Physical Sciences and Mathematics Commons^™

Dynamics Of Anisotropic Gold Nanopartilces In Synthetic And Biopolymer Solutions, Sharmine Alam

Wayne State University Dissertations

Soft matter is a subfield of condensed matter physics including systems such as polymers, colloids, amphiphiles and liquid crystals. Understanding their interaction and dynamics is essential for many interdisciplinary fields of study as well as important for technological advancements. We used gold nanorods (AuNRs) to investigate the length-scale dependent dynamics in semidilute polymer solutions, their conjugation and interaction with a protein bovine serum albumin (BSA), and the effect of shape anisotropy on the dynamics within a crowded solution of spheres. Multiphoton fluctuation correlation spectroscopy (MP-FCS) technique was used to investigate the translation and rotational diffusion of AuNRs. For polymer solutions, …

A Control-Theoretic Design And Analysis Framework For Resilient Hard Real-Time Systems, Pradeep Mahendra Hettiarachchi

Wayne State University Dissertations

We introduce a new design metric called system-resiliency which characterizes the maximum unpredictable

external stresses that any hard-real-time performance mode can withstand. Our proposed systemresiliency

framework addresses resiliency determination for real-time systems with physical and hardware

limitations. Furthermore, our framework advises the system designer about the feasible trade-offs between

external system resources for the system operating modes on a real-time system that operates in a

multi-parametric resiliency environment.

Modern multi-modal real-time systems degrade the system’s operational modes as a response to unpredictable

external stimuli. During these mode transitions, real-time systems should demonstrate a reliable

and graceful degradation of service. Many …

Resource Management In Cloud And Big Data Systems, Lena Mashayekhy

Wayne State University Dissertations

Cloud computing is a paradigm shift in computing, where services are offered and acquired on demand in a cost-effective way. These services are often virtualized, and they can handle the computing needs of big data analytics. The ever-growing demand for cloud services arises in many areas including healthcare, transportation, energy systems, and manufacturing. However, cloud resources such as computing power, storage, energy, dollars for infrastructure, and dollars for operations, are limited. Effective use of the existing resources raises several fundamental challenges that place the cloud resource management at the heart of the cloud providers' decision-making process. One of these challenges …

Development Of New Algorithms For Exploring The Potential Energy Landscape Of Chemical Reactions, Adam Benjamin Birkholz

Wayne State University Dissertations

The research presented in this dissertation is divided into 5 chapters. In Chapter 2, a method for reducing the number of coordinates required to accurately reproduce a known chemical reaction pathway by applying principal component analysis to a number of geometries along the pathway (expressed in either Cartesian coordinates or redundant internal coordinates) is described and applied to 9 example reactions. Chapter 3 introduces new methods for estimating the structure of and optimizing transition states by utilizing information about the atomic bonding in the reactants and products. These methods are then benchmarked against a standard transition state optimization approach utilizing …

Interaction Forces And Reaction Kinetics Of Ligand-Cell Receptor Systems Using Atomic Force Microscopy, Anwesha Sarkar

Wayne State University Dissertations

Atomic Force Microscopy (AFM) provides superior imaging resolution and the ability to measure forces at the nanoscale. It is an important tool for studying a wide range of bio-molecular samples from proteins, DNA to living cells. We developed AFM measurement procedures to measure protein interactions on live cells at the single molecular level. These measurements can be interpreted by using proper statistical approaches and can yield important parameters about ligand-receptor interactions on live cells. However, the standard theory for analyzing rupture force data does not fit the experimental rupture force histograms. Most of the experimental measurements of rupture force data …

Object Tracking: Appearance Modeling And Feature Learning, Raed Almomani

Wayne State University Dissertations

Object tracking in real scenes is an important problem in computer vision due to increasing usage of tracking systems day in and day out in various applications such as surveillance, security, monitoring and robotic vision. Object tracking is the process of locating objects of interest in every frame of video frames. Many systems have been proposed to address the tracking problem where the major challenges come from handling appearance variation during tracking caused by changing scale, pose, rotation, illumination and occlusion.

In this dissertation, we address these challenges by introducing several novel tracking techniques. First, we developed a multiple object …

Strong Field Ionization Of Radicals And Reaction Intermediates, Fadia Cudry

Wayne State University Dissertations

This work presents results of adapting SFI probe for detection of radicals and their isomers. Radicals and reaction intermediates were produced using an established method flash pyrolysis. This combination allows for new insight in studying radicals and provide complementary results to the other detection methods used. This is the first study reporting the use of SFI to detect radicals. This detection will also provide structural information of the radicals under study.

For acetone and isoprene, a detailed study shows the SFI flash pyrolysis mass spectra. These mass spectra were then compared to the spectra produced by other detection techniques. We …

Biochemical And Structural Characterization Of The Core Subunits Of Gpi Transamidase, Dilani G. Gamage

Wayne State University Dissertations

BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF THE CORE SUBUNITS OF GPI TRANSAMIDASE

by

DILANI G GAMAGE

May 2015

Advisor: Prof. Tamara L. Hendrickson

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Glycosylphosphatidylinositol transamidase (GPI-T) is a complicated, membrane-bound, multi-subunit enzyme that catalyzes an essential post-translational modification. This enzyme attaches GPI anchors to the C-termini of various proteins that contain a proper GPI-T signal sequence. Gpi8, Gaa1, Gpi16, Gpi17 and Gab1 are the five known subunits that may encompass the fungal GPI-T; Gpi8 is the catalytic subunit, but the functions of the other subunits remain essentially unknown. In humans, different GPI-T subunits are …

Dna Aptamers Selected Against Wild-Type Helix 69 Ribosomal Rna And Their Implications In Combating Antibiotic Resistance, Sakina Miriam Hill

Wayne State University Dissertations

Outbreaks of advanced antibiotic-resistant strains of microbes have hastened the need to identify new viable molecular targets for the development of novel anti-infectives. For this purpose, helix 69 (H69, or m3a 19-nucleotide (nt) hairpin motif that is highly conserved throughout phylogeny and rich in modified nucleotides, including pseudouridine () and 3-methylpseudouridine (m3) was chosen as a potential target. Helix 69, which is located in domain IV of Escherichia coli 23S ribosomal RNA (rRNA), undergoes conformational changes when in close proximity to the decoding region of 16S rRNA and transfer RNAs (tRNAs) in the peptidyl-transferase center (PTC). Functionally, the exact biological …

The Loss Of Genomic Uracil Homeostasis And Aid-Dependent Accumulation Of Dna Damage In B Cell Lymphomas, Sophia Shalhout

Wayne State University Dissertations

Activation-induced deaminase (AID) is a sequence-selective DNA cytosine deaminase that introduces uracils in immunoglobulin genes. This DNA mutator is required for somatic hypermutation and class switch recombination- processes involved in the affinity maturation and diversification of antibodies. AID, however, can also lead to deleterious mutations and translocations promoting lymphomagenesis. The introduction of uracils throughout the genome of activated B cells and the ability of UNG2 glycosylase to excise these uracils is examined here. This interplay was also studied in cancerous B cells, with different results emerging in transformed cells versus healthy cells. Genomic uracil levels are found to remain at …

A Prediction Modeling Framework For Noisy Welding Quality Data, Junheung Park

Wayne State University Dissertations

Numerous and various research projects have been conducted to utilize historical manufacturing process data in product design. These manufacturing process data often contain data inconsistencies, and it causes challenges in extracting useful information from the data. In resistance spot welding (RSW), data inconsistency is a well-known issue. In general, such inconsistent data are treated as noise data and removed from the original dataset before conducting analyses or constructing prediction models. This may not be desirable for every design and manufacturing applications since every data can contain important information to further explain the process. In this research, we propose a prediction …

Investigation Of New Ligand Architechtures Towards Proton And Water Reduction Catalysis By Cobalt Complexes, Debashis Basu

Wayne State University Dissertations

We designed several redox-active ligand architectures to optimize and understand the redox, electronic, and catalytic properties of their respective cobalt complexes. Ligand design was varied from pentadentate donor phenolate to tetradentate acceptor oxime in order to reduce the overpotential of hydrogen generation in organic solvents. We altered the substitution, axial ligands and axial ligand substitutions to vary electronic and catalytic properties for such tetra- or pentadentate ligand systems. Knowledge of the nature of the active species for catalysis enabled us to design the pentadentate oxime ligand which exhibited rich reaction chemistry along with suitable catalytic property in organic solvent. Presence …

On The Nature Of Excited States In Ruthenium Complexes: Towards Renewable Energy, Ryan A. Thomas

Wayne State University Dissertations

The 77 K radiative properties (spectra, quantum yields and lifetimes) of ruthenium-polypyridyl complexes are investigated to better understand the effects of electronic mixing on metal-to-ligand-charge-transfer (3MLCT) excited state properties and how metal-centered (3MC) excited states affect the properties of potential ruthenium photosensitizers.The radiative rate of relaxation (kRAD) determines the maximum possible excited state lifetime when all other relaxation pathways are blocked (kn = 0 for all n  RAD). Thus, the excited state will relax only by means of an emission characteristic of the polypyridyl chromophore. kRAD is expected to increase as the excited state energy increases while the value …

Estimating Cold Nuclear Matter Effects Using Jets In P-Pb Collisions At √Snn = 5.02 Tev With The Alice Detector, Christopher Ghanim Yaldo

Wayne State University Dissertations

In heavy-ion collisions at RHIC and the LHC, a suppression of the nuclear modifi- cation factor for jets along with other strongly interacting particles has been observed relative to proton-proton collisions. To unambiguously determine if this suppression is due to the creation of a strongly interacting medium of de-confied partons referred to as the Quark-Gluon Plasma, or due to Cold Nuclear Matter effects, a "control experiment" is required. Proton-lead collisions serve as this control experiment, because these colli- sions are expected to be sensitive to cold nuclear matter effects while not producing a QGP at this collision energy (√sNN = …

Noncovalent Interactions Between Alkali Metal Cation And Aza/Thia-Crown Macrocycles: Mass Spectrometric Techniques And Theoretical Studies, Calvin A. Austin

Wayne State University Dissertations

Macrocyclic complexes have been useful in understanding many systems encountered in biology, along with having widespread use in analytical, pharmaceutical, and synthetic chemistry. My goal was to provide a quantitative experimental and theoretical description of cation-aza-crown and thia-crown ether interactions with alkali metal cations. Infrared multiple photon dissociation (IRMPD) action spectroscopy and energy-resolved collision-induced dissociation (CID) techniques were used in conjunction with theoretical electronic structure calculations to characterize the structures, binding interactions, and stability of cation-aza-crown ether interactions. Quantum chemical calculations at several levels of theory were employed to characterize the structures and stabilities of the isolated cations and aza-crown …

Semantic Web Based Relational Database Access With Conflict Resolution, Fayez Khazalah

Wayne State University Dissertations

This thesis focuses on (1) accessing relational databases through Semantic Web technologies and (2) resolving conflicts that usually arises when integrating data from heterogeneous source schemas and/or instances.

In the first part of the thesis, we present an approach to access relational databases using Semantic Web technologies. Our approach is built on top of Ontop framework for Ontology Based Data Access. It extracts both Ontop mappings and an equivalent OWL ontology from an existing database schema. The end users can then access the underlying data source through SPARQL queries. The proposed approach takes into consideration the different relationships between the …

Stochastic Approximation Algorithms With Applications To Particle Swarm Optimization, Adaptive Optimization, And Consensus, Quan Yuan

Wayne State University Dissertations

In this dissertation, we present three problems arising in recent applications of stochastic approximation methods. In Chapter 2, we use stochastic approximation to analyze Particle Swarm Optimization (PSO) algorithm. We introduce four coefficients and rewrite the PSO procedure as a stochastic approximation type iterative algorithm. Then we analyze its convergence using weak convergence method. It is proved that a suitably scaled sequence of swarms converge to the solution of an ordinary differential equation. We also establish certain stability results. Moreover, convergence rates are ascertained by using weak convergence method. A centered and scaled sequence of the estimation errors is shown …

Chirped-Pulse Fourier Transform Microwave Spectroscopy In Pulsed Uniform Supersonic Flows, Chamara S.W Abeysekera

Wayne State University Dissertations

This dissertation is focused on the development of a new experimental apparatus that combines two powerful techniques: Chirped-Pulse Fourier-Transform Microwave (CP-FTMW) spectroscopy and uniform supersonic flows. This combination promises a nearly universal detection method that can deliver quantitative isomer, conformer, and vibrational level specific detection; characterize unstable reaction products and intermediates; and perform unique spectroscopic, kinetics and dynamics measurements.

Thus, a new high-power Ka band (26 – 40 GHz) chirped pulse spectrometer with sub-MHz resolution was designed and constructed. In order to study smaller molecules, E-band (60 – 90 GHz) capabilities were also added to the spectrometer. A novel strategy …

Dynamics Of Biopolymers On Nanomaterials Studied By Quasielastic Neutron Scattering And Mdsimulations, Gurpreet Dhindsa

Wayne State University Dissertations

Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, β-Casein and Inorganic Pyrophosphatase (IPPase).

RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and …

On A Multi-Dimensional Singular Stochastic Control Problem: The Parabolic Case, Nhat Do Minh Nguyen

Wayne State University Dissertations

This dissertation considers a stochastic dynamic system which is governed by a multidimensional diffusion process with time dependent coefficients. The control acts additively on the state of the system. The objective is to minimize the expected cumulative cost associated with the position of the system and the amount of control exerted. It is proved that Hamilton-Jacobi-Bellman’s equation of the problem has a solution, which corresponds to the optimal cost of the problem. We also investigate the smoothness of the free boundary arising from the problem.

In the second part of the dissertation, we study the backward parabolic problem for a …

Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph, Narjes Sadat Movahedi Tabrizi

Wayne State University Dissertations

Recent progress in DNA amplification techniques, particularly multiple displacement

amplification (MDA), has made it possible to sequence and assemble bacterial

genomes from a single cell. However, the quality of single cell genome assembly has

not yet reached the quality of normal multi-cell genome assembly due to the coverage

bias (including uneven depth of coverage and region blackout) and errors caused by

MDA. Computational methods try to mitigates the amplification bias. In this document

we introduce a de novo co-assembly method using colored de Bruijn graph,

which can overcome the problem of blackout regions due to amplification bias. The

algorithm is …

New Characterizations Of Sobolev Spaces On Heisenberg And Carnot Groups And High Order Sobolev Spaces On Eucliean Spaces, Xiaoyue Cui

Wayne State University Dissertations

This dissertation focuses on new characterizations of Sobolev spaces .

It encompasses an in-depth study of Sobolev spaces on Heisenberg groups, as well as Carnot groups, second order and high order Sobolev spaces on Euclidean spaces.

Biological Evaluation Of The Vaccine Candidate Tf-Ps A1 And A One-Pot Multicomponent Coupling/Cyclization For Natural Product Herbicide (±)-Thaxtomin A, Jean Paul Bourgault

Wayne State University Dissertations

ABSTRACT

BIOLOGICAL EVALUATION OF THE VACCINE CANDIDATE TF-PS A1 AND A ONE-POT MULTICOMPONENT COUPLING/CYCLIZATION FOR NATURAL PRODUCT HERBICIDE (±)-THAXTOMIN A

By

JEAN PAUL BOURGAULT

August 2015

Advisor: Prof. Peter R. Andreana

Major: Chemistry (Organic)

Degree: Doctor of Philosophy

The -aminooxy derivative of the Thomsen–Friedenreich tumor associated carbohydrate antigen has been synthesized in 11 steps utilizing a D-GalN3 acceptor carrying a pre-installed -N-hydroxysuccinimidyl moiety. The natural  linkage was prepared in high selectivity employing a suitably protected D-GalN3-thioglycoside donor with N-hydroxysuccinimide. With access to -TF-ONH2, the preparation of the TF-PS A1 vaccine candidate ensued smoothly through oxime bond formation. This construct …

Efficient Algorithms And Optimizations For Scientific Computing On Many-Core Processors, Kamel Rushaidat

Wayne State University Dissertations

Designing efficient algorithms for many-core and multicore architectures requires using different strategies to allow for the best exploitation of the hardware resources on those architectures. Researchers have ported many scientific applications to modern many-core and multicore parallel architectures, and by doing so they have achieved significant speedups over running on single CPU cores. While many applications have achieved significant speedups, some applications still require more effort to accelerate due to their inherently serial behavior.

One class of applications that has this serial behavior is the Monte Carlo simulations. Monte Carlo simulations have been used to simulate many problems in statistical …

Multiple Dalitz Plot Analysis At Cleo-C, Mackenzie Smith

Wayne State University Dissertations

Dalitz Plot analysis is a standard technique for the study of weak hadronic 3-body decays. This technique allows us to extract the relative amplitudes, phases, and fit fractions of the resonances that are the primary product of such decays. A Dalitz analysis is complicated by the presence of two or more interfering resonances that appear at the same place on the plot. In this analysis I attempt to resolve the $K^{0}_{s} a_{0}(980)^{0}$ and $K^{0}_{s} f_{0}(980)$ in the decay of $D^{0} \to K^{0}_{s} K^{+} K^{-}$. Using the $K^{0}_{s} a_{0}(980)^{0}$ resonance found in $D^{0} \to K^{0}_{s} \pi^{0} \eta$, I compare equating a …

(I)Chromatographic Methods For Solute Descriptor Determinations (Ii)Ruthenium Substrate-Catalyzed Growth Of Nickel Nitride Thin Films By Atomic Layer Deposition, Thiloka Chandima Ariyasena

Wayne State University Dissertations

Determination of distribution levels of environmentally important compounds in various environmental compartments is a major procedure in many fields including environmental risk assessment, food and drug safety, and the perfumery industry. Models for direct estimation of environmental properties were developed using gas chromatography and liquid-liquid partitioning. The developed models were used to derive descriptor values for environmentally important organic compounds. The accuracy of the developed models and descriptor values were demonstrated by the application to the estimation of standard environmental properties and by comparison with experimental solute property values.

Quantitative structure property relationships were constructed for totally organic biphasic partition …

Synthesis, Characterization, And Rna Reactivity Of Amino-Acid-Linked Cisplatin Analogues, Xun Bao

Wayne State University Dissertations

The essential role of ribosomal RNA (rRNA) in the cell life cycle is highlighted by protein synthesis; therefore, the ribosome is considered to be an ideal drug target. Ribosomal RNAs exhibit a high level of structural diversity. The well-known anticancer drug cisplatin was previously applied as a chemical probe of rRNA structure to determine solvent accessible purines (guanosine) in vivo and in vitro. Cisplatin accumulates faster on RNA than DNA, with less chance of repair. As such, designing new RNA-targeting Pt compounds is not only a promising direction for chemical-probing applications, but also for the design of anticancer drugs that …

Enhancement In Electrochemical Performance Of Advanced Battery Electrodes Using Carbon- Nanomaterial Composites, Kulwinder Dhindsa

Wayne State University Dissertations

LiFePO4 has attracted great interest as a cathode material for lithium ion batteries due to its reasonably high theoretical capacity (170mAh/g), thermal stability, high Li ion reversibility and low cost. However, prohibitively low electronic conductivity (~10-9 S/cm) of LiFePO4 leads to high impedance, low capacity and low rate capability. To overcome this bottleneck, we have developed multiple approaches to improve the conductivity of LiFePO4. Motivated by the outstanding electronic and mechanical properties as well as high surface area of graphene, we prepared LiFePO4/graphene nano-composites by a sol-gel method. The phase purity of the nano LiFePO4/Graphene composite was confirmed by X-Ray …

Developing A Toolbox To Probe Reaction Dynamics With Strong Field Ionization And Non-Linear Attosecond Spectroscopy, Thushani Nikeshala Herath

Wayne State University Dissertations

Electronic motions which happen in 10 to 100 of attoseconds are the heart of all processes in nature. Therefore monitoring and extracting details in this fundamental level will provide new prospect to the areas as information technology, basic energy science, medicine and life sciences. The challenge being, develop a tool to reach such a fast time scale for real time observation in atomic level. In this thesis work we have address this matter using two interesting approaches related to the laser matter interaction: strong field ionization and nonlinear attosecond spectroscopy. The first part is based on the studies related to …

Shape Analysis Using Spectral Geometry, Jiaxi Hu

Wayne State University Dissertations

Shape analysis is a fundamental research topic in computer graphics and computer vision. To date, more and more 3D data is produced by those advanced acquisition capture devices, e.g., laser scanners, depth cameras, and CT/MRI scanners. The increasing data demands advanced analysis tools including shape matching, retrieval, deformation, etc. Nevertheless, 3D Shapes are represented with Euclidean transformations such as translation, scaling, and rotation and digital mesh representations are irregularly sampled. The shape can also deform non-linearly and the sampling may vary. In order to address these challenging problems, we investigate Laplace-Beltrami shape spectra from the differential geometry perspective, focusing more …