Physical Sciences and Mathematics Commons^™

On The Approximability Of The Exemplar Adjacency Number Problem For Genomes With Gene Repetitions, Zhinxiag Chen, Bin Fu, Randy Goebel, Guohui Lin, Weitian Tong, Jinhui Xu, Boting Yang, Zhiyu Zhao, Binhai Zhu

Computer Science Faculty Publications and Presentations

In this paper, we apply a measure, exemplar adjacency number, which complements and extends the well-studied breakpoint distance between two permutations, to measure the similarity between two genomes (or in general, between any two sequences drawn from the same alphabet). For two genomes and drawn from the same set of n gene families and containing gene repetitions, we consider the corresponding Exemplar Adjacency Number problem (EAN), in which we delete duplicated genes from and such that the resultant exemplar genomes (permutations) G and H have the maximum adjacency number. We obtain the following results. First, we prove that the one-sided …

Energy And Potential Enstrophy Flux Constraints In Quasi-Geostrophic Models, Eleftherios Gkioulekas

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

We investigate an inequality constraining the energy and potential enstrophy flux spectra in two-layer and multi-layer quasi-geostrophic models. Its physical significance is that it can diagnose whether any given multi-layer model that allows co-existing downscale cascades of energy and potential enstrophy can allow the downscale energy flux to become large enough to yield a mixed energy spectrum where the dominant k−3 scaling is overtaken by a subdominant k−5/3 contribution beyond a transition wavenumber kt situated in the inertial range. The validity of the flux inequality implies that this scaling transition cannot occur within the inertial range, whereas a violation of …

Advances In Molecular Quantum Chemistry Contained In The Q-Chem 4 Program Package, Yihan Shao, Zhengting Gan, Evgeny Epifanovsky, Andrew T. B. Gilbert, Michael Wormit, Shervin Fatehi

Chemistry Faculty Publications and Presentations

A summary of the technical advances that are incorporated in the fourth major release of the Q-CHEM quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of …

Theoretical And Experimental Infrared Spectra Of Hydrated And Dehydrated Sulfonated Poly(Ether Ether Ketone), Jonathan Doan, Erin Kingston, Ian Kendrick, Kierstyn Anderson, N. Dimakis, Philippe Knauth, Maria Luisa Di Vona, Eugene S. Smotkina

Physics and Astronomy Faculty Publications and Presentations

Time-dependent FT-IR spectra of sulfonated poly(ether ether ketone) during dehydration show diminishing 1081 cm−1 and 1023 cm−1 band intensities concurrent with the emergence and shifting of bands at 1362 cm−1 and 898 cm−1. Animations of density functional theory calculated normal modes enable assignment of the 1081 cm−1 and 1023 cm−1 bands as group modes that include a sulfonate exchange site with C3v local symmetry, while the 1362 cm−1 and 898 cm−1 bands are assigned as group modes that include an associated sulfonic acid with no local symmetry (C1). In contrast to analogously assigned Nafion group mode bands, the SPEEK C3v …

Publisher’S Note: “Derivative Couplings Between Tddft Excited States Obtained By Direct Differentiation In The Tamm-Dancoff Approximation” [J. Chem. Phys. 141, 024114 (2014)], Qi Ou, Shervin Fatehi, Ethan Alguire, Yihan Shao, Joseph Subotnik

Chemistry Faculty Publications and Presentations

No abstract provided.

The Green Bank Northern Celestial Cap Pulsar Survey. I. Survey Description Data Analysis And Initial Results, K. Stovall, R. S. Lynch, S. M. Ransom, A. M. Archibald, S. Banaszak, C. M. Biwer, J. Boyles, L. P. Dartez, D. Day, A. J. Ford, J. Flanigan, A. Garcia, J. W.T. Hessels, J. Hinojosa, F. A. Jenet, D. L. Kaplan, C. Karako-Argaman, V. M. Kaspi, V. I. Kondratiev, S. Leake, D. R. Lorimer, G. Lunsford, J. G. Martinez, A. Mata, M. A. Mclaughlin, M. S.E. Roberts, M. D. Rohr, X. Siemens, I. H. Stairs, J. Van Leeuwen

Physics and Astronomy Faculty Publications and Presentations

We describe an ongoing search for pulsars and dispersed pulses of radio emission, such as those from rotating radio transients (RRATs) and fast radio bursts, at 350 MHz using the Green Bank Telescope. With the Green Bank Ultimate Pulsar Processing Instrument, we record 100 MHz of bandwidth divided into 4096 channels every 81.92 μs. This survey will cover the entire sky visible to the Green Bank Telescope (δ > -40°, or 82% of the sky) and outside of the Galactic Plane will be sensitive enough to detect slow pulsars and low dispersion measure (<30 pc cm-3) millisecond pulsars (MSPs) with a 0.08 duty cycle down to 1.1 mJy. For pulsars with a spectral index of -1.6, we will be 2.5 times more sensitive than previous and ongoing surveys over much of our survey region. Here we describe the survey, the data analysis pipeline, initial discovery parameters for 62 pulsars, and timing solutions for 5 new pulsars. PSR J0214+5222 is an MSP in a long-period (512 days) orbit and has an optical counterpart identified in archival data. PSR J0636+5129 is an MSP in a very short-period (96 minutes) orbit with a very low mass companion (8 M J). PSR J0645+5158 is an isolated MSP with a timing residual RMS of 500 ns and has been added to pulsar timing array experiments. PSR J1434+7257 is an isolated, intermediate-period pulsar that has been partially recycled. PSR J1816+4510 is an eclipsing MSP in a short-period orbit (8.7 hr) and may have recently completed its spin-up phase. © 2014. The American Astronomical Society. All rights reserved..

Exposure To Traffic Pollution, Acute Inflammation And Autonomic Response In A Panel Of Car Commuters, Jeremy A. Sarnat, Rachel Golan, Roby Greenwald, Amit U. Raysoni, Priya Kewada, Andrea Winquist, Stefanie E. Sarnat, W. Dana Flanders, Maria C. Mirabelli, Jennifer E. Zora

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

Background

Exposure to traffic pollution has been linked to numerous adverse health endpoints. Despite this, limited data examining traffic exposures during realistic commutes and acute response exists. Objectives: We conducted the Atlanta Commuters Exposures (ACE-1) Study, an extensive panel-based exposure and health study, to measure chemically-resolved in-vehicle exposures and corresponding changes in acute oxidative stress, lipid peroxidation, pulmonary and systemic inflammation and autonomic response.

Methods

We recruited 42 adults (21 with and 21 without asthma) to conduct two 2-h scripted highway commutes during morning rush hour in the metropolitan Atlanta area. A suite of in-vehicle particulate components were measured in …

Fast Radio Burst Discovered In The Arecibo Pulsar Alfa Survey, L. G. Spitler, J. M. Cordes, J. W.T. Hessels, D. R. Lorimer, M. A. Mclaughlin, S. Chatterjee, F. Crawford, J. S. Deneva, V. M. Kaspi, R. S. Wharton, B. Allen, S. Bogdanov, A. Brazier, F. Camilo, P. C.C. Freire, F. A. Jenet, C. Karako-Argaman, B. Knispel, P. Lazarus, K. J. Lee, J. Van Leeuwen, R. Lynch, S. M. Ransom, P. Scholz, X. Siemens, I. H. Stairs, K. Stovall, J. K. Swiggum, A. Venkataraman, W. W. Zhu

Physics and Astronomy Faculty Publications and Presentations

Recent work has exploited pulsar survey data to identify temporally isolated, millisecond-duration radio bursts with large dispersion measures (DMs). These bursts have been interpreted as arising from a population of extragalactic sources, in which case they would provide unprecedented opportunities for probing the intergalactic medium; they may also be linked to new source classes. Until now, however, all so-called fast radio bursts (FRBs) have been detected with the Parkes radio telescope and its 13-beam receiver, casting some concern about the astrophysical nature of these signals. Here we present FRB 121102, the first FRB discovery from a geographic location other than …

Efficient Evaluation Of Sparql Property Path Queries Over Prov-Dm Provenance Graphs In An Rdbms, Rodolfo E. Roman Velasco

Theses and Dissertations - UTB/UTPA

Millions of useful resources on the Web are enhanced with machine-processable annotations using W3C Resource Description Framework (RDF). It is crucial to design efficient data management techniques to support querying of existing RDF datasets using standard SPARQL queries. To address this challenge, we use a Relational Database Management System (RDBMS) for efficient and scalable storage and querying backend for RDF data. Our solution requires designing novel algorithms for translating SPARQL queries into equivalent SQL queries, such that the latter can be efficiently executed in an RDBMS. The focus of this work is on the translation of SPARQL property paths queries. …

Prediction Of Time-To-Graduation For Stem Hispanic Undergraduate Students, Gejun Zhu

Theses and Dissertations - UTB/UTPA

In this thesis, we study the time-to-graduation problem for STEM Hispanic undergraduate students. The response, time-to-graduation, was treated in two different ways: as a binary variable with graduated (by the 6th year) and not-graduated values, and as an ordinal variable with values year-4, year-5, year-6, and not-graduate. Mathematics education plays critical role in students’ timely graduation, especially for STEM students. We used students records data obtained from The University of Texas-Pan American to illustrate how mathematics background factors (including SAT math score, ACT math score, TASP math score) and mathematics performance variables (including mathematics GPA, number of dropped mathematics courses, …

An Empirical Study Of Some Branching Processes With Upper Barrier, Alejandro Aguilar

Theses and Dissertations - UTB/UTPA

We consider discrete time branching processes with a reflecting upper barrier. The processes differ in their offspring distributions being either binary splitting or binomial one. Two important factors for the behavior of the processes characteristics are studied as follows: time to extinction and total progeny up to the n th generation. More specifically, we investigate the distribution and expected value of the time to extinction as well as the probability mass functions of the total progeny. The tools used are basic results for a finite state Markov chain.

Dynamics For The Compound Burgers-Kdv Equation, Xiangqian Zheng

Theses and Dissertations - UTB/UTPA

In this thesis, we study the Two-Dimensional Burgers-Korteweg-de Vries (2D-BKdV) equation and Two-Dimensional Compound Burgers-Korteweg-de Vries (2D-Compound BKdV) by analyzing the first integral equation, which indicates that under some particular conditions, the 2D-BKdV equation and 2D-Compound BKdV have exact traveling wave solutions. By using the elliptic integral and some transformations, traveling wave solution to the 2D-BKdV equation and 2DCompound BKdV are expressed explicitly.

Balanced Modular Parameterizations, Esteban J. Melendez

Theses and Dissertations - UTB/UTPA

In this thesis, we show that Classical representations for certain modular forms have symmetric form. These symmetric formulations are interpreted in terms of more general balanced homogeneous polynomial representations resulting from a permutative action of Hecke congruence subgroups on quotients of theta functions. For prime levels between 5 and 19, sets of permuted theta quotients are constructed that generate the corresponding vector spaces of modular forms of weight one.

Anxiety, Depression And Smoking Status Among Adults Of Mexican Heritage On The Texas-Mexico Border, Anna V. Wilkinson, Kristina Vatcheva, Adriana Pérez, Belinda M. Reininger, Joseph B. Mccormick, Susan P. Fisher-Hoch

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

The goal of the current analysis is to examine relationships between smoking status and anxiety and depression among adults of Mexican heritage to inform the development of culturally relevant smoking cessations efforts. Mexican heritage residents (N=1,791) of the city of Brownsville, TX, aged 18 years or older, enrolled in the Cameron County Hispanic Cohort, were selected through two stage cluster sampling of randomly selected census tracts from the first and third quartile of SES using Census 2000. Among current smokers, anxiety and depression scores were highest among women who had not completed high school (p<0.05). Former smoking women, but not men, with at least a high school education and former smoking women born in the United States reported higher levels of anxiety and depression than never smoking women. Negative affective states may represent a greater barrier to smoking cessation among women than men.

Illustrations And Supporting Texts For Sound Standing Waves Of Air Columns In Pipes In Introductory Physics Textbooks, Liang Zeng, Chris Smith, G. Herold Poelzer, Jennifer Rodriguez, Edgar Corpuz, George Yanev

Physics and Astronomy Faculty Publications and Presentations

In our pilot studies, we found that many introductory physics textbook illustrations with supporting text for sound standing waves of air columns in open-open, open-closed, and closed-closed pipes inhibit student understanding of sound standing wave phenomena due to student misunderstanding of how air molecules move within these pipes. Based on the construct of meaningful learning from cognitive psychology and semiotics, a quasiexperimental study was conducted to investigate the comparative effectiveness of two alternative approaches to student understanding: a traditional textbook illustration approach versus a newly designed air molecule motion illustration approach. Thirty volunteer students from introductory physics classes were randomly …

Reconstruction Of Structured Quadratic Pencils From Eigenvalues On Ellipses And Parabolas, R. Ibragimov, Vesselin Vatchev

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

In the present paper we study the reconstruction of a structured quadratic pencil from eigenvalues distributed on ellipses or parabolas. A quadratic pencil is a square matrix polynomial

QP(λ) = M λ²+Cλ +K,

where M, C, and K are real square matrices. The approach developed in the paper is based on the theory of orthogonal polynomials on the real line. The results can be applied to more general distribution of eigenvalues. The problem with added single eigenvector is also briefly discussed. As an illustration of the reconstruction method, the eigenvalue problem …

Derivative Couplings Between Tddft Excited States Obtained By Direct Differentiation In The Tamm-Dancoff Approximation, Qi Ou, Shervin Fatehi, Ethan Alguire, Yihan Shao, Joseph Subotnik

Chemistry Faculty Publications and Presentations

Working within the Tamm-Dancoff approximation, we calculate the derivative couplings between time-dependent density-functional theory excited states by assuming that the Kohn-Sham superposition of singly excited determinants represents a true electronic wavefunction. All Pulay terms are included in our derivative coupling expression. The reasonability of our approach can be established by noting that, for closely separated electronic states in the infinite basis limit, our final expres- sion agrees exactly with the Chernyak-Mukamel expression (with transition densities from response theory). Finally, we also validate our approach empirically by analyzing the behavior of the derivative couplings around the T1/T2 conical intersection of benzaldehyde.

Detection And Estimation Of Unmodeled Narrowband Nonstationary Signals: Application Of Particle Swarm Optimization In Gravitational Wave Data Analysis, Soumya Mohanty

Physics and Astronomy Faculty Publications and Presentations

The extraction of weak signals from instrumental noise is a critical task in ongoing searches for gravitational waves. A detection and estimation method, made feasible by Particle Swarm Optimization, is presented for a particularly challenging class of signals expected from astrophysical sources.

Biodegradable Electrospun Nanofibers Coated With Platelet-Rich Plasma For Cell Adhesion And Proliferation, Luis Diaz-Gomez, Carmen Alvarez-Lorenzo, Angel Concheiro, Maite Silva, Fernando Dominguez, Faheem A. Sheikh, Travis Cantu, Raj Desai, Vanessa L. Garcia, Javier Macossay-Torres

Chemistry Faculty Publications and Presentations

Biodegradable electrospun poly(ε-caprolactone) (PCL) scaffolds were coated with platelet-rich plasma (PRP) to improve cell adhesion and proliferation. PRP was obtained from human buffy coat, and tested on human adipose-derived mesenchymal stem cells (MSC) to confirm cell proliferation and cytocompatibility. Then, PRP was adsorbed on the PCL scaffolds via lyophilization, which resulted in uniform sponge-like coating of 2.85 (s.d. 0.14) mg/mg. The scaffolds were evaluated regarding mechanical properties (Young’s modulus, tensile stress and tensile strain), sustained release of total protein and growth factors (PDGF-BB, TGF-β1 and VEGF), and hemocompatibility. MSC seeded on the PRP-PCL nanofibers showed an increased adhesion and proliferation …

Globular Cluster Simulations By Mocca Code, Dongming Jin

Theses and Dissertations - UTB/UTPA

The MOCCA code is one of the most advanced codes that has the capacity to simulate a realistic sized star cluster with a full dynamical history including stellar evolution using Monte Carlo methods for the cluster evolution and the Fewbody code for scattering. The dynamical evolution of a cluster can result in the formation of many binary systems. Some of these binaries may be very close. Close double white dwarf binaries (double WDBs) may be promising gravitational wave sources. Our work uses MOCCA to simulate 90 globular clusters with different numbers of stars, binary fractions, metallicities and power-law indices of …

The Born Approximation, Multiple Scattering, And The Butterfly Algorithm, Alejandro F. Martinez

Theses and Dissertations - UTB/UTPA

Radar works by focusing a beam of light and seeing how long it takes to reflect. To see a large region the beam is pointed in different directions. The focus of the beam depends on the size of the antenna (called an aperture). Synthetic aperture radar (SAR) works by moving the antenna through some region of space. A fundamental assumption in SAR is that waves only bounce once. Several imaging algorithms have been designed using that assumption. The scattering process can be described by iterations of a badly behaving integral. Recently a method for efficiently evaluating these types of integrals …

The Generation Model Of Internal Waves In A Forced Rotation-Modified Ocean, Daqi Xin

Theses and Dissertations - UTB/UTPA

A two-layer model which contains the forcing term due to the barotropic tides which flow over a comparatively large bottom topography in the ocean was derived previously. The model can be used to describe the generation of nonlinear dispersive internal tides and the following disintegration into internal waves. We studied the influence of Coriolis effect. A numerical simulation shows that the Earth’s rotation affects the generation of the internal waves since it hampers the disintegration of internal tides into internal waves.

Isolation And Characterization Of Polychlorinated Biphenyl (Pcb) Degrading Bacteria Isolated From A Pcb Contaminated Reservoir In Donna, Tx, Sergio Cepeda

Theses and Dissertations - UTB/UTPA

The Donna Irrigation System (DIS) located in Donna, Hidalgo County, TX, was confirmed to be contaminated with polychlorinated biphenyls (PCBs) in 1993 and remediation of the site will be attempted in the future. The need to isolate novel PCB degrading bacteria for bioremediation has been an active area of research in recent decades; thus, it was hypothesized that a variety of microorganisms able to degrade PCBs could be isolated from sediments taken from the DIS. Two genes of the PCB degradation pathway, bphA1 and bphC, were detected in 43 bacterial isolates grown from DIS sediments using molecular and culture-based methodology, …

Radar Image Processing And Its Applications Based On Convolution Back Projection, Qitong Li

Theses and Dissertations - UTB/UTPA

A general synthetic aperture radar (SAR) signal model is derived from the Maxwell’s equations, and a SAR image processing algorithm called Convolution Back Projection (CBP) will be introduced in this thesis, which can be applied to data gathered by a Synthetic Aperture Radar (SAR) system to produce high resolution images. The purpose of this thesis is starting from Maxwell’s equations to study the CBP algorithm as it is applied to SAR image processing. Two different image simulation results will be provided by this method.

Using The Differential Fay Identities For Ribbon Graph Enumeration, Indalecio Soto Jr.

Theses and Dissertations - UTB/UTPA

In this paper we are exploiting connections between the Differential Fay Identities and the partition function of Gaussian Unitary Random Matrices. The partition function has a asymptotic expression whose terms give the generating function for the enumeration of ribbon graphs partitioned by genus. These ribbon graphs (k; j), of k vertices of degree j have an orientation in genus g where the edges are represented as ribbons. Furthermore, we will develop connections between the Differential Fay Identities and introduce several theorems between the hierarchies of the identities. Lastly, we will briefly explore the first Differential Fay Identity that contains the …

Studies Of A Mathematical Model For Generating Rhythmic Behavior With A Simple Brain, Juan C. Morales

Theses and Dissertations - UTB/UTPA

The rhythmic behavior of feeding in the pond snail, Lymnaea stagnalis can be described computationally by a model describing its central pattern generator network (CPG). The model includes coupled Hodgkin-Huxley type nonlinear ordinary differential equations describing four neurons connected by both inhibitory and excitatory synapses. We studied the system’s dependence on current parameters to generate periodic behavior. We also considered the effect of eliminating specific connections from the network. In addition, experiments on the biological system were used to motivate application of the model in Parkinson’s disease.

Illustrations And Supporting Texts For Sound Standing Waves Of Air Columns In Pipes In Introductory Physics Textbooks, Liang Zeng, Chris Smith, G. Herold Poelzer, Jennifer Rodriguez, Edgar Corpuz, George Yanev

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

In our pilot studies, we found that many introductory physics textbook illustrations with supporting text for sound standing waves of air columns in open-open, open-closed, and closed-closed pipes inhibit student understanding of sound standing wave phenomena due to student misunderstanding of how air molecules move within these pipes. Based on the construct of meaningful learning from cognitive psychology and semiotics, a quasiexperimental study was conducted to investigate the comparative effectiveness of two alternative approaches to student understanding: a traditional textbook illustration approach versus a newly designed air molecule motion illustration approach. Thirty volunteer students from introductory physics classes were randomly …

Turbidimetric Determination Of Anionic Polyacrylamide In Low Carbon Soil Extracts, James Jihoon Kang, Tyler D. Sowers, Owen W. Duckworth, Aziz Amoozegar, Joshua L. Heitman, Richard A. Mclaughlin

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

Concerns over runoff water quality from agricultural lands and construction sites have led to the development of improved erosion control practices, including application of polyacrylamide (PAM). We developed a quick and reliable method for quantifying PAM in soil extracts at low carbon content by using a turbidimetric reagent, Hyamine 1622. Three high-molecular weight anionic PAMs differing in charge density (7, 20, and 50 mol%) and five water matrices, deionized (DI) water and extracts from four different soils, were used to construct PAM calibration curves by reacting PAM solutions with hyamine and measuring turbidity development from the PAM–hyamine complex. The PAM …

Methods And Results Of A Search For Gravitational Waves Associated With Gamma-Ray Bursts Using The Geo 600, Ligo, And Virgo Detectors, J. Aasi, B. P. Abbott, H. Daveloza, Mario C. Diaz, Soma Mukherjee, Volker Quetschke, Malik Rakhmanov, K. E. Ramirez, Robert Stone, Cristina V. Torres

Physics and Astronomy Faculty Publications and Presentations

In this paper we report on a search for short-duration gravitational wave bursts in the frequency range 64 Hz–1792 Hz associated with gamma-ray bursts (GRBs), using data from GEO 600 and one of the LIGO or Virgo detectors. We introduce the method of a linear search grid to analyze GRB events with large sky localization uncertainties, for example the localizations provided by the Fermi Gamma-ray Burst Monitor (GBM). Coherent searches for gravitational waves (GWs) can be computationally intensive when the GRB sky position is not well localized, due to the corrections required for the difference in arrival time between detectors. …

Exponential Replication Of Patterns In The Signal Tile Assembly Model, Alexandra Keenan, Robert Schweller, Xingsi Zhong

Computer Science Faculty Publications and Presentations

Chemical self-replicators are of considerable interest in the field of nanomanufacturing and as a model for evolution. We introduce the problem of self-replication of rectangular two-dimensional patterns in the practically motivated Signal Tile Assembly Model (STAM) [9]. The STAM is based on the Tile Assembly Model (TAM) which is a mathematical model of self-assembly in which DNA tile monomers may attach to other DNA tile monomers in a programmable way. More abstractly, four-sided tiles are assigned glue types to each edge, and self-assembly occurs when singleton tiles bind to a growing assembly, if the glue types match and the glue …