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Regarding diameter of geometry

Posted: Sat Sep 05, 2020 7:31 pm
by tuh36651
Hello, I am have imported a cell (in the gui, I am a little new to using) and I am running Hodgkin Huxley Channel simulation on the cell. I am modifying the geometric parameter: diameter and biophysical parameter Ra and Cm. I have set the diameter to 1.4e-6, kept Ra and Cm to default, and I am noticing that the wave speed of the AP is significantly less (by orders of 100 less ~0.01 m/s) then what is biologically possible 0.5 m/s to 10 m/s. I think I am not specifying the diameter parameter correctly, but I am not sure if there are other parameters in the gui that can affect the ap propagation speed.
1) Are there other parameters that if I do not specify correctly will produce unusual ap propagation speeds?
2) Are the parameters (such as Ra and Cm) usually left to default?
3) Should I be specifying 1.4 instead of 1.4e-6, I ask because it shows (um) in the label.

Re: Regarding diameter of geometry

Posted: Tue Sep 08, 2020 11:25 am
by ted
Never apologize for using the GUI--the GUI has many tools that are powerful and easy to use.

A quick way to learn a lot of useful information is to go straight to the Documentation page at NEURON's web site
and check out the links under
For NEURON beginners
and especially to read the short article mentioned in the first suggestion on the
Help for the total beginner
page. Yes, that article was written before NEURON started using Python, but it introduces concepts that are valid regardless of whether you're using hoc or Python.

With regard to your specific questions, the answers are
1) Of course.
2) Parameter values are generally assigned values that are based on experimental observations and the assumptions that the modeler wishes to evaluate. A good way to get a sense of actual practice is to read the Methods sections of a few modeling papers, particulary papers that combine modeling and experimentation. You may find some examples of interest to you in ModelDB
3) To learn the units that are used in NEURON, see the item
What units are used in NEURON?
in the Hot tips area of the NEURON Forum viewforum.php?f=28 (hint: it's the oldest hot tip, so you may have to go past the first page).