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Full-Text Articles in Engineering

The Irreversible Momentum Of Clean Energy, Barack Obama Jan 2017

The Irreversible Momentum Of Clean Energy, Barack Obama

US Department of Energy Publications

The release of carbon dioxide (CO2) and other greenhouse gases (GHGs) due to human activity is increasing global average surface air temperatures, disrupting weather patterns, and acidifying the ocean. Left unchecked, the continued growth of GHG emissions could cause global average temperatures to increase by another 4°C or more by 2100 and by 1.5 to 2 times as much in many midcontinent and far northern locations. Although our understanding of the impacts of climate change is increasingly and disturbingly clear, there is still debate about the proper course for U.S. policy—a debate that is very much on display …


Identification And Characterization Of Mtoa: A Decaheme C-Type Cytochrome Of The Neutrophilic Fe(Ii)-Oxidizing Bacterium Sideroxydans Lithotrophicus Es-1, Juan Liu, Zheming Wang, Sara M. Belchik, Marcus J. Edwards, Chongxuan Liu, David W. Kennedy, Eric D. Merkley, Mary S. Lipton, Julea N. Butt, David J. Richardson, John M. Zachara, James K. Fredrickson, Kevin M. Rosso, Liang Shi Feb 2012

Identification And Characterization Of Mtoa: A Decaheme C-Type Cytochrome Of The Neutrophilic Fe(Ii)-Oxidizing Bacterium Sideroxydans Lithotrophicus Es-1, Juan Liu, Zheming Wang, Sara M. Belchik, Marcus J. Edwards, Chongxuan Liu, David W. Kennedy, Eric D. Merkley, Mary S. Lipton, Julea N. Butt, David J. Richardson, John M. Zachara, James K. Fredrickson, Kevin M. Rosso, Liang Shi

US Department of Energy Publications

The Gram-negative bacterium Sideroxydans lithotrophicus ES-1(ES-1) grows on FeCO3 or FeS at oxic–anoxic interfaces at circumneutral pH, and the ES-1-mediated Fe(II) oxidation occurs extracellularly. However, the molecular mechanisms underlying ES-1’s ability to oxidize Fe(II) remain unknown. Survey of the ES-1 genome for candidate genes formicrobial extracellular Fe(II) oxidation revealed that it contained a three-genecluster encoding homologs of Shewanella oneidensis MR-1(MR-1) MtrA, MtrB, and CymA that are involved in extracellular Fe(III) reduction. Homologs of MtrA and MtrB were also previously shown to be involved in extracellular Fe(II) oxidation by Rhodopseudomonas palustris TIE-1. To distinguish them from those found in MR-1, …


Dielectric Function Spectra And Critical-Point Energies Of Cu2znsnse4 From 0.5 To 9.0 Ev, S. . G. Choi, H. . Y. Zhao, C. Persson, C. L. Perkins, A Donohue, B To, A. G. Norman, J Li, I. L. Repins Jan 2012

Dielectric Function Spectra And Critical-Point Energies Of Cu2znsnse4 From 0.5 To 9.0 Ev, S. . G. Choi, H. . Y. Zhao, C. Persson, C. L. Perkins, A Donohue, B To, A. G. Norman, J Li, I. L. Repins

US Department of Energy Publications

We present dielectric function e=e1+ie2spectra and critical-point energies of Cu2ZnSnSe4 determined by spectroscopic ellipsometry from 0.5 to 9.0 eV. We reduce artifacts from surface overlayers to the maximum extent possible by performing chemical-mechanical polishing and wet-chemical etching of the surface of a Cu2ZnSnSe4 thin film. Ellipsometric data are analyzed by the multilayer model and the e spectra are extracted. The data exhibit numerous spectral features associated with critical points, whose energies are obtained by fitting standard lineshapes to second energy derivatives of the data. The experimental results are in good …


The Sintering Behavior Of Close-Packed Spheres, R. Bjørk, V. Tikare, H. L. Frandsen, N. Pryds Jan 2012

The Sintering Behavior Of Close-Packed Spheres, R. Bjørk, V. Tikare, H. L. Frandsen, N. Pryds

US Department of Energy Publications

The sintering behavior and microstructural evolution of a powder compact is influenced strongly by initial properties, such as the relative density, the particle and pore size distribution, and the powder packing. While the influence of the former parameters on the microstructural evolution has been investigated in some detail, the impact of the initial packing of the powder has been mostly overlooked. However, research has shown that the sintering behavior of a powder can be significantly improved if the powder is regularly packed.

This has been shown for monodisperse spherical TiO2 particles [1], which sintered 10 times faster and exhibited almost …


The Hardness And Strength Of Metal Tribofilms: An Apparent Contradiction Between Nanoindentation And Pillar Compression, Corbett C. Battaile, Brad L. Boyce, Christopher Weinberger, Somuri Prasad, Joseph R. Michael, Blythe G. Clark Jan 2012

The Hardness And Strength Of Metal Tribofilms: An Apparent Contradiction Between Nanoindentation And Pillar Compression, Corbett C. Battaile, Brad L. Boyce, Christopher Weinberger, Somuri Prasad, Joseph R. Michael, Blythe G. Clark

US Department of Energy Publications

After sliding contact of a hard spherical counterface on a metal surface, the resulting wear scar possesses a complex microstructure consisting of dislocations, dislocation cells, ultrafine or nanocrystalline grains, and material that has undergone dynamic recovery. There remains a controversy as to the mechanical properties of the tribolayer formed in this wear scar. To investigate the properties of this thin layer of damaged material in single crystal nickel, we employed two complementary techniques: pillar compression and nanoindentation. In both techniques, the tests were tailored to characterize the near surface properties associated with the top 500 nm of material, where the …


Sparse Pseudospectral Approximation Method, Paul G. Constantine, Michael Eldred, Eric Phipps Jan 2012

Sparse Pseudospectral Approximation Method, Paul G. Constantine, Michael Eldred, Eric Phipps

US Department of Energy Publications

Multivariate global polynomial approximations – such as polynomial chaos or stochastic collocation methods – are now in widespread use for sensitivity analysis and uncertainty quantification. The pseudospectral variety of these methods uses a numerical integration rule to approximate the Fourier-type coefficients of a truncated expansion in orthogonal polynomials. For problems in more than two or three dimensions, a sparse grid numerical integration rule offers accuracy with a smaller node set compared to tensor product approximation. However, when using a sparse rule to approximately integrate these coefficients, one often finds unacceptable errors in the coefficients associated with higher degree polynomials.

By …


Pore Scale Analysis Of The Impact Of Mixing-Induced Reaction Dependent Viscosity Variations, S.M. Davison, H. Yoon, M. J. Martinez Jan 2012

Pore Scale Analysis Of The Impact Of Mixing-Induced Reaction Dependent Viscosity Variations, S.M. Davison, H. Yoon, M. J. Martinez

US Department of Energy Publications

Expanding interest in enhanced subsurface natural resource recovery and carbon sequestration motivates study of reacting flows in porous media. In this work, we examine the case of reaction products that increase or decrease the viscosity of the fluid. Parallel reactant streams flow through porous media and react transversely along the centerline. We utilize a pore scale, finite element numerical method that couples the reaction with fluid flow through two arrangements of porous media at three Damkohler (Da) numbers and two viscosity conditions. When the product increases the fluid viscosity, the flow velocity is reduced and higher amounts of …


Raman/Rayleigh Scattering And Co-Lif Measurements In Laminar And Turbulent Jet Flames Of Dimethyl Ether, Frederik Fuest, Robert S. Barlow, Jyh-Yuan Chen, Andreas Dreizler Jan 2012

Raman/Rayleigh Scattering And Co-Lif Measurements In Laminar And Turbulent Jet Flames Of Dimethyl Ether, Frederik Fuest, Robert S. Barlow, Jyh-Yuan Chen, Andreas Dreizler

US Department of Energy Publications

To reduce the impact of combustion of fossil fuels on air quality and climate change, dimethyl ether (DME) is a promising alternative diesel fuel candidate. Technical combustion processes, including formation of pollutants, are influenced by turbulence–chemistry interaction. Therefore, accurate prediction by computational combustion models of combustion systems burning DME must account for multiple scalars and scalar gradients. The testing of such models requires detailed experiments. Here a study is presented on the feasibility of simultaneous species and temperature measurements in turbulent dimethyl ether flames, using line-imaged Raman/Rayleigh scattering of the major species H2, O2, N2 …


The Fundamental Equation Of Eddy Covariance And Its Application In Flux Measurements, Lianhong Gu, William J. Massman, Ray Leuning, Stephen Pallardy, Tilden Meyers, Paul Hanson, Jeffery Riggs, Kevin Hosman, Bai Yang Jan 2012

The Fundamental Equation Of Eddy Covariance And Its Application In Flux Measurements, Lianhong Gu, William J. Massman, Ray Leuning, Stephen Pallardy, Tilden Meyers, Paul Hanson, Jeffery Riggs, Kevin Hosman, Bai Yang

US Department of Energy Publications

A fundamental equation of eddy covariance (FQEC) is derived that allows the net ecosystem exchange (NEE) N̅s of a specified atmospheric constituent s to be measured with the constraint of conservation of any other atmospheric constituent (e.g. N2, argon, or dry air). It is shown that if the condition │N̅s│ ˃˃ │X̅s│ │N̅co2│is true, the conservation of mass can be applied with the assumption of no net ecosystem source or sink of dry air and the FQEC is reduced to the following equation and its approximation for horizontally homogeneous mass fluxes:

s = c̅dw’X’s …


A Non-Premixed Combustion Model Based On Flame Structure Analysis At Supercritical Pressures, Guilhem Lacaze, Joseph Oefelein Jan 2012

A Non-Premixed Combustion Model Based On Flame Structure Analysis At Supercritical Pressures, Guilhem Lacaze, Joseph Oefelein

US Department of Energy Publications

This work presents a study of non-premixed flames at supercritical-pressure conditions. Emphasis is placed on flame stability in liquid rocket engines fueled with liquid oxygen and gaseous hydrogen. The flame structure sensitivity to strain, pressure, temperature and real-fluid effects was investigated in detailed opposed-jet flames calculations. It is shown that the flame is very robust to strain, that the flamelet assumption is valid for the conditions of interest, and that real-fluid phenomena can have a significant impact on flame topology. At high-pressure supercritical conditions, small pressure or temperature variations can induce strong changes of thermodynamic properties across the flame. A …


Field Ion Source Development For Neutron Generators, B. Bargsten Johnson, P. R. Schwoebel, C. E. Holland, P. J. Resnick, K L. Hertz, D L. Chichester Jan 2012

Field Ion Source Development For Neutron Generators, B. Bargsten Johnson, P. R. Schwoebel, C. E. Holland, P. J. Resnick, K L. Hertz, D L. Chichester

US Department of Energy Publications

An ion source based on the principles of electrostatic field desorption is being developed to improve the performance of existing compact neutron generators. The ion source is an array of gated metal tips derived from field electron emitter array micro fabrication technology. A comprehensive summary of development and experimental activities is presented. Many structural modifications to the arrays have been incorporated to achieve higher tip operating fields, while lowering fields at the gate electrode to prevent gate field electron emission which initiates electrical breakdown in the array. The latest focus of fabrication activities has been on rounding the gate electrode …


Numerical Simulation Of Expansion And Charring Of Carbon-Epoxy Laminates In Fire Environments, Matthew Mcgurn, Paul Desjardin, Amanda Dodd Jan 2012

Numerical Simulation Of Expansion And Charring Of Carbon-Epoxy Laminates In Fire Environments, Matthew Mcgurn, Paul Desjardin, Amanda Dodd

US Department of Energy Publications

A thermal model is developed for the response of carbon-epoxy composite laminates in fire environments. The model is based on a porous media description that includes the effects of gas transport within the laminate along with swelling. Model comparisons are conducted against the data from Quintiere et al. [34]. Verifications are conducted for both coupon level and intermediate scale one-sided heating tests. Comparisons of the heat release rate (HRR) and time-to-ignition as well as the final products (mass fractions, volume percentages, porosity, etc.) are conducted. Overall, the agreement between available the data and model is good considering the simplified approximations …


Saturated–Unsaturated Flow In A Compressible Leaky-Unconfined Aquifer, Phoolendra Mishra, Velimir Vesselinov, Kristopher Kuhlman Jan 2012

Saturated–Unsaturated Flow In A Compressible Leaky-Unconfined Aquifer, Phoolendra Mishra, Velimir Vesselinov, Kristopher Kuhlman

US Department of Energy Publications

An analytical solution is developed for three-dimensional flow towards a partially penetrating largediameter well in an unconfined aquifer bounded below by a leaky aquitard of finite or semi-infinite extent. The analytical solution is derived using Laplace and Hankel transforms, then inverted numerically. Existing solutions for flow in leaky unconfined aquifers neglect the unsaturated zone following an assumption of instantaneous drainage due to Neuman. We extend the theory of leakage in unconfined aquifers by (1) including water flow and storage in the unsaturated zone above the water table, and (2) allowing the finite-diameter pumping well to partially penetrate the aquifer. The …


Combined Finite Element And Peridynamic Analyses For Predicting Failure In A Stiffened Composite Curved Panel With A Central Slot, Erkan Oterkus, Erdogan Madenci, Olaf Weckner, Stewart Silling, Philip Bogert, Alexander Tessler Jan 2012

Combined Finite Element And Peridynamic Analyses For Predicting Failure In A Stiffened Composite Curved Panel With A Central Slot, Erkan Oterkus, Erdogan Madenci, Olaf Weckner, Stewart Silling, Philip Bogert, Alexander Tessler

US Department of Energy Publications

This study presents an analysis approach based on a merger of the finite element method and the peridynamic theory. Its validity is established through qualitative and quantitative comparisons against the test results for a stiffened composite curved panel with a central slot under combined internal pressure and axial tension. The predicted initial and final failure loads, as well as the final failure modes, are in close agreement with the experimental observations. This approach demonstrates the capability of the PD approach to assess the durability of complex composite structures.


A Reaction Progress Variable Modeling Approach For Non-Ideal Multiphase Explosives, K. P. Ruggirello, P. E. Desjardin, M. R. Baer, M. J. Kaneshige, E. S. Hertel Jan 2012

A Reaction Progress Variable Modeling Approach For Non-Ideal Multiphase Explosives, K. P. Ruggirello, P. E. Desjardin, M. R. Baer, M. J. Kaneshige, E. S. Hertel

US Department of Energy Publications

This study concerns the development of a mixture fraction based reaction progress variable formulation for aluminized explosives. Highlights of the formulation include a fully compressible treatment of both the gas and solid phases (both aluminum and alumina), heterogenous and homogenous reactions, and effects of group combustion. Isolated particle simulations are validated against experimental data and DNS and show good agreement of burn times over a range of pressure and oxygen environments. The new models are implemented in the CTH shock physics code using a fractional step approach to allow for efficient computation of particle dynamics. Comparisons are made to experimental …


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

US 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 …


An Experimental And Theoretical Study Of Heat And Mass Transfer During The Venting Of Gas From Pressure Vessels, W. S. Winters, G. H. Evans, S. F. Rice, R. Greif Jan 2012

An Experimental And Theoretical Study Of Heat And Mass Transfer During The Venting Of Gas From Pressure Vessels, W. S. Winters, G. H. Evans, S. F. Rice, R. Greif

US Department of Energy Publications

Non condensing gas flow and heat transfer during venting of vessels are studied using experiments and analysis. A high pressure helium supply vessel is connected to a low pressure receiver via orifice and tubing. A single control volume analysis and a multi-dimensional analysis are used to predict pressure and mass-averaged temperature in the supply. Experiments utilizing transient PVT methods are conducted to obtain transient pressure and mass-averaged temperature data for validating the analysis. Measured transient pressures and mass-averaged temperatures in the supply are reproduced by analysis. Heat transfer is due to natural convection except for the early part of transfer.


A Functional Description Of Cyma, An Electron-Transfer Hub Supporting Anaerobic Respiratory Flexibility In Shewanella, Sophie J. Marritt, Thomas G. Lowe, Jordan Bye, Duncan G. G. Mcmillan, Liang Shi, James K. Fredrickson, John M. Zachara, David J. Richardson, Myles R. Cheesman, Lars J. C. Jeuken, Julea N. Butt Jan 2012

A Functional Description Of Cyma, An Electron-Transfer Hub Supporting Anaerobic Respiratory Flexibility In Shewanella, Sophie J. Marritt, Thomas G. Lowe, Jordan Bye, Duncan G. G. Mcmillan, Liang Shi, James K. Fredrickson, John M. Zachara, David J. Richardson, Myles R. Cheesman, Lars J. C. Jeuken, Julea N. Butt

US Department of Energy Publications

CymA (tetrahaem cytochrome c) is a member of the NapC/NirT family of quinol dehydrogenases. Essential for the anaerobic respiratory flexibility of shewanellae, CymA transfers electrons from menaquinol to various dedicated systems for the reduction of terminal electron acceptors including fumarate and insoluble minerals of Fe(III). Spectroscopic characterization of CymA from Shewanella oneidensis strain MR-1 identifies three lowspin His/His co-ordinated c-haems and a single high-spin chaem with His/H2O co-ordination lying adjacent to the quinolbinding site. At pH 7, binding of the menaquinol analogue, 2-heptyl-4-hydroxyquinoline-N-oxide, does not alter the midpoint potentials of the high-spin (approximately −240 mV) …


Exploring The Biochemistry At The Extracellular Redox Frontier Of Bacterial Mineral Fe(Iii) Respiration, David J. Richardson, Marcus J. Edwards, Gaye F. White, Nanakow Baiden, Robert S. Hartshorne, James K. Fredrickson, Liang Shi, John M. Zachara, Andrew J. Gates, University Of East Anglia, Thomas Clarke Jan 2012

Exploring The Biochemistry At The Extracellular Redox Frontier Of Bacterial Mineral Fe(Iii) Respiration, David J. Richardson, Marcus J. Edwards, Gaye F. White, Nanakow Baiden, Robert S. Hartshorne, James K. Fredrickson, Liang Shi, John M. Zachara, Andrew J. Gates, University Of East Anglia, Thomas Clarke

US Department of Energy Publications

Many species of the bacterial Shewanella genus are notable for their ability to respire in anoxic environments utilizing insoluble minerals of Fe(III) and Mn(IV) as extracellular electron acceptors. In Shewanella oneidensis, the process is dependent on the decahaem electron-transport proteins that lie at the extracellular face of the outer membrane where they can contact the insoluble mineral substrates. These extracellular proteins are charged with electrons provided by an inter-membrane electron-transfer pathway that links the extracellular face of the outer membrane with the inner cytoplasmic membrane and thereby intracellular electron sources. In the present paper, we consider the common structural …


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

US 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 …


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

US 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 …


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

US 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 …


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

US 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 …


Img: The Integrated Microbial Genomes Database And Comparative Analysis System, Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides Jan 2012

Img: The Integrated Microbial Genomes Database And Comparative Analysis System, Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides

US Department of Energy Publications

The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG’s data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations …


Complete Genome Sequence Of Thauera Aminoaromatica Strain Mz1t, Ke Jiang, John Sanseverino, Archana Chauhan, Susan Lucas, Alex Copeland, Alla Lapidus, Tijana Glavina Del Rio, Eileen Dalin, Hope Tice, David Bruce, Lynne Goodwin, Sam Pitluck, David Sims, Thomas Brettin, John C. Detter, Cliff Han, Y.J. Chang, Frank Larimer, Miriam Land, Loren Hauser, Nikos C. Kyrpides, Natalia Mikhailova, Scott Moser, Patricia Jegier, Dan Close, Jennifer M. Debruyn, Ying Wang, Alice C. Layton, Michael S. Allen, Gary S. Sayler Jan 2012

Complete Genome Sequence Of Thauera Aminoaromatica Strain Mz1t, Ke Jiang, John Sanseverino, Archana Chauhan, Susan Lucas, Alex Copeland, Alla Lapidus, Tijana Glavina Del Rio, Eileen Dalin, Hope Tice, David Bruce, Lynne Goodwin, Sam Pitluck, David Sims, Thomas Brettin, John C. Detter, Cliff Han, Y.J. Chang, Frank Larimer, Miriam Land, Loren Hauser, Nikos C. Kyrpides, Natalia Mikhailova, Scott Moser, Patricia Jegier, Dan Close, Jennifer M. Debruyn, Ying Wang, Alice C. Layton, Michael S. Allen, Gary S. Sayler

US Department of Energy Publications

Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysaccharide and degrade various aromatic compounds with nitrate as an electron acceptor. These properties, if fully understood at the genome-sequence level, can aid in environmental processing of organic matter in anaerobic cycles by short-circuiting a central anaerobic metabolite, acetate, from microbiological conversion to methane, a critical greenhouse gas. Strain MZ1T is the first strain from the genus Thauera with a completely sequenced genome. The 4,496,212 bp chromosome and 78,374 bp plasmid …


The Crystal Structure Of The Extracellular 11-Heme Cytochromeundareveals A Conserved 10-Heme Motif And Defined Binding Site For Soluble Iron Chelates, Marcus J. Edwards, Andrea Hall, Liang Shi, James K. Fredrickson, John M. Zachara, Julea N. Butt, David J. Richardson, Thomas A. Clarke Jan 2012

The Crystal Structure Of The Extracellular 11-Heme Cytochromeundareveals A Conserved 10-Heme Motif And Defined Binding Site For Soluble Iron Chelates, Marcus J. Edwards, Andrea Hall, Liang Shi, James K. Fredrickson, John M. Zachara, Julea N. Butt, David J. Richardson, Thomas A. Clarke

US Department of Energy Publications

Members of the genus Shewanella translocate decaor undeca-heme cytochromes to the external cell surface thus enabling respiration using extracellular minerals and polynuclear Fe(III) chelates. The high resolution structure of the first undeca-heme outer membrane cytochrome, UndA, reveals a crossed heme chain with four potential electron ingress/ egress sites arranged within four domains. Sequence and structural alignment of UndA and the deca-heme MtrF reveals the extra heme of UndA is inserted between MtrF hemes 6 and 7. The remaining UndA hemes can be superposed over the heme chain of the decaheme MtrF, suggesting that a ten heme core is conserved between …


Three-Dimensional Bayesian Geostatistical Aquifer Characterization At The Hanford 300 Area Using Tracer Test Data, Xingyuan Chen, Haruko Murakami, Melanie S. Hahn, Glenn E. Hammond, Mark Rockhold, John M. Zachara, Yoram Rubin Jan 2012

Three-Dimensional Bayesian Geostatistical Aquifer Characterization At The Hanford 300 Area Using Tracer Test Data, Xingyuan Chen, Haruko Murakami, Melanie S. Hahn, Glenn E. Hammond, Mark Rockhold, John M. Zachara, Yoram Rubin

US Department of Energy Publications

Tracer tests performed under natural or forced gradient flow conditions can provide useful information for characterizing subsurface properties, through monitoring, modeling, and interpretation of the tracer plume migration in an aquifer. Nonreactive tracer experiments were conducted at the Hanford 300 Area, along with constant-rate injection tests and electromagnetic borehole flow meter tests. A Bayesian data assimilation technique, the method of anchored distributions (MAD) (Rubin et al., 2010), was applied to assimilate the experimental tracer test data with the other types of data and to infer the three-dimensional heterogeneous structure of the hydraulic conductivity in the saturated zone of the Hanford …


Analysis Of Phase Separation In High Performance Pbte–Pbs Thermoelectric Materials, Steven N. Girard, Klaus Schmidt-Rohr, Thomas C. Chasapis, Euripides Hatzikraniotis, B. Njegic, E. M. Levin, A. Rawal, Konstantinos M. Paraskevopoulos, Mercouri G. Kanatzidis Jan 2012

Analysis Of Phase Separation In High Performance Pbte–Pbs Thermoelectric Materials, Steven N. Girard, Klaus Schmidt-Rohr, Thomas C. Chasapis, Euripides Hatzikraniotis, B. Njegic, E. M. Levin, A. Rawal, Konstantinos M. Paraskevopoulos, Mercouri G. Kanatzidis

US Department of Energy Publications

Phase immiscibility in PbTe–based thermoelectric materials is an effective means of top-down synthesis of nanostructured composites exhibiting low lattice thermal conductivities. PbTe1− x Sx thermoelectric materials can be synthesized as metastable solid solution alloys through rapid quenching. Subsequent post-annealing induces phase separation at the nanometer scale, producing nanostructures that increase phonon scattering and reduce lattice thermal conductivity. However, there has yet to be any study investigating in detail the local chemical structure of both the solid solution and nanostructured variants of this material system. Herein, quenched and annealed (i.e., solid solution and phase-separated) samples of PbTe–PbS are analyzed …


Nanoscale Structure And Structural Relaxation In Zr50cu45al5 Bulk Metallic Glass, Jinwoo Hwang, Z. H. Melgarejo, Y. E. Kalay, I. Kalay, Matthew J. Kramer, D. S. Stone, P. M. Voyles Jan 2012

Nanoscale Structure And Structural Relaxation In Zr50cu45al5 Bulk Metallic Glass, Jinwoo Hwang, Z. H. Melgarejo, Y. E. Kalay, I. Kalay, Matthew J. Kramer, D. S. Stone, P. M. Voyles

US Department of Energy Publications

Hybrid reverse Monte Carlo simulations of the structure of Zr50Cu45Al5 bulk metallic glass incorporating medium-range structure from fluctuation electron microscopy data and short-range structure from an embedded atom potential produce structures with significant fractions of icosahedral- and crystal-like atomic clusters. Similar clusters group together into nanometer-scale regions, and relaxation transforms crystal-like clusters into icosahedral clusters. A model refined against only the potential does not agree with the fluctuation microscopy data and contains few crystal-like clusters.


Antiferromagnetic Order In The Quasicrystal Approximant Cd6tb Studied By X-Ray Resonant Magnetic Scattering, M. G. Kim, G. Beutier, A. Kreyssig, T. Hiroto, T. Yamada, J. W. Kim, M. De Boissieu, R. Tamura, A. I. Goldman Jan 2012

Antiferromagnetic Order In The Quasicrystal Approximant Cd6tb Studied By X-Ray Resonant Magnetic Scattering, M. G. Kim, G. Beutier, A. Kreyssig, T. Hiroto, T. Yamada, J. W. Kim, M. De Boissieu, R. Tamura, A. I. Goldman

US Department of Energy Publications

We have used x-ray resonant magnetic scattering at the Tb L2 edge to elucidate the nature of magnetic ordering in Cd6Tb, a 1/1 approximant closely related to the Cd-Mg-R (R = rare earth) icosahedral alloys. Below TN ≈ 24 K, the ordered moments associated with the icosahedral clusters at the corners and body center of the pseudocubic unit cell are antiferromagnetically correlated, and long-range magnetic order is realized.