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Item Exploring exchange and transport dynamics in complex systems through nuclear magnetic resonance(Montana State University - Bozeman, College of Letters & Science, 2021) Nelson, Madison Lee; Chairperson, Graduate Committee: Joseph D. Seymour and Sarah L. Codd (co-chair); This is a manuscript style paper that includes co-authored chapters.Nuclear magnetic resonance (NMR) is uniquely qualified for non-invasive studies of systems providing insights into macro-, meso-, and microscale structures. NMR relaxation and diffusion methods are applied to characterize transport and magnetization exchange dynamics in various complex systems. These techniques are highly sensitive to molecular mobility restrictions which correlate to the ability to monitor thermodynamic phase transitions and changes in molecular environment. NMR diffusion and relaxation measurements are applied to characterize the effect of xylose on transport within zeolite beads. The ability for NMR to explore the transport phenomenon on multiple length and time scales is exploited to characterize how the introduction of xylose effects the transport structure of the bead. Eigenvector simulations of magnetization evolution within a coupled pore system during multidimensional NMR measurements, T1-T2 relaxation correlation experiments, allowed for insights into complex diffusion and exchange occurring within multiple systems. Additionally, multidimensional relaxation NMR measurements, in the form of varying echo-time spin-spin relaxation dispersion T2(tau) and spin-spin relaxation exchange T2-T2 experiments, are demonstrated to successfully characterize thermodynamic structural rearrangements of two natural straight-chained hydrocarbons and a natural wax. Temperature dependent magnetization exchange was found in both the longitudinal and transverse magnetization. The results indicate the ability of NMR relaxometry to detect magnetization exchange without mass or molecular exchange, also known as spin diffusion, including in the transverse magnetization. Spatial domain extent can be inferred from the exchange timescale and an estimate of the spin diffusion coefficient. NMR relaxometry methods were extended to glycerol behenate, a common pharmaceutical component. Glycerol behenate was decomposed into its three base components to explore how polymorphic structure and exchange depend on temperature within each pure lipid through T2(tau) and T2-T2 NMR relaxation experiments. These methods allowed for in-situ monitoring of thermodynamic dependent exchange across domains in addition to decoupling of transverse and longitudinal exchange. The results allow for calculation of exchange length scales across the micro- and mesoscales within the lipids. Ultimately, multidimensional NMR relaxometry is successfully demonstrated to be an effective technique for characterizing and monitoring structural changes in lipids across various phase transition temperatures and time and length scales.Item Improving transport in hydrogels for 3D bioprinting applications(Montana State University - Bozeman, College of Engineering, 2021) Abbasi, Reha; Chairperson, Graduate Committee: James Wilking; Aaron D. Benjamin was an author and Madison Owens, Robert J. Olsen, Danica J. Walsh, Thomas B. LeFevre and James N. Wilking were co-authors of the article, 'Light-based 3D printing of hydrogels with high-resolution channels' in the journal 'Biomedical physics & engineering express' which is contained within this dissertation.; Thomas B. LeFevre was an author and Aaron D. Benjamin, Isaak J. Thornton, and James N. Wilking were co-authors of the article, 'Coupling fluid flow to hydrogel fluidic devices with reversible "pop-it" connections' in the journal 'Lab on a chip' which is contained within this dissertation.; Zahra Mahdieh was an author and Galip Yiyen, Robert A. Walker and James N. Wilking were co-authors of the article, 'Light-based 3D bioprinting of hydrogels containing colloidal calcium peroxide' submitted to the journal 'Bioprinting' which is contained within this dissertation.Hydrogels are soft, water-based gels with widespread applications in medicine, tissue engineering, and biotechnology. Many of these applications require structuring hydrogels in three-dimensional space. Light-based 3D printers offer exquisite spatial control; however, technologies for light-based 3D-printing of hydrogels remain limited. This is mainly caused by poor material transportation through the hydrogel. For example, limited transport of oxygen and other nutrients through 3D printed tissue constructs containing living cells leads to low cell viability. Here, we describe three experimental research studies focused on improving material transport in 3D-printed hydrogels. In the first part of this thesis, we describe a generalizable method for light-based 3D printing of hydrogels containing open, well-defined, submillimeter-scale channels with any orientation. These submillimeter channels allow for bulk liquid flow through the hydrogel to improve nutrient and oxygen transport. In the second part of this thesis, we describe a simple, reversible, plug-based connector designed to couple tubing to a hydrogel-based fluidic device to allow for pressurized liquid flow through the system. The resulting connection can withstand liquid pressures significantly greater than traditional, connector-free approaches, enabling long-term flow through 3D-printed hydrogels. In the third part of this thesis, we characterize the printability of photopolymerizable resins containing particles that slowly dissolve to release oxygen and thereby improve cell viability. The light-based 3D bioprinting technologies we describe in this thesis will improve material transport through 3D printed hydrogels and enable a wide variety of applications in 3D bioprinting and hydrogel fluidics.Item Multivalently presented carbohydrates can be used as drug delivery vehicles and to study protein carbohydrate interactions(Montana State University - Bozeman, College of Letters & Science, 2018) VanKoten, Harrison Wesley; Chairperson, Graduate Committee: Mary J. Cloninger; Wendy M. Dlakic, Robert Engel and Mary J. Cloninger were co-authors of the article, 'Synthesis and biological activity of highly cationic dendrimer antibiotics' in the journal 'Molecular pharmaceutics' which is contained within this thesis.; Rebecca Moore, Coleen Murphy and Mary J. Cloninger were co-authors of the article, 'Probing the LEC-1 and LEC-10 oxidative stress pathway in Caenorhabditis elegans using GALBeta1-4FUC dendrimers' which is contained within this thesis.Dendrimers in general excel as drug delivery vehicles since there are many different ways they can be assembled and different ways to tailor them to the system being studied. Glycodendrimers are generally nontoxic and can be further developed to meet the needs of what is being studied. For instance, in the studies below, a quaternity ammonium compound (QAC) has been attached to a glycodendrimer to determine the antimicrobial activity of a multivalently presented QAC in studies of minimum inhibitory concentration (MIC), biofilm prevention, and bacterial resistance. Results include comparable MICs to those of established antibiotics, prevention of biofilm formation but not disruption of an established biofilm, and establishment of multivalency as a strategy to counteract bacterial resistance. Another heterogeneously functionalized dendrimer was synthesized to study drug release characteristics of a prodrug attached to a cleavable substrate. In these studies, the upregulation of several proteins during cancer progression was taken advantage of including; MMP-2, -7, -9, and galectin-3. Glycodendrimers are tools used to study protein carbohydrate interactions. Study of galectins and their corresponding Beta-galactosides have illuminated their role in several essential biological processes. Multivalency plays a crucial role in many protein-carbohydrate interactions. Galectins are known to interact multivalently with various ligands. Although the role of galectins in this process is not yet fully understood, galectins have been proposed to serve as protective proteins during periods of high oxidative stress. We describe the synthesis of GalBeta1-4Fuc functionalized poly(amidoamine) (PAMAM) dendrimers in order to test C. elegans' response to high oxidative stress. In order to test the function of GalBeta1-4Fuc in vivo, C. elegans were treated with RNAi to knockdown lec-1 or lec-10, and then treated with glycodendrimer and exposed to oxidative stress. C. elegans that were pre-treated with the glycodendrimers were less susceptible to oxidative stress than untreated controls. The glycodendrimers mainly appeared within the digestive tract of the worms, and uptake into the vulva and proximal gonads could also be observed in some instances. This study indicates that multivalently presented GalBeta1-4Fuc can protect C. elegans from oxidative stress by binding to galectins.Item Characterizing excited state dynamics and carrier transport in hybrid organic-inorganic lead halide perovskites via ultrafast microscopy(Montana State University - Bozeman, The Graduate School, 2018) Hill, Andrew Hinson; Chairperson, Graduate Committee: Erik Grumstrup; Kori E. Smyser, Casey L. Kennedy, Eric S. Massaro and Erik M. Grumstrup were co-authors of the article, 'Ultrafast microscopy of methylammonium lead iodide perovskite thin films: heterogeneity of excited state spatial and temporal evolution' which is contained within this thesis.; Kori E. Smyser, Casey L. Kennedy, Eric S. Massaro and Erik M. Grumstrup were co-authors of the article, 'Screened charge carrier transport in methylammonium lead iodide perovskite thin films' in the journal 'Journal of physical chemistry letters' which is contained within this thesis.; Casey L. Kennedy, Eric S. Massaro and Erik M. Grumstrup were co-authors of the article, 'Perovskite carrier transport: disentangling the impacts of effective mass and scattering time through microscopic optical detection' in the journal 'Journal of physical chemistry letters' which is contained within this thesis.; Casey L. Kennedy and Erik M. Grumstrup were co-authors of the article, 'Determining the effects of A-site cation substitution on the optical response and transport properties of lead tri-bromide perovskites' submitted to the journal 'Journal of physical chemistry letters' which is contained within this thesis.Lead tri-halide perovskites have recently emerged as cost-effective alternatives to silicon for use in photovoltaic devices. A large contributor to their reduced cost compared to silicon is the simple solution processed techniques employed in their fabrication. While these methods can produce effective photovoltaic devices, heterogeneity endemic to solution processing makes characterization of tri-halide perovskites a challenging task. Most spectroscopic techniques use large sample interrogation volumes which often results in the indiscriminate sampling of grain boundaries and other heterogeneities which impact the spectroscopic observable. To circumvent this issue, pump-probe microscopy is used to dramatically shrink the sample volume, reducing the contributions from chemical and morphological heterogeneities and providing a more accurate measure of the sample's inherent properties. This work begins with a study of the recombination and transport dynamics methylammonium lead tri-iodide (MAPbI 3) perovskite. After identifying the main recombination pathways and contributions to the transient signal, experimental focus is shifted to the transport properties of MAPbI 3. The key contributing factors to the high diffusivities reported in MAPbI 3 are found to be strong electron-phonon coupling and a high static dielectric constant which serves to screen carriers from interactions with charged defects and other carriers. Then the development a new all-optical method capable of uniquely determining the two fundamental parameters that govern carrier transport (the mean scattering time and optical mass of photogenerated carriers) is reported. This method was applied to a series of different perovskite materials including MAPbI 3, cesium lead bromide di-iodide (CsPbBrI 2), methylammonium lead tri-bromide (MAPbBr 3), formamidinium lead tri-bromide (FAPbBr 3), and cesium lead tri-bromide (CsPbBr 3). The results of these experiments have led to the characterization of the role each perovskite constituent (namely, the identity of the organic cation and the halide stoichiometry) plays in determining the transport properties of the resulting material. The work presented in this dissertation characterizes the transport properties of lead halide perovskites. Measurements collected across multiple discrete and highly crystalline domains of multiple perovskite species have helped establish a relationship between the functionality and the local structure of these materials. Additionally, the design and first application of a new methodology to disentangle the effects of mean scattering time and the photogenerated carrier mass on carrier transport is reported. This technique will not only continue to aid in the characterization of lead-halide perovskites but will likely also see use on a host of other material systems to advance understanding of carrier transport in a variety of materials.Item Solution-phase dynamics of the Hepatitis B virus capsid : kinetics-based assays for study of supramolecular complexes(Montana State University - Bozeman, College of Letters & Science, 2009) Hilmer, Jonathan Kyle; Chairperson, Graduate Committee: Brian BothnerViruses are the most abundant form of life on the planet. Many forms are pathogenic and represent a major threat to human health, but viruses can also be useful nanoscale tools: as adjuvants, gene therapy agents, antimicrobials, or functionalized nanoscale building blocks. Viruses have historically been viewed as static and rigid delivery vehicles, but over the last few decades they have been recognized as flexible structures. Their structural dynamics are a crucial element of their functionality, and they represent a substantial target for antiviral strategies. To overcome the inherent problems of characterizing the biophysics of supramolecular complexes, we have developed a set of kinetic assays to probe capsid motion at several different amplitudes. The first assay, kinetic hydrolysis, works via the differential cleavage of folded versus unfolded proteins, and reports on large-scale conformational changes. The second assay, hydrogen-deuterium exchange, is a probe of small-amplitude dynamics. Both of these assays were used to study the solution-phase dynamics of the hepatitis B virus (HBV) capsid under the influence of assembly effectors and temperature. The results of these assays indicate that the HBV capsid adopts multiple conformations in response to the external environment. The dimeric subunit becomes primed for assembly via an entropically-driven process, but once assembled the capsid has reduced dependence on hydrophobic contacts. Depending on the assembly state, the subunit protein has varying response to assembly effectors, with changes to both small-amplitude and large-amplitude motions. The sum of the assay results indicate that the HBV capsid protein is capable of rotational translocations of the alpha-helices, while maintaining most of the secondary structure. Concerted structural shifts are implied, consistent with an allosteric model, which helps to explain previously observed allostery of capsid assembly and response to drugs.Item Pathogen transport and capture in a porous media biofilm reactor(Montana State University - Bozeman, College of Engineering, 2007) Grabinski, Kevin John; Chairperson, Graduate Committee: Warren JonesDrinking water distribution systems pose the potential to transport biological and chemical contaminants to the consumers' tap that can be responsible for widespread waterborne disease outbreaks (WBDO). A need exists to improve the ability to monitor contaminants that can attach to the distribution system's interior surfaces and to obtain samples for diagnosing both the cause of a WBDO and the extent of contamination within the system. In this study, a porous media reactor colonized with a mixed-species drinking water biofilm was used to study the capture of Salmonella typhimurium as a model pathogen. Parallel reactors were operated under constant flow (CF) and constant head (CH) to compare flow-regime induced spatial variations in biofilm accumulation and the resulting pathogen capture. Parallel test reactors were operated with 0.5 mg/L supplemental carbon until the accumulation of biofilm in the CH reactor reduced the flowrate to the target sampling point (CF flowrate). Both test reactors were then inoculated with slug doses of approximately 3x109 CFU S. typhimurium. Effluent water samples were collected for five pore-volumes, followed by the destructive sampling of the reactor.