Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin
| Autor: | Esposito, S, Cofini, M, Rigante, D, Leonardi, A, Lucchetti, L, Cipolla, C, Lanciotti, L, Penta, L. |
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| Přispěvatelé: | Annunziatella, Carlo, Chiariello, Andrea M., Esposito, Andrea, Bianco, Simona, Fiorillo, Luca, Nicodemi, Mario |
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Theoretical computer science Polymers Computer science Molecular Dynamics Simulation General Biochemistry Genetics and Molecular Biology Mice 03 medical and health sciences Molecular dynamics Cryptorchidism computer simulation Animals Humans Child Molecular Biology Cell Nucleus Structure (mathematical logic) Biochemistry Genetics and Molecular Biology (all) Genome Models Genetic String (computer science) Puberty SOX9 Transcription Factor Folding (DSP implementation) Inhibin B Chromatin 030104 developmental biology Genetic Loci Polymer physics Polymer physic State (computer science) |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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