Data for Multiphase separation in postsynaptic density regulated by membrane geometry via interaction valency and volume

Representative Trajectories of 4 Postsynaptic density Systems in 3D and 2D Simulations This dataset contains representative simulation trajectories of molecular simulation with 4 PSD proteins (AMPAR, PSD-95, NMDAR, CaMKII), generated under various activation and valency conditions. The data were produced using particle-based reaction-diffusion simulatior, ReaDDy2. Directory Structure: 3Dsystem/: Simulations in a 3D cytosolic environment. active_CaMKII/: Active CaMKII (R = r). active_CaMKII_half/: Active CaMKII wit reduced radius (R = 1/2 r). active_CaMKII_twothirds/: Active CaMKII wit reduced radius (R = 2/3 r). inactive_CaMKII/: Inactive CaMKII. 2Dsystem/: Simulations on a 2D surface (membrane). active_CaMKII/: CaMKII in the fully active state (valency = 12). active_CaMKII_valency6/: CaMKII with reduced valency (valency = 6). active_CaMKII_valency3/: CaMKII with reduced valency (valency = 3). inactive_CaMKII/: CaMKII in the inactive state (valency = 0). Each subfolder contains: HDF5 trajectory files (e.g., PSD4_cube_activated.h5) Folders with HDF5 checkpoint files from the simulation (e.g.,checkpoints_PSD4_activate/checkpoint_*.h5) Python scripts used to set up and run the simulation (e.g., cube_nmdar_act_camk2.py) Note that “_[n]” refers to the simulation result that continues from the final structure of “_[n-1]”. Related Work: If you use this data, please cite the publication:https://doi.org/10.7554/eLife.106602.1