ReDiClus in Matlab
Live 3D simulation space
2D surface plot with PSD areas marked with boxes
SAP cluster for PSD1. For most simulations the starting SAP cluster size for this PSD is 7x7 or 49 SAP molecules. The diffusion rate 'D' of the extrasynaptic area (D.es) is scaled in the PSD (D.psd) by the current total number of SAPs present (SAP.t), such that [D.psd = D.ec/SAP.t]. So if D.es = .3 µm²/s and there are 10 SAPs in PSD1, then D.psd1 = .03 µm²/s.
PSD1: post synaptic density area "1". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD areas are scaled as a function of the total SAP expressed at their surface (D.psd = D.ec/SAP). So if the extracellular diffusion rate is 0.3 µm²/s and there are 10 SAP molecules in PSD1, then PSD1 diffusion rate would be D.psd = .3/10 = 0.03 µm²/s which are empirically relevant values.
This is the diffusion rate meter (aka D-Ometer) for PSD1. It provides information on the moment-to-moment diffusion rate inside PSD1. Note the meter is log scaled from .001 µm²/s to 1.0 µm²/s.
This is the diffusion rate meter (aka D-Ometer) for PSD2. It provides information on the moment-to-moment diffusion rate inside PSD2. Note the meter is log scaled from .001 µm²/s to 1.0 µm²/s.
These bar graphs represent the number of AMPAR (red) particles in a defined region: EC (extracellular), PSD1, PSD2, and PSDT (the total combined number of receptors in both PSD areas). In most simulations, if PSDT > 50, PSD clusters tend to shrink, and if PSDT < 30 SAP clusters tend to grow. This is due to the repulsion lattice changes, globally, based on the total number of receptors in synapses.
This the the boundary for the periPSD area, aka the perisynaptic pad for PSD2 that represents a non-PSD portion of a dendritic spine. This area has its own diffusion rate, and separate D-rates for GluR1 and GluR2 particles
This is the boundary for the PSD area of PSD-2. This area has a lower diffusion rate (D) compared to the surrounding periPSD area box. It also has a lower diffusion rate for GluR2 than GluR1 during baseline conditions.
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