On this thesis work, design and construction of an up to date complete RF excitation system was intended. This excitation system is mainly based on highly efficient switching power generators and proper coupling of the power to the object plasma. This new excitation system design should answer the demands of today&#039 / s progressed CO2 lasers on various power ranges. Though it could be used by a large variety of applications including RF plasma and RF heating, on the first occasion in order to define design considerations, this system is to be exploited by RF excited fast flow and RF excited slab CO2 laser constructions.

Wideband and dual band stacked microstrip patch antennas are investigated for the new wideband and dual band applications in the area of telecommunications. In this thesis, aperture-coupled stacked patch antennas are used to increase the bandwidth of the microstrip patch antenna. By this technique, antennas with 51% bandwidth at 6.1 GHz and 43% bandwidth at 8 GHz satisfying S11&lt / -15 dB are designed, manufactured and measured. A dual-band aperture coupled stacked microstrip patch antenna operating at 1.8 GHz with 3.8% bandwidth and at 2.4 GHz with 1.6% bandwidth is designed, produced and measured for mobile phone and WLAN applications. In addition, an aperture coupled stacked microstrip patch antenna which operates at PCS frequencies in 1.7-1.95 GHz band is designed. Dual and circularly polarized stacked aperture coupled microstrip patch antennas are also investigated. A triple band dual polarized aperture coupled stacked microstrip patch antenna is designed to operate at 900 MHz, at 1.21 GHZ and at 2.15 GHz. Mutual coupling between aperture coupled stacked microstrip patch antennas are examined and compared with the coupling of aperture coupled microstrip patch antennas

Understanding the function of membrane proteins is crucial to elucidate the molecular mechanisms by which transmembrane signaling based physiological processes,i. e., the interactions of extracellular ligands with membrane-bound receptors, are regulated. In this work, synthetic transmembrane segments derived from the visual photoreceptor rhodopsin, the full length system rhodopsin and mutants of opsin are used to study physical processes that underlie the function of this prototypical class-A G-protein coupled Receptor. The dependency of membrane protein hydration and protein-lipid interactions on side chain charge neutralization is addressed by fluorescence spectroscopy on synthetic transmembrane segments in detergent and lipidic environment constituting transmembrane segments of rhodopsin in the membrane. Results from spectroscopic studies allow us to construct a structural and thermodynamical model of coupled protonation of the conserved ERY motif in transmembrane helix 3 of rhodopsin and of helix restructuring in the micro-domain formed at the protein/lipid water phase boundary. Furthermore, synthesized peptides and full length systems were studied by time resolved FTIR-Fluorescence Cross Correlation Hydration Modulation, a technique specifically developed for the purpose of this study, to achieve a full prospect of time-resolved hydration effects on lipidic and proteinogenic groups, as well as their interactions. Multi-spectral experiments and time-dependent analyses based on 2D correlation where established to analyze large data sets obtained from time-resolved FTIR difference spectra and simultaneous static fluorescence recordings. The data reveal that lipids play a mediating role in transmitting hydration to the subsequent membrane protein response followed by water penetration into the receptor structure or into the sub-headgroup region in single membrane-spanning peptides carrying the conserved proton uptake site (monitored by the fluorescence emission of hydrophobic buried tryptophan). Our results support the assumption of the critical role of the lipid/water interface in membrane protein function and they prove in particular the important influence of electrostatics, i. e., side chain charges at the phase boundary, and hydration on that function. / Für die Aufklärung der molekularen Wirkungsweise von physiologischen, auf Signaltransduktion, d. h. dem Zusammenspiel von extrazellulären Reizen und membrangebundenen Rezeptoren, beruhenden Prozessen ist das Verständnis der Funktion von Membranproteinen unerlässlich. In dieser Arbeit werden von Rhodopsin abgleitete, synthetische transmembrane Segmentpeptide, Opsin-Mutanten und der vollständige Photorezeptor Rhodopsin untersucht, um die physikalischen Prozesse zu beleuchten, die der Funktionen dieses prototypischen Klasse-A G-Protein gekoppelten Rezeptors zugrunde liegen. Die Abhängigkeit der Membranprotein-Hydratation und der Lipid-Protein-Wechselwirkung von der Ladung einer Aminosäuren-Seitenkette wird erforscht. Hierzu werden synthetische, transmembrane Segmentpeptide in Lipid und Detergenz, als Modell transmembraner Segmente von Rhodopsin in der Membran mittels Fluoreszenzspektroskopie untersucht. Aus den erhaltenen Ergebnissen wird ein thermodynamisches und strukturelles Modell hergeleitet, welches die Kopplung der Protonierung des hochkonservierten ERY-Motivs in Transmembranhelix 3 von Rhodopsin an die Restrukturierung der Helix in der Mikroumgebung der Lipid-Wasser-Phasengrenze erklärt. Des Weiteren werden sowohl die Segementpeptide als auch die vollständigen Systeme Opsin und Rhodopsin mittels zeitaufgelöster FTIR-Fluoreszenz-Kreuzkorrelations-Hydratations-Modulation untersucht. Diese Technik wurde eigens zur Aufklärung von zeitabhängigen Hydratationseffekten auf Lipide und Proteine oder Peptide entwickelt. Dabei werden zeitaufgelöste FTIR Differenz-Spektren und gleichzeitig statische Fluoreszenzsignale aufgenommen und diese zeitabhängigen multispektralen Datensätze mittels 2D Korrelation analysiert. Die Auswertung der Experimente enthüllt einen sequentiellen Hydratationsprozess. Dieser beginnt mit der Bildung von Wasserstoffbrückenbindungen an der Carbonylgruppe des Lipids, gefolgt von Strukturänderungen der Transmembranproteine und abgeschlossen durch das Eindringen von Wasser in das Proteininnere. Letzteres wird nachgewiesen durch die Fluoreszenz von Tryptophan im hydrophoben Peptid- oder Proteininneren. Die Ergebnisse dieser Arbeit unterstreichen die Annahme, dass Lipid-Protein-Wechselwirkungen eine entscheidende Rolle in der Funktion von Membranproteinen spielen und das insbesondere Elektrostatik, in Form von Ladungen an der Phasengrenze, und die Hydratisierung einen kritischen Einfluss auf diese Funktion haben.

The notion of designing circuits based on charge sensing, charge adaptation, and charge programming is explored in this research. This design concept leads to a low-power capacitive sensing interface circuit that has been designed and tested with a MEMS microphone and a capacitive micromachined ultrasonic transducer. Moreover, by using the charge programming technique, a designed floating-gate based large-scale field-programmable analog array (FPAA) containing a universal sensor interface sets the stage for reconfigurable smart sensory systems. Based on the same charge programming technique, a compact programmable analog radial-basis-function (RBF) based classifier and a resultant analog vector quantizer have been developed and tested. Measurement results have shown that the analog RBF-based classifier is at least two orders of magnitude more power-efficient than an equivalent digital processor. Furthermore, an adaptive bump circuit that can facilitate unsupervised learning in the analog domain has also been proposed. A projection neural network for a support vector machine, a powerful and more complicated binary classification algorithm, has also been proposed. This neural network is suitable for analog VLSI implementation and has been simulated and verified on the transistor level. These analog classifiers can be integrated at the interface to build smart sensory systems.

EPR spectroscopy and isotopic substitution were used to gain increased knowledge about the proton-coupled electron transfer (PCET) mechanism for the reduction of the tyrosine D radical (YD*) in photosystem II. pL dependence (where pL is either pH or pD) of both the rate constant and kinetic isotope effect (KIE) was examined for YD* reduction. Second, the manner in which protons are transferred during the rate-limiting step for YD* reduction at alkaline pL was determined. Finally, high field electron paramagnetic resonance (EPR) spectroscopy was used to study the effect of pH on the environment surrounding both the tyrosine D radical and the tyrosine Z radical (YZ*). At alkaline pL, it was determined that the proton and electron are both transferred in the rate-limiting step of YD* reduction. At acidic pL, the proton transfer occurs first followed by electron transfer. Proton inventory experiments indicate that there is more than one proton donation pathway available to YD* during PCET reduction at alkaline pL. Additionally, the proton inventory experiments indicate that at least one of those pathways is multiproton. High field EPR experiments indicate that both YD* and YZ* are hydrogen bonded to neutral species. The EPR gx component for YD* is invariant with respect to pH. Analysis of the EPR gx component for Yz* indicates that its environment becomes more electropositive as the pH is increased. This is most likely due to changes in the hydrogen bond strength

The accurate and efficient simulation of coupled neutron-photon problems is necessary for several important radiation detection applications. Examples include the detection of nuclear threats concealed in cargo containers and prompt gamma neutron activation analysis for nondestructive determination of elemental composition of unknown samples. In these applications, high-resolution gamma-ray spectrometers are used to preserve as much information as possible about the emitted photon flux, which consists of both continuum and characteristic gamma rays with discrete energies. Monte Carlo transport is the most commonly used modeling tool for this type of problem, but computational times for many problems can be prohibitive. This work explored the use of coupled Monte Carlo-deterministic methods for the simulation of neutron-induced photons for high-resolution gamma-ray spectroscopy applications. A method was developed for the implementation of coupled neutron-photon problems into RAdiation Detection Scenario Analysis Toolbox (RADSAT), a computer code that couples the complementary strengths of discrete-ordinate and Monte Carlo approaches to obtain high-resolution detector responses. Central to this work was the development of a method for generating multi-group neutron-photon cross-sections in a way that separates the discrete and continuum photon emissions so that the key signatures in neutron activation analysis (i.e., the characteristic line energies) are preserved. The mechanics of the cross-section preparation method are described and contrasted with standard neutron-gamma cross-section sets. These custom cross-sections were then applied to several benchmark problems using the method developed in this work. Multi-group results for neutron and photon flux are compared to MCNP results. Finally, calculated responses of high-resolution spectrometers were compared. The added computational efficiency of the coupled Monte Carlo-deterministic method and the positive agreement achieved in the code-to-code verification make the integration of the coupled neutron-photon method into RADSAT a promising endeavor.

The effect of in-situ or redistributed stress on solute transport in fractured rocks is one of the major concerns for many subsurface engineering problems. However, it remains poorly understood due to the difficulties in experiments and numerical modeling. The main aim of this thesis is to systematically investigate the influences of stress on solute transport in fractured rocks, at scales of single fractures and fracture networks, respectively. For a single fracture embedded in a porous rock matrix, a closed-form solution was derived for modeling the coupled stress-flow-transport processes without considering damage on the fracture surfaces. Afterwards, a retardation coefficient model was developed to consider the influences of damage of the fracture surfaces during shear processes on the solute sorption. Integrated with particle mechanics models, a numerical procedure was proposed to investigate the effects of gouge generation and microcrack development in the damaged zones of fracture on the solute retardation in single fractures. The results show that fracture aperture changes have a significant influence on the solute concentration distribution and residence time. Under compression, the decreasing matrix porosity can slightly increase the solute concentration. The shear process can increase the solute retardation coefficient by offering more sorption surfaces in the fracture due to gouge generation, microcracking and gouge crushing. To study the stress effects on solute transport in fracture systems, a hybrid approach combing the discrete element method for stress-flow simulations and a particle tracking algorithm for solute transport was developed for two-dimensional irregular discrete fracture network models. Advection, hydrodynamic dispersion and matrix diffusion in single fractures were considered. The particle migration paths were tracked first by following the flowing fluid (advection), and then the hydrodynamic dispersion and matrix diffusion were considered using statistic methods. The numerical results show an important impact of stress on the solute transport, by changing the solute residence time, distribution and travel paths. The equivalent dispersion coefficient is scale dependent in an asymptotic or exponential form without stress applied or under isotropic compression conditions. Matrix diffusion plays a dominant role in solute transport when the hydraulic gradient is small. Outstanding issues and main scientific achievements are also discussed. / QC 20111011

The interaction between two 6 kDa proteins has been investigated. The studied complex of micromolar affinity (Kd) consists of the Z domain derived from staphylococcal protein A and the related protein ZSPA-1, belonging to a group of binding proteins denoted affibody molecules generated via combinatorial engineering of the Z domain. Affibody-target protein complexes are good model systems for structural and thermodynamic studies of protein-protein interactions. With the Z:ZSPA-1 pair as a starting point, we determined the solution structure of the complex and carried out a preliminary characterization of ZSPA-1. We found that the complex contains a rather large (ca. 1600 Å2) interaction interface with tight steric and polar/nonpolar complementarity. The structure of ZSPA-1 in the complex is well-ordered in a conformation that is very similar to that of the Z domain. However, the conformation of the free ZSPA-1 is best characterized by comparisons with protein molten globules. It shows a reduced secondary structure content, aggregation propensity, poor thermal stability, and binds the hydrophobic dye ANS. This molten globule state of ZSPA-1 is the native state in the absence of the Z domain, and the ordered state is only adopted following a stabilization that occurs upon binding. A more extensive characterization of ZSPA-1 suggested that the average topology of the Z domain is retained in the molten globule state but that it is represented by a multitude of conformations. Furthermore, the molten globule state is only marginally stable, and a significant fraction of ZSPA-1 exists in a completely unfolded state at room temperature. A complete thermodynamic characterization of the Z:ZSPA-1 pair suggests that the stabilization of the molten globule state to an ordered three helix structure in the complex is associated with a significant conformational entropy penalty that might influence the binding affinity negatively and result in an intermediate-affinity (µM) binding protein. This can be compared to a dissociation constant of 20-70 nM for the complex Z:Fc of IgG where Z uses the same binding surface as in Z:ZSPA-1. Structure analyses of Z in the free and bound state reveal an induced fit response upon complex formation with ZSPA-1 where a conformational change of several side chains in the binding surface increases the accessible surface area with almost 400 Å2 i.e. almost half of the total interaction surface in the complex. Two cysteine residues were introduced at specific positions in ZSPA-1 for five mutants in order to stabilize the conformation of ZSPA-1 by disulfide bridge formation. The mutants were thermodynamically characterized and the binding affinity of one mutant showed an improvement by more than a factor of ten. The improvement of the introduced cysteine bridge correlates with an increase in binding enthalpy rather than with entropy. Further analysis of the binding entropy suggests that the conformational entropy change in fact is reduced but its favorable contribution is opposed by a less favorable desolvation enthalpy change. These studies illustrate the structural and thermodynamic complexity of protein-protein interactions, but also that this complexity can be dissected and understood. In this study, a comprehensive characterization of the ZSPA-1 affibody has gained insight into the intricate mechanisms involved in complex formation. These theories were supported by the design of a ZSPA-1 mutant with improved binding affinity. / QC 20100924

Two areas of particular importance in prostate cancer progression are primary tumour development and metastasis. These processes involve a number of physiological events, the mediators of which are still being discovered and characterised. Serine proteases have been shown to play a major role in cancer invasion and metastasis. The recently discovered phenomenon of their activation of a receptor family known as the protease activated receptors (PARs) has extended their physiological role to that of signaling molecule. Several serine proteases are expressed by malignant prostate cancer cells, including members of the kallikreinrelated peptidase (KLK) serine protease family, and increasingly these are being shown to be associated with prostate cancer progression. KLK4 is highly expressed in the prostate and expression levels increase during prostate cancer progression. Critically, recent studies have implicated KLK4 in processes associated with cancer. For example, the ectopic over-expression of KLK4 in prostate cancer cell lines results in an increased ability of these cells to form colonies, proliferate and migrate. In addition, it has been demonstrated that KLK4 is a potential mediator of cellular interactions between prostate cancer cells and osteoblasts (bone forming cells). The ability of KLK4 to influence cellular behaviour is believed to be through the selective cleavage of specific substrates. Identification of relevant in vivo substrates of KLK4 is critical to understanding the pathophysiological roles of this enzyme. Significantly, recent reports have demonstrated that several members of the KLK family are able to activate PARs. The PARs are relatively new members of the seven transmembrane domain containing G protein coupled receptor (GPCR) family. PARs are activated through proteolytic cleavage of their N-terminus by serine proteases, the resulting nascent N-terminal binds intramolecularly to initiate receptor activation. PARs are involved in a number of patho-physiological processes, including vascular repair and inflammation, and a growing body of evidence suggests roles in cancer. While expression of PAR family members has been documented in several types of cancers, including prostate, the role of these GPCRs in prostate cancer development and progression is yet to be examined. Interestingly, several studies have suggested potential roles in cellular invasion through the induction of cytoskeletal reorganisation and expression of basement membrane-degrading enzymes. Accordingly, this program of research focussed on the activation of the PARs by the prostate cancer associated enzyme KLK4, cellular processing of activated PARs and the expression pattern of receptor and agonist in prostate cancer. For these studies KLK4 was purified from the conditioned media of stably transfected Sf9 insect cells expressing a construct containing the complete human KLK4 coding sequence in frame with a V5 epitope and poly-histidine encoding sequences. The first aspect of this study was the further characterisation of this recombinant zymogen form of KLK4. The recombinant KLK4 zymogen was demonstrated to be activatable by the metalloendopeptidase thermolysin and amino terminal sequencing indicated that thermolysin activated KLK4 had the predicted N-terminus of mature active KLK4 (31IINED). Critically, removal of the pro-region successfully generated a catalytically active enzyme, with comparable activity to a previously published recombinant KLK4 produced from S2 insect cells. The second aspect of this study was the activation of the PARs by KLK4 and the initiation of signal transduction. This study demonstrated that KLK4 can activate PAR-1 and PAR-2 to mobilise intracellular Ca2+, but failed to activate PAR-4. Further, KLK4 activated PAR-1 and PAR-2 over distinct concentration ranges, with KLK4 activation and mobilisation of Ca2+ demonstrating higher efficacy through PAR-2. Thus, the remainder of this study focussed on PAR-2. KLK4 was demonstrated to directly cleave a synthetic peptide that mimicked the PAR-2 Nterminal activation sequence. Further, KLK4 mediated Ca2+ mobilisation through PAR-2 was accompanied by the initiation of the extra-cellular regulated kinase (ERK) cascade. The specificity of intracellular signaling mediated through PAR-2 by KLK4 activation was demonstrated by siRNA mediated protein depletion, with a reduction in PAR-2 protein levels correlating to a reduction in KLK4 mediated Ca2+mobilisation and ERK phosphorylation. The third aspect of this study examined cellular processing of KLK4 activated PAR- 2 in a prostate cancer cell line. PAR-2 was demonstrated to be expressed by five prostate derived cell lines including the prostate cancer cell line PC-3. It was also demonstrated by flow cytometry and confocal microscopy analyses that activation of PC-3 cell surface PAR-2 by KLK4 leads to internalisation of this receptor in a time dependent manner. Critically, in vivo relevance of the interaction between KLK4 and PAR-2 was established by the observation of the co-expression of receptor and agonist in primary prostate cancer and prostate cancer bone lesion samples by immunohistochemical analysis. Based on the results of this study a number of exciting future studies have been proposed, including, delineating differences in KLK4 cellular signaling via PAR-1 and PAR-2 and the role of PAR-1 and PAR-2 activation by KLK4 in prostate cancer cells and bone cells in prostate cancer progression.

[Truncated abstract] The analysis and subsequent interpretation of trace evidence is of paramount importance to the forensic scientist. While a variety of methods are available to facilitate comparison between recovered and control samples, the use of a specific analytical method depends upon both the physical and chemical nature of the material itself and the material to which it is to be compared. Elemental analysis of evidentiary material is one such method of sample comparison and has been extensively applied to this purpose following the introduction of neutron activation analysis in the early 1960s. However, over the last 15 years, another instrumental technique has taken centre stage in the analytical armoury of the forensic scientist: laser ablation–inductively coupled plasma-mass spectrometry (LA-ICP-MS). The modification and adaptation of this technique, to a point where it is possible to distinguish between glass materials produced only hours apart on the same production line, is detailed in this thesis. Additional protocols have also been developed for the analysis of fibreglass and plastic crime scene debris. Finally, a method for quantification of elemental concentrations in headlamp plastics has also been developed to facilitate inter-comparison of data between both different analytical techniques and different laboratories. Glass material is one of the most common varieties of trace evidence and the forensic examination of glass traditionally involves the determination of its refractive index (RI). ... The analytical protocol involves the analysis of 46 analytes on material comprising the exterior surface of the lens. Using this data, it was found that although minor variations in elemental composition exist within a single headlamp lens, discrimination between lenses produced from a single manufacturing plant over a short period of time could still be achieved. Discrimination between all headlamp lenses, with the exception of some lenses produced on the same day, could be facilitated using the analytical protocol developed. Furthermore, an interpretational protocol has been developed that has successfully classified all unknown headlamp lens samples investigated in this study, within the discrimination limits of the analytical method. The semi-quantitative analysis of glass and plastic samples has also been examined using LA-ICP-MS. The concentrations of 16 analytes in container and float glass samples were determined. However, the levels of discrimination afforded by the semi-quantitative data were inferior to those achieved using qualitative data. Finally, a series of plastic-based standards, containing 25 analytes of known concentrations, was produced. Using these standards, relative concentrations of the study analytes were determined in polycarbonate headlamp lenses. Interpretation of the data produced made it possible to discriminate between all study samples. Consequently, the total analytical and interpretational protocol developed in this study has established the foundation for LA-ICP-MS to be adopted internationally as a recognised method for the analysis of plastic crime scene debris.