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

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.

生物膜（Biofilm）是一类由微生物组成的群落，可在几乎所有具备充足营养的表面定植生长，涵盖水生与工业水处理系统、医疗设备等场景。生物膜属于结构复杂的群落，其中微生物种群的生长、代谢与种间竞争过程，会与扩散、对流、附着及脱离等物理过程相互耦合。本研究构建了搅拌釜反应器内的一维生物膜模型，可涵盖上述各类复杂相互作用过程。该模型基于现代Julia编程语言实现，可为各类生物膜及微生物所形成的复杂群落的研究提供高效分析工具。本文详述了这款名为Biofilm.jl的新型软件的相关细节，涵盖其数学模型、代码架构与运行流程。本文展示了使用Biofilm.jl建模的多类生物膜示例，包括单一异养菌、硫化物氧化细菌（sulfide-oxidizing bacteria, SOB）与硫酸盐还原细菌（sulfate-reducing bacteria, SRB），以及光能营养菌（phototroph）。本文还介绍了配套的后处理工具，可帮助Biofilm.jl用户生成可视化图表、从求解结果中提取特定数值，并对模拟得到的生物膜结果开展探索分析。