A Computational Kinetics Model To Quantify Radiation Induced Chemical Products Of Atmospheric Gas Mixtures,
2023
The University of Southern Mississippi
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 …
Heterochiral Dna Nanotechnology For Biomedical Applications,
2023
University of New Mexico
Heterochiral Dna Nanotechnology For Biomedical Applications, Tracy L. Mallette
Biomedical Engineering ETDs
In the past 30 years, there have been major advancements on how to treat and diagnose disease because of the improvement and increase in accessibility of sequencing technology. Nucleic acid-based therapeutics can manipulate protein expression. Likewise, pathogens can be identified and detected with single nucleotide specificity. However, the underlying oligonucleotide technology requires protection against natural defense systems that have evolved to destroy foreign nucleic acids. Many chemical modifications that can protect nucleotides also have significant cytotoxic side effects and must be carefully designed into the strands. A novel way to protect against nuclease-mediated degradation is through the use of mirror-image, …
Uncertainty In The Physical Basis Of Estimates Of Relative Biological Effectiveness In Carbon Radiotherapy,
2023
The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Uncertainty In The Physical Basis Of Estimates Of Relative Biological Effectiveness In Carbon Radiotherapy, Shannon Hartzell, Shannon Hartzell Ph.D.
Dissertations and Theses (Open Access)
Carbon ion radiotherapy is a novel modality used for the treatment of tumors that are unresectable, close to critical structures, or resistant to standard radiotherapy. A unique benefit of this therapy is the relative biological effectiveness (RBE) of the beam (i.e., how biologically potent carbon ions are as compared to x-rays), which is significantly elevated. This RBE also varies as a function of many parameters, and there are currently several models implemented in clinical and research-based treatment planning systems with which to predict RBE. These algorithms are computationally expensive and there are currently no means of validating their implementation within …
The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution,
2023
Clemson University
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 …
Impacts And Applications Of Vegetable Glycerin On Nanocellulose,
2023
University of Northern Iowa
Impacts And Applications Of Vegetable Glycerin On Nanocellulose, Elise Hong-Miller, Dylan Seiffert, T. E. Kidd
Summer Undergraduate Research Program (SURP) Symposium
Nanocellulose is created by breaking down cellulose, the most common organic molecule found in nature. Nanocellulose has attractive properties, such as a very high strength-to-weight ratio, for many different applications. A major challenge is that nanocellulose has a very high shrinkage % (~90%) when it is dried, as well as a strong probability to crack. Different additives can be added in varying amounts to either mitigate or intensify these aspects, as well as affect its drying conditions. This investigation is helping the National Aeronautics and Space Administration (NASA) and the U.S. Army to find a use for this highly renewable …
Flow Through Processing Of Nanocellulose For Space Exploration Applications,
2023
University of Northern Iowa
Flow Through Processing Of Nanocellulose For Space Exploration Applications, Dylan Seiffert, T. E. Kidd
Summer Undergraduate Research Program (SURP) Symposium
Nanocellulose is synthesized from cellulose, which is the most abundant organic molecule found in nature. Nanocellulose solids are biodegradable and have a strength-to-weight ratio eight times that of steel1. The production of nanocellulose solids is challenging due to the large volume loss that occurs during the curing process as well as the time and cost associated with ultrasonic processing. The loss of volume during curing often results in cracking and deformation of the cured solid. The issues caused by the large volume loss can be mitigated using additives that do not compromise the strength, shape, or machineability of …
Molybdenum Disulfide (Mos₂) As A Nanocellulose Substrate,
2023
University of Northern Iowa
Molybdenum Disulfide (Mos₂) As A Nanocellulose Substrate, Mariana Torres, Dylan Seiffert, Elise Hong-Miller, T. E. Kidd
Summer Undergraduate Research Program (SURP) Symposium
Cellulose is a substance abundant in nature, found in fruits and vegetables, plant cell walls (National Center for Biotechnology Information, 2023), and wood (Sjostrom, 1993). The abundance of cellulose is attributable to its linear chemical structure, as it is composed of long strands of glucose molecules linked together by hydrogen atoms, which enable the substance to withstand significant pressure without breaking (Rongpipi et al., 2019). This property—known as high tensile strength—is joined by its non-toxicity and sustainability, given cellulose may be degraded and renewed naturally (Kaur, 2021). These various properties indicate versatility, and its resultant current and desired uses—such as …
The Applicability Of The Postmortem Submersion Interval Estimation Formula For Human Remains Found In Subtropical Aquatic Environments,
2023
University of South Florida
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,
2023
California Polytechnic State University, San Luis Obispo
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 …
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,
2023
CUNY Graduate Center
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 …
Flash-Rt: Using High-Dose Radiation For Clinical Radiation Therapy,
2023
Portland State University
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 …
Vibrational, Rotational And Electronic Spectroscopy For Possible Interstellar Detection Of Alnh2 And Halnh,
2023
University of Pennsylvania
Vibrational, Rotational And Electronic Spectroscopy For Possible Interstellar Detection Of Alnh2 And Halnh, Tarek Trabelsi, Vincent J. Esposito, Joseph S. Francisco
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
We obtained accurate vibrational frequencies, rotational constants, and vertical transition energy for AlNH2(X1A1) and HAlNH(X1A′) isomers using ab initio calculations at various levels of theory. These two isomers are potential candidates for astronomical observation. AlNH2 and HAlNH are thermodynamically stable, with Al-NH2 and HAl-NH bond dissociation energies predicted to be 4.39 and 3.60 eV, respectively. The two isomers are characterized by sizable dipole moments of 1.211 and 3.64 D, respectively. The anharmonic frequencies and spectroscopic constants reported for the two isomers should facilitate their experimental differentiation. In addition, we evaluated …
Photoisomerizable Membrane Active Peptides,
2023
Seton Hall University
Photoisomerizable Membrane Active Peptides, Cristina Ventura
Seton Hall University Dissertations and Theses (ETDs)
Membrane active peptides (MAPs) bind and partition into the cell membrane thus causing permeabilization. Many α-helical membrane active peptides contain central proline residues that distinguish the hydrophobic and hydrophilic faces of the helix. The proline induces a bend that produces a helix-hinge-helix motif. Mutation of these proline residues has a significant effect on the activity of the MAP. Azobenzene is a photoisomerizable molecule that switches from its trans to cis isomer upon excitation with ultraviolet (UV) light and from its cis to trans isomer upon excitation with visible light (VL). In this work it is hypothesized that the hinge function …
Maximum Likelihood Estimation Of Glandular Fraction For Mammography,
2023
Louisiana State University and Agricultural and Mechanical College
Maximum Likelihood Estimation Of Glandular Fraction For Mammography, Bryce Smith
LSU Master's Theses
Breast tissue is a mixture of adipose and fibro glandular tissue with a glandular fraction on average of 20%-30%. Previous studies have confirmed that there is a risk of undetected breast cancer related to the amount of glandular tissue present in the breast. Since a higher glandular fraction can lead to an increased cancer risk, it is important for radiologists to know quantitative glandular fraction when diagnosing a patient. Another increasingly popular protocol for mammography is to eliminate the anti-scatter grid and use software algorithms to reduce scatter. This work focuses on using a maximum likelihood algorithm to estimate the …
The Use Of Fluorescence Resonance Energy Transfer And Bent Dna To Study Dna And Ion Interactions,
2023
University of Arkansas, Fayetteville
The Use Of Fluorescence Resonance Energy Transfer And Bent Dna To Study Dna And Ion Interactions, Kaitlin Bullard
Physics Undergraduate Honors Theses
Studying DNA interactions is advantageous to developments in the medical field since DNA and its interactions affect our health greatly. In addition, it is important to understand how the bendability of DNA depends on metal ions, which are essential for various fundamental processes in cells. In this work, we investigate the use of FRET and self-assembled bent DNA molecules to quantify DNA interactions with magnesium ions. We measured that the FRET efficiency increased at higher concentrations of magnesium ions. We also ran simulations to further understand the mechanisms. These observations show that magnesium ions increase the stability and flexibility of …
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 …
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 …
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 …
