# Biological Basis of the Computational Model Code The provided code is designed to simulate antidromic action potentials in a neuronal model using the NEURON simulation environment. The key biological aspects of this model are discussed below. ## Target Neuron Type The model is based on a layer 5 pyramidal neuron from the prefrontal cortex of postnatal day 19 (p19) rats, as described by Diana Smetters. Layer 5 pyramidal neurons are key excitatory cells in the cortex that have extensive apical dendrites and are involved in various neural processing tasks, including the integration of synaptic inputs and the initiation of action potentials. ## Membrane and Ion Channel Dynamics ### Ion Channels The model implements Hodgkin-Huxley type kinetics (Huguenard/McCormick formulations) for sodium (Na⁺) and potassium (K⁺) channels. Ion channels are crucial for the generation and propagation of action potentials: - **Na⁺ Channels (`na3`)**: These are inserted in the dendrites, soma, axon initial segment (AIS), hillock, and nodes of Ranvier, with conductance levels defined (`gna_dend` for dendrites and `gna_node` for axonal compartments). - **K⁺ Channels (`kd3`)**: These are inserted in the somatic and basal dendrite compartments, providing the repolarizing K⁺ currents crucial for action potential termination. ### Passive Properties The passive properties, including axial resistance (`ra`), membrane resistance (`rm`), and membrane capacitance (`c_m`), are specified. Different passive properties are applied to the myelinated sections (`cm = 0.04`) to reflect the insulating properties of myelin. ### Reversal Potentials The reversal potentials for Na⁺ and K⁺ are set (`Ena = 60 mV` and `Ek = -90 mV`), which influence the driving force and dynamics of ion current flow across the membrane when channels are open. ## Temperature The simulation temperature is set at 23°C, which can affect ion channel kinetics as they are temperature-sensitive. ## Simulation Objectives ### Antidromic Action Potentials The primary biological focus of this model is to simulate antidromic action potentials, which are action potentials propagating from the axon terminal back toward the cell body. This is relevant to the study by Stuart and Sakmann (1994), which explored how action potentials invade the soma and dendrites from their initiation point in the axon. ### Current Injection Protocols Two types of current injection simulations are provided: 1. **Soma Injection**: An electric current is applied directly to the soma, simulating how input at the cell body can influence action potential dynamics. 2. **Dendrite Injection**: Current is injected at a specified dendritic site, allowing exploration of how distal inputs can affect action potential initiation and propagation. ## Graphical Output The code includes configuration for graphical output, which allows visualization of membrane potentials at specified locations (e.g., soma and AIS) within the neuron. In summary, the code models the complex biophysical characteristics of a layer 5 pyramidal neuron, focusing on the simulation of action potentials and their propagation, which is fundamental for understanding neuronal signaling and processing.