NUFEB: A massively parallel simulator for individual-based modelling of microbial communities

Area of Science:

• Computational Biology
• Microbial Ecology
• Bioinformatics

Background:

• Microbial communities exhibit complex emergent behaviors arising from individual interactions.
• Simulating these dynamics requires sophisticated computational tools capable of handling large numbers of individuals and diverse processes.

Purpose of the Study:

• To introduce NUFEB, a novel open-source software for simulating the 3D dynamics of microbial communities.
• To provide a flexible and efficient platform for modeling microbial systems, with a focus on biofilms.

Main Methods:

• Utilizes the Individual-based Modelling (IbM) approach, representing microbes as discrete units.
• Built upon the LAMMPS molecular dynamics simulator, extended with IbM functionalities.
• Implements a wide range of biological, physical, and chemical processes for explicit microbial system modeling.

Main Results:

• NUFEB is fully parallelized, enabling simulations of large microbial populations (10^7 individuals and beyond).
• Employs a domain decomposition scheme for efficient parallel processing.
• Includes post-processing routines for visualization and analysis of simulation data.

Conclusions:

• NUFEB offers a powerful and flexible tool for studying emergent behaviors in microbial communities.
• The software facilitates detailed modeling of microbial systems, particularly biofilms.
• Provides a valuable resource for researchers in microbial ecology and computational biology.