5. Unimolecular Reactions

5.1. Tutorial Overview

This tutorial will define a single unimolecular 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 single_molecule.blend to unimol_reactions.blend

• Click Save As Blender File button

5.2.2. Define a Reaction

• Click the Reactions button.

• Click the “plus” sign (+) to the right of the Defined Reactions box

• Type a in the Reactants text field

• Type NULL (all upper case) in the Products text field

• Type 5e3 in the Forward Rate text field

5.2.3. Release More Molecules

• Click the Molecule Placement button

• Change the Quantity to Release to 1000

5.2.4. Define Reaction Data to be Saved for Plotting

• Click the Plot Output Settings button

• Click the “plus” sign (+) to the right of the Reaction Data Output box

• Ignore the error which indicates an incomplete definition at this time

• Select a from the Molecule selector (should clear the error)

• Note the descriptive item “Count a in World” in the list

5.2.5. Simulate the Model

• Click the Run Simulation button to return to the Run Simulation panel

• Click the Export & Run button

• Wait for the simulation to complete

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

5.2.6. Use the Time Line

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

• Stop the simulation by clicking the “Pause” () button below the time line

• Click (or Click-and-Drag) in the time line to view the simulation at different points in time

5.2.7. Plot the Reaction Data

• Click the Plot Output Settings button

• Select MatPlotLib Plotter from the plotter drop-down list if it’s available.

• Click the Plot button.

5.2.8. Save Your File

• File > Save