Wave Function For Time-Dependent Harmonically Confined Electrons In A Time-Dependent Electric Field, 2013 Ningbo University
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, 2013 Technological University Dublin
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, 2013 Wesleyan University
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, 2013 Northeastern University
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, 2013 University of Tennessee, Knoxville
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, 2013 University of Richmond
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, 2013 Cornell University
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, 2013 Northeastern University
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, 2013 Florida International University
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, 2013 Florida International University
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, 2013 Gettysburg College
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, 2013 California Polytechnic State University - San Luis Obispo
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, 2013 Clemson University
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, 2013 National Institute of Health
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, 2013 California Polytechnic State University - San Luis Obispo
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, 2013 University of Texas at Brownsville
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, 2013 Technological University Dublin
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, 2013 University of Tennessee - Knoxville
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 …
Novel Materials For Use In Homeland Security Research, 2013 Western Kentucky University
Novel Materials For Use In Homeland Security Research, Jason Osgood Ewen Young
Masters Theses & Specialist Projects
Organometallic pyridazines and compounds derived from them have been of interest in polymer research due to their atypical environmental stability (as compared to other non-aromatic organic semiconductors) as well as their conductivity. The off-metal synthesis and characterization of several pyridazyl thallium, manganese, and rhenium complexes, beginning with fulvenes 1,2- C5H3(COHR)(COR), are reported here. The diacyl fulvenes were treated with hydrazine hydrate to ring close to pyridazines. Next, the pyridazines were converted to their respective thallium salts through treatment with thallium (I) ethoxide. Lastly, the salts were transmetallated into the respective rhenium or manganese complexes through treatment with the respective metal …
The Role Of Protonation States In Ligand-Receptor Recognition And Binding, 2013 Clemson University
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 …