Investigation of AlInN barrier ISFET structures with GaN capping for pH detection

The pH response of GaN/AlInN/AlN/GaN ion-sensitive field effect transistor (ISFET) on Si substrates has been characterized. We analyzed the variation of the surface potential (ΔVsp/ΔpH) and current (ΔIds/ΔpH) with solution pH in devices with the same indium content (17%, in-plane lattice-matched to GaN) and different AlInN thickness (6 nm and 10 nm), and compared with the literature. The shrinkage of the barrier, that has the effect to increase the transconductance of the device, makes the 2-dimensional electron density (2DEG) at the interface very sensitive to changes in the surface. Although the surface potential sensitivity to pH is similar in the two devices, the current change with pH (ΔIds/ΔpH), when biasing the ISFET by a Ag/AgCl reference electrode, is almost 50% higher in the device with 6 nm AlInN barrier, compared to the device with 10 nm barrier. When measuring the current response (ΔIds/ΔpH) without reference electrode, the device with thinner AlInN layer has a larger response than the thicker one, of a factor of 140%, and that current response without reference electrode is only 22% lower than its maximum response obtained using reference electrode.

Experimental and numerical study of cracking of concrete due to reinforcement corrosion

La corrosión del acero es una de las patologías más importantes que afectan a las estructuras de hormigón armado que están expuestas a ambientes marinos o al ataque de sales fundentes. Cuando se produce corrosión, se genera una capa de óxido alrededor de la superficie de las armaduras, que ocupa un volumen mayor que el acero inicial; como consecuencia, el óxido ejerce presiones internas en el hormigón circundante, que lleva a la fisuración y, ocasionalmente, al desprendimiento del recubrimiento de hormigón. Durante los últimos años, numerosos estudios han contribuido a ampliar el conocimiento sobre el proceso de fisuración; sin embargo, aún existen muchas incertidumbres respecto al comportamiento mecánico de la capa de óxido, que es fundamental para predecir la fisuración. Por ello, en esta tesis se ha desarrollado y aplicado una metodología, para mejorar el conocimiento respecto al comportamiento del sistema acero-óxido-hormigón, combinando experimentos y simulaciones numéricas. Se han realizado ensayos de corrosión acelerada en condiciones de laboratorio, utilizando la técnica de corriente impresa. Con el objetivo de obtener información cercana a la capa de acero, como muestras se seleccionaron prismas de hormigón con un tubo de acero liso como armadura, que se diseñaron para conseguir la formación de una única fisura principal en el recubrimiento. Durante los ensayos, las muestras se equiparon con instrumentos especialmente diseñados para medir la variación de diámetro y volumen interior de los tubos, y se midió la apertura de la fisura principal utilizando un extensómetro comercial, adaptado a la geometría de las muestras. Las condiciones de contorno se diseñaron cuidadosamente para que los campos de corriente y deformación fuesen planos durante los ensayos, resultando en corrosión uniforme a lo largo del tubo, para poder reproducir los ensayos en simulaciones numéricas. Se ensayaron series con varias densidades de corriente y varias profundidades de corrosión. De manera complementaria, el comportamiento en fractura del hormigón se caracterizó en ensayos independientes, y se midió la pérdida gravimétrica de los tubos siguiendo procedimientos estándar. En todos los ensayos, la fisura principal creció muy despacio durante las primeras micras de profundidad de corrosión, pero después de una cierta profundidad crítica, la fisura se desarrolló completamente, con un aumento rápido de su apertura; la densidad de corriente influye en la profundidad de corrosión crítica. Las variaciones de diámetro interior y de volumen interior de los tubos mostraron tendencias diferentes entre sí, lo que indica que la deformación del tubo no fue uniforme. Después de la corrosión acelerada, las muestras se cortaron en rebanadas, que se utilizaron en ensayos post-corrosión. El patrón de fisuración se estudió a lo largo del tubo, en rebanadas que se impregnaron en vacío con resina y fluoresceína para mejorar la visibilidad de las fisuras bajo luz ultravioleta, y se estudió la presencia de óxido dentro de las grietas. En todas las muestras, se formó una fisura principal en el recubrimiento, infiltrada con óxido, y varias fisuras secundarias finas alrededor del tubo; el número de fisuras varió con la profundidad de corrosión de las muestras. Para muestras con la misma corrosión, el número de fisuras y su posición fue diferente entre muestras y entre secciones de una misma muestra, debido a la heterogeneidad del hormigón. Finalmente, se investigó la adherencia entre el acero y el hormigón, utilizando un dispositivo diseñado para empujar el tubo en el hormigón. Las curvas de tensión frente a desplazamiento del tubo presentaron un pico marcado, seguido de un descenso constante; la profundidad de corrosión y la apertura de fisura de las muestras influyeron notablemente en la tensión residual del ensayo. Para simular la fisuración del hormigón causada por la corrosión de las armaduras, se programó un modelo numérico. Éste combina elementos finitos con fisura embebida adaptable que reproducen la fractura del hormigón conforme al modelo de fisura cohesiva estándar, y elementos de interfaz llamados elementos junta expansiva, que se programaron específicamente para reproducir la expansión volumétrica del óxido y que incorporan su comportamiento mecánico. En el elemento junta expansiva se implementó un fenómeno de despegue, concretamente de deslizamiento y separación, que resultó fundamental para obtener localización de fisuras adecuada, y que se consiguió con una fuerte reducción de la rigidez tangencial y la rigidez en tracción del óxido. Con este modelo, se realizaron simulaciones de los ensayos, utilizando modelos bidimensionales de las muestras con elementos finitos. Como datos para el comportamiento en fractura del hormigón, se utilizaron las propiedades determinadas en experimentos. Para el óxido, inicialmente se supuso un comportamiento fluido, con deslizamiento y separación casi perfectos. Después, se realizó un ajuste de los parámetros del elemento junta expansiva para reproducir los resultados experimentales. Se observó que variaciones en la rigidez normal del óxido apenas afectaban a los resultados, y que los demás parámetros apenas afectaban a la apertura de fisura; sin embargo, la deformación del tubo resultó ser muy sensible a variaciones en los parámetros del óxido, debido a la flexibilidad de la pared de los tubos, lo que resultó fundamental para determinar indirectamente los valores de los parámetros constitutivos del óxido. Finalmente, se realizaron simulaciones definitivas de los ensayos. El modelo reprodujo la profundidad de corrosión crítica y el comportamiento final de las curvas experimentales; se comprobó que la variación de diámetro interior de los tubos está fuertemente influenciada por su posición relativa respecto a la fisura principal, en concordancia con los resultados experimentales. De la comparación de los resultados experimentales y numéricos, se pudo extraer información sobre las propiedades del óxido que de otra manera no habría podido obtenerse. Corrosion of steel is one of the main pathologies affecting reinforced concrete structures exposed to marine environments or to molten salt. When corrosion occurs, an oxide layer develops around the reinforcement surface, which occupies a greater volume than the initial steel; thus, it induces internal pressure on the surrounding concrete that leads to cracking and, eventually, to full-spalling of the concrete cover. During the last years much effort has been devoted to understand the process of cracking; however, there is still a lack of knowledge regarding the mechanical behavior of the oxide layer, which is essential in the prediction of cracking. Thus, a methodology has been developed and applied in this thesis to gain further understanding of the behavior of the steel-oxide-concrete system, combining experiments and numerical simulations. Accelerated corrosion tests were carried out in laboratory conditions, using the impressed current technique. To get experimental information close to the oxide layer, concrete prisms with a smooth steel tube as reinforcement were selected as specimens, which were designed to get a single main crack across the cover. During the tests, the specimens were equipped with instruments that were specially designed to measure the variation of inner diameter and volume of the tubes, and the width of the main crack was recorded using a commercial extensometer that was adapted to the geometry of the specimens. The boundary conditions were carefully designed so that plane current and strain fields were expected during the tests, resulting in nearly uniform corrosion along the length of the tube, so that the tests could be reproduced in numerical simulations. Series of tests were carried out with various current densities and corrosion depths. Complementarily, the fracture behavior of concrete was characterized in independent tests, and the gravimetric loss of the steel tubes was determined by standard means. In all the tests, the main crack grew very slowly during the first microns of corrosion depth, but after a critical corrosion depth it fully developed and opened faster; the current density influenced the critical corrosion depth. The variation of inner diameter and inner volume of the tubes had different trends, which indicates that the deformation of the tube was not uniform. After accelerated corrosion, the specimens were cut into slices, which were used in post-corrosion tests. The pattern of cracking along the reinforcement was investigated in slices that were impregnated under vacuum with resin containing fluorescein to enhance the visibility of cracks under ultraviolet lightening and a study was carried out to assess the presence of oxide into the cracks. In all the specimens, a main crack developed through the concrete cover, which was infiltrated with oxide, and several thin secondary cracks around the reinforcement; the number of cracks diminished with the corrosion depth of the specimen. For specimens with the same corrosion, the number of cracks and their position varied from one specimen to another and between cross-sections of a given specimen, due to the heterogeneity of concrete. Finally, the bond between the steel and the concrete was investigated, using a device designed to push the tubes of steel in the concrete. The curves of stress versus displacement of the tube presented a marked peak, followed by a steady descent, with notably influence of the corrosion depth and the crack width on the residual stress. To simulate cracking of concrete due to corrosion of the reinforcement, a numerical model was implemented. It combines finite elements with an embedded adaptable crack that reproduces cracking of concrete according to the basic cohesive model, and interface elements so-called expansive joint elements, which were specially designed to reproduce the volumetric expansion of oxide and incorporate its mechanical behavior. In the expansive joint element, a debonding effect was implemented consisting of sliding and separation, which was proved to be essential to achieve proper localization of cracks, and was achieved by strongly reducing the shear and the tensile stiffnesses of the oxide. With that model, simulations of the accelerated corrosion tests were carried out on 2- dimensional finite element models of the specimens. For the fracture behavior of concrete, the properties experimentally determined were used as input. For the oxide, initially a fluidlike behavior was assumed with nearly perfect sliding and separation; then the parameters of the expansive joint element were modified to fit the experimental results. Changes in the bulk modulus of the oxide barely affected the results and changes in the remaining parameters had a moderate effect on the predicted crack width; however, the deformation of the tube was very sensitive to variations in the parameters of oxide, due to the flexibility of the tube wall, which was crucial for indirect determination of the constitutive parameters of oxide. Finally, definitive simulations of the tests were carried out. The model reproduced the critical corrosion depth and the final behavior of the experimental curves; it was assessed that the variation of inner diameter of the tubes is highly influenced by its relative position with respect to the main crack, in accordance with the experimental observations. From the comparison of the experimental and numerical results, some properties of the mechanical behavior of the oxide were disclosed that otherwise could not have been measured.

Determinação do contorno pulmonar orientado em sequências temporais de imagens de RM pela transformada de Hough.

O estudo do movimento pulmonar é assunto de grande interesse na área médica. A observação direta do mesmo é inviável, uma vez que o pulmão colapsa quando a caixa torácica é aberta. Dentre os meios de observação indireta, escolheu-se o imageamento por ressonância magnética em respiração livre e sem uso de nenhum gás para melhorar o contraste ou qualquer informação de sincronismo. Esta escolha propõe diversos desafios, como: a superar a alta variação na qualidade das imagens, que é baixa, em geral, e a suscetibilidade a artefatos, entre outras limitações a serem superadas. Imagens de Tomografia Computadorizada apresentam melhor qualidade e menor tempo de aquisição, mas expõem o paciente a níveis consideráveis de radiação ionizante. É apresentada uma metodologia para segmentação do pulmão, produzindo um conjunto de pontos coordenados. Isto é feito através do processamento temporal da sequência de imagens de RM. Este processamento consiste nas seguintes etapas: geração de imagens temporais (2DSTI), transformada de Hough modificada, algoritmo de contornos ativos e geração de silhueta. A partir de um dado ponto, denominado centro de rotação, são geradas diversas imagens temporais com orientações variadas. É proposta uma formulação modificada da transformada de Hough para determinar curvas parametrizadas que sejam síncronas ao movimento diafragmático, chamados movimentos respiratórios. Também são utilizadas máscaras para delimitar o domínio de aplicação da transformada de Hough. São obtidos movimentos respiratórios que são suavizados pelo algoritmo de contornos ativos e, assim, permitem a geração de contornos para cada quadro pertencente a sequência e, portanto, de uma silhueta do pulmão para cada sequência.

Boston, Massachusetts Region LIDAR First Return Elevation Data, 2002

LIDAR (LIght Detection And Ranging) first return elevation data of the Boston, Massachusetts region from MassGIS at 1-meter resolution. This LIDAR data was captured in Spring 2002. LIDAR first return data (which shows the highest ground features, e.g. tree canopy, buildings etc.) can be used to produce a digital terrain model of the Earth's surface. This dataset consists of 74 First Return DEM tiles. The tiles are 4km by 4km areas corresponding with the MassGIS orthoimage index. This data set was collected using 3Di's Digital Airborne Topographic Imaging System II (DATIS II). The area of coverage corresponds to the following MassGIS orthophoto quads covering the Boston region (MassGIS orthophoto quad ID: 229890, 229894, 229898, 229902, 233886, 233890, 233894, 233898, 233902, 233906, 233910, 237890, 237894, 237898, 237902, 237906, 237910, 241890, 241894, 241898, 241902, 245898, 245902). The geographic extent of this dataset is the same as that of the MassGIS dataset: Boston, Massachusetts Region 1:5,000 Color Ortho Imagery (1/2-meter Resolution), 2001 and was used to produce the MassGIS dataset: Boston, Massachusetts, 2-Dimensional Building Footprints with Roof Height Data (from LIDAR data), 2002 [see cross references].

Locating a strand of the Seattle Fault Zone in southeast Seattle, Washington through topographic analysis, borehole analysis and ground penetrating radar

Contributing to the evaluation of seismic hazards, a previously unmapped strand of the Seattle Fault Zone (SFZ), cutting across the southwest side of Lake Washington and southeast Seattle, is located and characterized on the basis of bathymetry, borehole logs, and ground penetrating radar (GPR). Previous geologic mapping and geophysical analysis of the Seattle area have generally mapped the locations of some strands of the SFZ, though a complete and accurate understanding of locations of all individual strands of the fault system is still incomplete. A bathymetric scarp-like feature and co-linear aeromagnetic anomaly lineament defined the extent of the study area. A 2-dimensional lithology cross-section was constructed using six boreholes, chosen from suitable boreholes in the study area. In addition, two GPR transects, oblique to the proposed fault trend, served to identify physical differences in subsurface materials. The proposed fault trace follows the previously mapped contact between the Oligocene Blakeley Formation and Quaternary deposits, and topographic changes in slope. GPR profiles in Seward Park and across the proposed fault location show the contact between the Blakeley Formation and unconsolidated glacial deposits, but it does not constrain an offset. However, north-dipping beds in the Blakely Formation are consistent with previous interpretations of P-wave seismic profiles on Mercer Island and Bellevue, Washington. The profiles show the mapped location of the aeromagnetic lineament in Lake Washington and the inferred location of the steeply-dipping, high-amplitude bedrock reflector, representing a fault strand. This north-dipping reflector is likely the same feature identified in my analysis. I characterize the strand as a splay fault, antithetic to the frontal fault of the SFZ. This new fault may pose a geologic hazard to the region.

Seismically-Induced Rock-Slope Failure: Numerical Investigation using the Bonded Particle Model

Thesis (Ph.D.)--University of Washington, 2016-06

Crystal structures of fusion proteins with large-affinity tags

The fusion of a protein of interest to a large-affinity tag, such as the maltose-binding protein (MBP), thioredoxin (TRX), or glutathione-S-transferase (GST), can be advantageous in terms of increased expression, enhanced solubility, protection from proteolysis, improved folding, and protein purification via affinity chromatography. Unfortunately, crystal growth is hindered by the conformational heterogeneity induced by the fusion tag, requiring that the tag is removed by a potentially problematic cleavage step. The first three crystal structures of fusion proteins with large-affinity tags have been reported recently. All three structures used a novel strategy to rigidly fuse the protein of interest to MBP via a short three- to five-amino acid spacer. This strategy has the potential to aid structure determination of proteins that present particular experimental challenges and are not conducive to more conventional crystallization strategies (e.g., membrane proteins). Structural genomics initiatives may also benefit from this approach as a way to crystallize problematic proteins of significant interest.

Detection of surfactant protein A (SP-A) and surfactant protein D (SP-D) in equine synovial fluid with immunoblotting

Once considered unique to the lung, surfactant proteins have been clearly identified in the intestine and peritoneum and are suggested to exist in several other organs. In the lung, surfactant proteins assist in the formation of a monolayer of surface-active phospholipid at the liquid-air interface of the alveolar lining, reducing the surface tension at this surface. In contrast, surface-active phospholipid adsorbed to articular surfaces has been identified as the load-bearing boundary lubricant of the joint. This raises the question of whether surfactant proteins in synovial fluid (SF) are required for the formation of the adsorbed layer in normal joints. Proteins from small volumes of equine SF were resolved by 1- and 2-dimensional polyacrylamide gel electrophoresis and detected by Western blotting to investigate the presence of surfactant proteins. The study showed that surfactant proteins A and D (SP-A and SP-D) are present in the SF of normal horses. We suggest that, like surface-active phospholipid, SP-A and SP-D play a significant role in the functioning of joints. Next will be clarification of the roles of surfactant proteins as disease markers in a variety of joint diseases, such as degenerative joint disease and inflammatory problems.

Evidence for energy relaxation via a radiative cascade in surface-passivated PbS quantum dots

Multiple emission peaks have been observed from surface passivated PbS nanocrystals displaying strong quantum confinement. The emission spectra are shown to be strongly dependent on the excited-state parity. We also find that intraband energy relaxation from initial states excited far above the band-edge is nearly three orders of magnitude slower than that found in other nanocrystal quantum dots, providing evidence of inefficient energy relaxation via phonon emission. The initial-state parity dependence of the photoluminescent emission properties suggests that energy relaxation from the higher excited states occurs via a radiative cascade, analogous to energy relaxation in atomic systems. Such radiative cascade emission is possible from ideal zero-dimensional semiconductors, where electronic transitions can be decoupled from phonon modes.

Milk Proteomics

Milk proteins have been studied continuously for over 50 years. Knowledge of this complex protein system has evolved incrementally in recent decades, largely coinciding with advances in technology. Proteomics and associated technologies have the potential to facilitate further advances in our knowledge of milk proteins. Proteomics allows for the detection, identification and characterization of milk proteins. More importantly, proteomics facilitates the analysis of large numbers of milk proteins simultaneously. In the first part of this review we provide a description of the key techniques used within proteomic methodologies, with an emphasis on their general uses within proteomics. In the second part we summarize recent applications of proteomics to milk proteins and highlight the potential for new and rapid advances in the analysis of milk proteins. In particular, we emphasise the effectiveness of two-dimensional gel electrophoresis in combination with various mass spectrometry techniques for the detailed characterization of milk proteins. (C) 2004 Elsevier Ltd. All rights reserved.

Pulling out threads from the cosmic tapestry: Defining filaments of galaxies

Filaments of galaxies are the dominant feature of modern large-scale redshift surveys. They can account for up to perhaps half of the baryonic mass budget of the Universe and their distribution and abundance can help constrain cosmological models. However, there remains no single, definitive way in which to detect, describe, and define what filaments are and their extent. This work examines a number of physically motivated, as well as statistical, methods that can be used to define filaments and examines their relative merits.

A new algorithm for the detection of intercluster galaxy filaments using galaxy orientation alignments

We present a new algorithm for detecting intercluster galaxy filaments based upon the assumption that the orientations of constituent galaxies along such filaments are non-isotropic. We apply the algorithm to the 2dF Galaxy Redshift Survey catalogue and find that it readily detects many straight filaments between close cluster pairs. At large intercluster separations (> 15 h(-1) Mpc), we find that the detection efficiency falls quickly, as it also does with more complex filament morphologies. We explore the underlying assumptions and suggest that it is only in the case of close cluster pairs that we can expect galaxy orientations to be significantly correlated with filament direction.

Various topological excitations in the SO(4) gauge field in higher dimensions

Following the original analysis Of Zhang and Hu for the 4-dimensional generalization of Quantum Hall effect, there has been much work from different viewpoints on the higher dimensional condensed matter systems. In this paper, we discuss three kinds of topological excitations in the SO(4) gauge field of condensed matter systems in 4-dimension-the instantons and anti-instantons, the 't Hooft-Polyakov monopoles, and the 2-membranes. Using the phi-mapping topological theory, it is revealed that there are 4-, 3-, and 2-dimensional topological currents inhering in the SO (4) gauge field, and the above three kinds of excitations can be directly and explicitly derived from these three kinds of currents, respectively. Moreover, it is shown that the topological charges of these excitations are characterized by the Hopf indices and Brouwer degrees of phi-mapping. (c) 2005 Elsevier Inc. All rights reserved.

Efffluent flux prediction in variably saturated soil zones within a septic tank-soil absorption trench

The treatment and hydraulic mechanisms in a septic tank-soil absorption system ( SAS) are highly influenced by the clogging layer or biomat zone which develops on bottom and lower sidewall surfaces within the trench. Flow rates through the biomat and sub-biomat zones are governed largely by the biomat hydraulic properties (resistance and hydraulic conductivity) and the unsaturated hydraulic conductivity of the underlying soil. One- and 2-dimensional models were used to investigate the relative importance of sidewall and vertical flow rates and pathways in SAS. Results of 1-dimensional modelling show that several orders of magnitude variation in saturated hydraulic conductivity (Ks) reduce to a 1 order of magnitude variation in long-term flow rates. To increase the reliability of prediction of septic trench hydrology, HYDRUS-2D was used to model 2-dimensional flow. In the permeable soils, under high trench loading, effluent preferentially flowed in the upper region of the trench where no resistant biomat was present (the exfiltration zone). By comparison, flow was more evenly partitioned between the biomat zones and the exfiltration zones of the low permeability soil. An increase in effluent infiltration corresponded with a greater availability of exfiltration zone, rather than a lower resistance of biomat. Results of modelling simulations demonstrated the important role that a permeable A horizon may play in limiting surface surcharge of effluent under high trench hydraulic loading.

Molecular diversity in venom from the Australian Brown Snake, Pseudonaja textilis

Venom from the Australian elapid Pseudonaja textilis (Common or Eastern Brown snake), is the second most toxic snake venom known and is the most common cause of death from snake bite in Australia. This venom is known to contain a prothrombin activator complex, serine proteinase inhibitors, various phospholipase A(2)s, and pre-and postsynaptic neurotoxins. In this study, we performed a proteomic identification of the venom using two- dimensional gel electrophoresis, mass spectrometry, and de novo peptide sequencing. We identified most of the venom proteins including proteins previously not known to be present in the venom. In addition, we used immunoblotting and post-translational modification-specific enzyme stains and antibodies that reveal the complexity and regional diversity of the venom. Modifications observed include phosphorylation, gamma-carboxylation, and glycosylation. Glycoproteins were further characterized by enzymatic deglycosylation and by lectin binding specificity. The venom contains an abundance of glycoproteins with N-linked sugars that include glucose/mannose, N-acetylgalactosamine, N-acetylglucosamine, and sialic acids. Additionally there are multiple isoforms of mammalian coagulation factors that comprise a significant proportion of the venom. Indeed two of the identified proteins, a procoagulant and a plasmin inhibitor, are currently in development as human therapeutic agents.