Can we model DNA at the mesoscale?
Modelling DNA is useful for understanding its properties better but it is also challenging because many of these properties involve hundreds of base pairs or more, or time scales which are much longer than the time scales accessible to molecular dynamics. It is therefore necessary to develop models at a mesoscale, which include enough details to describe the properties of interest, for instance the biological sequence, while staying sufficiently simple and realistic.We discuss here two examples: a dynamical model to study the mechanical denaturation of DNA, which probes the sequence on various scales, and a model for the self assembly of DNA which describes the formation of hairpins and allows us to study its kinetics.
Dept. Física de la Materia Condensada, Universidad de Zaragoza, c/Pedro Cerbuna s/n 50009 Zaragoza, Spain  ; Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée d'Iltalie, 69364 Lyon cedex 07, France  ; Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain.
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Cuesta-López
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Errami
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Falo
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Peyrard