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ChromFold: Multi-scale coarse-grain polymer model for interphase chromosomes and nuclear organization

external link: https://sites.google.com/site/angelosissa/winterschoolphysicscell-unitn2020

developed by Angelo Rosa (SISSA, Trieste, Italy) & Ralf Everaers (Ecole Normale Supérieure de Lyon, France)

Description

The method combines Monte Carlo and Molecular Dynamics numerical tools into an efficient coarse-grain scheme suitable for generating putative conformations of interphase chromosomes. The method is based on rigorous arguments of polymer physics and it may be easily adapted and generalized to simulate chromosomes under diverse external conditions. The algorithm proceeds via two main steps: (1) "slow" relaxation of the large scale chromosome structure by Monte Carlo; (2) "fast" relaxation of the local degrees of freedom via Molecular Dynamics.

How to cite

  1. A. Rosa, R. Everaers. Structure and dynamics of interphase chromosomes. Plos Computational Biology 4, e1000153 (2008) - https://doi.org/10.1371/journal.pcbi.1000153
  2. A. Rosa, R. Everaers. Ring polymers in the melt state: The physics of crumpling. Physical Review Letters 112, 118302 (2014) - https://doi.org/10.1103/PhysRevLett.112.118302
  3. M. Valet, A. Rosa. Viscoelasticity of model interphase chromosomes. Journal of Chemical Physics 141, 245101 (2014) - https://aip.scitation.org/doi/full/10.1063/1.4903996
  4. A. Rosa, R. Everaers Computer simulations of melts of randomly branching polymers. Journal of Chemical Physics 145, 164906 (2016) - https://doi.org/10.1063/1.4965827