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Talk- Ada Sedova

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Ab initio simulations of nucleic acid oligonucleotides and building blocks using the Oak Ridge Leadership Computing Facility (OLCF) Supercomputers.

  • cmb seminar
When Apr 09, 2018
from 11:00 AM to 12:30 PM
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I will present my latest research on solution-state molecular dynamics of small nucleic acids using explicit water and ions at the density functional theory (DFT) level. These are some of the first simulations of biomolecules at the ab initio level that have included explicit water and ions, and using periodic systems larger than the van der Waals cutoff. Using the linear-scaling self-consistent field method provided by the program CP2K and the OLCF supercomputers, achieving tens of picoseconds of simulation time on systems close to 1000 atoms iscurrently possible within 1-2 weeks, without the use of semi-empirical methods such as tight binding, presenting exciting prospects for advances of this method in future exascale computing efforts. We find that the effects of polarization and fully non-rigid water molecules seem to be highly significant in the conformational preferences of these molecules, which have been difficult to parameterize using classical force fields. Comparison to classical molecular dynamics is also presented.

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