Biological Basis of the Code

This code is a computational representation of a neural network model focusing on cortical structures and their interactions, inspired by the study by Benita et al. (2012). The objective is to simulate the neurophysiological dynamics within the cerebral cortex, including both the intrinsic cellular properties and the synaptic interactions. Here's a breakdown of the biological elements represented within the code:

Key Components

Cell Populations

1. Pyramidal Cells (PY cells):

   • PYdr (Pyramidal Dendritic Region): This population represents the dendritic compartments of pyramidal neurons, which are the principal excitatory neurons in the cortex. They play a critical role in integrating synaptic inputs and generating output signals.
   • PYso (Pyramidal Somatic Region): This population represents the somatic compartments of pyramidal neurons. The somatic region is typically responsible for the initiation of action potentials and is crucial for neuron firing regulation.

2. Interneurons (IN cells):

   • These represent inhibitory neurons within the cortex, which modulate the activity of pyramidal neurons and contribute to the balance of excitation and inhibition in the network.

3. Thalamic Cells:

   • TC (Thalamocortical Neurons): These neurons are responsible for relaying sensory information to the cortex and are involved in oscillatory activities that contribute to cortical rhythms.
   • TRN (Thalamic Reticular Nucleus Neurons): These are GABAergic neurons that play a role in the modulation of thalamic signals and are crucial for attention and sleep-wake cycles.

Ionic Currents and Mechanisms

• Ion Channels:

  • Ionic currents such as sodium (Na(^+)), potassium (K(^+)), calcium (Ca(^{2+})), and hyperpolarization-activated cation channels are modeled. These channels are responsible for generating and regulating action potentials and synaptic activities.

• Synaptic Currents:

  • AMPA, NMDA, and GABA Receptors:
    • AMPA and NMDA receptors mediate fast excitatory synaptic transmission, while GABA receptors mediate inhibitory transmission. The code features these synaptic mechanisms to model the dynamic interactions between excitatory and inhibitory neurons.
  • Intercompartmental Currents:
    • The code includes dendro-somatic interactions that are critical for integrating synaptic inputs.

Network Structure and Interactions

• The connectivity between pyramidal cells (PY), interneurons (IN), and thalamic cells (TC and TRN) is defined to capture the network's functional dynamics. This includes both intracortical (within the cortex) and thalamo-cortical (between the thalamus and cortex) connections.

Biological Phenomena Modeled

• Cortical Oscillations:

  • The model simulates slow oscillatory activity, which is a hallmark of certain states of consciousness such as sleep.

• Synaptic Depression:

  • Mention of mechanisms related to synaptic depression suggests an inclusion of plasticity effects, which are vital in learning and memory.

Conclusion

This computational model replicates various biological features of neuronal networks in the cerebral cortex and thalamus. By leveraging these components, the model aims to capture the complex electrophysiological behavior of brain regions involved in sensory processing, cognitive function, and state-dependent activity such as wakefulness and sleep.