Published May 8, 2023
| Version v1
Journal article
Open
Source Code - Polymer folding through active processes recreates features of genome organization
Authors/Creators
- 1. Massachusetts Institute of Technology
Description
This repository contains the source code for the polymer simulations, the source code for exact numerical calculations that determine the steady state conformation of a linear phantom polymer, and several Mathematica notebook that illustrates analytic calculations, for the article "Polymer folding through active processes recreates features of genome organization" published in Proceedings of the National Academy of Sciences of the United States of America 120, e2221726120.
| File | Description |
|---|---|
| Active-Polymer-Conformation.zip | Mathematica notebooks that illustrate the analytical calculations, Julia code for calculating the steady-state conformation of an active polymer, and Julia code for inferring a candidate distribution of independent active processes that best reproduces a given target steady state. |
| active-polymers-main.zip | Python code for running Brownian dynamics simulations of active Rouse chains without self-avoidance. |
| HiC_analysis.zip | Python code for analyzing Hi-C data. |
| polychrom_analysis.zip |
Python scripts interfacing with polychrom (https://github.com/open2c/polychrom) to run and analyze active polymer simulations with self-avoidance. |
Files
Active-Polymer-Conformation.zip
Additional details
Related works
- Is supplement to
- Journal article: 10.1073/pnas.2221726120 (DOI)
- Preprint: 10.1101/2022.12.24.521789 (DOI)