ExternalPotential Plugin

Chemotaxis plugin is used to cause directional cell movement in response to chemical gradient. Another way to achieve directional movement is to use ExternalPotential plugin. This plugin is responsible for imposing a directed pressure (or rather force) on cells. It is used to implement persistent motion of cells and its applications can be very diverse.

Example usage of this plugin looks as follows:

<Plugin Name="ExternalPotential">
   <Lambda x="-0.5" y="0.0" z="0.0"/>

Lambda is a vector quantity and determines components of force along three axes. In this case we apply force along x pointing in the positive direction.


Positive component of Lambda vector pushes cell in the negative direction and negative component pushes cell in the positive direction

We can also apply external potential to specific cell types:

<Plugin Name="ExternalPotential">
    <ExternalPotentialParameters CellType="Body1" x="-10" y="0" z="0"/>
    <ExternalPotentialParameters CellType="Body2" x="0" y="0" z="0"/>
    <ExternalPotentialParameters CellType="Body3" x="0" y="0" z="0"/>

Where in ExternalPotentialParameters we specify which cell type is subject to external potential (Lambda is specified using x , y , z attributes).

We can also apply external potential to individual cells. In that case, in the CC3DML section we only need to specify:

<Plugin Name="ExternalPotential"/>

and in the Python file we change lambdaVecX, lambdaVecY, lambdaVecZ, which are properties of cell. For example in Python we could write:

cell.lambdaVecX = -10

Calculations done by ExternalPotential Plugin are by default based on direction of pixel copy (similarly as in chemotaxis plugin). One can, however, force CC3D to do calculations based on movement of center of mass of cell. To use algorithm based on center of mass movement we use the following CC3DML syntax:

<Plugin Name="ExternalPotential">



In the pixel-based algorithm the typical value of pixel displacement used in calculations is of the order of 1 (pixel) whereas typical displacement of center of mass of cell due to single pixel copy is of the order of 1/cell volume (pixels) – ~ 0.1 pixel. This implies that to achieve compatible behavior of cells when using center of mass algorithm we need to multiply lambda’s by appropriate factor, typically of the order of 10.