Biological and Chemical Physics Commons^™

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 …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Jwst: Deuterated Pahs, Pah-Nitriles, And Pah 4 Overtone And Combination Bands I: Program Description And First Look, C. Boersma, L. J. Allamandola, Vincent J. Esposito, A. Maragkoudakis, J. D. Bregman, P. Temi, T. J. Lee, R. C. Fortenberry, E. Peeters

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A first look is taken at the NIRSpec 1–5 μm observations from James Webb Space Telescope program 1591 that targets seven objects along the low-mass stellar life cycle with polycyclic aromatic hydrocarbon (PAH) emission. Spectra extracted from a 1'.'5 radius circular aperture are explored, showing a wealth of features, including the 3 μm PAH complex, the PAH continuum, and atomic and molecular emission lines from H i, He, H₂, and other species. CO₂- and H₂O-ice absorption and CO emission is also seen. Focusing on the bright-PDR position in M17, the PAH CH stretch falls …

Raman Spectroscopic Analysis Of Human Serum Samples Of Convalescing Covid-19 Positive Patients, Hugh Byrne, Naomi Jackson, Jaythoon Hassan

Articles

Rapid screening, detection and monitoring of viral infection is of critical importance, as exemplified by the rapid spread of SARS-CoV-2, leading to the worldwide pandemic of COVID-19. This is equally the case for the stages of patient convalescence as for the initial stages of infection, to understand the medium and long terms effects, as well as the efficacy of therapeutic interventions. Optical spectroscopic techniques potentially offer an alternative to currently employed techniques of screening for the presence, or the response to infection. In this study, the ability of Raman spectroscopy to distinguish between samples of the serum of convalescent COVID-19 …

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

Langevin Dynamic Models For Smfret Dynamic Shift, David Frost, Keisha Cook Dr, Hugo Sanabria Dr

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Entanglements Of Teenage Food Security Within High School Pantries In Pinellas County, Florida, Karen T. Díaz Serrano

USF Tampa Graduate Theses and Dissertations

Food insecurity has the ability to shape an individual’s or a family’s everyday life and take emotional, psychological, and physical tolls. Among adolescents, not having access to nutritious food could lead to physical effects during growth and development. Moreover, the stress and anxiety of not knowing where their next meal is coming from and the social stigma associated with being food insecure can have negative effects on mental health. A recent solution to these issues is locating food pantries in high schools. Purpose: This exploratory study examined how high school students in Pinellas County, Florida perceive the use of a …

Biosynthesis Of Mgo Nanoparticles And Their Impact On The Properties Of The Pva/Gelatin Nanocomposites For Smart Food Packaging Applications, Mohamed Morsy

Nanotechnology Research Centre

No abstract provided.

Anharmonic Ir Absorption Spectra Of The Prototypical Interstellar Pahs Phenanthrene, Pyrene, And Pentacene In Their Neutral And Cation States, Vincent J. Esposito, Louis J. Allamandola, Christiaan Boersma, Jesse D. Bregman, Ryan C. Fortenberry, Alexandros Maragkoudakis, Pasquale Temi

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Combination band and overtone transitions of polycyclic aromatic hydrocarbon (PAH) cations in the 2000–2900 cm^-1 (5-3.5 µm) region are implicated as carriers of the ‘quasi-continuum’ observed in the near-infrared (IR) emission spectra of many astronomical objects. In neutral PAHs, the strongest absorption features are concentrated in the 700–900 cm^-1 (14–11 µm) range, which are associated with CH out-of-plane bending motions. Upon ionization, this shifts to the 1000–1600 cm^-1 (10–6 µm) range, where bands are associated with C=C stretches and CH in-plane bends. Anharmonicity is required to accurately characterize the IR absorption spectrum of PAHs, indicated herein by …

Anharmonicity And Deuteration In The Ir Absorption And Emission Spectra Of Phenylacetylene, Vincent J. Esposito, Pierro Ferrari, Wybren Jan Buma, Christiaan Boersma, Cameron J. Mackie, Alessandra Candian, Ryan C. Fortenberry, Alexander G. G. M. Tielens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Anharmonic cascade emission simulations, herein evinced by full reproduction and deep insights into recent emission spectroscopy experiments of phenylacetylene, are integral to the future successful analysis of JWST observational spectra. Experimental infrared absorption experiments conducted in this study reveal a complex spectrum dominated by quantum effects that are uncovered by anharmonic computational analysis. From this work, it becomes clear that phenylacetylene exhibits strong resonance coupling between fundamental and two-quanta combination modes as well as giving indication for coupling with higher-order, three-quanta combination bands. This study benchmarks the development of advanced computational methods that will be extended to larger systems of …