Making cylindrical space in Repast Simphony?

Question

I am trying to model the interior of an epithelial space and am stuck on movement around the interior edges of a cylindrical space. Basically, I'm trying to implement StickyBorders and keep agents on those borders in a cylindrical space that I am creating.

Is there a way to use cylindrical coordinates in Repast Simphony? I found this example (https://www.researchgate.net/publication/259695792_An_Agent-Based_Model_of_Vascular_Disease_Remodeling_in_Pulmonary_Arterial_Hypertension) where they seem to have done something similar, but the paper doesn't explain methods in much depth, and I don't believe this is an example in the repast simphony models.

Currently, I have a class of epithelial cells that are set up to form a cylinder and other agents start just inside that cylinder. To move, they are choosing their most desired spot (similar to the Zombie code) then pointing to a new location in the direction of that desired location within one grid square of that original location. They check that new point before moving to it and make sure that there are at least two other epithelial cells in the immediate moore neighborhood, to ensure they stay against the wall.

GridPoint intendedpt = new GridPoint((int)Math.rint(alongX),(int)Math.rint(alongY),(int)Math.rint(alongZ));
        GridCellNgh<EpithelialCell> nearEpithelium = new GridCellNgh<EpithelialCell>(mac_grid, intendedpt, EpithelialCell.class, 1,1,1);    
        List<GridCell<EpithelialCell>> EpiCells = nearEpithelium.getNeighborhood(false);
        int nearbyEpiCellsCount=0;
        for (GridCell<EpithelialCell> cell: EpiCells) {
            nearbyEpiCellsCount++;
        }
        if (nearbyEpiCellsCount<2) {
            System.out.println(this + " leaving epithelial wall /r");
            RunEnvironment.getInstance().pauseRun();

            //TODO: where to go if false
        }

I am wondering if there is a way to either set the boundaries of the space to be a cylinder or to check which side of the agent is against the wall and restrict its movement in that direction.

score 4 · Answer 1 · answered Oct 24 '18 at 12:58

The sticky border code (StickyBorders.java) essentially just checks if the point that the agent moves to is beyond any of the space's dimensions, and if so the point is clamped to that dimension. So, for example, if the space is 3x4 and an agent's movement would take it to 4,2, then that point becomes 3,2 and the agent is placed there. Can you do something like that in this case? If not, can you edit your question to explain why not and maybe that will help us understand better.

score 3 · Answer 2 · answered Oct 24 '18 at 16:15

The approach we took in that model was to use a 3D grid space with custom borders and query methods. The space itself was still Cartesian - we just visualized it as a cylinder using custom display code. Using the Cartesian grid was an reasonable approximation for this application since the cell dimensions were significantly smaller that the vessel radius, so curvature effects were neglected. The boundary conditions on the vessel space were wrap around in the angular dimension, so that cells could move continuously around the circumference of the vessel, and the axial boundary conditions were also wrapped, as we assumed a long enough vessel length that this would be reasonable. The wall thickness dimension had hard boundaries at the basement membrane (y=0) and at the fluid interface (y=wall thickness).

Depending on which type of space you are using, you will need to implement a PointTranslator or GridPointTranslator that performs the border functions. If you want specific examples of the code I suggest you reach out to the author's directly.

Making cylindrical space in Repast Simphony?

2 Answers2