Reading Pinsky and Rinzel (1999) about a model of a pyramidal neuron, I stumbled upon the following. They have developed a twocompartmental model in which the currents are normalized per unit surface area. The two compartments are coupled, and current is allowed to flow between compartments by a coupling conductance gc.
In the paper, the resistance between the two compartments is calculated as the axonal resistance of half of the first compartment plus the axonal resistance of half the second compartment, which are both cylinders. I understand that this is the same as calculating the axonal resistance of half of the total cylinder (compartment 1 + 2).
To calculate the conductance between two compartments per unit area, they use the constants provided in Traub(1991). I looked them up and calculated the conductance myself, but I ended up with a value in the range of 10^-10 S/um^2. Can someone tell me what went wrong?
r=[4.23; 2.89; 2.42] %um
l=[125; 120; 110] %um
Ri=100e4; %Ohm um
Pinsky & Rinzel (1999)
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Here's a fundamental problem: the model described by Traub et al. contains 19 compartments--an 8 compartment basal dendrite, a soma with 1 compartment, and an apical dendrite with 10 compartments. Somehow Pinsky & Rinzel reduced that to a 2 compartment model. How did they combine the apical and basal dendrites, which had different lengths and diameters, into a single equivalent compartment? Did you discover exactly where they spelled that out? When they wrote that they used "the values from Traub et al. (1991) for these constants" (i.e. for compartment radius, and length), which values did they intend to use for the non-soma compartment? Without this information, you're stuck. ModelDB does contain an XPPAUT implementation of the Pinsky-Rinzel model; maybe you can work backwards from that to figure out what they did. Or maybe Pinsky or Rinzel can explain it.