Digital Commons Network^™

Component Trees For The Exploration Of Macromolecular Structures In Biology, Lucas Oliveira

Dissertations, Theses, and Capstone Projects

Understanding the three-dimensional structure of a macromolecular complex is essential for understanding its function. A component tree is a topological and geometric image descriptor that captures information regarding the structure of an image based on the connected components determined by different grayness thresholds. This dissertation presents a novel interactive framework for visual exploration of component trees of the density maps of macromolecular complexes, with the purpose of improved understanding of their structure. The interactive exploration of component trees together with a robust simplification methodology provide new insights in the study of macromolecular structures. An underlying mathematical theory is introduced and …

Synthesis Of Biologically Important C-Glycosides From Simple C-Glycosyl Alkenes, Ahmad Sabri Altiti

Dissertations, Theses, and Capstone Projects

C-Glycosides are carbohydrate analogues in which the glycosidic oxygen is replaced with a methylene substituent. Because of their stability under acidic hydrolysis or enzymatic cleavage, they are widely used as mimetics of their parent O-glycosides in medicinal chemistry. This thesis describes the development of new synthetic methods for C-glycosides, which center on the use of readily available, simple C-allyl glycosides as precursors. C- glycosides of three structurally distinct and pharmacologically interesting carbohydrates, the immunostimulatory glycolipid C-KRN700, the insulin mimetic glycoinositol β-galactosamine-(1→4)-3-O-methyl-D-chiro-inositiol (INS-2), and α-mannose-(1→6)-D-myo-inositiol, a subunit of the cell wall in Mycobacterium tuberculosis, will be used as test cases for …

The Effect Of Income On Health After Hurricane Katrina, Jang Wook Lee

Dissertations, Theses, and Capstone Projects

There is a large literature that documents a positive correlation between income and a variety of measures of good health. This correlation may reflect causality in both directions and may also reflect omitted "third variables" that are positively related to income and health. In my dissertation, I employ an exogenous negative shock to income due to a natural disaster to estimate the true causal impact of income on health. The shock I will use is Hurricane Katrina, which severely damaged counties in Alabama, Mississippi, and Louisiana in August 2005. I use these treatment counties and a variety of alternative sets …

Carbon And Nitrogen Dynamics From Slow Pools Of Soil Organic Matter In A Temperate Forest: Pyrogenic Organic Matter And And Root Litter, Fernanda Dos Santos

Dissertations, Theses, and Capstone Projects

Soil organic matter (SOM) is the dominant reservoir of organic carbon (OC) in terrestrial ecosystems, storing approximately three times the size of the C pool in the atmosphere. In temperate forests, a major fraction of the SOM consists of slowly decaying soil organic C (SOC) pools. While slowly cycling C pools constitute a large reservoir of stable C in soils, the dominant environmental factors controlling this C pool remain unresolved. This research investigates two significant, but poorly characterized slowly decaying C pools: fine root litter (< 2mm) and thermally altered plant biomass (pyrogenic organic matter, PyOM). Specifically, I used compound-specific stable isotope analysis (¹³C and ¹⁵N) as my main methodological approach to examine the (1) …

Characterization Of Wide Band Gap Semiconductors And Multiferroic Materials, Bo Cai

Dissertations, Theses, and Capstone Projects

Structural, optical and electrical properties of zinc oxide (ZnO), aluminum nitride (AlN), and lutetium ferrite (LuFe₂O4) have been investigated. Temperature dependent Hall Effect measurements were performed between 80 and 800 K for phosphorus (P) and arsenic (As) doped ZnO thin films grown on c-plane sapphire substrate by RF magnetron sputtering. These samples exhibited n-type conductivity throughout the temperature range with carrier concentration of 3.85 × 10 ¹⁶ cm^-3 and 3.65 × 10 ¹⁷ cm^-3 at room temperature for P-doped and As-doped ZnO films, respectively. The Arrhenius plots of free electron concentration of those doped samples showed …

Motivic Integration Over Nilpotent Structures, Andrew Ryan Stout

Dissertations, Theses, and Capstone Projects

This thesis concerns developing the notion of Motivic Integration in such a way that it captures infinitesimal information yet reduces to the classical notion of motivic integration for reduced schemes. Moreover, I extend the notion of Motivic Integration from a discrete valuation ring to any complete Noetherian ring with residue field $\kappa$, where $\kappa$ is any field. Schoutens' functorial approach (as opposed to the traditional model theoretic approach) allows for some very general notions of motivic integration. However, the central focus is on using this general framework to study generically smooth schemes, then non-reduced schemes, and then, finally, formal schemes. …

Systematic Comparison Of Cross-Lingual Projection Techniques For Low-Density Nlp Under Strict Resource Constraints, Joshua Waxman

Dissertations, Theses, and Capstone Projects

The field of low-density NLP is often approached from an engineering perspective, and evaluations are typically haphazard - considering different architectures, given different languages, and different available resources - without a systematic comparison. The resulting architectures are then tested on the unique corpus and language for which this approach has been designed. This makes it difficult to truly evaluate which approach is truly the "best," or which approaches are best for a given language.

In this dissertation, several state-of-the-art architectures and approaches to low-density language Part-Of-Speech Tagging are reimplemented; all of these techniques exploit a relationship between a high-density (HD) …

Development Of Cell-Active Inhibitors And Activity-Based Probe Of Cysteine Cathepsins, Dibyendu Dana

Dissertations, Theses, and Capstone Projects

Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cellular processes, and are implicated in various types of human diseases. Still however, many of their cellular function remain poorly understood. Chemical biology approaches employing small molecules can be utilized for this purpose. Unfortunately small molecule probes that are cell-permeable and non-peptidyl in nature are scarcely available.

In this work, first a library of sulfonyloxiranes is synthesized. From this library, 2-(2-ethylphenylsulfonyl)oxirane is identified as a selective inhibitor of cysteine cathepsins. Cell-based study reveals that 2-(2-ethylphenylsulfonyl)oxirane is a cell-permeable, covalent, and irreversible inhibitor of cathepsin B with …

Combinatorial Properties Of Polyiamonds, Christopher Larson

Dissertations, Theses, and Capstone Projects

Polyiamonds are plane geometric figures constructed by pasting together equilateral triangles edge-to-edge. It is shown that a diophantine equation involving vertices of degrees 2, 3, 5 and 6 holds for all polyiamonds; then an Eberhard-type theorem is proved, showing that any four-tuple of non-negative integers that satisfies the diophantine equation can be realized geometrically by a polyiamond. Further combinatorial and graph-theoretic aspects of polyiamonds are discussed, including a characterization of those polyiamonds that are three-connected and so three-polytopal, a result on Hamiltonicity, and constructions that use minimal numbers of triangles in realizing four-vectors.

An Algorithmic Approach To The Differential Galois Theory Of Second-Order Linear Differential Equations With Differential Parameters, Carlos Eduardo Arreche Aguayo

Dissertations, Theses, and Capstone Projects

We present algorithms to compute the differential Galois group G associated via the parameterized Picard-Vessiot theory to a parameterized second-order linear differential equation with respect to d/dx, with coefficients in the field of rational functions F(x) over a differential field F, where we think of the derivations on F as being derivations with respect to parameters. We build on an earlier procedure, developed by Dreyfus, that computes G when the equation is unimodular, assuming either that G is reductive, or else that its maximal reductive quotient is differentially constant. We first show how to modify the space of parametric derivations …

Dynamics Of Nanoparticles In Fluids And At Interfaces, Weikang Chen

Dissertations, Theses, and Capstone Projects

In this thesis, we use molecular dynamics simulation to study three basic behaviors or properties of nanoparticles: deposition during droplets evaporation, slip boundary condition and Brownian motion. These three problems address the need for an in-depth understanding of the dynamics of nanoparticles in fluids and at interfaces. In the first problem, evaporation of the droplets dispersed with particles, we investigated the distribution of evaporative flux, inner flow field, density and temperature. And we use these numerical experiments to check on our hydrodynamic theory of the "coffee ring" phenomenon. The simulations reveal the connection between the particle interactions and the deposit …

Planetary Improvement: Discourses And Practices Of Green Capitalism In The Cleantech Space, Jesse Adam Goldstein

Dissertations, Theses, and Capstone Projects

There is money to be made in saving the planet. A whole host of actors, such as investors, entrepreneurs, engineers, and policy makers have mobilized around our ecological problems, seeking to innovate new `green' and `clean' technologies that can serve a rapidly changing environment. The presumption that such technologies are both necessary and necessarily profitable anchors visions of a `green' capitalism that can and must be brought into existence.

However, just as free markets have never been all that free, why should we presume that green capitalism would be all that green? Instead of attempting to arbit whether or not …

Synthesis, Fabrication And Characterization Of Magnetic And Dielectric Nanoparticles And Nanocomposite Films, Xiaohua Liu

Dissertations, Theses, and Capstone Projects

Materials science is an interdisciplinary field investigating the structure-property relationship in solid-state materials scientifically and technologically. Nanoscience is concerned with the distinctive properties that matter exhibits when confined to physical dimensions on the order of 10^-9 meters. At these length scales, behaviors of particles or elaborate structures are often governed by the rules of quantum mechanics in addition to the physical properties associated with the bulk material.

The work reported here seeks to employ nanocystals, binary nanocomposites and thin films of materials, to build versatile, functional systems and devices. With a focus on dielectric, ferroelectric, and magnetoelectric performance, a …

Oxocarbenium Ion And Alkene Metathesis Strategies For The Synthesis Of Complex Cyclohexanes, Clayton Errol Mattis

Dissertations, Theses, and Capstone Projects

Highly oxygenated cyclohexanes comprise the structures of a number of pharmacologically interesting molecules, including potently bioactive natural products and carbapyranosides. The latter, which are unnatural analogues of carbohydrates in which the ring oxygen of the parent sugar is replaced with a methylene group, have attracted interest as hydrolytically stable mimetics of their parent O-glycosides. This research reports the development of two general methodologies for the synthesis of highly oxygenated cyclohexanes: (1) Oxocarbenium Ion Cyclization (OCC) and (2) Ring Closing Metathasis (RCM).

Chapter one gives a review of the literature on the synthesis for highly oxygenated cyclohexanes.

Previous results from this …

Optical Spectroscopy Of Xenon-Related Defects In Diamond, Yury Dziashko

Dissertations, Theses, and Capstone Projects

The work presents the results of optical studies of Xe-related defect in diamond. This defect is one of a few having narrow zero-phonon line in the near-infrared part of the photo-luminescence spectra. It appears in diamond after Xe+ ion implantation followed by thermal annealing. Given unique physical properties of diamond (hardness, optical transparency in wide spectral range, chemical inertness, high thermal conductivity, low thermal expansion coefficient) and stability of Xe-related center it can be viewed as an potential candidate for the source of single-photons, or as optically manipulated qubit, not unlike nitrogen-vacancy center. However, compared to the latter Xe-related center …

Canvas: A Fast And Accurate Geometric Sentence Alignment System Using Lexical Cues Within Complex Misalignment Settings, Hussein M. Ghaly

Dissertations, Theses, and Capstone Projects

In this paper, we present a new sentence alignment system (Canvas), which is a Python implementation of a geometric approach to sentence alignment, based on lexical cues. Canvas system is designed mainly to handle parallel texts exhibiting complex misalignment patterns, namely within English-Arabic pairs for United Nations documents. The system relies heavily on pre-indexing words/tokens in the source and target texts, and it creates correspondences between the token indexes. From this point onward, the alignment problem is reduced to a geometric problem of finding the path that runs through the True Correspondence Points (TCPs). The likelihood of a point being …

Martingales For Uniformly Quasisymmetric Circle Endomorphisms, Yunchun Hu

Dissertations, Theses, and Capstone Projects

The main subject studied in this thesis is the space of all uniformly quasisymmetric circle endomorphisms preserving the Lebesgue measure. Although many of our arguments work for any degree d≥2, our proof will be mainly written for degree 2 maps.

We will introduce a sequence of Markov partitions of the unit circle by using preimages of the fixed point of such circle endomorphism f. The uniform quasisymmetry condition is equivalent to the bounded nearby geometry condition of the Markov partitions. In Chapter 2 of this thesis, for each f, we use the Lebesgue invariant condition and the …

The Computational Complexity Of Some Games And Puzzles With Theoretical Applications, Vasiliki Despoina Mitsou

Dissertations, Theses, and Capstone Projects

The subject of this thesis is the algorithmic properties of one- and two-player

games people enjoy playing, such as Sudoku or Chess. Questions asked about puzzles

and games in this context are of the following type: can we design efficient computer

programs that play optimally given any opponent (for a two-player game), or solve

any instance of the puzzle in question?

We examine four games and puzzles and show algorithmic as well as intractability

results. First, we study the wolf-goat-cabbage puzzle, where a man wants to transport

a wolf, a goat, and a cabbage across a river by using a …

The Interaction Between Arsenic And Struvite During Coprecipitation And Adsorption Processes, Ning Ma

Dissertations, Theses, and Capstone Projects

The formation of struvite, MgNH4PO4*6H2O (MAP), from wastes is one of the methods that can be used to recover P from wastes efficiently. However, since there are usually toxic components in the wastes, like arsenic (As), the possibility of having toxic contaminants in MAP is a big concern. So, the interaction between As and MAP during coprecipitation (CPT) and adsorption (ADS) processes were studied at pH 8-11. MAP precipitated without As at pH 8-11 was also characterized.

During CPT process, the MAP was precipitated from a MgCl2-(NH4)2HPO4-NaCl-H2O system spiked with As at an initial pH (pHi) of 8-11. The batch …

All At One Point: The New Physics Of Italo Calvino And Jorge Luis Borges, Mark Thomas Rinaldi

Dissertations, Theses, and Capstone Projects

This work of comparative literary criticism focuses on the presence of mathematical and scientific concepts and imagery in the works of Italo Calvino and Jorge Luis Borges, beginning with an historical overview of scientific philosophy and an introduction to the most significant scientific concepts of the last several centuries, before shifting to deep, scientifically-driven analyses of numerous individual fictions, and finally concluding with a meditation on the unexpectedly fictive aspects of science and mathematics. The close readings of these authors' fictions are contextualized with thorough explanations of the potential literary implications of theories from physics, mathematics, neuroscience and chaos theory. …

Selva Simbólica Selva Simbiótica Apuntes Para Una Ecocritica Latinoamericana, Liza Pamela Rosas-Bustos

Dissertations, Theses, and Capstone Projects

This dissertation focuses on Latin America's selvatic territories. It argues for prevailing ecological principles as revealed in the selected works of three twentieth-century Latin American story-writers and poets. They portray rainforests as multisensorial lands that encompass bewildering events from which a principle of local authority emerges. This analysis is based on Francisco Coloane's short stories "Tierra del Fuego" and "Cabo de Hornos," Rosario Castellanos'Balún Canán, and Luis Sepúlveda's Un viejo que leía novelas de amor. Such phenomenology is also present on the environmental poetics from Marosa di Giorgio, Cecilia Vicuña, and Leonel Lienlaf linked to emotions of fear, urgency, …

Message Passing Techniques For Statistical Physics And Optimization In Complex Systems, Lin Bo

Dissertations, Theses, and Capstone Projects

Optimization problem has always been considered as a central topic in various areas of science and engineering. It aims at finding the configuration of a large number of variables with which the objective function is optimal. The close relation between optimization problems and statistical physics through the probability measure of the Boltzmann type has brought new theoretical tools from statistical physics of disordered systems to optimization problems. In this thesis, we use message passing techniques, in particular cavity method, developed in the last decades within spin glass theory to study optimization problems in complex systems. In the study of force …

Randomized Search Of Graphs In Log Space And Probabilistic Computation, Wen-Ju Cheng

Dissertations, Theses, and Capstone Projects

Reingold has shown that L = SL, that s-t connectivity in a poly-mixing digraph is complete for promise-RL, and that s-t connectivity for a poly-mixing out-regular digraph with known stationary distribution is in L. Several properties that bound the mixing times of random walks on digraphs have been identified, including the digraph conductance and the digraph spectral expansion. However, rapidly mixing digraphs can still have exponential cover time, thus it is important to specifically identify structural properties of digraphs that effect cover times. We examine the complexity of random walks on a basic parameterized family of unbalanced digraphs called Strong …

Second Quantum State Transition In Gaas/Algaas Resonant Bragg Structure Probed By Modulation Reflectance Spectroscopy, Yuechao Chen

Dissertations, Theses, and Capstone Projects

Modulation spectroscopy, ever since its introduction by B.O. Seraphin in 1964, has been considered and widely used as a sensitive experiment technique for studying and characterizing the properties of varieties of semiconductor materials. Compared to general optical reflectance spectrum which measures the absolute reflection, the modulation spectroscopy evaluates the interpretation of the changes in the optical response from the sample caused by a periodic physical perturbation applied to the sample, such as temperature, electric fields, hydrostatic pressure, uniaxial stress, etc.Those modulation spectroscopies with an external electric field perturbation are known as electroreflectance spectroscopy, which provides sharp and derivative-like spectral features …

Science Identity Transformations Through Place-Based Teaching And Learning In The Natural World, Amy Defelice

Dissertations, Theses, and Capstone Projects

This dissertation includes three main components related through a sociocultural lens of identity transformation. The first component describes the Field Studies program for ninth grade students at Brooklyn Academy of Science and the Environment (BASE High School), and explores how outdoor settings and place-based pedagogies can be used to enhance urban students' science identities. Student researchers took digital photographs of their Field Studies experiences and met in cogenerative dialogues with me, their teacher, where we shared our reflections. The second component explains students' experiences and reactions to a week-long place-based geoscience program held over spring break at Prospect Park. This …

Variable Pressure Nuclear Magnetic Resonance Studies Of Ionic Liquids And Electrophoretic Probe Design, Armando Julio Rua

Dissertations, Theses, and Capstone Projects

Energy storage materials play a key role in, efficient, clean, and versatile use of energy, and are crucial for the exploitation of renewable energy. The improve efficiency of energy use stimulates the development of energy storage such as batteries or super capacitors, toward higher power and energy density, which significantly depends upon the advancement of new materials used in these devices. The new materials need better understanding and description in the electrochemical properties. Nuclear Magnetic Resonance (NMR) has been an important tool in the characterization of ionic liquids and solids. The measurements of the relaxation times and the diffusion coefficient …

Quantum Crystallography Of Hydronium Cations, Sonjae Sycoria Wallace

Dissertations, Theses, and Capstone Projects

Cationic hydronium clusters of the form [HaOb]^c,(c>0), have been investigated. After investigating over 2000 crystal structures containing hydronium cations found in the Cambridge Structural Database. The hydronium cationic compounds that were most unusual, mischaracterized, or those of apparent aggregates, were investigated further by geometry optimization and in some cases with the Quantum Theory of Atoms in Molecules (QTAIM). The results of our investigations yielded the first reports of stable conformations of cyclic dihydronium cationic clusters. In a second investigation we reported the first theoretically confirmed transition state of a H7O3+conformer captured within a crystal. A third product from our …

Self-Referentiality In Constructive Semantics Of Intuitionistic And Modal Logics, Junhua Yu

Dissertations, Theses, and Capstone Projects

This thesis explores self-referentiality in the framework of justification logic. In this framework initialed by Artemov, the language has formulas of the form t:F, which means "the term t is a justification of the formula F." Moreover, terms can occur inside formulas and hence it is legal to have t:F(t), which means "the term t is a justification of the formula F about t itself." Expressions like this is not only interesting in the semantics of justification logic, but also, as we will see, necessary in applications of justification logic in formalizing constructive contents implicitly carried by modal and intuitionistic …

Text Extraction From Natural Scene: Methodology And Application, Chucai Yi

Dissertations, Theses, and Capstone Projects

With the popularity of the Internet and the smart mobile device, there is an increasing demand for the techniques and applications of image/video-based analytics and information retrieval. Most of these applications can benefit from text information extraction in natural scene. However, scene text extraction is a challenging problem to be solved, due to cluttered background of natural scene and multiple patterns of scene text itself. To solve these problems, this dissertation proposes a framework of scene text extraction.

Scene text extraction in our framework is divided into two components, detection and recognition. Scene text detection is to find out the …

Transport And Optical Properties Of Low-Dimensional Complex Systems, Andrii Iurov

Dissertations, Theses, and Capstone Projects

Over the last five years of my research work, I, my research was mainly concerned with certain crucial tunneling, transport and optical properties of novel low-dimensional graphitic and carbon-based materials as well as topological insulators. Both single-electron and many-body problems were addressed. We investigated the Dirac electrons transmission through a potential barrier in the presence of circularly polarized light. An anomalous photon-assisted enhanced transmission is predicted and explained in a comparison with the well-known Klein paradox. It is demonstrated that the perfect transmission for nearly-head-on collision in an infinite graphene is suppressed in gapped dressed states of electrons, which is …