NUFEB - a LAMMPS user package for individual-based modelling of microbial communities

We present NUFEB (Newcastle University Frontiers in Engineering Biology), a LAMMPS user package for modelling 3D dynamics of microbial communities. The tool is based on Individual-based Modelling (IbM) approach, which allows users to explicitly describe the dynamics of each microbe as well as the internal and external processes that result in microbial growth, decay, motility, etc. NUFEB allows studying population behaviours that emerge from the interaction between individuals and their environment. The novelty of NUFEB lies in its parallelisation and generic model specification, enabling realistic modelling and simulation of systems with over 10^7 microbes and a wide range of biological, physical, and chemical processes at millimetre scale.

In this talk, we give an overview of NUFEB’s functionalities. We showcase the type of microbial systems NUFEB can be used to model and simulate. Examples include microbial growth within a continuous nutrient field, large-scale biofilm simulation, rod-shaped microbial representation, and biofilm deformation and detachment under fluid dynamics (LAMMPS/NUFEB - OpenFOAM coupling).