This repository contains all the scripts to perform the molecular dynamics simulations and model analysis in
Marco Di Stefano, Hans-Wilhelm Nützmann, Marc A. Marti-Renom, Daniel Jost. Polymer modelling unveils the roles of heterochromatin and nucleolar organizing regions in shaping 3D genome organization in Arabidopsis thaliana, Nucleic Acids Research, Volume 49, Issue 4, 26 February 2021, Pages 1840–1858, https://doi.org/10.1093/nar/gkaa1275.
In the actual implementation, this repository relies on TADdyn [TADdyn]_ for the preparation of the single-chromosome initial conformations, on LAMMPS [Plimpton]_ for the implementation of the simulations.
Bibliography
.. [TADdyn] Di Stefano, M., Stadhouders, R., Farabella, I., Castillo, D., Serra, F., Graf, T., Marti-Renom, M.A. Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs. Nature Communications 11, 2564 (2020).
.. [Plimpton] Plimpton, S. Fast Parallel Algorithms for Short-Range Molecular Dynamics. J Comp Phys 117, 1-19 (1995) and Fiorin, G., Klein, M.L. & Hénin, J. Using collective variables to drive molecular dynamics simulations. Molecular Physics 111, 3345-3362 (2013).