SERC MD seminar 15th May, 16:00, FA31 Albanova

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The talk will be given by Aymeric Naômé.

Title: Coarse-graining of DNA systems using Inverse Monte Carlo
Time: 15th May, 2014, 16:00

Place: FA31, AlbaNova Univ Center (http://www.biox.kth.se/contact/maps/map1.htm), 3rd floor (2 floors down if you enter from South and 2 up if from North)

Abstract:
We present an application of the inverse Monte Carlo method to B-DNA.
Following a Newton inversion scheme, we constructed a class of
coarse-grained force fields (FFs) consisting of discretized effective
solvent-mediated potentials for molecular simulations of DNA with
explicit ions and electrostatics. Sets of DNA intramolecular- and
DNA-ions intermolecular interaction potentials are obtained from the
corresponding radial distribution functions averaged on
microsecond-long all-atom molecular dynamics trajectories. The FF
constructed is suited for simulations of micrometre-sized duplex DNA
fragments in the microsecond time scale. Our model, reducing a
nucleotide to one interaction site without distinction of the
nucleobase, succeeds in quantitatively reproducing the persistence
length of DNA and its dependence on ionic concentration. This key
property determines the flexibility of DNA and is thus of great
importance to further study DNA association with proteins where it
often undergoes major bending. We also investigate the formation of
superhelical structures in supercoiled DNA minicircles. Those
mechanical features of DNA are also of utmost importance for the
condensation and packaging of the genome into the tight structures
found in the cell nuclei. We also present the early developments of a
DNA-protein FF following the same methodology.