# Biological Basis of the Computational Model The code provided is part of a computational neuroscientific model that aims to simulate ionic flux dynamics across the membrane of neuronal voxels. This simulation represents critical biological processes involved in the functioning of neurons, primarily focusing on ion channels and the ionic currents that traverse them. Here are the biological foundations captured by the code: ## 1. **Voxel and Ion Channels** - **Voxel**: In the context of computational neuroscience, a voxel represents a three-dimensional pixel of neuronal tissue, consisting of several neurons or parts thereof. The model simulates ionic currents in these small volumetric partitions, updated over time. ## 2. **Ionic Currents** - **Ion Fluxes (jk, jna, jca)**: The code models the movement of several key ions across voxel membranes. - **Jk (Potassium ions, K\(^+\))**: Represents the flux of potassium ions, integral to repolarizing the membrane after an action potential and maintaining the resting membrane potential. - **Jna (Sodium ions, Na\(^+\))**: Models the flux of sodium ions, crucial for the depolarization phase of an action potential. - **Jca (Calcium ions, Ca\(^{2+}\))**: Represents calcium ion flux, essential in neurotransmitter release and other cellular signaling pathways. ## 3. **Synaptic and Capacitive Currents** - **Isyn (Synaptic Current)**: The synaptic current results from neurotransmitter action, modeled as part of the unknown ion flux (jx). This part of the simulation captures how synaptic activity contributes to neuronal activity by modulating ionic currents. - **Icap (Capacitive Current)**: Refers to the current associated with the charging and discharging of the cell membrane's capacitor-like properties. This is critical for understanding how voltage across the membrane changes in response to currents. ## 4. **Membrane Current and Unspecified Ion Flux (Ix)** - **Imemb (Total Membrane Current)**: A total current across the membrane, integrating individual ion currents (ik, ina, ica) and unspecified currents. - **Ix (Unspecified Ion Current)**: Captures the cumulative effect of unspecified ion movements, including any leak currents (il), hyperpolarization-activated currents (ih), and synaptic currents (isyn). ## 5. **Units and Conversion** - The biological data is transformed into SI units for quantitative analysis. Currents are expressed in Amperes (then converted to mol/s using the Faraday constant), ensuring accuracy and consistency with biological measurements. ## 6. **Electrochemical Transformations** - The code leverages the Faraday constant (F), a fundamental component in electrochemical calculations, to convert electrical current to moles of ion flux, accounting for the specific valence charges of each ion. This model provides insights into the dynamic interplay of ionic currents that lead to neuronal excitability and synaptic transmission, fundamental to understanding how neurons communicate within networks and how brain activities manifest at a cellular level.