Physical Sciences and Mathematics Commons^™

Experimental And Statistical Techniques To Probe Extraordinary Electronic Properties Of Molecules, Byron Hager Smith

Doctoral Dissertations

The existence of an additional electron or hole in the presence of an electric monopole is a well understood physical system, but this ideality is far from the true physical properties of many molecules. Examples of such irregular electronic states include the attachment of an excess charge to a molecule's dipole moment, electronic correlation spanning a molecule, or attachment of multiple excess charges. Current theoretical and experimental interpretations widely vary for these states and further elucidation of the nature of irregular electronic structure may provide solutions to unexplained observations and the impetus for industrial application. For example, in the case …

Mechanisms Of Hemolysis-Associated Platelet Activation, Christine C. Helms, M. Marvel, W. Zhao, M. Stahle, R. Vest, G. J. Kato, J. S. Lee, G. Christ, M. T. Gladwin, R. R. Hantgan, D. B. Kim-Shapiro

Physics Faculty Publications

Background

Intravascular hemolysis occurs after blood transfusion, in hemolytic anemias, and in other conditions, and is associated with hypercoagulable states. Hemolysis has been shown to potently activate platelets in vitro and in vivo, and several mechanisms have been suggested to account for this, including: (i) direct activation by hemoglobin (Hb); (ii) increase in reactive oxygen species (ROS); (iii) scavenging of nitric oxide (NO) by released Hb; and (iv) release of intraerythrocytic ADP.

Objective

To elucidate the mechanism of hemolysis-mediated platelet activation.

Methods

We used flow cytometry to detect PAC-1 binding to activated platelets for in vitro experiments, and a …

Hydrogen Evolution Reaction Measurements Of Dealloyed Porous Nicu, Kyla Koboski, Evan Nelsen, Jennifer R. Hampton

Faculty Publications

Porous metals are of interest for their high surface area and potential for enhanced catalytic behavior. Electrodeposited NiCu thin films with a range of compositions were electrochemically dealloyed to selectively remove the Cu component. The film structure, composition, and reactivity of these samples were characterized both before and after the dealloying step using scanning electron microscopy, energy-dispersive spectroscopy, and electrochemical measurements. The catalytic behavior of the dealloyed porous Ni samples towards the hydrogen evolution reaction was measured and compared to that of the as-deposited samples. The dealloyed samples were generally more reactive than their as-deposited counterparts at low overpotentials, making …

Interactive Wireless Sensor For Remote Trace Detection And Recognition Of Hazardous Gases, Audrey Lama

Masters Theses & Specialist Projects

The interactive wireless sensor detects many hazardous gases such as Hexane, Propane, Carbon monoxide and Hydrogen. These gases are highly toxic and used in different kinds of manufacturing industries, domestic purpose and so on. So, building a sensor that can detect this kind of gases can save the environment; prevent the potential for explosion, and endangering human life. In long term, interactive wireless sensor can also prevent the financial losses that might occur due to the hazardous incident that might occur due to these toxic gases.

Hexane is a colorless, strong gas which inhaled in significant amounts by a person …

Radiogenic Second Cancer Risk Differences In Female Hodgkin Lymphoma Patients Treated With Proton Versus Photon Radiotherapies, Kenneth L. Homann

Dissertations & Theses (Open Access)

Hodgkin Lymphoma (HL) is the most common cancer diagnosis of young adults in the United States. Advances in curative treatments for HL, including the use of photon radiation therapy (RT) techniques, have increased 10 year survival rates to approximately 90% among young patients. These RT treatments, however, contribute to an increased incidence of radiogenic second cancer (RSC) formation to the healthy tissue surrounding the tumor volume relative to the general population. These RSCs are the leading cause of death among long-term HL survivors. Proton therapy has been shown to reduce the therapeutic dose, and therefore, the risk of developing a …

Molecular Mechanisms Of Disease-Causing Missense Mutations, Shannon Stefl, Hafumi Nishi, Marharyta Petukh, Anna R. Panchenko, Emil Alexov

Publications

Genetic variations resulting in a change of amino acid sequence can have a dramatic effect on stability, hydrogen bond network, conformational dynamics, activity and many other physiologically important properties of proteins. The substitutions of only one residue in a protein sequence, so-called missense mutations, can be related to many pathological conditions, and may influence susceptibility to disease and drug treatment. The plausible effects of missense mutations range from affecting the macromolecular stability to perturbing macromolecular interactions and cellular localization. Here we review the individual cases and genome-wide studies which illustrate the association between missense mutations and diseases. In addition we …

Solution Scattering And Fret Studies Of Nucleosomes Reveal Dna: Unwrapping Effects Of H3 And H4 Tail Removal, Kurt Andresen, Isabel Jimenez-Useche, Steven C. Howell, Chongli Yuan, Xiangyun Qiu

Physics and Astronomy Faculty Publications

Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes …

Structure And Dynamics Of Model Systems: From Ferrofluids To Brain Membranes, Matthew A. Barrett

Matthew J. Barrett

Soft condensed matter systems are a very diverse and challenging subject to study. To understand the complex macro-properties of such systems one approach is to characterize the microscopic structure and dynamics. A powerful technique for determining micro and nanoscale properties is scattering of radiation sources. Light, electron and neutron scattering techniques provide insight into the complicated molecular structures and the processes happening on these small scales. We have used neutron and x-ray scattering techniques to determine structural and dynamical information from two different types of soft condensed matter systems. The microscopic nature of a cobalt magnetic fluid was studied using …

Fabricating Cost-Effective Nanostructures For Biomedical Applications, Erden Ertorer

Electronic Thesis and Dissertation Repository

In this thesis we described inexpensive alternatives to fabricate nanostructures on planar substrates and provided example applications to discuss the efficiency of fabricated nanostructures.

The first method we described is forming large area systematically changing multi-shape nanoscale structures on a chip by laser interference lithography. We analyzed the fabricated structures at different substrate positions with respect to exposure time, exposure angle and associated light intensity profile. We presented experimental details related to the fabrication of symmetric and biaxial periodic nanostructures on photoresist, silicon surfaces, and ion-milled glass substrates. Behavior of osteoblasts and osteoclasts on the nanostructures was investigated. These results …

Wave Function For Time-Dependent Harmonically Confined Electrons In A Time-Dependent Electric Field, Yu-Qi Li, Xiao-Yin Pan, Viraht Sahni

Publications and Research

The many-body wave function of a system of interacting particles confined by a time-dependent harmonic potential and perturbed by a time-dependent spatially homogeneous electric field is derived via the Feynman path-integral method. The wave function is comprised of a phase factor times the solution to the unperturbed time-dependent Schrödinger equation with the latter being translated by a time-dependent value that satisfies the classical driven equation of motion. The wave function reduces to that of the Harmonic Potential Theorem wave function for the case of the time-independent harmonic confining potential.

Experimental Microwave Breast Cancer Detection With Oil-On-Gelatin Phantom, Giuseppe Ruvio, Raffaele Solimene, Antonio Cuccaro, Jacinta Browne, Domenico Gaetano, Max Ammann

Conference Papers

Limitations of conventional X-ray mammography has induced a recent interest into radio frequency based diagnostic approaches in order to take advantage of the sharpest dielectric contrast between benign and malignant breast tissues in the microwave frequency range [1]. Dielectric contrast is notably higher than the radiographic density exploited by X-ray mammography. Consequences of the superior sensitivity of RF-based techniques can have a huge social and cost impact. By reducing the false response percent, a dramatic reduction of costs for the health system together with a diminution of traumatic experiences for the patients can be achieved. The antenna properties play a …

Escherichia Coli Heptosyltransferase I: Investigation Of Protein Dynamics Of A Gt-B Structural Enzyme, Erika A. Taylor, Daniel J. Czyzyk, Shreya S. Sawant, Carlos A. Ramirez-Mondragon

Erika A. Taylor, Ph.D.

Heptosyltransferase I (HepI), the enzyme responsible for the transfer of l-glycero-d-manno-heptose to a 3-deoxy-α-d-manno-oct-2-ulopyranosonic acid (Kdo) of the growing core region of lipopolysaccharide, is a member of the GT-B structural class of enzymes. Crystal structures have revealed open and closed conformations of apo and ligand-bound GT-B enzymes, implying that large-scale protein conformational dynamics play a role in their reaction mechanism. Here we report transient kinetic analysis of conformational changes in HepI reported by intrinsic tryptophan fluorescence and present the first real-time evidence of a GT-B enzyme undergoing a substrate binding-induced transition from an open to closed state prior to catalysis.

Computational Design Optimization For Microfluidic Magnetophoresis, Brian Dennis Plouffe, Laura H. Lewis, Shashi Krishna Murthy

Laura H. Lewis

Current macro- and microfluidic approaches for the isolation of mammalian cells are limited in both efficiency and purity. In order to design a robust platform for the enumeration of a target cell population, high collection efficiencies are required. Additionally, the ability to isolate pure populations with minimal biological perturbation and efficient off-chip recovery will enable subcellular analyses of these cells for applications in personalized medicine. Here, a rational design approach for a simple and efficient device that isolates target cell populations via magnetic tagging is presented. In this work, two magnetophoretic microfluidic device designs are described, with optimized dimensions and …

Three-Dimensional Electrokinetic Trapping Of A Single Fluorescent Nanoparticle In Solution, Jason Keith King

Doctoral Dissertations

This dissertation presents the development of an instrument for effectively trapping a single fluorescent nanoparticle that is freely diffusing in solution in all three dimensions. The instrument is expected to have applications for studies of single nanoparticles or molecules for which prolonged observations are required, but without immobilization or proximity to a surface, which may alter behavior. The trapping technique depends on rapid three-dimensional position measurements of the nanoparticle with sub-micron precision, which are used for real-time control of induced electrokinetic motion, so as to counteract Brownian motion. While anti-Brownian electrokinetic trapping experiments in one and two dimensions have previously …

Hemoglobin-Mediated Nitric Oxide Signaling, Christine C. Helms, D. B. Kim-Shapiro

Physics Faculty Publications

The rate that hemoglobin reacts with nitric oxide (NO) is limited by how fast NO can diffuse into the heme pocket. The reaction is as fast as any ligand/protein reaction can be and the result, when hemoglobin is in its oxygenated form, is formation of nitrate in what is known as the dioxygenation reaction. As nitrate, at the concentrations made through the deoxygenation reaction, is biologically inert, the only role hemoglobin was once thought to play in NO signaling was to inhibit it. However, there are now several mechanisms that have been discovered by which hemoglobin may preserve, control, and …

Ion Competition In Condensed Dna Arrays In The Attractive Regime, Xiangyun Qiu, John Giannini, Steven C. Howell, Qi Xia, Fuyou Ke, Kurt Andresen

Physics and Astronomy Faculty Publications

Physical origin of DNA condensation by multivalent cations remains unsettled. Here, we report quantitative studies of how one DNA-condensing ion (Cobalt³⁺ Hexammine, or Co³⁺Hex) and one nonDNA-condensing ion (Mg²⁺) compete within the interstitial space in spontaneously condensed DNA arrays. As the ion concentrations in the bath solution are systematically varied, the ion contents and DNA-DNA spacings of the DNA arrays are determined by atomic emission spectroscopy and x-ray diffraction, respectively. To gain quantitative insights, we first compare the experimentally determined ion contents with predictions from exact numerical calculations based on nonlinear Poisson-Boltzmann equations. Such calculations …

Computational Design Optimization For Microfluidic Magnetophoresis, Brian Plouffe, Laura Lewis, Shashi Murthy

Shashi K. Murthy

Current macro- and microfluidic approaches for the isolation of mammalian cells are limited in both efficiency and purity. In order to design a robust platform for the enumeration of a target cell population, high collection efficiencies are required. Additionally, the ability to isolate pure populations with minimal biological perturbation and efficient off-chip recovery will enable subcellular analyses of these cells for applications in personalized medicine. Here, a rational design approach for a simple and efficient device that isolates target cell populations via magnetic tagging is presented. In this work, two magnetophoretic microfluidic device designs are described, with optimized dimensions and …

An Ethnographic Study: Becoming A Physics Expert In A Biophysics Research Group, Idaykis Rodriguez

Idaykis Rodriguez

Expertise in physics has been traditionally studied in cognitive science, where physics expertise is understood through the difference between novice and expert problem solving skills. The cognitive perspective of physics experts only create a partial model of physics expertise and does not take into account the development of physics experts in the natural context of research. This dissertation takes a social and cultural perspective of learning through apprenticeship to model the development of physics expertise of physics graduate students in a research group. I use a qualitative methodological approach of an ethnographic case study to observe and video record the …

An Ethnographic Study: Becoming A Physics Expert In A Biophysics Research Group, Idaykis Rodriguez

FIU Electronic Theses and Dissertations

Expertise in physics has been traditionally studied in cognitive science, where physics expertise is understood through the difference between novice and expert problem solving skills. The cognitive perspective of physics experts only create a partial model of physics expertise and does not take into account the development of physics experts in the natural context of research. This dissertation takes a social and cultural perspective of learning through apprenticeship to model the development of physics expertise of physics graduate students in a research group. I use a qualitative methodological approach of an ethnographic case study to observe and video record the …

Elucidating Internucleosome Interactions And The Roles Of Histone Tails, Steven C. Howell, Kurt Andresen, Isabel Jimenez-Useche, Chongli Yuan, Xiangyun Qiu

Physics and Astronomy Faculty Publications

The nucleosome is the first level of genome organization and regulation in eukaryotes where negatively charged DNA is wrapped around largely positively charged histone proteins. Interaction between nucleosomes is dominated by electrostatics at long range and guided by specific contacts at short range, particularly involving their flexible histone tails. We have thus quantified how internucleosome interactions are modulated by salts (KCl, MgCl₂) and histone tail deletions (H3, H4 N-terminal), using small-angle x-ray scattering and theoretical modeling. We found that measured effective charges at low salts are ∼1/5th of the theoretically predicted renormalized charges and that H4 tail deletion …

Dynamics Of The Fitzhugh-Nagumo Neuron Model, Zechariah Thurman

Physics

In this paper, the dynamical behavior of the Fitzhugh-Nagumo model is examined. The relationship between neuron input current and the firing frequency of the neuron is characterized. Various coupling schemes are also examined, and their effects on the dynamics of the system is discussed. The phenomenon of stochastic resonance is studied for a single uncoupled Fitzhugh-Nagumo neuron.

Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov

Publications

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization …

Cancer Missense Mutations Alter Binding Properties Of Proteins And Their Interaction Networks, Hafumi Nisha, Manoj Tyagi, Shaolei Teng, Benjamin A. Shoemaker, Kosuke Hashimoto, Emil Alexov, Stefan Wuchty, Anna R. Panchenko

Publications

Many studies have shown that missense mutations might play an important role in carcinogenesis. However, the extent to which cancer mutations might affect biomolecular interactions remains unclear. Here, we map glioblastoma missense mutations on the human protein interactome, model the structures of affected protein complexes and decipher the effect of mutations on protein-protein, protein-nucleic acid and protein-ion binding interfaces. Although some missense mutations over-stabilize protein complexes, we found that the overall effect of mutations is destabilizing, mostly affecting the electrostatic component of binding energy. We also showed that mutations on interfaces resulted in more drastic changes of amino acid physico-chemical …

Organic Polymer Solar Cells: The Effects Of Device Packaging On Cell Lifetime, Spencer Herrick

Physics

As the earth runs out of nonrenewable energy sources and climate change starts to have drastic effects on the environment, the world is becoming increasingly desperate for cost efficient, renewable energy sources. Organic polymer based solar technology is a cutting edge approach to meeting the world’s energy demands. We fabricate single-layer, organic photovoltaics devices that utilize the electrical characteristics of semi-conductive polymers. These solution processable materials are beneficial due to their low material cost, lightweight, and simple fabrication requirements. Our devices utilize multiple photoactive polymers, P3HT and PCPDTBT, to absorb photons over a wide spectral range. We optimized various device …

Simulation Of Electronic Processes Of Nanoenergetic Gas Generator Using Cabrera Mott Oxidation Model, Zamart Ramazanova

Theses and Dissertations - UTB/UTPA

This research study is a theoretical framework for understanding rapid thermal processes which occur during the performance of new Nanoenergetic Gas-Generators (NGG) systems that rapidly release a large amount of gaseous products and generate a fast-moving thermal wave during the explosion. The kinetics of rapid oxidation of metal nanoparticles acquires practical importance with the quickly developing nanoenergetic systems. The thin film oxidation theory of Cabrera-Mott model was examined for a spherically symmetric case and used to analyze the physical importance of the exothermic processes for prediction of the reaction time and front velocity. A rapid kinetic of oxide growth on …

Raman Spectroscopic Analysis Of Human Skin Tissue Sections Ex-Vivo: Evaluation Of The Effects Of Tissue Processing And Dewaxing, Syed Mehmood Ali, Franck Bonnier, Ali Tfayli, Helen Lambkin, Kathleen Flynn, Vincent Mcdonagh, Claragh Healy, Thomas Lee, Fiona Lyng, Hugh Byrne

Articles

Raman spectroscopy coupled with K-means clustering analysis (KMCA) is employed to elucidate the biochemical structure of human skin tissue sections, and the effects of tissue processing. Both hand and thigh sections of human cadavers were analysed in their unprocessed and formalin fixed paraffin processed (FFPP) and subsequently dewaxed forms. In unprocessed sections, KMCA reveals clear differentiation of the stratum corneum, intermediate underlying epithelium and dermal layers for sections from both anatomical sites. The stratum corneum is seen to be relatively rich in lipidic content; the spectrum of the subjacent layers is strongly influenced by the presence of melanin, while that …

Application Of Computational Molecular Biophysics To Problems In Bacterial Chemotaxis, Davi Ortega

Doctoral Dissertations

The combination of physics, biology, chemistry, and computer science constitutes the promising field of computational molecular biophysics. This field studies the molecular properties of DNA, protein lipids and biomolecules using computational methods. For this dissertation, I approached four problems involving the chemotaxis pathway, the set of proteins that function as the navigation system of bacteria and lower eukaryotes.

In the first chapter, I used a special-purpose machine for molecular dynamics simulations, Anton, to simulate the signaling domain of the chemoreceptor in different signaling states for a total of 6 microseconds. Among other findings, this study provides enough evidence to propose …

The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov

Publications

In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states when provided with the structures of the unbound …

Biophysical Characterization Of Optimized Self-Assembling Protein Nanoparticles As A Malaria Vaccine, Sophia Walker

Honors Scholar Theses

Malaria is an infectious disease that affects several million individuals worldwide and is a significant international public health issue. While there is currently a malaria vaccine in phase III clinical trials, recent results demonstrate that it is only about 35% effective in reducing the incidence of the disease. The use of self-assembling protein nanoparticles (SAPNs) that display epitopes of the repeat sequence of the circumsporozoite protein of Plasmodium falciparum, the parasite that causes malaria, has been shown to elicit a strong immune response. This prototype has potential for further improvement by altering the epitope regions of the nanoparticles to …

In Silico Modeling The Effect Of Single Point Mutations And Rescuing The Effect By Small Molecules Binding, Zhe Zhang

All Dissertations

Single-point mutation in genome, for example, single-nucleotide polymorphism (SNP) or rare genetic mutation, is the change of a single nucleotide for another in the genome sequence. Some of them will result in an amino acid substitution in the corresponding protein sequence (missense mutations); others will not. This investigation focuses on genetic mutations resulting in a change in the amino acid sequence of the corresponding protein. This choice is motivated by the fact that missense mutations are frequently found to affect the native function of proteins by altering their structure, interaction and other properties and cause diseases. A particular disease is …