The available methods of computer modeling of biofilms and their development trends

The object of this research is the available means of computer modeling of bacterial communities-biofilms. Such communities include the majority (95-99%) of bacteria and are ubiquitous. Biofilms are much more resistant than single bacteria to antibiotics and other antibacterial means due to weak permeability of intercellular environment and moderation of metabolism of some specimen of the community. Examination of influence techniques on biofilms is an important problem of biology; its solution requires various computer modeling tools that allow achieving significant scientific results. The subject of this research is the mathematical models used in modern techniques of biofilm modeling, and as well as the software for their implementation. The conclusion is made that the available methods of biofilm modeling are capable of successful reproduction of multiple behavioral aspects of these bacteria communities, including growth, destruction, and self-regulation; however, certain relevant problems are yet to be resolved. This is associated with the fact that the development of modern software for two-dimensional and three-dimensional agent modeling of biofilms – BSim, iDynoMiCS, CellModeller, require competent programmers for describing the interactions between simulated objects. Most promising direction in further development of this software implies a more active usage of tools for describing behavior and interaction of agents applied in the sphere of artificial intelligence, for example, fin-state automaton or production rules systems, with mandatory preservation of biological content of the models.

A framework for good biofilm reactor modeling practice (GBRMP)

A researcher or practitioner can employ a biofilm model to gain insight into what controls the performance of a biofilm process and for optimizing its performance. While a wide range of biofilm-modeling platforms is available, a good strategy is to choose the simplest model that includes sufficient components and processes to address the modeling goal. In most cases, a one-dimensional biofilm model provides the best balance, and good choices can range from hand-calculation analytical solutions, simple spreadsheets, and numerical-method platforms. What is missing today is clear guidance on how to apply a biofilm model to obtain accurate and meaningful results. Here, we present a five-step framework for good biofilm reactor modeling practice (GBRMP). The first four steps are (1) obtain information on the biofilm reactor system, (2) characterize the influent, (3) choose the plant and biofilm model, and (4) define the conversion processes. Each step demands that the model user understands the important components and processes in the system, one of the main benefits of doing biofilm modeling. The fifth step is to calibrate and validate the model: System-specific model parameters are adjusted within reasonable ranges so that model outputs match actual system performance. Calibration is not a simple ‘by the numbers’ process, and it requires that the modeler follows a logical hierarchy of steps. Calibration requires that the adjusted parameters remain within realistic ranges and that the calibration process be carried out in an iterative manner. Once each of steps 1 through 5 is completed satisfactorily, the calibrated model can be used for its intended purpose, such as optimizing performance, trouble-shooting poor performance, or gaining deeper understanding of what controls process performance.

From biofilm ecology to reactors: a focused review

Biofilms are complex biostructures that appear on all surfaces that are regularly in contact with water. They are structurally complex, dynamic systems with attributes of primordial multicellular organisms and multifaceted ecosystems. The presence of biofilms may have a negative impact on the performance of various systems, but they can also be used beneficially for the treatment of water (defined herein as potable water, municipal and industrial wastewater, fresh/brackish/salt water bodies, groundwater) as well as in water stream-based biological resource recovery systems. This review addresses the following three topics: (1) biofilm ecology, (2) biofilm reactor technology and design, and (3) biofilm modeling. In so doing, it addresses the processes occurring in the biofilm, and how these affect and are affected by the broader biofilm system. The symphonic application of a suite of biological methods has led to significant advances in the understanding of biofilm ecology. New metabolic pathways, such as anaerobic ammonium oxidation (anammox) or complete ammonium oxidation (comammox) were first observed in biofilm reactors. The functions, properties, and constituents of the biofilm extracellular polymeric substance matrix are somewhat known, but their exact composition and role in the microbial conversion kinetics and biochemical transformations are still to be resolved. Biofilm grown microorganisms may contribute to increased metabolism of micro-pollutants. Several types of biofilm reactors have been used for water treatment, with current focus on moving bed biofilm reactors, integrated fixed-film activated sludge, membrane-supported biofilm reactors, and granular sludge processes. The control and/or beneficial use of biofilms in membrane processes is advancing. Biofilm models have become essential tools for fundamental biofilm research and biofilm reactor engineering and design. At the same time, the divergence between biofilm modeling and biofilm reactor modeling approaches is recognized.