Showing papers by "Oak Ridge National Laboratory published in 2009"

Trends in the sources and sinks of carbon dioxide

Abstract: Efforts to control climate change require the stabilization of atmospheric CO2 concentrations. This can only be achieved through a drastic reduction of global CO2 emissions. Yet fossil fuel emissions increased by 29% between 2000 and 2008, in conjunction with increased contributions from emerging economies, from the production and international trade of goods and services, and from the use of coal as a fuel source. In contrast, emissions from land-use changes were nearly constant. Between 1959 and 2008, 43% of each year's CO2 emissions remained in the atmosphere on average; the rest was absorbed by carbon sinks on land and in the oceans. In the past 50 years, the fraction of CO2 emissions that remains in the atmosphere each year has likely increased, from about 40% to 45%, and models suggest that this trend was caused by a decrease in the uptake of CO2 by the carbon sinks in response to climate change and variability. Changes in the CO2 sinks are highly uncertain, but they could have a significant influence on future atmospheric CO2 levels. It is therefore crucial to reduce the uncertainties.

Conduction at domain walls in oxide multiferroics

Abstract: Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO3. The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features. Domain walls may be important in future electronic devices, given their small size as well as the fact that their location can be controlled. In the case of insulating multiferroic oxides, domain walls are now discovered to be electrically conductive, suggesting their possible use in logic and memory applications.

Porous Graphene as the Ultimate Membrane for Gas Separation

Abstract: We investigate the permeability and selectivity of graphene sheets with designed subnanometer pores using first principles density functional theory calculations. We find high selectivity on the order of 10(8) for H(2)/CH(4) with a high H(2) permeance for a nitrogen-functionalized pore. We find extremely high selectivity on the order of 10(23) for H(2)/CH(4) for an all-hydrogen passivated pore whose small width (at 2.5 A) presents a formidable barrier (1.6 eV) for CH(4) but easily surmountable for H(2) (0.22 eV). These results suggest that these pores are far superior to traditional polymer and silica membranes, where bulk solubility and diffusivity dominate the transport of gas molecules through the material. Recent experimental investigations, using either electron beams or bottom-up synthesis to create pores in graphene, suggest that it may be possible to employ such techniques to engineer variable-sized, graphene nanopores to tune selectivity and molecular diffusivity. Hence, we propose using porous graphene sheets as one-atom-thin, highly efficient, and highly selective membranes for gas separation. Such a pore could have widespread impact on numerous energy and technological applications; including carbon sequestration, fuel cells, and gas sensors.

Transient Simulation of Last Deglaciation with a New Mechanism for Bølling-Allerød Warming

Abstract: We conducted the first synchronously coupled atmosphere-ocean general circulation model simulation from the Last Glacial Maximum to the Bolling-Allerod (BA) warming. Our model reproduces several major features of the deglacial climate evolution, suggesting a good agreement in climate sensitivity between the model and observations. In particular, our model simulates the abrupt BA warming as a transient response of the Atlantic meridional overturning circulation (AMOC) to a sudden termination of freshwater discharge to the North Atlantic before the BA. In contrast to previous mechanisms that invoke AMOC multiple equilibrium and Southern Hemisphere climate forcing, we propose that the BA transition is caused by the superposition of climatic responses to the transient CO 2 forcing, the AMOC recovery from Heinrich Event 1, and an AMOC overshoot.

Hierarchically Structured Sulfur/Carbon Nanocomposite Material for High-Energy Lithium Battery

Abstract: We report herein a hierarchically structured sulfur−carbon (S/C) nanocomposite material as the high surface-area cathode for rechargeable lithium batteries. A porous carbon with a uniform distribution of mesopores of 7.3 nm has been synthesized through a soft-template synthesis method. The potassium hydroxide activation of this mesoporous carbon results in a bimodal porous carbon with added microporosity of less than 2 nm to the existing mesopores without deterioration of the integrity of the original mesoporous carbon. Elemental sulfur has been loaded to the micropores through a solution infiltration method. The resulted S/C composites with various loading level of sulfur have a high surface areas and large internal porosities. These materials have been tested as novel cathodes for Li/S batteries. The results show that the cyclability and the utilization of sulfur in the Li/S batteries have been significantly improved. The large internal porosity and surface area of the micromesoporous carbon is essentia...

Priming in systemic plant immunity.

Abstract: Plants possess inducible systemic defense responses when locally infected by pathogens. Bacterial infection results in the increased accumulation of the mobile metabolite azelaic acid, a nine-carbon dicarboxylic acid, in the vascular sap of Arabidopsis that confers local and systemic resistance against the pathogen Pseudomonas syringae. Azelaic acid primes plants to accumulate salicylic acid (SA), a known defense signal, upon infection. Mutation of the AZELAIC ACID INDUCED 1 (AZI1) gene, which is induced by azelaic acid, results in the specific loss of systemic immunity triggered by pathogen or azelaic acid and of the priming of SA induction in plants. Furthermore, the predicted secreted protein AZI1 is also important for generating vascular sap that confers disease resistance. Thus, azelaic acid and AZI1 are components of plant systemic immunity involved in priming defenses.

Coordinatively Unsaturated Al3+ Centers as Binding Sites for Active Catalyst Phases of Platinum on γ-Al2O3

Abstract: In many heterogeneous catalysts, the interaction of metal particles with their oxide support can alter the electronic properties of the metal and can play a critical role in determining particle morphology and maintaining dispersion. We used a combination of ultrahigh magnetic field, solid-state magic-angle spinning nuclear magnetic resonance spectroscopy, and high-angle annular dark-field scanning transmission electron microscopy coupled with density functional theory calculations to reveal the nature of anchoring sites of a catalytically active phase of platinum on the surface of a γ-Al 2 O 3 catalyst support material. The results obtained show that coordinatively unsaturated pentacoordinate Al 3+ (Al 3+ penta ) centers present on the (100) facets of the γ-Al 2 O 3 surface are anchoring Pt. At low loadings, the active catalytic phase is atomically dispersed on the support surface (Pt/Al 3+ penta = 1), whereas two-dimensional Pt rafts form at higher coverages.

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

Abstract: The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial-microbial and microbial-host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.

MIRD Pamphlet No. 21: A Generalized Schema for Radiopharmaceutical Dosimetry—Standardization of Nomenclature

Abstract: The internal dosimetry schema of the Medical Internal Radiation Dose (MIRD) Committee of the Society of Nuclear Medicine has provided a broad framework for assessment of the absorbed dose to whole organs, tissue subregions, voxelized tissue structures, and individual cellular compartments for use in both diagnostic and therapeutic nuclear medicine. The schema was originally published in 1968, revised in 1976, and republished in didactic form with comprehensive examples as the MIRD primer in 1988 and 1991. The International Commission on Radiological Protection (ICRP) is an organization that also supplies dosimetric models and technical data, for use in providing recommendations for limits on ionizing radiation exposure to workers and members of the general public. The ICRP has developed a dosimetry schema similar to that of the MIRD Committee but has used different terminology and symbols for fundamental quantities such as the absorbed fraction, specific absorbed fraction, and various dose coefficients. The MIRD Committee objectives for this pamphlet are 3-fold: to restate its schema for assessment of absorbed dose in a manner consistent with the needs of both the nuclear medicine and the radiation protection communities, with the goal of standardizing nomenclature; to formally adopt the dosimetry quantities equivalent dose and effective dose for use in comparative evaluations of potential risks of radiation-induced stochastic effects to patients after nuclear medicine procedures; and to discuss the need to identify dosimetry quantities based on absorbed dose that address deterministic effects relevant to targeted radionuclide therapy.

A class of parallel tiled linear algebra algorithms for multicore architectures

Abstract: As multicore systems continue to gain ground in the high performance computing world, linear algebra algorithms have to be reformulated or new algorithms have to be developed in order to take advantage of the architectural features on these new processors. Fine grain parallelism becomes a major requirement and introduces the necessity of loose synchronization in the parallel execution of an operation. This paper presents algorithms for the Cholesky, LU and QR factorization where the operations can be represented as a sequence of small tasks that operate on square blocks of data. These tasks can be dynamically scheduled for execution based on the dependencies among them and on the availability of computational resources. This may result in out of order execution of tasks which will completely hide the presence of intrinsically sequential tasks in the factorization. Performance comparisons are presented with LAPACK algorithms where parallelism can only be exploited at the level of the BLAS operations and vendor implementations.

HPCTOOLKIT: tools for performance analysis of optimized parallel programs

Abstract: SUMMARY HPCTOOLKIT is an integrated suite of tools that supports measurement, analysis, attribution, and presentation of application performance for both sequential and parallel programs. HPCTOOLKIT can pinpoint and quantify scalability bottlenecks in fully-optimized parallel programs with a measurement overhead of only a few percent. Recently, new capabilities were added to HPCTOOLKIT for collecting call path profiles for fully-optimized codes without any compiler support, pinpointing and quantifying bottlenecks in multithreaded programs, exploring performance information and source code using a new user interface, and displaying hierarchical space-time diagrams based on traces of asynchronous call stack samples. This paper provides an overview of HPCTOOLKIT and illustrates its utility for performance analysis of parallel applications.

Near-degeneracy of several pairing channels in multiorbital models for the Fe pnictides

Abstract: Weak-coupling approaches to the pairing problem in the iron pnictide superconductors have predicted a wide variety of superconducting ground states. We argue here that this is due both to the inadequacy of certain approximations to the effective low-energy band structure, and to the natural near degeneracy of different pairing channels in superconductors with many distinct Fermi surface sheets. In particular, we review attempts to construct two-orbital effective band models, the argument for their fundamental inconsistency with the symmetry of these materials, and compare the dynamical susceptibilities of two- and five-orbital tight-binding models. We then present results for the magnetic properties, pairing interactions and pairing instabilities within a five-orbital tight-binding random phase approximation model. We discuss the robustness of these results for different dopings, interaction strengths and variations in band structures. Within the parameter space explored, an anisotropic, sign-changing s-wave (A1g) state and a (B1g) state are nearly degenerate, due to the near nesting of Fermi surface sheets.

Terascale direct numerical simulations of turbulent combustion using S3D

Abstract: Computational science is paramount to the understanding of underlying processes in internal combustion engines of the future that will utilize non-petroleum-based alternative fuels, including carbon-neutral biofuels, and burn in new combustion regimes that will attain high efficiency while minimizing emissions of particulates and nitrogen oxides. Next-generation engines will likely operate at higher pressures, with greater amounts of dilution and utilize alternative fuels that exhibit a wide range of chemical and physical properties. Therefore, there is a significant role for high-fidelity simulations, direct numerical simulations (DNS), specifically designed to capture key turbulence-chemistry interactions in these relatively uncharted combustion regimes, and in particular, that can discriminate the effects of differences in fuel properties. In DNS, all of the relevant turbulence and flame scales are resolved numerically using high-order accurate numerical algorithms. As a consequence terascale DNS are computationally intensive, require massive amounts of computing power and generate tens of terabytes of data. Recent results from terascale DNS of turbulent flames are presented here, illustrating its role in elucidating flame stabilization mechanisms in a lifted turbulent hydrogen/air jet flame in a hot air coflow, and the flame structure of a fuel-lean turbulent premixed jet flame. Computing at this scale requires close collaborations between computer and combustion scientists to provide optimized scaleable algorithms and software for terascale simulations, efficient collective parallel I/O, tools for volume visualization of multiscale, multivariate data and automating the combustion workflow. The enabling computer science, applied to combustion science, is also required in many other terascale physics and engineering simulations. In particular, performance monitoring is used to identify the performance of key kernels in the DNS code, S3D and especially memory intensive loops in the code. Through the careful application of loop transformations, data reuse in cache is exploited thereby reducing memory bandwidth needs, and hence, improving S3D's nodal performance. To enhance collective parallel I/O in S3D, an MPI-I/O caching design is used to construct a two-stage write-behind method for improving the performance of write-only operations. The simulations generate tens of terabytes of data requiring analysis. Interactive exploration of the simulation data is enabled by multivariate time-varying volume visualization. The visualization highlights spatial and temporal correlations between multiple reactive scalar fields using an intuitive user interface based on parallel coordinates and time histogram. Finally, an automated combustion workflow is designed using Kepler to manage large-scale data movement, data morphing, and archival and to provide a graphical display of run-time diagnostics.

Tracking the rhythm of the seasons in the face of global change: phenological research in the 21st century.

Abstract: Phenology is the study of recurring life-cycle events, classic examples being the flowering of plants and animal migration. Phenological responses are increasingly relevant for addressing applied environmental issues. Yet, challenges remain with respect to spanning scales of observation, integrating observations across taxa, and modeling phenological sequences to enable ecological forecasts in light of future climate change. Recent advances that are helping to address these questions include refined landscape-scale phenology estimates from satellite data, advanced, instrument-based approaches for field measurements, and new cyberinfrastructure for archiving and distribution of products. These breakthroughs are improving our understanding in diverse areas, including modeling land-surface exchange, evaluating climate–phenology relationships, and making land-management decisions.

Shotgun metaproteomics of the human distal gut microbiota.

Abstract: The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

Electric modulation of conduction in multiferroic Ca-doped BiFeO3 films

Abstract: Many interesting materials phenomena such as the emergence of high-Tc superconductivity in the cuprates and colossal magnetoresistance in the manganites arise out of a doping-driven competition between energetically similar ground states. Doped multiferroics present a tantalizing evolution of this generic concept of phase competition. Here, we present the observation of an electronic conductor-insulator transition by control of band-filling in the model antiferromagnetic ferroelectric BiFeO3 through Ca doping. Application of electric field enables us to control and manipulate this electronic transition to the extent that a p-n junction can be created, erased and inverted in this material. A 'dome-like' feature in the doping dependence of the ferroelectric transition is observed around a Ca concentration of approximately 1/8, where a new pseudo-tetragonal phase appears and the electric modulation of conduction is optimized. Possible mechanisms for the observed effects are discussed on the basis of the interplay of ionic and electronic conduction. This observation opens the door to merging magnetoelectrics and magnetoelectronics at room temperature by combining electronic conduction with electric and magnetic degrees of freedom already present in the multiferroic BiFeO3.

First-order magnetic and structural phase transitions in Fe1+ySexTe1-x

Abstract: We use bulk magnetic susceptibility, electronic specific heat, and neutron scattering to study structural and magnetic phase transitions in Fe1+ySexTe1-x. Fe1.068Te exhibits a first-order phase transition near 67 K with a tetragonal-to-monoclinic structural transition and simultaneously develops a collinear antiferromagnetic (AF) order responsible for the entropy change across the transition. Systematic studies of the FeSe1-xTex system reveal that the AF structure and lattice distortion in these materials are different from those of FeAs-based pnictides. These results call into question the conclusions of present density-functional calculations, where FeSe1-xTex and FeAs-based pnictides are expected to have similar Fermi surfaces and therefore the same spin-density wave AF order.

Polarization Control of Electron Tunneling into Ferroelectric Surfaces

Abstract: We demonstrate a highly reproducible control of local electron transport through a ferroelectric oxide via its spontaneous polarization. Electrons are injected from the tip of an atomic force microscope into a thin film of lead-zirconate titanate, Pb(Zr0.2Ti0.8)O3, in the regime of electron tunneling assisted by a high electric field (Fowler-Nordheim tunneling). The tunneling current exhibits a pronounced hysteresis with abrupt switching events that coincide, within experimental resolution, with the local switching of ferroelectric polarization. The large spontaneous polarization of the PZT film results in up to 500-fold amplification of the tunneling current upon ferroelectric switching. The magnitude of the effect is subject to electrostatic control via ferroelectric switching, suggesting possible applications in ultrahigh-density data storage and spintronics.

Knowledge discovery from data streams

Abstract: Since the beginning of the Internet age and the increased use of ubiquitous computing devices, the large volume and continuous flow of distributed data have imposed new constraints on the design of learning algorithms. Exploring how to extract knowledge structures from evolving and time-changing data, Knowledge Discovery from Data Streams presents a coherent overview of state-of-the-art research in learning from data streams. The book covers the fundamentals that are imperative to understanding data streams and describes important applications, such as TCP/IP traffic, GPS data, sensor networks, and customer click streams. It also addresses several challenges of data mining in the future, when stream mining will be at the core of many applications. These challenges involve designing useful and efficient data mining solutions applicable to real-world problems. In the appendix, the author includes examples of publicly available software and online data sets. This practical, up-to-date book focuses on the new requirements of the next generation of data mining. Although the concepts presented in the text are mainly about data streams, they also are valid for different areas of machine learning and data mining.

Bulk superconductivity at 14 K in single crystals of Fe 1 + y Te x Se 1 − x

Abstract: Resistivity, magnetic susceptibility, and heat-capacity measurements are reported for single crystals of Fe{sub 1+y}Te{sub x}Se{sub 1-x} grown via a modified Bridgeman method with 0 < y < 0.15 and x = 1, 0.9, 0.75, 0. 67, 0.55, and 0.5. Although resistivity measurements show traces of superconductivity near 14 K for all x except x = 1, only crystals grown with compositions near x = 0.5 exhibit bulk superconductivity. The appearance of bulk superconductivity correlates with a reduction in the magnitude of the magnetic susceptibility at room temperature and smaller values of y, the concentration of Fe in the Fe(2) site.

Carbon-nitrogen interactions regulate climate-carbon cycle feedbacks: results from an atmosphere-ocean general circulation model

Abstract: Inclusion of fundamental ecological interactions between carbon and nitrogen cycles in the land component of an atmosphere-ocean general circulation model (AOGCM) leads to decreased carbon uptake associated with CO2 fertil- ization, and increased carbon uptake associated with warm- ing of the climate system. The balance of these two oppos- ing effects is to reduce the fraction of anthropogenic CO2 predicted to be sequestered in land ecosystems. The primary mechanism responsible for increased land carbon storage un- der radiatively forced climate change is shown to be fertiliza- tion of plant growth by increased mineralization of nitrogen directly associated with increased decomposition of soil or- ganic matter under a warming climate, which in this partic- ular model results in a negative gain for the climate-carbon feedback. Estimates for the land and ocean sink fractions of recent anthropogenic emissions are individually within the range of observational estimates, but the combined land plus ocean sink fractions produce an airborne fraction which is too high compared to observations. This bias is likely due in part to an underestimation of the ocean sink frac- tion. Our results show a significant growth in the airborne fraction of anthropogenic CO2 emissions over the coming

Power-law scaling and fractal nature of medium-range order in metallic glasses.

Abstract: Understanding the short- and medium-range structure of metallic glasses remains a difficult challenge The observation that the medium-range order has the characteristics of a fractal network may have broader implications in the understanding of the relation between structure and mechanical properties in metallic glasses The atomic structure of metallic glasses has been a long-standing scientific problem Unlike crystalline metals, where long-range ordering is established by periodic stacking of fundamental building blocks known as unit cells, a metallic glass has no long-range translational or orientational order, although some degrees of short- and medium-range order do exist1,2,3 Previous studies1,2,3,4 have identified solute- (minority atom)-centred clusters as the fundamental building blocks or short-range order in metallic glasses Idealized cluster packing schemes, such as efficient cluster packing on a cubic lattice1 and icosahedral packing3 as in a quasicrystal, have been proposed and provided first insights on the medium-range order in metallic glasses However, these packing schemes break down beyond a length scale of a few clusters Here, on the basis of neutron and X-ray diffraction experiments, we propose a new packing scheme—self-similar packing of atomic clusters We show that the medium-range order has the characteristics of a fractal network with a dimension of 231, and is described by a power-law correlation function over the medium-range length scale Our finding provides a new perspective of order in disordered materials and has broad implications for understanding their structure–property relationship, particularly those involving a change in length scales

Facile ionothermal synthesis of microporous and mesoporous carbons from task specific ionic liquids.

Abstract: An expedient, template-free, high-yield, and solventless route to nitrogen-rich micro- and mesoporous carbons is reported based on direct, atmospheric-pressure carbonization of task-specific ionic liquids bearing one or more nitrile side chains. The resulting textural properties (pore regime, surface area) are highly dependent upon the structural motifs of the ions comprising the corresponding parent ionic liquid, and uniform carbon films are routinely deposited with this novel methodology, highlighting excited new opportunities in the development of advanced functional carbon composites.

Toward Exascale Resilience

Abstract: Over the past few years resilience has became a major issue for high-performance computing (HPC) systems, in particular in the perspective of large petascale systems and future exascale systems. These systems will typically gather from half a million to several millions of central processing unit (CPU) cores running up to a billion threads. From the current knowledge and observations of existing large systems, it is anticipated that exascale systems will experience various kind of faults many times per day. It is also anticipated that the current approach for resilience, which relies on automatic or application level checkpoint/ restart, will not work because the time for checkpointing and restarting will exceed the mean time to failure of a full system. This set of projections leaves the community of fault tolerance for HPC systems with a difficult challenge: finding new approaches, which are possibly radically disruptive, to run applications until their normal termination, despite the essentially unstable nature of exascale systems. Yet, the community has only five to six years to solve the problem. This white paper synthesizes the motivations, observations and research issues considered as determinant of several complimentary experts of HPC in applications, programming models, distributed systems and system management.