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Using SPARK as a Solver for Modelica

Description: Modelica is an object-oriented acausal modeling language that is well positioned to become a de-facto standard for expressing models of complex physical systems. To simulate a model expressed in Modelica, it needs to be translated into executable code. For generating run-time efficient code, such a translation needs to employ algebraic formula manipulations. As the SPARK solver has been shown to be competitive for generating such code but currently cannot be used with the Modelica language, we report in this paper how SPARK's symbolic and numerical algorithms can be implemented in OpenModelica, an open-source implementation of a Modelica modeling and simulation environment. We also report benchmark results that show that for our air flow network simulation benchmark, the SPARK solver is competitive with Dymola, which is believed to provide the best solver for Modelica.
Date: June 30, 2008
Creator: Wetter, Michael; Wetter, Michael; Haves, Philip; Moshier, Michael A. & Sowell, Edward F.
Partner: UNT Libraries Government Documents Department
open access

Image-Based Modeling Reveals Dynamic Redistribution of DNA Damageinto Nuclear Sub-Domains

Description: Several proteins involved in the response to DNA doublestrand breaks (DSB) f orm microscopically visible nuclear domains, orfoci, after exposure to ionizing radiation. Radiation-induced foci (RIF)are believed to be located where DNA damage occurs. To test thisassumption, we analyzed the spatial distribution of 53BP1, phosphorylatedATM, and gammaH2AX RIF in cells irradiated with high linear energytransfer (LET) radiation and low LET. Since energy is randomly depositedalong high-LET particle paths, RIF along these paths should also berandomly distributed. The probability to induce DSB can be derived fromDNA fragment data measured experimentally by pulsed-field gelelectrophoresis. We used this probability in Monte Carlo simulations topredict DSB locations in synthetic nuclei geometrically described by acomplete set of human chromosomes, taking into account microscope opticsfrom real experiments. As expected, simulations produced DNA-weightedrandom (Poisson) distributions. In contrast, the distributions of RIFobtained as early as 5 min after exposure to high LET (1 GeV/amu Fe) werenon-random. This deviation from the expected DNA-weighted random patterncan be further characterized by "relative DNA image measurements." Thisnovel imaging approach shows that RIF were located preferentially at theinterface between high and low DNA density regions, and were morefrequent than predicted in regions with lower DNA density. The samepreferential nuclear location was also measured for RIF induced by 1 Gyof low-LET radiation. This deviation from random behavior was evidentonly 5 min after irradiation for phosphorylated ATM RIF, while gammaH2AXand 53BP1 RIF showed pronounced deviations up to 30 min after exposure.These data suggest that DNA damage induced foci are restricted to certainregions of the nucleus of human epithelial cells. It is possible that DNAlesions are collected in these nuclear sub-domains for more efficientrepair.
Date: August 3, 2007
Creator: Costes Sylvain V.; Ponomarev, Artem; Chen, James L.; Nguyen, David; Cucinotta, Francis A. & Barcellos-Hoff, Mary Helen
Partner: UNT Libraries Government Documents Department
open access

Horizontal gene transfer and the evolution of transcriptionalregulation in Escherichia coli

Description: Background: Most bacterial genes were acquired by horizontalgene transfer from other bacteria instead of being inherited bycontinuous vertical descent from an ancient ancestor}. To understand howthe regulation of these {acquired} genes evolved, we examined theevolutionary histories of transcription factors and of regulatoryinteractions from the model bacterium Escherichia coli K12. Results:Although most transcription factors have paralogs, these usually arose byhorizontal gene transfer rather than by duplication within the E. colilineage, as previously believed. In general, most neighbor regulators --regulators that are adjacent to genes that they regulate -- were acquiredby horizontal gene transfer, while most global regulators evolvedvertically within the gamma-Proteobacteria. Neighbor regulators wereoften acquired together with the adjacent operon that they regulate, sothe proximity might be maintained by repeated transfers (like "selfishoperons"). Many of the as-yet-uncharacterized (putative) regulators havealso been acquired together with adjacent genes, so we predict that theseare neighbor regulators as well. When we analyzed the histories ofregulatory interactions, we found that the evolution of regulation byduplication was rare, and surprisingly, many of the regulatoryinteractions that are shared between paralogs result from convergentevolution. Another surprise was that horizontally transferred genes aremore likely than other genes to be regulated by multiple regulators, andmost of this complex regulation probably evolved after the transfer.Conclusions: Our results highlight the rapid evolution of niche-specificgene regulation in bacteria.
Date: December 20, 2007
Creator: Price, Morgan N.; Dehal, Paramvir S. & Arkin, Adam P.
Partner: UNT Libraries Government Documents Department
open access

BDDC for nonsymmetric positive definite and symmetric indefinite problems

Description: The balancing domain decomposition methods by constraints are extended to solving both nonsymmetric, positive definite and symmetric, indefinite linear systems. In both cases, certain nonstandard primal constraints are included in the coarse problems of BDDC algorithms to accelerate the convergence. Under the assumption that the subdomain size is small enough, a convergence rate estimate for the GMRES iteration is established that the rate is independent of the number of subdomains and depends only slightly on the subdomain problem size. Numerical experiments for several two-dimensional examples illustrate the fast convergence of the proposed algorithms.
Date: December 10, 2008
Creator: Tu, Xuemin & Li, Jing
Partner: UNT Libraries Government Documents Department
open access

LOWER BOUNDS ON SELF-FOCUSING SO AS TO MAINTAIN RING INTEGRITY NEAR THE INITIATION OF ACCELERATION IN AN ELECTRON RING ACCELERATOR

Description: Relationships necessary for ring stability are derived between the self-focusing forces of an electron ring and the magnetic field gradient defocusing forces present near and just subsequent to the start of ring acceleration.
Date: April 16, 1970
Creator: Pellegrini, Claudio & Sessler, Andrew.
Partner: UNT Libraries Government Documents Department
open access

Measurement of Fast Voltage Transients in High-Performance Nb3Sn Magnets

Description: The Superconducting Magnet group at Lawrence Berkeley National Laboratory has been developing Nb{sub 3}Sn high-field accelerator magnet technology for the last fifteen years. In order to support the magnet R&D effort, we are developing a diagnostic system that can help identify the causes of performance limiting quenches by recording small flux-changes within the magnet prior to quench-onset. These analysis techniques were applied to the test results from recent Nb{sub 3}Sn magnets. This paper will examine various types of events and their distinguishing characteristics. The present measurement techniques are discussed along with the design of a new data acquisition system that will substantially improve the quality of the recorded signals.
Date: June 1, 2008
Creator: Lietzke, A. F.; Sabbi, G. L.; Ferracin, P.; Caspi, S.; Zimmerman, S.; Joseph, J. et al.
Partner: UNT Libraries Government Documents Department
open access

Mechanical and charge transport properties of alkanethiol self-assembled monolayers on Au (111) surface: The Role of Molecular Tilt

Description: The relationship between charge transport and mechanical properties of alkanethiol self-assembled monolayers (SAM) on Au(111) films has been investigated using an atomic force microscope with a conductive tip. Molecular tilts induced by the pressure applied by the tip cause stepwise increases in film conductivity. A decay constant {beta} = 0.57 {+-} 0.03 {angstrom}{sup -1} was found for the current passing through the film as a function of tip-substrate separation due to this molecular tilt. This is significantly smaller than the value of {approx} 1 {angstrom}{sup -1} found when the separation is changed by changing the length of the alkanethiol molecules. Calculations indicate that for isolated dithiol molecules S-bonded to hollow sites, the junction conductance does not vary significantly as a function of molecular tilt. The impact of S-Au bonding on SAM conductance is discussed.
Date: November 12, 2007
Creator: Mulleregan, Alice; Qi, Yabing; Ratera, Imma; Park, Jeong Y.; Ashby, Paul D.; Quek, Su Ying et al.
Partner: UNT Libraries Government Documents Department
open access

THz radiation as a bunch diagnostic forlaser-wakefield-accelerated electron bunches

Description: Experimental results are reported from two measurementtechniques (semiconductor switching and electro-optic sampling) thatallow temporal characterization of electron bunches produced by alaser-driven plasma-based accelerator. As femtosecond electron bunchesexit the plasma-vacuum interface, coherent transition radiation (at THzfrequencies) is emitted. Measuring the properties of this radiationallows characterization of the electron bunches. Theoretical work on theemission mechanism is represented, including a model that calculates theTHz waveform from a given bunch profile. It is found that the spectrum ofthe THz pulse is coherent up to the 200 mu m thick crystal (ZnTe)detection limit of 4 THz, which corresponds to the production of sub-50fs (root-mean-square) electron bunch structure. The measurementsdemonstrate both the shot-to-shot stability of bunch parameters that arecritical to THz emission (such as total charge and bunch length), as wellas femtosecond synchrotron between bunch, THz pulse, and laserbeam.
Date: February 15, 2006
Creator: van Tilborg, J.; Schroeder, C. B.; Filip, C. V.; Toth, Cs.; Geddes, C. G. R.; Fubiani, G. et al.
Partner: UNT Libraries Government Documents Department
open access

Three-dimensional lithographically-defined organotypic tissue arrays for quantitative analysis of morphogenesis and neoplastic progression

Description: Here we describe a simple micromolding method to construct three-dimensional arrays of organotypic epithelial tissue structures that approximate in vivo histology. An elastomeric stamp containing an array of posts of defined geometry and spacing is used to mold microscale cavities into the surface of type I collagen gels. Epithelial cells are seeded into the cavities and covered with a second layer of collagen. The cells reorganize into hollow tissues corresponding to the geometry of the cavities. Patterned tissue arrays can be produced in 3-4 h and will undergo morphogenesis over the following one to three days. The protocol can easily be adapted to study a variety of tissues and aspects of normal and neoplastic development.
Date: February 13, 2008
Creator: Nelson, Celeste M.; Inman, Jamie L. & Bissell, Mina J.
Partner: UNT Libraries Government Documents Department
open access

A RESONANCE IN THE Lambda pi SYSTEM

Description: The authors report a study of the reaction K{sup -} + p {yields} {Lambda}{sup 0} + {pi}{sup +} + {pi}{sup -} produced by 1.15 Gev/c K{sup -} mesons and observed in the Lawrence Radiation Laboratory's 15-in. hydrogen bubble chamber. A preliminary report of these results was presented at the 1960 Rochester Conference. The beam was purified by two velocity spectrometers. A hyperon/observed during the run and the preliminary cross sections for various K{sup -} reactions at 1.15 Bev/c have been reported previously. Reaction (1) was the first one selected for detailed study, because it appeared to take place with relatively large probability and because the event, a 2-prong interaction accompanied by a V, was easily identified. In a volume of the chamber sufficiently restricted so that the scanning efficiency was near 100%, 255 such events were found. These events were measured, and the track data supplied to a computer which tested each event for goodness of fit to various kinematic hypotheses. The possible reactions, the distribution of events, and the corresponding cross sections are given in Table I. An event was placed in a given category of Table I if the {chi}{sup 2} probability for the other hypotheses was < 1%. It appears likely that the majority of the events in group(e) are also reactions of type (I). This belief is based on the following arguments: (1) since the kinematics of a {Lambda} {pi}{pi} fit (four constraints) are more overdetermined than those of a {Sigma}{sup 0} {pi}{pi} fit(two constraints), it is relatively easy for a {Lambda} {pi}{pi} reaction to fit a {Sigma}{sup 0} {pi}{pi} reaction, but only very few {Sigma}{sup 0} configurations can fit the {Lambda} {pi}{pi} reactions. (2) The events of group(e) when treated as {Sigma}{sup 0} {pi}{pi} reactions give a {chi}{sup 2} distribution which is much worse than …
Date: October 24, 1960
Creator: Alston, Margaret; Alvarez, Luis W.; Eberhard, Philippe & Wojcicki, Stanley G.
Partner: UNT Libraries Government Documents Department
open access

Resonant Soft X-Ray Contrast Variation Methods as Composition-Specific Probes of Thin Polymer Film Structure

Description: We have developed complementary soft x-ray scattering and reflectometry techniques that allow for the morphological analysis of thin polymer films without resorting to chemical modification or isotopic 2 labeling. With these techniques, we achieve significant, x-ray energy-dependent contrast between carbon atoms in different chemical environments using soft x-ray resonance at the carbon edge. Because carbon-containing samples absorb strongly in this region, the scattering length density depends on both the real and imaginary parts of the atomic scattering factors. Using a model polymer film of poly(styrene-b-methyl methacrylate), we show that the soft x-ray reflectivity data is much more sensitive to these atomic scattering factors than the soft x-ray scattering data. Nevertheless, fits to both types of data yield useful morphological details on the polymer?slamellar structure that are consistent with each other and with literature values.
Date: April 4, 2008
Creator: Welch, Cynthia; Welch, Cynthia F.; Hjelm, Rex P.; Mang, Joseph T.; Hawley, Marilyn E.; Wrobleski, Debra A. et al.
Partner: UNT Libraries Government Documents Department
open access

Magnet R&D for the US LHC Accelerator Research Program (LARP)

Description: In 2004, the US DOE established the LHC Accelerator Research Program (LARP) with the goal of developing a technology base for future upgrades of the LHC. The focus of the magnet program, which is a collaboration of three US laboratories, BNL, FNAL and LBNL, is on development of high gradient quadrupoles using Nb{sub 3}Sn superconductor. Other program components address issues regarding magnet design, radiation-hard materials, long magnet scale-up, quench protection, fabrication techniques and conductor and cable R&amp;D. This paper presents an overall view of the program with emphasis on the current quadrupole project and outlines the long-term goals of the program.
Date: June 1, 2006
Creator: Gourlay, S. A.; Ambrosio, G.; Andreev, N.; Anerella, M.; Barzi, E.; Bossert, R. et al.
Partner: UNT Libraries Government Documents Department
open access

X-ray spectroscopic study of the charge state and local orderingof room-temperature ferromagnetic Mn oped ZnO

Description: The charge state and local ordering of Mn doped into a pulsed laser deposited single-phase thin film of ZnO are investigated by using X-ray absorption spectroscopy at the O K-, Mn K- and L-edges, and X-ray emission spectroscopy at the O K- and Mn L-edge. This film is found to be ferromagnetic at room temperature. EXAFS measurement shows that Mn{sup 2+} replaces Zn site in tetrahedral symmetry, and there is no evidence for either metallic Mn or MnO in the film. Upon Mn doping, the top of O 2p valence band extends into the bandgap indicating additional charge carries being created.
Date: August 7, 2007
Creator: Guo, J.-H.; Gupta, Amita; Sharma, Parmanand; Rao, K.V.; Marcus,M.A.; Dong, C.L. et al.
Partner: UNT Libraries Government Documents Department
open access

Evolution of the Surface Science of Catalysis from Single Crystals to Metal Nanoparticles under Pressure

Description: Vacuum studies of metal single crystal surfaces using electron and molecular beam scattering revealed that the surface atoms relocate when the surface is clean (reconstruction) and when it is covered by adsorbates (adsorbate induced restructuring). It was also discovered that atomic steps and other low coordination surface sites are active for breaking chemical bonds (H-H, O=O, C-H, C=O and C-C) with high reaction probability. Investigations at high reactant pressures using sum frequency generation (SFG)--vibrational spectroscopy and high pressure scanning tunneling microscopy (HPSTM) revealed bond breaking at low reaction probability sites on the adsorbate-covered metal surface, and the need for adsorbate mobility for continued turnover. Since most catalysts (heterogeneous, enzyme and homogeneous) are nanoparticles, colloid synthesis methods were developed to produce monodispersed metal nanoparticles in the 1-10 nm range and controlled shapes to use them as new model catalyst systems in two-dimensional thin film form or deposited in mesoporous three-dimensional oxides. Studies of reaction selectivity in multipath reactions (hydrogenation of benzene, cyclohexene and crotonaldehyde) showed that reaction selectivity depends on both nanoparticle size and shape. The oxide-metal nanoparticle interface was found to be an important catalytic site because of the hot electron flow induced by exothermic reactions like carbon monoxide oxidation.
Date: March 6, 2008
Creator: Somorjai, Gabor A. & Park, Jeong Y.
Partner: UNT Libraries Government Documents Department
open access

NERSC News

Description: This month's issue has the following 3 articles: (1) Kathy Yelick is the new director for the National Energy Research Scientific Computing Center (NERSC); (2) Head of the Class--A cray XT4 named Franklin passes a rigorous test and becomes an official member of the NERSC supercomputing family; and (3) Model Comparisons--Fusion research group published several recent papers examining the results of two types of turbulence simulations and their impact on tokamak designs.
Date: November 25, 2007
Creator: Wang, Ucilia
Partner: UNT Libraries Government Documents Department
open access

CARBON-13 NMR STUDIES OF LIQUID CRYSTALS

Description: High resolution, proton decoupled {sup 13}C nmr are observed for a series of neat nematic liquid crystals, the p-alkoxyazoxybenzenes, and a smectic-A liquid crystal, diethylazoxydibenzoate in a magnetic field of 23 kG. The (uniaxial) order parameters S = &lt;P{sub 2}(cos{theta})&gt; are found to be about 0.4 and 0.9 for the nematic and smectic-A phase respectively at the clearing points. The order parameter increases with decreasing temperature in the nematic phase but is constant, or nearly so, with temperature in the smectic-A phase. In the nematic series studied, the ordering exhibits an even-odd alternation along the series and qualitative agreement with a recent theory due to Marcelja is found. In both phases, the spectra show that the molecule rotates rapidly about its long axis. Tentative conclusions about molecular conformational motion and {sup 14}N spin relaxation are presented for both nematic and smectic-A phases. In the smectic-A phase, the sample is rotated about an axis perpendicular to H{sub 0} and the resulting spectra are discussed. The theory of observed chemical shifts in liquid crystals is treated in an appendix. Equations are derived which relate the nmr spectra of liquid-crystals to the order parameters. A model for the smectic-C phase due to Luz and Meiboom and Doane is described and lineshapes are determined on the basis of this model for special cases. Experiments on smectic-C liquid crystals are currently underway for comparison with the theory. Also treated in an appendix is the dependence of the order parameters on the molecular potential which give rise to the various degrees of order in the different liquid crystalline phases. To a good approximation the functional dependence of the order parameters on the molecular potential is shown to be a simple one in the limit of small tilt angle in the smectic-C phase.
Date: June 1, 1975
Creator: Allison, Stuart
Partner: UNT Libraries Government Documents Department
open access

Breaking the Curse of Cardinality on Bitmap Indexes

Description: Bitmap indexes are known to be efficient for ad-hoc range queries that are common in data warehousing and scientific applications. However, they suffer from the curse of cardinality, that is, their efficiency deteriorates as attribute cardinalities increase. A number of strategies have been proposed, but none of them addresses the problem adequately. In this paper, we propose a novel binned bitmap index that greatly reduces the cost to answer queries, and therefore breaks the curse of cardinality. The key idea is to augment the binned index with an Order-preserving Bin-based Clustering (OrBiC) structure. This data structure significantly reduces the I/O operations needed to resolve records that cannot be resolved with the bitmaps. To further improve the proposed index structure, we also present a strategy to create single-valued bins for frequent values. This strategy reduces index sizes and improves query processing speed. Overall, the binned indexes with OrBiC great improves the query processing speed, and are 3 - 25 times faster than the best available indexes for high-cardinality data.
Date: April 4, 2008
Creator: Wu, Kesheng; Wu, Kesheng; Stockinger, Kurt & Shoshani, Arie
Partner: UNT Libraries Government Documents Department
open access

Summary of Workshop: Barriers to Energy Efficient Residential Ventilation

Description: The objectives for this workshop were to bring together those with different viewpoints on the implementation of energy efficient ventilation in homes to share their perspectives. The primary benefit of the workshop is to allow the participants to get a broader understanding of the issues involved and thereby make themselves more able to achieve their own goals in this area. In order to achieve this objective each participant was asked to address four objectives from their point of view: (1) Drivers for energy efficient residential ventilation: Why is this an important issue? Who cares about it? Where is the demand: occupants, utilities, regulation, programs, etc? What does sustainability mean in this context? (2) Markets & Technologies: What products, services and systems are out there? What kinds of things are in the pipeline? What is being installed now? Are there regional or other trends? What are the technology interactions with other equipment and the envelope? (3) Barriers to Implementation: What is stopping decision makers from implementing energy-efficient residential ventilation systems? What kind of barriers are there: technological, cost, informational, structural, etc. What is the critical path? (4) Solutions: What can be done to overcome the barriers and how can/should we do it? What is the role of public vs. private institutions? Where can investments be made to save energy while improving the indoor environment? Ten participants prepared presentations for the workshop. Those presentations are included in sections at the end of this workshop report. These presentations provided the principal context for the discussions that happened during the workshop. Critical path issues were raised and potential solutions discussed during the workshop. As a secondary objective they have listed key issues and some potential consensus items which resulted from the discussions.
Date: January 10, 2008
Creator: Sherman, Max & Sherman, Max
Partner: UNT Libraries Government Documents Department
open access

Surface species formed by the adsorption and dissociation of water molecules on Ru(0001) surface containing a small coverage of carbon atoms studied by scanning tunneling microscopy

Description: The adsorption and dissociation of water on a Ru(0001) surface containing a small amount ({le} 3 %) of carbon impurities was studied by scanning tunneling microscopy (STM). Various surface species are formed depending on the temperature. These include molecular H{sub 2}O, H{sub 2}O-C complexes, H, O, OH and CH. Clusters of either pure H{sub 2}O or mixed H{sub 2}O-OH species are also formed. Each of these species produces a characteristic contrast in the STM images and can be identified by experiment and by ab initio total energy calculations coupled with STM image simulations. Manipulation of individual species via excitation of vibrational modes with the tunneling electrons has been used as supporting evidence.
Date: April 26, 2008
Creator: UCB, Dept of Materials Science and Engineering
Partner: UNT Libraries Government Documents Department
open access

Compensatory Paracrine Mechanisms That Define The Urothelial Response to Injury in Partial Bladder Outlet Obstruction

Description: Diseases and conditions affecting the lower urinary tract are a leading cause of dysfunctional sexual health, incontinence, infection, and kidney failure. The growth, differentiation, and repair of the bladder&#39;s epithelial lining are regulated, in part, by fibroblast growth factor (FGF)-7 and -10 via a paracrine cascade originating in the mesenchyme (lamina propria) and targeting the receptor for FGF-7 and -10 within the transitional epithelium (urothelium). The FGF-7 gene is located at the 15q15-q21.1 locus on chromosome 15 and four exons generate a 3.852-kb mRNA. Five duplicated FGF-7 gene sequences that localized to chromosome 9 were predicted not to generate functional protein products, thus validating the use of FGF-7-null mice as an experimental model. Recombinant FGF-7 and -10 induced proliferation of human urothelial cells in vitro and transitional epithelium of wild-type and FGF-7-null mice in vivo.To determine the extent that induction of urothelial cell proliferation during the bladder response to injury is dependent on FGF-7, an animal model of partial bladder outlet obstruction was developed. Unbiased stereology was used to measure the percentage of proliferating urothelial cells between obstructed groups of wild-type and FGF-7-null mice. The stereological analysis indicated that a statistical significant difference did not exist between the two groups, suggesting that FGF-7 is not essential for urothelial cell proliferation in response to partial outlet obstruction. In contrast, a significant increase in FGF-10 expression was observed in the obstructed FGF-7-null group, indicating that the compensatory pathway that functions in this model results in urothelial repair.
Date: June 21, 2007
Creator: Bassuk, James; Lendvay, Thomas S.; Sweet, Robert; Han, Chang-Hee; Soygur, Tarkan; Cheng, Jan-Fang et al.
Partner: UNT Libraries Government Documents Department
open access

Control of the Magnetic and Magnetotransport Properties of La0.67Sr0.33MnO3 Thin Films Through Epitaxial Strain

Description: The influence of epitaxial strain, in the form of tetragonal distortions, on the magnetic and magnetotransport properties of La{sub 0.67}Sr{sub 0.33}MnO{sub 3} thin films was studied. The tetragonal distortion (c/a ratio) was modulated through the choice of the substrate, ranging from c/a=1.007 on (001)-oriented (LaAlO{sub 3}){sub 0.3}(Sr{sub 2}AlTaO{sub 6}){sub 0.7} substrates to 0.952 on (110)-oriented GdScO{sub 3} substrates. In agreement with previous theoretical predictions, these large values of tensile strain cause the Curie temperature and the saturation magnetization to decrease, alter the temperature dependence of the resistivity and magnetoresistance, and increase the resistivity several orders of magnitude.
Date: December 20, 2007
Creator: Arenholz, Elke; Takamura, Y.; Chopdekar, R.V.; Arenholz, E. & Suzuki, Y.
Partner: UNT Libraries Government Documents Department
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