Biological and Chemical Physics Commons^™

6d Single-Fluorogen Orientation-Localization Microscopy For Elucidating The Architecture Of Beta-Sheet Assemblies And Biomolecular Condensates, Tingting Wu, Weiyan Zhou, Jai S. Rudra, Rohit V. Pappu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We develop six-dimensional single-molecule orientation-localization microscopy (SMOLM) to measure the 3D positions and 3D orientations simultaneously of single fluorophores. We show how careful optimization of phase and polarization modulation components can encode phase, polarization, and angular spectrum information from each fluorescence photon into a microscope’s dipole-spread function. We used the transient binding and blinking of Nile red (NR) to characterize the helical structure of fibrils formed by designed amphipathic peptides, KFE8^L and KFE8^D, and the pathological amyloid-beta peptide Aβ42. We also deployed merocyanine 540 to uncover the interfacial architectures of biomolecular condensates.

Spectralomics – Towards A Holistic Adaptation Of Label Free Spectroscopy, Hugh Byrne

Articles

Vibrational spectroscopy, largely based on infrared absorption and Raman scattering techniques, is much vaunted as a label free approach, delivering a high content, holistic characterisation of a sample, with demonstrable applications in a broad range of fields, from process analytical technologies and preclinical drug screening, to disease diagnostics, therapeutics, prognostics and personalised medicine. However, in the analysis of such complex systems, a trend has emerged in which spectral analysis is reduced to the identification of individual peaks, based on reference tables of assignments derived from literature, which are then interpreted as biomarkers. More sophisticated analysis attempts to unmix the spectrum …

A Causal Inference Approach For Spike Train Interactions, Zach Saccomano

Dissertations, Theses, and Capstone Projects

Since the 1960s, neuroscientists have worked on the problem of estimating synaptic properties, such as connectivity and strength, from simultaneously recorded spike trains. Recent years have seen renewed interest in the problem coinciding with rapid advances in experimental technologies, including an approximate exponential increase in the number of neurons that can be recorded in parallel and perturbation techniques such as optogenetics that can be used to calibrate and validate causal hypotheses about functional connectivity. This thesis presents a mathematical examination of synaptic inference from two perspectives: (1) using in vivo data and biophysical models, we ask in what cases the …

Toward The Ir Detection Of Carbon Acid: Absorption And Emission Spectrum, Ryan C. Fortenberry, Vincent J. Esposito

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

With the recent radioastronomical detection of cis-trans-carbonic acid (H₂CO₃) in a molecular cloud toward the Galactic center, the more stable but currently unobserved cis-cis conformer is shown here to have strong IR features. While the higher-energy cis-trans-carbonic acid was detected at millimeter and centimeter wavelengths, owing to its larger dipole moment, the vibrational structure of cis-cis-carbonic acid is more amenable to its observation at micron wavelengths. Even so, both conformers have relatively large IR intensities, and some of these fall in regions not dominated by polycyclic aromatic hydrocarbons. Water features may inhibit observation …

Synthesis Of Cu-Cy Nanoparticles For Treating Pfas In Water, Ligang Wang

Physics Theses - Archive

This work aims to address the cumulative harm caused by perfluoroalkyl and polyfluoroalkyl substances (PFAS) in water to human health and the ecological environment around the world. Reducing or removing PFAS pollution is an urgent need. Cu-Cy nanoparticles are photosensitizers, which were developed for photodynamic therapy of cancer in the first place. In this work, we use Cu-Cy for the catalytic degradation of PFAS. Synthesis of Cu-Cy nanoparticles in deionized water at 90 degrees Celsius is a low-cost and efficient method. We demonstrated the detailed process of synthesizing Cu-Cy nanoparticles. Under ultraviolet illumination, the synthesized Cu-Cy nanoparticles turned yellow as …

Next-Generation Alpha Irradiation Platform: Design, Development, And Applications In Radiobiological Research, Harsh Arya

Physics Dissertations - Archive

This dissertation unveils the innovative design, development, and application of a next-generation alpha irradiation platform, specifically crafted for pre-clinical and university-level radiobiological research. Driven by the quest to overcome the inherent limitations of existing alpha particle irradiators, this study explores the profound therapeutic potential of alpha particles in cancer treatment. Known for their exceptional high linear energy transfer (LET), alpha particles exhibit a unique prowess in inducing clustered DNA damage, sparking intriguing possibilities for highly targeted cancer therapies. Yet, their application has been historically constrained by their limited range of biological tissues and the absence of precise delivery systems.

Our …

Outpatient Fall Prevention In Ambulatory Adults 65 Years Old And Over, Dorothy L. Osborne-White

Doctor of Nursing Practice (DNP) Scholarly Projects - Archive

Background: In the United States (U.S.), falls are the leading cause of injury among adults 65 and over, resulting in 36 million falls yearly (Moreland et al., 2020). According to the Centers for Disease Control and Prevention (CDC, 2023), one in four older adults experiences a fall each year. Falls are the world's second most prominent cause of accidental deaths (World Health Organization [WHO], 2021). Falls are the leading cause of both fatal and non-fatal injuries among older adults (Moreland et al., 2020).

Methods: A quality improvement project that included a fall bundle was implemented in a primary clinic. A …

Spiral Wave Teleportation And Multiplex Network Synchronization In Light Sensitive Belousov-Zhabotinsky Systems, Shannyn Alicia Tyler

Graduate Theses, Dissertations, and Problem Reports (ETD)

We experimentally and computationally investigate dynamical behaviors in excitable and oscillatory media using light sensitive Belousov-Zhabotinsky (BZ) systems. These systems are not in a state of thermodynamic equilibrium, and have been proven to show various interesting phenomena including spatiotemporal patterns, self-organization, and chaos. We utilize the BZ reaction, a nonlinear chemical reaction, known for its relaxation-type oscillations, to explore the dynamics of these systems.

We examine spiral wave teleportation in an excitable media as an effective alternate defibrillation method. Spiral waves have emerged as a key phenomenon associated with the initiation and persistence of cardiac arrhythmias. Using a light sensitive …

Plant Root Hair Adhesion Mediated Through Variation In Sodium Ion Concentration, Natasha Mulenga

Honors Program Theses

This study investigates the effects of sodium ion (Na+) concentration on the adhesion of Brassica Rapa root hairs using atomic force microscopy (AFM). Plant root hair adhesion to soil particles plays a crucial role in anchoring plants and facilitating nutrient uptake. Previous research has shown that calcium ions (Ca2+) cross-link pectin molecules in the cell wall, increasing rigidity and reducing adhesion. As Na+ binds to pectin without cross-linking, we expected that root hairs exposed to sodium chloride (NaCl) solutions would exhibit longer adhesive interactions and similar binding forces compared to those exposed to calcium chloride (CaCl2) solutions of equal concentrations. …

Transient Diode Laser Absorption Spectroscopy For Measuring Collisional Quenching Rates Of Co And Its Potential For Studying H2o, Jordan M. Polvere

Master’s Theses

Motivated by the necessity of non-LTE models that account for species that are not in Local Thermodynamic Equilibrium (LTE) in Titan’s and Earth’s atmospheres, collisional quenching rates of CO and H2O_(g) have been studied. Providing more accurate and precise values of collisional quenching rate coefficients is crucial in the development of more advanced atmospheric models, which are important to fields of science such as meteorology and astronomy. Rates of collisional quenching of CO(v=1,2) by CO and CO(v=2) by N₂ at approximately 301-321 K were measured by transient diode laser absorption spectroscopy. The rate coefficients of CO(v=1)-CO, CO(v=2)-CO, and …

Orbital And Spin Angular Momentum Light Generation, Interactions, Special Photons, And Applications In Liquids, Solids, Vapors And Biological Tissue Media, Sandra Mamani Reyes

Dissertations and Theses

Photons possess many characteristics such as wavelength, coherence, speed, polarization and wavefront. The aim of this thesis is the study of two salient properties of light exploring light carrying polarization and space degree of freedom of the wavefront. The wavefront of light is complex with different states of polarization. Special light beams are generated and characterized for interaction with liquids, solids, vapors, and bio- materials to understand fundamental processes such as Transmission, Raman scattering, and Optical Kerr Effect in steady state and temporal domains.

It has been more than hundred years since it is known that light can carry other …

Mathematical Analysis Of Eukaryotic Pericentromere, Puranjan Ghimire

Theses and Dissertations

The centromere is crucial for chromosomal stability and their proper segregation during cell division in eukaryotes. Surrounding the centromere are pericentromeres, made of repetitive DNA elements called pericentromeric repeats, varying from 10 in fission yeast to thousands in humans. These repeats form densely packed heterochromatin, where genes are usually silenced. The silencing mechanism across different pericentromeric repeats remains unclear.

Despite variations in sequence and length, pericentromeric repeats are conserved across eukaryotes, indicating their functional importance. This dissertation presents mathematical models to quantify gene silencing in fission yeast and humans. In fission yeast, my model predicts that silencing occurs only with …