Analysis of polychrom simulations

This folder contains scripts to interface with the open2c/polychrom simulation software package in order to run the simulations in¹. To use these scripts, first create a clean conda environment and install openMM and other dependencies using the install.sh script.

conda create -n polychrom python=3.9
conda activate polychrom
bash install.sh

The contrib folder contains custom Brownian dynamics integrators for polymers driven by active forces that vary in magnitude and can potentially be correlated. The examples folder contains the scripts used to run polychrom simulations using these custom integrators. The post_processing folder contains scripts for analyzing the output of polychrom simulations. The data folder contains the A/B identities of a 1000-mer chain derived from Hi-C data for the 35-60Mb region of chromosome 2 in murine erythroblast cells (Zhang et al. Nat. Commun. 2021).

Footnotes

1. A. Goychuk, D. Kannan, A. K. Chakraborty, and M. Kardar. Polymer folding through active processes recreates features of genome organization. bioRxiv (2022) https://doi.org/10.1101/2022.12.24.521789 ↩