Neuron Simulation Lab
Run the simulation by double-clicking on trymeneuron.hoc. In this
simulation, you will be examining the relationships between the behavior of
channels proposed in the Hodgkin-Huxley model of the neuron, and the
neuron properties of threshold and refractoriness.
A) In this simulation, there are two stimuli introduced one end of a long
axon. Parameters of Stimulus 1 and Stimulus 2 are controllable through the
windows titled IClamp[0] and IClamp[1], respectively. There are three time
graphs associated with this simulation. The first (top) is a graph of
membrane voltage near the end of the axon well orthodromic to the
stimulation electrodes. The middle graph shows the Hodgkin-Huxley model
parameters m, h, and n at the patch of membrane right under the stimulating
electrodes. The bottom graph is the membrane voltage right beneath the
recording electrodes, with a zoomed in time axis.
While leaving the amplitude of the second stimulus (IClamp[1]) zero, vary
the amplitude of the first stimulus to determine the current threshold for this
soma. (Click the Init and Run Button to run the simulation).
1) What is the current threshold for this soma? What is the voltage
threshold?
After determining this threshold, set stimulus 1 to be six times the current
threshold, then vary the delay (parameter del) of stimulus 2. Start at 5ms,
and increase the delay by 3ms, until you reach 40ms. For each delay, vary
the stimulus amplitude of Stimulus 2 to determine the threshold for the
second stimulus, within 5% of the threshold value (greater precision is not
called for). If the threshold of the second pulse is greater than 2000
milliamps, assume the threshold is infinite.
Saving Graph Data to a text file:
You can save your data to a text file by selecting the window menu from
the NEURON main menu, and opening the Print & File Window Manager.
This will open up a screen, with outlines of Neuron windows on your
desktop, and a mock page of what will get printed when you print. If you
click on the graphics windows of interest, youll see that they get copied to
the mock print sheet. If you run your simulation, then use the Print window
to print in ASCII format, youll get prompted for a file name. If you use the
extension .txt, you wont have much trouble importing this data into Excel
or Matlab. Use this technique to save enough data to generate your lab
report and answer any questions. Keep a log of file names you save, and
what type of runs they were associated with so you can reconstruct your
session later.
2) Plot (by hand, or using whatever software package you choose)
the threshold versus the difference between delay 2 and delay 1.
3) How long is the absolute refractory period?
4) How long is the relative refractory period?
5) Relate the absolute and relative refractory period to the state of
the channels shown in the graph Channel States, which shows
m (roughly corresponds to Na activation), h (roughly corresponds
to Na in activation), and n (roughly corresponds to K activation)
in different colors.
B) Close NEURON. Run the passiveaxon simulation by double clicking
passiveaxon2010.hoc. This is an example of an axon of unknown diameter
with passive channels (i.e, no voltage-modulated gated channels). In this
simulation, we will determine how axonal and membrane resistance, as well
as membrane capacitance, change as a function of axon geometry.
Run the simulation. Right-click in the graph entitled Time Plot. While
continuing to hold down the Right mouse button, select View, and then
Set View in the submenu that pops up. Set the x-axis to be between 30
and 40, and leave the y-axis at its defaults. Right-click in the same graph
once again, and select Crosshair. Now, by left-clicking on the curve in the
graph, a crosshair will appear, and the corresponding x and y values on the
curve will appear in the window title bar for that graph.
6) Use the methods described immediately above to collect a number
of points on the decaying exponential. Use this data to estimate
the time constant of this axon.
In the RunControl window, edit the Tstop parameter to be 30 ms (third
box from the bottom). Run the simulation again. The graph titled Space
Plot shows axon voltage in mV (y-axis) as a function of distance along the
axon (x-axis, in microns).
7) Given that the stimulating electrode is at 25000 microns, use
methods described above to calculate the length constant of this
axon in centimeters.
8) Given that the stimulus is 50nA, what is the input resistance r
input
of this axon?
Close the simulation. Restart it to reinitialize all the graphs. Go to the
window containing the NEURON command line, and type axon.diam=20
(without the quotes) to set the diameter of the axon at 20 microns. Run the
simulation again. Use the same techniques described above to answer the
following questions.
9) Is the time constant greater, less than, or unchanged from its
original value?
10) Is the input resistance greater, less than, or unchanged from its
original value?
11) Is the length constant greater, less than, or unchanged from its
original value?
12) What was the diameter of the original axon, prior to changing
the diameter to 20 microns?
