problem with conductance unit in NEURON

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xin
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Joined: Thu Jun 18, 2015 8:54 pm

problem with conductance unit in NEURON

Post by xin » Tue Jun 23, 2015 10:12 am

Greetings,
I am confused about the conductance unit in NEURON. Use the Destexhe et al.1994 model as example (https://senselab.med.yale.edu/ModelDB/s ... model=3670). The unit of conductance in the gaba.mod file is 1 (umho). The unit of conductance in HH2.mod for sodium is mho/cm2. I am trying to understand how to convert this two units. From RE.tem file, the RE cell surface is 1000 um^2. Does the sodium conductance 0.1mho/cm2 in this certain cell equivalent to 1umho?

However, when I change the unit in the HH2 from 0.1 mho/cm2 to 0.1 umho then compile. The output of the cell are same. So in the code, it looks like 0.1 mho/cm2 with 1000 um^2 surface = 0.1 umho which conflicts with my unit convert in the first paragraph. I am not sure where I got lost.
Thanks

ted
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Re: problem with conductance unit in NEURON

Post by ted » Tue Jun 23, 2015 12:14 pm

You need to understand the difference between density mechanisms (AKA distributed mechanisms), which are used for channels that are distributed over the surface of a cell, and "point processes" which are used to represent localized current sources such as synapses or current and voltage clamps. Suggest you read chapters 5 and 6 of the NEURON Book or at the very least read
Hines, M.L. and Carnevale, N.T. The NEURON simulation environment. Neural Computation 9:1179-1209, 1997.
which is available from a link at
http://www.neuron.yale.edu/neuron/nrnpubs
xin wrote:I am trying to understand how to convert this two units.
This is a bit like asking how to convert oranges to apples, as you will see after reading the above.
However, when I change the unit in the HH2 from 0.1 mho/cm2 to 0.1 umho
Bad idea. Don't do that. You're setting a trap for yourself and anyone who uses your modified code.

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