Variable Rate Constants

In this tutorial, you will learn how to use a rate constant that varies with respect to time.

Create Variable Rate Constant Text File

Using any text editor, create a new file called rate_constant.txt. Add the following text in the file:

0      0
5E-4   1E4

The first column is the time (seconds), and the second column is the rate constant at that time. The units for the reaction rate are the same as used earlier in the Reactions section.

The example shown above is a very simple case where the reaction only changes once. You could just as well have it change every time step, like this:

0      0
1E-6   1.0E5
2E-6   1.1E5
3E-6   1.2E5
...

Save the file and quit.

Set Project Directory

After you start Blender, save the file (and set the project directory) by hitting Ctrl-s, typing ~/mcell_tutorial/var_rate_constant (or C:\mcell_tutorial\var_rate_constant on Windows) into the directory field, var_rate_constant.blend into the file name field, and hit the Save As Blender File button.

Set Project Parameters

Set the following parameters:

  • Create a Cube and add it to the Model Objects list.

  • Create a volume molecule called vol1 with a diffusion constant of 1e-6.

    _images/defined_molecules1.png
  • Create a release site with the following properties:

    • Set the Site Name to vol1_rel.
    • Set the Molecule to vol1.
    • Set the Release/Shape to Object/Region.
    • Set the Object/Region to Cube.
    • Set the Quantity to Release to 1000.
    _images/molecule_placement1.png

Create Reaction with Variable Rate Constant

  • Hit the Reactions button.
  • Hit the + button.
  • Set Reactants to vol1.
  • Set Products to NULL.
  • Click the Enable Variable Rate Constant check box.
  • Hit the Add Variable Rate Constant button.
  • Navigate to the rate_constant.txt file and select it.

A green check mark should appear next to the file name if everything worked correctly.

_images/var_rate_constant.png

Run and Visualize the Simulation

  • Save the Blender file (Ctrl-s).
  • Hit the Run Simulation button.
  • Lastly, hit the Export & Run button.

Once the simulation has finished running, hit Reload Visualization Data. Hit Alt-a to play back the animation.

For the first 500 iterations of the simulation, the molecules will diffuse around in the box undisturbed. After that point, they will begin to disappear. By the end of the simulation, almost all of them will be gone.