No description available.

Preparative mass spectrometry is a gas-phase ion deposition technique aimed at deposition of monodisperse ion beams on a surface. This is accomplished through the implementation of a soft-landing ion mobility system which allows for high ion flux of conformationally selected ion packets. The soft-landing ion mobility system has been applied to a number of unique chemical problems including the deposition of insulators on graphene, the preparation of reusable surface enhanced Raman spectroscopic substrates, and the deposition of uranium nanoparticles. Soft-landing ion mobility provided a platform for the quick deposition of usable amounts of materials, which is the major objective of preparative mass spectrometry. Soft-landing ion mobility is unique when compared to other preparative mass spectrometric techniques in that the ion packets are conformationally separated, not separated on mass to charge ratio. This provides orthogonal complementary data to traditional mass spectrometric techniques and allows for the study of conformationally monodisperse surfaces. The diversity of problems that have been and continued to be explored with soft-landing ion mobility highlight the utility of the technique as a novel tool for the study of multiple ion/surface interactions.

The trapping behavior of deuterium and helium in polycrystalline tungsten (PCW) under D+-only, He+-only, sequential and simultaneous irradiation was studied as a function of incident ion fluences and irradiation temperature. Deuterium implanted at 300 and 500 K gets trapped at surface adsorption sites, vacancy-related traps, or extended defects. No deuterium was trapped for 700 K implantations. Results were affected by tungsten-carbide impurities in PCW specimens. It is suggested that He trapping occurs via the formation of He clusters, at impurity sites, or as part of He-vacancy complexes. For sequential implantations, D and He were found to de-trap each other, with He impeding the trapping of D when implanted first at 300 K. Under simultaneous irradiation a decrease in D inventories was observed for all cases, and a re-distribution of He to higher energy traps (associated with He-vacancy complex formation) was observed for higher fluences and temperatures.

The trapping behavior of deuterium and helium in polycrystalline tungsten (PCW) under D+-only, He+-only, sequential and simultaneous irradiation was studied as a function of incident ion fluences and irradiation temperature. Deuterium implanted at 300 and 500 K gets trapped at surface adsorption sites, vacancy-related traps, or extended defects. No deuterium was trapped for 700 K implantations. Results were affected by tungsten-carbide impurities in PCW specimens. It is suggested that He trapping occurs via the formation of He clusters, at impurity sites, or as part of He-vacancy complexes. For sequential implantations, D and He were found to de-trap each other, with He impeding the trapping of D when implanted first at 300 K. Under simultaneous irradiation a decrease in D inventories was observed for all cases, and a re-distribution of He to higher energy traps (associated with He-vacancy complex formation) was observed for higher fluences and temperatures.

Solution nuclear magnetic resonance (NMR) spectroscopy is a valuable analytical technique that is nondestructive, highly reproducible, and relatively quick to identify and quantify many chemical compounds. Quantitative NMR is a technique commonly used in many medical applications such as drug analysis, metabolomics, and protein-nanoparticle (P-NP) interactions. The most common technique used is the proton (1H) NMR experiment. The 1H NMR analysis provides a quick snapshot of the interested compounds in solution. However, as the compounds become more complex the spectrum becomes overpopulated. This dissertation focuses on various quantitative NMR techniques applied to metabolic and protein competition studies. Specifically, we investigated the effect of biochar on Escherichia coli (E. coli) growth to provide insight on how the metabolic pathways were influenced with the addition of biochar in the RPMI media. A 1H NMR spectrum was recorded at various time points to monitor the metabolic changes over time as E. coli grew in the presence and absence of biochar. The spectra were compared to an in-house metabolite library to identify and quantify the metabolic changes in E. coli. To enhance our metabolic library analysis, we utilized a pure shift analysis attached to the TOCSY pulse program to deconvolute spin systems by using a second dimension for analysis. DIPSI-PSYCHE TOCSY was applied to investigate a metabolite mixture sample and Streptococcus pneumoniae (S. pneumoniae) extracellular metabolites to better resolve the spin systems that significantly overlap each other in the 1H NMR spectra. Our novel approach suggests that adding a pure shift to the TOCSY pulse program is extremely beneficial to investigate various metabolic profiles. Finally, we investigated the protein competition to the AuNP surfaces using a 2D 1H-15N HSQC pulse program. Specifically, we used 1H-15N HSQC technique to quantify the binding capacity for each protein to the AuNP surface before we investigated the competition of two proteins, GB3-Ubq (model protein mixture) or AM-R2ab (biofilm forming protein mixture) to the surface. We also employed a model to study the kinetics of the protein competition to the surface. Our model suggests that GB3-Ubq does not specifically behave kinetically but AM-R2ab is strictly kinetically controlled.

Doctor of Philosophy / Department of Chemical Engineering / Peter H. Pfromm / One area of considerable importance in modern biotechnology is the preparation of highly active and selective enzyme based biocatalysts for applications in organic solvents. A major challenge is posed by the tendency of enzymes to cluster when suspended in organic solvents. Because the clusters obstruct the transport of substrates to the active site of the enzyme, the observed activity is often severely reduced. Over the past two decades, many strategies have been proposed to mitigate this problem. We have tackled this major hurdle by devising an immobilization strategy that utilizes fumed silica as carrier for the enzyme molecules. Fumed silica is a non-porous nanoparticulated fractal aggregate with unique absorptive properties. The enzyme/fumed silica preparation is formed in two steps. The buffered enzyme molecules are physically adsorbed on the fumed silica and then lyophilized. This protocol was shown to be successful with two enzymes of industrial relevance, Candida antarctica Lipase B (CALB) and subtilisin Carlsberg. The maximum observed catalytic activity in hexane reached or even exceeded commercial immobilizates and nonbuffer salt based preparations. The results demonstrated that catalytic activity has an intricate relationship with the nominal surface coverage (%SC) of the support by the enzyme molecules. s. Carlsberg exhibited an ever increasing activity as more surface area was provided per enzyme molecule. The activity leveled off when a sparse surface population was reached. CALB showed a maximum in catalytic activity at an intermediate surface coverage with steep decreases at both lower and higher surface coverage. It was shown that this maximum results from the presence of three distinct surface loading regimes after lyophilization: 1. a low surface coverage where opportunities for multi-attachment to the surface likely lead to detrimental conformational changes, 2. an intermediate surface coverage where interactions with neighboring proteins and the surface help to maintain a higher population of catalytically competent enzyme molecules, and 3. a multi-layer coverage where mass transfer limitations lead to a decrease in the apparent catalytic activity. Conformational stability analyses with both fluorescence and CD spectroscopy showed evidence that these regimes are most likely formed during the adsorption step of our protocol. A low conformational stability region was detected at low surface coverage while adsorbates with highly stable enzyme ensembles were observed at high surface coverage. Secondary structural analysis of the lyophilized nanobiocatalysts with FTIR confirmed a substantial decrease in the alpha-helical components at low surface coverage. In summary, the work presented here traces the phenomenological observation of the catalytic behavior of a nanobiocatalyst to molecular-level: enzyme-enzyme and enzyme-support interactions, which are specific to the intricate properties of the enzyme molecules.

Arctic climate is changing fast, but weather forecast and climate models have serious deficiencies in representing the Arctic atmosphere, because of the special conditions that occur in this region. The cold ice surface and the advection of warm air aloft from the south result in a semi-continuous presence of a temperature inversion, known as the “Arctic inversion”, which is governed by interacting large-scale and local processes, such as surface fluxes and cloud formation. In this thesis these poorly understood interactions are investigated using observations from field campaigns on the Swedish icebreaker Oden: The Arctic Summer Cloud Ocean Study (ASCOS) in 2008 and the Arctic Clouds in Summer Experiment (ACSE) in 2014. Two numerical models are also used to explore these data: the IFS global weather forecast model from the European Center for Medium-range Weather Forecasts and the MIMICA LES from Stockholm University. Arctic clouds can persist for a long time, days to weeks, and are usually mixed-phase; a difficult to model mixture of super-cooled cloud droplets and ice crystals. Their persistence has been attributed to several mechanisms, such as large-scale advection, surface evaporation and microphysical processes. ASCOS observations indicate that these clouds are most frequently decoupled from the surface; hence, surface evaporation plays a minor role. The determining factor for cloud-surface decoupling is the altitude of the clouds. Turbulent mixing is generated in the cloud layer, forced by cloud-top radiative cooling, but with a high cloud this cannot penetrate down to the surface mixed layer, which is forced primarily by mechanical turbulence. A special category of clouds is also found: optically thin liquid-only clouds with stable stratification, hence insignificant in-cloud mixing, which occur in low-aerosol conditions. IFS model fails to reproduce the cloud-surface decoupling observed during ASCOS. A new prognostic cloud physics scheme in IFS improves simulation of mixed-phase clouds, but does not improve the warm bias in the model, mostly because IFS fails to disperse low surface-warming clouds when observations indicate cloud-free conditions. With increasing summer open-water areas in a warming Arctic, there is a growing interest in processes related to the ice marginal zones and the summer-to-autumn seasonal transition. ACSE included measurements over both open-water and sea-ice surfaces, during melt and early freeze. The seasonal transition was abrupt, not gradual as would have been expected if it was primarily driven by the gradual changes in net solar radiation. After the transition, the ocean surface remained warmer than the atmosphere, enhancing surface cooling and facilitating sea-ice formation. Observations in melt season showed distinct differences in atmospheric structure between the two surface types; during freeze-up these largely disappear. In summer, large-scale advection of warm and moist air over melting sea ice had large impacts on atmospheric stability and the surface. This is explored with an LES; results indicate that while vertical structure of the lowest atmosphere is primarily sensitive to heat advection, cloud formation, which is of great importance to the surface energy budget, is primarily sensitive to moisture advection. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

Lipases are enzymes that play fundamental roles in fat digestion and metabolism, and function at the interface formed between hydrophobic molecules and the surrounding aqueous environment. These interfacial interactions are thought to induce conformational changes in a "lid" region of the lipase, leading to a dramatic increase in activity. This thesis aims to provide insight into the interactions that govern lipase association with interfaces of di erent structural characteristics, and the possible conformational changes that arise as a function of these interactions. A multi-scale molecular simulation approach (combining atomistic and coarse-grained methods) was applied to study two different lipases with a range of interfaces, including "soft" biological surfaces and "hard" non-biological surfaces. Three major insights were gained from these studies. First, interactions of a small bacterial lipase (M37) with lipid interfaces resulted in substantial structural changes in a lid region, uncovering of the underlying active site. A mechanism of interfacial ac- tivation is proposed for this lipase. Second, the interaction of M37 with non-biological interfaces di er from lipid interfaces, leading to altered interfacial orientations with possible functional consequences. Third, the amino acid composition of the lid region of a yeast lipase (TLL) is shown to play crucial roles in lipase activation and structural stability.

Atom-surface interactions are becoming an integral part of the field of atom optics. Here the role of van der Waals atom-surface interactions in atom wave diffraction and interferometry are investigated. In particular, it is shown that van der Waals interactions influence the intensity and phase of atomic diffraction patterns obtained from material gratings. As a result the atomic diffraction patterns are utilized to make an accurate determination of the interaction strength and verify the spatial variation of the atom-surface potential. A theory for describing the modified atom wave diffraction patterns is developed through an analogy with optical waves. An atom interferometer is used to directly measure the de Broglie wave phase shift induced by atom-surface interactions. More specifically, the phases of the zeroth, first, and second diffraction orders are measured. A proposal for using electromagnetic fields to modify the van der Waals interaction is put forth. Several of the important experimental components for observing such an effect are also demonstrated.

Au nanoparticles are increasingly being used in biological applications. Their use is of interest based upon their unique properties that are achieved at the nanoscale, which includes strong optical absorbances that are size and aggregation state dependent. Such absorbances can be used in sensitive chemical/biological detection schemes where bioligands can be directly attached to the nanoparticle surface using facile methods. Unfortunately, a number of complications persist that prevent their wide-scale use. These limitations include minimal nanoparticle stability in biological-based media of high ionic strength, unknown surface functionalization effects using simple biomolecules, and determining the binding motifs of the ligands to the nanoparticle surface. This situation can be further complicated when employing shaped materials where crystallographic facets can alter the binding potential of the bioligands. We have attempted to address these issues using traditional nanoparticle functionalization techniques that are able to be characterized using readily available analytical methods. By exploiting the optical properties of Au nanomaterials, we have been able to determine the solution stability of Au nanorods in a buffered medium and site-specifically functionalized Au nanomaterials of two different shapes: spheres and rods. Such abilities are hypothesized to be intrinsic to the bioligand once bound to the surface of the materials. Our studies have focused mainly on simple amino acids that have demonstrated unique assembly abilities for the materials in solution, resulting in the formation of specific patterns. The applications for such capabilities can range from the use of the materials as sensitive biochemical sensors to their directed assembly for use as device components.