Showing papers by "Argonne National Laboratory published in 2001"

The Anatomy of the Grid: Enabling Scalable Virtual Organizations

Abstract: "Grid" computing has emerged as an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high performance orientation. In this article, the authors define this new field. First, they review the "Grid problem," which is defined as flexible, secure, coordinated resource sharing among dynamic collections of individuals, institutions, and resources--what is referred to as virtual organizations. In such settings, unique authentication, authorization, resource access, resource discovery, and other challenges are encountered. It is this class of problem that is addressed by Grid technologies. Next, the authors present an extensible and open Grid architecture, in which protocols, services, application programming interfaces, and software development kits are categorized according to their roles in enabling resource sharing. The authors describe requirements that they believe any such mechanisms must satisfy and discuss the importance of defining a compact set of intergrid protocols to enable interoperability among different Grid systems. Finally, the authors discuss how Grid technologies relate to other contemporary technologies, including enterprise integration, application service provider, storage service provider, and peer-to-peer computing. They maintain that Grid concepts and technologies complement and have much to contribute to these other approaches.

The Anatomy of the Grid - Enabling Scalable Virtual Organizations

Abstract: "Grid" computing has emerged as an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high-performance orientation. In this article, we define this new field. First, we review the "Grid problem," which we define as flexible, secure, coordinated resource sharing among dynamic collections of individuals, institutions, and resources-what we refer to as virtual organizations. In such settings, we encounter unique authentication, authorization, resource access, resource discovery, and other challenges. It is this class of problem that is addressed by Grid technologies. Next, we present an extensible and open Grid architecture, in which protocols, services, application programming interfaces, and software development kits are categorized according to their roles in enabling resource sharing. We describe requirements that we believe any such mechanisms must satisfy, and we discuss the central role played by the intergrid protocols that enable interoperability among different Grid systems. Finally, we discuss how Grid technologies relate to other contemporary technologies, including enterprise integration, application service provider, storage service provider, and peer-to-peer computing. We maintain that Grid concepts and technologies complement and have much to contribute to these other approaches.

IFEFFIT: interactive XAFS analysis and FEFF fitting.

Abstract: IFEFFIT, an interactive program and scriptable library of XAFS algorithms is presented. The core algorithms of AUTOBK and FEFFIT have been combined with general data manipulation and interactive graphics into a single package. IFEFFIT comes with a command-line program that can be run either interactively or in batch-mode. It also provides a library of functions that can be used easily from C or Fortran, as well as high level scripting languages such as Tcl, Perl and Python. Using this library, a Graphical User Interface for rapid 'online' data analysis is demonstrated. IFEFFIT is freely available with an Open Source license. Outside use, development, and contributions are encouraged.

6-31G* basis set for third-row atoms

Abstract: Medium basis sets based upon contractions of Gaussian primitives are developed for the third-row elements Ga through Kr. The basis functions generalize the 6-31G and 6-31G* sets commonly used for atoms up to Ar. A reexamination of the 6-31G* basis set for K and Ca developed earlier leads to the inclusion of 3d orbitals into the valence space for these atoms. Now the 6-31G basis for the whole third-row K through Kr has six primitive Gaussians for 1s, 2s, 2p, 3s, and 3p orbitals, and a split-valence pair of three and one primitives for valence orbitals, which are 4s, 4p, and 3d. The nature of the polarization functions for third-row atoms is reexamined as well. The polarization functions for K, Ca, and Ga through Kr are single set of Cartesian d-type primitives. The polarization functions for transition metals are defined to be a single 7f set of uncontracted primitives. Comparison with experimental data shows good agreement with bond lengths and angles for representative vapor-phase metal complexes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 976–984, 2001

Condor-G: a computation management agent for multi-institutional grids

Abstract: In recent years, there has been a dramatic increase in the amount of available computing and storage resources, yet few have been able to exploit these resources in an aggregated form. We present the Condor-G system, which leverages software from Globus and Condor to allow 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.

Crystal Structure of the Extracellular Segment of Integrin αVβ3

Abstract: Integrins are αβ heterodimeric receptors that mediate divalent cation-dependent cell-cell and cell-matrix adhesion through tightly regulated interactions with ligands. We have solved the crystal structure of the extracellular portion of integrin αVβ3 at 3.1 A resolution. Its 12 domains assemble into an ovoid “head” and two “tails.” In the crystal, αVβ3 is severely bent at a defined region in its tails, reflecting an unusual flexibility that may be linked to integrin regulation. The main inter-subunit interface lies within the head, between a seven-bladed β-propeller from αV and an A domain from β3, and bears a striking resemblance to the Gα/Gβ interface in G proteins. A metal ion–dependent adhesion site (MIDAS) in the βA domain is positioned to participate in a ligand-binding interface formed of loops from the propeller and βA domains. MIDAS lies adjacent to a calcium-binding site with a potential regulatory function.

The role of hydrogen in tribological properties of diamond-like carbon films☆

Abstract: Extensive research on diamond and diamondlike carbon (DLC) films in our laboratory has further confirmed that hydrogen plays an important role in the tribological properties of these films. Specifically, model experiments in inert gas environments revealed a very close relationship between the hydrogen-to-carbon (H/C) ratios of source gases and the friction and wear coefficients of the resultant DLC films. The friction coefficient of films grown in source gases with very high H/C ratios (e.g. 10) was superlow (0.003), whereas that of hydrogen-free DLC films (with essentially zero H/C ratio) was very high (0.65). The friction coefficients of films grown in source gases with intermediate H/C ratios were between 0.003 and 0.65. Experiments also revealed that the frictional properties of these films were very sensitive to test environments. Specifically, when tested in open air, the friction coefficient of hydrogen-free DLC dropped to 0.25, whereas that of highly-hydrogenated DLC increased to 0.06. Fundamental knowledge combined with surface analytical and tribological studies have led to the conclusion that the type and extent of chemical interactions between carbon–carbon, carbon–hydrogen, and carbon–adsorbate atoms at the sliding-contact interfaces determine the friction and wear properties of DLC films.

Elliptic flow in Au + Au collisions at √SNN = 130 GeV

Abstract: Elliptic flow from nuclear collisions is a hadronic observable sensitive to the early stages of system evolution. We report first results on elliptic flow of charged particles at midrapidity in Au+Au collisions at √(sNN) = 130 GeV using the STAR Time Projection Chamber at the Relativistic Heavy Ion Collider. The elliptic flow signal, v₂, averaged over transverse momentum, reaches values of about 6% for relatively peripheral collisions and decreases for the more central collisions. This can be interpreted as the observation of a higher degree of thermalization than at lower collision energies. Pseudorapidity and transverse momentum dependence of elliptic flow are also presented.

Designer magnets containing cyanides and nitriles.

Abstract: Magnets synthesized from molecules have contributed to the renaissance in the study of magnetic materials. Three-dimensional network solids exhibiting magnetic ordering have been made from several first-row metal ions and bridging unsaturated cyanide, tricyanomethanide, and/or dicyanamide ligands. These materials possess several different structural motifs, and the shorter the bridge, the stronger the interaction (i.e., C⋮N > N⋮CN ≫ N⋮CNC⋮N = N⋮CCC⋮N). Cyanide additionally has the ability to discriminate between C- and N-bonding to form ordered heterobimetallic magnets, and the strong coupling can lead to ferro- or ferrimagnetic ordering substantially above room temperature. Tricoordination of tricyanomethanide results in spin-frustrated systems, which possess interpenetrating rutile-like networks. In contrast, single rutile-like frameworks are formed by μ3-bonded dicyanamide, which leads to ferromagnetics and weak ferromagnetics.

Realistic models of pion-exchange three-nucleon interactions

Abstract: We present realistic models of pion-exchange three-nucleon interactions obtained by fitting the energies of all the 17 bound or narrow states of $3l~Al~8$ nucleons, calculated with less than 2% error using the Green's function Monte Carlo method. The models contain two-pion-exchange terms due to $\ensuremath{\pi}N$ scattering in S and P waves, three-pion-exchange terms due to ring diagrams with one $\ensuremath{\Delta}$ in the intermediate states, and a phenomenological repulsive term to take into account relativistic effects, the suppression of the two-pion-exchange two-nucleon interaction by the third nucleon, and other effects. The models have five parameters, consisting of the strength of the four interactions and the short-range cutoff. The 17 fitted energies are insufficient to determine all of them uniquely. We consider five models, each having three adjustable parameters and assumed values for the other two. They reproduce the observed energies with an rms error $l1%$ when used together with the Argonne ${v}_{18}$ two-nucleon interaction. In one of the models the $\ensuremath{\pi}N$ S-wave scattering interaction is set to zero; in all others it is assumed to have the strength suggested by chiral effective-field theory. One of the models also assumes that the $\ensuremath{\pi}N$ P-wave scattering interaction has the strength suggested by effective-field theories, and the cutoff is adjusted to fit the data. In all other models the cutoff is taken to be the same as in the ${v}_{18}$ interaction. The effect of relativistic boost correction to the two-nucleon interaction on the strength of the repulsive three-nucleon interaction is estimated. Many calculated properties of $Al~8$ nuclei, including radii, magnetic dipole, and electric quadrupole moments, isobaric analog energy differences, etc., are tabulated. Results obtained with only Argonne ${v}_{8}^{\ensuremath{'}}$ and ${v}_{18}$ interactions are also reported. In addition, we present results for seven- and eight-body neutron drops in external potential wells.

Actinide partitioning—a review

Abstract: Reagents and methods that have been developed during the past 20 years for hydrometallurgical partitioning of actinides from different types of transuranium (TRU) wastes and dissolved fuels are reviewed. Emphasis is placed on the extraction performance of the fully-optimized reagents rather than on the structural iterations that were undertaken (and in some cases are still being conducted) to identify the optimum species. Particular attention is paid to separation processes that have been demonstrated in batch and counter-current solvent extraction, and batch and column mode extraction chromatography. The salient features of the various techniques and reagents for actinide recycle are compared. Sections of the review focus on neptunium behavior in hydrometallurgy and on characterization of those reagents best suited to the separation of trivalent actinides from fission product lanthanides. Selected flowsheets that have been reported for the separation and recovery of actinides from TRU wastes are presented.

Synthesis and characterization of highly-conducting nitrogen-doped ultrananocrystalline diamond films

Abstract: Ultrananocrystalline diamond (UNCD) films with up to 0.2% total nitrogen content were synthesized by a microwave plasma-enhanced chemical-vapor-deposition method using a CH4(1%)/Ar gas mixture and 1%–20% nitrogen gas added. The electrical conductivity of the nitrogen-doped UNCD films increases by five orders of magnitude (up to 143 Ω−1 cm−1) with increasing nitrogen content. Conductivity and Hall measurements made as a function of film temperature down to 4.2 K indicate that these films have the highest n-type conductivity and carrier concentration demonstrated for phase-pure diamond thin films. Grain-boundary conduction is proposed to explain the remarkable transport properties of these films.

Molecular-Scale Density Oscillations in Water Adjacent to a Mica Surface

Abstract: High-resolution specular x-ray reflectivity of the mica(001)-water interface under ambient conditions reveals oscillations in water oxygen density in the surface-normal direction, giving evidence of interfacial water ordering. The spacings between neighboring water layers in the near-surface, strongly oscillatory region are 2.5(2)-2.7(2) A, approximately the size of the water molecule. The density oscillations extend to about 10 A above the surface and do not strictly maintain a solvent-size periodicity as that in interfacial liquid metal and hard-sphere molecular liquids. We interpret this oscillatory density profile of the interfacial water as due to the "hard-wall" effect of the molecularly smooth mica surface.

Studies of Mg-substituted Li4-xMgxTi5O12 spinel electrodes (0 ≤ x ≤ 1) for lithium batteries

Abstract: Magnesium-substituted Li{sub 4-x}Mg{sub x}Ti{sub 5}O{sub 12} spinel electrodes (0

Hydroxylation of camphor by reduced oxy-cytochrome P450cam: mechanistic implications of EPR and ENDOR studies of catalytic intermediates in native and mutant enzymes.

Abstract: We have employed γ-irradiation at cryogenic temperatures (77 K and also ∼6 K) of the ternary complexes of camphor, dioxygen, and ferro-cytochrome P450cam to inject the “second” electron of the catalytic process. We have used EPR and ENDOR spectroscopies to characterize the primary product of reduction as well as subsequent states created by annealing reduced oxyP450, both the WT enzyme and the D251N and T252A mutants, at progressively higher temperatures. (i) The primary product upon reduction of oxyP450 4 is the end-on, “H-bonded peroxo” intermediate 5A. (ii) This converts even at cryogenic temperatures to the hydroperoxo-ferriheme species, 5B, in a step that is sensitive to these mutations.Yields of 5B are as high as 40%. (iii) In WT and D251N P450s, brief annealing in a narrow temperature range around 200 K causes 5B to convert to a product state, 7A, in which the product 5-exo-hydroxycamphor is coordinated to the ferriheme in a nonequilibrium configuration. Chemical and EPR quantitations indicate the ...

High-level multireference methods in the quantum-chemistry program system COLUMBUS: Analytic MR-CISD and MR-AQCC gradients and MR-AQCC-LRT for excited states, GUGA spin–orbit CI and parallel CI density

Abstract: Development of several new computational approaches within the framework of multi-reference ab initio molecular electronic structure methodology and their implementation in the COLUMBUS program system are reported. These new features are: calculation of the analytical MR-CI gradient for excited states based on state-averaged MCSCF orbitals, the extension of the MR-ACPF/AQCC methods to excited states in the framework of linear-response theory, spin–orbit CI for molecules containing heavy atoms and the development of a massively-parallel code for the computation of the one- and two-particle density matrix elements. Illustrative examples are given for each of these cases.

A Java commodity grid kit

Abstract: In this paper we report on the features of the Java Commodity Grid Kit. The Java CoG Kit provides middleware for accessing Grid functionality from the Java framework. Java CoG Kit middleware is general enough to design a variety of advanced Grid applications with quite different user requirements. Access to the Grid is established via Globus protocols, allowing the Java CoG Kit to communicate also with the C Globus reference implementation. Thus, the Java CoG Kit provides Grid developers with the ability to utilize the Grid, as well as numerous additional libraries and frameworks developed by the Java community to enable network, Internet, enterprise, and peer-to peer computing. A variety of projects have successfully used the client libraries of the Java CoG Kit to access Grids driven by the C Globus software. In this paper we also report on the efforts to develop server side Java CoG Kit components. As part of this research we have implemented a prototype pure Java resource management system that enables one to run Globus jobs on platforms on which a Java virtual machine is supported, including Windows NT machines.

Specific Heat of Mg 11 B 2 : Evidence for a Second Energy Gap

Abstract: Measurements of the specific heat of ${\mathrm{Mg}}^{11}{\mathrm{B}}_{2}$ from 1 to 50 K, in magnetic fields to 9 T, give the Debye temperature, $\ensuremath{\Theta}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1050\mathrm{K}$, the coefficient of the normal-state electron contribution, ${\ensuremath{\gamma}}_{n}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}2.6\mathrm{mJ}{\mathrm{mol}}^{\ensuremath{-}1}{\mathrm{K}}^{\ensuremath{-}2}$, and a discontinuity in the zero-field specific heat of $133\mathrm{mJ}{\mathrm{mol}}^{\ensuremath{-}1}{\mathrm{K}}^{\ensuremath{-}1}$ at ${T}_{c}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}38.7\mathrm{K}$. The estimated value of the electron-phonon coupling parameter, $\ensuremath{\lambda}\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}0.62$, could account for the observed ${T}_{c}$ only if the important phonon frequencies are unusually high relative to $\ensuremath{\Theta}$. At low $T$, there is a strongly field-dependent feature that suggests the existence of a second energy gap, about 4 times smaller than the major gap.

The GrADS Project: Software Support for High-Level Grid Application Development

Abstract: Advances in networking technologies will soon make it possible to use the global information infrastructure in a qualitatively different way--as a computational as well as an information resource. As described in the recent book The Grid: Blueprint for a New Computing Infrastructure, this Grid will connect the nation's computers, databases, instruments, and people in a seamless web of computing and distributed intelligence, which can be used in an on-demand fashion as a problem-solving resource in many fields of human endeavor--and, in particular, science and engineering. The availability of grid resources will give rise to dramatically new classes of applications, in which computing resources are no longer localized but, rather, distributed, heterogeneous, and dynamic; computation is increasingly sophisticated and multidisciplinary; and computation is integrated into our daily lives and, hence, subject to stricter time constraints than at present. The impact of these new applications will be pervasive, ranging from new systems for scientific inquiry, through computing support for crisis management, to the use of ambient computing to enhance personal mobile computing environments. To realize this vision, significant scientific and technical obstacles must be overcome. Principal among these is usability. The goal of the Grid Application Development Software (GrADS) project is to simplify distributed heterogeneous computing in the same way that the World Wide Web simplified information sharing over the Internet. To that end, the project is exploring the scientific and technical problems that must be solved to make it easier for ordinary scientific users to develop, execute, and tune applications on the Grid. In this paper, the authors describe the vision and strategies underlying the GrADS project, including the base software architecture for grid execution and performance monitoring, strategies and tools for construction of applications from libraries of grid-aware components, and development of innovative new science and engineering applications that can exploit these new technologies to run effectively in grid environments.

Measurement of the neutral current cross section and F-2 structure function for deep inelastic e(+)p scattering at HERA

Abstract: The cross section and the proton structure function \(F_2\) for neutral current deep inelastic \(e^+p\) scattering have been measured with the ZEUS detector at HERA using an integrated luminosity of 30 pb\(^{-1}\). The data were collected in 1996 and 1997 at a centre-of-mass energy of 300 GeV. They cover the kinematic range \(2.7 < Q^2 < 30000\) GeV\(^2\) and \(6\cdot 10^{-5} < x < 0.65\). The variation of \(F_2\) with x and \(Q^2\) is well described by next-to-leading-order perturbative QCD as implemented in the DGLAP evolution equations.

Proliferating Cell Nuclear Antigen (PCNA): Ringmaster of the Genome

Abstract: Proliferating cell nuclear antigen (PCNA) protein is one of the central molecules responsible for decisions of life and death of the cell. The PCNA gene is induced by p53, while PCNA protein interacts with p53-controlled proteins Gadd45, MyD118, CR6 and, most importantly, p21, in the process of deciding cell fate. If PCNA protein is present in abundance in the cell in the absence of p53, DNA replication occurs. On the other hand, if PCNA protein levels are high in the cell in the presence of p53, DNA repair takes place. If PCNA is rendered non-functional or is absent or present in low quantities in the cell, apoptosis occurs. The evolution from prokaryotes to eukaryotes involved a change of function of PCNA from a 'simple' sliding clamp protein of the DNA polymerase complex to an executive molecule controlling critical cellular decision pathways. The evolution of multicellular organisms led to the development of multicellular processes such as differentiation, senescence and apoptosis. PCNA, already an essential molecule in the life of single cellular organisms, then became a protein critical for the survival of multicellular organisms.

Pressure-induced amorphization and an amorphous–amorphous transition in densified porous silicon

Abstract: Crystalline and amorphous forms of silicon are the principal materials used for solid-state electronics and photovoltaics technologies. Silicon is therefore a well-studied material, although new structures and properties are still being discovered. Compression of bulk silicon, which is tetrahedrally coordinated at atmospheric pressure, results in a transition to octahedrally coordinated metallic phases. In compressed nanocrystalline Si particles, the initial diamond structure persists to higher pressure than for bulk material, before transforming to high-density crystals. Here we report compression experiments on films of porous Si, which contains nanometre-sized domains of diamond-structured material. At pressures larger than 10 GPa we observed pressure-induced amorphization. Furthermore, we find from Raman spectroscopy measurements that the high-density amorphous form obtained by this process transforms to low-density amorphous silicon upon decompression. This amorphous-amorphous transition is remarkably similar to that reported previously for water, which suggests an underlying transition between a high-density and a low-density liquid phase in supercooled Si (refs 10, 14, 15). The Si melting temperature decreases with increasing pressure, and the crystalline semiconductor melts to a metallic liquid with average coordination approximately 5 (ref. 16).

Secure, Efficient Data Transport and Replica Management for High-Performance Data-Intensive Computing

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.