Biofilm.jl: a fast solver for one-dimensional biofilm chemistry and ecology

TL;DR

Biofilm.jl is a Julia-based software tool that efficiently models one-dimensional biofilm growth, metabolism, and interactions, enabling detailed simulation and analysis of complex microbial communities in various environments.

Contribution

The paper introduces Biofilm.jl, a new software package that models complex biofilm processes in one dimension with improved efficiency and usability compared to existing tools.

Findings

Successfully modeled diverse biofilm types including heterotrophs, SOB, SRB, and phototrophs.

Demonstrated the software's capability to generate detailed plots and extract data from simulations.

Provided a comprehensive mathematical and software framework for biofilm modeling in Julia.

Abstract

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.