Setting default reversal potential for an ionic species

NMODL and the Channel Builder.
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Joined: Fri Jun 25, 2010 6:52 pm

Setting default reversal potential for an ionic species

Post by dave_arthurs »


I am very new to NEURON and have a basic question. Specifically, I am wondering if there is a way to specify the default reversal potential for an ionic species, for example, potassium, such that all ion channels that use this ion will have the same default reversal potential.

The one way I have found to set the reversal potential is to specify it when defining the section, as in

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soma {
      nseg = 1
      diam = 18.8
      L = 18.8
      Ra = 123.0
      insert hh
      ena = 71.5
      ek = -89.1
      gl_hh = .0001666
      el_hh = -60.0
      insert CaT
      eca = 126.1
However, one has to do this for every section, which can be cumbersome. I notice that, if ek=-89.1 is not specified, the ek value will default to -77. Ideally, one way to accomplish what I am asking would be to change this default value, but I am not sure how to access it.

The other method I have been attempting is to specify a default value in the mod file. For example, I noticed that the Neuron example script "nrn/nrn/share/examples/nrniv/nmodl/hh1.mod" contains lines in the PARAMETER section attempting to set the default ek and ena values

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        v (mV)
        celsius = 6.3 (degC)
        dt (ms)
        gnabar = .12 (mho/cm2)
        ena = 50 (mV)
        gkbar = .036 (mho/cm2)
        ek = -77.5 (mV)
        gl = .0003 (mho/cm2)
        el = -54.3 (mV)
However, when I ran this code, psection() returned the default value of -77 mV, and not -77.5 mV, so it seems that this segment of the code is overridden by the default (I guess perhaps there is some lower-level process for calculating the reversal potential?).

So, in short, it would be great if someone could suggest a more elegant mechanism for dealing with this. As a back up plan, I will just specify a global variable to use to hold the reversal potential.

Thank you!
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Re: Setting default reversal potential for an ionic species

Post by ted »

Ionic equilibrium potential is a complex topic, good for you for asking about it. Sometimes one wants to treat them as constant parameters, other times it is necessary to calculate them from the Nernst equation--it all depends on what you want. NEURON allows modelers a completely free hand with this. Reading the material mentioned in this post
may or may not answer all of your questions, but at the very least it will give you what you need to know so that we can have a more focussed discussion.
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