Open Conference Systems, StatPhys 27 Main Conference

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A new coarse-grained model for the investigation of 3D chromatin organization
Stephen Farr

##manager.scheduler.building##: Edificio Santa Maria
##manager.scheduler.room##: Auditorio San Agustin
Date: 2019-07-10 12:00 PM – 03:45 PM
Last modified: 2019-06-14

Abstract


Chromatin is the macromolecular complex of DNA and proteins found in eukaryotic cells, its primary functions are to package DNA into dense structures suitable for cell division and to facilitate gene expression. It is now well established that the 3D structure of chromatin is intimately linked to gene function. However, the detailed structure of chromatin and the mechanisms explaining how structure controls gene expression are still poorly understood. This is due to the large size of the molecules and long timescales limiting the applicability of atomistic molecular simulation, and the dense structures limiting in-vivo experimental imaging techniques from achieving sufficient resolution. We have created a new coarse-grained chromatin model which represents DNA at base-pair level and proteins at residue level. The model is implemented in LAMMPS molecular dynamics software package using bespoke forcefields. We are able to investigate the dynamics (e.g. force-extension, DNA unwrapping, and DNA sliding) and the equilibrium structural properties of chromatin at high resolution for large system sizes as a function of DNA sequence and epigenetic modifications.