models/chapter3

buffering	Calcium buffering. The reaction scheme shows Ca binding with a buffer, B, to produce the bound complex CaB. The graph to the upper left shows how the concentrations evolve, during a series of calcium injections, (upper right). Change the forward and reverse rates of the buffering reaction to see how the calcium concentration behaves. To eliminate buffering altogether, hold the blue dot at the center of the reaction arrow with the right mouse button and drag it away. Dragging it back will reconnect it. To change the calcium injection, drag the point at the top left of the series of square pulese, or at the bottom right. All the other points are scaled to these two for the example because it is so easy to make a mess of the profile. To make your own from scratch, select edit from the conc profile menu. This brings up a window for editing profiles. Select new default from the top left menu to start making a new one. To apply the new profile, select it in the conc profile menu on the reaction scheme.
RapidExcess	The buffering scheme contains two reaction arrows. One has relatively slow kinetics, the other fast kinetics. Remove the active one (hold the middle with the right mouse button and drag) and replace it with the spare one. To compare the results directly use the keep in background option under the data menu for one and then switch them over. For the fast kinetics, the calcium concentration rises smoothly and doesn't fall back: in effect injected calcium comes to the new equilibrium immediately. This is equivalent to the rapid buffering approximation. Note that although the transients are different, the final concentrations are the same. Now use the slow kinetics arrow, and click the buffer pool. In the left hand panel, switch the buffering from free to C-0. This means that the buffer itself is buffered, with its concentration fixed at its initial value. This corresponds to the excess buffer approximation. The calcium profile agrees well for the first couple of pulses, but then diverges when in the full calculation the buffer begins to get used up.
BufferedDomain	Calcium domain formation. The buffering ReactionScheme is shown at the bottom right. To change the diffusion constants of Calcium, the buffer or the bound complex, click on the coresponding node and set its D-diff value. The model has a 5ms injection of calcium at the center of a sphere. The resulting concentration history is shown color coded as a function of distance from the injection site (X) and time (Y). To examine details of the profile, use the little white arrows (more can be torn off the blue one at the end). For each white arrow a horizontal (constant time) or vertical(constant radius) slice is exported to the graph on the left. The checkboxes on the right select which of the available variables are exported. Those on the left select which are shown in the image. Controls for the discretization in space and time are at the far left. These are set relatively coarse so the model doesn't run too slowly. The number of points can be increased or the timestep reduced to get better resolution. To see the effect of buffering on the size of the domain, disconnect the arrow entirely (drag with right mouse) in the reaction scheme window. How does changing the rate of the reaction or the mobilities of the various species affect the extent of the domain? This is the injection profile in the domain example. Use the top left control point to change its amplitude and the top right one to change the duration.