Physical Sciences and Mathematics Commons^™

Structure Of Polc Reveals Unique Dna Binding And Fidelity Determinants, Ronald J. Evans, Douglas R. Davies, James M. Bullard, Jeffrey Christensen, Louis S. Green, Joseph W. Guiles, Janice D. Pata, Wendy K. Ribble, Nebojsa Janjic, Thale C. Jarvis

Chemistry Faculty Publications and Presentations

PolC is the polymerase responsible for genome duplication in many Gram-positive bacteria and represents an attractive target for antibacterial development. We have determined the 2.4-Å resolution crystal structure of Geobacillus kaustophilus PolC in a ternary complex with DNA and dGTP. The structure reveals nascent base pair interactions that lead to highly accurate nucleotide incorporation. A unique β-strand motif in the PolC thumb domain contacts the minor groove, allowing replication errors to be sensed up to 8 nt upstream of the active site. PolC exhibits the potential for large-scale conformational flexibility, which could encompass the catalytic residues. The structure suggests a …

Locality And Stability Of The Cascades Of Two-Dimensional Turbulence, Eleftherios Gkioulekas

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

We investigate and clarify the notion of locality as it pertains to the cascades of two-dimensional turbulence. The mathematical framework underlying our analysis is the infinite system of balance equations that govern the generalized unfused structure functions, first introduced by L’vov and Procaccia. As a point of departure we use a revised version of the system of hypotheses that was proposed by Frisch for three-dimensional turbulence. We show that both the enstrophy cascade and the inverse energy cascade are local in the sense of nonperturbative statistical locality. We also investigate the stability conditions for both cascades. We have shown that …

Uv-Vis Investigations On Ion Beam Irradiated Polycarbonate, Mircea Chipara, Dorina M. Chipara

Physics and Astronomy Faculty Publications and Presentations

UV-VIS investigations on polycarbonate irradiated with accelerated U ions are reported. The experimental data are consistent with the decrease of the energy gap due to irradiation and indicate the formation of isolated conjugated structures. The relatively weak decrease of the energy gap and the shape of the electron spin resonance lines indicate that the conjugated structures are isolated within the polymeric matrix. published: 8 November, 2008.

Search For Gravitational-Wave Bursts From Soft Gamma Repeaters, B. P. Abbott, R. Abbott, Mario C. Diaz, R. Grosso, K. Hayama, Soma Mukherjee, Soumya Mohanty, Joseph D. Romano, Robert Stone

Physics and Astronomy Faculty Publications and Presentations

We present a LIGO search for short-duration gravitational waves (GWs) associated with soft gamma ray repeater (SGR) bursts. This is the first search sensitive to neutron star f modes, usually considered the most efficient GW emitting modes. We find no evidence of GWs associated with any SGR burst in a sample consisting of the 27 Dec. 2004 giant flare from SGR 1806−20 and 190 lesser events from SGR 1806−20 and SGR 1900+14. The unprecedented sensitivity of the detectors allows us to set the most stringent limits on transient GW amplitudes published to date. We find upper limit estimates on the …

Pulsar Timing As A Probe Of Non-Einsteinlan Polarizations Of Gravitational Waves, K. J. Lee, F. A. Jenet, Richard H. Price

Physics and Astronomy Faculty Publications and Presentations

Einstein's theory of gravity predicts waves of the distortion of spacetime with two degrees of polarization; alternative theories predict more polarizations, up to a maximum of six. Although laser interferometric gravity wave detectors can be used to search for at least some of the non-Einsteinian polarizations, their configuration is not optimal for the task. By contrast, the angular distribution of pulsars in the sky makes pulsar timing a flexible tool for detecting all polarizations. We give here an analysis of the sensitivity of pulsar timing to an isotropic stochastic gravitational wave background of waves with non-Einsteinian polarizations and conclude that …

A Teaching Intervention To Increase Achievement Of Hispanic Nonscience Majors Taking Physical Science Courses, G. Herold Poelzer, Liang Zeng

Physics and Astronomy Faculty Publications and Presentations

This quasi-experimental pilot study of nonscience majors taking a physical science course at a university in South Texas was conducted on Hispanic undergraduate students, and is theory based--an application of attribution theory. That the treatment group outperformed the comparison group provides evidence of the positive effect of having students reflect on controllable reasons for their grades and on their subsequent planning of strategies to maintain or improve those grades. (Contains 1 table and 2 figures.)

Cluster Analysis Of Simulated Gravitationalwave Triggers Using S-Means And Constrained Validation Clustering, Lappoon R. Tang, Hansheng Lei, Soma Mukherjee, Soumya Mohanty

Computer Science Faculty Publications and Presentations

The fifth Science run of LIGO (S5) has been concluded recently. The data collected over two years of the run calls for a thorough analysis of the glitches seen in the gravitational wave channels, as well as in the auxiliary and environmental channels. The study presents two new techniques for cluster analysis of gravitational wave burst triggers. Traditional approaches to clustering treats the problem as an optimization problem in an “open” search space of clustering models. However, this can lead to problems with producing models that over-fit or under-fit the data as the search is stuck on local minima. The …

S-Means: Similarity Driven Clustering And Its Application In Gravitational-Wave Astronomy Data Mining, Hansheng Lei, Lappoon R. Tang, Juan R. Iglesias, Soma Mukherjee, Soumya Mohanty

Computer Science Faculty Publications and Presentations

Clustering is to classify unlabeled data into groups. It has been well researched for decades in many disciplines. Clustering in massive amount of astronomical data generated by multi-sensor networks has become an emerging new challenge; assumptions in many existing clustering algorithms are often violated in these domains. For example, K means implicitly assumes that underlying distribution of data is Gaussian. Such an assumption is not necessarily observed in astronomical data. Another problem is the determination of K, which is hard to decide when prior knowledge is lacking. While there has been work done on discovering the proper value for K …

Optimization And Validation Of An Enzymatic Method To Quantify Glucose In Potato Tubers, Engil Isadora Pujol Pereira, Tatiana Emanuelli, Dilson Antonio Bisognin, Sergio T. De Freitas

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

The processing industry requires potato tubers with low levels of reduced sugars, glucose and fructose, which is responsible for the whiteness of the chip color. The objective of this research was to optimize and validate a simple, inexpensive, and precise enzymatic method to quantify glucose in potato tubers. This method will be useful in breeding programs to select clones for processing purposes with low levels of glucose. The validation procedure followed the recommendations described in INMETRO document DOQ-CGCRE-008 in 2003. The method was linear between 1.25 to 40µg of glucose in the sample. The quantification limit was 0.319mg g-1 of …

Implications For The Origin Of Grb 070201 From Ligo Observations, B. Abbott, R. Abbott, R. Adhikari, J. Agresti, P. Ajith, B. Allen, R. Amin, S. B. Anderson, W. G. Anderson, M. Arain, M. Araya, H. Armandula, M. Ashley, S. Aston, P. Aufmuth, C. Aulbert, S. Babak, S. Ballmer, H. Bantilan, B. C. Barish, C. Barker, D. Barker, B. Barr, P. Barriga, M. A. Barton, K. Bayer, J. Betzwieser, P. T. Beyersdorf, B. Bhawal, I. A. Bilenko

Physics and Astronomy Faculty Publications and Presentations

We analyzed the available LIGO data coincident with GRB 070201, a short-duration, hard-spectrum γ-ray burst (GRB) whose electromagnetically determined sky position is coincident with the spiral arms of the Andromeda galaxy (M31). Possible progenitors of such short, hard GRBs include mergers of neutron stars or a neutron star and a black hole, or soft γ-ray repeater (SGR) flares. These events can be accompanied by gravitational-wave emission. No plausible gravitational-wave candidates were found within a 180 s long window around the time of GRB 070201. This result implies that a compact binary progenitor of GRB 070201, with masses in the range …

Some Applications Of Dirac's Delta Function In Statistics For More Than One Random Variable, Santanu Chakraborty

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

In this paper, we discuss some interesting applications of Dirac's delta function in Statistics. We have tried to extend some of the existing results to the more than one variable case. While doing that, we particularly concentrate on the bivariate case.

Correlation Between Luminescent Properties And Local Coordination Environment For Erbium Dopant In Yttrium Oxide Nanotubes, Yuanbing Mao, John Bargar, Michael Toney, Jane P. Chang

Chemistry Faculty Publications and Presentations

The local dopant coordination environment and its effect on the photoluminescent (PL) spectral features of erbium-doped yttrium oxide nanotubes (NTs) were probed by synchrotron-based x-ray diffraction (XRD), x-ray absorption near-edge spectroscopy (XANES), and extended x-ray absorption fine structure (EXAFS). XRD, XANES, and EXAFS data demonstrate that single phase solid solutions of Y (2-x) Erx O3 were formed at 0≤x

Winterberg’S Conjectured Breaking Of The Superluminal Quantum Correlations Over Large Distances, Eleftherios Gkioulekas

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

We elaborate further on a hypothesis by Winterberg that turbulent fluctuations of the zero point field may lead to a breakdown of the superluminal quantum correlations over very large distances. A phenomenological model that was proposed by Winterberg to estimate the transition scale of the conjectured breakdown, does not lead to a distance that is large enough to be agreeable with recent experiments. We consider, but rule out, the possibility of a steeper slope in the energy spectrum of the turbulent fluctuations, due to compressibility, as a possible mechanism that may lead to an increased lower-bound for the transition scale. …

Rapid Evolution In Introduced Species, ‘Invasive Traits’ And Recipient Communities: Challenges For Predicting Invasive Potential, Kenneth D. Whitney, Christopher A. Gabler

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

The damaging effects of invasive organisms have triggered the development of Invasive Species Predictive Schemes (ISPS). These schemes evaluate biological and historical characteristics of species and prioritize those that should be the focus of exclusion, quarantine, and/or control. However, it is not clear how commonly these schemes take microevolutionary considerations into account. We review the recent literature and find that rapid evolutionary changes are common during invasions. These evolutionary changes include rapid adaptation of invaders to new environments, effects of hybridization, and evolution in recipient communities. Strikingly, we document 38 species in which the specific traits commonly associated with invasive …

Comparison Of Polymerase Chain Reaction And Bacterial Culture For Salmonella Detection In The Muscovy Duck In Trinidad And Tobago, Joanne Rampersad-Ammons, Jenelle Johnson, Gabriel Brown, Michael S. Samlal, David R. Ammons

Chemistry Faculty Publications and Presentations

Objectives: The purpose of this study was to investigate the presence and serovar identity of Salmonella, at the national level, in farmed Muscovy ducks (Cairina moschata) in Trinidad and Tobago, and to compare the relative benefits of bacterial culture to those of polymerase chain reaction (PCR) for use in the routine detection and surveillance of Salmonella in these ducks.

Methods: From March-September 2003, 110 fecal samples were collected from 82 farms across the islands of Trinidad and Tobago. Salmonella was isolated from fresh and frozen samples and the serotype of each was determined through bacterial culture. An in-house, nested PCR …

Arecibo H I Absorption Measurements Of Pulsars And The Electron Density At Intermediate Longitudes In The First Galactic Quadrant, J. M. Weisberg, S. Stanimirović, K. Xilouris, A. Hedden, A. De La Fuente, S. B. Anderson, F. A. Jenet

Physics and Astronomy Faculty Publications and Presentations

We have used the Arecibo telescope to measure the H I absorption spectra of eight pulsars. We show how kinematic distance measurements depend on the values of the Galactic constants R0 and Θ0, and we select our preferred current values from the literature. We then derive kinematic distances for the low-latitude pulsars in our sample and electron densities along their lines of sight. We combine these measurements with all others in the inner Galactic plane visible from Arecibo to study the electron density in this region. The electron density in the interarm range 48° < l < 70° is 0.017-0.007+0.012(68% c.1.) cm-3. This is 0.75-0.22+0.49(68% c.1.) of the value calculated by the Galactic electron density model of Cordes & Lazio. The model agrees more closely with electron density measurements toward Arecibo pulsars lying closer to the Galactic center, at 30° < l < 48°. Our analysis leads to the best current estimate of the distance of the relativistic binary pulsar B1913+16: d = 9.0 ± 3 kpc We use the high-latitude pulsars to search for small-scale structure in the interstellar hydrogen observed in absorption over multiple epochs. PSR B0301+19 exhibited significant changes in its absorption spectrum over 22 yr, indicating H I structure on a ∼500 AU scale. © 2008. The American Astronomical Society. All rights reserved.

Psr J1856+0245: Arecibo Discovery Of A Young Energetic Pulsar Coincident With The Tev G-Ray Source Hess J1857+026, J. W.T. Hessels, D. J. Nice, B. M. Gaensler, V. M. Kaspi, D. R. Lorimer, D. J. Champion, A. G. Lyne, M. Kramer, J. M. Cordes, P. C.C. Freire, F. Camilo, S. M. Ransom, J. S. Deneva, N. D.R. Bhat, I. Cognard, F. Crawford, F. A. Jenet, L. Kasian, P. Lazarus, J. Van Leeuwen, M. A. Mclaughlin, I. H. Stairs, B. W. Stappers, A. Venkataraman

Physics and Astronomy Faculty Publications and Presentations

We present the discovery of the Vela-like radio pulsar J1856+0245 in the Arecibo PALFA survey. PSR J1856+0245 has a spin period of 81 ms, a characteristic age of 21 kyr, and a spin-down luminosity Ä– p 4.6 x 10 36 ergs s-1. It is positionally coincident with the TeV γ-ray source HESS J1857+026, which has no other known counterparts. Young, energetic pulsars create wind nebulae, and more than a dozen pulsar wind nebulae have been associated with very high energy (100 GeV-100 TeV) γ-ray sources discovered with the HESS telescope. The γ-ray emission seen from HESS J1857+026 is potentially produced …

Beating The Spin-Down Limit On Gravitational Wave Emission From The Crab Pulsar, B. P. Abbott, R. Abbott, R. Adhikari, P. Ajith, B. Allen, G. Allen, R. Amin, S. B. Anderson, W. G. Anderson, M. A. Arain, M. Araya, H. Armandula, P. Armor, Y. Aso, S. Aston, P. Aufmuth, C. Aulbert, S. Babak, S. Ballmer, H. Bantilan, B. C. Barish, C. Barker, D. Barker, B. Barr, P. Barriga, M. A. Barton, M. Bastarrika, K. Bayer, J. Betzwieser, P. T. Beyersdorf

Physics and Astronomy Faculty Publications and Presentations

We present direct upper limits on gravitational wave emission from the Crab pulsar using data from the first 9 months of the fifth science run of the Laser Interferometer Gravitational-wave Observatory (LIGO). These limits are based on two searches. In the first we assume that the gravitational wave emission follows the observed radio timing, giving an upper limit on gravitational wave emission that beats indirect limits inferred from the spin-down and braking index of the pulsar and the energetics of the nebula. In the second we allow for a small mismatch between the gravitational and radio signal frequencies and interpret …

Search Of S3 Ligo Data For Gravitational Wave Signals From Spinning Black Hole And Neutron Star Binary Inspirals, B. P. Abbott, R. Grosso, Mario C. Diaz, Soumya Mohanty, Soma Mukherjee, Cristina V. Torres

Physics and Astronomy Faculty Publications and Presentations

We report on the methods and results of the first dedicated search for gravitational waves emitted during the inspiral of compact binaries with spinning component bodies. We analyze 788 hours of data collected during the third science run (S3) of the LIGO detectors. We searched for binary systems using a detection template family specially designed to capture the effects of the spin-induced precession of the orbital plane. We present details of the techniques developed to enable this search for spin-modulated gravitational waves, highlighting the differences between this and other recent searches for binaries with nonspinning components. The template bank we …

Search For Gravitational Waves From Binary Inspirals In S3 And S4 Ligo Data, B. P. Abbott, R. Abbott, Mario C. Diaz, R. Grosso, Soumya Mohanty, Soma Mukherjee, Cristina V. Torres

Physics and Astronomy Faculty Publications and Presentations

We report on a search for gravitational waves from the coalescence of compact binaries during the third and fourth LIGO science runs. The search focused on gravitational waves generated during the inspiral phase of the binary evolution. In our analysis, we considered three categories of compact binary systems, ordered by mass: (i) primordial black hole binaries with masses in the range 0.35M⊙

Physiological Aging Of Potato Tubers Produced During Fall And Spring Growing Seasons And Stored Under Different Temperatures, Dilson A. Bisognin, Sergio T. De Freitas, Auri Brackmann, Jeronimo Luiz Andriolo, Engil Isadora Pujol Pereira, Douglas Renator Muller, Mauricio Guerra Bandinelli

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Adequate tuber storage is necessary to maintain a good availability of potato tubers in the market and to get seeds with adequate physiological age at planting. The objective of this work was to determine the effect of different storage temperatures on tuber physiological aging of three potato clones produced during fall and spring growing seasons. The experiment was carried out as factorial of three clones (Asterix, SMIJ461-1 and SMINIA793101-3) by four storage temperatures (4, 8, 12 and 25 ºC) and two growing seasons (fall and spring) in a random design with four replications. At 30-day intervals, tubers were evaluated from …

All-Sky Search For Periodic Gravitational Waves In Ligo S4 Data, B. P. Abbott, R. Abbott, Mario C. Diaz, R. Grosso, Soumya Mohanty, Soma Mukherjee, Cristina V. Torres

Physics and Astronomy Faculty Publications and Presentations

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50–1000 Hz and with the frequency’s time derivative in the range −1×10−8  Hz s−1 to zero. Data from the fourth LIGO science run (S4) have been used in this search. Three different semicoherent methods of transforming and summing strain power from short Fourier transforms (SFTs) of the calibrated data have been used. The first, known as StackSlide, averages normalized power from each SFT. A “weighted Hough” scheme is also developed and used, which also allows for a multi-interferometer search. The third method, …

Kinetics And Thermodynamics Of Salt-Dependent T7 Gene 2.5 Protein Binding To Single- And Double-Stranded Dna., Leila Shokri, Boriana Marintcheva, Mootaz Eldib, Andreas Hanke, Ioulia Rouzina, Mark C. Williams

Physics and Astronomy Faculty Publications and Presentations

Bacteriophage T7 gene 2.5 protein (gp2.5) is a single-stranded DNA (ssDNA)-binding protein that has essential roles in DNA replication, recombination and repair. However, it differs from other ssDNA-binding proteins by its weaker binding to ssDNA and lack of cooperative ssDNA binding. By studying the rate-dependent DNA melting force in the presence of gp2.5 and its deletion mutant lacking 26 C-terminal residues, we probe the kinetics and thermodynamics of gp2.5 binding to ssDNA and double-stranded DNA (dsDNA). These force measurements allow us to determine the binding rate of both proteins to ssDNA, as well as their equilibrium association constants to dsDNA. …

Denaturation Transition Of Stretched Dna, Andreas Hanke, Martha G. Ochoa, Ralf Metzler

Physics and Astronomy Faculty Publications and Presentations

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent c, for which we find the new value c=4ν−1/2 such that the transition is second order with c=1.85DNA, corresponding to a lower melting temperature T(F), in agreement with single-molecule DNA stretching experiments.

Search For Gravitational Waves Associated With 39 Gamma-Ray Bursts Using Data From The Second, Third, And Fourth Ligo Runs, B. P. Abbott, R. Abbott, Mario C. Diaz, R. Grosso, Wm. R. Johnston, Soumya Mohanty, Soma Mukherjee, Cristina V. Torres

Physics and Astronomy Faculty Publications and Presentations

We present the results of a search for short-duration gravitational-wave bursts associated with 39 gamma-ray bursts (GRBs) detected by gamma-ray satellite experiments during LIGO’s S2, S3, and S4 science runs. The search involves calculating the crosscorrelation between two interferometer data streams surrounding the GRB trigger time. We search for associated gravitational radiation from single GRBs, and also apply statistical tests to search for a gravitational-wave signature associated with the whole sample. For the sample examined, we find no evidence for the association of gravitational radiation with GRBs, either on a single-GRB basis or on a statistical basis. Simulating gravitational-wave bursts …

Splitting Np-Complete Sets, Christian Glaßer, A. Pavan, Alan L. Selman, Liyu Zhang

Computer Science Faculty Publications and Presentations

We show that a set is m-autoreducible if and only if it is m-mitotic. This solves a long-standing open question in a surprising way. As a consequence of this unconditional result and recent work by Glaßer et al., complete sets for all of the following complexity classes are m-mitotic: NP, coNP, ⊕P, PSPACE, and NEXP, as well as all levels of PH, MODPH, and the Boolean hierarchy over NP. In the cases of NP, PSPACE, NEXP, and PH, this at once answers several well-studied open questions. These results tell us that complete sets share a redundancy that was not known …

An Action For A Classical String, The Equation Of Motion And Group Invariant Classical Solutions, Paul Bracken

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

A string action which is essentially a Willmore functional is presented and studied. This action determines the physics of a surface in Euclidean three space which can be used to model classical string configurations. By varying this action an equation of motion for the mean curvature of the surface is obtained which is shown to govern certain classical string configurations. Several classes of classical solutions for this equation are discussed from the symmetry group point of view and an application is presented.

A Fragment On Euler's Constant In Ramanujan's Lost Notebook, Bruce C. Berndt, Timothy Huber

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

A formula for Euler’s constant found in Ramanujan’s lost notebook and also in a problem he submitted to the Journal of the Indian Mathematical Society is proved and discussed.

Quantum Phases For A Generalized Harmonic Oscillator, Paul Bracken

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

An effective Hamiltonian for the generalized harmonic oscillator is determined by using squeezed state wavefunctions. The equations of motion over an extended phase space are determined and then solved perturbatively for a specific choice of the oscillator parameters. These results are used to calculate the dynamic and geometric phases for the generalized oscillator with this choice of parameters.

Rapid Evolution In Introduced Species, ‘Invasive Traits’ And Recipient Communities: Challenges For Predicting Invasive Potential, Kenneth D. Whitney, Christopher A. Gabler

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

The damaging effects of invasive organisms have triggered the development of Invasive Species Predictive Schemes (ISPS). These schemes evaluate biological and historical characteristics of species and prioritize those that should be the focus of exclusion, quarantine, and/or control. However, it is not clear how commonly these schemes take microevolutionary considerations into account. We review the recent literature and find that rapid evolutionary changes are common during invasions. These evolutionary changes include rapid adaptation of invaders to new environments, effects of hybridization, and evolution in recipient communities. Strikingly, we document 38 species in which the specific traits commonly associated with invasive …