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"/>
</Plugin>
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.
Note
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"/>
</Plugin>
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">
<Algorithm>CenterOfMassBased</Algorithm>
…
</Plugin>
Note
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
.