3. Single Molecule Diffusion¶
3.1. Required software¶
This tutorial is designed to be used with the CellBlender 3.5 bundle. Please download it from here if you haven’t done so yet.
3.2. Tutorial Overview¶
This tutorial will define a single molecule and show its diffusion.
3.3. Initial Configuration¶
Install the CellBlender 3.5 bundle if you haven’t already done so.
Start Blender
Note
On MacOS you will have to open Blender from the command line unless you have built CellBlender from scratch.
Select all objects (press the a key until all objects are orange)
Delete all objects (press the x key and click the “Delete” pop up button)
3.3.1. Save the Startup File¶
File > Save Startup File
Confirm Save Startup File
You will only have to do this once. After this, every time you start Blender you will get a clean slate.
3.3.2. Save the File with a New Name in Your Working Directory¶
Select File > Save As…
Change untitled.blend to single_molecule.blend
Click Save As Blender File button
3.3.3. Open CellBlender Panel¶
From the Tool shelf on the left hand side open click on the CellBlender tab

If prompted click Initialize CellBlender
3.3.4. Define a Molecule “species”¶
Click the Molecules button

Click the “plus” sign (+) to the right of the Defined Molecules box

Click in the Name field, type the letter a and press the Enter key
The new molecule a should have a green check mark in the Defined Molecules box
Click in the Diffusion Constant box, type 1e-6 and press the Enter key

3.3.5. Release a Single Molecule into the Simulation¶
Click the Molecule Placement button

Click the “plus” sign (+) to the right of the Release/Placement Sites box
Click in the Molecule field and type a then hit enter
Note
CellBlender will allow you to type in a name of a molecule you have not defined, however this will result in an error when running the simulation.
Click in the Quantity to Release field and set it to 1

3.3.6. Simulate the Model¶
Click the Run Simulation button

Click the Export & Run button

A green check mark will appear in the list of MCell Processes when the simulation is complete
Press the Reload Visualization Data button to load the results of the simulation

Zoom in (mouse scroll wheel) to see molecule(s) at the origin
3.3.7. Change Settings to See Results¶
Hide the “Manipulator” near the bottom middle of the screen


Click the Molecules button

Open the Display Options subpanel
Change the Sphere_1 to Torus
Change the Scale to 5
Change the color to a bright yellow

Note
You’ll notice that there are actually two torus objects. One of them should be moving as the simulation is played, and the other should be stationary at the origin. The torus at the origin is really a “template” molecule used by Blender. There will always be a template molecule at the origin for every molecule species you define.
3.3.8. Use the Time Line¶

Press the “Play” (
) button below the time line
Use the mouse scroll wheel to zoom in or out until you can see the moving torus

Stop the simulation by clicking the “Pause” (
) button below the time line
Click at various locations on the time line to see the molecule state at that time
Click and drag in the time line to “scrub” the simulation results through time
3.3.9. Save Your File¶
File > Save