Time derivative of the membrane potential in NMODL

NMODL and the Channel Builder.
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daniel.krieg

Time derivative of the membrane potential in NMODL

Post by daniel.krieg » Thu Dec 09, 2010 10:40 am

Hi,
is there a simple way of accessing the time derivative of membrane potential v' in a mod file?
I want to do something like this

Code: Select all

BREAKPOINT {
	SOLVE state METHOD cnexp
	i = g*(v - e)
}

DERIVATIVE state {
	g' = -g/tau
	w' = v'*i
}
Btw: is it a problem if a state derivative depends on another state? Do I have to use a different integration method? I thought I've read something like this somewhere...

Thanks
Daniel

ted
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Re: Time derivative of the membrane potential in NMODL

Post by ted » Fri Dec 10, 2010 12:07 am

Tell me if I understand correctly--you want a learning rule that adjusts synaptic weight according to the product of synaptic current and local dv/dt?

daniel.krieg

Re: Time derivative of the membrane potential in NMODL

Post by daniel.krieg » Fri Dec 10, 2010 4:07 am

Right

ted
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Re: Time derivative of the membrane potential in NMODL

Post by ted » Fri Dec 10, 2010 10:14 am

Every section has built-in range variables that include i_cap and cm--compute dvdt from those.
In the NEURON block declare
RANGE dvdt
In the ASSIGNED block declare
i_cap (mA/cm2)
cm (micorfarad/cm2)
dvdt (mV/ms)
As the final statement in the INITIAL block declare
dvdt = (1000)*i_cap/cm
and whenever you need the current value of dvdt, calculate it as
dvdt = (1000)*i_cap/cm

Further considerations:

If your synaptic mechanism's learning rule depends only on dvdt at the instant of synaptic activation, you should compute the new w in the NET_RECEIVE block. This will allow stream-specific plasticity, i.e. regardless of how many NetCons converge on a single instance of your synaptic mechanism, the weight associated with each afferent event stream will depend only on the history of that stream.

If you have some other conceptual model of the relationship between synaptic weight and local dvdt, a very different implementation may be required. If this is the case, perhaps we should have a private discussion via email or Skype so that I can properly advise you how to carry that out.

daniel.krieg

Re: Time derivative of the membrane potential in NMODL

Post by daniel.krieg » Fri Dec 10, 2010 12:45 pm

dvdt is nan, because both i_cap and cm are zero all the time, which i checked with a printf.
No matter if I do it in the BREAKPOINT or NET_RECEIVE block.
Running modlunit was ok.

ted
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Re: Time derivative of the membrane potential in NMODL

Post by ted » Fri Dec 10, 2010 8:32 pm

So neither cm nor i_cap is automatically known to code within an NMODL-defined mechanism. No problem. Only needs a few minor additions to what I have already recommended.

Add these declarations to the NEURON block of the NMODL code for your synaptic mechanism:
RANGE cm : set equal to cm in relevant segment
POINTER icap : link to i_cap in relevant segment

All that remains is to use the necessary hoc statements to assign a value to cm and link icap to i_cap in the segment to which the synaptic mechanism is attached. So consider the completely arbitrary example of a synaptic mechanism that is an instance of the class Whatever (i.e. the mechanism's NEURON block declares POINT_PROCESS Whatever) attached to the middle of a section called erewhon:

Code: Select all

objref syn
erewhon {
  syn = new Whatever(0.5)
  syn.cm = cm(0.5)
  setpointer syn.icap, i_cap(0.5)
}
And you're off to the races.

daniel.krieg

Re: Time derivative of the membrane potential in NMODL

Post by daniel.krieg » Sun Mar 27, 2011 11:38 am

Hi Ted,

thanks for your help. so far it work great. But now I was trying to speed up the simulations by using variable time step with cvode. But i_cap is fluctuating pretty much when using this and also dvdt is behaving strange because it is not any longer a linearly scaled version of i_cap. So I tried to set the tolerance with the atolscale method but this didn't work.

Code: Select all

syn_sec.sec tol = cvode.atolscale(&i_cap(0.5),0.01)
/usr/local/nrn/x86_64/bin/nrniv: i_cap is not a STATE
Is there another way to do this?

ted
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Re: Time derivative of the membrane potential in NMODL

Post by ted » Sun Mar 27, 2011 12:08 pm

I don't know, but there are other ways to speed up simulations. On a multicore PC or Mac it is often possible to get significant speedups without requing any revisions to your hoc code (some mod files may need changing to make them threadsafe) by using multithreaded simulations--see
http://www.neuron.yale.edu/phpBB/viewto ... =22&t=1476

daniel.krieg

Re: Time derivative of the membrane potential in NMODL

Post by daniel.krieg » Sun Mar 27, 2011 12:48 pm

Thanks for your quick response. I was just about to edit my post because I found out what the problem seems to be. My pointprocess which has a pointer to i_cap also inserts a NONSPECIFIC_CURRENT (which then influences i_cap).

So, just using a different mechansim to insert the current resolves the problem.

ted
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Re: Time derivative of the membrane potential in NMODL

Post by ted » Sun Mar 27, 2011 2:37 pm

Great, finding one's own bug can be very hard to do. Glad it works now.

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Re: Time derivative of the membrane potential in NMODL

Post by hines » Mon Mar 28, 2011 9:43 am

It would be a good idea to do a bit of accuracy testing by decreasing dt for the fixed step method
and decreasing tolerance for cvode. Neither method is designed for the case where dv/dt appears on the
right hand side of the y' = f(y) equations inside f. For the fixed step method, one expects 1st order
accuracy since i_cap is calculated just before solving the equations in state blocks. i.e i_cap is evaluated using
v(t+dt)-v(t)/dt and that value is the one you are using as a constant for the integration interval t-dt/2 to t+dt/2.
It your case it is fine to use cnexp since v' and i are constants during the integration interval.

For cvode it would be nice to be able to use v' directly since it just so happens that the evaluation of
y' = f(y) does the v's prior to the nmodl states. Therefore, in principle, one could reach into the y' vector when
it is time to evaluate w'. However, also in principle, cvode could slow down since there is no provision in the
jacobian for terms involving y' on the right hand side. I see that when cvode is used, i_cap is evaluated after the
nmodl ode's y' are evaluated. So you are using the value from the previous evaluation of f(y).
You might experiment with editing nrn/src/nrncvode/occvode.cpp . Notice the two fragments having the lines:

do_ode(nt);
// divide by cm and compute capacity current
nrn_div_capacity(nt, z.cmlcap_->ml);

just reverse the do_ode and nrn_div_capacity statements.
Again, though, this does not improve the jacobian.

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