Figure 1.

Synaptic model used in the MCell simulations. A simple model in which the synapse is represented by a box with dimensions 1 × 2 × 0.05 μm. Receptors are located on the lower x-y surface (postsynaptic membrane) only. The front and rear x-z surfaces are clamped to the desired ligand concentration and all other surfaces reflect ligand molecules. The box is divided into 10 numbered sections for the purpose of counting receptors and ligands at different distances from the clamped sides. In the figure, sections that have the same distance from a clamped side (e.g., 1 and 10,) are considered together. The synaptic cleft thickness, t_cleft, is varied in some simulations.