microcompartments (and compartments (and loop extrusion))

Polymer simulations of compartments and extrusion for modeling the mitosis-to-G1 transition and, more generally, chromatin compartmentalization with or without loop extrusion. See Refs [1-2].

Also see: The polychrom library (https://github.com/open2c/polychrom/) [3], a wrapper for the OpenMM MD package [4]. 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.

Additionally, the examples directory contains data from short, small runs as examples, along with the commands (with command line options) used to run the simulations.

Running microcompartment simulations

To run steady-state simulations simulations in the compartment/microcompartment configuration used to model the Dag1 locus, provide the configuration files as inputs in the command line. e.g.:

python compSim.py comppath=dag1/comps.dat microcomppath=dag1/microcompsAnaTelo.dat

Other parameters can be set/changed by command line inputs as well. For more details:

python compSim.py ?

M-to-G1 simulations of the Dag1 locus are run similarly (with the addition of an input for CTCF positions):

python m-to-g1_transition.py comppath=dag1/comps.dat microcomppath=dag1/microcompsAnaTelo.dat ctcfpath=dag1/ctcf.dat

Additional notes

Code will run from directory without additional setup (provided that polychrom and OpenMM are also installed). Simulations were originally run on GPUs on machines running Ubuntu 22.04.5 OS.

References

[1] VY Goel et al. Dynamics of microcompartment formation at the mitosis-to-G1 transition. Nat. Struct. Mol Biol. 32:2614 (2025). https://www.biorxiv.org/content/10.1101/2024.09.16.611917

[2] G Wutz, IF Davidson, EJ Banigan et al. PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes. Mol. Cell 86:1614 (2026). https://www.biorxiv.org/content/10.1101/2025.08.30.67324

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

[4] P Eastman et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. J Phys Chem B 128:109-116 (2023). https://arxiv.org/abs/2310.03121