Functional description of glutamatergic synapse 3D model

Zagubnaya O.A., Nartsissov Y.R.

Institute of Cytochemistry and Molecular Pharmacology, Russian Federation, 115404, Moscow, ul. 6-ya Radialnaya d. 24 str. 14, +7 (495) 327-49-87, E-mail:

Glutamatergic neurotransmission plays an important role in synaptic plasticity which forms the basis of cognition, memory and learning. High (excitotoxic) level of extracellular glutamate is in attendance on many neurodegenerative diseases and brain injury.

A 3D model of isolated glutamatergic synapse was built using COMSOL Multiphysics in accordance with earlier proposed isolated synapse model [1,2]. The presynaptic neuronal membrane possesses geometrically adjusted vesicular localization system with conceivable places of neurotransmitter partial release as consistent with experimental structural data [3].

Functional parameters of glutamate release from varied number of vesicles with distinct localization were defined following this specified model. Convectional diffusion of neurotransmitter with its reuptake by glutamate transporters was also calculated in the area of interstitial fluid. It was shown that peripheral glutamate release from a few vesicles results in substantially smaller transmitter concentration amplitude in the proximity of postsynaptic glutamate receptors area than if released from one central vesicle only. Moreover, amount of glutamate transporters influences on neurotransmitter concentration in the described system.

The obtained results of 3D modelling enable to describe glutamate concentration changes within synaptic functioning in more detail and to predict possible reasons for excitotoxicity induction.


1. Nartsissov Y.R. A novel algorithm of the digital nervous tissue phantom creation based on 3D Voronoi diagram application // Journal of Physics: Conference Series 2090, 012009, 2021.

2. Nartsissov Y.R., Ivontsin L.A. Mathematical Modelling of Physiological Effects Caused by a Glycine Receptors Post-Synaptic Density Spatial Polymorphism // Mathematics 11, 2499, 2023.

3. Nartsissov Y.R., Zagubnaya O.A. A digital 3D reconstruction of a synaptic cleft which can be used for further modeling of neuromediators convectional diffusion in a nervous tissue // AIP Conference Proceedings 2872, 120003, 2023.


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