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” (
) button below the time line
6.2.8. Save Your File¶
File > Save