2023/07/12 by Mark Owkes, Kai Coblentza, Owkes, Mark +7
Chemical Engineering · Environmental Science · #Biological Physics (physics.bio-ph) #FOS: Physical sciences #Microbial Community Ecology and Physiology #Odor and Emission Control Technologies #Wastewater Treatment and Nitrogen Removal
paper · pdf · doi:10.48550/arxiv.2307.06153
openalex publication_date 2023/07/12 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of growth, metabolism, and competition between species interact with physical processes of diffusion, convection, attachment, and detachment. This work describes a model of a one-dimensional biofilm in a stirred tank reactor that incorporates these complexities. The model is implemented in the modern Julia programming language providing an efficient tool for studying a large variety of biofilms and the intricate communities the microorganisms create. Details of the new software, known as Biofilm.jl, including the mathematical model and organization and execution of the code, are provided. Examples of biofilms modeled using Biofilm.jl are presented such as a single heterotroph, a sulfide-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB), and a phototroph. Postprocessing tools are described that allow a Biofilm.jl user to make plots and extract specific values from the solution and explore the simulated biofilm results.