Suggest you read the FAQ entry
What units does NEURON use for current, concentration, etc.?. There's a link to the FAQ list at NEURON's Documentation page
http://www.neuron.yale.edu/neuron/docs.
manyi wrote:I want to fit some data from voltage clamp experiments. Now I have a multi-compartment model
Then your voltage clamp will only control membrane potential in the near vicinity of the clamp electrode, and the current that the clamp collects will be contaminated with cable charging artifact, and confounded by the facts that membrane is not isopotential, and the clamp won't be capturing all of the membrane current. But maybe you're not interested in the current recorded by the clamp.
and use VClamp(0.5)
Use SEClamp, not VClamp. See
What is the difference between SEClamp and VClamp, and which should I use?
in the FAQ list. This won't eliminate the problems related to the extended architecture of your model, but at least you won't be piling additional artifacts on top of others.
In my code,
Code: Select all
vector_current.record(&soma.ik(.5))
So you are recording the potassium current density associated with the node at the middle of soma--something that can't be done in real life. OK, that's one of the strengths of computational modeling.
I got a reasonable trace of the recorded current, but what is the unit of the values in vector_current?
mA/cm2, as you will discover from the first FAQ list item that I mentioned.
Actually I expect to obtain something with current unit ampere, not per unit area, in order to compare the current that the soma electrode see in experiments.
Sorry to dash your expectations, but
1. In real experiments, the clamp electrode will capture current from more than just the soma. As I pointed out above, experiments on cells with extended architectures produce "dirty" results because of cable filtering and imperfect space clamp.
2. In NEURON, transmembrane ionic currents have units of current density. From this I infer that there may be additional items that need clarification, so let me suggest that you read chapters 5 and 6 of The NEURON Book, or this article
Hines, M.L. and Carnevale, N.T.
The NEURON simulation environment.
Neural Computation 9:1179-1209, 1997
(available for download from
http://www.neuron.yale.edu/neuron/nrnpubs)
The most convenient way to study a voltage gated channel in NEURON is to insert it into a single compartment model that has no other ionic currents, attach an SEClamp to the model, and record the SEClamp's i variable, which has units of nA. Also, set the SEClamp's rs (series resistance) parameter to a very small value, e.g. 1e-3. The current record will then have a brief brief capacitive artifact at every abrupt change of command potential, but it will be free of electrode series resistance artifact. Final tip: it is convenient to make the surface area of the model 100 um2, since this ensures that total current in nA is numerically equal to current density in mA/cm2.