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

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, 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.