Physics Commons^™

Protein Nano-Object Integrator (Pronoi) For Generating Atomic Style Objects For Molecular Modeling, Nicholas Smith, Brandon Campbell, Lin Li, Chuan Li, Emil Alexov

Publications

Background

With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system.

Results

Here we report the Protein Nano-Object Integrator (ProNOI) which allows for …

Spectroscopic Signature For Bundling, Edge States And Impurities In 1d And 0d Materials, Kiran Kumar Lingam

All Dissertations

Study of nanomaterials has gained interest of researchers from various fields of science and technology due to their unique electronic and vibrational properties as compared to their bulk counterparts. In particular, carbon nanotechnology has evolved rapidly over the past few decades and nowadays, carbon nanotubes are used in various fields such as energy storage, electronics etc. However, the quest for new properties of this material is never ending and the invention of graphene generated enormous interest in the scientific community due to its excellent properties such as strength, high electron mobility, thermal conductivity etc. In this thesis, I aim at …

Understanding Nanoparticle-Cell Interaction, Ran Chen

All Dissertations

Nanotechnology has revolutionalized the landscape of modern science and technology, including materials, electronics, therapeutics, bioimaging, sensing, and the environment. Along with these technological advancements, there arises a concern that engineered nanomaterials, owing to their high surface area and high reactivity, may exert adverse effects upon discharge to compromise biological and ecological systems. Research in the past decade has examined the fate of nanomaterials in vitro and in vivo, as well as the interactions between nanoparticles and biological and ecosystems using primarily toxicological and ecotoxicological approaches. However, due to the versatility in the physical and physicochemical properties of nanoparticles, and due …

Ultraluminous X-Ray Sources In Andromeda Galaxy: Two Recent Discoveries And Their Implications, Amanpreet Kaur

All Theses

Ultraluminous X-ray sources are believed to be associated with X-ray binaries, in which an accreting black hole generates X-ray luminosities in excess of 10 39 erg/s. The nature of the companion star and the underlying physics of the accretion process is not yet established with certainty. In particular, whether or not the accretion is super/sub Eddington is an open question, as is the mass of the companion star. We discuss the first two ULXs recently discovered in M31 and investigate the nature of their underlying sources. We present the X-ray observations for ULX-1 in detail and discuss its implications for …

Highly Efficient And Exact Method For Parallelization Of Grid-Based Algorithms And Its Implementation In Delphi, Chuan Li, Lin Li, Jie Zhang, Emil Alexov

Publications

The Gauss–Seidel (GS) method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the GS method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here, we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of processes or computing units. In …

Thermoelectric Properties Of Silicon Germanium: An In-Depth Study To The Reduction Of Lattice Thermal Conductivity, Daniel Thompson

All Dissertations

Thermoelectric materials provide a solid state route for the direct conversion between thermal and electrical energy. Hence, thermal gradients can be used to generate power of up to several KW, or driven DC power can be used to pump heat in or out of a system. Recent pushes in thermoelectric research are for power generation materials with higher efficiency. These materials can be used to recover energy from the waste heat of vehicles' exhaust systems, and as power generators for extraterrestrial exploration when coupled with a radioactive heat source.
The goal of this dissertation will be to demonstrate a new …

Intense And Highly Energetic Atmospheric Pressure Plasma Jet Arrays, John Furmanski

All Theses

This thesis documents the efforts taken to produce highly ionized and concentrated atmospheric pressure plasma using an arrayed atmospheric pressure plasma jet (APPJ) system. The honeycomb-shaped array features seven plasma jets operating in close enough proximity to one another to exhibit jet-to-jet coupling behavior. Optimal gas flow rates for the system were determined and intense plasma plumes composed of argon and/or helium are generated. Optical emission spectroscopy was employed to observe the charged particles responsible for the emissions of each gas discharge and APPJ operation mode. Plasma etching of indium tin oxide glass was conducted to verify the highly energetic …

Probing And Controlling Fluid Rheology At Microscale With Magnetic Nanorods, Alexander Tokarev

All Dissertations

This Dissertation is focused on the development of new methods for characterization and control of fluid rheology using magnetic nanorods. This Dissertation consists of five chapters. In the first chapter, we review current microrheologial methods and develop a Magnetic Rotational Spectroscopy (MRS) model describing nanorod response to a rotating magnetic field. Using numerical modeling, we analyze the effects of materials parameters of nanorods and fluids on the MRS characteristic features. The model is designed for a specific experimental protocol. We introduce and examine physical parameters which can be measured experimentally. The model allows identification of MRS features enabling the calculation …

Predicting Nonspecific Ion Binding Using Delphi, Marharyta Petukh, Maxim Zhenirovskyy, Chuan Li, Lin Li, Lin Wang, Emil Alexov

Publications

Ions are an important component of the cell and affect the corresponding biological macromolecules either via direct binding or as a screening ion cloud. Although some ion binding is highly specific and frequently associated with the function of the macromolecule, other ions bind to the protein surface nonspecifically, presumably because the electrostatic attraction is strong enough to immobilize them. Here, we test such a scenario and demonstrate that experimentally identified surface-bound ions are located at a potential that facilitates binding, which indicates that the major driving force is the electrostatics. Without taking into consideration geometrical factors and structural fluctuations, we …

Delphi: A Comprehensive Suite For Delphi Software And Associated Resources, Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov

Publications

Background

Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions.

Results

Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding …

Highly Charged Ion Interactions With Ultrathin Dielectric Films, Russell Lake

All Dissertations

The excitations occurring at a solid surface due to slow highly charged ion (HCI) impacts are interesting from the perspective of fundamental processes in atomic collisions and materials science. This thesis focuses on two questions: 1) How much HCI potential energy deposition is required to form permanent surface modifications?, 2) How does the presence of a thin dielectric surface film change the classical over-the-barrier picture for neutralization above a clean metal?
I describe a measurement of craters in thin dielectric films formed by XeQ+ (26 ≤ Q ≤ 44) projectiles. Tunnel junction devices with ion-irradiated barriers were used to amplify …

Analyzing Effects Of Naturally Occurring Missense Mutations, Zhe Zhang, Maria A. Miteva, Lin Wang, Emil Alexov

Publications

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 produce an amino acid substitution in the corresponding protein sequence (missense mutations); others will not. This paper focuses on genetic mutations resulting in a change in the amino acid sequence of the corresponding protein and how to assess their effects on protein wild-type characteristics. The existing methods and approaches for predicting the effects of mutation on protein stability, structure, and dynamics are outlined and discussed with respect to their underlying …