Scholarly Work - Center for Biofilm Engineering
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/9335
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Item NMR relaxation measurements of biofouling in model and geological porous media(2011-09) Codd, Sarah L.; Vogt, Sarah J.; Hornemann, Jennifer A.; Phillips, Adrienne J.; Maneval, James E.; Romanenko, K. R.; Hansen, L.; Cunningham, Alfred B.; Seymour, Joseph D.Recently 2D nuclear magnetic resonance (NMR) relaxation techniques have been able to access changes in pore structures through surface and diffusion based relaxation measurements. This research investigates the applicability of these methods for measuring pore and surface changes due to biofilm growth in various model porous systems and natural geological media. Model bead packs of various construction containing 100 lm borosilicate and soda lime glass beads were used to demonstrate how changes in the measured relaxation rates can be used to non-invasively verify and quantify biofilm growth in porous media. However significant challenges are shown to arise when trying to implement the same techniques to verify biofilm growth in a natural geological media.Item Magnetic resonance analysis of capillary formation reaction front dynamics in alginate gels(2011-09) Maneval, James E.; Bernin, D.; Fabich, H. T.; Seymour, Joseph D.; Codd, Sarah L.The formation of heterogeneous structures in biopolymer gels is of current interest for biomedical applications and is of fundamental interest to understanding the molecular level origins of structures generated from disordered solutions by reactions. The cation-mediated physical gelation of alginate by calcium and copper is analyzed using magnetic resonance measurements of spatially resolved molecular dynamics during gel front propagation. Relaxation time and pulse-field gradient methods are applied to determine the impact of ion front motion on molecular translational dynamics. The formation of capillaries in alginate copper gels is correlated to changes in translational dynamics.Item NMR measurement of hydrodynamic dispersion in porous media subject to biofilm mediated precipitation reactions(2011-03) Fridjonsson, E. O.; Seymour, Joseph D.; Schultz, Logan N.; Gerlach, Robin; Cunningham, Alfred B.; Codd, Sarah L.Noninvasive measurements of hydrodynamic dispersion by nuclear magnetic resonance (NMR) are made in a model porous system before and after a biologically mediated precipitation reaction. Traditional magnetic resonance imaging (MRI) was unable to detect the small scale changes in pore structure visualized during light microscopy analysis after destructive sampling of the porous medium. However, pulse gradient spin echo nuclear magnetic resonance (PGSE NMR) measurements clearly indicated a change in hydrodynamics including increased pore scale mixing. These changes were detected through time-dependent measurement of the propagator by PGSE NMR. The dynamics indicate an increased pore scale mixing which alters the preasymptotic approach to asymptotic Gaussian dynamics governed by the advection diffusion equation. The methods described here can be used in the future to directly measure the transport of solutes in biomineral-affected porous media and contribute towards reactive transport models, which take into account the influence of pore scale changes in hydrodynamics.Item Detection of biological uranium reduction using magnetic resonance(2012-04) Vogt, Sarah J.; Stewart, B. D.; Seymour, Joseph D.; Peyton, Brent M.; Codd, Sarah L.The conversion of soluble uranyl ions (UO22+) by bacterial reduction to sparingly soluble uraninite (UO2(s)) is being studied as a way of immobilizing subsurface uranium contamination. Under anaerobic conditions, several known types of bacteria including iron and sulfate reducing bacteria have been shown to reduce U (VI) to U (IV). Experiments using a suspension of uraninite (UO2(s)) particles produced by Shewanella putrefaciens CN32 bacteria show a dependence of both longitudinal (T1) and transverse (T2) magnetic resonance (MR) relaxation times on the oxidation state and solubility of the uranium. Gradient echo and spin echo MR images were compared to quantify the effect caused by the magnetic field fluctuations (T*2 ) of the uraninite particles and soluble uranyl ions. Since the precipitate studied was suspended in liquid water, the effects of concentration and particle aggregation were explored. A suspension of uraninite particles was injected into a polysaccharide gel, which simulates the precipitation environment of uraninite in the extracellular biofilm matrix. A reduction in the T2 of the gel surrounding the particles was observed. Tests done in situ using three bioreactors under different mixing conditions, continuously stirred, intermittently stirred, and not stirred, showed a quantifiable T2 magnetic relaxation effect over the extent of the reaction.Item Microbial and algal alginate gelation characterized by magnetic resonance(2012-10) Fabich, H. T.; Vogt, Sarah J.; Sherick, Matthew L.; Seymour, Joseph D.; Brown, Jennifer R.; Franklin, Michael J.; Codd, Sarah L.Advanced magnetic resonance (MR) relaxation and diffusion correlation measurements and imaging provide a means to non-invasively monitor gelation for biotechnology applications. In this study, MR is used to characterize physical gelation of three alginates with distinct chemical structures; an algal alginate, which is not O-acetylated but contains poly guluronate (G) blocks, bacterial alginate from Pseudomonas aeruginosa, which does not have poly-G blocks, but is O-acetylated at the C2 and/or C3 of the mannuronate residues, and alginate from a P. aeruginosa mutant that lacks O-acetyl groups. The MR data indicate that diffusion-reaction front gelation with Ca2+ ions generates gels of different bulk homogeneities dependent on the alginate structure. Shorter spin–spin T2 magnetic relaxation times in the alginate gels that lack O-acetyl groups indicate stronger molecular interaction between the water and biopolymer. The data characterize gel differences over a hierarchy of scales from molecular to system size.Item Nuclear magnetic resonance measurement of hydrodynamic dispersion in porous media: Preasymptotic dynamics, structure and nonequilibrium statistical mechanics(2012-10) Codd, Sarah L.; Seymour, Joseph D.Measurement of displacement time and length scale dependent dynamics by pulsed gradient spin echo nuclear magnetic resonance in porous media directly provides the preasymptotic hydrodynamic dispersion coefficient. This allows for comparison with nonequilibrium statistical mechanics models of hydrodynamics dispersion in porous media. Preasymptotic dispersion data and models provide characterization of porous media structure length scales relevant to transport and are related to the permeability and sample heterogeneity.Item Biofilm detection in natural unconsolidated porous media using a low-field magnetic resonance system(2013-04) Sanderlin, A. B.; Vogt, Sarah J.; Grunewald, E.; Bergin, B. A.; Codd, Sarah L.The extent to which T2 relaxation measurements can be used to determine biofouling in several natural geological sand media using a low-field (275 kHz, 6.5 mT) NMR system has been demonstrated. It has been previously shown that, at high laboratory strength fields (300 MHz, 7 T), T2 techniques can be used as a bioassay to confirm the growth of biofilm inside opaque porous media with low magnetic susceptibilities such as borosilicate or soda lime glass beads. Additionally decreases in T2 can be associated with intact biofilm as opposed to degraded biofilm material. However, in natural geological media, the strong susceptibility gradients generated at high fields dominated the T2 relaxation time distributions and biofilm growth could not be reliably detected. Samples studied included Bacillus mojavensis biofilm in several sand types, as well as alginate solution and alginate gel in several sand types. One of the sand types was highly magnetic. Data was collected with a low-field (275 kHz, 6.5 mT) benchtop NMR system using a CPMG sequence with an echo time of 1.25 ms providing the ability to detect signals with T2 greater than 1 ms. Data presented here clearly demonstrate that biofilm can be reliably detected and monitored in highly magnetically susceptible geological samples using a low-field NMR spectrometer indicating that low-field NMR could be viable as a biofilm sensor at bioremedation sites.Item Permeability of a growing biofilm in a porous media fluid flow analyzed by magnetic resonance displacement-relaxation correlations(2013-05) Vogt, Sarah J.; Sanderlin, A. B.; Seymour, Joseph D.; Codd, Sarah L.Biofilm growth in porous media is difficult to study non-invasively due to the opaqueness and heterogeneity of the systems. Magnetic resonance is utilized to non-invasively study water dynamics within porous media. Displacement-relaxation correlation experiments were performed on fluid flow during biofilm growth in a model porous media of mono-dispersed polystyrene beads. The spin–spin T2 magnetic relaxation distinguishes between the biofilm phase and bulk fluid phase due to water–biopolymer interactions present in the biofilm, and the flow dynamics are measured using PGSE NMR experiments. By correlating these two measurements, the effects of biofilm growth on the fluid dynamics can be separated into a detailed analysis of both the biofilm phase and the fluid phase simultaneously within the same experiment. Within the displacement resolution of these experiments, no convective flow was measured through the biomass. An increased amount of longitudinal hydrodynamic dispersion indicates increased hydrodynamic mixing due to fluid channeling caused by biofilm growth. The effect of different biofilm growth conditions was measured by varying the strength of the bacterial growth medium.Item Direct numerical simulation of pore-scale flow in a bead pack: Comparison with magnetic resonance imaging observations(2013-04) Yang, Xinmin; Scheibe, T. D.; Richmond, M. C.; Perkins, W. A.; Vogt, Sarah J.; Codd, Sarah L.; Seymour, Joseph D.; McKinley, M. I.A significant body of current research is aimed at developing methods for numerical simulation of flow and transport in porous media that explicitly resolve complex pore and solid geometries, and at utilizing such models to study the relationships between fundamental pore-scale processes and macroscopic manifestations at larger (i.e., Darcy) scales. A number of different numerical methods for pore-scale simulation have been developed, and have been extensively tested and validated for simplified geometries. However, validation of pore-scale simulations of fluid velocity for complex, three-dimensional (3D) pore geometries that are representative of natural porous media is challenging due to our limited ability to measure pore-scale velocity in such systems. Recent advances in magnetic resonance imaging (MRI) offer the opportunity to measure not only the pore geometry, but also local fluid velocities under steady-state flow conditions in 3D and with high spatial resolution. In this paper, we present a 3D velocity field measured at sub-pore resolution (tens of micrometers) over a centimeter-scale 3D domain using MRI methods. We have utilized the measured pore geometry to perform 3D simulations of Navier–Stokes flow over the same domain using direct numerical simulation techniques. We present a comparison of the numerical simulation results with the measured velocity field. It is shown that the numerical results match the observed velocity patterns well overall except for a variance and small systematic scaling which can be attributed to the known experimental uncertainty in the MRI measurements. The comparisons presented here provide strong validation of the pore-scale simulation methods and new insights for interpretation of uncertainty in MRI measurements of pore-scale velocity. This study also provides a potential benchmark for future comparison of other pore-scale simulation methods. © 2012 Elsevier Science. All rights reserved.Item Anomalous preasymptotic colloid transport by hydrodynamic dispersion in microfluidic capillary flow(2014-07) Fridjonsson, E. O.; Seymour, Joseph D.; Codd, Sarah L.The anomalous preasymptotic transport of colloids in a microfluidic capillary flow due to hydrodynamic dispersion is measured by noninvasive nuclear magnetic resonance (NMR). The data indicate a reduced scaling of mean squared displacement with time from the 〈z(t)^{2}〉_{c}∼t^{3} behavior for the interaction of a normal diffusion process with a simple shear flow. This nonequilibrium steady-state system is shown to be modeled by a continuous time random walk (CTRW) on a moving fluid. The full propagator of the motion is measured by NMR, providing verification of the assumption of Gaussian jump length distributions in the CTRW model. The connection of the data to microrheology measurements by NMR, in which every particle in a suspension contributes information, is established.