Source Code for the paper 'Oct4 clusters promote DNA accessibility by enhancing chromatin plasticity'
We are delighted to share our model for chromatin structure in the presence of Oct4. Please use it freely and cite our paper: preprint https://www.biorxiv.org/content/10.1101/2025.10.20.683403v1
For questions, contact Jan Huertas: jh2366[at]cam.ac.uk
For compiling the chromatin multiscale model, please follow the instructions in https://github.com/CollepardoLab/CollepardoLab_Chromatin_Model/tree/plugin-dev
The files needed to run a typical simulation from the paper are in the demo folder. Please download the whole folder, and run using at least 16 cores, for example:
mpirun -np 16 ./lmp -in run.in
We recommend using OVITO (https://www.ovito.org/) or VMD (https://www.ks.uiuc.edu/Research/vmd) for visualising the trajectory.