Physical Sciences and Mathematics Commons^™

Multi-Scale Modeling Of Microbial Defection In The Presence Of Antibiotics, Darshan Dilip Nahar

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Limited environmental resources push life into competition. In terms of microbes, we assume that the only goal is to grow and competition means to grow faster than the peers. Organisms tend to adapt to their environmental conditions and improve their efficiency in using the common resources to grow faster. While different organisms compete they engage into various social behaviors like cooperation to work together towards a common goal, e.g., production of public goods that benefits the entire population. Hence a part of the resources at hand is dedicated to participate in cooperative activities if the cost-to-benefit ratio is less than …

Pathway Pioneer: Heterogeneous Server Architecture For Scientific Visualization And Pathway Search In Metabolic Network Using Informed Search, Vipul Kantilal Oswal

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

PathwayPioneer is a website to visualize the biological models. The complex metabolic models are hard to perceive when read through text format. It is even more difficult to understand the flow of network and different subsystem or pathways. PathwayPioneer organizes different subsystems into simple graphical representation. We simplify the complex network based on subsystem and compartment. Users can do computation (flux balance analysis) through the user interface and perceive the changed model visually. Our system is one of its kind to handle large model files with quick response time.

Biologists are often interested in knowing different alternative pathways targeting a …

Multiversejava, Vishal Sharma

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Sequenced semantics, which was first proposed in the context of temporal databases, is the semantics for the evaluation of a program on values annotated with time metadata. The time metadata records when each value is “live” (is valid or has existence). Sequenced semantics stipulates that a computation on values annotated with temporal metadata must be equivalent to, in effect, running the computation at every time point with only the values alive at that time. Sequenced semantics is challenging to program because it is more than just a re-interpretation of the run-time behavior of a program; for instance, a sequenced “if-else” …

The Kimama Core: A 6.4 Ma Record Of Volcanism, Sedimentation, And Magma Petrogenesis On The Axial Volcanic High, Snake River Plain, Id, Katherine Elizabeth Potter

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Snake River Plain (SRP) is one of the best-preserved examples of continental hotspot volcanis, with a continuous record of volcanism that extends over 16 Ma to the present. Yellowstone-Snake River Plain records the migration of plume-tail volcanism from inception at the Bruneau-Jarbridge caldera complex at 12.6 Ma to its present locus, under the Yellowstone Plateau.

Records kept by the Snake River Plain volcanic actions include rhyolite lavas and ignimbritesm minor coeval basalts, and an overlying veneer of younger basalts. The central SRP has received comparatively little attention in the past. The Kimama core hole was drilled as part of …

Landscape Evolution Of The Needles Fault Zone, Utah, Investigated Through Chronostratigraphic And Terrain Analyses, Faye L. Geiger

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Arcing eastward from the deep gorge of Cataract Canyon on the Colorado River is a series of aligned valleys (graben) and ridges (horst). This unusual landscape has formed as subsurface salt deforms toward the river and dissolves away, causing the overlying rocks to fault, slide, and subside. Geologists have long been interested in this actively evolving area they call the Needles fault zone, because understanding its mechanics and origin may shed light on how faults work in general and similar, yet inaccessible places like offshore rift zones or even the surface of the Moon. Despite this interest, the timing and …

In Situ Stress And Geology From The Mh-2 Borehole, Mountain Home, Idaho: Implications For Geothermal Exploration From Fractures, Rock Properties, And Geomechanics, James Andrew Kessler

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Geothermal energy is being explored as a supplement to traditional fossil fuel resources to meet growing energy demand and reduce carbon emissions. Geothermal energy plants harvest heat stored in the Earth’s subsurface by bringing high temperature fluids to the surface and generating steam to produce electricity. Development of geothermal resources is often inhibited by large upfront risk and expense. Successful mitigation of those costs and risks begins with efficient characterization of the resource before development. A typically successful geothermal reservoir consists of a fractured reservoir that conducts hydrothermal fluids and a cap rock seal to limit convective heat loss through …

Automated Reverse Engineering Of Malware To Develop Network Signatures To Match With Known Network Signatures, Dan Sinema

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Illicit software that seeks to steal user information, deny service, or cause general mayhem on computer networks is often discovered after the damage has been done. The ability to discover network behavior of software before a computer network is utilized would allow administrators to protect and preserve valuable resources. Static reverse engineering is the process of discovering in a offline environment how a software application is built and how it will behave. By automating static reverse engineering, software behavior can be discovered before it is executed on client devices. Fingerprints are then built from the discovered behavior which is matched …

Are Experimentally Derived Estimates Of Thermal Tolerance Useful In Interpreting Species Distribution Models, Iva Sokolovska

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Species distribution models are frequently used in ecology to predict the spatial and temporal occurrence of organisms. Direct interpretation of these models assumes that the relationships between the organisms and their environment are manifestations of causal mechanisms. However, in general, the mechanisms producing these associations have not been experimentally validated, which questions our confidence in their interpretation and application. Temperature is one of the most important factors influencing the fitness and distribution of aquatic organisms, and studying the thermal physiology of aquatic invertebrates could provide a useful approach for validating predictions of the species distribution models.

Experimental thermal tolerance studies, …

Hamiltonicity, Pancyclicity, And Cycle Extendability In Graphs, Deborah C. Arangno

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A significant portion of Graph Theory is devoted to determining the characteristics which guarantee the existence of long cycles.

Long cycles have roles in applications to civil engineering, chemistry, and communications, among many others, but the problem, in and of itself, of determining whether a graph has a cycle of some fixed and typically large length is one of the most important problems of both pure Mathematics and Computer Science.

A cycle containing all the vertices of the graph is called a Hamiltonian cycle, and a graph which possesses such a cycle is said to be Hamiltonian. If …

Family-Wise Error Rate Control In Quantitative Trait Loci (Qtl) Mapping And Gene Ontology Graphs With Remarks On Family Selection, Garrett Saunders

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

One of the great aims of statistics, the science of collecting, analyzing, and interpreting data, is to protect against the probability of falsely rejecting an accepted claim, or hypothesis, given observed data stemming from some experiment. This is generally known as protecting against a Type I Error, or controlling the Type I Error rate. The extension of this protection against Type I Errors to the situation where thousands upon thousands of hypotheses are examined simultaneously is known as multiple hypothesis testing. This dissertation presents an improvement to an existing multiple hypothesis testing approach, the Focus Level method, specific to gene …

Traditional Lecture Versus An Activity Approach For Teaching Statistics: A Comparison Of Outcomes, Jennifer L. Loveland

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Many educational researchers have proposed teaching statistics with less lecture and more active learning methods. However, there are only a few comparative studies that have taught one section of statistics with lectures and one section with activity-based methods; of those studies, the results are contradictory. To address the need for more research on the actual effectiveness of active learning methods in introductory statistics, this research study was undertaken.

An introductory, university level course was divided into two sections. One section was taught entirely with traditional lecture. The other section was taught using active learning methods and a minimal amount of …

Rock Strength Of Caprock Seal Lithologies: Evidence For Past Seal Failure, Migration Of Fluids And The Analysis Of The Reservoir Seal Interface In Outcrop And The Subsurface, Elizabeth Sandra Petrie

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Scientists have proposed that in order to avoid damaging climate change further accumulations of anthropogenic atmospheric carbon dioxide (CO₂) must be limited. One of several proposed techniques for reducing the amount CO₂ reaching the atmosphere is carbon capture and storage (CCS). This emerging technology stores CO₂ Emissions captured from large point sources (i.e. power plants or industrial facilities), in deep geologic formations, including depleted hydrocarbon reservoirs and saline aquifers. For successful CCS design, implementation and appropriate site selection and subsurface trapping mechanisms must be ensured over the 100's to 1000's of year timescale.

A key component …

Detailed Analysis Of The Domains Of Mtr4 And How They Regulate Helicase Activity, Lacy Leigh Taylor

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The central dogma states that DNA is transcribed into RNA, which is then translated into protein. This concept conveys a minimal view of the role of RNA, portraying it simply as an intermediary between DNA and protein. However, it is now known that the role of RNA in the cell is critical in regulating protein expression both directly and indirectly. RNA in the cell typically goes through modifications to become active (on) and inactive (off) to eventually become targeted for degradation and start the cycle all over again. The protein complex that regulates the proper maturation and degradation of RNA …

Decision Making Using Trust And Risk In Self-Adaptive Agent Organization, Kamilia Ahmadi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Interaction between agents is one of the key factors in multi-agent societies in order to cooperatively execute complex tasks which are beyond the capability of a single agent. In the self-adaptation society, agents try to keep best neighbors around themselves. Agents use history of past iterations to evaluate their neighbors and locally modify their structural links. Main characteristics of this model are its decentralization, dynamicity and no need of external control. This research at first deals with implementing self-adaptive agent organization. Then it focuses on evaluating cooperation peers in decision making. Trust as an evaluation mechanism lies at the core …

Physically Based Preconditioning Techniques Applied To The First Order Particle Transport And To Fluid Transport In Porous Media, Michael Rigley

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Solving linear systems is at the heart of many scientific applications from the PreAlgebra's student solving for x and y for basic geometry problems to the computational scientist solving billions of equations with billions of variables for weather forecasting, modeling fusion reactions, or web search algorithms. In this study we look at improving the efficiency of solving large linear systems that result from two applications. The first includes linear systems that result from solving differential equations for the movement of atomic particles in particle emitting, void, and absorbing regions. The second includes solving linear systems that result from solving differential …

Fault And Fluid Interactions In The Elsinore Fault-West Salton Detachment Fault Damage Zones, Agua Caliente County Park, California, Rebekah Erin Wood

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This study area provides a unique opportunity to study the intersection of the Elsinore and West Salton detachment faults in southern California, effusing warm springs, and alteration products in the midst of the fault intersection. Structural mapping and compiling previous maps supply an interpretation of the fault zone geometries within the Tierra Blanca Mountains. Geochemical analysis of the crystalline basement and altered protolith help determine the effects of faulting and fluid flow in the study area. In the Tierra Blanca Mountains, the Elsinore strike-slip fault system transitions from the double-stranded Julian segment and Earthquake Valley fault in the northwest, to …

Implementation And Application Of The Curds And Whey Algorithm To Regression Problems, John Kidd

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A common statistical problem is trying to predict two or more variables using a set of predictor variables. The simplest model for this situation is called multivariate linear regression. This method uses each set of predictor variables to predict each of the response variables separately. This approach seems counter-intuitive as any possible relationship between the variables being predicted is ignored.

Breiman and Friedman found a way to take advantage of relationships among the response variables to increase the accuracy of the predictions for each of the predicted variables with an algorithm they called Curds and
Whey. It uses other statistical …

Computational Topics In Lie Theory And Representation Theory, Thomas J. Apedaile

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The computer algebra system Maple contains a basic set of commands for working with Lie algebras and matrices. The purpose of this thesis was to extend the functionality of these Maple packages in a number of important areas. First, programs for defining multiplication in several different types of algebras were created to allow users to perform a wider variety of calculations. Second, commands were created for calculating some basic properties of matrix representations of semisimple Lie algebras. This allows a user to identify a given matrix representation by a collection of integers which do not change when the basis of …

Family-Wise Error Rate Control In Quantitative Trait Loci (Qtl) Mapping And Gene Ontology Graphs With Remarks On Family Selection, Garrett Saunders

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

One of the great aims of statistics, the science of collecting, analyzing, and interpreting data, is to protect against the probability of falsely rejecting an accepted claim, or hypothesis, given observed data stemming from some experiment. This is generally known as protecting against a Type I Error, or controlling the Type I Error rate. The extension of this protection against Type I Errors to the situation where thousands upon thousands of hypothesis are examined simultaneously is known as multiple hypothesis testing. This dissertation presents an improvement to an existing multiple hypothesis testing approach, the Focus Level method, specific to gene …

Gravitational Wave Astrophysics With Compact Binary Systems, Eric Addison

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Gravitational waves are ripples in the fabric of spacetime that convey information about changing gravitational fields. Large-scale detection projects are currently in operation, and more advanced detectors are being designed and built. Though we have yet to make a direct detection of a gravitational wave signal, upgrades to current detectors are expected to bring the first detections within the next year or two.

Gravitational waves will bring us information about astrophysical phenomena that is complementary to the information gained from photon-based observations (e.g., telescopes and radio receivers). One of the primary sources of gravitational waves are binary systems: two massive …

A Computer-Aided Training (Cat) System For Short Track Speed Skating, Chenguang Liu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Short track speed skating was adopted by the International Skating Union in 1967, and upgraded to full winter Olympic sport status in 1992. Even though its history is short compared with long track speed skating, it became popular around the world because it is more intense and more entertaining for audiences. The demands of having a CAT system for gathering and analyzing competition data automatically is raising drastically due to its growing popularity all around the world.

There have been some commercial systems for some other sports, which are able to provide extrinsic feedback information to coaches and athletes. However, …

Molecular Systematics, Historical Biogeography, And Evolution Of Spider Wasps (Hymenoptera: Pompilidae), Juanita Rodriguez

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The study of the diversity and classification of any group of organisms provides a foundation for further scientific studies in ecology, evolution, and conservation. Insects are among the most diverse organisms that inhabit the planet, but knowledge of their diversity and classification is still limited. One understudied group of insects is spider wasps. These are solitary parasitoids that use one spider to lay a single egg. There are approximately 5,000 described species, and many more to be described. Unfortunately, fewer than 10 scientists worldwide study these insects. One reason the group has not been very well studied is the difficulty …

Pathway Pioneer: A Web-Based Graphical Tool For The Organization And Flux Analysis Of Metabolic Networks, Sumit Kumar Singh

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Every so often the field of genome-scale metabolic networks undergoes radical changes, each bringing its own complexity and challenges. The existing visualization tools, owing to their inability to assist in generating layouts suitable for easy readability and conceptualization, hinder further advancement. The lack of in-depth comprehensible representation of the intricacies of interaction and arrangements within the network topology prevents researchers from being able to advance at a faster speed despite the growing number of networks and systems. The far and wide diverse standards, layout schemas and network formats of the biological realm contribute to the existing challenges of developing visualization …

Pathway Pioneer: A Web-Based Metabolic Network Layout Extension, Harsh Dosi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The number and complexity of genome-scale metabolic networks have seen a rapid growth in the past 10 years. Today, more than 450 genome-scale metabolic reconstructions of biological systems are characterized and existing models are extended. With the growing influence of these reconstructions on biomedical and biological research, the field has observed a shift from an inward focus on method development to an outward focus on application development.

Static state analysis of metabolic networks in textual format is too cumbersome and time consuming. In addition, visualization and arrangement of these networks to facilitate their analysis is an open research problem. A …

Mesoscale Deformational Features Near Outcrop Analogs Of A Reservoir-Seal Interface: Implications For Seal Failure, Santiago L. Flores

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The boundary that separates reservoir rocks from caprock seals is generally considered a flow barrier for reservoir fluids. Buoyant fluids do no flow through the caprocks because they have low permeability and molecular forces at the base of the caprock resist upward flow. Deformation at the reservoir/caprock boundary may include fractures that increase permeability and lessen the effect of the molecular forces.

The injection and storage of carbon dioxide (CO₂) in porous sandstone with effective top seals below earth’s surface is a possible solution for reducing the amount of human-created CO₂ in the atmosphere. Uplift and erosion …

Beetles, Fungi And Trees: A Story For The Ages? Modeling And Projecting The Multipartite Symbiosis Between The Mountain Pine Beetle, Dendroctonus Ponderosae, And Its Fungal Symbionts, Grosmannia Clavigera And Ophiostoma Montium, Audrey L. Addison

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As data collection and modeling improve, ecologists increasingly discover that interspecies dynamics greatly affect the success of individual species. Models accounting for the dynamics of multiple species are becoming more important. In this work, we explore the relationship between mountain pine beetle (MPB, Dendroctonus ponderosae Hopkins) and two mutualistic fungi, Grosmannia clavigera and Ophiostoma montium. These species are involved in a multipartite symbiosis, critical to the survival of MPB, in which each species benefits.

Extensive phenological modeling has been done to determine how temperature affects the timing of life events and cold-weather mortality of MPB. The fungi have also …

Soil Water Flux Estimates From Streaming Potential And Penta-Needle Heat Pulse Probe Measurements, Pawel J. Szafruga

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Growing populations, coupled with climate change and resource depletion, have heightened concern about water management. The growing need to better manage agricultural systems, including irrigation and fertilizer application, as well the lasting consequences of excess application of nitrogen and other nutrients, could be remedied with an improved method to monitor soil water movement. Despite huge technological advances, a tool to measure soil water flow at the low rates found in the field has not been developed. Current methods lack the precision to provide the needed accuracy to fully understand soil-water dynamics, as well as the ability to provide instantaneous information. …

Structure And Multi-Center Bonding: From Atomic Clusters To Solid Phase Materials, Timur R. Galeev

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work presented in this dissertation has been focused on structure, stability, and chemical bonding of atomic clusters and solid-state compounds. The common thread was development of theoretical models and methods capable of interpreting bonding and hence, structures of these species. A major part of this work presents joint experimental and theoretical studies of a large series of doped boron clusters. The dissertation introduces a new theoretical tool for interpretation of bonding of solid phase materials in chemically intuitive terms of localized and multi-center bonds. Understanding how interactions between atoms in sub-nano clusters and solid-state compounds determine their structures, physical …

Computational Models Of Intracellular And Intercellular Processes In Developmental Biology, Ahmadreza Ghaffarizadeh

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Systems biology takes a holistic approach to biological questions as it applies mathematical modeling to link and understand the interaction of components in complex biological systems. Multiscale modeling is the only method that can fully accomplish this aim. Mutliscale models consider processes at different levels that are coupled within the modeling framework. A first requirement in creating such models is a clear understanding of processes that operate at each level. This research focuses on modeling aspects of biological development as a complex process that occurs at many scales. Two of these scales were considered in this work: cellular differentiation, the …

Statistical Modeling, Exploration, And Visualization Of Snow Water Equivalent Data, James Beguah Odei

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Due to a continual increase in the demand for water as well as an ongoing regional drought, there is an imminent need to monitor and forecast water resources in the Western United States. In particular, water resources in the Intermountain West rely heavily on snow water storage. Thus, the need to improve seasonal forecasts of snowpack and considering new techniques would allow water resources to be more effectively managed throughout the entire water-year. Many available models used in forecasting snow water equivalent (SWE) measurements require delicate calibrations.

In contrast to the physical SWE models most commonly used for forecasting, we …