The code provided is a simulation of a cortical column model with Intra-Cortical Microstimulation (ICMS), referencing modifications based on works by Markram et al., 2015, and Aberra et al., 2018. Below are the key biological components and processes being modeled in this simulation: ### Cortical Columns - **Cortical Columns:** The primary focus of this code is on simulating cortical columns, which are cylindrical processing units in the mammalian neocortex. Each column is composed of multiple types of neurons and synapses arranged in layers, playing important roles in sensory processing, perception, and higher cognitive functions. ### Neuron and Synapse Modeling - **Neuron Morphology:** The code references neuron morphology modification (`editMorphology.hoc`) which likely involves loading and adjusting the detailed cell models that represent the neurons within the cortical column. This includes their dendritic trees and axons that are crucial for determining the connectivity and computation abilities of the neurons. - **Membrane Dynamics:** This simulation employs mechanisms to simulate the membrane potential dynamics of cells, particularly by setting the initial conditions and running through time steps to observe membrane potential changes over time (notably, the `recvm` and `rec_vm_axon` procedures). - **Synapses:** Synaptic mechanisms are invoked (e.g., `synapses.load_synapses`), which indicates the presence of synaptic transmission modeling. These synapses are adjusted during the simulation to reflect connections between neurons that influence action potential firing and signal propagation through the network. ### Stimulation Protocols - **ICMS Stimulation:** The code is intended to model the effects of electrical microstimulation on the cortical column. Parameters such as delay (`DEL`), duration (`DUR`), amplitude (`AMP`), and frequency (`FREQ`) are set to simulate the ICMS, which is a method used experimentally to probe and modulate neuronal circuitry. - **Electrode Placement:** The positions of two electrodes (`ELECx1`, `ELECy1`, `ELECz1`, etc.) are defined. These parameters suggest the modeling of the spatial interaction of the electric field with the cortical tissue, allowing for the analysis of stimulation effects on neurons at different locations within the cortical column. ### Extracellular Dynamics - **Extracellular Resistivity:** The code involves calculations (`calcesI`) to simulate the effect of electrical fields generated by the stimulating electrodes on the neurons, including contributions from extracellular resistivity (`sigma_e`). These computations are crucial for understanding how the electric field influences neuronal excitability and synaptic activity. ### Temperature Effects - **Physiological Temperature:** The simulation sets the model at a physiological temperature of 37°C, which is critical as it influences the kinetic properties of ion channels and overall neuronal activity. ### High-Level Functions - **Parallel Simulations:** The code is designed to run batch simulations using multiple cell instances, suggesting that the model is used to explore variability in response to ICMS across different types or configurations of cortical columns. By simulating these components and processes, the model aims to provide insights into the electrical properties and network interactions of cortical columns under electrical stimulation conditions. This could be used to inform experimental and clinical applications, including neural prosthetics and brain-computer interfaces.