Digital Commons Network^™

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 & Astronomy Faculty Publications

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. …

Beating The Spin-Down Limit On Gravitational Wave Emission From The Crab Pulsar, B. P. Abbott, R. Abbott, R. Adhikari, Mario C. Diaz, Roberto Grosso, Kazuhiro Hayama, Soumya Mohanty, Soma Mukherjee, Joseph D. Romano, Robert Stone

Physics & Astronomy Faculty Publications

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 …

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

Physics & Astronomy Faculty Publications

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 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 & Astronomy Faculty Publications

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 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 & Astronomy Faculty Publications

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 …

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, Fredrick A. Jenet

Physics & Astronomy Faculty Publications

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 …

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 & Astronomy Faculty Publications

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⊙

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 & Astronomy Faculty Publications

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, …

The Collegian (2007-12-03), Isis Lopez

UTB/TSC Archives - The Collegian [Newspaper]

Vol. 60, No. 14

On Mathematical Modeling, Nonlinear Properties And Stability Of Secondary Flow In A Dendrite Layer, Daniel N. Riahi

School of Mathematical & Statistical Sciences Faculty Publications

This paper studies instabilities in the flow of melt within a horizontal dendrite layer with deformed upper boundary and in the presence or absence of rotation during the solidification of a binary alloy. In the presence of rotation, it is assumed that the layer is rotating about a vertical axis at a constant angular velocity. Linear and weakly nonlinear stability analyses provide results about various flow features such as the critical mode of convection, neutral stability curve, preferred flow pattern and the solid fraction distribution within the dendrite layer. The preferred shape of the deformed upper boundary of the layer, …

Zinc Cysteine Active Sites Of Metalloproteins: A Density Functional Theory And X-Ray Absorption Fine Structure Study, Nicholas Dimakis, Mohammed Junaid Farooqi, Emily Sofia Garza, Grant Bunker

Physics & Astronomy Faculty Publications

Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal …

The Pan American (2007-11-29), Sandra Gonzalez

UTPA Archives - The Pan American Newspaper

58th Year, No. 13

The Collegian (2007-11-12), Isis Lopez

UTB/TSC Archives - The Collegian [Newspaper]

Vol. 60, No. 12

Microwave Spectra And Ab Initio Studies Of Ar-Propane And Ne-Propane Complexes: Structure And Dynamics, Karen I. Peterson, David Pullman, Wei Lin, Andrea J. Minei, Stewart E. Novick

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Microwave spectra in the 7-26 MHz region have been measured for the van der Waals complexes, Ar-C H3 C H2 C H3, Ar- C13 H3 C H2 C H3, Ne20 -C H3 C H2 C H3, and Ne22 -C H3 C H2 C H3. Both a - and c -type transitions are observed for the Ar-propane complex. The c -type transitions are much stronger indicating that the small dipole moment of the propane (0.0848 D) is aligned perpendicular to the van der Waals bond axis. While the 42 transition lines observed for the primary argon complex are well fitted to …

An Overview Of The Genus Nardostachys, Asima Chatterjee, Utpal Dutta, Debasish Bandyopadhyay, Anupam Nayak, Bidyut Basak, Avijit Banerji, Julie Banerji

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Nardostachys jatamansi, a medicinally important herb of Nepalese origin, has been used for centuries in the Ayurvedic and Unani systems of medicine. In combination with Marsilea minuta it is being used as an antistress and anticonvulsant drug and also finds use in the treatment of epilepsy. Recently, it has been reported that N. jatamansi, which plays an important role in protecting from cerebral ischemia and liver damage, is also used for the treatment of osteoporosis and hypercalcemia. The other member of the genus Nardostachys, N. chinensis, possesses antifungal and antimalarial properties. It is also used in the treatment of skin …

In-House Polymerase Chain Reaction For Affordable And Sustainable Chlamydia Trachomatis Detection In Trinidad And Tobago, Joanne Rampersad, Xiaohui Wang, Helen Gayadeen, Samuel Ramsewak, David Ammons

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Objectives: To provide a preliminary assessment of in-house polymerase chain reaction (PCR) as an alternative to the more costly commercial test for detection of asymptomatic infection by Chlamydia trachomatis and to provide much needed demographic data on infection indicators within the Trinidad and Tobago public health care system.

Methods: An inexpensive in-house nested-PCR with an Internal Amplification Control was used to detect C. trachomatis and Neisseria gonorrhoeae in urine samples collected from 273 apparently healthy, pregnant women from March-September 2004 in Trinidad, West Indies. Demographic information on participants was collected and subjected to statistical analyses.

Results: C. trachomatis was detected …

The Collegian (2007-10-22), Isis Lopez

UTB/TSC Archives - The Collegian [Newspaper]

Vol. 60, No. 9

The Pan American (2007-10-18), Sandra Gonzalez

UTPA Archives - The Pan American Newspaper

58th Year, No. 8

The Collegian (2007-10-15), Isis Lopez

UTB/TSC Archives - The Collegian [Newspaper]

Vol. 60, No. 8

The Collegian (2007-10-08), Isis Lopez

UTB/TSC Archives - The Collegian [Newspaper]

Vol. 60, No. 7

Utpa Stats At A Glance - Fall 2007, University Of Texas-Pan American

UTPA Archives - Stats At A Glance

No abstract provided.

Utpa Commencement – Fall 2007, University Of Texas-Pan American

Edinburg Archives - Legacy Commencement Programs

No abstract provided.

Los Arcos - Fall 2007, University Of Texas-Pan American

UTPA Archives - Los Arcos Magazine

No abstract provided.

The Legacy Of Joan Vollmer: The Short Significant Life Of A Beat Woman, Christopher Carmona

Theses and Dissertations - UTB/UTPA

In this thesis, I have endeavored to flesh out the life of Joan Vollmer. Joan Vollmer was an essential figure in the Beat Generation of Writers even though she never published a word. Through researching the life of Joan Vollmer, the role that she played in the creation of the Beat Generation becomes clear. Joan Vollmer is mentioned in the major Beat texts, but there is no definitive look at her life and importance. Therefore, I set out to do what no one has done and write about Joan Vollmer' s life. I have collected as many letters that still …

Fundamental Emission Via Wave Advection From A Collapsing Wave Packet In Electromagnetic Strong Plasma Turbulence, Fredrick A. Jenet, A. Melatos, P. A. Robinson

Physics & Astronomy Faculty Publications

Zakharov simulations of nonlinear wave collapse in continuously driven two-dimensional, electromagnetic strong plasma turbulence with electron thermal speeds v⩾0.01c show that for v≲0.1c, dipole radiation occurs near the plasma frequency, mainly near arrest, but for v≳0.1c, a new mechanism applies in which energy oscillates between trapped Langmuir and transverse modes until collapse is arrested, after which trapped transverse waves are advected into incoherent interpacket turbulence by an expanding annular density well, where they detrap. The multipole structure, Poynting flux, source current, and radiation angular momentum are computed.

Upper Limit Map Of A Background Of Gravitational Waves, B. P. Abbott, R. Abbott, Mario C. Diaz, R. Grosso, Soumya Mohanty, Soma Mukherjee, Cristina V. Torres

Physics & Astronomy Faculty Publications

We searched for an anisotropic background of gravitational waves using data from the LIGO S4 science run and a method that is optimized for point sources. This is appropriate if, for example, the gravitational wave background is dominated by a small number of distinct astrophysical sources. No signal was seen. Upper limit maps were produced assuming two different power laws for the source strain power spectrum. For an f−3 power law and using the 50 Hz to 1.8 kHz band the upper limits on the source strain power spectrum vary between 1.2×10−48  Hz−1 (100  Hz/f)3 and 1.2×10−47  Hz−1 (100  Hz/f)3, …

Searches For Periodic Gravitational Waves From Unknown Isolated Sources And Scorpius X-1: Results From The Second Ligo Science Run, B. P. Abbott, R. Abbott, Mario C. Diaz, R. Grosso, Wm. R. Johnston, Soumya Mohanty, Soma Mukherjee, Cristina V. Torres

Physics & Astronomy Faculty Publications

We carry out two searches for periodic gravitational waves using the most sensitive few hours of data from the second LIGO science run. Both searches exploit fully coherent matched filtering and cover wide areas of parameter space, an innovation over previous analyses which requires considerable algorithm development and computational power. The first search is targeted at isolated, previously unknown neutron stars, covers the entire sky in the frequency band 160–728.8 Hz, and assumes a frequency derivative of less than 4×10−10  Hz/s. The second search targets the accreting neutron star in the low-mass x-ray binary Scorpius X-1 and covers the frequency …

The Pan American (2007-09-27), Sandra Gonzalez

UTPA Archives - The Pan American Newspaper

58th Year, No. 5

The Collegian (2007-09-24), Isis Lopez

UTB/TSC Archives - The Collegian [Newspaper]

Vol. 60, No. 5

The Collegian (2007-09-17), Isis Lopez

UTB/TSC Archives - The Collegian [Newspaper]

Vol. 60, No. 4