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Synaptic transmission is the main process providing cross-connecting activity among neurons in the central nervous system (CNS). In the present study, the 3D mathematical model of a neuronal bouton with a cluster localization of glycine receptors (GlyRs) on the post-synaptic membrane was developed. The number and eventual position of the receptors are defined by the structural data of the GlyR-gephyrin complex. Furthermore, the forming of inhibitory post-synaptic potential (IPSP) and an electro-diffusion of chloride ions were evaluated by applying the boundary problems for a Poisson’s equation and a non-steady-state diffusion equation, respectively. It was shown that local changes in the chloride ion concentration near the post-synaptic membrane, mediated by GlyRs activation, can raise up to 80–110% from the initial level. The average value of the concentration increase was as high as 10% in a pike of activity under the full activation of GlyRs. The central spatial localization of GlyRs in the cluster had a considerable difference both in the chloride ion concentration changes (6%) and IPSP (17%) compared to the divided or rear localization. Thus, a spatial polymorphism of the post-synaptic density of GlyRs is important to form a physiological response to a neuromediator release.

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