6. Bimolecular Reactions

6.1. Tutorial Overview

This tutorial will define a single bimolecular reaction.

6.2. Initial Configuration

This tutorial builds upon what was done in Unimolecular Reactions. Either complete that tutorial yourself or use the unimol_reactions.blend file to get started.

6.2.1. 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

6.2.2. Define a New Molecule Type

  • Click the Molecules button

  • 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


6.2.3. Release “b” Molecules 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, type b and hit enter

  • 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


6.2.4. Define a Bimolecular Reaction

  • Click the Reactions button.

  • Change the Reactants text field from a to a + b

  • Type 1e8 in the Forward Rates text field


6.2.5. Simulate the Model

  • Click the Run Simulation button

  • Change the Time Step to 1e-5

  • Click the Export & Run button

  • Wait for the simulation to complete

  • Press the “Reload Visualization Data” button to load the results of the simulation.


6.2.6. Change the Shape of “b”

  • Click the Molecules button

  • Open the Display Options subpanel if it isn’t already

  • Change the Sphere_1 to Cube

  • Change the Scale to 2.5

  • Change the color to a bright red

6.2.7. View the Results

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

6.2.8. Save Your File

  • File > Save