# Biological Basis of the Code This code models the diffusion of glutamate in a 3D space without boundary constraints, simulating neurotransmitter dynamics following synaptic release. Here are the key biological concepts represented in the code: ## Glutamate Dynamics - **Glutamate Release and Diffusion**: Glutamate (glu), a primary excitatory neurotransmitter in the brain, is released into the synaptic cleft. The code models how glutamate concentrations decrease over time and space, simulating its diffusion away from the release site. ## Synaptic Anatomy - **Release Sites**: The parameter `nu` represents the density of glutamate release sites, indicative of the capacity for neurotransmitter release in the synapse. - **Cleft Width**: The cleft width (`h`) denotes the physical space through which glutamate must diffuse to affect surrounding neurons. ## Diffusion and Uptake - **Effective Diffusion Coefficient (`Deff`)**: This parameter is crucial for simulating how quickly glutamate disperses in the extracellular space. - **Absorbing Boundaries**: The radius of absorbing boundaries (`rabs`) can represent uptake by neurons and glial cells or diffusion away limits. - **Volume Fraction**: `alpha` is an inverse measure related to the extracellular medium's volume fraction, affecting how concentration diffuses. ## Receptor Interactions - **Post-synaptic Density (PSD)**: `rPSD` signifies the radius of the post-synaptic density, where receptors are densely packed. - **AMPA Receptor Dynamics**: The code models dynamics of AMPA receptor open probability (`Popeak`) affected by glutamate concentration. It segments glutamate's synaptic action into direct and spillover components (`Podir` and `Pospill` respectively). ## Neurotransmitter Spillover - **Spillover Dynamics**: Glutamate's propagation beyond its immediate release site is captured by the spillover calculation. The effective concentration adjacent to release sites involves integration across presynaptic terminal bounds (`meandist`) to larger mossy fiber terminals (`Rmf`). ## Temporal Dynamics - **Timing Adjustments**: Delays in AMPA receptor current onset (`tm1`, `td1`, `ts1`) enable modeling of realistic synaptic timing from experimental data. Overall, this simulation describes the interplay between neurotransmitter diffusion, receptor activation, and synaptic architecture, reflecting complex physiological processes that underlie synaptic transmission in the cerebellum, as inferred from variables such as `GrC` (Granule Cell), a common site of study for glutamatergic synapses. The model emphasizes the rapid yet spatially constrained nature of synaptic signaling in such neural environments.