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Articles 1 - 17 of 17
Full-Text Articles in Physical Sciences and Mathematics
Unusually Low Thermal Conductivity In The Argyrodite Ag8gete6 Attributed To Strong Anharmonicity, Dale Hitchcock
Unusually Low Thermal Conductivity In The Argyrodite Ag8gete6 Attributed To Strong Anharmonicity, Dale Hitchcock
All Dissertations
Arguably the main focus of thermoelectric materials research over the last decade has been the reduction of lattice thermal conductivity through nanostructuring. This approach has proved quite effective in many instances, but has several inherent drawbacks including not only the metastability of many of the nanostructures used, but also difficulty decoupling the effects on the thermal properties of materials from the effects on their electrical properties. Some more recent research has focused on reduced thermal conductivity in materials with strong anharmonicity. In these systems anharmonicty in the crystal structure, whose strength can be gauged by the so-called Gruneissen parameter leads …
Chasing Polys: Interdisciplinary Affinity And Its Connection To Physics Identity, Tyler Scott
Chasing Polys: Interdisciplinary Affinity And Its Connection To Physics Identity, Tyler Scott
All Dissertations
This research is based on two motivations that merge by means of the frameworks of interdisciplinary affinity and physics identity. First, a goal of education is to develop interdisciplinary abilities in students' thinking and work. But an often ignored factor is students interests and beliefs about being interdisciplinary. Thus, this work develops and uses a framework called interdisciplinary affinity. It encompasses students interests in making connections across disciplines and their beliefs about their abilities to make those connections. The second motivation of this research is to better understand how to engage more students with physics. Physics identity describes how a …
Majorana Fermions In Chiral Topological Superconductors, Eugen Florin Dumitrescu
Majorana Fermions In Chiral Topological Superconductors, Eugen Florin Dumitrescu
All Dissertations
Majorana fermions were first proposed in the context of high energy physics by Ettore Majorana in 1937, just before his mysterious disappearance. Now, over 70 years later, signatures of condensed matter ana-logues of Majorana fermions are finally appearing in low-dimensional superconductor-based heterostructures. In low-dimensional systems, these order parameter, defect-bound Majorana quasiparticles obey non-Abelian quantum statistics and can therefore be used as the building blocks of a topological quantum computer. In this thesis we will analyze the signatures associated with, and the robustness of, Majorana bound states in a variety of one-dimensional superconducting platforms. Our main result is the finding that …
Fast Fission Neutron Detection Using The Cherenkov Effect, Matthew Millard
Fast Fission Neutron Detection Using The Cherenkov Effect, Matthew Millard
All Theses
The Cherenkov effect in optically clear media of varying indices of refraction and composition was investigated for quantification of fast neutrons. The ultimate application of the proposed detection system is criticality monitoring. The optically clear medium, composed of select target nuclei, was coupled to a photomultiplier tube. Neutron reaction products of the target nuclei contained within the optical medium emit beta particles and gamma rays that produce Cherenkov photons within the medium which can be detected. Assessed media include quartz (SiO2), sapphire (Al2O3), spinel (MgAl2O4), and zinc sulfide (ZnS), which were irradiated with un-moderated 252Cf. Monte Carlo N-Particle (MCNP) code …
Rational Design Of Small-Molecule Stabilizers Of Spermine Synthase Dimer By Virtual Screening And Free Energy-Based Approach, Zhe Zhang, Virginie Martiny, David Lagorce, Yoshihiko Ikeguchi, Emil Alexov, Maria A. Miteva
Rational Design Of Small-Molecule Stabilizers Of Spermine Synthase Dimer By Virtual Screening And Free Energy-Based Approach, Zhe Zhang, Virginie Martiny, David Lagorce, Yoshihiko Ikeguchi, Emil Alexov, Maria A. Miteva
Publications
Snyder-Robinson Syndrome (SRS) is a rare mental retardation disorder which is caused by the malfunctioning of an enzyme, the spermine synthase (SMS), which functions as a homo-dimer. The malfunctioning of SMS in SRS patients is associated with several identified missense mutations that occur away from the active site. This investigation deals with a particular SRS-causing mutation, the G56S mutation, which was shown computationally and experimentally to destabilize the SMS homo-dimer and thus to abolish SMS enzymatic activity. As a proof-of-concept, we explore the possibility to restore the enzymatic activity of the malfunctioning SMS mutant G56S by stabilizing the dimer through …
Mechanical Properties Of Low Dimensional Materials, Deepika Saini
Mechanical Properties Of Low Dimensional Materials, Deepika Saini
All Dissertations
Recent advances in low dimensional materials (LDMs) have paved the way for unprecedented technological advancements. The drive to reduce the dimensions of electronics has compelled researchers to devise newer techniques to not only synthesize novel materials, but also tailor their properties. Although micro and nanomaterials have shown phenomenal electronic properties, their mechanical robustness and a thorough understanding of their structure-property relationship are critical for their use in practical applications. However, the challenges in probing these mechanical properties dramatically increase as their dimensions shrink, rendering the commonly used techniques inadequate. This Dissertation focuses on developing techniques for accurate determination of elastic …
Energy Loss Of Ions Implanted In Mos Dielectric Films, Radhey Shyam
Energy Loss Of Ions Implanted In Mos Dielectric Films, Radhey Shyam
All Dissertations
Energy loss measurements of ions in the low kinetic energy regime have been made on as-grown SiO2(170-190nm) targets. Singly charged Na+ ions with kinetic energies of 2-5 keV and highly charged ions Ar+Q (Q=4, 8 and 11) with a kinetic energy of 1 keV were used. Excitations produced by the ion energy loss in the oxides were captured by encapsulating the irradiated oxide under a top metallic contact. The resulting Metal-Oxide-Semiconductor (MOS) devices were probed with Capacitance-Voltage (C V) measurements and extracted the flatband voltages from the C-V curves. The C-V results for singly charged ion experiments reveal …
A Biophysical Understanding Of The Applications And Implications Of Nanomaterials, Nicholas Geitner
A Biophysical Understanding Of The Applications And Implications Of Nanomaterials, Nicholas Geitner
All Dissertations
The last few decades have seen an explosion in the study and application of nanomaterials that continues to grow at a dizzying pace. Despite exciting applications in nano-enabled electronics, materials, medicine, and environmental remediation, an understanding of the interactions of these materials with natural materials and systems and the resulting implications lags severely behind. The purpose of this Dissertation is to illuminate these interactions as well as develop novel environmental applications from a biophysical perspective. Following an introduction and literature review in Chapter 1, Chapters 2-4 will explore the application of dendritic polymers as novel and biocompatible oil dispersants for …
Protein Nano-Object Integrator: Generating Atomic-Style Objects For Use In Molecular Biophysics, Nicholas Smith
Protein Nano-Object Integrator: Generating Atomic-Style Objects For Use In Molecular Biophysics, Nicholas Smith
All Theses
As researchers obtain access to greater and greater amounts of computational power, focus has shifted towards modeling macroscopic objects while still maintaining atomic-level details. The Protein Nano-Object Integrator (ProNOI) presented here has been designed to provide a streamlined solution for creating and designing macro-scale objects with atomic-level details to be used in molecular simulations and tools. To accomplish this, two different interfaces were developed: a Protein Data Bank (PDB), PDB-focused interface for generating regularly-shaped three-dimensional atomic objects and a 2D image-based interface for tracing images with irregularly shaped objects and then extracting three-dimensional models from these images. Each interface is …
Fourth Moment Approximation Of Instrinsic Mode Lifetimes In Solids, Yang Gao
Fourth Moment Approximation Of Instrinsic Mode Lifetimes In Solids, Yang Gao
All Dissertations
A new method (second moment approximation method) of calculating mode lifetimes of materials has been proposed by Dickel and Daw [14, 15]. The method was tested on an anharmonic lattice model, and it shows consistency with results from using traditional method (molecular dy-namics with Green-Kubo [2]) at high temperatures, but deviates at low temperatures. Based on this method, we developed the fourth moment approximation method, and tested it on various models from 1D anharmonic chain to the FCC cube with Lennard-Jones potential. Calculations showed that the fourth moment approximation method provides a fast and reliable scheme to calculate mode lifetimes …
Problm Web Server: Protein And Membrane Placement And Orientation Package, Taylor Kimmett, Nicholas Smith, Shawn Witham, Marharyta Petukh, Subhra Sarkar, Emil Alexov
Problm Web Server: Protein And Membrane Placement And Orientation Package, Taylor Kimmett, Nicholas Smith, Shawn Witham, Marharyta Petukh, Subhra Sarkar, Emil Alexov
Publications
The 3D structures of membrane proteins are typically determined without the presence of a lipid bilayer. For the purpose of studying the role of membranes on the wild type characteristics of the corresponding protein, determining the position and orientation of transmembrane proteins within a membrane environment is highly desirable. Here we report a geometry-based approach to automatically insert a membrane protein with a known 3D structure into pregenerated lipid bilayer membranes with various dimensions and lipid compositions or into a pseudomembrane. The pseudomembrane is built using the Protein Nano-Object Integrator which generates a parallelepiped of user-specified dimensions made up of …
Computational And Experimental Approaches To Reveal The Effects Of Single Nucleotide Polymorphisms With Respect To Disease Diagnostics, Tugba G. Kucukkal, Ye Yang, Susan C. Chapman, Weiguo Cao, Emil Alexov
Computational And Experimental Approaches To Reveal The Effects Of Single Nucleotide Polymorphisms With Respect To Disease Diagnostics, Tugba G. Kucukkal, Ye Yang, Susan C. Chapman, Weiguo Cao, Emil Alexov
Publications
DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and …
Chronic Beryllium Disease: Revealing The Role Of Beryllium Ion And Small Peptides Binding To Hla-Dp2, Marharyta Petukh, Bohua Wu, Shannon Stefl, Nick Smith, David Hyde-Volpe, Li Wang, Emil Alexov
Chronic Beryllium Disease: Revealing The Role Of Beryllium Ion And Small Peptides Binding To Hla-Dp2, Marharyta Petukh, Bohua Wu, Shannon Stefl, Nick Smith, David Hyde-Volpe, Li Wang, Emil Alexov
Publications
Chronic Beryllium (Be) Disease (CBD) is a granulomatous disorder that predominantly affects the lung. The CBD is caused by Be exposure of individuals carrying the HLA-DP2 protein of the major histocompatibility complex class II (MHCII). While the involvement of Be in the development of CBD is obvious and the binding site and the sequence of Be and peptide binding were recently experimentally revealed [1], the interplay between induced conformational changes and the changes of the peptide binding affinity in presence of Be were not investigated. Here we carry out in silico modeling and predict the Be binding to be within …
On The Modeling Of Polar Component Of Solvation Energy Using Smooth Gaussian-Based Dielectric Function, Lin Li, Chuan Li, Emil Alexov
On The Modeling Of Polar Component Of Solvation Energy Using Smooth Gaussian-Based Dielectric Function, Lin Li, Chuan Li, Emil Alexov
Publications
Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine …
On The Electrostatic Properties Of Homodimeric Proteins, Brandon Campbell, Marharyta Petukh, Emil Alexov, Chuan Li
On The Electrostatic Properties Of Homodimeric Proteins, Brandon Campbell, Marharyta Petukh, Emil Alexov, Chuan Li
Publications
A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology, 9(2), e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily …
A Novel P.Leu(381)Phe Mutation In Presenilin 1 Is Associated With Very Early Onset And Unusually Fast Progressing Dementia As Well As Lysosomal Inclusions Typically Seen In Kufs Disease, Natalia Dolzhanskaya, Michael A. Gonzalez, Fiorella Sperziani, Shannon Stefl, Jeffrey Messing, Guang Y. Wen, Emil Alexov, S Stephan Zuchner, Milen Velinov
A Novel P.Leu(381)Phe Mutation In Presenilin 1 Is Associated With Very Early Onset And Unusually Fast Progressing Dementia As Well As Lysosomal Inclusions Typically Seen In Kufs Disease, Natalia Dolzhanskaya, Michael A. Gonzalez, Fiorella Sperziani, Shannon Stefl, Jeffrey Messing, Guang Y. Wen, Emil Alexov, S Stephan Zuchner, Milen Velinov
Publications
Whole exome sequencing in a family with suspected dominant Kufs disease identified a novel Presenilin 1 mutation p.Leu(381)Phe in three brothers who, along with their father, developed progressive dementia and motor deficits in their early 30s. All affected relatives had unusually rapid disease progression (on average 3.6 years from disease onset to death). In silico analysis of mutation p.Leu(381)Phe predicted more detrimental effects when compared to the common Presenilin 1 mutation p.Glu(280)Ala. Electron microscopy study of peripheral fibroblast cells of the proband showed lysosomal inclusions typical for Kufs disease. However his brain autopsy demonstrated typical changes of Alzheimer disease.
Multidimensional Simulations Of Non-Linear Cosmic Ray Production In Supernova Remnant Evolution, Joshua Wood
Multidimensional Simulations Of Non-Linear Cosmic Ray Production In Supernova Remnant Evolution, Joshua Wood
All Dissertations
When a high-mass star (& 4Msun) explodes at the end of its life, a supernova occurs, leaving its degenerate core and a fast-moving shell of matter, known as a supernova remnant (SNR). The SNR shell lasts for many thousands of years, generating emissions from low-frequency radio (~ 10-7 eV) up to γ-ray regime (~ 1015 eV). It is also believed that SNRs are the predominant source of galactic cosmic rays, accelerating a population of thermal ions, primarily protons, up to relativistic energies by means of the diffusive shock acceleration (DSA) mechanism. The small population of thermal (Boltzmann) particles, p ~ …