Physics Commons^™

Microstructure-Based Modeling Of Primary Cilia Mechanics, Nima Mostafazadeh, Andrew Resnick, Y.-N. Young, Zhangli Peng

Physics Faculty Publications

A primary cilium, made of nine microtubule doublets enclosed in a cilium membrane, is a mechanosensing organelle that bends under an external mechanical load and sends an intracellular signal through transmembrane proteins activated by cilium bending. The nine microtubule doublets are the main load-bearing structural component, while the transmembrane proteins on the cilium membrane are the main sensing component. No distinction was made between these two components in all existing models, where the stress calculated from the structural component (nine microtubule doublets) was used to explain the sensing location, which may be totally misleading. For the first time, we developed …

The Accumulation And Growth Of Pseudomonas Aeruginosa On Surfaces Is Modulated By Surface Mechanics Via Cyclic-Di-Gmp Signaling, Liyun Wang, Yu-Chern Wong, Joshua M. Correira, Megan Wancura, Chris J. Geiger, Shanice S. Webster, Ahmed Touhami, Benjamin J. Butler, George A. O’Toole, Richard M. Langford

Physics and Astronomy Faculty Publications and Presentations

Attachment of bacteria onto a surface, consequent signaling, and accumulation and growth of the surface-bound bacterial population are key initial steps in the formation of pathogenic biofilms. While recent reports have hinted that surface mechanics may affect the accumulation of bacteria on that surface, the processes that underlie bacterial perception of surface mechanics and modulation of accumulation in response to surface mechanics remain largely unknown. We use thin and thick hydrogels coated on glass to create composite materials with different mechanics (higher elasticity for thin composites; lower elasticity for thick composites) but with the same surface adhesivity and chemistry. The …

Exploring The Interaction Of Minor-Groove-Binder Netropsin With Dna Using Optical Tweezers, Irbazhusain Shaikh

Honors Program Theses and Projects

Netropsin is an antibiotic that binds in the minor grooves of DNA, which also exhibits anticancer properties. There have been many previous studies that explored the binding of this drug to DNA using traditional methods where an ensemble averaging is used. In this study we explore the interaction of Netropsin with DNA at a single molecule level using dual beam optical tweezers. We trapped and stretched a single DNA molecule using optical tweezers to measure the force experienced by the DNA as a function of extension in the absence and presence of various concentrations of Netropsin. Our results show the …

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 …

Volume 14, Ireland Seagle, Dalton C. Whitby, Cassandra Poole, Rachel Cannon, Heidi Parker-Combes, Devon G. Shifflett, Antonio Harvey

Incite: The Journal of Undergraduate Scholarship

Table of Contents:

• Introduction: Dr. Amorette Barber
• From the Editor: Dr. Larissa "Kat" Tracy
• From the Designers: Rachel English, Rachel Hanson
• Hungry Like the Wolf: The Wolf as Metaphor in Paramount Network’s Yellowstone: Ireland Seagle
• “Floating Cities”: Illustrating the Commercial and Conservation Conflict of Alaskan Cruise Ship Tourism: Dalton C. Whitby
• What Can You Do When Your Genes are the Enemy? Current Applications of Gene Manipulation and the Associated Ethical Considerations: Cassandra Poole
• La doble cara: un tema romántico en las obras de Larra y Hawthorne: Rachel Cannon
• Resolving a Conflict: How to …

Ultrasound-Assisted Air-Jet Spinning Of Silk Fibroin-Soy Protein Nanofiber Composite Biomaterials., Futian Yang, Fang Wang, Janine Mazahreh, Xiao Hu

Faculty Scholarship for the College of Science & Mathematics

Ultrasound utilizes a non-radiation technology that can meet modern standards to gain access to cheap, reliable and sustainable modern energy. Ultrasound technology can be implemented in the field of biomaterials for its exceptional potential in controlling the shape of nanomaterials. This study presents the first example of the production of soy and silk fibroin protein composite nanofibers in various ratios via combining ultrasonic technology with air-spray spinning. Characterization of ultrasonic spun nanofibers was performed by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), X-ray powder diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric (TG) analysis, water contact angle, water retention, enzymatic …

Long-Range Aceo Phenomena In Microfluidic Channel, Diganta Dutta, Keifer Smith, Xavier Palmer

Electrical & Computer Engineering Faculty Publications

Microfluidic devices are increasingly utilized in numerous industries, including that of medicine, for their abilities to pump and mix fluid at a microscale. Within these devices, microchannels paired with microelectrodes enable the mixing and transportation of ionized fluid. The ionization process charges the microchannel and manipulates the fluid with an electric field. Although complex in operation at the microscale, microchannels within microfluidic devices are easy to produce and economical. This paper uses simulations to convey helpful insights into the analysis of electrokinetic microfluidic device phenomena. The simulations in this paper use the Navier–Stokes and Poisson Nernst–Planck equations solved using COMSOL …

Quantification Of Spent Coffee Ground Extracts By Roast And Brew Method, And Their Utility In A Green Synthesis Of Gold And Silver Nanoparticles, Brian G Yust, Niny Z Rao, Evan T Schwarzmann, Madisyn H Peoples

College of Life Sciences Faculty Papers

Nanotechnology has become increasingly important in modern society, and nanoparticles are routinely used in many areas of technology, industry, and commercial products. Many species of nanoparticle (NP) are typically synthesized using toxic or hazardous chemicals, making these methods less environmentally friendly. Consequently, there has been growing interest in green synthesis methods, which avoid unnecessary exposure to toxic chemicals and reduce harmful waste. Synthesis methods which utilize food waste products are particularly attractive because they add value and a secondary use for material which would otherwise be disposed of. Here, we show that spent coffee grounds (SCGs) that have already been …

Bbt Acoustic Alternative Top Bracing Cadd Data Set-Norev-2022jun28, Bill Hemphill

STEM Guitar Project’s BBT Acoustic Kit

This electronic document file set consists of an overview presentation (PDF-formatted) file and companion video (MP4) and CADD files (DWG & DXF) for laser cutting the ETSU-developed alternate top bracing designs and marking templates for the STEM Guitar Project’s BBT (OM-sized) standard acoustic guitar kit. The three (3) alternative BBT top bracing designs in this release are
(a) a one-piece base for the standard kit's (Martin-style) bracing,
(b) 277 Ladder-style bracing, and
(c) an X-braced fan-style bracing similar to traditional European or so-called 'classical' acoustic guitars.

The CADD data set for each of the three (3) top bracing designs includes …

Evaluation Of Silver Nanoparticles Attached To Methylene Blue As An Antimicrobial Agent And Its Cytotoxicity, Somon Hakimov

Masters Theses & Specialist Projects

Antibiotics resistance is considered as one of the greatest public health challenges of our time. In this work, we have synthesized silver nanoparticles (Ag NPs) using pulsed liquid ablation in different medium of growth and later combined with methylene blue (MB) to evaluate its potential as an effective photodynamic therapy agent. Ag NPs were synthesized by pulsed laser ablation technique in Polyvinylpyrrolidone (PVP), citrate, and Polyvinyl alcohol (PVA). The Ag NPs were characterized using transmission electron microscopy (TEM), UV-Visible (UV-Vis), and photoluminescence (PL) spectra. Next, Ag NPs were coupled with MB and used to deactivate the Gram-negative bacteria, Escherichia coli …

The Role Of Conformational Changes In Viral And Bacterial Protein Functions, Md Lokman Hossen

FIU Electronic Theses and Dissertations

Proteins do versatile work in cells. They require a cascade of structural changes to perform different tasks like binding to the other neighboring biomolecules, transporting small chemicals, activating a chemical reaction, etc. The structural conformations of proteins can be critical in changing their working ability. In this dissertation, I investigated the role of conformational changes of viral protein, e.g., spike and envelope protein of SARS-CoV-2, and bacterial protein, e.g., multidrug transporter and toxic extrusion protein- PfMATE from Pyrococcus furiosus. Also, I performed molecular docking-based drug screening targeting the E protein to suggest a set of drugs that can be repurposed …

Bbt Side Mold Assy, Bill Hemphill

STEM Guitar Project’s BBT Acoustic Kit

This electronic document file set covers the design and fabrication information of the ETSU Guitar Building Project’s BBT (OM-sized) Side Mold Assy for use with the STEM Guitar Project’s standard acoustic guitar kit. The extended 'as built' data set contains an overview file and companion video, the 'parent' CADD drawing, CADD data for laser etching and cutting a drill &/or layout template, CADD drawings in AutoCAD .DWG and .DXF R12 formats of the centerline tool paths for creating the mold assembly pieces on an AXYZ CNC router, and support documentation for CAM applications including router bit specifications, feeds, speed, multi-pass …

Contributions Of Vibrational Spectroscopy To Virology: A Review, Iqra Chaudhary, Naomi Jackson, Denise Denning, Luke O'Neill, Hugh Byrne

Articles

Vibrational spectroscopic techniques, both infrared absorption and Raman scattering, are high precision, label free analytical techniques which have found applications in fields as diverse as analytical chemistry, pharmacology, forensics and archeometrics and, in recent times, have attracted increasing attention for biomedical applications. As analytical techniques, they have been applied to the characterisation of viruses as early as the 1970s, and, in the context of the coronavirus disease 2019 (COVID-19) pandemic, have been explored in response to the World Health Organisation as novel methodologies to aid in the global efforts to implement and improve rapid screening of viral infection. This review …

Combining Pharmacokinetics And Vibrational Spectroscopy: Mcr-Als Hard-And-Soft Modelling Of Drug Uptake In Vitro Using Tailored Kinetic Constraints, David Perez-Guaita, Guillermo Quintas, Zeineb Farhane, Roma Tauler, Hugh Byrne

Articles

Raman microspectroscopy is a label-free technique which is very suited for the investigation of pharmacokinetics of cellular uptake, mechanisms of interaction, and efficacies of drugs in vitro. However, the complexity of the spectra makes the identification of spectral patterns associated with the drug and subsequent cellular responses difficult. Indeed, multivariate methods that relate spectral features to the inoculation time do not normally take into account the kinetics involved, and important theoretical information which could assist in the elucidation of the relevant spectral signatures is excluded. Here, we propose the integration of kinetic equations in the modelling of drug uptake and …

Volume 13, Payton Davenport, Audrey Lemons, Jacob Shope, Haley Smith, Cassandra Poole, Rachel Cannon, Rachel Boch, Suzanne Stetson

Incite: The Journal of Undergraduate Scholarship

Introduction Dr. Roger A. Byrne, Dean

From the Editor Dr. Larissa “Kat” Tracy

From the Designers Rachel English, Rachel Hanson

The Effect of Compliment Type on the Estimated Value of the Compliment by Payton Davenport, Audrey Lemons, and Jacob Shope

The Imperial Japanese Military: A New Identity in the Twentieth Century, 1853–1922 by Haley Smith

Longwood University’s campus: Human-cultivated Soil has Higher Microbial Diversity than Soil Collected from Wild Sites by Cassandra Poole

Reminiscent Modernism: Poetry Magazine’s Modernist Nostalgia for the Past by Rachel Cannon

Challenges Faced by Healthcare Workers During the COVID-19 Pandemic: A Preliminary Study of Age and …

Impact Of Introductory Physics For The Life Sciences In A Senior Biology Capstone Course, Benjamin D. Geller , '01, Jack Rubien , '20, Sara Hiebert Burch, Catherine Hirshfeld Crouch

Physics & Astronomy Faculty Works

A goal of introductory physics for life sciences (IPLS) curricula is to prepare students to effectively use physical models and quantitative reasoning in biological and medical settings. To assess whether this goal is being met, we conducted a longitudinal study of the impact of IPLS on student work in later biology and chemistry courses. We report here on one part of that study, a comparison of written responses by students with different physics backgrounds on a diffusion task administered in a senior biology capstone course. We observed differences in student reasoning that were found to be associated with prior or …

Examining Ecological Succession Of Diatoms In California Current System Cyclonic Mesoscale Eddies, Zuzanna M. Abdala, Sophie Clayton, Sveinn V. Einarsson, Kimberly Powell, Claire P. Till, Tyler H. Coale, P. Dreux Chappell

OES Faculty Publications

The California Current System is a diatom-dominated region characterized by seasonal coastal upwelling and additional elevated mesoscale activity. Cyclonic mesoscale eddies in the region trap productive coastal waters with their planktonic communities and transport them offshore with limited interaction with surrounding waters, effectively acting as natural mesocosms, where phytoplankton populations undergo ecological succession as eddies age. This study examines diatom community composition within two mesoscale cyclonic eddies that formed in the same region of the California Current System 2 months apart and in the California Current waters surrounding them. The diatom communities were analyzed in the context of shifting environmental …

Loren Haarsma - When Did Sin Begin?, Loren Haarsma

University Faculty Publications and Creative Works

Patrick Hamilton speaks to Calvin University Professor, Loren Haarsma, about the origins of sin and various ways to make sense of the doctrine of original sin in light of evolutionary origins. Other topics of conversation include psychology, free will and the theology of Saint Augustine.

Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li

Chemistry: Faculty Publications and Other Works

Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r …

Experimental Evidence That Metapopulation Structure Can Accelerate Adaptive Evolution, Partha Pratim Chakraborty, Louis R. Nemzer, Rees Kassen

Chemistry and Physics Faculty Articles

Whether the spatial arrangement of a population influences adaptive evolution has been a long-standing question in population genetics. In contrast to standard population genetic models, evolutionary graph theory (EGT) predicts certain topologies amplify (increase) the probability that a beneficial mutation will spread in the population relative to a well-mixed population. Here, we test these predictions empirically by tracking the fixation dynamics of an antibiotic resistant mutant under positive selection as it spreads through networks of different topologies both in vitro and in silico. We show that star-like topologies involving bi-directional dispersal between a central hub and peripheral leaves can …

Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei

Mathematics Faculty Publications

While automated feature extraction has had tremendous success in many deep learning algorithms for image analysis and natural language processing, it does not work well for data involving complex internal structures, such as molecules. Data representations via advanced mathematics, including algebraic topology, differential geometry, and graph theory, have demonstrated superiority in a variety of biomolecular applications, however, their performance is often dependent on manual parametrization. This work introduces the auto-parametrized weighted element-specific graph neural network, dubbed AweGNN, to overcome the obstacle of this tedious parametrization process while also being a suitable technique for automated feature extraction on these internally complex …

Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye

Biology: Faculty Publications and Other Works

Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the …

Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner

Publications and Research

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome …

The Biomechanics Of The Softball Swing In Seven Stages: Optimizing Exit Velocity, Ceara A. Larson

Lawrence University Honors Projects

The study of sports biomechanics is a rapidly developing field that can be used to analyze an athlete’s most critical motions and improve their performance. In the world of baseball, sports biomechanists, scientists dedicated to the field of sports biomechanics, help keep pitchers healthy, optimize pitch performance, and improve a batter’s swing efficiency. Because of their surface-level similarities, the findings of baseball biomechanical studies have been projected onto the sport of women’s fastpitch softball, despite their substantial differences in physiology, field dimensions, pitch delivery, and classifications of hitters. The purpose of this study is to produce a biomechanical analysis unique …

Rapid Production And Purification Of Dye-Loaded Liposomes By Electrodialysis-Driven Depletion, Gamid Abatchev, Andrew Bogard, Zoe Hutchinson, Jason Ward, Daniel Fologea

Physics Faculty Publications and Presentations

Liposomes are spherical-shaped vesicles that enclose an aqueous milieu surrounded by bilayer or multilayer membranes formed by self-assembly of lipid molecules. They are intensively exploited as either model membranes for fundamental studies or as vehicles for delivery of active substances in vivo and in vitro. Irrespective of the method adopted for production of loaded liposomes, obtaining the final purified product is often achieved by employing multiple, time consuming steps. To alleviate this problem, we propose a simplified approach for concomitant production and purification of loaded liposomes by exploiting the Electrodialysis-Driven Depletion of charged molecules from solutions. Our investigations show that …

Cholesterol And Cholesterol Bilayer Domains Inhibit Binding Of Alpha-Crystallin To The Membranes Made Of The Major Phospholipids Of Eye Lens Fiber Cell Plasma Membranes, Raju Timsina, Geraline Trossi-Torres, Matthew O'Dell, Nawal K. Khadka, Laxman Mainali

Physics Faculty Publications and Presentations

The concentration of α-crystallin decreases in the eye lens cytoplasm, with a corresponding increase in membrane-bound α-crystallin during cataract formation. The eye lens’s fiber cell plasma membrane consists of extremely high cholesterol (Chol) content, forming cholesterol bilayer domains (CBDs) within the membrane. The role of high Chol content in the lens membrane is unclear. Here, we applied the continuous-wave electron paramagnetic resonance spin-labeling method to probe the role of Chol and CBDs on α-crystallin binding to membranes made of four major phospholipids (PLs) of the eye lens, i.e., phosphatidylcholine (PC), sphingomyelin (SM), phosphatidylserine (PS), and phosphatidylethanolamine (PE). Small unilamellar vesicles …

Liposomes Prevent In Vitro Hemolysis Induced By Streptolysin O And Lysenin, Marcelo Ayllon, Gamid Abatchev, Andrew Bogard, Rosey Whiting, Sarah E. Hobdey, Daniel Fologea

Physics Faculty Publications and Presentations

The need for alternatives to antibiotics in the fight against infectious diseases has inspired scientists to focus on antivirulence factors instead of the microorganisms themselves. In this respect, prior work indicates that tiny, enclosed bilayer lipid membranes (liposomes) have the potential to compete with cellular targets for toxin binding, hence preventing their biological attack and aiding with their clearance. The effectiveness of liposomes as decoy targets depends on their availability in the host and how rapidly they are cleared from the circulation. Although liposome PEGylation may improve their circulation time, little is known about how such a modification influences their …

Investigating The Use Of Ultraviolet Light Emitting Diodes (Uv-Leds) For The Inactivation Of Bacteria In Powdered Food Ingredients, Laura Nyhan, Milosz Przyjalgowski, Liam O'Faolain, Máire Begley, Michael Callanan

Cappa Publications

The addition of contaminated powdered spices and seasonings to finished products which do not undergo further processing represents a significant concern for food manufacturers. To reduce the incidence of bacterial contamination, seasoning ingredients should be subjected to a decontamination process. Ultraviolet light emitting diodes (UV-LEDs) have been suggested as an alternative to UV lamps for reducing the microbial load of foods, due to their increasing efficiency, robustness and decreasing cost. In this study, we investigated the efficacy of UV-LED devices for the inactivation of four bacteria (Listeria monocytogenes, Escherichia coli, Bacillus subtilis and Salmonella Typhimurium) on a plastic surface and …

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) …

The Resistive Barrier Discharge: A Brief Review Of The Device And Its Biomedical Applications, Mounir Laroussi

Electrical & Computer Engineering Faculty Publications

This paper reviews the principles behind the design and operation of the resistive barrier discharge, a low temperature plasma source that operates at atmospheric pressure. One of the advantages of this plasma source is that it can be operated using either DC or AC high voltages. Plasma generated by the resistive barrier discharge has been used to efficiently inactivate pathogenic microorganisms and to destroy cancer cells. These biomedical applications of low temperature plasma are of great interest because in recent times bacteria developed increased resistance to antibiotics and because present cancer therapies often are accompanied by serious side effects. Low …