Physical Sciences and Mathematics Commons^™

Evaluation Of Gpu Acceleration For Wrf–Sfire, Joshua Benz

Master's Projects

WRF–SFIRE is an open source, atmospheric–wildfire model that couples the WRF model with the level set fire spread model to simulate wildfires in real time. This model has many applications and more scientific questions can be asked and answered if the model can be run faster. Nvidia has put a lot of effort into easing the barrier of entry for accelerating applications with their tools to be run on GPUs. Various physical simulations have been successfully ported to utilize GPUs and have benefited from the speed increase. In this research, we take a look at WRF-SFIRE and try to use …

The Carrying Capacity Of Pure And Oversown Giant Star Grass (Cynodon Nlemfuensis Vanderyst) Under Different Stocking Rate In South-Western Islands Of Japan, Yasuhiro Kawamoto, T. Namihira, Y. Imura, M. Nagano

IGC Proceedings (1977-2023)

The objective of this study was firstly to know the potential carrying capacity, pasture production, pasture utilization of giant star grass under different stocking rates in intensive rotational grazing system, and to evaluate a carrying capacity of giant star grass (Cynodon nlemfuensis Vanderyst) pasture oversown with annual hybrid ryegrass (Lolium multiflorum X Lolium perenne) on short low productive winter pasture in South-western Islands of Japan. High herbage availability and good quality forage to bring about effective animal productions were produced by using relatively heavy stocking rates of 6 - 8 heads/ha, and achieved optimum pasture utilization of …

Residual Forage And Animal Performance From A Kikuyo Pasture Under Mixed Grazing And Supplementation, F. C. Gómez-Merino, Pedro A. Martínez-Hernández, J. Pérez-Pérez, Alfonso Hernández-Garay

IGC Proceedings (1977-2023)

Five grazing strategies were compared: grazing by ewes only and mixed grazing (ewes + heifers), in mixed grazing heifers received no supplement or one of three supplements. Ruminal undegradable protein (RUP) varied among supplement: 4.25, 9.11 and 9.13%, the supplement with the highest RUP included protected methionine. All supplements were 21% crude protein and 3.0 Mcal/kg of metabolizable energy. Grazing was on kikuyu, ratio was 30 kg of ewe per 100 kg of heifer in the mixed grazing treatments. Experimental grazing lasted 84 days. Variables measured were residual forage, proline content in residual forage and liveweight gains per animal and …

Stubble Height Effects On Limpograss Pasture Characteristics And Performance Of Beef Heifers, Y. C. Newman, Lynn E. Sollenberger, W. E. Kunkle, D. B. Bates, C. G. Chambliss, A. M. Fox

IGC Proceedings (1977-2023)

Limpograss (Hemarthria altissima [Poir.] Stapf. & C.E. Hubb.) is a C₄ species used in Florida beef production systems because of its cool-season growth, persistence on poorly drained soils, and high yield and digestibility. Animal performance on limpograss pastures, however, has been limited by low herbage crude protein (CP). This study evaluated the effect of canopy height of limpograss pastures and N supplementation of grazing cattle on sward characteristics and weight gain and blood urea N (BUN) concentration of yearling beef heifers. Under continuous stocking, six treatments were imposed that included all combinations of three stubble heights (20, 40, …

The Duration Of Regrowth Period And The Structural Traits In A Rotationally Grazed Panicum Maximum Sward, Carlos A. M. Gomide, J. A. Gomide

IGC Proceedings (1977-2023)

Panicum maximum 'cv'. Mombaça was rotationally grazed by steers. Three regrowth periods based on the number of expanded leaves per tiller: 2.5; 3.5 and 4.5, were compared. Three groups of seven tester steers, one for each treatment, grazed the replications of each experimental paddocks, the animals being removed from a paddock after 4 to 5 day grazing period when its sward leaf area index (LAI) was 1.5, on the average. Sward height and available biomass increased while tiller population density and leaf-stem ratio decreased with regrowth period. Overall averages observed for LAI and photosyntheticly active radiation interception by the end …

Effect Of Different Strategies Of Management Of Elephantgrass On Pasture Availability And Milk Yield Of Crossbred Holstein X Zebu Cows, Fermino Deresz

IGC Proceedings (1977-2023)

The trial was done to study different strategies of pasture management on milk production of cows grazing Elephantgrass (Pennisetum purpureum, Schum.). The treatments were: Elephantgrass with 30 days of resting and fertilized monthly (30MF), fertilized every two months (30BF). Elephantgrass with 45 days of resting and a stubble height of 90-100 cm (45HS) or a stubble height of 40-50 cm (45LS). The stubble height for treatments 30MF and 30BF was 90-100 cm. The study was done using six crossbred Holstein x Zebu cows/treatment, with 100 days of lactation, on average. The experimental design was a completely randomized block …

Seedemu: The Seed Internet Emulator, Honghao Zeng

Theses - ALL

I studied and experimented with the idea of building an emulator for the Internet. While there are various already available options for such a task, none of them takes the emulation of the entire Internet as an important feature in mind. Those emulators and simulators can handle small-scale networks pretty well, but lacks the ability to handle large-size networks, mainly due to:

- Not being able to run many nodes, or requires very powerful hardware to do so,- Lacks convenient ways to build a large emulation, and - Lacks reusability: once something is built, it is very hard to re-use …

A Brief Treatise On Bayesian Inverse Regression., Debashis Chatterjee Dr.

Doctoral Theses

Inverse problems, where in a broad sense the task is to learn from the noisy response about some unknown function, usually represented as the argument of some known functional form, has received wide attention in the general scientific disciplines. However, apart from the class of traditional inverse problems, there exists another class of inverse problems, which qualify as more authentic class of inverse problems, but unfortunately did not receive as much attention.In a nutshell, the other class of inverse problems can be described as the problem of predicting the covariates corresponding to given responses and the rest of the data. …

High-Resolution Cryo-Electron Microscopy Structure Of Photosystem Ii From The Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803, Christopher J. Gisriel, Jimin Wang, Jinchan Liu, David A. Flesher, Krystle M. Reiss, Hao-Li Huang, Ke R. Yang, William H. Armstrong, M. R. Gunner, Victor S. Batista, Richard J. Debus, Gary W. Brudvig

Publications and Research

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a highresolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the …

Developing Novel Molecular Detection Techniques For Hemlock Woolly Adelgid (Adelges Tsugae), Meg Sanders

Masters Theses

Hemlock forests in eastern North America face a deadly threat: the invasive insect, hemlock woolly adelgid (HWA), Adelges tsugae. Early detection of this pest remains a key focus for management groups to ensure rapid response to control and stop the spread of HWA. In Chapter II, our goals were to develop an affordable, easy-to-use trap that is compatible with airborne eDNA sampling techniques and assess its efficiency as a monitoring tool for HWA. We tested three potential trap designs (i.e., passive trap, funnel trap, and motorized trap) against a standard sticky trap. Our passive, funnel, and motorized traps estimated …

Buckling Patterns And Mechanics Of Thin Interfacial Polymer Films, Monica M. Ripp

Dissertations - ALL

Thin elastic solids are easily deformed and will readily collapse into complex buckling modes. They can also transition between distinct buckling modes when the confining forces evolve over time, forming a variety of robust and striking patterns. Here we explore how thin interfacial films and the buckling modes they present couple with evolving macroscopic forces and how multi-scale features of the systems give rise to patterns.

In the indentation of a circular film floating on a liquid bath three buckling modes arise: wrinkling, crumpling, and folding. This work shows that striking transitions between these states accompany four regimes in the …

Exploration Of Carbon-Oxygen And Carbon-Nitrogen Bond Formation Utilizing Trichloroacetimidates And Investigations Of New Reactions Mediated By Oxoammonium Salts, Rowan Meador

Dissertations - ALL

Mono-O-alkylated 1,1′-bi-2-naphthols (BINOLs) are often used as the source of chirality for catalysts or ligand systems that are employed in asymmetric organic transformations. However, these BINOLs can be hard to synthesize. The O-alkylation of BINOL can be accomplished with primary and secondary alkyl halides or under Mitsunobu conditions, the yields of these alkylations with tertiary halides or alcohols are very low. A new protocol was developed utilizing trichloroacetamide electrophiles to install bulky groups onto one of the phenolic oxygens. Trichloroacetimidates are also shown to be useful reactions for the synthesis of esters. These reagents proceeded through a symbiotic activation pathway. …

The Phase Behavior Of Ubqln Proteins And Implications For Protein Quality Control, Yiran Yang

Dissertations - ALL

The ubiquitin-proteasome system (UPS) and autophagy are essential pathways for maintaining protein quality control (PQC) in cells. Misfolded proteins and large aggregates are cleared by UPS and autophagy signaled by ubiquitin (Ub) or polyubiquitin (polyUb) chains. Shuttle proteins facilitate cargo transporting by interacting with both ubiquitin and degradation machineries. Previously, our lab discovered that the shuttle protein Ubiquilin-2 (UBQLN2) is recruited to stress granules in cells and undergoes liquid-liquid phase separation (LLPS) in vitro. LLPS is a biophysical process by which proteins separate themselves from the surrounding aqueous solution by forming protein-rich droplets. The overarching goals of this work are …

Direct Single Molecule Imaging Of Enhanced Diffusion For Enzymes And Enzyme-Conjugated Dna Origami, Mengqi Xu

Dissertations - ALL

Enzymes have been shown to diffuse faster in the presence of their substrates. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT) with total internal reflection fluorescence (TIRF) microscopy. We found that the mobility of individual enzymes was enhanced three-fold in the presence of the substrate, and the motion remained Brownian. We showed that the relative increase in diffusion is independent of the total enzyme concentrations; and the oligomerization state of enzymes did not change during the catalytic turnover. These experiments ruled out the possibility that the enhanced enzyme diffusion was caused by the …

Distribution And Characterization Of Rhyolites Of The Strawberry Volcanics -- Evolution Of A Major Rhyolite Field Associated With Columbia River Basalt Magmatism, Eastern Oregon, Usa, Chanel Leigh Dvorak

Dissertations and Theses

The Strawberry Rhyolites constitute a significant rhyolite field among the largest in Oregon. Aerial coverage of approximately 386 km² and an overall estimated volume of ~67 km³ using a median thickness for each unit. On the other hand, the total volume could be greater than 100 km³ if greater thicknesses apply. The Strawberry Rhyolites, a largely unknown mid-Miocene silicic volcanic rocks, crop out amongst voluminous flood basalt flows of the Columbia River Basalt Group (CRBG) in eastern Oregon. The eruptive activity of the Strawberry Rhyolites is currently constrained to span a period of about 2 million years, …

Fine Scales, Broad Consequences: Drivers And Effects Of Microclimatic Variation In Great Smoky Mountains National Park, Jordan Rebecca Stark

Theses - ALL

Climate is highly variable at scales that are not captured by most weather and climate models due to local effects of topography and living systems. This variation in microclimate has been noted for many decades but has been difficult to incorporate into quantitative understanding of ecological systems and processes due to the large amount of data and complex models required to adequately describe fine-scale patterns across complex landscapes. In recent years, models of thermal microclimate variation have been developed using low-cost temperature sensors, but few of these models have been used to predict the effects of microclimatic variation on ecological …

First Measurement Of B(Ξc0 → Π−Λ+C ), Michael Kent Wilkinson

Dissertations - ALL

The first measurement of the branching fraction of the Ξc0 baryon in its decay to π− and Λ+c hadrons, B(Ξc0 → π−Λ+c ), is presented. This measurement was conducted with the LHCb detector, located on the Large Hadron Collider, using 13 TeV proton-proton collisions. There have been a number of theoretical predictions for the size of this branching fraction, spanning more than an order of magnitude; this large difference is primarily due to differing assumptions about the internal interactions contributing to the decay. The branching fraction measured here provides the first experimental evidence for the nature of these interactions; it …

A Solid-State Phase Camera For Advanced Gravitational Wave Detectors, Erik Muniz

Dissertations - ALL

I present a novel way of wavefront sensing using a commercially available, continuouswavetime-of- ight camera with QVGA-resolution. This CMOS phase camera is capable of sensing externally modulated light sources with frequencies up to 100 MHz. The high-spatial-resolution of the sensor, combined with our integrated control electronics, allows the camera to image power modulation index as low as -62 dBc/second/pixel. The phase camera is applicable to problems where alignment and mode-mismatch sensing is needed and suited for diagnostic and control applications in gravitationalwave detectors. Specically, I explore the use of the phase camera in sensing the beat signals due to thermal …

Observation Of Ω Contribution In The C1(3872) → Π+Π−J/Ψ Decays, Baasansuren Batsukh

Dissertations - ALL

Resonant structure in the dipion mass spectrum produced via \decay{\Bu}{\X\Kp}, \decay{\X}{\jpsi \pip \pim}, with \decay{\jpsi}{\mu^+\mu^-} is analyzed using Run 1 and Run 2 data samples from the LHCb experiment. The spectrum is dominated by $\rhoz\to\pi^+\pi^-$, but cannot be described by this contribution alone. A significant $\omega\to\pi^+\pi^-$ contribution, interfering with $\rhoz$, is observed for the first time. This is a more significant observation ($>7.1\sigma$) of $\X\to\omega\jpsi$ decays, than previously achieved with $\omega\to\pi^+\pi^-\pi^0$ decays. The relative contribution of $\omega$ to the total $\X\to\pi^+\pi^-\jpsi$ rate is at the level expected from the measured $\X\to(\omega\to\pi^+\pi^-\pi^0)\jpsi$ rate, if the interference between the $\rho^0$ and …

Utilizing Parity Violating Electron Scattering As A Probe To Measure The Neutron Radius Of 208-Pb, David Eric King

Dissertations - ALL

The Lead Radius Experiment 2 (PREX-II) and Calcium Radius Experiment (CREX) carried out in Hall A of the Thomas Jefferson National Accelerator Facility were designed to measure the neutron skins of 208-Pb and 48-Ca nuclei by measuring the parity-violating asymmetry APV of the elastic scattering of polarized electrons on 208-Pb and 48-Ca targets. In order to achieve a precision measurement of the neutron skins of 208-Pb and 48-Ca it is imperative to maintain precise control over many experimental parameters–one of which is a precision measurement of the electron beam polarization (which is the largest contributor to experimental error making control …

Formation Of Pyrroloindolines And Alkylation Of N-Heterocycles With Trichloroacetimidates And Synthesis Of Quinoline Based Small Molecule Inhibitors Of Ghrelin O-Acyltransferase (Goat), Bhaskar Joshi

Dissertations - ALL

Pyrroloindolines and related systems are present in a large number of complex natural products. These core structures have generated considerable synthetic interest, as many of the compounds possess challenging, elaborate structures and interesting biological properties. Recently we have focused on using trichloroacetimidates for the synthesis of these fascinating molecules. Trichloroacetimidates can be used an electrophilic source of an alkyl group to form the pyrroloindoline directly from tryptamine derivatives. In this manner trichloroacetimidates provide a flexible solution to accessing highly functionalized pyrroloindoline core structures, needing only a catalytic amount of a Lewis acid to effect the requisite transformations.

Isatin (1H-indol-2,3-dione) based …

Effects Of Nitrogen Fertilization On The Production Of Panicum Maximum Cv. Ipr 86 Under Grazing, S. M. B. Lugão, L. R. De A. Rodrigues, E. B. Malheiros, J. J. Dos S. Abrahão, A. De Morais

IGC Proceedings (1977-2023)

The experiment was conducted at the Experimental Station of Paranavaí/IAPAR-PR-Brazil, from October 1998 to May 1999, to evaluate the effects of N fertilization on Panicum maximum cv. IPR 86 pastures. Four doses of N (0; 150; 300; and 450 kg.ha^-1.year^-1) were applied to pastures under rotational grazing with grazing cycles (GCs) of 40 days (5 days-grazing and 35 days-rest). It was used a randomized complete block design, with split-plots, and two replications per treatment, being the N-doses studied in the main plots and the GCs in the sub-plots. In all GCs the variables dry matter of …

Effects Of Management Strategies On Seed Production And Seedling Recruitment In Birdsfoot Trefoil-White Clover Mixtures, W. Ayalá, M. Carámbula, D. F. Risso, J. Hodgson, Peter D. Kemp

IGC Proceedings (1977-2023)

The effects of grazing management on seed production, seed bank size and seedling emergence patterns of Trifolium repens cv. Zapicán (WC) and Lotus corniculatus cv. San Gabriel (BFT) oversown swards were evaluated. A complete randomized block design with 4 replicate blocks was used, in which 4 grazing strategies (grazing all year (SI), summer spelling for seed production (S2), winter rest plus summer spelling (S3) and autumn rest plus summer spelling (S4)), were combined with two defoliation severalties (4 and 10 cm height post-grazing residuals). Plots of 110 m² were grazed monthly by sheep. Seed production, soil seed bank and …

Genetic Contributors Of Incident Stroke In 10,700 African Americans With Hypertension: A Meta-Analysis From The Genetics Of Hypertension Associated Treatments And Reasons For Geographic And Racial Differences In Stroke Studies, Nicole D. Armstrong, Vinodh Srinivasasainagendra, Amit Patki, Rikki M. Tanner, Bertha A. Hidalgo, Hemant K. Tiwari, Nita A. Limdi, Ethan M. Lange, Leslie A. Lange, Donna K. Arnett, Marguerite R. Irvin

Epidemiology and Environmental Health Faculty Publications

Background: African Americans (AAs) suffer a higher stroke burden due to hypertension. Identifying genetic contributors to stroke among AAs with hypertension is critical to understanding the genetic basis of the disease, as well as detecting at-risk individuals.

Methods: In a population comprising over 10,700 AAs treated for hypertension from the Genetics of Hypertension Associated Treatments (GenHAT) and Reasons for Geographic and Racial Differences in Stroke (REGARDS) studies, we performed an inverse variance-weighted meta-analysis of incident stroke. Additionally, we tested the predictive accuracy of a polygenic risk score (PRS) derived from a European ancestral population in both GenHAT and REGARDS AAs …

Adopting Agility In Academia Through Pilot Projects, Omar Ochoa, Massood Towhidnejad

Papers

This innovate practice work in progress paper presents our initial findings about the application of agile process in the day to day operation of an academic department. The benefits of agile methods, which are processes that are lightweight and people-oriented, are well-known. Agile methods provide the ability to respond faster to the changing needs of stakeholders, improved product quality, team over individual goals, and better transparency. Therefore, one would expect adaption of the agile process within academic environment would be welcomed, however, unique issues exist within faculty that impact adoption; faculty have different goals that change through their tenure, and …

Dysregulation Of Dna Methylation And Epigenetic Clocks In Prostate Cancer Among Puerto Rican Men, Anders Berglund, Jaime Matta, Jarline Encarnación-Medina, Carmen Ortiz-Sanchéz, Julie Dutil, Raymond Linares, Joshua Marcial, Caren Abreu-Takemura, Natasha Moreno, Ryan Putney, Ratna Chakrabarti, Hui Yi Lin, Kosj Yamoah, Carlos Diaz Osterman, Liang Wang, Jasreman Dhillon, Youngchul Kim, Seung Joon Kim, Gilberto Ruiz-Deya, Jong Y. Park

School of Public Health Faculty Publications

In 2021, approximately 248,530 new prostate cancer (PCa) cases are estimated in the United States. Hispanic/Latinos (H/L) are the second largest racial/ethnic group in the US. The objective of this study was to assess DNA methylation patterns between aggressive and indolent PCa along with ancestry proportions in 49 H/L men from Puerto Rico (PR). Prostate tumors were classified as aggressive (n = 17) and indolent (n = 32) based on the Gleason score. Genomic DNA samples were extracted by macro-dissection. DNA methylation patterns were assessed using the Illumina EPIC DNA methylation platform. We used ADMIXTURE to estimate global ancestry proportions. …

Temperature Relaxation And Magnetically Suppressed Expansion In Strongly Coupled Ultracold Neutral Plasmas, Robert Tucker Sprenkle

Theses and Dissertations

Ultracold neutral plasmas provide a platform for studying transport properties in an idealized environment. In this dissertation, transport properties in a Ca$^+$/Yb$^+$ dual species ultracold neutral plasma and a Ca$^+$ magnetized ultracold neutral plasma are studied. In dual species plasmas, we study ion-ion temperature relaxation. We compare measured relaxation rates with atomistic simulations and a range of popular theories. Our work validates the assumptions and capabilities of molecular dynamic simulations and invalidates theoretical models in this regime. This work illustrates an approach for precision determinations of detailed material properties in Coulomb mixtures across a wide range of conditions. We also …

An Instructional Guide To Environmental Campaigns For K-12 Schools, Erin Mccarty

University Honors Theses

Evidence suggests environmental education can correlate with both short- and long-term behavioral changes, but existing research on the effectiveness of popular environmental education tactics show mixed results. Qualitative research was used in this study to assess student engagement and behavioral change within the context of environmental education campaigns. Ideally, students exposed to environmental campaigns become more informed on environmental issues and adjust their behavior to align with the campaign’s objectives. However, only a portion of environmental campaigns have these desired effects on their students. Based on a preliminary literature review, I anticipated the defining catalyst on post-campaign behavioral engagement would …

Winter 2021

In The Loop

2021 Emmy Nominees; Animator Tapped by Cartoon Network; IndieCade Horizons 2021; Hack4Space; Security Daemons Prevail; Role Models: DePaul Originals Game Studio students build industry-level skills that benefit themselves and others; Frames and Fortune: Eugene Bush programmed his indie video studio with patience and planning; Reality Check: Heather Snyder Quinn augments reality to question systems of unchecked power

Linking Migration To Community Resilience In The Receiving Basin Of A Large-Scale Water Transfer Project, Anna Erwin, Zhao Ma, Ruxandra Popovici, Emma Patricia Salas O’Brien, Laura Zanotti, Chelsea A. Silva, Eliseo Zeballos Zeballos, Jonathan Bauchet, Nelly Ramírez Calderón, Glenn Roberto Arce Larreah

School of Earth, Environmental, & Marine Sciences Faculty Publications

Large-scale water transfer projects (LWTPs) transfer water to urban and agricultural areas. The Majes-Siguas canal, established in 1983, is an LWTP that created a thriving agricultural area through irrigating the Majes district in the Atacama Desert of Peru. Like other LWTP receiving basins, the project has attracted an influx of migrants who work on the farms. At the same time, the Majes LWTP is the district’s only source of water and has an aging infrastructure which presents significant risks. While many studies critically analyze the consequences of LWTPs in water supply basins, few evaluate the resilience of communities living in …