Showing papers by "Argonne National Laboratory published in 2002"
TL;DR: It is shown that performance profiles combine the best features of other tools for performance evaluation to create a single tool for benchmarking and comparing optimization software.
Abstract: We propose performance profiles — distribution functions for a performance metric — as a tool for benchmarking and comparing optimization software. We show that performance profiles combine the best features of other tools for performance evaluation.
3,729 citations
TL;DR: In this paper, the authors explore four possible explanations for the anomalous thermal conductivity of nanofluids: Brownian motion of the particles, molecular-level layering of the liquid at the liquid/particle interface, the nature of heat transport in the nanoparticles, and the effects of nanoparticle clustering.
2,008 citations
TL;DR: In this paper, the authors focus on the nature of the services that respond to protocol messages and propose a set of services that can be aggregated in various ways to meet the needs of virtual organizations, which themselves can be defined by the services they operate and share.
Abstract: Increasingly, computing addresses collaboration, data sharing, and interaction modes that involve distributed resources, resulting in an increased focus on the interconnection of systems both within and across enterprises. These evolutionary pressures have led to the development of Grid technologies. The authors' work focuses on the nature of the services that respond to protocol messages. Grid provides an extensible set of services that can be aggregated in various ways to meet the needs of virtual organizations, which themselves can be defined in part by the services they operate and share.
1,816 citations
TL;DR: The crystal structure of the extracellular segment of integrin αVβ3 in complex with a cyclic peptide presenting the Arg-Gly-Asp sequence is reported and ligand binding induces small changes in the orientation of αV relative to β3.
Abstract: The structural basis for the divalent cation-dependent binding of heterodimeric alphabeta integrins to their ligands, which contain the prototypical Arg-Gly-Asp sequence, is unknown. Interaction with ligands triggers tertiary and quaternary structural rearrangements in integrins that are needed for cell signaling. Here we report the crystal structure of the extracellular segment of integrin alphaVbeta3 in complex with a cyclic peptide presenting the Arg-Gly-Asp sequence. The ligand binds at the major interface between the alphaV and beta3 subunits and makes extensive contacts with both. Both tertiary and quaternary changes are observed in the presence of ligand. The tertiary rearrangements take place in betaA, the ligand-binding domain of beta3; in the complex, betaA acquires two cations, one of which contacts the ligand Asp directly and the other stabilizes the ligand-binding surface. Ligand binding induces small changes in the orientation of alphaV relative to beta3.
1,598 citations
TL;DR: The cubic complex Ginzburg-Landau equation is one of the most-studied nonlinear equations in the physics community as mentioned in this paper, it describes a vast variety of phenomena from nonlinear waves to second-order phase transitions, from superconductivity, superfluidity, and Bose-Einstein condensation to liquid crystals and strings in field theory.
Abstract: The cubic complex Ginzburg-Landau equation is one of the most-studied nonlinear equations in the physics community. It describes a vast variety of phenomena from nonlinear waves to second-order phase transitions, from superconductivity, superfluidity, and Bose-Einstein condensation to liquid crystals and strings in field theory. The authors give an overview of various phenomena described by the complex Ginzburg-Landau equation in one, two, and three dimensions from the point of view of condensed-matter physicists. Their aim is to study the relevant solutions in order to gain insight into nonequilibrium phenomena in spatially extended systems.
1,557 citations
TL;DR: In this article, the authors compare the results of equilibrium and nonequilibrium methods to compute thermal conductivity using Sillinger-Weber silicon as a model system, addressing issues related to nonlinear response, thermal equilibration, and statistical averaging.
Abstract: We compare the results of equilibrium and nonequilibrium methods to compute thermal conductivity. Using Sillinger-Weber silicon as a model system, we address issues related to nonlinear response, thermal equilibration, and statistical averaging. In addition, we present an analysis of finite-size effects and demonstrate how reliable results can be obtained when using nonequilibrium methods by extrapolation to an infinite system size. For the equilibrium Green-Kubo method, we show that results for the thermal conductivity are insensitive to the choice of the definition of local energy from the many-body part of the potential. Finally, we show that the results obtained by the equilibrium and nonequilibrium methods are consistent with each other and for the case of Si are in reasonable agreement with experimental results.
1,410 citations
Book•
19 Aug 2002
TL;DR: In this article, the authors present an approach for approximating the Stokes and Navier-Stokes equations for elliptic problems with respect to orthogonal polynomials and discrete transforms.
Abstract: Preface 1. Fluid mechanics and computation: an introduction 2. Approximation methods for elliptic problems 3. Parabolic and hyperbolic problems 4. Mutidimensional problems 5. Steady Stokes and Navier-Stokes equations 6. Unsteady Stokes and Navier-Stokes equations 7. Domain decomposition 8. Vector and parallel implementations Appendix A. Preliminary mathematical concepts Appendix B. Orthogonal polynomials and discrete transforms.
917 citations
TL;DR: It is demonstrated that, in contrast to coarse-grained Al, mechanical twinning may play an important role in the deformation behaviour of nanocrystalline Al, and large-scale molecular-dynamics simulations are used to elucidate this intricate interplay during room-temperature plastic deformation of model nanocrystaline Al microstructures.
Abstract: The mechanical behaviour of nanocrystalline materials (that is, polycrystals with a grain size of less than 100 nm) remains controversial. Although it is commonly accepted that the intrinsic deformation behaviour of these materials arises from the interplay between dislocation and grain-boundary processes, little is known about the specific deformation mechanisms. Here we use large-scale molecular-dynamics simulations to elucidate this intricate interplay during room-temperature plastic deformation of model nanocrystalline Al microstructures. We demonstrate that, in contrast to coarse-grained Al, mechanical twinning may play an important role in the deformation behaviour of nanocrystalline Al. Our results illustrate that this type of simulation has now advanced to a level where it provides a powerful new tool for elucidating and quantifying--in a degree of detail not possible experimentally--the atomic-level mechanisms controlling the complex dislocation and grain-boundary processes in heavily deformed materials with a submicrometre grain size.
823 citations
TL;DR: Condor-G as discussed by the authors leverages software from Globus and Condor to enable users to harness multi-domain resources as if they all belong to one personal domain, and it handles job management, resource selection, security, and fault tolerance.
Abstract: In recent years, there has been a dramatic increase in the number of available computing and storage resources. Yet few tools exist that allow these resources to be exploited effectively in an aggregated form. We present the Condor-G system, which leverages software from Globus and Condor to enable users to harness multi-domain resources as if they all belong to one personal domain. We describe the structure of Condor-G and how it handles job management, resource selection, security, and fault tolerance. We also present results from application experiments with the Condor-G system. We assert that Condor-G can serve as a general-purpose interface to Grid resources, for use by both end users and higher-level program development tools.
792 citations
TL;DR: High-pressure Raman, infrared, x-ray, and neutron studies show that H2 and H2O mixtures crystallize into the sII clathrate structure with an approximate H2/H2Omolar ratio of 1:2.
Abstract: High-pressure Raman, infrared, x-ray, and neutron studies show that H2 and H2O mixtures crystallize into the sII clathrate structure with an approximate H2/H2O molar ratio of 1:2. The clathrate cages are multiply occupied, with a cluster of two H2 molecules in the small cage and four in the large cage. Substantial softening and splitting of hydrogen vibrons indicate increased intermolecular interactions. The quenched clathrate is stable up to 145 kelvin at ambient pressure. Retention of hydrogen at such high temperatures could help its condensation in planetary nebulae and may play a key role in the evolution of icy bodies.
790 citations
TL;DR: This work studied the topology and protocols of the public Gnutella network to evaluate costs and benefits of the peer-to-peer (P2P) approach and to investigate possible improvements that would allow better scaling and increased reliability in Gnutsella and similar networks.
Abstract: We studied the topology and protocols of the public Gnutella network. Its substantial user base and open architecture make it a good large-scale, if uncontrolled, testbed. We captured the network's topology, generated traffic, and dynamic behavior to determine its connectivity structure and how well (if at all) Gnutella's overlay network topology maps to the physical Internet infrastructure. Our analysis of the network allowed us to evaluate costs and benefits of the peer-to-peer (P2P) approach and to investigate possible improvements that would allow better scaling and increased reliability in Gnutella and similar networks. A mismatch between Gnutella's overlay network topology and the Internet infrastructure has critical performance implications.
TL;DR: It is shown that nanocrystalline diamond thin-films covalently modified with DNA oligonucleotides provide an extremely stable, highly selective platform in subsequent surface hybridization processes, suggesting that diamond thin -films may be a nearly ideal substrate for integration of microelectronics with biological modification and sensing.
Abstract: Diamond, because of its electrical and chemical properties, may be a suitable material for integrated sensing and signal processing. But methods to control chemical or biological modifications on diamond surfaces have not been established. Here, we show that nanocrystalline diamond thin-films covalently modified with DNA oligonucleotides provide an extremely stable, highly selective platform in subsequent surface hybridization processes. We used a photochemical modification scheme to chemically modify clean, H-terminated nanocrystalline diamond surfaces grown on silicon substrates, producing a homogeneous layer of amine groups that serve as sites for DNA attachment. After linking DNA to the amine groups, hybridization reactions with fluorescently tagged complementary and non-complementary oligonucleotides showed no detectable non-specific adsorption, with extremely good selectivity between matched and mismatched sequences. Comparison of DNA-modified ultra-nanocrystalline diamond films with other commonly used surfaces for biological modification, such as gold, silicon, glass and glassy carbon, showed that diamond is unique in its ability to achieve very high stability and sensitivity while also being compatible with microelectronics processing technologies. These results suggest that diamond thin-films may be a nearly ideal substrate for integration of microelectronics with biological modification and sensing.
CERN1, Royal Holloway, University of London2, Fermilab3, University of Bonn4, University of Montpellier5, University of Michigan6, University of California, Davis7, University of California, Santa Cruz8, University of Wisconsin-Madison9, Brookhaven National Laboratory10, Stanford University11, Lawrence Berkeley National Laboratory12, University of Warsaw13, Northern Illinois University14, RWTH Aachen University15, University of Florida16, University of Antwerp17, University of Colorado Boulder18, University of Minnesota19, Austrian Academy of Sciences20, University of Zurich21, Northwestern University22, California Institute of Technology23, Argonne National Laboratory24, University of Chicago25, University of Kansas26
TL;DR: The "Snowmass Points and Slopes" (SPS) as mentioned in this paper are a set of benchmark points and parameter lines in the MSSM parameter space corresponding to different scenarios in the search for Supersymmetry at present and future experiments.
Abstract: The ”Snowmass Points and Slopes” (SPS) are a set of benchmark points and parameter lines in the MSSM parameter space corresponding to different scenarios in the search for Supersymmetry at present and future experiments. This set of benchmarks was agreed upon at the 2001 ”Snowmass Workshop on the Future of Particle Physics” as a consensus based on different existing proposals.
TL;DR: In this article, surface modification of nanocrystalline metal oxide particles with enediol ligands was found to result in altered optical properties of nanoparticles, and the surface modification results in a red shift of the semiconductor absorption compared to unmodified nanocrystites.
Abstract: Surface modification of nanocrystalline metal oxide particles with enediol ligands was found to result in altered optical properties of nanoparticles. The surface modification results in a red shift of the semiconductor absorption compared to unmodified nanocrystallites. The optical shift is correlated to the dipole moment of the Ti−ligand complexes at the particle surface and decreases with the ligand size. The binding was found to be exclusively characteristic of colloids in the nanocrystalline domain(<20 nm). X-ray near-edge structure measurements at Ti K edge indicate that in this size domain the surface Ti atoms adjust their coordination environment to form undercoordinated sites. These five-coordinated defect sites are the source of novel enhanced and selective reactivity of the nanoparticle toward bidentate ligand binding as observed using IR spectroscopy. Enediol ligands have the optimal geometry for chelating surface Ti atoms, resulting in a five-membered ring coordination complex and restored si...
24 Jul 2002
TL;DR: The Chimera virtual data system is developed, which combines avirtual data catalog for representing data derivation procedures and derived data, with a virtual data language interpreter that translates user requests into data definition and query operations on the database.
Abstract: A lot of scientific data is not obtained from measurements but rather derived from other data by the application of computational procedures. We hypothesize that explicit representation of these procedures can enable documentation of data provenance, discovery of available methods, and on-demand data generation (so-called "virtual data"). To explore this idea, we have developed the Chimera virtual data system, which combines a virtual data catalog for representing data derivation procedures and derived data, with a virtual data language interpreter that translates user requests into data definition and query operations on the database. We couple the Chimera system with distributed "data grid" services to enable on-demand execution of computation schedules constructed from database queries. We have applied this system to two challenge problems, the reconstruction of simulated collision event data from a high-energy physics experiment, and searching digital sky survey data for galactic clusters, with promising results.
TL;DR: In this paper, it was shown that the mass of the KK photon and the neutrino can be inferred from the spectrum of the first-tier KK modes, and that the photon can have appropriate annihilation cross sections to account for the dark matter.
Abstract: In models with universal extra dimensions (i.e. in which all Standard Model fields, including fermions, propagate into compact extra dimensions) momentum conservation in the extra dimensions leads to the conservation of Kaluza--Klein (KK) number at each vertex. KK number is violated by loop effects because of the orbifold imposed to reproduce the chiral Standard Model with zero modes, however, a KK parity remains at any order in perturbation theory which leads to the existence of a stable lightest KK particle (LKP). In addition, the degeneracy in the KK spectrum is lifted by radiative corrections so that all other KK particles eventually decay into the LKP. We investigate cases where the Standard Model lives in five or six dimensions with compactification radius of TeV$^{-1}$ size and the LKP is the first massive state in the KK tower of either the photon or the neutrino. We derive the relic density of the LKP under a variety of assumptions about the spectrum of first tier KK modes. We find that both the KK photon and the KK neutrino, with masses at the TeV scale, may have appropriate annihilation cross sections to account for the dark matter, $\Omega_M \sim 0.3$.
Posted Content•
TL;DR: MPICH-G2 as discussed by the authors is a Grid-enabled implementation of the Message Passing Interface (MPI) that allows a user to run MPI programs across multiple computers, at the same or different sites, using the same commands that would be used on a parallel computer.
Abstract: Application development for distributed computing "Grids" can benefit from tools that variously hide or enable application-level management of critical aspects of the heterogeneous environment. As part of an investigation of these issues, we have developed MPICH-G2, a Grid-enabled implementation of the Message Passing Interface (MPI) that allows a user to run MPI programs across multiple computers, at the same or different sites, using the same commands that would be used on a parallel computer. This library extends the Argonne MPICH implementation of MPI to use services provided by the Globus Toolkit for authentication, authorization, resource allocation, executable staging, and I/O, as well as for process creation, monitoring, and control. Various performance-critical operations, including startup and collective operations, are configured to exploit network topology information. The library also exploits MPI constructs for performance management; for example, the MPI communicator construct is used for application-level discovery of, and adaptation to, both network topology and network quality-of-service mechanisms. We describe the MPICH-G2 design and implementation, present performance results, and review application experiences, including record-setting distributed simulations.
01 May 2002
TL;DR: A high-speed transport service that extends the popular FTP protocol with new features required for Data Grid applications, such as striping and partial file access and a replica management service that integrates a replica catalog with GridFTP transfers to provide for the creation, registration, location, and management of dataset replicas.
Abstract: An emerging class of data-intensive applications involve the geographically dispersed extraction of complex scientific information from very large collections of measured or computed data. Such applications arise, for example, in experimental physics, where the data in question is generated by accelerators, and in simulation science, where the data is generated by supercomputers. So-called Data Grids provide essential infrastructure for such applications, much as the Internet provides essential services for applications such as e-mail and the Web. We describe here two services that we believe are fundamental to any Data Grid: reliable, high-speed transport and replica management. Our high-speed transport service, GridFTP, extends the popular FTP protocol with new features required for Data Grid applications, such as striping and partial file access. Our replica management service integrates a replica catalog with GridFTP transfers to provide for the creation, registration, location, and management of dataset replicas. We present the design of both services and also preliminary performance results. Our implementations exploit security and other services provided by the Globus Toolkit.
TL;DR: In this paper, X-ray photoelectron spectroscopy and scanning electron microscopy were used to study electrode samples obtained from 18650-type lithium-ion cells subjected to accelerated calendar-life testing at temperatures ranging from 25 to 70 C and at states of charge from 40 to 80%.
Abstract: X-ray photoelectron spectroscopy and scanning electron microscopy were used to study electrode samples obtained from 18650-type lithium-ion cells subjected to accelerated calendar-life testing at temperatures ranging from 25 to 70 C and at states-of-charge from 40 to 80%. The cells contained LiNi{sub 0.8}Co{sub 0.2}O{sub 2}-based positive electrodes (cathodes), graphite-based negative electrodes (anodes), and a 1 M LiPF{sub 6} ethylene carbonate:diethyl carbonate (1:1) electrolyte. The results from electrochemically treated samples showed surface film formation on both electrodes. The positive electrode laminate surfaces contained a mixture of organic species that included polycarbonates, and LiF, Li{sub x}PF{sub y}-type and Li{sub x}PF{sub y}O{sub z}-type compounds. The same surface compounds were observed regardless of test temperature, test duration, and state-of-charge. On the negative electrode laminates lithium alkyl carbonates (ROCO{sub 2}Li) and Li{sub 2}CO{sub 3} were found in addition to the above-mentioned compounds. Decomposition of lithium alkyl carbonates to Li{sub 2}CO{sub 3} occurred on negative electrodes stored at elevated temperature. Initial depth-profiling results suggest that the surface layer thickness is greater on positive electrode samples from cells stored at high temperature than on samples from cells stored at room temperature. This observation is significant because positive electrode impedance, and more specifically, charge-transfer resistance at the electrode/electrolytemore » interface, has been shown to be the main contributor to impedance rise in these cells.« less
TL;DR: As computer networks become cheaper and more powerful, a new computing paradigm is poised to transform the practice of science and engineering.
Abstract: As computer networks become cheaper and more powerful, a new computing paradigm is poised to transform the practice of science and engineering.
TL;DR: Using Cytofectin GSV to deliver both inhibitors, the siRNAs appear to be quantitatively more efficient and its effect is lasting for a longer time in cell culture and in mice, an activity of siRNA but not of antisense oligonucleotides is observed.
TL;DR: A new LIC vector is developed, pMCSG7, that incorporates the tobacco etch virus (TEV) protease cleavage site into the leader sequence and includes a pair of adjacent, unique restriction sites that will allow insertion of additional modules between the his-tag and the Cleavage site of the leader sequences to generate a family of vectors suitable for high-throughput production of proteins.
TL;DR: In this article, the authors presented Mn $3s$ x-ray photoelectron spectra of manganese oxides with the Mn formal valency from $2+$ to $4+.
Abstract: We present Mn $3s$ x-ray photoelectron spectra of manganese oxides with the Mn formal valency from $2+$ to $4+.$ We found that the ${\mathrm{Sr}}^{2+}$ doping or cation deficiency in manganites do not change the Mn $3s$ splitting in manganites with the Mn formal valency from $3.0+$ to $3.3+.$ We suggest that doping holes are localized in O $2p$ states.
TL;DR: In this paper, the transverse momentum distributions of charged hadrons within 0.2 < p T < 6.0 GeV/c have been measured over a broad range of centrality for Au + Au collisions at S N N = 130 GeV.
Abstract: Inclusive transverse momentum distributions of charged hadrons within 0.2 < p T < 6.0 GeV/c have been measured over a broad range of centrality for Au + Au collisions at S N N = 130 GeV. Hadron yields are suppressed at high PT in central collisions relative to peripheral collisions and to a nucleon-nucleon reference scaled for collision geometry. Peripheral collisions are not suppressed relative to the nucleon-nucleon reference. The suppression varies continuously at intermediate centralities. The results indicate significant nuclear medium effects on high-p T hadron production in heavy-ion collisions at high energy.
TL;DR: In this article, the observation of periodic 180 degrees stripe domains below the ferroelectric transition in thin thin films was studied using x-ray scattering and the dependence of Lambda on d agrees well with theory including epitaxial strain effects, while the suppression of T(C) for thinner films is significantly larger than that expected solely from stripe domains.
Abstract: We report the observation of periodic 180 degrees stripe domains below the ferroelectric transition in thin films. Epitaxial PbTiO3 films of thickness d=1.6 to 42 nm on SrTiO3 substrates were studied using x-ray scattering. Upon cooling below T(C), satellites appeared around Bragg peaks indicating the presence of 180 degrees stripe domains of period Lambda=3.7 to 24 nm. The dependence of Lambda on d agrees well with theory including epitaxial strain effects, while the suppression of T(C) for thinner films is significantly larger than that expected solely from stripe domains.
16 Nov 2002
TL;DR: A parameterized architectural framework is described, which is name Giggle (for GIGa-scale Global Location Engine), within which a wide range of RLSs can be defined, and initial performance results for an RLS prototype are presented, demonstrating that RLS systems can be constructed that meet performance goals.
Abstract: In wide area computing systems, it is often desirable to create remote read-only copies (replicas) of files. Replication can be used to reduce access latency, improve data locality, and/or increase robustness, scalability and performance for distributed applications. We define a replica location service (RLS) as a system that maintains and provides access to information about the physical locations of copies. An RLS typically functions as one component of a data grid architecture. This paper makes the following contributions. First, we characterize RLS requirements. Next, we describe a parameterized architectural framework, which we name Giggle (for GIGa-scale Global Location Engine), within which a wide range of RLSs can be defined. We define several concrete instantiations of this framework with different performance characteristics. Finally, we present initial performance results for an RLS prototype, demonstrating that RLS systems can be constructed that meet performance goals.
TL;DR: TraR of Agrobacterium tumefaciens was solved as a complex with the pheromone N-3-oxooctanoyl-l-homoserine lactone and its TraR DNA-binding site and the structure of a LuxR-type protein is presented.
Abstract: Many proteobacteria are able to monitor their population densities through the release of pheromones known as N-acylhomoserine lactones. At high population densities, these pheromones elicit diverse responses that include bioluminescence, biofilm formation, production of antimicrobials, DNA exchange, pathogenesis and symbiosis. Many of these regulatory systems require a pheromone-dependent transcription factor similar to the LuxR protein of Vibrio fischeri. Here we present the structure of a LuxR-type protein. TraR of Agrobacterium tumefaciens was solved at 1.66 A as a complex with the pheromone N-3-oxooctanoyl-L-homoserine lactone (OOHL) and its TraR DNA-binding site. The amino-terminal domain of TraR is an alpha/beta/alpha sandwich that binds OOHL, whereas the carboxy-terminal domain contains a helix turn helix DNA-binding motif. The TraR dimer displays a two-fold symmetry axis in each domain; however, these two axes of symmetry are at an approximately 90 degree angle, resulting in a pronounced overall asymmetry of the complex. The pheromone lies fully embedded within the protein with virtually no solvent contact, and makes numerous hydrophobic contacts with the protein as well as four hydrogen bonds: three direct and one water-mediated.
24 Jul 2002
TL;DR: A resource management model is defined that distinguishes three kinds of resource-independent service level agreements (SLAs), formalizingag reements to deliver capability, perform activities, and bind activities to capabilities, respectively.
Abstract: A fundamental problem in distributed computing is to map activities such as computation or data transfer onto resources that meet requirements for performance, cost, security, or other quality of service metrics. The creation of such mappings requires negotiation among application and resources to discover, reserve, acquire, configure, and monitor resources. Current resource management approaches tend to specialize for specific resource classes, and address coordination across resources only in a limited fashion. We present a new approach that overcomes these difficulties.We define a resource management model that distinguishes three kinds of resource-independent service level agreements (SLAs), formalizingag reements to deliver capability, perform activities, and bind activities to capabilities, respectively. We also define a Service Negotiation and Acquisition Protocol (SNAP) that supports reliable management of remote SLAs. Finally, we explain how SNAP can be deployed within the context of the Globus Toolkit.
01 Aug 2002
TL;DR: In this paper, a massively parallel molecular-dynamics code for the simulation of polycrystal plasticity is used to elucidate the intricate interplay between dislocation and GB processes during room-temperature plastic deformation of model nanocrystalline-Al microstructures.