Chapter 4.  HOW TO APPROACH AND WRITE-UP THE SIMULATION EXERCISES

PLEASE PRINT OUT THESE PAGES FIRST AND THEN KEEP THE PRINTED TEXT BESIDE YOU AS A GUIDE WHEN YOU LOAD AND RUN "NEURON". THIS WILL SAVE YOU HAVING TO JUGGLE BETWEEN NEURON AND NETSCAPE WINDOWS ONCE YOU HAVE THE SIMULATION LOADED.

To begin working with this chapter you should have downloaded and installed Neuron, as described in Chapter 1 .

Philosophy Behind the Exercises
In creating these exercises, it is not my intention that you should point and click your way through a series of commands. Rather, I would like to encourage you to understand the experimental situation that is being simulated by Neuron and to use Neuron to test some hypotheses about the way that nerve cells work. The previous chapters should have provided you with enough basic information to use Neuron and to understand what is being simulated. More will be provided for specific exercises. If you have trouble later, read them again, ask your T/A or email me. So my intention is simply to ask you to test a hypothesis using a given model simulation. You must provide a written report describing what is being simulated, the method  by which the hypothesis can be tested, and what the outcome of the "experiments' are - in terms of copies of the graphical output of voltage, current etc., the parameters used to produce each graph and the conclusions drawn.


Example Exercise

Exercise:
Use the action potential simulation (as described in Chapter 1) to test the hypothesis that the action potential requires voltage-dependent sodium and potassium channels, as described by Hodgkin and Huxley, to be present in the neuronal membrane.

Report:

1. What is being simulated?
The action potential simulation describes the behavior of a small patch of neuronal membrane impaled by voltage and current electrodes. The membrane potential is recorded under current clamp conditions. The neuronal membrane contains either passive voltage-independent  (pas) channels only or Hodkin-Huxley type channels (hh).

2. Experiment(s)  performed to test the hypothesis.
With the hh channels checked in the Insert/Remove channels Window:
  [Remember that if you want to illustrate what you did, you can copy any Window into WordPad by pressing Alt-Prtsc when the Window is active and then pasting it into WordPad (which can be activated from  the Start>Programs>Accessories menu)]
 
 

The response to a stimulating current pulse of amplitude 90 nA, duration 2 ms consisted of a single action potential, as shown in the plot of membrane potential (mV) vs time (ms), below:

With the pas channels inserted and the hh channels removed:

The membrane's response to the same simulating current was:

 

3. Conclusion
The hh channels are necessary to produce an action potential.

Now try the exercises in Chapter 5.