4. Unimolecular Reactions

4.1. Tutorial Overview

This tutorial will define a single unimolecular reaction.

4.2. Initial Configuration

This tutorial builds upon what was done in Single Molecule Diffusion. Either complete that tutorial yourself or use the single_molecule.blend file to get started.

4.2.1. 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

4.2.2. Define a Reaction

  • Click the Reactions button.
_images/reactions_panel_h.png
  • Click the "plus" sign (+) to the right of the Defined Reactions box
  • Ignore the error (indicates that you haven't fully defined a reaction yet)
  • 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
_images/define_reactions1.png

4.2.3. Release More Molecules

  • Click the Molecule Placement button
  • Change the Quantity to Release to 1000
_images/release_1000.png

4.2.4. Define Reaction Data to be Saved for Plotting

  • Click the Plot Output Settings button
_images/plot_panel_h.png
  • Click the "plus" sign (+) to the right of the Reaction Data Output box
  • Again, ignore the error which indicates an incomplete definition at this time
  • Select a from the Molecule selector (should clear the error)
_images/plot1.png
  • Note the descriptive item "Count a in World" in the list

4.2.5. Simulate the Model

  • Click the Run Simulation button to return to the Run Simulation panel
_images/run_panel_h.png
  • Click the Export & 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_h.png

4.2.6. Use the Time Line

  • Press the "Play" (play) button below the time line
_images/150_iters.png _images/750_iters.png
  • Stop the simulation by clicking the "Pause" (pause) button below the time line
  • Click (or Click-and-Drag) in the time line to view the simulation at different points in time

4.2.7. 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.
_images/plot2.png _images/plot3.png

4.2.8. Save Your File

  • File > Save