Showing papers by "Pacific Northwest National Laboratory published in 2008"

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).

Abstract: Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.

Model for Simulating Aerosol Interactions and Chemistry (MOSAIC)

Abstract: This paper describes the development and evaluation of a new Model for Simulating Aerosol Interactions and Chemistry (MOSAIC), with a special focus on addressing the long-standing issues associated with solving the dynamic partitioning of semi-volatile inorganic gases (HNO3, HCl, and NH3) to size-distributed atmospheric aerosol particles. The coupled ordinary differential equations (ODE) for dynamic gas-particle mass transfer are extremely stiff, and the available numerical techniques are either too expensive or produce oscillatory and/or inaccurate steady-state solutions. These limitations are overcome in MOSAIC, which couples an accurate and computationally efficient thermodynamic module [Zaveri et al., 2005a,b] with a new dynamic gas-particle partitioning module described here. The algorithm involves time-split integrations of non-volatile and semi-volatile species, and a new concept of “dynamic pH” and an adaptive time-stepping scheme hold the key to smooth, accurate, and efficient solutions over the entire relative humidity range. MOSAIC is found to be in excellent agreement with a benchmark version of the model that uses LSODES (a Gear solver) for rigorously integrating the stiff ODEs. The steady-state MOSAIC results for monodisperse aerosol test cases are also in excellent agreement with those obtained with the benchmark equilibrium model AIM. MOSAIC is also evaluated within a 3-D model, andmore » the average CPU speed is estimated to be over 100 times faster than the dynamic aerosol model MADM [Pilinis et al., 2000]. These results suggest that MOSAIC is highly attractive for use in 3-D aerosol and air quality models in which both accuracy and efficiency are critically important.« less

Towards environmental systems biology of Shewanella

Abstract: Bacteria of the genus Shewanella are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of the various terminal electron acceptors that they encounter in their stratified environments. Owing to their diverse metabolic capabilities, shewanellae are important for carbon cycling and have considerable potential for the remediation of contaminated environments and use in microbial fuel cells. Systems-level analysis of the model species Shewanella oneidensis MR-1 and other members of this genus has provided new insights into the signal-transduction proteins, regulators, and metabolic and respiratory subsystems that govern the remarkable versatility of the shewanellae.

High-capacity hydrogen storage in lithium and sodium amidoboranes

Abstract: The safe and efficient storage of hydrogen is widely recognized as one of the key technological challenges in the transition towards a hydrogen-based energy economy. Whereas hydrogen for transportation applications is currently stored using cryogenics or high pressure, there is substantial research and development activity in the use of novel condensed-phase hydride materials. However, the multiple-target criteria accepted as necessary for the successful implementation of such stores have not yet been met by any single material. Ammonia borane, NH3BH3, is one of a number of condensed-phase compounds that have received significant attention because of its reported release of approximately 12 wt% hydrogen at moderate temperatures (approximately 150 degrees C). However, the hydrogen purity suffers from the release of trace quantities of borazine. Here, we report that the related alkali-metal amidoboranes, LiNH2BH3 and NaNH2BH3, release approximately 10.9 wt% and approximately 7.5 wt% hydrogen, respectively, at significantly lower temperatures (approximately 90 degrees C) with no borazine emission. The low-temperature release of a large amount of hydrogen is significant and provides the potential to fulfil many of the principal criteria required for an on-board hydrogen store.

Visual Analytics: Scope and Challenges

Abstract: In today's applications data is produced at unprecedented rates. While the capacity to collect and store new data rapidly grows, the ability to analyze these data volumes increases at much lower rates. This gap leads to new challenges in the analysis process, since analysts, decision makers, engineers, or emergency response teams depend on information hidden in the data. The emerging field of visual analytics focuses on handling these massive, heterogenous, and dynamic volumes of information by integrating human judgement by means of visual representations and interaction techniques in the analysis process. Furthermore, it is the combination of related research areas including visualization, data mining, and statistics that turns visual analytics into a promising field of research. This paper aims at providing an overview of visual analytics, its scope and concepts, addresses the most important research challenges and presents use cases from a wide variety of application scenarios.

Recent developments in proton exchange membranes for fuel cells

Abstract: Proton exchange membranes (PEMs) that operate at temperatures above 120 °C are needed to avoid catalyst poisoning, enhance electrochemical reactions, simplify the design and reduce the cost of fuel cells This review summarizes developments in PEMs over the last five years In order to design new membranes for elevated temperature operation, one must understand the chemistry, morphology and dynamics of protons and water molecules in existing membranes The integration of experiment with modelling and simulation can shed light on the hierarchical structure of the membrane and dynamical processes associated with molecular transport Based on such a fundamental understanding, membranes can be modified by controlling the polymer chemistry and architecture or adding inorganic fillers that can retain water under low relative humidity conditions The development of anhydrous membranes based on phosphoric acid doped polymers, ionic liquid-infused polymer gels and solid acids can enable fuel cell operation above 150 °C Considerable work remains to be done to identify proton transport mechanisms in novel membranes and evaluate membrane durability under real world operating conditions

Fundamentals of Traveling Wave Ion Mobility Spectrometry

Abstract: Traveling wave ion mobility spectrometry (TW IMS) is a new IMS method implemented in the Synapt IMS/mass spectrometry system (Waters). Despite its wide adoption, the foundations of TW IMS were only qualitatively understood and factors governing the ion transit time (the separation parameter) and resolution remained murky. Here we develop the theory of TW IMS using derivations and ion dynamics simulations. The key parameter is the ratio (c) of ion drift velocity at the steepest wave slope to wave speed. At low c, the ion transit velocity is proportional to the squares of mobility (K) and electric field intensity (E), as opposed to linear scaling in drift tube (DT) IMS and differential mobility analyzers. At higher c, the scaling deviates from quadratic in a way controlled by the waveform profile, becoming more gradual with the ideal triangular profile but first steeper and then more gradual for realistic profiles with variable E. At highest c, the transit velocity asymptotically approaches the wave speed. ...

Environmental genomics reveals a single-species ecosystem deep within Earth.

Abstract: DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earth's crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

Flexible (Breathing) Interpenetrated Metal−Organic Frameworks for CO2 Separation Applications

Abstract: A breathing 2-fold interpenetrated microporous metal-organic framework was synthesized with a flexible tetrahedral organic linker and Zn(2) clusters that sorb CO(2) preferably over N(2) and H(2).

DAnTE: a statistical tool for quantitative analysis of -omics data

Abstract: Summary: Data Analysis Tool Extension (DAnTE ) is a statistical tool designed to address challenges associated with quantitative bottomup, shotgun proteomics data. This tool has also been demonstrated for microarray data and can easily be extended to other highthroughput data types. DAnTE features selected normalization methods, missing value imputation algorithms, peptide-to-protein rollup methods, an extensive array of plotting functions and a comprehensive hypothesis-testing scheme that can handle unbalanced data and random effects. The graphical user interface (GUI) is designed to be very intuitive and user friendly. Availability: DAnTE may be downloaded free of charge at http://omics.pnl.gov/software/

GridLAB-D: An open-source power systems modeling and simulation environment

Abstract: GridLAB-D is a new power system modeling and simulation environment developed by the US Department of Energy. This paper describes its basic design concept, method of solution, and the initial suite of models that it supports.

Oriented nanostructures for energy conversion and storage.

Abstract: Recently, the role of nanostructured materials in addressing the challenges in energy and natural resources has attracted wide attention. In particular, oriented nanostructures demonstrate promising properties for energy harvesting, conversion, and storage. In this Review, we highlight the synthesis and application of oriented nanostructures in a few key areas of energy technologies, namely photovoltaics, batteries, supercapacitors, and thermoelectrics. Although the applications differ from field to field, a common fundamental challenge is to improve the generation and transport of electrons and ions. We highlight the role of high surface area to maximize the surface activity and discuss the importance of optimum dimension and architecture, controlled pore channels, and alignment of the nanocrystalline phase to optimize the transport of electrons and ions. Finally, we discuss the challenges in attaining integrated architectures to achieve the desired performance. Brief background information is provided for the relevant technologies, but the emphasis is focused mainly on the nanoscale effects of mostly inorganic-based materials and devices.

Development of transferable interaction potentials for water. V. Extension of the flexible, polarizable, Thole-type model potential (TTM3-F, v. 3.0) to describe the vibrational spectra of water clusters and liquid water.

Abstract: We present a new parametrization of the flexible, polarizable Thole-type model for water [J. Chem. Phys. 116, 5115 (2002); J. Phys. Chem. A 110, 4100 (2006)], with emphasis in describing the vibrational spectra of both water clusters and liquid water. The new model is able to produce results of similar quality with the previous versions for the structures and energetics of water clusters as well as structural and thermodynamic properties of liquid water evaluated with classical and converged quantum statistical mechanical atomistic simulations. At the same time it yields accurate redshifts for the OH vibrational stretches of both water clusters and liquid water.

Simple Synthesis of Functionalized Superparamagnetic Magnetite/Silica Core/Shell Nanoparticles and their Application as Magnetically Separable High‐Performance Biocatalysts

Abstract: Uniformly sized silica-coated magnetic nanoparticles (magnetite@silica) are synthesized in a simple one-pot process using reverse micelles as nanoreactors. The core diameter of the magnetic nanoparticles is easily controlled by adjusting the w value ([polar solvent]/[surfactant]) in the reverse-micelle solution, and the thickness of the silica shell is easily controlled by varying the amount of tetraethyl orthosilicate added after the synthesis of the magnetite cores. Several grams of monodisperse magnetite@silica nanoparticles can be synthesized without going through any size-selection process. When crosslinked enzyme molecules form clusters on the surfaces of the magnetite@silica nanoparticles, the resulting hybrid composites are magnetically separable, highly active, and stable under harsh shaking conditions for more than 15 days. Conversely, covalently attached enzymes on the surface of the magnetite@silica nanoparticles are deactivated under the same conditions.

Catalytic hydrothermal gasification of biomass.

Abstract: A recent development in biomass gasification is the use of a pressurized water-processing environment to avoid drying of the biomass. This paper reviews the research undertaken developing this new option for biomass gasification. This review does not cover wet oxidation or near-atmospheric-pressure steam-gasification of biomass. Laboratory research on hydrothermal gasification of biomass focusing on the use of catalysts is reviewed here, and a companion review focuses on non-catalytic processing. Research includes liquid-phase, subcritical processing as well as supercritical water processing. The use of heterogeneous catalysts in such a system allows effective operation at lower temperatures, and the issues around the use of catalysts are presented. This review attempts to show the potential of this new processing concept by comparing the various options under development and the results of the research. © 2008 Society of Chemical Industry and John Wiley & Sons, Ltd

Initial review of methods for cascading failure analysis in electric power transmission systems IEEE PES CAMS task force on understanding, prediction, mitigation and restoration of cascading failures

Abstract: Large blackouts are typically caused by cascading failure propagating through a power system by means of a variety of processes. Because of the wide range of time scales, multiple interacting processes, and the huge number of possible interactions, the simulation and analysis of cascading blackouts is extremely complicated. This paper defines cascading failure for blackouts and gives an initial review of the current understanding, industrial tools, and the challenges and emerging methods of analysis and simulation.

Long-term black carbon dynamics in cultivated soil

Abstract: Black carbon (BC) is a quantitatively important C pool in the global C cycle due to its relative recalcitrance compared with other C pools. However, mechanisms of BC oxidation and accompanying molecular changes are largely unknown. In this study, the long-term dynamics in quality and quantity of BC were investigated in cultivated soil using X-ray photoelectron spectroscopy (XPS), Fourier-transform infrared (FTIR) and nuclear magnetic resonance (NMR) techniques. BC particles and changes in BC stocks were obtained from soil collected in fields that were cleared from forest by fire at 8 different times in the past (2, 3, 5, 20, 30, 50, 80 and 100 years before sampling) in western Kenya. BC contents rapidly decreased from 12.7 to 3.8 mg C g−1 soil during the first 30 years following deposition, after which they slowly decreased to a steady state at 3.5 mg C g−1 soil. BC-derived C losses from the top 0.1 m over 100 years were estimated at 6,000 kg C ha−1. The initial rapid changes in BC stocks resulted in a mean residence time of only around 8.3 years, which was likely a function of both decomposition as well as transport processes. The molecular properties of BC changed more rapidly on surfaces than in the interior of BC particles and more rapidly during the first 30 years than during the following 70 years. The Oc/C ratios (Oc is O bound to C) and carbonyl groups (C=O) increased over the first 10 and 30 years by 133 and 192%, respectively, indicating oxidation was an important process controlling BC quality. Al, Si, polysaccharides, and to a lesser extent Fe were found on BC particle surfaces within the first few years after BC deposition to soil. The protection by physical and chemical stabilization was apparently sufficient to not only minimize decomposition below detection between 30 and 100 years after deposition, but also physical export by erosion and vertical transport below 0.1 m.

Linked reactivity at mineral-water interfaces through bulk crystal conduction.

Abstract: The semiconducting properties of a wide range of minerals are often ignored in the study of their interfacial geochemical behavior. We show that surface-specific charge density accumulation reactions combined with bulk charge carrier diffusivity create conditions under which interfacial electron transfer reactions at one surface couple with those at another via current flow through the crystal bulk. Specifically, we observed that a chemically induced surface potential gradient across hematite (α-Fe 2 O 3 ) crystals is sufficiently high and the bulk electrical resistivity sufficiently low that dissolution of edge surfaces is linked to simultaneous growth of the crystallographically distinct (001) basal plane. The apparent importance of bulk crystal conduction is likely to be generalizable to a host of naturally abundant semiconducting minerals playing varied key roles in soils, sediments, and the atmosphere.

Geometry-Based Edge Clustering for Graph Visualization

Abstract: Graphs have been widely used to model relationships among data. For large graphs, excessive edge crossings make the display visually cluttered and thus difficult to explore. In this paper, we propose a novel geometry-based edge-clustering framework that can group edges into bundles to reduce the overall edge crossings. Our method uses a control mesh to guide the edge-clustering process; edge bundles can be formed by forcing all edges to pass through some control points on the mesh. The control mesh can be generated at different levels of detail either manually or automatically based on underlying graph patterns. Users can further interact with the edge-clustering results through several advanced visualization techniques such as color and opacity enhancement. Compared with other edge-clustering methods, our approach is intuitive, flexible, and efficient. The experiments on some large graphs demonstrate the effectiveness of our method.

Stability of black carbon in soils across a climatic gradient

Abstract: [1] The recalcitrant properties of black carbon (BC) grant it to be a significant pool of stable organic C (OC) in soils. Up to now, however, the longevity of BC under different climates is still unclear. In this study, we used BC samples from historical charcoal blast furnace sites to examine the stability of BC across a climatic gradient of mean annual temperatures (MAT) from 3.9 to 17.2°C. The results showed that OC concentration and OC storage in the BC-containing soils at a soil depth of 0–0.2 m were 9.0 and 4.7 times higher than those in adjacent soils, respectively. Organic C in the BC-containing soils was more stable, with a significantly lower amount of the labile OC fraction (4.4 mg g−1 OC versus 27.5 mg g−1 OC) and longer half-life of the recalcitrant OC fraction (59 years versus 9 years) than the adjacent soils determined by incubation experiments. The stability of BC was primarily due to its inherently recalcitrant chemical composition as suggested by short-term incubation and solid state 13C nuclear magnetic resonance spectra of isolated BC particles. A significant negative relationship between OC storage and MAT further indicated that OC storage was decreased with warmer climate. However, the lack of a relationship between MAT and BC mineralization suggested that the stability of the remaining BC was similar between sites with very different MAT. Despite the fact that warming or cooling result in immediate consequences for BC stocks, it may have little impact on the stability of remaining BC over the period studied.

Radiation Detector Materials: An Overview

Abstract: Due to events of the past two decades, there has been new and increased usage of radiation-detection technologies for applications in homeland security, nonproliferation, and national defense. As a result, there has been renewed realization of the materials limitations of these technologies and greater demand for the development of next-generation radiation-detection materials. This review describes the current state of radiation-detection material science, with particular emphasis on national security needs and the goal of identifying the challenges and opportunities that this area represents for the materials-science community. Radiation-detector materials physics is reviewed, which sets the stage for performance metrics that determine the relative merit of existing and new materials. Semiconductors and scintillators represent the two primary classes of radiation detector materials that are of interest. The state-of-the-art and limitations for each of these materials classes are presented, along with possible avenues of research. Novel materials that could overcome the need for single crystals will also be discussed. Finally, new methods of material discovery and development are put forward, the goal being to provide more predictive guidance and faster screening of candidate materials and thus, ultimately, the faster development of superior radiation-detection materials.

Development of a low-temperature photoelectron spectroscopy instrument using an electrospray ion source and a cryogenically controlled ion trap.

Abstract: The ability to control ion temperatures is critical for gas phase spectroscopy and has been a challenge in chemical physics. A low-temperature photoelectron spectroscopy instrument has been developed for the investigation of complex anions in the gas phase, including multiply charged anions, solvated species, and biological molecules. The new apparatus consists of an electrospray ionization source, a three dimensional (3D) Paul trap for ion accumulation and cooling, a time-of-flight mass spectrometer, and a magnetic-bottle photoelectron analyzer. A key feature of the new instrument is the capability to cool and tune ion temperatures from 10to350K in the 3D Paul trap, which is attached to the cold head of a closed cycle helium refrigerator. Ion cooling is accomplished in the Paul trap via collisions with a background gas and has been demonstrated by observation of complete elimination of vibrational hot bands in photoelectron spectra of various anions ranging from small molecules to complex species. Further evidence of ion cooling is shown by the observation of H2-physisorbed anions at low temperatures. Cold anions result in better resolved photoelectron spectra due to the elimination of vibrational hot bands and yield more accurate energetic and spectroscopic information. Temperature-dependent studies are made possible for weakly bonded molecular and solvated clusters, allowing thermodynamic information to be obtained.

On model selection criteria in multimodel analysis

Abstract: [1] Hydrologic systems are open and complex, rendering them prone to multiple conceptualizations and mathematical descriptions. There has been a growing tendency to postulate several alternative hydrologic models for a site and use model selection criteria to (1) rank these models, (2) eliminate some of them, and/or (3) weigh and average predictions and statistics generated by multiple models. This has led to some debate among hydrogeologists about the merits and demerits of common model selection (also known as model discrimination or information) criteria such as AIC, AICc, BIC, and KIC and some lack of clarity about the proper interpretation and mathematical representation of each criterion. We examine the model selection literature to find that (1) all published rigorous derivations of AIC and AICc require that the (true) model having generated the observational data be in the set of candidate models; (2) though BIC and KIC were originally derived by assuming that such a model is in the set, BIC has been rederived by Cavanaugh and Neath (1999) without the need for such an assumption; and (3) KIC reduces to BIC as the number of observations becomes large relative to the number of adjustable model parameters, implying that it likewise does not require the existence of a true model in the set of alternatives. We explain why KIC is the only criterion accounting validly for the likelihood of prior parameter estimates, elucidate the unique role that the Fisher information matrix plays in KIC, and demonstrate through an example that it imbues KIC with desirable model selection properties not shared by AIC, AICc, or BIC. Our example appears to provide the first comprehensive test of how AIC, AICc, BIC, and KIC weigh and rank alternative models in light of the models' predictive performance under cross validation with real hydrologic data.

Synthesis and Li-Ion Insertion Properties of Highly Crystalline Mesoporous Rutile TiO2

Abstract: Mesoporous TiO2 has attracted great attention as a promising Li insertion electrode material with improved cycling life, rate capability, and high power density. Up to date, mesoporous anatase TiO2 has been investigated for Li insertion. Recent studies have shown that nanosized rutile could be an excellent candidate for anode materials for higher Li insertion capacity and improved stability. However, synthesis of highly crystalline mesoporous rutile has met with limited success so far. There has been no report on Li insertion of mesoporous rutile TiO2. In this paper, we report a new low-temperature solution growth of TiO2 nanocrystals within an anionic surfactant matrix to produce highly crystalline mesoporous rutile and investigate Li insertion properties of the mesoporous crystalline rutile. X-ray diffraction (XRD) patterns and N2 sorption isotherms reveal that mesoporous structure in the highly crystalline mesoporous TiO2 directly results from the anionic surfactant templating effects with high surface...

Organic liquid CO2 capture agents with high gravimetric CO2 capacity

Abstract: We report a new class of CO2 binding organic liquids that chemically capture and release CO2 much more efficiently than aqueous alkanolamine systems. Mixtures of organic alcohols and amidine/guanidine bases reversibly bind CO2 chemically as liquid amidinium/guanidinium alkylcarbonates. The free energy of CO2 binding in these organic systems is very small and dependent on the choice of base, approximately −9 kJ mol−1 for DBU and Barton's base and +2 kJ mol−1 for 1,1,3,3-tetramethylguanidine. These CO2 capturing agents do not require an added solvent because they are liquid, and therefore have high CO2 capacities of up to 19% by weight for neat systems, and slightly less when dissolved in acetonitrile. The rate of CO2 uptake and release by these organic systems is limited by the rate of dissolution of CO2 into and out of the liquid phase. Gas absorption is selective for CO2 in both concentrated and dilute gas streams. These organic systems have been shown to bind and release CO2 for five cycles without losing activity or selectivity.

A Photoelectron Spectroscopic and Theoretical Study of B16− and B162−: An All-Boron Naphthalene

Abstract: The structure and chemical bonding of B16− were studied using ab initio calculations and photoelectron spectroscopy. Its global minimum is found to be a quasi-planar and elongated structure (C2h). Addition of an electron to B16− resulted in a perfectly planar and closed shell B162− (D2h), which is shown to possess 10 π electrons with a π-bonding pattern similar to that of naphthalene and can thus be considered as an “all-boron naphthalene”, a new member in the growing family of hydrocarbon analogues of boron clusters.

Functionalized carbon nanotubes and nanofibers for biosensing applications.

Abstract: This review summarizes recent advances in electrochemical biosensors based on carbon nanotubes (CNTs) and carbon nanofibers (CNFs) with an emphasis on applications of CNTs. CNTs and CNFs have unique electric, electrocatalytic and mechanical properties, which make them efficient materials for developing electrochemical biosensors. We discuss functionalizing CNTs for biosensors. We review electrochemical biosensors based on CNTs and their various applications (e.g., measurement of small biological molecules and environmental pollutants, detection of DNA, and immunosensing of disease biomarkers). Moreover, we outline the development of electrochemical biosensors based on CNFs and their applications. Finally, we discuss some future applications of CNTs.