Physical Sciences and Mathematics Commons^™

Applications Of Statistical Physics To Ecology: Ising Models And Two-Cycle Coupled Oscillators, Vahini Reddy Nareddy

Doctoral Dissertations

Many ecological systems exhibit noisy period-2 oscillations and, when they are spatially extended, they undergo phase transition from synchrony to incoherence in the Ising universality class. Period-2 cycles have two possible phases of oscillations and can be represented as two states in the bistable systems. Understanding the dynamics of ecological systems by representing their oscillations as bistable states and developing dynamical models using the tools from statistical physics to predict their future states is the focus of this thesis. As the ecological oscillators with two-cycle behavior undergo phase transitions in the Ising universality class, many features of synchrony and equilibrium …

Frontiers In The Self-Assembly Of Charged Macromolecules, Khatcher O. Margossian

Doctoral Dissertations

The self-assembly of charged macromolecules forms the basis of all life on earth. From the synthesis and replication of nucleic acids, to the association of DNA to chromatin, to the targeting of RNA to various cellular compartments, to the astonishingly consistent folding of proteins, all life depends on the physics of the organization and dynamics of charged polymers. In this dissertation, I address several of the newest challenges in the assembly of these types of materials. First, I describe the exciting new physics of the complexation between polyzwitterions and polyelectrolytes. These materials open new questions and possibilities within the context …

Intracellular Delivery Of Therapeutic Biomolecules Through Versatile Polymer Nanotechnology, David C. Luther

Doctoral Dissertations

Advancing pharmaceutical technology has made it possible to treat diseases once considered ‘undruggable.’ Access to these new pharmaceutical targets is possible thanks to the advent of protein and nucleic acid therapeutics. Responses to the COVID-19 pandemic, as well as cutting-edge treatments for cancer and multiple sclerosis have centered on these biologic therapies, promising even greater value in the future. However, their utility is limited at a cellular level by inability to cross the plasma membrane. Nanocarrier technologies encapsulate therapeutics and facilitate uptake into the cell but are often trapped and degraded in endosomes. Arginine-functionalized gold nanoparticles (Arg-NPs) provide efficient, direct …

Quantification Of Hydrologic Response To Forest Disturbance In Western U.S. Watersheds, Sara A. Goeking '92

Doctoral Dissertations

Forested watersheds produce more than half of the water supply in the United States. Forests affect how precipitation is partitioned into available water versus evapotranspiration. This dissertation investigated how water yield and snowpack responded to forest disturbance following recent disturbances in western U.S. forests during the period 2000-2019.

Chapter 2 systematically reviewed 78 recent studies that examined how water yield or snowpack changed after forest disturbances. Water yield and snowpack often increased after disturbance, but decreased in some circumstances. Decreased water yield was most likely to occur following disturbances that did not remove the entire forest canopy. It was also …

Better Understanding Genomic Architecture With The Use Of Applied Statistics And Explainable Artificial Intelligence, Jonathon C. Romero

Doctoral Dissertations

With the continuous improvements in biological data collection, new techniques are needed to better understand the complex relationships in genomic and other biological data sets. Explainable Artificial Intelligence (X-AI) techniques like Iterative Random Forest (iRF) excel at finding interactions within data, such as genomic epistasis. Here, the introduction of new methods to mine for these complex interactions is shown in a variety of scenarios. The application of iRF as a method for Genomic Wide Epistasis Studies shows that the method is robust in finding interacting sets of features in synthetic data, without requiring the exponentially increasing computation time of many …

Design And Development Of The Urban Population Health Observatory To Improve Disease Surveillance And Response, Whitney Brakefield

Doctoral Dissertations

Chronic and infectious diseases have a profound impact on the quality and length of life of populations that suffer from these conditions. Scientists, physicians, and health officials are seeking innovative approaches to decrease the morbidity and mortality of deadly diseases. Incorporating artificial intelligence and data science techniques across the health science domain could improve disease surveillance, intervention planning, and policymaking. In this dissertation, we describe the design and development of the Urban Population Health Observatory (UPHO), an explainable knowledge-based multimodal big data analytics platform. A common challenge for conducting multimodal big data analytics is integrating multidimensional heterogeneous data sources, which …

Perceptions Of Historical Climate Change And Park Policy: The Impact On The Fremont Cottonwood In Zion National Park, Kathleen Kavarra Corr

Doctoral Dissertations

Despite its “natural” appearance and the Organic Act 1916 mandate for preservation of the natural environment in National Parks, the Virgin River as it flows through Zion National Park’s Zion Canyon was transformed through massive flood control re-engineering projects in the 1930s. The armoring of the river has had significant impacts on riparian vegetation, particularly on the stands of native Fremont Cottonwood trees that once filled the narrow valley. What was the motivation for this massive flood control project carried out in an arid region with less than 15 inches of rain per year? This dissertation explores the motivations which …

Deciphering Protein Higher-Order Structure And Interactions Via Diethylpyrocarbonate Labeling-Mass Spectrometry, Xiao Pan

Doctoral Dissertations

The study of protein higher-order structures is vital because it is closely related to the investigation of protein folding, aggregation, interaction and protein therapeutics. Consequently, numerous biochemical and biophysical tools have been developed to study protein higher-order structures in many different situations. The combination of covalent labeling (CL) and mass spectrometry (MS) has emerged as a powerful tool for studying protein structures and offers many advantages over other traditional techniques, such as better structural coverage, high throughput, high sensitivity, and the ability to study proteins in mixtures. This dissertation focuses on diethylpyrocarbonate (DEPC) as an effective CL reagent that can …

Quantitative Imaging Of Tensile Forces At Cell-Cell Junction With Dna-Based Probes, Puspam Keshri

Doctoral Dissertations

Mechanical forces are an integral part in biology, they regulate several cellular properties, such as morphology, proliferation, migration. These forces are also involved in receptor signaling and the differentiation of different cell types. Different proteins and biomolecules such as cadherin, integrin, notch proteins are essential elements of these processes. Measuring these intercellular forces are challenging considering the minimal intensity (piconewton-level) of these molecular forces. In our lab, we have developed a membrane DNA tension probe (MDTP) that uses a DNA hairpin module to sense tensile forces and has a lipid anchor to modify onto live-cell membranes. The programmability of DNA …

Design And Synthesis Of Purine Based Neuroprotectors And Novel Synthetic Methods For The Trifluoromethylation Of Aldehyde Hydrazones, Puspa Aryal

Doctoral Dissertations

"Purine-derived compounds are widely investigated as cyclin-dependent kinase inhibitors that have broad applications in the design of pharmaceuticals for treating diseases, such as diabetes, atherosclerosis, and cancers. Towards the goal of effective AGE-inhibitors, and neuroprotector compounds we have synthesized a series of novel purine-based triazoles and investigated their neuroprotective effects, using SHSY-3Y human neuroblastoma cell line. Through these studies, we have identified purine-based neuroprotector compounds that favorably modulate oxidative stress induced by the Fenton reaction-generated reactive oxygen species (ROS).

The C(sp²−H)-trifluoromethylation of hydrazones would give access to the αtrifluoromethylated hydrazones that can serve as intermediates in the synthesis …