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surf_class_surf_mol.rst

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Surface Classes and Surface Molecules

Note

The simulations and visualizations in this tutorial were generated using Blender 2.70a and CellBlender 1.0. It may or may not work with other versions.

We have already discussed surface classes at length, but we haven't touched on how they can affect the diffusion of surface molecules. Their effects are manifested at the boundaries of the surface regions that they are applied to. For example, if a surface is Reflective to surf1, then any surf1 can't get in or out of that that surface region. It acts as a fence of sorts corralling the molecules in one region. The Absorptive surface class also acts somewhat like a fence, but, instead of molecules harmlessly "bouncing" off of it, they are destroyed whenever they touch it. Transparent surface classes don't affect surface molecules, so we can ignore them in this context.

Set Project Directory

Start Blender. Hit the Scene button in the Properties Editor.

./images/scene_button.png

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

Creating and Assigning Surface Regions

With the default Cube selected, hit the Object button in the Properties Editor.

./images/object_button.png

Expand the Define Surface Regions panel. Hit + twice so that you have two new surface regions.

./images/surf_class_surf_mol/region_0_1.png

Click on the first one and change its name in the text field to top. Next, click on the second entry and change its name to bottom.

./images/surf_class_surf_mol/bottom_top.png

Move your cursor to the 3D View window and hit Tab to switch into Edit Mode. Hit Ctrl-t to triangulate the faces.

./images/triangulate.png

Then hit Ctrl-Tab and select Face.

./images/ctrl_tab.png

Hold Shift and right click on the top faces

./images/select_top.png

Select the top surface region from the list and click Assign.

./images/surf_class_surf_mol/bottom_top_assign.png

Next move your mouse back to the 3D View window and hold the middle mouse button down and drag upward so that the bottom faces are shown. Make sure everything is deselected (Hit a until all the faces are gray). Then hold Shift and right click on the bottom faces, select bottom from the list of regions, and click Assign.

Add Cube to Model Objects List

Hit the Scene button on the Properties Editor.

./images/scene_button.png

Expand the Model Objects panel. Hit the + button and Cube will appear in the list.

./images/surf_class_surf_mol/model_objects.png

Set Simulation Parameters

Next, expand the Model Initialization panel. Make the following changes:

  • Change Iterations to 1000.
  • Change Time Step to 1e-4.

./images/surf_class_surf_mol/model_init.png

Define a Surface Molecule

Expand the Define Molecules panel and hit the + button.

  • Change the Molecule Name to surf1.
  • Change the Molecule Type to Surface Molecule.
  • Change the Diffusion Constant to 1e-6.

./images/surf_class_surf_mol/surf1.png

Define a Release Site

Expand the Molecule Release/Placement panel and hit the + button.

  • Change Site Name to surf1_rel.
  • Change Molecule to surf1.
  • Leave Initial Orientation set to Top Front.
  • Leave Release Shape set to Object/Region.
  • Change Object/Region to Cube.
  • Change Quantity to Release to 1000.

./images/surf_class_surf_mol/release_surf1.png

Add the Surface Class

Expand the Define Surface Classes panel. Then, hit the + button to create a new surface class called Surface_Class. Rename it to absorb.

Hit the + button beside the empty absorb Properties list.

  • Select surf1 from the Molecule Name field.
  • Leave Orientation set to Top/Front.
  • Leave Type set to Absorptive.

./images/surf_class_surf_mol/absorb.png

Repeat this process, except call the surface class reflect and change the Type to Reflective.

./images/surf_class_surf_mol/reflect.png

Modify the Surface Regions

Now that we have created our surface class, we need to assign it to our mesh. Expand the Modify Surface Regions panel. Hit the + to begin modifying a surface region.

  • In the Surface Class Name field, select absorb.
  • Under Object Name, select the newly created Cube object.
  • For Region Name, select top.

./images/surf_class_surf_mol/assign_absorb.png

Repeat this process, except select reflect for the Surface Class Name and bottom for the region.

./images/surf_class_surf_mol/assign_reflect.png

In this example, we have two surface classes, absorb and reflect. absorb is applied to top and reflect is applied to bottom. The faces in the middle do not have a surface region assigned to them. surf1 molecules are released all over the Cube, not just one surface region.

The effect of the absorb class is that all the surf1 molecules are destroyed when they hit the boundary between the top region and the undefined middle section. The effect of the reflect class is that molecules cannot pass the boundary between the bottom region and the undefined middle section. Therefore, all the surf1 molecules that start inside of the bottom region never escape and the surf1 molecules starting in the middle section and top region will ultimately be destroyed.

Run the Simulation and Visualize the Results

Select Export All under Visualization Output Settings.

Save the Blender file (Ctrl-s) and hit the Run Simulation button under the Run Simulation panel.

Once the simulation has finished running, hit Read Viz Data under the Visualize Simulation Results panel. Hit Alt-a to play back the animation. You should notice the surf1 molecules being destroyed by the absorptive surface boundary.