NUFEB 2.0: Computational modelling of waste water microbial communities

Microbial communities are ubiquitous in nature and play key roles in the ecosystems of our planet, e.g. microbial communities present in activated-sludge or biofilm reactors are responsible for most of the carbon and nutrient removal from sewage and thus represent the core component of every biological waste water treatment plant (WWTP). With current molecular techniques we can characterise these systems in unprecedented detail. However, such methods provide little mechanistic insight into how the dynamic couplings between individual microorganisms give rise to their dynamic activities. To address this challenge, computational modelling is necessary for generating and testing biological hypotheses by systematically reconciling experimental data with model predictions.

In this talk, I will present the development of a comprehensive individual-based model which incorporates detailed micro-scale biology, chemistry and physics to enable the prediction of emergent properties of a wide range of bacterial communities. The individual-based model is developed on the open source molecular dynamic simulator LAMMPS. Bacteria growth, division, decay, mechanical interactions and chemical reactions are included. The 3D model allows to answer research questions such as variation in biofilm structure with respect to the nutrient availability, shear flow, and particle interactions.