Biological Basis of the Computational Model Code

The provided code is part of a computational neuroscience model simulating synaptic connections and neural interactions between two types of neurons: P23RSb and P5IBd. The model aims to capture the dynamics and characteristics of synaptic transmission and propagation within a neural network. Below are the biological aspects modeled by each section of the code:

Neuronal Types

• P23RSb Neurons: These possibly represent pyramidal neurons in cortical layer 2/3, which are known for their regular spiking behavior. Pyramidal cells are the primary excitatory neurons in the cortex and play critical roles in integrating synaptic inputs and sending outputs to various regions of the brain.
• P5IBd Neurons: These likely represent layer 5 intrinsic bursting neurons. Such neurons are known for their ability to generate bursts of action potentials intrinsically and are typically involved in projecting outputs to subcortical regions, thereby facilitating communication between the cortex and other brain regions.

Synaptic Connections

The code establishes synaptic connections between the P23RSb (presynaptic) and P5IBd (postsynaptic) neurons using both AMPA and NMDA receptor-mediated transmission:

• AMPA Receptors: These are ionotropic glutamate receptors that mediate fast synaptic transmission in the brain. Activation of AMPA receptors results in the rapid influx of sodium ions, which depolarizes the postsynaptic neuron.
• NMDA Receptors: These are also glutamate receptors but are slower to activate and play a crucial role in synaptic plasticity and memory formation due to their voltage-dependent magnesium block and calcium permeability.

Synaptic Location

• The code defines multiple synapses onto various dendritic compartments (apdend5 to apdend12). This reflects the biological distribution of synapses across the dendritic tree, influencing how excitatory inputs integrate within a neuron.

Connection Probability and Masking

• Probability: A defined probability (0.12500*{P23RSb_P5IBd_prob}) governs the likelihood of synapse formation, simulating the non-deterministic nature of synaptic connectivity in the brain.
• Spatial Masks: The use of masks (sourcemask, destmask) defines the spatial boundaries and geometry within which synaptic connections can occur. These parameters replicate the constrained anatomical layout of neurons in the cortex.

Synaptic Delays and Weights

• Delays: Transmission delays are added with variability (using Gaussian distribution), reflecting the time it takes for an action potential to travel along axons and initiate postsynaptic responses. This delay is influenced by factors like axonal length and propagation velocity (CABLE_VEL).
• Weights: Synaptic weights determine the strength of synaptic transmission and are crucial for simulating neural circuit function and plasticity. The use of a decay function with max and min weights models synaptic depression or potentiation over interactions, aligning with principles like Hebbian learning.

General Biological Context

The model seeks to replicate aspects of cortical microcircuits, emphasizing synaptic transmission and plasticity. These interactions are essential for functions like sensory processing, decision making, and learning. Parameters such as velocity, probability, and spatial constraints ensure the model remains an accurate representation of biological phenomena, making it useful for investigating neural circuit dynamics and their functional implications.