sodium ion accumulation without diffusion

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ipv1313
Posts: 5
Joined: Wed Nov 09, 2022 3:51 am
Location: Indian Institute of Technology Delhi

sodium ion accumulation without diffusion

Post by ipv1313 »

Hello all.,

I am a complete beginner to NEURON. I am trying to implement a cell with voltage-gated sodium, calcium, and potassium channels. I have inserted pumps and now focussing on managing ion diffusion across the membrane. I came across this mechanism on modelDB. https://senselab.med.yale.edu/ModelDB/s ... mod#tabs-2

Code: Select all

TITLE Sodium ion accumulation without diffusion

NEURON {
	SUFFIX nabalan
	USEION na READ ina WRITE nai
	RANGE nainit,f
}

UNITS {
	(mM) = (milli/liter)
	(um) = (micron)
	FARADAY = (faraday) (coulomb)
	PI = (pi) (1)
}

PARAMETER {
        nainit = 0.8 (mM) 
        f = 2.00
}

ASSIGNED {
	ina (milliamp/cm2)
	diam (um)
}

STATE {
	nai (mM) <1e-4>
}

BREAKPOINT {
	SOLVE state METHOD sparse
}

INITIAL{
        nai=nainit
}

KINETIC state {
	COMPARTMENT PI*diam*diam/4 {nai}
	~ nai << (-f*ina*PI*diam*(1e4)/(FARADAY))

What is 'f' here and how can I decide the initial concentration here, when the initial sodium internal concentration is 10 mM?
ted
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Location: Yale University School of Medicine
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Re: sodium ion accumulation without diffusion

Post by ted »

Beats me. Why does the model initialize nai to 0.8 mM? What do the model's authors say about these oddities?
ted
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Joined: Wed May 18, 2005 4:50 pm
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Re: sodium ion accumulation without diffusion

Post by ted »

In case anyone else is curious, here's a little gift for the holidays.

The source code that prompted ipv1313's questions is associated with the paper

Kuznetsova AY, Huertas MA, Kuznetsov AS, Paladini CA, Canavier CC (2010)
Regulation of firing frequency in a computational model of a midbrain dopaminergic neuron.
J Comput Neurosci 28:389-403

which is available at no charge from the Journal of Neurophysiology's web site. Neither the model's source code nor this paper says anything about the parameter f. Source code for another paper from the same lab used a rather similar mechanism to describe intracellular sodium accumulation, but that mod file assigned a value of 1 to f--again without discussion of the parameter's significance.

My guess is that the authors tacitly assume that the volume of distribution of intracellular sodium is less than the intracellular volume--that sodium is restricted to some fraction of intracellular volume. That fraction would range from 0 to 1, and would be numerically equal to 1/f.

The rationale for initializing nai to 0.8 mM is not discussed in these papers.

My advice to those who might want to reuse this particular mechanism: don't alter the NMDOL code. Just use hoc or Python statements to assign your desired values to nainit and f. These parameters are RANGE variables, so they can have different values in each segment if you like.
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