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Faculty Publications

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Articles 3001 - 3030 of 4118

Full-Text Articles in Physical Sciences and Mathematics

Measurement Of Prompt Photons With Associated Jets In Photoproduction At Hera, S. Chekanov, M. Derrick, S. Magill, S. Miglioranzi, B. Musgrave, D. Nicholass, J. Repond, R. Yoshida, Margarita C. K. Mattingly, N. Pavel, A. G. Yagües Molina, S. Antonelli, P. Antonioli, G. Bari, M. Basile, L. Bellagamba, M. Bindi, D. Boscherini, A. Bruni, G. Bruni, L. Cifarelli, F. Cindolo, A. Contin, M. Corradi, S. De Pasquale, G. Iacobucci, A. Margotti, R. Nania, A. Polini, L. Rinaldi, G. Sartorelli Jan 2007

Measurement Of Prompt Photons With Associated Jets In Photoproduction At Hera, S. Chekanov, M. Derrick, S. Magill, S. Miglioranzi, B. Musgrave, D. Nicholass, J. Repond, R. Yoshida, Margarita C. K. Mattingly, N. Pavel, A. G. Yagües Molina, S. Antonelli, P. Antonioli, G. Bari, M. Basile, L. Bellagamba, M. Bindi, D. Boscherini, A. Bruni, G. Bruni, L. Cifarelli, F. Cindolo, A. Contin, M. Corradi, S. De Pasquale, G. Iacobucci, A. Margotti, R. Nania, A. Polini, L. Rinaldi, G. Sartorelli

Faculty Publications

The photoproduction of prompt photons, together with an accompanying jet, has been studied in ep collisions at a centre-of-mass energy of 318 GeV with the ZEUS detector at HERA using an integrated luminosity of 77 pb-1. Cross sections were measured for the transverse energy of the photon and the jet larger than 5 and 6 GeV, respectively. The differential γ+jet cross sections were reconstructed as functions of the transverse energy, pseudorapidity and xγobs, the fraction of the incoming photon momentum taken by the photon-jet system. Predictions based on leading-logarithm parton-shower Monte Carlo models and next-to-leading-order (NLO) QCD generally underestimate the …

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Multiple Mixed-Type Attractors In A Competition Model, J. M. Cushing, Shandelle M. Henson, Chantel C. Blackburn Jan 2007

Multiple Mixed-Type Attractors In A Competition Model, J. M. Cushing, Shandelle M. Henson, Chantel C. Blackburn

Faculty Publications

We show that a discrete-time, two-species competition model with Ricker (exponential) nonlinearities can exhibit multiple mixed-type attractors. By this is meant dynamic scenarios in which there are simultaneously present both coexistence attractors (in which both species are present) and exclusion attractors (in which one species is absent). Recent studies have investigated the inclusion of life-cycle stages in competition models as a casual mechanism for the existence of these kinds of multiple attractors. In this paper we investigate the role of nonlinearities in competition models without life-cycle stages. © 2007 Taylor & Francis Group, LLC.

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Spatial Ecology Of The Coachwhip, Masticophis Flagellum (Squamata: Colubridae), In Eastern Texas, Richard W. Johnson, Robert R. Fleet, Michael B. Keck, D. Craig Rudolph Jan 2007

Spatial Ecology Of The Coachwhip, Masticophis Flagellum (Squamata: Colubridae), In Eastern Texas, Richard W. Johnson, Robert R. Fleet, Michael B. Keck, D. Craig Rudolph

Faculty Publications

We radio-tracked nine Masticophis flagellum (Coachwhips) to determine home range, habitat use, and movements in eastern Texas from April to October 2000. Home ranges of Coachwhips contained more oak savanna macrohabitat than early-successional pine plantation or forested seep, based on the availability of these three macrohabitats in the study area. Likewise, within their individual home ranges, Coachwhips used oak savanna more than the other two macrohabitats, based on availability. An analysis of microhabitat use revealed that, relative to random sites within their home range, Coachwhips were found at sites with fewer pine trees and more herbaceous vegetation taller than 30 …

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Search For Stop Production In R-Parity-Violating Supersymmetry At Hera, S. Chekanov, M. Derrick, S. Magill, S. Miglioranzi, B. Musgrave, D. Nicholass, J. Repond, R. Yoshida, Margarita C. K. Mattingly, N. Pavel, A. G. Yagües Molina, S. Antonelli, P. Antonioli, G. Bari, M. Basile, L. Bellagamba, M. Bindi, D. Boscherini, A. Bruni, G. Bruni, L. Cifarelli, F. Cindolo, A. Contin, M. Corradi, S. De Pasquale, G. Iacobucci, A. Margotti, R. Nania, A. Polini, L. Rinaldi, G. Sartorelli Jan 2007

Search For Stop Production In R-Parity-Violating Supersymmetry At Hera, S. Chekanov, M. Derrick, S. Magill, S. Miglioranzi, B. Musgrave, D. Nicholass, J. Repond, R. Yoshida, Margarita C. K. Mattingly, N. Pavel, A. G. Yagües Molina, S. Antonelli, P. Antonioli, G. Bari, M. Basile, L. Bellagamba, M. Bindi, D. Boscherini, A. Bruni, G. Bruni, L. Cifarelli, F. Cindolo, A. Contin, M. Corradi, S. De Pasquale, G. Iacobucci, A. Margotti, R. Nania, A. Polini, L. Rinaldi, G. Sartorelli

Faculty Publications

A search for stop production in R-parity-violating supersymmetry has been performed in e+p interactions with the ZEUS detector at HERA, using an integrated luminosity of 65 pb-1. At HERA, the R-parity-violating coupling λ' allows resonant squark production, e+d→̃ q. Since the lowest-mass squark state in most supersymmetry models is the light stop, ̃t, this search concentrated on production of ̃t, followed either by a direct R-parity-violating decay, or by the gauge decay to b̃x1+. No evidence for stop production was found and limits were set on λ'131 as a function of the stop mass in the framework of the minimal …

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Biogeography And The Cambrian Radiation Of Arachnomorph Arthropods, Jonathan R. Hendricks, Bruce S. Lieberman Jan 2007

Biogeography And The Cambrian Radiation Of Arachnomorph Arthropods, Jonathan R. Hendricks, Bruce S. Lieberman

Faculty Publications

Biogeographic patterns in primarily Cambrian arachnomorph taxa are investigated using a recently constructed phylogenetic hypothesis in order to explore the biogeographic context of the Cambrian radiation. A modified version of Brooks Parsimony Analysis is employed to elucidate patterns of vicariance and geodispersal in taxa from six regions (Laurentia, Baltica, Siberia, Australia, Africa and China). Well resolved vicariance and geodispersal trees are very similar and reconstruct Laurentia and China as sister areas. This close area relationship between Laurentia and China provides extensive evidence for congruent vicariance and range expansion in Cambrian arachnomorphs, while data from trilobites do not show this pattern. …

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Comment: Boosting Algorithms: Regularization, Prediction And Model Fitting, A. Buja, David Mease, A. Wyner Jan 2007

Comment: Boosting Algorithms: Regularization, Prediction And Model Fitting, A. Buja, David Mease, A. Wyner

Faculty Publications

The authors are doing the readers of Statistical Science a true service with a well-written and up-to-date overview of boosting that originated with the seminal algorithms of Freund and Schapire. Equally, we are grateful for high-level software that will permit a larger readership to experiment with, or simply apply, boosting-inspired model fitting. The authors show us a world of methodology that illustrates how a fundamental innovation can penetrate every nook and cranny of statistical thinking and practice. They introduce the reader to one particular interpretation of boosting and then give a display of its potential with extensions from classification (where …

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Application Of The Empirical Mode Decomposition And Hilbert-Huang Transform To Seismic Reflection Data, Bradley M. Battista, Camelia C. Knapp, Tom Mcgee, Vaughn Goebel Jan 2007

Application Of The Empirical Mode Decomposition And Hilbert-Huang Transform To Seismic Reflection Data, Bradley M. Battista, Camelia C. Knapp, Tom Mcgee, Vaughn Goebel

Faculty Publications

Advancements in signal processing may allow for improved imaging and analysis of complex geologic targets found in seismic reflection data. A recent contribution to signal processing is the empirical mode decomposition (EMD) which combines with the Hilbert transform as the Hilbert- Huang transform (HHT). The EMD empirically reduces a time series to several subsignals, each of which is input to the same time-frequency environment via the Hilbert transform. The HHT allows for signals describing stochastic or astochastic processes to be analyzed using instantaneous attributes in the time-frequency domain. The HHT is applied herein to seismic reflection data to: (1) assess …

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A Cognitive Robotics Approach To Comprehending Human Language And Behaviors, Deryle W. Lonsdale, D. Paul Benjamin, Damian Lyons Jan 2007

A Cognitive Robotics Approach To Comprehending Human Language And Behaviors, Deryle W. Lonsdale, D. Paul Benjamin, Damian Lyons

Faculty Publications

The ADAPT project is a collaboration of researchers in linguistics, robotics and artificial intelligence at three universities. We are building a complete robotic cognitive architecture for a mobile robot designed to interact with humans in a range of environments, and which uses natural language and models human behavior. This paper concentrates on the HRI aspects of ADAPT, and especially on how ADAPT models and interacts with humans.

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Cybercraft: Protecting Electronic Systems With Lightweight Agents, Daniel R. Karrels, Gilbert L. Peterson Jan 2007

Cybercraft: Protecting Electronic Systems With Lightweight Agents, Daniel R. Karrels, Gilbert L. Peterson

Faculty Publications

The United States military is seeking new and innovative methods for securing and maintaining its computing and network resources locally and world-wide. This document presents a work-in-progress research thrust toward building a system capable of meeting many of the US military’s network security and sustainment requirements. The system is based on a Distributed Multi-Agent System (DMAS), that is secure, small, and scalable to the large networks found in the military. It relies on a staged agent architecture capable of dynamic configuration to support changing mission environments. These agents are combined into Hierarchical Peer-to-Peer (HP2P) networks to provide scalable solutions. They …

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On Strongly Asymptotic L(P) Spaces And Minimality, S J. Dilworth, V Ferenczi, Denka Kutzarova, E Odell Jan 2007

On Strongly Asymptotic L(P) Spaces And Minimality, S J. Dilworth, V Ferenczi, Denka Kutzarova, E Odell

Faculty Publications

No abstract provided.

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Clustering Streaming Music Via The Temporal Similarity Of Timbre, Jacob Merrell, Bryan S. Morse, Dan A. Ventura Jan 2007

Clustering Streaming Music Via The Temporal Similarity Of Timbre, Jacob Merrell, Bryan S. Morse, Dan A. Ventura

Faculty Publications

We consider the problem of measuring the similarity of streaming music content and present a method for modeling, on the fly, the temporal progression of a song’s timbre. Using a minimum distance classification scheme, we give an approach to classifying streaming music sources and present performance results for auto-associative song identification and for content-based clustering of streaming music. We discuss possible extensions to the approach and possible uses for such a system.

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Generating Ontologies Via Language Components And Ontology Reuse, Deryle W. Lonsdale, Yihong Ding, David W. Embley, Martin Hepp, Li Xu Jan 2007

Generating Ontologies Via Language Components And Ontology Reuse, Deryle W. Lonsdale, Yihong Ding, David W. Embley, Martin Hepp, Li Xu

Faculty Publications

Realizing the Semantic Web involves creating ontologies, a tedious and costly challenge. Reuse can reduce the cost of ontology engineering. Semantic Web ontologies can provide useful input for ontology reuse. However, the automated reuse of such ontologies remains underexplored. This paper presents a generic architecture for automated ontology reuse. With our implementation of this architecture, we show the practicality of automating ontology generation through ontology reuse. We experimented with a large generic ontology as a basis for automatically generating domain ontologies that fit the scope of sample natural-language web pages. The results were encouraging, resulting in five lessons pertinent to …

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Demonstration Of Magnetoelectric Scanning Probe Microscopy, Jason R. Hattrick-Simpers, Liyang Dai, Manfred Wuttig, Ichiro Takeuchi, Eckhard Quandt Jan 2007

Demonstration Of Magnetoelectric Scanning Probe Microscopy, Jason R. Hattrick-Simpers, Liyang Dai, Manfred Wuttig, Ichiro Takeuchi, Eckhard Quandt

Faculty Publications

A near-field room temperature scanning magnetic probe microscope has been developed using a laminated magnetoelectric sensor. The simple trilayer longitudinal-transverse mode sensor, fabricated using Metglas as the magnetostrictive layer and polyvinylidene fluoride as the piezoelectric layer, shows an ac field sensitivity of 467±3μV∕Oe in the measured frequency range of 200Hz–8kHz. The microscope was used to image a 2mm diameter ring carrying an ac current as low as 10−5A. ac fields as small as 3×10−10T have been detected.

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Rapid Structural Mapping Of Ternary Metallic Alloy Systems Using The Combinatorial Approach And Cluster Analysis, C. J. Long, Jason R. Hattrick-Simpers, M. Murakami, R. C. Srivastava, I. Takeuchi, V. L. Karen, X. Li Jan 2007

Rapid Structural Mapping Of Ternary Metallic Alloy Systems Using The Combinatorial Approach And Cluster Analysis, C. J. Long, Jason R. Hattrick-Simpers, M. Murakami, R. C. Srivastava, I. Takeuchi, V. L. Karen, X. Li

Faculty Publications

We are developing a procedure for the quick identification of structural phases in thin film composition spread experiments which map large fractions of compositional phase diagrams of ternary metallic alloy systems. An in-house scanning x-ray microdiffractometer is used to obtain x-ray spectra from 273 different compositions on a single composition spread library. A cluster analysissoftware is then used to sort the spectra into groups in order to rapidly discover the distribution of phases on the ternary diagram. The most representative pattern of each group is then compared to a database of known structures to identify known phases. Using this method, …

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Exafs Characterization Of Dendrimer‐Derived Pt/Γ‐Al2O3, A. Siani, Oleg S. Alexeev, Christopher T. Williams, Harry J. Ploehn, Michael D. Amiridis Jan 2007

Exafs Characterization Of Dendrimer‐Derived Pt/Γ‐Al2O3, A. Siani, Oleg S. Alexeev, Christopher T. Williams, Harry J. Ploehn, Michael D. Amiridis

Faculty Publications

The various steps involved in the preparation of a Pt/γ‐Al2O3 material using hydroxyl‐terminated generation four (G4OH) PAMAM dendrimers as templates were monitored by EXAFS. The results indicate that Cl ligands in the Pt precursors (H2PtCl6 and K2PtCl4) were partially replaced by aquo ligands upon hydrolysis to form [PtCl3(H2O)3]+ and [PtCl2(H2O)2] species. After interaction of such species with G4OH, Cl ligands from the first coordination shell of Pt were further replaced by nitrogen atoms from the dendrimer interior, …

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On The Kauffman Bracket Skein Module Of The Quaternionic Manifold, Patrick M. Gilmer, John M. Harris Jan 2007

On The Kauffman Bracket Skein Module Of The Quaternionic Manifold, Patrick M. Gilmer, John M. Harris

Faculty Publications

We use recoupling theory to study the Kauffman bracket skein module of the quaternionic manifold over Z[A(+/- 1)] localized by inverting all the cyclotomic polynomials. We prove that the skein module is spanned by five elements. Using the quantum invariants of these skein elements and the Z(2)-homology of the manifold, we determine that they are linearly independent.

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Threshold Meson Production And Cosmic Ray Transport, John W. Norbury, Lawrence W. Townsend, Ryan B. Norman Jan 2007

Threshold Meson Production And Cosmic Ray Transport, John W. Norbury, Lawrence W. Townsend, Ryan B. Norman

Faculty Publications

An interesting accident of nature is that the peak of the cosmic ray spectrum, for both protons and heavier nuclei, occurs near the pion production threshold. The Boltzmann transport equation contains a term which is the cosmic ray flux multiplied by the cross section. Therefore when considering pion and kaon production from proton - proton reactions, small cross sections at low energy can be as important as larger cross sections at higher energy. This is also true for subthreshold kaon production in nuclear collisions, but not for subthreshold pion production.

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Differential Cross Sections For Electromagnetic Dissociation, John W. Norbury, Anne Adamczyk Jan 2007

Differential Cross Sections For Electromagnetic Dissociation, John W. Norbury, Anne Adamczyk

Faculty Publications

Differential cross; sections for electromagnetic dissociation in nucleus-nucleus collisions are calculated. The kinetic energy distributions is parameterized with a Boltzmann distribution and the angular distribution is assumed isotropic in the projectile frame. In order to be useful for three-dimensional transport codes, these cross sections are available in both the projectile and lab frames. Comparison between theory and experiment is good. The formalism applies to single and multiple nucleon removal, a particle removal, and fission in electromagnetic reactions of nuclei. (c) 2006 Elsevier B.V. All rights reserved.

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Parameterized Total Cross Sections For Pion Production In Nuclear Collisions, John W. Norbury, Lawrence W. Townsend Jan 2007

Parameterized Total Cross Sections For Pion Production In Nuclear Collisions, John W. Norbury, Lawrence W. Townsend

Faculty Publications

Total inclusive cross sections for neutral and charged pion production in proton–nucleus and nucleus–nucleus reactions have been calculated and compared to experiment. Nucleon–nucleon theoretical cross sections have been scaled up to nuclear collisions using a scaling factor similar to (APAT)2/3, where AP and AT are the nucleon numbers of the projectile and target nuclei. Variations in the power of this scaling factor have been studied and a good fit to experiment is obtained with a small modification of the power. Theoretical cross sections are written in a form that is very …

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A New View Of Ridge Segmentation And Near-Axis Volcanism At The East Pacific Rise, 8˚–12˚N, From Em300 Multibeam Bathymetry, Scott M. White, Rachel M. Haymon, S M. Carbotte Dec 2006

A New View Of Ridge Segmentation And Near-Axis Volcanism At The East Pacific Rise, 8˚–12˚N, From Em300 Multibeam Bathymetry, Scott M. White, Rachel M. Haymon, S M. Carbotte

Faculty Publications

New, high-resolution bathymetry for the East Pacific Rise between 8˚N and 12˚N was collected over a6 km wide swath centered on the ridge axis using the 30 kHz Simrad EM300 multibeam system. Thecoverage area corresponds latitudinally to the designated Ridge2000 Integrated Studies Site (ISS) for fastspreading ridges. The EM300 data, gridded at 30 m latitude by 50 m longitude, represent a greater than 4Ximprovement in horizontal resolution over previously available multibeam data and a 2X improvement indepth resolution. The new bathymetry was used to update the locations and hierarchy of ridge offsets forthis area. Among the many applications for this …

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Theory Of Cavity-Polariton Self-Trapping And Optical Strain In Polymer Chains, M. V. Katkov, Yuriy V. Pershin Dr, C. Piermarocchi Dec 2006

Theory Of Cavity-Polariton Self-Trapping And Optical Strain In Polymer Chains, M. V. Katkov, Yuriy V. Pershin Dr, C. Piermarocchi

Faculty Publications

We consider a semiconductor polymer chain coupled to a single electromagnetic mode in a cavity. The excitations of the chain have a mixed exciton-photon character and are described as polaritons. Polaritons are coupled to the lattice by the deformation potential interaction and can propagate in the chain. We find that the presence of optical excitation in the polymer induces strain on the lattice. We use a BCS variational wave function to calculate the chemical potential of the polaritons as a function of their density. We analyze first the case of a short chain with only two unit cells in order …

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Eliminating Redundant And Less-Informative Rss News Articles Based On Word Similarity And A Fuzzy Equivalence Relation, Ian Garcia, Yiu-Kai D. Ng Nov 2006

Eliminating Redundant And Less-Informative Rss News Articles Based On Word Similarity And A Fuzzy Equivalence Relation, Ian Garcia, Yiu-Kai D. Ng

Faculty Publications

The Internet has marked this era as the information age. There is no precedent in the amazing amount of information, especially network news, that can be accessed by Internet users these days. As a result, the problem of seeking information in online news articles is not the lack of them but being overwhelmed by them. This brings huge challenges in processing online news feeds, e.g., how to determine which news article is important, how to determine the quality of each news article, and how to filter irrelevant and redundant information. In this paper, we propose a method for filtering redundant …

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Tetrakis(N-Ethyl-9-Oxo-4-Azonia-5-Aza-9h-Fluorene) Tetra-Μ3-Iodo-Hexa-Μ2-Iodo-Dodecaiodohexabismuthate, Meredith A. Tershany, Andrea M. Goforth, Mark D. Smith, Leroy Peterson Jr., Hans-Conrad Zur Loye Nov 2006

Tetrakis(N-Ethyl-9-Oxo-4-Azonia-5-Aza-9h-Fluorene) Tetra-Μ3-Iodo-Hexa-Μ2-Iodo-Dodecaiodohexabismuthate, Meredith A. Tershany, Andrea M. Goforth, Mark D. Smith, Leroy Peterson Jr., Hans-Conrad Zur Loye

Faculty Publications

The new iodobismuthate compound (C13H11N2O)4[Bi6I22] has been synthesized solvothermally by reacting BiI3, Zn(NO3)2·6H2O and 4,5-diazafluoren-9-one in a water/ethanol solvent mixture. The asymmetric unit of the compound contains two independent [N-ethyl-4,5-dafo]+ cations and one-half of a centrosymmetric [Bi6I22]4- anion. The average terminal Bi-I, Bi-2-I and Bi-3-I bond lengths in the anion are 2.8923 (2), 3.1403 (2) and 3.3022 (2) Å, respectively.

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Subtidal Inner Shelf Currents Off Cartagena De Indias, Caribbean Coast Of Colombia, Mauro Maza, George Voulgaris, Bulusu Subrahmanyam Nov 2006

Subtidal Inner Shelf Currents Off Cartagena De Indias, Caribbean Coast Of Colombia, Mauro Maza, George Voulgaris, Bulusu Subrahmanyam

Faculty Publications

Seasonal trends in inner shelf subtidal circulation off the coast of Cartagena de Indias, Colombia, are examined through the analysis of current profiles, hydrographic, meteorological and satellite data collected from 1999 to 2002. During the dry season (December–April) the water column is well-mixed and along-shelf currents flow southwestward following the steady trade winds. In the rainy season (May –November) the water column experiences continuous events of stratification and the along-shelf currents flow northeastward, opposing the weak southwestward winds. In the dry season the along shelfcirculation is mostly driven by wind forcing, while in the rainy season, the circulation is set …

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Dynamic Modeling And Statistical Analysis Of Event Times, Edsel A. Pena Nov 2006

Dynamic Modeling And Statistical Analysis Of Event Times, Edsel A. Pena

Faculty Publications

This review article provides an overview of recent work in the modeling and analysis of recurrent events arising in engineering, reliability, public health, biomedicine and other areas. Recurrent event modeling possesses unique facets making it different and more difficult to handle than single event settings. For instance, the impact of an increasing number of event occurrences needs to be taken into account, the effects of covariates should be considered, potential association among the interevent times within a unit cannot be ignored, and the effects of performed interventions after each event occurrence need to be factored in. A recent general class …

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An Improved Distance Heuristic Function For Directed Software Model Checking, Eric G. Mercer, Neha Rungta Nov 2006

An Improved Distance Heuristic Function For Directed Software Model Checking, Eric G. Mercer, Neha Rungta

Faculty Publications

State exploration in directed software model checking is guided using a heuristic function to move states near errors to the front of the search queue. Distance heuristic functions rank states based on the number of transitions needed to move the current program state into an error location. Lack of calling context information causes the heuristic function to underestimate the true distance to the error; however, inlining functions at call sites in the control flow graph to capture calling context leads to an exponential growth in the computation. This paper presents a new algorithm that implicitly inlines functions at call sites …

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Ordering Tendencies In The Binary Alloys Of Rh, Pd, Ir, And Pt: Density Functional Calculations, Gus L. W. Hart, Brian Kolb, Stefan Müller, David B. Botts Oct 2006

Ordering Tendencies In The Binary Alloys Of Rh, Pd, Ir, And Pt: Density Functional Calculations, Gus L. W. Hart, Brian Kolb, Stefan Müller, David B. Botts

Faculty Publications

The binary alloys of Rh, Pd, Ir, and Pt are important because of their high catalytic potential. We report in this paper that the Rh1-xIrx and Rh1-xPtx systems, long thought to phase separate at low temperatures, actually exhibit miscibility over the entire concentration and temperature range. We find low critical ordering temperatures, indicating that long-range order is unlikely to be observed experimentally. These results are compared with previous theoretical predications for the other binary alloys of Rh, Pd, Ir, and Pt and with calculations performed here on the Pt1-xIrx and Pd1-xIrx systems. We discuss these results and investigate the mechanisms …

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Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson Oct 2006

Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson

Faculty Publications

We examine consequences of the non-Boltzmann nature of probability distributions for one-particle kinetic energy, momentum, and velocity for finite systems of classical hard spheres with constant total energy and nonidentical masses. By comparing two cases, reflecting walls (NVE or microcanonical ensemble) and periodic boundaries (NVEPG or molecular dynamics ensemble), we describe three consequences of the center-of-mass constraint in periodic boundary conditions: the equipartition theorem no longer holds for unequal masses, the ratio of the average relative velocity to the average velocity is increased by a factor of [N/(N–1)]^1/2, and the ratio of average collision energy to average kinetic energy is …

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Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell Oct 2006

Effects Of Gap Open And Gap Extension Penalties, Hyrum Carroll, Mark J. Clement, Perry Ridge, Quinn O. Snell

Faculty Publications

Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence alignment, and consequently on phylogeny scores are not as well understood. We use exhaustive phylogeny searching to explore the effects of varying the gap open and gap extension penalties for three nuclear ribosomal data sets. Particular attention is given to optimal phylogeny scores for 200 alignments of a range of gap open and gap extension penalties and their respective …

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Large Grain Size Stochastic Optimization Alignment, Hyrum Carroll, Mark J. Clement, Perry Ridge, Dan Sneddon, Quinn O. Snell Oct 2006

Large Grain Size Stochastic Optimization Alignment, Hyrum Carroll, Mark J. Clement, Perry Ridge, Dan Sneddon, Quinn O. Snell

Faculty Publications

DNA sequence alignment is a critical step in identifying homology between organisms. The most widely used alignment program, ClustalW, is known to suffer from the local minima problem, where suboptimal guide trees produce incorrect gap insertions. The optimization alignment approach, has been shown to be effective in combining alignment and phylogenetic search in order to avoid the problems associated with poor guide trees. The optimization alignment algorithm operates at a small grain size, aligning each tree found, wasting time producing multiple sequence alignments for suboptimal trees. This research develops and analyzes a large grain size algorithm for optimization alignment that …

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