Multi-Compartment Model

[thats_karlo]

Dear Friends,

suppose insted of one compartment model , you like to have 3 comaprtment model.

so, it means insted of one RC-circuit, you will have 3 RC-circuits


1-compartment model -----RC-----

3-compartment model ----RC---/\/\/\---RC---/\/\/\----RC

where /\/\/\ shows resistance!


and my question:

1-Dose 'nseg=1' mean 1-compartment model and 'nseg=3' mean 3-compartment model?

2- The resistance between RC-circuit is cytoplasmic resistance(right?)
that is shown by Ra in Neuron. what should i do if i want to have diffrent Ra
between RC-circuits?


Thank's in advance!

[ted]

1-Dose 'nseg=1' mean 1-compartment model and 'nseg=3' mean 3-compartment model?

You should read
Hines, M.L. and Carnevale, N.T. The NEURON simulation environment.
Neural Computation 9:1179-1209, 1997.
which you can get from a link at
http://www.neuron.yale.edu/neuron/bib/nrnpubs.html
There you will see that nseg specifies the number of compartments that are used to
represent a section.

2- The resistance between RC-circuit is cytoplasmic resistance(right?)
that is shown by Ra in Neuron. what should i do if i want to have diffrent Ra
between RC-circuits?

Ra is cytoplasmic resistivity in [ohm cm]. This is the resistance of a 1x1x1 cm cube of
cytoplasm, measured between two 1 cm2 electrodes separated by 1 cm distance.

The resistance between two locations in a neurite depends not just on Ra, but also
on the diameter of the neurite and the distance between the points. NEURON's built-in
function ri() computes this value--see
http://www.neuron.yale.edu/neuron/stati ... ry.html#ri
Also read
Hines, M.L. and Carnevale, N.T. The NEURON simulation environment.
Neural Computation 9:1179-1209, 1997

Ra is a "section variable" which means that it has the same value along the entire
length of a section. diam is a "range variable" which means that it can vary with
position along the length of a section.

Therefore ri() can vary with position--just change diam. But of course that changes
total membrane capacitance and conductance in the affected segments. If you need
to control ri() alone, your best strategy is to use more than one section.

--Ted

[thats_karlo]

Dear Ted

Thank's for your answers! but unfotunatly i didn't get one point,

i have one section, say "A", when i define nseg=1, and i'm gonig to "Plot what?" i can find A.v(0.5), and for nseg=3 , i just can find A.v(0.166)

what should i do,if i like to plot A.v(0.5), in case nseg=3?

in the "Plot what?" it ,"Enter sybmol name" , accepts A.v(0.5) but v(0.5) dosent appear in symbol name list in second column!


Thank's again!

[ted]

Have you read the pdf preprint for this paper
Hines, M.L. and Carnevale, N.T. The NEURON simulation environment.
Neural Computation 9:1179-1209, 1997
? Especially the part about range and range variables.

--Ted

[TWA]

I know what Karlo is talking about. Even though I'm sure Karlo has figured this out by now, I thought I would post an answer for future reference for the less initiated who will be confused by what they see when they click stuff in the plot what? window. Also, I have seen another post by someone who wanted to plot something from a certain section that wasn't showing up in the plot what? window.

The answer is the same for both: double click on something close to what you want in the plot what? window, for example A.v(0.166). When you have it showing in the top field, click on it there and edit it to read what you really want, for example A.v(0.5).

I have often pondered the mysteries of what shows up in the plot what? window, thinking there must be a link to NEURON's inner mind... but the answer seems to be just out of reach.

Corey

[ted]

TWA got it right. I missed what Karlo was getting at. Sorry, Karlo, and
many thanks, TWA!

When you use the Plot what? tool to examine the name of a range variable,
the tool shows only one location--usually the first internal node, which is
at 0.16666666... when nseg==3. This is because the value of nseg can be
very large, so it would be cumbersome if each node's location were
displayed.