Structure Of N-Heptane/Air Triple Flames In Partially-Premixed Mixing Layers,
2011
Sandia National Laboratories, Livermore, CA
Structure Of N-Heptane/Air Triple Flames In Partially-Premixed Mixing Layers, J. Prager, H. N. Najm, M. Valorani, D.A. Goussis
United States Department of Energy: Publications
Results of a detailed numerical analysis of an n-heptane/air edge flame are presented. The equations of a low-Mach number reacting flow are solved in a two-dimensional domain using detailed models for species transport and chemical reactions. The reaction mechanism involves 560 species and 2538 reversible reactions. We consider an edge flame that is established in a mixing layer with a uniform velocity field. The mixing layer spans the equivalence ratios between pure air and 3.5. The detailed model enables us to analyze the chemical structure of the n-heptane edge flame. We identify major species profiles, discuss reactions causing the heat-release, …
Roaming Radicals In The Thermal Decomposition Of Dimethyl Ether:
Experiment And Theory,
2011
Argonne National Laboratory, Argonne, IL
Roaming Radicals In The Thermal Decomposition Of Dimethyl Ether: Experiment And Theory, R. Sivaramakrishnan, J. Michael, A. Wagner, R. Dawes, A. Jasper, L. Harding, Y. Georgievskii, S. Klippenstein
United States Department of Energy: Publications
The thermal dissociation of dimethyl ether has been studied with a combination of reflected shock tube experiments and ab initio dynamics simulations coupled with transition state theory based master equation calculations. The experiments use the extraordinary sensitivity provided by H-atom ARAS detection with an unreversed light source to measure both the total decomposition rate and the branching to radical products versus molecular products, with the molecular products arising predominantly through roaming according to the theoretical analysis. The experimental observations also provide a measure of the rate coefficient for H + CH3OCH3. An evaluation of the available experimental results for H …
A Review Of Polymer Electrolyte Membrane Fuel Cells: Technology, Applications,
And Needs On Fundamental Research,
2011
The University of California, Irvine, Irvine, CA
A Review Of Polymer Electrolyte Membrane Fuel Cells: Technology, Applications, And Needs On Fundamental Research, Yun Wang, Ken Chen, Jeffrey Mishler, Sung Chan Cho, Xavier Cordobes Adroher
United States Department of Energy: Publications
Polymer electrolyte membrane (PEM) fuel cells, which convert the chemical energy stored in hydrogen fuel directly and efficiently to electrical energy with water as the only byproduct, have the potential to reduce our energy use, pollutant emissions, and dependence on fossil fuels. Great deal of efforts has been made in the past, particularly during the last couple of decades or so, to advance the PEM fuel cell technology and fundamental research. Factors such as durability and cost still remain as the major barriers to fuel cell commercialization. In the past two years, more than 35% cost reduction has been achieved …
Direct Numerical Simulations Of Ignition Of A Lean N-Heptane/Air Mixture With
Temperature Inhomogeneities At Constant Volume: Parametric Study,
2011
Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
Direct Numerical Simulations Of Ignition Of A Lean N-Heptane/Air Mixture With Temperature Inhomogeneities At Constant Volume: Parametric Study, Chun Sang Yoo, Tianfeng Lu, Jacqueline Chen, Chung K. Law
United States Department of Energy: Publications
The effect of thermal stratification on the ignition of a lean homogeneous n-heptane/air mixture at constant volume and high pressure is investigated by direct numerical simulations (DNS) with a new 58- species reduced kinetic mechanism developed for very lean mixtures from the detailed LLNL mechanism (H.J. Curran et al., Combust. Flame 129 (2002) 253–280). Two-dimensional DNS are performed in a fixed volume with a two-dimensional isotropic velocity spectrum and temperature fluctuations superimposed on the initial scalar fields. The influence of variations in the initial temperature field, imposed by changing the mean and variance of temperature, and the ratio of turbulence …
Solution And Microbial Controls On The Formation Of Reduced
U(Iv) Species,
2011
Argonne National Laboratory
Solution And Microbial Controls On The Formation Of Reduced U(Iv) Species, Maxim I. Boyanov, Kelly E. Fletcher, Man Jae Kwon, Xue Rui, Edward J. O’Loughlin, Frank E. Löffler, Kenneth M. Kemner
United States Department of Energy: Publications
Reduction of UVI to UIV as the result of direct or indirect microbial activity is currently being explored for in situ remediation of subsurface U plumes, under the assumption that UIV solubility is controlled by the low solubility mineral uraninite (UIV-dioxide). However, recent characterizations of U in sediments from biostimulated field sites, as well as laboratory UVI bioreduction studies, report on the formation of UIV species that lack the U=O2=U coordination of uraninite, suggesting that phases other than uraninite may be controlling UIV solubility in environments with complexing surfaces and ligands. …
Identification And Characterization Of Undahrcr-6, An Outer Membrane
Endecaheme C-Type Cytochrome Of Shewanella Sp. Strain Hrcr-6,
2011
Pacific Northwest National Laboratory
Identification And Characterization Of Undahrcr-6, An Outer Membrane Endecaheme C-Type Cytochrome Of Shewanella Sp. Strain Hrcr-6, Liang Shi, Sara M. Belchik, Zheming Wang, David W. Kennedy, Alice C. Dohnalkova, Matthew J. Marshall, John M. Zachara, James K. Fredrickson
United States Department of Energy: Publications
UndAHRCR-6 was identified from the metal-reducing bacterium Shewanella sp. strain HRCR-6. Both in vivo and in vitro characterization results indicate that UndAHRCR-6 is an outer membrane endecaheme c-type cytochrome and probably has a key functional role in the extracellular reduction of iron [Fe(III)] oxides and uranium [U(VI)] by Shewanella sp. HRCR-6.
Purification And Characterization Of The [Nife]-Hydrogenase Of
Shewanella Oneidensis Mr-1,
2011
Pacific Northwest National Laboratory
Purification And Characterization Of The [Nife]-Hydrogenase Of Shewanella Oneidensis Mr-1, Liang Shi, Sara M. Belchik, Andrew E. Plymale, Steve Heald, Alice C. Dohnalkova, Kateryna Sybirna, Herve Bottin, Thomas C. Squier, John M. Zachara, James K. Fredrickson
United States Department of Energy: Publications
Shewanella oneidensis MR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H2ase) that has been implicated in H2 production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H2ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H2ase were cloned and then expressed in an MR-1 mutant without hyaB and hydA genes. Expression of recombinant MR-1 [NiFe]-H2ase in trans restored the mutant’s ability to produce H2 at 37% of that for the wild type. Following purification, MR-1 [NiFe]-H2ase coupled H2 oxidation to …
Microbial Reduction Of Chlorite And Uranium Followed By Air Oxidation,
2011
Chinese Academy of Sciences
Microbial Reduction Of Chlorite And Uranium Followed By Air Oxidation, Gengxin Zhang, William D. Burgos, John M. Senko, Michael E. Bishop, Hailiang Dong, Maxim Boyanov, Kenneth M. Kemner
United States Department of Energy: Publications
To evaluate the stability of biogenic nanoparticulate U(IV) in the presence of an Fe(II)-rich iron-bearing phyllosilicate, we examined the reduction of structural Fe(III) in chlorite CCa-2 and uranium(VI) by Shewanella oneidensis MR-1, and the reoxidation of these minerals (after pasteurization) via the introduction of oxygen. Bioreduction experiments were conducted with combinations of chlorite, U(VI), and anthraquinone-2,6-disulfonate (AQDS). Abiotic experiments were conducted to quantify the reduction of U(VI) by chemically-reduced chlorite-associated Fe(II), the oxidation of nanoparticulate U(IV) by unaltered structural Fe(III) in chlorite, and the sorption of U(VI) to chlorite, to elucidate interactions between U(VI)/ U(IV) and Fe(II)/Fe(III)-chlorite. Solids were characterized …
Competitive Reduction Of
Pertechnetate (99tco4-) By
Dissimilatory Metal Reducing
Bacteria And Biogenic Fe(Ii),
2011
Pacific Northwest National Laboratory
Competitive Reduction Of Pertechnetate (99tco4-) By Dissimilatory Metal Reducing Bacteria And Biogenic Fe(Ii), Andrew Plymale, James K. Fredrickson, John M. Zachara, Alice Dohnalkova, Steve Heald, Dean Moore, David Kennedy, Matthew Marshall, Chongmin Wang, Charles Resch, Ponnusamy Nachimuthu
United States Department of Energy: Publications
The fate of pertechnetate (99Tc(VII)O4 -) during bioreduction was investigated in the presence of 2-line ferrihydrite (Fh) and various dissimilatory metal reducing bacteria (DMRB) (Geobacter, Anaeromyxobacter, Shewanella) in comparison with TcO4 - bioreduction in the absence of Fh. In the presence of Fh, Tc was present primarily as a fine-grained Tc(IV)/Fe precipitate that was distinct from the Tc(IV)O2 ·nH2O solids produced by direct biological Tc(VII) reduction. Aqueous Tc concentrations (<0.2 μm) in the bioreduced Fh suspensions (1.7 to 3.2 × 10-9 mol L-1) were over 1 order of magnitude lower than when TcO4 - …
Effect Of Grain Size On Uranium(Vi) Surface Complexation
Kinetics And Adsorption Additivity,
2011
Pacific Northwest National Laboratory
Effect Of Grain Size On Uranium(Vi) Surface Complexation Kinetics And Adsorption Additivity, Jianying Shang, Chongxuan Liu, Zheming Wang, John M. Zachara
United States Department of Energy: Publications
The contribution of variable grain sizes to uranium adsorption/ desorption was studied using a sediment from the US DOE Hanford site. The sediment was wet sieved into four size fractions: coarse sand (1−2 mm), medium sand (0.2−1 mm), fine sand (0.053−0.2 mm), and clay/silt fraction (<0.053 mm). For each size fraction and their composite (sediment), batch and flow-cell experiments were performed to determine uranium adsorption isotherms and kinetic uranium adsorption and subsequent desorption. The results showed that uranium adsorption isotherms and adsorption/desorption kinetics were size specific, reflecting the effects of size-specific adsorption site concentration and kinetic rate constants. The larger-size fraction had a larger mass percentage in the sediment but with a smaller adsorption site concentration and generally a slower uranium adsorption/desorption rate. The same equilibrium surface complexation reaction and reaction constant could describe uranium adsorption isotherms for all size fractions and the composite after accounting for the effect of adsorption site concentration. Mass-weighted, linear additivity was observed for both uranium adsorption isotherms and adsorption/desorption kinetics in the composite. One important implication of this study is that grain-size distribution may be used to estimate uranium adsorption site and adsorption/desorption kinetic rates in heterogeneous sediments from a common location.
Determining Individual Mineral Contributions To U(Vi)
Adsorption In A Contaminated Aquifer Sediment:
A Fluorescence Spectroscopy Study,
2011
Pacific Northwest National Laboratory
Determining Individual Mineral Contributions To U(Vi) Adsorption In A Contaminated Aquifer Sediment: A Fluorescence Spectroscopy Study, Zheming Wang, John M. Zachara, Jean-Francois Boily, Yuanxian Xia, Tom C. Resch, Dean A. Moore, Chongxuan Liu
United States Department of Energy: Publications
The adsorption and speciation of U(VI) was investigated on contaminated, fine grained sediment materials from the Hanford 300 area (SPP1 GWF) in simulated groundwater using cryogenic laser-induced U(VI) fluorescence spectroscopy combined with chemometric analysis. A series of reference minerals (montmorillonite, illite, Michigan chlorite, North Carolina chlorite, California clinochlore, quartz and synthetic 6-line ferrihydrite) was used for comparison that represents the mineralogical constituents of SPP1 GWF. Surface area-normalized Kd values were measured at U(VI) concentrations of 5 X 10−7 and 5 X 10−6 mol L−1 that displayed the following affinity series: 6-line-ferrihydrite > North Carolina chlorite ≈ California clinochlore …
The Mineralogic Transformation Of Ferrihydrite Induced By
Heterogeneous Reaction With Bioreduced Anthraquinone
Disulfonate (Aqds) And The Role Of Phosphate,
2011
Pacific Northwest National Laboratory
The Mineralogic Transformation Of Ferrihydrite Induced By Heterogeneous Reaction With Bioreduced Anthraquinone Disulfonate (Aqds) And The Role Of Phosphate, John M. Zachara, Ravi K. Kukkadapu, Tanya Peretyazhko, Mark Bowden, Chongmin Wang, David Kennedy, Dean Moore, Bruce Arey
United States Department of Energy: Publications
Bioreduced anthraquinone-2,6-disulfonate (AH2DS; dihydro-anthraquinone) was reacted with a 2-line, Si-substituted ferrihydrite under anoxic conditions at neutral pH in PIPES buffer. Phosphate (P) and bicarbonate (C); common adsorptive oxyanions and media/buffer components known to effect ferrihydrite mineralization; and Fe(II)aq (as a catalytic mineralization agent) were used in comparative experiments. Heterogeneous AH2DS oxidation coupled with Fe(III) reduction occurred within 0.13–1 day, with mineralogic transformation occurring thereafter. The product suite included lepidocrocite, goethite, and/or magnetite, with proportions varing with reductant:oxidant ratio (r:o) and the presence of P or C. Lepidocrocite was the primary product at low r:o in the absence of P …
Interfacial Reactivity Of Radionuclides:
Emerging Paradigms From Molecular-Level Observations,
2011
Pacific Northwest National Laboratory
Interfacial Reactivity Of Radionuclides: Emerging Paradigms From Molecular-Level Observations, A.R. Felmy, E.S. Ilton, K.M. Rosso, John M. Zachara
United States Department of Energy: Publications
Over the past few decades an increasing array of molecular-level analytical probes has provided new detailed insight into mineral and radionuclide interfacial reactivity in subsurface environments. This capability has not only helped change the way mineral surface reactivity is studied but also how field scale contaminant migration problems are addressed and ultimately resolved. Here we review relatively new interfacial reactivity paradigms and assess their implications for future research directions. Specific examples include understanding the following: the role of site-to-site electron conduction at mineral surfaces and through bulk mineral phases and the effects of local chemical environment on the stability of …
Structure Of A Bacterial Cell Surface
Decaheme Electron Conduit,
2011
University of East Anglia
Structure Of A Bacterial Cell Surface Decaheme Electron Conduit, Thomas A. Clarke, Marcus Edwards, Andrew J. Gates, Andrea Hall, Gaye F. White, Justin Bradley, Catherine L. Reardon, Liang Shi, Alexander Beliaev, Matthew Marshall, Zheming Wang, Nicholas Watmough, James K. Fredrickson, John M. Zachara, Julea Butt, David J. Richardson
United States Department of Energy: Publications
Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of transouter- membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along “nanowire” appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to …
Sop For Pathway Inference In Integrated Microbial Genomes (Img),
2011
DOE Joint Genome Institute
Sop For Pathway Inference In Integrated Microbial Genomes (Img), Iain Anderson, Amy Chen, Victor Markowitz, Nikos Kyrpides, Natalia Ivanova
United States Department of Energy: Publications
One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG terms, which are organized into IMG pathways. Based on manual and automatic assignment of IMG terms, the presence or absence of IMG pathways is automatically inferred. The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown. In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding …
Complete Genome Sequence Of The Cellulolytic Thermophile
Clostridium Thermocellum Dsm1313,
2011
Mascoma Corporation
Complete Genome Sequence Of The Cellulolytic Thermophile Clostridium Thermocellum Dsm1313, Lawrence Feinberg, Justine Foden, Trisha Barrett, Karen Walston Davenport, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Alla Lapidus, Susan Lucas, Jan-Fang Cheng, Samuel Pitluck, Tanja Woyke, Natalia Ivanova, Natalia Mikhailova, Miriam Land, Loren Hauser, D. Aaron Argyros, Lynne Goodwin, David Hogsett, Nicky Caiazza
United States Department of Energy: Publications
Clostridium thermocellum DSM1313 is a thermophilic, anaerobic bacterium with some of the highest rates of cellulose hydrolysis reported. The complete genome sequence reveals a suite of carbohydrate-active enzymes and demonstrates a level of diversity at the species level distinguishing it from the type strain ATCC 27405.
Img/M: The Integrated Metagenome Data
Management And Comparative Analysis System,
2011
Lawrence Berkeley National Laboratory
Img/M: The Integrated Metagenome Data Management And Comparative Analysis System, Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides
United States Department of Energy: Publications
The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context. IMG/M integrates metagenome data sets with isolate microbial genomes from the IMG system. IMG/M’s data content and analytical capabilities have been extended through regular updates since its first release in 2007. IMG/M is available at http://img.jgi.doe.gov/m. A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER: http://img.jgi.doe.gov/mer).
Complete Genome Sequence Of Lactobacillus Buchneri Nrrl
B-30929, A Novel Strain From A Commercial Ethanol Plant,
2011
National Center for Agricultural Utilization Research
Complete Genome Sequence Of Lactobacillus Buchneri Nrrl B-30929, A Novel Strain From A Commercial Ethanol Plant, Siqing Liu, Timothy D. Leathers, Alex Copeland, Olga Chertkov, Lynne Goodwin, David A. Mills
United States Department of Energy: Publications
Lactobacillus buchneri strain NRRL B-30929 was a contaminant obtained from a commercial ethanol fermentation. This facultative anaerobe is unique because of its rapid growth on xylose and simultaneous fermentation of xylose and glucose. The strain utilizes a broad range of carbohydrate substrates and possesses a high tolerance to ethanol and other stresses, making it an attractive candidate for bioconversion of biomass substrates to various bioproducts. The genome sequence of NRRL B-30929 will provide insight into the unique properties of this lactic acid bacterium.
Vista Region Viewer (Rviewer)—A Computational System For
Prioritizing Genomic Intervals For Biomedical Studies,
2011
Lawrence Berkeley National Laboratory
Vista Region Viewer (Rviewer)—A Computational System For Prioritizing Genomic Intervals For Biomedical Studies, Igor Lukashin, Pavel Novichkov, Dario Boffelli, Alex R. Paciorkowski, Simon Minovitsky, Song Yang, Inna Dubchak
United States Department of Energy: Publications
Summary:
Current genome browsers are designed for linear browsing of individual genomic regions, but the high-throughput nature of experiments aiming to elucidate the genetic component of human disease makes it very important to develop user-friendly tools for comparing several genomic regions in parallel and prioritizing them based on their functional content. We introduce VISTA Region Viewer (RViewer), an interactive online tool that allows for efficient screening and prioritization of regions of the human genome for follow-up studies. The tool takes as input genetic variation data from different biomedical studies, determines a number of various functional parameters for both coding …
Complete Genome Sequence Of The Plant Growth-Promoting
Endophyte Burkholderia Phytofirmans Strain Psjn,
2011
AIT Austrian Institute of Technology GmbH
Complete Genome Sequence Of The Plant Growth-Promoting Endophyte Burkholderia Phytofirmans Strain Psjn, Alexandra Weilharter, Birgit Mitter, Maria V. Shin, Patrick S. G. Chain, Jerzy Nowak, Angela Sessitsch
United States Department of Energy: Publications
Burkholderia phytofirmans PsJNT is able to efficiently colonize the rhizosphere, root, and above-ground plant tissues of a wide variety of genetically unrelated plants, such as potatoes, canola, maize, and grapevines. Strain PsJN shows strong plant growth-promoting effects and was reported to enhance plant vigor and resistance to biotic and abiotic stresses. Here, we report the genome sequence of this strain, which indicates the presence of multiple traits relevant for endophytic colonization and plant growth promotion.
