Parametrizations of Coarse-Grain Sequence-Dependent Models of DNA Mechanics

John Maddocks
École Polytechnique Fédérale de Lausanne (EPFL)

I will describe ongoing efforts to effect the passage from all atom Molecular Dynamic (MD) simulations of DNA fragments, which are of necessity still short both in duration of simulation and length of oligomer, to coarser grain sequence-dependent models involving rigid base, rigid base-pair, and continuum descriptions. These coarser grain models in principle allow quantitative, sequence-dependent modelling of experiments on DNA involving several tens to a few hundreds of base pairs, e.g. cyclization rates of minicircles, but detailed parametrizations of the energies in these models must be passed up from a finer resolution description

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