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Transcriptional And Post-Transcriptional Regulation Of Gene Expression, Jun Ding
Transcriptional And Post-Transcriptional Regulation Of Gene Expression, Jun Ding
Electronic Theses and Dissertations
Regulation of gene expression includes a variety of mechanisms to increase or decrease specific gene products. Gene expression can be regulated at any stage from transcription to post-transcription and it's essential to almost all living organisms, as it increases the versatility and adaptability by allowing the cell to express the needed proteins. In this dissertation, we comprehensively studied the gene regulation from both transcriptional and post-transcriptional points of view. Transcriptional regulation is by which cells regulate the transcription from DNA to RNA, thereby directing gene activity. Transcriptional factors (TFs) play a very important role in transcriptional regulation and they are …
A Comparison Of Concurrent Correctness Criteria For Shared Memory Based Data Structure, Dipanjan Bhattacharya
A Comparison Of Concurrent Correctness Criteria For Shared Memory Based Data Structure, Dipanjan Bhattacharya
Electronic Theses and Dissertations
Developing concurrent algorithms requires safety and liveness to be defined in order to understand their proper behavior. Safety refers to the correctness criteria while liveness is the progress guarantee. Nowadays there are a variety of correctness conditions for concurrent objects. The way these correctness conditions differ and the various trade-offs they present with respect to performance, usability, and progress guarantees is poorly understood. This presents a daunting task for the developers and users of such concurrent algorithms who are trying to better understand the correctness of their code and the various trade-offs associated with their design choices and use. The …
Analysis Of Commutativity With State-Chart Graph Representation Of Concurrent Programs., Kishore Debnath
Analysis Of Commutativity With State-Chart Graph Representation Of Concurrent Programs., Kishore Debnath
Electronic Theses and Dissertations
We present a new approach to check for Commutativity in concurrent programs from their run-time state-chart graphs. Two operations are said to be commutative if changing the order of their execution do not change the resultant effect on the working object. Commutative property is capable of boosting performance in concurrent transactions such that transactional concurrency is comparable to a non-blocking linearizable version of a similar data structure type. Transactional concurrency is a technique that analyses object semantics, as object states, to determine conflicts and recovery between conflicting operations. Processes that commute at object level can be executed concurrently at transaction …
Self-Assembly Of Rous Sarcoma Virus Capsid Protein, Probed By Solid-State Nmr And Tem, Jaekyun Jeon
Self-Assembly Of Rous Sarcoma Virus Capsid Protein, Probed By Solid-State Nmr And Tem, Jaekyun Jeon
Electronic Theses and Dissertations
The retroviral capsid protein (CA) is derived from the cleavage of Gag polyprotein during the maturation process, and self-assembles into a polymorphic fullerene-like shell encasing the viral genome materials. The orthoretroviral CAs, for instance, Human Immunodeficiency Virus (HIV) and Rous Sarcoma Virus (RSV) CA, has little similarity in their sequence composition but a common 3D structure. They form distinct capsid assembly in vivo and a range of similar assemblies in vitro. Due to the substantial polymorphism, such assemblies are not amenable for conventional structural biology techniques such as X-ray diffraction crystallography and cryo-electron microscopy (cryo-EM). Solid-state NMR spectroscopy is the …
A Mathematical Model For Feral Cat Ecology With Application To Disease., Jeff Sharpe
A Mathematical Model For Feral Cat Ecology With Application To Disease., Jeff Sharpe
Electronic Theses and Dissertations
We formulate and analyze a mathematical model for feral cats living in an isolated colony. The model contains compartments for kittens, adult females and adult males. Kittens are born at a rate proportional to the population of adult females and mature at equal rates into adult females and adult males. Adults compete with each other in a manner analogous to Lotka-Volterra competition. This competition comes in four forms, classified by gender. Native house cats, and their effects are also considered, including additional competition and abandonment into the feral population. Control measures are also modeled in the form of per-capita removal …
Ultrafast Mechanisms Of Nonlinear Refraction And Two-Photon Photochromism, Peng Zhao
Ultrafast Mechanisms Of Nonlinear Refraction And Two-Photon Photochromism, Peng Zhao
Electronic Theses and Dissertations
Derived from a material's third-order nonlinearity, nonlinear refraction (NLR) occurs at any wavelength in any material, and may exhibit noninstantaneous dynamics depending on its physical origins. The main subject of this dissertation is to investigate the underlying mechanisms responsible for the NLR response in different phases of matter, e.g. liquids, gases, and semiconductors, by extensively using our recently developed ultrafast Beam Deflection (BD) technique. An additional subject includes the characterization of a novel two-photon photochromic molecule. In molecular liquids, the major nonlinear optical (NLO) response can be decomposed into a nearly instantaneous bound-electronic NLR (Kerr effect), originating from the real …
Hybrid Integrated Photonic Platforms And Devices, Jeffrey Chiles
Hybrid Integrated Photonic Platforms And Devices, Jeffrey Chiles
Electronic Theses and Dissertations
Integrated photonics has the potential to revolutionize optical systems by achieving drastic reductions in their size, weight and power. Remote spectroscopy, free-space communications and high-speed telecommunications are critical applications that would benefit directly from these advancements. However, many such applications require extremely wide spectral bandwidths, leading to significant challenges in their integration. The choice of integrated platform influences the optical transparency and functionality which can be ultimately achieved. In this work, several new platforms and technologies have been developed to meet these needs. First, the silicon-on-lithium-niobate (SiLN) platform is discussed, on which the first compact, integrated electro-optic modulator in the …
Habitat Selection In Transformed Landscapes And The Role Of Novel Ecosystems For Native Species Persistence, Lina Maria Sanchez Clavijo
Habitat Selection In Transformed Landscapes And The Role Of Novel Ecosystems For Native Species Persistence, Lina Maria Sanchez Clavijo
Electronic Theses and Dissertations
To understand native species persistence in transformed landscapes we must evaluate how individual behaviors interact with landscape structure through ecological processes such as habitat selection. Rapid, widespread landscape transformation may lead to a mismatch between habitat preference and quality, a phenomenon known as ecological traps that can have negative outcomes for populations. I applied this framework to the study of birds inhabiting landscapes dominated by forest remnants and shade coffee plantations, a tropical agroforestry system that retains important portions of native biodiversity. I used two different approaches to answer the question: What is the role of habitat selection in the …
Electrical Parasitic Bandwidth Limitations Of Oxide-Free Lithographic Vertical-Cavity Surface-Emitting Lasers, Xu Yang
Electronic Theses and Dissertations
Nowadays, Vertical-Cavity Surface-Emitting Lasers (VCSELs) are the most popular optical sources in short-reach data communications. In the commercial oxide VCSEL technology, an oxide aperture is created inside resonant cavity in realizing good mode and current confinement, however, high electrical resistance comes along with forming the oxide aperture and the electrical parasitic bandwidth becomes the main limitation in modulation speed. In this report, electrical bandwidths of oxide-free lithographic VCSELs have been studied along with their general lasing properties. Due to the new ways of fabricating the aperture, record low resistances have been achieved in oxide-free lithographic VCSELs with various sizes, while …
On Randic Energy Of Graphs, Brittany Burns
On Randic Energy Of Graphs, Brittany Burns
Electronic Theses and Dissertations
In this research, we explore the subject of graph energy. We first discuss the connections between linear algebra and graph theory and review some important definitions and facts of these two fields. We introduce graph energy and provide some historical perspectives on the subject. Known results of graph energy are also mentioned and some relevant results are proven. We discuss some applications of graph energy in the physical sciences. Then, Randic energy is defined and results are given and proved for specific families of graphs. We focus on simple, connected graphs that are commonly studied in graph theory. Also, the …
Techniques For Automated Parameter Estimation In Computational Models Of Probabilistic Systems, Faraz Hussain
Techniques For Automated Parameter Estimation In Computational Models Of Probabilistic Systems, Faraz Hussain
Electronic Theses and Dissertations
The main contribution of this dissertation is the design of two new algorithms for automatically synthesizing values of numerical parameters of computational models of complex stochastic systems such that the resultant model meets user-specified behavioral specifications. These algorithms are designed to operate on probabilistic systems – systems that, in general, behave differently under identical conditions. The algorithms work using an approach that combines formal verification and mathematical optimization to explore a model's parameter space. The problem of determining whether a model instantiated with a given set of parameter values satisfies the desired specification is first defined using formal verification terminology, …
Study Of Polychlorinated Biphenyl Dechlorination By Zero Valent Magnesium With And Without Activated Carbon In Acidified Ethanol-Ethyl Lactate System, Fiona Zullo
Electronic Theses and Dissertations
Polychlorinated biphenyls (PCBs) are synthetic organic chemicals that ca de detected in the environment worldwide. PCBs were banned in the U.S in 1979 owing to their toxicity and persistence in the environment. Today PCBs are classified as human carcinogens and are among the top ten of the U.S Environmental Protection Agency's (EPA) most toxic chemicals. Many researchers have shown soil to be contaminated with PCBs at concentrations as high as 750 ppm. Given the toxicity of PCBs, there is an urgent need to extract and degrade such chemicals from contaminated soil in a cost effective way. Prior work revealed a …
Broad Bandwidth Optical Frequency Combs From Low Noise, High Repetition Rate Semiconductor Mode-Locked Lasers, Anthony Klee
Broad Bandwidth Optical Frequency Combs From Low Noise, High Repetition Rate Semiconductor Mode-Locked Lasers, Anthony Klee
Electronic Theses and Dissertations
Mode-locked lasers have numerous applications in the areas of communications, spectroscopy, and frequency metrology. Harmonically mode-locked semiconductor lasers with external ring cavities offer a unique combination of benefits in that they can produce high repetition rate pulse trains with low timing jitter, achieve narrow axial mode linewidths, have the potential for entire monolithic integration on-chip, feature high wall-plug efficiency due to direct electrical pumping, and can be engineered to operate in different wavelength bands of interest. However, lasers based on InP/InGaAsP quantum well devices which operate in the important telecom C-band have thus far been relatively limited in bandwidth as …
Dynamical Formation Of Protoplanetesimals, Akbar Whizin
Dynamical Formation Of Protoplanetesimals, Akbar Whizin
Electronic Theses and Dissertations
The seeds of planetesimals that formed in the gaseous protoplanetary disk (PPD) have many barriers to overcome in their growth from millimeter to meter-sized and larger bodies. Centimeter-sized aggregates are weakly bound and self-gravity is almost non-existent so surface forces play a critical role in holding small loosely-bound rubble-piles together. Their orbital motions and effects form disk processes impart relative velocities leading to collisions so understanding the macroscopic disk environment is also necessary. To this end we analyze the dynamics of particles in Saturn's F ring as an analogue to understanding the orbital evolution of proto-planetesimals embedded in a PPD. …
Spatiotemporal Graphs For Object Segmentation And Human Pose Estimation In Videos, Dong Zhang
Spatiotemporal Graphs For Object Segmentation And Human Pose Estimation In Videos, Dong Zhang
Electronic Theses and Dissertations
Images and videos can be naturally represented by graphs, with spatial graphs for images and spatiotemporal graphs for videos. However, for different applications, there are usually different formulations of the graphs, and algorithms for each formulation have different complexities. Therefore, wisely formulating the problem to ensure an accurate and efficient solution is one of the core issues in Computer Vision research. We explore three problems in this domain to demonstrate how to formulate all of these problems in terms of spatiotemporal graphs and obtain good and efficient solutions. The first problem we explore is video object segmentation. The goal is …
Investigating The Predictive Power Of Student Characteristics On Success In Studio-Mode, Algebra-Based Introductory Physics Courses, Jarrad Pond
Electronic Theses and Dissertations
As part of a project to explore the differential success of similar implementations of the studio-mode of physics instruction, the objective of this work is to investigate the characteristics of students enrolled in algebra-based, studio-mode introductory physics courses at various universities in order to evaluate what effects these characteristics have on different measures of student success, such as gains in conceptual knowledge, shifts to more favorable attitudes toward physics, and final course grades. In my analysis, I explore the strategic self-regulatory, motivational, and demographic characteristics of students in algebra-based, studio-mode physics courses at three universities: the University of Central Florida …
Computational Approaches For Binning Metagenomic Reads, Ying Wang
Computational Approaches For Binning Metagenomic Reads, Ying Wang
Electronic Theses and Dissertations
Metagenomics uses sequencing technologies to study genetic sequences from whole microbial communities. Binning metagenomic reads is the most fundamental step in metagenomic studies, which is essential for the understanding of microbial functions, compositions, and interactions in environmental samples. Various taxonomy-dependent and taxonomy-independent approaches have been developed based on information such as sequence similarity, sequence composition, or k-mer frequency. However, there is still room for improvement, and it is still challenging to bin reads from species with similar or low abundance or to bin reads from unknown species. In this dissertation, we introduce one taxonomy-independent and three taxonomy-dependent approaches to improve …
Design And Engineering Of Ultrafast Amplifier Systems, Benjamin Webb
Design And Engineering Of Ultrafast Amplifier Systems, Benjamin Webb
Electronic Theses and Dissertations
Recently, the design and engineering of ultrafast laser systems have led to an extraordinary increase in laser power and performance which have brought about advances in many fields such as medicine, material processing, communications, remote sensing, spectroscopy, nonlinear optics, and atomic physics. In this work, several ultrafast amplification techniques -- including chirped-pulse amplification (CPA), optical parametric chirped-pulse amplification (OPCPA), and divided-pulse amplification (DPA) -- are described and demonstrated in the design and construction of two ultrafast laser facilities. An existing Ti:Sapphire laser system was completely redesigned with an increased power of 10 TW for experiments capable of generating hundreds of …
Optical Parity Time Metasurface Structures, Ahmed El Halawany
Optical Parity Time Metasurface Structures, Ahmed El Halawany
Electronic Theses and Dissertations
In the last few years, optics has witnessed the emergence of two fields namely metasurfaces and parity-time (PT) symmetry. Optical metasurfaces are engineered structures that provide unique responses to electromagnetic waves, absent in natural materials. Optical metasurfaces are known for their reduced dimensionality i.e. subwavelength and consequently lower losses are anticipated. The other paradigm is the PT symmetric materials, also known as photonic synthetic matter. PT symmetry has emerged from quantum mechanics when a new class of non-Hermitian Hamiltonian quantum systems was highlighted to have real eigenvalues, hence eradicating Hermiticity of the Hamiltonian as an essential condition to the existence …
Novel Photodynamic Cancer Therapy Agent And Biochemical Phosphate Sensor Based On Nanomaterials, Alaa Fadhel
Novel Photodynamic Cancer Therapy Agent And Biochemical Phosphate Sensor Based On Nanomaterials, Alaa Fadhel
Electronic Theses and Dissertations
Biochemical research and clinical studies have revolutionized the field of medicine in both diagnosis and therapy. Researchers in the field of biochemistry and biotechnology are using nanomaterials in different applications to develop devices and materials that offer benefits to both patients and the health care industry. These include biochemical sensors, enzyme encapsulation, biomarkers, and drug delivery improvements for the treatment of cancer. This dissertation focuses on investigating two biochemical aspects using nanomaterials; namely therapy and clinical diagnosis. For therapy purposes, Silica nanoparticles were used as drug delivery system to develop a new photodynamic cancer therapy agent photo-acid generator (PAG) that …
Internal Degrees Of Freedom And Spin Transitions In Single Molecule Magnets, James Atkinson
Internal Degrees Of Freedom And Spin Transitions In Single Molecule Magnets, James Atkinson
Electronic Theses and Dissertations
This thesis covers a range of work detailing the transitions between spin eigenstates in molecular magnet systems. Broadly speaking, these transitions can be divided into two kinds: Those that involve a the tunneling of spin through a potential barrier to a resonant state on the other side, a phenomenon known as quantum tunneling of magnetization, and those that occur through the absorption or emission of a photon. In this latter case, the energy of the photon must match the difference between two eigenstates with a difference in angular momentum of ?. We will detail research performed on single molecule magnets, …
Monolithically Integrated Inp-Based Unidirectional Circulators Utilizing Non-Hermiticity And Nonlinearity, Parinaz Aleahmad
Monolithically Integrated Inp-Based Unidirectional Circulators Utilizing Non-Hermiticity And Nonlinearity, Parinaz Aleahmad
Electronic Theses and Dissertations
The need to integrate critical optical components on a single chip has been an ongoing quest in both optoelectronics and optical communication systems. Among the possible devices, elements supporting non-reciprocal transmission are of great interest for applications where signal routing and isolation is required. In this respect, breaking reciprocity is typically accomplished via Faraday rotation through appropriate magneto-optical arrangements. Unfortunately, standard light emitting optoelectronic materials like for example III-V semiconductors, lack magneto-optical properties and hence cannot be directly used in this capacity. To address these issues, a number of different tactics have been attempted in the last few years. These …
Coupling Of Laser Beams For Filament Propagation, Daniel Kepler
Coupling Of Laser Beams For Filament Propagation, Daniel Kepler
Electronic Theses and Dissertations
Laser filamentation is a nonlinear process involving high-energy, ultrashort pulses that create narrow, non-diffracting structures over many times the Raleigh length. While many of the characteristics of filaments can vary greatly depending on the physical parameters used to create them, they share several defining features: a high intensity core, a lower intensity cladding of photons that serves as an energy reservoir to the core, and spectral broadening into a supercontinuum. While there have been many studies on the creation and control of multiple filaments from one laser pulse and a few studies on the interaction of two single filaments, many …
Model Nanocatalysts With Tunable Reactivity: Tailoring The Structure And Surface Chemistry Of Nanomaterials For Energy And Alternative Fuels Catalysis, Hemma Mistry
Electronic Theses and Dissertations
One of the most pressing challenges of our time is meeting growing global energy demands while limiting human impact on the environment. To meet this challenge, new catalysts are needed to enable carbon neutral energy production processes and low cost synthesis of alternative fuels. In order to design new catalysts for such processes, fundamental understanding is needed on how the structural and chemical properties of nanostructured materials influences their surface chemistry. In this dissertation, I explore how the properties of nanoparticles, such as particle size, shape, composition, and chemical state, can be used to tune their reactivity. For this work, …
Analysis Of Employment And Earnings Using Varying Coefficient Models To Assess Success Of Minorities And Women, Amanda Goedeker
Analysis Of Employment And Earnings Using Varying Coefficient Models To Assess Success Of Minorities And Women, Amanda Goedeker
Electronic Theses and Dissertations
The objective of this thesis is to examine the success of minorities (black, and Hispanic/Latino employees) and women in the United States workforce, defining success by employment percentage and earnings. The goal of this thesis is to study the impact gender, race, passage of time, and national economic status reflected in gross domestic product have on the success of minorities and women. In particular, this thesis considers the impact of these factors in Science, Technology, Engineering and Math (STEM) industries. Varying coefficient models are utilized in the analysis of data sets for national employment percentages and earnings.
Multi-Purpose Device For Analyzing And Measuring Ultra-Short Pulses, Naman Anilkumar Mehta
Multi-Purpose Device For Analyzing And Measuring Ultra-Short Pulses, Naman Anilkumar Mehta
Electronic Theses and Dissertations
Intensity auto correlator is device to measure pulse widths of ultrashort pulses on the order of picoseconds and femtoseconds. I have built an in-house, compact, portable, industry standard intensity auto correlator for measuring ultrashort pulse-widths. My device is suitable for pulse-widths from 500 ps to 50 fs. The impetus for developing this instrument stemmed from our development of a multicore-fiber laser for high power laser applications, which also produces very short pulses that cannot be measured with an oscilloscope. As techniques for measuring short pulse-widths have been well studied, what made my journey exciting was the process of taking an …
Interval Edge-Colorings Of Graphs, Austin Foster
Interval Edge-Colorings Of Graphs, Austin Foster
Electronic Theses and Dissertations
A proper edge-coloring of a graph G by positive integers is called an interval edge-coloring if the colors assigned to the edges incident to any vertex in G are consecutive (i.e., those colors form an interval of integers). The notion of interval edge-colorings was first introduced by Asratian and Kamalian in 1987, motivated by the problem of finding compact school timetables. In 1992, Hansen described another scenario using interval edge-colorings to schedule parent-teacher conferences so that every person's conferences occur in consecutive slots. A solution exists if and only if the bipartite graph with vertices for parents and teachers, and …
Size, Shape, Composition And Chemical State Effects In Nanocatalysis, Mahdi Ahmadi
Size, Shape, Composition And Chemical State Effects In Nanocatalysis, Mahdi Ahmadi
Electronic Theses and Dissertations
The field of nanocatalysis has gained significant attention in the last decades due to the numerous industrial applications of nanosized catalysts. Size, shape, structure, and composition of the nanoparticles (NPs) are the parameters that can affect the reactivity, selectivity and stability of nanocatalysts. Therefore, understanding how these parameters affect the catalytic properties of these systems is required in order to engineer them with a given desired performance. It is also important to gain insight into the structural evolution of the NP catalysts under different reaction conditions to design catalysts with long durability under reaction condition. In this dissertation a synergistic …
Structure-Preserving Finite Difference Methods For Linearly Damped Differential Equations, Ashish Bhatt
Structure-Preserving Finite Difference Methods For Linearly Damped Differential Equations, Ashish Bhatt
Electronic Theses and Dissertations
Differential equations (DEs) model a variety of physical phenomena in science and engineering. Many physical phenomena involve conservative or dissipative forces, which manifest themselves as qualitative properties of DEs that govern these phenomena. Since only a few and simplistic models are known to have exact solutions, approximate solution techniques, such as numerical integration, are used to reveal important insights about solution behavior and properties of these models. Numerical integrators generally result in undesirable quantitative and qualitative errors . Standard numerical integrators aim to reduce quantitative errors, whereas geometric (numerical) integrators aim to reduce or eliminate qualitative errors, as well, in …
Conformations And Dynamics Of Semi-Flexible Polymers, Aiqun Huang
Conformations And Dynamics Of Semi-Flexible Polymers, Aiqun Huang
Electronic Theses and Dissertations
In this dissertation, we investigate the conformations, transverse fluctuations and dynamics of two-dimensional (2D) semi-flexible polymers both in the bulk and under channel confinement. We present unified scaling relations in regard to various quantities of interest for a broad range of combinations of chain length and chain stiffness using Langevin dynamics simulation. We also present a three-dimensional (3D) heterogeneous semi-flexible chain model for a double stranded DNA (dsDNA). Our model not only confirms the established findings for homogeneous dsDNA, but also predicts new physical phenomenon for heterogeneous dsDNA. The problems studied in this dissertation are relevant to analysis of the …