## Biological Basis of the Code The provided code is a computational model aiming to simulate synaptic transmission in neurons, specifically focusing on two types of glutamate receptors: AMPAR (Alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor) and NMDAR (N-Methyl-D-aspartate receptor). These receptors are crucial for synaptic plasticity, learning, and memory. ### AMPA Receptors (AMPAR) **AMPA Receptors** are responsible for fast excitatory synaptic transmission. They are ionotropic receptors that conduct sodium (Na⁺) and potassium (K⁺) ions upon glutamate binding, leading to excitatory postsynaptic potentials (EPSPs). - **Modeling Aspect**: - The AMPAR is implemented using the `AlphaSynapse` built-in function, which mimics the receptor's fast kinetics. - The `AMPAtau` parameter defines the time constant for the synaptic conductance change, reflecting the rapid opening and closing of AMPA channels. - `AMPAgmax` represents the maximum conductance, indicative of the synaptic strength this receptor type provides. ### NMDA Receptors (NMDAR) **NMDA Receptors** are also ionotropic glutamate receptors, but they have slower kinetics compared to AMPARs. They are unique due to their voltage dependency and permeability to calcium ions (Ca²⁺), which is crucial for synaptic plasticity processes like long-term potentiation (LTP). - **Modeling Aspect**: - The NMDA component uses the `NMDA_Mg_T` mechanism based on Kampa et al. (2004), reflecting encapsulated kinetic and blocking properties. - NMDARs have a voltage-dependent block by magnesium ions (Mg²⁺), which is lifted during postsynaptic depolarization, allowing calcium (Ca²⁺) influx. - `NMDAgmax` specifies the maximal conductance in the absence of Mg²⁺ block. The note about "Popen is 0.2 so effective gmax" reflects that the maximal conductance is limited by the average probability that the channel is open. - The pointer mechanism (`setpointer`) links the presynaptic release events to NMDA channel activation, modeling the triggering of synaptic currents by actual neurotransmitter release. ### Synaptic Modeling The model specifies synaptic placement based on data from `"./synapse_loc.dat"`, which would typically contain information about the dendritic locations where synapses are formed. The creation of synapses at specific dendritic positions (`dendid` and `pos`) represents a more realistic anatomical setup of neuronal connections. - **Procedures**: - **`init_syn_params`** establishes baseline parameters for AMPAR and NMDAR synapses. - **`init_syns`** initializes synapses at multiple locations specified in the synapse location file. - **`addAMPA`** and **`addNMDA`** establish the properties of each synapse, tuned to reflect biological kinetics and conductivity. - **`addPRE`** sets up a custom presynaptic terminal with neurotransmitter release dynamics, represented here by parameters like `dur_rel` (release duration) and `amp_rel` (amplitude of release). This code models synaptic transmission, integrating receptor dynamics and synaptic locations to simulate how neurons communicate and change over time through long-term potentiation and depression mechanisms. This level of modeling is pivotal for understanding neural circuit functions and how synapses contribute to the overall behavior of neurons and networks in the brain.