Physical Sciences and Mathematics Commons^™

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 …

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 …

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 …

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 …

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 …

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. …

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 …

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. …

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, …

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 (1993-2023)

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 (1993-2023)

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 …

Segmentation And Classification Algorithms Applied To Sentinel-2a Images For Geological Mapping: Case Of The Al Glo’A Sheet (1/50000), Morocco, Abdessamad El Atillah, Mouhssine El Atillah, Zine El Abidine El Morjani, Khalid El Fazazy, Mustapha Souhassou

Bulletin of the Mineral Research and Exploration

The multispectral image, of Landsat 7 and 8; Aster and Sentinel-2A, has good results in lithological, structural, hydrothermal and mineralogical alteration mapping. Segmentation and image classification are two complementary steps as they are allowed the most important operations in the field of image processing. In this sense, this work aims at evaluating the potential of segmentation and classification algorithms for the generation of surface geological maps, hydrothermal alterations and lineaments. Given the good resolution of the Sentinel 2A (10m), the three images, (11/12; 11/2; 11/8), 12.8.2, main component 1, 2 and 3 (11.12.2), processed by five algorithms (K-means, Isodata, watershed, …

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

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 …

Twin Anomaly Detection System, Paaras Chand

Master's Projects

Anomaly detection performs well in situations where signature (and other rule-based) methods fail; there is no need to identify every threat as long as it is different from the norm. The tradeoff is that anomaly detection often results in a large number of false positives. While previous work has capitalized on the data imbalance problem to train models with only one set of data (one-class classification), few have utilized the limiting set for anything other than testing purposes. This paper seeks to utilize two anomaly detectors: one that is trained on the positive set and one that is trained on …

All I Want For Christmas..., Channon Visscher

Faculty Work Comprehensive List

"JWST [the James Webb Space Telescope] will let us see clearer and further into the ancient and beautiful story of creation."

Posting about new developments in spacecraft from In All Things - an online journal for critical reflection on faith, culture, art, and every ordinary-yet-graced square inch of God’s creation.

https://inallthings.org/all-i-want-for-christmas/

Temperature-Immune Self-Referencing Fabry–Pérot Cavity Sensors, Hengky Chandrahalim, Jonathan W. Smith

AFIT Patents

A passive microscopic Fabry-Pérot Interferometer (FPI) sensor an optical fiber a three-dimensional microscopic optical structure formed on a cleaved tip of an optical fighter that reflects a light signal back through the optical fiber. The reflected light is altered by refractive index changes in the three-dimensional structure that is subject to at least one of: (i) thermal radiation; and (ii) volatile organic compounds.

A Hybrid Machine Learning Framework For Predicting Students’ Performance In Virtual Learning Environment, Edmund Evangelista

All Works

Virtual Learning Environments (VLE), such as Moodle and Blackboard, store vast data to help identify students' performance and engagement. As a result, researchers have been focusing their efforts on assisting educational institutions in providing machine learning models to predict at-risk students and improve their performance. However, it requires an efficient approach to construct a model that can ultimately provide accurate predictions. Consequently, this study proposes a hybrid machine learning framework to predict students' performance using eight classification algorithms and three ensemble methods (Bagging, Boosting, Voting) to determine the best-performing predictive model. In addition, this study used filter-based and wrapper-based feature …

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 …

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. …

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, and Marine Sciences Faculty Publications and Presentations

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 …

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 …

Progressive Destabilization And Triggering Mechanism Analysis Using Multiple Data For Chamoli Rockslide Of 7 February 2021, Wenfei Mao, Lixin Wu, Ramesh P. Singh, Yuan Qi, Busheng Xie, Yingjia Liu, Yifan Ding, Zilong Zhou, Jia Li

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A catastrophic rockslide occurred on 7 February 2021 in Chamoli area in the high Himalaya. In the absence of field data, multiple satellites data of decade span have been used to investigate and understand the progressive destabilization of rockslide body. A 3D geometric model was developed using geospatial information about geology, terrain, and ice cover to understand the triggering mechanism. Several causes are uncovered as: the pronounced long-term change of land surface temperature facilitated local permafrost degradation and led to ice cover shrinking since 2010; the occurrence of ice avalanche nearby in 2016 accompanying with sidewall-to-bedrock fracturing enhanced the ice …

Sheep Performance In Italian Ryegrass Swards At Contrasting Sward Heights, Paulo C. De F. Carvalho, L. S. Pontes, E. O. Silveira, C. H. E. C. Poli, Carlos Nabinger, O. A. Pereira Neto, G. E. Maraschin

IGC Proceedings (1993-2023)

The objective of this study was to assess the effect of Italian ryegrass (Lolium multiflorum Lam.) sward height on lamb performance. The experiment was carried out at the Research Station of UFRGS, Eldorado do Sul, Brazil. Yearling no-castrated male lambs were assessed in terms of individual animal performance and gain per hectare. The experiment was carried out in a randomised block design with three replications of four treatments: 5, 10, 15 and 20 cm of sward surface height (SSH), which were maintained using continuous variable stocking, and monitored by a sward stick. Samples of 0.25 m² were cut …

Animal Performance In Pastures Of Panicum Maximum Cv. Ipr 86 Fertilized With Nitrogen, S. M. B. Lugão, L. R. De A. Rodrigues, E. B. Malheiros, J. J. Dos S. Abrahão, A. De Morais

IGC Proceedings (1993-2023)

The experiment was carried out at the Experimental Station of the IAPAR in Paranavaí– PR, Brazil, from October 1998 to May 1999 to evaluate the response of crossbred steers grazing pastures of Panicum maximum cv. IPR 86 fertilized with four doses of N (0; 150; 300 and 450 kg.ha^-1.year). The grass was grazed according to a rotational grazing system with grazing cycles (GCs) of 40 days (grazing period of 5 days and rest period of 35 days). It was used a randomized complete block design, with split-plots, and two replications per treatment, being the N-doses studied in the …

Dairy Cow Performance On Pasture-Based Feeding Systems And In Confinement, Renato S. Fontaneli, Lynn E. Sollenberger, C. R. Staples

IGC Proceedings (1993-2023)

Interest in grazing systems is growing among farmers in the USA as a means of reducing feed costs for lactating dairy cows. An experiment was conducted near Gainesville, FL to compare milk production and composition and milk income minus feed costs from two pasture-based systems with those of a conventional confinement housing system over a 276-d period. System 1 was based on a mixture of rye (Secale cereale L.), annual ryegrass (Lolium multiflorum Lam.), crimson clover (Trifolium incarnatum L.), and red clover (Trifolium pratense L.) during the winter-spring seasons and pearl millet (Pennisetum glaucum [L.] …

Comparative Analysis Of Rgb-Based Eye-Tracking For Large-Scale Human-Machine Applications, Brett Thaman, Trung Cao

Posters-at-the-Capitol

Gaze tracking has become an established technology that enables using an individual’s gaze as an input signal to support a variety of applications in the context of Human-Computer Interaction. Gaze tracking primarily relies on sensing devices such as infrared (IR) cameras. Nevertheless, in the recent years, several attempts have been realized at detecting gaze by acquiring and processing images acquired from standard RGB cameras. Nowadays, there are only a few publicly available open-source libraries and they have not been tested extensively. In this paper, we present the result of a comparative analysis that studied a commercial eye-tracking device using IR …

Weather And Climate Research At The Kentucky Climate Center Based On Mesonet Observations, Brittany Pekara, Eric Rappin

Posters-at-the-Capitol

The Kentucky Mesonet is a great asset for the Commonwealth of Kentucky in a multitude of ways, from real-time storm monitoring to building a detailed climate record. A detailed climate record is essential as causality between observations and extreme weather can be identified, making it a great tool in an evolving climate system. The climate record being developed at the 75+ Kentucky Mesonet observation stations consists of approximately 75 indices that reflect frequency, extremes, range, duration, trends of precipitation, droughts, and extreme temperatures. Calculations are done for daily, weekly, monthly, seasonal, bi-annual, and annual aggregation periods. Tools will also be …

Design And Construction Of A Modular Nai(Tl) Detector Array For Use In The Parity- And Time Reversal Violation Measurements For Noptrex, Jon Mills, Jason Fry

Posters-at-the-Capitol

The goal of the NOPTREX collaboration is to probe the Standard Model by utilizing the properties of low energy neutron-nucleus resonances to find evidence of parity- and time-reversal-odd violations. In order to conduct these sensitive experiments, it is needed to design and simulate an array of modular, high precision NaI(Tl) detectors. These detectors will be designed to operate in both pulse and current modes. We have tentative beam time at LANSCE to perform a search for new parity violation in heavy nuclei as candidates for time reversal and to perform a research and development effort on the n+d=t+gamma experiment. We …