Mass spectrometry (MS) has proven itself to be indispensable for the analysis of biomolecules and molecular systems. This research has three goals: (1) expand on prior work toward the discovery of novel diagnostic targets for Valley Fever, (2) evaluate current mass spectrometry based proteomics for the discovery of non-host protein in complex host biological samples, and (3) investigate the potential for two gas phase techniques, surface induced dissociation, and ion mobility for the analysis of carbohydrate based molecules. Mass spectrometry has allowed for great advances in the identification of proteins in biological samples through implementing liquid chromatography tandem mass spectrometry and bioinformatics techniques known as proteomics. Proteomics techniques were used to elucidate a portion of the biosignature of Valley Fever (VF), a disease of great importance in the arid regions of the western United States. Current diagnostics for this fungal lung disease are remarkably unreliable which creates a need for an unfailing diagnostic method. Using a new generation of instrumentation along with directed methods, four previously discovered VF marker proteins were evaluated for their presence in mouse plasma, lung homogenate and bronchoalveolar lavage fluid samples. Due to inconclusive data, discovery proteomics approaches were then used to identify possible diagnostic targets in both human and mouse bronchoalveolar lavage fluid. In human bronchoalveolar lavage fluid, one potential target was discovered in five out of eight VF positive samples, and two further identifications of VF in negative samples. Mouse bronchoalveolar lavage fluid also showed the presence of this protein. Multiple-reaction monitoring based validation, using two-dimensional online separations for the presence of either the newly discovered protein or the four previously discovered proteins, was inconclusive. Emerging from the difficulties observed by the author and colleagues in identifying infectious agent proteins in complex host biological samples, an investigation of the feasibility of undertaking such endeavors was performed. One of the main complications thwarting the discovery of infectious agent proteins is the dynamic range of protein concentration in the host biological sample. This issue was resolved by using commercially available mass spectrometry and a two-dimensional liquid chromatographic separations platform. This enhanced separation combined with cost-effective protein normalization techniques, identified non-host proteins with good sequence coverage and spectral counts. Combining antibody-based depletion of highly abundant plasma proteins in bronchoalveolar lavage fluid, with at least a three fraction sample analysis enabled detection of a low abundant non-host protein (2pmol in 50μg host protein) with high sequence coverage. Glycosylation, an abundant post-translational modification of protein composed of carbohydrate oligomers may hold within its structure more biologically relevant information than the DNA that encoded the protein on which the glycan resides. The analysis of glycosylation plays a critical role in understanding biology. Carbohydrate based moieties pose many distinct challenges to their analysis; two of which are isobaric fundamental units and complex branching chemistry. Mass spectrometry provides a way of overcoming some of these challenges. To examine the complex biomolecules, a gas phase ion separation technique, known as ion mobility, and a non-traditional ion activation technique, surface-induced dissociation, were used. Surface-induced dissociation provides analogous fragmentation patterns to those generated via collision-induced dissociation (CID); however, much more extensive fragmentation can be achieved in a single tandem MS experiment. Using the gas-phase separations power of ion mobility showed that multiple conformations were adopted by relatively simple oligosaccharides. Ion mobility was also successfully used to determine fragment ion lineage of isobaric fragment ions, through inline separation between two differential fragmentation experiments.

The interaction of a rectangular turbulent jet with a free surface for three jet-exit aspect ratios is experimentally investigated using Particle Image Velocimetry (PIV). The jet exits from a sharp edged rectangular orifice plate, parallel to the free surface and has a jet width of d = 10 mm. Aspect ratios of 1, 2 and 4 are studied with a fixed offset of 3d from the free surface. Reynolds and Froude numbers based on the bulk velocity are 6900 and 1.27 respectively. Detailed 2-D velocity fields are captured using the PIV in the central x-y plane for 0 < x/d < 23.5. The distribution of Reynolds shear stresses and turbulent kinetic energy show that they are suppressed in the vicinity of the free surface due to confinement. There was a significant effect of nozzle geometry on the reattachment point and recirculation region of the jets. / May 2016

Three-dimensional (3D) non-contact optical methods for surface inspection are of significant interest to many industrial sectors. Many aspects of manufacturing processes have become fully automated resulting in high production volumes. However, this is not necessarily the case for surface defect inspection. Existing human visual analysis of surface defects is qualitative and subject to varying interpretation. Automated 3D non-contact analysis should provide a robust and systematic quantitative approach. However, different 3D optical measurement technologies use different physical principles, interact with surfaces and defects in diverse ways, leading to variation in measurement data. Instrument s native software processing of the data may be non-traceable in nature, leading to significant uncertainty about data quantisation. Sub-millimetric level surface defect artefacts have been created using Rockwell and Vickers hardness testing equipment on various substrates. Four different non-contact surface measurement instruments (Alicona InfiniteFocus G4, Zygo NewView 5000, GFM MikroCAD Lite and Heliotis H3) have been utilized to measure different defect artefacts. The four different 3D optical instruments are evaluated by calibrated step-height created using slipgauges and reference defect artefacts. The experimental results are compared to select the most suitable instrument capable of measuring surface defects in robust manner. This research has identified a need for an automatic tool to quantify surface defect and thus a mathematical solution has been implemented for automatic defect detection and quantification (depth, area and volume) in 3D. A simulated defect softgauge with a known geometry has been developed in order to verify the implemented algorithm and provide mathematical traceability. The implemented algorithm has been identified as a traceable, highly repeatable, and high speed solution to quantify surface defect in 3D. Various industrial components with suspicious features and solder joints on PCB are measured and quantified in order to demonstrate applicability.

Planarization techniques such as Surface planer (better known as Fly-cut) and chemical-mechanical polishing (CMP) can be used to improve the bump roughness and bump height uniformity within the die and wafer which can be beneficial for solder based bump stacking and Cu-Cu direct bonding [1]. In this paper the influence of both planarization techniques on 20μm pitch Cu and CuNiSn bumps embedded in polymer are studied. The polymer protects the bumps from the shearing force of the planarization process and will later serve as a underfill material for the resulting gap of a 3D stack. The microbump planarization process will be discussed. Furthermore characterization of the bump height uniformity across the wafer using SEM and High Resolution Profilometry (HRP) is reported.

The stationary phase on chemically modified supports for liquid chromatography is described as a mixture of the surface-bonded species, the active unmodified surface, and associated mobile phase components. Each of these three factors in stationary phase formation is examined and improved qualitative and quantitative descriptions of the stationary phase are provided. The role of the active unmodified surface was examined by synthesizing a carbon support and chemically modifying it with octyl groups. The modified carbon had a greater affinity for lipophilic probes than an octyl silica. The lipophilicity of the octyl carbon was attenuated relative to the unmodified carbon. The physical state of the bonded species in C(,18) and C(,8) packings was studied using carbon-13 NMR. Peak widths of 2-7 ppm indicated a liquid-like nature but with restricted movement. Only the 7 to 10 carbons in a C(,18) chain farthest from the surface were sufficiently motile to produce a signal. The C(,8) packing showed more rigid chains with only the top 3 or 4 carbons responding. The liquid-like nature of a C(,18) chain increased with the lipophilic character of the solvent, indicating that solvation of the bonded species was directly related to the mobile phase composition. Changes in temperature had little effect on the physical state of the bonded species, but chromatographic enthalpy measurements showed that changes in stationary phase composition could be induced by warming the column and held by subsequent cooling. Quantitative measurements of stationary phase compositions revealed linear distribution isotherms for the organic modifiers methanol, acetonitrile, and tetrahydrofuran. Chromatographic selectivities for homologous n-alkanols correlated linearly with organic modifier concentrations in the stationary phases. The stationary phase volumes, which increased with increasing modifier concentrations, are interpreted as constituting filling of the pores in the support with a gradient of modifier enrichment toward the surface.

published_or_final_version / Physics / Master / Master of Philosophy

published_or_final_version / abstract / Electrical and Electronic Engineering / Master / Master of Philosophy

Convection at the interior surface of a building represents a significant portion of the heat transfer in office buildings with large glazing areas. While a large number of these office buildings utilize ceiling slot diffusers at the glazed building perimeter, convection correlations specific to these diffusers have not yet been investigated. This paper describes convection correlations developed for ceiling slot diffusers and examines the effect of temperature, various window geometries, and diffuser jet momentum on these correlations. The paper also examines the effect of venetian blinds on the overall correlations at various blind angle configurations: open, partially open, and closed. The results of the examined phenomena are validated in both heating and cooling conditions. All together, this paper represents the effort of over 100 individual experiments. The results show that forced convection is dominant at all air flow rates, and correlations are developed as a function of air volumetric flow rate with supply air temperature utilized as the reference. The correlations are found to rely only on window position, and are independent of temperature difference between surface and supply, diffuser position, and diffuser jet momentum. With respect to the blinds, the only relevant parameter is the angle of the blinds except when the blinds are open. When the blinds are open and at 45º, convective heat transfer is enhanced. Conversely, convection is decreased when the blinds are closed and at -45º. There is also a decrease in the convective heat transfer with a full window in contrast to a half window when the blinds are open. Finally, there is little difference between the convection correlations developed for heated and cooled environments. / text

<p>Two methods for the measurement of micro-scale stressvariations of press felt surfaces were developed. The methodswere based on a thin plastic film that was coated with anopaque stress-sensitive layer (Cronapress conversion film). Thefilm was compressed between a felt and a smooth surface. Uponapplication of load the opaque layer became partiallytransparent at the locations where load was applied by thesurface fibres of the felt. The degree of transparency was afunction of the locally applied stress. The spatial resolutionof the method was 6.3 µm, which means that even details ofthe order of the diameter of a batt fibre diameter can beresolved.</p><p>Parameters characterising the stress variations were used toquantitatively describe the extent of the stress variations,the size of the contact areas and the distance between them.The applicability of these contact characterisation parameterswas evaluated in laboratory wet pressing experiments and inpilot paper machine trials for two sets of specially designedpress felts. In general, the dewatering result was mainlyinfluenced by the diameter of the felt surface batt fibres andby the web grammage. For a specific pulp type and operatingconditions a multivariate model was formulated based on themeasured web dryness, web grammage and each contactcharacterisation parameter. The model was able to describe thedewatering capability of the different felts tested. Contactcharacterisation parameters related to contact properties (e.g.contact area ratio) gave the best prediction for low grammagewebs, while parameters related to flow properties (e.g. size ofopenings) gave the best prediction for high grammage webs.</p><p>Furthermore it was found that at a certain web grammage, thesurface batt fibre diameter did not have an influence on thedewatering result. This grammage was termed "transitiongrammage". Below the transition grammage a fine surface gavesignificantly better dewatering, while the opposite trend wasobserved above the transition grammage. Based on these results,a modified dewatering hypothesis was formulated. Thishypothesis links the non-uniform compression of the wet webwith different dewatering situations for low and high grammagewebs.</p><p><b>Keywords</b>Press felts, Roughness, Smoothness, SurfaceStructure, Uniformity, Wet pressing, Batt fibre, Base weave,Stress variations, Micro-scale.</p>

<p>Chlorite is a ferrous silicate mineral occurring as afracture filling mineral in the Swedish granite bedrock thatsurrounds the area of the candidate Swedish geologicalrepositories for nuclear waste.</p><p>To investigate the importance of chlorites as a naturalbarrier for radionuclide migration sorption of Ni(II) onto anatural chlorite was chosen as the studied system. The sorptionbehaviour was studied using batch technique under differentexperimental conditions by varying the concentration ofbackground electrolyte, pH and initial nickel concentration.Our experiments showed that sorption is dependent of pH; belowpH 4 no sorption occurs and in the pH range 7-11 the sorptionmaxima was found. The sorption shows no dependence of ionicstrength in our experiments and together with pH dependency weconclude that the sorption of nickel to chlorite is mostlyoccurring through surface complexation. The distributioncoefficient, K<i>d</i>, was determined for our results and in the range formaximal sorption the K<i>d</i>is approximately 10³cm³/g.</p><p>Our experimental data were described using a diffuse doublelayer model, including strong and weak surface sites, in thesoftware PHREECQ and the results obtained from PHREEQC werealso used for a fit of the data in the software FITEQL. Thesurface complexes that dominate the sorption of nickel tochlorite from our model are Chl_ONi⁺(weak) and for pH above 9 Chl_ONi(OH)^-(weak). Flow-through technique was used in ourinvestigations regarding the dissolution rate of a naturalchlorite and the experimental results show that the dissolutionrate of chlorite is strongly pH dependent and at pH 2 thehighest dissolution rate (R_Si) could be determined to 7• 10^-11mol/(m²s) based on silica data.</p><p><b>Keywords:</b>chlorite, nickel, sorption, surfacecomplexation, dissolution rate.</p>