Physical Sciences and Mathematics Commons^™

Structure And Dynamics Of The Membrane Protein Bacteriorhodopsin Studied By Mass Spectrometry, Yan Pan

Electronic Thesis and Dissertation Repository

Membrane proteins continue to represent a major challenge for most analytical techniques. Using bacteriorhodopsin (BR) as model system, this work aims to develop mass spectrometry (MS)-based approaches for exploring the structure, dynamics and folding of membrane proteins.

As the first step, BR in its native lipid environment was exposed to hydroxyl radicals, which were produced by laser photolysis of hydrogen peroxide. It was found that the resulting methionine (Met) labeling pattern was consistent with the known BR structure. This finding demonstrates that laser-induced oxidative Met labeling can provide structural information on membrane proteins. In subsequent experiments, the effects of different …

Classic Mosaics And Visual Correspondence Via Graph-Cut Based Energy Optimization, Yu Liu

Electronic Thesis and Dissertation Repository

Computer graphics and computer vision were traditionally two distinct research fields focusing on opposite topics. Lately, they have been increasingly borrowing ideas and tools from each other. In this thesis, we investigate two problems in computer vision and graphics that rely on the same tool, namely energy optimization with graph cuts.

In the area of computer graphics, we address the problem of generating artificial classic mosaics, still and animated. The main purpose of artificial mosaics is to help a user to create digital art. First we reformulate our previous static mosaic work in a more principled global optimization framework. Then, …

Three-Dimensional Modeling Of Electrostatic Precipitator Using Hybrid Finite Element - Flux Corrected Transport Technique, Niloofar Farnoosh

Electronic Thesis and Dissertation Repository

This thesis presents the results of a three-dimensional simulation of the entire precipitation process inside a single-electrode one-stage electrostatic precipitator (ESP). The model was designed to predict the motion of ions, gas and solid particles. The precipitator consists of two parallel grounded collecting plates with a corona electrode mounted at the center, parallel to the plates and excited with a high dc voltage. The complex mutual interaction between the three coexisting phenomena of electrostatic field, fluid dynamics and the particulate transport, which affect the ESP process, were taken into account in all the simulations. The electrostatic field and ionic space …

Electronic And Magnetic Excitations In Graphene And Magnetic Nano-Ribbons, Maher Zakaria Ahmed Selim

Electronic Thesis and Dissertation Repository

The discovery of graphene - a 2D material with superior physical properties - in 2004 was important for the intensive global research to find alternatives to three-dimensional (3D) semiconductor materials in industry. At the same time there have been exciting advances for 2D magnetic materials on the nanometer scale. The superior properties of graphene are mainly attributed to its crystal structure and its relatively short-range interactions. These properties show that natural and artificial 2D materials are promising for new applications.

In this thesis we have carried out a comprehensive investigation of the effects of the 2D lattice structures, the roles …

Development Of Single And Multimodality Imaging Probes For Pet, Spect And Fluorescence Imaging, Babak Behnam Azad

Electronic Thesis and Dissertation Repository

This dissertation is in an integrated format discussing three major projects centered around probe development. In the first project, novel metal-chelated and fluorinated GLP-1 derivatives were prepared all containing D-Ala-8, a modification known to improve resistance towards degradation by dipeptidyl-peptidase IV. The effect of increased distance between DOTA and the peptide chain was investigated using a spacer, in order to reduce steric effects imposed by DOTA. Placement of linker and DOTA moieties were varied within the GLP-1 sequence to test for optimal metal-complex location. Binding affinity of peptide derivatives was determined in vitro with CHO/GLP-1R cell line and shown to …

Addressing Computational Complexity Of High Speed Distributed Circuits Using Model Order Reduction, Ehsan Rasekh

Electronic Thesis and Dissertation Repository

Advanced in the fabrication technology of integrated circuits (ICs) over the last couple of years has resulted in an unparalleled expansion of the functionality of microelectronic systems. Today’s ICs feature complex deep-submicron mixed-signal designs and have found numerous applications in industry due to their lower manufacturing costs and higher performance levels. The tendency towards smaller feature sizes and increasing clock rates is placing higher demands on signal integrity design by highlighting previously negligible interconnect effects such as distortion, reflection, ringing, delay, and crosstalk. These effects if not predicted in the early stages of the design cycle can severely degrade circuit …

Hyperthermal H2 Induced C–H Bond Cleavage: A Novel Approach To Cross-Linking Of Organic Molecules, Tomas Trebicky

Electronic Thesis and Dissertation Repository

The development of simple and effective methods of incorporating molecular moieties with desirable properties into new functional materials is one of the ultimate goals of material scientists. The work presented in this thesis demonstrates an easy way to accomplish this using a beam of gaseous H₂, which we call hyperthermal hydrogen induced cross-linking (HHIC). We prove theoretically and experimentally that when the kinetic energy of H₂ is raised to ~20 eV, it becomes a light-mass projectile which is energetic enough to knock hydrogen atoms off of organic molecules, but not other heavier atoms. By developing a reactor …

Uncovering New Bonding Motifs: The Synthesis Of Chalcogen And Phosphorus Complexes Supported By Nitrogen Based Ligands, Caleb D. Martin

Electronic Thesis and Dissertation Repository

The chemistry of the main group elements with nitrogen based ligands has been an area that has received little attention in comparison to transition metals. The preliminary investigations have focused on groups 13 and 14 revealing new bonding motifs and interesting reactivity. This has motivated us to synthesize group 15 and 16 derivatives in new bonding arrangements capable of activating small molecules.

In pursuit of isolating such species, the reactivity of sulfur dichloride and “S(OTf)2” with a series of diazabutadiene (DAB) ligands was explored. The substitution on the ligand was extremely influential on the outcome of the reaction. Alkyl groups …

Improving Search Engine Results By Query Extension And Categorization, Guo Mei

Electronic Thesis and Dissertation Repository

Since its emergence, the Internet has changed the way in which information is distributed and it has strongly influenced how people communicate. Nowadays, Web search engines are widely used to locate information on the Web, and online social networks have become pervasive platforms of communication.

Retrieving relevant Web pages in response to a query is not an easy task for Web search engines due to the enormous corpus of data that the Web stores and the inherent ambiguity of search queries. We present two approaches to improve the effectiveness of Web search engines. The first approach allows us to retrieve …

Advances In Graph-Cut Optimization: Multi-Surface Models, Label Costs, And Hierarchical Costs, Andrew T. Delong

Electronic Thesis and Dissertation Repository

Computer vision is full of problems that are elegantly expressed in terms of mathematical optimization, or energy minimization. This is particularly true of "low-level" inference problems such as cleaning up noisy signals, clustering and classifying data, or estimating 3D points from images. Energies let us state each problem as a clear, precise objective function. Minimizing the correct energy would, hypothetically, yield a good solution to the corresponding problem. Unfortunately, even for low-level problems we are confronted by energies that are computationally hard—often NP-hard—to minimize. As a consequence, a rather large portion of computer vision research is dedicated to proposing …

Active Learning With Generalized Queries, Jun Du

Electronic Thesis and Dissertation Repository

We study active learning with generalized queries in the thesis.

In contrast to supervised learning, active learning can usually achieve the same predictive accuracy with much fewer labeled training examples, thus significantly reducing the labeling cost. However, previous studies of active learning mostly assume that the learner can only ask specific queries (i.e., require labels for specific examples by providing all feature values). For instance, if the task is to predict osteoarthritis based on a patient data set with 30 features, the previous active learners could only ask the specific queries as: does this patient have osteoarthritis, if ID is …

Molecular Dynamics Simulations Of Charged Nanodroplets, Elias Ahadi

Electronic Thesis and Dissertation Repository

Charged nanodroplets represent a fascinating research area due to their unique dynamics and physical properties. These nanodroplets play a key role in electrospray mass spectrometry (ESI-MS), which is a method for analyzing organic/inorganic molecules as well as proteins and other biomolecular species. The mechanism whereby these analytes are transferred into the gas phase as intact ions remains incompletely understood. Two competing models have been proposed to explain the process, the charged residue model (CRM) and the ion evaporation model (IEM). Under the CRM, evaporation of the droplet proceeds until dryness, at which point the analyte ion is left behind. Under …

The Analysis Of Extreme Synoptic Winds, David A. Gatey

Electronic Thesis and Dissertation Repository

Time histories of wind speed and direction from 394 surface observation stations were obtained to calculate synoptic 50-year return period wind speeds for 11 countries in Europe. Preliminary investigation indicated wind speed differences along national borders were successfully reduced by application of a simple consistent methodology to wind speed data. This study considers the ideal methodology for calculating synoptic 50-year return period wind speeds.

Wind speed data requires standardisation through quality control measures, exposure correction and adjustment for disjunct sampling. A quality control algorithm was successfully applied to identify shifts of monthly mean wind speeds and data conversion issues. Three …

Solving Polynomial Systems Via Triangular Decomposition, Changbo Chen

Electronic Thesis and Dissertation Repository

Finding the solutions of a polynomial system is a fundamental problem with numerous applications in both the academic and industrial world. In this thesis, we target on computing symbolically both the real and the complex solutions of nonlinear polynomial systems with or without parameters. To this end, we improve existing algorithms for computing triangular decompositions. Based on that, we develop various new tools for solving polynomial systems and illustrate their effectiveness by applications.

We propose new algorithms for computing triangular decompositions of polynomial systems incrementally. With respect to previous works, our improvements are based on a weakened notion of a …

Asymptotic Theory Of General Multivariate Garch Models, Weibin Jiang

Electronic Thesis and Dissertation Repository

Generalized autoregressive conditional heteroscedasticity (GARCH) models are widely used in financial markets. Parameters of GARCH models are usually estimated by the quasi-maximum likelihood estimator (QMLE). In recent years, economic theory often implies equilibrium between the levels of time series, which makes the application of multivariate models a necessity. Unfortunately the asymptotic theory of the multivariate GARCH models is far from coherent since many algorithms on the univariate case do not extend to multivariate models naturally. This thesis studies the asymptotic theory of the QMLE under mild conditions. We give some counterexamples for the parameter identifiability result in Jeantheau [1998] and …

Ice-Movement History And Kimberlite Indicator Mineral Dispersal Study, Pelly Bay, Lower Boothia Peninsula, And Wager Plateau Areas, Nunavut, Canada, Carl Ozyer

Electronic Thesis and Dissertation Repository

This study reconstructs the ice flow history of the eastern portion of the Keewatin sector of the Laurentide Ice Sheet by integrating field work, remote imagery, and work by others. The study reveals at least seven ice flow phases during the Wisconsinan, including ice streams. A model was developed using inverse distance weighed (IDW) interpolation with GIS to identify and isolate potential kimberlite bedrock sources in kimberlite indicator mineral-rich areas in the Pelly Bay area, Nunavut. Kimberlite indicator mineral (KIM) data were normalized by “peer size” to better understand how KIM grains from three kimberlite sources are distributed within three …

Validation And Application Of Wind Profiler Measurements Of Atmospheric Turbulence, Armin Dehghan

Electronic Thesis and Dissertation Repository

This thesis focuses on the investigation of the reliability of turbulence measurements by radars when the spectral-width method is used. This method employs the spectral widths observed by radar (experimental spectral width) to determine turbulence. However, the experimental width can be affected by non-turbulent effects, including radar geometry. Therefore, the spectral width due to non-turbulent effects (theoretical spectral width) must be removed from the experimental width. This can occasionally lead to negative values of turbulence.

It is our aim (1) to study the effects of both experimental and theoretical spectral widths on the accuracy of turbulence measurements, (2) to study …

Exploring Bacterial Nanowires: From Properties To Functions And Implications, Kar Man Leung

Electronic Thesis and Dissertation Repository

The discovery of electrically conductive bacterial nanowires from a broad range of microbes provides completely new insights into microbial physiology. Shewanella oneidensis strain MR-1, a dissimilatory metal-reducing bacterium, produces extracellular bacterial nanowires up to tens of micrometers long, with a lateral dimension of ~10 nm. The Shewanella bacterial nanowires are efficient electrical conductors as revealed by scanning probe techniques such as CP-AFM and STM.

Direct electrical transport measurements along Shewanella nanowires reveal a measured nanowire resistivity on the order of 1 Ω∙cm. With electron transport rates up to 10⁹/s at 100 mV, bacterial nanowires can serve as a …

Rational Design And Advanced Fabrication Of Metallic Nanostructures For Surface-Enhanced Raman Spectroscopy, Betty Cristina Galarreta

Electronic Thesis and Dissertation Repository

One of the main challenges in analytical science and technology is to develop devices that provide unambiguously the chemical nature of the material of interest with the minimum intrusiveness, the smallest amount of analyte, and the shortest acquisition time. Among the promising methods for such purpose, optical spectroscopy such as surface-enhanced Raman scattering is considered a suitable option. This spectroscopic technique takes advantage of the interaction between an optical field and metallic nanostructures to magnify the electromagnetic field in the vicinity of the nanostructure, resulting in an amplified signal of the vibrational fingerprints of the adsorbed molecules onto the metallic …

Some Single And Combined Operations On Formal Languages: Algebraic Properties And Complexity, Bo Cui

Electronic Thesis and Dissertation Repository

In this thesis, we consider several research questions related to language operations in the following areas of automata and formal language theory: reversibility of operations, generalizations of (comma-free) codes, generalizations of basic operations, language equations, and state complexity.

Motivated by cryptography applications, we investigate several reversibility questions with respect to the parallel insertion and deletion operations. Among the results we obtained, the following result is of particular interest. For languages L₁, L₂ ⊆ Σ^∗, if L₂ satisfies the condition L₂ΣL₂ ∩ Σ⁺L₂Σ⁺ = ∅, then …

Workflow-Net Based Cooperative Multi-Agent Systems, Yehia T. Kotb

Electronic Thesis and Dissertation Repository

Workflow-nets are mathematical frameworks that are used to formally describe, model and implement workflows. First, we propose critical section workflow nets (abbreviated WFCSnet). This framework allows feedbacks in workflow systems while ensuring the soundness of the workflow. Feedback is generally not recommended in workflow systems as they threaten the soundness of the system. The proposed WFCSnet allows safe feedback and limits the maximum number of activities per workflow as required. A theorem for soundness of WFCSnet is presented. Serializability, Separability, Quasi-liveness and CS-Properties of WFCSnet are examined and some theorems and lemmas are proposed to mathematically formalize them. In this …

Microrheology And Microstructure Of Poly(Vinyl Alcohol)-Based Physical Gels, Nan Yang

Electronic Thesis and Dissertation Repository

We study the microrheology and microstructure of physically cross-linked poly(vinyl alcohol) (PVA) gels using atomic force microscopy, dynamic light scattering and particle tracking. We compare the microscopic rheological properties with the bulk properties measured using conventional shear rheometry, and correlate the rheological properties to the structure of the materials.

We develop a new technique for investigating the viscoelastic properties of soft materials using the atomic force microscope. The electronic feedback of an atomic force microscope is modified by adding a small oscillatory voltage to the deflection signal, and the amplitude and phase of the motion of the sample stage is …

Ergodicity And Seismicity Clustering With Applications In Statistical Seismology, Nelson Cho

Electronic Thesis and Dissertation Repository

The implications of understanding fault networks as ergodic systems are addressed here by using the Thirumalai-Mountain metric that identifies effective ergodic periods, when long but finite time intervals are considered. This framework was proven to be useful in statistical seismology studies. Initially, it was established that that the metric can be used to quantify seismicity clustering. Periods of effective ergodicity were characterized by the occurrence of declustered seismicity. This interpretation was implemented for synthetic and seismic data from southern California and Canadian mines.

Next, methods used in the estimation of regional seismic hazard were applied to mining induced seismicity. The …

Strategies For The Thermal And Photochemical Modification Of Gold Nanoparticles (Aunps) And The Fabrication Of Aunp Hybrid Materials, Hossein Ismaili

Electronic Thesis and Dissertation Repository

Among the existing approaches for the functionalization of the gold nanoparticle (AuNP), a direct interfacial organic reaction of terminal functional groups exposed on the surface of template nanoparticles with various reactants has been shown as a promising strategy to incorporate desired functionality onto the AuNP monolayer. In our own attempts to extend the types of reactions that can be utilized for efficient interfacial modifications of AuNPs, we examined uncatalyzed Huisgen 1,3-dipolar click-type cycloaddition of azide-modified AuNPs to terminal alkynes. These particular reactions were found to be generally too slow to be useful at ambient temperatures but it was shown that …

Noncommutative Complex Geometry Of Quantum Projective Spaces, Ali Moatadelro

Electronic Thesis and Dissertation Repository

In this thesis, we study complex structures of quantum projective
spaces that was initiated in [19] for the quantum projective line,
$\mathbb{C}P^1_q$. In Chapters 2 and 3, which are the main parts of this thesis, we generalize the the results of [19] to the spaces $\mathbb{C}P^{2}_q$ and $\mathbb{C}P^{\ell}_q$. We consider a natural holomorphic structure on the quantum projective space already presented in [11,9],
and define holomorphic structures on its canonical quantum line bundles.
The space of holomorphic sections of these line bundles then will determine
the quantum homogeneous coordinate ring of the quantum projective space as the space of twisted …

X-Ray Photoelectron Spectroscopy Studies On The Oxidation Processes Of Nickel, Chromium And Their Alloys, Bradley P. Payne

Electronic Thesis and Dissertation Repository

The reaction of polycrystalline Ni metal surfaces with low pressures (~ 130 Pa) of O₂ gas or H₂O vapour produced thin defective nickel oxide films containing both Ni²⁺ and Ni³⁺ species at 25^oC and 300^oC. Exposure of Ni metal samples to H₂O vapour resulted in a much slower reaction rate when compared to similar doses of O₂ gas. This difference was attributed to a slower place exchange with a surface hydroxyl (OH (ads)) intermediate compared to that of an adsorbed oxygen atom (O (ads)). This OH (ads) species …

Gkm Theory Of Rationally Smooth Group Embeddings, Richard P. Gonzales

Electronic Thesis and Dissertation Repository

This thesis is concerned with the study of rationally smooth group embeddings. We prove that the equivariant cohomology of any of these compactifications
can be described, via GKM-theory, as certain ring of piecewise polynomial functions.
Moreover, building on previous work of Renner, we show that the embeddings under consideration come equipped with both a canonical decomposition into rational cells and a filtration by equivariantly formal closed subvarieties.

The techniques developed in this monograph supply a method for constructing free
module generators on the equivariant cohomology of Q-filtrable GKM-varieties.
Our findings extend the earlier work of Arabia and Guillemin-Kogan on equivariant …

Diagnostic Checking, Time Series And Regression, Esam Mahdi

Electronic Thesis and Dissertation Repository

In this thesis, a new univariate-multivariate portmanteau test is derived. The proposed test statistic can be used for diagnostic checking ARMA, VAR, FGN, GARCH, and TAR time series models as well as for checking randomness of series and goodness-of- fit VAR models with stable Paretian errors. The asymptotic distribution of the test statistic is derived as well as a chi-square approximation. However, the Monte-Carlo test is recommended unless the series is very long. Extensive simulation experiments demonstrate the usefulness of this test and its improved power performance compared to widely used previous multivariate portmanteau diagnostic check. The contributed R package …

Double Helical Hydrogen-Bonded Aaa-Ddd Complexes And Supramolecular Polymers, Hong-Bo Wang

Electronic Thesis and Dissertation Repository

The design and characterization of linear oligomers that self-assemble into double helical structures has been a subject of interest to chemists since the elucidation of the double helix structure of DNA in 1953. Transition metal templates have been widely used in the construction of artificial double helical complexes from linear multidentate ligands. The use of other non-covalent interactions as the driving force in the self-assembly of these types of complexes is less common. Aromatic stacking interactions, anion templates, and salt-bridges have all been applied in this context. The great majority of these investigations have been concerned with the dimerization of …

The Complex Paragenetic History Of Basal Negaunee Iron Formation Iron Ores, Tilden Mine, Marquette District, Upper Michigan, Natalie J. Pietrzak

Electronic Thesis and Dissertation Repository

Variable mineral chemistry and textures of basal Negaunee iron ores mined in the Main Tilden Pit have led to metallurgical difficulties. Core-logging and detailed petrography supported by microprobe investigations, identify three upward fining lithofacies within the Main Pit Carbonate and overlying Martite ore domains: 1) Basal Clastics; 2) Medial BIF; and 3) Granular Iron Formation. Growth fault related subsidence controlled deposition of the Basal Clastics, comprised of detrital quartz dispersed in a matrix of chlorite, cemented by ferri-hydrite, chert and Mg-siderite. Subsequent starvation of any clastic input led to cyclic iron-silica precipitation throughout the deposition of Medial BIF. Increasing wave …