Use the SimBiology app to create a model in which ligand L and receptor R
species form receptor-ligand complexes through reversible binding reactions. These
reactions are defined using mass action kinetics by , where kon and
koff are forward and reverse rate
C are the
concentrations of ligand, receptor, and receptor-ligand complex respectively.
Open the app by typing
simbiology at the command line or clicking
the app icon on the Apps tab. Then on the
Home tab of the app, select Add
Model > Create New Blank Model. Enter a
name for the model, such as
m1. Open the Diagram view by selecting
Open > Diagram.
Drag and drop three species blocks and one reaction block into the compartment. Rename the species and
compartment by double-clicking the default text. For instance, change
To connect the species to the reaction, press and hold the Ctrl key (onWindows® and Linux® systems) or the Option key (on Macintosh® systems), click the species block, and drag the line.
Define the reaction properties:
Double-click the reaction block to open the Block Property Editor.
In the Settings tab, select Reversible.
Set KineticLaw to MassAction.
For Forward Rate Parameter, set the name to
kon and the value to
0.05. Set the
liter/nanomole/hour. For Reverse
Rate Parameter, set the name to
and the value to
0.1 with the unit
Update the initial amounts of
10 with the unit
Open the SimBiology Model Analyzer app by typing
simBiologyModelAnalyzer at the command line or clicking the app
icon from the Home tab.
To simulate this reaction, select Program > Simulate Model in the Project section from the Home tab. Set the Stop Time to 20 seconds in the Simulation step since the model reaches a saturated state after that. Click Run from the Home tab.
Running the program plots the results in the Plot1 tab. The plot shows the simulated responses in different colors. The program stores the simulation results in the LastRun folder of the program.