Biological Basis of the Computational Model Code

The provided code represents a computational model involving different types of neurons in the auditory cortex, specifically focusing on pyramidal cells and fast spiking basket cells. Here is an explanation of the biological concepts the code aims to capture:

Resting Membrane Potential and Equilibrium Potentials

• Resting Membrane Potential (EREST_ACT): The default value is set at -0.07 volts for auditory cortex cells. It represents the baseline electrical charge difference across the neuron's membrane.
• Sodium (ENA) and Potassium (EK) Equilibrium Potentials: These values are critical for understanding the ionic basis of action potentials. Sodium equilibrium potential (0.045 volts) and potassium equilibrium potential (-0.082 volts) are set to reflect ionic gradients and their contributions to action potential dynamics.

Neuronal Compartments

• Compartmental Modeling: Compartmental models break down a neuron into distinct sections, allowing for simulation of electrical activity across different parts of the cell. This is crucial for capturing the spatial dynamics of signal propagation.

Ion Channels

The code defines various ion channels that mimic the ionic currents across the neuronal membrane, which are essential for generating action potentials:

• Sodium Channels (Na_pyr, Na_bask): These channels are critical for the rapid depolarization phase of the action potential.
• Potassium Channels (Kdr_pyr, Kdr_bask): These are responsible for repolarizing the neuron after an action potential.
• Calcium Channels (Ca_hip_traub91): Calcium currents are important for various intracellular processes including neurotransmitter release and modulation of other channel activities.
• Kahp Channel: Represents a calcium-dependent potassium current which plays a role in afterhyperpolarization and neural adaptation.

Synaptic Channels

• AMPA and GABA Channels (AMPA_pyr, GABA_pyr, AMPA_bask, GABA_bask): These channels model synaptic inputs. AMPA channels are typically excitatory, allowing sodium entry into the cell, while GABA channels are inhibitory, allowing chloride influx or potassium efflux, stabilizing the resting potential.

Spike Generation

• Spike Generator: The spikegen object simulates action potential firing in response to specific input conditions, defined by threshold and refractory parameters. This reflects the intrinsic excitability and timing of neuron firing.

Neuronal Types

• Pyramidal Cells: These are the principal excitatory neurons in the cortex, characterized by pyramidal shapes with distinct apical and basal dendritic trees. The model includes channels (Na_pyr, Kdr_pyr, etc.) tailored to mimic the unique ionic currents of pyramidal neurons.

• Fast Spiking Basket Cells: Known for their rapid and brief action potentials, these inhibitory interneurons regulate the excitability of nearby neurons and overall network oscillations. The code includes fast-spiking channels (Na_bask, Kdr_bask, etc.) to reproduce the distinct electrophysiological properties of these interneurons.

In summary, this code underpins a detailed computational model that seeks to replicate the behavior and interactions of auditory cortical neurons, focusing on ionic currents, synaptic interactions, and neuronal firing properties. The model strives to mimic biological processes in a controlled and quantifiable manner, reflecting the complex dynamics of cell populations in a cortical region.