Stress granules plug and stabilize damaged endolysosomal membranes

This data repository contains all the relevant simulation and analysis code used for the study of stress-granule condensation and plugging of damaged vesicles in molecular dynamics. This research is part of the work published in "Stress granules plug and stabilize damaged endolysosomal membranes", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.



Content:

examples/ folder containing three relevant examples of scripts to reproduce typical simulations used in this work on LAMMPS. See note below for instructions on how to run these simulations.
analysis/ folder containing all the necessary code to reproduce the data analysis performed for this work on simulation output. See note below for instructions on how to run the analysis.



Simulations:

These simulations were performed using the LAMMPS Molecular Dynamics software package. We recommend using the LAMMPS version from November 3rd 2022 or a later one. The ylz potential (which is not present in older versions) is required for these simulations. You will need to build LAMMPS with ASPEHRE, EXTRA-PAIR, MOLECULE and MISC. To run a simulation just execute the LAMMPS executable (lmp_mpi / lmp_serial) within the simulation folder as: /$YOURPATHTOLAMMPS/lmp_mpi -in in.local

Please refer to the Supplementary Information of the publication for details on how to adjust parameters in the scripts to reproduce different regimes.



Analysis:

For the analysis performed the surface reconstruction library developped by Miguel Amaral (Saric lab) is required. This is freely available at https://github.com/Saric-Group/monolayer_shared