The provided code models the dynamics of neuronal behavior through an extended version of the "EDPR model," which likely involves cellular and ionic processes that contribute to neuronal signal propagation. The model incorporates several key components that are fundamental to neuronal physiology:

Biological Elements in the Model

Ionic Species

The model tracks concentrations of several crucial ions within different compartments of the neuron:

• Sodium (Na⁺)
• Potassium (K⁺)
• Chloride (Cl⁻)
• Calcium (Ca²⁺)

These ions are essential for generating electrical signals in neurons, such as action potentials, through their movement across cell membranes. Their concentrations are often different inside versus outside cells, creating electrochemical gradients that drive ion flows via channels and transporters.

Gating Variables

The model utilizes gating variables (n, h, s, c, q, z) to represent the state of ion channels, which is quintessential in neuronal signaling:

• n, h, s, c, q, z: These likely correspond to parameters governing the opening and closing kinetics of various ion channels (akin to the Hodgkin-Huxley model), influencing how ions contribute to membrane potential dynamics.

Membrane Potentials

The model calculates several membrane potentials:

• phi_si, phi_se, phi_di, phi_de: These are transmembrane potentials in various neuronal compartments, crucial for action potential propagation.
• Reversal Potentials: (E_Na_s, E_Na_d, E_K_s, E_K_d, E_Cl_s, E_Cl_d, E_Ca_s, E_Ca_d) are the potentials at which there is no net flow of respective ions across the membrane.

Charge Balance

• The model ensures charge conservation (q_si, q_se, q_di, q_de) which is critical given that ions carry electrical charges, and imbalances can affect cellular excitability and signaling.

Temperature

• Temperature (T = 309.14 K): This is a biological temperature setting that influences the kinetics of biochemical processes and ion channel dynamics.

Model Dynamics and Stimulus

The model incorporates a stimulation paradigm through I_stim parameters, meant to simulate external inputs to the neuron, possibly mimicking synaptic input or experimental current injections.

Biological Interpretation

Overall, the code models the biophysical basis of neuronal function, focusing on ion dynamics and membrane potential regulation. This simulation allows for exploring how variations in ion concentrations, channel kinetics, and external stimuli impact neuronal behavior, which is fundamental for understanding nervous system function and pathologies. The inclusion of calcium ions and their separate initial conditions suggests a concern with intracellular signaling pathways often implicated in synaptic plasticity and other long-lasting neuronal changes.