Physical Sciences and Mathematics Commons^™

Exploration Of Nucleic Acid Hydrogran Bonding Using Molecular Mechanics And Dft Calculations, Simi Kaur

Biological Sciences

Many recent theoretical and experimental techniques have been developed to probe the structurefunction relationships of complex biomolecules. The roles of RNAs are dependent upon various intricate structural motifs and interactions, including hairpins, pseudoknots, long range territory contacts, bulges and internal loops, that are not easily captured by these methods. We had previously developed an enhanced replica exchange molecular dynamics method that incorporated secondary structure information in the form of distance restraints in order to effectively overcome kinetic barriers and sample conformational space. In several structures, restrained RNA base pairs near large bulges displayed a preference for stacking over hydrogen bonding …

Wrinkles In Time : An Exploration Of Non-Uniform Temporal Resolution In Network Data, Daniel John Ditursi

Legacy Theses & Dissertations (2009 - 2024)

The continued proliferation of timestamped network data demands increasing sophistication in the analysis of that data. In particular, the literature amply demonstrates that the choice of temporal resolution has a profound impact on the solutions produced by many different methods in this domain -- answers differ when data is viewed second-by-second as opposed to week-by-week. Additionally, research also shows quite clearly that the rates at which network events happen are not constant -- some times are "faster" or "slower" than others, and these variations are not necessarily predictable. Given the above, it is clear that there must be problem settings …

Pose Based Human Activity Recognition, Wenbo Li

Legacy Theses & Dissertations (2009 - 2024)

Pose based human activity recognition is an important step towards video understanding. The last decade has witnessed the great progress in this field which is driven by multiple technical innovations, i.e., kinect, pose estimation techniques, deep learning, etc.

Fingerprint Analysis: Moving Toward Multiattribute Determination Via Individual Markers, Morgan Eldridge

Chemistry

Forensic science will be forever revolutionized if law enforcement can identify personal attributes of a person of interest solely from a fingerprint. For the past five years, the goal of the Halamek Lab has been to establish a way to identify originator attributes. Specifically, biological sex has been accomplished and the ultimate goal is to continue to accomplish this using a single analyte for each. To date, an enzymatic assay and two chemical assays have been developed for the analysis of multiple analytes. In this thesis, an additional enzymatic assay has been developed. This time, however, the assay utilizes only …

Potential Impact Of Climate Change On The Distribution Of Alpine Tundra In The Adirondack Mountains Of New York, Terry Allard

Atmospheric & Environmental Sciences

Given the potential for significant changes in climate over the next century, understanding how biome locations may shift in response to these changes may be useful in informing conservation efforts. In this work the potential effect of climate change on the distribution of alpine tundra in the Adirondack Mountains of New York is examined. The ecological niche modelling software Maxent was used to analyze the distribution of alpine tundra relative to 30 year 800m PRISM climate normal data and terrain aspect over the Adirondacks. Random points from surveyed areas of alpine tundra in the Adirondacks were used as presence data …

Antecedent North Pacific Jet Regimes Conducive To The Development Of Cool Season Continental U.S. Tornado Outbreaks, Jessica Blair

Atmospheric & Environmental Sciences

The occurrence of tornado outbreaks are often associated with considerable societal and economic impacts. The U.S. averages nearly 1000 tornadoes per year that result in 1500 injuries and 80 fatalities, many of which are associated with outbreak days. Additionally, one outbreak alone can cause millions of dollars in property damage. The location of these outbreaks can vary temporally throughout the cool season (September–May) and can vary substantially in terms of their severity.

This study focuses on continental U.S. tornado outbreaks during the cool season and their relation to the state and evolution of the North Pacific jet (NPJ) stream 0–5 …

Weyl Groups And The Nil-Hecke Algebra, Arta Holaj

Mathematics and Statistics

We begin this paper with a short survey on finite reflection groups. First we establish what a reflection in Euclidean space is. Then we introduce a root system, which is then partitioned into two sets: one of positive roots and one with negative roots. Th is articulates our understanding of groups generated by simple reflections. Furthermore, we develop our insight to Weyl groups and crystallographic groups before exploring crystallographic root systems. The section section of this paper examines the twisted group algebra along with the Demazure element Xi and the Demazure-Lusztig element Ti. Lastly, the third section of this paper …

Raman Spectroscopic Examination Of Bloodstains For Forensic Purposes : Background And Race Determination, Ewelina M. Mistek

Legacy Theses & Dissertations (2009 - 2024)

Chapter 1 of this thesis critically overviews recent developments in forensic trace evidence analysis since 2016. It covers improvements to existing techniques as well as new methods for the analysis of fibers, hair, paint, glass, gunshot residue (GSR), and explosives.

Characterizing Body Fluids With Raman Spectroscopy : Towards Real World Application, Marisia Ann Fikiet

Legacy Theses & Dissertations (2009 - 2024)

This project continues the research on a new method of body fluid identification and furthers its field capabilities. This method of identification uses Raman spectroscopy and advanced chemometrics to distinguish between body fluids. It is an improvement on current methods because it is confirmatory, non-destructive, and has simple sample preparation. The first objective of this research is to create a model for differentiating body fluids for a new desktop instrument. It was determined that due to resolution differences from a research grade instrument, a new model needed to be made for this the desktop instrument. This model will be able …

16-Day Free-Traveling Rossby Waves And Their Association With Northern Hemisphere Blocking, Ernesto W. Findlay

Legacy Theses & Dissertations (2009 - 2024)

An analysis of the 16-day free Rossby wave is performed. The behavior of this wave includes a barotropic vertical structure that is independent of local forcing. An Empirical Orthogonal Function (EOF) analysis was performed on 15–30-day filtered geopotential height anomalies to extract the spatial patterns of the wave. Results show that the first two EOFs are in quadrature with each other, representing a westward moving signal with an average period of around 23 days and a phase velocity of. The Principal Components (PCs) from these EOFs were used to construct a 16-day wave index, which was employed as a tool …

Synthesis And Adsorption Experiments With Metal-Organic Frameworks For High School And Undergraduate Laboratory Settings, Kate Holley

Legacy Theses & Dissertations (2009 - 2024)

Seven experiments are described and outlined here that introduce high school and undergraduate students to metal–organic frameworks (MOFs) and their applications. The experiments were designed to be completed with basic laboratory equipment and supplies and without the use of expensive characterization instruments, simulating typical high school chemistry laboratory conditions. Students synthesized two well-known MOFs, HKUST-1 and aluminum fumarate, using simple, safe, and rapid methods (fast enough to be performed within the time constrains of a typical high school class). Students then use their synthesized MOFs to explore their inherent sorption properties. In one set of experiments, the synthesized MOFs are …

Measurement Of Bottom Quark Pair Production, In Association With Z Bosons And Top Quarks, With The Atlas Detector, Stewart Swift

Legacy Theses & Dissertations (2009 - 2024)

This thesis uses 36.1 fb-1 of proton-proton collision data collected with the ATLAS detector situated at the Large Hadron Collider at sqrt(s) = 13 TeV to measure the associated production of Z bosons with b-quark jets. The differential cross-sections for events containing a Z boson with 1 and 2 additional b-quark-jets are measured and compared with leading and next-to-leading order theoretical predictions.

Towards The Development Of A Concurrent Programming Language, Marrium Ayesha

Legacy Theses & Dissertations (2009 - 2024)

In order to fully utilize the potential of current architectures, programmers must program withconcurrency in mind. Concurrent processes can be extremely challenging to reason about due tounexpected program behavior that may emerge from interaction between processes. One approachto deal with this difficulty is to study new programming languages that offer an abstraction forconcurrency. This thesis focuses on developing a logical interpretation for concurrent processesand incorporating it in an existing functional programming language called SML. We developthis feature upon the fact that a proof of a theorem in logic can be expressed as a program in aprogramming language. This relation allows …

Quantification Of Hemoglobin In Human Blood To Differentiate Individuals From One Another, Audrey Jeanne Auleley

Legacy Theses & Dissertations (2009 - 2024)

Blood is one of the principal sources of evidence in crime scene investigations. The level of hemoglobin in human blood is known to hardly fluctuate over time in a healthy adult patient. Using a method like the sodium lauryl sulfate (SLS) method for hemoglobin level determination is beneficial because SLS converts any other derivates of hemoglobin into methemoglobin. The amount of hemoglobin would be determined using the linear correlation between the absorbance of methemoglobin and its amount in blood samples. Those curves differ significantly from sample to sample. Therefore, a differentiation can be observed between the blood samples of different …

Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan

Legacy Theses & Dissertations (2009 - 2024)

Computational methods can be used for a wide range of applications, especially regarding DNA and RNA. Interactions such as sugar torsions, receptor-ligand interactions, ligand docking/drug docking, receptor modeling, and drug design are excellent candidates for computational analysis and in silico experiments. The use of molecular dynamics software (GROMACS) coupled with molecular design software (MOE) produce insights that may have been otherwise difficult to assess. All these problems are academic in nature but have practical uses outside of academia. Understanding alternate linkages can lead to antibiotic assays to address potential superbug epidemics. Modeling DNA superstructures can provide insight into how large …

Synergistic Effects Of Midlevel Dry Air And Vertical Wind Shear On Tropical Cyclone Development, Joshua James Alland

Legacy Theses & Dissertations (2009 - 2024)

This dissertation seeks to better understand how midlevel moisture and vertical wind shear (VWS) modulate tropical cyclone (TC) development. The first component of this dissertation simplifies the objective by focusing solely on how midlevel moisture modulates TC development, utilizing an axisymmetric modeling framework. Results show that low-entropy midlevel air affects the upward vertical mass flux in these experiments through subsidence into the subcloud layer, which results in a longer recovery time before deep convection develops. This process, as well as descending motion closer to the inner core, limits the radial width of deep convection, reduces the area of upward motions, …

Convection-Permitting Ensemble Forecasts Of The 10-12 December 2013 Lake-Effect Snow Event: : Sensitivity To Microphysical, Planetary Boundary Layer, And Surface Layer Parameterizations, William Massey Bartolini

Legacy Theses & Dissertations (2009 - 2024)

Lake-effect snow (LeS) presents a substantial forecast challenge for convection-permitting models, due in part to uncertainties in the parameterization of microphysical (MP) and planetary boundary layer / surface layer (PBL/SL) processes. Here we focus on understanding these uncertainties for a LeS event that occurred during 10–12 December 2013 during the Ontario Winter Lake-effect Systems (OWLeS) field campaign. Throughout this event, long-lake-axis-parallel snowbands persisted downwind of the eastern shore of Lake Ontario, leading to snowfall accumulations as high as 105 cm (liquid precipitation equivalent of 64.5 mm) on the Tug Hill Plateau.

Investigation Of Optical Second Harmonic Generation From Si (100) With Process Tailored Surface & Embedded Ag Nanostructures For Advanced Si Nonlinear Nanophotonics, Gourav Bhowmik

Legacy Theses & Dissertations (2009 - 2024)

The challenge of current microelectronic architecture in transmission bandwidth and power consumption can be potentially solved by using silicon photonics technologies that are compatible with modern CMOS fabrication. One of the critical active photonic devices for Si photonics is a Si based optical modulator. Most of the reported silicon modulators rely on the free carrier plasma dispersion effect. In those cases, a weak change of the refractive index obtained by carrier accumulation, injection or depletion is utilized in a Mach-Zehnder interferometer or a microring resonator to achieve intensity modulation, rendering them difficult for chip-level implementation due to a large footprint …

An Underground World : Creative Writing In The Dystopian Genre, Mary Kathleen Brown

Legacy Theses & Dissertations (2009 - 2024)

Despite its importance for the creation of a compelling story, world-building is often overlooked in literary studies due to its complexity, with studies instead favoring analysis of plot, character, or situation. The dystopian genre dictates why world-building is a crucial element for fictional writing because it showcases a manipulated relationship between writer and reader. Using the overlap in possible worlds and actual worlds, this paper explores how world-building incites change in the actual world due to a reader correlating the possible world with their own. By way of example, my paper features the first three chapters of my dystopian novel, …

Evaluation Of Fingerprint Content For Forensic Crime Scene Analysis And Drug Metabolite Detection, Erica Kathryn Brunelle

Legacy Theses & Dissertations (2009 - 2024)

With respect to criminal investigations, one key piece of evidence that often gets overlooked are fingerprints. For years, fingerprint samples have been believed to be useful only for matching purposes using their unique ridges, shapes, and sizes. With the rapid growth of forensic science, it has become evident that the development of fingerprint analysis has been stagnant. The traditional approach has been advantageous for the identification of many individuals; however, many fingerprint samples have been labeled “unusable” due to smudging, smearing, or any one of a myriad of reasons that could cause inconclusive matches. These samples can, however, still be …

Tribute From The Underworld : The Historical Ecology Of The Maya Postclassic Fish Trade With Isotopic Analysis Of Otoliths From MayapáN And Caye Coco, Jeffrey Michael Bryant

Legacy Theses & Dissertations (2009 - 2024)

This dissertation investigates the Maya fish trade through the extensive analysis of fish otoliths (ear stones), from the Postclassic sites of Mayapán, and Caye Coco, and provides an initial foundation for the development of a historical ecology program. Through osteometry, thin-section microscopy of growth rings, and microscale stable isotope analysis (δC13 and δO18), a spectrum of data is produced to characterize the Postclassic fish trade. These data are used to illuminate themes of the seasonality of the fish harvest, diet, biodiversity, fish population demography, environmental change, sustainability, and resilience. The timing of a seasonal intensification of the harvest is viewed …

Applying Forecast Track And Intensity Diagnostics To High-Impact Northeast Winter Storms, Tomer Burg

Legacy Theses & Dissertations (2009 - 2024)

A conventional forecasting notion is that as lead time decreases, numerical weather prediction models exhibit a leftward (i.e., west) trend in the forecast position of low-pressure systems along the East Coast of the U.S. This left trend, which may turn seemingly weak ocean cyclones into high-impact weather events for the Northeast U.S., is attributed to various potential causes, such as variability in upstream shortwave troughs, or the representation of latent heat release in the NWP models downstream of the trough associated with the incipient cyclone. This study seeks to address whether this rule of thumb holds any significant merit, and …

A Multiscale Analysis Of The Rainband And Cellular Structure In Hurricanes Harvey And Irma (2017) Using The Ncar Ensemble, Dylan Card

Legacy Theses & Dissertations (2009 - 2024)

Tropical cyclones pose a significant threat to life and property, and exhibit many severe weather hazards as they make landfall, such as storm surge, strong winds, flooding rains, and tornadoes. Tropical cyclone rainbands are associated with nearly all of these hazards, which can extend hundreds of kilometers inland. Thus, understanding tropical cyclone rainband structure, and the individual convective cells of which rainbands are composed, is important to mitigating risk. Several previous studies have documented the overall structure of tropical cyclone rainbands, including the cells of which they are comprised and the environments in which they are embedded. These studies have …

Potential Effects Of Regional Soil Moisture Anomalies On The Great Plains Low-Level Jet, Matthew Arturo Campbell

Legacy Theses & Dissertations (2009 - 2024)

The Great Plains low-level jet (GPLLJ) contributes to Great Plains (GP) warm season water resources (precipitation), wind resources, and severe weather outbreaks. Past research has shown that synoptic and local mesoscale physical mechanisms (Holton and Blackadar mechanisms) are jointly required to explain GPLLJ variability. Although local mechanistic theories hinge upon soil moisture-planetary boundary layer (PBL) interactions, the effect of regional soil moisture anomalies on GPLLJ speed, northward penetration, and propensity for severe weather is not well known.

Permanently Heated Micro-Wire Electrodes For Electrochemistry Above The Boiling Point, Zhihua Chang

Legacy Theses & Dissertations (2009 - 2024)

Heated micro-wire electrodes offer lots of advantages, such as, accurate temperature control, enhanced diffusion and accelerated reaction kinetics through micro-stirring effect, easy cleaning, and low cost, etc. Its application in high temperature electrochemistry has gained lots of interests since its debut in the mid-1990s. A maximum of 250 °C has been reported using heating pulses in duration of 5 ms. For various applications, permanently heating would be more useful. In this study, two types of micro-wire electrodes were successfully developed for electrochemistry above the boiling point with acetaminophen as model compound and a continuous heating time of at least 2 …

Detection And Attribution Of Wind Energy Changes In The Contiguous United States, North Atlantic Ocean And European Sector In The Twentieth Century, Shengzhe Chen

Legacy Theses & Dissertations (2009 - 2024)

Wind power is playing a greater role as an alternative energy resource to fossil fuels. The prediction skills for hourly and daily forecasts of hub-height (80 – 100 m) wind power are increasingly reliable. However, regarding historical trends in wind energy availability (an important variable for determining wind farm capacity factors), little is known about the interannual and decadal variability of the hub-height wind speed. With climate change uncertainty now incorporated into wind energy resource assessment, insight into the relative contribution from the internal variability of the climate system versus the external forcing is presently lacking. Here, Empirical Orthogonal Function …

Precipitation Characteristics And Their Dependence On Data Resolution And Model Physics, Di Chen

Legacy Theses & Dissertations (2009 - 2024)

To fully characterize precipitation, one often needs not only the accumulative amount (A), but also its frequency (F), intensity (I) and duration (D). These characteristics have large impacts on Earth’s hydrologic cycle. Aiming for a comprehensive understanding, this dissertation investigates precipitation characteristics and their dependence on data resolution and model physics using observational datasets and comprehensive global climate models (GCMs).

The Sensitivity Of The December 2014 New York Mixed Precipitation Event To Initial Condition And Microphysics Uncertainty, Meghan Conway

Legacy Theses & Dissertations (2009 - 2024)

The prediction of wintertime precipitation type and amount can be a challenging undertaking, partly due to uncertainties in meteorological parameters such as temperature (horizontal and vertical), moisture, and wind. During Dec. 9-10, 2014, a mixed precipitation event occurred in the upper Hudson River Valley. This storm produced an unexpected heavy mesoscale snowband during rush hour in the Capitol region, after winter weather advisories had been cancelled.

Variability Of African Easterly Waves, Yuan-Ming Cheng

Legacy Theses & Dissertations (2009 - 2024)

African Easterly Waves (AEWs) are the most important rain modulators in the sub-Saharan Africa and precursors for tropical cyclone genesis in the Atlantic. While most previous studies have focused on the mean structure and dynamics of AEWs, evidence has shown that AEWs can vary substantially in terms of their structure and characteristics. Therefore, the overarching goal of this dissertation is to document the variability of AEWs and understand its causes. The goal is accomplished through two different but complementary approaches: (1) statistical analysis and (2) vorticity tracking.

Design And Implementation Of The New York State Mesonet Flux Tower Network, Jason Michael Covert

Legacy Theses & Dissertations (2009 - 2024)

The New York State Mesonet (NYSM) was established in 2014 to provide high-quality real-time meteorological data for weather monitoring and forecasting, emergency management, and research aimed at improving numerical weather prediction. The mainstay of the network consists of 126 surface weather stations located throughout New York State with an average spacing of 30 km. In 2017, 17 of the sites (“flux” sites) were equipped with additional (permanent) instrumentation to measure short and long-wave radiation components, soil heat flux, and turbulent fluxes of momentum, sensible and latent heat, and carbon dioxide (CO2). The mesoscale resolution of the 17-site NYSM Flux Tower …