Mesoscale molecular assembly is favored by the active, crowded cytoplasm (PRX Life, 2024)

(Tong Shu, Gaurav Mitra, Jonathan Alberts, Matheus P. Viana, Emmanuel D. Levy, Glen M. Hocky, Liam J. Holt)

This folder contains the simulation framework for running the MD simulations for the formation of biomolecular condensates from an in silico Coarse-Grained system synDrops perfomed using HOOMD-Blue. The simulation_setup folder contains the Python and Bash scripts for setting up the MD simulations, the analysis folder contains scripts for performing different types of analysis and for the generation of plots used in the paper and finally, the dybond folder contains the C++ code for the dynamic binding / unbinding plugin. The data_from_analyses folder contains all the data from simulations which were used in making plots/figures in this paper, and lastly the final_figures folder contains all the plots made from these analyses, some of whichwere used in the paper.