Kinematics

Virtual Cell supports moving boundary applications for 2D geometries using a moving boundary solver. Specifying a velocity field for objects using the Kinematics tab in the Geometry workspace automatically invokes use of the moving boundary solver for simulations. Either a constant value or a function can be used to describe the velocity of defined spatial objects within the simulation.

The kinematics tab in the geometry workspace displays two Tables.

The top Spatial Objects Table identifies the different spatial objects in the BioModel along with the associated properties that can be used in kinematic expressions for each object.

Volume Objects are defined by the BioModel structures and can use properties of centroid, velocity and size.
Surface Objects are defined by the BioModel structures and can use properties of unit normal, velocity, distance, direction, and size.
Point Objects are defined in the kinematics and can use properties of position (x and y coordinates), velocity, direction, and distance.

Each type of Object has a Properties Pane that allows the user to select the properties that will be used to define the kinematics. See the appropriate Properties Pane information for each type of spatial Object.

Add a new Point Object in the Spatial Objects table using the New button.

Delete a selected Point Object in the Spatial Objects table using the Delete button.

The lower Spatial Process table defines the movement of objects in the simulation.

Point Location Processes (pproc) define point locations over time (x and y coordinates)
Point Kinematics (pproc) is not currently supported
Surface Kinematics (sproc) define membrane velocities
Volume Kinematics (vproc) define volume velocities

Add a new Spatial Process by first selecting a spatial object and then use the dropdown box in the New button in the Spatial Process Table.

Add or Edit the expression for velocity using the properties enabled for that object. See the Properties Pane information for each type of spatial process.