%0 Journal Article %1 owkes2023biofilmjl %A Owkes, Mark %A Coblentz, Kai %A Eriksson, Austen %A Kammerzell, Takumi %A Stewart, Philip S. %D 2023 %J Computer Physics Communications %K 92c70-microbiology 92d40-ecology biofilm julialang %P 108890 %R https://doi.org/10.1016/j.cpc.2023.108890 %T Biofilm.jl: A fast solver for one-dimensional biofilm chemistry and ecology %U https://www.sciencedirect.com/science/article/pii/S0010465523002357 %V 293 %X 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. Program summary Program Title: Biofilm.jl CPC Library link to program files: https://doi.org/10.17632/n8sgj48nvd.1 Developer's repository link: https://github.com/markowkes/Biofilm.jl Code Ocean capsule: https://codeocean.com/capsule/2341966 Licensing provisions: MIT Programming language: Julia (Developed on v1.8, tested on v1.9) Supplementary material: https://markowkes.github.io/Biofilm.jl Nature of problem: This software solves for the temporal and spatial dynamics of an arbitrary number of solutes and particulates (biomass species) in a one-dimensional biofilm. The model includes the growth of particulates and the associated solute consumption (or production), the biofilm thickness dynamics due to growth within and detachment from the top of the biofilm. Additionally, source terms can be used to model the death of biomass or other effects. Discontinuous inputs, such as the diurnal cycle or periodic dosing, can be included. Solution method: The software solves for the temporal dynamics of particulates, solutes, and biofilm thickness, which are described by differential equations. These equations are discretized using a finite volume method and organized into a single system of ordinary differential equations that are solved using the DifferentialEquations.jl library. The software includes a collection of postprocessing tools to assist the user with exploring the simulation results.

@article{owkes2023biofilmjl, 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. Program summary Program Title: Biofilm.jl CPC Library link to program files: https://doi.org/10.17632/n8sgj48nvd.1 Developer's repository link: https://github.com/markowkes/Biofilm.jl Code Ocean capsule: https://codeocean.com/capsule/2341966 Licensing provisions: MIT Programming language: Julia (Developed on v1.8, tested on v1.9) Supplementary material: https://markowkes.github.io/Biofilm.jl Nature of problem: This software solves for the temporal and spatial dynamics of an arbitrary number of solutes and particulates (biomass species) in a one-dimensional biofilm. The model includes the growth of particulates and the associated solute consumption (or production), the biofilm thickness dynamics due to growth within and detachment from the top of the biofilm. Additionally, source terms can be used to model the death of biomass or other effects. Discontinuous inputs, such as the diurnal cycle or periodic dosing, can be included. Solution method: The software solves for the temporal dynamics of particulates, solutes, and biofilm thickness, which are described by differential equations. These equations are discretized using a finite volume method and organized into a single system of ordinary differential equations that are solved using the DifferentialEquations.jl library. The software includes a collection of postprocessing tools to assist the user with exploring the simulation results.}, added-at = {2023-11-28T23:03:59.000+0100}, author = {Owkes, Mark and Coblentz, Kai and Eriksson, Austen and Kammerzell, Takumi and Stewart, Philip S.}, biburl = {https://www.bibsonomy.org/bibtex/23e865d65ff491efdeca34d92a8293fd7/gdmcbain}, description = {Biofilm.jl: A fast solver for one-dimensional biofilm chemistry and ecology - ScienceDirect}, doi = {https://doi.org/10.1016/j.cpc.2023.108890}, interhash = {24947399fbd2ab24d69da08b98fd23b8}, intrahash = {3e865d65ff491efdeca34d92a8293fd7}, issn = {0010-4655}, journal = {Computer Physics Communications}, keywords = {92c70-microbiology 92d40-ecology biofilm julialang}, pages = 108890, timestamp = {2023-11-28T23:03:59.000+0100}, title = {Biofilm.jl: A fast solver for one-dimensional biofilm chemistry and ecology}, url = {https://www.sciencedirect.com/science/article/pii/S0010465523002357}, volume = 293, year = 2023 }