Release Patterns

Release patterns allow you to release molecules at specified time intervals. One thing this can be useful for is simulating a synaptic vesicle releasing neurotransmitter.

Start New Project

After you start Blender, save the file (and set the project directory) by hitting Ctrl-s, typing ~/mcell_tutorial/rel_pattern (or C:\mcell_tutorial\rel_pattern on Windows) into the directory field, rel_pattern.blend into the file name field, and hit the Save As Blender File button.

Set Project Parameters

Set the following parameters:

  • Create a volume molecule called vol1.
  • Set the diffusion constant of 1e-6.
  • Create a reaction with the following properties:
    • Set Reactants to vol1.
    • Set Products to NULL.
    • Set Forward Rate to 1e5.
  • Count all the vol1 molecules in the World.

Create Release Pattern

  • Hit the Release Pattern button.
  • Hit the + button to create a new release pattern.
  • Set the Site Name to rel_pat1.
  • Set the Release Pattern Delay to 50e-6.
  • Set the Release Interval to 50e-6.
  • Set the Train Duration to 200e-6.
  • Set the Train Interval to 300e-6
  • Set the Number of Trains to 3
_images/rel_pat.png

A release pattern consists of one or more "trains." Each train can last for a certain period of time (Train Duration), and an interval between trains can be set (Train Interval). Within a given train, you can release molecules at specific intervals (Release Interval). And lastly, the Delay indicates when the first train will start. This may sound more confusing than it really is. Plotting the reaction data should help illustrate what's happening for this specific release pattern.

Create Release Site

Create a release site with the following properties:

  • Set the Site Name to vol1_rel.
  • Set the Molecule to vol1.
  • Set the Quantity to Release to 100.
  • Set the Release Pattern to rel_pat1.
_images/vol1_rel.png

Running the Simulation and Visualizing the Results

  • Save the Blender file (Ctrl-s).
  • Hit the Run Simulation button.
  • Lastly, hit the Export & Run button.

Once the simulation has finished running, hit Reload Visualization Data. Hit Alt-a to play back the animation.

At the origin, you should see small bursts of molecules being created (due to the actions of the release site and release pattern) and quickly decaying (from the reaction). You may want to zoom in to get a better look.

Additionally, let's plot the reaction data using the plotting tool of your choice.

_images/plot.png

As you can see, there are three distinct trains and within each train a release event happens every 50 microseconds. Overlays have been added to point out the effects that all the release pattern properties had on the creation of vol1.