Datasets on elastic shell model

This repository includes simulation and analyses codes for the Attar et al, 2023. Nucleus_Generator_F.py -> Generates the data file containing the shell model for the nuclear lamina and the polymer blocks representing the chromatin. To generate the polymer blocks, it reads 'mm9_domains_200k.npy' and uses the Hi-C compartment sequences. BondingMin.py -> It uses the data file generated from the minimization simulation and reassigns bonds for the simulation efficiency. Dumpread_FS.py -> Reads the dump file generated using LAMMPS MD simulations and exports the average radial distance, density, and tensors. FFT_steady.py -> Reads the dump file and exports a CSV file that contains the amplitudes and the corresponding wavenumbers. Input files folder contains the input files required for running the simulations. Data files folder contains the example data file for initial model, conventional and inverted simulation results. References: Attar, A. G., Paturej, J., Banigan, E. J., & Erbas, A. (2023). Polymer modeling suggests correlations between chromatin phase separation and nuclear shape fluctuations. bioRxiv. https://doi.org/10.1101/2023.12.16.571697