Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints,
2023
University of Connecticut
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 …
An Investigation On The Effect Of Conserved Hinge Histidine On Influenza Hemagglutinin(Ha2) Protein Conformation Using Md Simulations,
2023
University of Arkansas, Fayetteville
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 …
Simulating Mass Extinctions In An Agent-Based Evolutionary Model,
2023
University of Missouri-St. Louis
Simulating Mass Extinctions In An Agent-Based Evolutionary Model, Emily Vastola, Will Hayes, Joe Milliano, Tyler Hanke, Ian Heye, Dawn M. King, Sonya Bahar
Undergraduate Research Symposium
In an agent-based model of evolutionary dynamics which has been shown to undergo a nonequilibrium phase transition from extinction to survival, we apply coalescent theory to investigate the responses of population lineages to simulated mass extinctions. In the model, organisms reproduce via assortative mating on a neutral fitness landscape; parameters including the mutability (distance offspring may be distributed away from their parents in the fitness landscape) and the death parameter (percentage of organisms randomly removed during each generation) control the phase transition. Lineage structure can be characterized using the time to most recent common ancestor (TMRCA). We examine how this …
An Ab Initio Computation Of The Potential Energy Surfaces Of The Dna Bases,
2023
Southern Adventist University
An Ab Initio Computation Of The Potential Energy Surfaces Of The Dna Bases, Anjali F. Filinovich, Vola Andrianarijaona
Campus Research Month
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,
2023
Murray State University
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 …
United Properties Of Single-Origin Chocolates,
2023
Utah State University
United Properties Of Single-Origin Chocolates, Joseph Cooney
Student Research Symposium
In small production facilities, such as those used to manufacture single origin chocolate, cocoa nibs are ground to reduce the particle size to levels below 20 microns. This is a very important step during chocolate production, since chocolates with particles greater than 20 microns will have a grainy texture and unacceptable mouthfeel. The objective of this research was to evaluate changes in viscosity during chocolate grinding as affected by chocolate formulation. Three different types of chocolates were evaluated: 70% dark, 50% milk, and a Swiss-style milk chocolate. Chocolates were processed in a stone grinder and samples were taken as a …
Modeling Excited State Processes In Molecular Aggregates By Constructing An Adaptive Basis For The Hierarchy Of Pure States,
2023
Southern Methodist University
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 …
Novel As-S-Se Compositions Of Solution-Processed Chalcogenide Thin Films For Infrared Optics,
2023
Ursinus College
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 …
Developing Carbon Quantum Dots As Multimodal Contrast Agents,
2023
Rowan University
Developing Carbon Quantum Dots As Multimodal Contrast Agents, Nicholas Whiting
College of Science & Mathematics Departmental Research
No abstract provided.
Reconversion Of Parahydrogen Gas In Surfactant-Coated Glass Nmr Tubes,
2023
Rowan University
Reconversion Of Parahydrogen Gas In Surfactant-Coated Glass Nmr Tubes, Robert V. Chimenti, James Daley, James Sack, Jennifer Necsutu, Nicholas Whiting
College of Science & Mathematics Departmental Research
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,
2023
CUNY Graduate Center
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,
2023
The Children’s Hospital at Westmead, Sydney, Australia
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,
2023
Technological University Dublin
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 …
Long-Range And Chaotic Active Mixing Of Swimming Microbes In A Vortex Chain Flow,
2023
Bucknell University
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 …
Analysis Of Biologically Effective Dose For Retroactive Yttrium-90 Trans-Arterial Radioembolization Treatment Optimization,
2023
Claremont McKenna College
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 …
First Review Of Equilibrium Landscape Of Ingress/Egress Channels And Gating Residues Of The Cytochrome P450 3a4,
2023
Southern Illinois University Edwardsville
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".
Homopurine Guanine-Rich Sequences In Complex With N-Methyl Mesoporphyrin Ix Form Parallel G-Quadruplex Dimers And Display A Unique Symmetry Tetrad,
2023
Swarthmore College
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 …
Optical Tweezers: Exerting Force With Light,
2023
Scripps College
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 …
Review-Electrode Kinetics And Electrolyte Stability In Vanadium Flow Batteries,
2023
Technological University of the Shannon, Ireland
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 …
Fabrication And Investigation Of Microfluidic Devices That Produce Non-Linear Chemical Gradients,
2023
Georgia Southern University
Fabrication And Investigation Of Microfluidic Devices That Produce Non-Linear Chemical Gradients, Elijah L. Waters
College of Graduate Studies: Theses & 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 …
