Physical Sciences and Mathematics Commons^™

New Methods For Exafs Analysis In Structural Genomics, Grant Bunker, N. Dimakis, Gocha Kelashvili

Physics and Astronomy Faculty Publications and Presentations

Data analysis is one of the remaining bottlenecks in high-throughput EXAFS for structural genomics. Here some recent developments in methodology are described that offer the potential for rapid and automated XAS analysis of metalloproteins.

Xafs Debye-Waller Factors For Zn Metalloproteins, N. Dimakis, Grant Bunker

Physics and Astronomy Faculty Publications and Presentations

An accurate and practical method for the calculation and use of thermal x-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) in active sites of metalloproteins is presented. These factors are calculated on model clusters within the local density functional approximation with nonlocal corrections. The DWFs are mapped out and parametrized as a function of the first shell distance and an angle (where applicable), for all significant single and multiple scattering paths, as well as the sample temperature. This approach is applied to the biologically essential but spectroscopically silent Zn+2 active sites composed of histidines, cysteines, and carboxylate ligands in homogeneous …

Setting Upper Limits On The Strength Of Periodic Gravitational Waves From Psr J1939+2134 Using The First Science Data From The Geo 600 And Ligo Detectors, B. P. Abbott, R. Abbott, Mario C. Diaz, Wm. R. Johnston, Joseph D. Romano, Cristina V. Torres

Physics and Astronomy Faculty Publications and Presentations

Data collected by the GEO 600 and LIGO interferometric gravitational wave detectors during their first observational science run were searched for continuous gravitational waves from the pulsar J1939+2134 at twice its rotation frequency. Two independent analysis methods were used and are demonstrated in this paper: a frequency domain method and a time domain method. Both achieve consistent null results, placing new upper limits on the strength of the pulsar’s gravitational wave emission. A model emission mechanism is used to interpret the limits as a constraint on the pulsar’s equatorial ellipticity.

Parametric Classification In Domains Of Characters, Numerals, Punctuation, Typefaces And Image Qualities, Osama Ahmed Khan

Theses and Dissertations - UTB/UTPA

This thesis contributes to the Optical Font Recognition problem (OFR), by developing a classifier system to differentiate ten typefaces using a single English character ‘e’. First, features which need to be used in the classifier system are carefully selected after a thorough typographical study of global font features and previous related experiments. These features have been modeled by multivariate normal laws in order to use parameter estimation in learning. Then, the classifier system is built up on six independent schemes, each performing typeface classification using a different method. The results have shown a remarkable performance in the field of font …

Generation Of The Transient Electrical And Spontaneous Magnetic Fields By Solid State Combustion, Karen S. Martirosyan, J. R. Claycomb, J. H. Miller Jr., D. Luss

Physics and Astronomy Faculty Publications and Presentations

Experiments revealed that transient electric field intensities up to 2.5 V/cm were generated during the initial period of combustion synthesis of the ferromagnetic products before the maximum temperature was reached. This occurred when the iron particles were partially oxidized and the reaction product was mainly magnetite sFe3O4d. The electromagnetic field caused spontaneous magnetization of the product in the postcombustion zone. Magnetic field values up to 4 µT formed after the sample temperature fell below the Curie temperature and the initial reactants were completely converted to the ferromagnetic phase PbFe12O19. Increasing the volume of the samples increases the absolute residual magnetic …

Data Analysis In The Antes System, Yavuz Tor

Theses and Dissertations - UTB/UTPA

Acanthosis nigricans is a skin condition that can be used as an indicator for the risk of developing type 2 diabetes in the future. Border Health Office, in University of Texas - Pan American, organizes screenings in schools for acanthosis nigricans. Screening results are, then, collected and evaluated in the Border Health Office. The ANTES System is a computer system that stores and manages the data collected in those screenings.

This study is on the analysis of those collected data to track the progress of data entry, to evaluate the progress on obesity and related problems, and to discover the …

Visualization Of Internet Web Pages Based On Authority And Word Frequency, David Navarro

Theses and Dissertations - UTB/UTPA

The growth, accessibility, and integration of the World Wide Web with contemporary information utilization provides a rich domain in which to explore information retrieval systems. One approach in the evolution of retrieval systems couples successful and long-standing techniques of information retrieval with new techniques, such as visualization. The system developed and reported in this thesis takes this approach. It builds upon well-known techniques of information retrieval including stemming, keyword matching, and cosine similarity. It also incorporates the new and relatively successful hubs and authority approach, which describes Web documents by their reference by other documents. Finally, it develops a new …

Antes: A Web-Based Acanthosis Nigricans And Other Obesity Related Information System, Chunyue Wang

Theses and Dissertations - UTB/UTPA

Acanthosis nigricans is a cutaneous marker associated with systemic disorders and may serve as an indicator for risk of Type 2 diabetes. Acanthosis nigricans screening can help identify children who have high insulin levels and who may be at-risk for developing Type 2 diabetes. The ANTES system is a computerization attempt for acanthosis nigricans control of the student population from elementary schools and secondary schools in Texas. A general description of the system and the medical and history background of the ANTES program is given. The technology applied to the system is demonstrated. An overview of the system operation status …

Gravitational Radiation From Pulsating White Dwarfs, M. Benacquista, D. M. Sedrakian, M. V. Hairapetyan, K. M. Shahabasyan, A. A. Sadoyan

Physics and Astronomy Faculty Publications and Presentations

Rotating white dwarfs undergoing quasi-radial oscillations can emit gravitational radiation in a frequency range from 0.1 to 0.3 Hz. Assuming that the energy source for the gravitational radiation comes from the oblateness of the white dwarf induced by the rotation, the strain amplitude is found to be ∼10-27 for a white dwarf at ∼50 pc. The Galactic population of these sources is estimated to be ∼107 and may produce a confusion-limited foreground for proposed advanced detectors in the frequency band between space-based and ground-based interferometers. Nearby oscillating white dwarfs may provide a clear enough signal to investigate white dwarf interiors …

Using The Intensity Modulation Index To Test Pulsar Radio Emission Models, Fredrick A. Jenet, Janusz Gil

Physics and Astronomy Faculty Publications and Presentations

This Letter explores the possibility of testing pulsar radio emission models by observing pulse-to-pulse intensity modulation. It is shown that a relationship between a pulsar's period, period derivative, and intensity modulation is a natural consequence of at least one theoretical model of radio pulsar emission. It is proposed that other models may also predict a similar correlation. The exact form of the relationship will depend on the model in question. Hence, observations of intensity modulation should be able to determine the validity of the various emission models. In an attempt to search for the predicted dependencies, the modulation properties of …

Normal And Lateral Casimir Forces Between Deformed Plates, Thorsten Emig, Andreas Hanke, Ramin Golestanian, Mehran Kardar

Physics and Astronomy Faculty Publications and Presentations

The general path-integral formulation was set up for Casimir energy of the electromagnetic gauge field. By separating into transversal electric and magnetic modes, the problem was reduced to two decoupled problems for scalar fields which differ only in their boundary conditions. In each case, the Casimir energy was calculated for general plate deformations perturbatively. Results on both the normal and the lateral force between sinusoidally corrugated plates were outlined.

Mode-Cleaning And Injection Optics Of The Gravitational-Wave Detector Geo600, S. Goßler, M. M. Casey, A. Grant, H. Grote, Volker Quetschke

Physics and Astronomy Faculty Publications and Presentations

The British–German interferometric gravitational-wave detector GEO600 uses two high-finesse triangular ring cavities of 8 m optical pathlength each, as an optical mode-cleaning system. The modecleaner system is housed in an ultrahigh-vacuum environment to avoid contamination of the optics and to minimize both the influence of refractive index variations of the air and acoustic coupling to the optics. To isolate the cavities from seismic noise, all optical components are suspended as double pendulums. These pendulums are damped at their resonance frequencies at the upper pendulum stage with magnet-coil actuators. A suspended reaction mass supports three coils matching magnets bonded onto the …

Comment On ‘‘Why Is The Dna Denaturation Transition First Order?’’, Andreas Hanke, Ralf Metzler

Physics and Astronomy Faculty Publications and Presentations

A Comment on the Letter by . The authors of the Letter offer a Reply.

Recent Applications Of Fractional Calculus To Science And Engineering, Lokenath Debnath

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

This paper deals with recent applications of fractional calculus to dynamical systems in control theory, electrical circuits with fractance, generalized voltage divider, viscoelasticity, fractional-order multipoles in electromagnetism, electrochemistry, tracer in fluid flows, and model of neurons in biology. Special attention is given to numerical computation of fractional derivatives and integrals.

Category Of Nonlinear Evolution Equations, Algebraic Structure, And R-Matrix, Zhijun Qiao, Cewen Cao, Walter Strampp

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

In this paper we deal with the category of nonlinear evolution equations ~NLEEs! associated with the spectral problem and provide an approach for constructing their algebraic structure and r-matrix. First we introduce the category of NLEEs, which is composed of various positive order and negative order hierarchies of NLEEs both integrable and nonintegrable. The whole category of NLEEs possesses a generalized Lax representation. Next, we present two different Lie algebraic structures of the Lax operator: one of them is universal in the category, i.e., independent of the hierarchy, while the other one is nonuniversal in the hierarchy, i.e., dependent on …

Spontaneous Magnetization Generated By Spin, Pulsating, And Planar Combustion Synthesis, Karen S. Martirosyan, J. R. Claycomb, G. Gogoshin, R. A. Yarbrough, J. H. Miller Jr., D. Luss

Physics and Astronomy Faculty Publications and Presentations

The motion of the high temperature front during combustion synthesis of ferrite materials generates residual magnetization in cylindrical product samples. The combustion wave created a current density of up to 10 A/cm2, which influenced the magnetization distribution. The measured peak magnetic field intensity was up to 8 mT. Qualitatively different magnetic field maps were generated in ferrite samples synthesized by different combustion modes. The average magnetization vector generated by either planar or pulsating combustion was oriented at a smaller angle with respect to the pellet axis ~f<45°! than those generated by spin combustion ~60°

Alignment, Mechanical And Thermo-Physical Characterization Of Nanofiber-Reinforced Polyethylene, Veronica M. Diaz-Serrato

Theses and Dissertations - UTB/UTPA

Alignment of vapor grown carbon nano-reinforced polyethylene composites was performed using conventional extrusion processing methods. The alignment of the nanofibers within polyethylene, PE; the matrix, produced a material with anisotropic behavior. Mechanical and thermo-physical properties of the nanocomposite were studied. Enhancements in mechanical properties were investigated for pure PE, misaligned, and aligned specimens for stress versus strain, maximum load, and Young's modulus as high as 185, 273, and 80%, respectively. In fact, toughness was considerably high for the 10 rpm specimen when compared to other samples of different windup speeds. Thermo-physical studies were performed using differential scanning calorimetry (DSC) and …

Horizontal-Branch Morphology And The Photometric Evolution Of Old Stellar Populations, Hyun Chul Lee, Young Wook Lee, Brad K. Gibson

Physics and Astronomy Faculty Publications and Presentations

Theoretical integrated broadband colors ranging from far-UV to near-IR have been computed for old stellar systems from our evolutionary population synthesis code. These models take into account, for the first time, the detailed systematic variation of horizontal-branch (HB) morphology with age and metallicity. Our models show that some temperature-sensitive color indices are significantly affected by the presence of blue HB stars. In particular, B-V does not become monotonically redder as metallicity increases at given ages, but becomes bluer by as much as ∼0.15 mag because of the contribution from blue HB stars. Similar trends are also found in the Washington …

Equilibrium Shapes Of Flat Knots, Ralf Metzler, Andreas Hanke, Paul G. Dommersnes, Yacov Kantor, Mehran Kardar

Physics and Astronomy Faculty Publications and Presentations

The equilibrium shapes of prime and composite knots were studied. It was showed that the topological details of prime knots were localized on a small portion of the larger ring polymer due to self-avoiding effects. The original knot configuration could assume a hierarchy of contracted shape, the dominating one given by one small loop, within this region. For the flat trefoil knot, this hierarchy was studied in detail and corroborated by Monte Carlo simulations.

Dna Polymerase Iii Holoenzyme From Thermus Thermophilus Identification Expression Purification Of Components And Use To Reconstitute A Processive Replicase, James M. Bullard, Jennifer C. Williams, Wendy K. Acker, Carsten Jacobi, Nebojsa Janjic, Charles S. Mchenry

Chemistry Faculty Publications and Presentations

DNA replication in bacteria is performed by a specialized multicomponent replicase, the DNA polymerase III holoenzyme, that consist of three essential components: a polymerase, the β sliding clamp processivity factor, and the DnaX complex clamp-loader. We report here the assembly of the minimal functional holoenzyme from Thermus thermophilus (Tth), an extreme thermophile. The minimal holoenzyme consists of α (pol III catalytic subunit), β (sliding clamp processivity factor), and the essential DnaX (τ/γ), δ and δ′ components of the DnaX complex. We show with purified recombinant proteins that these five components are required for rapid and processive DNA synthesis …

A Three-Domain Structure For The Delta Subunit Of The Dna Polymerase Iii Holoenzyme Delta Domain Iii Binds Delta' And Assembles Into The Dnax Complex, James M. Bullard, Arthur E. Pritchard, Min Sun Song, Bradley P. Glover, Anna Wieczorek, Joe Chen, Nebojsa Janjic, Charles S. Mchenry

Chemistry Faculty Publications and Presentations

Using ψ-BLAST, we have developed a method for identifying the poorly conserved δ subunit of the DNA polymerase III holoenzyme from all sequenced bacteria. This approach, starting withEscherichia coli δ, leads not only to the identification of δ but also to the DnaX and δ′ subunits of the DnaX complex and other AAA⁺-class ATPases. This suggests that, although not an ATPase, δ is related structurally to the other subunits of the DnaX complex that loads the β sliding clamp processivity factor onto DNA. To test this prediction, we aligned δ sequences with those of δ′ and, using …

Tightness Of Slip-Linked Polymer Chains, Ralf Metzler, Andreas Hanke, Paul G. Dommersnes, Yacov Kantor, Mehran Kardar

Physics and Astronomy Faculty Publications and Presentations

We study the interplay between entropy and topological constraints for a polymer chain in which sliding rings (slip links) enforce pair contacts between monomers. These slip links divide a closed ring polymer into a number of subloops which can exchange length among each other. In the ideal chain limit, we find the joint probability density function for the sizes of segments within such a slip-linked polymer chain (paraknot). A particular segment is tight (small in size) or loose (of the order of the overall size of the paraknot) depending on both the number of slip links it incorporates and its …

Group-Fitted Ab Initio Single- And Multiple-Scattering Exafs Debye-Waller Factors, N. Dimakis, Grant Bunker

Physics and Astronomy Faculty Publications and Presentations

X-ray absorption fine structure (XAFS) spectroscopy is one of the few direct probes of the structure of metalloprotein binding that is equally applicable to proteins in crystals, solutions, and membranes. Despite considerable progress in the calculation of the photoelectron scattering aspects of XAFS, calculation of the vibrational aspects has lagged because of the difficulty of the calculations. We report here initial results that express single- and multiple-scattering Debye-Waller factors as polynomial functions of first shell radial distance for metal-peptide complexes, enabling quantitatively accurate full multiple-scattering XAFS data analysis of active sites of unknown structure at arbitrary temperatures without the use …

Correlation Functions Near Modulated And Rough Surfaces, Andreas Hanke, Mehran Kardar

Physics and Astronomy Faculty Publications and Presentations

In a system with long-ranged correlations, the behavior of correlation functions is sensitive to the presence of a boundary. We show that surface deformations strongly modify this behavior as compared to a flat surface. The modified near surface correlations can be measured by scattering probes. To determine these correlations, we develop a perturbative calculation in the deformations in height from a flat surface. Detailed results are given for a regularly patterned surface, as well as for a self-affinely rough surface with roughness exponent ζ. By combining this perturbative calculation in height deformations with the field-theoretic renormalization-group approach, we also estimate …

The First Detection Of Coherent Emission From Radio Pulsars, F. A. Jenet, S. B. Anderson, T. A. Prince

Physics and Astronomy Faculty Publications and Presentations

The statistical properties of the radio emission from the pulsars B0823+26, B0950+08, B1133+16, and B1937+21 are studied using high time resolution observations taken at the Arecibo Observatory in Puerto Rico. Temporally coherent non-Gaussian emission has been detected in three of the four observed objects. This is the first time such a phenomenon has been observed. The results have been interpreted using a generalized shot noise model, and various basic physical quantities pertaining to the magnetospheric plasma have been estimated.

Data Conditioning For Gravitational Wave Detectors: A Kalman Filter For Regressing Suspension Violin Modes, L. S. Finn, S. Mukherjee

Physics and Astronomy Faculty Publications and Presentations

Interferometric gravitational wave detectors operate by sensing the differential light travel time between free test masses. Correspondingly, they are sensitive to anything that changes the physical distance between the test masses, including physical motion of the masses themselves. In ground-based detectors the test masses are suspended as pendula, in order that they be approximately \"free\" above the pendulumn frequency. Still, thermal or other excitations of the suspension wires' violin modes do impart a force on the masses that appears as a strong, albeit narrow-band, \"signal\" in the detectors waveband. Gravitational waves, on the other hand, change the distance between the …

Visual Iconic Object-Oriented Programming To Advance Computer Science Education And Novice Programming, Nancy Silva Martinez

Theses and Dissertations - UTB/UTPA

Learning how to program a computer is difficult for most people. Computer programming is a cognitively challenging, time consuming, labor intensive, and frustrating endeavor. Years of formal study and training are required to learn a programming language's world of algorithms and data structures. Instructions are coded in advance before the computer demonstrates the desired behavior. Seeing all the programming steps and instruction code is complicated. There exists a tremendous gap between the representations the human brain uses when thinking about a problem and the representations used in programming a computer. Often people are much better at dealing with specific, concrete …

Verification Of A Distortion In The Microstructure Of Gan Detected By Exafs Using Ab Initio Density Functional Theory Calculations, N. Dimakis, Grant Bunker, M. Katsikini, E. C. Paloura

Physics and Astronomy Faculty Publications and Presentations

X-ray absorption fine structure (XAFS) measurements on a series of epitaxially grown GaN samples have shown a distortion in the microstructure of GaN. More specifically the central N atom is 4-fold coordinated but the four Ga atoms are not equidistant. It has been shown that 2.9 to 3.5 of them (depending on the growth conditions) are found in the expected from XRD distance of 1.94 A and the remaining are at a distance longer by approximately 15%. Second derivative calculation of the conformation energy using the Density Functional Theory (DFT) is used to investigate if the symmetric GaN cluster as …

Probing The Strong Boundary Shape Dependence Of The Casimir Force, Thorsten Emig, Andreas Hanke, Ramin Golestanian, Mehran Kardar

Physics and Astronomy Faculty Publications and Presentations

We study the geometry dependence of the Casimir energy for deformed metal plates by a path integral quantization of the electromagnetic field. For the first time, we give a complete analytical result for the deformation induced change in Casimir energy δE in an experimentally testable, nontrivial geometry, consisting of a flat and a corrugated plate. Our results show an interesting crossover for δE as a function of the ratio of the mean plate distance H, to the corrugation length λ: For λ≪H we find a slower decay ∼H−4, compared to the H−5 behavior predicted by the commonly used pairwise summation …

Polymer Depletion Interaction Between Two Parallel Repulsive Walls, F. Schlesener, Andreas Hanke, R. Kimpel, S. Dietrich

Physics and Astronomy Faculty Publications and Presentations

The depletion interaction between two parallel repulsive walls confining a dilute solution of long and flexible polymer chains is studied by field-theoretic methods. Special attention is paid to self-avoidance between chain monomers relevant for polymers in a good solvent. Our direct approach avoids the mapping of the actual polymer chains on effective hard or soft spheres. We compare our results with recent Monte Carlo simulations [A. Milchev and K. Binder, Eur. Phys. J. B 3, 477 (1998)] and with experimental results for the depletion interaction between a spherical colloidal particle and a planar wall in a dilute solution of nonionic …