TU Delft
Short description of structure of the framework's program

The framework introduced in this article was implemented in the Java programming language following object oriented programming techniques. The structure adopted allows the description of biofilm systems with any number of bacterial and solute species, as well as bioconversions in which the species are involved. Following are diagrams of two important parts of the program used to implement the modelling framework: (1) the species and reactions module and (2) the classes used by the multigrid solver. The diagrams shown conform to the Unified Modelling Language (UML), a specification commonly used for the representation of object oriented programs.

Class diagram (UML) for biomass species, particulate species, solute species and reactions, which constitutes the basic structure for the mass balances in the biofilm-modelling framework. The generality of the framework allows for arbitrary numbers of species and reactions to be defined, providing the infrastructure for the creation of 2D/3D biofilm models with any type of microbe/chemicals interactions.
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Class diagram (UML) for all classes used by the multigrid solver implementing relative diffusivity values (RelativeDiffusivity), boundary layer scenarios (classes inheriting from BoundaryLayer) and the concentration fields of particulates (ParticulateSpecies) and solutes (SoluteSpecies). The hierarchy used for implementation of diverse bulk concentration behaviours is also shown.
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2004 - Biofilm Modeling group at the TU Delft