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2011

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Articles 3751 - 3780 of 5802

Full-Text Articles in Engineering

Reducing Error And Measurement Time In Impedance Spectroscopy Using Model Based Optimal Experimental Design, Francesco Ciucci, Thomas Carraro, William Chueh, Wei Lai Jan 2011

Reducing Error And Measurement Time In Impedance Spectroscopy Using Model Based Optimal Experimental Design, Francesco Ciucci, Thomas Carraro, William Chueh, Wei Lai

United States Department of Energy: Publications

In this work we introduce several novel tools for the reduction of errors in parameters estimated with electrochemical impedance spectroscopy experiments. An optimization strategy is developed that minimizes an estimate of the errors on the parameters while bounding the experimental time. The approach is also used to reduce experimental time while keeping a bound on the parameter errors. This feature is particularly critical in systems changing significantly within the experimental time. The paper uses a fuel cell electrode model to test this methodology and presents a real time algorithm for coupling experiment with the parameter estimation and experimental optimization.

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Real-Space Study Of The Growth Of Magnesium On Ruthenium, T. Herranz, B. Santos, K.F. Mccarty, J. De La Figuera Jan 2011

Real-Space Study Of The Growth Of Magnesium On Ruthenium, T. Herranz, B. Santos, K.F. Mccarty, J. De La Figuera

United States Department of Energy: Publications

The growth of magnesium on ruthenium has been studied by low-energy electron microscopy (LEEM) and scanning tunneling microscopy (STM). In LEEM, a layer-by-layer growth is observed except in the first monolayer, where the completion of the first layer in inferred by a clear peak in electron reflectivity. Desorption from the films is readily observable at 400 K. Real-space STM and low-energy electron diffraction confirm that sub-monolayer coverage presents a moiré pattern with a 12 Å periodicity, which evolves with further Mg deposition by compressing the Mg layer to a 22 Å periodicity. Layer-by-layer growth is followed in LEEM up to …

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Methods For Probabilistic Modeling Of Concentrating Solar Power Plants, Clifford Ho, Siri S. Khalsa, Gregory J. Kolb Jan 2011

Methods For Probabilistic Modeling Of Concentrating Solar Power Plants, Clifford Ho, Siri S. Khalsa, Gregory J. Kolb

United States Department of Energy: Publications

Probabilistic modeling of concentrating solar power technologies provides important information regarding uncertainties and sensitivities not available from deterministic models. Benefits of using probabilistic models include quantification of uncertainties inherent in the system and characterization of their impact on system performance and economics. This paper presents the tools necessary to conduct probabilistic modeling of concentrating solar technologies. The probabilistic method begins with the identification of uncertain variables and the assignment of appropriate distributions for those variables. Those parameters are then sampled using a stratified method (Latin Hypercube Sampling) to ensure complete and representative sampling from each distribution. Models of performance, reliability, …

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Magnetically Driven Hyper-Velocity Launch Capability At The Sandia Z Accelerator, R. W. Lemke, M. D. Knudson,, J. P. Davis Jan 2011

Magnetically Driven Hyper-Velocity Launch Capability At The Sandia Z Accelerator, R. W. Lemke, M. D. Knudson,, J. P. Davis

United States Department of Energy: Publications

The intense magnetic field generated by the Z accelerator at Sandia National Laboratories is used as a pressure source for material science studies. A current of ∼20 MA can be delivered to the loads used in experiments on a time scale of ∼100-600 ns. Magnetic fields (pressures) exceeding 1200 T (600 GPa) have been produced in planar configurations. In one application we have developed, the magnetic pressure launches a flyer plate to ultra-high velocity in a plate impact experiment; equation of state data is obtained on the Hugoniot of a material that is shock compressed to multi-megabar pressure. This capability …

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Multiple Benzene-Formation Paths In A Fuel-Rich Cyclohexane Flame, Wenjun Li, Matthew Law, Phillip Westmoreland, Tina Kasper, Nils Hansen, Katharina Kohse-Höinghaus Jan 2011

Multiple Benzene-Formation Paths In A Fuel-Rich Cyclohexane Flame, Wenjun Li, Matthew Law, Phillip Westmoreland, Tina Kasper, Nils Hansen, Katharina Kohse-Höinghaus

United States Department of Energy: Publications

Detailed data and modeling of cyclohexane flames establish that a mixture of pathways contributes to benzene formation and that this mixture changes with stoichiometry. Mole-fraction profiles are mapped for more than 40 species in a fuel-rich, premixed flat flame (Φ = 2.0, cyclohexane/O2/30% Ar, 30 Torr, 50.0 cm/s) using molecular-beam mass spectrometry with VUV-photoionization at the Advanced Light Source of the Lawrence Berkeley National Laboratory. The use of a newly constructed set of reactions leads to an excellent simulation of this flame and an earlier stoichiometric flame (M.E. Law et al., Proc. Combust. Inst. 31 (2007) 565–573), …

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Structure Of N-Heptane/Air Triple Flames In Partially-Premixed Mixing Layers, J. Prager, H. N. Najm, M. Valorani, D.A. Goussis Jan 2011

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, …

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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 Jan 2011

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 …

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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 Jan 2011

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 …

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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 Jan 2011

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 …

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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 Jan 2011

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. …

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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 Jan 2011

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.

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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 Jan 2011

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 …

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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 Jan 2011

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 …

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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 Jan 2011

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 - …

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Effect Of Grain Size On Uranium(Vi) Surface Complexation Kinetics And Adsorption Additivity, Jianying Shang, Chongxuan Liu, Zheming Wang, John M. Zachara Jan 2011

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.

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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 Jan 2011

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 …

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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 Jan 2011

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 …

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Interfacial Reactivity Of Radionuclides: Emerging Paradigms From Molecular-Level Observations, A.R. Felmy, E.S. Ilton, K.M. Rosso, John M. Zachara Jan 2011

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 …

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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 Jan 2011

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 …

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Sop For Pathway Inference In Integrated Microbial Genomes (Img), Iain Anderson, Amy Chen, Victor Markowitz, Nikos Kyrpides, Natalia Ivanova Jan 2011

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 …

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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 Jan 2011

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.

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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 Jan 2011

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).

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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 Jan 2011

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.

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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 Jan 2011

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 …

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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 Jan 2011

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.

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Characterization Of The Intragranular Water Regime Within Subsurface Sediments: Pore Volume, Surface Area, And Mass Transfer Limitations, Michael B. Hay, Deborah L. Stoliker, James A. Davis, John M. Zachara Jan 2011

Characterization Of The Intragranular Water Regime Within Subsurface Sediments: Pore Volume, Surface Area, And Mass Transfer Limitations, Michael B. Hay, Deborah L. Stoliker, James A. Davis, John M. Zachara

United States Department of Energy: Publications

Although ‘‘intragranular’’ pore space within grain aggregates, grain fractures, and mineral surface coatings may contain a relatively small fraction of the total porosity within a porous medium, it often contains a significant fraction of the reactive surface area, and can thus strongly affect the transport of sorbing solutes. In this work, we demonstrate a batch experiment procedure using tritiated water as a high-resolution diffusive tracer to characterize the intragranular pore space. The method was tested using uranium contaminated sediments from the vadose and capillary fringe zones beneath the former 300A process ponds at the Hanford site (Washington). Sediments were contacted …

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Multispecies Diffusion Models: A Study Of Uranyl Species Diffusion, Chongxuan Liu, Jianying Shang, John M. Zachara Jan 2011

Multispecies Diffusion Models: A Study Of Uranyl Species Diffusion, Chongxuan Liu, Jianying Shang, John M. Zachara

United States Department of Energy: Publications

Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found …

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Transient Groundwater Chemistry Near A River: Effects On U(Vi) Transport In Laboratory Column Experiments, Jun Yin, Roy Haggerty, Deborah L. Stoliker, Douglas B. Kent, Jonathan D. Istok, Janek Greskowiak, John M. Zachara Jan 2011

Transient Groundwater Chemistry Near A River: Effects On U(Vi) Transport In Laboratory Column Experiments, Jun Yin, Roy Haggerty, Deborah L. Stoliker, Douglas B. Kent, Jonathan D. Istok, Janek Greskowiak, John M. Zachara

United States Department of Energy: Publications

In the 300 Area of a U(VI)-contaminated aquifer at Hanford, Washington, USA, inorganic carbon and major cations, which have large impacts on U(VI) transport, change on an hourly and seasonal basis near the Columbia River. Batch and column experiments were conducted to investigate the factors controlling U(VI) adsorption/desorption by changing chemical conditions over time. Low alkalinity and low Ca concentrations (Columbia River water) enhanced adsorption and reduced aqueous concentrations. Conversely, high alkalinity and high Ca concentrations (Hanford groundwater) reduced adsorption and increased aqueous concentrations of U(VI). An equilibrium surface complexation model calibrated using laboratory batch experiments accounted for the decrease …

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Simulating Adsorption Of U(Vi) Under Transient Groundwater Flow And Hydrochemistry: Physical Versus Chemical Nonequilibrium Model, Janek Greskowiak, Michael Hay, Henning Prommer, Chongxuan Liu, Vincent Post, Rui Ma, James Davis, Chunmiao Zheng, John M. Zachara Jan 2011

Simulating Adsorption Of U(Vi) Under Transient Groundwater Flow And Hydrochemistry: Physical Versus Chemical Nonequilibrium Model, Janek Greskowiak, Michael Hay, Henning Prommer, Chongxuan Liu, Vincent Post, Rui Ma, James Davis, Chunmiao Zheng, John M. Zachara

United States Department of Energy: Publications

Coupled intragrain diffusional mass transfer and nonlinear surface complexation processes play an important role in the transport behavior of U(VI) in contaminated aquifers. Two alternative model approaches for simulating these coupled processes were analyzed and compared: (1) the physical nonequilibrium approach that explicitly accounts for aqueous speciation and instantaneous surface complexation reactions in the intragrain regions and approximates the diffusive mass exchange between the immobile intragrain pore water and the advective pore water as multirate first-order mass transfer and (2) the chemical nonequilibrium approach that approximates the diffusion-limited intragrain surface complexation reactions by a set of multiple first-order surface complexation …

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Transition Of Cellulose Crystalline Structure And Surface Morphology Of Biomass As A Function Of Ionic Liquid Pretreatment And Its Relation To Enzymatic Hydrolysis, Gang Cheng, Patanjali Varanasi, Chenlin Li, Hanbin Liu, Yuri B. Melnichenko, Blake A. Simmons, Michael S. Kent, Seema Singh Jan 2011

Transition Of Cellulose Crystalline Structure And Surface Morphology Of Biomass As A Function Of Ionic Liquid Pretreatment And Its Relation To Enzymatic Hydrolysis, Gang Cheng, Patanjali Varanasi, Chenlin Li, Hanbin Liu, Yuri B. Melnichenko, Blake A. Simmons, Michael S. Kent, Seema Singh

United States Department of Energy: Publications

Cellulose is inherently resistant to breakdown, and the native crystalline structure (cellulose I) of cellulose is considered to be one of themajor factors limiting its potential in terms of cost-competitive lignocellulosic biofuel production. Here we report the impact of ionic liquid pretreatment on the cellulose crystalline structure in different feedstocks, including microcrystalline cellulose (Avicel), switchgrass (Panicum virgatum), pine (Pinus radiata), and eucalyptus (Eucalyptus globulus), and its influence on cellulose hydrolysis kinetics of the resultant biomass. These feedstocks were pretreated using 1-ethyl-3-methyl imidazolium acetate ([C2mim][OAc]) at 120 and 160°C for 1, 3, 6, and 12 …

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