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United States Department of Energy: Publications

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Application Of Pdf Mixing Models To Premixed Flames With Differential Diffusion, Edward Richardson, Jacqueline Chen Jan 2012

Application Of Pdf Mixing Models To Premixed Flames With Differential Diffusion, Edward Richardson, Jacqueline Chen

United States Department of Energy: Publications

Differential diffusion alters the balance of reaction and diffusion in turbulent premixed combustion, affecting the performance and emissions of combustion devices. Modelling combustion devices with Probability or Filtered Density Function (PDF or FDF) methods provides an exact treatment for the change in composition due to chemical reaction, while molecular mixing has to be modelled. Previous PDF molecular mixing models do not account for differential diffusion in a manner which satisfies realizability requirements. A new approach for treating differential diffusion, which ensures realizability, is proposed for pairwise-exchange mixing models in general, and applied in the Interaction by Exchange with the Mean …

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Pore-Scale Characterization Of Biogeochemical Controls On Iron And Uranium Speciation Under Flow Conditions, Carolyn I. Pearce, Michael J. Wilkins, Changyong Zhang, Steve M. Heald, James K. Fredrickson, John M. Zachara Jan 2012

Pore-Scale Characterization Of Biogeochemical Controls On Iron And Uranium Speciation Under Flow Conditions, Carolyn I. Pearce, Michael J. Wilkins, Changyong Zhang, Steve M. Heald, James K. Fredrickson, John M. Zachara

United States Department of Energy: Publications

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both Xray microprobe and X-ray absorption spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively …

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Quantitative 3-D Elemental Mapping By La-Icp-Ms Of A Basaltic Clast From The Hanford 300 Area, Washington, Usa, Sheng Peng, Qinhong Hu, Robert Ewing, Chongxuan Liu, John M. Zachara Jan 2012

Quantitative 3-D Elemental Mapping By La-Icp-Ms Of A Basaltic Clast From The Hanford 300 Area, Washington, Usa, Sheng Peng, Qinhong Hu, Robert Ewing, Chongxuan Liu, John M. Zachara

United States Department of Energy: Publications

Laser ablation with inductively coupled plasma-mass spectrometry (LA-ICP-MS) was used to measure elemental concentrations at the 100-μm scale in a 3-dimensional manner within a basaltic clast sample collected from the Hanford 300 Area in south-central Washington State, United States. A calibration method was developed to quantify the LAICP- MS signal response using a constant-sum mass fraction of eight major elements; the method produced reasonable concentration measurements for both major and trace elements when compared to a standard basalt sample with known concentrations. 3-Dimensional maps (stacked 2-D contour layers, each representing 2100 μm × 2100 μm) show …

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Molecular Underpinnings Of Fe(Iii) Oxide Reduction By Shewanella Oneidensis Mr-1, Liang Shi, Kevin Rosso, Tomas Clarke, David Richardson, John M. Zachara, James K. Fredrickson Jan 2012

Molecular Underpinnings Of Fe(Iii) Oxide Reduction By Shewanella Oneidensis Mr-1, Liang Shi, Kevin Rosso, Tomas Clarke, David Richardson, John M. Zachara, James K. Fredrickson

United States Department of Energy: Publications

In the absence of O2 and other electron acceptors, the Gram-negative bacterium Shewanella oneidensis MR-1 can use ferric [Fe(III)] (oxy) (hydr) oxideminerals as the terminal electron acceptors for an aerobic respiration. At circumneutral pH and in the absence of strong complexing ligands, Fe(III) oxides are relatively insoluble and thus are external to the bacterial cells. S. oneidensis MR-1 and related strains of metal-reducing Shewanella have evolved machinery (i.e.,metal-reducing or Mtr pathway) for transferring electrons from the inner-membrane, through the periplasmanda cross the outer-membrane to the surface of extracellular Fe(III) oxides. The protein components identified to date for the Mtr …

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The ‘Porin–Cytochrome’ Model For Microbe-To-Mineral Electron Transfer, David Richardson, Julea Butt, James K. Fredrickson, John M. Zachara, Liang Shi, Marcus Edwards, Gaye White, Nanakow Baiden, Andrew Gates, Sophie Marritt, Thomas Clarke Jan 2012

The ‘Porin–Cytochrome’ Model For Microbe-To-Mineral Electron Transfer, David Richardson, Julea Butt, James K. Fredrickson, John M. Zachara, Liang Shi, Marcus Edwards, Gaye White, Nanakow Baiden, Andrew Gates, Sophie Marritt, Thomas Clarke

United States Department of Energy: Publications

Many species of bacteria can couple anaerobic growth to the respiratory reduction of insoluble minerals containing Fe(III) or Mn(III/IV). It has been suggested that in Shewanella species electrons cross the outer membrane to extracellular substrates via ‘porin–cytochrome’ electron transport modules. The molecular structure of an outer-membrane extracellular-facing deca-haem terminus for such a module has recently been resolved. It is debated how, once outside the cells, electrons are transferred from outer-membrane cytochromes to insoluble electron sinks. This may occur directly or by assemblies of cytochromes, perhaps functioning as ‘nanowires’, or via electron shuttles. Here we review recent work in this field …

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The Genome Portal Of The Department Of Energy Joint Genome Institute, Igor V. Grigoriev, Henrik Nordberg, Igor Shabalov, Andrea Aerts, Mike Cantor, David Goodstein, Alan Kuo, Simon Minovitsky, Roman Nikitin, Robin A. Ohm, Robert Otillar, Alex Poliakov, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak Nov 2011

The Genome Portal Of The Department Of Energy Joint Genome Institute, Igor V. Grigoriev, Henrik Nordberg, Igor Shabalov, Andrea Aerts, Mike Cantor, David Goodstein, Alan Kuo, Simon Minovitsky, Roman Nikitin, Robin A. Ohm, Robert Otillar, Alex Poliakov, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak

United States Department of Energy: Publications

The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user …

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Bioenergy Feedstock-Specific Enrichment Of Microbial Populations During High-Solids Thermophilic Deconstruction, Amitha P. Reddy, Martin Allgaier, Steven W. Singer, Terry C. Hazen, Blake A. Simmons, Philip Hugenholtz, Jean S. Vandergheynst Sep 2011

Bioenergy Feedstock-Specific Enrichment Of Microbial Populations During High-Solids Thermophilic Deconstruction, Amitha P. Reddy, Martin Allgaier, Steven W. Singer, Terry C. Hazen, Blake A. Simmons, Philip Hugenholtz, Jean S. Vandergheynst

United States Department of Energy: Publications

Thermophilic microbial communities that are active in a high-solids environment offer great potential for the discovery of industrially relevant enzymes that efficiently deconstruct bioenergy feedstocks. In this study, finished green waste compost was used as an inoculum source to enrich microbial communities and associated enzymes that hydrolyze cellulose and hemicellulose during thermophilic high-solids fermentation of the bioenergy feedstocks switchgrass and corn stover. Methods involving the disruption of enzyme and plant cell wall polysaccharide interactions were developed to recover xylanase and endoglucanase activity from deconstructed solids. Xylanase and endoglucanase activity increased by more than a factor of 5, upon four successive …

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Comparison Of Dynamic Compression Behavior Of Single Crystal Sapphire To Polycrystalline Alumina, G. J. Kleiser, L.C. Chhabildas, W.D. Reinhart Jan 2011

Comparison Of Dynamic Compression Behavior Of Single Crystal Sapphire To Polycrystalline Alumina, G. J. Kleiser, L.C. Chhabildas, W.D. Reinhart

United States Department of Energy: Publications

Due to the considerable interest in the shock loading behavior of aluminum oxide whether it is in the polycrystalline phase or in the single crystal phase well-controlled experiments were conducted to probe differences in shock loading behavior between these two materials. Previous studies concluded that the behavior was similar but careful examination of well-controlled experiments has revealed the two materials are different.Although the experimental results appear to have the same behavior in the shock velocity vs. particle velocity plane, they are considerably different in the stressevolume compression plane and evidence is provided that indicates the single crystal remains crystalline up …

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Persistence Of Uranium Groundwater Plumes: Contrasting Mechanisms At Two Contaminated Doe Sites, John M. Zachara, James A. Davis, Philip E. Long, Kenneth H. Williams, Mark Freshley, James P. Mckinley Jan 2011

Persistence Of Uranium Groundwater Plumes: Contrasting Mechanisms At Two Contaminated Doe Sites, John M. Zachara, James A. Davis, Philip E. Long, Kenneth H. Williams, Mark Freshley, James P. Mckinley

United States Department of Energy: Publications

We examine subsurface uranium (U) plumes at two U.S. Department of Energy sites located near large river systems. Following excavation of contaminated materials, both sites were projected to naturally flush remnant uranium contamination to levels below regulatory limits (e.g., 30 μg/L), within 10 years at the Hanford 300 Area (Columbia River) and 12 years at the Rifle site (Colorado River). The observed rate of attenuation was much lower than expected at both sites. Current understanding suggests that the two sites have common, but also differing mechanisms controlling plume persistence. At Hanford, the persistent source is adsorbed U(VI) in the deep …

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Monarch: A High-Assurance Java-To-Java (J2j) Source-Code Migrator, Victor L. Winter, Jonathan Guerrero, Carl Reinke, James T. Perry Jan 2011

Monarch: A High-Assurance Java-To-Java (J2j) Source-Code Migrator, Victor L. Winter, Jonathan Guerrero, Carl Reinke, James T. Perry

United States Department of Energy: Publications

JVM-based processors used in embedded systems are often scaled back versions of the standard JVM which do not support the full set of Java byte codes and native methods assumed by a JVM. As a result, code bases such as Java libraries must be migrated in order make them suitable for execution on the embedded JVM-based processor. This paper describes Monarch, a high-assurance Java-to-java (J2j) source code migrator that we are developing to assist such code migrations.

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Effects Of Damköhler Number On Flame Extinction And Reignition In Turbulent Non-Premixed Flames Using Dns, David Lignell, Jacqueline Chen, Hans Schmutz Jan 2011

Effects Of Damköhler Number On Flame Extinction And Reignition In Turbulent Non-Premixed Flames Using Dns, David Lignell, Jacqueline Chen, Hans Schmutz

United States Department of Energy: Publications

Results from a parametric study of flame extinction and reignition with varying Damköhler number using direct numerical simulation are presented. Three planar, non-premixed ethylene jet flames were simulated at a constant Reynolds number of 5120. The fuel and oxidizer stream compositions were varied to adjust the steady laminar extinction scalar dissipation rate, while maintaining constant flow and geometric conditions. Peak flame extinction varies from approximately 40% to nearly global blowout as the Damköhler number decreases. The degree of extinction significantly affects the development of the jets and the degree of mixing of fuel, oxidizer, and combustion products prior to reignition. …

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Variational Theory And Domain Decomposition For Nonlocal Problems, Burak Aksoylu, Michael L. Parks Jan 2011

Variational Theory And Domain Decomposition For Nonlocal Problems, Burak Aksoylu, Michael L. Parks

United States Department of Energy: Publications

In this article we present the first results on domain decomposition methods for nonlocal operators. We present a nonlocal variational formulation for these operators and establish the well-posedness of associated boundary value problems, proving a nonlocal Poincaré inequality. To determine the conditioning of the discretized operator, we prove a spectral equivalence which leads to a mesh size independent upper bound for the condition number of the stiffness matrix. We then introduce a nonlocal two-domain variational formulation utilizing nonlocal transmission conditions, and prove equivalence with the single-domain formulation. A nonlocal Schur complement is introduced. We establish condition number bounds for the …

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Automated Analysis Of Mouse Serum Peptidome Using Restricted Access Media And Nanoliquid Chromatography–Tandem Mass Spectrometry, Geun-Cheol Gil, Jim Brennan, Dan Throckmorton, Steven Branda, Gabriela Chirica Jan 2011

Automated Analysis Of Mouse Serum Peptidome Using Restricted Access Media And Nanoliquid Chromatography–Tandem Mass Spectrometry, Geun-Cheol Gil, Jim Brennan, Dan Throckmorton, Steven Branda, Gabriela Chirica

United States Department of Energy: Publications

We demonstrate use of restricted access media with reversed phase functionality (RAM-RP) for analysis of low molecular weight proteins and peptides in mouse serum (75ml) using a custom designed modular automated processing system (MAPS). RAM-RP fractionation with simultaneous removal of high molecular weight and high abundance proteins is integrated with a follow-on buffer exchange module (BE) to ensure compatibility with subsequent processing steps (trypsin digestion and intact peptide separation prior to mass spectrometric analysis). The high sample capacity afforded by chromatographic methods generates enough sample to achieve comprehensive serum peptidome identification (357 proteins) through tandem mass spectrometric analysis of both …

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An Experimental And Kinetic Modeling Study Of Methyl Formate Low-Pressure Flames, S. Dooley, F. L. Dryer, B. Yang, J. Wang, T. A. Cool, T. Kasper, N. Hansen Jan 2011

An Experimental And Kinetic Modeling Study Of Methyl Formate Low-Pressure Flames, S. Dooley, F. L. Dryer, B. Yang, J. Wang, T. A. Cool, T. Kasper, N. Hansen

United States Department of Energy: Publications

The oxidation of methyl formate (CH3OCHO), the simplest methyl ester, is studied in a series of burnerstabilized laminar flames at pressures of 22–30 Torr and equivalence ratios (Φ) from 1.0 to 1.8 for flame conditions of 25–35% fuel. Flame structures are determined by quantitative measurements of species mole fractions with flame-sampling molecular-beam synchrotron photoionization mass spectrometry (PIMS). Methyl formate is observed to be converted to methanol, formaldehyde and methane as major intermediate species of mechanistic relevance. Smaller amounts of ethylene and acetylene are also formed from methyl formate oxidation. Reactant, product and major intermediate species profiles …

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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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