Biological Basis of the Computational Model

The provided code is a simulation script intended to model the synaptic interactions and electrical behavior of pyramidal cells within a neuronal circuit. This type of model is frequently employed in computational neuroscience to understand complex synaptic integration and network properties. Below, key biological components represented in the code are outlined:

Pyramidal Cells

The code initializes multiple instances of PyramidalCell objects, each representing a pyramidal neuron. These neurons are the primary excitatory cells in regions like the cerebral cortex and hippocampus. Pyramidal cells have distinct morphological features, including a triangular soma, a single long apical dendrite, and multiple basal dendrites, which are involved in different synaptic inputs.

Synaptic Inputs

The model incorporates various synaptic connections to pyramidal cells, representing complex interactions:

• AMPA-mediated Synapses:

  • These synapses use glutamate as a neurotransmitter and are critical for fast excitatory transmission. MyExp2Syn objects with specified tau1, tau2, and reversal potential (e.g., e = 0) are used to model AMPA receptor kinetics. The code models inputs from different sources to various parts of the pyramidal cell dendrites.

• GABA-mediated Synapses:

  • These synapses utilize GABA as a neurotransmitter and provide inhibitory effects on the postsynaptic neuron. The presence of both GABA_A and GABA_B type synapses indicates the simulation of both fast and slow inhibitory postsynaptic potentials. The reversal potential is set to -75 mV, typical of GABAergic synapses.

Synaptic Targets and Regions

The model specifies synaptic placement on different dendritic compartments, highlighting the spatial complexity of synaptic integration:

• Apical Dendrites: Receive excitatory inputs reflecting distant sources, such as entorhinal cortex (EC) and CA3 regions via AMPA synapses.
• Basal Dendrites: Targeted by synapses representing inputs from broader regions and local circuits.
• Soma and Axon Initial Segment: Targeted specifically by inhibitory synapses, such as those originating from basket cells (BC) or axoaxonic cells (AAC), which are crucial for regulating action potential initiation and propagation.

Voltage Clamp

The code employs voltage clamp techniques (VClamp) on soma regions to control and measure the ionic currents while keeping the membrane potential at a fixed level. This serves to isolate synaptic responses and study the properties of synaptic conductances more clearly.

Temporal Parameters

The simulation time (tstop) and the stimulus properties (e.g., NetStim) are used to model neuronal dynamics over a short period, capturing the transient synaptic events and their integration without the confounds of long-term plasticity mechanisms.

Output and Data Collection

The model records the synaptic currents (i_ca1 vectors) generated through these networks, enabling the analysis of synaptic effectiveness and integration at multiple input sites.

In conclusion, the script models the input from a network of excitatory and inhibitory synapses on pyramidal neurons, capturing synaptic dynamics and potential regulatory mechanisms. Such models are foundational in understanding synaptic integration's role in neural computation and network behavior.