Biological and Chemical Physics Commons^™

Review-Electrode Kinetics And Electrolyte Stability In Vanadium Flow Batteries, Andrea Bourke, Daniela Oboroceanu, Nathan Quill, Catherine Lenihan, Maria Alhajji Safi Maria Alhajji Safi, Mallory A. Miller, Robert F. Savinell, Jesse S. Wainright, Varsha Sasikumarsp, Maria Rybalchenko, Pupak Amini, Niall Dalton, Robert P. Lynch, D. Noel Buckley

Articles

Two aspects of vanadium flow batteries are reviewed: electrochemical kinetics on carbon electrodes and positive electrolyte stability. There is poor agreement between reported values of kinetic parameters; however, most authors report that kinetic rates are faster for VIV/VV than for VII/VIII. Cycling the electrode potential increases the rates of both reactions initially due to roughening but when no further roughening is observed, the VII/VIII and VIV/VV reactions are affected oppositely by the pretreatment potential. Anodic pretreatment activates the electrode for the VII/VIII reaction, and deactivates it for VIV/VV. Three states of the carbon surface are suggested: reduced and oxidized states …

Analysis Of Biologically Effective Dose For Retroactive Yttrium-90 Trans-Arterial Radioembolization Treatment Optimization, Mj Lindsey

CMC Senior Theses

Trans-arterial radioembolization (TARE) is a protracted modality of radiation therapy where radionuclides labeled with Yttrium-90 (⁹⁰Y) are inserted inside a patient's hepatic artery to treat hepatocellular carcinoma (HCC). While TARE has been shown to be a clinically effective and safe treatment, there is little understanding of the radiobiological relationship between absorbed dose and tissue response, and thus there is no dosimetric standard for treatment planning. The Biologically Effective Dose (BED) formalism, derived from the Linear-Quadratic model of radiobiology, is used to weigh the absorbed dose by the time pattern of delivery. BED is a virtual dose that can …

Homopurine Guanine-Rich Sequences In Complex With N-Methyl Mesoporphyrin Ix Form Parallel G-Quadruplex Dimers And Display A Unique Symmetry Tetrad, Ming Ye, Erin V. Chen, Shawn H. Pfeil, Kailey N. Martin, Tamanaa Atrafi, Sara Yun, Zahara Martinez, Liliya A. Yatsunyk

Physics & Engineering Faculty Publications

DNA can fold into G-quadruplexes (GQs), non-canonical secondary structures formed by pi-pi stacking of G-tet-rads. GQs are important in many biological processes, which makes them promising therapeutic targets. We identified a 42-nucleotide long, purine-only G-rich sequence from human genome, which contains eight G- stretches connected by A and AAAA loops. We divided this sequence into five unique segments, four guanine stretches each, named GA1-5. In order to investigate the role of adenines in GQ structure formation, we per-formed biophysical and X-ray crystallographic studies of GA1-5 and their complexes with a highly selective GQ ligand, N-methyl mesoporphyrin IX (NMM). Our data …

Long-Range And Chaotic Active Mixing Of Swimming Microbes In A Vortex Chain Flow, Nghia Le

Honors Theses

We present experiments studying the motion and active mixing of swimming mi- crobes in laminar, vortex-dominated fluid flows. We are testing a theory that predicts the existence of swimming invariant manifolds (SwIMs) - invisible, one-way barriers blocking the paths of self-propelled tracers in the flow in one direction. We also pro- pose that the SwIMs together can form chute structures in three-dimensional phase space that facilitate cross-vortex transport of the microbes. We also observe evidence of how these structures promote long-range transport at different non-dimensional velocities (microbe’s velocity relative to flow velocity). Long-range transport is quan- tified by measuring the …

Optical Tweezers: Exerting Force With Light, Gabriella Seifert

Scripps Senior Theses

Photons carry momentum. When a tightly-focused beam of photons hit a particle, they transfer some of their momentum to the particle, exerting a force. Optical tweezers take advantage of this phenomenon to trap (or “tweeze”) a spherical bead just after the focus of a diverging laser beam, creating a potential well that pulls in beads. In this thesis, I predict the force exerted on trapped beads and measure the actual force using an optical tweezers setup that I built. To predict the force, I follow the path of all possible rays from a diverging beam incident on a spherical bead …

Fabrication And Investigation Of Microfluidic Devices That Produce Non-Linear Chemical Gradients, Elijah L. Waters

Electronic Theses and Dissertations

Investigation of cell chemotaxis requires controlled chemical gradients. We investigated microfluidic devices that could enhance small populations' cell assays because of their ability to generate various chemical gradients. Our five designs generate different chemical concentration landscapes that we can easily convert into tools to study cell response to growth factors. Gradient landscapes occurred by splitting and mixing two input fluid concentrations using bifurcations, trifurcations, and Y-mixing junctions in three consecutive steps. Such fluid flow manipulations resulted in nine concentration streams entering a 0.54-mm-wide gradient chamber. The first design used a 1:1 ratio Y-mixer (unbiased) when blending two concentrations, resulting in …

First Review Of Equilibrium Landscape Of Ingress/Egress Channels And Gating Residues Of The Cytochrome P450 3a4, Edward Ackad Ph.D, Maria Kontoyianni

SIUE Faculty Research, Scholarship, and Creative Activity

The review document and changes made to "Equilibrium Landscape of Ingress/Egress Channels and Gating Residues of the Cytochrome P450 3A4".

Behaviors For Which Deinonychosaurs Used Their Feet, Alexander King

Honors Projects

This paper seeks to show for what purpose deinonychosaurs used their feet. Fowler et al., (2011) showed that D. antirrhopus’s feet were closest in function to accipitrids, as they found it was more built for grasping prey than running.

I answered this question by using 2D images of the feet of three modern birds (Buteo jamaicensis, Phasianus colchicus, and Gallus gallus domesticus), one eudromaeosaur (Deinonychus antirrhopus), and one troodontid (Borogovia gracilicrus). I used ImageJ to apply 73 landmarks to each foot, capturing the variation between species in the metatarsals and pedal phalanges. These data were then uploaded to the software …

Cell Division Dynamics Of Escherichia Coli In Extreme Environments, Steven P. Murray

Graduate Theses and Dissertations

Life is remarkable in how resilient it can be. Many organism, classified as ex- tremophiles, can not only survive in extreme environments, but they can thrive in them. In the search for extraterrestrial life, the best candidates to harbor life exist with some kind of extreme condition. Europa, for example, is a favorite for the possibility of accommodating life as we know it within our solar system. Thought there is believed to be a liquid ocean under its icy surface, this habitat would be under immense pressures and high salinity. To best know where to look for extraterrestrial life, it …

A Method For Exploring The Habitability Of Earth-Like Exoplanets: Applications To Tess Objects Of Interest 203 B, 256 B, And 700 D, Paul Bonney

Graduate Theses and Dissertations

The Transiting Exoplanet Survey Satellite (TESS) has and is continuing to discover a multitude of potentially habitable planet candidates. As more planets are detected and confirmed, it becomes increasingly important to strategically search for signs of habitability with which to differentiate and prioritize them for further observation, in particular with the James Webb Space Telescope (JWST). To facilitate this, I have created a method for prioritizing TESS planet candidates based on parameters derived from their light curves and have applied the method to the TESS Candidate Target List (CTL). This data set uses preliminary fits to transit modeling which can …

Fluid-Structure Interaction Modelling Of Neighboring Tubes With Primary Cilium Analysis, Nerion Zekaj, Shawn D. Ryan, Andrew Resnick

Mathematics and Statistics Faculty Publications

We have developed a numerical model of two osculating cylindrical elastic renal tubules to investigate the impact of neighboring tubules on the stress applied to a primary cilium. We hypothesize that the stress at the base of the primary cilium will depend on the mechanical coupling of the tubules due to local constrained motion of the tubule wall. The objective of this work was to determine the in-plane stresses of a primary cilium attached to the inner wall of one renal tubule subject to the applied pulsatile flow, with a neighboring renal tube filled with stagnant fluid in close proximity …

Using Protonation Microstates And Hydrogen Bond Networks To Track Proton Transfer Pathways In Complex I, Umesh Khaniya

Dissertations, Theses, and Capstone Projects

Complex I, NADH-ubiquinone oxidoreductase, is the first enzyme in the mitochondrial and bacterial aerobic respiratory chain. It pumps four protons through four transiently open pathways from the high pH, negative, N- side of the membrane to the positive, P-side driven by the exergonic transfer of electrons from NADH to a quinone. Three protons transfer through subunits descended from Mrp antiporters, while the fourth, E-channel is unique. Because of the complex possible paths thorough the many buried polar residues and lack of high-resolution crystal structure, the path for protons through the E-channel is elusive.

In this dissertation, the E-channel proton pumping …

The Interaction Of Different Primary Producers And Physical And Chemical Dynamics Of An Urban Shallow Lake, Majid Sahin

Dissertations, Theses, and Capstone Projects

An artificial urban shallow lake, Prospect Park Lake (PPL), is situated on a terminal moraine in Brooklyn New York, and supplied with municipal water treated with ortho-phosphates. The constant input of the phosphate nutrient is the primary source of eutrophication in the lake. The numerous pools along the water course houses various aquatic phototrophs, which influence the water quality and the state of the system, driving conditions into favoring the survival of their species. In the first half of the dissertation, the focus of the project is on analyzing how the different primary producers in different regions of PPL affect …

Coupled Oscillators: Protein And Acoustics, Angelique N. Mcfarlane

Theses

This work encompassed three different vibrational energy transfer studies of coupled resonators (metal, topological, and microtubule comparison) inspired by the lattices of microtubules from regular and cancerous cells. COMSOL Multiphysics 5.4 was utilized to design the experiment. The simulation starts with an acoustic pressure study to examine the vibrational modes present in coupled cylinders, representing α-, β-tubulin heterodimers. The Metal Study consisted of 3 models (monomer, dimer, and trimer) to choose the correct height (40 mm) and mode (Mode 1) for study. The Topological Study was run to predict and understand how the lattice structure changes over a parametric sweep …

Mathematics For Biomedical Physics, Jogindra M. Wadehra

Open Textbooks

Mathematics for Biomedical Physics is an open access peer-reviewed textbook geared to introduce several mathematical topics at the rudimentary level so that students can appreciate the applications of mathematics to the interdisciplinary field of biomedical physics. Most of the topics are presented in their simplest but rigorous form so that students can easily understand the advanced form of these topics when the need arises. Several end-of-chapter problems and chapter examples relate the applications of mathematics to biomedical physics. After mastering the topics of this book, students would be ready to embark on quantitative thinking in various topics of biology and …

Revealing The Role Of Electrostatics In Molecular Recognition, Ion Binding And Ph-Dependent Phenomena, Mihiri Hewa Bosthanthirige

All Dissertations

In this dissertation, we study the role of electrostatics in molecular recognition, ion binding and pH-dependent phenomena. In this work that includes three different research projects, the Poisson-Boltzmann (PB) model is used to describe the biological system and Delphi (which is a popular tool for solving the PB equation (PBE)) to study the electrostatics of biomolecular systems.

Chapter two aims to investigate the role of electrostatic forces in molecular recognition. We calculated electrostatic forces between binding partners separated at various distances. To accomplish this goal, we developed a method to find an appropriate direction to move one chain of protein …

A Computational Model Of The Line-1 Retrotransposon Life Cycle And Visualization Of Metabolic Networks In 3-Dimensions., Michael D. Martin

Electronic Theses and Dissertations

Computational modeling of metabolic reactions and cellular systems is evolving as a tool for quantitative prediction of metabolic parameters and reaction pathway analysis. In this work, the basics of computational cell biology are presented as well as a summary of physical processes within the cell, and the algorithmic methods used to find time dependent solutions. Protein-protein and enzyme-substrate interactions are mathematically represented via mass action kinetics to construct sets of linear differential equations that describe reaction rates and formation of protein complexes. Using mass action methods, examples of reaction networks and their solutions are presented within the Virtual Cell simulation …

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 …

Symmetry-Inspired Analysis Of Biological Networks, Ian Leifer

Dissertations, Theses, and Capstone Projects

The description of a complex system like gene regulation of a cell or a brain of an animal in terms of the dynamics of each individual element is an insurmountable task due to the complexity of interactions and the scores of associated parameters. Recent decades brought about the description of these systems that employs network models. In such models the entire system is represented by a graph encapsulating a set of independently functioning objects and their interactions. This creates a level of abstraction that makes the analysis of such large scale system possible. Common practice is to draw conclusions about …

A Molecular Dynamics Study Of Polymer Chains In Shear Flows And Nanocomposites, Venkat Bala

Electronic Thesis and Dissertation Repository

In this work we study single chain polymers in shear flows and nanocomposite polymer melts extensively through the use of large scale molecular dynamics simulations through LAMMPS. In the single polymer chain shear flow study, we use the Lattice Boltzmann method to simulate fluid dynamics and also include thermal noise as per the \emph{fluctuation-dissipation} theorem in the system. When simulating the nanocomposite polymer melts, we simply use a Langevin thermostat to mimic a heat bath. In the single polymer in shear flow study we investigated the margination of a single chain towards solid surfaces and how strongly the shear flow …

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 …

Dr. Lawrence J. Berliner, Anit Tyagi

DU Undergraduate Research Journal Archive

An interview with Dr. Lawrence J. Berliner.

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 …

Supertertiary Structural Dynamics Modulate Function In Postsynaptic Density Protein 95, George L. Hamilton Iii

All Dissertations

Proteins, RNA, and DNA serve as the primary sub-cellular machinery that give rise to the necessary functions of life. The long-standing paradigm has been that the structures of biomolecules, or the arrangement of the subunits that make up a biomolecule, determine biological function. However, biomolecules are not static objects. Instead, they often undergo structural rearrangements that are crucial to enabling and regulating their functions. In my thesis I present several studies of the interplay between the structures, dynamics, and functions of biomolecules that combine experimental fluorescence spectroscopy and computational methods to probe these systems at the single-molecule level. In particular, …

Optimization Of Modular, Long-Range, Ultra-Fast Optical Tweezers With Fluorescence Capabilities For Single-Molecule And Single-Cell Based Biophysical Measurements, Subash C. Godar

All Dissertations

An Optical tweezer is a tightly focused laser beam that applies and senses precise and localized optical force to a dielectric microsphere and offers a unique and effective tool for manipulating the single cell or cell components, including nucleotides and dynein motor proteins. Here, I used highly stabilized optomechanical components and ultra-sensitive detection modules to significantly improve the measurement capabilities over a wide range of temporal and spatial scales. I combined the optical tweezer-based force spectroscopy technique with fluorescence microscopy to develop an integrated high-resolution force-fluorescence system capable of measuring displacements at sub-nanometer, forces at sub-piconewton over a temporal range …

Prediction Of Pathogenic Mutations In Spermine/Spermidine Synthases, Shannon Bonomi

All Theses

As genetic technology and information become continuously more sophisticated and applied to the prevention and treatment of diseases, the need to understand the effects of genetic variants becomes an important task with regards to assessing disease risk. In the specific case of intellectual disabilities, prenatal screenings is an important diagnostic tool that prepares families and health professionals for the arrival of a child who may need immediate, specialized care. Cell Free DNA screenings are routine for determining sex and provide the opportunity to discover genetic anomalies. However, this has little value unless mutations can be recognized as pathogenic and are …

Scale-Free Behavioral Dynamics Directly Linked With Scale-Free Cortical Dynamics, Sabrina Jones

Physics Undergraduate Honors Theses

In organisms, an interesting phenomenon occurs in both behavior and neuronal activity: organization with fractal, scale-free fluctuations over multiple spatiotemporal orders of magnitude (1,2). In regard to behavior, this sort of complex structure-- which manifests itself from small scale fidgeting to purposeful, full body movements-- may support goals such as foraging (3-6), visual search (4), and decision making (7,8). Likewise, the presence of this sort of structure in the cerebral cortex in the form of spatiotemporal cascades, coined “neuronal avalanches,” may offer optimal information transfer (9). Thus, when considering the functional relationship between the cerebral cortex and movements of the …

Ongoing Calculus In The Cerebral Cortex, Luke Long

Physics Undergraduate Honors Theses

Various modes of neuronal computations have long been theorized to be possible based on the structure and geometry of the brain. These computations also seem necessary for many of the integral functions of the brain, like information processing and regulatory processes in the body. However, experimental data directly supporting these claims have been rare.

In this study, data collected in mice from a large number of neurons over a long period of time provided the opportunity to search for some of these computations, specifically change detection and squaring calculations. Using Matlab, the goal of this analysis was to find statistically …

Generation & Kinetic Studies Of Porphyrin Chromium-Oxo Intermediates, Iyanu Olumide Ojo

Masters Theses & Specialist Projects

Recent emerging applications of chromium porphyrin complexes are generating increasing interest in oxidation chemistry and catalysis. Its recent application as metal-organic frames in spintronic devices supports the rich electronic system of chromium metal. Through the past decades, first-row transition metalloporphyrins have served as biomimetic oxidation catalysts and models of cytochrome P450 enzymes. However, the oxygen atom transfer mechanism of chromium porphyrin complexes, most especially in sulfide oxidation reactions, has been scarcely investigated.

In this study, high-valent chromium-oxo porphyrin species, namely Cr^IV-oxo and Cr^V-oxo species, with electron-donating tetramesitylporphyrin(TMP) ligand were successfully generated and characterized with UV-vis, ESI-MS, …

Estimating The Analytical Performance Of Raman Spectroscopy For Quantification Of Active Ingredients In Human Stratum Corneum, Hichem Kichou, Emilie Munnier, Yuri Dancik, Kamilia Kemel, Hugh Byrne, Ali Tfayli, Dominique Bertrand, Martin Soucé, Igor Chourpa, Franck Bonnier

Articles

Confocal Raman microscopy (CRM) has become a versatile technique that can be applied routinely to monitor skin penetration of active molecules. In the present study, CRM coupled to multivariate analysis (namely PLSR—partial least squares regression) is used for the quantitative measurement of an active ingredient (AI) applied to isolated (ex vivo) human stratum corneum (SC), using systematically varied doses of resorcinol, as model compound, and the performance is quantified according to key figures of merit defined by regulatory bodies (ICH, FDA, and EMA). A methodology is thus demonstrated to establish the limit of detection (LOD), precision, accuracy, sensitivity (SEN), and …