The provided code is a part of a computational neuroscience model simulating synaptic transmission, specifically focusing on the diffusion and uptake of glutamate in the synaptic cleft and surrounding extracellular space. The process being modeled is relevant to understanding how neurotransmitter dynamics affect synaptic signaling, particularly within cerebellar granule cells.
Glutamate Release and Diffusion:
Deff
, the effective diffusion coefficient, which influences how quickly glutamate spreads within the synaptic cleft and beyond.Synaptic Geometry:
rPSD
(radius of the postsynaptic density), rabs
(radius of absorbing boundary), and h
(width of the synaptic cleft) define the physical constraints within which glutamate diffusion occurs.Rmf
refers to the radius of the mossy fiber terminal, indicative of the presynaptic geometry and its interaction with the postsynaptic cell.Receptor Binding and Kinetics:
gludir
and gluspill
, representing the direct synaptic and spillover concentration of glutamate, respectively.Popeak
, Podir
, and Pospill
) based on glutamate concentration and kinetics. This is biologically significant because AMPA receptors mediate fast synaptic transmission.Spillover Effects:
inclugluspill
to account for glutamate reaching beyond the synaptic cleft, potentially impacting neighboring synapses (termed spillover), which can influence neural circuit dynamics beyond immediate synaptic partners.Temporal Dynamics:
tm1
, td1
, ts1
) that shift experimental measures of miniature excitatory postsynaptic currents (mEPSCs), direct EPSCs, and spillover EPSCs, indicating the temporal aspect of synaptic transmission.Boundary Conditions:
rabs
parameter reflects the model's closed boundary for simulation, representing the limits within which glutamate is absorbed or taken up, correlating to synaptic cleft clearance mechanisms in a biological setting.Overall, the code attempts to create a detailed simulation of synaptic dynamics, capturing both the geometric and kinetic complexities of neurotransmitter diffusion, binding to receptors, and resultant postsynaptic effects in a neuronal context.