Physical Sciences and Mathematics Commons^™

Geant4 Study Of Protons - Body Interactions, Omar Hernandez Rodriguez

Open Access Theses & Dissertations

Proton beam therapy for cancer treatment uses high-energy protons to destroy cancer cells, a problem that needs immediate attention is the determination of where in the body the protons are hitting, in real time, i.e. during the irradiation. One possibility is to pay attention to the gamma rays produced during the irradiation, and use the information they carry to infer the body part that produced the gamma ray.

This Thesis presents the results of an investigation of the interaction of protons with different body parts. Focusing on gamma ray-producing interactions, the goal is to determine the type of interaction that …

Improving Time-Of-Flight And Other Depth Images: Super-Resolution And Denoising Using Variational Methods, Salvador Canales Andrade

Open Access Theses & Dissertations

Depth information is a new important source of perception for machines, which allow them to have a better representation of the surroundings. The depth information provides a more precise map of the location of every object and surfaces in a space of interest in comparison with conventional cameras. Time of flight (ToF) cameras provide one of the techniques to acquire depth maps, however they produce low spatial resolution and noisy maps. This research proposes a framework to enhance and up-scale depth maps by using two different regularization terms: Total Generalized Variation (TGV) and Total Generalized Variation with a Structure Tensor …

Using Data Mining To Model Student Achievement On The 4th Grade Timss 2015 Mathematics Assessment: A Five Nation Sudy, Annette M. Siemssen

Open Access Theses & Dissertations

Data mining has been successfully used by financial and retail companies since the mid-1960's to create predictive models and reveal unexpected relationships. However, it remains underutilized as a tool in educational research. Large-scale standardized assessment programs such as the Trends in International Mathematics and Science Study (TIMSS) provide vast amounts of data with the potential for providing new insights in education. Five nations, the Republic of Korea, the United States, Germany, Kuwait, and Kazakhstan were selected based on General Response Style theory to represent a spectrum of cultural backgrounds, from acquiescent to midpoint to individualistic (Hastedt, D. & van de …

Towards Foundations Of Fuzzy Utility: Taking Fuzziness Into Account Naturally Leads To Intuitionistic Fuzzy Degrees, Christian Servin, Vladik Kreinovich

Departmental Technical Reports (CS)

The traditional utility-based decision making theory assumes that for every two alternatives, the user is either absolutely sure that the first alternative is better, or that the second alternative is better, or that the two alternatives are absolutely equivalent. In practice, when faced with alternatives of similar value, people are often not fully sure which of these alternatives is better. To describe different possible degrees of confidence, it is reasonable to use fuzzy logic techniques. In this paper, we show that, somewhat surprisingly, a reasonable fuzzy modification of the traditional utility elicitation procedure naturally leads to intuitionistic fuzzy degrees.

Geant4 Study Of A Gamma Ray Collimator For Proton Therapy, Selim Romero

Open Access Theses & Dissertations

This Thesis presents the results of an investigation of the use of collimators in proton therapy. The problem to solve is that in the proton therapy, we do not have the certainty if the target-tumor is receiving all the energy to destroy it or if we are really shooting at this one, so the remaining question is: where the beam is hitting? How to know it? to answer those questions our work has the propose of study proton therapy to determine where the proton interactions occur, these kinds of interactions usually produce gamma rays, and we simulated in GEANT4 the …

Mathematical Modeling Of Tumor Growth For Free-Boundary Problem By Enhanced Finite Volume Method, Mashriq Ahmed Saleh

Open Access Theses & Dissertations

Modeling tumor growth due to infiltration of immune cells presents several challenges in numerical computations. First, it involves multiple cell species whose total number should be a constant, due to the incompressibility assumption; second, by mapping the Eulerian coordinate of the free-boundary problem onto a fixed logical domain, geometric source terms appear and they need to be addressed properly in numerical methods. In this work, we use a simplified model that contains two species and prescribed infiltration velocity and to show that the conventional finite volume methods fail to preserve the trivial (constant) solutions. To this end, we introduce the …

Estimating The Optimal Cutoff Point For Logistic Regression, Zheng Zhang

Open Access Theses & Dissertations

Binary classification is one of the main themes of supervised learning. This research is concerned about determining the optimal cutoff point for the continuous-scaled outcomes (e.g., predicted probabilities) resulting from a classifier such as logistic regression. We make note of the fact that the cutoff point obtained from various methods is a statistic, which can be unstable with substantial variation. Nevertheless, due partly to complexity involved in estimating the cutpoint, there has been no formal study on the variance or standard error of the estimated cutoff point.

In this Thesis, a bootstrap aggregation method is put forward to estimate the …

Effects Of Gradation And Moisture Content On Resistivity Of Mechanically Stabilized Earth Wall Backfill Materials, Jose Luis Arciniega

Open Access Theses & Dissertations

The service life of mechanically stabilized earth (MSE) walls depends on the corrosion rate of the metallic reinforcement used in their construction. The resistivity of the backfill aggregates needs to be measured accurately in order to estimate realistically the corrosion rate of the reinforcement. Resistivity testing is usually performed using the traditional soil box on the portion of the aggregates that passes a No. 10 or No. 8 sieve to either select or reject the backfill. For a more reasonable characterization of the corrosivity of coarse backfills, it is desirable to use their actual gradations. To that end, several resistivity …

Gravitational Analysis And Fault Identification Within An Active Rift Basin: The Mesilla Valley Bolson In Western Texas - Southern New Mexico, Jose Pablo Cervantes

Open Access Theses & Dissertations

The metropolitan region of El Paso Texas and Ciudad Juárez, Chihuahua, located within the northern Chihuahua Desert, contains approximately two million inhabitants. The two main aquifers that supply groundwater to this region are the Mesilla and Hueco Bolsons. Both bolsons have been tapped for decades without sustainable recharge. This study's purpose is to use geophysical methods coupled with published geochemical analyses to determine the structural and stratigraphic controls on the quality and quantity of groundwater in the southern Mesilla Bolson.

The Mesilla Bolson is one of many fault-controlled basins within the Rio Grande Rift - southern Basin and Range. Faults …

Variety-Dependent Physiologic And Biochemical Effects Of Copper Nano Particles On Rosie And Green Bok Choy (Brassica Rapa) Phenotypes, Chaoyi Deng

Open Access Theses & Dissertations

The effects of Cu-based nanoparticles (NPs) in bok choy (Brassica rapa subsp. chinensis) are unknown. In this study, Rosie and Green, two varieties of bok choy, with different anthocyanin content, were cultivated for 70 days in soil amended with copper oxide nanoparticles (nano CuO), bulk copper oxide (bulk CuO) and copper chloride (CuCl2) at 75, 150, 300 and 600 mg Cu/kg soil. Cu and essential elements in tissues, and relative chlorophyll content, were determined. In both varieties, nano CuO treatments caused significantly more Cu uptake in roots and shoots, compared with bulk CuO and ion CuCl2 (p ≤ 0.05). Additionally, …

Hierarchical Multiplicity Control Methods For Linear Models, Dimuthu Dilshan Fernando

Open Access Theses & Dissertations

HypoThesis testing is a commonly used statistical inference technique on which a statement of the population is investigated through the evidence from a representative sample of the population. With simultaneous testing of more than one null hypotheses need for an appropriate multiple comparison method is essential. With motivation from the study of Bogomolov et al. (2017) we have modified a multiple comparison tree structure to build the required comparisons and focus on controlling the FWER (Family Wise Error Rate) using the Bonferroni procedure. The proposed method has advantages such as controlling the global error rates separately at each level, families …

Evaluating Fold And Thrust Systems Within An Inverted Basin: Indio Mounntains, West Texas, Myra Guerrero

Open Access Theses & Dissertations

Fold and thrust belts often are complicated by out of sequence thrust faulting and inverted basins display these structures particularly often due to reactivation of original normal faults as well as complex topographic evolution. The Indio Mountains lie along the northern margin of the Chihuahua trough which formed as a mid-Cretaceous extensional basin and was subsequently shortened during the Laramide orogeny, making the Indio Mountains an exceptional site for studies of structures produced by large scale basin inversion. This study focuses on the subsurface structures in a complexly imbricated thrust window developed along the paleo rift basin margin.

This study …

Attributes Of The Fisher Valley Megaflap And Comparison To The Gypsum Valley Megaflap, Paradox Basin, Utah And Colorado: Implications For Controls On Megaflap Formation, Kate Grisi

Open Access Theses & Dissertations

Megaflaps are panels of steeply dipping to overturned strata that extend kilometers up the side of a salt diapir or equivalent weld. They often form important components of salt-diapir related hydrocarbon systems, though little is known about their geologic characteristics or how they form. In this study, I collected structural, stratigraphic, and sedimentologic data of the Fisher Valley megaflap and compared these attributes to the previous studied Gypsum Valley megaflap to test the differential sediment loading model proposed for initiation of megaflap formation. This model predicts that the sediment source proximal megaflap of Fisher Valley should have started rotation earlier, …

Deep Learning Models For Scoring Protein-Ligand Interaction Energies, Md Mahmudulla Hassan

Open Access Theses & Dissertations

In recent years, the cheminformatics community has seen an increased success with machine learning-based scoring functions for estimating binding affinities. The prediction of protein-ligand binding affinities is crucial for drug discovery research. Many physics-based scoring functions have been developed over the years. Lately, machine learning approaches are proven to boost the performance of traditional scoring functions. In this study, two scoring functions were developed; one is based on the Convolutional Neural Networks and the other one, called DLSCORE, is based on an ensemble of fully connected neural networks. Both the models were trained on the refined PDBbind (v.2016) dataset using …

Matroid - Based Variable Selection For Complex Data Structures, Wimarsha Thathsarani Jayanetti

Open Access Theses & Dissertations

This research project has the objective to extend use of the matroid algorithm using statistically based criteria, Joint/Multivariate Cumulants (Speed, 1983) and Effective Dependence (Pena & Rodriguez, 2003) to capture linear as well as non-linear higher order dependencies. We also improve variable selection for complex data structures using the proposed matroid algorithm. The limiting distribution of the joint cumulant was defined using U-statistics theory by Hoeffding (1948). U-statistics variance as theorized by Hoeffding provide a lower bound for the estimated variance, and our simulation results justify the use of Hoeffding U-statistic variance for determining a threshold for joint cumulants deviation …

Analysis Of High Performance Scientific Programming Workflows, Withana Kankanamalage Umayanganie Klaassen

Open Access Theses & Dissertations

Substantial time is spent on building, optimizing and maintaining large-scale software that is run on supercomputers. However, little has been done to utilize overall resources efficiently when it comes to including expensive human resources. The community is beginning to acknowledge that optimizing the hardware performance such as speed and memory bottlenecks contributes less to the overall productivity than does the development lifecycle of high-performance scientific applications. Researchers are beginning to look at overall scientific workflows for high performance computing. Scientific programming productivity is measured by time and effort required to develop, configure, and maintain a simulation experiment and its constituent …

The Inverse And Direct Hofmeister Series Of Hen Egg White Lysozyme At Ph Below The Isoelectric Point (Pi) As Seen By Small Angle X-Ray Scattering(Saxs), Pawan Koirala

Open Access Theses & Dissertations

The structural changes of Hen Egg White Lysozyme (HEWL) in the intermediate stages leading up to Hofmeister anion-induced aggregation were measured using small-angle x-ray Scattering (SAXS). We used three concentrations of HEWL: 10mg/ml, 60mg/ml and 200mg/ml and two concentrations of salts: 0.1M and 1.0M, mostly in a Tris-buffer solution with a pH of 9.0. For 200mg/ml in Di-water solution, the scattering signal was best fit using an ellipsoidal form factor with equatorial radius of 28.4±0.1 Å and polar radius of 11.3±0.1 Å, and a screened Coulomb repulsive structure factor with an effective radius of 19.9±0.1 Å and protein surface charge …

Magnetic And Catalytic Properties Of Transition Metal Doped Mos2 Nanocrystals, Luis Martinez

Open Access Theses & Dissertations

Magnetism and catalytic activity of nanoscale layered two-dimensional (2D) transition metal dichalcogenides (TMDs) have gained an increasing research interest in the recent past. To broaden the current knowledge and understanding on this subject, in this work, together with my collaborators, I study the magnetic and electrocatalytic properties of hydrothermally grown pristine and transition metal doped (10% of Co, Ni, Fe and Mn) 2H-MoS2 nanosheets/nanocrystals (NCs), with the particle size of 25-30 nm. A broad range of experimental measurements such as x-ray diffraction, transmission electron microscopy, x-ray photo absorption spectroscopy, Raman spectroscopy, magnetic, catalytic and electron spin resonance have been employed …

Exposure Of Kidney Bean (Phaseolus Vulgaris) Plants To Coated And Uncoated Zinc Oxide Nanomaterials Under Different Soil Conditions: Effects On Plant Growth And Seed Quality, Illya Aidee Medina Velo

Open Access Theses & Dissertations

Soil exposure to engineered nanomaterials (NMs) occurs through the intentional use of nano-agrochemicals, incidental contamination from industrial-waste release, irrigation with wastewater and gray water, or amendment with NM-loaded sludge. Although there are several reports about the effects of NMs in terrestrial plants, there is still a lack of knowledge about the effects of NMs in crop plants and their edible portions.

Among the large list of produced NMs, it is estimated that 34,000 tons of ZnO NMs are produced yearly. Due to their growing applications in cosmetics and personal care products, there is a high possibility that the ZnO NMs …

Parallelization And Scalability Analysis Of The \\[1pc] 3d Spatially Variant Lattice Algorithm, Henry Roger Moncada Lopez

Open Access Theses & Dissertations

The purpose of this research is to design a faster implementation of an algorithm to generate 3D spatially variant lattices (SVL) and improve its performance when it is running on a parallel computer system. The algorithm is used to synthesize a SVL for a periodic structure. The algorithm has the ability to spatially vary the unit cell, the orientation of the unit cells, lattice spacing, fill fraction, material composition, and lattice symmetry. The algorithm produces a lattice that is smooth, continuous and free of defects. The lattice spacing remains strikingly uniform even when the lattice is spatially varied. This is …

Type-2 Fuzzy Analysis Explains Ubiquity Of Triangular And Trapezoid Membership Functions, Olga Kosheleva, Vladik Kreinovich, Shahnaz Shahbazova

Departmental Technical Reports (CS)

In principle, we can have many different membership functions. Interestingly, however, in many practical applications, triangular and trapezoidal membership functions are the most efficient ones. In this paper, we use fuzzy approach to explain this empirical phenomenon.

Facies Changes Associated With Formation Of An Extensive Salt Shoulder By The Coastal And Eolian Carmel And Entrada Formations, Gypsum Valley, Colorado, Ryan Burtron Ronson

Open Access Theses & Dissertations

A salt shoulder forms a zone at the margin of a salt diapir where that margin steps relatively abruptly inward. These shoulders form when the salt rise rate near the diapir margin substantially decreases or stops relative to the salt rise rate at the inboard central part of the diaper. Based on current models of interactions between these salt shoulders and overlying sediment, it was anticipated that the thickness changes of the Entrada and Carmel formations would be only gradual and that any notable thinning would take place proximal to the neck portion of the diapir that would still have …

Integrated Immunoassays On Paper/Polymer Hybrid Microfluidic Devices For Low-Cost Detection Of Disease Biomarkers, Sanjay Sharma Timilsina

Open Access Theses & Dissertations

Infectious diseases and cancers have been the major cause of global death and disability causing a significant impact on global health and economies. Enzyme-linked immunosorbent assay (ELISA) is one of the most widely used laboratory diagnostic methods for infectious diseases and cancer. ELISA detects proteins based on their binding to immobilized antibodies or antigen. Even though most ELISAs performed today in 96-well plates are well suited for high throughput assays, performing ELISA in low-resource settings is limited by several factors, such as long incubation time, large volumes of precious reagents, and well-equipped laboratories. Herein, we have developed multiple simple, miniaturized …

Geometry, Timing, And Kinematics Of Neogene Extensional And Transtensional Structures Of Southern Death Valley: Implications For Regional Reconstructions And A Corrective Method For Rigid Body Rotations, Zachariah Fleming

Open Access Theses & Dissertations

Chapter 1:Advancements in computing capabilities over the last decade have allowed for the routine creation of Structure from Motion-Multiview Stereo (SfM-MVS) terrain models that can serve as base for high resolution geologic mapping. Outcrops models developed from these systems are high-resolution, photo-realistic 3D base providing unprecedented capability for geometric analysis. Yet, before this technology becomes a mainstay of field geology, the potential errors associated with it must be well understood. Here, we compare orientation measurements from multi-point analyses on the SfM-MVS point clouds to those taken in the field with the objective of resolving the geometry of complex folds within …

Electrocatalysts Based On Organic Macrocycles For Electrochemical Water Splitting, Yanyu Wu

Open Access Theses & Dissertations

Water splitting, which is the dissociation of water into hydrogen and oxygen gases, can be separated into two half reactions corresponding to the hydrogen evolution reaction and oxygen evolution reaction (HER and OER, respectively). Both reactions offer a promising way for storing energy into the form of chemical bonds, which is an important strategy for the development of clean-energy technologies. A main area of interest while studying HER and OER is to design effective and robust electrocatalysts made from earth-abundant materials. This dissertation describes several homogeneous and heterogeneous systems for the electrocatalytic generation of hydrogen and oxygen gases.

In Chapter …

A Mixed Finite Element Method For The Coupling Of Linear Elasticity And Stokes Flow, Maranda Bean

Open Access Theses & Dissertations

The complex interaction between fluids and structures require the coupling the laws concerning structure mechanics and fluid dynamics and are of vital importance to many scientific and engineering fields. We propose a method for modeling the coupling of a linearly elastic solid and slow fluid flow modeled by Stokes equations. The model equations are expressed in terms of displacement, velocity and stress. With these primary variables, we use a single mixed finite element space based on the Hellinger-Reissner variational principle for linear elasticity to discretize the resulting system spatially. This results in more accurate approximations for stress than those obtained …

Investigating The 2016 Jackson, Wyoming Earthquake Sequence Using Waveform Cross-Correlation And Seismic Array Methods, Emily Jo Graves

Open Access Theses & Dissertations

During a visual inspection of PDAR data extracted for the catalog events, I observed additional, unreported events, which is to be expected during an energetic swarm or seismic sequence. The casual observation of missed events strongly implied that more such missed events could be found in the data, which could improve the completeness of the earthquake catalog for the Jackson, Wyoming area. Catalog completeness improves our assessment of a region's tectonic behavior and earthquake exposure. To search for recurring swarm or earthquake sequence behavior, I applied waveform correlation methods to scan nearly two decades of continuous PDAR waveforms, comparing to …

Grenvillian Tectonomagmatic Evolution Of Southwestern Laurentia; Virtual Tour Of Multidimensional Orders Of Scale; Two Methods To Describe The Vastness Of Time; Math Concepts Utilizing Google Earth; Systematic Approach To Motion Analyses; Mathematics And Earth Science-Based Knowledge And Learning, Anthony M. Alvarez

Open Access Theses & Dissertations

This Dissertation is the product of several individual multi-disciplinary investigations that cover a variety of topics in mathematics, physics, geology, and geoscience education. The first chapter formulates a better understanding of the timings, magma source, and relationships between dikes and associated magmatic bodies of the Red Bluff Granitic Complex to provide a clearer picture of the evolution of post-Grenville magmatism and tectonism of southwestern USA. The second chapter provides an improved method for representing spatial information in the form of a multidimensional virtual tour where the background map is used as a central object. The third chapter describes two methods …

Backward Elimination Algorithm For High Dimensional Variable Screening, Sophia Korkor Foli

Open Access Theses & Dissertations

In recent times, variable selection in high-dimensional data has become a challenging prob- lem. We investigate here a popular but classical variable screening method, the Back- ward Elimination (BE) in a high dimensional setup (small-n-large P). The BE method as a variable screening method reduces the dimension of small-n-large P data into a lower dimensional data and then established shrinkage methods such as: LASSO, SCAD and MCP can be applied directly. To overcome the problems in high dimensional data, Chen and Chen (2008) recently developed a family of Extended Bayesian Information Criterion (EBIC) which is consistent with finite sample properties …

Development Of A Dna Aptamer That Specifically Inhibits Human Carbonic Anhydrase Ii, Afroz Karim

Open Access Theses & Dissertations

Carbonic anhydrases (CA) are a family of enzymes that catalyze the rapid interconversion of carbon dioxide and water to bicarbonate. Carbonic anhydrase II is the most abundant protein in the cytosol. CA II inhibitors are emergent therapeutic targets for the development of antiglaucoma agents. Glaucoma is a disease affecting large number of people and characterized by an elevated intraocular pressure due to excessive secretion of aqueous humor. The enzyme CA II is responsible for the secretion of aqueous humor. Isoforms of CA II such as CA IV and CA I are present in many tissues and organs other than the …