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Description
Microfluidic devices represent a growing technology in the world of analytical chemistry. Serial femtosecond crystallography (SFX) utilizes microfluidic devices to generate droplets of an aqueous buffer containing protein crystals, which are then fired out as a jet in the beam of an X-ray free electron laser (XFEL). A crucial part of the device is its method of droplet detection. This project presents a design for a capacitive sensor that uses a unique electrode configuration to detect the difference in capacitance between the aqueous and oil phases. This design was developed using MATLAB and COMSOL Multiphysics simulations and printed using high-resolution 3D printing. Results show that this design can successfully distinguish between the two immiscible liquids, confirming it as a possible detection method in future SFX experiments.
ContributorsCorder, Cameron Dean (Author) / Ros, Alexandra (Thesis director) / Williams, Peter (Committee member) / Hayes, Mark (Committee member) / School of Molecular Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
A new challenge on the horizon is to utilize the large amounts of protein found in the atmosphere to identify different organisms from which the protein originated. Included here is work investigating the presence of identifiable patterns of different proteins collected from the air and biological samples for the purposes of remote identification. Protein patterns were generated using high performance liquid chromatography (HPLC). Patterns created could identify high-traffic and low-traffic indoor spaces. Samples were collected from the air using air pumps to draw air through a filter paper trapping particulates, including large amounts of shed protein matter. In complimentary research aerosolized biological samples were collected from various ecosystems throughout Ecuador to explore the relationship between environmental setting and aerosolized protein concentrations. In order to further enhance protein separation and produce more detailed patterns for the identification of individual organisms of interest; a novel separation device was constructed and characterized. The separation device incorporates a longitudinal gradient as well as insulating dielectrophoretic features within a single channel. This design allows for the production of stronger local field gradients along a global gradient allowing particles to enter, initially transported through the channel by electrophoresis and electroosmosis, and to be isolated according to their characteristic physical properties, including charge, polarizability, deformability, surface charge mobility, dielectric features, and local capacitance. Thus, different types of particles are simultaneously separated at different points along the channel distance given small variations of properties. The device has shown the ability to separate analytes over a large dynamic range of size, from 20 nm to 1 μm, roughly the size of proteins to the size of cells. In the study of different sized sulfate capped polystyrene particles were shown to be selectively captured as well as concentrating particles from 103 to 106 times. Qualitative capture and manipulation of β-amyloid fibrils were also shown. The results demonstrate the selective focusing ability of the technique; and it may form the foundation for a versatile tool for separating complex mixtures. Combined this work shows promise for future identification of individual organisms from aerosolized protein as well as for applications in biomedical research.
ContributorsStaton, Sarah J. R (Author) / Hayes, Mark A. (Committee member) / Anbar, Ariel D (Committee member) / Shock, Everett (Committee member) / Williams, Peter (Committee member) / Arizona State University (Publisher)
Created2011
Description
In-situ environmental transmission electron microscopy (ETEM) is a powerful tool for following the evolution of supported metal nanoparticles under different reacting gas conditions at elevated temperatures. The ability to observe the events in real time under reacting gas conditions can provide significant information on the fundamental processes taking place in catalytic materials, from which the performance of the catalyst can be understood. The first part of this dissertation presents the application of in-situ ETEM studies in developing structure-activity relationship in supported metal nanoparticles. In-situ ETEM studies on nanostructures in parallel with ex-situ reactor studies of conversions and selectivities were performed for partial oxidation of methane (POM) to syngas (CO+H2) on Ni/SiO2, Ru/SiO2 and NiRu/SiO2 catalysts. During POM, the gas composition varies along the catalyst bed with increasing temperature. It is important to consider these variations in gas composition in order to design experiments for in-situ ETEM. In-situ ETEM experiments were performed under three different reacting gas conditions. First in the presence of H2, this represents the state of the fresh catalyst for the catalytic reaction. Later in the presence of CH4 and O2 in 2:1 ratio, this is the composition of the reacting gases for the POM reaction and this composition acts as an oxidizing environment. Finally in the presence of CH4, this is the reducing gas. Oxidation and reduction behavior of Ni, Ru and NiRu nanoparticles were followed in an in-situ ETEM under reacting gas conditions and the observations were correlated with the performance of the catalyst for POM. The later part of the dissertation presents a technique for determining the gas compositional analysis inside the in-situ ETEM using electron energy-loss spectroscopy. Techniques were developed to identify the gas composition using both inner-shell and low-loss spectroscopy of EELS. Using EELS, an "operando TEM" technique was successfully developed for detecting the gas phase catalysis inside the ETEM. Overall this research demonstrates the importance of in-situ ETEM studies in understanding the structure-activity relationship in supported-metal catalysts for heterogeneous catalysis application.
ContributorsChenna, Santhosh (Author) / Crozier, Peter A. (Thesis advisor) / Carpenter, Ray (Committee member) / Sieradzki, Karl (Committee member) / Petuskey, William (Committee member) / Arizona State University (Publisher)
Created2011
Description
In an effort to begin validating the large number of discovered candidate biomarkers, proteomics is beginning to shift from shotgun proteomic experiments towards targeted proteomic approaches that provide solutions to automation and economic concerns. Such approaches to validate biomarkers necessitate the mass spectrometric analysis of hundreds to thousands of human samples. As this takes place, a serendipitous opportunity has become evident. By the virtue that as one narrows the focus towards "single" protein targets (instead of entire proteomes) using pan-antibody-based enrichment techniques, a discovery science has emerged, so to speak. This is due to the largely unknown context in which "single" proteins exist in blood (i.e. polymorphisms, transcript variants, and posttranslational modifications) and hence, targeted proteomics has applications for established biomarkers. Furthermore, besides protein heterogeneity accounting for interferences with conventional immunometric platforms, it is becoming evident that this formerly hidden dimension of structural information also contains rich-pathobiological information. Consequently, targeted proteomics studies that aim to ascertain a protein's genuine presentation within disease- stratified populations and serve as a stepping-stone within a biomarker translational pipeline are of clinical interest. Roughly 128 million Americans are pre-diabetic, diabetic, and/or have kidney disease and public and private spending for treating these diseases is in the hundreds of billions of dollars. In an effort to create new solutions for the early detection and management of these conditions, described herein is the design, development, and translation of mass spectrometric immunoassays targeted towards diabetes and kidney disease. Population proteomics experiments were performed for the following clinically relevant proteins: insulin, C-peptide, RANTES, and parathyroid hormone. At least thirty-eight protein isoforms were detected. Besides the numerous disease correlations confronted within the disease-stratified cohorts, certain isoforms also appeared to be causally related to the underlying pathophysiology and/or have therapeutic implications. Technical advancements include multiplexed isoform quantification as well a "dual- extraction" methodology for eliminating non-specific proteins while simultaneously validating isoforms. Industrial efforts towards widespread clinical adoption are also described. Consequently, this work lays a foundation for the translation of mass spectrometric immunoassays into the clinical arena and simultaneously presents the most recent advancements concerning the mass spectrometric immunoassay approach.
ContributorsOran, Paul (Author) / Nelson, Randall (Thesis advisor) / Hayes, Mark (Thesis advisor) / Ros, Alexandra (Committee member) / Williams, Peter (Committee member) / Arizona State University (Publisher)
Created2011
Description
Signal processing techniques have been used extensively in many engineering problems and in recent years its application has extended to non-traditional research fields such as biological systems. Many of these applications require extraction of a signal or parameter of interest from degraded measurements. One such application is mass spectrometry immunoassay (MSIA) which has been one of the primary methods of biomarker discovery techniques. MSIA analyzes protein molecules as potential biomarkers using time of flight mass spectrometry (TOF-MS). Peak detection in TOF-MS is important for biomarker analysis and many other MS related application. Though many peak detection algorithms exist, most of them are based on heuristics models. One of the ways of detecting signal peaks is by deploying stochastic models of the signal and noise observations. Likelihood ratio test (LRT) detector, based on the Neyman-Pearson (NP) lemma, is an uniformly most powerful test to decision making in the form of a hypothesis test. The primary goal of this dissertation is to develop signal and noise models for the electrospray ionization (ESI) TOF-MS data. A new method is proposed for developing the signal model by employing first principles calculations based on device physics and molecular properties. The noise model is developed by analyzing MS data from careful experiments in the ESI mass spectrometer. A non-flat baseline in MS data is common. The reasons behind the formation of this baseline has not been fully comprehended. A new signal model explaining the presence of baseline is proposed, though detailed experiments are needed to further substantiate the model assumptions. Signal detection schemes based on these signal and noise models are proposed. A maximum likelihood (ML) method is introduced for estimating the signal peak amplitudes. The performance of the detection methods and ML estimation are evaluated with Monte Carlo simulation which shows promising results. An application of these methods is proposed for fractional abundance calculation for biomarker analysis, which is mathematically robust and fundamentally different than the current algorithms. Biomarker panels for type 2 diabetes and cardiovascular disease are analyzed using existing MS analysis algorithms. Finally, a support vector machine based multi-classification algorithm is developed for evaluating the biomarkers' effectiveness in discriminating type 2 diabetes and cardiovascular diseases and is shown to perform better than a linear discriminant analysis based classifier.
ContributorsBuddi, Sai (Author) / Taylor, Thomas (Thesis advisor) / Cochran, Douglas (Thesis advisor) / Nelson, Randall (Committee member) / Duman, Tolga (Committee member) / Arizona State University (Publisher)
Created2012
Description
Gold-silver alloy nanoparticles (NPs) capped with adenosine 5'-triphosphate were synthesized by borohydride reduction of dilute aqueous metal precursors. High-resolution transmission electron microscopy showed the as-synthesized particles to be spherical with average diameters ~4 nm. Optical properties were measured by UV-Visible spectroscopy (UV-Vis), and the formation of alloy NPs was verified across all gold:silver ratios by a linear shift in the plasmon band maxima against alloy composition. The molar absorptivities of the NPs decreased non-linearly with increasing gold content from 2.0 x 108 M-1 cm-1 (fÉmax = 404 nm) for pure silver to 4.1 x 107 M-1 cm-1 (fÉmax = 511 nm) for pure gold. The NPs were immobilized onto transparent indium-tin oxide composite electrodes using layer-by-layer (LbL) deposition with poly(diallyldimethylammonium) acting as a cationic binder. The UV-Vis absorbance of the LbL film was used to calculate the surface coverage of alloy NPs on the electrode. Typical preparations had average NP surface coverages of 2.8 x 10-13 mol NPs/cm2 (~5% of cubic closest packing) with saturated films reaching ~20% of ccp for single-layer preparations (1.0 ~ 10-12 mol NPs/cm2). X-ray photoelectron spectroscopy confirmed the presence of alloy NPs in the LbL film and showed silver enrichment of the NP surfaces by ~9%. Irreversible oxidative dissolution (dealloying) of the less noble silver atoms from the NPs on LbL electrodes was performed by cyclic voltammetry (CV) in sulfuric acid. Alloy NPs with higher gold content required larger overpotentials for silver dealloying. Dealloying of the more-noble gold atoms from the alloy NPs was also achieved by CV in sodium chloride. The silver was oxidized first to cohesive silver chloride, and then gold dealloyed to soluble HAuCl4- at higher potentials. Silver oxidation was inhibited during the first oxidative scan, but subsequent cycles showed typical, reversible silver-to-silver chloride voltammetry. The potentials for both silver oxidation and gold dealloying also shifted to more oxidizing potentials with increasing gold content, and both processes converged for alloy NPs with >60% gold content. Charge-mediated electrochemistry of silver NPs immobilized in LbL films, using Fc(meOH) as the charge carrier, showed that 67% of the NPs were electrochemically inactive.
ContributorsStarr, Christopher A (Author) / Buttry, Daniel A (Thesis advisor) / Petuskey, William (Committee member) / Jones, Anne (Committee member) / Arizona State University (Publisher)
Created2014
Description
Alkali treated aluminosilicate (geopolymer) was functionalized by surfactant to increase the hydrophobicity for making Pickering emulsion for the first part of this work. In the first part of this study, alkali treated metakaolin was functionalized with cetyltrimethylammonium bromide ((C16H33)N(CH3)3Br, CTAB). The electrostatic interaction between this quaternary ammonium and the surface of the aluminosilicate which has negative charge has taken place. The particles then were used to prepare Pickering emulsion. The resulting stable dispersions, obtained very fast at very simple conditions with low ratio of aluminosilicate to liquid phase. In the second part, the interaction between geopolymer and glycerol was studied to see the covalent grafting of the geopolymer for making geopolymer composite. The composite material would be the basis material to be used as support catalyst, thin coating reagent and flame retardant material and so on, Variety of techniques, Thermogravimetric (TGA), Particle-induced X-ray emission (PIXE), FTIR, Solid state NMR, Powder X-ray diffraction (PXRD), BET surface area, Elemental analysis (CHN), TEM, SEM and Optical microscopy were used to characterize the functionalized geopolymer.
ContributorsMesgar, Milad (Author) / Seo, Dong-Kuyn (Thesis advisor) / Petuskey, William (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012
Description
Mass spectrometric analysis requires that atoms from the sample be ionized in the gas phase. Secondary ion mass spectrometry achieves this by sputtering samples with an energetic primary ion beam. Several investigations of the sputtering and ionization process have been conducted. Oxygen is commonly used in secondary ion mass spectrometry (SIMS) to increase ion yields, but also can complicate the interpretation of SIMS analyses. An 18O implant in silicon has been used to quantify the oxygen concentration at the surface of sputtered silicon in order to study the dependence on oxygen of several sputtering and depth profile phenomena. The ion yield dependence of trace elements in silicon on the surface oxygen concentration is a function of the ionization potential of the element. The ion yield is high and unaffected by oxygen for elements with low ionization potential and ranges over several orders of magnitude for elements with high ionization potential. Depth resolution in sputter profiles has been shown to be degraded by the presence of oxygen, the mechanism of this effect has been investigated using an 18O implant to quantify oxygen levels and it is shown that the process does not appear to be a consequence of surface oxide formation. Molecular ions are a source of mass interference in SIMS analysis, and multiply charged atomic ion signals might be interference-free due to the possible instability of multiply-charged molecular ions. Sputtered SiH2+, AlH2+, BeH2+, Mo22+ and Mg22+ ions have been observed and appear surprisingly stable. The formation mechanism of some of these species has been explored.
ContributorsSobers, Richard Carlisle, Jr (Author) / Williams, Peter (Thesis advisor) / Hayes, Mark (Committee member) / Petuskey, William (Committee member) / Arizona State University (Publisher)
Created2012
Description
Cancer claims hundreds of thousands of lives every year in US alone. Finding ways for early detection of cancer onset is crucial for better management and treatment of cancer. Thus, biomarkers especially protein biomarkers, being the functional units which reflect dynamic physiological changes, need to be discovered. Though important, there are only a few approved protein cancer biomarkers till date. To accelerate this process, fast, comprehensive and affordable assays are required which can be applied to large population studies. For this, these assays should be able to comprehensively characterize and explore the molecular diversity of nominally "single" proteins across populations. This information is usually unavailable with commonly used immunoassays such as ELISA (enzyme linked immunosorbent assay) which either ignore protein microheterogeneity, or are confounded by it. To this end, mass spectrometric immuno assays (MSIA) for three different human plasma proteins have been developed. These proteins viz. IGF-1, hemopexin and tetranectin have been found in reported literature to show correlations with many diseases along with several carcinomas. Developed assays were used to extract entire proteins from plasma samples and subsequently analyzed on mass spectrometric platforms. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric techniques where used due to their availability and suitability for the analysis. This resulted in visibility of different structural forms of these proteins showing their structural micro-heterogeneity which is invisible to commonly used immunoassays. These assays are fast, comprehensive and can be applied in large sample studies to analyze proteins for biomarker discovery.
ContributorsRai, Samita (Author) / Nelson, Randall (Thesis advisor) / Hayes, Mark (Thesis advisor) / Borges, Chad (Committee member) / Ros, Alexandra (Committee member) / Arizona State University (Publisher)
Created2012
Description
Nanoporous crystalline oxides with high porosity and large surface areas are promising in catalysis, clean energy technologies and environmental applications all which require efficient chemical reactions at solid-solid, solid-liquid, and/or solid-gas interfaces. Achieving the balance between open porosity and structural stability is an ongoing challenge when synthesizing such porous materials. Increasing porosity while maintaining an open porous network usually comes at the cost of fragility, as seen for example in ultra low density, highly random porous aerogels. It has become increasingly important to develop synthetic techniques that produce materials with these desired properties while utilizing low cost precursors and increasing their structural strength. Based on non-alkoxide sol-gel chemistry, two novel synthetic methods for nanoporous metal oxides have been developed. The first is a high temperature combustion method that utilizes biorenewable oil, affording gamma alumina (Al2O3) with a surface area over 300 cm3/g and porosity over 80% and controllable pore sizes (average pore width 8 to 20 nm). The calcined crystalline products exhibit an aerogel-like textural mesoporosity. To demonstrate the versatility of the new method, it was used to synthesize highly porous amorphous silica (SiO2) which exhibited increased mechanical robustness while achieving a surface area of 960 m2/g and porosity of 85%. The second method utilizes sequential gelation of inorganic and organic precursors forming an interpenetrating inorganic/organic gel network. The method affords yttria-stabilized zirconia with surface area over 90 cm3/g and porosity over 60% and controllable pore sizes (average pore width 6 to 12 nm). X-ray diffraction, gas sorption analysis, Raman spectroscopy, nuclear magnetic resonance spectroscopy and electron microscopy were all used to characterize the structure, morphology, and the chemical structure of the newly afforded materials. Both novel methods produce products that show superior pore properties and robustness compared to equivalent commercially available and currently reported materials.
ContributorsLadd, Danielle (Author) / Seo, Don (Thesis advisor) / Häussermann, Ulrich (Committee member) / Petuskey, William (Committee member) / Arizona State University (Publisher)
Created2012