# Biological Basis of the Computational Model The provided code is a computational model that simulates the electrophysiological behavior of a neuron, specifically incorporating aspects seen in Ratte et al. 2018. Below are the key biological components and mechanisms captured by the model: ## Membrane Potential Dynamics - **Membrane Potential (V):** The model simulates the time-dependent change in the membrane potential of a neuron (`dv/dt`). The equation includes various ionic currents that influence the potential across the neuronal membrane. ## Ionic Currents 1. **Sodium Current (INa):** - Modeled by `gna*minf(V)*(V-Vna)`, representing the fast sodium current responsible for the rapid depolarization phase of action potentials. - **Gating Variable (m):** `minf(v)` is an activation function influenced by voltage. 2. **Potassium Current (IK):** - Expressed as `gk*w*(V-VK)`, representing the delayed rectifier potassium current responsible for repolarization post-action potential. - **Gating Variable (w):** The activation of this current is described by `dw/dt`, influencing the recovery phase. 3. **Leak Current (IL):** - Represented by `gl*(V-Vl)`, contributing to the resting membrane potential. 4. **Calcium-Activated Non-Selective Current (ICAN):** - Modeled by `gcan*p2*(V-Vcan)`, linked to intracellular calcium concentration changes. - **Gating Variable (p2):** Reflects the influence of intracellular calcium (`cai`) on channel activation. 5. **Afterhyperpolarization Currents (IAHP):** - Several forms (`gahp*q*(v-Vk)`, `gahp2*q2*(v-Vk)`, `gahp3*q3*(v-Vk)`) are modeled to capture the concept of calcium-dependent potassium currents that contribute to afterhyperpolarization following action potentials. - **Gating Variables (q, q2, q3):** These variables are functions of voltage and decay over time, responsible for the adaptation phenomenon. ## Calcium Dynamics - **Intracellular Calcium (cai):** - Modeled by `dcai/dt`, reflecting calcium influx through voltage-gated calcium channels (`gca*p*(V-Vca)`) and its decay over time. - Calcium dynamics are crucial for activating calcium-dependent processes such as ICAN and IAHP. ## Stimulation Protocols - **Current Stimulation (I_stim):** The model uses several time-dependent current injections (`I1a`, `I1b`, etc.) to simulate external stimuli, often used for triggering spikes or sustained depolarizations/plateaus. ## Neuronal Geometry - **Spherical Soma:** The model assumes a spherical soma (cell body) to calculate surface area-to-volume (`SAvol`) ratios affecting ionic dynamics. ## Summary This code is designed to simulate neuronal behavior by modeling key ion channel dynamics, including sodium, potassium, and calcium currents, as well as calcium-dependent processes. It exemplifies a biophysically realistic neuron model used to study action potential generation, afterhyperpolarization, and stimulus response, reflecting the complex interplay of ionic movements and intracellular signaling essential for neural activity.