microcompartments

Polymer simulations of compartments and extrusion for modeling the mitosis-to-G1 transition

Reference: VY Goel, NG Aborden, JM Jusuf, H Zhang, L Mori, LA Mirny, G Blobel, EJ Banigan, AS Hansen. "Dynamics of microcompartment formation at the mitosis-to-G1 transition." bioRxiv 611917 (2024). https://www.biorxiv.org/content/10.1101/2024.09.16.611917

Also see: The polychrom library (https://github.com/open2c/polychrom/) [1], a wrapper for the OpenMM MD package [2]. Beyond using the polychrom library, the code in this repository used examples and methods found in polychrom as a starting point.

There are two simulation codes here:

1. comp_extr - This code is used for equilibrated polymer sims (used in parameter sweeps)
2. m-to-g1 - A code for performing time-calibrated polymer simulations that progress from mitotic-like chromosomes to interphase-like chromosomes.

References

[1] VY Goel et al. Dynamics of microcompartment formation at the mitosis-to-G1 transition. bioRxiv 611917 (2024).

[2] M Imakaev, A Goloborodoko, HB Brandao. polychrom v0.1.0. Zenodo: https://zenodo.org/records/3579473 DOI: 10.5281/zenodo.3579472

[3] P Eastman et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. J Phys Chem B 128:109-116 (2023).