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
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 rate constants,
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
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
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
block, and drag the line to
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:
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
the value for Forward Rate Parameter, and
1E-4 for Reverse
Update the initial amounts of reactant species by entering
values respectively. Click Close.
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.