DiffuTrapKv

DiffuTrapKv2 Simulation of diffusion and trapping of a tetramer of size “molecule diameter” onto fixed interaction sites. In the tetramer there are “Cter” number of interacting subunits. Reference: Paupiah et al (2025) Epileptic encephalopathy-related Kv2.1 mutants impair channel clustering and membrane distribution but not neuronal excitability bioRxiv https://doi.org/10.1101/2025.10.13.681825 Enter the parameters in the pop up window: Number of Cter – number of molecules: Enter the number of subunits bearing the entire Cter (with a PRC domain) and the number of molecules with these characteristics (two numbers, separated by a space): Example: 2 100 -> means a simulation with 100 molecules (tetramers) with 2 PRC domains. If you combine two groups, enter the values for one after the other: Example: 2 100 4 100 Diffusion coefficient: In µm2/s (mean value of a gaussian distribution of D). Trajectory length: Duration of the simulation, in “SPT” frames. Circle diameter: Circular space, in the middle of the simulation space, where interactions may occur. Simulation space: Size of the bounding box where molecules diffuse. Kon and koff: Effective constants for the scaffolding interaction (each PRC acting independently). Time between images, Pixel size, Localization accuracy: The same than the SPT experiment that the simulation wants to reproduce. Molecule diameter: Size of the diffusing molecule (circle). Output : - SPT-like trajectory files (.trc, a txt file), in \trc folder with: Files ctergroup#-simulation#.trc : trajectories of each group separately Files sim-simulation#-all.trc : all groups together - A report file with the parameters (main folder) molecule # time (frame) x position y position group # (# Cter)