2. Single Molecule Diffusion

2.1. 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).

Note

Other versions may work as well.

2.2. Tutorial Overview

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

2.3. Initial Configuration

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

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

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

2.3.2. Define a Molecule "species"

  • Click the Molecules button
_images/molecules.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

2.3.3. Release a Single Molecule into the Simulation

  • Click the Molecule Placement button
_images/molecule_placement.png
  • Click the "plus" sign (+) to the right of the Release/Placement Sites box
  • Click in the Molecule field and select the a molecules
  • Click in the Quantity to Release field and set it to 1
_images/release_one.png

2.3.4. Simulate the Model

  • Click the Run Simulation button
_images/run_sim_button.png
  • Click the 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_data.png

2.3.5. Change Settings to See Results

  • Hide the "Manipulator" near the bottom middle of the screen
_images/hide_manipulator.png
  • Click the Molecules button
_images/molecules.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.

2.3.6. Use the Time Line

_images/timeline.png
  • Press the "Play" (play) button below the time line
  • Use the scroll wheel to zoom in 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 through time

2.3.7. Save Your File

  • File > Save