The snippet from the model code provided appears to pertain to the computational modeling of neuronal activity and calcium dynamics in a neuron, likely a pyramidal neuron or similar, that uses compartmental modeling to simulate different parts (segments) of a neuron.

Biological Basis

1. Membrane Potential (Vm):

   • SomaVm: This variable suggests the tracking of the somatic membrane potential over time. Membrane potential is crucial for understanding how neurons generate and propagate electrical signals. The soma is the cell body, a key area for processing synaptic inputs and generating action potentials.

2. Dendritic Compartments:

   • tert1volavg, tert5volavg, tert9volavg, tert13volavg: These variables most likely represent average voltages or volumes in different dendritic compartments or branches. Dendrites are critical for receiving synaptic inputs and can influence neuronal excitability and synaptic integration, impacting the overall activity of the neuron.

3. Calcium Dynamics:

   • tert1CaMN, tert5CaMN, tert9CaMN, tert13CaMN: These variables are likely modeling calcium ion concentrations ([Ca(^2+)]) in the cytoplasm of dendritic compartments. Calcium plays a pivotal role in a variety of cellular processes, including synaptic plasticity, neurotransmitter release, and gene expression. The suffix "MN" may indicate a specific measurement or model used to calculate calcium activity, such as mean concentration.

   • tert1CaMC, tert5CaMC, tert9CaMC, tert13CaMC: These might represent calcium ion concentrations in another cellular location, possibly the mitochondrial calcium concentration or bound calcium in the cytoplasm. "MC" could refer to mitochondria, modeling the role of mitochondria in buffering calcium, or it could represent a form of calcium buffering in the dendrite.

4. Calbindin (cb):

   • tert1cb, tert5cb, tert9cb, tert13cb: These could refer to the concentration of calbindin in each compartment, a calcium-binding protein known to buffer intracellular calcium levels and modulate neuronal activity. Calbindin is involved in protecting neurons from calcium overload, which can be toxic, and plays a role in shaping calcium transients related to neuronal signaling and plasticity.

Summary

The code is modeling the dynamic activity of neuron compartments, specifically focusing on the understanding of membrane potentials and calcium dynamics, which are vital for neuronal signaling, plasticity, and overall brain function. It examines how changes in electrical and chemical signals might occur across different parts (compartments) of a neuron's dendritic tree and soma, revealing insights into the intricate workings of neurons in the context of computational neuroscience.