# Biological Basis of the Code The provided code is concerned with simulating the electrical properties of a myelinated axon in response to extracellular electrical stimulation. Here's a detailed breakdown of the biological context: ## Myelinated Axons Myelinated axons are nerve fibers enveloped by a myelin sheath, which serves as an insulating layer, increasing the speed of electrical impulse propagation. In this model, the axon is represented with nodes and internodes: - **Nodes of Ranvier**: These are gaps in the myelin sheath where voltage-gated sodium and potassium channels are concentrated, allowing for saltatory conduction. - **Internodes**: The myelinated segments between the nodes, characterized by lower ionic channel density due to the insulating properties of myelin. ## Electrical Stimulation The model simulates the response of a myelinated axon to an external electric field aligned along the axon's length. The intent is to observe how an electric stimulus can evoke an action potential (AP), a rapid rise and fall in membrane potential that constitutes a nerve impulse. ### Key Concepts: 1. **Extracellular Field (E)**: A homogeneous electric field is applied along the x-axis where the axon is aligned. The intensity and effect of the field depend on the distance from the origin along the axon. 2. **Spike Initiation**: The code aims to capture spike initiation events that may occur when an external field induces a membrane potential change significant enough to cross the threshold for generating an AP. 3. **Resting Potential**: The axon is initialized to a resting potential of -70 mV, close to physiological conditions for neurons. ## Electrical Properties - **Extracellular Resistivity (RHOE)**: The parameter RHOE specifies the resistivity of the extracellular space, affecting how the electric field influences the axon. - **Capacitive and Conductive Properties**: The code models the axon's biophysical behavior by setting parameters for membrane capacitance (cm) and extracellular channel conductivities (xg and xc). The latter simulates the insulating property of myelin as a "perfect insulator." ## Simulation Goals The code aims to determine the threshold stimulus intensity required to elicit an AP. It does so by varying stimulus parameters and using counters to detect spikes: - **APCount**: An object placed to monitor AP occurrence, reflecting the physiological concept of neural firing upon reaching a certain membrane potential threshold. - **Threshold Identification**: The code utilizes a process whereby stimulus intensity is adapted to find the minimal threshold required for action potential generation, tested under different protocols. ## Protocols Through various protocols, the axon's response to different patterns of stimulus (pulse, square wave) is tested, mimicking experimental conditions to understand neuron behavior under various extracellular stimuli. --- Overall, the model amalgamates anatomical, biophysical, and computational principles to simulate how neurons behave in an extracellular field, a fundamental exercise in understanding neural responses in electrophysiological experiments or therapeutic interventions.