Digital Commons Network^™

Applications Of Electronic Structure Theory To Problems In Strong-Field Chemistry, Inorganic Chemistry, And Nanomaterial Systems, Jason Anthony Sonk

Wayne State University Dissertations

This dissertation covers research performed on applications of electronic structure theory to various fields of chemistry and is divided into eight chapters. Chapters 2 through 4 describe a series of related works which explore applications of excited state electronic structure methods to problems in strong field chemistry. Chapters 5, 6, and 7 discuss the application of electronic structure theory methods to solving problems in inorganic chemistry. Finally, Chapter 8 looks at an application of electronic structure theory to nanomaterials.

Chapter 2 covers the modeling of electron dynamics of butadiene interacting with a short, intense laser pulse in the absence of …

Metal Complexes Of Non-Heme Ligands: Biological Applications, Jai Prakash

Wayne State University Dissertations

Oxidative inactivation of proteins (carbonic anhydrase–I, trypsin, chymotrypsin and 20S proteasome) by non–heme iron complexes, and glutathionylation of non–heme cobalt complexes mimicking the N5 coordination environment like that of biologically important cofactor cobalamin or B₁₂ (Cbl) are reported. Different non–heme ligand sets or inhibitors were used to inactivate different proteins. Carbonic anhydrase–I (CA–I) and 20S proteasome were inactivated by iron complexes in the presence of O₂ and a reductant (DTT), consistent with a pathway involving the reductive activation of O₂, whereas serine proteases trypsin and chymotrypsin were inactivated by ferryls (single turnover), and by an iron …

"Fine-Tuning" Of Ribosomal Structure And Functions By Pseudouridylation And Rna-Protein Interactions, Jun Jiang

Wayne State University Dissertations

ABSTRACT

"Fine-tuning" of ribosomal structure and functions by pseudouridylation and RNA-protein interactions

by

JUN JIANG

AUGUST 2012

Advisor: Prof. John SantaLucia Jr.

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Ribosomal structure and functions appear to be "fine-tuned" by pseudouridylation and RNA-protein interactions. Pseudouridylation may promote base stacking interactions by mediating the base stacking between residues on both sides. In the RNA duplex region, this enhanced stacking interaction contributes to stabilization of duplex folding. In the loop region, enhanced stacking in one structural motif may destabilize the conformation of adjacent structural residues. This hypothesis is supported by both UV-melting experiments, where …

State-Resolved Slice Imaging Of Photochemical Dynamics, Herath Mudiyans Nuradhika Herath

Wayne State University Dissertations

This dissertation focuses on the understanding the unimolecular photochemistry and dynamics

utilizing state-resolved slice imaging approach combined with the quantum-state selective

spectroscopy technique called resonance enhanced multi photon ionization (REMPI)

method. This powerful technique allows selecting the initial quantum states of the reactants

and determining the nal quantum states, energy, the orientation and alignments of

the products. In the investigations of photodissociation dynamics of acetone at 230 nm,

a bimodal distribution for the resulting CO photoproduct is identied. This observation

indicated the presence of unimolecular dissociation mechanism analogues to the roaming

dynamics reported in formaldehyde photodissociation. Moreover, another type of …

Measurement Of Branching Factions Of D Meson With Final State Including Kk, Peng Zhou

Wayne State University Dissertations

Using 818pb−1 of CLEO-c data at √s =3770 MeV, we measure precisely the branching ratios for four D+ → K+K−X hadronic channels. Our measurement improves the errors of B(D+ → K+K−π+π0) and B(D+ → φπ+π0) by factors of 10 respectively. We report first observation of the decay D+ → φρ+, as well as branching ratio measurements for two rare decays.

Nodal Geometry Of Eigenfunctions On Smooth Manifolds And Hardy-Littlewood-Sobolev Inequalities On The Heisenberg Group, Xiaolong Han

Wayne State University Dissertations

Part I: Let (M,g) be a n dimensional smooth, compact, and connected Riemannian manifold without boundary, consider the partial differential equation on M:

-Δu=Λu,

in which Δ is the Laplace-Beltrami operator. That is, u is an eigenfunction with eigenvalue Λ. We analyze the asymptotic behavior of eigenfunctions as Λ go to ∞ (i.e., limit of high energy states) in terms of the following aspects.

(1) Local and global properties of eigenfunctions, including several crucial estimates for further investigation.

(2) Write the nodal set of u as N={u=0}, estimate the size of N using Hausdorff measure. Particularly, surrounding the conjecture that …

Location Privacy In Emerging Network-Based Applications, Yong Xi

Wayne State University Dissertations

With the wide spread of computer systems and networks, privacy has become an issue that increasingly attracts attention. In wireless sensor networks, the location of an event source may be subject to unintentional disclosure through traffic analysis by the attacker. In vehicular networks, authentication leaves a trail to tie a driver to a sequence of time and space coordinates. In a cloud-based navigation system, the location information of a sensitive itinerary is disclosed. Those scenarios have shown that privacy protection is a far-reaching problem that could span many different aspects of a computer/network system, especially on a diversified landscape of …

Effective Semantic-Based Keyword Search Over Relational Databases For Knowledge Discovery, Sina Fakhraee

Wayne State University Dissertations

Keyword-based search has been popularized by Internet web search engines such as Google which is the most commonly used search engine to locate the information on the web. On the other hand while traditional database management systems offer powerful query languages such as SQL, they do not provide keyword-based search similar to the one provided by web search engines. The current amount of text data in relational databases is massive and is growing fast. This increases the importance and need for non-technical users to be able to search for such information using simple keyword search just as how they would …

A New Semantic Similarity Join Method Using Diffusion Maps And Long String Table Attributes, Bilal Hani Hawashin

Wayne State University Dissertations

With the rapid increase of the distributed data sources, and in order to make information integration, there is a need to combine the information that refers to the same entity from different sources. However, there are no global conventions that control the format of the data, and it is impractical to impose such global conventions. Also, there could be some spelling errors in the data as it is entered manually in most of the cases. For such reasons, the need to find and join similar records instead of exact records is important in order to integrate the data. Most of …

Effect Of Low Endogenous Brain-Derived Neurotrophic Factor Levels On Striatal Dopamine Dynamics, Francis Kabui Maina

Wayne State University Dissertations

Many neurological diseases and disorders are a result of alterations with neurotransmitters, neuromodulators, and/or proteins. Specifically, one protein that has been linked to numerous neurological diseases and disorders such as Parkinson's disease, Huntington's disease, addiction, attention deficit hyperactivity disorder (ADHD), and depression is brain-derived neurotrophic factor (BDNF). As a trophic factor, BDNF role is to assist in the growth, survival, and differentiation of neurons. However, there is increasing evidence that BDNF may mediate neurotransmitter dynamics. Our goals were to understand how endogenous BDNF levels and aging modulate the dopamine (DA) dynamics in the mouse striatum. Two complementary neurochemical techniques, slice …

The Structural Requirements Of Histone Deacetylase (Hdac) Inhibitors: Suberoylanilide Hydroxamic Acid (Saha) Analogues Modified At C3, C6, And C7 Positions Enhance Selectivity, Sun Ea Choi

Wayne State University Dissertations

Histone deacetylase (HDAC) proteins are targets for drug design towards the treatment of cancers since overexpression of HDAC is linked to cancer. Several HDAC inhibitors, including the FDA approved drug suberoylanilide hydroxamic acid (SAHA, Vorinostat), have cleared clinical trials and emerged as anti-cancer drugs. However, SAHA inhibits all of the 11 metal ion-dependent HDAC proteins. Therefore, we synthesized several libraries of small molecule HDAC inhibitors based on SAHA to help understand the structural requirements of inhibitory potency and isoform selectivity.

In previous work, SAHA analogues functionalized at the C2 position (C2-SAHA analogues) near the metal binding hydroxamic acid displayed decreased …

New Adaptations Of Analytical Tools For The Study Of Dynamic Interactions Of Lanthanide-Based Catalysis In Aqueous Media, Prabani Lakmanthi Dissanayake

Wayne State University Dissertations

Lewis acid catalyzed carbon-carbon bond-forming reactions are of great interest in organic synthesis. However, many conventional Lewis acids, and almost all enantioselective Lewis acid catalysts, must be used under strictly anhydrous conditions to avoid hydrolysis and the difficulties associated with recovery and reuse of the catalysts. Due to these drawbacks of conventional Lewis acids, there is a growing desire to perform many organic transformations using more environmentally friendly aqueous-stable catalysts. The advantages of using aqueous-stable catalysts include the ability to use unprotected functional groups, ease of product separation and catalyst recovery, and avoidance of costly solvent drying procedures. Lanthanide trifluoronmethanesulfonates …

Development Of A Cargo Delivery System And Inhibition Studies Focused On Clostridium Difficile Toxin A, Stephanie Marie Kern

Wayne State University Dissertations

Virulence factors of pathogenic bacteria are to be blamed for life-threatening infections such as diphtheria, anthrax, botulism, and tentanus. In the case of enzymatic exotoxins, disease arises from cytotoxic proteins, and cytotoxicity is acheived only after cell entry. This intrinsic mechanism for cell entry is intriguing from research and medical views. Along with a review on existing cargo delivery systems utilizing protein toxins and the usefulness of such a system, here is described the first reported Clostridium difficile toxin A fusion protein, luciferase-TcdA, and evidence of the successful transport of an active enzyme, luciferase, into the cytosol of vero cells. …

Synthesis, Spectroscopic, And Electrochemical Properties Of 3d Metal And Ruthenium Complexes With Phenolate And Catecholate Ligands, Frank Donald Lesh

Wayne State University Dissertations

The integration of amphiphilic properties into transition metal coordination systems is a pertinent step toward the development of candidate metallosurfactant precursors for the formation of responsive monolayer films. This concept is intended to preserve the solution-observed redox, spectroscopic, and magnetic responses onto solid surfaces for potential application. Selected metal ions and various ligand designs are investigated to address the effect of coordination and protonation preferences on amphiphilic behavior, the aspects of new modular approaches for Langmuir film precursors of differentiated topologies to extend amphiphilicity and redox behavior, and the introduction of photosensitizing properties into electroactive metallosurfactant precursors. In an attempt …

Multi-Component Ab2 Metal Hydride Alloys For Nickel Metal Hydride Battery Applications, Jean Nei

Wayne State University Dissertations

Compared to the mish metal-based AB₅ MH alloy commonly used in Ni/MH batteries, the transition metal-based AB₂ MH alloy not only reduces the rare earth dependency, it also has higher specific energy. In order to further improve the performance of AB₂ MH alloy, it's crucial to full understand its multi-phase nature, which includes the main C14/C15 Laves phases and the secondary non-Laves phases.

In order to optimize the gaseous phase and electrochemical advantages of both the C14 and C15 Laves phases, a study was established to recognize the factors that affect the C14/C15 phase abundance. Average electron …

Stabilization And Classification Of Poincare Duality Embeddings, John Whitson Peter

Wayne State University Dissertations

We define a space E(K,X) of Poincare Duality embeddings and show that such spaces admit a highly connected stabilization map.

This serves as a tool for classifying Poincare Duality embeddings in terms of the homotopy types of their complements. In

particular, a Poincare embedding gives rise to a fiberwise duality

map in the category of retractive spaces over X. We use this construction to obtain a highly connected classification map with target a moduli space of unstable complements for Poincare embeddings. As consequences, we obtain stabilization and classication results for

smooth embeddings.

Exploring Conformational Variability Of An Rna Domain In The Ribosome: From Structure And Function To Potential Antibiotic Targeting, Yogo Sakakibara

Wayne State University Dissertations

RNA in nature is modified at many specific sites to order to gain extra functions or to expand the genetic code. One of such RNAs is ribosomal RNA (rRNA), which contains several modified bases, particularly around the functionally significant sites. We have focused on understanding the influences of modified base on RNA structure and function by employing helix 69 (H69), which is a good region to evaluate the roles of modified bases since it contains three pseudouridines in the loop region and exists at the core of the ribosome.

Previous model studies using small hairpin H69 showed the conformational differences …

Drug Resistance Mechanisms And Drug Design Strategies For Human Immunodeficiency Virus And Hepatitis C Virus Proteases, Yong Wang

Wayne State University Dissertations

The antiviral drug development has improved steadily to treat the infections of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) which represent heavy public health burdens. The viral protease plays an indispensable role in viral maturation and therefore becomes one of the most important targets for drug design. Nine HIV-1 protease inhibitors and two HCV protease inhibitors have been developed and approved by the U.S. Food and Drug Administration. However, mutations in the protease decrease reduce the efficacy the drugs. In this study, the enzyme assays indicate that darunavir and tipranavir exhibit the most potent inhibition against the multi-drug …

Probing The Dynamics Of Radical Reactions With Polyatomic Hydrocarbons By Crossed-Beam Dc Slice Imaging, Armando Dura Estillore

Wayne State University Dissertations

This work presents results of crossed molecular beam imaging studies on the reaction of radicals (Cl and CN) with polyatomic hydrocarbons of different functionalities such as pentane isomers, deuterated alkanes, alkenes, and alcohols. The reactively scattered alkyl radicals are probed as a function of collision energy using single photon ionization. The scattering results for pentane are quite similar for all reactants, suggesting that the nature of the abstraction site has surprisingly little influence on the dynamics studied at ~5 and ~9 kcal/mol. The angular distributions are broad with a backscattered peak at low collision energy and a sharp forward peak …

Raman Spectroscopy And Diffuse Reflectance Spectroscopy For Diagnosis Of Human Cancer And Acanthosis Nigricans, Suneetha Devpura

Wayne State University Dissertations

Cancer and diabetes are common chronic diseases in today's world causing numerous deaths in adults as well as children. Most common types of cancers in adults include prostate, lung, breast, colorectal and head and neck squamous cell carcinoma, while among children; leukemia, and brain and central nervous system cancers are quite common. In each of these cases, early detection of the cancer or disease dramatically increases the chances of successful treatment. In recent years, there has been much interest in using Raman spectroscopy and diffuse reflectance spectroscopy as analytical optical spectroscopic methods for early diagnosis of diseases. Raman spectroscopy can …

Competencies Of Expert Web-Based Instruction Designers, Yonghui Chen

Wayne State University Dissertations

Web-based instruction has been increasingly accepted in education, business and industry, military and government, healthcare and other sectors as a dominant means to deliver instruction beyond time and geographical constraints. However, the overall quality of WBI courses or programs remains a concern. The reasons for the ineffectiveness can be many, of which is the lack of sufficient competencies and skills in existing professionals. This study attempts to identify the domains, competencies, performance statement for instructional designers in WBI at the expert level. IBSTPI competency model has been used as the conceptual framework, utilizing mixed methods.

As a result, 91 performance …

Hierarchical Multi-Label Classification For Protein Function Prediction Going Beyond Traditional Approaches, Noor Al Aydie

Wayne State University Dissertations

Hierarchical multi-label classification is a variant of traditional classification in which the

instances can belong to several labels, that are in turn organized in a hierarchy. Functional classification of genes is a challenging problem in functional genomics due to several reasons. First, each gene participates in multiple biological activities. Hence, prediction models should support multi-label classification. Second, the genes are organized and classified according to a hierarchical classification scheme that represents the relationships between the functions of the genes. These relationships should be maintained by the prediction models. In addition, various bimolecular data sources, such as gene expression data and …

Single Molecule Studies Of Rna-Target Interactions, Sharla Leann Wood

Wayne State University Dissertations

We have used FRET, single molecule spectroscopy, and several other biophysical techniques to study how the folding of RNA allows it to perform its various functions by recognizing and binding a target ligand. We have shown that the c-di-GMP riboswitch undergoes a large, global conformational change upon binding of the ligand. The folding dynamics of the c-di-GMP riboswitch upon Mg2+ binding help to pre-organize the aptamer for efficient ligand binding and ultimately efficient gene expression. We have also investigated two instances, a fluorophore-binding aptamer and molecular beacon, where the folding of RNA can be used to detect an analyte. We …

System Support For Robust Data Collection In Wireless Sensing Systems, Guoxing Zhan

Wayne State University Dissertations

This dissertation studied how to provide system support for robust data collection in wireless sensing systems through addressing a few urgent design issues in the existing systems. A wireless sensing system may suffer issues arising at the sensors, during the data transmission, and during the data access by applications. Due to the unique characteristics of wireless sensing systems, certain conventional solutions for networked systems may not work well with these issues. We developed approaches to resolve these urgent problems in the design of wireless sensing systems. Specially, we have achieved the following: (1) we developed a resilient trust model to …

Search For Contact Interactions In The Dimuon Channel In P-P Collisions At Sqrt(S) = 7 Tev At Cms, Sowjanya Gollapinni

Wayne State University Dissertations

The standard model (SM) fails to explain the variety of observed quark and lepton flavors and their masses suggesting that there might exist a more fundamental basis. If quarks and leptons are composite

particles made up of more basic constituents, a new physics

interaction in the form of a four-fermion contact interaction

arises between them. Experimentally the signal is manifest as

a deviation from the SM prediction in the high-mass tail for

the invariant mass distribution of the opposite-sign dimuon pairs.

The Large Hadron Collider (LHC) experiment at the Center for

European Nuclear Research (CERN) is built to explore new …

The Dependent Samples T And Wilcoxon Sign Rank Maximum Test, Saverpierre Maggio

Wayne State University Dissertations

A maximum test using the parametric dependent samples t-test and the non-parametric Wilcoxon sign rank test was created using a FORTRAN program and various subroutines of the International Mathematical and Statistical Libraries (IMSL, 1980). Two tailed critical values were derived from a mixed normal distribution. Critical values obtained were at the 0.05, 0.025, 0.01 and 0.005 alpha levels via sample sizes (n) 8 through 30, 45, 60, 90 and 120. Critical values were compared to values obtained through the application of the Bonferroni correction method. It was concluded that the Bonferroni is an unnecessary method. Findings of the study are …

New Precursors And Chemistry For The Growth Of Transition Metal Films By Atomic Layer Deposition, Thomas Joseph Knisley

Wayne State University Dissertations

The advancing complexity of advanced microelectronic devices is placing rigorous demands on currently used PVD and CVD deposition techniques. The ALD deposition method is proposed to meet the film thickness and conformality constraints needed by the semiconductor industry in future manufacturing processes. Unfortunately, there is a limited number of chemical precursors available that have high thermal stability, reactivity, and vapor pressure suitable for ALD film growth to occur. These properties collectively contribute to the lack of suitable transition metal precursors available for use in ALD. In this thesis, we report the discovery of a series of novel transition metal diazadienate …

Determination Of Descriptors By Liquid-Liquid Partition And Chromatographic Methods, Thushara Namal Karunasekara

Wayne State University Dissertations

ABSTRACT

DETERMINATION OF DESCRIPTORS BY LIQUID-LIQUID PARTITION AND CHROMATOGRAPHIC METHODS

by

THUSHARA KARUNASEKARA

September 2012

Advisor: Prof. Colin F. Poole

Major: Chemistry (Analytical)

Degree: Doctor of Philosophy

Partition coefficients for varied compounds were determined for several totally organic biphasic systems using formamide, propylene carbonate, ethylene glycol or dimethyl sulfoxide as the base solvent and n-heptane, 1,2-dichloroethane, 1-octanol or isopentyl ether as the counter solvent. These partition coefficient databases are analyzed using the solvation parameter model facilitating a quantitative comparison of these systems with other totally organic and water-based partition systems. These totally organic biphasic solvent systems offer a complementary approach …

Systems Support For Genomics Computing In Cloud Environments, Tung Thanh Nguyen

Wayne State University Dissertations

Genomics research has enormous applications in many areas such as health care, forensic, agriculture, etc. Most recent achievements in this field come from the availability of the unprecedented genomic data. However, new sequencing technologies in genomics keep producing data at a faster pace resulting a very huge amount of data. This poses great challenges on how to store, manage, process and analyze the data efficiently. To deal with these, genomics research groups often equip themselves with a small scale server room composed of high storage capacity and computing ability machines. This solution is not only costly, unscalable but also inefficient. …

Rethinking The Design And Implementation Of The I/O Software Stack For High-Performance Computing, Xuechen Zhang

Wayne State University Dissertations

Current I/O stack for high-performance computing is composed of multiple software layers in order to hide users from complexity of I/O performance optimization. However, the design and implementation of a specific layer is usually carried out separately with limited consideration of its impact on other layers, which could result in suboptimal I/O performance because data access locality is weakened, if not lost, on hard disk, a widely used storage medium in high-end storage systems.

In this dissertation, we experimentally demonstrated such issues in four different layers, including operating system process management layer and MPI-IO middleware layer on compute server side, …