Physical Sciences and Mathematics Commons^™

Complexity In Overmarsh Circulation, Jessica Chassereau Sullivan

Theses and Dissertations

Overmarsh circulation is highly complex with variations in current direction over very short timescales and flowpaths that differ substantially between flood and ebb cycles. Understanding such flow complexities in salt marshes is important because they inherently impact the distribution of sediment, larvae and nutrients throughout the marsh, and hence, the ecogeomorphic feedbacks that control landscape evolution. The purpose this Ph.D. research is to quantitatively evaluate the effects of salt marsh topography on overmarsh circulation in a Georgia salt marsh. This dissertation is comprised of three parts. First, digital elevation models (DEMs) were compared to characterize how well airborne lidar (light …

Illuminating The Interactions And Functions Of Glutaredoxins, Bola Proteins, And Erv1 In Iron Homeostasis, Adrian Colleen Dlouhy

Theses and Dissertations

Iron is a redox-active protein cofactor required for essential cellular functions such as respiration, however excess intracellular iron can generate damaging reactive oxygen species. Understanding how cells regulate iron levels is critical for treatment of human diseases that span from anemia to iron overload disorders. Glutaredoxins (Grxs) with a CGFS active site are highly conserved proteins shown to have roles in iron homeostasis and iron-sulfur cluster assembly, thus earning them the title “the Iron Whores”. They can exist either as a [2Fe-2S] cluster-bound dimer or an apo monomer, suggesting conservation of structure and function. In addition, Grxs interact with the …

Modeling And Computations Of Cellular Dynamics Using Complex-Fluid Models, Jia Zhao

Theses and Dissertations

Cells are fundamental units in all living organisms as all living organisms are made up of cells of different varieties. The study of cells is therefore an essential part of research in life science. Cells can be classified into two basic types: prokaryotic cells and eukaryotic cells. One typical organisms of prokaryotes is bacterium. And eukaryotes mainly consist of animal cells. In this thesis, we focus on developing predictive models mathematically to study bacteria colonies and animal cell mitotic dynamics.

Instead of living alone, bacteria usually survive in a biofilm, which is a microorganism where bacteria stick together by extracellular …

Neutrino And Antineutrino Induced Meson Production, Libo Jiang

Theses and Dissertations

Coherent meson production measurement is very important in physics research. First, the coherent pion production is a potential background to v oscillation in next generation of Long Base Line Experiment(ELBNF/DUNE); second, coherent pion and coherent p production provide a detailed test of CVC and PCAC hypothesis; third, coherent meson production can be used to monitor the neutrino and anti-neutrino fluxes in the experiment. This dissertation focuses on two parts: coherent pi production in NOMAD, and coherent p simulation using LBNF fluxes. With the NOMAD data, the ratio between cross-sections of coherent pi- and v charged current interactions was measured and …

Bayesian Semi- And Non-Parametric Analysis For Spatially Correlated Survival Data, Haiming Zhou

Theses and Dissertations

Flexible incorporation of both geographical patterning and risk effects in cancer survival models is becoming increasingly important, due in part to the recent availability of large cancer registries. The analysis of spatial survival data is challenged by the presence of spatial dependence and censoring for survival times. Accurately modeling the risk factors and geographical pattern that explain the differences in survival is particularly of interest. Within this dissertation, the first chapter reviews commonlyused baseline priors, semiparametric and nonparametric Bayesian survival models and recent approaches for accommodating spatial dependence, both conditional and marginal. The last three chapters contribute three flexible survival …

Propagated Image Segmentation Using Edge-Weighted Centroidal Voronoi Tessellation Based Methods, Youjie Zhou

Theses and Dissertations

Propagated image segmentation is the problem of utilizing the existing segmentation of an image for obtaining a new segmentation of, either a neighboring image in a sequence, or the same image but in different scales. We name these two cases as the inter-image propagation and the intra-image propagation respectively. The inter-image propagation is particularly important to material science, where efficient and accurate segmentation of a sequence of 2D serial-sectioned images of 3D material samples is an essential step to understand the underlying micro-structure and related physical properties. For natural images with objects in different scales, the intra-image propagation, where segmentations …

A Silylation-Based Kinetic Resolution Of Hydroxy Lactones And Lactams With Subsequent Mechanistic Investigations, Robert W. Clark

Theses and Dissertations

The work contained herein focuses on the methodology and design of new reactions for the production of stereoenriched compounds. The primary focus of research discussed is kinetic resolution, a classic and powerful methodology for the separation of a single enantiomer from a racemic mixture. In 2011, a silylation-based resolution catalyzed by a chiral isothiourea produced synthetically useful selectivity factors for mono-functional secondary alcohols. In chapter 2, this methodology was subsequently expanded to include α-hydroxy lactones with selectivity factors up to 100. This study resulted in the most selective reaction reported to date for the aforementioned silylation-based resolution. In addition to …

Assessing The Magnitude And Impact Of Seawater/Pore Water Exchange In Salt Marsh Systems, Carrie Lee Milliken

Theses and Dissertations

Submarine groundwater discharge is a hydrological process that is important to study and understand as it impacts biogeochemical processes and hydrological cycles. Particularly in coastal salt marsh systems, it is an important process to analyze as these systems serve as crucial interfaces between terrestrial and marine waters and particulates. There is evidence that these systems, typically thought to have little exchange across the interface due to impermeable sediments, could actually allow for significant flow of water and particulates at shallow depths. In order to measure and quantify this flow, a method using 224Ra as a tracer has been tested. The …

Trees, Partitions, And Other Combinatorial Structures, Heather Christina Smith

Theses and Dissertations

This dissertation contains work on three main topics.

Chapters 1 through 4 provide complexity results for the single cut-or-join model for genome rearrangement. Genomes will be represented by binary strings. Let S be a finite collection of binary strings, each of the same length. Define M to be the collection of medians – binary strings μ which minimize Sigma v belongs to S H(μ,v) where H is the Hamming distance. For any non-negative function f(x), define Z(f(x), S) to be (Sigma μ belongs to M) (Pi v belongs to S)f(H(μ,v)). We study the complexity of calculating Z(f(x), S), with respect …

The Development Of Efficient Geminal-Based Methods For Quantum Chemical Calculations, Brett Allen Cagg

Theses and Dissertations

Incorporation of electron correlation to improve the accuracy of computations remains a driving force in quantum chemical method development. Traditionally, electron correlation effects are divided into static and dynamic correlation parts, and the inclusion of both results in methods that are impractical for large chemical systems. The goal of this doctoral research is to develop a method that efficiently accounts for both components of electron correlation in a separate but balanced manner. The approach focuses on combining a geminal method, called the antisymmetrized product of singlet-type, strongly orthogonal geminals (SSG), with dynamic correlation by either density functionals or a recently …

Avoiding Doubled Words In Strings Of Symbols, Michael Lane

Theses and Dissertations

A word on the n-letter alphabet is a finite length string of symbols formed from a set of n letters. A word is doubled if every letter that appears in the word appears at least twice. A word w avoids a word u if there is no non-erasing homomorphism h (a map that respects concatenation) such that h (u) is a subword of w. Finally, a word w is n-avoidable if there is an infinite list of words on the n-letter alphabet that avoid w. In 1906, Thue showed that the simplest doubled word, namely xx, is 3-avoidable. In 1984, …

Integrated Assessment Of Interactions Between Surface Water And Groundwater Under Climate Variability And Change In The White Volta Basin, Ghana, Felix Mensah Oteng

Theses, Dissertations and Culminating Projects

The Nasia River, a tributary of the White Volta River system in Northern Ghana, is an important water resource for the area. In this research, a hydrological model that is able to simulate surface and subsurface flows in the Nasia catchment reasonably well was developed. The model was calibrated and verified using discharge and hydraulic head observations for the period 2000-2010. The complete simulation showed that the model was able to simulate the streamflow at the Nasia outlet quite well (Nash-Sutcliffe coefficient of 0.65, and correlation coefficient 0.805). The flow dynamics at three groundwater monitoring stations (HAP5, HAP 10, and …

Analysis And Visualization Of Flow Fields Using Information-Theoretic Techniques And Graph-Based Representations, Jun Ma

Dissertations, Master's Theses and Master's Reports - Open

Three-dimensional flow visualization plays an essential role in many areas of science and engineering, such as aero- and hydro-dynamical systems which dominate various physical and natural phenomena. For popular methods such as the streamline visualization to be effective, they should capture the underlying flow features while facilitating user observation and understanding of the flow field in a clear manner.

My research mainly focuses on the analysis and visualization of flow fields using various techniques, e.g. information-theoretic techniques and graph-based representations. Since the streamline visualization is a popular technique in flow field visualization, how to select good streamlines to capture flow …

Generating Plans In Concurrent, Probabilistic, Over-Subscribed Domains, Li Li

Dissertations, Master's Theses and Master's Reports - Open

Planning in realistic domains typically involves reasoning under uncertainty, operating under time and resource constraints, and finding the optimal subset of goals to work on. Creating optimal plans that consider all of these features is a computationally complex, challenging problem. This dissertation develops an AO* search based planner named CPOAO* (Concurrent, Probabilistic, Over-subscription AO*) which incorporates durative actions, time and resource constraints, concurrent execution, over-subscribed goals, and probabilistic actions. To handle concurrent actions, action combinations rather than individual actions are taken as plan steps. Plan optimization is explored by adding two novel aspects to plans. First, parallel steps that serve …

Enabling Techniques For Expressive Flow Field Visualization And Exploration, Jun Tao

Dissertations, Master's Theses and Master's Reports

Flow visualization plays an important role in many scientific and engineering disciplines such as climate modeling, turbulent combustion, and automobile design. The most common method for flow visualization is to display integral flow lines such as streamlines computed from particle tracing. Effective streamline visualization should capture flow patterns and display them with appropriate density, so that critical flow information can be visually acquired. In this dissertation, we present several approaches that facilitate expressive flow field visualization and exploration. First, we design a unified information-theoretic framework to model streamline selection and viewpoint selection as symmetric problems. Two interrelated information channels are …

The Mass Profile And Shape Of Bars In The Spitzer Survey Of Stellar Structure In Galaxies (S4g) : Search For An Age Indicator For Bars., Taehyun Kim, Kartik Sheth, Dimitri A. Gadotti, Myung Gyoon Lee, Dennis Zaritsky, Bruce G. Elmegreen, E. Athanassoula, Albert Bosma, Benne W. Holwerda, Luis C. Ho, Sebastien Comeron, Johan H. Knapen, Joannah Hinz, Juan Carlos Munoz-Mateos, Santiago Erroz-Ferrer, Ronald J. Buta, Minjin Kim, Eija Laurikainen, Heikki Salo, Barry F. Madore, Jarkko Laine, Karin Menendez-Delmestre, Michael Regan, Bonita De Swardt, Armando Gil De Paz, Mark Seibert, Trisha Mizusawa

Faculty and Staff Scholarship

We have measured the radial light profiles and global shapes of bars using two-dimensional 3.6μm image decompositions for 144 face-on barred galaxies from the Spitzer Survey of Stellar Structure in Galaxies. The bar surface brightness profile is correlated with the stellar mass and bulge-to-total (B/T) ratio of their host galaxies. Bars in massive and bulge-dominated galaxies (B/T > 0.2) show a flat profile, while bars in less massive, disk-dominated galaxies (B/T ∼ 0) show an exponential, disk-like profile with a wider spread in the radial profile than in the bulge-dominated galaxies. The global two-dimensional shapes of bars, however, are rectangular/boxy, independent …

The Contribution Of Non-Thermal And Advanced Oxidation Technologies Towards Dissipation Of Pesticide Residues, N. Misra

Articles

Background

The use of pesticides has stabilised the food production to a great extent and their usage cannot be avoided anymore. Nevertheless, common food processing operations always allowed dissipating pesticide residues in foods to some extent. Within the food science community and the food processing sector, non-thermal food technologies are being researched and commercialised at a great pace over the past three decades.

Scope and Approach

In this review we provide a critical analysis of the literature pertinent to the fate of pesticide residues during non-thermal processing of solid and liquid foods. We also identify the opportunities for further development …

Computational Development Of Selective Nnos Inhibitors: Binding Modes And Pharmacokinetic Considerations, Adam Curtin, Gemma K. Kinsella, John Stephens

Articles

Abstract: Neuronal nitric oxide synthase (nNOS) produces the key signalling mediator nitric oxide, (NO). This gaseous, free radical molecule modulates a vast array of biological processes, from vascular pressure to immune responses and neurological signalling cascades. Overproduction of NO has been implicated in conditions including Alzheimer’s disease, Parkinson’s disease and schizophrenia. Inhibition of nNOS therefore offers a potential therapeutic approach for treatment of these conditions. This endeavour is made more complex by the fact that there are two other isoforms of nitric oxide synthase (NOS), endothelial NOS (eNOS) and inducible NOS (iNOS). The selectivity of nNOS inhibitors is therefore a …

A Framework And System For A Multi-Model Decision Aid For Sustainable Farming Practices, Kasi Bharath Vegesana

Computational Modeling & Simulation Engineering Theses & Dissertations

Decision support systems (DSS) for farmers address the need for modeling multiple processes and scenarios that affect farmer decision making. Existing DSS have various drawbacks that stop them from being deployed as decision support tools. This research proposes a multi-model simulation framework that can be used to analyze farm management practices at the crop level, individual farm level and at the community level to show the impact and alternatives for smallholder farming practices. A generic crop growth model is proposed, based on existing equations. We run sensitivity analysis on the model to identify important variables. The outputs from the crop …

Modeling And Simulation Of Molecular Couette Flows And Related Flows, Wei Li

Mathematics & Statistics Theses & Dissertations

In this thesis, molecular Couette flow is clearly defined and the modeling and simulation of this kind of flow is systematically investigated. First, the integral equations for the velocity of gaseous Couette flow and related flows are derived from linearized Boltzmann BGK equation with Maxwell boundary condition and solved with high precision by using Chebyshev collocation and chunk-based collocation methods. The velocity profiles of gaseous Couette flows and related flows with a wide range of Knudsen number and the Maxwell boundary condition of various accommodation ratios are obtained. Moreover, the order of convergence of the numerical methods is also discussed …

De Novo Protein Structure Modeling And Energy Function Design, Lin Chen

Computer Science Theses & Dissertations

The two major challenges in protein structure prediction problems are (1) the lack of an accurate energy function and (2) the lack of an efficient search algorithm. A protein energy function accurately describing the interaction between residues is able to supervise the optimization of a protein conformation, as well as select native or native-like structures from numerous possible conformations. An efficient search algorithm must be able to reduce a conformational space to a reasonable size without missing the native conformation. My PhD research studies focused on these two directions.

A protein energy function—the distance and orientation dependent energy function of …

On The Uncertainty Of Sea-Ice Isostasy, Cathleen Geiger, Peter Wadhams, Hans-Reinhard Müller, Jacqueline Richter-Menge

Dartmouth Scholarship

During late winter 2007, coincident measurements of sea ice were collected using various sensors at an ice camp in the Beaufort Sea, Canadian Arctic. Analysis of the archived data provides new insight into sea-ice isostasy and its related R-factor through case studies at three scales using different combinations of snow and ice thickness components. At the smallest scale (<1 m; point scale), isostasy is not expected, so we calculate a residual and define this as �� (‘zjey’) to describe vertical displacement due to deformation. From 1 to 10 m length scales, we explore traditional isostasy and identify a specific sequence of thickness calculations which minimize freeboard and elevation uncertainty. An effective solution exists when the R-factor is allowed to vary: ranging from 2 to 12, with mean of 5.17, mode of 5.88 and skewed distribution. At regional scales, underwater, airborne and spaceborne platforms are always missing thickness variables from either above or below sea level. For such situations, realistic agreement is found by applying small-scale skewed ranges for the R-factor. These findings encourage a broader isostasy solution as a function of potential energy and length scale. Overall, results add insight to data collection strategies and metadata characteristics of different thickness products.

Mouse Aorta-Derived Mesenchymal Progenitor Cells Contribute To And Enhance The Immune Response Of Macrophage Cells Under Inflammatory Conditions, Jodi F. Evans Ph.D., Veronica Salvador, Sheela George, Cristina Trevino-Gutierrez, Catherine Nunez

Faculty Works: BCES (1999-2023)

Abstract

Introduction: Mesenchymal progenitor cells interact with immune cells and modulate inflammatory responses. The cellular characteristics required for this modulation are under fervent investigation. Upon interaction with macrophage cells, they can contribute to or suppress an inflammatory response. Current studies have focused on mesenchymal progenitors derived from bone marrow, adipose, and placenta. However, the arterial wall contains many mesenchymal progenitor cells, which during vascular disease progression have the potential to interact with macrophage cells. To examine the consequence of vascular-tissue progenitor cell-macrophage cell interactions in an inflammatory environment, we used a recently established mesenchymal progenitor cell line derived from the …

Acth Enhances Lipid Accumulation In Bone-Marrow Derived Mesenchymal Stem Cells Undergoing Adipogenesis, Jodi F. Evans Ph.D., Thomas Rhodes, Michelle Pazienza

Faculty Works: BCES (1999-2023)

ACTH is a major hormone of the stress axis or hypothalamic-pituitary-adrenal (HPA) axis. It is derived from pro-opiomelanocortin (POMC) the precursor to the melanocortin family of peptides. POMC produces the biologically active melanocortin peptides via a series of enzymatic steps in a tissue-specific manner, yielding the melanocyte-stimulating hormones (MSHs), corticotrophin (ACTH) and β-endorphin. The melanocortin system plays an imperative role in energy expenditure, insulin release and insulin sensitivity. Bone marrow derived mesenchymal stem cells circulate in the blood stream and as progenitor cells have the potential to differentiate into many cell types such as osteoblasts, chondrocytes and adipocytes. Here we …

Vascular Tissue-Resident Mesenchymal Stem Cells; Friend Or Foe?, Jodi F. Evans Ph.D., Heather Renna, Lauren Mchugh, Eddie Bochynski, Victoria Flemm

Faculty Works: BCES (1999-2023)

Mesenchymal stem cells (MSC) are ideal candidates for stem cell-based therapies of vascular inflammation. They are progenitor cells that can replace damaged cells and they can modulate immune response cells. MSC from bone marrow and adipose tissue regulate inflammation by promoting the switch of macrophage cell from an inflammatory to an anti-inflammatory phenotype. Much less is known about the tissue resident MSC’s and their interaction with macrophage cells. We hypothesized that aortaderived mesenchymal stem cells (mAo MSC) would also promote the expression of the antiinflammatory phenotype among macrophage cells. The interaction of mAo MSC with the macrophage was examined by …

Reconciling The Two Cultures : A Case Study Of The University Of Northern Iowa, Elizabeth Ann Collins

Dissertations and Theses @ UNI

In 1959, chemist and author Charles Percy Snow gave a Rede Lecture at the University of Cambridge in which he named “Two Cultures”—the sciences and the humanities—which, according to his experience as someone who worked in both, were at odds with one another. His words elicited impassioned responses from critics who either agreed with Snow, believing this to be a detriment to society, or vehemently disagreed, believing Snow’s statements to be unfounded, and even antagonistic. This conversation, which had also found relevance in the United States, continues to be important today, and has changed over the years as institutions of …

Matrix Multiplication, Trilinear Decompositions, Apa Algorithms, And Summation, Victor Pan

Publications and Research

Matrix multiplication (hereafter we use the acronym MM) is among the most fundamental operations of modern computations. The efficiency of its performance depends on various factors, in particular vectorization, data movement and arithmetic complexity of the computations, but here we focus just on the study of the arithmetic cost and the impact of this study on other areas of modern computing. In the early 1970s it was expected that the straightforward cubic time algorithm for MM will soon be accelerated to enable MM in nearly quadratic arithmetic time, with some far fetched implications. While pursuing this goal the mainstream research …

A Principle Of Economy Predicts The Functional Architecture Of Grid Cells, Xue-Xin Wei, Jason Prentice, Vijay Balasubramanian

Publications and Research

Grid cells in the brain respond when an animal occupies a periodic lattice of ‘grid fields’ during navigation. Grids are organized in modules with different periodicity. We propose that the grid system implements a hierarchical code for space that economizes the number of neurons required to encode location with a given resolution across a range equal to the largest period. This theory predicts that (i) grid fields should lie on a triangular lattice, (ii) grid scales should follow a geometric progression, (iii) the ratio between adjacent grid scales should be √e for idealized neurons, and lie between 1.4 and 1.7 …

Azimuthal Asymmetries And The Emergence Of “Collectivity” From Multi-Particle Correlations In High-Energy Pa Collisions, Adrian Dumitru, Larry Mclerran, Vladimir Skokov

Publications and Research

We show how angular asymmetries ∼ cos 2φ can arise in dipole scattering at high energies. We illustrate the effects due to anisotropic fluctuations of the saturation momentum of the target with a finite correlation length in the transverse impact parameter plane, i.e. from a domain-like structure. We compute the two-particle azimuthal cumulant in this model including both one-particle factorizable as well as genuine two-particle non-factorizable contributions to the two-particle cross section. We also compute the full BBGKY hierarchy for the four-particle azimuthal cumulant and find that only the fully factorizable contribution to c₂{4} is negative while …

Automated Computation Of Scattering Amplitudes From Integrand Reduction To Monte Carlo Tools, Hans Van Deurzen, Gionata Luisoni, Pierpaolo Mastrolia, Giovanni Ossola, Zhibai Zhang

Publications and Research

After a general introduction about the calculation of one-loop scattering amplitudes via integrand-level techniques, which led to the construction of efficient and automated computational tools for NLO predictions, we briefly describe an approach to the reduction of scattering amplitudes based on integrand-level reduction via multivariate polynomial division also applicable beyond one-loop amplitudes. We also review the main features of the GoSam 2.0 automated framework for NLO calculations and show some of its application to Standard Model processes involving the production massive particles, such as the Higgs boson or top-quark pairs, obtained embedding of the virtual amplitudes produced by GoSam within …