Physics Commons^™

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 …

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.

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 …

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 …

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 …

The Fate Of The Crossbridge After Phosphate Rebinding: Implications For Fatigue, Christopher P. Marang

Doctoral Dissertations

In response to repeated intense contractile activity, a muscle’s ability to generate force decreases due to the created state of muscular fatigue. This compromised force production state is dependent on changes within the microenvironment of muscle thought to alter the function of the force generating, contractile protein myosin. For example, phosphate (P_i), elevated during fatigue, has been suggested to alter how myosin generates force. However, the effects of P_i are not straightforward, as muscle fiber data suggest that P_i's interaction with myosin may be force-dependent. In particular, P_i has no effect on maximal shortening …

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.

A Computational Kinetics Model To Quantify Radiation Induced Chemical Products Of Atmospheric Gas Mixtures, Patrick Ables

Dissertations

This research is focused on the development of a computational model which will calculate the effects of radiation on the chemical composition of the atmosphere. The approach utilizes the open-source chemical kinetics toolkit Cantera to model the creation of radiation-induced reactant species within irradiated air mixtures. Chemical solutions are iteratively stepped toward chemical equilibrium within a ‘constantly stirred’ (homogeneous) reactor of fixed volume. Three different radiation chemistry models are implemented in several different pulsed and continuous radiation schemes. The first model includes the mechanisms and rates of a pulse radiation model from the literature to test the validity of the …

Dinitrogen Functionalization Using A Molybdenum Atom: Bridging The Gap Between Small And Coordination Complexes Via Quantum Mechanical Methods, Maria Virginia White

Doctoral Dissertations

Chemistry devotes a significant amount of its research to understanding small molecule activation from an electronic structure perspective to help with the investigation of the reaction pathways of catalytically active substances that can promote biomimetic catalysis. A large portion of the energy used annually in our planet is used for the artificial nitrogen fixation (Haber-Bosch process), which renders dinitrogen activation a subject of study. Molybdenum, a fourth row transitional metal, has demonstrated its effectiveness as an essential component of the dinitrogen reduction catalytic process. To better understand the multiple dinitrogen molybdenum binding modes, the work described herein combines wave function …

The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess

All Dissertations

The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions ¹. The experimental data¹ evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …

The Applicability Of The Postmortem Submersion Interval Estimation Formula For Human Remains Found In Subtropical Aquatic Environments, Kara L. Dicomo

USF Tampa Graduate Theses and Dissertations

Within the past decade, several attempts have been made to standardize a method for estimating postmortem submersion intervals (PMSI); however, the majority of these studies have focused on data from a temperate climate which cannot be taken as representative of large portions of the globe. Thus, there are large portions of the earth in which the methodology from these studies may not be able to accurately estimate PMSI which has the potential to leave investigators in these other climatic zones at a disadvantage. This presentation presents a case study into the applicability of two Total Body Scoring Systems (TADS) utilized …

Optimization Of Flagellar Locomotion In The Low Reynolds Number Regime, Aidan M. Trodden, Aidan M. Trodden

Physics

This report investigates the computational and theoretical techniques - modeled by E. Lauga and C. Eloy - used to optimize the shape of an activated flagellum for enhanced cell motility. Cell motility is ubiquitous and has a large affect on biological systems such as marine life ecosystems, reproduction, and infection. The physical principles governing flagellar propulsion are explored using computational fluid dynamics simulations, mathematical modeling, and the sequential quadratic programming (SQP) optimization algorithm. Through iterative refinement, we can identify optimized flagellar shapes that would minimize the energetic cost dependent on a single dimensionless sperm numbers (Sp). The computation of the …

Flash-Rt: Using High-Dose Radiation For Clinical Radiation Therapy, Deja Stubbs

University Honors Theses

This paper is a literature review on the possible mechanisms behind the FLASH effect and why such research can advance the world of radiology treatment by modifying current clinical linear accelerators to produce ultra-high doses of radiation. Radiation Therapy, also known as external Beam Radiation Therapy, is a common type of cancer treatment. Globally, cancer is the second-leading cause of death, but has seen an increase in survival rates over the past couple of years. Cancer can develop in almost any part of the body since cancer is defined as uncontrolled cell growth. The FLASH Effect is seen when treating …

Characterization Of Boreal-Arctic Vegetation Growth Phases And Active Soil Layer Dynamics In The High-Latitudes Of North America: A Study Combining Multi-Year In Situ And Satellite-Based Observations, Michael G. Brown

Dissertations, Theses, and Capstone Projects

This dissertation examined the seasonal freeze/thaw activity in boreal-Arctic soils and vegetation physiology in Alaska, USA and Alberta, Canada, using in situ environmental measurements and passive microwave satellite observations. The boreal-Arctic high-latitudes have been experiencing ecosystem changes more rapidly in comparison to the rest of Earth due to the presently warming climatic conditions having a magnified effect over Polar Regions. Currently, the boreal-Arctic is a carbon sink; however, recent studies indicate a shift over the next century to become a carbon source. High-latitude vegetation and cold soil dynamics are influenced by climatic shifts and are largely responsible for the regions …

An Investigation On The Effect Of Conserved Hinge Histidine On Influenza Hemagglutinin(Ha2) Protein Conformation Using Md Simulations, Nada Tolba

Chemistry & Biochemistry Undergraduate Honors Theses

Hemagglutinin is a protein on the surface of Human Influenza Viruses.¹ It is composed of two glycopolypeptide domains, the HA1 and HA2 domains. Previous studies have found that across different strains of Influenza viruses, HIS435 residues remain conserved.⁴ In studies where mutations occurred in hinge-site histadine residues, the Influenza virus was inactive.⁴ These investigations indicated a significant role of HIS435 (hinge-site histadines) in virulence. Four systems were created using Molecular dynamics (MD) simulations. Each system was composed of an Isolated HA2 trimer solvated in a 150 mM NaCl rectangular water box at 310 K under isobaric and …

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

Modelling Cell Population Growth, Mahmood Mazarei

Electronic Thesis and Dissertation Repository

The growth of biological matter, e.g., tumor invasion, depends on various factors, mainly the tissue’s mechanical properties, implying elasticity, stiffness, or apparent viscosity. These properties are impacted by the characteristics of the tissue’s extracellular matrix and constituent cells, including, but not limited to, cell membrane stiffness, cell cytoskeleton mechanical properties, and the intensity and distribution of focal adhesions over the cell membrane. To compute and study the mechanical properties of tissues during growth and confluency, a theoretical and computational framework, called CellSim3D, was developed in our group based on a three-dimensional kinetic division model.

In this work, CellSim3D is …

An Ab Initio Computation Of The Potential Energy Surfaces Of The Dna Bases, Anjali F. Filinovich, Vola Andrianarijaona

Campus Research Day

The potential energy surfaces of atoms in DNA can be analyzed and compared to show how their bonds break. This DNA potential energy reference data is very useful to understanding how DNA damage occurs, however, a dataset of relevant potential energy surfaces is not available for scientific use. We obtain the potential energy surfaces of various atoms in the four DNA bases adenine, thymine, guanine, and cytosine, by moving an atom in these molecules in three orthogonal directions using ORCA, an ab initio quantum chemistry software. Density functional theory is
used to compute potential energies as an atom is moved, …

Analysis And Methodology Of Helical And Flexible Homopolymer Monte Carlo Simulations, Nathan Roberts

Honors College Theses

The purpose of my work is to analyze the results of Monte Carlo simulations of various types of polymers: a helical homopolymer and a flexible homopolymer. Specific applications of Monte Carlo polymer simulations and parallel tempering replica exchanges are presented. Using temporal analysis, I aim to measure the efficiency of each type of simulation as it relates to equilibration time. For the helical homopolymer model, equilibration time is expanded upon to analyze the rate of structure generation and relevant hyper-phase diagram. Stable states for helical homopolymers will use data generated from parallel tempering replica exchange Monte Carlo simulations created by …

Novel As-S-Se Compositions Of Solution-Processed Chalcogenide Thin Films For Infrared Optics, Annabella Orsini

Physics and Astronomy Honors Papers

Chalcogenide glasses (ChGs) have a wide range of interdisciplinary applications. In industry, ChGs are used to vastly improve infrared sight abilities. There are, however, improvements that can be made to the films’ stability, cost, and flexibility. Our project seeks to produce thin films that have these improvements, with capabilities comparable or better than what is widely used in the field. Thin films created through solution-based processes have proven to be much more flexible in comparison to bulk glass versions. Other elements in Group 16, such as Sulfur and Selenium have shown across literature to be a cost-effective alternative to Tellurium …

Modeling Excited State Processes In Molecular Aggregates By Constructing An Adaptive Basis For The Hierarchy Of Pure States, Leonel Varvelo

Chemistry Theses and Dissertations

Simulating excitation energy transfer (EET) in molecular materials is of crucial importance for the development of and understanding of materials such as organic photovoltaics and photosynthetic systems and further development of novel materials. The Hierarchy of Pure States (HOPS) is an exact framework for the time evolution of an open quantum system in which a hierarchy of stochastic wave functions are propagated in time. The adaptive HOPS (adHOPS) method achieves size-invariant scaling with the number of simulated molecules for sufficiently large aggregates by using an adaptive basis that moves with the excitation through the material. To demonstrate the power of …

Developing Carbon Quantum Dots As Multimodal Contrast Agents, Nicholas Whiting

Faculty Scholarship for the College of Science & Mathematics

No abstract provided.

Reconversion Of Parahydrogen Gas In Surfactant-Coated Glass Nmr Tubes, Robert V. Chimenti, James Daley, James Sack, Jennifer Necsutu, Nicholas Whiting

Faculty Scholarship for the College of Science & Mathematics

The application of parahydrogen gas to enhance the magnetic resonance signals of a diversity of chemical species has increased substantially in the last decade. Parahydrogen is prepared by lowering the temperature of hydrogen gas in the presence of a catalyst; this enriches the para spin isomer beyond its normal abundance of 25% at thermal equilibrium. Indeed, parahydrogen fractions that approach unity can be attained at sufficiently low temperatures. Once enriched, the gas will revert to its normal isomeric ratio over the course of hours or days, depending on the surface chemistry of the storage container. Although parahydrogen enjoys long lifetimes …

Dynamics In Designed Elastins And Enzymes, Jonathan M. Preston

Dissertations, Theses, and Capstone Projects

In this dissertation I present experimental results on the structure and dynamics of elastin, an elastomeric extracellular component in vertebrates that, in mammals, provides structure and elasticity to the circulatory system, lungs, skin and joints. These experiments, using a set of designed elastin like proteins with properties analogous to the natural protein, show that elastin is highly disordered and connect this disorder to its mechanism of assembly and elasticity. In addition, I also present preliminary work on imparting flexibility into a set of computationally designed metalloenzymes to broaden the range of catalytic activities they perform.

Minimal Expression Of Dysferlin Prevents Development Of Dysferlinopathy In Dysferlin Exon 40a Knockout Mice, Joe Yasa, Claudia E. Reed, Adam M. Bournazos, Frances J. Evesson, Ignatius Pang, Mark E. Graham, Jesse R. Wark, Brunda Nijagal, Kim H. Kwan, Thomas Kwiatkowski, Rachel Jung, Noah Weisleder, Sandra T. Cooper, Frances A. Lemckert

Chemistry Faculty Publications

Dysferlin is a Ca2+-activated lipid binding protein implicated in muscle membrane repair. Recessive variants in DYSF result in dysferlinopathy, a progressive muscular dystrophy. We showed previously that calpain cleavage within a motif encoded by alternatively spliced exon 40a releases a 72 kDa C-terminal minidysferlin recruited to injured sarcolemma. Herein we use CRISPR/Cas9 gene editing to knock out murine Dysf exon 40a, to specifically assess its role in membrane repair and development of dysferlinopathy. We created three Dysf exon 40a knockout (40aKO) mouse lines that each express different levels of dysferlin protein ranging from similar to 90%, similar to 50% and …

The Clinical Transferability Of Raman Micro-Spectroscopic Systems For Cervical Cytopathology, Rubina Shaikh Dr, Sarah Loughlin, Alison Malkin, John J. O'Leary, Cara M. Martin, Fiona Lyng

Conference papers

The clinical potential for Raman microscopic systems is well established for early diagnosis via cytology. Although Raman systems offer a complementary diagnostic tool providing molecular information, it is not yet utilised substantially in clinics. A few challenges for the clinical implementation of Raman spectroscopy are system and user variability. In this study, we asked how much variability occurs due to different Raman systems or users. To address these questions, we measured the same set of cells using two different Raman microscopes and by two different users. And classification models were generated using multivariate partial least squares discriminant analysis (PLS-DA) and …