Hormonally-triggered regulatory hierarchies play a major role in organismal development. Disruption of a single member of such a hierarchy can lead to irregular development and disease. Therefore, knowledge of the members involved and the mechanisms controlling signaling through such pathways is of great importance in understanding how resulting developmental defects occur. Type II transmembrane serine proteases (TTSPs) make up a family of cell surface-associated proteases that play important roles in the development and homeostasis of a number of mammalian tissues. Aberrant expression of TTSPs is linked to several human disorders, including deafness, heart and respiratory disease and cancer. However, the mechanism by which these proteases function remains unknown. The ecdysone-responsive Stubble TTSP of Drosophila serves as a good model in which to study the functional mechanism of the TTSP family. The Stubble protease interacts with the intracellular Rho1 (RhoA) pathway to control epithelial development in imaginal discs. The Rho1 signaling pathway regulates cellular behavior via control of gene expression and actin cytoskeletal dynamics. However, the mechanism by which the Stubble protease interacts with the Rho1 pathway to control epithelial development, in particular leg imaginal disc morphogenesis, has yet to be elucidated. The Stubble protein consists of several conserved domains. One approach to a better understanding of the mechanism of action of Stubble in regulating Rho1 signaling is to define which of the conserved domains within the protease are required for proper function. Sequence analysis of twelve recessive Stubble mutant alleles has revealed that the proteolytic domain is essential for proper function. Alleles containing mutations which disrupt regions of the protease domain necessary for protease activation or substrate binding, as well as those with deletions or truncations that remove some portion of the proteolytic domain, result in defective epithelial development in vivo. In contrast, mutations in other regions of the Stubble protein, including the disulfide-knotted and cytoplasmic domains, were not observed. Another important step for defining the connection between Stubble and Rho1 signaling is to identify a Stubble target that acts as an upstream regulator of the Rho1 pathway. We performed a genetic screen in which 97 of the 147 Drosophila non-olfactory and non-gustatory G-protein-coupled receptors (GPCRs), a family of proteins that has been shown to be protease-activated and to activate Rho1 signaling, were tested for interactions with a mutant allele of Stubble. We found 4 genomic regions uncovering a total of 7 GPCRs that interact genetically when in heterozygous combination with a Stubble mutant. Further analysis of these genes is necessary to determine if any of these GPCRs is targeted by Stubble during activation of the Rho1 pathway.

In this dissertation, a novel semiconductor mode-locked oscillator which is an extension of eXtreme Chirped Pulse Amplification (XCPA) is investigated. An eXtreme Chirped Pulse Oscillator (XCPO) implemented with a Theta cavity also based on a semiconductor gain is presented for generating more than 30ns frequency-swept pulses with more than 100pJ of pulse energy and 3.6ps compressed pulses directly from the oscillator. The XCPO shows the two distinct characteristics which are the scalability of the output energy and the mode-locked spectrum with respect to repetition rate. The laser cavity design allows for low repetition rate operation < 100MHz. The cavity significantly reduces nonlinear carrier dynamics, integrated self phase modulation (SPM), and fast gain recovery in a Semiconductor optical Amplifier (SOA). Secondly, a functional device, called a Grating Coupled Surface Emitting Laser (GCSEL) is investigated. For the first time, passive and hybrid mode-locking of a GCSEL is achieved by using saturable absorption in the passive section of GCSEL. To verify the present limitation of the GCSEL for passive and hybrid mode-locking, a dispersion matched cavity is explored. In addition, a Grating Coupled surface emitting Semiconductor Optical Amplifier (GCSOA) is also investigated to achieve high energy pulse. An energy extraction experiment for GCSOA using stretched pulses generated from the colliding pulse semiconductor mode-locked laser via a chirped fiber bragg grating, which exploits the XCPA advantages is also demonstrated. Finally, passive optical cavity amplification using an enhancement cavity is presented. In order to achieve the interferometric stability, the Hänsch-Couillaud Method is employed to stabilize the passive optical cavity. The astigmatism-free optical cavity employing an acousto-optic modulator (AOM) is designed and demonstrated. In the passive optical cavity, a 7.2 of amplification factor is achieved with a 50 KHz dumping rate.

A linearly-polarized aperture coupled patch antenna design is characterized and optimized using HFSS antenna simulation software. This thesis focuses on the aperture coupled patch antenna due to the lack of fabrication and tuning documentation for the design of this antenna and its usefulness in arrays and orthogonally polarized communications. The goal of this thesis is to explore dimension effects on aperture coupled antenna performance, to develop a design and tuning procedure, and to describe performance effects through electromagnetic principles. Antenna parameters examined in this study include the dimensions and locations of the substrates, feed line, ground plane coupling slot, and patch. The operating frequency, input VSWR, percent bandwidth, polarization ratio, and broadside gain are determined for each antenna configuration. The substrate material is changed from RT Duroid (material in nominal HFSS design) to FR4 due to lower cost and availability. The operating frequency is changed from 2.3GHz (specified in nominal HFSS design) to 2.4GHz for wireless communication applications. Required dimensional adjustments when changing substrate materials and operating frequencies for this antenna are non-trivial and the new design procedure is used to tune the antenna. The antenna is fabricated using 59mil thick double and single sided FR4 boards joined together with double sided 45mil thick acrylic tape. The antenna is characterized in an anechoic chamber and experimental results are compared to theoretical predictions. The results show that the new design procedure can be successfully applied to aperture coupled antenna design.

Tooth enamel is among the most durable substances in the human body and as such has high recoverability in forensic anthropology cases. Its crystalline hydroxyapatite matrix has a slightly variable chemical composition which incorporates biologically available trace elements. The trace elements are derived from an individual's diet and the water he or she consumes during the period of enamel formation. As a result, trace element profiles of enamel can reflect the geology, pollution, and certain cultural dietary factors of the area in which the individual resided during this period. This research examines a sample of teeth with known demographic information from the Antioquia Modern Skeletal Reference Collection in Medellin, Colombia. A sample set of 75 teeth from 61 individuals born in areas throughout northwestern Colombia were analyzed using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), a minimally destructive, semi-quantitative technique. Analysis was performed at the Center for Archaeology, Materials, and Applied Spectroscopy (CAMAS) at Idaho State University. 33 elements were analyzed in the sample. Nonparametric methods were used to assess the relationship between elemental profiles and region of origin. Sr, Mo, Ag, Ba, Eu, and Tm concentration profiles were found to vary among regional groups. Al, Ni, Cr, Mn, Co, Sr, Cd, Sb, Sm, Eu, and U were found to predict region of origin. Differences in municipality were classified with 72% accuracy, variation across the department of Antioquia was classified with 67% accuracy, and the age of the geologic substrate was classified with 67% accuracy. The results suggest that trace element analysis of permanent tooth enamel may be of some use in estimating an individual's region of origin in forensic anthropological contexts. Further research with both larger sample sizes and more geographic variation is necessary.

There are a lot of interesting problems in surface chemistry where quantum chemistry could give great insight, like reaction mechanisms in heterogeneous catalysis, the effect of surface functionalization on semiconductors, or the influence of defects on the reactivity of crystal surfaces. Plane wave based methods applied to crystals cannot handle problems that are localized in nature like surface defects and adsorbates. On the other hand, molecular electronic structure techniques, which describe these effects and the locality of the electronic correlation well, are too computationally expensive to use on these systems. In this work, we introduce translationally-transformed coupled-cluster (TT-CC) theory, a new electronic structure method that incorporates the periodicity of crystals and the locality of electronic correlation. This is accomplished by encoding the periodicity into the amplitudes, instead of using plane waves, in order to be able to use a local basis to reflect the decay of the electronic correlation at sufficiently large distances. This avoids the calculation of redundant amplitudes. Perfectly periodic surfaces are envisioned as reference wavefunctions for localized defects and chemical reactions. The working equations in one dimension are derived starting from the amplitude equations of conventional coupled cluster singles and doubles (CCSD) on an infinite system and rearranging them such that the distance to an anonymous cell is an explicit degree of freedom, L. The formally infinite summations can be truncated by systematically neglecting numerically insignificant amplitudes. The generalization of the amplitude equations to higher dimensions is straightforward, albeit laborious. We show a general strategy to incorporate defects. These will be subjects of future dissertations. We present a proof of principle for 1-dimensional chemical systems of increasing size (He, H2, Be, Ne and N2) using the 6-31G basis set. We compute the energies, with TT-CCSD, at different distances and compared them against the perfectly periodic intensive energy (PPIE) using conventional CCSD. All results, up to L=3, show that the energies of TT-CCSD converge to the PPIE. For neon, TT-CCSD shows an error of -6.2x10-6 Eh per cell against the PPIE at the bonding distance with the potential computational cost of 7 cells using CCSD, as an upper bound. For nitrogen, TT-CCSD shows an error of -2.2x10-9 Eh at 7.5 Å per cell with the same potential cost as upper bound.

The local structures of the iron atoms for a series of strongly coupled Fe 2 (TIED)L 4 complexes (TIED = tetraiminethylenedimacrocycle, L = axail ligand) have been investigated by K-edge X-ray Absorption Spectroscopy (XAS). These complexes include not only the well characterized iso-valence CH 3 CN complex, mixed-valence CH 3 CN and Cl − complexes, and previously reported iso-valence CO complex but also the new isolated solids of iso-valence Fe 2 TIED complexes with Cl − , Br − , imidazole, pyridine, histidine, N,N-dimethyformamide (DMF), SCN − , and CN − as axial ligands and mixed-valence complexes with Br − and imidazole as axial ligands. The average Fe-N distances for the first coordination sphere of the iron atom obtained by EXAFS analysis are 1.94, 1.94, 1.95, 1.96, 1.94, 1.93, 1.96, 1.96, 1.96, and 1.96 Å for the iso- and mixed-valence CH 3 CN and imidazole complexes and iso-valence complexes with SCN − , CN − , CO, pyridine, histidine, and DMF as axial ligands, respectively. Two-shell fitting analyses of the complexes gave average iron to the four planar coordinated nitrogen distance of 1.90, 1.91, 1.91, 1.92, and 1.92 Å for the Fe 2 (TIED)L 4 with L = DMF, pyridine, Cl − , Br − , imidazole, and histidine complexes, respectively. The average distances from the center iron to: N(DMF), 2.05; N(pyridine), 2.05; Cl − , 2.33; Br − , 2.45; N(imidazole), 2.08; and N(histidine), 2.07 Å. They are all comparable to related bond distances in the literature. The above data indicate that there is no significant difference in the average Fe-N distances between each of the iso- and mixed-valence pairs. Also different axial ligands do not cause significant impact on the average Fe-N distances from the iron atom to the four coordinated N in the TIED ligand. The threshold edge positions shift about +1 eV from the iso-valence CH 3 CN, Cl − , and Br − complexes to their corresponding mixed-valence complexes. The relatively small shift compared with the normal +2 [special characters omitted] +3 eV edge shift from Fe 2+ to Fe 3+ reflects the oxidation state change of iron from Fe 2+ to Fe 2.5+ . The edge energy of the isovalence diiron complexes with different axial ligands increases in the order of the spectrochemical series of the axial Iigands from strong to weak field Iigands as follows [58, 59]: [special characters omitted] All the complexes studied here have a weak dipole-forbidden 1s → 3d pre-edge transition. The low intensity indicates only a small distortion of the octahedral coordination geometry of the central iron atom.

The Neolithic and late Iron Age pottery from the settlement site of Pool, Sanday, Orkney, was studied on two levels. Firstly, a morphological and technological study was carried out to establish a sequence for the site. Secondly an assessment was made of the usefulness of X-ray Fluorescence Analysis, Inductively Coupled Plasma Spectrometry and Petrological analysis to coarse ware studies, using the Pool assemblage as a case study. Recording of technological and typological attributes allowed three phases of Neolithic pottery to be identified. The earliest phase included sherds of Unstan Ware. This phase was followed by an assemblage characterised by pottery with incised decoration, which was stratified below a traditional Grooved Ware assemblage. The change in pottery styles and manufacturing methods with the Grooved Ware indicated that it evolved elsewhere. Grass tempered and burnished pottery characterised the Iron Age assemblage. Pottery samples from all phases of the site were analysed by XRF and ICPS. In addition, pottery from late Iron Age sites in the area was analysed for comparison with the Pool Iron Age pottery. XRF and ICPS analyses did not distinguish between either different phases at Pool or different Orcadian sites. This was attributed to the similarities in geological deposits over much of Orkney and the variations which can occur within a clay source. A clay survey was carried out in the vicinity of the site, and samples taken for comparison with the Pool pottery. Identification of rocks and minerals in thin section, and grain-size analysis, indicated that the Pool pottery was made locally to the site, and that both primary and secondary clays were used. It was concluded that petrological analysis is more suitable than elemental analysis in the study of coarse wares. / Science-based Archaeology'Committee of the Science and Engineering Research Council.

No abstract is provided. / Thesis / Master of Engineering (MEngr) / Scope and contents: The aim of this thesis is to present a finite difference method, for analysing coupled shear walls with constant or variable cross-section, resting on rigid or elastic foundations and with elastic or inelastic connecting beams. It is also intended to compare the finite difference method with the continuous connection method, which can be developed using Rosman's approach or Newmark's concept for analysing composite beams or the energy approach, and with the finite element method. An analysis of coupled shear walls with multiple piers is presented.

This thesis describes the analytical study of a structural system under the combined action of noncirculatory or circulatory loading and oscillating base motion. The model is a double inverted pendulum composed of two rigid weightless bars of equal length with two concentrated masses at the ends of each bar, on an oscillating base. Noncirculatory or circulatory loading is applied at the free end. At the hinges restoring moments are produced by spring and damping forces. Damping coefficients are taken as positive, and gravitational effects are considered. The stability of the system under the combined action of the noncirculatory or circulatory loading and the parametric excitation can be investigated by Hsu's method. This method is applied to solve the coupled Mathieu equations by the given system and determine the unstable resonance, a nonlinear analysis is used to find the steady state response. / Thesis / Master of Engineering (MEngr)

The present work applies the hybrid Voronoi cell finite element method (VCFEM) within geomechanics. Coupled seepage and deformation analysis using the VCFEM incorporating body forces allows accurate analysis of earth dams. The development of a novel approach for simulating granular material behaviour using the combined finite-discrete element method (VCFEM-DEM) provides new insights into strain localization in granular materials. Chapter 1 provides background including summary literature reviews for all concepts in the title including seepage analysis, micromechanical and continuum mechanics theory, Voronoi diagrams, finite elements (FEM), discrete elements (DEM) and combined FEM-DEM. Chapter 1 concludes by detailing the contributions of the present work. Chapter 2 presents the VCFEM for seepage analysis. The numerical examples include an investigation of mesh sensitivity and a comparison of conforming shape functions. Polygonal elements with more than four nodes show a decrease in mesh sensitivity in free surface problems, compared with four-node quadrilateral elements. The choice of conforming shape function within the VCFEM analysis did not affect the results. Chapter 3 formulates and applies the VCFEM-DEM, showing that strain localization effects in granular materials are important at all scales. The VCFEM-DEM captures shear banding in biaxial compression tests, demonstrating that global shear strains and inhomogeneities in the shear stress field present after consolidation are early precursors to the failure mode. At the field scale, strain localization can lead to significant non-uniformity in subsurface stress distribution owing to self-weight. Chapter 4 presents the coupled VCFEM for seepage and deformation. A practical example of the design of an earth dam demonstrates the application of general body forces within a hybrid formulation, notably lacking in the literature. Chapter 5 concludes by summarizing the key observations of the present work, and providing direction for future research. The Appendix provides additional details related to numerical integration within the VCFEM. / Thesis / Doctor of Philosophy (PhD) / The focus of the present work is the simulation of geomechanical behaviour at multiple scales. This ranges from simulating the interaction of grains of sand in a laboratory compression test to the seepage of water through and deformation of a large dam constructed of granular material. The simulations use a numerical tool called the Voronoi cell finite element method (VCFEM), which the present work extends to allow accurate analysis of the flow of fluid through a porous medium, deformation of a granular material under load and coupled analysis of these phenomena. The development and testing of this numerical tool for use in geomechanical analysis is itself a contribution. The present work also contains new insights into how localized stresses and strains in a granular material that are present well before the peak strength can have an important influence on the mode of failure.