The procedures and results of experimental and/or theoretical studies of four transient molecules, GeO, WO, BeH, and MgH are reported in the thesis. Two of them, GeO and WO, are diatomic molecules composed of relatively ...

Plant development is complex and highly regulated. Tens of thousands of genes have been sequenced for the model plant Arabidopsis thaliana, yet few have been functionally annotated and characterized. This thesis describes the expression analysis and characterization of four genes in Arabidopsis. Three of these belong to the eukaryotic translation initiation factor 5A (eIF5A) gene family, and the fourth encodes diacylglycerol acyltransferase 1 (DGAT1). Putative roles for these genes in the development of Arabidopsis thaliana are described. <br /><br /> eIF5A is the only known protein to contain the amino acid hypusine. It has been demonstrated previously that eIF5A acts as a shuttle protein, moving specific mRNAs from the nucleus to the cytoplasm for translation. In Arabidopsis thaliana (At), there are three isoforms of eIF5A, and it is clear from the present study that they each have a unique temporal and spatial expression pattern. AteIF5A-1 and -2 are up-regulated during natural senescence and wounding/pathogenesis, respectively, and it is proposed that they regulate the onset of programmed cell death during these events. AteIF5A-3 is up-regulated in elongating meristem of the root, and it is proposed that this isoform is involved in cell growth. <br /><br /> Over-expression of the individual AteIF5A isoforms in planta resulted in pleiotropic phenotypes. When AteIF5A-1 or AteIF5A-2 was over-expressed, the phenotypes observed were indicative of their putative roles in the translation of proteins required for programmed cell death. When AteIF5A-3 was over-expressed, the phenotypes were indicative of a role for this protein in the regulation of cell and tissue elongation. <br /><br /> Lipid analysis of rosette leaves from Arabidopsis thaliana revealed an accumulation of triacylglycerol with advancing leaf senescence coincident with an increase in the abundance and size of plastoglobuli. The terminal step in the biosynthesis of triacylglycerol in Arabidopsis is catalyzed by DGAT1. When gel blots of RNA isolated from rosette leaves at various stages of development were probed with the Arabidopsis EST clone, E6B2T7, which has been annotated as DGAT1, a steep increase in DGAT1 transcript levels was evident in the senescing leaves coincident with the accumulation of triacylglycerol. The increase in DGAT1 transcript correlated temporally with enhanced levels of DGAT1 protein detected immunologically. Two lines of evidence indicated that the triacylglycerol of senescing leaves is synthesized in chloroplasts and sequesters fatty acids released from the catabolism of thylakoid galactolipids. First, triacylglycerol isolated from senescing leaves proved to be enriched in hexadecatrienoic acid (16:3) and linolenic acid (18:3), which are normally present in thylakoid galactolipids. Second, DGAT1 protein in senescing leaves was found to be associated with chloroplast membranes. These findings collectively indicate that DGAT1 plays a role in senescence by sequestering fatty acids de-esterified from galactolipids into triacylglycerol....

Better understanding of protein folding process can provide physical insights on the function of proteins and makes it possible to benefit from genetic information accumulated so far. Protein folding process normally takes place in less than seconds but even seconds are beyond reach of current computational power for simulations on a system of all-atom detail. Hence, to model and explore protein folding process it is crucial to construct a proper model that can adequately describe the physical process and mechanism for the relevant time scale. We discuss the reduced off-lattice model that can express &alpha;-helix and &beta;-hairpin conformations defined solely by a given sequence in order to investigate a protein folding mechanism of conformations such as a &beta;-hairpin and also to investigate conformational conversions in proteins. The first two chapters introduce and review essential concepts in protein folding modelling physical interaction in proteins, various simple models, and also review computational methods, in particular, the Metropolis Monte Carlo method, its dynamic interpretation and thermodynamic Monte Carlo algorithms. Chapter 3 describes the minimalist model that represents both &alpha;-helix and &beta;-sheet conformations using simple potentials. The native conformation can be specified by the sequence without particular conformational biases to a reference state. In Chapter 4, the model is used to investigate the folding mechanism of &beta;-hairpins exhaustively using the dynamic Monte Carlo and a thermodynamic Monte Carlo method an effcient combination of the multicanonical Monte Carlo and the weighted histogram analysis method. We show that the major folding pathways and folding rate depend on the location of a hydrophobic. The conformational conversions between &alpha;-helix and &beta;-sheet conformations are examined in Chapter 5 and 6. First, the conformational conversion due to mutation in a non-hydrophobic system and then the conformational conversion due to mutation with a hydrophobic pair at a different position at various temperatures are examined....

As optical fiber systems evolve to higher data rates, the importance of polarization control and manipulation steadily increases. Polarization manipulating devices, such as polarization splitters and converters, can be realized by introducing material anisotropy or geometric asymmetry. Compared to active devices, passive polarization converters are more simply fabricated and controlled; therefore they have attracted increasing attention during the past two decades. However, materials employed in previous polarization rotating waveguides are mainly limited to low index-contrast III-V semiconductors such as InP and GaAs. Such III-V devices possess large radiation loss, large curvature loss, and low coupling efficiency to single-mode fibers; in addition, due to the weak optical confinement, the device spacing has to be large, which prevents high-density and large-scale integration in optoelectronic integrated circuits (OEIC) and planar lightwave circuits (PLC). <br /><br /> In this dissertation, the silicon-on-insulator (SOI) technology is introduced to the design and fabrication of passive polarization rotators (PR). Efficient and accurate full-vectorial finite-element eigenmode solvers as well as propagation schemes for characterizing novel SOI PRs are developed because commercial software packages based on finite-difference techniques are inefficient in dealing with arbitrary waveguide geometries. <br /><br /> A set of general design procedures are accordingly developed to design a series of slanted-angle polarization converters, regardless of the material system (SOI or III-V), outer-slab layer configuration (symmetric or asymmetric), and longitudinal loading (single- or multi-section). In particular, our normalized design charts and simple empirical formula for SOI polarization converters are applicable to a wide range of silicon-guiding-film thickness, e. g. , from 1 to 30 &mu;m, enabling fast and accurate polarization rotator design on most commercial SOI wafers. With these procedures, in principle 100% polarization conversion efficiency can be achieved by optimizing waveguide geometric parameters. <br /><br /> A novel configuration with asymmetric external waveguiding layers is proposed, which is advantageous for fabrication procedure, manufacturing tolerance, single-mode region, and conversion efficiency. By etching along the crystallographic plane, the angled-facet can be perfectly fabricated. Completely removing external waveguiding layer beside the sloped sidewall not only simplifies production procedures but also enhances fabrication tolerances. <br /><br /> To accurately and efficiently characterize asymmetric slanted-angle SOI polarization converters, adaptive mesh generation procedures are incorporated into our finite-element method (FEM) analysis. In addition, anisotropic perfectly-matched-layer (PML) boundary condition (BC) is employed in the beam propagation method (BPM) in order to effectively suppress reflections from the edges of the computation window. For the BPM algorithm, the power conservation is strictly monitored, the non-unitarity is thoroughly analyzed, and the inherent numerical dissipation is reduced by adopting the quasi-Crank-Nicholson scheme and adaptive complex reference index. <br /><br /> Advantages of SOI polarization rotators over III-V counterparts are studied through comprehensive research on power exchange, single-mode condition, fabrication tolerance, wavelength stability, bending characteristics, loss and coupling properties. The performance of SOI PRs is stable for wavelengths in the ITU-T C-band and L-band, making such devices quite suitable for DWDM applications. Due to the flexible cross-section of SOI polarization converters, the coupling loss to laser diodes and single mode fibers (SMF) can be designed to be very small and can be further reduced by a tapered waveguide with cross-sections always satisfying the single-mode criteria. Slanted-angle SOI polarization rotators display asymmetric bending characteristics and permit extremely small curvatures with negligible radiation loss when the angled-facet is located at the outer bend radius. Moreover, SOI polarization rotators can be manufactured with low-price processing techniques that are fully compatible with CMOS integrated circuits (IC) technology, and thus can be integrated on both photonic and electronic chips. <br /><br /> Experimental verifications have shown good agreement with theoretical analysis and have confirmed the promising characteristics of our novel asymmetric SOI polarization converters. Similar asymmetric-outer-slab geometry has recently been employed by peer researchers to fabricate high performance III-V polarization rotators. We therefore believe that results in this dissertation will contribute much to related research fields....

Software reliability has not kept pace with computing hardware. Despite the use reliability improvement techniques and methods, faults remain that lead to software errors and failures. Runtime monitoring can improve software reliability by detecting certain errors before failures occur. Monitoring is also useful for online and electronic services, where resource management directly impacts reliability and quality. For example, resource ownership errors can accumulate over time (e. g. , as resource leaks) and result in software aging. Early detection of errors allows more time for corrective action before failures or service outages occur. In addition, the ability to monitor individual software concerns, such as application resource ownership structure, can help support autonomic computing for self-healing, self-adapting and self-optimizing software. <br /><br /> This thesis introduces ResOwn - an application resource ownership ontology for interactive session-oriented services. ResOwn provides software monitoring with enriched concepts of application resource ownership borrowed from real-world legal and ownership ontologies. ResOwn is formally defined in OWL-DL (Web Ontology Language Description Logic), verified using an off-the-shelf reasoner, and tested using the call processing software for a small private branch exchange (PBX). The ResOwn Prime Directive states that every object in an operational software system is a resource, an owner, or both simultaneously. Resources produce benefits. Beneficiary owners may receive resource benefits. Nonbeneficiary owners may only manage resources. This approach distinguishes resource ownership use from management and supports the ability to detect when a resource's role-based runtime capacity has been exceeded. <br /><br /> This thesis also presents a greybox approach to concern-specific, dynamic software structure monitoring including a monitor architecture, greybox interpreter, and algorithms for deriving monitoring model from a monitored target's formal specifications. The target's requirements and design are assumed to be specified in SDL, a formalism based on communicating extended finite state machines. Greybox abstraction, applicable to both behavior and structure, provides direction on what parts, and how much of the target to instrument, and what types of resource errors to detect. <br /><br /> The approach was manually evaluated using a number of resource allocation and ownership scenarios. These scenarios were obtained by collecting actual call traces from an instrumented PBX. The results of an analytical evaluation of ResOwn and the monitoring approach are presented in a discussion of key advantages and known limitations. Conclusions and recommended future work are discussed at the end of the thesis....

In this work, three aluminum sheet alloys, AA5754, AA5182 and AA6111, which are prime candidates for replacing mild steel in automobile structures, are tested in tension at quasi-static and high strain rates. <br /><br ...

In this study two nonlinear analysis methods are proposed for investigation of nonlinear effects of high temperature superconductive(HTSC) thin film planar microwave circuits. The MoM-HB combination method is based on ...

UV disinfection performance was investigated under the influence of representative particle sources, including wastewater particles from secondary effluent in a wastewater treatment plant, river particles from surface ...

The importance of social capital can be characterized by a well-known quote: "it's not just what you know, but whom you know". Firms with rich social capital are more informed, more capable, and more competitive, because networks of resources are within their reach. Social capital is embedded in social networks, and social network analysis is the chief topic of this research. The network being examined contains 1126 venture capital (VC) programs, 206 of them being corporate venture programs, and the rest consisting of independent venture capital firms. Venture programs co-invest in portfolio firms following an identifiable pattern. This research attempts to explain this co-investment pattern using social network analysis. Four attributes of social networks are explored during this analysis: prominence, range, brokerage, and cohesion. The findings of the corporate venture capital network provide a number of implications for the theory of social capital. The objective of the thesis is using social capital to examine the syndication patterns in a corporate VC network. The analysis of the corporate VC co-investment pattern supports four hypotheses. First, the corporate VC network is not cohesive. Second, most relationships in the network are indirect. Third, most prominent VCs are also the most powerful resource brokers in the network. Lastly, prominent VCs are likely to syndicate with other prominent VCs....

This work deals with the control of the human immune system. A standard immune system model is modified by introducing control signals corresponding to drug cocktail and immune suppressor treatments. The ultimate ...