vol.83, issue.8, p.4069, 1985.
DOI : 10.1063/1.449071

K. Drukker and G. C. Schatz, A Model for Simulating Dynamics of DNA Denaturation, The Journal of Physical Chemistry B, vol.104, issue.26, p.6108, 2000.
DOI : 10.1021/jp000550j

M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids. Oxford science publications, 1989.

M. Sayar, Twist-writhe partitioning in a coarse-grained DNA minicircle model, Physical Review E, vol.81, issue.4, pp.81-041916, 2010.
DOI : 10.1103/PhysRevE.81.041916

H. Limbach, ESPResSo???an extensible simulation package for research on soft matter systems, Computer Physics Communications, vol.174, issue.9, p.704, 2006.
DOI : 10.1016/j.cpc.2005.10.005

E. Sambriski, A Mesoscale Model of DNA and Its Renaturation, Biophysical Journal, vol.96, issue.5, pp.96-1675, 2009.
DOI : 10.1016/j.bpj.2008.09.061

A. Florescu and M. Joyeux, Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide, The Journal of Chemical Physics, vol.135, issue.8, pp.135-085105, 2011.
DOI : 10.1063/1.3626870

T. E. Ouldridge, Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model, The Journal of Chemical Physics, vol.134, issue.8, pp.134-085101, 2011.
DOI : 10.1063/1.3552946

T. E. Ouldridge, DNA Nanotweezers Studied with a Coarse-Grained Model of DNA, Physical Review Letters, vol.104, issue.17, 2010.
DOI : 10.1103/PhysRevLett.104.178101

H. R. Warner, Kinetic Theory and Rheology of Dilute Suspensions of Finitely Extendible Dumbbells, Industrial & Engineering Chemistry Fundamentals, vol.11, issue.3, p.11, 1972.
DOI : 10.1021/i160043a017

K. Kremer and G. S. Grest, Dynamics of entangled linear polymer melts:??? A molecular???dynamics simulation, The Journal of Chemical Physics, vol.92, issue.8, p.92, 1990.
DOI : 10.1063/1.458541

S. Whitelam, The role of collective motion in examples of coarsening and self-assembly, Soft Matter, vol.93, issue.6, p.1251, 2009.
DOI : 10.1039/B810031D

S. P. Mielke, Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA, The Journal of Chemical Physics, vol.123, issue.12, pp.123-124911, 2005.
DOI : 10.1063/1.2038767

S. P. Mielke, Brownian dynamics of double-stranded DNA in periodic systems with discrete salt, Physical Review E, vol.77, issue.3, pp.77-031924, 2008.
DOI : 10.1103/PhysRevE.77.031924

M. C. Linak, Moving beyond WatsonCrick models of coarse grained DNA dynamics, The Journal of Chemical Physics, p.135, 2011.

S. Niewieczerza and M. Cieplak, Stretching and twisting of the DNA duplexes in coarse-grained dynamical models, Journal of Physics: Condensed Matter, vol.21, issue.47, p.474221, 2009.
DOI : 10.1088/0953-8984/21/47/474221

A. Morriss-andrews, A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality, The Journal of Chemical Physics, vol.132, issue.3, pp.132-035105, 2010.
DOI : 10.1063/1.3269994

S. Buyukdagli, Towards more realistic dynamical models for DNA secondary structure, Chemical Physics Letters, vol.419, issue.4-6, p.419, 2006.
DOI : 10.1016/j.cplett.2005.12.009

URL : https://hal.archives-ouvertes.fr/hal-00015832

A. K. Dasanna, Slow closure of denaturation bubbles in DNA: Twist matters, Physical Review E, vol.87, issue.5, p.52703, 2013.
DOI : 10.1103/PhysRevE.87.052703

URL : https://hal.archives-ouvertes.fr/hal-00822680

M. Doi and S. F. Edwards, The Theory of Polymer Dynamics, 1986.

C. Bouchiat and M. Mézard, Elasticity Model of a Supercoiled DNA Molecule, Physical Review Letters, vol.80, issue.7, p.1556, 1998.
DOI : 10.1103/PhysRevLett.80.1556

N. L. Goddard, Sequence Dependent Rigidity of Single Stranded DNA, Physical Review Letters, vol.85, issue.11, 2000.
DOI : 10.1103/PhysRevLett.85.2400

C. Ke, Direct measurements of base stacking interactions in dna by singlemolecule atomic-force spectroscopy, Physical Review Letters, pp.99-018302, 2007.

S. B. Smith, Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules, Science, vol.271, issue.5250, pp.271-795, 1996.
DOI : 10.1126/science.271.5250.795

B. Tinland, Persistence Length of Single-Stranded DNA, Macromolecules, vol.30, issue.19, 1997.
DOI : 10.1021/ma970381+

M. Manghi and R. R. Netz, Variational theory for a single polyelectrolyte chain revisited, The European Physical Journal E, vol.11, issue.1, p.14, 2004.
DOI : 10.1140/epje/i2004-10007-3

URL : https://hal.archives-ouvertes.fr/hal-00123826

S. Chandrasekhar, Stochastic Problems in Physics and Astronomy, Reviews of Modern Physics, vol.15, issue.1, 1943.
DOI : 10.1103/RevModPhys.15.1

C. W. Gardiner, Handbook of stochastic methods : for physics, chemistry and the natural sciences. Springer series in synergetics, 2002.

R. Kubo, Statistical Physics II: Nonequilibrium Statistical Mechanics (Springer Series in Solid-State Sciences, 31), 1995.

D. Poland and H. A. Scheraga, Theory of helix-coil transitions in biopolymers: statistical mechanical theory of order-disorder transitions in biological macromolecules, 1970.

D. Panja, Non-equilibrium dynamics of single polymer adsorption to solid surfaces, Journal of Physics: Condensed Matter, vol.21, issue.24, 2009.
DOI : 10.1088/0953-8984/21/24/242101

A. Ferrantini and E. Carlon, Anomalous zipping dynamics and forced polymer translocation, Journal of Statistical Mechanics: Theory and Experiment, vol.2011, issue.02, pp.2011-02020, 2011.
DOI : 10.1088/1742-5468/2011/02/P02020

URL : http://arxiv.org/abs/1102.2714

K. Luo, Driven polymer translocation through nanopores: Slow-vs.-fast dynamics, EPL (Europhysics Letters), vol.88, issue.6, p.88, 2009.
DOI : 10.1209/0295-5075/88/68006

Y. Yin and X. S. Zhao, Kinetics and Dynamics of DNA Hybridization, Accounts of Chemical Research, vol.44, issue.11, p.1172, 2011.
DOI : 10.1021/ar200068j

T. Sakaue, Sucking genes into pores: Insight into driven translocation, Physical Review E, vol.81, issue.4, pp.81-041808, 2010.
DOI : 10.1103/PhysRevE.81.041808

A. Y. Grosberg, How long does it take to pull an ideal polymer into a small hole? Physical Review Letters, pp.96-228105, 2006.

Y. Kantor and M. Kardar, Anomalous dynamics of forced translocation, Physical Review E, vol.69, issue.2, pp.69-021806, 2004.
DOI : 10.1103/PhysRevE.69.021806

N. Destainville, Microscopic Mechanism for Experimentally Observed Anomalous Elasticity of DNA in Two Dimensions, Biophysical Journal, vol.96, issue.11, p.96, 2009.
DOI : 10.1016/j.bpj.2009.03.035

URL : https://hal.archives-ouvertes.fr/hal-00417510

M. Guéron, A single mode of DNA base-pair opening drives imino proton exchange, Nature, vol.328, issue.6125, p.328, 1987.
DOI : 10.1038/328089a0

M. Bandyopadhyay, DNA breathing dynamics: Analytic results for distribution functions of relevant Brownian functionals, Physical Review E, vol.83, issue.3, pp.83-031905, 2011.
DOI : 10.1103/PhysRevE.83.031905

B. S. Alexandrov, Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter, PLoS Computational Biology, vol.10, issue.3, p.1000313, 2009.
DOI : 10.1371/journal.pcbi.1000313.g007

J. F. Marko, Stretching must twist DNA, Europhysics Letters (EPL), vol.38, issue.3, 1997.
DOI : 10.1209/epl/i1997-00223-5

J. M. Huguet, Single-molecule derivation of salt dependent base-pair free energies in DNA, Proceedings of the National Academy of Sciences, vol.107, issue.35, p.15431, 2010.
DOI : 10.1073/pnas.1001454107

D. L. Ermak and J. A. Mccammon, Brownian dynamics with hydrodynamic interactions, The Journal of Chemical Physics, vol.69, issue.4, pp.69-1352, 1978.
DOI : 10.1063/1.436761

J. Rotne and S. Prager, Variational Treatment of Hydrodynamic Interaction in Polymers, The Journal of Chemical Physics, vol.50, issue.11, pp.50-4831, 1969.
DOI : 10.1063/1.1670977

H. Yamakawa, Transport Properties of Polymer Chains in Dilute Solution: Hydrodynamic Interaction, The Journal of Chemical Physics, vol.53, issue.1, pp.53-436, 1970.
DOI : 10.1063/1.1673799

M. Peyrard, Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules, Journal of Physics: Condensed Matter, vol.21, issue.3, p.34103, 2009.
DOI : 10.1088/0953-8984/21/3/034103

URL : https://hal.archives-ouvertes.fr/ensl-00309191

J. Santalucia, A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proceedings of the National Academy of Sciences, pp.95-1460, 1998.
DOI : 10.1073/pnas.95.4.1460

S. Geggier and A. Vologodskii, Sequence dependence of DNA bending rigidity, Proceedings of the National Academy of Sciences, p.15421, 2010.
DOI : 10.1073/pnas.1004809107

H. Zhou, Elastic property of single double-stranded DNA molecules: Theoretical study and comparison with experiments, Physical Review E, vol.62, issue.1, pp.62-1045, 2000.
DOI : 10.1103/PhysRevE.62.1045

S. Cocco, Unzipping dynamics of long DNAs, Physical Review E, vol.66, issue.5, p.51914, 2002.
DOI : 10.1103/PhysRevE.66.051914

S. Cocco, Force and kinetic barriers to initiation of DNA unzipping, Physical Review E, vol.65, issue.4, pp.65-041907, 2002.
DOI : 10.1103/PhysRevE.65.041907

E. Orlandini, Mechanical denaturation of DNA: existence of a low-temperature denaturation, Journal of Physics A: Mathematical and General, vol.34, issue.50, pp.34-751, 2001.
DOI : 10.1088/0305-4470/34/50/104

F. Romano, Coarse-grained simulations of DNA overstretching, The Journal of Chemical Physics, vol.138, issue.8, p.85101, 2013.
DOI : 10.1063/1.4792252

M. Manghi, Mesoscopic models for DNA stretching under force: New results and comparison with experiments, The European Physical Journal E, vol.98, issue.10, p.35, 2012.
DOI : 10.1140/epje/i2012-12110-2

URL : https://hal.archives-ouvertes.fr/hal-00745436