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Statistical Mechanics in Systems Biology: Villa Orlandi, Anacapri ~ May 29 - June 1, 2012 |
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Davide Marenduzzo School of Physics, University of Edinburgh (UK) Modelling the three-dimensional organisation of eukaryotic chromosomes While we now know in details the sequence of most eukaryotic genomes, we still have only a rudimentary idea of how these genomes fold in space, or how structure affects function. In eukaryotes, DNA is invariably associated with a number of proteins, such as histones, polymerases, promoters etc. Rather than merely using DNA as a track on which to diffuse around or track along, these proteins often profoundly change the 3-dimensional structure of the genome. I will present a coarse grained Brownian dynamics simulation study of chromatin fragments, and human chromosomes, in which the force field is either inferred from the accepted properties of active and inactive DNA (euchromatin and heterochromatin respectively), or from the sequence. I will also present a finer grained molecular dynamics study of chromosome 14, comparing the structure we obtain in simulations with the contacts found by our experimental collaborators via fluorescence in situ hybridization (FISH) and chromosome conformation capture (3C) experiments. |
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