Using Ca2+ currents in point and distributed processes

NMODL and the Channel Builder.
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hkur

Using Ca2+ currents in point and distributed processes

Post by hkur » Thu Mar 25, 2010 8:44 am

Hello,
I want to add a synapse as a point process with an NMDA receptors in which
Ca2+ current is expressed by ica (nA).
But I also want to use a distributed process for a voltage-gated Ca2+ conductance
in which Ca2+ current is expressed by ica (mA/cm2), simultaneously.
Is it possible?

ted
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Re: Using Ca2+ currents in point and distributed processes

Post by ted » Thu Mar 25, 2010 2:13 pm

Yes. Have you read chapters 5 and 6 of The NEURON Book? Or at least
Hines, M.L. and Carnevale, N.T. The NEURON simulation environment. Neural Computation 9:1179-1209, 1997
(available from http://www.neuron.yale.edu/neuron/nrnpubs).

hkur

Re: Using Ca2+ currents in point and distributed processes

Post by hkur » Fri Mar 26, 2010 5:03 am

Sorry.
I should explain my problem clearly.
I would like to model a dynamics of calcium concentration.
So, I use a NMODL file for dynamics of Ca2+ concentration in which
'USEION ca READ ica, cai WRITE cai'
is inserted.
Similary, 'USEION ca READ cai WRITE ica' and 'USEION ca READ eca WRITE ica' are used
in the files for NMDA synapse and voltage-gated Ca2+ channel, respectively.
Because the unit of ica in the file for Ca2+ dynamics is mA/cm2 and the same as the one in the file for voltage-gated Ca2+ channel,
simultaneous usage of the mechanis for Ca2+ dynamics and voltage-gated Ca2+ channel work all right.
However, if I add the mechanism for NMDA synapse in which the unit of ica is nA and differs from the ones in the other mechanisms,
dose it work?

ted
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Re: Using Ca2+ currents in point and distributed processes

Post by ted » Fri Mar 26, 2010 10:59 am

Yes. NEURON has distributed (density) mechanisms and point mechanisms ("point processes") precisely for the purpose of enabling the construction of models that may contain representations of any combination of distributed and localized transmembrane currents and ion fluxes. Currents generated by density mechanisms are specified in units of mA/cm2, and currents generated by point mechanisms are specified in units of nA.

menica
Posts: 67
Joined: Wed Sep 02, 2015 11:02 am

Re: Using Ca2+ currents in point and distributed processes

Post by menica » Tue Dec 05, 2017 7:21 am

hi,
I have a similar problem.
I have a chloride leak current expressed in mA/cm2 and an accumulation mechanisms.
I had a gabaa synapse point process which writes a ligand-gated chloride current in nA. I would like to counterbalance with the cl pump the activity of the leak and cl current generated by gabaa.
Is my accumulation mechanisms considering the icl generated by all the density and point process mechanism?
When I look at the cl current generated by the gabaa, is it automatically converted by neuron in mA/cm2 or I need to convert it from nA?


I did this modification to the gaba point process:

Code: Select all

TITLE is :Inhibitory synapse in the pyramidal cell

NEURON {	
	POINT_PROCESS is
        RANGE tau1, tau2, icl,i, g
	USEION cl READ ecl WRITE icl VALENCE -1	   		   
	POINTER e
}

UNITS{
PI		= (pi) (1)
}

PARAMETER {
	tau1 = 2   (ms)
	tau2 = 6   (ms)
}

ASSIGNED {
	v    (mV)
	e    (mV)
	ecl  (mV)
i (nA)
	icl  (mA/cm2)
  g (microsiemens)
  factor
}

STATE {
   A (microsiemens)
   B (microsiemens)
}

INITIAL {
 LOCAL tp
 if (tau1/tau2 > .9999) {
     tau1 = .9999*tau2
 }
 A = 0
 B = 0
 tp = (tau1*tau2)/(tau2 - tau1) * log(tau2/tau1)
 factor = -exp(-tp/tau1) + exp(-tp/tau2)
 factor = 1/factor
}

BREAKPOINT {
 SOLVE state METHOD cnexp
 g = B - A
i= g*(v - e)
 icl = i*0.000001/(PI*diam*diam)
}

DERIVATIVE state {
 A' = -A/tau1
 B' = -B/tau2
}

 NET_RECEIVE(weight (microsiemens)) {
 A = A + weight*factor
 B = B + weight*factor
} 
is it ok?

ted
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Re: Using Ca2+ currents in point and distributed processes

Post by ted » Tue Dec 05, 2017 11:05 am

I have a chloride leak current expressed in mA/cm2 and an accumulation mechanisms.
An accumulation mechanism for what? Chloride?
I had a gabaa synapse point process which writes a ligand-gated chloride current in nA. I would like to counterbalance with the cl pump
Just guessing here--your accumulation mechanism is a chloride accumulation mechanism, and it includes a chloride pump?
Is my accumulation mechanisms considering the icl generated by all the density and point process mechanism . . .
When I look at the cl current generated by the gabaa, is it automatically converted by neuron in mA/cm2 or I need to convert it from nA? . . .
I did this modification to the gaba point process . . . is it ok?
Have you checked this mod file with modlunit? This is a point process, so the units of the current it WRITEs must be nA. There is absolutely no need to do this calculation
icl = i*0.000001/(PI*diam*diam)
NEURON will take care of that for you--it will automatically add up all of chloride currents produced by density mechanisms and point processes, and it takes surface area into account. So just declare icl to be in nA and replace
icl = i*0.000001/(PI*diam*diam)
with
icl = i
and your synaptic mechanism will be OK as far as chloride current is concerned.

But what's this e variable that is a POINTER? Why bother to READ ecl but then ignore ecl?

menica
Posts: 67
Joined: Wed Sep 02, 2015 11:02 am

Re: Using Ca2+ currents in point and distributed processes

Post by menica » Tue Dec 05, 2017 3:29 pm

Dear Ted,
Thanks.
Yes I have a Cl accumulation mechanism and a simple pump mechanism which writes the current passing through the Cl pump icl_pump=const*(cli-cli0).
Do you mean that the icl I am using in the accumulation mechanism takes into account the icl of the point process because neuron changes automatically the units from nA to mA/cm2?
How can I save and plot the icl written by the point process in mA/cm2 ?
I mean, how can I check this?
At the moment I am calculating the area under the currents curves. I need to check that the area under the Cl pump current is equal to the sum of the area under the leak and ligand-gated chloride current. I got a discrepancy in this values.

I modified the synaptic mechanism...I eliminate the READ ecl, and I am not defining anymore the units of icl as mA/cm2:

Code: Select all

NEURON {	
	POINT_PROCESS is
        RANGE tau1, tau2,  g,icl
	USEION cl WRITE icl VALENCE -1	   		   
	POINTER e
}


PARAMETER {
	tau1 = 2   (ms)
	tau2 = 6   (ms)
}

ASSIGNED {
	v    (mV)
	e    (mV)
	ecl  (mV)
	icl  (nanoamp)
  g (microsiemens)
  factor
}

STATE {
   A (microsiemens)
   B (microsiemens)
}

INITIAL {
 LOCAL tp
 if (tau1/tau2 > .9999) {
     tau1 = .9999*tau2
 }
 A = 0
 B = 0
 tp = (tau1*tau2)/(tau2 - tau1) * log(tau2/tau1)
 factor = -exp(-tp/tau1) + exp(-tp/tau2)
 factor = 1/factor
}

BREAKPOINT {
 SOLVE state METHOD cnexp
 g = B - A
icl= g*(v - e)
}

DERIVATIVE state {
 A' = -A/tau1
 B' = -B/tau2
}

 NET_RECEIVE(weight (microsiemens)) {
 A = A + weight*factor
 B = B + weight*factor
} 

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