Digital Commons Network^™

Mixture Modeling Of Next Generation Sequencing Data And Its Applications To Genotyping And Estimating Genotype Frequencies, Jayon Lihm

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Estimating the probability that an individual has a base pair nucleodite different from the reference nucleotide is important in next generation sequencing (NGS) research. I present a method for modeling the frequency of single nucleotide polymorphism variants in the exome capturing sequence data of an individual. A mixture distribution was used to model the proportion of alternative alleles at a specified base pair position assuming a biallelic single nucleotide polymorphism model. I measured the proportion of alternative alleles for positions in chromosome 1 exome sequencing data fro two trios taken from the Pilot 3 data in the 1000 Genomes Project. …

Novel Catalytic Nanoparticles And Nanostructures For Environmental And Energy Applications, Shen Zhao

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Semiconductor photocatalysis is a dynamic field at the forefront of environmental and energy research. This dissertation has focused on the development of novel nanomaterials to exceed performance for environmental and energy related applications in both liquid and gas phases as compared to traditional materials. This project investigated the impact of size of noble metal clusters on photocatalytic activity induced by UV and visible light. Compared to larger particles, sub-nanometer particles have shown much better activity for catalytic reactions in both liquid and gas phases. These nanoclusters supported on various semiconductors, such as TiO2 and CdS showed outstanding catalytic properties for …

Forward Analysis Of Transversely Isotropic Thin Film By Indentation Method, Zheng Zhi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Instrument indentation based methods for determining elasto-plastic properties of bulk specimen or thin film have received considerable and continue growing attention for recent decades, due to its simplicity, operability, and potential applications. However, the researches of transversely isotropic thin film are still at the beginning stage. In order to obtain a deeper understand of the relationship between P&ndashh curve and thin film properties, both dimensional analysis method and finite element method were applied in the present work. Extensive computational analysis of 630 sets of materials properties was carried out here. Through systematical studies, a more reasonable and intrinsic relationship, between …

Threading Dislocation Characterization And Stress Mapping Depth Profiling Via Ray Tracing Technique, Tianyi Zhou

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Zinc oxide (ZnO) has been well known as a transparent, dielectric, piezoelectric and wide band gap material. The potential capabilities have been demonstrated for a wide range of applications such as piezoelectric transducer, gas sensor, optical waveguides and transparent electrode. It could also be applied as a substrate material for GaN-based devices. However, while some applications have already been realized, issues relating to crystalline defects remain a barrier to the successful realization of several others. In this thesis, the central focus of Chapter II is to characterize threading dislocations in hydrothermal grown ZnO substrates through simulation work as well as …

Real Rational Curves Of Low Degree, Shane Dmello

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In the first part of the talk we will consider real planar rational curves of degree 4. We will prove that the rigid isotopy classification of real rational curves of degree 4 in the projective plane can be solved by considering their chord diagrams. In the second part of the talk, we will consider real rational knots on the 3-sphere. The 3-sphere can be realized as a subvariety of the projective space of dimension 4. Real rational knots in the 3-sphere are curves in the 4-dimensional projective space that lie on the 3-sphere. We will prove a rigid isotopy classification …

Computation Of Floer Invariant Of (2,2n)-Torus Link Complement, Jaepil Lee

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

A closed three manifold invariant Heegaard Floer homology was generalized to bordered Heegaard Floer homology, defined by Robert Lipshitz, Peter Ozsváth and Dylan Thurston. Bordered Heegaard Floer homology is an invariant of three manifold with connected boundary, and its variant doubly bordered Floer homology is a bimodule defined on three manifold with two disconnected boundary components. In this thesis, we compute bordered Floer homology of (2,2n)-torus link complement. | A closed three manifold invariant Heegaard Floer homology was generalized to bordered Heegaard Floer homology, defined by Robert Lipshitz, Peter Ozsváth and Dylan Thurston. Bordered Heegaard Floer homology is an invariant …

Super-Hydrophobic Metallic Surface Formation By Short Pulsed Lasers, Di Liu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Surface texturing in micro/nanoscale plays an important role in many application fields including enhanced light trapping in solar cell, self-cleaning and anti-icing surfaces by achieving super-hydrophobicity in wind turbine and airplane wings, and enhanced convective and radiative heat transfer from surface. For metals such as copper and stainless steel which have been widely used in modern industries, formation of super-hydrophobic surfaces can offer significant benefits in terms of reliable and efficient operation by enabling, for instance, surfaces free from corrosion, contamination, freezing, and crack with improved heat dissipation. Super-hydrophobic surface is a highly hydrophobic surface typically with water contact angle …

Laser Processing Of Carbon Nanotube Transparent Conducting Films, Andrew Mann

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Transparent conducting films, or TCFs, are 2D electrical conductors with the ability to transmit light. Because of this, they are used in many popular electronics including smart phones, tablets, solar panels, and televisions. The most common material used as a TCF is indium tin oxide, or ITO. Although ITO has great electrical and optical characteristics, it is expensive, brittle, and difficult to pattern. These limitations have led researchers toward other materials for the next generation of displays and touch panels. The most promising material for next generation TCFs is carbon nanotubes, or CNTs. CNTs are cylindrical tubes of carbon no …

High Performance Two-Phase Thermosyphon For Energy-Efficient Refrigeration Applications: Modeling And Experiments, Chunlei Mei

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The Two-Phase Closed Thermosyphon (TPCT) is a device that transfers heat from its bottom to top and because phase change phenomenon happens both in its bottom and top, its performance is ten times better than pure metal. It has three heat transfer regimes, condenser, adiabatic section and evaporator. The mechanism of thermosyphon is the phase change cycle: liquid absorbs heat in evaporator and then vaporizes into vapor; finally the vapor condenses along the condenser wall and flow back to evaporator liquid pool. Firstly, detailed heat transfer mechanism will be discussed. Many empirical equations will be reviewed. Geometrically, TPCT contains three …

Synchrotron X-Ray Scattering Characterization Of Soft Materials: Rubber And Plastics, Justin Che

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Synchrotron X-ray scattering and diffraction techniques have been widely used to study the structure and property relationships of materials. It is important to first identify the driving physics and basic understanding of the structure change during mechanical usage before leading to material design for potential applications. In this thesis, the combined wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS) techniques have been used to analyze in-situ structure formation over a large range of length scale from 1 nm to 100 nm during mechanical deformation. In specific, the in-situ structural development and morphological changes in polymer plastics and rubber during …

Untangling The Interactions: Structural Basis Of Nitric Oxide Regulated Cyclic-Di-Gmp Metabolism In Bacteria, Tanaya Lahiri

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Bacteria use numerous small molecules for cellular signaling. These primary and secondary messengers act within the cell to relay signal transduction and regulate distinct pathways. Among these the diatomic gas molecule nitric oxide (NO) and the nucleotide cyclic-di-GMP play central role in virulence, quorum sensing, and biofilm formation. In this dissertation, we have focused on H-NOX, a heme-nitric oxide/oxygen binding protein in the biofilm-dwelling bacterium Shewanella woodyi (Sw), which mediates NO-induced biofilm dispersal by modulating the activity of a dual-functioning diguanylate cyclase/phosphodiesterase enzyme that we have named HaCE, (H-NOX-associated cyclic-di-GMP enzyme). These enzymes tightly regulate the intracellular spatio-temporal concentrations of …

Macrocyclic Host-Guest Framework For Polymerization Of Diiodobutadiyne, Xianzhi Liu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Conjugated organic polymers have optical and electronic properties that make them candidates for applications in organic field effect transistors (OFETs) and light emitting materials. Polydiacetylenes (PDAs) are an important branch of conjugated polymers with alternating poly(ene-yne) structure. The all-carbon polymer without any side groups is carbyne, which has only alternating single and triple carbon-carbon bonds. Carbyne provides a good opportunity to investigate the inherent properties of conjugated polymers. Polydiiododiacetylene (PIDA), a simple PDA with only iodine atom substituents, can be successfully obtained by the topochemical polymerization of the monomer diiodobutadiyne. This polymerization is achieved through the use of bis(nitrile) or …

Poly(Diiododiacetylene): A Potential Precursor For New All-Carbon Materials, Daniel Joseph Resch

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Poly(diiododiacetylene) (PIDA) is a polymer consisting entirely of carbon and iodine. The polymer is prepared by cocrystallizing a bis(nitrile) oxalamide host with the monomer diiodobutadiyne. These compounds are held together by a halogen bond and an ordered 1,4-topochemical polymerization occurs in the solid state. The formation of the monomer cocrystals was found to be highly solvent dependent. Acetonitrile was found to greatly improve the yield of cocrystals over solvents used in the past. Cocrystals could not be obtained from other solvents such as dimethoxyethane and acetone. THF did give some cocrystal but the yield was poor. The use of acetonitrile …

Rational Design Of Cu-Based Nanocatalysts For The Production Of Methanol, Yixiong Yang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The synthesis of methanol (CH3OH) from CO2 hydrogenation (CO2+3H2=CH3OH+H2O) has attracted considerable attention recently due to its industrial and environmental significance. It is a promising way to convert CO2, a greenhouse gas, into a renewable liquid fuel, CH3OH. Commercially, the reaction is conducted over a Cu-ZnO/Al2O3 catalyst under high temperature (220-240°C) and high pressure (50-100 bar) conditions, but the conversion is limited to ~20%. In this work, a combined theoretical and experimental study was carried out in order to derive general principles to improve the performance of Cu-based catalysts. Density Functional Theory (DFT) calculations were carried out to elucidate the …

Systematic Modeling And Characterization Of Analog Circuits Using Symbolic And Data Mining Techniques, Cristian Ferent

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Analog circuit design activities mainly depend on designers' expertise and their ability to produce new designs by combining basic devices, sub-circuits, and ideas from similar solutions as the source for innovation. There are very few systematic methods that can characterize similarities and differences between analog circuits while maintaining the correlation between design variables, performance, and trade-offs. Moreover, many computer-aided design tools are focused only on routine tasks, like transistor sizing and layout design. This dissertation presents novel techniques to automatically characterize the analog design space based on feature uniqueness and variety and to perform systematic circuit comparisons using symbolic models. …

New Development On Market Microstructure And Macrostructure: Patterns Of U.S. High Frequency Data And A Unified Factor Model Framework, Xu Dong

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this thesis we study the problem of modeling cross-sectional volatility structure of U.S. stock market. The thesis contains two parts. In the first part we identify a particular volatility spike phenomenon, that the cross-sectional volatility is significantly stronger at every 5 minute. An empirical spike study is conducted on individual stock level by applying Lee-Mykland jump detector. By constructing spike ratio statistics, the evolving paths of this spike phenomenon is studied during the 1993 to 2009 time period. In the second part, we model the volatility structure using factor structures. Particular, we propose two approaches to build a better …

La Biografã­A Difusa De Sombra Castaã±Eda: Un Anã¡Lisis Histã³Rico-Literario | La Biografía Difusa De Sombra Castañeda: Un Análisis Histórico-Literario, Mr Ramón Fernádez

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The novelist Marcio Veloz Maggiolo is one of the most prolific Dominican writers of the last decades. In this thesis we devote our attention to the novel biografía difusa de Sombra Castañeda. We go through many of the modulation of the construct Dominican cultural identity presented in the novel. Trying to objectively define the construct Dominican Cultural identity, La biografía difusa de Sombra Castañeda explores its character's way of life, displaying the complex relationships between the dictator, Sombra Castañeda, and his subordinates, the Dominican people. We analyze these relationships with an eye on the way in which the subordinates are …

Eikonal Scattering At Strong Coupling, Melvin Eloy Irizarry-Gelpi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The scattering of subatomic particles is a source of important physical phenomena. Decades of work have yielded many techniques for the computation of scattering amplitudes. Most of these techniques involve perturbative quantum field theory and thus apply only at weak coupling. Complementary to scattering is the formation of bound states, which are intrinsically nonperturbative. Regge theory arose in the late 1950s as an attempt to describe, with a single framework, both scattering and the formation of bound states. In Regge theory one obtains an amplitude with bound state poles after analytic continuation of a nonperturbative scattering amplitude, corresponding to a …

Uncovering The Structure Of (Super)Conformal Field Theories, Pedro Liendo

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Conformal field theories (CFTs) are of central importance in modern theoretical physics, with applications that range from condensed matter physics to particle theory phenomenology. In this Ph.D. thesis we study CFTs from two somehow orthogonal (but complementary) points of view. In the first approach we concentrate our efforts in two specific examples: the Veneziano limit of N=2 and N=1 superconformal QCD. The addition of supersymmetry makes these theories amenable to analytical analysis. In particular, we use the correspondence between single trace operators and states of a spin chain to study the integrability properties of each theory. Our results indicate that …

Translational Symmetry Breaking In Materials: First-Principles Wannier Function Study, Chia-Hui Lin

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The spatial periodicity of the crystal structure dictates the electronic band structure theory as the fundamental paradigm in solid state physics. The original translation in materials is commonly broken with an enlarged unit cell required by spontaneously developed long-range order or multiple competing periodicities. The former happens in the systems undergoing the phase transition to antiferromagnetism, charge/spin density waves or lattice distortion. The latter originates from the intrinsic arrangement of the multiple atom system or the externally introduced impurities. The emergence of the broken symmetry can significantly modify the electronic structure, shift the chemical potential, and change the electric, magnetic …

Multi-Dimensional Workload Analysis And Synthesis For Modern Storage Systems, Vasily Tarasov

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Modern computer systems produce and process an overwhelming amount of data at an increasing rates. The performance of storage hardware components, however, cannot keep up with the required speed at a practical cost. To mitigate this discrepancy, storage vendors incorporate many workload-driven optimizations in their products. Emerging applications cause workload patterns to change rapidly and significantly. One of the prominent examples is a rapid shift towards virtualized environments. Virtual machines mix I/O streams from different applications and perturb applications' access patterns. In addition, modern users demand more convenience features, such as deduplication, snapshotting, and encryption. Stringent performance requirements, changing I/O …

Species Composition And Reproductive Strategies Of Commensal Synalpheus Shrimp (Decapoda:Alpheidae) Occupying The Sponges Spheciospongia Vesparium And Spongia Sp. Of The Florida Reef Tract, Brittnee Nicole Barris

HCNSO Student Theses and Dissertations

Synalpheus shrimp species of the gambarelloides group are the only marine organisms displaying the highest level of social functioning, eusociality. Their social hierarchies are equally complex compared to the reproductive abnormalities that have been recently discovered. For instance, snapping shrimp of the genus Synalpheus were thought to be gonochoric, i.e. developing as independent sexes, until scanning electron microscopy studies revealed intersexed gonopores in several species. This project analyzed both the species composition, and accompanying reproductive structures, of Synalpheus spp. (Caridea: Alpheidae) comprised of densely aggregating communal and pair-living colonies in the Florida Keys, Florida.

Colonies of pair-living and communal Synalpheus …

Racial Differences In Human Platelet Par4 Reactivity Reflect Expression Of Pctp And Mir-376c., Leonard Edelstein, Lukas M Simon, Raúl Teruel Montoya, Michael Holinstat, Edward S Chen, Angela Bergeron, Xianguo Kong, Srikanth Nagalla, Narla Mohandas, David E Cohen, Jing-Fei Dong, Chad Shaw, Paul Bray

Cardeza Foundation for Hematologic Research

Racial differences in the pathophysiology of atherothrombosis are poorly understood. We explored the function and transcriptome of platelets in healthy black (n = 70) and white (n = 84) subjects. Platelet aggregation and calcium mobilization induced by the PAR4 thrombin receptor were significantly greater in black subjects. Numerous differentially expressed RNAs were associated with both race and PAR4 reactivity, including PCTP (encoding phosphatidylcholine transfer protein), and platelets from black subjects expressed higher levels of PC-TP protein. PC-TP inhibition or depletion blocked PAR4- but not PAR1-mediated activation of platelets and megakaryocytic cell lines. miR-376c levels were differentially expressed by race and …

Commencement Program 2013 December: School Of Social Work; School Of Urban And Public Affairs; University College, The University Of Texas At Arlington

Commencement Programs, Photos, and Video

No abstract provided.

Commencement Program 2013 December: College Of Education And Health Professions, The University Of Texas At Arlington

Commencement Programs, Photos, and Video

No abstract provided.

Commencement Program 2013 December: College Of Liberal Arts, The University Of Texas At Arlington

Commencement Programs, Photos, and Video

No abstract provided.

Scholarships Awarded To Mcnair Scholars, The Mcnair Team

McNair Scholars Research Journal

No abstract provided.

Granite State College, University System Of New Hampshire 2013-2014 Undergraduate Catalog, Granite State College

Granite State College Catalogs

No abstract provided.

Systematic Parameter Analysis For Selective Laser Melting (Slm) Of Silver-Based Materials., Harald Rieper

Electronic Theses and Dissertations

Selective Laser Melting (SLM) is a growing technology for the additive manufacturing of parts and structures. Based on a powder layer technique, a laser locally melts the powder and forms new structures. [1] In this approach, silver-based alloy powders will be used. The processing of this kind of material is considered difficult compared to other powder materials such as mild steels or tool steels. Silver powder is a highly reflecting material and has excellent thermal conductivity. Both properties make it difficult to process using Selective Laser Melting. Due to its high price, industries use silver parts as economically as possible …

The Impact Of Kindergarten Teachers' Theoretical Orientation To Reading On Curricular Planning And Classroom Practice In Literacy., Jacquelyn J. Singleton

Electronic Theses and Dissertations

Using case-study analysis, this dissertation is a qualitative examination of kindergarten teachers’ beliefs, theoretical orientation toward reading, and outside pressures and their impact upon the educators’ classroom practice for literacy instruction. Selected for the study based upon their scores on DeFord’s Theoretical Orientation to Reading Profile (1985), eight teachers participated in two in-depth interviews and two separate 30-minute classroom observations for which they provided lesson plans. They also completed the Reading Interest-A-Lyzer (Reis, 2005). The results were coded with a coding scheme developed around the Theoretical Orientation to Reading Profile and Vygotsky’s Activity Theory—the theoretical framework for the current study. …