Biophysical Society Thematic Meeting| Les Houches 2019

Multiscale Modeling of Chromatin: Bridging Experiment with Theory

Poster Abstracts

19-POS Board 19 PERSISTENCE LENGTH OF DNA USING INVERSE MONTE CARLO: COMPARISON OF DIFFERENT FORCE FIELDS Vishal Minhas 1 ; Nikolay Korolev 1 ; Lars Nordenskiold 1 ; Alexander Lyubartsev 2 ; 1 Nanyang Technological University , School of Biological Sciences, Singapore, North-West, Singapore 2 Stockholm University, Department of Materials and Environmental Chemistry, Stockholm , Stockholms län, Sweden A multiscale computational model is developed to understand the packing of DNA in a physiological ionic environment. We use bottom-up coarse-graining to bridge all-atom and meso-atom representations of all the principal chromatin components. To achieve this, 2 microsecond long all-atom MD simulations of underlying systems are performed, which are then bead-mapped to a coarse-grained representation and used for the calculation of the radial distribution functions (RDF), which are then used to derive the effective potentials using the Inverse Monte-Carlo method. Also, the RDFs obtained from the bead-mapped representation are then reproduced in the coarse-grained simulation using the effective potentials obtained to ensure structure properties of the system are conserved. Finally, to validate the model, coarse-grained MD simulations using the effective potentials are run to calculate the persistence length of DNA and a comparison with experiments is done. Two most popular nucleic acid force fields AMBER and CHARMM are compared on their prediction of persistence length of DNA using this model.

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