Create Model of Receptor-Ligand Kinetics

This example shows how to create and simulate a simple model of receptor-ligand kinetics using the SimBiology Model Builder and SimBiology Model Analyzer apps.

In this model, ligand L and receptor R species form receptor-ligand complexes through reversible binding reactions. These reactions are defined using mass action kinetics by $$\frac{dC}{dt}=k_f\cdot L\cdot R-k_r\cdot C$$, where k_f and k_r are forward and reverse rate constants. L, R, and C are the concentrations of the ligand, receptor, and receptor-ligand complex, respectively.

Open Model Builder App

Click the SimBiology Model Builder icon on the Apps tab or enter simBiologyModelBuilder at the command line.

Build Model

1. On the Home tab of the app, select Model > Create New Blank Model. Enter m1 as the name for the model. The app creates an empty compartment unnamed and displays the compartment on the Diagram tab.

2. Drag and drop three species blocks and one reaction block into the compartment. Optionally, you can rename the species and compartment by double-clicking the default names. For instance, change unnamed to cell.

   

3. To connect the species to the reaction, press and hold the Ctrl key (on Windows^® and Linux^®) or the Option key (on macOS), click the species block, and drag the line.

   

4. Click the reaction block to see its properties in the Property Editor pane. Set the following parameters.

   • Select Reversible > true.

   • In the States table, update the values of L to 5 and R to 10. Set the units of the L, R, and C species to nanomole/liter.

   • Set the value of the forward rate parameter k_f to 0.05. Set the unit to liter/nanomole/hour.

   • Set the value of the reverse rate parameter k_r to 0.1 with the unit 1/hour.

   

5. Click the cell compartment in the diagram. In the Property Editor pane, set its Units to liter.

Simulate Model

1. On the Home tab, click the Model Analyzer icon to open the SimBiology Model Analyzer app.

2. In the Model Analyzer app, select Program > Simulate Model on the Home tab. The Program1 tab opens.

3. In the Simulation step of the program, set the Stop Time to 20 seconds because the model reaches a saturated state after that.

   

4. Click Run from the Home tab.

5. 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.