Physical Sciences and Mathematics Commons^™

Development Of An Integrated Workflow For Nucleosome Modeling And Simulations, Ran Sun

Doctoral Dissertations

Nucleosomes are the building blocks of eukaryotic genomes and thus fundamental to to all genetic processes. Any protein or drug that binds DNA must either cooperate or compete with nucleosomes. Given that a nucleosome contains 147 base pairs of DNA, there are approximately 4^147 or 10^88 possible sequences for a single nucleosome. Exhaustive studies are not possible. However, genome wide association studies can identify individual nucleosomes of interest to a specific mechanism, and today's supercomputers enable comparative simulation studies of 10s to 100s of nucleosomes. The goal of this thesis is to develop and present and end-to-end workflow that serves …

Multi-Scale Computational Modeling Of Metal/Ceramic Interfaces, Abu Shama Mohammad Miraz

Master's Theses

Multi-scale atomistic calculations were carried out to understand the interfacial features that dictate the mechanical integrity of the metal/ceramic nanolaminates. As such, first principles density functional theory (DFT) calculations were performed to understand the electronic and atomistic factors governing adhesion and resistance to shear for simple metal/ceramic interfaces, whereas molecular dynamics (MD) simulations were performed to observe the impact of interfacial structures, such as misfit dislocation network geometries and orientation relationships, on interfacial mechanical properties.

For the DFT investigation, we choose metals with different crystal structures, namely - Cu (fcc), Cr (bcc) and Ti (hcp) along with a variety of …

Multi-Scale Computational Modeling Of Metal/Ceramic Interfaces, Abu Shama Mohammad Miraz

Doctoral Dissertations

Multi-scale atomistic calculations were carried out to understand the interfacial features that dictate the mechanical integrity of the metal/ceramic nanolaminates. As such, first principles density functional theory (DFT) calculations were performed to understand the electronic and atomistic factors governing adhesion and resistance to shear for simple metal/ceramic interfaces, whereas molecular dynamics (MD) simulations were performed to observe the impact of interfacial structures, such as misfit dislocation network geometries and orientation relationships, on interfacial mechanical properties.

For the DFT investigation, we choose metals with different crystal structures, namely - Cu (fcc), Cr (bcc) and Ti (hcp) along with a variety of …

The Megaprocessor As An Educational Tool Making The Abstract Concrete, Jonathon Beauregard Ii

Master's Theses

Computer architecture courses can be difficult for students to engage with and learn from. This is because, unlike most core courses for a computer science student, learning architecture is an abstract process. To address this, universities have implemented methods for teaching course material other than purely descriptive methods. This typically means using simulations to model some aspect of a CPU or FPGA (fieldprogrammable gate array) boards for hands-on experimentation in CPU design. However, there are issues with these tools. Simulations can only cover a few topics well, are prone to being abandoned, and introduce additional abstraction layers. FPGAs, while great …

The Parity-Violating Asymmetry In The N→Δ Transition At Low Q2, Thamraa A. Alshayeb

Doctoral Dissertations

Qweak has used the parity violating asymmetry to test the Standard Model (SM) by constantly flipping helicity states of a longitudinally polarized electron beam that scatters in the unpolarized LH2 target. The main focus of the Qweak experiment at Jefferson Lab was the recently published determination of the proton’s weak charge. In order to make corrections to the measured asymmetry at low 𝑄 2 due to inelastically scattered electrons, dedicated measurements were made of the parity violating asymmetry in the N→∆ transition at two different beam energies.

The measured inelastic asymmetries are used to extract the low energy constant dΔ, …

Poisoning Attacks On Learning-Based Keystroke Authentication And A Residue Feature Based Defense, Zibo Wang

Doctoral Dissertations

Behavioral biometrics, such as keystroke dynamics, are characterized by relatively large variation in the input samples as compared to physiological biometrics such as fingerprints and iris. Recent advances in machine learning have resulted in behaviorbased pattern learning methods that obviate the effects of variation by mapping the variable behavior patterns to a unique identity with high accuracy. However, it has also exposed the learning systems to attacks that use updating mechanisms in learning by injecting imposter samples to deliberately drift the data to impostors’ patterns. Using the principles of adversarial drift, we develop a class of poisoning attacks, named Frog-Boiling …

A Framework Of Multi-Dimensional And Multi-Scale Modeling With Applications, Zilong Li

Doctoral Dissertations

In this dissertation, a framework for multi-dimensional and multi-scale modeling is proposed. The essential idea is based on oriented space curves, which can be represented as a 3D slender object or 1D step parameters. SMILES and Masks provide functionalities that extend slender objects into branched and other objects. We treat the conversion between 1D, 2D, 3D, and 4D representations as data unification. A mathematical analysis of different methods applied to helices (a special type of space curves) is also provided. Computational implementation utilizes Model-ViewController design principles to integrate data unification with graphical visualizations to create a dashboard. Applications of multi-dimensional …

Social Media Based Algorithmic Clinical Decision Support Learning From Behavioral Predispositions, Radhika V. Medury

Doctoral Dissertations

Behavioral disorders are disabilities characterized by an individual’s mood, thinking, and social interactions. The commonality of behavioral disorders amongst the United States population has increased in the last few years, with an estimated 50% of all Americans diagnosed with a behavioral disorder at some point in their lifetime. AttentionDeficit/Hyperactivity Disorder is one such behavioral disorder that is a severe public health concern because of its high prevalence, incurable nature, significant impact on domestic life, and peer relationships. Symptomatically, in theory, ADHD is characterized by inattention, hyperactivity, and impulsivity. Access to providers who can offer diagnosis and treat the disorder varies …

Adaptive Feature Engineering Modeling For Ultrasound Image Classification For Decision Support, Hatwib Mugasa

Doctoral Dissertations

Ultrasonography is considered a relatively safe option for the diagnosis of benign and malignant cancer lesions due to the low-energy sound waves used. However, the visual interpretation of the ultrasound images is time-consuming and usually has high false alerts due to speckle noise. Improved methods of collection image-based data have been proposed to reduce noise in the images; however, this has proved not to solve the problem due to the complex nature of images and the exponential growth of biomedical datasets. Secondly, the target class in real-world biomedical datasets, that is the focus of interest of a biopsy, is usually …

Feature Space Modeling For Accurate And Efficient Learning From Non-Stationary Data, Ayesha Akter

Doctoral Dissertations

A non-stationary dataset is one whose statistical properties such as the mean, variance, correlation, probability distribution, etc. change over a specific interval of time. On the contrary, a stationary dataset is one whose statistical properties remain constant over time. Apart from the volatile statistical properties, non-stationary data poses other challenges such as time and memory management due to the limitation of computational resources mostly caused by the recent advancements in data collection technologies which generate a variety of data at an alarming pace and volume. Additionally, when the collected data is complex, managing data complexity, emerging from its dimensionality and …

A Multicarrier Technique For Monte Carlo Simulation Of Electrothermal Transport In Nanoelectronics, Tyler J. Spence

Doctoral Dissertations

The field of microelectronics plays an important role in many areas of engineering and science, being ubiquitous in aerospace, industrial manufacturing, biotechnology, and many other fields. Today, many micro- and nanoscale electronic devices are integrated into one package. e capacity to simulate new devices accurately is critical to the engineering design process, as device engineers use simulations to predict performance characteristics and identify potential issues before fabrication. A problem of particular interest is the simulation of devices which exhibit exotic behaviors due to non-equilibrium thermodynamics and thermal effects such as self-heating. Frequently, it is desirable to predict the level of …

Increasing The Functionality Of Additive Manufacturing Through Atmospheric Microplasma And Nanotechnology, Alexander Jon Ulrich

Doctoral Dissertations

Additive Manufacturing (AM) has been changing the manufacturing landscape for the last 20 years. As the interest and demand for both polymer and metal-based 3D printing has grown, the materials and machines used have increased in capabilities. Despite the growth and advancement, there are still a large number of improvements that can be made to add functionality to 3D printers. Metal AM, a subcategory of 3D printing, has garnered much attention among industrial applications with large companies such as General Electric trying to implement the technology to increase innovative designs for motors. Some of the limitations on AM have to …

Organically Modified Inorganic Nanoparticles For Halochromic Ionophores And Nucleic Acids, William Johnston

Doctoral Dissertations

In this dissertation, four nanoparticle reaction schemes were developed as substrates for halochromic dyes or nucleic acids. The reaction schemes include the use of two substrates: silica nanoparticles and halloysite nanotubes. The protocols can incorporate silica (SiO2) nanoparticles and halloysite aluminosilicate (AlO2SiO2) nanotubes due to the presence of silane groups on the surface of either substrate. The reaction schemes are presented along with detailed protocols which were written to facilitate both reproducibility and to serve as an aid to further study and for easy modification of the protocol to suit a researcher's needs. The data is discussed in the materials …

Effective Magnetic And Electric Response Of Composite Materials, Mona Hassan Alsaleh

Doctoral Dissertations

Metamaterials (MMs) are nanocomposite materials consisting of metal-dielectric resonators much smaller in size than the wavelength of the incident light. Common examples of metamaterials are based on split ring resonators (SRRs), parallel wires or strips and fishnet structures. These types of materials are designed and fabricated in order to provide unique optical responses to the incident electromagnetic radiation that are not available in naturally existing materials. The MMs can exhibit unusual properties such as strong magnetism at terahertz (THz) and optical frequencies. Additionally, negative index materials (NIMs) can provide negative index of refraction which can be used in many applications …

Multidimensional Feature Engineering For Post-Translational Modification Prediction Problems, Norman Mapes Jr.

Doctoral Dissertations

Protein sequence data has been produced at an astounding speed. This creates an opportunity to characterize these proteins for the treatment of illness. A crucial characterization of proteins is their post translational modifications (PTM). There are 20 amino acids coded by DNA after coding (translation) nearly every protein is modified at an amino acid level. We focus on three specific PTMs. First is the bonding formed between two cysteine amino acids, thus introducing a loop to the straight chain of a protein. Second, we predict which cysteines can generally be modified (oxidized). Finally, we predict which lysine amino acids are …

Electromagnetic Wave-Matter Interactions In Complex Opto-Electronic Materials And Devices, Raj Kumar Vinnakota

Doctoral Dissertations

This dissertation explores the fundamentals of light-matter interaction towards applications in the field of Opto-electronic and plasmonic devices. In its core, this dissertation attempts and succeeds in the the modeling of light-matter interactions, which is of high importance for better understanding the rich physics underlying the dynamics of electromagnetic field interactions with charged particles. Here, we have developed a self-consistent multi-physics model of electromagnetism, semiconductor physics and thermal effects which can be readily applied to the field of plasmotronics and Selective Laser Melting (SLM). Plasmotronics; a sub-field of photonics has experienced a renaissance in recent years by providing a large …

A Complete Characterization Of Near Outer-Planar Graphs, Tanya Allen Lueder Genannt Luehr

Doctoral Dissertations

A graph is outer-planar (OP) if it has a plane embedding in which all of the vertices lie on the boundary of the outer face. A graph is near outer-planar (NOP) if it is edgeless or has an edge whose deletion results in an outer-planar graph. An edge of a non outer-planar graph whose removal results in an outer-planar graph is a vulnerable edge. This dissertation focuses on near outer-planar (NOP) graphs. We describe the class of all such graphs in terms of a finite list of excluded graphs, in a manner similar to the well-known Kuratowski Theorem for planar …

Spatiotemporal Subspace Feature Tracking By Mining Discriminatory Characteristics, Richard D. Appiah

Doctoral Dissertations

Recent advancements in data collection technologies have made it possible to collect heterogeneous data at complex levels of abstraction, and at an alarming pace and volume. Data mining, and most recently data science seek to discover hidden patterns and insights from these data by employing a variety of knowledge discovery techniques. At the core of these techniques is the selection and use of features, variables or properties upon which the data were acquired to facilitate effective data modeling. Selecting relevant features in data modeling is critical to ensure an overall model accuracy and optimal predictive performance of future effects. The …

Understanding The Surface Fouling Mechanism Of Ultrananocrystalline Diamond Microelectrodes Using Microfluidics For Neurochemical Detection, An-Yi Chang

Doctoral Dissertations

Electrochemical methods are widely used for chronic neurochemical sensing, but thus far, the organic solution redox reactions fouled the electrodes' surface. It caused the reduction of sensitivity and the electrodes' lifetime.

Here, we present the boron-doped nanocrystalline diamond microelectrodes (BDUNCD) as the next generation electrode material for neurochemical sensor development. To aid in long-term chronic monitoring of neurochemicals, they have a wide window of electrochemical potential, extremely low background current, and excellent chemical inertness. The main research goal is to reduce the rate of electrode fouling due to the reaction by-products, and significantly extend their useful lifetime.

We systematically characterize …

Electrochemical Behavior Of Dense Electrodes For Impedancemetric Nox Sensors, Nabamita Pal

Doctoral Dissertations

NOx (NO and NO2) exhaust gas sensors for diesel powered vehicles have traditionally consisted of porous platinum (Pt) electrodes along with a dense ZrO2 based electrolyte. Advancement in diesel engine technology results in lower NOx emissions. Although Pt is chemically and mechanically tolerant to the extreme exhaust gas environment, it is also a strong catalyst for oxygen reduction, which can interfere with the detection of NOx at concentrations below 100 ppm. Countering this behavior can add to the complexity and cost of the conventional NO x sensor design. Recent studies have shown that dense electrodes are less prone to heterogeneous …

Full Simulation For The Qweak Experiment At 1.16 And 0.877 Gev And Their Impact On Extracting The Pv Asymmetry In The N→Δ A Transition, Hend Abdullah Nuhait

Doctoral Dissertations

The Qweak project is seeking to find new physics beyond the Standard Model. It is aimed to measure the weak charge of the proton, which has never been measured, at 4% precision at low momentum transfer. The experiment is performed by scattering electrons from protons and exploiting parity violation in the weak interaction at low four-momentum transfer.

In this experiment, two measurements were considered: which are elastic and inelastic. The elastic is to measure the proton's weak charge. In addition, the inelastic asymmetry measurement, which will extract the low energy constant dΔ. That measurement works in the neutral current …

Motion-Capture-Based Hand Gesture Recognition For Computing And Control, Andrew Gardner

Doctoral Dissertations

This dissertation focuses on the study and development of algorithms that enable the analysis and recognition of hand gestures in a motion capture environment. Central to this work is the study of unlabeled point sets in a more abstract sense. Evaluations of proposed methods focus on examining their generalization to users not encountered during system training.

In an initial exploratory study, we compare various classification algorithms based upon multiple interpretations and feature transformations of point sets, including those based upon aggregate features (e.g. mean) and a pseudo-rasterization of the capture space. We find aggregate feature classifiers to be balanced across …

An Improved Imaging Method For Extended Targets, Sui Zhang

Doctoral Dissertations

The dissertation presents an improved method for the inverse scattering problem to obtain better numerical results. There are two main methods for solving the inverse problem: the direct imaging method and the iterative method. For the direct imaging method, we introduce the MUSIC (MUltiple SIgnal Classification) algorithm, the multi-tone method and the linear sampling method with different boundary conditions in different cases, which are the smooth case, the one corner case, and the multiple corners case. The dissertation introduces the relations between the far field data and the near field data.

When we use direct imaging methods for solving inverse …

Synthesis, Characterization, And Activity Of Co/Fe Alumina/Silica Supported Ft Catalysts And The Study Of Promoter Effect Of Ruthenium, Sunday Azubike Esumike

Doctoral Dissertations

The alumina and hybrid alumina-silica FT catalyst were prepared by one-step solgel/oil-drop methods using metal-nitrate-solutions (method-I), and nanoparticle-metaloxides (method-2). The nanoparticle-metal-oxides did not participate in solubility equilibria in contrast to metal nitrate in method-1 causing no metal ion seepage; therefore, method-2 yields higher XRF metal loading efficiency than method-1. The thermal analysis confirmed that the metal loading by method-1 and method-2 involved two different pathways. Method-1 involves solubility equilibria in the conversion of metal-nitrate to metal- hydroxide and finally to metal-oxide, while in method-2 nanoparticle-metal-oxide remained intact during sol-gel-oil-drop and calcination steps.

The alumina supported catalysts were dominated by γ-alumina …

A Study Of Mathematics Achievement, Placement, And Graduation Of Engineering Students, Sara Hahler Blazek

Doctoral Dissertations

The purpose of this study was to determine how background knowledge impacts freshmen engineering students' success at Louisiana Tech University in terms of grades in two different freshman classes and graduation. To determine what factors impact students, three different studies were implemented. The first study used linear regression to analyze which demographic and academic variables significantly impacted freshman math and engineering courses. Using regression discontinuity, the second study determined if the university's placement requirement for Pre-Calculus was appropriate. The final study analyzed factors that impact graduation for engineering students as well as other disciplines to determine which significant variables were …

Embedding Oriented Graphs In Books, Stacey R. Mcadams

Doctoral Dissertations

A book consists of a line L in [special characters omitted]3, called the spine, and a collection of half planes, called pages, whose common boundary is L. A k-book is book with k pages. A k-page book embedding is a continuous one-to-one mapping of a graph G into a book such that the vertices are mapped into L and the edges are each mapped to either the spine or a particular page, such that no two edges cross in any page. Each page contains a planar subgraph of G. The book thickness, denoted bt( …

Anxiolytic Effects Of Propranolol And Diphenoxylate On Mice And Automated Stretch-Attend Posture Analysis, Kevin Scott Holly

Doctoral Dissertations

The prevention of social anxiety, performance anxiety, and social phobia via the combination of two generic drugs, diphenoxylate HC1 (opioid) plus atropine sulfate (anticholinergic) and propranolol HCl (beta blocker) was evaluated in mice through behavioral studies. A patent published on a September 8, 2011 by Benjamin D. Holly, US 2011/0218215 Al, prompted the research. The drug combination of diphenoxylate and atropine plus propranolol could be an immediate treatment for patients suffering from acute phobic and social anxiety disorders. Demonstrating the anxiolytic effects of the treatment on mice would validate a mouse model for neuroscientist to be used to detect the …

Generalized Partial Directed Coherence And Centrality Measures In Brain Networks For Epileptogenic Focus Localization, Joshua Aaron Adkinson

Doctoral Dissertations

Accurate epileptogenic focus localization is required prior to surgical resection of brain tissue for treatment of patients with intractable temporal lobe epilepsy, a clinical need that is partially fulfilled to date through a subjective, and at times inconclusive, evaluation of the recorded electroencephalogram (EEG). Using brain connectivity analysis, patterns of causal interactions between brain regions were derived from multichannel EEG of 127 seizures in nine patients with focal, temporal lobe epilepsy (TLE). The statistically significant directed interactions in the reconstructed brain networks were estimated from three second intracranial multi-electrode EEG segments using the Generalized Partial Directed Coherence (GPDC) and validated …

Thermal Analysis In A Triple-Layered Skin Structure With Embedded Vasculature, Tumor, And Gold Nanoshells, Casey O. Orndorff

Doctoral Dissertations

In hyperthermia skin cancer treatment, the objective is to control laser heating of the tumor (target temperatures of 42-46 °C) so that the temperatures of the normal tissue surrounding the tumor remains low enough not to damage the normal tissue. However, obtaining accurate temperature distributions in living tissue related to hyperthermia skin cancer treatment without using an intruding sensor is a challenge. The objective of this dissertation research is to develop a mathematical model that can accurately predict the temperature distribution in the tumor region and surrounding normal tissue induced by laser irradiation. The model is based on a modified …

Direct And Inverse Scattering Problems For Domains With Multiple Corners, Jiang Yihong

Doctoral Dissertations

Direct and inverse scattering problems have wide applications in geographical exploration, radar, sonar, medical imaging and non-destructive testing. In many applications, the obstacles are not smooth. Corner singularity challenges the design of a forward solver. Also, the nonlinearity and ill-posedness of the inverse problem challenge the design of an efficient, robust and accurate imaging method.

This dissertation presents numerical methods for solving the direct and inverse scattering problems for domains with multiple corners. The acoustic wave is sent from the transducers, scattered by obstacles and received by the transducers. This forms the response matrix data. The goal for the direct …