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After the firing of a neuron, the sodium and potassium concentration differences vanish.

It requires some time for cell to actively transport the ions in and out to re-establish the balance.

Does the HH model incorporate this effect?

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Welcome to the site. Please don't simultaneously cross-post on multiple stack exchange sites. biology.stackexchange.com/questions/6944/… –  Jeromy Anglim Jan 28 '13 at 3:30
    
The concentration differences do not vanish! An action potential requires extremely small ion fluxes, and thus the concentrations of sodium and potassium ions are mostly unaffected. In very small cells, with continuous activity, the internal concentration of ions can shift slightly. This is not a factor in the HH experiment, where the volumes both internally and externally are large and an infinite reservoir of ions is a reasonable approximation. –  yamad Jan 30 '13 at 19:24

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up vote 4 down vote accepted

HH doesn't "count ions", it pretends the reservoirs are infinite.

Specifically, the "reversal potential" for each ion species is a constant. This constant is calculated from the Goldman Hodgkins Katz equation which uses the concentrations on either side of the membrane to calculate the reversal potential given the concentration gradient.

We could hypothetically keep this a function of the individual species concentrations and add a current to the model to represent the pump, but you would gain little in predictive power and much in computational complexity.

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I didn't remember enough (and didn't have a chance to look it up), but some of the later models have a refractory constant, I think? –  Chuck Sherrington Jan 27 '13 at 21:41
    
If we're not crossing terminologies here, the refractory period comes from a variable (the inactivation curve described by h) and refers to the time-delayed inactivation of individual ion species channels after being activated. It has no direct dependence on the ion concentration –  Keegan Keplinger Jan 27 '13 at 22:18

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