How does NEURON calculate the membrane potential?

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asa
Posts: 1
Joined: Tue Apr 25, 2006 3:46 am

How does NEURON calculate the membrane potential?

Post by asa » Tue Apr 25, 2006 5:30 am

How does NEURON calculate the membrane potential? Is there any diffrences between ion current (such like 'ica') and nonspecific current i?

We have build a two compartement model containing soma and dend. In the dend we have inserted r-Type voltage gated channels 'car.mod' by the commend "insert car", and AMPA receptors. To trigger the AMPA receptors we used 'NetCon()' function.

By plotting the membrane potential and the currents we found although the r-Type VGCC (ica) is big, it doesn't seem to contribute as much as it should to the membrane potential. In the plot the ion current from r-Type VGCC (ica) is as big as the the nonspecific AMPA current (i) but they do not contrubute the same. Also by blocking r-Type VGCC (ica) there is nearly no difference in the membrane potential. Both the ion current and the non specific current are in current density (mA/cm^2).


Could the problem be the way NEURON handles the two kinds of current (nonspecific and ion current)?


the main code for the two compartment model
--------------------------------------------------------------
...
access soma
access dend
celldef()



forsec "dend" {

insert car
insert canmda
insert cad
}

dend[0].gcabar_car=5
......

objref synAmpa
dend[0] synAmpa = new ampa(0.5)

objref nc1, nil
nc1 = new NetCon(nil, synAmpa)
nc1.weight = 10
nc1.delay = 0

objref syntimes
syntimes = new Vector(1)
syntimes.x[0] = 10


objref fih
fih = new FInitializeHandler("loadqueue()")
proc loadqueue() { local ii
for ii=0,syntimes.size()-1 {
nc1.event(syntimes.x[ii])
}
}

------------------------------------------------

ted
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Re: How does NEURON calculate the membrane potential?

Post by ted » Tue Apr 25, 2006 11:37 am

asa wrote:How does NEURON calculate the membrane potential?
Numerical integration of the cable equation. See chapter 5 of
The NEURON Book, or read
Hines, M.L. and Carnevale, N.T. The NEURON simulation environment. In: The Handbook of Brain Theory and Neural Networks, 2nd ed, edited by M.A. Arbib. Cambridge, MA: MIT Press, 2003, pp. 769-773
or
Hines, M.L. and Carnevale, N.T. The NEURON simulation environment. Neural Computation 9:1179-1209, 1997
downloadable from
http://www.neuron.yale.edu/neuron/bib/nrnpubs.html
Is there any diffrences between ion current (such like 'ica') and nonspecific current i?
Both affect charge balance. Currents associated with a specific ion
affect concentration and equilibrium potential if there is a corresponding
ion accumulation mechanism.
By plotting the membrane potential and the currents we found although the r-Type VGCC (ica) is big, it doesn't seem to contribute as much as it should to the membrane potential. In the plot the ion current from r-Type VGCC (ica) is as big as the the nonspecific AMPA current (i) but they do not contrubute the same. Also by blocking r-Type VGCC (ica) there is nearly no difference in the membrane potential. Both the ion current and the non specific current are in current density (mA/cm^2).
Not so. Your calcium current is produced by a density mechanism, but
your AMPA current is generated by a point process. The units are mA/cm2
and nA, respectively. Only if surface area is 100 um2, will the ca current
density in mA/cm2 be numerically identical to the total ca current in nA.
Could the problem be the way NEURON handles the two kinds of current (nonspecific and ion current)?
Not likely.
access soma
access dend
Not a good idea to use access more than once. Search this Forum for the
keyword "access."
celldef()
What is this?

Lei
Posts: 3
Joined: Thu Jan 05, 2006 8:28 am

Re: How does NEURON calculate the membrane potential?

Post by Lei » Thu Apr 27, 2006 8:52 am

thank you ted!
Not so. Your calcium current is produced by a density mechanism, but
your AMPA current is generated by a point process. The units are mA/cm2
and nA, respectively. Only if surface area is 100 um2, will the ca current
density in mA/cm2 be numerically identical to the total ca current in nA.
does it mean there are only two current class units: current density in (mA/cm2) and current in (nA)?

Does only point_process mechanism use current in (nA)? I mean how can I tell NEURON which unit should be chosen for calculating the membrane potential?

Thanks a lot!

ted
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Joined: Wed May 18, 2005 4:50 pm
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Units

Post by ted » Thu Apr 27, 2006 9:55 am

See this item
What units does NEURON use for current, concentration, etc.?
in the FAQ list
http://www.neuron.yale.edu/neuron/faq

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