5. Bimolecular Reactions

5.1. Tutorial Overview

This tutorial will define a single bimolecular reaction.

5.2. Initial Configuration

This tutorial builds upon what was done in Add Simple Mesh Geometry. Either complete that tutorial yourself or use the add_meshgeom.blend file to get started.

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

  • Select File > Save As...
  • Change add_meshgeom.blend to bimol_reactions.blend
  • Click Save As Blender File button

5.2.2. Define a New Molecule Type

  • Click the Molecules button
_images/molecules.png
  • Click the "plus" sign (+) to the right of the Defined Molecules box
  • Click in the Molecule Name field, type the letter b and press the Enter key
  • Click in the Diffusion Constant box, type 1e-6 and press the Enter key
_images/define_b.png

5.2.3. Release "b" Molecules 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
  • Change the Site Name to Release_Site2
  • Click in the Molecule field and select the b molecules
  • Change Release Shape to Object/Region
  • Type Icosphere in the Object/Region field
  • Click in the Quantity to Release field and set it to 1000
_images/release_site2.png

5.2.4. Define a Bimolecular Reaction

  • Click the Reactions button.
_images/reactions_button.png
  • Change the Reactants text field from a to a + b
  • Type 5e3 in the Forward Rates text field
_images/change_reaction.png

5.2.5. Simulate the Model

  • Click the Run Simulation button
_images/run_sim_button.png
  • Change the Time Step to 1e-5
  • Click the Run button
_images/run_sim.png
  • Wait for the simulation to complete
  • Press the "Reload Visualization Data" button to load the results of the simulation.
_images/reload_viz_data.png

5.2.6. Change the Shape of "b"

  • Click the Molecules button
_images/molecules.png
  • Open the Display Options subpanel if it isn't already
  • Change the Cone to Sphere_2
  • Change the Scale to 2.5
  • Change the color to a bright red

5.2.7. View the Results

  • Press the "Play" (play) button below the time line

5.2.8. Save Your File

  • File > Save