na3 Mechanism parameter

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lb5999
Posts: 56
Joined: Mon Oct 11, 2010 9:12 am

na3 Mechanism parameter

Post by lb5999 » Tue Sep 27, 2011 11:40 am

Hi Ted,

I should start by saying thank you for your reply to my previous thread regarding serial computing in BlueCrystal (Bristol's supercomputer).. we pretty much have it working, and its awesome! More importantly, it is very good to hear from you too!

I have been studying the mechanism na3.mod, as I used a slightly modified version of it in my neurone model. Here is the senselab link for the sodium mechanism:

http://senselab.med.yale.edu/modeldb/Sh ... %5Cna3.mod

You will notice that one of the gating variables is "s", and that the steady-state for this gating variable is defined by:

Code: Select all

	c=alpv(vm)
        sinf = c+a2*(1-c)
Now, I can't for the life of me find out what "a2" is; I have scoured the na3.mod file and all I can find is "ar2" which takes the value 1... equating a2=ar2 would give a steady-state value of 1, for any membrane potential, which obviously gives silly s-dynamics and messes with the dynamics of my XPP file! So I can only assume that a2 is something different, but I don't know what.

Am I missing something here? I can only assume I am being an invalid, and I would be really grateful if you could point out why.

Kindest regards,

Linford

ted
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Location: Yale University School of Medicine
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Re: na3 Mechanism parameter

Post by ted » Wed Sep 28, 2011 10:12 am

Here's the answer:

Code: Select all

PROCEDURE trates(vm,a2,sh2) {  
 . . .
        sinf = c+a2*(1-c)
that is, a2 is the 2nd argument when trates() is called.

When this kind of thing happens to me, it usually means I have been staring at source code so long that I can't see it. Getting out into the sun/fog/rain for an hour or so usually helps.

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