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京都大学 / 新制・課程博士 / 博士(理学) / 甲第23731号 / 理博第4821号 / 新制||理||1689(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 谷村 吉隆, 教授 林 重彦, 教授 渡邊 一也 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

<p>Bacteria of the genus <em>Deinococcus</em> are perhaps the most resilient life forms ever discovered, demonstrating extreme resistance to ionizing radiation, ultraviolet radiation, desiccation, and a variety of mutagenic chemical agents. The most studied member of this genus, <em>D. radiodurans</em>, has been observed to rapidly reassemble its genome following severe fragmentation by hundreds of γ-radiation induced double-strand DNA breaks. Amongst the numerous factors contributing to DNA repair, a single-stranded annealing protein, DdrB, is believed to play an important role during the initial phases of recovery. The work described in this thesis represents the first structural characterization of DdrB, revealing a novel fold for single-stranded DNA binding. Together with biochemical data delineating the DNA-binding interface, two crystal structures of the DdrB/ssDNA complex were also solved, providing a comprehensive illustration of this interaction. Quaternary assemblies observed in these crystal structures also informed on the potential contribution of higher-order nucleoprotein complexes to the function of DdrB in single-stranded annealing. Most significantly, a face-to-face assembly of DdrB/ssDNA complexes provided insight into the mechanism by which DdrB mediates annealing of DNA, which may represent a common mechanism shared by other single-stranded annealing proteins.<strong></strong></p> / Doctor of Philosophy (PhD)

Intercritically annealed medium manganese steels are a promising third-generation advanced high-strength steel candidate, relying on large fractions of Mn-enriched retained austenite for excellent strength-ductility combinations. The present study proposes a novel cyclic intercritical annealing to promote nucleation and efficient stabilization of austenite in a medium Mn microstructure. Design of the heat treatment is driven by the hypothesis that the distribution of ductile austenite is key in mitigating the strain incompatibility that accelerates failure in these steels. Development and preliminary testing of the heat treatment are first detailed and compared with literature results for equivalent isothermal annealing. The effects of cyclic annealing parameters on the amount and stability of retained austenite are also explored through diffraction methods and mechanical testing. Finally, steps are taken towards quantifying austenite formation during the cyclic treatment, and recommendations are made for adapting the designed heat treatment to thicker gauges.

Yeast Rad1-Rad10 is a structure specific nuclease that processes branched double-strand break (DSB) repair intermediates; the persistence of which can impede normal DNA metabolism. The single strand annealing (SSA) mechanism of DSB repair acts when homologous repeats flank both sides of the DSB. End resection from the 5′ ends of the break exposes complementary sequences at the flanking repeats, which are annealed to form 3′ non-homologous flap structures. Saw1 recruits Rad1-Rad10 recruits to these 3′ non-homologous flaps, where Rad1-Rad10 incises the DNA and removes the flap. Saw1 has affinity towards branched DNA structures and forms a stable complex with Rad1-Rad10. The mechanism of both structure specific recruitment and nucleolytic activity of the Saw1-Rad1-Rad10 complex is currently unknown. To study this nuclease complex, we need to produce large quantities of pure, stable, and active recombinant protein. Using dynamic light scattering (DLS) and differential scanning fluorimetry (DSF)-based high throughput thermal stability assays, we have developed a method for large-scale production of recombinant Saw1. This optimized method has increased the stability and yield of protein, thereby allowing for future biochemical investigation of Saw1. Similarly, we have optimized the large-scale production of the higher molecular-weight complex (Saw1-Rad1-Rad10) and improved the homogeneity of the recombinant complex. We have also biochemically characterized the minimal branched DNA substrates for both Saw1 and Saw1-Rad1-Rad10. This work allows for biochemical investigation into the molecular mechanism of eukaryotic 3′ non-homologous flap removal during SSA. / Thesis / Master of Science (MSc)

McMaster University DOCTOR OF PHILOSOPHY (2017) Hamilton, Ontario (Engineering Physics) TITLE: Luminescent Silicon Carbonitride Thin Films Grown using ECR PECVD: Fabrication and Characterization AUTHOR: Zahra Khatami , M.A.Sc. (Shahid Behehsti University) SUPERVISOR: Professor Peter Mascher NUMBER OF PAGES: xx, 268 / Silicon, the cornerstone semiconductor of microelectronics, has seen growing interest as a low-cost material in photonics. Nanoscience has employed various strategies to overcome its fundamentally inefficient visible light emission such as developing new silicon-based nanostructures and materials. Each of the proposed materials has its own advantages and disadvantages in attempting to reach commercialization. Silicon carbonitride (SiCxNy) is a less-studied and multi-functional material with tunable optical features. Despite reports on promising mechanical properties of SiCxNy thin films, they have not yet been well explored optically. This thesis presents the first in-depth analysis of the luminescent properties of SiCxNy thin films at a broad range of compositions and temperatures. To better understand this ternary structure, the reported data of the two fairly well studied binary structures was used as a reference. Therefore, three classes of silicon-based materials were produced and explored; SiCxNy, SiNx, and SiCx. Samples were fabricated using one of the common methods in the semiconductor industry; electron cyclotron resonance plasma enhanced chemical vapour deposition (ECR PECVD). A multitude of characterization techniques were utilized including; optical methods (ultraviolet-visible spectroscopy (UVVIS), variable angle spectroscopic ellipsometry (VASE), photoluminescence (PL)) and structural techniques (elastic recoil detection (ERD), Rutherford backscattering spectrometry (RBS), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), high-resolution transmission electron microscopy (HR-TEM)). In view of the exploring of emission properties of SiCxNy materials, our approach was towards the enhancement of the visible emission by adjusting the film composition and subsequent thermal treatment. First, a systematic study of the influence of carbon on the optical, compositional, and structural properties of SiCxNy was carried out. This investigation was followed by an exploration of influence of growth conditions on the visible emission and its connection with the other film properties including hydrogen concentration, microstructure, and composition. In addition, hydrogen diffusion was explored and associated with two featured annealing temperatures. The key element of this thesis is the comprehensive report on the interdependency of the visible light emission and all optical, structural, and compositional features of SiCxNy structures. Unlocking the potential of this ternary and less studied material can appeal to the silicon photonics community to implement it in anti-reflection, solar cell, and sensing applications, and in particular as a substitution of SiNx used in existing microelectronic devices. / Thesis / Doctor of Philosophy (PhD)

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Yes / Multidimensional data streams are a major paradigm in data science. This work focuses on possibilistic clustering algorithms as means to perform clustering of multidimensional streaming data. The proposed approach exploits fuzzy outlier analysis to provide good learning and tracking abilities in both concept shift and concept drift.

Due to a variety of political, economic, and technological factors, many national electricity industries around the globe are transforming from non-competitive monopolies with centralized systems to decentralized operations with competitive business units. This process, commonly referred to as deregulation (or liberalization) is driven by the belief that a monopolistic industry fails to achieve economic efficiency for consumers over the long run. Deregulation has occurred in a number of industries such as: aviation, natural gas, transportation, and telecommunications. The most recent movement involving the deregulation of the electricity marketplace is expected to yield consumer benefit as well. To facilitate deregulation of the electricity marketplace, competitive business units must be established to manage various functions and services independently. In addition, these business units must be given physical property rights for certain parts of the transmission and distribution network in order to provide reliable service and make effective business decisions. However, partitioning a physical power grid into economically viable districts involves many considerations. We refer to this complex problem as the electrical power districting problem. This research is intended to identify the necessary and fundamental characteristics to appropriately model and solve an electrical power districting problem. Specifically, the objectives of this research are five-fold. First, to identify the issues relevant to electrical power districting problems. Second, to investigate the similarities and differences of electrical power districting problems with other districting problems published in the research literature. Third, to develop and recommend an appropriate solution methodology for electrical power districting problems. Fourth, to demonstrate the effectiveness of the proposed solution method for a specific case of electric power districting in the Republic of Ghana, with data provided by the World Bank. Finally, to develop a decision support system for the decision makers at the World Bank for solving Ghana's electrical power districting problem. / Ph. D.

Generalized hill climbing (GHC) algorithms provide a framework for using local search algorithms to address intractable discrete optimization problems. Many well-known local search algorithms can be formulated as GHC algorithms, including simulated annealing, threshold accepting, Monte Carlo search, and pure local search (among others). This dissertation develops a mathematical framework for simultaneously addressing a set of related discrete optimization problems using GHC algorithms. The resulting algorithms, termed simultaneous generalized hill climbing (SGHC) algorithms, can be applied to a wide variety of sets of related discrete optimization problems. The SGHC algorithm probabilistically moves between these discrete optimization problems according to a problem generation probability function. This dissertation establishes that the problem generation probability function is a stochastic process that satisfies the Markov property. Therefore, given a SGHC algorithm, movement between these discrete optimization problems can be modeled as a Markov chain. Sufficient conditions that guarantee that this Markov chain has a uniform stationary probability distribution are presented. Moreover, sufficient conditions are obtained that guarantee that a SGHC algorithm will visit the globally optimal solution over all the problems in a set of related discrete optimization problems. Computational results are presented with SGHC algorithms for a set of traveling salesman problems. For comparison purposes, GHC algorithms are also applied individually to each traveling salesman problem. These computational results suggest that optimal/near optimal solutions can often be reached more quickly using a SGHC algorithm. / Ph. D.