3. Single Molecule Diffusion

3.1. Required software

This tutorial is designed to be used with the CellBlender 1.1 bundle (linux, windows). If using OSX, please install CellBlender from scratch (CellBlender Installation (for Developers and Advanced Users), note: install Blender first).


Other versions may work as well.

3.2. Tutorial Overview

This tutorial will define a single molecule and show its diffusion.

3.3. Initial Configuration

Install the CellBlender 1.1 bundle if you haven't already done so.

3.3.1. Save the File with a New Name in Your Working Directory

  • Start Blender
  • 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)
  • Select File > Save As...
  • Change untitled.blend to single_molecule.blend
  • Click Save As Blender File button

3.3.2. 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

3.3.3. 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 select the a molecule type
  • Click in the Quantity to Release field and set it to 1

3.3.4. 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

3.3.5. 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
  • Open the Display Options subpanel
  • Change the Sphere_1 to Torus
  • Change the Scale to 5
  • Change the color to a bright yellow


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.

3.3.6. Use the Time Line

  • 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
  • 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

3.3.7. Save Your File

  • File > Save