ArticlePLoS computational biology2019
NUFEB: A massively parallel simulator for individual-based modelling of microbial communities.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Wrinkle-like structures emerge from matrix complementarity and mechanical discontinuity in heterogenous biofilms.NPJ biofilms and microbiomes · 2026Article
- Spatial structure: shaping the ecology and evolution of microbial communities.FEMS microbiology reviews · 2026Review
- A continuum multi-species bacterial growth model with a novel interaction scheme.Archive of applied mechanics = Ingenieur-Archiv · 2026Article
- Dissecting the physics of bacterial biofilms with agent-based simulations.Current opinion in solid state & materials science · 2025Article
- Individual-based modeling unravels spatial and social interactions in bacterial communities.The ISME journal · 2025Review
- Article
- A Hamilton principle-based model for diffusion-driven biofilm growth.Biomechanics and modeling in mechanobiology · 2024Article
- Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0.PLoS computational biology · 2024Article
- BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering.Bioinformatics advances · 2024Article
- From microbiome composition to functional engineering, one step at a time.Microbiology and molecular biology reviews : MMBR · 2023Review
- Quantifying drift-selection balance using an agent-based biofilm model of identical heterotrophs under low-nutrient conditions.Interface focus · 2023Article
- Numerical and experimental investigation of multi-species bacterial co-aggregation.Scientific reports · 2023Article
- Predicting partner fitness based on spatial structuring in a light-driven microbial community.PLoS computational biology · 2023Article
- Article
- Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective.Open biology · 2022Review
- Agent-Based Modeling of Microbial Communities.ACS synthetic biology · 2022Review
- Calibrating spatiotemporal models of microbial communities to microscopy data: A review.PLoS computational biology · 2022Review
- Coupled CFD-DEM modeling to predict how EPS affects bacterial biofilm deformation, recovery and detachment under flow conditions.Biotechnology and bioengineering · 2022Article
- CAMDLES: CFD-DEM Simulation of Microbial Communities in Spaceflight and Artificial Microgravity.Life (Basel, Switzerland) · 2022Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present NUFEB (Newcastle University Frontiers in Engineering Biology), a flexible, efficient, and open source software for simulating the 3D dynamics of microbial communities. The tool is based on the Individual-based Modelling (IbM) approach, where microbes are represented as discrete units and their behaviour changes over time due to a variety of processes. This approach allows us to study population behaviours that emerge from the interaction between individuals and their environment. NUFEB is built on top of the classical molecular dynamics simulator LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator), which we extended with IbM features. A wide range of biological, physical and chemical processes are implemented to explicitly model microbial systems, with particular emphasis on biofilms. NUFEB is fully parallelised and allows for the simulation of large numbers of microbes (107 individuals and beyond). The parallelisation is based on a domain decomposition scheme that divides the domain into multiple sub-domains which are distributed to different processors. NUFEB also offers a collection of post-processing routines for the visualisation and analysis of simulation output. In this article, we give an overview of NUFEB's functionalities and implementation details. We provide examples that illustrate the type of microbial systems NUFEB can be used to model and simulate.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.