Perspectives on the Coarse-Grained Models of DNA

University of Maryland, College Park, Maryland 20742, USA Institute for Physical Science and Technology, 

DNA is a highly charged, semi-flexible polyelectrol)Ae. In eukaiyotic cells, DNA chains are packed inside the microscopic volume of the nucleus in an ordered, yet dynamical way. To overcome the electrostatic repulsion that hinders compaction, DNA molecules associate with a variety of counterions and proteins to condensate into a hierarchical and tunable architecture named chromatin. Besides DNA condensation, chromatin also plays a key role in gene regulation by making DNA accessible for transcription in a dynamical and specific way. Consequently, understanding the physicochemical properties of DNA chains at the molecular and mesoscopic scales is a required step to elucidate how cells regulate 

Many-Body Effects and Electrostatics in Biomolecules Edited by Qiang Cui, Markus Meuwly, and Pengyu Ren Copyright 2016 Pan Stanford Publishing Pte. Ltd. 

When deriving CG potentials, physically distinct contributions are usually treated as independent and additive, hence, it is important to avoid double counting of these interactions. In this context. 

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