Making efficient coarse-grain models for long polymers: application to chromatin folding

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Dr Surya Ghosh (Post Doc)


The physical organization of a chromosome is very crucial for cell functions. Chromosomes are, in general, long and dense-packed polymers. Emphasizing on these characteristics, we developed a generic strategy to develop efficient coarse-grain homopolymer models for chromosomes. From a proper time mapping using the monomer mean-squared displacement, we show that our simulation scheme not only captures the equilibrium properties of the system but also track the same dynamics at different coarse-graining. Our results strongly suggest that accounting properly for the initial configuration, the polymer entanglement length and the base pair density are crucial for quantitatively describing the sequence average behavior of chromosome folding. Finally, we use our formalism to study more precisely the 3D organization of chromosome 3R in drosophila. We show that a combination of our coarse-graining strategy with a one-parameter block copolymer model integrating epigenomic-driven interactions can quantitatively reproduce experimental HiC data at the chromosome-scale and make interesting predictions on the dynamics of chromosome folding.

Primary author

Dr Surya Ghosh (Post Doc)


Dr Daniel Jost (CNRS TIMC-IMAG) Dr cedric vaillant (Laboratoire de Physique ENS de Lyon CNRS)

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