Biological and Chemical Physics Commons^™

Determination Of The Rydberg Constant From The Emission Spectra Of H And He+, Kyle D. Shaffer

Ramifications

Abstract

In this experiment, the Rydberg constants for the hydrogen atom and He⁺ were determined by analysis of the emission spectra of Hand He, respectively, in comparison to the principal quantum numbers of each transition. Using both a hydrogen and then a helium atomic lamp attached to a 0.5 m grating spectrometer and a photomultiplier detector (PMT), a change in voltage detected by the PMT can be paired with a corresponding wavelength passing through the spectrometer from each emission peak in the visible to ultraviolet range. The peaks acquired from this change in voltage were analyzed to find their …

The Potential Of Raman Spectroscopy In The Diagnosis Of Dysplastic And Malignant Oral Lesions, Ola Ibrahim, M. Toner, Steven Flint, Hugh Byrne, Fiona Lyng

Articles

Early diagnosis, treatment and/or surveillance of oral premalignant lesions are important in preventing progression to oral squamous cell carcinoma (OSCC). The current gold standard is through histopathological diagnosis, which is limited by inter and intra observer and sampling errors. The objective of this work was to use Raman spectroscopy to discriminate between benign, mild, moderate and severe dysplasia and OSCC in formalin fixed paraffin preserved (FFPP) tissues. The study included 72 different pathologies from which 17 were benign lesions, 20 mildly dysplastic, 20 moderately dysplastic, 10 severely dysplastic and 5 invasive OSCC. The glass substrate and paraffin wax background were …

Biomedical Applications Of Vibrational Spectroscopy: Oral Cancer Diagnostics, Hugh Byrne, Isha Behl, Genecy Calado, Ola Ibrahim, M. Toner, Sheila Galvin, Claire M. Healy, Steven Flint, Fiona Lyng

Articles

Vibrational spectroscopy, based on either infrared absorption or Raman scattering, has attracted increasing attention for biomedical applications. Proof of concept explorations for diagnosis of oral potentially malignant disorders and cancer are reviewed, and recent advances critically appraised. Specific examples of applications of Raman microspectroscopy for analysis of histological, cytological and saliva samples are presented for illustrative purposes, and the future prospects, ultimately for routine, chairside in vivo screening are discussed.

Using The Marcus Inverted Region And Artificial Cofactors To Create A Charge Separated State In De Novo Designed Proteins, Eskil Me Andersen

Dissertations, Theses, and Capstone Projects

To create an efficient de novo photosynthetic protein it is important to create long lived charge separated states. Achieving stable charge separation leads to an increase in the efficiency of the photosynthetic reaction which in turn leads to higher yields of end products, such as biofuels, electrical charge, or synthetic chemicals. In an attempt to create charge separated states in de novo proteins we hypothesized that we could engineer the free energy gaps in the proteins from excited primary donor (PD) to acceptor (A), and A back to ground state PD such that the forward electron transfer (ET) would be …

Frozen In Time: A Numerical Modeling Approach To The Study Of Ice Bearing Planetesimals Through Carbonaceous Chondrites, Jasmine M. Bayron

Dissertations, Theses, and Capstone Projects

Icy planetesimals are significant objects of study for meteoritics, planetary science, and astrobiology due to their connections to the origins of life and liquid water on Earth. An existing closed system aqueous alteration model was adapted to simulate several scenarios involving early Solar System geologic processes occurring in an icy planetesimal interior. The model described in this work has been developed not only to test the validity of constraints currently thought to apply to CM1 parent bodies, but to directly compare the implications of these constraints for the isotopic composition and the modal mineralogy of carbonaceous chondrites. Isotopic ratios of …

Mechanism Of Action Of Dihydropteridine Reductase, Gabriela Arias De La Rosa

Dissertations, Theses, and Capstone Projects

Human dihydropteridine reductase is an enzyme that transfers a hydride from NADH to reduce quinonoid 7,8-dihydropterin (qBH₂) to 5,6,7,8-tetrahydropterin (BH₄), which is a cofactor important in the production of neurotransmitters.DHPR deficiency causes a drastic form of the neurological genetic disease phenylketonuria (PKU) that does not benefit from a phenylalanine-free diet.From site-directed mutagenesis studies, mostly on Rat DHPR, we know that certain residues are important for cofactor binding, substrate binding, and hydride transfer; however, there are still some questions about how DHPR works, particularly, because there is not a crystal structure of the tertiary complex: What is …

Enhancement And Evaluation Of Proton Pencil Beam Spot Placement Algorithms, Mahboob Ur Rehman

Electronic Theses and Dissertations, 2020-

Intensity modulated proton therapy (IMPT) in the form of pencil beam scanning (PBS) has shown improvement in treatment plan quality as compared to conventional proton and photon-based radiotherapy techniques. However, in IMPT maintaining a sharp lateral dose falloff is crucial for sparing organs at risk (OARs), especially when they are in close proximity to the target volume. The most common approach to improve lateral dose falloff is through the use of physical beam shaping devices, such as brass apertures or collimator-based systems. This work has shown that IMPT can be further improved by implementation of advanced spot placement techniques by …

Biophysical Analysis Of The Structure And Aggregation Of Amyloid Beta Peptide, Faisal Abedin

Electronic Theses and Dissertations, 2020-

Alzheimer's disease (AD) is the major cause of dementia and is characterized by neuronal death and brain atrophy. The amyloid ß (Aß) peptide is tightly associated with neuronal dysfunction during AD, but the molecular mechanism underlying the neurotoxic effect of Aß is poorly understood. Extracellular fibrillar deposits (plaques) of Aß were initially believed to be the cause of AD, but currently there is overwhelming evidence that the prefibrillar Aß oligomers are the major toxic entities. Structural characterization of Aß oligomers and fibrils is important for understanding the structural features determining the toxic potency of the peptide. This project has studied …

Monitoring Stem Cell Differentiation Using Raman Microspectroscopy: Chondrogenic Differentiation, Towards Cartilage Formation, Francesca Ravera, Esen Efeoglu, Hugh Byrne

Articles

Mesenchymal Stem Cells (MSCs) have the ability to differentiate into chondrocytes, the only cellular components of cartilage and are therefore ideal candidates for cartilage and tissue repair technologies. Chondrocytes are surrounded by cartilage-like extracellular matrix (ECM), a complex network rich in glycosaminoglycans, proteoglycans, and collagen, which, together with a multitude of intracellular signalling molecules, trigger the chondrogenesis and allow the chondroprogenitor to acquire the spherical morphology of the chondrocytes. However, although the mechanisms of the differentiation of MSCs have been extensively explored, it has been difficult to provide a holistic picture of the process, in situ. Raman Micro Spectroscopy (RMS) …

Acoustic Communication In The Atlantic Mudskipper, Periopthalmus Barbarus, Seth Hoffman

Mahurin Honors College Capstone Experience/Thesis Projects

Mudskippers are intertidal fishes that can survive both in and out of the water. They are territorial and exhibit behaviors to attract mates and defend against competitors. Recently, it has been shown that vibrations are produced and transmitted through the mud during such displays in one species, Periophthalmodon septemradiatus. To see if similar vibrations are produced in other species of mudskippers, I recorded the behavioral interactions of pairs of the mudskipper Periophthalmus barbarus via digital video and acoustic signals via accelerometer. Comparative analysis of fish mass, sex, contest length, and contest outcome coupled with acoustic characteristics within dyadic pairings …

Modeling Disorder In Proteins Yields Insights Into The Evolution Of Stability And Function, Jonathan Huihui

Electronic Theses and Dissertations

The central dogma of molecular biology dictates that a DNA sequence codes for an RNA sequence, which in turn codes for a sequence of amino acids that comprises a protein. Proteins are responsible with performing myriad functions within living organisms and most proteins require a folded structure in order to perform their function. The protein's structure is the direct link from sequence to function. This is known as the sequence - structure - function paradigm. However, this does not mean that the unfolded state is unimportant. In order to properly model the stability of the folded state, one needs to …

Structure Of Unmodified And Pyroglutamylated Amyloid Beta Peptide In Lipid Membranes, Rowan Hassan

Honors Undergraduate Theses

Alzheimer's Disease (AD) is a devastating neurodegenerative disease that is characterized by brain atrophy, neuronal and synaptic loss, cognitive decline, trouble handling activities of daily life, and ultimately leads to death. Worldwide, at least 30 million people suffer from AD, with 5.8 million suffering in the US alone. Despite extensive basic and clinical research, the underlying molecular mechanisms behind AD remain largely unknown. There are four FDA-approved compounds are used for alleviating symptoms but have no curative potency. The first potentially disease-modifying AD drug, aducanumb, was approved by FDA in June 2021. The main histopathological traits of AD are the …

Dual Beam Frequency Comb Ftir Spectroscopy, Connor Kelly

Electronic Theses and Dissertations, 2020-

A visible and Infrared (IR) range dual beam frequency comb Fourier transform spectrometer was developed. Using dual mode-locked Ti:Sapphire lasers a comb-interferogram was generated in the visible range. This spectrum was calculated and used to measure the transmittance of a Nd-doped crystal. The system was further developed to generate an IR interferogram by Difference Frequency Generation (DFG) using a Gallium Selenide (GaSe) crystal placed in the mode-locked pump beam. Numerical work was done to calculate the expected DFG spectrum confirming the necessary IR range can be reached. This has been conducted in support of an IR holographic spectroscopic microscopy spatial …

Numerical Simulations Of Capsule Deformation Using A Dual Time-Stepping Lattice Boltzmann Method, Charles Armstrong, Yan Peng

Mathematics & Statistics Faculty Publications

In this work a quasisteady, dual time-stepping lattice Boltzmann method is proposed for simulation of capsule deformation. At each time step the steady-state lattice Boltzmann equation is solved using the full approximation storage multigrid scheme for nonlinear equations. The capsule membrane is modeled as an infinitely thin shell suspended in an ambient fluid domain with the fluid structure interaction computed using the immersed boundary method. A finite element method is used to compute the elastic forces exerted by the capsule membrane. Results for a wide range of parameters and initial configurations are presented. The proposed method is found to reduce …

Predicting Material Properties: Applications Of Multi-Scale Multiphysics Numerical Modeling To Transport Problems In Biochemical Systems And Chemical Process Engineering, Tom Pace

Theses and Dissertations--Physics and Astronomy

Material properties are used in a wide variety of theoretical models of material behavior. Descriptive properties quantify the nature, structure, or composition of the material. Behavioral properties quantify the response of the material to an imposed condition. The central question of this work concerns the prediction of behavioral properties from previously determined descriptive properties through hierarchical multi-scale, multiphysics models implemented as numerical simulations. Applications covered focus on mass transport models, including sequential enzyme-catalyzed reactions in systems biology, and an industrial chemical process in a common reaction medium.

Power Amplification Strategies Across Animals, Rayhan Asif

Williams Honors College, Honors Research Projects

Animals use muscles for movement, but some have evolved mechanisms to exceed maximum power used in a motion known as power amplification. In this literature review, I analyzed and compared the evolution of structures capable of power amplification between species. Structures capable of power amplification were broken down into the basic components of the engine, amplifier, and tool. The species analyzed were found to possess necessary structures for power amplification which were relatively similar to each other in morphology, but varied greatly in function. The ease with which these structures evolved was evaluated based on the amount of divergence which …

The Effects Of Increasing Positively Charged Metal Ions Within Synovial Fluid, Kandisi Anyabwile

Williams Honors College, Honors Research Projects

Osteoarthritis is a degenerative joint disease that affects 10% of men and 13% of women over age of 60. It is the degradation of the cartilage between two bones; obesity, age, overuse, or injury are major contributors to the development of this disease. The joint is incapsulated by the synovial sac filled with a viscous solution that aids in lubrication referred to as synovial fluid. If the synovial sac is ruptured due to injury, positive ions (K⁺, Na⁺, Ca²⁺, and Fe³⁺) may affect viscoelastic properties within the sac. The purpose of this …

Development And Characterization Of Nb₃N/Al₂0₃ Superconducting Multilayers For Particle Accelerators, Chris Sundahl, Junki Makita, Paul B. Welander, Yi-Feng Su, Fumitake Kametani, Lin Xie, Huimin Zhang, Lian Li, Alex Gurevich, Chang-Beom Eom

Physics Faculty Publications

Superconducting radio-frequency (SRF) resonator cavities provide extremely high quality factors > 10¹⁰ at 1-2 GHz and 2 K in large linear accelerators of high-energy particles. The maximum accelerating field of SRF cavities is limited by penetration of vortices into the superconductor. Present state-of-the-art Nb cavities can withstand up to 50 MV/m accelerating gradients and magnetic fields of 200-240 mT which destroy the low-dissipative Meissner state. Achieving higher accelerating gradients requires superconductors with higher thermodynamic critical fields, of which Nb₃Sn has emerged as a leading material for the next generation accelerators. To overcome the problem of low vortex penetration …

Tri-Molybdenum Phosphide (Mo3P) And Multi-Walled Carbon Nanotube Junctions For Volatile Organic Compounds (Vocs) Detection, Baleeswaraiah Muchharla, Praveen Malali, Brenna Daniel, Alireza Kondori, Mohammad Asadi, Wei Cao, Hani E. Elsayed-Ali, Mickaël Castro, Mehran Elahi, Adetayo Adedeji, Kishor Kumar Sadasivuni, Muni Raj Mauya, Kapil Kumar, Abdennaceur Karoui, Bijandra Kumar

Electrical & Computer Engineering Faculty Publications

Detection and analysis of volatile organic compounds’ (VOCs) biomarkers lead to improvement in healthcare diagnosis and other applications such as chemical threat detection and food quality control. Here, we report on tri-molybdenum phosphide (Mo₃P) and multi- walled carbon nanotube (MWCNT) junction-based vapor quantum resistive sensors (vQRSs), which exhibit more than one order of magni- tude higher sensitivity and superior selectivity for biomarkers in comparison to pristine MWCNT junctions based vQRSs. Transmission electron microscope/scanning tunneling electron microscope with energy dispersive x-ray spectroscopy, x-ray diffraction, and x-ray photo- electron spectroscopy studies reveal the crystallinity and the presence of Mo and …

Composite Network Of Actin And Microtubule Filaments, Self-Organization And Steady-State Dynamics, Leila Farhadi

Doctoral Dissertations

Actin and microtubule filaments, with their auxiliary proteins, enable the cytoskeleton to perform vital processes in the cell by tuning the organizational, mechanical properties and dynamics of the network. Despite their critical importance and interactions in cells, we are only beginning to uncover information about the composite network. Here, I use florescence microscopy to explore the role of filaments characteristics, interactions and activities in the self-organization and steady-state dynamics of the composite network of filaments. First, I discuss active self-organization of semiflexible actin and rigid microtubule filaments in the 2D composite network while myosin II and kinesin-1 motor proteins propel …