An Algorithm for Creating a Synaptic Cleft Digital Phantom Suitable for Further Numerical Modeling

One of the most significant applications of mathematical numerical methods in biology is the theoretical description of the convectional reaction–diffusion of chemical compounds. Initial biological objects must be appropriately mimicked by digital domains that are suitable for further use in computational modeling. In the present study, an algorithm for the creation of a digital phantom describing a local part of nervous tissue—namely, a synaptic contact—is established. All essential elements of the synapse are determined using a set of consistent Boolean operations within the COMSOL Multiphysics software 6.1. The formalization of the algorithm involves a sequence of procedures and logical operations applied to a combination of 3D Voronoi diagrams, an experimentally defined inner synapse area, and a simple ellipsoid under different sets of biological parameters. The obtained digital phantom is universal and may be applied to different types of neuronal synapses. The clear separation of the designed domains reveals that the boundary’s conditions and internal flux dysconnectivity functions can be set up explicitly. Digital domains corresponding to the parts of a synapse are appropriate for further application of the derived numeric meshes, with various capacities of the included elements. Thus, the obtained digital phantom can be effectively used for further modeling of the convectional reaction–diffusion of chemical compounds in nervous tissue.