Fluctuation Compensator Solver Add-On¶
Fluctuation Compensator is an optional PDE solver add-on introduced in v4.1.2 to account for Metropolis surface fluctuations in field solutions in both a feasible and sensible way. The algorithm is based on that which is described by Marée et. al  and imposes total mass conservation in all cellular domains and the medium over the spin flips of a Monte Carlo step. The algorithm does not impose advection by domain deformation, but rather homogeneously applies a correction factor in each subdomain to all field solutions of a solver such that the total amount of each simulated species in each subdomain is unchanged over all spin flips.
The Fluctuation Compensator algorithm consists of the following three rules.
- Rule 1 (mass conservation): In each subdomain, the total amount of each species is unchanged over an arbitrary number of spin flips.
- Rule 2 (uniform correction): Corrections applied to values in each subdomain so to impose mass conservation are uniformly applied.
- Rule 3 (Neumann condition): The amount of species in the copying site of a spin flip are exactly copied to the site of the flip.
Fluctuation Compensator is supported in DiffusionSolverFE and ReactionDiffusionSolverFE.
Exactly one Fluctuation Compensator can be attached to each supported solver instance.
An attached Fluctuation Compensator performs corrections on all fields of the solver
to which it is attached. A Fluctuation Compensator can be attached to a solver in
CC3DML using the tag
<FluctuationCompensator/> at the level of field specification.
For example, to attach a Fluctuation Compensator to a simple use-case with
DiffusionSolverFE might look like the following.
<Steppable Type="DiffusionSolverFE"> <FluctuationCompensator/> <DiffusionField Name="ATTR"/> </Steppable>
Demos showing basic usage and comparison are available in
PDE solution field values can be modified outside of the solver routines without
invalidating the correction factors of Fluctuation Compensators so long as
they are notified that field values have been modified. The CompuCell3D library has
a convenience method to do exactly this:
updateFluctuationCompensators. Call this
method after modifying field values and before the next PDE solution step to refresh
Fluctuation Compensators according to your changes.
|||Marée, Athanasius FM, Verônica A. Grieneisen, and Leah Edelstein-Keshet. “How cells integrate complex stimuli: the effect of feedback from phosphoinositides and cell shape on cell polarization and motility.” PLoS Computational Biology 8.3 (2012).|