The provided code simulates a computational model of a type of nerve fiber known as a C fiber. C fibers are unmyelinated nerve fibers found in the peripheral nervous system, typically responsible for conveying slow pain or noxious thermal stimuli. The specific model aims to investigate the role of ion pumps and ionic currents in the transmission of action potentials, as well as the potential for spike failure at a T-junction of such a fiber. This is grounded in the work by Sundt et al. (JNP 2015), focusing on computational approaches to studying neural activity. ### Biological Basis 1. **Neuron Structure:** - The simulation defines a multi-compartment model of a neuron consisting of sections such as the peripheral axon (`peri`), T-junction (`tjperi`, `tjcentral`), central axon (`central`), stem, and soma. T-junctions are critical points where the axon bifurcates and are common locations for spike failure due to the complex geometry influencing current flow. 2. **Ion Channels and Conductances:** - **Na+ (Sodium) Channels:** The model inserts sodium channels (`nahh`), which are crucial for the initiation and propagation of action potentials. The density (`gnabar_nahh`) regulates how many channels per unit area are available to conduct Na+ ions. - **K+ (Potassium) Channels:** Delayed rectifier K+ channels (`borgkdr`) are included to represent the repolarization phase of the action potential, where K+ ions move out of the neuron, restoring the membrane potential. - **Ca2+ (Calcium) Channels:** The high voltage-activated Ca2+ channels (`cal`) and associated SK channels represent mechanisms by which calcium signals are integrated into cell activity, often contributing to after-hyperpolarization and other slow dynamics. 3. **Ion Pumps:** - **Na+/K+ Pump (`pump`):** The inclusion of ion pumps illustrates their role in maintaining electrochemical gradients by moving Na+ out and K+ into the cell, effectively regulating resting potential and recovery post-action potential. The `PUMP` flag toggles the inclusion of pump dynamics. 4. **Simulation Conditions:** - **Temperature (`celsius`):** Set to 35°C, approximating the physiological temperature for mammals, affecting the kinetics of channel gating and ion movement. - **Stimulation Protocol:** A train of electrical pulses is used to stimulate the peripheral axon section at a given frequency (`FREQ`) to evoke action potentials. This simulates repetitive physiological stimulation that might occur in pain signaling. 5. **Ionic Equilibrium Potentials:** - The various sections of the neuron are initialized with specific ionic conditions and equilibrium potentials (e.g., K+ equilibrium potential `ek` at -80 mV). These values are critical for driving the ionic currents that underlie action potentials. The overall objective of the code is to assess how changes in channel conductances, especially sodium and potassium currents, along with pump activities, influence the potential for spike failure at the T-junction. This model might help understand certain neuropathies or pain conditions where such failures could alter sensory signal transmission. By simulating various parameters and observing the impact on neural activity, the model contributes to the broader understanding of peripheral nervous system function and its disruptions.