CompuCell3d manual and Tutorial Version 2
V.D Bacterium-and-Macrophage Simulation
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V.D Bacterium-and-Macrophage SimulationIn the two simulations we have presented so far, the cellular pattern develops without fields. Often, however, biological patterning mechanisms require us to introduce and evolve chemical fields and to have cells’ behaviors depend on the fields. To illustrate the use of fields, we model the in vitro behavior of bacteria and macrophages in blood. In the famous experimental movie taken in the 1950s by David Rogers at Vanderbilt University, the macrophage appears to chase the bacterium, which seems to run away from the macrophage. We can model both behaviors using cell secretion of diffusible chemical signals and movement of the cells in response to the chemical (chemotaxis): the bacterium secretes a signal (a chemoattractant) that attracts the macrophage and the macrophage secretes a signal (a chemorepellant) which repels the bacterium (97). Listing 4 shows the CC3DML configuration file for the bacterium-and-macrophage simulation. bacterium_macrophage_2D_wall_v3.pif Listing 4. CC3DML configuration file for the bacterium-and-macrophage simulation. The simulation has five generalized-cell types: Medium, Bacterium, Macrophage, Red blood cells and a surrounding Wall. It also has two diffusible fields, representing a chemoattractant, ATTR, and a chemorepellent, REP. Because the default boundary-energy between any generalized-cell type and the edge of the cell lattice is zero, we define a surrounding wall to prevent cells from sticking to the cell-lattice boundary. As in our previous simulations, we assign cell types using the CellType plugin. Note the new syntax in the line specifying the cell type making up the walls:
The Freeze="" attribute excludes generalized cells of type Wall from participating in index copies, which makes the walls immobile. We replace the Volume plugin with VolumeFlex and add the plugin SurfaceFlex. These plugins allow independent assignment of target values and constraint strengths in the volume-constraint and surface-constraint energies (equations and ). These plugins require a line for each generalized-cell type, specifying the type name and the target volume (or target surface area), and  (or  ) for that generalized-cell type, e.g.:
We implement the actual bacterium-macrophage “chasing” mechanism using the Chemotaxis plugin, which specifies how a generalized cell of a given type responds to a field. The Chemotaxis plugin biases a cell’s motion up or down a field gradient by changing the calculated effective-energy change used in the acceptance function, equation . For a field  :
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