Parameter analysis in model translation

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.

Parameter analysis in model translation

Postby pdennevis » Fri Jun 30, 2017 4:02 pm

Hi all!

Recently I have been trying to translate a Matlab model of a single cell neuron to the NEURON environment. So far, I have finished the NEURON code, but due to differences in the approaches, the neuron doesn't give me the same spikes yet. The soma part of the model contains 4 types of channels: Sodium, Low-treshold Calcium, Potassium and Potassium delayed rectifier.

I have already tried tuning the different parameters (time constants, midpoint voltages) of the channels, but still don't get the same results. ALso it turns out when I change the channels' conductance (even put it to 0) the spikes don't change.

This is how I want them to look:

This is where I started:

This is where I am now, by changing only the time constant of the h-gate of the potassium channel:

It is close already, but the wrinkles in the plateau still irritate me. I don't have a background in the underlying biological mechanisms so I was hoping one of you could tell me which channel, or even which parameter, is responsible for this behaviour? Is this a response of one of the potassium channels?

Looking forward to hear from you!
Kind regards,
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Re: Parameter analysis in model translation

Postby ted » Mon Jul 03, 2017 9:14 am

In the absence of any real information about your model, I can only make the most general of suggestions.
1. Most models that are not implemented with NEURON use "absolute" units to specify maximum channel conductances, but NEURON uses S/cm2 for channels that are distributed over the cell surface. Make sure that the product of your model's surface area and channel densities are correct.
2. Some non-NEURON model implementations approximate "fast channels" by an algebraic equation that maps membrane potential to the corresponding steady state ionic conductance or current. This can introduce instabilities.
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