NUFEB 2.0: An advanced simulator for individual-based modelling of cell populations

Cell systems are intricate and dynamic, characterized by complex interactions between individual cells and their micro-environment. Understanding their behaviour and emergent properties is crucial for advancing our knowledge in fields such as tissue engineering, community ecology, and disease modelling. Here, we present NUFEB 2.0 (Newcastle University Frontier in Engineer Biology) - a 3D individual-based simulator for modelling and simulating cell populations. The software is built on top of LAMMPS framework and extended with biological and biochemical features. It incorporates various functionalities such as cell metabolism and division, bioreactor coupling, substrate diffusion and pH based on mesh grid structure. Additionally, NUFEB is integrated with OpenFOAM through the SediFoam interface, enabling CFD-DEM simulation.

In NUFEB 2.0, we have refactored the codebase and made significant improvements to enhance its usability. Key new features and improvements include: 1) expanding cell representation options with sphere, rod and ellipsoid shape, 2) GPU acceleration based on the LAMMPS Kokkos framework, 3) packages for modelling plasmid dynamics and epidermis formation; 4) comprehensive documentation and tutorial materials. In this talk, I will give an brief overview of NUFEB 2.0 and showcase several biological applications.