Chapter 7. Programming Simulations

7.3 MECHANISM ASSIGNMENTS.

A. By Program

Mechanisms are invoked and assigned as shown in the program below.

Box 3. mechanisms.hoc


     soma	{ insert hh	gnabar_hh = .5 gkbar_hh = .5 gl_hh = .5
		 insert NaCax}
		// inserts into soma Hodgkin & Huxley channels
 		// (but sets channel density at 0.5 the normal HH value)
		// and inserts the sodium-calcium exchange mechanism

     axon	 insert hh
		// inserts Hodgkin & Huxley channels into axon 
		// with standard channel densities

For more detailed and controlled assignment of channels in a complex structure, an EXAMPLE is available where the assignments are carried out by the procedure membrane().
A. By Graphical Interface

By Pressing the "Distributed Mechanisms" button on the NEURON Main Panel panel, selecting "Managers" then "Inserter" to bring up the "Insert browser" which shows the soma as the accessed section in red.
When a new section is selected (here dendrite[0]) , it is high lighted in red and the soma color is changed to black. Acceptance of this selection brings up the "Inserter" list for selection of mechanisms to be inserted in the newly selected section. This example is taken from the Single Compartment Simulator described in Chapter 6.

As soon as the mechanisms have been inserted, the default values of their parameters again can be viewed by pressing the "Distributed Mechanisms" button on the Main Menu Panel; this brings up the submenu panels as before. A double-click on the soma now brings up a panel listing the Hodgkin-Huxley set of parameters.

Any of these may be changed as follows:

a) Fill in a new value:place mouse cursor in the white space beside value button, fill in the desired value, and hit the "enter" key or click on the label. Immediately the value shows up in parameter panel with RED checkmark beside it.
Alternatively the current value may be changed by placing the cursor at its right end, writing a mathematical operation (e.g. current value*5; current value/2, current value+4), and hitting the "enter" key or clicking on the label; again the new value shows up in the parameter panel with a RED checkmark.
b)Toggle betweeen values: once a new value has been entered in this way, a click on flag box next to the value button will cause the value to toggle between the value in the field when the window was created and the last entered value.
c) Reset the parameter in the "hoc" interpreter: in the hoc intrepreter window, type in an expression for the desired parameter (e.g. "gnabar_hh = 0.6") & enter. Immediately this value shows up in parameter panel, again with RED checkmark beside it.
Reference potential in Hodgkin-Huxley equations
Because they had no absolute voltage,in their equations Hodgkin and Huxley gave the membrane potential with respect to an intracellular resting level (v=0mV). With the advent of microelectrodes, membrane potentials could be measured with respect to an extracellular ground and this is the convention of choice today. For ease of comparison with experimental observations using this convention, the reference point for the HH equations in NEURON has been translated from the original HH convention to today's conventional extracellular reference as ground. This required the choice of an OFFSET voltage; -65mv was selected to give reasonable fit to in vivo intracellular measurements of resting and action potentials in squid axons by Cole and Moore 1960a.
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