This example shows how to create and simulate a simple model of receptor-ligand kinetics using the SimBiology Desktop.
In this model, ligand
L and receptor
species form receptor-ligand complexes through reversible binding reactions.
Using the mass action kinetics, the kinetic rate equation for the rate of change
in concentration of receptor-ligand complex can be defined as , where kon and
koff are forward and reverse
C are the concentrations of ligand, receptor, and
receptor-ligand complex respectively. The objective of this simulation is to
find the concentrations of all three species (
C) as the reaction progresses
given initial amounts of species and rate constants.
Open the SimBiology® desktop by typing
simbiology in the MATLAB® Command Window or clicking SimBiology
on the Apps tab.
On the Home tab, select Add
Model > Create New Blank Model.
Name the model as
m1 when prompted.
Select Open > Diagram to open the diagram view.
Rename the compartment to
cell by double-clicking the text
Drag and drop three species blocks and one reaction block inside the
Rename the species to
C as follows.
To connect the ligand species block to the reaction block, press and hold the
Ctrl key (Windows® and Linux®) or the Option key (Macintosh®), click the
L species block, and drag the line to
reaction_1. Similarly connect
reaction_1 properties to set the reaction as a
reversible reaction, select mass action as kinetic law, and define the forward
and reverse rate parameters:
reaction_1 block to open the
Reaction Properties dialog box.
On the Settings tab, select Reversible.
From KineticLaw drop-down list, select MassAction.
Under Quantities Used by Reaction,
kon as the name and
2.0E6 as the value for Forward
Rate Parameter, and
1E-4 for Reverse Rate
Update the initial amounts of reactant species by entering
L species values respectively. Click
On the Model tab, select Add Task > Simulate model. This opens a new window called Task Editor, where you can edit and run the task. Given the previous initial amounts and rate parameters, the reaction reaches a saturated state after 300 seconds. Therefore, set the simulation stop time to 300 seconds instead of 10 seconds, which is the default stop time. To do so, expand the Task Stop Time section, select Use a Stop Time specific to this task only, and enter 300.
To simulate the model, click the Run button.
Once the simulation is finished, the Live Plots section shows the States versus Time plot for each species.