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Molecular Dynamics simulations of the Strings and Binders Switch Model of chromatin

Item Type:Article
Title:Molecular Dynamics simulations of the Strings and Binders Switch Model of chromatin
Creators Name:Annunziatella, C. and Chiariello, A.M. and Esposito, A. and Bianco, S. and Fiorillo, L. and Nicodemi, M.
Abstract:In recent years interest has grown on the applications of polymer physics to model chromatin folding in order to try to make sense of the complexity of experimental data emerging from new technologies such as Hi-C or GAM, in a principled way. Here we review the methods employed to efficiently implement Molecular Dynamics computer simulations of polymer models, focusing in particular on the String&Binders Switch (SBS) model. The constant improvement of such methods and computer power is returning increasingly more accurate insights on the structure and molecular mechanisms underlying the spatial organization of chromosomes in the cell nucleus. We aim to provide an account of the state of the art of computational techniques employed in this type of investigations and to review recent applications of such methods to the description of real genomic loci, such as the Sox9 locus in mESC.
Keywords:Cell Nucleus, Chromatin, Genetic Loci, Genetic, Models, Genome, Molecular Dynamics Simulation, Polymers, SOX9 Transcription Factor, Animals, Mice
Source:Methods
ISSN:1046-2023
Publisher:Elsevier / Academic Press (U.S.A.)
Volume:142
Page Range:81-88
Date:1 June 2018
Official Publication:https://doi.org/10.1016/j.ymeth.2018.02.024
PubMed:View item in PubMed

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