Biological Basis of the Provided Code

The code models a specific type of synaptic transmission in the brain, particularly focusing on inhibitory synapses. Inhibition is crucial in modulating neuronal excitability and synchronizing network activity. The synapses modeled here are characterized by the neurotransmitter systems they involve and various molecular markers.

Key Aspects of the Model

Synaptic Transmission

The code is based on an extended form of the Exp2Syn model, which is commonly used to simulate synaptic currents. The model takes into account the rise and decay kinetics of a postsynaptic conductance following the release of neurotransmitters. Biological synapses typically exhibit such dynamics due to the binding and unbinding of neurotransmitters to their receptors.

• Rise and Decay Time Constants (tau1, tau2): These constants define the temporal profile of the synaptic conductance change, where tau1 is the rise time and tau2 is the decay time. The assumption is that decay is slower than the rise, as is usually the case in biological synapses.

Inhibitory Synapses

This extension explicitly models inhibitory synapses. These synapses generally use neurotransmitters like γ-aminobutyric acid (GABA) to induce hyperpolarization or stabilize the membrane potential of the postsynaptic neuron, reducing its likelihood to fire an action potential.

• Reversal Potential (e): Set at -70 mV, typical for inhibitory synapses that work primarily with GABAergic mechanisms, which often aim to stabilize the membrane potential close to the resting potential of neurons.

Synaptic Markers and Functionality

The model incorporates additional attributes to track and control specific types of inhibitory synapses:

• Markers (vgat, sst, npy, pv): These parameters reflect the molecular makeup of the synapses:

  • vgat: Represents synapses that transport and store GABA.
  • sst: Represents synapses marked by somatostatin, a neuropeptide that typically modulates GABAergic activity.
  • npy: Represents synapses associated with neuropeptide Y, which can modulate neuronal excitability and synaptic plasticity.
  • pv: Reflects the presence of parvalbumin, a calcium-binding protein often found in fast-spiking interneurons.

• isOn: A functional switch determining whether the synapse is active or inactive, allowing for simulation of genetic conditions or altered states of synaptic function.

Voltage-Dependent Outward Rectification

The added functionality includes a voltage-dependent outward rectification mechanism:

• rect(v): A function that modulates the synaptic conductance based on the membrane potential, potentially modeling more complex, nonlinear behavior seen in some synapse types. This could represent potassium channel conductances that show voltage sensitivity, affecting how inhibition can change with the postsynaptic cell's membrane potential.

Summary

Overall, the code is designed to represent the physiological behavior of inhibitory synapses with various neurochemical identities and dynamic properties, incorporating both conventional synaptic kinetics and extending them with influence from membrane potential to simulate more complex inhibitory roles in neuronal networks.