# Biological Basis of the Code The code is designed to model a glutamatergic synapse with short-term plasticity (STP), focusing on the dynamics of AMPA and NMDA receptors, and their interactions with calcium (Ca²⁺) ions. This type of synapse is crucial in neuronal communication and synaptic plasticity. ## Key Biological Concepts ### 1. **Glutamatergic Synapse** - **Glutamate** is the primary excitatory neurotransmitter in the central nervous system. It binds to various receptor types, primarily AMPA and NMDA receptors, which mediate excitatory synaptic transmission. ### 2. **AMPA and NMDA Receptors** - **AMPA Receptors** respond quickly to glutamate and mediate the initial, rapid excitatory post-synaptic current. They are modeled with two decay constants (`tau1_ampa` and `tau2_ampa`) that define the fast kinetics of AMPA channel dynamics. - **NMDA Receptors** have slower kinetics and are voltage-dependent due to a magnesium (Mg²⁺) block, which is relieved upon depolarization. This code models the voltage-dependence using a gating function (`mggate`). The NMDA receptors allow calcium ions to enter the neuron when activated, having a prolonged effect on the synaptic current (`tau1_nmda` and `tau2_nmda`). ### 3. **Short-Term Plasticity** - **Short-term facilitation and depression** refer to transient increases or decreases in synaptic strength due to the history of synaptic activity. This code implements these dynamics through several parameters such as `tauR`, `tauF`, and `U`, which correspond to recovery and facilitation time constants and the baseline utilization of synaptic efficacy. ### 4. **Calcium Dynamics** - Calcium influx through NMDA receptors is crucial for many forms of synaptic plasticity. This code models calcium contributions (`ca_ratio_ampa` and `ca_ratio_nmda`) stemming from the activity of AMPA and NMDA receptors. ### 5. **Magnesium Block** - The NMDA receptor activity is modulated by extracellular magnesium (`mg`), which blocks the receptor in a voltage-dependent manner. This code accounts for the magnesium block through the `mggate` variable, which adjusts the NMDA conductance based on membrane potential. ### 6. **Biophysical Properties** - The synapse model includes properties such as synaptic conductance (`g`), synaptic current (`i`), and other state variables (`A_ampa, B_ampa, A_nmda, B_nmda`) that are updated per the reaction to presynaptic spikes (NET_RECEIVE). ## Conclusion This code models the complex dynamics of glutamatergic synapses, incorporating fast AMPA receptor-mediated transmission, slower NMDA receptor kinetics, and calcium permeability. By including mechanisms for short-term synaptic plasticity such as facilitation and depression, the model provides a framework to study synaptic responses to varying frequency and patterns of neuronal activity. These dynamics are crucial for understanding synaptic integration and the physiological basis of learning and memory.