Channels based on kinetic schemes, KSChannel, are defined by the possible transitions between different states of the channel. The state diagram can be constructed by tearing off states or transitions and sticking them together. The transitions rates may be constant or depend on the voltage, or agent concentrations, and can be controlled with the corresponding voltage dependence or binding curves.
The state diagram is constructed by dragging states and transitions from the top and sticking them together. Transitions stick to states, but not the converse. A transition can be lifted off with the right mouse button. See the CcmbNetEditor for general properties of node-and-link components.
Each state has its own relative conductance which appears near the middle on the right when the state is highlighted and can be set with the slider. State colors can be set from the menu on the state button when a state is highlighted.
There are five types of transitions, from the left in the top of the main window:
1) time and voltage dependent, with the expression parameterized by the forward and reverse rates at zero membrane potential, effective charge, asymmetry and saturation. This provides a smooth transition between voltage dependent and independent rates.
2) Time dependent only, defined by forward and reverse lifetimes for this transition (nothing to do with lifetimes of the channel).
3) Voltage dependent, following Borg-Graham, parameterized as the effective gating 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.
4) Agent dependent, indicated by a + sign above the binding transition. The rates are defined by the dissociation constant K-d and the off rate tau-r.
5) Multiplicative: the transition must contain a pointer to some other transition in the system and constant multipliers for the forward and reverse reaction.
Transition parameters can be set by dragging the corresponding curves in the lower graphs, or with the sliders. When values are changed with the curves, the sliders do not continuously update but will do so if you move the mouse over them. The transitions of types 1 and 3 are formally equivalent, except for z = 0 when 3 breaks down, and the lower two displays are identical. Indeed, internally, reactions specified as type 3 are converted to type 1.
A kinetic scheme may contain multiple gating complexes simply by defining disjoint blocks on the diagram. In this case, the relative conductance of the channel is the product of the relative conductances of all the complexes on it. Each state has a field Nserial which sets the number of identical repeats of the complex to which it belongs. It is sufficient to set Nserial for just one of the states on any complex to duplicate the whole complex.