Create Model of Receptor-Ligand Kinetics

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

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 dCdt=konLRkoffC, where kon and koff are forward and reverse rate constants. L, R, and 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 unnamed to cell.

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 unit to liter/nanomole/hour. For Reverse Rate Parameter, set the name to koff and the value to 0.1 with the unit 1/hour.

  • Update the initial amounts of L to 5 and R to 10 with the unit nanomole/liter.

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.

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