Physical Sciences and Mathematics Commons^™

Development Of Correction Algorithm For Pulsed Terahertz Computed Tomography (Thz-Ct), Suman Mukherjee

Dissertations

For last couple of decades, there has been a considerable improvement in Terahertz (THz) science, technology, and imaging. In particular, the technique of 3-D computed tomography has been adapted to the THz range. However, it has been widely recognized that a fundamental limitation to THz computed tomography imaging is the refractive effects of the sample under study. The finite refractive index of materials in the THz range can severally refract THz beams which probe the internal structure of a sample during the acquisition of tomography data. Refractive effects lead to anomalously high local absorption coefficients in the reconstructed image near …

Structural Indicators For Effective Quality Assurance Of Snomed Ct, Ankur Agrawal

Dissertations

The Standardized Nomenclature of Medicine -- Clinical Terms (SNOMED CT -- further abbreviated as SCT) has been endorsed as a premier clinical terminology by many national and international organizations. The US Government has chosen SCT to play a significant role in its initiative to promote Electronic Health Record (EH R) country-wide. However, there is evidence suggesting that, at the moment, SCT is not optimally modeled for its intended use by healthcare practitioners. There is a need to perform quality assurance (QA) of SCT to help expedite its use as a reference terminology for clinical purposes as planned for EH R …

Solar Eclipse Observation On May 21, 2012 From Jvla, Shaheda Begum Shaik

Theses

The annular solar eclipse occurred on May 21, 2012 is studied using the radio data from the Jansky Very Large Array (JVLA), Sorrocco, Mexico. The eclipse is observed in the solar minimum activity period of solar cycle 24. The centimeter wavelength observation of the Sun's surface during the solar eclipse helps in determining the spatially well resolved features not obtained by the man made advanced technology. Even though, the activity on the Sun is observed to be low in the period of eclipse, the study provides a good opportunity to understand the quiet Sun features in the regions occulted by …

Investigations Into B-O Defect Formation-Dissociation In Cz-Silicon And Their Effect On Solar Cell Performance, Prakash M. Basnyat

Dissertations

About 30% of the total market share of industrial manufacture of silicon solar cells is taken by single crystalline Czochralski (CZ) grown wafers. The efficiency of solar cells fabricated on boron-doped Czochralski silicon degrades due to the formation of metastable defects when excess electrons are created by illumination or minority carrier injection during forward bias. The recombination path can be removed by annealing the cell at about 200° C but recombination returns on exposure to light.

Several mono-crystalline and multi-crystalline solar cells have been characterized by methods such as laser beam induced current (LBIC), Four-Probe electrical resistivity etc. to better …

Concept Graphs: Applications To Biomedical Text Categorization And Concept Extraction, Said Bleik

Dissertations

As science advances, the underlying literature grows rapidly providing valuable knowledge mines for researchers and practitioners. The text content that makes up these knowledge collections is often unstructured and, thus, extracting relevant or novel information could be nontrivial and costly. In addition, human knowledge and expertise are being transformed into structured digital information in the form of vocabulary databases and ontologies. These knowledge bases hold substantial hierarchical and semantic relationships of common domain concepts. Consequently, automating learning tasks could be reinforced with those knowledge bases through constructing human-like representations of knowledge. This allows developing algorithms that simulate the human reasoning …

Novel Color And Local Image Descriptors For Content-Based Image Search, Sugata Banerji

Dissertations

Content-based image classification, search and retrieval is a rapidly-expanding research area. With the advent of inexpensive digital cameras, cheap data storage, fast computing speeds and ever-increasing data transfer rates, millions of images are stored and shared over the Internet every day. This necessitates the development of systems that can classify these images into various categories without human intervention and on being presented a query image, can identify its contents in order to retrieve similar images.

Towards that end, this dissertation focuses on investigating novel image descriptors based on texture, shape, color, and local information for advancing content-based image search. Specifically, …

Mechanical, Electronic And Optical Properties Of Multi-Ternary Semiconductor Alloys, Dongguo Chen

Dissertations

The ability to obtain tunable properties with composition makes multi-ternary alloys extremely useful for a variety of applications in semiconductor devices and is of significant interest in experimental and theoretical research. This dissertation investigates the mechanical, electronic and optical properties of multi-ternary, i.e., binary, ternary and quaternary, semiconductor alloys using analytical methods and first-principles calculations.

For the calculations of mechanical properties, existing models on the average shear modulus of III-V & II-VI binary semiconductors are revised. New expressions are developed for the average Young’s modulus as well as the shear modulus and Young’s modulus on (111) plane for these compounds. …

Stability And Precipitation Of Diverse Nanoparticles, Chintal Desai

Dissertations

Nanotechnology is a rapidly growing industry that is exploiting the novel characteristics of materials manufactured at the nanoscale. Carbon based nanomaterials such as Carbon Nanotubes (CNTs) and Detonation Nanodiamond (DND) possess unique properties and find a wide range of industrial applications. With the advent of mass production of such materials, there is a possibility of contamination of water resources. Depending on the surface properties and structures, they might aggregate and settle down, or be dispersed and transported by the water. Therefore, there is a need to develop an understanding of the fate of such materials in aqueous media. The understanding …

The Application Of Bayesian Adaptive Design And Markov Model In Clinical Trials, Xiaoyu Lu

Dissertations

In this research, two new designs in clinical trials are proposed. The first problem is a new Bayesian adaptive dose-finding design and its application in an oncology clinical trial. This design is used for phase IB studies with the biomarker as the endpoint and with the fewer patients. The second problem is another new Bayesian adaptive dose-finding design with longitudinal analysis and its application in phase II depression clinical trial. This design is best fit for phase II dosing-finding clinical trials with clinical endpoints. MTD information has been obtained before the trials.

In adaptive dose-finding clinical trials, the strategy is …

Application Of Hydrogen Peroxide As Brown Tide Bloom Control Agent, Varunpreet Randhawa

Dissertations

Harmful algal blooms (HABs) are growing problem across the globe. One such HAB that’s recurring in the coastal waters of New York and New Jersey since mid-1980s, and has been reported in other countries recently, is brown tide bloom. The causal organism is a minute pel agophyte (cell diameter ~- 2µ m) Aureococcus anophagefferens. The brown tide bloom has been responsible for the severe ecological damage and economic loss (e.g. shellfishery) in the affected areas. This research focuses on finding a method to control brown tide blooms and explores the potential of natural chemical biocide hydrogen peroxide (H_{2 …}

Study Of Deep Level Defects Of N+-Cds/P-Cdte Solar Cells, Poonam Rani Kharangarh

Dissertations

Among various photovoltaic materials, polycrystalline cadmium telluride thin film is now the most promising material, due to its low production cost excellent stability and reliability. Current-voltage and capacitance-voltage measurements of CdTe photovoltaic devices at different temperatures can provide valuable information about non-idealities in the n-p semiconductor junction. There are certain limitations which limit the efficiency of CdTe solar cells. There is no real distinction between defects and impurities in CdTe solar cells as both act as beneficial dopants or detrimental traps unlike Si where intentional shallow dopants and traps are distinctly different. Therefore, the role of defect states on CdTe …

Study Of Elementary Reactions Of Combustion Importance At Elevated Temperatures And Pressures, Manuvesh Sangwan

Dissertations

The aim of the present study is to study the kinetics of elementary reactions of combustion importance at elevated temperatures and pressures. High pressure is encountered in many systems of practical importance such as internal combustion engines and rocket combustion chambers. Several reactions of OH, CH₃ and HO₂ radicals are studied. The pressure range covered in this study is 1 - 100 bar and the temperature range is 292 - 834 K. The experimental approach used is laser photolysis coupled to UV transient absorption spectroscopy. A unique high pressure heatable flow reactor is employed and a novel approach …

Thermochemistry Reaction Paths And Oxidation Kinetics On Ketonyl And Aldehydic Nitrogen Oxides, Propene And Isooctane: A Theoretical Study, Suarwee Snitsiriwat

Dissertations

Thermochemical properties for several atmospheric and combustion related species are determined using computational chemical methods coupled with fundamentals of thermodynamics and statistical mechanics. Enthalpies of formation (ΔH_f°₂₉₈) are determined using isodesmic reaction analysis at the CBS-QB3 composite and the B3LYP density functional methods. Entropies (S°₂₉₈) and heat capacities (Cp°(T)) are determined using geometric parameters and vibration frequencies; internal rotor contributions are included in S and Cp(T) values in place of torsion frequencies. Kinetic parameters are calculated versus pressure and temperature for the chemical activated …

Escherichia Coli 2-Oxoglutarate Dehydrogenase Multienzyme Complex: E1 And E2 Substrate Specificty, E1 Carboligase Activity, And E2 Interchain Succinyl Transfer, Da Jeong Shim

Dissertations

Escherichia coli (E. coli) 2-oxoglutarate dehydrogenase multienzyme complex (OGDHc) contains three components: a thiamin di phosphate (ThD P) dependent 2-oxogl utarate dehydrogenase (E1 o), a di hydrol i poylsucci nyl transferase (E2o), and a di hydrol i poyl dehydrogenase (E3). The first two components carry out the principal reactions for succinyl CoA formation while the third one reoxidizes dihydrolipoamide to lipoamide. This mechanism is similar to other 2-oxoacid dehydrogenase complexes, including pyruvate dehydrogenases (PDHc) and branched-chain dehydrogenases.

E1o of the E. coli OGDHc was engineered to accept unnatural substrates. The natural substrate for E1 o is 2-oxogl utarate …

Computational Thermochemistry Of Hydrocarbons, Oxygenates, Cyclic Alkanes, And Furans, Jason Michael Hudzik

Dissertations

Fundamental thermochemical properties including enthalpies (ΔH°_{f 298}), entropies (S° (T)), heat capacities (C_p(T)), and bond dissociation energies (BDEs) for several common and complex hydrocarbon fuel species are determined using computational chemical methods. ΔH° _{f 298} values are calculated using work reactions with the B3LY P (6-31 G(d,p) and 6-311G(2d,2p) basis sets), CBS-QB3, and G3MP2B3 calculation methods. Structures, moments of inertia, vibrational frequencies, and internal rotor potentials are calculated for contributions to entropies and heat capacities. Kinetic rate parameters are calculated for hydrogen abstraction and chemical activation reactions.

Recommended ΔH° …

A Statistical Study Of Plasmawaves And Energetic Particles In The Outer Magnetosphere, Kyungguk Min

Dissertations

The Earth magnetosphere contains energetic particles undergoing specific motions around Earth’s magnetic field, and interacting with a variety of waves. The dynamics of energetic particles are often described in terms of three kinds of adiabatic invariants. Energetic electrons are often unstable to the whistler-mode chorus waves, and ions, to the electromagnetic ion cyclotron (EMIC) instability. These waves play an important role in the dynamics of the magnetosphere by energizing electrons to form a radiation belt, extracting energy from the hot, anisotropic ions and causing pitch angle scattering of energetic ions and relativistic electrons into the loss cone. EMIC waves correspond …

Mathematical Models For Bistable Nematic Liquid Crystal Displays, Chenjing Cai

Dissertations

Bistable Liquid Crystal Displays (LCDs) offer the potential for considerable power savings, compared with conventional (monostable) LCDs. The existence of two (or more) stable field-free states that are optically-distinct means that contrast can be maintained in a display without an externally-applied electric field. An applied field is required only to switch the device from one state to the other, as needed. This dissertation focuses on theoretical models of a possible bistable nematic device, whose operating principle relies on controlling surface anchoring conditions. Switching between the two stable steady states is achieved by application of a transient electric field. A 1D …

A Numerical Method For Electro-Kinetic Flow With Deformable Interfaces, Manman Ma

Dissertations

We consider two-phase flow of ionic fluids whose motion is driven by an imposed electric field. At a fluid-fluid interface, a screening cloud of ions develops and forms an electro-chemical double layer or ‘Debye layer’. The applied electric field acts on the ionic cloud it induces, resulting in a strong slip flow near the interface. This is known as ‘induced-charge electro-kinetic flow’, and is an important phenomenon in microfluidic applications and in the manipulation of biological cells. The models with two different cases including the fast or slow charging time scales are studied both analytically and numerically. We address a …

Genome Wide Search For Pseudo Knotted Non-Coding Rnas, Meghana S. Vasavada

Theses

Non-coding RNAs (ncRNAs) are the functional RNA molecules that are involved in many biological processes including gene regulation, chromosome replication and RNA modification. Searching genomes using computational methods has become an important asset for prediction and annotation of ncRNAs. To annotate an individual genome for a specific family of ncRNAs, a computational tool is interpreted to scan through the genome and align its sequence segments to some structure model for the ncRNA family. With the recent advances in detecting an ncRNA in the genome, heuristic techniques are designed to perform an accurate search and sequence-structure alignment. This study uses a …

Rna-Sequence Analysis Of Human Melanoma Cells, Jharna Miya

Theses

RNA-sequencing refers to the use of high throughput sequencing technologies that are used to sequence cDNA in order to get the complete information of a sample’s RNA content. The objective of this study is to analyze this data in different aspects and to characterize gene expression. Besides this characterization, the data was also used to investigate the effect of sequencing depth on gene expression measurements.

This research focuses on quantitative measurement of expression levels of genes and their transcripts. In this study, complementary DNA fragments of cultured human melanoma cells are sequenced and a total of 139,501,106 million 200-bp reads …

Performance Comparison Of Five Rna-Seq Alignment Tools, Yuanpeng Lu

Theses

Aligning millions of short reads to a reference genome is a critical task in high throughput sequencing. In recent years, a large number of mapping algorithms have been developed, all of which have in common that they align a vast number of reads to genomic or transcriptomic sequences. RNA-Seq data is discrete in nature, therefore with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. To provide guidance in the choice of alignment algorithms, five different alignment tools for RNA-Seq data are evaluated. In order to compare the …

Polyaseeker: A Computational Framework For Identifying Polyadenylation Cleavage Site From Rna-Seq, Xiao Ling

Theses

Alternative polyadenylation (APA) of mRNA plays a crucial role for post-transcriptional gene regulation. Recently, advances in next generation sequencing technology have made it possible to efficiently characterize the transcriptome and identify the 3’end of polyadenylated RNAs. However, no comprehensive bioi nformatic pipelines have fulfilled this goal. The PolyASeeker, a computational framework for identifying polyadenylation cleavage sites from RNA-Seq data is proposed in this thesis. By using the simulated RNA-seq dataset, a novel method is developed to evaluate the performance of the proposed framework versus the traditional A-stretch approach, and compute accurate Precisions and Recalls that previous estimation could not get. …

Validation Of Solar Flare Forecasting & Evolution Of Magnetic Helicity Of Two Active Regions, Qin Li

Theses

This thesis includes two components: (1) Validation of the NJIT flare-forecasting model that was established in recent years is carried out based on the statistical correlation between solar magnetic parameters and flare productivity of active regions (ARs). 378 ARs are examined, comparing observation with prediction. It is found that the accuracy rate to some extent decreases with the level of flares. (2) The temporal evolution of the relative magnetic helicity of two ARs, AR 11072 and 11158 is investigated. The former is flare-quiet while the latter is flare-productive over the 5-day observation period. It is found that for both regions, …

A Gpu Program To Compute Snp-Snp Interactions In Genome-Wide Association Studies, Srividya Ramakrishnan

Theses

With the recent advances in the next generation sequencing technologies, short read sequences of human genome are made more accessible. Paired end sequencing of short reads is currently the most sensitive method for detecting somatic mutations that arise during tumor development. In this study, a novel approach to optimize the detection of structural variants using a new short read alignment program is presented.

Pairwise interaction effects of the Single Nucleotide Polymorphisms (SNPs) have proven to uncover the underlying complex disease traits. Computing the disease risk based on the interaction effects of SNPs on a case - control study is a …

Synthesis And Characterization Of New Light Emitting Probes For Sensitive Detection Of Bio-Molecules And Live Cells, Shyamala Pravin Pillai

Dissertations

A variety of contemporary analytical platforms in technical and biological applications take advantage of labeling the objects of interest with fluorescent or luminescent tracers. Luminescent tracers take advantage of the unique property of some lanthanide metals to absorb and emit light. Long lifetime of lanthanide emission allows temporal gating of the signal, which avoids the short-lived background of interfering sample components. This property in combination with large Stokes shift contributes to extreme sensitivity of detection (ca. 10^-13-10^-14 M), which makes lanthanide-based probes suitable for large variety of challenging tasks ( e.g., intracellular detection of single DNA/RNA, or …

Extension To Pv Optics To Include Front Electrode Design In Solar Cells, Debraj Guhabiswas

Dissertations

Proper optical designing of solar cells and modules is of paramount importance towards achieving high photovoltaic conversion efficiencies. Modeling softwares such as PV OPTICS, BIRANDY and SUNRAYS have been created to aid such optical designing of cells and modules; but none of these modeling packages take the front metal electrode architecture of a solar cell into account.

A new model, has been developed to include the front metal electrode architecture to finished solar cells for optical calculations. This has been implemented in C++ in order to add a new module to PV OPTICS (NREL’s photovoltaic modeling tool) to include …

Modeling Cell Proliferation In A Perfusion Tissue Engineering Bioreactor, Jeffrey Vincent Pohlmeyer

Dissertations

In this dissertation we develop a comprehensive model to simulate a tissue engineering experiment. The experiment takes place in a bioreactor in which a cell seeded porous scaffold is placed, and the scaffold experiences a perfused flow of a nutrient-rich culture medium. The goal of the model is to assist experimentalists in evaluation of different parameter scenarios as the time needed to simulate an experiment is significantly less than the time needed for the experiment itself. We provide the full two-dimensional model development, as well as investigation into possible variations of specific model choices, and we demonstrate the robustness and …

The Goodness-Of-Fit Tests For Geometric Models, Feiyan Chen

Dissertations

We propose two types of goodness-of-fit tests for geometric distribution and for a bivariate geometric distribution called BGD(B&D), based on their probability generating function (PGF). The first type is a special-case application of the general testing procedure for discrete distributions proposed by Kocherlakota and Kocherlakota (1986). The second type utilizes the supremum of the absolute value of the standardized difference between the PGF’s maximum likelihood estimator (MLE) and its empirical counterpart as the test statistic. We verify the asymptotic properties of the test statistics for the first type of test and explore the asymptotic behaviors of the test statistics for …

Development Of Luminescent Probes For Ultrasensitive Detection Of Biopolymers, Their Complexes, And Living Cells, Laura A. Wirpsza

Dissertations

New luminescent probes with enhanced brightness convenient for bioconjugation were synthesized and tested in major biological applications including the detection of nucleic acids and living cells. The first project used luminescent lanthanide ion probes that take advantage of hyper-sensitive acquisition of their long-lived emission signal in time- resolved mode, which avoids short-lived background fluorescence of the medium. Two model carbostyril fluorophores (cs 124-CH₃ and cs 124-CF₃) were modified by inclusion of two spacers (diamino and bi-phenyl) for the attachment of amine and thiol reactive cross-linking groups. In this project, time-resolved measurements are presented for spectroscopy and microscopy. …

Eye Detection Using Discriminatory Features And An Efficient Support Vector Machine, Shuo Chen

Dissertations

Accurate and efficient eye detection has broad applications in computer vision, machine learning, and pattern recognition. This dissertation presents a number of accurate and efficient eye detection methods using various discriminatory features and a new efficient Support Vector Machine (eSVM).

This dissertation first introduces five popular image representation methods - the gray-scale image representation, the color image representation, the 2D Haar wavelet image representation, the Histograms of Oriented Gradients (HOG) image representation, and the Local Binary Patterns (LBP) image representation - and then applies these methods to derive five types of discriminatory features. Comparative assessments are then presented to evaluate …