Thesis (Ph.D.)--Washington State University, August 2005. / Includes bibliographical references.

University, Diss., 2006--Würzburg.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

The guided wave technique is an ultrasonic technique which is used to monitor large structures in a variety of industry sectors to safeguard against catastrophic failure. The guided wave technique for pipeline inspection has been commercially used since the early 2000s and this facilitates rapid inspection where from a single location over 100 metres of pipeline can be inspected. This technique is currently being used in pipeline infrastructure across the globe. For the technique to be successful it is highly dependent on a numerous of factors including, frequency selection, array designs and pipeline geometries. The transducers used on pipeline are dry coupled and the magnitude of the signal transmitted is dependent on the normal force applied to it. If this force is not controlled the signal being transmitted can degrade and lead to the difficult analysis of a complex signal. In this thesis studies have been undertaken to understand the relationship between dry force coupling of the transducer and the signal received, aligning this connection to classical contact theory. This is then further to extended to the influence surface contact conditions have on the transmission of signal from the transducer. Analysis of the results detected a peak in the operational frequency response which in turn initiated electrical impedance and structural resonance measurements to identify the presence of resonances which are induced by dry coupling. This behaviour was then modelled in FEA software and the validity of the FEA approach was tested against several prototype transducers. This thesis has been funded in joint collaboration between the Engineering Physics and Science Research Council and TWI ltd.

During skeletal muscle stimulation, there is a summation of local events of Ca2+ release from the sarcoplasmic reticulum, known as Ca2+ sparks. Ca2+ sparks originate from groups of skeletal ryanodine receptors (RyR1) that activate and close in synchrony. This synchrony allows for the rapid and massive release of Ca2+ from the sarcoplasmic reticulum to initiate contraction and, more important, would provide a mechanism to terminate Ca2+ release under conditions where independent RyR1 are normally active. RyR1 mutations can result in abnormal intracellular Ca2+ signaling that is associated with numerous skeletal muscle disorders including malignant hyperthermia and central core disease. Therefore, investigating the mechanisms that control RyR1 function can help identify how these mutations cause deleterious Ca2+ handling. Currently, most published research on RyR1s gating utilizes single RyR1 reconstituted into planar lipid bilayers to test isolated RyR1. However, in vivo, arrays of RyR1 function in synchrony. Attempts to reconstitute RyR1s into planar lipid bilayers result in experiments that contain multiple channels, which under specific conditions may gate in synchrony, also known as coupled gating. Coupled RyR1 gating was first reported by A. Marks' laboratory and attributed to FK-506 binding protein 12 (FKBP12) associating with neighboring RyR1s the stabilization of RyR1-RyR1 interactions that promote coupled gating. Previous studies suggested that ATP is required for coupled RyR1 gating; however, the mechanism by which ATP promotes the coordinated activity of RyR1s has not been elucidated and is the focus of this thesis. Therefore, my hypothesis is that the agonist action of ATP and FKBP12 bound to RyR1 are required for coupled RyR1 gating. In addition, new pharmacological tools are required to better understand coupled RyR gating. Thus, an additional goal is to identify pharmacological agents that modulate RyR1s in an innovative manner, i.e., help to uncover novel aspects of RyR1 gating and conduction. This investigation suggests that the adenosine based nucleotides, ATP, ADP and AMP, are agonists of RyR1s and promote coupled RyR1 gating in planar lipid bilayers. However, ADP and AMP were unable to maintain coupled RyR1 gating with physiological levels of Mg2+. This suggests that coupled gating would be impaired when the levels ATP decrease, as in muscle fatigue. When ATP was compared to other nucleotides (GTP, ITP, and TTP), the results suggest that the nucleotide agonist action on RyR1s is dependent on the phosphate groups and amino group on the nucleobase. As ATP is the most efficient nucleotide for coupled gating, I also investigated the indirect action of ATP to act as a kinase substrate or alter the cytoskeletal network. The addition of kinases, phosphatases and cytoskeletal modulators did not produce a significant disruption of coupled RyR1 gating. I also tested the role of addition of exogenous FKBP12 to RyR1s that gated independently or had partial coupling, but coupled gating was never improved. Also, the addition of high doses of rapamycin to remove FKBP12 from coupled RyR1 failed to functionally uncouple the channels. Finally, I attempted to find pharmacological agents that could aid in the understanding of coupled RyR1. Some agents were found to modulate RyR1s; however, I did not find a probe that would affect kinetics/conductance of RyR1s and was suitable for comparing coupled gating in bilayers with Ca2+ sparks in cells. Overall, coupled RyR gating is dependent on the physiological modulators ATP and Mg2+. This thesis represents a step forward in identifying the requirements for coupled RyR1 gating and understanding how RyR1s function in cells. Until an understanding of how these receptors communicate in cells is obtained, how different mutations alter the Ca2+ leak will continue to be quite difficult to study.

This thesis is focused on non-contact air-coupled ultrasonic Non-Destructive Evaluation (NDE) of Carbon-Carbon (C/C) disc brake materials. The minimum detectable defect size in the C/C composite disc brakes up to the maximum thickness of 1 7/16" (36.33 mm) using 120, 225 and 400 kHz transducers was investigated in the experimental section of this thesis. The effect of scanning increment step size on resolution of the final C-scan image was also investigated. The results indicated that the 12.7 mm diameter flat bottom drilled holes were reliably detectable using 225 kHz transducers. The flat bottom drilled holes and the side drilled holes of 6.35 mm in diameter were detectable on the final C-scan images of 225 kHz testing mainly due to the known locations of the defects. Results showed that testing frequency of 120 kHz provides very transparent C-scans. Testing frequency of 225 kHz provides also good transparency and better resolution. Testing frequency of 400 kHz did not provide satisfactory results. No advanced signal filtering techniques were utilized during the experiments. The relationship between the speed of sound in C/C material and the carbon fiber orientation in the carbon matrix needs to be investigated. The air-coupled ultrasonic testing of the C/C composite disc brake samples was conducted at the Center for Non-Destructive Evaluation at Iowa State University.

In this thesis, the Smoothed Particle Hydrodynamics (SPH) method is applied to elastic dynamics and fracture. More specifically, two coupling methods are presented which make use of both the Eulerian and Total Lagrangian formulations. These coupling methods are intended for problems whereby SPH particles, which constitute the domain, are required to convert from a Total Lagrangian kernel to an Eulerian kernel once a damage criterion is activated. The conservation equations are derived for the Eulerian and Total Lagrangian formulations, in a consistent manner which naturally presents the conditions required for the conservation of momentum and energy. These derivations are written such that they make no use of the symmetrical nature of the kernel function or the anti-symmetrical nature of the kernel function gradient. The conservation of momentum and energy is then enforced, along with improving the consistency of the formulations, by implementing the mixed kernel-and-gradient correction. This mixed correction can be applied to both the Eulerian and Total Lagrangian formulations without detracting from the energy and momentum preserving properties provided that the kernel gradient anti-symmetry property is not exploited. The symmetry terms, which are often found in SPH, are included in the derivation of the conservation equations. This is done both to reduce the number of calculations required and to simplify the first coupling procedure. Both coupled formulations are further expanded by highlighting how artificial viscosity can be introduced. A disadvantage of the first coupling method, this being the incompatibility with artificial stress, is also detailed. The equations of state and the plasticity and damage models used in this work are outlined. Additionally, a number of practical details concerning numerical implementation are given. These include the coupled implementations of ghost particle boundary conditions, memory storage, OpenMP implementation, and the Predict, Evaluate, Correct (PEC) form of leapfrog time integration used. Lastly, the proposed formulations and models are verified and validated. This is done by modelling progressively more complex simulations that verify individual aspects of the formulations. Either analytical or experimental results are used for validation where possible. The final simulations highlight how high velocity impacts can be modelled using the proposed coupled mixed correction Eulerian Total Lagrangian SPH method.

Plasmon resonances have attracted a lot of recent research interest for their potential applications, including bio-sensing, sub-wavelength optics, negative refractive index metamaterials and their ability to produce massively enhanced electromagnetic fields. Localised surface plasmon resonances (LSPR) in metallic nanostructures can offer large electromagnetic field enhancements, and nanometre-scale localisation of electric fields. Their resonance wavelengths and properties can be tuned by variation of the nanostructure geometry and are sensitive to environmental refractive index. Coupling of localised plasmon resonances can: Create new hybrid modes that cannot be supported by individual nanostructures, overcome some of the limitations of individual LSPR, and open up possibilities for new applications and active control of plasmon resonances. This thesis contains results from samples exploiting near-field, far-field and resistive coupling of localised plasmon resonances to create novel resonance modes that may make them suitable for important applications. Firstly results are presented from samples exhibiting strong collective plasmon resonances at normal incidence, which could be used to improve the spatial resolution of, miniaturise and add new functionality to highly sensitive surface plasmon resonance based approaches to bio-sensing. A very high bio-sensing figure of merit is calculated for the nanostructure arrays fabricated. Results are also presented from samples designed to produce the highest quality factor resonances possible when excited with light at grazing incidence. The highest resonance quality factors measured were conservatively estimated to be >210, which to our knowledge are the highest values of quality factor measured in diffraction coupled arrays at the resonance wavelengths around 1.5 μm. Evidence for the existence of a presently largely unrecognised resistive coupling mechanism is also presented from an array of gold nanostripes covered with a graphene layer. If further work is successful, this could allow extremely rapid modulation of theoptical properties of a plasmonic array by application of gate voltage to the graphenelayer. Finally an improvement to the fabrication procedure for established near-field coupled composite plasmonic nanostructures that create a cascaded electromagnetic field enhancement effect is presented.

Group III-nitride semiconductors possess unique properties, which make them versatile materials for suiting many applications. Structuring vertical and exceptionally smooth GaN profiles is crucial for efficient optical device operation. The processing requirements for laser devices and ridge waveguides are stringent as compared to LEDs and other electronic devices. Due to the strong bonding and chemically inert nature of GaN, dry etching becomes a critical fabrication step. The surface morphology and facet etch angle are analyzed using SEM and AFM measurements. The influence of different mask materials is also studied including Ni as well as a SiO2 and resist bilayer. The high selectivity Ni Mask is found to produce high sidewall angles ~79°. Processing parameters are optimized for both the mask material and GaN in order to achieve a highly anisotropic, smooth profile, without resorting to additional surface treatment steps. An optimizing a SF6/O2 plasma etch process resulted in smooth SiO2 mask sidewalls. The etch rate and GaN surface roughness dependence on the RF power was also examined. Under a low 2mTorr pressure, the RF and ICP power were optimized to 150W and 300W respectively, such that a smooth GaN morphology and sidewalls was achieved with reduced ion damage. The The AFM measurements of the etched GaN surface indicate a low RMS roughness ranging from 4.75 nm to 7.66 nm.

In this study, a novel method based on biotinylated antibodies and streptavidin coated magnetic beads was used to separate the thrombocyte subpopulations from zebrafish whole blood. DiI-C18, a lipophilic dye, labels only young thrombocytes when used at low concentrations. Commercially available biotinylated anti-Cy3 antibody was used to label the chromophore of DiI-C18 on the young thrombocytes and streptavidin coated magnetic beads were added subsequently, to separate young thrombocytes. The remaining blood cells were probed with custom-made biotinylated anti-GPIIb antibody and streptavidin magnetic beads to separate them from other cells. Further, thrombocytes are equivalents of mammalian platelets. Platelets play a crucial role in thrombus formation. The G-protein coupled receptors (GPCRs) present on the platelet surface are involved during platelet activation and aggregation processes. So, thrombocytes were studied for the presence of GPCRs. The GPCR mRNA transcripts expressed in the young and mature thrombocytes were subjected to densitometry analysis and pixel intensities of the bands were compared using one way ANOVA. This analysis did not show significant differences between the young and mature GPCR mRNA transcripts but identified a novel GPCR, GPR18 that was not reported in platelets earlier. To study the function of this GPCR, it was knocked down using GPR18 specific antisense morpholino and vivo morpholino. The immunofluorescence experiment indicated the presence of GPR18 on thrombocytes. The results of the assays, such as, time to occlusion (TTO) and time to aggregation (TTA) in response to N-arachidonyl glycine (NAG) as an agonist, showed prolongation of time in GPR18 larval and adult morphants respectively, suggesting that GPR18 plays a role in thrombus formation in zebrafish. In conclusion, our results indicate that GPR18 may be present in zebrafish thrombocytes, it may be involved in thrombus formation and that NAG may be an agonist at GPR18 on thrombocytes.