Biological and Chemical Physics Commons^™

Stability Of Group Four Monochalcogenides In Water And Air, William Shattuck

Graduate Theses and Dissertations

Previously published works have simulated the behavior of monolayer group IV monochalcogenides and predicted them to have very useful electronic properties. These simulations have also predicted that monolayers of group IV monochalcogenides will degrade quickly when exposed to water, even in extremely low concentrations. We hypothesize that thin samples of these materials will show signs of degradation if left in air and in water for an extended period of time.

Samples of each of the four monochalcogenides (GeS, GeSe, SnS and SnSe) were exfoliated onto clean oxidized silicon substrates. Chemical analysis showed the SnSe samples were contaminated, so they were …

Hyperpolarized Carbon-13 Magnetic Resonance Measurements Of Tissue Perfusion And Metabolism, Keith Michel

Dissertations and Theses (Open Access)

Hyperpolarized Magnetic Resonance Imaging (HP MRI) is an emerging modality that enables non-invasive interrogation of cells and tissues with unprecedented biochemical detail. This technology provides rapid imaging measurements of the activity of a small quantity of molecules with a strongly polarized nuclear magnetic moment. This polarization is created in a polarizer separate from the imaging magnet, and decays continuously towards a non-detectable thermal equilibrium once the imaging agent is removed from the polarizer and administered by intravenous injection. Specialized imaging strategies are therefore needed to extract as much information as possible from the HP signal during its limited lifetime.

In …

Nuclear-Targeted Gold Nanoparticles Enhance The Effects Of Radiation Therapy With And Without Liposomal Delivery, Maureen Aliru

Dissertations and Theses (Open Access)

Less that 10% of pancreatic cancer patients are eligible for curative resection, and clinical trials evaluating chemoradiation in locally advanced patients with unresectable disease have been largely disappointing. New and creative therapeutic approaches are needed to address the unment need for treatment options. The objective of this thesis is to advance radiosensitization of treatment-resistant densely desmoplastic pancreatic cancer using nanoparticles to surmount biological barriers to effective particle distribution for DNA-targeting.

Clinical translation of radiosensitizing nanoparticles has stalled owing to technical challenges. Current strategies to use AuNPs for radiosensitization require large quantities of gold, kilovoltage x-rays, immediate irradiation after intravenous administration, …

Characterizing Childhood And Diet In Migration Period Hungary, Kirsten A. Verostick

USF Tampa Graduate Theses and Dissertations

This project investigates children, childhood and diet of two different Migration Period (4^th-8^th century AD) populations, the Gepids and the Avars, in the Great Hungarian Plain. The main goal was to assess whether there are differences in treatment of children and differences in breastfeeding and weaning practices in these distinct sites and populations. Secondarily, this research also focused on characterizing diet for the Gepids and the Avars at four different sites from the Migration Period, to understand how the migration and settling into the region and the assimilation of other groups into the two populations affected their …

Maternal Social Status, Offspring 2d:4d Ratio And Postnatal Growth, In Macaca Mulatta (Rhesus Macaques), Juan Pablo Arroyo

USF Tampa Graduate Theses and Dissertations

Early life exposure to stressors can disrupt growth and development, resulting in long-term compromised function and increased risk for disease throughout the lifecourse. Maternal exposure to psychosocial stressors (i.e., stressors derived from social status, social inequalities, and social interactions) during pregnancy has been associated with reduced fetal growth, adverse birth outcomes, and increased morbidity for the offspring later in life. Maternal hormonal responses to stress, such as fluctuations in glucocorticoids (e.g., cortisol) and androgens (e.g., testosterone), can result in increased developmental instability, interfere with offspring growth in-utero, and may alter developmental processes of sexual dimorphism. Second digit to fourth digit …

High Level Ab Initio Study Of The Energetic And Spectroscopic Properties Of [Al,S,O]X (X=0,+1) And Its Potential For Detection In Space, Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Highly reliable molecular properties have been computed for the [Al, S, O]^x (x = 0, +1) molecular system. Spectroscopic parameters are predicted from analysis of each isomer’s 3D potential energy surface calculated using the explicitly correlated multireference configuration interaction method, including the Davidson correction (MRCI-F12+Q). These parameters provide an accurate prediction of spectroscopic data that can be used in laboratory and observational studies of these molecules. Linear-SAlO is expected to have a large permanent dipole moment suitable for detection in the circumstellar envelopes of large, evolved, oxygen-rich stars such as VY Canis Majoris, IK Tauri, and R Doradus. …

Protein Conformational Entropy Is Not Slaved To Water, Bryan S Marques, Matthew A Stetz, Christine Jorge, Kathleen G Valentine, A Joshua Wand, Nathaniel V Nucci

College of Science & Mathematics Departmental Research

Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The "solvent slaving" model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side …

Period Estimation And Noise In A Neutrally Stable Stochastic Oscillator, Kevin R. Sanft, Ben F. M. Intoy

Spora: A Journal of Biomathematics

The periods of the orbits for the well-mixed cyclic three-species Lotka-Volterra model far away from the fixed point are studied. For finite system sizes, a discrete stochastic approach is employed and periods are found via wavelet analysis. As the system size is increased, a hierarchy of approximations ranging from Poisson noise to Gaussian noise to deterministic models are utilized. Based on the deterministic equations, a mathematical relationship between a conserved quantity of the model and the period of the population oscillations is found. Exploiting this property we then study the deterministic conserved quantity and period noise in finite size systems.

Water-Soluble Graphene In Agar Gel As Electrolyte For Magnesium-Air Battery, Liew Siaw Ying

Student Works (2020-2029)

Presently, ever-increasing demands on energy and the global environmental issues have given the impetus to investigate the new battery systems which are inexpensive, efficient, having high performance, and also green to the environment. Among all the battery technologies, magnesium-air (Mg-air) battery is an attractive battery to be developed owing to the interesting properties of the Mg anode. Mg has high specific energy (6.46 kWh kg-1) and reactivity, apart from its high abundance, lower cost, low toxicity, and comparatively safe to handle in the atmosphere. Nevertheless, Mg-air battery is still not being widely investigated as compared to the other batteries. Electrolyte …

Pressure-Stabilized Divalent Ozonide Cao3 And Its Impact On Earth’S Oxygen Cycles, Yanchao Wang, Meiling Xu, Liuxiang Yang, Bingmin Yan, Qin Qin, Xuecheng Shao, Yunwei Zhang, Dajian Huang, Xiaohuan Lin, Jian Lv, Dongzhou Zhang, Huiyang Gou, Ho-Kwang Mao, Changfeng Chen, Yanming Ma

Physics & Astronomy Faculty Research

High pressure can drastically alter chemical bonding and produce exotic compounds that defy conventional wisdom. Especially significant are compounds pertaining to oxygen cycles inside Earth, which hold key to understanding major geological events that impact the environment essential to life on Earth. Here we report the discovery of pressure-stabilized divalent ozonide CaO3 crystal that exhibits intriguing bonding and oxidation states with profound geological implications. Our computational study identifies a crystalline phase of CaO3 by reaction of CaO and O2 at high pressure and high temperature conditions; ensuing experiments synthesize this rare compound under compression in a diamond anvil cell with …

Pressure Driven Desalination Utilizing Nanomaterials, Fangyou Xie

Master's Theses

Nanomaterials such as graphene oxide and carbon nanotubes, have demonstrated excellent properties for membrane desalination, including decrease of maintenance, increase of flux rate, simple solution casting, and impressive chemical inertness. Here, two projects are studied to investigate nanocarbon based membrane desalination. The first project is to prepare hybrid membranes with amyloid fibrils intercalated with graphene oxide sheets. The addition of protein amyloid fibrils expands the interlayer spacing between graphene oxide nanosheets and introduces additional functional groups in the diffusion pathways, resulting in increase of flux rate and rejection rate for the organic dyes. Amyloid fibrils also provide structural assistance to …

Embedded Gold Nanoparticles For Metal Enhanced Photoluminescence, Hasna Alali

Dissertations

Noble metal nanoparticles (MNPs) have attracted great attention in electronics, solar cells and catalysis. Their unique optical properties and biocompatibility makes them useful in biological applications like imaging, drug delivery, therapy and diagnostic. At the surface of MNPs the collective oscillation of free electrons resonates with a particular wavelength of incident light, generating the Localized Surface Plasmons Resonance (LSPR). LSPR results in absorption and scattering of incident light. Scattering results in reflecting photons and absorption leads to enhanced photoluminescence and quenching of fluorophores, if the fluorophore is in the vicinity of MNPs.

Most of the studies in this regard have …

Improved Antimicrobial Properties Of Silver Nanoparticles With Methylene Blue, Ermek Belekov

Masters Theses & Specialist Projects

Photosensitizing agents are the cornerstone of photodynamic therapy (PDT) that play essential role in deactivation process of multidrug resistant pathogens and tumor treatments. In this work we studied a photosensitizing agent made from mixture of silver nanoparticles (Ag NPs) and methylene blue (MB) which possess improved important characteristics like high photostability and high singlet oxygen yield. Ag NPs were synthesized by pulsed laser ablation technique in different aqueous solutions like Polyvinylpyrrolidone (PVP), citrate and Deionized (DI) water. The synthesized Ag NPs were characterized in depth using with transmission electron microscopy (TEM), UVVisible (UV-Vis), and photoluminescence (PL) spectra. Ag NPs were …

Investigation Of The Structural, Electronic, And Thermoelectric Properties Of Mono- Chalcogenides, Aida Sheibani

Graduate Theses and Dissertations

The structural, electronic, and thermoelectric properties of GeTe are studied using density functional theory and Boltzmann transport equations. This material has a rhombohedral crystal structure in ambient temperature with a ferroelectric behavior due to lack of inversion symmetry. This study suggests that the presence of asymmetry in GeTe can lead to an improvement in the thermoelectric properties of this material. In addition, studies on introducing Group III, IV, and V dopants to GeSe show that while these impurities can improve the power factor and decrease the lattice thermal conductivity, they cannot enhance the figure of merit.

Visualization Of Brown Fat Using X-Ray Dark Field Imaging, Troy D. Jacobs

LSU Master's Theses

Introduction: Obesity has become a major societal issue. Many researchers are looking for ways to combat this growing epidemic. Brown adipose tissue (BAT) might be a way to help individuals overcome the challenges associated with weight loss and maintenance of weight loss, but a better understanding of BAT and how to control and utilize it is needed. BAT differs from white adipose tissue (WAT) in that BAT is rich with mitochondria and therefore is metabolically active. BAT is a source of non-shivering thermogenesis and can be activated both by cold exposure and pharmacologically. Current methods of assessing BAT activity are …

Circuits With Broken Fibration Symmetries Perform Core Logic Computations In Biological Networks, Ian Leifer, Flaviano Morone, Saulo D. S. Reis, José S. Andrade Jr., Mariano Sigman, Hernán A. Makse

Publications and Research

We show that logic computational circuits in gene regulatory networks arise from a fibration symmetry breaking in the network structure. From this idea we implement a constructive procedure that reveals a hierarchy of genetic circuits, ubiquitous across species, that are surprising analogues to the emblematic circuits of solid-state electronics: starting from the transistor and progressing to ring oscillators, current-mirror circuits to toggle switches and flip-flops. These canonical variants serve fundamental operations of synchronization and clocks (in their symmetric states) and memory storage (in their broken symmetry states). These conclusions introduce a theoretically principled strategy to search for computational building blocks …

Non-Adiabatic Quantum Dynamics Of The Ultracold Li+Lina→ Li2+Na Chemical Reaction, B. K. Kendrick, M. Li, H. Li, S. Kotochigova, J. F.E. Croft, Balakrishnan Naduvalath

Chemistry and Biochemistry Faculty Research

We report non-adiabatic dynamics of the Li+LiNa→Li2+Na chemical reaction at cold and ultracold temperatures employing accurate ab initio electronic potential energy surfaces in a quantum dynamics formulation employing a diabatic representation. Results are compared against those from a single adiabatic ground state potential energy surface and a universal model based on the long-range interaction potential. We discuss signatures of non-universal behavior in the total rate coefficients as well as strong non-adiabatic effects in the state-to-state rotationally resolved rate coefficients.

Testing A Thermodynamic Approach To Collective Animal Behavior In Laboratory Fish Schools, Julia A. Giannini, James G. Puckett

Physics and Astronomy Faculty Publications

Collective behaviors displayed by groups of social animals are observed frequently in nature. Understanding and predicting the behavior of complex biological systems is dependent on developing effective descriptions and models. While collective animal systems are characteristically nonequilibrium, we can employ concepts from equilibrium statistical mechanics to motivate the measurement of material-like properties in laboratory animal aggregates. Here, we present results from a new set of experiments that utilize high speed footage of two-dimensional schooling events, particle tracking, and projected static and dynamic light fields to observe and control the behavior of negatively phototaxic fish schools (Hemigrammus bleheri). First, …

Proton Pumping Mechanism In Cytochrome C Oxidase, Xiuhong Cai

Dissertations, Theses, and Capstone Projects

Cytochrome c Oxidase (CcO), is the terminal electron acceptor in the membrane bound aerobic respiratory chain. It reduces O₂ to water. The energy released by this reaction is stored by pumping protons from the high pH, N-side of the membrane to the low pH, P-side. The generated proton gradient provides the motive force for synthesis of ATP by the ATP synthase.

Building a proton gradient across the membrane requires that proton transport must occur along controllable proton pathways to prevent proton leakage to the N-side. It has been suggested that CcO function requires proton transfer channels in both the …

Emergence, Mechanics, And Development: How Behavior And Geometry Underlie Cowrie Seashell Form, Michael G. Levy, Michael R. Deweese

Biology and Medicine Through Mathematics Conference

No abstract provided.

Additive Modulation Of Dna-Dna Interactions By Interstitial Ions, Wei Meng, Raju Timsina, Abby Bull, Kurt Andresen, Xiangyun Qiu

Physics and Astronomy Faculty Publications

Quantitative understanding of biomolecular electrostatics, particularly involving multivalent ions and highly charged surfaces, remains lacking. Ion-modulated interactions between nucleic acids provide a model system in which electrostatics plays a dominant role. Using ordered DNA arrays neutralized by spherical cobalt3+ hexammine and Mg2+ ions, we investigate how the interstitial ions modulate DNA-DNA interactions. Using methods of ion counting, osmotic stress, and x-ray diffraction, we systematically determine thermodynamic quantities, including ion chemical potentials, ion partition, DNA osmotic pressure and force, and DNA-DNA spacing. Analyses of the multidimensional data provide quantitative insights into their interdependencies. The key finding of this study is that …

Determining The Kinetic Isotope Effect Of Ruthenium Compound Ru(Bpy)₂(Bpyno)(Pf₆)₂ Using Artificial Photosynthesis, Alexandra I. Kirkvold

Honors Thesis

The world’s demand for energy is ever-increasing, but its fuel resources are being depleted at an alarming rate. A potential solution for this crisis lies in using ruthenium-based compounds to produce hydrogen for use in fuel cells. This research uses the process of artificial photosynthesis to learn more about a promising ruthenium-based compound, Ru(bpy)₂(bpyNO)(PF₆)₂. The experiment tests the reaction for oxygen production in both H₂O and D₂O to determine the Kinetic Isotope Effect of the compound and, thus, aid future research working to understand the reaction mechanisms. The analysis shows that the reaction demonstrates an inverse …

Silicon Quantum Dots Conjunctive With Stable Radicals: Potential Application In Non-Invasive Cancer Diagnostics, Daylan R. Post

Honors College Theses

Quantum Dots, and nanomaterials in general, are one of the most promising areas of current physical study, especially their potential medical uses. In this study we introduced Nitroxide free radicals into a Silicon Quantum Dot (SiQD) solution and conducted experiments on the modified SiQDs in order to characterize their physical properties. We gathered emission, excitation, absorption and electron spin resonance (ESR) spectra of both modified and unmodified SiQDs. Previous studies have shown the possibility of using proteins as markers for cancer detection. Our measurements show the potential of using the interaction between these protein markers and SiQDs as a form …

Vibration Overtone Hyperpolarizability Measured For H2, Rachel M. Ellis, David P. Shelton

Physics & Astronomy Faculty Research

The second hyperpolarizability (γ) of the H2 molecule was measured by gas-phase electric field induced second harmonic generation at the frequencies of the one-photon resonance for the 3–0 Q(J) overtone transitions (v, J = 0, J → 3, J for J = 0, 1, 2, and 3). The magnitude of the resonant contribution to γ was measured with 2% accuracy using the previously determined non-resonant γ for calibration. Pressure broadening and frequency shift for the transitions were also measured. A theoretical expression for the resonant vibrational γ contribution in terms of transition polarizabilities is compared to the observations. The measured …

The Generality Of The Guga Mrci Approach In Columbus For Treating Complex Quantum Chemistry, Hans Lischka, Ron Shepard, Thomas Müller, Peter G. Szalay, Russell M. Pitzer, Adelia J. A. Aquino, Carol A. Parish, Et Al.

Chemistry Faculty Publications

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calcu- lations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of dia- batization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully vari- ational …

Sulfur Dioxide From The Atmospheric Chemistry Experiment Satellite, Doug Cameron

College of Sciences Posters

The version 4.0 dataset from the Atmospheric Chemistry Experiment – Fourier Transform Spectrometer (ACE-FTS) on SCISAT, released in March of 2019, has sulfur dioxide (SO₂) volume mixing ratio (VMR) profiles as a routine data product. From this dataset, global SO₂ distributions between the altitudes of 10.5 km and 23.5 km are analyzed. The global distribution of all SO₂ VMR data by altitude is broken down into 30° and 5° latitude zones. Seasonality of the global SO₂ distribution is explored. Volcanic SO₂ plumes are isolated in the dataset and compared with extinction data from the …

Fibration Symmetries Uncover The Building Blocks Of Biological Networks, Flaviano Morone, Ian Leifer, Hernán A. Makse

Publications and Research

A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these networks as a set of input trees, one for each node, which contains all pathways along which information can be transmitted in the network. In this representation, we find remarkable symmetries in the input trees that deconstruct the network into functional building blocks called fibers. Nodes in a fiber have isomorphic input trees and thus process equivalent dynamics and synchronize their activity. Each …

Laser-Induced Breakdown Spectroscopy For Elemental Analysis In Bioarchaeology And Forensic Anthropology, Kelsi N. Kuehn

USF Tampa Graduate Theses and Dissertations

Within bioarchaeology and forensic anthropology, the current processes of differentiating between individual human skeletal remains are imprecise, costly, and inefficient. A novel analytical technique within anthropology, laser-induced breakdown spectroscopy (LIBS) can aid in the identification of human remains using rapid laser ablation occurring at the micro-scale, making the technique virtually non-destructive to the sample. Considering this, LIBS could offer a superior method for materials discrimination and human identification. This research sought to examine whether LIBS can be used to obtain elemental signatures within bones to distinguish individuals from one another in a rapid, non-destructive manner. Seven human skeletal donors and …

Similarities Between Insect Swarms And Isothermal Globular Clusters, Dan Gorbonos, Kasper Van Der Vaart, Michael Sinhuber, James G. Puckett, Andrew M. Reynolds, Nicholas T. Ouellette, Nir S. Gov

Physics and Astronomy Faculty Publications

Previous work has suggested that disordered swarms of flying insects can be well modeled as self-gravitating systems, as long as the “gravitational” interaction is adaptive. Motivated by this work, we compare the predictions of the classic, mean-field King model for isothermal globular clusters to observations of insect swarms. Detailed numerical simulations of regular and adaptive gravity allow us to expose the features of the swarms' density and velocity profiles that are due to long-range interactions and are captured by the King model phenomenology, and those that are due to adaptivity and short-range repulsion. Our results provide further support for adaptive …

Examining Artifacts Of The Watershed Segmentation, Emily Jo Armitage

Electronic Theses and Dissertations

The watershed segmentation is an algorithm used to systematically track cell intercalary behaviors during germ band extension of the Drosophila embryo. Neighboring cells share a contracting vertical interface, called a T1, which continues contracting to a single point, a T2, and extending in the horizontal direction to create what is called a T3 interface (Fig. 1). Additionally, higher order vertices called rosettes occur when five or more cells meet at a common vertex. Simulated T2 events demonstrate that cell angle and not noise level in the image contributes to the incorrect detection of artifactual T1s in more acute angled cells …