agentGrid
All agents in biofilm simulations are stored and tracked using a grid called the agentGrid, which is similar to the grid for the solutes but serves a different purpose unique to agents. There are several parameters that need to be specified for the grid, and this is done with the agentGrid mark-up.
The first parameter (computationDomain) specifies the domain in which the grid is to be used, and the second parameter (resolution) specifies the size of each grid element in physical units. The resolution should be chosen to match the size of the individuals (should be near the diameter of the largest species) and the resolution of the solute grid. It is best to choose a size that is a factor of two different from the size of the solute grid, i.e. if the solute grid has a resolution of 8 µm, the agentGrid should have a resolution of 4, 8, or 16 µm. If unsure, use 8 µm.
The detachment mark-up defines one way in which the outside world may affect growth of the biofilm system via erosion acting at the surface of the growing biofilm. There are two detachment types currently available in iDynoMiCS: ‘DS_Quadratic’ and ‘DS_Biomass’. The desired form of detachment is set using the class attribute. The ‘DS_Quadratic’ type (illustrated above) sets the erosion strength to be a parameter kDet times the square of the local biofilm height, and the parameter kDet must be specified in the mark-up. You must also set the maximum thickness that the biofilm may reach (maxTh), which should be used as a safety catch to ensure that the biofilm region remains within the computation domain; any biomass growing above this height will be removed from the system, or in order to keep the biofilm to a certain thickness below the top of the domain. The second detachment class is ‘DS_Biomass’, which is similar to the ‘DS_Quadratic’ class but with the added property that the erosion is scaled by the ocal biomass concentration; this means that higher concentrations of biomass will be less susceptible to detachment. The mark-up looks as follows:
(Recall the conversion 1 fg/µm3 = 1 g/L, which you might use in relating this detachment parameter to the height-based parameter above.)
As the biofilm grows, it sometimes happens that decay and erosion outpace growth in the lower reaches of the biofilm. When this occurs, agents may be removed because they have become too small, and if this happens for many agents it is possible that large chunks of biofilm may no longer be connected to the substratum. The sloughDetachedBiomass parameter sets whether you would like biofilm pieces that are no longer connected to the substratum to be removed from the domain. The default value is true, to remove those pieces, but some applications might require the pieces to remain; in those cases, set the flag to false.
Finally, the remaining parameters set the behaviour of the shoving algorithm, whose purpose is to move agents as they grow and compete for space in the biofilm. In general, it is not necessary to modify these values, but again for completeness we describe their purpose. The shovingFraction parameter sets the allowed cut-off for moving agents; when the fraction of still-moving agents is below this value, the agent positions are accepted as equilibrated and the simulation continues. The shovingMaxIter parameter sets the maximal number of iterations allowed to reach the final agent positions. Finally, the shovingMutual parameter sets whether the shoving motion is applied to both agents or only to one when two agents overlap.