Marc Joyeux - Melting dynamics of DNA

Melting dynamics of DNA

We are interested in the thermal denaturation of DNA, that is, the separation of the two strands upon heating. To this end, we develop mesoscopic dynamical models and investigate their properties using a combination of Molecular Dynamics simulations (i.e., numerical integration of Langevin equations) and Transfer Integral calculations. We characterized in some detail the phase transition that takes place at the critical temperature, for both homogeneous and inhomogeneous sequences

Representation of the kind of models we use to investigate the denaturation dynamics of DNA

Time evolution of the temperature of a 2399 bp sequence below (325 K) and at (335 K) the melting temperature, obtained from dynamics simulations using a dynamical model. Each pixel corresponds to the temperature averaged over ten successive bps and 50 ns.

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78 -	Free-energy landscape and characteristic forces for the initiation of DNA unzipping A. Mentes, A.-M. Florescu, E. Brunk, J. Wereszczynski, M. Joyeux and I. Andricioaei, Biophys. J. 108 (2015) 1727-1738 (1-12) [full text] copyright : Elsevier ([Abstract])
72 -	Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide A.-M. Florescu and M. Joyeux, J. Chem. Phys. 135 (2011) 085105 (1-12) [full text] copyright : The American Institute of Physics ([Abstract])
69 -	On the Pseudo-Schrödinger Equation approximation of the Transfer-Integral operator for 1-dimensional DNA models M. Joyeux, J. Nonlin. Math. Phys. 18 (2011) 339-357 [full text] copyright : World Scientific Publishing ([Abstract])
66 -	Mapping between the order of thermal denaturation and the shape of the critical line of mechanical unzipping in 1-dimensional DNA models S. Buyukdagli and M. Joyeux, Chem. Phys. Lett. 484 (2010) 315-320 [Abstract] [Ask for an electronic reprint by email] [arXiv preprint]
64 -	Modeling of two-dimensional DNA display A.-M. Florescu, M. Joyeux and B. Lafay, Electrophoresis 30 (2009) 3649-3656 [Abstract] [Ask for an electronic reprint by email] [arXiv preprint]
61 -	Dynamical versus statistical mesoscopic models for DNA denaturation M. Joyeux and A.-M. Florescu, J. Phys. : Condens. Matter 21 (2009) 034101 (1-12) (special issue on DNA melting) [full text] copyright : Institute of Physics Publishing ( [Abstract])
60 -	Comment on "Bubble nucleation and cooperativity in DNA melting" M. Sanrey and M. Joyeux, Phys. Rev. Letters 102 (2009) 029601 (1-1) [full text] copyright : The American Physical Society ( [Abstract])
59 -	Statistical physics of the melting of inhomogeneous DNA S. Buyukdagli and M. Joyeux, Phys. Rev. E 77 (2008) 031903 (1-10) [full text] copyright : The American Physical Society ([Abstract])
58 -	Theoretical investigation of finite size effects at DNA melting S. Buyukdagli and M. Joyeux, Phys. Rev. E 76 (2007) 021917 (1-11) [full text] copyright : The American Physical Society ([Abstract])
57 -	1/f fluctuations of DNA temperature at thermal denaturation M. Joyeux, S. Buyukdagli and M. Sanrey, Phys. Rev. E 75 (2007) 061914 (1-9) [full text] copyright : The American Physical Society ([Abstract])
54 -	Scaling laws at the phase transition of systems with divergent order parameter and/or internal length : the example of DNA denaturation S. Buyukdagli and M. Joyeux, Phys. Rev. E 73 (2006) 051910 (1-6) [full text] copyright : The American Physical Society ([Abstract])
52 -	Towards more realistic dynamical models for DNA secondary structure S. Buyukdagli, M. Sanrey and M. Joyeux, Chem. Phys. Lett. 419 (2006) 434-438 [Abstract] [Ask for an electronic reprint by email] [arXiv preprint]
51 -	Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation M. Joyeux and S. Buyukdagli, Phys. Rev. E 72 (2005) 051902 (1-5) [full text] copyright : The American Physical Society ([Abstract])