NUFEB

NUFEB simulates three-dimensional dynamics of microbial communities using individual-based modeling (IbM) to represent microbes as discrete agents interacting through biological, physical, and chemical processes.

Key Features:

• Individual-based Modeling (IbM): Represents microbes as discrete units whose behaviors evolve over time due to biological, physical, and chemical processes.
• LAMMPS integration: Built upon the molecular dynamics simulator LAMMPS and extended with IbM capabilities.
• Parallelization and domain decomposition: Implements full parallelization via domain decomposition that divides the simulation domain into sub-domains distributed across processors, enabling simulations of up to 10^7 individuals.
• Explicit multi-physics processes: Incorporates a wide array of biological, physical, and chemical processes to explicitly simulate interactions within microbial communities.
• Biofilm and fluid dynamics support: Supports simulation of biofilm systems with fluid dynamics, multiple microbial functional groups, and nutrient dynamics.
• Post-processing routines: Includes routines for visualization and analysis of simulation outputs.
• Extensibility: Allows model extension and customization to represent diverse microbial scenarios.

Scientific Applications:

• Biofilm modeling: Simulates biofilm development, structure, and dynamics under coupled biological, physical, and chemical interactions.
• Multispecies community simulations: Models complex biofilms involving multiple microbial functional groups and nutrient interactions.
• Emergent population dynamics: Studies emergent behaviors and large-scale microbial system dynamics up to 10^7 individuals.

Methodology:

NUFEB extends LAMMPS with Individual-based Modelling features, uses domain decomposition for parallelization across processors, and provides post-processing routines for output visualization and analysis.