Physical Sciences and Mathematics Commons^™

Ultrafast Electronic Relaxation Pathways Of The Molecular Photoswitch Quadricyclane, Kurtis D. Borne, Joseph C. Cooper, Michael N. R. Ashfold, Julien Bachmann, Surjendu Bhattacharyya, Rebecca Boll5, Matteo Bonanomi, Michael Bosch, Carlo Callegari, Martin Centurion, Marcello Coreno, Basile F. E. Curchod, Miltcho B. Danailov, Alexander Demidovich, Michele Di Fraia, Benjamin Erk, Davide Faccialà, Raimund Feifel, Ruaridh J. G. Forbes, Christopher S. Hansen, David M. P. Holland, Rebecca A. Ingle, Roland Lindh, Lingyu Ma, Henry G. Mcghee, Sri Bhavya Muvva, Joao Pedro Figueira Nunes, Asami Odate, Shashank Pathak, Oksana Plekan, Kevin C. Prince, Primoz Rebernik, Arnaud Rouzée, Artem Rudenko, Alberto Simoncig, Richard J. Squibb, Anbu Selvam Venkatachalam, Caterina Vozzi, Peter M. Weber, Adam Kirrander, Daniel Rolles

Martin Centurion Publications

The light-induced ultrafast switching between molecular isomers norbornadiene and quadricyclane can reversibly store and release a substantial amount of chemical energy. Prior work observed signatures of ultrafast molecular dynamics in both isomers upon ultraviolet excitation but could not follow the electronic relaxation all the way back to the ground state experimentally. Here we study the electronic relaxation of quadricyclane after exciting in the ultraviolet (201 nanometres) using time-resolved gas-phase extreme ultraviolet photoelectron spectroscopy combined with non-adiabatic molecular dynamics simulations. We identify two competing pathways by which electronically excited quadricyclane molecules relax to the electronic ground state. The fast pathway (<100 femtoseconds) is distinguished by effective coupling to valence electronic states, while the slow pathway involves initial motions across Rydberg states and takes several hundred femtoseconds. Both pathways facilitate interconversion between the two isomers, albeit on different timescales, and we predict that the branching ratio of norbornadiene/ quadricyclane products immediately after returning to the electronic ground state is approximately 3:2.

Soft Microreactors For The Deposition Of Microstructures And The Related Surface Chemistries Of Polymeric Materials, Jessica Wagner

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

The precise control over small volumes of liquids is of great interest to various fields such as biotechnology, drug development, and diagnostics. Working at small scales reduces cost, time, and waste, which is why microfluidic lab – on – chip technologies have become popular in a wide range of industries and applications. Additionally, there are differences in properties such as mass transport and heat dissipation at the micron scale compared to in bulk. Microfluidic devices contain several interfaces to consider when preparing to fabricate devices. The substrate/device, substrate/solution, and solution/device interfaces are all of importance and must carefully be tuned …

Game-Theoretic Approaches To Optimal Resource Allocation And Defense Strategies In Herbaceous Plants, Molly R. Creagar

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

Empirical evidence suggests that the attractiveness of a plant to herbivores can be affected by the investment in defense by neighboring plants, as well as investment in defense by the focal plant. Thus, allocation to defense may not only be influenced by the frequency and intensity of herbivory but also by defense strategies employed by other plants in the environment. We incorporate a neighborhood defense effect by applying spatial evolutionary game theory to optimal resource allocation in plants where cooperators are plants investing in defense and defectors are plants that do not. We use a stochastic dynamic programming model, along …

The Development And Evolution Of The Soil Health Nutrient Tool (Aka Haney Test) After Ten Years Of Implementation In A Commercial Agricultural Laboratory, Lance Michael Gunderson

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

The growing focus on soil health and regenerative agriculture has brought about the need for new integrated approaches for the analysis of soil. Prior, commercial agricultural laboratories relied on methods to measure chemical properties of the soil, such as pH and nutrients. The Soil Health Nutrient Tool (aka. Haney Test) developed by Dr. Rick Haney (USDA-ARS Blackland Research and Extension Station, Temple, TX) integrates chemical and biological properties to provide a more holistic understanding of soil fertility management. Following adoption by commercial laboratories in 2013, criticisms regarding variability in measurements and lack of calibration were apparent. In this research, we …

Formal Concept Analysis For Image Classification And Machine Learning Models For Anti-Crispr Protein Discovery In Bioinformatics, Minal Khatri

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

This study investigates two critical areas in bioinformatics: enhancing transparency in medical image analysis and advancing the discovery of Anti-CRISPR (Acr) proteins, which have potential in developing more precise and controlled CRISPR-Cas gene editing tools. While CNN’s are increasingly applied in critical fields like medical diagnosis, understanding their decision-making process remains a challenge. Although visualization techniques like Saliency maps offer insights into CNN’s decision-making for individual images, they do not explicitly establish a relationship between the high-level features learned by CNN’s and the class labels across dataset. To bridge this gap, Formal Concept Analysis (FCA) framework is leveraged as a …

Relativistic Ultrafast Electron Diffraction At High Repetition Rates, K. M. Siddiqui, D. B. Durham, F. Cropp, F. Ji, S. Paiagua, C. Ophus, N. C. Andresen, L. Jin, J. Wu, S. Wang, X. Zhang, W. You, M. Murnane, Martin Centurion, X. Wang, D. S. Slaughter, R. A. Kaindl, P. Musumeci, A. M. Minor, D. Filippetto

Department of Physics and Astronomy: Faculty Publications

The ability to resolve the dynamics of matter on its native temporal and spatial scales constitutes a key challenge and convergent theme across chemistry, biology, and materials science. The last couple of decades have witnessed ultrafast electron diffraction (UED) emerge as one of the forefront techniques with the sensitivity to resolve atomic motions. Increasingly sophisticated UED instruments are being developed that are aimed at increasing the beam brightness in order to observe structural signatures, but so far they have been limited to low average current beams. Here, we present the technical design and capabilities of the HiRES (High Repetition-rate Electron …

The Influence Of Invasive Species On Fishers’ Satisfactions, Caroline M. Laplante

School of Natural Resources: Dissertations, Theses, and Student Research

Invasives species are prevalent and widespread in North America. Outdoor recreational activities, such as fishing, introduce a point in which humans may interact with invasive species and have to adapt their own behaviors. Bigheaded carp in the Missouri River below Gavin’s Point Dam are a group of invasive fish species that were thought to be negatively relating to recreational fishers’ satisfactions. Using a content analysis and an importance-grid, we conclude that invasive species do not strongly relate to recreational paddlefish fishers’ satisfactions. Paddlefish fishers represent a small sub-set of recreational fishers in Nebraska and South Dakota. The content analysis revealed …

Understanding Avidities Of Recreational Activities For People Possessing Fishing Licenses And Residing In Urban Environments, Kyle F. Hansen

School of Natural Resources: Dissertations, Theses, and Student Research

Recreational fishing is one of the world's most popular pastimes, wherein participation is associated with sociodemographic factors. Even so, fishing license sales are declining in the USA in conjunction with a reduction in rural populations as people move to urban areas. Thus, urban areas are constantly growing in population size, population diversity, and geographic size suggesting a need to understand fishing participation in these growing areas. Natural resource managers often use participation to understand recreationists, yet avidity could provide a new way to understand recreationists. The goal of our study is to understand what sociodemographic factors influence the fishing avidity …

Wonderstone And Its Connection To Liesegang, Microbes, And Beyond, Haden S. Mandery

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

In the western and southwestern United States, the term wonderstone is used to describe volcanic, volcaniclastic, and sedimentary rocks with variegated banding produced by iron oxide mineralization or staining. This iron oxide mineralization is typically described as Liesegang banding. In this paper I will (1) test if the banding in wonderstone follows the spacing and width laws characteristic of Liesegang, (2) identify the source of iron that ultimately precipitated in the bands, and (3) examine the role that microbes played in the formation of the mineralization in these rocks. I conclude that the iron oxide mineralization is not Liesegang banding. …

Population Demography Of A Glacial-Relict Stream Fish Mediated Via Anthropogenic Alteration, Joseph M. Spooner

School of Natural Resources: Dissertations, Theses, and Student Research

Northern Pearl Dace Margariscus nachtriebi are a small-bodied glacial-relict fish species of greatest conservation need (SGCN) found throughout Canada and the northern United Sates. Their distribution within the Nebraska Sandhills Ecoregion is isolated from the northern core distribution of the species following the last glaciation period approximately 18,000 years ago. Headwater streams within the Nebraska Sandhills Ecoregion are predominately groundwater fed and provide the cool water temperatures needed to support Northern Pearl Dace and other glacial-relict SGCN. Headwater streams within the Nebraska Sandhills Ecoregion have been geomorphically altered through anthropogenic processes such as channelization whereby habitat homogenization has occurred. Evidence …

Habitat Heterogeneity In Nebraska Streams And Distribution Prediction For Tier-1 Cyprinids Using Multi-Scale Modeling Of Fluvial And Landscape Features, Connor P. Hart

School of Natural Resources: Dissertations, Theses, and Student Research

Multiscale environmental processes determine in-stream habitat conditions which drive species distributions. Habitat constitutes the physical template upon which ecological processes occur and species conduct life stage activities. Habitat heterogeneity promotes biodiversity of aquatic systems. Stream classification informs freshwater conservation by providing a useful framework to account for habitat heterogeneity, often based on landscape regions of similar environmental processes. A greater understanding of landscape-based classification frameworks as means to classify stream systems may improve understanding of drivers of biodiversity. Using Nebraska as a case study, on a statewide scale, objectives were 1) to characterize habitat availability for several at-risk fish species, …

Assessing The Morphological And Physiological Traits Of Smooth Brome Pastures Under Long Term Grazing And Nutrient Enrichment In Eastern Nebraska, Hassan Shehab

School of Natural Resources: Dissertations, Theses, and Student Research

Climate change together with the increase in demands for food, feed, fuel, and fiber are becoming a threat to sustainability and resilience of agriculture and pasture lands. Bromus inermis (smooth bromegrass) dominates pastures for cattle grazing in Eastern Nebraska, US, where it is planted in monocultures, and is considered high quality forage because of its palatability and high nutritional value for cattle, especially under intensive management practices. Sustainable management of these pastures is key to long-term resilience. This study aims to assess the performance of smooth bromegrass pastures to the combined effects of long-term management practices (since 2005) of fertilization …

Human Dimensions Of Woody Encroachment Management In Nebraska, Emily Rowen

School of Natural Resources: Dissertations, Theses, and Student Research

Woody plant encroachment (WPE) is a social-ecological problem that will challenge conservation professionals and agricultural producers to adapt their management strategies. This research first examined WPE from the perspective of individual conservation professionals through an online survey. Conservation professionals’ attitudes about adaptation to vegetation transitions, such as WPE, were of interest because these attitudes are one measure of how prepared this group is to respond to WPE. Hypothesized predictors of adaptation attitude were tested through linear regression modeling. These predictors included ecological change, observation of WPE, or risk perception. It was found that risk perception was the strongest predictor of …

The Essential Role Of Fossil Fuels In Combating Climate Change, Ivye Meyer

Op-Eds from ENSC230 Energy and the Environment: Economics and Policies

Fossil fuels have been essential to the living standards enjoyed by the industrialized and developed world. Since the Industrial Revolution, non-renewable sources, including coal, oil, and natural gas, have been our first choice in energy generation. Fossil fuels have also become appealing to developing nations, as they require inexpensive sources of energy to increase their standards of living. These factors contribute to fossil fuels comprising over 80 percent of the current global primary energy demand, undeniably making them a vital part of our daily lives. The necessity for upcoming change in energy production does not require the exclusion of fossil …

Navigating The Green Skies: Why Saf Is The Wrong Path To Take, Cameron Cannon

Op-Eds from ENSC230 Energy and the Environment: Economics and Policies

With its promise of a significant decrease in greenhouse gas emissions, sustainable aviation fuels, or SAFs, have been hailed as an environmentally friendly substitute for conventional aviation fuels. SAFs are made from sustainable resources such as plant biomass, waste oils, or agricultural wastes and are intended to mitigate environmental issues. On closer examination, though, this solution's intricacy becomes clear. Grab your mental compass and journey with me as we discover why SAFs would lead us the wrong way.

The Broadwater Formation (Pliocene) Of Nebraska And Southeastern Wyoming, Robert F. Diffendal Jr., James B. Swinehart

Robert F. Diffendal, Jr., Publications

The Broadwater Formation, initially defined in 1945, is a Pliocene-aged coarse-grained alluvial deposit in Nebraska and southeastern Wyoming. It is characterized by a complex stratigraphic history and debated geologic interpretations. The formation is a rich resource of groundwater for the citizens of Nebraska and the Central Great Plains. We aim to synthesize and redefine the Broadwater Formation, shedding light on its distribution, geological characteristics, and paleoenvironmental significance. While historical hypotheses on Broadwater Formation paleovalley trajectories suggested northwest-southeast trending valleys, later investigations proposed wind-driven erosional patterns to explain the unique topographic features observed. The Broadwater is divided into an unnamed Upper …

Why We Should Have More Walkable Cities, Alexander Huddleston

Op-Eds from ENSC230 Energy and the Environment: Economics and Policies

The walkable city is something that is seen all over Europe but is a rarity in the United States. The rise of cheap oil in the first half of the 20th century led to the expansion of the suburbs and a car culture that we just can’t get away from. Our cities are now so spread out, causing more and more pollution and damage done to our environment. There is a lot that we know about this issue and the solutions that we can get done to fix it. America is stuck in a car culture that is so hard …

Eminent Domain: Unconstitutional, Unjust, And Unnecessary, Ashley Norris

Op-Eds from ENSC230 Energy and the Environment: Economics and Policies

Perhaps the most important undertaking of our time is the ubiquity of sustainable energy vital for the continuation and improvement of living conditions worldwide. The utmost care must be taken with the means used to achieve this feat. The fossil fuel industry has used and abused eminent domain since its inception. Ironically, environmental advocates now propose the same means to a cleaner, greener end. The taking of private land for private development, regardless of intent, is unconstitutional, unjust, and unnecessary. The Fifth Amendment states: “…nor shall private property be taken for public use, without just compensation.”

As stated by the …

Sound Energy Could Change The World, Tyler Bugiel

Op-Eds from ENSC230 Energy and the Environment: Economics and Policies

The energy crisis is a problem that has been growing more concerning for many years, and yet there has not seemed to be a good solution to the problem. That being said, I think that there is a solution that has not been explored thoroughly enough, that solution being sound energy. Solar and wind are both energy systems that use natural resources and things that occur on a day to day basis to convert those things into energy, but sound has not been explored as much.

Game-Theoretic Approaches To Optimal Resource Allocation And Defense Strategies In Herbaceous Plants, Molly R. Creagar

Department of Mathematics: Dissertations, Theses, and Student Research

Empirical evidence suggests that the attractiveness of a plant to herbivores can be affected by the investment in defense by neighboring plants, as well as investment in defense by the focal plant. Thus, allocation to defense may not only be influenced by the frequency and intensity of herbivory but also by defense strategies employed by other plants in the environment. We incorporate a neighborhood defense effect by applying spatial evolutionary game theory to optimal resource allocation in plants where cooperators are plants investing in defense and defectors are plants that do not. We use a stochastic dynamic programming model, along …

On Dyadic Parity Check Codes And Their Generalizations, Meraiah Martinez

Department of Mathematics: Dissertations, Theses, and Student Research

In order to communicate information over a noisy channel, error-correcting codes can be used to ensure that small errors don’t prevent the transmission of a message. One family of codes that has been found to have good properties is low-density parity check (LDPC) codes. These are represented by sparse bipartite graphs and have low complexity graph-based decoding algorithms. Various graphical properties, such as the girth and stopping sets, influence when these algorithms might fail. Additionally, codes based on algebraically structured parity check matrices are desirable in applications due to their compact representations, practical implementation advantages, and tractable decoder performance analysis. …

Unexpectedness Stratified By Codimension, Frank Zimmitti

Department of Mathematics: Dissertations, Theses, and Student Research

A recent series of papers, starting with the paper of Cook, Harbourne, Migliore, and Nagel on the projective plane in 2018, studies a notion of unexpectedness for finite sets Z of points in N-dimensional projective space. Say the complete linear system L of forms of degree d vanishing on Z has dimension t yet for any general point P the linear system of forms vanishing on Z with multiplicity m at P is nonempty. If the dimension of L is more than the expected dimension of t−r, where r is N+m−1 choose …

The Perception Of Natural Resource Management In Nebraska: Efforts For Cross-Boundary Collaborative Management, Daniel Morales

School of Natural Resources: Dissertations, Theses, and Student Research

Nebraska’s agricultural landscapes are rapidly changing, affecting natural resources and their successful management. I utilized two surveys and scenario planning (Chapters 1: statewide survey, 2: local survey, and 3: scenario-planning workshop) to investigate attitudes and perceptions of natural resource management and cross-boundary collaboration. My first objective focused on determining what prevents Nebraskans from addressing natural resources challenges, considering demographics amongst generations and the type of areas they live in (rural versus urban). The second objective focused on whether landowners engaged with their community in managing natural resources. The third objective was to develop alternative future scenarios for the Denton Hills …

Ecological Impacts Of Restoring Fire-Grazing Interaction In Sandhills Prairie Through Patch-Burn Grazing, Nolan P. Sipe

School of Natural Resources: Dissertations, Theses, and Student Research

A Collaborative Adaptive Management (CAM) Project was started at the University of Nebraska in 2020 to address some of the key uncertainties related to the management of grasslands in the Nebraska Sandhills through stakeholder driven experiments and the adaptive management cycle. Patch-burn grazing was selected by CAM as a management tool to generate heterogeneity across the landscape and promote biodiversity while balancing economic and ecological trade-offs. The patch-burn grazing system was implemented with controlled burns in May of 2022 and March of 2023. Other parties in CAM will be examining the impact that patch-burn grazing has on forage and livestock …

Bingroup2: Statistical Tools For Infection Identification Via Group Testing, Christopher R. Bilder, Brianna D. Hitt, Brad J. Biggerstaff, Joshua M. Tebbs, Christopher S. Mcmahan

Department of Statistics: Faculty Publications

Group testing is the process of testing items as an amalgamation, rather than separately, to determine the binary status for each item. Its use was especially important during the COVID-19 pandemic through testing specimens for SARS-CoV-2. The adoption of group testing for this and many other applications is because members of a negative testing group can be declared negative with potentially only one test. This subsequently leads to significant increases in laboratory testing capacity. Whenever a group testing algorithm is put into practice, it is critical for laboratories to understand the algorithm’s operating characteristics, such as the expected number of …

Reimagining Large River Management Using The Resist–Accept–Direct (Rad) Framework In The Upper Mississippi River, Nicole K. Ward, Abigail J. Lynch, Erik A. Beever, Joshua Booker, Kristen L. Bouska, Holly Embke, Jeffrey N. Houser, John F. Kocik, Joshua Kocik, David J. Lawrence, Mary Grace Lemon, Doug Limpinsel, Madeline R. Magee, Bryan M. Maitland, Owen Mckenna, Andrew Meier, John M. Morton, Jeffrey D. Muehlbauer, Robert Newman, Devon C. Oliver, Heidi M. Rantala, Greg G. Sass, Aaron Shultz, Laura M. Thompson, Jennifer L. Wilkening

School of Natural Resources: Faculty Publications

Background: Large-river decision-makers are charged with maintaining diverse ecosystem services through unprecedented social-ecological transformations as climate change and other global stressors intensify. The interconnected, dendritic habitats of rivers, which often demarcate jurisdictional boundaries, generate complex management challenges. Here, we explore how the Resist–Accept–Direct (RAD) framework may enhance large-river management by promoting coordinated and deliberate responses to social-ecological trajectories of change. The RAD framework identifies the full decision space of potential management approaches, wherein managers may resist change to maintain historical conditions, accept change toward different conditions, or direct change to a specified future with novel conditions. In the Upper Mississippi …

Good Practices And Common Pitfalls In Climate Time Series Changepoint Techniques: A Review, Robert B. Lund, Claudie Beaulieu, Rebecca Killick, Qiqi Lu, Xueheng Shi

Department of Statistics: Faculty Publications

Climate changepoint (homogenization) methods abound today, with a myriad of techniques existing in both the climate and statistics literature. Unfortunately, the appropriate changepoint technique to use remains unclear to many. Further complicating issues, changepoint conclusions are not robust to perturbations in assumptions; for example, allowing for a trend or correlation in the series can drastically change changepoint conclusions. This paper is a review of the topic, with an emphasis on illuminating the models and techniques that allow the scientist to make reliable conclusions. Pitfalls to avoid are demonstrated via actual applications. The discourse begins by narrating the salient statistical features …

Accelerated Evolution Of Sars-Cov-2 In Free-Ranging White-Tailed Deer, Dillon S. Mcbride, Sofya K. Garushyants, John Franks, Andrew F. Magee, Steven H. Overend, Devra Huey, Amanda M. Williams, Seth A. Faith, Ahmed Kandeil, Sanja Trifkovic, Lance Miller, Trushar Jeevan, Anami Patel, Jacqueline M. Nolting, Michael J. Tonkovich, J. Tyler Genders, Andrew J. Montoney, Kevin Kasnyik, Timothy J. Linder, Sarah N. Bevins, Julianna B. Lenoch, Jeffrey C. Chandler, Thomas J. Deliberto, Eugene V. Koonin, Marc A. Suchard, Philippe Lemey, Richard J. Webby, Martha I. Nelson, Andrew S. Bowman

United States Department of Agriculture Wildlife Services: Staff Publications

The zoonotic origin of the COVID-19 pandemic virus highlights the need to fill the vast gaps in our knowledge of SARS-CoV-2 ecology and evolution in non-human hosts. Here, we detected that SARS-CoV-2 was introduced from humans into white-tailed deer more than 30 times in Ohio, USA during November 2021-March 2022. Subsequently, deer-to-deer transmission persisted for 2–8 months, disseminating across hundreds of kilometers. Newly developed Bayesian phylogenetic methods quantified how SARS-CoV-2 evolution is not only three-times faster in white-tailed deer compared to the rate observed in humans but also driven by different mutational biases and selection pressures. The long-term effect of …

Rapid Evolution Of A(H5n1) Influenza Viruses After Intercontinental Spread To North America, Ahmed Kandeil, Christopher Patton, Jeremy C. Jones, Trushar Jeevan, Walter N. Harrington, Sanja Trifkovic, Jon P. Seiler, Thomas Fabrizio, Karlie Woodard, Jasmine C. Turner, Jeri Carol Crumpton, Lance Miller, Adam Rubrum, Jennifer Debeauchamp, Charles J. Russell, Elena A. Govorkova, Peter Vogel, Mia Kim-Torchetti, Yohannes Berhane, David Stallknecht, Rebecca Poulson, Lisa Kercher, Richard J. Webby

United States Department of Agriculture Wildlife Services: Staff Publications

Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b underwent an explosive geographic expansion in 2021 among wild birds and domestic poultry across Asia, Europe, and Africa. By the end of 2021, 2.3.4.4b viruses were detected in North America, signifying further intercontinental spread. Here we show that the western movement of clade 2.3.4.4b was quickly followed by reassortment with viruses circulating in wild birds in North America, resulting in the acquisition of different combinations of ribonucleoprotein genes. These reassortant A(H5N1) viruses are genotypically and phenotypically diverse, with many causing severe disease with dramatic neurologic involvement in mammals. The proclivity of …

Enhancing Urban Water Quality Through Biological-Chemical Treatment: Aquatic Macroinvertebrate Community And Temporal Chlorophyll-A Response, Matthew Chaffee

Department of Biological Systems Engineering: Dissertations and Theses

With a growing human population, urbanization is impeding a plethora of natural waterways. Of these, urban ponds play a vital role in nutrient sequestration, flood prevention, and habitat sanctuaries. However, nutrient loading can reduce habitat effectiveness and promote harmful algae blooms. To reduce internal nutrient loads, a biological-chemical treatment strategy consisting of floating treatment wetlands (FTWs) and lanthanum were applied to two urban retention ponds, Densmore and Wilderness Ridge Ponds. To measure effectiveness, chlorophyll-a samples were collected and correlated with Sentinel-2. A novel band algorithm termed 3BR1 produced a strong correlation (R² = 0.72) to physical chlorophyll-a …