Physical Sciences and Mathematics Commons^™

Using Protonation Microstates And Hydrogen Bond Networks To Track Proton Transfer Pathways In Complex I, Umesh Khaniya

Dissertations, Theses, and Capstone Projects

Complex I, NADH-ubiquinone oxidoreductase, is the first enzyme in the mitochondrial and bacterial aerobic respiratory chain. It pumps four protons through four transiently open pathways from the high pH, negative, N- side of the membrane to the positive, P-side driven by the exergonic transfer of electrons from NADH to a quinone. Three protons transfer through subunits descended from Mrp antiporters, while the fourth, E-channel is unique. Because of the complex possible paths thorough the many buried polar residues and lack of high-resolution crystal structure, the path for protons through the E-channel is elusive.

In this dissertation, the E-channel proton pumping …

An Analysis Of The Friendship Paradox And Derived Sampling Methods, Yitzchak Novick

Dissertations, Theses, and Capstone Projects

The friendship paradox (FP) is the famous sampling-bias phenomenon that leads to the seemingly paradoxical truth that, on average, people’s friends have more friends than they do. Among the many far-reaching research findings the FP inspired is a sampling method that samples neighbors of vertices in a graph in order to acquire random vertices that are of higher expected degree than average.

Our research examines the friendship paradox on a local level. We seek to quantify the impact of the FP on an individual vertex by defining the vertex’s “friendship index”, a measure of the extent to which the phenomenon …

The Separation Of Charm And Bottom Decays Measured In P+Au Collisions At 200 Gev, Zhiyan Wang

Dissertations, Theses, and Capstone Projects

It has long been observed experimentally, from previous heavy-flavor electron measurements, that heavy quarks are subject to substantial modifications of their momentum spectrum. Using the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC), measurements of the production of open heavy flavor hadrons with charm and bottom quarks in p+Au collisions at 200 GeV are studied and presented in this thesis. Distance of closest approach analysis of electron tracks is used to study the semileptonic decay electrons from charm and bottom hadrons. The results include invariant yield and fraction of bottom electrons. In addition to the p+p and Au+Au collisions’ …

Catalyzed And Uncatalyzed N1 Modifications Of Inosine And 2'-Deoxyinosine And N-Directed Remote Aroylation Of C6-Aryl Purine Nucleosides, Casina Malinchak

Dissertations, Theses, and Capstone Projects

Nucleosides, and their analogs, are important biological molecules that are integral to cell signaling, metabolism, and DNA and RNA synthesis. Because of their presence in all living systems, they are ideal candidates for drug development. Although extensive literature exists on the alkylation and alkenylation at N1 of inosine and 2’-deoxyinosine, few reports have been published on arylation at this position. Using diaryliodonium salts, a copper-catalyzed method has been developed for the efficient N1-arylation of silyl group-protected inosine and 2’-deoxyinosine. Diaryliodonium salts are easily synthesized and allow for the use of mild conditions to promote transfer of aryl groups to the …

Driven Dipolaritons In Van Der Waals Transition Metal Dichalcogenide Heterostructures: Properties And Applications, Patrick Serafin

Dissertations, Theses, and Capstone Projects

The need for advances in optical computation leads us toward the investigation of novel methods of re-routing light in optical circuits. The behavior and properties of electrically driven exciton-dipolaritons in van der Waals transition metal dichalcogenides are investigated as a platform for realizing working elements of a polaritronic transistor. In this work, we consider exciton-dipolaritons, which are three-way superposition of cavity photons, direct excitons, and indirect excitons in a bilayer semiconducting system embedded in an optical microcavity. We start by providing motivation for our study of polaritons and then survey the fundamental properties of exciton-dipolaritons. We also survey the basic …

Sensitized Photooxidation Of Prenylated Compounds: Mechanisms Of Downstream Dark Effects And Phototoxicity Priming, Shakeela Jabeen

Dissertations, Theses, and Capstone Projects

This thesis consists of four chapters as detailed below.

Chapter 1 discusses a singlet oxygen priming mechanism. Airborne singlet oxygen derived from photosensitization of triplet dioxygen is shown to react with an alkene surfactant (8-methylnon-7-ene-1 sulfonate) leading to ‘ene’ hydroperoxides that in the dark inactivate planktonic E. coli. The ‘ene’ hydroperoxide photoproducts are not toxic on their own, but they become toxic after the bacteria are pretreated with singlet oxygen. The total quenching rate constant (k_T) of singlet oxygen of the alkene surfactant was measured to be 1.1 × 10⁶ M⁻¹ s^{− …}

Nutrient Dynamics And Ecosystem Development Of Urban Forests, Gisselle A. Mejía

Dissertations, Theses, and Capstone Projects

Urban growth and expansion are a major component of global environmental change, with impacts on climate, air and water quality, biodiversity, and human well-being. Forests embedded in urban landscapes are critical in mitigating these impacts at local, regional, and continental scales. However, assessing urban forests is difficult because cities are heterogenous in physical, chemical, biological, and social dimensions. This heterogeneity has constrained how urban forests are defined, and therefore, how they are studied. The objective of this dissertation is to determine how these biophysical and social factors drive ecological processes in urban forests and will address three outstanding challenges in …

Data-Centric Machine Learning For Speech And Audio, Ali Raza Syed

Dissertations, Theses, and Capstone Projects

There is growing recognition of the importance of data-centric methods for building machine learning systems. Data-centric methods assume a fixed model and iterate over the data to improve system performance. This is in contrast to traditional model-centric approaches, which assume a fixed dataset and iterate over models for the same ends. Data-centric machine learning is driven by the observation that, beyond the size of the training data, model performance depends on factors such as the quality of the annotations, and whether the data are representative of conditions in which models will be deployed. This is particularly of interest in the …

Conformation Of The U12-U6atac Snrna Complex Of The Minor Spliceosome And Binding By Ntc-Related Protein Rbm22, Joanna Ciavarella

Dissertations, Theses, and Capstone Projects

Splicing of precursor messenger (pre-m)RNA is a critical process in eukaryotes in which the non-coding regions, called introns, are removed and coding regions, or exons, are ligated to form a mature mRNA. This process is catalyzed by the spliceosome, a multi-mega Dalton ribonucleoprotein complex assembled from five small nuclear ribonucleoproteins (snRNP) in the form of small nuclear (sn)RNA-protein complexes (U1, U2, U4, U5 and U6) and >100 proteins. snRNA components catalyze the two transesterification reactions while proteins perform critical roles in assembly and rearrangement. U2 and U6 snRNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA. …

Removal Of Anisotropic Background From Neutral Pion And Tagged Direct Photon–Hadron Correlations Of Au+Au 200 Gev Collisions, Zachary Rowan

Dissertations, Theses, and Capstone Projects

A reaction plane dependent event mixing technique is developed to remove the collective background from two particle correlation measurements in heavy ion collisions. The method eliminates the need for any external flow measurements and is well suited for studying the path length dependence of particle production in quark-gluon plasma. Central to mid-central, as well as in vs out-of-plane, per neutral pion trigger integrated away-side hadron yield comparisons are made. Results suggest a significant path length dependent partonic energy loss in the medium. A tagging method is also introduced to measure the direct photon yield for various collision criteria. Direct photon …

Engineering Rare-Earth Based Color Centers In Wide Bandgap Semiconductors For Quantum And Nanoscale Applications, Gabriel I. López-Morales

Dissertations, Theses, and Capstone Projects

For many years, atomic point-defects have been readily used to tune the bulk properties of solid-state crystalline materials, for instance, through the inclusion of elemental impurities (doping) during growth, or post-processing treatments such as ion bombardment or high-energy irradiation. Such atomic point-defects introduce local ‘incompatible’ chemical interactions with the periodic atomic arrangement that makes up the crystal, resulting for example in localized electronic states due to dangling bonds or excess of electrons. When present in sufficient concentrations, the defects interact collectively to alter the overall bulk properties of the host material. In the low concentration limit, however, point-defects can serve …

Witness-Authenticated Key Exchange, Kelsey G. Melissaris

Dissertations, Theses, and Capstone Projects

In this dissertation we investigate Witness-Authenticated Key Exchange (WAKE), a key agreement protocol in which each party is authenticated through knowledge of a witness to an arbitrary NP statement. We provide both game-based and universally composable definitions. Thereby, this thesis presents solutions for the most flexible and general method of authentication for group key exchange, providing simple constructions from (succinct) signatures of knowledge (SOK) and a two round UC-secure protocol.

After a discussion of flaws in previous definitions for WAKE we supply a new and improved game-based definition along with the first definition for witness-authenticated key exchange between groups of …

On The Cryptographic Deniability Of The Signal Protocol, Nihal Vatandas

Dissertations, Theses, and Capstone Projects

Offline deniability is the ability to a posteriori deny having participated in a particular communication session. This property has been widely assumed for the Signal messaging application, yet no formal proof has appeared in the literature. In this work, we present the first formal study of the offline deniability of the Signal protocol. Our analysis shows that building a deniability proof for Signal is non-trivial and requires strong assumptions on the underlying mathematical groups where the protocol is run.

To do so, we study various implicitly authenticated key exchange protocols, including MQV, HMQV, and 3DH/X3DH, the latter being the core …

Asymptotic Classes, Pseudofinite Cardinality And Dimension, Alexander Van Abel

Dissertations, Theses, and Capstone Projects

We explore the consequences of various model-theoretic tameness conditions upon the behavior of pseudofinite cardinality and dimension. We show that for pseudofinite theories which are either Morley Rank 1 or uncountably categorical, pseudofinite cardinality in ultraproducts satisfying such theories is highly well-behaved. On the other hand, it has been shown that pseudofinite dimension is not necessarily well-behaved in all ultraproducts of theories which are simple or supersimple; we extend such an observation by constructing simple and supersimple theories in which pseudofinite dimension is necessarily ill-behaved in all such ultraproducts. Additionally, we have novel results connecting various forms of asymptotic classes …

The Interaction Of Different Primary Producers And Physical And Chemical Dynamics Of An Urban Shallow Lake, Majid Sahin

Dissertations, Theses, and Capstone Projects

An artificial urban shallow lake, Prospect Park Lake (PPL), is situated on a terminal moraine in Brooklyn New York, and supplied with municipal water treated with ortho-phosphates. The constant input of the phosphate nutrient is the primary source of eutrophication in the lake. The numerous pools along the water course houses various aquatic phototrophs, which influence the water quality and the state of the system, driving conditions into favoring the survival of their species. In the first half of the dissertation, the focus of the project is on analyzing how the different primary producers in different regions of PPL affect …

Stability Of Two-Dimensional Magnetic Skyrmions, Amel Derras-Chouk

Dissertations, Theses, and Capstone Projects

Magnetic skyrmions are whirls formed by magnetic moments in a crystal. They have attracted attention largely due to their topological protection, which provides an avenue for technology like next-generation memory storage. The idea of topologically protected solutions of a quantum field theory was originally proposed by Tony Skyrme when he developed a model to explain the stability of hadrons in particle physics. His work has extended far beyond his original intent to several areas of condensed matter physics. Here we focus on skyrmions in magnetic materials.

Skyrme's original theory modeled excitations which exist in three spatial dimensions, a requirement for …

Astrophysics, Cosmology And Particle Phenomenology At The Energy Frontier, Jorge Fernandez Soriano

Dissertations, Theses, and Capstone Projects

This dissertation consists of two parts, treating significantly separated fields. Each part consists on several chapters, each treating a somewhat isolated topic from the rest. In each chapter, I present some of the work developed during my passage through the graduate program, which has mostly been published elsewhere.

Part I – Cosmic Rays and Particle Physics

• Chapter 1: In this chapter we present an introduction to the topic of cosmic ray physics, with an special focus on the so-called ultra high energy cosmic rays: their potential origins, effects during their propagation between their sources and Earth, the different techniques used …

Stacking The Gamma-Ray Sky To Search For Faint Astrophysical Populations, Yuzhe Song

Dissertations, Theses, and Capstone Projects

Gamma-ray emission can be generated from a wide variety of high-energy astrophysical phenomena, from stellar flares to pulsating neutron stars, and from interstellar clouds to the center of the Milky Way Galaxy. Entering the 13th year of its orbit around Earth, the Fermi Space Gamma-ray Telescope has been continually surveying the γ-ray sky with its Large Area Telescope (LAT) on board. The latest Fermi source catalog contains over 6000 sources. Yet, a lot of sources that are expected to emit γ-rays are not detected, and only small percentages of some populations are detected. For example, solar flares are detected in …

The Microscopical Evidence Traces Analysis Of Household Dust And Its Statistical Significance As A Definitive Identification Technique, Stephanie Polifroni

Dissertations, Theses, and Capstone Projects

Evidence found at crime scenes is used to assist in creating a link the suspect, the victim, and the scene. As stated by the Locard’s Principle, every contact leaves a trace, that evidence can be used to link together an investigation. Traces are collected in hopes that they can be identified and associated to an individual or individuals to help solve that particular crime. However, the strongest conclusion for evidence traces is an association to a source, and unless a physical match of some kind is found, an individualization cannot be established even when known sample is available. However, having …

Dynamics Of Cubic Rational Maps Under Certain Constraints On Critical Points, Arkady Etkin

Dissertations, Theses, and Capstone Projects

There is a neat dichotomy for the Julia sets of quadratic rational maps; that is, they are either connected or a Cantor set. In contrast to the quadratic case, the Julia sets of rational maps of of degree ≥ 3 have more variations. In this project, we study the Julia sets of cubic rational maps under some constraints. We first extend the Julia set dichotomy to the cubic rational maps with all critical points escaping to an attracting fixed point. Then we consider two more classes of cubic rational maps: one class consists of the cubic rational maps with two …

Control Of Nonlinear Properties Of Van Der Waals Materials, Rezlind Bushati

Dissertations, Theses, and Capstone Projects

Van der Waals materials are a broad class of materials that exhibit unique optoelectronic properties. They provide a rich playground for which they can be integrated into current on-chip devices due to their nanometer-scale size, and be utilized for studying fundamental physics. Strong coupling of emitters to microcavities provides many opportunities for new exotic physics through the formation of hybrid quasi-particles exciton-polaritons. This thesis
focuses on exploring and enhancing nonlinearity of van der Waals materials through strongly coupling to microcavities. By taking advantage of the stacking order of TMDs, we show intense second-harmonic generation from bulk, centrosymmetric TMD systems. In …

Magnetic Field Effects On The Physics Of Neutron Stars, Aric A. Hackebill

Dissertations, Theses, and Capstone Projects

In the context of neutron stars (NS), dense-magnetized quark and hadron models have been well studied under the assumption that the system's pressures are isotropic. However, the pressures determined from semi-classical statistical averaging of the energy momentum tensor in the presence of a uniform background magnetic field are anisotropic with different pressures arising along and perpendicular to the magnetic field direction. Since large magnetic fields are expected to be present in the interior of NS, it is important to understand the roll the pressure anisotropy plays. While considering the pressure anisotropy, we revisit some important calculations in NS physics.

We …

The Local Lifting Problem For Curves With Quaternion Actions, George Mitchell

Dissertations, Theses, and Capstone Projects

The lifting problem asks whether one can lift Galois covers of curves defined over positive characteristic to Galois covers of curves over characteristic zero. The lifting problem has an equivalent local variant, which asks if a Galois extension of complete discrete valuation rings over positive characteristic, with algebraically closed residue field, can be lifted to characteristic zero. In this dissertation, we content ourselves with the study of the local lifting problem when the prime is 2, and the Galois group of the extension is the group of quaternions. In this case, it is known that certain quaternion extensions cannot be …

Visible Light Photocatalysis Of Organic Reactions In H2o, Sankarsan Biswas

Dissertations, Theses, and Capstone Projects

Visible-light photocatalysis in H₂O provides an attractive, green alternative to typical organic synthesis, which often involves toxic solvents, metal catalysts, and large energy demands. Hence, there is a growing need for an efficient photocatalytic methods that use either aqueous media as a solvent or can proceed solvent-free. However, commercially available photocatalysts do not work well for aqueous photocatalysis. Supramolecular systems in particular have been explored recently to address these issues associated with aqueous photocatalysis. Chapter 1 will review recent advances in aqueous supramolecular photocatalysis with examples of different supramolecular systems and how they have addressed some of the …

Application Of Peo-Ppo-Peo Triblock Copolymers In Synthesis Of Silica And Organosilica Nanomaterials, Shu Zhang

Dissertations, Theses, and Capstone Projects

In this dissertation, the research work focused on the application of Pluronic triblock copolymers, poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO), in the synthesis of mesoporous material, such as double-helical silica nanotube structures as well as bridged organosilica nanotubes by using swollen micelles of Pluronic surfactants and their mixtures. Chapter 1 introduced the background and several important mesoporous structures, and the relevant topics in this dissertation, such as, silica nanotubes, helical silica nanotubes, silica vesicles and organosilica nanotubes. Chapter 2, continued research works from earlier published paper (ACS Nano 2021, 15, 1016-1029), discussed static treatment and stirring effect on the formation of …

Electron Transport In Quantum Systems With Interaction, Sara Abedi

Dissertations, Theses, and Capstone Projects

No abstract provided.

Topological Shadow Of Higher-Order Topological Phases And Non-Hermitian Phases Protected By Generalized Rotational Symmetry, Kai Chen

Dissertations, Theses, and Capstone Projects

Topological phenomena in condensed matter physics have been investigated intensively in the past decades since the discovery of the integer quantum Hall effect (IQHE). For the IQHE, the energy band can be characterized by its topological invariants (Chern number or TKNN invariant), which relates to the quantized Hall conductance directly. Later, this expression was recognized as the first Chern class of a U(1) principal fiber bundle on a torus, where the fibers and torus correspond respectively to the magnetic Bloch waves and the magnetic Brillouin zone. And then, the discoveries of time-reversal symmetric topological insulators in two and three dimensions …

Asian Hate Speech Detection On Twitter During Covid-19, Amir Toliyat, Sarah Ita Levitan, Zeng Peng, Ronak Etemadpour

Publications and Research

Coronavirus disease 2019 (COVID-19) started in Wuhan, China, in late 2019, and after being utterly contagious in Asian countries, it rapidly spread to other countries. This disease caused governments worldwide to declare a public health crisis with severe measures taken to reduce the speed of the spread of the disease. This pandemic affected the lives of millions of people. Many citizens that lost their loved ones and jobs experienced a wide range of emotions, such as disbelief, shock, concerns about health, fear about food supplies, anxiety, and panic. All of the aforementioned phenomena led to the spread of racism and …

A Decade Review Of Disease Surveillance Research Trends In The International Journal Of Health Geographics (2009 To 2018), Rose Jimenez, Paradorn Wongchanapai

Publications and Research

The field of health geographics is rapidly growing in its methods and epistemologies. This is a review of the open-source journal International Journal of Health Geographics, and the trends in disease surveillance over ten years (2009-2018). Drawing from research review methodologies, we wrote a Python script to quantify research trends within the field of geographic disease surveillance, finding many articles focusing on population health, techniques of GIS, qualitative techniques, and geospatial technology for health monitoring. This was foundational in conducting an in-depth qualitative lexical analysis of article content and epistemologies. Overall, we concluded that over the time period, the …

(2022 Revision) Chapter 6: Essential Aspects Of Physical Design And Implementation Of Relational Databases, Tatiana Malyuta, Ashwin Satyanarayana

Open Educational Resources

No abstract provided.