Calculating kappa

[Vladimir Nikolić]

Hi!

For Biocellion v1.2, the function prototype to update kappa value is:

void updateIfSubgridKappa( const VIdx& vIdx, const VIdx& subgridVOffset, const UBAgentData& ubAgentData, const UBEnv& ubEnv, REAL& gridKappa )

If I understand correctly, kappa lets us reduce space available in a grid box for molecular concentration due to presence of cells (or possibly other objects?) that occupy space. This function provides UBAgentData with agents in the grid box, but isn't NbrUBAgentData what we need in order to find all the agents that occupy some space in the given grid box? Correct me if I'm wrong, but UBAgentData does not contain agents whose center is in the neighbouring grid box but whose volume overlaps a bit with the given grid box.

Cheers,

Vladimir

[Boris Aguilar]

Hi Vladimir,

Yes you are right, kappa is used to include space reduction due to
agents in a given Voxel. It would be ideal to have NbrUBAgentData as a
parameter of the function but for efficiency, we don't want to read
information about neighboring voxels too often in the code. The
synchronization between agents and grid properties is done in the
'updateIfGridVar' function which can be called before the PDE solver.

The way we used this feature before, is by first computing the
excluded volume in the function 'updateIfGridVar' and saving it into a
Voxel variable, then compute kappa form the Voxel variable, this way
kappa can include excluded volume of agents overlapping with a voxel
because updateIfGridVar can access all neighboring voxels and their
agents.

Note also that if the grid size is much larger than the agent sizes,
then the error of not including overlapping agents with voxels should
be very small, but of course, that will require some testing.

Please let us know if you have further questions.

Boris



Boris

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[Vladimir Nikolić]

Hey Boris,

That makes sense, thanks for clarifying! As for interface grid size vs agent size, although my agents are small, they're grouped together and take up some space, so that's why I thought about implementing kappa.

Cheers,

Vlad

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