A multispecies, two- and three-dimensional model was developed, based on a previously published planar biofilm model, and the biochemical structure of the ADM1. Several soluble substrates diffuse and react in the granule. Local pH is calculated from acid-base equilibria and charge balance. The model uses individual-based representation of biomass particles within the granule (biofilm), and describes spreading by an iterative pushing technique. The overall computational domain consists of one granule, and is divided into a grid with Cartesian coordinates. The number of grid elements does not limit the number of biomass particles, and it is not necessary to use grid-spreading techniques, such as cellular automata, which result in Cartesian artefacts. The model represents both microscopic and macroscopic features in granule structure, previously observed using in-situ molecular techniques, and can be effectively used to interpret these results.

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