Physics Commons^™

A Generalized Force-Modified Potential Energy Surface For Mechanochemical Simulations, Gopinath Subramanian, Nithin Mathew, Jeff Leiding

Faculty Publications

We describe the modifications that a spatially varying external load produces on a Born-Oppenheimer potential energy surface (PES) by calculating static quantities of interest. The effects of the external loads are exemplified using electronic structure calculations (at the HF/6-31G- level) of two different molecules: ethane and hexahydro-1,3,5-trinitro-s-triazine (RDX). The calculated transition states and Hessian matrices of stationary points show that spatially varying external loads shift the stationary points and modify the curvature of the PES, thereby affecting the harmonic transition rates by altering both the energy barrier as well as the prefactor. The harmonic spectra of both molecules are blueshifted …

Lorentz Invariant Spacelike Surfaces Of Constant Mean Curvature In Anti-De Sitter 3-Space, Jamie Patrick Lambert

Master's Theses

In this thesis, I studied Lorentz invariant spacelike surfaces with constant mean curvature H = c in the anti-de Sitter 3-space H³₁(−c²) of constant curvature −c². In particular, I construct Lorentz invariant spacelike surfaces of constant mean curvature c and maximal Lorentz invariant spacelike surfaces in H³₁(−c²). I also studied the limit behavior of those constant mean curvature c surfaces in H³₁(−c²). It turns out that they approach a maximal catenoid in Minkowski 3-space E³₁ as c → …

Structural Variation Of Alpha-Synuclein With Temperature By A Coarse-Grained Approach With Knowledge-Based Interactions, Peter Mirau, Barry L. Farmer, Ras B. Pandey

Faculty Publications

Despite enormous efforts, our understanding the structure and dynamics of α-synuclein (ASN), a disordered protein (that plays a key role in neurodegenerative disease) is far from complete. In order to better understand sequence-structure-property relationships in α-SYNUCLEIN we have developed a coarse-grained model using knowledge-based residue-residue interactions and used it to study the structure of free ASN as a function of temperature (T) with a large-scale Monte Carlo simulation. Snapshots of the simulation and contour contact maps show changes in structure formation due to self-assembly as a function of temperature. Variations in the residue mobility profiles reveal clear distinction among three …

Self-Assembly Dynamics For The Transition Of A Globular Aggregate To A Fibril Network Of Lysozyme Proteins Via A Coarse-Grained Monte Carlo Simulation, Ras B. Pandey, Barry L. Farmer, Bernard S. Gerstman

Faculty Publications

The self-organizing dynamics of lysozymes (an amyloid protein with 148 residues) with different numbers of protein chains, Nc = 1,5,10, and 15(concentration 0.004 – 0.063) is studied by a coarse-grained Monte Carlo simulation with knowledge-based residue-residue interactions. The dynamics of an isolated lysozyme (Nc = 1) is ultra-slow (quasi-static) at low temperatures and becomes diffusive asymptotically on raising the temperature. In contrast, the presence of interacting proteins leads to concentration induced protein diffusion at low temperatures and concentration-tempering sub-diffusion at high temperatures. Variation of the radius of gyration of the protein with temperature shows a …

Relativistic And Non-Relativistic Proton-Nucleus Scattering, Kinsey Ann Elisabeth Zarske-Williamson

Honors Theses

Calculations for proton-nucleus scattering often rely on transition amplitudes. We implement new transition amplitudes [7] with the relativistic equations. We can find the matrix elements of the operators between the usual Dirac spinor basis or the helicity spinor basis. The operators can also be written as a linear combination of non-relativistic spin operators. To transform from one basis to another, we need to find a transformation matrix. We must establish what one of the factors that appears in the transformed expression means in order to correctly complete our transformation matrix. Once this is resolved, our transformation matrix will be complete.

Impact Of Homogeneous Strain On Uranium Vacancy Diffusion In Uranium Dioxide, Anuj Goyal, Simon R. Phillpot, Gopinath Subramanian, David A. Andersson, Chris R. Stanek, Blas P. Uberuaga

Faculty Publications

We present a detailed mechanism of, and the effect of homogeneous strains on, the migration of uranium vacancies in UO₂. Vacancy migration pathways and barriers are identified using density functional theory and the effect of uniform strain fields are accounted for using the dipole tensor approach. We report complex migration pathways and noncubic symmetry associated with the uranium vacancy in UO₂ and show that these complexities need to be carefully accounted for to predict the correct diffusion behavior of uranium vacancies. We show that under homogeneous strain fields, only the dipole tensor of the saddle with respect …

Lifetime Measurement Of The Cesium 6p3/2 Level Using Ultrafast Pump-Probe Laser Pulses, B. M. Patterson, J. F. Sell, T. Ehrenreich, M. A. Gearba, G. M. Brooke, J. Scoville, R. J. Knize

Faculty Publications

Using the inherent timing stability of pulses from a mode-locked laser, we measure the cesium 6P_3/2 excited-state lifetime. An initial pump pulse excites cesium atoms in two counterpropagating atomic beams to the 6P_3/2 level. A subsequent synchronized probe pulse ionizes atoms that remain in the excited state and the photoions are collected and counted. By selecting pump pulses that vary in time with respect to the probe pulses, we obtain a sampling of the excited-state population in time, resulting in a lifetime value of 30.462(46) ns. The measurement uncertainty (0.15%) is slightly larger than our previous report of …

Momentum Distributions For 2H (E, E' P), William P. Ford, Sabine Jeschonnek, J. W. Van Orden

Faculty Publications

Background: A primary goal of deuteron electrodisintegration is the possibility of extracting the deuteron momentum distribution. This extraction is inherently fraught with difficulty, as the momentum distribution is not an observable and the extraction relies on theoretical models dependent on other models as input.

Purpose: We present a new method for extracting the momentum distribution which takes into account a wide variety of model inputs thus providing a theoretical uncertainty due to the various model constituents. To test the extraction, pseudodata were generated, and the extracted “experimental” distribution, which has theoretical uncertainty accounted by this extraction method, can be compared …

Elastic Differential Cross Sections For Space Radiation Applications, Charles M. Werneth, Khin M. Maung, William P. Ford, John W. Norbury, Michael D. Vera

Faculty Publications

The eikonal, partial wave (PW) Lippmann-Schwinger, and three-dimensional Lippmann-Schwinger (LS3D) methods are compared for nuclear reactions that are relevant for space radiation applications. Numerical convergence of the eikonal method is readily achieved when exact formulas of the optical potential are used for light nuclei (>A≤>16), and the momentum-space representation of the optical potential is used for heavier nuclei. The PW solution method is known to be numerically unstable for systems that require a large number of partial waves, and, as a result, the LS3D method is employed. The effect of relativistic kinematics is studied with the PW and …

Development And Applications Of The Expanded Equivalent Fluid Method, Bharath Kumar Kandula

Dissertations

Ocean acoustics is the study of sound in the oceans. Electromagnetic waves attenuate rapidly in the water medium. Sound is the best means to transmit information underwater. Computational numerical simulations play an important role in ocean acoustics. Simulations of acoustic propagation in the oceans are challenging due to the complexities involved in the ocean environment. Different methods have been developed to simulate underwater sound propagation. The Parabolic-Equation (PE) method is the best choice in several ocean acoustic problems. In shallow water acoustic experiments, sound loses some of its energy when it interacts with the bottom. An equivalent fluid technique was …

Binding Of Solvated Peptide (Eplqlkm) With A Graphene Sheet Via Simulated Coarse-Grained Approach, Somayyeh Sheikholeslami, R. B. Pandey, Nadiya Dragneva, Wely Floriano, Oleg Rubel, Stephen A. Barr, Zhifeng Kuang, Rajiv Berry, Rajesh Naik, Barry Farmer

Faculty Publications

Binding of a solvated peptide A1 (¹E ²P ³L ⁴Q ⁵L ⁶K ⁷M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of temperature (T). Quantitative differences (e.g., the extent of binding within a temperature range) and qualitative similarities are observed in results from three simulated potentials. Differences in variations of both local and …

Conformational Response To Solvent Interaction And Temperature Of A Protein (Histone H3.1) By A Multi-Grained Monte Carlo Simulation, Ras B. Pandey, Barry L. Farmer

Faculty Publications

Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.1) in effective solvent media. The structural response is examined as a function of the solvent-residue interaction strength (based on hydropathy index) in a range of temperatures (spanning low to high) involving a knowledge-based (Miyazawa-Jernigan(MJ)) residue-residue interaction. The protein relaxes rapidly from an initial random configuration into a quasi-static structure at low …

A Hierarchical Coarse-Grained (All-Atom-To-All-Residue) Computer Simulation Approach: Self-Assembly Of Peptides, Ras B. Pandey, Zhifeng Kuang, Barry L. Farmer

Faculty Publications

A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 (¹H ²S ³S ⁴Y ⁵W ⁶Y ⁷A ⁸F ⁹N ¹⁰N ¹¹K ¹²T) is considered as an example to illustrate the utility. We find that peptides assemble rather fast into globular …

Reification: A Process To Configure Java Realtime Processors, John Huddleston Heath

Dissertations

Real-time systems require stringent requirements both on the processor and the software application. The primary concern is speed and the predictability of execution times. In all real-time applications the developer must identify and calculate the worst case execution times (WCET) of their software. In almost all cases the processor design complexity impacts the analysis when calculating the WCET. Design features which impact this analysis include cache and instruction pipelining. With both cache and pipelining the time taken for a particular instruction can vary depending on cache and pipeline contents. When calculating the WCET the developer must ignore the speed advantages …

Microstructure, Vacancies And Voids In Hydrogenated Amorphous Silicon, Rajendra Timilsina

Dissertations

This dissertation presents a theoretical and computational study of microstructure, vacancies and voids in hydrogenated amorphous silicon (a-Si:H). The microstructure consists of all possible silicon-hydrogen bonding configurations such as SiH, SiH₂, SiH₃ and SiH₄. However, it is highly dominated (approximately 75% or even more) by monohydride (SiH) configurations. Furthermore, the hydrogen atoms locate in both clustered and diluted phases; as a result, the distribution becomes highly inhomogeneous. Approximately 5% of hydrogen atoms reside in a form of isolated monohydrides at the lower (7 at.%) concentration whereas such configurations do not appear at the higher concentrations …

Random Coil To Globular Thermal Response Of A Protein (H3.1) With Three Knowledge-Based Coarse-Grained Potentials, Ras B. Pandey, Barry L. Farmer

Faculty Publications

The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.1 undergoes a systematic (possibly continuous) structural transition from a random coil to a globular conformation on reducing the temperature. The range over which such a systematic response in variation of the radius of gyration (R_g) with the temperature (T) occurs, however, depends on the potential, i.e. ΔT_MJ ≈ 0.013–0.020, ΔT_BT ≈ 0.018–0.026 …

Effect Of Compactified Dimensions On The Ground State Energy Of The Hydrogen Atom, Floyd Maseda

Honors Theses

The three-dimensional Hydrogen atom has been explored extensively, and a wavefunction and energy expression can be found in closed form. Little work, however, has been done with higher-dimensional atoms. This discussion focuses on the effects of adding first one then two compactified dimensions to a Hydrogen atom. The metric of the 4-D Hydrogen atom is taken to be R3 × S1 while the 5-D metric is taken to be R3 × S2. We first determine the form of the Laplacian operator in each space and use it to find the respective atomic potentials. The variational method is used to determine …

Conformational Temperature-Dependent Behavior Of A Histone H2ax: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials, Miriam Fritsche, Ras B. Pandey, Barry L. Farmer, Dieter W. Heerman

Faculty Publications

Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input …

A System For Measuring Radiation Induced Chemical Products In Atmospheric Gases Using Optical Detection Methods, Tyler Webster Reese

Master's Theses

This research is a part of an effort to characterize the chemical products generated by radiation interacting with atmosphere. One method of detecting ionizing radiation is to monitor the radiation induced products in the atmosphere around the source. This project explored the potential for using Cavity Ringdown Spectroscopy to evaluate the presence of chemical products generated by the air-radiation interaction near an alpha radiation source. In particular, measurements of ozone concentration within a controlled atmosphere chamber as affected by radiation exposure were obtained.

The first portion of this thesis provides brief reviews of ionizing radiation and ozone formation as well …

Relativistic Studies Of The Charmonium And Bottomonium Systems Using The Sucher Equation, Charles Martin Werneth

Dissertations

In this dissertation, bound states of quarks and anti-quarks (mesons) are studied with a relativistic equation known as the Sucher equation. Prior to the work in this dissertation, the Sucher equation had never been used for meson mass spectra. Furthermore, a full angular momentum analysis of the Sucher equation has never been studied. The Sucher equation is a relativistic equation with positive energy projectors imposed on the interaction. Since spin is inherent to the equation, the Sucher equation is equivalent to a relativistic Schrödinger equation with a spin-dependent effective potential. Through a complete general angular momentum analysis of the equation, …

Studies Of Meson Mass Spectra In The Context Of Quark-Antiquark Bound States, Mallika Dhar

Dissertations

This dissertation deals with the computation of meson mass spectra in the context of quarkantiquark (q ¯ q) bound-state. Traditionally the q ¯ q bound-state problem is treated by solving the non-relativistic Schrödinger equation in position representation with a linear confining potential and a Coulomb-like attractive potential. For high energy, relativistic kinematics is necessary. It is well known that relativistic kinematics cannot be treated properly in position representation, but it can easily be handled in momentum representation. On the other hand, the linear potential and Coulomb-like potential have singularities in momentum-space and complicated subtraction procedure is necessary to treat the …

African-American College Student Attitudes Toward Physics And Their Effect On Achievement, Carl Timothy Drake

Dissertations

The purpose of this study was to investigate factors affecting the attitudes that African-American college students have towards introductory college physics. The population targeted for this study consisted of African-American males and females enrolled in introductory college physics classes at an urban public historical black college or university (HBCU) located in the southeastern United States. Nine of the Fennema- Sherman Mathematics Attitude Scales, modified for physics, were used to analyze the attitudes of the 135 participants enrolled in an introductory college physics class. The nine scales used to measure the students' attitudes were Attitude Toward Success in Physics Scale (AS), …

Conformation Of A Coarse-Grained Protein Chain (An Aspartic Acid Protease) Model In Effective Solvent By A Bond-Fluctuating Monte Carlo Simulation, Ras B. Pandey, B.L. Farmer

Faculty Publications

In a coarse-grained description of a protein chain, all of the 20 amino acid residues can be broadly divided into three groups: Hydrophobic (H), polar (P), and electrostatic (E). A protein can be described by nodes tethered in a chain with a node representing an amino acid group. Aspartic acid protease consists of 99 residues in a well-defined sequence of H, P, and E nodes tethered together by fluctuating bonds. The protein chain is placed on a cubic lattice where empty lattice sites constitute an effective solvent medium. The amino groups (nodes) interact with the solvent (S) sites with appropriate …

Real Space Information From Fluctuation Electron Microscopy: Applications To Amorphous Silicon, Parthapratim Biswas, Raymond Atta-Fynn, S. Chakraborty, D. A. Drabold

Faculty Publications

Ideal models of complex materials must satisfy all available information about the system. Generally, this information consists of experimental data, information implicit to sophisticated interatomic interactions and potentially other a priori information. By jointly imposing first-principles or tight-binding information in conjunction with experimental data, we have developed a method: experimentally constrained molecular relaxation (ECMR) that uses all of the information available. We apply the method to model medium range order in amorphous silicon using fluctuation electron microscopy (FEM) data as experimental information. The paracrystalline model of medium range order is examined, and a new model based on voids in amorphous …

Experimentally Constrained Molecular Relaxation: The Case Of Hydrogenated Amorphous Silicon, Parthapratim Biswas, Raymond Atta-Fynn, D. A. Drabold

Faculty Publications

We have extended our experimentally constrained molecular relaxation technique [P. Biswas et al., Phys. Rev. B 71, 54204 (2005)] to hydrogenated amorphous silicon: a 540-atom model with 7.4% hydrogen and a 611-atom model with 22% hydrogen were constructed. Starting from a random configuration, using physically relevant constraints, ab initio interactions, and the experimental static structure factor, we construct realistic models of hydrogenated amorphous silicon. Our models confirm the presence of a high-frequency localized band in the vibrational density of states due to Si-H vibration that has been observed in recent vibrational transient grating measurements on plasma enhanced chemical …

Relativistic Multiple Scattering Theory And The Relativistic Impulse Approximation, Khin Maung Maung, John W. Norbury, Trina Coleman

Faculty Publications

It is shown that a relativistic multiple scattering theory for hadron - nucleus scattering can be consistently formulated in four dimensions in the context of meson exchange. We give a multiple scattering series for the optical potential and discuss the differences between the relativistic and non- relativistic versions. We develop the relativistic multiple scattering series by separating out the one-boson exchange term from the rest of the Feynman series. However, this particular separation is not absolutely necessary and we discuss how to include other terms. We then show how to make a three- dimensional reduction for hadron - nucleus scattering …

Measurement Of Population Dynamics In Stimulated Raman Adiabatic Passage, Alina Gearba, H. A. Camp, M. L. Trachy, G. Veshapidze, M.H. Shah, H.U. Jang, B.D. Depaola

Faculty Publications

The temporal evolution of populations has been directly measured for a three-level ladder system undergoing coherent excitation by stimulated Raman adiabatic passage (STIRAP). The measurement technique makes use of charge transfer as diagnostic. The method is model independent and has a temporal resolution of a few nanoseconds. The temporal evolution is measured for several values of the delay between the pump and Stokes laser pulses that are part of the STIRAP excitation scheme. The corresponding quantum Liouville equations are solved and the results of the calculations are compared with experiment.

Multiscale Mode Dynamics Of A Tethered Membrane, Ras B. Pandey, Kelly L. Anderson, B. L. Farmer

Faculty Publications

Stochastic dynamics of a tethered membrane with a bond-fluctuating coarse-grained Monte Carlo simulation shows, in addition to diffusion, nondiffusive behavior sensitive to the type of membrane, its size, and quality of the solvent. Motion of the membrane’s center node is described by the variation of the mean-square displacement (R_2n) with time step (t), i.e., R_2n∝t2ν with the exponent ν≃1/8−1∕6 in the short time followed by subdiffusive power laws (i.e., ν∼1∕5, 1∕10) in the intermediate time regimes before reaching diffusion ν=1. The crossover between in-plane wrinkle modes is identified from the segmental (node) motion of the membrane.

Model-Independent Measurement Of The Excited Fraction In A Magneto-Optical Trap, M. H. Shah, H. A. Camp, M. L. Trachy, G. Veshapidze, M.A. Gearba, B.D. Depaola

Faculty Publications

In many experiments involving a magneto-optical trap (MOT) it is of great importance to know the fraction of atoms placed in an excited state due to the trapping process. Generally speaking, researchers have had to use overly simplistic and untested models to estimate this fraction. In this work, the excited fractions of ⁸⁷Rb atoms in a MOT are directly measured using a charge transfer technique, for a range of MOT parameters. Simple models are then fit to the measured fractions. Using the results of this work, the excited fraction of ⁸⁷Rb atoms trapped in a MOT can be …

Split Quaterionic Representation Of Sdym (Su(1,1) Instantons In S2- × S2+, Sungwook Lee, Khin Maung Maung

Faculty Publications

Using split‐quaternions, we find explicit SDYM SU(1,1) instanton solutions in S^2- × S²⁺ which is the conformal compactification of the semi‐Euclidean 4‐spacetime R²⁺² of split signature (-,-,+,+). It is also shows that SDYM and ASDYM fields in S^2- × S²⁺ can be described as simple split-quaternionic 2-forms.