Showing papers by "Oak Ridge National Laboratory published in 2007"

Scientific aspects of polymer electrolyte fuel cell durability and degradation.

Abstract: Rod Borup is a Team Leader in the fuel cell program at Los Alamos National Lab in Los Alamos, New Mexico. He received his B.S.E. in Chemical Engineering from the University of Iowa in 1988 and his Ph.D. from the University of Washington in 1993. He has worked on fuel cell technology since 1994, working in the areas of hydrogen production and PEM fuel cell stack components. He has been awarded 12 U.S. patents, authored over 40 papers related to fuel cell technology, and presented over 50 oral papers at national meetings. His current main research area is related to water transport in PEM fuel cells and PEM fuel cell durability. Recently, he was awarded the 2005 DOE Hydrogen Program R&D Award for the most significant R&D contribution of the year for his team's work in fuel cell durability and was the Principal Investigator for the 2004 Fuel Cell Seminar (San Antonio, TX, USA) Best Poster Award. Jeremy Meyers is an Assistant Professor of materials science and engineering and mechanical engineering at the University of Texas at Austin, where his research focuses on the development of electrochemical energy systems and materials. Prior to joining the faculty at Texas, Jeremy workedmore » as manager of the advanced transportation technology group at UTC Power, where he was responsible for developing new system designs and components for automotive PEM fuel cell power plants. While at UTC Power, Jeremy led several customer development projects and a DOE-sponsored investigation into novel catalysts and membranes for PEM fuel cells. Jeremy has coauthored several papers on key mechanisms of fuel cell degradation and is a co-inventor of several patents. In 2006, Jeremy and several colleagues received the George Mead Medal, UTC's highest award for engineering achievement, and he served as the co-chair of the Gordon Research Conference on fuel cells. Jeremy received his Ph.D. in Chemical Engineering from the University of California at Berkeley and holds a Bachelor's Degree in Chemical Engineering from Stanford University. Bryan Pivovar received his B.S. in Chemical Engineering from the University of Wisconsin in 1994. He completed his Ph.D. in Chemical Engineering at the University of Minnesota in 2000 under the direction of Profs. Ed Cussler and Bill Smyrl, studying transport properties in fuel cell electrolytes. He continued working in the area of polymer electrolyte fuel cells at Los Alamos National Laboratory as a post-doc (2000-2001), as a technical staff member (2001-2005), and in his current position as a team leader (2005-present). In this time, Bryan's research has expanded to include further aspects of fuel cell operation, including electrodes, subfreezing effects, alternative polymers, hydroxide conductors, fuel cell interfaces, impurities, water transport, and high-temperature membranes. Bryan has served at various levels in national and international conferences and workshops, including organizing a DOE sponsored workshop on freezing effects in fuel cells and an ARO sponsored workshop on alkaline membrane fuel cells, and he was co-chair of the 2007 Gordon Research Conference on Fuel Cells. Minoru Inaba is a Professor at the Department of Molecular Science and Technology, Faculty of Engineering, Doshisha University, Japan. He received his B.Sc. from the Faculty of Engineering, Kyoto University, in 1984 and his M.Sc. in 1986 and his Dr. Eng. in 1995 from the Graduate School of Engineering, Kyoto University. He has worked on electrochemical energy conversion systems including fuel cells and lithium-ion batteries at Kyoto University (1992-2002) and at Doshisha University (2002-present). His primary research interest is the durability of polymer electrolyte fuel cells (PEFCs), in particular, membrane degradation, and he has been involved in NEDO R&D research projects on PEFC durability since 2001. He has authored over 140 technical papers and 30 review articles. Kenichiro Ota is a Professor of the Chemical Energy Laboratory at the Graduate School of Engineering, Yokohama National University, Japan. He received his B.S.E. in Applied Chemistry from the University of Tokyo in 1968 and his Ph.D. from the University of Tokyo in 1973. He has worked on hydrogen energy and fuel cells since 1974, working on materials science for fuel cells and water electrolysis. He has published more than 150 original papers, 70 review papers, and 50 scientific books. He is now the president of the Hydrogen Energy Systems Society of Japan, the chairman of the Fuel Cell Research Group of the Electrochemical Society of Japan, and the chairman of the National Committee for the Standardization of the Stationary Fuel Cells. ABSTRACT TRUNCATED« less

Global and regional drivers of accelerating CO2 emissions

Abstract: CO2 emissions from fossil-fuel burning and industrial processes have been accelerating at a global scale, with their growth rate increasing from 1.1% y(-1) for 1990-1999 to >3% y(-1) for 2000-2004. The emissions growth rate since 2000 was greater than for the most fossil-fuel intensive of the Intergovernmental Panel on Climate Change emissions scenarios developed in the late 1990s. Global emissions growth since 2000 was driven by a cessation or reversal of earlier declining trends in the energy intensity of gross domestic product (GDP) (energy/GDP) and the carbon intensity of energy (emissions/energy), coupled with continuing increases in population and per-capita GDP. Nearly constant or slightly increasing trends in the carbon intensity of energy have been recently observed in both developed and developing regions. No region is decarbonizing its energy supply. The growth rate in emissions is strongest in rapidly developing economies, particularly China. Together, the developing and least-developed economies (forming 80% of the world's population) accounted for 73% of global emissions growth in 2004 but only 41% of global emissions and only 23% of global cumulative emissions since the mid-18th century. The results have implications for global equity.

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.

Abstract: From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding ‘higher’ Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H_2 metabolism, CO_2-reductive acetogenesis and N_2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-μl environment can be.

CO2 balance of boreal, temperate, and tropical forests derived from a global database

Abstract: Terrestrial ecosystems sequester 2.1 Pg of atmospheric carbon annually. A large amount of the terrestrial sink is realized by forests. However, considerable uncertainties remain regarding the fate of this carbon over both short and long timescales. Relevant data to address these uncertainties are being collected at many sites around the world, but syntheses of these data are still sparse. To facilitate future synthesis activities, we have assembled a comprehensive global database for forest ecosystems, which includes carbon budget variables (fluxes and stocks), ecosystem traits (e.g. leaf area index, age), as well as ancillary site information such as management regime, climate, and soil characteristics. This publicly available database can be used to quantify global, regional or biome-specific carbon budgets; to re-examine established relationships; to test emerging hypotheses about ecosystem functioning [e.g. a constant net ecosystem production (NEP) to gross primary production (GPP) ratio]; and as benchmarks for model evaluations. In this paper, we present the first analysis of this database. We discuss the climatic influences on GPP, net primary production (NPP) and NEP and present the CO2 balances for boreal, temperate, and tropical forest biomes based on micrometeorological, ecophysiological, and biometric flux and inventory estimates. Globally, GPP of forests benefited from higher temperatures and precipitation whereas NPP saturated above either a threshold of 1500 mm precipitation or a mean annual temperature of 10 degrees C. The global pattern in NEP was insensitive to climate and is hypothesized to be mainly determined by nonclimatic conditions such as successional stage, management, site history, and site disturbance. In all biomes, closing the CO2 balance required the introduction of substantial biome-specific closure terms. Nonclosure was taken as an indication that respiratory processes, advection, and non-CO2 carbon fluxes are not presently being adequately accounted for.

Complex systems analysis of series of blackouts: Cascading failure, critical points, and self-organization

Abstract: We give an overview of a complex systems approach to large blackouts of electric power transmission systems caused by cascading failure. Instead of looking at the details of particular blackouts, we study the statistics and dynamics of series of blackouts with approximate global models. Blackout data from several countries suggest that the frequency of large blackouts is governed by a power law. The power law makes the risk of large blackouts consequential and is consistent with the power system being a complex system designed and operated near a critical point. Power system overall loading or stress relative to operating limits is a key factor affecting the risk of cascading failure. Power system blackout models and abstract models of cascading failure show critical points with power law behavior as load is increased. To explain why the power system is operated near these critical points and inspired by concepts from self-organized criticality, we suggest that power system operating margins evolve slowly to near a critical point and confirm this idea using a power system model. The slow evolution of the power system is driven by a steady increase in electric loading, economic pressures to maximize the use of the grid, and the engineering responses to blackouts that upgrade the system. Mitigation of blackout risk should account for dynamical effects in complex self-organized critical systems. For example, some methods of suppressing small blackouts could ultimately increase the risk of large blackouts.

Chapter 2: Plasma confinement and transport

Abstract: The understanding and predictive capability of transport physics and plasma confinement is reviewed from the perspective of achieving reactor-scale burning plasmas in the ITER tokamak, for both core and edge plasma regions. Very considerable progress has been made in understanding, controlling and predicting tokamak transport across a wide variety of plasma conditions and regimes since the publication of the ITER Physics Basis (IPB) document (1999 Nucl. Fusion 39 2137-2664). Major areas of progress considered here follow. (1) Substantial improvement in the physics content, capability and reliability of transport simulation and modelling codes, leading to much increased theory/experiment interaction as these codes are increasingly used to interpret and predict experiment. (2) Remarkable progress has been made in developing and understanding regimes of improved core confinement. Internal transport barriers and other forms of reduced core transport are now routinely obtained in all the leading tokamak devices worldwide. (3) The importance of controlling the H-mode edge pedestal is now generally recognized. Substantial progress has been made in extending high confinement H-mode operation to the Greenwald density, the demonstration of Type I ELM mitigation and control techniques and systematic explanation of Type I ELM stability. Theory-based predictive capability has also shown progress by integrating the plasma and neutral transport with MHD stability. (4) Transport projections to ITER are now made using three complementary approaches: empirical or global scaling, theory-based transport modelling and dimensionless parameter scaling (previously, empirical scaling was the dominant approach). For the ITER base case or the reference scenario of conventional ELMy H-mode operation, all three techniques predict that ITER will have sufficient confinement to meet its design target of Q = 10 operation, within similar uncertainties.

A Synthesis of Progress and Uncertainties in Attributing the Sources of Mercury in Deposition

Abstract: A panel of international experts was convened in Madison, Wisconsin, in 2005, as part of the 8th International Conference on Mercury as a Global Pollutant. Our charge was to address the state of science pertinent to source attribution, specifically our key question was: "For a given location, can we ascertain with confidence the relative contributions of local, regional, and global sources, and of natural versus anthropogenic emissions to mercury deposition?" The panel synthesized new research pertinent to this question published over the past decade, with emphasis on four major research topics: long-term anthropogenic change, current emission and deposition trends, chemical transformations and cycling, and modeling and uncertainty. Within each topic, the panel drew a series of conclusions, which are presented in this paper. These conclusions led us to concur that the answer to our question is a "qualified yes," with the qualification being dependent upon the level of uncertainty one is willing to accept. We agreed that the uncertainty is strongly dependent upon scale and that our question as stated is answerable with greater confidence both very near and very far from major point sources, assuming that the "global pool" is a recognizable "source." Many regions of interest from an ecosystem-exposure standpoint lie in between, where source attribution carries the greatest degree of uncertainty.

The likely impact of elevated [CO2], nitrogen deposition, increased temperature and management on carbon sequestration in temperate and boreal forest ecosystems: a literature review.

Abstract: Temperate and boreal forest ecosystems contain a large part of the carbon stored on land, in the form of both biomass and soil organic matter. Increasing atmospheric [CO2], increasing temperature, elevated nitrogen deposition and intensified management will change this C store. Well documented single-factor responses of net primary production are: higher photosynthetic rate (the main [CO2] response); increasing length of growing season (the main temperature response); and higher leaf-area index (the main N deposition and partly [CO2] response). Soil organic matter will increase with increasing litter input, although priming may decrease the soil C stock initially, but litter quality effects should be minimal (response to [CO2], N deposition, and temperature); will decrease because of increasing temperature; and will increase because of retardation of decomposition with N deposition, although the rate of decomposition of high-quality litter can be increased and that of low-quality litter decreased. Single-factor responses can be misleading because of interactions between factors, in particular those between N and other factors, and indirect effects such as increased N availability from temperature-induced decomposition. In the long term the strength of feedbacks, for example the increasing demand for N from increased growth, will dominate over short-term responses to single factors. However, management has considerable potential for controlling the C store.

Fractionating recalcitrant lignocellulose at modest reaction conditions.

Abstract: Effectively releasing the locked polysaccharides from recalcitrant lignocellulose to fermentable sugars is among the greatest technical and economic barriers to the realization of lignocellulose biorefineries because leading lignocellulose pre-treatment technologies suffer from low sugar yields, and/or severe reaction conditions, and/or high cellulase use, narrow substrate applicability, and high capital investment, etc. A new lignocellulose pre-treatment featuring modest reaction conditions (50 degrees C and atmospheric pressure) was demonstrated to fractionate lignocellulose to amorphous cellulose, hemicellulose, lignin, and acetic acid by using a non-volatile cellulose solvent (concentrated phosphoric acid), a highly volatile organic solvent (acetone), and water. The highest sugar yields after enzymatic hydrolysis were attributed to no sugar degradation during the fractionation and the highest enzymatic cellulose digestibility ( approximately 97% in 24 h) during the hydrolysis step at the enzyme loading of 15 filter paper units of cellulase and 60 IU of beta-glucosidase per gram of glucan. Isolation of high-value lignocellulose components (lignin, acetic acid, and hemicellulose) would greatly increase potential revenues of a lignocellulose biorefinery.

GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes

Abstract: Owing to their vast diversity and as-yet uncultivated status, detection, characterization and quantification of microorganisms in natural settings are very challenging, and linking microbial diversity to ecosystem processes and functions is even more difficult. Microarray-based genomic technology for detecting functional genes and processes has a great promise of overcoming such obstacles. Here, a novel comprehensive microarray, termed GeoChip, has been developed, containing 24 243 oligonucleotide (50 mer) probes and covering 410 000 genes in 4150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation. The developed GeoChip was successfully used for tracking the dynamics of metal-reducing bacteria and associated communities for an in situ bioremediation study. This is the first comprehensive microarray currently available for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. It is particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions.

Current Production and Metal Oxide Reduction by Shewanella oneidensis MR-1 Wild Type and Mutants

Abstract: Shewanella oneidensis MR-1 is a gram-negative facultative anaerobe capable of utilizing a broad range of electron acceptors, including several solid substrates. S. oneidensis MR-1 can reduce Mn(IV) and Fe(III) oxides and can produce current in microbial fuel cells. The mechanisms that are employed by S. oneidensis MR-1 to execute these processes have not yet been fully elucidated. Several different S. oneidensis MR-1 deletion mutants were generated and tested for current production and metal oxide reduction. The results showed that a few key cytochromes play a role in all of the processes but that their degrees of participation in each process are very different. Overall, these data suggest a very complex picture of electron transfer to solid and soluble substrates by S. oneidensis MR-1.

Current and potential U.S. corn stover supplies.

Abstract: Agricultural residues such as corn (Zea mays L.) stover are a potential feedstock for bioenergy and bio-based products that could reduceU.S. dependence on foreign oil. Collection of such residues must take into account concerns that residue removal could increase erosion, reduce crop productivity, and deplete soil carbon and nutrients. This article estimates where and how much corn stover can be collected sustainably in the USA using existing commercial equipment and estimates costs of that collection. Erosion constraints to collection were considered explicitly, and crop productivity and soil nutrient constraints were considered implicitly, by recognizing the value of residues for maintaining soil moisture and including the cost of fertilizer to replace nutrients removed. Possible soil carbon loss was not considered in the analysis. With an annual production of 196 million Mg of corn grain (about9.2 billion bushels), the USA produces 196 million Mg of stover. Under current rotation and tillage practices, about 30% of this stover could be collected for less than $33 per Mg, taking into consideration erosion and soil moisture concerns and nutrient replacement costs. Wind erosion is a major constraint to stover collection. Analysis suggests three regions of the country (central Illinois, northern Iowa/southern Minnesota, and along themore » Platte River in Nebraska) produce sufficient stover to support large biorefineries with one million Mg per year feedstock demands and that if farmers converted to universal no-till production of corn, then over 100 million Mg of stover could be collected annually without causing erosion to exceed the tolerable soil loss.« less

Energy loss and flow of heavy quarks in Au+Au collisions at sNN=200GeV

Abstract: The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured electrons with 0.3 < p(T) < 9 GeV/c at midrapidity (y < 0.35) from heavy-flavor (charm and bottom) decays in Au + Au collisions at root s(NN) = 200 GeV. The nuclear modification factor R-AA relative to p + p collisions shows a strong suppression in central Au + Au collisions, indicating substantial energy loss of heavy quarks in the medium produced at RHIC energies. A large azimuthal anisotropy v(2) with respect to the reaction plane is observed for 0.5 < p(T) < 5 GeV/c indicating substantial heavy-flavor elliptic flow. Both R-AA and v(2) show a p(T) dependence different from those of neutral pions. A comparison to transport models which simultaneously describe R-AA(p(T)) and v(2)(p(T)) suggests that the viscosity to entropy density ratio is close to the conjectured quantum lower bound, i.e., near a perfect fluid.

A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity

Abstract: Here, we report a catalytic beacon sensor for uranyl (UO22+) based on an in vitro-selected UO22+-specific DNAzyme. The sensor consists of a DNA enzyme strand with a 3′ quencher and a DNA substrate with a ribonucleotide adenosine (rA) in the middle and a fluorophore and a quencher at the 5′ and 3′ ends, respectively. The presence of UO22+ causes catalytic cleavage of the DNA substrate strand at the rA position and release of the fluorophore and thus dramatic increase of fluorescence intensity. The sensor has a detection limit of 11 parts per trillion (45 pM), a dynamic range up to 400 nM, and selectivity of >1-million-fold over other metal ions. The most interfering metal ion, Th(IV), interacts with the fluorescein fluorophore, causing slightly enhanced fluorescence intensity, with an apparent dissociation constant of ≈230 μM. This sensor rivals the most sensitive analytical instruments for uranium detection, and its application in detecting uranium in contaminated soil samples is also demonstrated. This work shows that simple, cost-effective, and portable metal sensors can be obtained with similar sensitivity and selectivity as much more expensive and sophisticated analytical instruments. Such a sensor will play an important role in environmental remediation of radionuclides such as uranium.

Dual-frequency resonance-tracking atomic force microscopy

Abstract: A dual-excitation method for resonant-frequency tracking in scanning probe microscopy based on amplitude detection is developed. This method allows the cantilever to be operated at or near resonance for techniques where standard phase locked loops are not possible. This includes techniques with non-acoustic driving where the phase of the driving force is frequency and/or position dependent. An example of the latter is piezoresponse force microscopy (PFM), where the resonant frequency of the cantilever is strongly dependent on the contact stiffness of the tip–surface junction and the local mechanical properties, but the spatial variability of the drive phase rules out the use of a phase locked loop. Combined with high-voltage switching and imaging, dual-frequency, resonance-tracking PFM allows reliable studies of electromechanical and elastic properties and polarization dynamics in a broad range of inorganic and biological systems, and is illustrated using lead zirconate–titanate, rat tail collagen, and native and switched ferroelectric domains in lithium niobate.

The band excitation method in scanning probe microscopy for rapid mapping of energy dissipation on the nanoscale

Abstract: Mapping energy transformation pathways and dissipation on the nanoscale and understanding the role of local structure in dissipative behavior is a key challenge for imaging in areas ranging from electronics and information technologies to efficient energy production. Here we develop a family of novel scanning probe microscopy (SPM) techniques in which the cantilever is excited and the response is recorded over a band of frequencies simultaneously, rather than at a single frequency as in conventional SPMs. This band excitation (BE) SPM allows very rapid acquisition of the full frequency response at each point (i.e. transfer function) in an image and in particular enables the direct measurement of energy dissipation through the determination of the Q-factor of the cantilever–sample system. The BE method is demonstrated for force–distance and voltage spectroscopies and for magnetic dissipation imaging with sensitivity close to the thermomechanical limit. The applicability of BE for various SPMs is analyzed, and the method is expected to be universally applicable to ambient and liquid SPMs.

J/psi production versus centrality, transverse momentum, and rapidity in Au+Au collisions at root S-NN=200 GeV

Abstract: The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured J/psi production for rapidities -2.2 < y < 2.2 in Au+Au collisions at root s(NN)=200 GeV. The J/psi invariant yield and nuclear modification factor R-AA as a function of centrality, transverse momentum, and rapidity are reported. A suppression of J/psi relative to binary collision scaling of proton-proton reaction yields is observed. Models which describe the lower energy J/psi data at the CERN Super Proton Synchrotron invoking only J/psi destruction based on the local medium density predict a significantly larger suppression at RHIC and more suppression at midrapidity than at forward rapidity. Both trends are contradicted by our data.

Unique chemical reactivity of a graphene nanoribbon's zigzag edge.

Abstract: The zigzag edge of a graphene nanoribbon possesses a unique electronic state that is near the Fermi level and localized at the edge carbon atoms. The authors investigate the chemical reactivity of these zigzag edge sites by examining their reaction energetics with common radicals from first principles. A "partial radical" concept for the edge carbon atoms is introduced to characterize their chemical reactivity, and the validity of this concept is verified by comparing the dissociation energies of edge-radical bonds with similar bonds in molecules. In addition, the uniqueness of the zigzag-edged graphene nanoribbon is further demonstrated by comparing it with other forms of sp2 carbons, including a graphene sheet, nanotubes, and an armchair-edged graphene nanoribbon.

The phylum Cnidaria: A review of phylogenetic patterns and diversity 300 years after Linnaeus

Abstract: Systema Naturae includes representatives of every major lineage of the animal phylum Cnidaria. However, Linnaeus did not classify the members of the phylum as is now done, and the diversity of the group is not well represented. We contrast the Linnaean perspective on cnidarian diversity with the modern, phylogenetic perspective. For each order, we detail diversity at the family level, providing phylogenetic context where possible.

LandScan USA: a high-resolution geospatial and temporal modeling approach for population distribution and dynamics

Abstract: High-resolution population distribution data are critical for successfully addressing important issues ranging from socio-environmental research to public health to homeland security, since scientific analyses, operational activities, and policy decisions are significantly influenced by the number of impacted people. Dasymetric modeling has been a well-recognized approach for spatial decomposition of census data to increase the spatial resolution of population distribution. However, enhancing the temporal resolution of population distribution poses a greater challenge. In this paper, we discuss the development of LandScan USA, a multi-dimensional dasymetric modeling approach, which has allowed the creation of a very high-resolution population distribution data both over space and time. At a spatial resolution of 3 arc seconds (∼90 m), the initial LandScan USA database contains both a nighttime residential as well as a baseline daytime population distribution that incorporates movement of workers and students. Challenging research issues of disparate and misaligned spatial data and modeling to develop a database at a national scale, as well as model verification and validation approaches are illustrated and discussed. Initial analyses indicate a high degree of locational accuracy for LandScan USA distribution model and data. High-resolution population data such as LandScan USA, which describes both distribution and dynamics of human population, clearly has the potential to profoundly impact multiple domain applications of national and global priority.

Proactive fault tolerance for HPC with Xen virtualization

Abstract: Large-scale parallel computing is relying increasingly on clusters with thousands of processors. At such large counts of compute nodes, faults are becoming common place. Current techniques to tolerate faults focus on reactive schemes to recover from faults and generally rely on a checkpoint/restart mechanism. Yet, in today's systems, node failures can often be anticipated by detecting a deteriorating health status.Instead of a reactive scheme for fault tolerance (FT), we are promoting a proactive one where processes automatically migrate from "unhealthy" nodes to healthy ones. Our approach relies on operating system virtualization techniques exemplified by but not limited to Xen. This paper contributes an automatic and transparent mechanism for proactive FT for arbitrary MPI applications. It leverages virtualization techniques combined with health monitoring and load-based migration. We exploit Xen's live migration mechanism for a guest operating system (OS) to migrate an MPI task from a health-deteriorating node to a healthy one without stopping the MPI task during most of the migration. Our proactive FT daemon orchestrates the tasks of health monitoring, load determination and initiation of guest OS migration. Experimental results demonstrate that live migration hides migration costs and limits the overhead to only a few seconds making it an attractive approach to realize FT in HPC systems. Overall, our enhancements make proactive FT a valuable asset for long-running MPI application that is complementary to reactive FT using full checkpoint/restart schemes since checkpoint frequencies can be reduced as fewer unanticipated failures are encountered. In the context of OS virtualization, we believe that this is the first comprehensive study of proactive fault tolerance where live migration is actually triggered by health monitoring.

Size-dependent structural transformations of hematite nanoparticles. 1. Phase transition.

Abstract: Using Fourier Transform InfraRed (FTIR) spectroscopy, Raman spectroscopy, X-ray diffraction (XRD), and Transmission Electron Microscopy (TEM), we characterize the structure and/or morphology of hematite (α-Fe2O3) particles with sizes of 7, 18, 39 and 120 nm. It is found that these nanoparticles possess maghemite (γ-Fe2O3)-like defects in the near surface regions, to which a vibrational mode at 690 cm−1, active both in FTIR and Raman spectra, is assigned. The fraction of the maghemite-like defects and the net lattice disorder are inversely related to the particle size. However, the effect is opposite for nanoparticles grown by sintering of smaller hematite precursors under conditions when the formation of a uniform hematite-like structure throughout the aggregate is restricted by kinetic issues. This means that not only particle size but also the growth kinetics determines the structure of the nanoparticles. The observed structural changes are interpreted as size-induced α-Fe2O3 ↔ γ-Fe2O3 phase transitions. We develop a general model that considers spinel defects and absorbed/adsorbed species (in our case, hydroxyls) as dominant controls on structural changes with particle size in hematite nanoparticles, including solid-state phase transitions. These changes are represented by trajectories in a phase diagram built in three phase coordinates—concentrations of spinel defects, absorbed impurities, and adsorbed species. The critical size for the onset of the α → γ phase transition depends on the particle environment, and for the dry particles used in this study is about 40 nm. The model supports the existence of intermediate phases (protohematite and hydrohematite) during dehydration of goethite. We also demonstrate that the hematite structure is significantly less defective when the nanoparticles are immersed in water or KBr matrix, which is explained by the effects of the electrochemical double layer and increased rigidity of the particle environment. Finally, we revise the problem of applicability of IR spectroscopy to the lattice vibrations of hematite nanoparticles, demonstrating that structural comparison of different samples is much more reliable if it is based on the Eu band at about 460 cm−1 and the spinel band at 690 cm−1, instead of the A2u/Eu band at about 550 cm−1 used in previous work. The new methodology is applied to analysis of the reported IR spectra of Martian hematite.

Multiple Scales of Temporal Variability in Ecosystem Metabolism Rates: Results from 2 Years of Continuous Monitoring in a Forested Headwater Stream

Abstract: Headwater streams are key sites of nutrient and organic matter processing and retention, but little is known about temporal variability in gross primary production (GPP) and ecosystem respiration (ER) rates as a result of the short duration of most metabolism measurements in lotic ecosystems. We examined temporal variability and controls on ecosystem metabolism by measuring daily rates continuously for 2 years in Walker Branch, a first-order deciduous forest stream. Four important scales of temporal variability in ecosystem metabolism rates were identified: (1) seasonal, (2) day-to-day, (3) episodic (storm-related), and (4) inter-annual. Seasonal patterns were largely controlled by the leaf phenology and productivity of the deciduous riparian forest. Walker Branch was strongly net heterotrophic throughout the year with the exception of the open-canopy spring when GPP and ER rates were co-equal. Day-to-day variability in weather conditions influenced light reaching the streambed, resulting in high day-to-day variability in GPP particularly during spring (daily light levels explained 84% of the variance in daily GPP in April). Episodic storms depressed GPP for several days in spring, but increased GPP in autumn by removing leaves shading the streambed. Storms depressed ER initially, but then stimulated ER to 2–3 times pre-storm levels for several days. Walker Branch was strongly net heterotrophic in both years of the study, with annual GPP being similar (488 and 519 g O2 m−2 y−1 or 183 and 195 g C m−2 y−1) but annual ER being higher in 2004 than 2005 (−1,645 vs. −1,292 g O2 m−2 y−1 or −617 and −485 g C m−2 y−1). Inter-annual variability in ecosystem metabolism (assessed by comparing 2004 and 2005 rates with previous measurements) was the result of the storm frequency and timing and the size of the spring macroalgal bloom. Changes in local climate can have substantial impacts on stream ecosystem metabolism rates and ultimately influence the carbon source and sink properties of these important ecosystems.

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

Abstract: Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity-based ( blast hit distribution) and two sequence composition-based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.

Review of Atom Probe FIB-Based Specimen Preparation Methods

Abstract: Several FIB-based methods that have been developed to fabricate needle-shaped atom probe specimens from a variety of specimen geometries, and site-specific regions are reviewed. These methods have enabled electronic device structures to be characterized. The atom probe may be used to quantify the level and range of gallium implantation and has demonstrated that the use of low accelerating voltages during the final stages of milling can dramatically reduce the extent of gallium implantation.