subhasishg wrote:I had applied KCL=0 and tried to reverse calculate IClamp at section Y. That did not work.
Why would you expect it to?
I have a simple cell modeled with some sections and segments in each. I have HH Mechanism inserted.
It is no longer simple--it is a system that is distributed in space and has complex membrane properties.
1. First, I use a IClamp in section X and plot the voltage at section X & Y.
2. Next, I want to isolate section Y (i.e remove all other sections) and apply a suitable IClamp and generate voltage plot at Y only.
Both the plots in step 1 & 2 for Y should match.
How should I do this, what all things I need to consider.
Three steps are required.
The first step is to record the time course of v from Y under condition 1.
The second step is to use that waveform as the command for a voltage clamp under condition 2. The voltage clamp's series resistance should be very low, and it should be attached to Y at exactly the same point from which the voltage waveform was initially recorded. You should record the current delilvered by the voltage clamp.
The third step is to use a current clamp to inject exactly that current waveform into Y, again at the same point from which the voltage waveform was initially recorded. In theory this should produce the same voltage waveform in Y as step 2 did, but, if Y contains voltage gated currents, in practice you are likely to be in for a surprise (unlike steps 1 and 2 which should produce no unexpected result). If you are doing this as a homework assignment, expect to have an interesting discussion with your instructor about what happens.
Implementation suggestions:
Use an SEClamp, not a VClamp. See the explanation in the Forum's "Hot tips" area.
Set the SEClamp's series resistance to 1e-3 megohm or even smaller.
Use the Vector class's record() method to capture the time course of the waveforms that you will need into a pair of Vectors (one vector to capture the recorded variable, the other to capture time).
In step 2, use the Vector class's play() method to drive the time course of the SEClamp's amp1 parameter (make sure to set dur1 to a very large value, e.g. 1e9).
In step 3, use the Vector class's play() method to drive the time course of the IClamp's amp parameter (make sure to set del to 0 and dur to a very large value, e.g. 1e9).
You will want to read the Programmer's Reference entries on SEClamp, IClamp, and the Vector class--especially the latter's record() and play() methods.
The entire task will be more easily achieved if you structure it as a sequence of three separate stages, one stage for each of the three steps described above, where the code that accomplishes each stage is contained in its own hoc file (with load_file statements as appropriate for whatever ses files you may find helpful). This implies that stages 1 and 2 will involve writing results to output files, and stages 2 and 3 will involve reading the results that were saved from the previous stage. You will want to read the Programmer's Reference entries about the File class and its methods for saving and retrieving data from files.