Showing papers by "Sandia National Laboratories published in 2005"

Visualizing knowledge domains

Abstract: L'A. passe en revue les techniques de visualisation utilisees pour representer de facon cartographique la structure de domaine des disciplines scientifiques, et pour soutenir la recherche d'information et la classification. Un bref historique montre que la visualisation des domaines de connaissances s'enracine dans des disciplines telles que la scientometrie, la bibliometrie et l'analyse de citations, ainsi que la visualisation scientifique. L'A. analyse les principales etapes du processus de visualisation des domaines de connaissances : unites d'analyse, mesures, similarites entre unites. Differentes techniques couramment utilisees pour l'analyse et la visualisation des connaissances sont passees en revue : techniques de reduction de la dimensionnalite, analyse par clusters, configuration spatiale, visualisation et conception d'interaction. Differentes approches sont appliquees pour engendrer et comparer diverses representations cartographiques de la recherche sur la visualisation des domaines de connaissances. Ces cartes mettent en valeur les relations entre l'analyse de citations, la bibliometrie, la semantique et la visualisation de l'information. Augmenter l'accessibilite de la visualisation des domaines aupres des non-experts, appliquer la visualisation des domaines de connaissances pour mieux repondre a des questions pragmatiques, favoriser la collaboration et la diffusion des resultats entre chercheurs, developper des algorithmes plus robustes, comptent parmi les directions de recherche les plus prometteuses.

Synthesis, Properties, and Applications of Iron Nanoparticles

Abstract: Iron, the most ubiquitous of the transition metals and the fourth most plentiful element in the Earth's crust, is the structural backbone of our modern infrastructure. It is therefore ironic that as a nanoparticle, iron has been somewhat neglected in favor of its own oxides, as well as other metals such as cobalt, nickel, gold, and platinum. This is unfortunate, but understandable. Iron's reactivity is important in macroscopic applications (particularly rusting), but is a dominant concern at the nanoscale. Finely divided iron has long been known to be pyrophoric, which is a major reason that iron nanoparticles have not been more fully studied to date. This extreme reactivity has traditionally made iron nanoparticles difficult to study and inconvenient for practical applications. Iron however has a great deal to offer at the nanoscale, including very potent magnetic and catalytic properties. Recent work has begun to take advantage of iron's potential, and work in this field appears to be blossoming.

An overview of the Trilinos project

Abstract: The Trilinos Project is an effort to facilitate the design, development, integration, and ongoing support of mathematical software libraries within an object-oriented framework for the solution of large-scale, complex multiphysics engineering and scientific problems. Trilinos addresses two fundamental issues of developing software for these problems: (i) providing a streamlined process and set of tools for development of new algorithmic implementations and (ii) promoting interoperability of independently developed software.Trilinos uses a two-level software structure designed around collections of packages. A Trilinos package is an integral unit usually developed by a small team of experts in a particular algorithms area such as algebraic preconditioners, nonlinear solvers, etc. Packages exist underneath the Trilinos top level, which provides a common look-and-feel, including configuration, documentation, licensing, and bug-tracking.Here we present the overall Trilinos design, describing our use of abstract interfaces and default concrete implementations. We discuss the services that Trilinos provides to a prospective package and how these services are used by various packages. We also illustrate how packages can be combined to rapidly develop new algorithms. Finally, we discuss how Trilinos facilitates high-quality software engineering practices that are increasingly required from simulation software.

Mapping the backbone of science

Abstract: This paper presents a new map representing the structure of all of science, based on journal articles, including both the natural and social sciences. Similar to cartographic maps of our world, the map of science provides a bird’s eye view of today’s scientific landscape. It can be used to visually identify major areas of science, their size, similarity, and interconnectedness. In order to be useful, the map needs to be accurate on a local and on a global scale. While our recent work has focused on the former aspect 1 , this

Biochemistry: a cadmium enzyme from a marine diatom.

Abstract: The ocean biota contains a vast reservoir of genomic diversity. Here we present the sequence and preliminary characterization of a protein that is a cadmium-containing carbonic anhydrase from the marine diatom Thalassiosira weissflogii. The existence of a cadmium enzyme in marine phytoplankton may indicate that there is a unique selection pressure for metalloenzymes in the marine environment, and our discovery provides a long-awaited explanation for the nutrient-like behaviour of cadmium in the oceans.

Functional designed to include surface effects in self-consistent density functional theory

Abstract: We design a density-functional-theory (DFT) exchange-correlation functional that enables an accurate treatment of systems with electronic surfaces. Surface-specific approximations for both exchange and correlation energies are developed. A subsystem functional approach is then used: an interpolation index combines the surface functional with a functional for interior regions. When the local density approximation is used in the interior, the result is a straightforward functional for use in self-consistent DFT. The functional is validated for two metals (Al, Pt) and one semiconductor (Si) by calculations of (i) established bulk properties (lattice constants and bulk moduli) and (ii) a property where surface effects exist (the vacancy formation energy). Good and coherent results indicate that this functional may serve well as a universal first choice for solid-state systems and that yet improved functionals can be constructed by this approach.

The role of van der Waals forces in adhesion of micromachined surfaces

Abstract: Interfacial adhesion and friction are important factors in determining the performance and reliability of microelectro- mechanical systems. We demonstrate that the adhesion of micromachined surfaces is in a regime not considered by standard rough surface adhesion models. At small roughness values, our experiments and models show unambiguously that the adhesion is mainly due to van der Waals dispersion forces acting across extensive non-contacting areas and that it is related to 1/Dave2, where Dave is the average surface separation. These contributions must be considered because of the close proximity of the surfaces, which is a result of the planar deposition technology. At large roughness values, van der Waals forces at contacting asperities become the dominating contributor to the adhesion. In this regime our model calculations converge with standard models in which the real contact area determines the adhesion. We further suggest that topographic correlations between the upper and lower surfaces must be considered to understand adhesion completely.

Operation of terahertz quantum-cascade lasers at 164 K in pulsed mode and at 117 K in continuous-wave mode.

Abstract: We report the demonstration of a terahertz quantum-cascade laser that operates up to 164 K in pulsed mode and 117 K in continuous-wave mode at approximately 3.0 THz. The active region was based on a resonant-phonon depopulation scheme and a metal-metal waveguide was used for modal confinement. Copper to copper thermocompression wafer bonding was used to fabricate the waveguide, which displayed improved thermal properties compared to a previous indium-gold bonding method.

Unravelling combustion mechanisms through a quantitative understanding of elementary reactions

Abstract: This review of the role of reaction kinetics in combustion chemistry traces the historical evolution and present state of qualitative and quantitative understanding of a number of reaction systems. Starting from the H2–O2 system, in particular from the reaction between H and O2, mechanisms and key reactions for soot formation, for the appearance of NOx, and for processes of peroxy radicals in hydrocarbon oxidation are illustrated. The struggle for precise rate constants on the experimental and theoretical side is demonstrated for the example of the reaction H + O2 → OH + O. The intrinsic complexity of complex-forming bimolecular reactions, such as observed even in this reaction, also dominates most other key reactions of the systems considered and can be unravelled only with the help of quantum-chemical methods. The multi-channel character of these reactions often also requires the combination with master equation codes. Although kinetics provides an already impressive database for quantitative modelling of simple combustion systems, considerable effort is still required to quantitatively account for the complexities of more complicated fuel oxidation processes.

Predicting protein--protein interactions using signature products

Abstract: Motivation: Proteome-wide prediction of protein--protein interaction is a difficult and important problem in biology. Although there have been recent advances in both experimental and computational methods for predicting protein--protein interactions, we are only beginning to see a confluence of these techniques. In this paper, we describe a very general, high-throughput method for predicting protein--protein interactions. Our method combines a sequence-based description of proteins with experimental information that can be gathered from any type of protein--protein interaction screen. The method uses a novel description of interacting proteins by extending the signature descriptor, which has demonstrated success in predicting peptide/protein binding interactions for individual proteins. This descriptor is extended to protein pairs by taking signature products. The signature product is implemented within a support vector machine classifier as a kernel function. Results: We have applied our method to publicly available yeast, Helicobacter pylori, human and mouse datasets. We used the yeast and H.pylori datasets to verify the predictive ability of our method, achieving from 70 to 80% accuracy rates using 10-fold cross-validation. We used the human and mouse datasets to demonstrate that our method is capable of cross-species prediction. Finally, we reused the yeast dataset to explore the ability of our algorithm to predict domains. Contact:smartin@sandia.gov.

VisTrails: enabling interactive multiple-view visualizations

Abstract: VisTrails is a new system that enables interactive multiple-view visualizations by simplifying the creation and maintenance of visualization pipelines, and by optimizing their execution. It provides a general infrastructure that can be combined with existing visualization systems and libraries. A key component of VisTrails is the visualization trail (vistrail), a formal specification of a pipeline. Unlike existing dataflow-based systems, in VisTrails there is a clear separation between the specification of a pipeline and its execution instances. This separation enables powerful scripting capabilities and provides a scalable mechanism for generating a large number of visualizations. VisTrails also leverages the vistrail specification to identify and avoid redundant operations. This optimization is especially useful while exploring multiple visualizations. When variations of the same pipeline need to be executed, substantial speedups can be obtained by caching the results of overlapping subsequences of the pipelines. In this paper, we describe the design and implementation of VisTrails, and show its effectiveness in different application scenarios.

The Influence of Charge Dilution and Injection Timing on Low-Temperature Diesel Combustion and Emissions

Abstract: The effects of charge dilution on low-temperature diesel combustion and emissions were investigated in a small-bore single-cylinder diesel engine over a wide range of injection timing. The fresh air was diluted with additional N 2 and CO 2 , simulating 0 to 65% exhaust gas recirculation in an engine. Diluting the intake charge lowers the flame temperature T due to the reactant being replaced by inert gases with increased heat capacity. In addition, charge dilution is anticipated to influence the local charge equivalence ratio Φ prior to ignition due to the lower O 2 concentration and longer ignition delay periods. By influencing both Φ and T, charge dilution impacts the path representing the progress of the combustion process in the Φ-T plane, and offers the potential of avoiding both soot and NO x formation. In-cylinder pressure measurements, exhaust-gas emissions, and imaging of combustion luminosity were performed to clarify the path of the combustion process and the effects of charge dilution and injection timing on combustion and fuel conversion efficiency. Based on the findings, a postulated combustion process in the Φ-T plane is presented for different dilution levels and injection timings. Although the ignition delay increased with high dilution and early injection, the heat release analysis indicated that a large portion of the combustion and emissions formation processes was still dominated by the mixing-controlled phase rather than the premixed phase. Because of the incomplete premixing, and the need to mix a greater volume of charge with unbumed or partially-burned fuel to complete combustion, the diluted mixtures increased CO emissions. Injecting the fuel at earlier timings to extend the ignition delay helped alleviate this problem, but did not eliminate it. Fuel conversion efficiencies calculated for each dilution level and start of injection provide guidance as to the appropriate combustion phasing and practical levels of charge dilution for this low-temperature diesel combustion regime.

Peridynamic modeling of membranes and fibers

Abstract: The peridynamic theory of continuum mechanics allows damage, fracture, and long-range forces to be treated as natural components of the deformation of a material. In this paper, the peridynamic approach is applied to small thickness two- and one-dimensional structures. For membranes, a constitutive model is described appropriate for rubbery sheets that can form cracks. This model is used to perform numerical simulations of the stretching and dynamic tearing of membranes. A similar approach is applied to one-dimensional string like structures that undergrow stretching, bending, and failure. Long-range forces similar to van der Waals interactions at the nanoscale influence the equilibrium configurations of these structures, how they deform, and possibly self-assembly.

The Chemical and Structural Nature of Proton Exchange Membrane Fuel Cell Properties

Abstract: The chemical and structural (morphological) features of proton exchange membranes are directly tied to their fuel cell relevant transport properties. A large body of research has focused on characterizing the structure or investigating the properties of Nafion® and other proton exchange membranes, but few studies have linked chemical composition to membrane morphology, and resulting transport properties. This paper systematically discusses the key chemical and structural features of proton exchange membranes that impact properties critical for fuel cell applications. We focus our discussion on the fuel cell relevant transport properties of proton conductivity, methanol permeability, water diffusion coefficient, and electro-osmotic drag coefficient, using evidence from our work and from the literature to illustrate the connection between structure and properties in these materials. It is hoped that this document will serve as a guide to the rational, systematic design of new proton exchange membrane materials with improved properties.

Relationship Between Ignition Processes and the Lift-Off Length of Diesel Fuel Jets

Abstract: The reaction zone of a diesel fuel jet stabilizes at a location downstream of the fuel injector once the initial autoignition phase is over. This distance is referred to as flame lift-off length. Recent investigations have examined the effects of a wide range of parameters (injection pressure, orifice diameter, and ambient gas temperature, density and oxygen concentration) on lift-off length under quiescent diesel conditions. Many of the experimental trends in lift-off length were in agreement with scaling laws developed for turbulent, premixed flame propagation in gas-jet lifted flames at atmospheric conditions. However, several effects did not correlate with the gas-jet scaling laws, suggesting that other mechanisms could be important to lift-off stabilization at diesel conditions. This paper shows experimental evidence that ignition processes affect diesel lift-off stabilization. Experiments were performed in the same optically-accessible combustion vessel as the previous lift-off research. The experimental results show that the ignition quality of a fuel affects lift-off. Fuels with shorter ignition delays generally produce shorter lift-off lengths. In addition, a cool flame is found upstream of, or near the same axial location as, the quasi-steady lift-off length, indicating that first-stage ignition processes affect lift-off. High-speed chemiluminescence imaging also shows that high-temperature self-ignition occasionallymore » occurs in kernels that are upstream of, and detached from, the high-temperature reaction zone downstream, suggesting that the lift-off stabilization is not by flame propagation into upstream reactants in this instance. Finally, analysis of the previous lift-off length database shows that the time-scale for jet mixing from injector-tip orifice to lift-off length collapses to an Arrhenius-type expression, a common method for describing ignition delay in diesel sprays. This Arrhenius-based lift-off length correlation shows comparable accuracy as a previous power-law fit of the No.2 diesel lift-off length database.« less

Ionomeric Poly(phenylene) Prepared by Diels−Alder Polymerization: Synthesis and Physical Properties of a Novel Polyelectrolyte

Abstract: A series of poly(phenylene)-based polyelectrolytes were synthesized from 1,4-bis(2,4,5-triphenylcyclopentadienone)benzene and 1,4-diethynylbenzene by Diels−Alder polymerization. Postsulfonation of this high molecular weight and thermochemically stable poly(phenylene) with chlorosulfonic acid resulted in homogeneous polyelectrolytes with controllable ion content (IEC = 0.98−2.2 mequiv/g). Fuel cell relevant properties such as high proton conductivity (123 mS/cm), chemical/thermal stability, and film toughness suggest that this polyelectrolyte material shows promise as a potential candidate for polymer electrolyte membrane fuel cells. Physical properties of this material, such as water uptake, thermal stability, and proton conductivity, are reported with respect to ion exchange capacity and compared to Nafion and a series of sulfonated poly(ether sulfone)s.

Active Thermochemical Tables: thermochemistry for the 21st century

Abstract: Active Thermochemical Tables (ATcT) are a good example of a significant breakthrough in chemical science that is directly enabled by the US DOE SciDAC initiative. ATcT is a new paradigm of how to obtain accurate, reliable, and internally consistent thermochemistry and overcome the limitations that are intrinsic to the traditional sequential approach to thermochemistry. The availability of high-quality consistent thermochemical values is critical in many areas of chemistry, including the development of realistic predictive models of complex chemical environments such as combustion or the atmosphere, or development and improvement of sophisticated high-fidelity electronic structure computational treatments. As opposed to the traditional sequential evolution of thermochemical values for the chemical species of interest, ATcT utilizes the Thermochemical Network (TN) approach. This approach explicitly exposes the maze of inherent interdependencies normally ignored by the conventional treatment, and allows, inter alia, a statistical analysis of the individual measurements that define the TN. The end result is the extraction of the best possible thermochemistry, based on optimal use of all the currently available knowledge, hence making conventional tabulations of thermochemical values obsolete. Moreover, ATcT offer a number of additional features that are neither present nor possible in the traditional approach. With ATcT, new knowledge can be painlessly propagated through all affected thermochemical values. ATcT also allows hypothesis testing and evaluation, as well as discovery of weak links in the TN. The latter provides pointers to new experimental or theoretical determinations that can most efficiently improve the underlying thermochemical body of knowledge.

Poly(Arylene Ether Sulfone) Copolymers and Related Systems from Disulfonated Monomer Building Blocks: Synthesis, Characterization, and Performance – A Topical Review

Abstract: Research and development efforts have been focussed over the last five years towards the preparation of new, but potentially commercially viable low-cost copolymers for use as proton exchange membrane for fuel cell and other membrane applications. Our primary efforts centered on the direct synthesis of disulfonated copolymers via step-polycondensation methods. These novel series of disulfonated copolymers include optionally fluorinated poly(arylene ethers), poly(thioethers), polyimides, polybenzimidazoles, and polybenzoxazoles, as well as multiblock copolymer systems. The first generation of alternative proton exchange membranes (PEMs) has focused on wholly aromatic, disulfonated poly(arylene ether sulfone) random copolymers. Detailed herein are the development and current state of these disulfonated poly(arylene ether sulfone) copolymers and their fuel cell performance in both hydrogen-air PEMFCs and direct methanol fuel cells (DMFC).

Enols are common intermediates in hydrocarbon oxidation.

Abstract: Models for chemical mechanisms of hydrocarbon oxidation rely on spectrometric identification of molecular structures in flames. Carbonyl (keto) compounds are well-established combustion intermediates. However, their less-stable enol tautomers, bearing OH groups adjacent to carbon-carbon double bonds, are not included in standard models. We observed substantial quantities of two-, three-, and four-carbon enols by photoionization mass spectrometry of flames burning representative compounds from modern fuel blends. Concentration profiles demonstrate that enol flame chemistry cannot be accounted for purely by keto-enol tautomerization. Currently accepted hydrocarbon oxidation mechanisms will likely require revision to explain the formation and reactivity of these unexpected compounds.

Combustion at the focus: laser diagnostics and control

Abstract: Fifty years after the foundation of the Combustion Institute and almost 150 years after Michael Faraday's famous lectures on the combustion of a candle, combustion diagnostics have come a long way from visual inspection of a flame to detailed analysis of a combustion process with a multitude of sophisticated techniques, often using lasers. The extended knowledge on combustion phenomena gained by application of these diagnostic techniques, combined with equally advanced numerical simulation of the process, has been instrumental in designing modern combustion devices with efficient performance and reduced pollutant emission. Also, similar diagnostic techniques are now employed to develop sensors for process control in combustion. This article intends to give a perspective on the potential of combustion diagnostics by highlighting selected application examples and by guiding the reader to recent literature. In particular, techniques are emphasized, which permit measurement of important features of the chemical composition, sometimes in conjunction with flow field parameters. Although a complete image of present research and applications in combustion diagnostics and control is beyond the scope of this article, this overview may be a starting place where ideas may be found to solve specific combustion problems with the aid of diagnostics. (Less)

Sensor Placement in Municipal Water Networks

Abstract: We present a model for optimizing the placement of sensors in municipal water networks to detect maliciously injected contaminants. An optimal sensor configuration minimizes the expected fraction of the population at risk. We formulate this problem as a mixed-integer program, which can be solved with generally available solvers. We find optimal sensor placements for three test networks with synthetic risk and population data. Our experiments illustrate that this formulation can be solved relatively quickly and that the predicted sensor configuration is relatively insensitive to uncertainties in the data used for prediction.

Higher-order Web link analysis using multilinear algebra

Abstract: Linear algebra is a powerful and proven tool in Web search. Techniques, such as the PageRank algorithm of Brin and Page and the HITS algorithm of Kleinberg, score Web pages based on the principal eigenvector (or singular vector) of a particular non-negative matrix that captures the hyperlink structure of the Web graph. We propose and test a new methodology that uses multilinear algebra to elicit more information from a higher-order representation of the hyperlink graph. We start by labeling the edges in our graph with the anchor text of the hyperlinks so that the associated linear algebra representation is a sparse, three-way tensor. The first two dimensions of the tensor represent the Web pages while the third dimension adds the anchor text. We then use the rank-1 factors of a multilinear PARAFAC tensor decomposition, which are akin to singular vectors of the SVD, to automatically identify topics in the collection along with the associated authoritative Web pages.

Shape memory and pseudoelasticity in metal nanowires.

Abstract: Structural reorientations in metallic fcc nanowires are controlled by a combination of size, thermal energy, and the type of defects formed during inelastic deformation. By utilizing atomistic simulations, we show that certain fcc nanowires can exhibit both shape memory and pseudoelastic behavior. We also show that the formation of defect-free twins, a process related to the material stacking fault energy, nanometer size scale, and surface stresses is the mechanism that controls the ability of fcc nanowires of different materials to show a reversible transition between two crystal orientations during loading and thus shape memory and pseudoelasticity.