Crystal Structure Of Thermus Thermophilus Methylenetetrahydrofolate Dehydrogenase And Determinants Of Thermostability, 2020 University of South Florida
Crystal Structure Of Thermus Thermophilus Methylenetetrahydrofolate Dehydrogenase And Determinants Of Thermostability, Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele
USF St. Petersburg campus Faculty Publications
The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for …
Development Of A Comsol Microdialysis Model, Towards Creation Of Microdialysis On A Chip With Improved Geometries And Recovery, 2019 University of Arkansas, Fayetteville
Development Of A Comsol Microdialysis Model, Towards Creation Of Microdialysis On A Chip With Improved Geometries And Recovery, Patrick Pysz
Graduate Theses and Dissertations
Microdialysis (µD) sampling is a diffusion-limited sampling method that has been widely used in different biomedical fields for greater than 35 years. Device calibration for in vivo studies is difficult for current non-steady state analytes of interest correlated with both inflammatory response and microbial signaling molecules (QS); which exist in low ng/mL to pg/mL with molecular weights over a wide range of 170 Da to 70 kDa. The primary performance metric, relative recovery (RR), relating the collected sample to the extracellular space concentration varies from 10% to 60% per analyte even under controlled bench-top conditions. Innovations in microdialysis device design …
Characterization Of The Anomalous Ph Of Aqueous Nanoemulsions, 2019 University of Massachusetts Amherst
Characterization Of The Anomalous Ph Of Aqueous Nanoemulsions, Kieran P. Ramos
Doctoral Dissertations
Aqueous water-in-oil nanoemulsions have emerged as a versatile tool for use in microfluidics, drug delivery, single-molecule measurements, and other research. Nanoemulsions are often prepared with perfluorocarbons which are remarkably biocompatbile due to their stability, low surface tension, lipophobicity, and hydrophobicity. Therefore it is often assumed that droplet contents are unperturbed by the perfluorinated surface. However, in microemulsions, which are similar to nanoemulsions, it is known that either the pH of the aqueous phase or the ionization constants of encapsulated molecules are different from bulk solution. There is also recent evidence of low pH in perfluorinated aqueous nanoemulsions. The current underlying …
Analog Implementation Of The Hodgkin-Huxley Model Neuron, 2019 Illinois State University
Analog Implementation Of The Hodgkin-Huxley Model Neuron, Zachary D. Mobille, George H. Rutherford, Jordan Brandt-Trainer, Rosangela Follmann, Epaminondas Rosa
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Period Drift In A Neutrally Stable Stochastic Oscillator, 2019 Illinois State University
Period Drift In A Neutrally Stable Stochastic Oscillator, Kevin Sanft
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Odx: A Fitness Tracker-Based Device For Continuous Bacterial Growth Monitoring, 2019 Cancer Research@UCC, University College Cork, Cork T12 XF62, Ireland
Odx: A Fitness Tracker-Based Device For Continuous Bacterial Growth Monitoring, Venkata V.B. Yallapragada, Uday Gowda, David Wong, Liam O'Faolain, Mark Tangney, Ganga C.R. Devarapu
Cappa Publications
Continuous monitoring of bacterial growth in aqueous media is a crucial process in academic research as well as in the biotechnology industry. Bacterial growth is usually monitored by measuring the optical density of bacteria in liquid media, using benchtop spectrophotometers. Due to the large form factor of the existing spectrophotometers, they cannot be used for live monitoring of the bacteria inside bacterial incubation chambers. Additionally, the use of benchtop spectrometers for continuous monitoring requires multiple samplings and is labour intensive. To overcome these challenges, we have developed an optical density measuring device (ODX) by modifying a generic fitness tracker. The …
Effective Statistical Energy Function Based Protein Un/Structure Prediction, 2019 University of New Orleans
Effective Statistical Energy Function Based Protein Un/Structure Prediction, Avdesh Mishra
University of New Orleans Theses and Dissertations
Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D structure, have dynamic characteristics and therefore, exist in multiple states. Based on …
Quantifying Uncertainty In A Measurement-Based Assessment Of Relative Biological Effectiveness In Carbon Ion Radiotherapy, 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Quantifying Uncertainty In A Measurement-Based Assessment Of Relative Biological Effectiveness In Carbon Ion Radiotherapy, Shannon Hartzell
Dissertations & Theses (Open Access)
One of the largest inconsistencies in dose delivered during carbon ion therapy is due to uncertainties in relative biological effectiveness (RBE), a value that is calculated via one of several clinically implemented algorithms. This study investigates the uncertainty in measured microdosimetric parameters for RBE calculation by the Microdosimetric Kinetic Model (MKM), Repair Misrepair Fixation model (RMF), and Local Effect Model I (LEM) using a Tissue Equivalent Proportional Counter (TEPC).
Microdosimetric spectra, kinetic energy spectra, and dose fragment contributions were calculated using Monte Carlo (GEANT IV) for monoenergetic and SOBP carbon beams of clinical energy. From microdosimetric spectra, lineal energy values …
Modeling Proton Relative Biological Effectiveness Using Monte Carlo Simulations Of Microdosimetry, 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Modeling Proton Relative Biological Effectiveness Using Monte Carlo Simulations Of Microdosimetry, Mark A. Newpower
Dissertations & Theses (Open Access)
Proton therapy is a radiotherapy modality that can offer a better physical dose distribution when compared to photon radiotherapy by taking advantage of the Bragg peak, a narrow region of rapid energy loss. Proton therapy is also known to offer an enhanced relative biological effectiveness (RBE) compared to photons. In the current clinical standard, RBE is fixed at 1.1 at all points along the proton beam, meaning protons are assumed to require 10% less dose than photons to achieve target coverage and organ at risk (OAR) sparing. However, there is mounting clinical evidence, and a significant number of in vitro …
Commissioning Of Micro-Cube Thermoluminescent Dosimeters For Small Field Dosimetry Quality Assurance In Radiotherapy, 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Commissioning Of Micro-Cube Thermoluminescent Dosimeters For Small Field Dosimetry Quality Assurance In Radiotherapy, Brandon Luckett
Dissertations & Theses (Open Access)
Small field dosimetry presents complications and uncertainties that could be circumvented by using detectors which are smaller than the radiation field. This study evaluates the reproducibility and accuracy of TLD micro-cubes for use in stereotactic radiosurgery (SRS) remote auditing quality assurance (QA) for treatment centers participating in clinical trials. This study tested the hypothesis that TLD micro-cubes could be commissioned to evaluate small field dosimetry, and provide reproducibility within 3%, as well as assure agreement between measured dose and calculated doses to within 5%.
The aims of this thesis were to characterize and commission TLD micro-cubes as well as to …
Impact Of Excitation-Inhibition Balance/Imbalance On Dynamics Of Cortical Neural Networks, 2019 University of Arkansas, Fayetteville
Impact Of Excitation-Inhibition Balance/Imbalance On Dynamics Of Cortical Neural Networks, Vidit Agrawal
Graduate Theses and Dissertations
The purpose of this research is to study the implications of Excitation/Inhibition balance and imbalance on the dynamics of ongoing (spontaneous) neural activity in the cerebral cortex region of the brain.
The first research work addresses the question that why among the continuum of Excitation-Inhibition balance configurations, particular configuration should be favored? We calculate the entropy of neural network dynamics by studying an analytically tractable network of binary neurons. Our main result from this work is that the entropy maximizes at regime which is neither excitation-dominant nor inhibition-dominant but at the boundary of both. Along this boundary we see there …
A Comprehensive Assessment Of The Low-Temperature Thermal Properties And Thermodynamic Functions Of Ceo2, 2019 Texas A&M University
A Comprehensive Assessment Of The Low-Temperature Thermal Properties And Thermodynamic Functions Of Ceo2, Tyler D. Morrison, Elizabeth Sooby Wood, Phillippe F. Weck, Eunja Kim, Sung Oh Woo, Andrew T. Nelson, Donald G. Naugle
Physics & Astronomy Faculty Research
Reported is an experimental and computational investigation of the low temperature heat capacity, thermodynamic functions, and thermal conductivity of stoichiometric, polycrystalline CeO2. The experimentally measured heat capacity at T... (See full abstract in article).
Computational Investigation Of The Interactions Between Bioactive Compounds And Biological Assemblies, 2019 University of New Mexico - Main Campus
Computational Investigation Of The Interactions Between Bioactive Compounds And Biological Assemblies, Tye D. Martin
Biomedical Engineering ETDs
Small, biologically active molecules with unique properties and applications are potential solutions to a wide range of threats to global health including infectious agents and neurodegenerative disease. Experimental studies on a class of oligomeric p-phenylene ethynylenes (OPEs) have shown potential both as bioactive antimicrobials and fluorescent sensing agents for tracking amyloid-β (Aβ) aggregates found in Alzheimer’s Disease (AD). A second type of small molecule with potential applications in AD therapy, curcumin, has been found to interfere with Aβ fibril growth. Curcumin also attenuates Aβ-membrane interactions and Aβ toxicity. Our goal has been to use computational techniques to better understand the …
Reactive And Stimuli-Responsive Sulfonium-Based Polymer Zwitterions, 2019 University of Massachusetts Amherst
Reactive And Stimuli-Responsive Sulfonium-Based Polymer Zwitterions, Cristiam Santa Chalarca
Doctoral Dissertations
This dissertation describes the synthesis and characterization of novel monomers and (co)polymer zwitterions that incorporate trialkylsulfonium cations. The novel materials presented herein constitute a unique type of polymer zwitterions that exhibit salt- and temperature-dependent water solubility as well as inherent reactivity. The behavior of these polymers in aqueous solutions, as nanostructures, and at liquid-liquid interfaces was studied; in all cases, the inherent reactivity of the polymers was harnessed towards the fabrication of novel polymers and soft materials. Following an introductory chapter, Chapter 2 describes the synthesis of sulfonium sulfonate monomers and polymer zwitterions. Both styrenic and methacrylic monomers were synthesized …
Quantifying Complex Systems Via Computational Fly Swarms, 2019 Linfield College
Quantifying Complex Systems Via Computational Fly Swarms, Troy Taylor
Senior Theses
Complexity is prevalent both in natural and in human-made systems, yet is not well understood quantitatively. Qualitatively, complexity describes a phenomena in which a system composed of individual pieces, each having simple interactions with one another, results in interesting bulk properties that would otherwise not exist. One example of a complex biological system is the bird flock, in particular, a starling murmuration. Starlings are known to move in the direction of their neighbors and avoid collisions with fellow starlings, but as a result of these simple movement choices, the flock as a whole tends to exhibit fluid-like movements and form …
Magnetic Borophenes From An Evolutionary Search, 2019 Nankai University
Magnetic Borophenes From An Evolutionary Search, Meng-Hong Zhu, Xiao-Ji Weng, Guoying Gao, Shuai Dong, Ling-Fang Lin, Wei-Hua Wang, Qiang Zhu, Artem R. Oganov, Xiao Dong, Yongjun Tian, Xiang-Feng Zhou, Hui-Tian Wang
Physics & Astronomy Faculty Research
A computational methodology based on ab initio evolutionary algorithms and spin-polarized density functional theory was developed to predict two-dimensional magnetic materials. Its application to a model system borophene reveals an unexpected rich magnetism and polymorphism. A metastable borophene with nonzero thickness is an antiferromagnetic semiconductor from first-principles calculations, and can be further tuned into a half-metal by finite electron doping. In this borophene, the buckling and coupling among three atomic layers are not only responsible for magnetism, but also result in an out-of-plane negative Poisson's ratio under uniaxial tension, making it the first elemental material possessing auxetic and magnetic properties …
Topics In Three-Dimensional Imaging, Source Localization And Super-Resolution, 2019 University of New Mexico
Topics In Three-Dimensional Imaging, Source Localization And Super-Resolution, Zhixian Yu
Physics & Astronomy ETDs
The realization that twisted light beams with helical phasefronts could carry orbital angular momentum (OAM) that is in excess of the photon's spin angular momentum (SAM) has spawned various important applications. One example is the design of novel imaging systems that achieve three-dimensional (3D) imaging in a single snapshot via the rotation of point spread function (PSF).
Based on a scalar-field analysis, a particular simple version of rotating PSF imagery, which was proposed by my advisor Dr. Prasad, furnishes a practical approach to perform 3D source localization using a spiral phase mask that generates a combination of Bessel vortex beams. …
Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, 2019 University of Connecticut
Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre
Honors Scholar Theses
Abnormal ocular motility is a common manifestation of many underlying pathologies particularly those that are neurological. Dynamics of saccades, when the eye rapidly changes its point of fixation, have been characterized for many neurological disorders including concussions, traumatic brain injuries (TBI), and Parkinson’s disease. However, widespread saccade analysis for diagnostic and research purposes requires the recognition of certain eye movement parameters. Key information such as velocity and duration must be determined from data based on a wide set of patients’ characteristics that may range in eye shapes and iris, hair and skin pigmentation [36]. Previous work on saccade analysis has …
Scope Of Self-Interacting Thermal Wimps In A Minimal U(1) D Extension And Its Future Prospects, 2019 Indian Institute of Science
Scope Of Self-Interacting Thermal Wimps In A Minimal U(1) D Extension And Its Future Prospects, Rahool Kumar Barman, Biplob Bhattacherjee, Arindam Chatterjee, Arghya Choudhury, Aritra Gupta
Journal Articles
In this work we have considered a minimal extension of Standard Model by a local U(1) gauge group in order to accommodate a stable (fermionic) Dark Matter (DM) candidate. We have focussed on parameter regions where DM possesses adequate self-interaction, owing to the presence of a light scalar mediator (the dark Higgs), alleviating some of the tensions in the small-scale structures. We have studied the scenario in the light of a variety of data, mostly from dark matter direct searches, collider searches and flavor physics experiments, with an attempt to constrain the interactions of the standard model (SM) particles with …
Optical Enhancement In Periodic Plasmonic Gratings For Sers And Metal-Semiconductor-Metal Photodetectors (Msm-Pds) Applications, 2019 University of Arkansas, Fayetteville
Optical Enhancement In Periodic Plasmonic Gratings For Sers And Metal-Semiconductor-Metal Photodetectors (Msm-Pds) Applications, Ahmad Aziz Darweesh
Graduate Theses and Dissertations
This dissertation is aimed to numerically study the effect of plasmonic grating electrodes on the efficiency of metal-semiconductor-metal photodetectors (MSM PDs) and the sensitivity of Surface Enhanced Raman Spectroscopy (SERS). This research can benefit many areas of nanoscience and optics, including plasmonic applications, such as, super lenses, nano-scale optical circuits, optical filters, surface plasmon enhanced photo-detectors solar cells, imaging sensors, charge-coupled devices (CCD), and optical-fiber communication systems. Several parameters, wire widths and thickness, gap space, taper angle, and the incident wavelength and angle, were investigated. The goal of this research is to utilize the plasmonic phenomenon by using plasmonic gratings …