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

_images/cellblender_tab.png

  • If prompted click Initialize CellBlender

3.3.4. Define a Molecule “species”

  • Click the Molecules button

_images/molecules_panel_h.png

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

_images/define_molecule.png

  • 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

_images/define_molecule2.png

3.3.5. Release a Single Molecule into the Simulation

  • Click the Molecule Placement button

_images/release_placement_panel_h.png

  • 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

_images/release_one.png

3.3.6. Simulate the Model

  • Click the Run Simulation button

_images/run_panel_h.png

  • Click the Export & Run button

_images/run_sim.png

  • 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

_images/reload_viz_h.png

  • 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

_images/manipulater_location.png _images/hide_manipulator.png

  • Click the Molecules button

_images/molecules_panel_h.png

  • Open the Display Options subpanel

  • Change the Sphere_1 to Torus

  • Change the Scale to 5

  • Change the color to a bright yellow

_images/display_options.png

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

_images/timeline.png

  • Press the “Play” (play) button below the time line

  • Use the mouse scroll wheel to zoom in or out until you can see the moving torus

_images/single_diffusing_molec.png

  • Stop the simulation by clicking the “Pause” (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