# SAfSB Chapter 2

## Example 2.8 (Standard Modification)

The standard modification model is comprised of the two reactions U → W and W → U. Both reactions have mass action rate laws with propensity factors of 2. Open the file `examples/cain/SAfSB/Chapter2/Example-2_08-StdMod.xml`. In the recorder panel select all species and all reactions. Then click the launch button in the launcher panel to numerically solve the system of ordinary differential equations. Below we plot the species populations and the reaction rates. For the latter we use the Binned Reactions radio button in the plot configuration window.

## Example 2.9 (Heterodimerization)

Open the file `examples/cain/SAfSB/Chapter2/Example-2_09-HetDim.xml`. Below we plot the species populations and the reaction rates. (Note that because X1 and X2 have the same concentrations, we plot them with different line styles so that both lines are visible.)

## Example 2.10 (Lotka-Volterra)

Open the file `examples/cain/SAfSB/Chapter2/Example-2_10-LotVol.xml`. Below we plot the species populations and the reaction rates.

## Example 2.11 (Enzyme Kinetic Reaction)

Open the file `examples/cain/SAfSB/Chapter2/Example-2_11-EnzKin.xml`. Below we plot the species populations and the reaction rates. For the latter, we change the legend labels to the textual representation of the reactions in the plot configuration window.

## Example 2.12 (Schlogl)

Open the file `examples/cain/SAfSB/Chapter2/Example-2_12-Schlogl.xml`. Note that Cain does not support the concept of buffered species. Thus A and B are represented as parameters. Their population values are explicitly included in the reaction propensities. Below we plot the species populations and the reaction rates.

## Example 2.15 (Gene Regulation)

Open the file `examples/cain/SAfSB/Chapter2/Example-2_15-GeneReg.xml`. Below we plot the species populations and the reaction rates.