Center for Biofilm Engineering (CBE)
Permanent URI for this communityhttps://scholarworks.montana.edu/handle/1/9334
At the Center for Biofilm Engineering (CBE), multidisciplinary research teams develop beneficial uses for microbial biofilms and find solutions to industrially relevant biofilm problems. The CBE was established at Montana State University, Bozeman, in 1990 as a National Science Foundation Engineering Research Center. As part of the MSU College of Engineering, the CBE gives students a chance to get a head start on their careers by working on research teams led by world-recognized leaders in the biofilm field.
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Item Mathematical model of biofilm induced calcite precipitation(2010-08) Zhang, Tian-Yu; Klapper, IsaacMicrobially modulated carbonate precipitation is a fundamentally important phenomenon of both engineered and natural environments. In this paper, we propose a mixture model for biofilm induced calcite precipitation. The model consists of three phases—calcite, biofilm and solvent—which satisfy conservation of mass and momentum laws with addition of a free energy of mixing. The model also accounts for chemistry, mechanics, thermodynamics, fluid and electrodiffusion transport effects. Numerical simulations qualitatively capturing the dynamics of this process and revealing effects of kinetic parameters and external flow conditions are presented.Item Analysis of adaptive response to dosing protocols for biofilm control(2010-01) Szomolay, Barbara; Klapper, Isaac; Dindos, MartinBiofilms are sessile populations of microbes that live within a self-secreted matrix of extracellular polymers. They exhibit high tolerance to antimicrobial agents, and experimental evidence indicates that in many instances repeated doses of antimicrobials further reduce disinfection efficiency due to an adaptive stress response. In this investigation, a mathematical model of bacterial adaptation is presented consisting of an adapted-unadapted population system embedded within a moving boundary problem coupled to a reaction-diffusion equation. The action of antimicrobials on biofilms under different dosing protocols is studied both analytically and numerically. We find the limiting behavior of solutions under periodic and on-off dosing as the period is made very large or very small. High dosages often carry undesirable side effects so we specially consider low dosing regimes. Our results indicate that on-off dosing for small doses of biocide is more effective than constant dosing. Moreover, in a specific case, on-off dosing for short periods is again more effective regardless of the biocide dose. We also provide sufficient conditions for the eradication of biofilms under a constant dosing regime.Item Mathematical model of the effect of electrodiffusion on biomineralization(2011-05) Zhang, Tian-Yu; Klapper, IsaacBiofilm-induced mineral precipitation is a fundamentally important phenomenon with many potential applications including carbon sequestration and bioremediation. Based on a mixture model consisting of three phases (calcite, biofilm, and solvent) and also accounting for chemistry, mechanics, thermodynamics, fluid, and electrodiffusive transport effects, we describe the self-induced generation of an electric field due to different diffusivities of different ion species and study the effects of this field on ionic transport and calcite precipitation. Numerical simulations suggest that one of these effects is enhanced precipitation.Item An exclusion principle and the importance of mobility for a class of biofilm models(2011-01) Klapper, Isaac; Szomolay, BarbaraMuch of the earth’s microbial biomass resides in sessile, spatially structured communities such as biofilms and microbial mats, systems consisting of large numbers of single-celled organisms living within self-secreted matrices made of polymers and other molecules. As a result of their spatial structure, these communities differ in important ways from well-mixed (and well-studied) microbial systems such as those present in chemostats. Here we consider a widely used class of 1D biofilm models in the context of a description of their basic ecology. It will be shown via an exclusion principle resulting from competition for space that these models lead to restrictions on ecological structure. Mathematically, this result follows from a classification of steady-state solutions based on a 0-stability condition: 0-stable solutions are in some sense determined by competitive balance at the biofilm base, whereas solutions that are not 0-stable, while less dependent on conditions at the biofilm base, are unstable at the base. As a result of the exclusion principle, it is argued that some form of downward mobility, against the favorable substrate gradient direction, is needed at least in models and possibly in actuality.Item General theory for integrated analysis of growth, gene, and protein expression in biofilms(2013-12) Zhang, Tian-Yu; Pabst, Breana; Klapper, Isaac; Stewart, Philip S.A theory for analysis and prediction of spatial and temporal patterns of gene and protein expression within microbial biofilms is derived. The theory integrates phenomena of solute reaction and diffusion, microbial growth, mRNA or protein synthesis, biomass advection, and gene transcript or protein turnover. Case studies illustrate the capacity of the theory to simulate heterogeneous spatial patterns and predict microbial activities in biofilms that are qualitatively different from those of planktonic cells. Specific scenarios analyzed include an inducible GFP or fluorescent protein reporter, a denitrification gene repressed by oxygen, an acid stress response gene, and a quorum sensing circuit. It is shown that the patterns of activity revealed by inducible stable fluorescent proteins or reporter unstable proteins overestimate the region of activity. This is due to advective spreading and finite protein turnover rates. In the cases of a gene induced by either limitation for a metabolic substrate or accumulation of a metabolic product, maximal expression is predicted in an internal stratum of the biofilm. A quorum sensing system that includes an oxygen-responsive negative regulator exhibits behavior that is distinct from any stage of a batch planktonic culture. Though here the analyses have been limited to simultaneous interactions of up to two substrates and two genes, the framework applies to arbitrarily large networks of genes and metabolites. Extension of reaction-diffusion modeling in biofilms to the analysis of individual genes and gene networks is an important advance that dovetails with the growing toolkit of molecular and genetic experimental techniques.Item Estimation of a biofilm-specific reaction rate: kinetics of bacterial urea hydrolysis in a biofilm(2015-09) Connolly, James M.; Jackson, Benjamin; Rothman, Adam P.; Klapper, Isaac; Gerlach, RobinBackground/Objectives: Biofilms and specifically urea-hydrolysing biofilms are of interest to the medical community (for example, urinary tract infections), scientists and engineers (for example, microbially induced carbonate precipitation). To appropriately model these systems, biofilm-specific reaction rates are required. A simple method for determining biofilm-specific reaction rates is described and applied to a urea-hydrolysing biofilm. Methods: Biofilms were grown in small silicon tubes and influent and effluent urea concentrations were determined. Immediately after sampling, the tubes were thin sectioned to estimate the biofilm thickness profile along the length of the tube. Urea concentration and biofilm thickness data were used to construct an inverse model for the estimation of the urea hydrolysis rate. Results/Conclusions: It was found that urea hydrolysis in Escherichia coli MJK2 biofilms is well approximated by first-order kinetics between urea concentrations of 0.003 and 0.221 mol/l (0.186 and 13.3 g/l). The first-order rate coefficient (k1) was estimated to be 23.2±6.2 h−1. It was also determined that advection dominated the experimental system rather than diffusion, and that urea hydrolysis within the biofilms was not limited by diffusive transport. Beyond the specific urea-hydrolysing biofilm discussed in this work, the method has the potential for wide application in cases where biofilm-specific rates must be determined.