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NRSC 500

Neuron Simulator




Neuron simulator set-up and running.

Tim Murphy Neuroscience 500 Demo 2000-09-28.
Copyright © 1999-2000 N. T. Carnevale and M. L. Hines

To set-up Neuron 4.3.1 on set-up file and follow instructions.  Get file from install CD or at website: http://neuron.yale.edu/

A single file setup.exe (almost 6 MB long) is required.  Save this file to an empty directory, then use the "Add/Remove Programs" item in MSWin's Control Panel to install or download five pkzipped files, each of which is small enough to fit on a 1.44 MB floppy disk.

Use typical set-up and install into the C:\NRN directory.  Neuron works best on Pentium level computers probably greater than 100 MHz.  After installing neuron remember to restart computer.

Double click on Neuron demo icon.  From Neuron demonstrations menu select a demo.  First select the patch: HH (Hodgkin Huxley).  To reduce congestion on the screen minimize Neuron command line menu.  Also change the temperature default to 22 °C.  Whenever changes are made (to parameters) one needs to click the box to the left of the value insuring that a red check mark is present.

To run the demo find the Run Control window and press Init and Run the second entry.  On the window termed V (voltage) a single action potential is apparent.  Click on the window called IV clamp electrode on I clamp.  Increase the delay in ms to better see baseline and remember to click on the left box so you see a red check.  In the window designated IV clamp electrode decrease the amplitude of the current pulse to 0.1 and 0.5 nA.  At each setting hit Init and Run again to see the effect.  If the action potential is now off the window go back to the run control window and change the duration of the simulation.  For example in each place where 5 ms appears substitute with 10 ms.  Make sure to check the boxes.

Now alter the amount of Na and K conductance.  In the tools menu select distributed mechanisms and then select viewers, shape name, soma.  Double-click on soma and menu will come up with parameters for the soma.  In that Menu go down and adjust gNaBAR the amount of Hodgkin-Huxley Na current.  Reduce the conductance and observe what happens to the excitability of the cell and the action potential amplitude.  Now try increasing the K conductance and decreasing K conductance.  What happens if K conductance is decreased by a factor of 5? What happens to the action potential in zero K conductance and varied Na conductance? Now try to adjust the leak conductance gL.  Try increasing the leak by a factor of 5.  What happens to excitability? In the soma parameters menu you can also adjust concentrations of permeant ions such as Na and K.  Try adjusting the capacitance of the cell, increase it by a factor of 5 and see what happens to excitability.  Now examine the Na and K currents directly.  Go to Neuron main menu select graph, current axes, and then right mouse-click on the window of the graph, select plot what, double-click on soma, scroll down until you find INa (0.5), double-click on it, click accept.  Now run the simulation.  If the peak is overshooting the range of the graph right mouse-click on the legend that says soma.INa and then scroll up to view and then over to view = plot and it will autoscale.  Follow the same procedure and graph the K current graph current axes.

Close Neuron and start another demo.  This one would be on demonstrating principles of synaptic transmission.  Choose stylized neuron.  This is a myelinated neuron with 3 synapses.  Click on Init and Run and observe action potentials being plotted at the soma and at the first node of Ranvier.  In this demo there are 3 synapses on dendrite of a myelinated neuron and in the simulation window designated synaptic parameters it is possible to adjust the location of the 3 different synapses as well as the delays between them.  Adjust these and examine what effect they have on action potential generation.

 


 

 

 

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