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Ion channels following a Hodgkin-Huxley like formalism. The equilibrium open fraction and time constants are shown for each gate. They may be manipulated by dragging the curves, or with the corresponding sliders. Any number of gates may occur on a channel, and each gate can be raised to small integer powers to indicate identical serial copies.
To add a gate click the gate icon in the upper left. To remove one, click the center point on the gate and drag the gate up or down off the window. To reverse the slope of a gate, use the lower point on its activation curve and tip it over.
The gate power is set with the point just below the midpoint on each gate. When it is greater than 1 a second line is drawn showing the effective open fraction of the gate raised to that power. The ion to which this channel is permeant is selected in the top right - the context of the channel object defines the available ions.
The gating equation is taken from Borg-Graham and corresponds to a gating particle of effective charge (charge times the fraction of the field it moves through) z, moving between two wells which are of the same energy at a membrane potential V-half. The peak of the activation barrier is a fraction gamma of the way between the two wells. The rate is set through its reciprocals, the characteristic transition time tau-x, and saturates at some peak rate, the reciprocal of tau-m.
The HHChannel object is a special case of the more general KSChannel object which allows an equally compact and efficient representation of channels with HH kinetics as well as a wide variety of other channels. Most Catacomb objects involving ion channels use the KSChannel model rather than HHChannel.