Tackling the Triple-Threat Genome of Miscanthus x giganteus (2010 JGI User Meeting)

ScienceCinema

Moose, Steve

2018-02-05

Steve Moose from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Tackling the Triple-Threat Genome of Miscanthus x giganteus" on March 25, 2010 at the 5th Annual DOE JGI User Meeting.

Tackling the Triple-Threat Genome of Miscanthus x giganteus (2010 JGI User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moose, Steve

2010-03-25

Steve Moose from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on "Tackling the Triple-Threat Genome of Miscanthus x giganteus" on March 25, 2010 at the 5th Annual DOE JGI User Meeting.

CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-Scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shih, Patrick

2012-03-22

Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-Scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Shih, Patrick

2018-01-10

Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Next-Generation Genetics in Plants: Evolutionary Trade-off, Immunity and Speciation (2010 JGI User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiegel, Detlef

Detlef Wiegel from the Max Planck Institute for Developmental Biology on "Next-generation genetics in plants: Evolutionary tradeoffs, immunity and speciation" on March 25, 2010 at the 5th Annual DOE JGI User Meeting.

Next-Generation Genetics in Plants: Evolutionary Trade-off, Immunity and Speciation (2010 JGI User Meeting)

ScienceCinema

Wiegel, Detlef

2018-02-12

Detlef Wiegel from the Max Planck Institute for Developmental Biology on "Next-generation genetics in plants: Evolutionary tradeoffs, immunity and speciation" on March 25, 2010 at the 5th Annual DOE JGI User Meeting.

Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Zimmer, Carl [New York Times, New York, NY (United States)

2018-05-23

Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zimmer, Carl

Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy (2010 JGI User Meeting)

ScienceCinema

Khanna, Madhu

2018-02-19

Madhu Khanna from the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute on Competitiveness of Second Generation Biofuel Feedstocks: Role of Technology and Policy on March 25, 2010 at the 5th Annual DOE JGI User Meeting.

The Promise and Challenge of Producing Biofuel Feedstocks: An Ecological Perspective (2010 JGI User Meeting)

ScienceCinema

DeLucia, Evan

2018-02-13

Evan DeLucia of the University of Illinois at Urbana-Champaign and the Energy Biosciences Institute talks about The Promise and Challenge of Producing Biofuel Feedstocks: An Ecological Perspective on March 25, 2010 at the 5th Annual DOE JGI User Meeting.

Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

ScienceCinema

Tuskan, Gerry

2018-02-13

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gerry Tuskan of Oak Ridge National Laboratory on Resequencing in Populus: Towards Genome Wide Association Genetics at the 6th annual Genomics of Energy Environment Meeting on March 23, 2011.

The Laccaria and Tuber Genomes Reveal Unique Signatures of Mycorrhizal Symbiosis Evolution (2010 JGI User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, Francis

Francis Martin from the French National Institute for Agricultural Research (INRA) talks on how "The Laccaria and Tuber genomes reveal unique signatures of mycorrhizal symbiosis evolution" on March 24, 2010 at the 5th Annual DOE JGI User Meeting

Functional interaction between Cerebratulus lacteus cytolysin A-III and phospholipase A/sub 2/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, J.; Blumenthal, K.M.

A study on the interaction between bee venom phospholipase A/sub 2/ and Cerebratulus lacteus cytolysin A-III, a major hemolysin secreted by this organism has been carried out. The hemolytic activity of A-III in phosphate-buffered saline is increased 5-fold in the presence of phospholipase A/sub 2/ from bee venom. Dansylphosphatidylethanolamine (DPE) labeled, phosphatidylcholine-containing liposomes and human erythrocyte membranes were employed to study the interaction between these two proteins. In DPE-liposomes, A-III alone had no effect on DPE fluorescence nor did it enhance either the phospholipase A/sub 2/-dependent fluorescence increase or blue shift in emission maximum, indicating that the cytolysis is notmore » a major phospholipase A/sub 2/-activator. However, when DPE was incorporated into erythrocyte membranes, A-III alone induced a 40% fluorescence increase and a 5 nm blue shift, implying a transient activation of an endogenous phospholipase A/sub 2/. Further studies using synthetic lysophosphatidylcholine and free fatty acids demonstrated that the hemolytic activity of A-III is potentiated by free fatty acids, a product of phospholipid degradation catalyzed by phospholipase A/sub 2/. Subsequent analysis of this phenomenon by gel filtration chromatography, analytical ultracentrifugation, chemical cross-linking, and measurement of (/sup 14/C)oleic acid binding by the cytolysin demonstrated that binding of oleic acid to A-III causes aggregation of the toxin molecules to a tetrameric form which has a higher ..cap alpha..-helix content and a greater activity than the monomer.« less

The Turn-on of LCLS: the X-Ray Free Electron Laser at SLAC ( Keynote - 2011 JGI User Meeting)

ScienceCinema

Drell, Persis [SLAC National Accelerator Lab., Menlo Park, CA (United States)

2018-06-15

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. SLAC National Laboratory Director Persis Drell gives a keynote talk on "The Turn-on of LCLS: the X-Ray Free-Electron Laser at SLAC" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011

Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuskan, Gerry

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gerry Tuskan of Oak Ridge National Laboratory on Resequencing in Populus: Towards Genome Wide Association Geneticsmore » at the 6th annual Genomics of Energy Environment Meeting on March 23, 2011.« less

Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goldberg, Robert

2012-03-21

Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

ScienceCinema

Goldberg, Robert

2018-04-27

Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties (2011 JGI User Meeting)

ScienceCinema

Bork, Peer

2018-02-14

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Peer Bork of the European Molecular Biology Laboratory on Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

Genomics on the Half Shell: So, What do Oysters Have to do with Energy? (2010 JGI User Meeting)

ScienceCinema

Hedgecock, Dennis

2018-04-26

Dennis Hedgecock from the University of Southern California answers the question, "Genomics on the Half Shell: So, What Do Oysters Have to Do with Energy?" on March 24, 2010 at the 5th Annual DOE JGI User Meeting.

Regulatory Networks Controlling Plant Cold Acclimation or Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis (2011 JGI User Meeting)

ScienceCinema

Thomashow, Mike

2018-02-06

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Mike Thomashow of Michigan State University gives a presentation on on "Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011."

New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era (2010 JGI/ANL HPC Workshop)

ScienceCinema

Notredame, Cedric

2018-05-02

Cedric Notredame from the Centre for Genomic Regulation gives a presentation on New Challenges of the Computation of Multiple Sequence Alignments in the High-Throughput Era at the JGI/Argonne HPC Workshop on January 26, 2010.

Survey of A{sub LT'} asymmetries in semi-exclusive electron scattering on He4 and C12

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dan Protopopescu; et. Al.

2005-02-21

Single spin azimuthal asymmetries A{sub LT'} were measured at Jefferson Lab using 2.2 and 4.4 GeV longitudinally polarized electrons incident on {sup 4}He and {sup 12}C targets in the CLAS detector. A{sub LT'} is related to the imaginary part of the longitudinal-transverse interference and in quasifree nucleon knockout it provides an unambiguous signature for final state interactions (FSI). Experimental values of A{sub LT'} were found to be below 5%, typically |A{sub LT'}| < 3% for data with good statistical precision. Optical Model in Eikonal Approximation (OMEA) and Relativistic Multiple-Scattering Glauber Approximation (RMSGA) calculations are shown to be consistent with themore » measured asymmetries.« less

Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gallivan, Justin

2012-03-21

Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, CA.

Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Gallivan, Justin

2018-05-01

Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, CA.

Host Genetic Control of the Microbiome in Humans and Maize or Relating Host Genetic Variation to the Microbiome (2011 JGI User Meeting)

ScienceCinema

Ley, Ruth E. [Cornell Univ., Ithaca, NY (United States). Cornell Center for Comparative and Population Genomics, Dept. of Microbiology and Dept. of Molecular Biology and Genetics

2018-06-27

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy and Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Ruth Ley of Cornell University gives a presentation on "Relating Host Genetic Variation to the Microbiome" at the 6th annual Genomics of Energy and Environment Meeting on March 23, 2011.

Introduction to Metagenomics at DOE JGI: Program Overview and Program Informatics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Tringe, Susannah

2018-01-15

Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Host Genetic Control of the Microbiome in Humans and Maise or Relating Host Genetic Variation to the Microbiome (2011 JGI User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ley, Ruth

2011-03-23

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Ruth Ley of Cornell University gives a presentation on "Relating Host Genetic Variation to themore » Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.« less

Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Sayre, Richard; Kyrpides, Nikos

2018-05-03

Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Brady, Siobhan

2018-02-12

Siobhan Brady from University of California, Davis, gives a talk titled "Getting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brady, Siobhan

2012-03-22

Siobhan Brady from University of California, Davis, gives a talk titled "Getting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayre, Richard; Kyrpides, Nikos

2012-03-22

Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

ScienceCinema

Robinson, Gene

2018-02-05

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, CA. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gene Robinson of the University of Illinois on Genomic and Systems Biology Analyses of Social Behavior at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011.

Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Muchero, Wellington

2018-01-15

Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, Gene

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, CA. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gene Robinson of the University of Illinois on Genomic and Systems Biology Analyses of Socialmore » Behavior at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011.« less

TNF-{alpha} upregulates the A{sub 2B} adenosine receptor gene: The role of NAD(P)H oxidase 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

St Hilaire, Cynthia; Koupenova, Milka; Carroll, Shannon H.

2008-10-24

Proliferation of vascular smooth muscle cells (VSMC), oxidative stress, and elevated inflammatory cytokines are some of the components that contribute to plaque formation in the vasculature. The cytokine tumor necrosis factor-alpha (TNF-{alpha}) is released during vascular injury, and contributes to lesion formation also by affecting VSMC proliferation. Recently, an A{sub 2B} adenosine receptor (A{sub 2B}AR) knockout mouse illustrated that this receptor is a tissue protector, in that it inhibits VSMC proliferation and attenuates the inflammatory response following injury, including the release of TNF-{alpha}. Here, we show a regulatory loop by which TNF-{alpha} upregulates the A{sub 2B}AR in VSMC in vitromore » and in vivo. The effect of this cytokine is mimicked by its known downstream target, NAD(P)H oxidase 4 (Nox4). Nox4 upregulates the A{sub 2B}AR, and Nox inhibitors dampen the effect of TNF-{alpha}. Hence, our study is the first to show that signaling associated with Nox4 is also able to upregulate the tissue protecting A{sub 2B}AR.« less

An A{sub r} threesome: Matrix models, 2d conformal field theories, and 4dN=2 gauge theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schiappa, Ricardo; Wyllard, Niclas

We explore the connections between three classes of theories: A{sub r} quiver matrix models, d=2 conformal A{sub r} Toda field theories, and d=4N=2 supersymmetric conformal A{sub r} quiver gauge theories. In particular, we analyze the quiver matrix models recently introduced by Dijkgraaf and Vafa (unpublished) and make detailed comparisons with the corresponding quantities in the Toda field theories and the N=2 quiver gauge theories. We also make a speculative proposal for how the matrix models should be modified in order for them to reproduce the instanton partition functions in quiver gauge theories in five dimensions.

Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Benner, Steve

2018-05-08

Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benner, Steve

2012-03-22

Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

PubMed

Huntemann, Marcel; Ivanova, Natalia N; Mavromatis, Konstantinos; Tripp, H James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M; Kyrpides, Nikos C

2015-01-01

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.

Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Glass, N. Louise; Pennacchio, Len

2018-02-13

N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

DOE PAGES

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; ...

2015-10-26

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.

In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Mosier, Annika

2018-01-22

Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, CA.

Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Opportunitistic Enzymes, Catalytic Promiscuity and the Evolution of Chemodiversity in Nature (2010 JGI User Meeting)

ScienceCinema

Noel, Joseph

2018-04-26

Joseph Noel from the Salk Institute on "Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Enzymes, Catalytic Promiscuity and the Evolution of Chemodiversity in Nature" on March 26, 2010 at the 5th Annual DOE JGI User Meeting.

Role of adenosine A{sub 2A} receptor signaling in the nicotine-evoked attenuation of reflex cardiac sympathetic control

DOE Office of Scientific and Technical Information (OSTI.GOV)

El-Mas, Mahmoud M., E-mail: mahelm@hotmail.com; El-gowilly, Sahar M.; Fouda, Mohamed A.

Baroreflex dysfunction contributes to increased cardiovascular risk in cigarette smokers. Given the importance of adenosinergic pathways in baroreflex control, the hypothesis was tested that defective central adenosinergic modulation of cardiac autonomic activity mediates the nicotine-baroreflex interaction. Baroreflex curves relating changes in heart rate (HR) to increases or decreases in blood pressure (BP) evoked by i.v. doses (1-16 {mu}g/kg) of phenylephrine (PE) and sodium nitroprusside (SNP), respectively, were constructed in conscious rats; slopes of the curves were taken as measures of baroreflex sensitivity (BRS). Nicotine (25 and 100 {mu}g/kg i.v.) dose-dependently reduced BRS{sub SNP} in contrast to no effect on BRS{submore » PE}. BRS{sub SNP} was also attenuated after intracisternal (i.c.) administration of nicotine. Similar reductions in BRS{sub SNP} were observed in rats pretreated with atropine or propranolol. The combined treatment with nicotine and atropine produced additive inhibitory effects on BRS, an effect that was not demonstrated upon concurrent exposure to nicotine and propranolol. BRS{sub SNP} was reduced in preparations treated with i.c. 8-phenyltheophylline (8-PT, nonselective adenosine receptor antagonist), 8-(3-Chlorostyryl) caffeine (CSC, A{sub 2A} antagonist), or VUF5574 (A{sub 3} antagonist). In contrast, BRS{sub SNP} was preserved after blockade of A{sub 1} (DPCPX) or A{sub 2B} (alloxazine) receptors or inhibition of adenosine uptake by dipyridamole. CSC or 8-PT abrogated the BRS{sub SNP} depressant effect of nicotine whereas other adenosinergic antagonists were without effect. Together, nicotine preferentially impairs reflex tachycardia via disruption of adenosine A{sub 2A} receptor-mediated facilitation of reflex cardiac sympathoexcitation. Clinically, the attenuation by nicotine of compensatory sympathoexcitation may be detrimental in conditions such as hypothalamic defense response, posture changes, and ventricular rhythms

Crystallization and preliminary X-ray crystallographic analysis of the heterodimeric crotoxin complex and the isolated subunits crotapotin and phospholipase A{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santos, K. F.; Murakami, M. T.; Cintra, A. C. O.

2007-04-01

Crotoxin, a potent neurotoxin from the venom of the South American rattlesnake Crotalus durissus terrificus, exists as a heterodimer formed between a phospholipase A{sub 2} and a catalytically inactive acidic phospholipase A{sub 2} analogue (crotapotin). Large single crystals of the crotoxin complex and of the isolated subunits have been obtained. Crotoxin, a potent neurotoxin from the venom of the South American rattlesnake Crotalus durissus terrificus, exists as a heterodimer formed between a phospholipase A{sub 2} and a catalytically inactive acidic phospholipase A{sub 2} analogue (crotapotin). Large single crystals of the crotoxin complex and of the isolated subunits have been obtained.more » The crotoxin complex crystal belongs to the orthorhombic space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 38.2, b = 68.7, c = 84.2 Å, and diffracted to 1.75 Å resolution. The crystal of the phospholipase A{sub 2} domain belongs to the hexagonal space group P6{sub 1}22 (or its enantiomorph P6{sub 5}22), with unit-cell parameters a = b = 38.7, c = 286.7 Å, and diffracted to 2.6 Å resolution. The crotapotin crystal diffracted to 2.3 Å resolution; however, the highly diffuse diffraction pattern did not permit unambiguous assignment of the unit-cell parameters.« less

High pressure studies of A{sub 2}Mo{sub 3}O{sub 12} negative thermal expansion materials (A{sub 2}=Al{sub 2}, Fe{sub 2}, FeAl, AlGa)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, Lindsay; Gadient, Jennifer; Gao, Xiaodong

2016-05-15

High pressure powder X-ray diffraction studies of several A{sub 2}Mo{sub 3}O{sub 12} materials (A{sub 2}=Al{sub 2}, Fe{sub 2}, FeAl, and AlGa) were conducted up to 6–7 GPa. All materials adopted a monoclinic structure under ambient conditions, and displayed similar phase transition behavior upon compression. The initial isotropic compressibility first became anisotropic, followed by a small but distinct drop in cell volume. These patterns could be described by a distorted variant of the ambient pressure polymorph. At higher pressures, a distinct high pressure phase formed. Indexing results confirmed that all materials adopted the same high pressure phase. All changes were reversiblemore » on decompression, although some hysteresis was observed. The similarity of the high pressure cells to previously reported Ga{sub 2}Mo{sub 3}O{sub 12} suggested that this material undergoes the same sequence of transitions as all materials investigated in this paper. It was found that the transition pressures for all phase changes increased with decreasing radius of the A-site cations. - Graphical abstract: Overlay of variable pressure X-ray diffraction data of Al{sub 2}Mo{sub 3}O{sub 12} collected in a diamond anvil cell. Both subtle and discontinuous phase transitions are clearly observed. - Highlights: • The high pressure behavior of A{sub 2}Mo{sub 3}O{sub 12} (A=Al, Fe, (AlGa), (AlFe)) was studied. • All compounds undergo the same sequence of pressure-induced phase transitions. • The phase transition pressures correlate with the average size of the A-site cation. • All transitions were reversible with hysteresis. • Previously studied Ga{sub 2}Mo{sub 3}O{sub 12} undergoes the same sequence of transitions.« less

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

DOE PAGES

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; ...

2016-02-24

The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provide d via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation ismore » followed by functional annotation including assignment of protein product names and connection to various protein family databases.« less

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos

The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provide d via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation ismore » followed by functional annotation including assignment of protein product names and connection to various protein family databases.« less

Analysis of various types of single-polypeptide-chain (sc) heterodimeric A{sub 2A}R/D{sub 2}R complexes and their allosteric receptor–receptor interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamiya, Toshio, E-mail: kamiya@z2.keio.jp; Department of Neurology, Tokyo Metropolitan Institute for Neuroscience, 2-6 Musashidai, Fuchu, Tokyo 183-8526; Cell Biology Laboratory, School of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502

Highlights: • Various scA{sub 2A}R/D{sub 2}R constructs, with spacers between the two receptors, were created. • Using whole cell binding assay, constructs were examined for their binding activity. • Although the apparent ratio of A{sub 2A}R to D{sub 2}R binding sites should be 1, neither was 1. • Counter agonist-independent binding cooperativity occurred in context of scA{sub 2A}R/D{sub 2}R. - Abstract: Adenosine A{sub 2A} receptor (A{sub 2A}R) heteromerizes with dopamine D{sub 2} receptor (D{sub 2}R). However, these class A G protein-coupled receptor (GPCR) dimers are not fully formed, but depend on the equilibrium between monomer and dimer. In order tomore » stimulate the heteromerization, we have previously shown a successful design for a fusion receptor, single-polypeptide-chain (sc) heterodimeric A{sub 2A}R/D{sub 2}R complex. Here, using whole cell binding assay, six more different scA{sub 2A}R/D{sub 2}R constructs were examined. Not only in scA{sub 2A}R/D{sub 2}R ‘liberated’ with longer spacers between the two receptors, which confer the same configuration as the prototype, the A{sub 2A}R-odr4TM-D{sub 2L}R, but differ in size (Forms 1–3), but also in scA{sub 2A}R/D{sub 2L}R (Form 6) fused with a transmembrane (TM) of another type II TM protein, instead of odr4TM, neither of their fixed stoichiometry (the apparent ratios of A{sub 2A}R to D{sub 2}R binding sites) was 1, suggesting their compact folding. This suggests that type II TM, either odr4 or another, facilitates the equilibrial process of the dimer formation between A{sub 2A}R and D{sub 2L}R, resulting in the higher-order oligomer formation from monomer of scA{sub 2A}R/D{sub 2L}R itself. Also, in the reverse type scA{sub 2A}R/D{sub 2L}R, i.e., the D{sub 2L}R-odr4TM-A{sub 2A}R, counter agonist-independent binding cooperativity (cooperative folding) was found to occur (Forms 4 and 5). In this way, the scA{sub 2A}R/D{sub 2L}R system has unveiled the cellular phenomenon as a snapshot of the

A{sub n}{sup (1)} Toda solitons and the dressing symmetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belich, H.; Paunov, R.

We present an elementary derivation of the solitonlike solutions in the A{sub n}{sup (1)} Toda models which is an alternative to the previously used Hirota method. The solutions of the underlying linear problem corresponding to the N-solitons are calculated. This enables us to obtain explicit expression for the element which, by dressing group action, produces a generic soliton solution. In the particular example of monosolitons we suggest a relation to the vertex operator formalism, previously used by Olive, Turok, and Underwood. Our results can also be considered as generalization of the approach to the sine{endash}Gordon solitons, proposed by Babelon andmore » Bernard. {copyright} {ital 1997 American Institute of Physics.}« less

Gangliosides inhibit bee venom melittin cytotoxicity but not phospholipase A{sub 2}-induced degranulation in mast cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishikawa, Hirofumi; Kitani, Seiichi, E-mail: drkitani@kaiyodai.ac.jp

Sting accident by honeybee causes severe pain, inflammation and allergic reaction through IgE-mediated anaphylaxis. In addition to this hypersensitivity, an anaphylactoid reaction occurs by toxic effects even in a non-allergic person via cytolysis followed by similar clinical manifestations. Auto-injectable epinephrine might be effective for bee stings, but cannot inhibit mast cell lysis and degranulation by venom toxins. We used connective tissue type canine mast cell line (CM-MC) for finding an effective measure that might inhibit bee venom toxicity. We evaluated degranulation and cytotoxicity by measurement of {beta}-hexosaminidase release and MTT assay. Melittin and crude bee venom induced the degranulation andmore » cytotoxicity, which were strongly inhibited by mono-sialoganglioside (G{sub M1}), di-sialoganglioside (G{sub D1a}) and tri-sialoganglioside (G{sub T1b}). In contrast, honeybee venom-derived phospholipase A{sub 2} induced the net degranulation directly without cytotoxicity, which was not inhibited by G{sub M1}, G{sub D1a} and G{sub T1b}. For analysis of distribution of G{alpha}{sub q} and G{alpha}{sub i} protein by western blotting, lipid rafts were isolated by using discontinuous sucrose gradient centrifuge. Melittin disrupted the localization of G{alpha}{sub q} and G{alpha}{sub i} at lipid raft, but gangliosides stabilized the rafts. As a result from this cell-based study, bee venom-induced anaphylactoid reaction can be explained with melittin cytotoxicity and phospholipase A{sub 2}-induced degranulation. Taken together, gangliosides inhibit the effect of melittin such as degranulation, cytotoxicity and lipid raft disruption but not phospholipase A{sub 2}-induced degranulation in mast cells. Our study shows a potential of gangliosides as a therapeutic tool for anaphylactoid reaction by honeybee sting.« less

Synthesis, structure, and polymorphism of A{sub 3}LnSi{sub 2}O{sub 7} (A=Na, K; Ln=Sm, Ho, Yb)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Latshaw, Allison M.; Yeon, Jeongho; Smith, Mark D.

2016-03-15

Four new members of the A{sub 3}LnSi{sub 2}O{sub 7} family, K{sub 3}SmSi{sub 2}O{sub 7}, Na{sub 3}HoSi{sub 2}O{sub 7}, and two polymorphs of Na{sub 3}YbSi{sub 2}O{sub 7}, are reported. K{sub 3}SmSi{sub 2}O{sub 7} crystallizes in the hexagonal space group P6{sub 3}/mcm, Na{sub 3}HoSi{sub 2}O{sub 7} and Na{sub 3}YbSi{sub 2}O{sub 7} crystallize in the hexagonal space group P6{sub 3}/m, and Na{sub 3}YbSi{sub 2}O{sub 7} crystallizes in the trigonal space group P31c. The Na{sub 3}YbSi{sub 2}O{sub 7} composition that crystallizes in P31c is a new structure type. The magnetic properties for the Ho and Yb analogs are reported. - Graphical abstract: The differentmore » structure types and polymorphs of the A{sub 3}LnSi{sub 2}O{sub 7} family reported. - Highlights: • Four new members of the A{sub 3}LnSi{sub 2}O{sub 7} family are presented. • Na{sub 3}YbSi{sub 2}O{sub 7} is reported as two polymorphs, one is a new structure type. • Crystals synthesized out of molten fluoride fluxes.« less

Yor022c protein is a phospholipase A{sub 1} that localizes to the mitochondrial matrix

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urafuji, Kyosei; Arioka, Manabu

In mammals, three types of intracellular phospholipase A{sub 1} (iPLA{sub 1}) enzymes have been characterized and are thought to be involved in various cellular processes such as phospholipid metabolism, organelle biogenesis, and membrane trafficking. In this study we analyzed the unique iPLA{sub 1}-like protein, Yor022c, in the budding yeast Saccharomyces cerevisiae. By the mass spectrometry analysis, we demonstrate that Yor022c is actually a phospholipase displaying sn-1-specific activity toward phosphatidylcholine, phosphatidylethanolamine, and phosphatidic acid, generating 2-acyl lysophospholipids. GFP-fused Yor022c co-stained with the mitochondrial dye MitoTracker, indicating that, unlike its mammalian counterparts, it is a mitochondrial protein. Further biochemical fractionation experiment combinedmore » with protease sensitivity assay showed that Yor022c localizes to the mitochondrial matrix. Thus Yor022c is the first PLA{sub 1} putatively involved in the maintenance of sn-1 acyl chains of phospholipids in the mitochondrial inner membrane. - Highlights: • Yeast Yor022c protein displays phospholipase A{sub 1} activity to various phospholipids. • Yor022c-GFP fusion protein localizes to mitochondria. • Biochemical fractionation showed that Yor022c localizes to the mitochondrial matrix.« less

Preliminary X-ray crystallographic studies of a tetrameric phospholipase A{sub 2} formed by two isoforms of crotoxin B from Crotalus durissus terrificus venom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marchi-Salvador, D. P.; Corrêa, L. C.; Salvador, G. H. M.

2007-12-01

Crotoxin B is a basic phospholipase A{sub 2} found in the venom of C. durissus terrificus and is one of the subunits that constitute crotoxin. Here, the crystallization, X-ray diffraction data collection and molecular-replacement solution of a novel tetrameric complex formed by two dimers of crotoxin B isoforms are presented. Crotoxin B is a basic phospholipase A{sub 2} found in the venom of Crotalus durissus terrificus and is one of the subunits that constitute crotoxin. This heterodimeric toxin, which is the main component of C. d. terrificus venom, is completed by an acidic, nontoxic and non-enzymatic component (crotoxin A) andmore » is involved in important envenomation effects, such as neurological disorders, myotoxicity and renal failure. Although crotoxin was first crystallized in 1938, no crystal structure is currently available for crotoxin, crotoxin A or crotoxin B. In this work, the crystallization, X-ray diffraction data collection to 2.28 Å resolution and molecular-replacement solution of a novel tetrameric complex formed by two dimers of crotoxin B isoforms (CB1 and CB2) is presented.« less

Syntheses and characterization of one-dimensional alkali metal antimony(III) thiostannates(IV), A{sub 2}Sb{sub 2}Sn{sub 3}S{sub 10} (A=K, Rb, Cs)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yohannan, Jinu P.; Vidyasagar, Kanamaluru, E-mail: kvsagar@iitm.ac.in

2015-01-15

Three new isostructural quaternary antimony(III) thiostannates(IV), A{sub 2}Sb{sub 2}Sn{sub 3}S{sub 10} (A=K, Rb, Cs) have been synthesized by using alkali metal thiosulfate flux and structurally characterized by X-ray diffraction. Their structures contain A{sup +} ions around the [Sb{sub 2}Sn{sub 3}S{sub 10}]{sup 2−} chains, which are built from SbS{sub 3} pyramids, SnS{sub 6} octahedra and SnS{sub 4} tetrahedra. Raman and Mössbauer spectroscopic measurements corroborate the oxidation states and coordination environments of Sb(III) and Sn(IV). All three compounds are wide band gap semiconductors. Potassium compound undergoes partial exchange with strontium, cadmium and lead ions. - Graphical abstract: Syntheses, crystal structure, spectroscopic andmore » partial ion-exchange studies of new one-dimensional alkali metal antimony(III) thiostannates(IV), A{sub 2}Sb{sub 2}Sn{sub 3}S{sub 10} (A=K, Rb, Cs) are described. - Highlights: • Syntheses of new alkali metal antimony(III) thiostannates(IV), A{sub 2}Sb{sub 2}Sn{sub 3}S{sub 10} (A=K, Rb, Cs). • Wide band gap semiconductors with one-dimensional structure. • Topotactic partial exchange of K{sup +} ions of K{sub 2}Sb{sub 2}Sn{sub 3}S{sub 10} with Sr{sup 2+}, Cd{sup 2+} and Pb{sup 2+} ions.« less

Mutant quantity and quality in mammalian cells (A{sub L}) exposed to cesium-137 gamma radiation: Effect of caffeine

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGuinness, S.M.; Shibuya, M.L.; Ueno, A.M.

1995-06-01

We examined the effect of caffeine (1,3,7-trimethylxanthine) on the quantity and quality of mutations in cultured mammalian A{sub L} human-hamster hybrid cells exposed to {sup 137}Cs {gamma} radiation. At a dose (1.5 mg/ml for 16 h) that reduced the plating efficiency (PE) by 20%, caffeine was not itself a significant mutagen, but it increased by approximately twofold the slope of the dose-response curve for induction of S1{sup {minus}} mutants by {sup 137}Cs {gamma} radiation. Molecular analysis of 235 S1{sup {minus}} mutants using a series of DNA probes mapped to the human chromosome 11 in the A{sub L} hybrid cells revealedmore » that 73 to 85% of the mutations in unexposed cells and in cells treated with caffeine alone, {sup 137}Cs {gamma} rays alone or {sup 137}Cs {gamma} rays plus caffeine were large deletions involving millions of base pairs of DNA. Most of these deletions were contiguous with the region of the MIC1 gene at 11p13 that encodes the S1 cell surface antigen. In other mutants that had suffered multiple marker loss, the deletions were intermittent along chromosome 11. These {open_quotes}complex{close_quotes} mutations were rare for {sup 137}Cs {gamma} irradiation (1/63 = 1.5%) but relatively prevalent (23-50%) for other exposure conditions. Thus caffeine appears to alter both the quantity and quality of mutations induced by {sup 137}Cs {gamma} irradiation. 62 refs., 3 figs., 3 tabs.« less

Meson-meson scattering: K{anti K}-thresholds and f{sub 0}(980)-a{sub 0}(980) mixing

DOE Office of Scientific and Technical Information (OSTI.GOV)

O. Krehl; R. Rapp; J. Speth

1996-09-01

The authors study the influence of mass splitting between the charged and neutral pions and kaons in the Juelich meson exchange model for {pi}{pi} and {pi}{eta} scattering. The calculations are performed in the particle basis, which permits the use of physical masses for the pseudoscalar mesons and a study of the distinct thresholds associated with the neutral and the charged kaons. Within this model the authors also investigate the isospin violation which arises from the mass splitting and an apparent violation of G-parity in {pi}{pi} scattering which stems from the coupling to the K{anti K} channel. Nonvanishing cross sections formore » {pi}{pi} {r_arrow} {pi}{sup 0}{eta} indicate a mixing of the f{sub 0}(980) and a{sub 0}(980) states.« less

High-resolution laser spectroscopy and magnetic effect of the B{sup ~2}E′ ← X{sup ~2}A{sub 2}′ transition of {sup 14}NO{sub 3} radical

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tada, Kohei; Kashihara, Wataru; Baba, Masaaki

2014-11-14

Rotationally resolved high-resolution fluorescence excitation spectra of {sup 14}NO{sub 3} radical have been observed for the 662 nm band, which is assigned as the 0–0 band of the B{sup ~2}E′ ←X{sup ~2}A{sub 2}′ transition, by crossing a single-mode laser beam perpendicularly to a collimated molecular beam. More than 3000 rotational lines were detected in 15 070–15 145 cm{sup −1} region, but it is difficult to find the rotational line series. Remarkable rotational line pairs, whose interval is about 0.0246 cm{sup −1}, were found in the observed spectrum. This interval is the same amount with the spin-rotation splitting of the X{sup ~2}A{sub 2}′more » (υ = 0, k = 0, N = 1) level. From this interval and the observed Zeeman splitting up to 360 G, seven line pairs were assigned as the transitions to the {sup 2}E′{sub 3/2} (J′ = 1.5) levels and 15 line pairs were assigned as the transitions to the {sup 2}E′{sub 1/2} (J′ = 0.5) levels. From the rotational analysis, we recognized that the {sup 2}E′ state splits into {sup 2}E′{sub 3/2} and {sup 2}E′{sub 1/2} by the spin-orbit interaction and the effective spin-orbit interaction constant was roughly estimated as –21 cm{sup −1}. From the number of the rotational line pairs, we concluded that the complicated rotational structure of this 662 nm band of {sup 14}NO{sub 3} mainly owes to the vibronic interaction between the B{sup ~2}E′ state and the dark A{sup ~2}E″ state through the a{sub 2}″ symmetry vibrational mode.« less

Early age hydration of calcium sulfoaluminate (synthetic ye'elimite, C{sub 4}A{sub 3}S{sup ¯}) in the presence of gypsum and varying amounts of calcium hydroxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hargis, Craig W.; Kirchheim, Ana Paula; Monteiro, Paulo J.M., E-mail: monteiro@ce.berkeley.edu

Suspensions of synthetic ye'elimite (C{sub 4}A{sub 3}S{sup ¯}) in a saturated gypsum (CS{sup ¯}H{sub 2}) and calcium hydroxide (CH) solution were examined in-situ in a wet cell by soft X-ray transmission microscopy and ex-situ by scanning electron microscopy. The most voluminous hydration product observed was ettringite. Ettringite commonly displayed acicular, filiform, reticulated, and stellate crystal habits. Additionally, pastes with C{sub 4}A{sub 3}S{sup ¯}, 15% CS{sup ¯}H{sub 2}, and varying amounts of CH were prepared and examined with X-ray diffraction (XRD) and isothermal calorimetry. The XRD experiments showed that increasing CH content caused more solid solution (SO{sub 4}{sup 2−}/OH{sup −}) AFmmore » phases to form at early ages (< 1 d) and more monosulfate to form at later ages (> 1 d). Calorimetry indicated that the increased production of solid solution AFm was accompanied with an increase in the initial (< 30 min) rate of heat evolution, and increasing CH generally reduced the time till the second maximum rate of heat evolution due to the formation of ettringite and monosulfate.« less

A multireference configuration interaction study of the low-lying electronic states of ClO[sub 2][sup +] and the [ital X] [sup 1][ital A][sub 1] state of ClO[sub 2][sup [minus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peterson, K.A.; Werner, H.

1993-07-01

Near-equilibrium two-dimensional ([ital C][sub 2][ital v] symmetry) potential energy functions of the first seven electronic states of ClO[sub 2][sup +] and the ground [ital X] [sup 1][ital A][sub 1] electronic state of ClO[sub 2][sup [minus

Measurement of forward-backward asymmetry A{sub FB} and of the weak mixing angle in processes of dilepton production in proton-proton collisions at {radical} s = 7 TeV in the CMS experiment at the LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorbunov, I. N., E-mail: Ilya.Gorbunov@cern.ch; Shmatov, S. V., E-mail: shmatov@cern.ch

2013-09-15

The results obtained by measuring the forward-backward asymmetry (A{sub FB}) of Drell-Yan lepton pairs in proton-proton collisions at {radical} s = 7 TeV at the LHC are presented. This asymmetry is measured as a function of the dilepton mass and rapidity in the dielectron and dimuon channels. The values of A{sub FB} were found for invariant masses of dileptons in the range of 40 Less-Than-Or-Slanted-Equal-To M{sub ll} Less-Than-Or-Slanted-Equal-To 600 GeV. The results for the effective weak mixing angle that were deduced from data on dimuon production in Drell-Yan processes are also presented. The respective data sample was collected by usingmore » the Compact Muon Solenoid (CMS) detector over the period spanning the years 2010 and 2011. The measured asymmetry and the effective weak mixing are consistent with the respective Standard Model predictions.« less

DOE Joint Genome Institute 2008 Progress Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilbert, David

2009-03-12

While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imaginedmore » when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic technological change is presently underway at the JGI. The Sanger capillary-based sequencing

Fueling the Future with Fungal Genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor V.

2014-10-27

Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have beenmore » sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such ‘parts’ suggested by comparative genomics and functional analysis in these areas are presented here.« less

The Genome Portal of the Department of Energy Joint Genome Institute

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nordberg, Henrik; Cantor, Michael; Dushekyo, Serge

2014-03-14

The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Genome Portal in the past 2 years was significantly updated, with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI. A critical aspect of handling big data in genomics is the development of visualization and analysis tools that allow scientists to derive meaning from what are otherwise terrabases ofmore » inert sequence. An interactive visualization tool developed in the group allows us to explore contigs resulting from a single metagenome assembly. Implemented with modern web technologies that take advantage of the power of the computer's graphical processing unit (gpu), the tool allows the user to easily navigate over a 100,000 data points in multiple dimensions, among many biologically meaningful parameters of a dataset such as relative abundance, contig length, and G+C content.« less

Scalability of Comparative Analysis, Novel Algorithms and Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Mavrommatis, Kostas

2017-12-22

DOE JGI's Kostas Mavrommatis, chair of the Scalability of Comparative Analysis, Novel Algorithms and Tools panel, at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Synthesis and characterization of new fluoride-containing manganese vanadates A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} (A=Rb, Cs) and Mn{sub 2}VO{sub 4}F

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanjeewa, Liurukara D.; McGuire, Michael A.; Smith Pellizzeri, Tiffany M.

2016-09-15

Large single crystals of A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} (A=Rb, Cs) and Mn{sub 2}VO{sub 4}F were grown using a high-temperature (~600 °C) hydrothermal technique. Single crystal X-ray diffraction and powder X-ray diffraction were utilized to characterize the structures, which both possess MnO{sub 4}F{sub 2} building blocks. The A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} series crystallizes as a new structure type in space group Pbcn (No. 60), Z=4 (Rb{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2}: a=7.4389(17) Å, b=11.574(3) Å, c=10.914(2) Å; Cs{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2}: a=7.5615(15) Å, b=11.745(2) Å, c=11.127(2) Å). The structure is composed of zigzag chains ofmore » edge-sharing MnO{sub 4}F{sub 2} units running along the a-axis, and interconnected through V{sub 2}O{sub 7} pyrovanadate groups. Temperature dependent magnetic susceptibility measurements on this interesting one-dimensional structural feature based on Mn{sup 2+} indicated that Cs{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} is antiferromagnetic with a Neél temperature, T{sub N}=~3 K and a Weiss constant, θ, of −11.7(1) K. Raman and infrared spectra were also analyzed to identify the fundamental V–O vibrational modes in Cs{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2}. Mn{sub 2}(VO{sub 4})F crystalizes in the monoclinic space group of C2/c (no. 15), Z=8 with unit cell parameters of a=13.559(2) Å, b=6.8036(7) Å, c=10.1408(13) Å and β=116.16(3)°. The structure is associated with those of triplite and wagnerite. Dynamic fluorine disorder gives rise to complex alternating chains of five-and six-coordinate Mn{sup 2+}. These interpenetrating chains are additionally connected through isolated VO{sub 4} tetrahedra to form the condensed structure. - Graphical abstract: New vanadate fluorides A{sub 2}Mn{sub 2}V{sub 2}O{sub 7}F{sub 2} (A=Rb, Cs) and Mn{sub 2}(VO{sub 4})F have been synthesized hydrothermally. Upon cooling, the one-dimensional Mn(II) substructure results in

New simple A{sub 4} neutrino model for nonzero {theta}{sub 13} and large {delta}{sub CP}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ishimori, Hajime

In a new simple application of the non-Abelian discrete symmetry A{sub 4} to charged-lepton and neutrino mass matrices, we show that for the current experimental central value of sin{sup 2} 2{theta}{sub 13} Asymptotically-Equal-To 0.1, leptonic CP violation is necessarily large, i.e. Double-Vertical-Line tan{delta}{sub CP} Double-Vertical-Line > 1.3. We also consider T{sub 7} model with one parameter to be complex, thus allowing for one Dirac CP phase {delta}{sub CP} and two Majorana CP phases {alpha}{sub 1,2}. We find a slight modification to this correlation as a function of {delta}{sub CP}. For a given set of input values of {Delta}m{sup 2}{sub 21},more » {Delta}m{sup 2}{sub 32}, {theta}{sub 12}, and {theta}{sub 13}, we obtain sin{sup 2} 2{theta}{sub 23} and m{sub ee} (the effective Majorana neutrino mass in neutrinoless double beta decay) as functions of tan {delta}{sub CP}. We find that the structure of this model always yields small Double-Vertical-Line tan {delta}{sub CP} Double-Vertical-Line .« less

Fungal Genomics for Energy and Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor V.

2013-03-11

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for usersmore » to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.« less

Evaluation of the Cow Rumen Metagenome: Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Sczyrba, Alex

2018-02-13

DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Evaluation of the Cow Rumen Metagenome: Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sczyrba, Alex

2011-10-13

DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

New members of the A{sub 2}M′M{sub 2}{sup ″} structure family (A=Ca, Sr, Yb, La; M′=In,Sn,Pb; M″=Si,Ge)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jehle, Michael; Dürr, Ines; Fink, Saskia

The new mixed tetrelides Sr{sub 2}PbGe{sub 2} and Yb{sub 2}SnGe{sub 2}, several mixed Ca/Sr (A{sup II}) germanides A{sub 2}{sup II}(Sn,Pb)Ge{sub 2} and two polymorphs of La{sub 2}InSi{sub 2} represent new members of the general structure family of ternary alkaline-earth/lanthanoid main group silicides/germanides A{sub 2}M′M{sub 2}{sup ″}(M′=In,Sn,Pb;M″=Si,Ge). All compounds were synthesized from melts of the elements and their crystal structures have been determined by means of single crystal X-ray diffraction. Sr{sub 2}PbGe{sub 2} (Cmmm, a=402.36(11), b=1542.3(4), c=463.27(10) pm) crystallizes with the Mn{sub 2}AlB{sub 2}-type structure. In exhibiting infinite planar Ge zig-zag chains, it represents one border of the compound series. Themore » other borderline case, where only [Ge{sub 2}] dumbbells are left as Ge building units, is represented by the Ca/Yb tin germanides Ca{sub 2}SnGe{sub 2} and Yb{sub 2}SnGe{sub 2} (Mo{sub 2}FeB{sub 2}-type; P4/mbm, a=748.58(13)/740.27(7), c=445.59(8)/435.26(5) pm). In between these two border structures compounds with variable Si/Ge chain lengths could be obtained by varying the averaged size of the A{sup II} cations: Ca{sub 0.45}Sr{sub 1.55}PbGe{sub 2} (new structure type; Pbam, a=791.64(5), b=2311.2(2), c=458.53(3) pm) contains planar six-membered chain segments [Ge{sub 6}]. Tetrameric pieces [Ge{sub 4}] are the conspicuous structure elements in Ca{sub 1.16}Sr{sub 0.84}SnGe{sub 2} and La{sub 2}InSi{sub 2} (La{sub 2}InNi{sub 2}-type; Pbam, a=781.01(2)/762.01(13), b=1477.95(3)/1494.38(6), c=457.004(9)/442.1(3) pm). The tetragonal form of ’La{sub 2}InSi{sub 2}{sup ′} (exact composition: La{sub 2}In{sub 1.07}Si{sub 1.93}, P4/mbm, a=1309.11(12), c=443.32(4) pm) also crystallizes in a new structure type, containing only [Si{sub 3}] trimers as cutouts of the planar chains. In all structures the Si/Ge zig-zag chains/chain segments are connected by In/Sn/Pb atoms to form planar M layers, which are separated by pure A

Illumina Production Sequencing at the DOE Joint Genome Institute - Workflow and Optimizations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tarver, Angela; Fern, Alison; Diego, Matthew San

2010-06-18

The U.S. Department of Energy (DOE) Joint Genome Institute?s (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the DOE mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI?s Production Sequencing group, the Illumina Genome Analyzer pipeline has been established as one of three sequencing platforms, along with Roche/454 and ABI/Sanger. Optimization of the Illumina pipeline has been ongoing with the aim of continual process improvement of the laboratory workflow. These process improvement projects are being led by the JGI?s Process Optimization, Sequencing Technologies, Instrumentation&more » Engineering, and the New Technology Production groups. Primary focus has been on improving the procedural ergonomics and the technicians? operating environment, reducing manually intensive technician operations with different tools, reducing associated production costs, and improving the overall process and generated sequence quality. The U.S. DOE JGI was established in 1997 in Walnut Creek, CA, to unite the expertise and resources of five national laboratories? Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest ? along with HudsonAlpha Institute for Biotechnology. JGI is operated by the University of California for the U.S. DOE.« less

Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Canon, Shane

2018-01-24

DOE JGI's Zhong Wang, chair of the High-performance Computing session, gives a brief introduction before Berkeley Lab's Shane Canon talks about "Exploiting HPC Platforms for Metagenomics: Challenges and Opportunities" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Deinhibition of cardiac Na/sup +/-K/sup +/-ATPase after exposure to exogenous phospholipase A/sub 2/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colvin, R.A.

1987-01-01

After 2 h of exogenous phospholipase A/sub 2/ (PLA/sub 2/) exposure, membrane phospholipid decreased from 3.22 +/- 0.31 to 1.06 +/- 0.13 ..mu..mol/mg (33% of control). All classes of phospholipid, except sphingomyelin, were hydrolyzed, whereas total cholesterol content was unaffected. Increases in nonesterified fatty acids (NEFA) were reflected primarily in oleic (18:1), linoleic (18:2), and arachidonic (20:4). Na/sup +/-K/sup +/-adenosinetriphosphatase (ATPase) activity was inhibited to 29% of control by 2 h of PLA/sub 2/ treatment, and this inhibition was reversed (albeit, not completely after 5 min of PLA/sub 2/ treatment) by removal of the hydrolysis products with 0.1% bovine serummore » albumin (BSA). In contrast, the apparent binding capacity for (/sup 3/H)ouabain was not affected by PLA/sub 2/ treatment. Unmasking of latent (/sup 3/H)ouabain binding by alamethicin was utilized to estimate changes in the proportion of sealed vesicles present before and after PLA/sub 2/ treatment. PLA/sub 2/ treatment resulted in a time-dependent loss of sealed vesicles that paralleled the time course of phospholipid hydrolysis and was not reversed by washing with BSA. These studies demonstrate that cardiac Na/sup +/-K/sup +/-ATPase activity is inhibited by accumulation of endogenously produced lysophospholipids and NEFA. In contrast, loss of vesicle integrity may result from both accumulation of endogenously produced hydrolysis products and membrane phospholipid depletion.« less

Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Stepanauskas, Ramunas

2018-02-06

DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

High-resolution laser spectroscopy and magnetic effect of the B{sup ~2}E{sup ′}←X{sup ~2}A{sub 2}{sup ′} transition of the {sup 15}N substituted nitrate radical

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tada, Kohei; Teramoto, Kanon; Ishiwata, Takashi

2015-03-21

Rotationally resolved high-resolution fluorescence excitation spectra of the 0–0 band of the B{sup ~2}E{sup ′}←X{sup ~2}A{sub 2}{sup ′} transition of the {sup 15}N substituted nitrate radical were observed for the first time, by crossing a jet-cooled molecular beam and a single-mode dye laser beam at right angles. Several thousand rotational lines were detected in the 15 080–15 103 cm{sup −1} region. We observed the Zeeman splitting of intense lines up to 360 G in order to obtain secure rotational assignment. Two, nine, and seven rotational line pairs with 0.0248 cm{sup −1} spacing were assigned to the transitions from the X{supmore » ~2}A{sub 2}{sup ′} (υ″ = 0, k″ = 0, N″ = 1, J″ = 0.5 and 1.5) to the {sup 2}E{sub 3/2}{sup ′} (J′ = 1.5), {sup 2}E{sub 1/2}{sup ′} (J′ = 0.5), and {sup 2}E{sub 1/2}{sup ′} (J′ = 1.5) levels, respectively, based on the ground state combination differences and the Zeeman splitting patterns. The observed spectrum was complicated due to the vibronic coupling between the bright B{sup ~2}E{sup ′} (υ = 0) state and surrounding dark vibronic states. Some series of rotational lines other than those from the X{sup ~2}A{sub 2}{sup ′} (J = 0.5 and 1.5) levels were also assigned by the ground state combination differences and the observed Zeeman splitting. The rotational branch structures were identified, and the molecular constants of the B{sup ~2}E{sub 1/2}{sup ′} (υ = 0) state were estimated by a deperturbed analysis to be T{sub 0} = 15 098.20(4) cm{sup −1}, B = 0.4282(7) cm{sup −1}, and D{sub J} = 4 × 10{sup −4} cm{sup −1}. In the observed region, both the {sup 2}E{sub 1/2}{sup ′} and {sup 2}E{sub 3/2}{sup ′} spin-orbit components were identified, and the spin-orbit interaction constant of the B{sup ~2}E{sup ′} (υ = 0) state was estimated to be −12 cm{sup −1} as the lower limit.« less

Crystallization and preliminary X-ray diffraction analysis of a novel Arg49 phospholipase A{sub 2} homologue from Zhaoermia mangshanensis venom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murakami, Mário T.; Center for Applied Toxinology, CAT-CEPID, São Paulo, SP; Advanced Center for Genomics and Proteomics, UNESP-State University of São Paulo, São José do Rio Preto 15054-000

2007-07-01

A single crystal of zhaoermiatoxin with maximum dimensions of 0.2 × 0.2 × 0.5 mm was used for X-ray diffraction data collection to a resolution of 2.05 Å using synchrotron radiation and the diffraction pattern was indexed in the hexagonal space group P6{sub 4}, with unit-cell parameters a = 72.9, b = 72.9, c = 93.9 Å. Zhaoermiatoxin, an Arg49 phospholipase A{sub 2} homologue from Zhaoermia mangshanensis (formerly Trimeresurus mangshanensis, Ermia mangshanensis) venom is a novel member of the PLA{sub 2}-homologue family that possesses an arginine residue at position 49, probably arising from a secondary Lys49→Arg substitution that does notmore » alter the catalytic inactivity towards phospholipids. Like other Lys49 PLA{sub 2} homologues, zhaoermiatoxin induces oedema and strong myonecrosis without detectable PLA{sub 2} catalytic activity. A single crystal with maximum dimensions of 0.2 × 0.2 × 0.5 mm was used for X-ray diffraction data collection to a resolution of 2.05 Å using synchrotron radiation and the diffraction pattern was indexed in the hexagonal space group P6{sub 4}, with unit-cell parameters a = 72.9, b = 72.9, c = 93.9 Å.« less

A new structure related to the layered cuprates: The {open_quotes}1201{angstrom} shear-like phase Tl{sub 5}Ba{sub 3}Sr{sub 5}Cu{sub 3}O{sub 19}, third member of the series (TlA{sub 2}CuO{sub 5}){sub m}{center_dot}Tl{sub 2}A{sub 2}O{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Letouze, F.; Martin, C.; Hervieu, M.

1997-01-01

A thallium cuprate, Tl{sub 5}Ba{sub 3}Sr{sub 5}Cu{sub 3}O{sub 19}, whose structure can be derived by systematically shearing the {open_quotes}1201{close_quotes} structure has been synthesized for the first time. It crystallizes in an orthorhombic cell with a=3.7536(2) {angstrom}, b=30.631(2) {angstrom}, c=9.219(1) {angstrom}, and A-type symmetry. This new structure consists of {open_quotes}1201{close_quotes} ribbons parallel to (010) which are three CuO{sub 6} octahedra wide and are interconnected through {open_quotes}Tl{sub 2}A{sub 2}O{sub 4}{close_quotes} ribbons whose cationic configuration is that of the rock salt structure. This phase can be considered to be the m = 3 member of a new series with the generic formulation (TlA{submore » 2}CuO{sub 5}){sub m} {center_dot} Tl{sub 2}A{sub 2}O{sub 4} with A = Ba, Sr.« less

IMG/M: integrated genome and metagenome comparative data analysis system

DOE PAGES

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; ...

2016-10-13

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support formore » examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.« less

IMG/M: integrated genome and metagenome comparative data analysis system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support formore » examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.« less

IMG/M: integrated genome and metagenome comparative data analysis system

PubMed Central

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Palaniappan, Krishna; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Andersen, Evan; Huntemann, Marcel; Varghese, Neha; Hadjithomas, Michalis; Tennessen, Kristin; Nielsen, Torben; Ivanova, Natalia N.; Kyrpides, Nikos C.

2017-01-01

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system. PMID:27738135

Flash Updates of GSC projects (GSC8 Meeting)

ScienceCinema

Glockner, Frank Oliver; Markowitz, Victor; Kyrpides, Nikos; Meyer, Folker; Amaral-Zettler, Linda; Cole, James

2018-01-25

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. In quick succession Frank Oliver Glockner (MPI-Bremen), Victor Markowitz (LBNL), Nikos Kyripides (JGI), Folker Meyer (ANL), Linda Amaral-Zettler (Marine Biology Lab), and James Cole (Michigan State University) provide updates on a number of topics related to GSC projects at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Flash Updates of GSC projects (GSC8 Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glockner, Frank Oliver; Markowitz, Victor; Kyrpides, Nikos

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. In quick succession Frank Oliver Glockner (MPI-Bremen), Victor Markowitz (LBNL), Nikos Kyripides (JGI), Folker Meyer (ANL), Linda Amaral-Zettler (Marine Biology Lab), and James Colemore » (Michigan State University) provide updates on a number of topics related to GSC projects at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harwood, Caroline S.

Rhodopseudomonas palustris is a common soil and water bacterium that makes its living by converting sunlight to cellular energy and by absorbing atmospheric carbon dioxide and converting it to biomass. This microbe can also degrade and recycle components of the woody tissues of plants, wood being the most abundant polymer on earth. Because of its intimate involvement in carbon management and recycling, R. palustris was selected by the DOE Carbon Management Program to have its genome sequenced by the Joint Genome Institute (JGI). This award provided funds for the preparation of R. palustris genomic DNA which was then supplied tomore » the JGI in sufficient amounts to enable the complete sequencing of the R. palustris genome. The PI also supplied the JGI with technical information about the molecular biology of R. palustris.« less

Effects of environment of the activated nonradiative decay of the /sup 3/A/sub 2/ state of Rh/sub 2/(TMB)/sub 4//sup 2 +/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milder, S.J.

1985-10-09

The effect of environment on the temperature dependence of the nonradiative decay of the /sup 3/A/sup 2/ state of Rh/sub 2/(TMB)/sub 4//sup 2 +/ (TMB = 2,5-dimethyl-2,5-diisocyanohexane) is studied. The temperature dependence of the observed nonradiative decay rate can be approximately fit to an Arrhenius-like expression: k/sub obsd/ = k/sub 0/ + Ae/sup -E/sub a//RT/. Arrhenius parameters are obtained in seven different environments, with the activation energies varying from 1970 to 3420 cm/sup -1/. A plot of 1n A vs. E/sub a/, known as a Barclay-Butler plot, is linear, with slope = 3.3 x 10/sup -3/ cm and y interceptmore » = 20.0. The linear Barclay-Butler plot suggests that the activated decay from the /sup 3/A/sub 2/ state of Rh/sub 2/(TMB)/sub 4//sup 2 +/ has the same mechanism, regardless of environment. Single-crystal, dilute-plastic, and dilute-crystal environments have been tested. 13 references, 4 figures.« less

Metabolism of (/sup 3/H)gibberellin A/sub 5/ by immature seeds of apricot (Prunus armeniaca L. )

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Bottini, G.A.; Bottini, R.; Koshioka, M.

1987-01-01

Immature seeds of apricot (Prunus armeniaca L.) were fed the native gibberellin A/sub 5/ (GA/sub 5/) as 1- and 1,2-(/sup 3/H)GA/sub 5/ at doses 2 to 530 times the expected endogenous level. After 4 days of incubation, seeds were extracted and free (/sup 3/H)GA-like metabolites were separated from the highly H/sub 2/O-soluble (/sup 3/H)metabolites. For high specific activity feeds the retention times (Rts) of radioactive peaks were compared with Rts of authentic GAs on sequential gradient-eluted ..-->.. isocratic eluted reversed-phase C/sub 18/ high performance liquid chromatography (HPLC)-radiocounting (RC). From high substrate feeds (530 and 230 x expected endogenous levels) HPLC-RCmore » peak groupings were subjected to capillary gas chromatography-selected ion monitoring (GC-SIM), usually six characteristic ions. The major free GA metabolites of (/sup 3/H) GA/sub 5/ were identified as GA/sub 1/, GA/sub 3/, and GA/sub 6/ by GC-SIM. The major highly water soluble metabolite of (/sup 3/H)GA/sub 5/ at all levels of substrate GA/sub 5/ had chromatographic characteristics similar to authentic GA/sub 1/-glucosyl ester. Expressed as a percentage of recovered radioactivity, low substrate (/sup 3/H)GA/sub 5/ feeds (2 x expected endogenous level) yielded a broad spectrum of metabolites eluting at the Rts where GA/sub 1/, GA/sub 3/, GA/sub 5/ methyl ester, GA/sub 6/, GA/sub 22/, GA/sub 29/ (17, 14, 1.6, 7, 1.1, 0.5%, respectively) and GA glucosyl conjugates of GA/sub 1/, GA/sub 3/, GA/sub 5/, and GA/sub 8/ (33, 11, 1, 0.1%, respectively) elute.« less

IMG 4 version of the integrated microbial genomes comparative analysis system

PubMed Central

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Woyke, Tanja; Huntemann, Marcel; Anderson, Iain; Billis, Konstantinos; Varghese, Neha; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N.; Kyrpides, Nikos C.

2014-01-01

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu). PMID:24165883

IMG: the integrated microbial genomes database and comparative analysis system

PubMed Central

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

2012-01-01

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 (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp). PMID:22194640

IMG: the Integrated Microbial Genomes database and comparative analysis system.

PubMed

Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos C

2012-01-01

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 (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp).

IMG 4 version of the integrated microbial genomes comparative analysis system.

PubMed

Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Woyke, Tanja; Huntemann, Marcel; Anderson, Iain; Billis, Konstantinos; Varghese, Neha; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N; Kyrpides, Nikos C

2014-01-01

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG's data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG's annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).

A Taste of Algal Genomes from the Joint Genome Institute

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuo, Alan; Grigoriev, Igor

Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basicmore » and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.« less

Genomic Encyclopedia of Fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supportedmore » by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.« less

Assembly, Annotation, and Analysis of Multiple Mycorrhizal Fungal Genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Initiative Consortium, Mycorrhizal Genomics; Kuo, Alan; Grigoriev, Igor

Mycorrhizal fungi play critical roles in host plant health, soil community structure and chemistry, and carbon and nutrient cycling, all areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI). To this end we are building on our earlier sequencing of the Laccaria bicolor genome by partnering with INRA-Nancy and the mycorrhizal research community in the MGI to sequence and analyze dozens of mycorrhizal genomes of all Basidiomycota and Ascomycota orders and multiple ecological types (ericoid, orchid, and ectomycorrhizal). JGI has developed and deployed high-throughput sequencing techniques, and Assembly, RNASeq, and Annotation Pipelines. In 2012more » alone we sequenced, assembled, and annotated 12 draft or improved genomes of mycorrhizae, and predicted ~;;232831 genes and ~;;15011 multigene families, All of this data is publicly available on JGI MycoCosm (http://jgi.doe.gov/fungi/), which provides access to both the genome data and tools with which to analyze the data. Preliminary comparisons of the current total of 14 public mycorrhizal genomes suggest that 1) short secreted proteins potentially involved in symbiosis are more enriched in some orders than in others amongst the mycorrhizal Agaricomycetes, 2) there are wide ranges of numbers of genes involved in certain functional categories, such as signal transduction and post-translational modification, and 3) novel gene families are specific to some ecological types.« less

SPRUCE Deep Peat Heating (DPH) to Whole Ecosystem Warming (WEW) Metagenomes for Peat Samples Collected June 2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kluber, Laurel A; Yip, Daniel Z; Yang, Zamin K

This data set provides links to the results of metagenomic analyses of 44 peat samples collected on 13 June 2016 from SPRUCE experiment treatment and ambient plots. Experimental plots had received approximately 24 months of belowground warming (deep peat heating (DPH), Hanson et al. 2015) with the last 9 of those months including air warming for implementation of whole ecosystems warming (WEW – Hanson et al. 2016). WEW Metagenomes: Data from these metagenomes are archived in the U.S. Department of Energy Joint Genome Institute (DOE JGI) Integrated Microbial Genomes (IMG) system (http://img.jgi.doe.gov/) and are available at the accession numbers providedmore » below (Table 2) and in the accompanying inventory file. The easiest way to find results on IMG is at this link, https://img.jgi.doe.gov/cgi-bin/m/main.cgi, and then enter “June2016WEW” as a search term in the “Quick Genome Search:” box at the top of the page.« less

IMG 4 version of the integrated microbial genomes comparative analysis system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Finally, different IMG datamarts providemore » support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).« less

Phospholipid alterations in cardiac sarcoplasmic reticulum induced by xanthine oxidase: contamination of commercial preparations of xanthine oxidase by phospholipase A/sub 2/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gamache, D.A.; Kornberg, L.J.; Bartolf, M.

1986-05-01

Incubation of cardiac sarcoplasmic reticulum with xanthine oxidase alone at pH 7.0 resulted in a loss of lipid phosphorus that was potentiated by the addition of xanthine. Using autoclaved E.coli with 1-/sup 14/C-oleate in the 2-acyl position of membrane phospholipids, the authors demonstrate that many, but not all, commercial preparations of xanthine oxidase contain significant phospholipase A/sub 2/ (PLA/sub 2/) activity (64.3-545.6 nmols/min/mg). The PLA/sub 2/ was maximally active in the neutral-alkaline pH range, was Ca/sup 2 +/-dependent, and was unaffected by the addition of xanthine. PLA/sub 2/ activity was totally inhibited by 1mM EDTA whereas radical production by optimalmore » concentrations of xanthine/xanthine oxidase (X/XO) was unaffected by EDTA. Chromatographically purified xanthine oxidase (Sigma Grade III) contained high levels of PLA/sub 2/ activity (64.3 nmols/min/mg) compared to endogenous levels of neutral-active, Ca/sup 2 +/-dependent PLA/sub 2/ measured in various tissue homogenates (less than or equal to 0.5 nmols/ min/mg). Because X/XO mixtures are used extensively to study oxygen free radical-induced cell injury and membrane phospholipid alterations, the presence of a potent extracellular PLA/sub 2/ may have influenced previously published reports, and such studies should be interpreted cautiously.« less

Fungal Genomics Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor

The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scalemore » genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.« less

Preliminary X-ray crystallographic studies of BthTX-II, a myotoxic Asp49-phospholipase A{sub 2} with low catalytic activity from Bothrops jararacussu venom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corrêa, L. C.; Marchi-Salvador, D. P.; Cintra, A. C. O.

2006-08-01

A myotoxic Asp49-PLA{sub 2} with low catalytic activity from B. jararacussu (BthTX-II) was crystallized in the monoclinic crystal system; a complete X-ray diffraction data set was collected and a molecular-replacement solution was obtained. The oligomeric structure of BthTX-II resembles those of the Asp49-PLA{sub 2} PrTX-III and all bothropic Lys49-PLA{sub 2}s. For the first time, a complete X-ray diffraction data set has been collected from a myotoxic Asp49-phospholipase A{sub 2} (Asp49-PLA{sub 2}) with low catalytic activity (BthTX-II from Bothrops jararacussu venom) and a molecular-replacement solution has been obtained with a dimer in the asymmetric unit. The quaternary structure of BthTX-II resemblesmore » the myotoxin Asp49-PLA{sub 2} PrTX-III (piratoxin III from B. pirajai venom) and all non-catalytic and myotoxic dimeric Lys49-PLA{sub 2}s. In contrast, the oligomeric structure of BthTX-II is different from the highly catalytic and non-myotoxic BthA-I (acidic PLA{sub 2} from B. jararacussu). Thus, comparison between these structures should add insight into the catalytic and myotoxic activities of bothropic PLA{sub 2}s.« less

2013 Progress Report -- DOE Joint Genome Institute

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2013-11-01

In October 2012, we introduced a 10-Year Strategic Vision [http://bit.ly/JGI-Vision] for the Institute. A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the organism and ecosystem level. This involves the continued massive-scale generation of sequence data, complemented by orthogonal new capabilities to functionally annotate these large sequence data sets. Our Strategic Vision lays out a path to guide our decisions and ensure that the evolving set of experimental and computational capabilities available to DOE JGI users will continue to enable groundbreaking science.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor; Glass, N. Louise; Martin, Francis

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) managed by Lawrence Berkeley National Laboratory, is the only user facility in the world devoted to problems of energy and environment. With over one million species, fungi—which include mushrooms—represent one of the largest under-explored branches of the Tree of Life. Together with its community of more than 1,000 scientific collaborators, JGI helping to unlock the secrets encoded in the genomes of fungi to advance a better understanding of the global carbon cycle and to develop new biotechnology products, next-generation biofuels, and medicines.

Phytozome Comparative Plant Genomics Portal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goodstein, David; Batra, Sajeev; Carlson, Joseph

2014-09-09

The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilbert, David

2013-01-01

The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is to serve the diverse scientific community as a user facility, enabling the application of large-scale genomics and analysis of plants, microbes, and communities of microbes to address the DOE mission goals in bioenergy and the environment. The DOE JGI's sequencing efforts fall under the Eukaryote Super Program, which includes the Plant and Fungal Genomics Programs; and the Prokaryote Super Program, which includes the Microbial Genomics and Metagenomics Programs. In 2012, several projects made news for their contributions to energy and environment research.

Towards a Consensus Annotation System (GSC8 Meeting)

ScienceCinema

White, Owen

2018-02-01

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Towards Consensus Annotation at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 10, 2009.

Method and apparatus for enhancing microchannel plate data

DOEpatents

Thoe, R.S.

1983-10-24

A method and apparatus for determining centroid channel locations are disclosed for use in a system activated by one or more multichannel plates and including a linear diode array providing channels of information 1, 2, ...,n, ..., N containing signal amplitudes A/sub n/. A source of analog A/sub n/ signals, and a source of digital clock signals n, are provided. Non-zero A/sub n/ values are detected in a discriminator. A digital signal representing p, the value of n immediately preceding that whereat A/sub n/ takes its first non-zero value, is generated in a scaler. The analog A/sub n/ signals are converted to digital in an analog to digital converter. The digital A/sub n/ signals are added to produce a digital ..sigma..A/sub n/ signal in a full adder. Digital 1, 2, ..., m signals representing the number of non-zero A/sub n/ are produced by a discriminator pulse counter. Digital signals representing 1 A/sub p+1/, 2 A/sub p+2/, ..., m A/sub p+m/ are produced by pairwise multiplication in multiplier. These signal are added in multiplier summer to produce a digital ..sigma..nA/sub n/ - p..sigma..A/sub n/ signal. This signal is divided by the digital ..sigma..A/sub n/ signal in divider to provide a digital (..sigma..nA/sub n//..sigma..A/sub n/) -p signal. Finally, this last signal is added to the digital p signal in an offset summer to provide ..sigma..nA/sub n//..sigma..A/sub n/, the centroid channel locations.

Phylogeonomics and Ecogenomics of the Mycorrhizal Symbiosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuo, Alan; Grigoriev, Igor V.; Kohler, Annegret

Mycorrhizal fungi play critical roles in host plant health, soil community structure and chemistry, and carbon and nutrient cycling, all areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI). To this end we are building on our earlier sequencing of the Laccaria bicolor genome by partnering with INRA-Nancy and the mycorrhizal research community in the MGI to sequence and analyze 2 dozen mycorrhizal genomes of numerous known mycorrhizal orders and several ecological types (ectomycorrhizal [ECM], ericoid, orchid, and arbuscular). JGI has developed and deployed high-throughput pipelines for genomic, transcriptomic, and re-sequencing, and platforms formore » assembly, annotation, and analysis. In the last 2 years we have sequenced 21 genomes of mycorrhizal fungi, and resequenced 6 additional strains of L. bicolor. Most of this data is publicly available on JGI MycoCosm?s Mycorrhizal Fungi Portal (http://jgi.doe.gov/Mycorrhizal_fungi/), which provides access to both the genome data and tools with which to analyze the data. These data allow us to address long-standing issues in mycorrhizal evolution and ecology. For example, a major observation of mycorrhizal evolution is that each of the major ecological types appears to have evolved independently in multiple fungal clades. Using an ecogenomic approach we provide preliminary evidence that 2 clades (Cantharellales and Sebacinales) of a single symbiotic ecotype (orchid) utilize some common regulatory (protein tyrosine kinase) and metabolic (lipase) paths, the latter of which may be the product of HGT. Using a phylogenomic approach we provide preliminary evidence that a particular ecotype (ericoid) may have evolved more than once within a major clade (Leotiomycetes).« less

Standards and the INSDC: Submission of MIGS, MIMS, MIENS (GSC8 Meeting)

ScienceCinema

Mizrachi, Ilene

2017-12-21

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding. Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Ilene Mizrachi of the NCBI talks about submission of MIGS/MIMS/MIENS information at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Systems Biology Knowledgebase (GSC8 Meeting)

ScienceCinema

Cottingham, Robert W.

2018-01-04

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Robert W. Cottingham of Oak Ridge National Laboratory discusses the DOE Knowledge Base at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Annotations in Refseq (GSC8 Meeting)

ScienceCinema

Tatusova, Tatiana

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 10, 2009.

Gene Calling Standards (GSC8 Meeting)

ScienceCinema

Kyrpides, Nikos

2018-04-27

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses gene calling standards at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 10, 2009.

Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

ScienceCinema

Jansson, Janet

2018-01-04

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Oceanic Communities in a Changing Planet - The Tara Oceans Project (GSC8 Meeting)

ScienceCinema

Raes, Jeroen

2018-01-10

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Jeroen Raes of the University of Brussels discusses the Tara-Oceans expedition at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

The Biocurator Society (GSC8 Meeting)

ScienceCinema

Gaudet, Pascal

2018-01-10

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Pascal Gaudet of Northwestern University talks about "The Biocurator Society" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 11, 2009.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, X. J.; Zhong, J. X.; Glaser, R.

The unidentified infrared emission (UIE) features at 3.3, 6.2, 7.7, 8.6, and 11.3 μm, commonly attributed to polycyclic aromatic hydrocarbon (PAH) molecules, have recently been ascribed to mixed aromatic/aliphatic organic nanoparticles. More recently, an upper limit of <9% was placed on the aliphatic fraction (i.e., the fraction of carbon atoms in aliphatic form) of the UIE carriers based on the observed intensities of the 3.4 μm and 3.3 μm emission features by attributing them to aliphatic and aromatic C-H stretching modes, respectively, and assuming A{sub 3.4}/A{sub 3.3} ≈ 0.68 derived from a small set of aliphatic and aromatic compounds, wheremore » A{sub 3.4} and A{sub 3.3} are, respectively, the band strengths of the 3.4 μm aliphatic and 3.3 μm aromatic C-H bonds. To improve the estimate of the aliphatic fraction of the UIE carriers, here we analyze 35 UIE sources exhibiting both the 3.3 μm and 3.4 μm C-H features and determine I{sub 3.4}/I{sub 3.3}, the ratio of the power emitted from the 3.4 μm feature to that from the 3.3 μm feature. We derive the median ratio to be (I{sub 3.4}/I{sub 3.3}) ≈ 0.12. We employ density functional theory to compute A{sub 3.4}/A{sub 3.3} for a range of methyl-substituted PAHs. The resulting A{sub 3.4}/A{sub 3.3} ratio well exceeds ∼1.4, with an average ratio of A{sub 3.4}/A{sub 3.3} ≈ 1.76. By attributing the 3.4 μm feature exclusively to aliphatic C-H stretch (i.e., neglecting anharmonicity and superhydrogenation), we derive the fraction of C atoms in aliphatic form from I{sub 3.4}/I{sub 3.3} ≈ 0.12 and A{sub 3.4}/A{sub 3.3} ≈ 1.76 to be ∼2%. We therefore conclude that the UIE emitters are predominantly aromatic.« less

Crystal structure and X-ray photoemission spectroscopic study of A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dutta, Alo, E-mail: alo_dutta@yahoo.com; Saha, Sujoy; Kumari, Premlata

2015-09-15

The X-ray photoemission spectroscopic (XPS) study of the double perovskite oxides A{sub 2}LaMO{sub 6} [A=Ba, Ca; M=Nb, Ta] synthesized by the solid-state reaction technique has been carried out to investigate the nature of the chemical state of the constituent ions and the bonding between them. The Rietveld refinement of the X-ray diffraction patterns suggests the monoclinic crystal structure of all the materials at room temperature. The negative and positive chemical shifts of the core level XPS spectrum of O-1s and Nb-3d{sub 3/2}/Ta-4f{sub 5/2} respectively suggest the covalent bonding between Nb/Ta cations and O ion. The change of the bonding strengthmore » between the anion and the cations from one material to another has been analyzed. The vibrational property of the materials is investigated using the room temperature Raman spectra. A large covalency of Ta-based compound than Nb compound is confirmed from the relative shifting of the Raman modes of the materials. - Graphical abstract: Crystal structure of two perovskite oxides CLN and CLT is investigated. XPS study confirms the two different co-ordination environments of Ca and covalent bonding between B-site cations and O-ion. - Highlights: • Ordered perovskite structure obtained by Rietveld refinement of XRD patterns. • Study of nature of chemical bonding by X-ray photoemission spectroscopy. • Opposite chemical shift of d-states of Nb/Ta with respect to O. • Covalent bonding between d-states of Nb/Ta and O. • Relative Raman shifts of CLN and CLT substantiate the more covalent character of Ta than Nb.« less

Interlocking Detachable Coil Embolization by Technique of Dumbbell-Shaped Framing and Filling and Bridge Formation Under Balloon Dilatation for Huge Conglomerate Pulmonary Arteriovenous Malformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawai, Nobuyuki, E-mail: nobkawai@wakayama-med.ac.jp; Sato, Morio, E-mail: morisato@mail.wakayama-med.ac.jp; Minamiguchi, Hiroyuki, E-mail: hiromina4@hotmail.com

A 60-year-old woman presented with a conglomerate pulmonary arteriovenous malformation (PAVM) size 8.2 Multiplication-Sign 7.2 cm on chest X-ray. Feeding arteries were A{sub a}{sup 7} and A{sub b}{sup 7}, A{sup 8}, and A{sup 10}. The diameter and length of the A{sub b}{sup 7} neck were 15.5 and 16 mm, respectively. After percutaneous transcatheter embolization of A{sup 8} and A{sup 10}, PTE of A{sub a}{sup 7} and A{sub b}{sup 7} was conducted under balloon occlusion with interlocking detachable coils using a technique of dumbbell-shaped framing and filling, making a bridge from A{sub b}{sup 7} to the trunk of A{sup 9} andmore » A{sup 10}across A{sup 7}. Follow-up computed tomography 10 months after treatment showed marked shrinkage of the PAVM.« less

Liquid drop model for charged spherical metal clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seidl, M.; Brack, M.

1996-02-01

The average ground-state energy of a charged spherical metal cluster with {ital N} atoms and {ital z} excessive valence electrons, i.e., with net charge {ital Q}={minus}{ital ez} and radius {ital R}={ital r}{sub {ital sN}}{sup 1/3}, is presented in the liquid drop model (LDM) expansion {ital E}({ital N},{ital z})={ital a}{sub v}{ital N}+{ital a}{sub s}{ital N}{sup 2/3}+{ital a}{sub c}{ital N}{sup 1/3}+{ital a}{sub 0}({ital z})+{ital a}{sub {minus}1}({ital z}){ital N}{sup {minus}1/3}+{ital O}({ital N}{sup {minus}2/3}). We derive analytical expressions for the leading LDM coefficients {ital a}{sub v}, {ital a}{sub s}, {ital a}{sub c}, and, in particular, for the charge dependence of the further LDM coefficientsmore » {ital a}{sub 0} and {ital a}{sub {minus}1}, using the jellium model and density functional theory in the local density approximation. We obtain for the ionization energy {ital I}({ital R})={ital W}+{alpha}({ital e}{sup 2}/{ital R})+{ital O}({ital R}{sup {minus}2}), with the bulk work function {ital W}=[{Phi}(+{infinity}){minus}{Phi}(0)]{minus}{ital e}{sub b}, given first by Mahan and Schaich in terms of the electrostatic potential {Phi} and the bulk energy per electron {ital e}{sub b}, and a new analytical expression for the dimensionless coefficient {alpha}. We demonstrate that within classical theory {alpha}=1/2 but, in agreement with experimental information, {alpha} tends to {approximately}0.4 if quantum-mechanical contributions are included. In order to test and confirm our analytical expressions, we discuss the numerical results of semiclassical density variational calculations in the extended Thomas{endash}Fermi model. Copyright {copyright} 1996 Academic Press, Inc.« less

A GSC Global Genome Census (GSC8 Meeting)

ScienceCinema

Kyrpides, Nikos

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses the notion of a global genome census at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jansson, Janet

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI inmore » Walnut Creek, CA on Sept. 9, 2009.« less

The transition from the open minimum to the ring minimum on the ground state and on the lowest excited state of like symmetry in ozone: A configuration interaction study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theis, Daniel; Windus, Theresa L.; Ruedenberg, Klaus

The metastable ring structure of the ozone 1{sup 1}A{sub 1} ground state, which theoretical calculations have shown to exist, has so far eluded experimental detection. An accurate prediction for the energy difference between this isomer and the lower open structure is therefore of interest, as is a prediction for the isomerization barrier between them, which results from interactions between the lowest two {sup 1}A{sub 1} states. In the present work, valence correlated energies of the 1{sup 1}A{sub 1} state and the 2{sup 1}A{sub 1} state were calculated at the 1{sup 1}A{sub 1} open minimum, the 1{sup 1}A{sub 1} ring minimum,more » the transition state between these two minima, the minimum of the 2{sup 1}A{sub 1} state, and the conical intersection between the two states. The geometries were determined at the full-valence multi-configuration self-consistent-field level. Configuration interaction (CI) expansions up to quadruple excitations were calculated with triple-zeta atomic basis sets. The CI expansions based on eight different reference configuration spaces were explored. To obtain some of the quadruple excitation energies, the method of Correlation Energy Extrapolation by Intrinsic Scaling was generalized to the simultaneous extrapolation for two states. This extrapolation method was shown to be very accurate. On the other hand, none of the CI expansions were found to have converged to millihartree (mh) accuracy at the quadruple excitation level. The data suggest that convergence to mh accuracy is probably attained at the sextuple excitation level. On the 1{sup 1}A{sub 1} state, the present calculations yield the estimates of (ring minimum—open minimum) ∼45–50 mh and (transition state—open minimum) ∼85–90 mh. For the (2{sup 1}A{sub 1}–{sup 1}A{sub 1}) excitation energy, the estimate of ∼130–170 mh is found at the open minimum and 270–310 mh at the ring minimum. At the transition state, the difference (2{sup 1}A{sub 1}–{sup 1}A{sub 1

Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp)

PubMed Central

Spriggs, Andrew; Henderson, Steven T.; Hand, Melanie L.; Johnson, Susan D.; Taylor, Jennifer M.; Koltunow, Anna

2018-01-01

Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculata v1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has now been established in a collaboration between the Joint Genome Institute (JGI) and University California (UC) Riverside. Here we release supporting genomic and transcriptomic data for IT97K-499-35 and a second transformable cowpea variety, IT86D-1010. The transcriptome resource includes six tissue-specific datasets for each variety, with particular emphasis on reproductive tissues that extend and support the V. unguiculata v1.0 reference. Annotations have been included in our resource to allow direct mapping to the v1.0 cowpea reference. Access to this resource provided here is supported by raw and assembled data downloads. PMID:29528046

Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp).

PubMed

Spriggs, Andrew; Henderson, Steven T; Hand, Melanie L; Johnson, Susan D; Taylor, Jennifer M; Koltunow, Anna

2018-02-09

Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculata  v1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has now been established in a collaboration between the Joint Genome Institute (JGI) and University California (UC) Riverside. Here we release supporting genomic and transcriptomic data for IT97K-499-35 and a second transformable cowpea variety, IT86D-1010. The transcriptome resource includes six tissue-specific datasets for each variety, with particular emphasis on reproductive tissues that extend and support the V. unguiculata v1.0 reference. Annotations have been included in our resource to allow direct mapping to the v1.0 cowpea reference. Access to this resource provided here is supported by raw and assembled data downloads.

INFRARED SPECTROSCOPIC SURVEY OF THE QUIESCENT MEDIUM OF NEARBY CLOUDS. I. ICE FORMATION AND GRAIN GROWTH IN LUPUS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boogert, A. C. A.; Chiar, J. E.; Knez, C.

2013-11-01

Infrared photometry and spectroscopy (1-25 μm) of background stars reddened by the Lupus molecular cloud complex are used to determine the properties of grains and the composition of ices before they are incorporated into circumstellar envelopes and disks. H{sub 2}O ices form at extinctions of A{sub K} = 0.25 ± 0.07 mag (A{sub V} = 2.1 ± 0.6). Such a low ice formation threshold is consistent with the absence of nearby hot stars. Overall, the Lupus clouds are in an early chemical phase. The abundance of H{sub 2}O ice (2.3 ± 0.1 × 10{sup –5} relative to N{sub H}) ismore » typical for quiescent regions, but lower by a factor of three to four compared to dense envelopes of young stellar objects. The low solid CH{sub 3}OH abundance (<3%-8% relative to H{sub 2}O) indicates a low gas phase H/CO ratio, which is consistent with the observed incomplete CO freeze out. Furthermore it is found that the grains in Lupus experienced growth by coagulation. The mid-infrared (>5 μm) continuum extinction relative to A{sub K} increases as a function of A{sub K}. Most Lupus lines of sight are well fitted with empirically derived extinction curves corresponding to R{sub V} ∼ 3.5 (A{sub K} = 0.71) and R{sub V} ∼ 5.0 (A{sub K} = 1.47). For lines of sight with A{sub K} > 1.0 mag, the τ{sub 9.7}/A{sub K} ratio is a factor of two lower compared to the diffuse medium. Below 1.0 mag, values scatter between the dense and diffuse medium ratios. The absence of a gradual transition between diffuse and dense medium-type dust indicates that local conditions matter in the process that sets the τ{sub 9.7}/A{sub K} ratio. This process is likely related to grain growth by coagulation, as traced by the A{sub 7.4}/A{sub K} continuum extinction ratio, but not to ice mantle formation. Conversely, grains acquire ice mantles before the process of coagulation starts.« less

THE MID-INFRARED EXTINCTION LAW IN THE LARGE MAGELLANIC CLOUD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Jian; Jiang, B. W.; Xue, M. Y.

Based on photometric data from the Spitzer/SAGE survey, using red giants as extinction tracers, the mid-infrared (MIR) extinction laws in the Large Magellanic Cloud (LMC) are derived for the first time in the form of A{sub λ}/A{sub K{sub S}}. This quantity refers to the extinction in the four Infrared Array Camera (IRAC) bands (i.e., [3.6], [4.5], [5.8], and [8.0] μm) relative to the Two Micron All Sky Survey K{sub S} band at 2.16 μm. We obtain the near-infrared extinction coefficient to be E(J – H)/E(H – K{sub S} ) ≈ 1.29 ± 0.04 and E(J – K{sub S} )/E(H –more » K{sub S} ) ≈ 1.94 ± 0.04. The wavelength dependence of the MIR extinction A{sub λ}/A{sub K{sub S}} in the LMC varies from one sightline to another. The overall mean MIR extinction is A{sub [3.6]}/A{sub K{sub S}}∼0.72±0.03, A{sub [4.5]}/A{sub K{sub S}}∼0.94±0.03, A{sub [5.8]}/A{sub K{sub S}}∼0.58±0.04, and A{sub [8.0]}/A{sub K{sub S}}∼0.62±0.05. Except for the extinction in the IRAC [4.5] μm band, which may be contaminated by the 4.6 μm CO gas absorption of red giants used to trace LMC extinction, the extinction in the other three IRAC bands show a flat curve, close to the Milky Way R{sub V} = 5.5 model extinction curve, where R{sub V} is the optical total-to-selective extinction ratio. The possible systematic bias caused by the correlated uncertainties of K{sub S} – λ and J – K{sub S} is explored in terms of Monte Carlo simulations. We find that this bias could lead to an overestimation of A{sub λ}/A{sub K{sub S}} in the MIR.« less

Variable dimensionality and framework found in a series of quaternary zinc selenites, A{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}·xH{sub 2}O (A = Na, Rb, and Cs; 0≤x≤1) and Cs{sub 2}Zn{sub 2}(SeO{sub 3}){sub 3}·2H{sub 2}O

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lü, Minfeng; Jo, Hongil; Oh, Seung-Jin

Five new alkali metal zinc selenites, A{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}·xH{sub 2}O (A = Na, Rb, and Cs; 0≤x≤1) and Cs{sub 2}Zn{sub 2}(SeO{sub 3}){sub 3}·2H{sub 2}O have been synthesized by heating a mixture of ZnO, SeO{sub 2} and A{sub 2}CO{sub 3} (A = Na, Rb, and Cs), and characterized by X-ray diffraction (XRD) and spectroscopic analyses techniques. All of the reported materials revealed a rich structural chemistry with different frameworks and connection modes of Zn{sup 2+}. While Rb{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4} and Cs{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}·H{sub 2}O revealed three-dimensional frameworks consisting of isolated ZnO{sub 4} tetrahedra and SeO{submore » 3} polyhedra, Na{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}, Cs{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}, and Cs{sub 2}Zn{sub 2}(SeO{sub 3}){sub 3}·2H{sub 2}O contained two-dimensional [Zn{sub 3}(SeO{sub 3}){sub 4}]{sup 2-} layers. Specifically, whereas isolated ZnO{sub 4} tetrahedra and SeO{sub 3} polyhedra are arranged into two-dimensional [Zn{sub 3}(SeO{sub 3}){sub 4}]{sup 2-} layers in two cesium compounds, circular [Zn{sub 3}O{sub 10}]{sup 14-} chains and SeO{sub 3} linkers are formed in two-dimensional [Zn{sub 3}(SeO{sub 3}){sub 4}]{sup 2-} layers in Na{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4}. Close structural examinations suggest that the size of alkali metal is significant in determining the framework geometry as well as connection modes of transition metal cations. - Graphical abstract: Variable dimensions and frameworks were found in a series of quaternary zinc selenites, A{sub 2}Zn{sub 3}(SeO{sub 3}){sub 4} (A = Na, Rb and Cs). - Highlights: • Five novel quaternary zinc selenites are synthesized. • All the selenites with different structures contain polarizable d{sup 10} and lone pair cations. • The size of alkali metal cations is significant in determining the framework geometry.« less

Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Quake, Steve

2018-02-02

Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Genome Assembly Forensics: Metrics for Assessing Assembly Correctness (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Pop, Mihai

2018-04-27

University of Maryland's Mihai Pop on Genome Assembly Forensics: Metrics for Assessing Assembly Correctness at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quake, Steve

2011-10-12

Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

MIENS Minimum Information about an ENvironmental Sequence and The GSC's Not-for-Profit (GSC8 Meeting)

ScienceCinema

Yilmaz, Pelin; Kolker, Eugene

2018-01-24

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Pelin Yilmaz of the Max Planck Institute-Bremen talks about the MIENS specification and Eugene Kolker of Seattle Children's Hospital discusses the GSC's non-for-profit at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

ScienceCinema

Kolker, Eugene; Sansone, Susanna

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA. on Sept. 11, 2009.

The Genomes and Metagenomes (GEM) Catalogue (first presentation) and The ISA-GCDML Workshop (second presentation) (GSC8 Meeting)

ScienceCinema

Field, Dawn; Sansone, Susanna

2018-01-24

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding ''Research Coordination Network'' from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology & Hydrology briefly introduces the GEM Catalogue, followed by Susanna Sansone of the European Bioinformatics Institute who talks about the ISA-GCDML workshop at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knight, Rob

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Rob Knight of the University of Colorado gives a presentation on "Spatially and Temporally Resolvedmore » Studies of the Human Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.« less

Memory Efficient Sequence Analysis Using Compressed Data Structures (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Simpson, Jared

2018-01-24

Wellcome Trust Sanger Institute's Jared Simpson on Memory efficient sequence analysis using compressed data structures at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Secretory phospholipase A{sub 2}-mediated progression of hepatotoxicity initiated by acetaminophen is exacerbated in the absence of hepatic COX-2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhave, Vishakha S.; Donthamsetty, Shashikiran; Latendresse, John R.

2011-03-15

We have previously reported that among the other death proteins, hepatic secretory phospholipase A{sub 2} (sPLA{sub 2}) is a leading mediator of progression of liver injury initiated by CCl{sub 4} in rats. The aim of our present study was to test the hypothesis that increased hepatic sPLA{sub 2} released after acetaminophen (APAP) challenge mediates progression of liver injury in wild type (WT) and COX-2 knockout (KO) mice. COX-2 WT and KO mice were administered a normally non lethal dose (400 mg/kg) of acetaminophen. The COX-2 KO mice suffered 60% mortality compared to 100% survival of the WT mice, suggesting highermore » susceptibility of COX-2 KO mice to sPLA{sub 2}-mediated progression of acetaminophen hepatotoxicity. Liver injury was significantly higher at later time points in the KO mice compared to the WT mice indicating that the abatement of progression of injury requires the presence of COX-2. This difference in hepatotoxicity was not due to increased bioactivation of acetaminophen as indicated by unchanged cyp2E1 protein and covalently bound {sup 14}C-APAP in the livers of KO mice. Hepatic sPLA{sub 2} activity and plasma TNF-{alpha} were significantly higher after APAP administration in the KO mice. This was accompanied by a corresponding fall in hepatic PGE{sub 2} and lower compensatory liver regeneration and repair ({sup 3}H-thymidine incorporation) in the KO mice. These results suggest that hindered compensatory tissue repair and poor resolution of inflammation for want of beneficial prostaglandins render the liver very vulnerable to sPLA{sub 2}-mediated progression of liver injury. These findings are consistent with the destructive role of sPLA{sub 2} in the progression and expansion of tissue injury as a result of continued hydrolytic breakdown of plasma membrane phospholipids of perinecrotic hepatocytes unless mitigated by sufficient co-induction of COX-2.« less

Comparison of Normalized and Unnormalized Single Cell and Population Assemblies (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Hugenholtz, Phil

2018-02-12

University of Queensland's Phil Hugenholtz on "Comparison of Normalized and Unnormalized Single Cell and Population Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Won, Jong-Pil, E-mail: jpwon@konkuk.ac.kr; Hwang, Un-Jong; Lee, Su-Jin

This study evaluated the performance of shotcrete using high strength C{sub 12}A{sub 7} mineral-based accelerator that has been developed to improve the durability and long-term strength. Rebound, compressive strength and flexural strength were tested in the field. Test result showed that existing C{sub 12}A{sub 7} mineral-based accelerator exhibits better early strength than the high-strength C{sub 12}A{sub 7} mineral-based accelerator until the early age, but high-strength C{sub 12}A{sub 7} mineral-based accelerator shows about 29% higher at the long-term age of 28 days. Microstructural analysis such as scanning electron microscope (SEM), X-ray diffraction (XRD) and nitrogen adsorption method was evaluated to analyzemore » long-term strength development mechanism of high strength C{sub 12}A{sub 7} mineral-based accelerator. As analysis result, it had more dense structure due to the reaction product by adding material that used to enhanced strength. It had better resistance performance in chloride ion penetration, freezing–thawing and carbonation than shotcrete that used existing C{sub 12}A{sub 7} mineral-based accelerator.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seo, S.B.; Jun, J.H.; Choi, C.S.

The influence of prior deformation on reverse martensitic transformation temperature in Fe-high Ni alloys has been investigated by several workers. For example, Pope has studied the reverse transformation temperature of an Fe-30%Ni alloy with respect to deformation, and found that the start temperature of reverse transformation (A{sub s}) increased continuously with increasing deformation. Mel'nikov et al. have examined the variation in A{sub s} with deformation temperature in an Fe-30%Ni alloy, and reported that the deformation at ambient temperature shifted the A{sub s} to higher temperature, while deformation applied between 60 and 100 C lowered the A{sub s}. The above investigationmore » dealt only with the A{sub s} of lenticular martensite having partially twinned substructure, but few studies have been made on lath martensite with highly dislocated substructure of an Fe-Ni alloy. In the present study, lath martensite of an Fe-15%Ni and lenticular martensite of an Fe-31%Ni alloy were prepared, and the variation in A{sub s} with prior deformation at room temperature was investigated and compared with each other.« less

Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Li, Weizhong

2018-02-12

San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

ScienceCinema

Vaughan, Bob; Kaye, Jon

2018-01-24

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolker, Eugene; Sansone, Susanna

2011-09-11

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "Themore » ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA. on Sept. 11, 2009.« less

A New Arm of the GSC: The RCN4GSC and Curation of MIGS-compliant Data (GSC8 Meeting)

ScienceCinema

Field, Dawn; Sterk, Peter

2018-01-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology and Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology and Hydrology follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Exotic and qq-bar resonances in the pi+pi-pi- system produced in pi-p collisions at 18 GeV/c

DOE Office of Scientific and Technical Information (OSTI.GOV)

S. U. Chung; K. Danyo; R. W. Hackenburg

A partial-wave analysis of the reaction pi{sup -}p-->pi{sup +}pi{sup -}pi{sup -}p at 18 GeV/c has been performed on a data sample of 250 000 events obtained in the Brookhaven experiment E852. The well-known a{sub 1}(1260), a{sub 2}(1320) and pi{sub 2}(1670) resonant states are observed. The existence of the pi(1800), a{sub 1}(1700) and a{sub 4}(2040) states is confirmed. The a{sub 3}(1874) state is also observed. The exotic 1{sup -+} pi{sub 1}(1600) state produced in the natural parity exchange process is found to decay in the rho(770)pi{sup -} channel. A mass-dependent fit results in a resonance mass of 1593{+-}8{sub -47}{sup +29} MeV/c{supmore » 2} and a width of 168{+-}20{sub -12}{sup +150} MeV/c{sup 2}.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stacey, Gary

Gary Stacey, associate director of the National Center for Soybean Biotechnology at the University of Missouri, gives a talk simply titled "Soybean" on March 24, 2010 at the 5th Annual DOE JGI User Meeting.

Many light Higgs bosons in the next-to-minimal supersymmetric model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dermisek, Radovan; Gunion, John F.

2009-03-01

The next-to-minimal supersymmetric model with a light doubletlike CP-odd Higgs boson and small tan{beta} can satisfy all experimental limits on Higgs bosons even with light superpartners. In these scenarios, the two lightest CP-even Higgs bosons, h{sub 1} and h{sub 2}, and the charged Higgs boson, h{sup +}, can all be light enough to be produced at CERN LEP and yet have decays that have not been looked for or are poorly constrained by existing collider experiments. The channel h{sub 1}{yields}a{sub 1}a{sub 1} with a{sub 1}{yields}{tau}{sup +}{tau}{sup -} or 2j is still awaiting LEP constraints for m{sub h{sub 1}}>86 or 82more » GeV, respectively. LEP data may also contain e{sup +}e{sup -}{yields}h{sub 2}a{sub 1} events where h{sub 2}{yields}Za{sub 1} is the dominant decay, a channel that was never examined. Decays of the charged Higgs bosons are often dominated by H{sup {+-}}{yields}W{sup {+-}}{sup (}*{sup )}a{sub 1} with a{sub 1}{yields}gg, cc, and {tau}{sup +}{tau}{sup -}. This is a channel that has so far been ignored in the search for t{yields}h{sup +}b decays at the Tevatron. A specialized analysis might reveal a signal. The light a{sub 1} might be within the reach of B factories via {upsilon}{yields}{gamma}a{sub 1} decays. We study typical mass ranges and branching ratios of Higgs bosons in this scenario and compare these scenarios where the a{sub 1} has a large doublet component to the more general scenarios with arbitrary singlet component for the a{sub 1}.« less

Determination of orbits of comets: P/Kearns-Kwee, P/Gunn, including nongravitational effects in the comets' motion

NASA Technical Reports Server (NTRS)

Todorovic-Juchniewicz, Bozenna; Sitarski, Grzegorz

1992-01-01

To improve the orbits, all the positional observations of the comets were collected. The observations were selected and weighted according to objective mathematical criteria and the mean residuals a priori were calculated for both comets. We took into account nongravitational effects in the comets' motion using Marsden's method applied in two ways: either determining the three constant parameters, A(sub 1), A(sub 2), A(sub 3) or the four parameters A, eta, I, phi connected with the rotating nucleus of the comet. To link successfully all the observations, we had to assume for both comets that A(t) = A(sub O)exp(-B x t) where B was an additional nongravitational parameter.

Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Dehal, Paramvir

2018-02-06

Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Finding Fingerprints of Selection in Poplar Genomes

ScienceCinema

Tuskan, Gerald

2018-05-30

Jerry Tuskan of Oak Ridge National Laboratory and the DOE JGI talks about poplar trees as models for selective adaptation to an environment. This video complements a study published ahead online August 24, 2014 in Nature Genetics.

MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Sakakibara, Yasumbumi

2018-02-13

Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakakibara, Yasumbumi

2011-10-13

Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuskan, Gerald

Jerry Tuskan of Oak Ridge National Laboratory and the DOE JGI talks about poplar trees as models for selective adaptation to an environment. This video complements a study published ahead online August 24, 2014 in Nature Genetics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calva-Tellez, E.; Zepeda, A.

We discuss how weak neutral currents of popular gauge models manifest themselves in the process e/sup +/e/sup -/ ..-->.. ..pi../sup +/..pi../sup -/..pi../sup 0/ for an unpolarized initial state. We define three asymmetry parameters, A/sub c1/, A/sub c2/, and A/sub p/, which provide information about the presence of the neutral current. The former two give account of charge asymmetries in the ..pi../sup +/..pi../sup -/ final state, while A/sub p/ is nonzero when parity-violating effects occur. Using a phenomenological model for the hadronic vertices, we obtain that the maximum value of these parameters is approx. 3 to 4%, and that this valuemore » is reached at a beam energy approx. = 20 GeV. (AIP)« less

A Posteriori Correction of Forecast and Observation Error Variances

NASA Technical Reports Server (NTRS)

Rukhovets, Leonid

2005-01-01

Proposed method of total observation and forecast error variance correction is based on the assumption about normal distribution of "observed-minus-forecast" residuals (O-F), where O is an observed value and F is usually a short-term model forecast. This assumption can be accepted for several types of observations (except humidity) which are not grossly in error. Degree of nearness to normal distribution can be estimated by the symmetry or skewness (luck of symmetry) a(sub 3) = mu(sub 3)/sigma(sup 3) and kurtosis a(sub 4) = mu(sub 4)/sigma(sup 4) - 3 Here mu(sub i) = i-order moment, sigma is a standard deviation. It is well known that for normal distribution a(sub 3) = a(sub 4) = 0.

The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) Portal to the HMP (GSC8 Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weinstock, George; Wortman, Jennifer

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University ofmore » Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.« less

"A New Arm of the GSC: the RCN4GSC" and "Curation of MIGS-compliant Data" (GSC 8 Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Field, Dawn; Sterk, Peter

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology & Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology & Hydrologymore » follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.« less

A New Arm of the GSC: The RCN4GSC and Curation of MIGS-compliant Data (GSC8 Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Field, Dawn; Sterk, Peter

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology and Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology and Hydrologymore » follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.« less

Illumina GA IIx& HiSeq 2000 Production Sequenccing and QC Analysis Pipelines at the DOE Joint Genome Institute

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daum, Christopher; Zane, Matthew; Han, James

2011-01-31

The U.S. Department of Energy (DOE) Joint Genome Institute's (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI's Production Sequencing group, a robust Illumina Genome Analyzer and HiSeq pipeline has been established. Optimization of the sesequencer pipelines has been ongoing with the aim of continual process improvement of the laboratory workflow, reducing operational costs and project cycle times to increases ample throughput, and improving the overall quality of the sequence generated. A sequence QC analysismore » pipeline has been implemented to automatically generate read and assembly level quality metrics. The foremost of these optimization projects, along with sequencing and operational strategies, throughput numbers, and sequencing quality results will be presented.« less

Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaughan, Bob; Kaye, Jon

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Bettymore » Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.« less

The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) Portal to the HMP (GSC8 Meeting)

ScienceCinema

Weinstock, George; Wortman, Jennifer

2018-01-22

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University of Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

GenePRIMP: A Gene Prediction Improvement Pipeline For Prokaryotic Genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kyrpides, Nikos C.; Ivanova, Natalia N.; Pati, Amrita

2010-07-08

GenePRIMP (Gene Prediction Improvement Pipeline, Http://geneprimp.jgi-psf.org), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missing genes, and split genes. We show that manual curation of gene models using the anomaly reports generated by GenePRIMP improves their quality and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome sequencing and annotation technologies. Keywords in context: Gene model, Quality Control, Translation start sites, Automatic correction. Hardware requirements; PC, MAC; Operating System: UNIX/LINUX; Compiler/Version: Perl 5.8.5 or higher; Special requirements: NCBI Blast and nr installation; File Types:more » Source Code, Executable module(s), Sample problem input data; installation instructions other; programmer documentation. Location/transmission: http://geneprimp.jgi-psf.org/gp.tar.gz« less

Higher-order multipole amplitudes in charmonium radiative transitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Artuso, M.; Blusk, S.; Khalil, S.

2009-12-01

Using 24x10{sup 6} {psi}{sup '}{identical_to}{psi}(2S) decays in CLEO-c, we have searched for higher multipole admixtures in electric-dipole-dominated radiative transitions in charmonia. We find good agreement between our data and theoretical predictions for magnetic quadrupole (M2) amplitudes in the transitions {psi}{sup '}{yields}{gamma}{chi}{sub c1,c2} and {chi}{sub c1,c2}{yields}{gamma}J/{psi}, in striking contrast to some previous measurements. Let b{sub 2}{sup J} and a{sub 2}{sup J} denote the normalized M2 amplitudes in the respective aforementioned decays, where the superscript J refers to the angular momentum of the {chi}{sub cJ}. By performing unbinned maximum likelihood fits to full five-parameter angular distributions, we found the following values ofmore » M2 admixtures for J{sub {chi}}=1: a{sub 2}{sup J={sup 1}}=(-6.26{+-}0.63{+-}0.24)x10{sup -2} and b{sub 2}{sup J={sup 1}}=(2.76{+-}0.73{+-}0.23)x10{sup -2}, which agree well with theoretical expectations for a vanishing anomalous magnetic moment of the charm quark. For J{sub {chi}}=2, if we fix the electric octupole (E3) amplitudes to zero as theory predicts for transitions between charmonium S states and P states, we find a{sub 2}{sup J={sup 2}}=(-9.3{+-}1.6{+-}0.3)x10{sup -2} and b{sub 2}{sup J={sup 2}}=(1.0{+-}1.3{+-}0.3)x10{sup -2}. If we allow for E3 amplitudes we find, with a four-parameter fit, a{sub 2}{sup J={sup 2}}=(-7.9{+-}1.9{+-}0.3)x10{sup -2}, b{sub 2}{sup J={sup 2}}=(0.2{+-}1.4{+-}0.4)x10{sup -2}, a{sub 3}{sup J={sup 2}}=(1.7{+-}1.4{+-}0.3)x10{sup -2}, and b{sub 3}{sup J={sup 2}}=(-0.8{+-}1.2{+-}0.2)x10{sup -2}. We determine the ratios a{sub 2}{sup J={sup 1}}/a{sub 2}{sup J={sup 2}}=0.67{sub -0.13}{sup +0.19} and a{sub 2}{sup J={sup 1}}/b{sub 2}{sup J={sup 1}}=-2.27{sub -0.99}{sup +0.57}, where the theoretical predictions are independent of the charmed quark magnetic moment and are a{sub 2}{sup J={sup 1}}/a{sub 2}{sup J={sup 2}}=0.676{+-}0.071 and a{sub 2}{sup J={sup 1}}/b{sub 2}{sup

Phase relations in the system In{sub 2}O{sub 3}-TiO{sub 2}-Fe{sub 2}O{sub 3} at 1100 C in air

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, F.; Flores, M.J.R.; Kimizuka, N.

1999-04-01

Phase relations in the system In{sub 2}O{sub 3}-TiO{sub 2}-Fe{sub 2}O{sub 3} at 1100 C in air are determined by means of a classic quenching method. There exist In{sub 2}TiO{sub 5}, Fe{sub 2}TiO{sub 5} having a pseudo-Brookite-type phase and a new phase, In{sub 3}Ti{sub 2}FeO{sub 10} having a solid solution range from In{sub 2}O{sub 3}:TiO{sub 2}:Fe{sub 2}O{sub 3} = 4:6:1 to In{sub 2}O{sub 3}:TiO{sub 2}:Fe{sub 2}O{sub 3} = 0.384:0.464:0.152 (mole ratio) on the line InFeO{sub 3}-In{sub 2}Ti{sub 2}O{sub 7}. The crystal structures of In{sub 3}Ti{sub 2}FeO{sub 10} are pyrochlore related with a{sub m} = 5.9171 (5) {angstrom}, b{sub m} = 3.3696more » (3) {angstrom}, c{sub m} = 6.3885 (6) {angstrom}, and {beta} = 108.02 (1){degree} in a monoclinic crystal system at 1100 C, and a{sub 0} = 5.9089 (5) {angstrom}, b{sub 0} = 3.3679 (3) {angstrom}, and c{sub 0} = 12.130 (1) {angstrom} in an orthorhombic system at 1200 C. The relationship between the lattice constants of these phases and those of the cubic pyrochlore type are approximately as follows: a{sub m} = {minus}{1/4}a{sub p} + ({minus}{1/2})b{sub p} + ({minus}{1/4})c{sub p}, b{sub m} = {minus}{1/4}a{sub p} + (0)b{sub p} + ({1/4})c{sub p}, c{sub m} = {1/4}a{sub p} + ({minus}{1/2})b{sub p} + ({1/4})c{sub p} and {beta} = 109.47{degree} in the monoclinic system, and a{sub 0} = {minus}{1/4}a{sub p} + ({minus}{1/2})b{sub p} + ({minus}{1/4})c{sub p}, b{sub 0} = {minus}{1/4}a{sub p} + (0)b{sub p} + ({1/4})c{sub p}, and c{sub 0} = 2/3a{sub p} + ({minus}2/3)b{sub p} + (2/3)c{sub p} in the orthorhombic system, where a{sub p} = b{sub p} = c{sub p} = 9.90 ({angstrom}) are the lattice constants of In{sub 2}Ti{sub 2}O{sub 7} having the cubic pyrochlore type. All solid solutions of In{sub 3}Ti{sub 2}FeO{sub 10} have incommensurate structures with a periodicity of q {times} b{sup *} (q = 0.281--0.356) along the b{sup *} axis and the stoichiometric phase has q = 1/3. In FeO{sub 3} having a layered structure type is unstable between 750

ADP-ribosylation by cholera toxin: functional analysis of a cellular system that stimulates the enzymic activity of cholera toxin fragment A/sub 1/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gill, D.M.; Coburn, J.

1987-10-06

The authors have clarified relationships between cholera toxin, cholera toxin substrates, a membrane protein S that is required for toxin activity, and a soluble protein CF that is needed for the function of S. The toxin has little intrinsic ability to catalyze ADP-ribosylations unless it encounters the active form of the S protein, which is S liganded to GTP or to a GTP analogue. In the presence of CF, S x GTP forms readily, though reversibly, but a more permanent active species, S-guanosine 5'-O-(3-thiotriphosphate) (S x GTP..gamma..S), forms over a period of 10-15 min at 37/sup 0/C. Both guanosine 5'-O-(2-thiodiphosphate)more » and GTP block this quasi-permanent activation. Some S x GTP..gamma..S forms in membranes that are exposed to CF alone and then to GTP..gamma..S, with a wash in between, and it is possible that CF facilitates a G nucleotide exchange. S x GTP..gamma..S dissolved by nonionic detergents persists in solution and can be used to support the ADP-ribosylation of nucleotide-free substrates. In this circumstance, added guanyl nucleotides have no further effect. This active form of S is unstable, especially when heated, but the thermal inactivation above 45/sup 0/C is decreased by GTP..gamma..S. Active S is required equally for the ADP-ribosylation of all of cholera toxin's protein substrates, regardless of whether they bind GTP or not. They suggest that active S interacts directly with the enzymic A/sub 1/ fragments of cholera toxin and not with any toxin substrate. The activation and activity of S are independent of the state, or even the presence, of adenylate cyclase and seem to be involved with the cyclase system only via cholera toxin. S is apparently not related by function to certain other GTP binding proteins, including p21/sup ras/, and appears to be a new GTP binding protein whose physiologic role remains to be identified.« less

A Novel Method for Producing Transgenic Enzymes and Peptides

DTIC Science & Technology

2004-03-04

eutropha”. Biotechnol. Bioeng. 84(1): 114-120. Wieczorek, R., A. Steinbuchel, et al. (1996). “Occurrence of polyhydroxyalkanoic acid granule... polyhydroxyalkanoate (PHA), a biodegradable polymer, by ICI/Zeneca and later Monsanto. The genome has been sequenced (http://jgi.doe * Corresponding

Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Tremblay, Julien

2018-01-22

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lukjancenko, Oksana

2012-06-01

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tremblay, Julien

2012-06-01

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Lukjancenko, Oksana

2018-01-10

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

DUST IN ACTIVE GALACTIC NUCLEI: ANOMALOUS SILICATE TO OPTICAL EXTINCTION RATIOS?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyu, Jianwei; Hao, Lei; Li, Aigen, E-mail: haol@shao.ac.cn

Dust plays a central role in the unification theory of active galactic nuclei (AGNs). However, little is known about the nature (e.g., size, composition) of the dust that forms a torus around the AGN. In this Letter, we report a systematic exploration of the optical extinction (A{sub V} ) and the silicate absorption optical depth (Δτ{sub 9.7}) of 110 type 2 AGNs. We derive A{sub V} from the Balmer decrement based on the Sloan Digital Sky Survey data, and Δτ{sub 9.7} from the Spitzer/InfraRed Spectrograph data. We find that with a mean ratio of (A{sub V} /Δτ{sub 9.7}) ≲ 5.5, themore » optical-to-silicate extinction ratios of these AGNs are substantially lower than that of the Galactic diffuse interstellar medium (ISM) for which A{sub V} /Δτ{sub 9.7} ≈ 18.5. We argue that the anomalously low A{sub V} /Δτ{sub 9.7} ratio could be due to the predominance of larger grains in the AGN torus compared to that in the Galactic diffuse ISM.« less

Comment on twinning in YNbO sub 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsunekawa, S.

1992-04-01

The paper contains statements about an analogue of ZrO{sub 2} and the twins. The analogue is suggestive in connection with yttria-partially-stabilized zirconia, but an error is found in the description of the twins in YNbO{sub 4}. Because YNbO{sub 4} performs a pure, uncoupled ferroelastic transition (thermoelastic martensitic transformation), the composition plane is determined by the following formulas 4/mF2/m: x = pz and x = {minus}z/p, p = (b + (a{sup 2} + b{sup 2}){sup 1/2})/a a = (x{sub 33} {minus} x{sub 11})/2, b = {minus} tan ({beta} {minus} 90{degrees})/2) x{sub 11} = (a{sup I} {minus} a{sub 0})/a{sub 0}, x{sub 33}more » = (c{sup 1} {minus} a{sub 0})/a{sub 0} where a{sub 0} is the lattice parameter of a in the tetragonal phase, and a{sup I} and c{sup I} are the parameters of a and c, respectively, in the monoclinic phase represented by the I-lattice. The value of p at room temperature can be estimated by using the parameters included in this paper.« less

Comparative study of the scalar- and tensor-meson production in the reaction γγ{sup *} (Q{sup 2})→ ηπ{sup 0}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Achasov, N. N., E-mail: achasov@math.nsc.ru; Kiselev, A. V., E-mail: kiselev@math.nsc.ru; Shestakov, G. N., E-mail: shestako@math.nsc.ru

2016-05-15

The cross section for the reaction γγ{sup *} (Q{sup 2})→ ηπ{sup 0} was predicted on the basis of a simultaneous analysis of data from the Belle detector (Japan) on the reaction γγ → ηπ{sup 0} and data the KLOE detector (Italy) on the decay process ϕ → ηπ{sup 0}γ. The production of a{sub 0}(980) scalar and a{sub 2}(1320) tensor mesons was studied in detail. It is shown that the QCD-predicted asymptotic behavior of the cross section for the process γ{sup *}(Q{sup 2})γ → a{sub 2}(1320) → ηπ{sup 0} can be reproduced only upon taking into account the compensation of themore » contributions of ρ(770) and ω(782) mesons in the leading order by the contributions of their radial excitations in the Q{sup 2} channel. It is expected that, at large Q{sup 2}, the cross section is dominated by the a{sub 2}(1320) contribution, but that, at Q{sup 2} = 0, the a{sub 2}(1320) contribution is commensurate with the scalarmeson contribution.« less

ESR spectra of NSO/sub 4//sup 2 -/ in (NH/sub 4/)/sub 2/SO/sub 4/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bailey, C.E.

1981-03-01

The slow decay of NH/sub 3//sup +/ and NH/sub 2//sup +/ centers in ammonium sulfate produce a new, very stable, paramagnetic center that has been identified as NSO/sub 4//sup 2 -/. This center has g values of g/sub x/ = 2.012, g/sub y/ = 2.011, and g/sub z/ = 2.007 with the corresponding hfi constants A/sub x/ = A/sub y/ = 0.0 and A/sub z/ = 25.2 G. No change in this center is observed on passage of the crystal through the ferroelectric phase transition.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daum, Chris

Chris Daum of the DOE Joint Genome Institute discusses how the DOE JGI's Production Sequencing group optimizes the sequencer pipelines and assesses quality on the Production line on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

New Technology Drafts: Production and Improvements

ScienceCinema

Lapidus, Alla

2018-01-22

Alla Lapidus, head of the DOE Joint Genome Institute's Finishing group, gives a talk on how the DOE JGI's microbial genome sequencing pipeline has been adapted to accommodate next generation sequencing platforms at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, S.H.; Song, B.

The reoxidation behavior of steels by slag in the secondary steelmaking process was addressed by investigating the thermodynamic equilibria between the liquid iron containing Mn and P and CaO-MgO-SiO{sub 2}-Al{sub 2}O{sub 3}-P{sub 2}O{sub 5}-MnO-Fe{sub t}O ladle slag at 1873 K. The activity coefficient of Fe{sub t}O shows a maximum value in the vicinity of the basicity ((X{sub CaO} + X{sub MgO} + X{sub MnO})/(X{sub SiO{sub 2}} + X{sub Al{sub 2}O{sub 3}} + XP{sub 2}O{sub 5})) = 2.5 at the specific mole fraction range of Fe{sub t}O, while that of MnO seems to increase gradually with increasing the basicity. However, themore » values of {gamma}{sub Fe{sub t}O} and {gamma}{sub MnO} showed minima with respect to P{sub 2}O{sub 5} content of slag. In addition, the values of {gamma}{sub Fe{sub t}O} and {gamma}{sub MnO} increased as (pct CaO)/(pct Al{sub 2}O{sub 3}) ratio increased at given SiO{sub 2}, MgO, and P{sub 2}O{sub 5} contents. The conversion equations between the Fe{sub t}O and MnO activities and their calculated activities via regular solution model were derived by the correlation between the measured and calculated activities over the limited ranges of Fe{sub t}O and MnO contents. The regular solution model was used to estimate the oxygen potential in the slag. For MgO saturated slags, a{sub Fe{sub t}O{sub (l)}} = 0.864a{sub FeO{sub (R.S.)}}, a{sub MnO{sub (l)}} = 6.38a{sub MnO{sub (R.S.)}}. For Al{sub 2}O{sub 3} saturated slags, a{sub Fe{sub t}O{sub (l)}} = 2.086a{sub FeO{sub (R.S.)}}, a{sub MnO{sub (l)}} = 14.39a{sub MnO{sub (R.S.)}}.« less

Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Ze

2012-06-01

Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Peng, Ze

2018-01-24

Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

MycoCosm, an Integrated Fungal Genomics Resource

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shabalov, Igor; Grigoriev, Igor

2012-03-16

MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/monthmore » or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.« less

One-side forward-backward asymmetry at the LHC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang Youkai; Xiao Bo; Zhu Shouhua

2011-01-01

Forward-backward asymmetry A{sub FB} is an essential observable to study the nature of coupling in the standard model and physics beyond the standard model, as shown at LEP and Tevatron. As a proton-proton collider, the LHC does not have the preferred direction contrary to her counterparts, namely, LEP and Tevatron. Therefore, A{sub FB} is not applicable at the LHC. However, for the proton the momentum of the valence quark is usually larger than that of the sea quark. Utilizing this feature we have defined a so-called one-side forward-backward asymmetry A{sub OFB} for the top quark pair production at the LHCmore » in the previous work. In this paper we extend our studies to the charged leptons and bottom quarks as the final states. Our numerical results show that at the LHC A{sub OFB} can be utilized to study the nature of the couplings once enough events are collected.« less

Ab-initio calculations on melting of thorium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukherjee, D., E-mail: debojyoti@barc.gov.in; Sahoo, B. D.; Joshi, K. D.

2016-05-23

Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a{sub 0}){sup 3} and (1.02a{sub 0}){sup 3} and (1.04a{sub 0}){sup 3} increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a{sub 0} = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures asmore » melting point. The melting point of 2100 K is close to the experimental value of 2023 K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.« less

Phase formation in the (1-y)BiFeO{sub 3}-yBiScO{sub 3} system under ambient and high pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salak, A.N., E-mail: salak@ua.pt; Khalyavin, D.D., E-mail: dmitry.khalyavin@stfc.ac.uk; Pushkarev, A.V.

Formation and thermal stability of perovskite phases in the BiFe{sub 1-y}Sc{sub y}O{sub 3} system (0≤y≤0.70) were studied. When the iron-to-scandium substitution rate does not exceed about 15 at%, the single-phase perovskite ceramics with the rhombohedral R3c symmetry (as that of the parent compound, BiFeO{sub 3}) can be prepared from the stoichiometric mixture of the respective oxides at ambient pressure. Thermal treatment of the oxide mixtures with a higher content of scandium results in formation of two main phases, namely a BiFeO{sub 3}-like R3c phase and a cubic (I23) sillenite-type phase based on γ-Bi{sub 2}O{sub 3}. Single-phase perovskite ceramics of themore » BiFe{sub 1-y}Sc{sub y}O{sub 3} composition were synthesized under high pressure from the thermally treated oxide mixtures. When y is between 0 and 0.25 the high-pressure prepared phase is the rhombohedral R3c with the √2a{sub p}×√2a{sub p}×2√3a{sub p} superstructure (a{sub p} ~ 4 Å is the pseudocubic perovskite unit-cell parameter). The orthorhombic Pnma phase (√2a{sub p}×4a{sub p}×2√2a{sub p}) was obtained in the range of 0.30≤y≤0.60, while the monoclinic C2/c phase (√6a{sub p}×√2a{sub p}×√6a{sub p}) is formed when y=0.70. The normalized unit-cell volume drops at the crossover from the rhombohedral to the orthorhombic composition range. The perovskite BiFe{sub 1-y}Sc{sub y}O{sub 3} phases prepared under high pressure are metastable regardless of their symmetry. At ambient pressure, the phases with the compositions in the ranges of 0.20≤y≤0.25, 0.30≤y<0.50 and 0.50≤y≤0.70 start to decompose above 970, 920 and 870 K, respectively. - Graphical abstract: Formation of perovskite phases in the BiFe{sub 1-y}Sc{sub y}O{sub 3} system when y≥0.15 requires application of pressure of several GPa. The phases formed under high pressure: R3c (0.20≤y≤0.25), Pnma (0.30≤y≤0.60) and C2/c (y≥0.70) are metastable. - Highlights: • Maximal Fe-to-Sc substitution rate

A{sub 5}RE{sub 4}X[TO{sub 4}]{sub 4} crystal growth: Fluoride flux synthesis of Na{sub 5}Ln{sub 4}F[GeO{sub 4}]{sub 4} (Ln=Pr, Nd), the first quaternary germanate oxyfluorides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Latshaw, Allison M.; Wilkins, Branford O.; Morrison, Gregory

Crystals of Na{sub 5}Pr{sub 4}F[GeO{sub 4}]{sub 4} and Na{sub 5}Nd{sub 4}F[GeO{sub 4}]{sub 4} were synthesized using a eutectic sodium fluoride, sodium chloride flux. Both compounds crystallize in the tetragonal space group I-4 with lattice parameters of a=12.1173(4) Å and c=5.6795(2) Å (Pr) and of a=12.0642(17) Å and c=5.6674(11) Å (Nd). The structure of the reported compounds is three-dimensional with face and corner sharing lanthanide polyhedra which edge and corner share with isolated germanium tetrahedra. These novel compositions represent the first example of quaternary germanium containing oxyfluorides. - Graphical abstract: Structural image of the first examples of quaternary germanate oxyfluorides. Displaymore » Omitted - Highlights: • Molten flux growth of crystals of two lanthanide germanate oxyfluorides. • Expansion of the A{sub 5}RE{sub 4}X[TO{sub 4}]{sub 4} family into germanate oxyfluorides. • Synthesis of Na{sub 5}Nd{sub 4}F[GeO{sub 4}]{sub 4} and Na{sub 5}Pr{sub 4}F[GeO{sub 4}]{sub 4}.« less

Relativistic tidal properties of neutron stars

DOE Office of Scientific and Technical Information (OSTI.GOV)

Damour, Thibault; Nagar, Alessandro; ICRANet, 65122 Pescara

We study the various linear responses of neutron stars to external relativistic tidal fields. We focus on three different tidal responses, associated to three different tidal coefficients: (i) a gravito-electric-type coefficient G{mu}{sub l}=[length]{sup 2l+1} measuring the lth-order mass multipolar moment GM{sub a{sub 1}}{sub ...a{sub I}} induced in a star by an external lth-order gravito-electric tidal field G{sub a{sub 1}}{sub ...a{sub I}}; (ii) a gravito-magnetic-type coefficient G{sigma}{sub l}=[length]{sup 2l+1} measuring the lth spin multipole moment GS{sub a{sub 1}}{sub ...a{sub I}} induced in a star by an external lth-order gravito-magnetic tidal field H{sub a{sub 1}}{sub ...a{sub I}}; and (iii) a dimensionless 'shape'more » Love number h{sub l} measuring the distortion of the shape of the surface of a star by an external lth-order gravito-electric tidal field. All the dimensionless tidal coefficients G{mu}{sub l}/R{sup 2l+1}, G{sigma}{sub l}/R{sup 2l+1}, and h{sub l} (where R is the radius of the star) are found to have a strong sensitivity to the value of the star's 'compactness'c{identical_to}GM/(c{sub 0}{sup 2}R) (where we indicate by c{sub 0} the speed of light). In particular, G{mu}{sub l}/R{sup 2l+1}{approx}k{sub l} is found to strongly decrease, as c increases, down to a zero value as c is formally extended to the 'black hole (BH) limit'c{sup BH}=1/2. The shape Love number h{sub l} is also found to significantly decrease as c increases, though it does not vanish in the formal limit c{yields}c{sup BH}, but is rather found to agree with the recently determined shape Love numbers of black holes. The formal vanishing of {mu}{sub l} and {sigma}{sub l} as c{yields}c{sup BH} is a consequence of the no-hair properties of black holes. This vanishing suggests, but in no way proves, that the effective action describing the gravitational interactions of black holes may not need to be augmented by nonminimal worldline couplings.« less

Baecklund transformations of Toda chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andreev, V.A.

Baecklund transformations of the nonperiodic Toda chains corresponding to the algebras A/sub n/, B/sub n/, C/sub n/, G/sub 2/ and the periodic Toda chains corresponding to the algebras A/sub n/ and C/sub n/ are constructed. Baecklund transformations of matrix Toda chains are also considered.

An Empirical Expression for the Line Widths of Ammonia

NASA Technical Reports Server (NTRS)

Brown, Linda R.; Peterson, Dean B.

1994-01-01

The hydrogen-broadened line widths of 116 (sup 14)NH(sub 3) ground state transitions have been measured at 0.006 cm(sup -1) resolution using a Bruker spectrometer in the 24 to 210 cm(sup -1) region. The rotational variation of the experimental widths with J(sup '),K(sup ') = 1,0 to 10,10 has been reproduced to 2.4 % using an heuristically derived expression of the form

gamma = a(sub 0) + a(sub 1) J(sup ') + a (sub 2) K(sup ') + a(sub 3) J(sup ')(sup 2) + a(sub 4) J(sup ') K(sup ')

where J(sup ') and K(sup ') are the lower state symmetric top quantum numbers. This function has also been applied to the measured widths of the 58 transitions of nu(sub 1) at 3 (micro)m, each broadened by N(sub 2), O(sub 2), Ar, H(sub 2), and He. The rms of the observed minus calculated widths are 5% or better for the five foreign broadeners. The values of the fitted constants suggest that for some broadeners the expression might also be written as

gamma = a(sub 0) + b(sub 1) J(sup ') + b(sub 2)(J(sup ' )- K(sup ')) + b(sub 3) J(sup ')(J(sup ') - K(sup '))

.

Bellingshausen Sea Ice Extent Recorded in an Antarctic Peninsula Ice Core

NASA Technical Reports Server (NTRS)

Porter, Stacy E.; Parkinson, Claire L.; Mosley-Thompson, Ellen

2016-01-01

Annual net accumulation (A(sub n)) from the Bruce Plateau (BP) ice core retrieved from the Antarctic Peninsula exhibits a notable relationship with sea ice extent (SIE) in the Bellingshausen Sea. Over the satellite era, both BP A(sub n) and Bellingshausen SIE are influenced by large-scale climatic factors such as the Amundsen Sea Low, Southern Annular Mode, and Southern Oscillation. In addition to the direct response of BP A(sub n) to Bellingshausen SIE (e.g., more open water as a moisture source), these large-scale climate phenomena also link the BP and the Bellingshausen Sea indirectly such that they exhibit similar responses (e.g., northerly wind anomalies advect warm, moist air to the Antarctic Peninsula and neighboring Bellingshausen Sea, which reduces SIE and increases A(sub n)). Comparison with a time series of fast ice at South Orkney Islands reveals a relationship between BP A(sub n) and sea ice in the northern Weddell Sea that is relatively consistent over the twentieth century, except when it is modulated by atmospheric wave patterns described by the Trans-Polar Index. The trend of increasing accumulation on the Bruce Plateau since approximately 1970 agrees with other climate records and reconstructions in the region and suggests that the current rate of sea ice loss in the Bellingshausen Sea is unrivaled in the twentieth century.

Rare earth zirconium oxide buffer layers on metal substrates

DOEpatents

Williams, Robert K.; Paranthaman, Mariappan; Chirayil, Thomas G.; Lee, Dominic F.; Goyal, Amit; Feenstra, Roeland

2001-01-01

A laminate article comprises a substrate and a biaxially textured (RE.sub.x A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer over the substrate, wherein 0A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer can be deposited using sol-gel or metal-organic decomposition. The laminate article can include a layer of YBCO over the (RE.sub.x A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer. A layer of CeO.sub.2 between the YBCO layer and the (RE.sub.x A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer can also be include. Further included can be a layer of YSZ between the CeO.sub.2 layer and the (RE.sub.x A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer. The substrate can be a biaxially textured metal, such as nickel. A method of forming the laminate article is also disclosed.

Rate of intramolecular reduction of oxyferryl iron in horse heart myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fenwick, C.; Marmor, S.; Govindaraju, K.

1994-04-06

Like heme peroxidases and other heme enzymes, myoglobin forms oxyferryl (Fe[sup IV][triple bond]O) on reaction with peroxides. We have recently observed slow intramolecular electron transfer (ET) to the oxyferryl heme of cytochrome c peroxidase (CCP) from a[sub 5]Ru[sup II] (a[sub 5]Ru = pentaammineruthenium) bound at His60 and proposed a large reorganizational energy ([lambda]) for oxyferryl heme. An obvious test of this large postulated [lambda] is to directly compare intramolecular ET rates between oxyferryl and a[sub 5]Ru centers in myoglobin with the corresponding rates in zinc-substituted sperm whale (SWMb) and recombinant human myoglobins (RHMb). Since the oxyferryl heme of horse heartmore » myoglobin (HHMb) is significantly more stable than that of SWMb, the former protein was chosen for this study. A a[sub 5]Ru group was attached to the surface His48 of HHMb, and rates of ET over the 12.7-angstrom distance between the a[sub 5]Ru center and the ferric and oxyferryl hemes were measured by pulse radiolysis at Brookhaven National Laboratory. HHMb (0.5-10 [mu]M) solutions were prepared in N[sub 2]O-saturated sodium phosphate buffer at pH 7.0 (40 mM) containing 12 mM HCOONa to generate CO[sub 2][sup .[minus

Laminate article

DOEpatents

Williams, Robert K.; Paranthaman, Mariappan; Chirayil, Thomas G.; Lee, Dominic F.; Goyal, Amit; Feenstra, Roeland

2002-01-01

A laminate article comprises a substrate and a biaxially textured (RE.sub.x A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer over the substrate, wherein 0A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer can be deposited using sol-gel or metal-organic decomposition. The laminate article can include a layer of YBCO over the (RE.sub.x A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer. A layer of CeO.sub.2 between the YBCO layer and the (RE.sub.x A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer can also be include. Further included can be a layer of YSZ between the CeO.sub.2 layer and the (RE.sub.x A.sub.(1-x)).sub.2 O.sub.2-(x/2) buffer layer. The substrate can be a biaxially textured metal, such as nickel. A method of forming the laminate article is also disclosed.

On the formulation of D=11 supergravity and the composite nature of its three-form gauge field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bandos, Igor A.; Institute for Theoretical Physics, NSC 'Kharkov Institute of Physics and Technology', UA61108, Kharkov; Azcarraga, Jose A. de

2005-05-01

The underlying gauge group structure of the D=11 Cremmer-Julia-Scherk supergravity becomes manifest when its three-form field A{sub 3} is expressed through a set of one-form gauge fields, B1a1a2, B1a1...a5, {eta}{sub 1{alpha}}, and E{sup a}, {psi}{sup {alpha}}. These are associated with the generators of the elements of a family of enlarged supersymmetry algebras E-bar (528 vertical bar 32+32)(s) parametrized by a real number s. We study in detail the composite structure of A{sub 3} extending previous results by D'Auria and Fre, stress the equivalence of the above problem to the trivialization of a standard supersymmetry algebra E(11 vertical bar 32) cohomologymore » four-cocycle on the enlarged E-bar (528 vertical bar 32+32)(s) superalgebras, and discuss its possible dynamical consequences. To this aim we consider the properties of the first order supergravity action with a composite A{sub 3} field and find the set of extra gauge symmetries that guarantee that the field theoretical degrees of freedom of the theory remain the same as with a fundamental A{sub 3}. The extra gauge symmetries are also present in the so-called rheonomic treatment of the first order D=11 supergravity action when A{sub 3} is composite. Our considerations on the composite structure of A{sub 3} provide one more application of the idea that there exists an extended superspace coordinates/fields correspondence. They also suggest that there is a possible embedding of D=11 supergravity into a theory defined on the enlarged superspace {sigma}-bar (528 vertical bar 32+32)(s)« less

The relationship between IR, optical, and UV extinction

NASA Technical Reports Server (NTRS)

Cardelli, Jason A.; Clayton, Geoffrey C.; Mathis, John S.

1989-01-01

An analysis is presented for the variability of absolute IR, optical, and UV extinction, A(sub lambda), derived through the ratio of total-to-selective extinction, R, for 31 lines of sight for which reliable UV extinction parameters were derived. These data sample a wide range of environments and are characterized by 2.5 is less than or equal to R is less than or equal to 6.0. It was found that there is a strong linear dependence between extinction expressed as A(sub lambda)/A(sub V) and 1/R for 1.25 micron is less than or equal to lambda is less than or equal to 0.12 micron. Differences in the general shape of extinction curves are largely due to variations in shape of optical/near-UV extinction corresponding to changes in R, with A(sub lambda)/A(sub V) decreasing for increasing R. From a least-squares fit of the observed R-dependence as a function of wavelength for 0.8/micron is less than or greater than 1/lambda is less than or equal to 8.3/micron, an analytic expression was generated from which IR, optical, and UV extinction curves of the form A(sub lambda)/A(sub V) can be reproduced with reasonable accuracy from a knowledge of R. It was also found that the absolute bump strength normalized to A(sub V) shows a general decrease with increasing R, suggesting that some fraction of bump grains may be selectively incorporated into coagulated grains. Finally, it was found that absolute extinction normalized by suitably chosen color indices results in a minimization of the R-dependence of portions of the UV curve, allowing A(sub lambda) to be estimated for these wavelengths independent of R.

JGI's Carbon Cycling Studies on Restored Marshes

ScienceCinema

Tringe, Susannah; Theroux, Susanna

2018-02-14

DOE Joint Genome Institute Metagenome Program Head, Susannah Tringe, and postdoc, Susie Theroux, discuss the lessons to be learned from studying the microbial diversity of marshes that have been converted to other uses, and are now being restored, as well as the potential impacts on the global carbon cycle.

Generation of 2N + 1-scroll existence in new three-dimensional chaos systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yue; Guan, Jian; Ma, Chunyang

2016-08-15

We propose a systematic methodology for creating 2N + 1-scroll chaotic attractors from a simple three-dimensional system, which is named as the translation chaotic system. It satisfies the condition a{sub 12}a{sub 21} = 0, while the Chua system satisfies a{sub 12}a{sub 21} > 0. In this paper, we also propose a successful (an effective) design and an analytical approach for constructing 2N + 1-scrolls, the translation transformation principle. Also, the dynamics properties of the system are studied in detail. MATLAB simulation results show very sophisticated dynamical behaviors and unique chaotic behaviors of the system. It provides a new approach for 2N + 1-scroll attractors. Finally, to explore the potential usemore » in technological applications, a novel block circuit diagram is also designed for the hardware implementation of 1-, 3-, 5-, and 7-scroll attractors via switching the switches. Translation chaotic system has the merit of convenience and high sensitivity to initial values, emerging potentials in future engineering chaos design.« less

Effects of trace elements on the crystal field parameters of Nd ions at the surface of Nd{sub 2}Fe{sub 14}B grains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toga, Yuta; Suzuki, Tsuneaki; Sakuma, Akimasa, E-mail: sakuma@solid.apph.tohoku.ac.jp

2015-06-14

Using first-principles calculations, we investigate the positional dependence of trace elements such as O and Cu on the crystal field parameter A{sub 2}{sup 0}, proportional to the magnetic anisotropy constant K{sub u} of Nd ions placed at the surface of Nd{sub 2}Fe{sub 14}B grains. The results suggest the possibility that the A{sub 2}{sup 0} parameter of Nd ions at the (001) surface of Nd{sub 2}Fe{sub 14}B grains exhibits a negative value when the O or Cu atom is located near the surface, closer than its equilibrium position. At the (110) surface, however, O atoms located at the equilibrium position providemore » a negative A{sub 2}{sup 0}, while for Cu additions A{sub 2}{sup 0} remains positive regardless of Cu's position. Thus, Cu atoms are expected to maintain a positive local K{sub u} of surface Nd ions more frequently than O atoms when they approach the grain surfaces in the Nd-Fe-B grains.« less

Coherent states on the m-sheeted complex plane as m-photon states

NASA Technical Reports Server (NTRS)

Vourdas, Apostolos

1994-01-01

Coherent states on the m-sheeted complex plane are introduced and properties like overcompleteness and resolution of the identity are studied. They are eigenstates of the operators a(sub m)(+), a(sub m) which create and annihilate clusters of m-particles. Applications of this formalism in the study of Hamiltonians that describe m-particle clustering are also considered.

Measurements of Band Intensities, Herman-Wallis Parameters, and Self-Broadening Line-Widths of the 30011 - 00001 and 30014 - 00001 Bands of CO2 at 6503 cm(exp -1) and 6076 cm(exp -1)

NASA Technical Reports Server (NTRS)

Giver, L. P.; Brown, L. R.; Wattson, R. B.; Spencer, M. N.; Chackerian, C., Jr.; Strawa, Anthony W. (Technical Monitor)

1995-01-01

Rotationless band intensities and Herman-Wallis parameters are listed in HITRAN tabulations for several hundred CO2 overtone-combination bands. These parameters are based on laboratory measurements when available, and on DND calculations for the unmeasured bands. The DND calculations for the Fermi interacting nv(sub 1) + v(sub 3) polyads show the a(sub 2) Herman-Wallis parameter varying smoothly from a negative value for the first member of the polyad to a positive value for the final member. Measurements of the v(sub 1) + v(sub 3) dyad are consistent with the DND calculations for the a(sub 2) parameter, as are our recent measurements of the 4v(sub 1) + v(sub 3) pentad. However, the measurement-based values in the HITRAN tables for the 2v(sub 1) + v(sub 3) triad and the 3v(sub 1) + v(sub 3) tetrad do not support the DND calculated values for the a(sub 2) parameters. We therefore decided to make new measurements to improve some of these intensity parameters. With the McMath FTS at Kitt Peak National Observatory/National Solar Observatory we recorded several spectra of the. 4000 to 8000 cm(exp -1) region of pure CO2 at 0.011 cm(exp -1) resolution using the 6 meter White absorption cell. The signal/noise and absorbance of the first and fourth bands of the 3v(sub 1) + v(sub 3) tetrad of C-12O-16 were ideal on these spectra for measuring line intensities and broadening widths. Our selfbroadening results agree with the HITRAN parameterization, while our measurements of the rotationless band intensities are about 15% less than the HITRAN values. We find a negative value of a(sub 2) for the 30011-00001 band and a positive value for the 30014-00001 band, whereas the HITRAN values of a(sub 2) are positive for all four tetrad bands. Our a(sub 1) and a(sub 2) Herman-Wallis parameters are closer to DND calculated values than the 1992 HITRAN values for both the 30011-00001 and the 30014-00001 band.

Parameterizing Grid-Averaged Longwave Fluxes for Inhomogeneous Marine Boundary Layer Clouds

NASA Technical Reports Server (NTRS)

Barker, Howard W.; Wielicki, Bruce A.

1997-01-01

This paper examines the relative impacts on grid-averaged longwave flux transmittance (emittance) for Marine Boundary Layer (MBL) cloud fields arising from horizontal variability of optical depth tau and cloud sides, First, using fields of Landsat-inferred tau and a Monte Carlo photon transport algorithm, it is demonstrated that mean all-sky transmittances for 3D variable MBL clouds can be computed accurately by the conventional method of linearly weighting clear and cloudy transmittances by their respective sky fractions. Then, the approximations of decoupling cloud and radiative properties and assuming independent columns are shown to be adequate for computation of mean flux transmittance. Since real clouds have nonzero geometric thicknesses, cloud fractions A'(sub c) presented to isotropic beams usually exceed the more familiar vertically projected cloud fractions A(sub c). It is shown, however, that when A(sub c)less than or equal to 0.9, biases for all-sky transmittance stemming from use of A(sub c) as opposed to A'(sub c) are roughly 2-5 times smaller than, and opposite in sign to, biases due to neglect of horizontal variability of tau. By neglecting variable tau, all-sky transmittances are underestimated often by more than 0.1 for A(sub c) near 0.75 and this translates into relative errors that can exceed 40% (corresponding errors for all-sky emittance are about 20% for most values of A(sub c). Thus, priority should be given to development of General Circulation Model (GCM) parameterizations that account for the effects of horizontal variations in unresolved tau, effects of cloud sides are of secondary importance. On this note, an efficient stochastic model for computing grid-averaged cloudy-sky flux transmittances is furnished that assumes that distributions of tau, for regions comparable in size to GCM grid cells, can be described adequately by gamma distribution functions. While the plane-parallel, homogeneous model underestimates cloud transmittance by

Characterization of the patterns of polymorphism in a [open quotes]cryptic repeat[close quotes] reveals a novel type of hypervariable sequence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacobson, D.P.; Schmeling, P.; Sommer, S.S.

Alternating purine and pyrimidine repeats (RY(i)) are an abundant source of polymorphism. The subset with long tandem repeats of GT or AC (GT(i)) have been studied extensively, but cryptic RY(i) (i.e., no single tandem repeat predominates) have received little attention. The factor IX gene has a polymorphic cryptic RY(i) of 142-216 bp. Previously, there were four known polymorphic alleles, of the form AB, A[sub 2]B, A[sub 2]B[sub 2], and A[sub 3]B[sub 2], where A = (GT)(AC)[sub 3](AT)[sub 3](GT)(AT)[sub 4] and B = A with an additional 3' AT dinucleotide. To further characterize this locus, the authors examined more than 1,700more » additional human chromosomes and determined the sequences of the homologous sites in orangutans and chimpanzees. The novel alleles found in humans expand the repertoire of A/B alleles to A[sub 0-4]B[sub 1] and A[sub 1-3]B[sub 2]. The A[sub n]B[sub 2] series are abundant in Caucasians but are absent in blacks and Asians. Conversely, the A[sub 0]B[sub 1] allele is common in blacks but is not found in more than 1,700 Caucasian chromosomes. The data are compatible with a model in which recombination is more frequent than polymerase slippage at this locus. In orangutans, the RY(i) is present, but the sequence is markedly different. An A/B-type of pattern was discerned in which B differs from A by an additional six (AT) dinucleotides at the 3' end. In chimpanzees, the size of the RY(i) locus was greatly expanded, and the sequence showed a novel pattern of hypervariability in which there are many tandem repeats of the form (GT)[sub n](AC)[sub 0](AT)[sub p](GT)[sub q](AT)[sub s], where n, o, p, q, and s are different integers. The sequences of the factor IX intron 1 cryptic RY(i) in three primates provide perspective on the range of possible patterns of polymorphism. Analysis of the patterns suggests how the RY(i) can be conserved during evolution, while the precise sequence varies. 25 refs., 5 figs., 3 tabs.« less

Structural and dielectric properties of La and Ni-doped M-type BaFe{sub 12}O{sub 19} ceramics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, Poorva; Varshney, Dinesh, E-mail: vdinesh33@rediffmail.com, E-mail: dubea89@yahoo.com; Kumar, Ashwini

2016-05-23

BaFe{sub 12}O{sub 19} and Ba{sub 0.98}La{sub 0.02}Fe{sub 12-x}Ni{sub x}O{sub 19} (x = 0.02, 0.05) samples synthesized using solid-state reaction route crystallizes in hexagonal structure with space group P6{sub 3}/mmc as revealed from X-ray diffraction. A Raman spectrum shows seven strong and sharp modes at 291.9 (A{sub 1g}), 410.4 (E{sub 2g}), 496.09 (A{sub 1g}), 611.3 (E{sub 2g}), 681(A{sub 1g}), 1048.0 (A{sub 1g}+A{sub 1g}) and 1313.3 cm{sup −1} (A{sub 1g}+E{sub 2g}), identifying the presence of barium hexaferrite phase. The higher values of the dielectric constant at lower frequency and lower values at higher frequency indicate the dispersion due to interfacial polarization. Dielectricmore » constant decreases as the doping concentration of Ni increases due to increase in band gap. A resonance peak has been observed in all three sample and is attributed to the fact that hopping frequency of charge carrier matches well with the frequency of the applied field. Henceforth, Ba{sub 0.98}La{sub 0.02}Fe{sub 12-x}Ni{sub x}O{sub 19} (x = 0.02, 0.05) is suitable novel materials for microwave application with low dielectric constant and dielectric loss values.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oliva, R.; Ibanez, J.; Cusco, R.

We use Raman scattering to investigate the composition behavior of the E{sub 2h} and A{sub 1}(LO) phonons of In{sub x}Ga{sub 1-x}N and to evaluate the role of lateral compositional fluctuations and in-depth strain/composition gradients on the frequency of the A{sub 1}(LO) bands. For this purpose, we have performed visible and ultraviolet Raman measurements on a set of high-quality epilayers grown by molecular beam epitaxy with In contents over a wide composition range (0.25 < x < 0.75). While the as-measured A{sub 1}(LO) frequency values strongly deviate from the linear dispersion predicted by the modified random-element isodisplacement (MREI) model, we showmore » that the strain-corrected A{sub 1}(LO) frequencies are qualitatively in good agreement with the expected linear dependence. In contrast, we find that the strain-corrected E{sub 2h} frequencies exhibit a bowing in relation to the linear behavior predicted by the MREI model. Such bowing should be taken into account to evaluate the composition or the strain state of InGaN material from the E{sub 2h} peak frequencies. We show that in-depth strain/composition gradients and selective resonance excitation effects have a strong impact on the frequency of the A{sub 1}(LO) mode, making very difficult the use of this mode to evaluate the strain state or the composition of InGaN material.« less

Polyhedral realizations of crystal bases for quantum algebras of classical affine types

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoshino, A.

2013-05-15

We give the explicit forms of the crystal bases B({infinity}) for the quantum affine algebras of types A{sub 2n-1}{sup (2)}, A{sub 2n}{sup (2)}, B{sub n}{sup (1)}, C{sub n}{sup (1)}, D{sub n}{sup (1)}, and D{sub n+1}{sup (2)} by using the method of polyhedral realizations of crystal bases.

New color-octet axial vector boson revisited

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang Hao; Wang Youkai; Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190

2011-11-01

In this paper we reexamine how to utilize the previous proposed color-octet axial-vector boson Z{sub C} to explain the 3.4{sigma} anomaly of tt forward-backward (FB) asymmetry A{sub FB} for m{sub tt}>450 GeV observed by CDF. Our numerical results indicate that the best-fit parameters are g{sub A}{sup q}=0.07, g{sub A}{sup Q}=3, and M{sub C}=440 GeV, which are obtained by fitting the mass dependent A{sub FB} and total cross section data provided by a recent CDF measurement. Here g{sub A}{sup q}(g{sub A}{sup Q}) and M{sub C} are the axial couplings among Z{sub C} with the first two (the third) generation quarks, andmore » Z{sub C} mass, respectively. We also calculate one-side forward-backward asymmetry A{sub OFB} for top and bottom quark pair production at the LHC, focusing on the new contributions from Z{sub C}. Our studies show that A{sub OFB} can be utilized to measure the properties of new particle Z{sub C}.« less

Regarding the scalar mesons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu Yunhu; Shao Jianxin; Wang Xiaogang

Based on the main assumption that the D{sub sJ}(2860) belongs to the 2{sup 3}P{sub 0} qq multiplet, the masses of the scalar meson nonet are estimated in the framework of the relativistic independent quark model, Regge phenomenology, and meson-meson mixing. We suggest that the a{sub 0}(1005), K{sub 0}*(1062), f{sub 0}(1103), and f{sub 0}(564) constitute the ground scalar meson nonet; it is supposed that these states would likely correspond to the observed states a{sub 0}(980), {kappa}(900), f{sub 0}(980), and f{sub 0}(600)/{sigma}, respectively. Also a{sub 0}(1516), K{sub 0}*(1669), f{sub 0}(1788), and f{sub 0}(1284) constitute the first radial scalar meson nonet, it ismore » supposed that these states would likely correspond to the observed states a{sub 0}(1450), K{sub 0}*(1430), f{sub 0}(1710), and f{sub 0}(1370), respectively. The scalar state f{sub 0}(1500) may be a good candidate for the ground scalar glueball. The agreement between the present findings and those given by other different approaches is satisfactory.« less

Using Observations of Deep Convective Systems to Constrain Atmospheric Column Absorption of Solar Radiation in the Optically Thick Limit

NASA Technical Reports Server (NTRS)

Dong, Xiquan; Wielicki, Bruce A.; Xi, Baike; Hu, Yongxiang; Mace, Gerald G.; Benson, Sally; Rose, Fred; Kato, Seiji; Charlock, Thomas; Minnis, Patrick

2008-01-01

Atmospheric column absorption of solar radiation A(sub col) is a fundamental part of the Earth's energy cycle but is an extremely difficult quantity to measure directly. To investigate A(sub col), we have collocated satellite-surface observations for the optically thick Deep Convective Systems (DCS) at the Department of Energy Atmosphere Radiation Measurement (ARM) Tropical Western Pacific (TWP) and Southern Great Plains (SGP) sites during the period of March 2000 December 2004. The surface data were averaged over a 2-h interval centered at the time of the satellite overpass, and the satellite data were averaged within a 1 deg X 1 deg area centered on the ARM sites. In the DCS, cloud particle size is important for top-of-atmosphere (TOA) albedo and A(sub col) although the surface absorption is independent of cloud particle size. In this study, we find that the A(sub col) in the tropics is approximately 0.011 more than that in the middle latitudes. This difference, however, disappears, i.e., the A(sub col) values at both regions converge to the same value (approximately 0.27 of the total incoming solar radiation) in the optically thick limit (tau greater than 80). Comparing the observations with the NASA Langley modified Fu_Liou 2-stream radiative transfer model for optically thick cases, the difference between observed and model-calculated surface absorption, on average, is less than 0.01, but the model-calculated TOA albedo and A(sub col) differ by 0.01 to 0.04, depending primarily on the cloud particle size observation used. The model versus observation discrepancies found are smaller than many previous studies and are just within the estimated error bounds. We did not find evidence for a large cloud absorption anomaly for the optically thick limit of extensive ice cloud layers. A more modest cloud absorption difference of 0.01 to 0.04 cannot yet be ruled out. The remaining uncertainty could be reduced with additional cases, and by reducing the current

Solar Wind Helium Abundance as a Function of Speed and Heliographic Latitude: Variation through a Solar Cycle

NASA Technical Reports Server (NTRS)

Kasper, J. C.; Stenens, M. L.; Stevens, M. L.; Lazarus, A. J.; Steinberg, J. T.; Ogilvie, Keith W.

2006-01-01

We present a study of the variation of the relative abundance of helium to hydrogen in the solar wind as a function of solar wind speed and heliographic latitude over the previous solar cycle. The average values of A(sub He), the ratio of helium to hydrogen number densities, are calculated in 25 speed intervals over 27-day Carrington rotations using Faraday Cup observations from the Wind spacecraft between 1995 and 2005. The higher speed and time resolution of this study compared to an earlier work with the Wind observations has led to the discovery of three new aspects of A(sub He), modulation during solar minimum from mid-1995 to mid-1997. First, we find that for solar wind speeds between 350 and 415 km/s, A(sub He), varies with a clear six-month periodicity, with a minimum value at the heliographic equatorial plane and a typical gradient of 0.01 per degree in latitude. For the slow wind this is a 30% effect. We suggest that the latitudinal gradient may be due to an additional dependence of coronal proton flux on coronal field strength or the stability of coronal loops. Second, once the gradient is subtracted, we find that A(sub He), is a remarkably linear function of solar wind speed. Finally, we identify a vanishing speed, at which A(sub He), is zero, is 259 km/s and note that this speed corresponds to the minimum solar wind speed observed at one AU. The vanishing speed may be related to previous theoretical work in which enhancements of coronal helium lead to stagnation of the escaping proton flux. During solar maximum the A(sub He), dependences on speed and latitude disappear, and we interpret this as evidence of two source regions for slow solar wind in the ecliptic plane, one being the solar minimum streamer belt and the other likely being active regions.

A taxonomy of apatite frameworks for the crystal chemical design of fuel cell electrolytes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pramana, Stevin S.; Klooster, Wim T.; Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602

2008-08-15

Apatite framework taxonomy succinctly rationalises the crystallographic modifications of this structural family as a function of chemical composition. Taking the neutral apatite [La{sub 8}Sr{sub 2}][(GeO{sub 4}){sub 6}]O{sub 2} as a prototype electrolyte, this classification scheme correctly predicted that 'excess' oxygen in La{sub 9}SrGe{sub 6}O{sub 26.5} is tenanted in the framework as [La{sub 9}Sr][(GeO{sub 4}){sub 5.5}(GeO{sub 5}){sub 0.5}]O{sub 2}, rather than the presumptive tunnel location of [La{sub 9}Sr][(GeO{sub 4}){sub 6}]O{sub 2.5}. The implication of this approach is that in addition to the three known apatite genera-A{sub 10}(BO{sub 3}){sub 6}X{sub 2}, A{sub 10}(BO{sub 4}){sub 6}X{sub 2}, A{sub 10}(BO{sub 5}){sub 6}X{sub 2}-hybrid electrolytesmore » of the types A{sub 10}(BO{sub 3}/BO{sub 4}/BO{sub 5}){sub 6}X{sub 2} can be designed, with potentially superior low-temperature ion conduction, mediated by the introduction of oxygen to the framework reservoir. - Graphical abstract: Apatite framework taxonomy succinctly rationalises the crystallographic modifications of this structural family as a function of chemical composition. Neutron diffraction identified that the excess oxygen in La{sub 9}SrGe{sub 6}O{sub 26.5} is tenanted in the framework as [La{sub 9}Sr][(GeO{sub 4}){sub 5.5}(GeO{sub 5}){sub 0.5}]O{sub 2}. The implication of this approach is that in addition to the three known apatite genera-A{sub 10}(BO{sub 3}){sub 6}X{sub 2}, A{sub 10}(BO{sub 4}){sub 6}X{sub 2}, A{sub 10}(BO{sub 5}){sub 6}X{sub 2}-hybrid electrolytes of the types A{sub 10}(BO{sub 3}/BO{sub 4}/BO{sub 5}){sub 6}X{sub 2} can be designed.« less

Use of volumetric features for temporal comparison of mass lesions in full field digital mammograms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bozek, Jelena, E-mail: jelena.bozek@fer.hr; Grgic, Mislav; Kallenberg, Michiel

2014-02-15

Purpose: Temporal comparison of lesions might improve classification between benign and malignant lesions in full-field digital mammograms (FFDM). The authors compare the use of volumetric features for lesion classification, which are computed from dense tissue thickness maps, to the use of mammographic lesion area. Use of dense tissue thickness maps for lesion characterization is advantageous, since it results in lesion features that are invariant to acquisition parameters. Methods: The dataset used in the analysis consisted of 60 temporal mammogram pairs comprising 120 mediolateral oblique or craniocaudal views with a total of 65 lesions, of which 41 were benign and 24more » malignant. The authors analyzed the performance of four volumetric features, area, and four other commonly used features obtained from temporal mammogram pairs, current mammograms, and prior mammograms. The authors evaluated the individual performance of all features and of different feature sets. The authors used linear discriminant analysis with leave-one-out cross validation to classify different feature sets. Results: Volumetric features from temporal mammogram pairs achieved the best individual performance, as measured by the area under the receiver operating characteristic curve (A{sub z} value). Volume change (A{sub z} = 0.88) achieved higher A{sub z} value than projected lesion area change (A{sub z} = 0.78) in the temporal comparison of lesions. Best performance was achieved with a set that consisted of a set of features extracted from the current exam combined with four volumetric features representing changes with respect to the prior mammogram (A{sub z} = 0.90). This was significantly better (p = 0.005) than the performance obtained using features from the current exam only (A{sub z} = 0.77). Conclusions: Volumetric features from temporal mammogram pairs combined with features from the single exam significantly improve discrimination of benign and malignant lesions in FFDM

Studies of energy-transfer and electron-transfer processes involving the /sup 3/Au/sub 2u/ excited states of binuclear rhodium isocyanide complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milder, S.J.; Goldbeck, R.A.; Kliger, D.S.

1980-10-22

The lowest electronic excited states of Rh/sub 2/(br)/sub 4//sup 2 +/ (br = 1,3-diisocyanopropane) and Rh/sub 2/(TMB)/sub 4//sup 2 +/ (TMB = 2,5-dimethyl-2,5-diisocyanohexane) are relatively long-lived emissive triplets (/sup 3/A/sub 2u/). The /sup 3/A/sub 2u/ lifetimes in acetonitrile are 8.5 +- 0.5 ..mu..s for Rh/sub 2/(br)/sub 4//sup 2 +/ and 25 +- 5 ns for Rh/sub 2/(TMB)/sub 4//sup 2 +/ (21/sup 0/C). The triplet energy of Rh/sub 2/(br)/sub 4//sup 2 +/ has been estimated to be about 39 kcal/mol (approximately 1.7 eV, approximately 730 nm) from energy-transfer quenching experiments. The /sup 3/A/sub 2u/ excited states of Rh/sub 2/(br)/sub 4//sup 2more » +/ and Rh/sub 2/(TMB)/sub 4//sup 2 +/ undergo electron-transfer reactions with oxidative and reductive quenchers. Reductive quenching by N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD), and oxidative quenching by paraquat (PQ/sup 2 +/) have been studied in detail. In methanol solution, Rh/sub 2/(br)/sub 4//sup 2 +/*(/sup 3/A/sub 2u/) reacts with TMPD to give Rh/sub 2/(br)/sub 4//sup 2 +/ and TMPD/sup +/ (k/sub b/, the back-reaction rate constant, is 1 x 10/sup 9/ M/sup -1/s/sup -1/); similarly, Rh/sub 2/(TMB)/sub 4//sup 2 +/*(/sup 3/A/sub 2u/) reacts with TMPD to give Rh/sub 2/(TMB)/sub 4//sup +/ and TMPD/sup +/ (k/sub b/ = 1.4 x 10/sup 9/ M/sup -1/s/sup -1/). Oxidation of Rh/sub 2/(TMB)/sub 4//sup 2 +/*(/sup 3/A/sub 2u/) by PQ/sup 2 +/ in methanol gives Rh/sub 2/(TMB)/sub 4//sup 3 +/ and PQ/sup +/ (k/sub b/ = 2.2 x 10/sup 8/ M/sup -1/s/sup -1/; ..mu.. = 1.95 x 10/sup -2/ M). One-electron oxidation of Rh/sub 2/(br)/sub 4//sup 2 +/*(/sup 3/A/sub 2u/) by PQ/sup 2 +/ is observed, but the kinetics of the back-reaction are complex, owing to competing oligomerization processes.« less

Heavy ion irradiations on synthetic hollandite-type materials: Ba{sub 1.0}Cs{sub 0.3}A{sub 2.3}Ti{sub 5.7}O{sub 16} (A=Cr, Fe, Al)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Ming, E-mail: mtang@lanl.gov; Tumurugoti, Priyatham; Clark, Braeden

2016-07-15

The hollandite supergroup of minerals has received considerable attention as a nuclear waste form for immobilization of Cs. The radiation stability of synthetic hollandite-type compounds described generally as Ba{sub 1.0}Cs{sub 0.3}A{sub 2.3}Ti{sub 5.7}O{sub 16} (A=Cr, Fe, Al) were evaluated by heavy ion (Kr) irradiations on polycrystalline single phase materials and multiphase materials incorporating the hollandite phases. Ion irradiation damage effects on these samples were examined using grazing incidence X-ray diffraction (GIXRD) and transmission electron microscopy (TEM). Single phase compounds possess tetragonal structure with space group I4/m. GIXRD and TEM observations revealed that 600 keV Kr irradiation-induced amorphization on single phasemore » hollandites compounds occurred at a fluence between 2.5×10{sup 14} Kr/cm{sup 2} and 5×10{sup 14} Kr/cm{sup 2}. The critical amorphization fluence of single phase hollandite compounds obtained by in situ 1 MeV Kr ion irradiation was around 3.25×10{sup 14} Kr/cm{sup 2}. The hollandite phase exhibited similar amorphization susceptibility under Kr ion irradiation when incorporated into a multiphase system. - Graphical abstract: 600 keV Kr irradiation-induced amorphization on single phase hollandites compounds occurred at a fluence between 2.5×10{sup 14} Kr/cm{sup 2} and 5×10{sup 14} Kr/cm{sup 2}. The hollandite phase exhibited similar amorphization susceptibility under Kr ion irradiation when incorporated into a multiphase system. This is also the first time that the critical amorphization fluence of single phase hollandite compounds were determined at a fluence of around 3.25×10{sup 14} Kr/cm{sup 2} by in situ 1 MeV Kr ion irradiation. Display Omitted.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Dongbo; Zhao, Jinfeng, E-mail: jinfeng.zhao@tongji.edu.cn; Li, Libing

In this work, we applied a robust and fully air-coupled method to investigate the propagation of the lowest-order antisymmetric Lamb (A{sub 0}) mode in both a stubbed and an air-drilled phononic-crystal (PC) plate. By measuring simply the radiative acoustic waves of A{sub 0} mode close to the plate surface, we observed the band gaps for the stubbed PC plate caused by either the local resonance or the Bragg scattering, in frequency ranges in good agreement with theoretical predictions. We measured then the complete band gap of A{sub 0} mode for the air-drilled PC plate, in good agreement with the bandmore » structures. Finally, we compared the measurements made using the air-coupled method with those obtained by the laser ultrasonic technique.« less

Determining CDOM Absorption Spectra in Diverse Coastal Environments Using a Multiple Pathlength, Liquid Core Waveguide System. Measuring the Absorption of CDOM in the Field Using a Multiple Pathlength Liquid Waveguide System

NASA Technical Reports Server (NTRS)

Miller, Richard L.; Belz, Mathias; DelCastillo, Carlos; Trzaska, Rick

2000-01-01

We evaluated the accuracy, sensitivity and precision of a multiple pathlength, liquid core waveguide (MPLCW) system for measuring colored dissolved organic matter (CDOM) absorption in the UV-visible spectral range (370-700 nm). The MPLCW has four optical paths (2.0, 9.8, 49.3, and 204 cm) coupled to a single Teflon AF sample cell. Water samples were obtained from inland, coastal and ocean waters ranging in salinity from 0 to 36 PSU. Reference solutions for the MPLCW were made having a refractive index of the sample. CDOM absorption coefficients, a(sub CDOM), and the slope of the log-linearized absorption spectra, S, were compared with values obtained using a dual-beam spectrophotometer. Absorption of phenol red secondary standards measured by the MPLCW at 558 nm were highly correlated with spectrophotometer values (r > 0.99) and showed a linear response across all four pathlengths. Values of a(sub CDOM) measured using the MPLCW were virtually identical to spectrophotometer values over a wide range of concentrations. The dynamic range of a(sub CDOM) for MPLCW measurements was 0.002 - 231.5/m. At low CDOM concentrations (a(sub 370) < 0.1/m) spectrophotometric a(sub CDOM) were slightly greater than MPLCW values and showed larger fluctuations at longer wavelengths due to limitations in instrument precision. In contrast, MPLCW spectra followed an exponential to 600 nm for all samples. The maximum deviation in replicate MPLCW spectra was less than 0.001 absorbance units. The portability, sampling, and optical characteristics of a MPLCW system provide significant enhancements for routine CDOM absorption measurements in a broad range of natural waters.

Remote Sensing of the Absorption Coefficients and Chlorophyll a Concentration in the U.S. Southern Middle Atlantic Bight from SeaWiFS and MODIS-Aqua

NASA Technical Reports Server (NTRS)

Pan, Xiaoju; Mannino, Antonio; Russ, Mary E.; Hooker, Stanford B.

2008-01-01

At present, satellite remote sensing of coastal water quality and constituent concentration is subject to large errors as compared to the capability of satellite sensors in oceanic waters. In this study, field measurements collected on a series of cruises within U.S. southern Middle Atlantic Bight (SMAB) were applied to improve retrievals of satellite ocean color products in order to examine the factors that regulate the bio-optical properties within the continental shelf waters of the SMAB. The first objective was to develop improvements in satellite retrievals of absorption coefficients of phytoplankton (a(sub ph)), colored dissolved organic matter (CDOM) (a(sub g)), non-pigmented particles (a(sub d)), and non-pigmented particles plus CDOM (a(sub dg)), and chlorophyll a concentration ([Chl_a]). Several algorithms were compared to derive constituent absorption coefficients from remote sensing reflectance (R(sub rs)) ratios. The validation match-ups showed that the mean absolute percent differences (MAPD) were typically less than 35%, although higher errors were found for a(sub d) retrievals. Seasonal and spatial variability of satellite-derived absorption coefficients and [Chl_a] was apparent and consistent with field data. CDOM is a major contributor to the bio-optical properties of the SMAB, accounting for 35-70% of total light absorption by particles plus CDOM at 443 nm, as compared to 30-45% for phytoplankton and 0-20% for non-pigmented particles. The overestimation of [Chl_a] from the operational satellite algorithms may be attributed to the strong CDOM absorption in this region. River discharge is important in controlling the bio-optical environment, but cannot explain all of the regional and seasonal variability of biogeochemical constituents in the SMAB.

Algorithm Development and Validation for Satellite-Derived Distributions of DOC and CDOM in the US Middle Atlantic Bight

NASA Technical Reports Server (NTRS)

Mannino, Antonio; Russ, Mary E.; Hooker, Stanford B.

2007-01-01

In coastal ocean waters, distributions of dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) vary seasonally and interannually due to multiple source inputs and removal processes. We conducted several oceanographic cruises within the continental margin of the U.S. Middle Atlantic Bight (MAB) to collect field measurements in order to develop algorithms to retrieve CDOM and DOC from NASA's MODIS-Aqua and SeaWiFS satellite sensors. In order to develop empirical algorithms for CDOM and DOC, we correlated the CDOM absorption coefficient (a(sub cdom)) with in situ radiometry (remote sensing reflectance, Rrs, band ratios) and then correlated DOC to Rrs band ratios through the CDOM to DOC relationships. Our validation analyses demonstrate successful retrieval of DOC and CDOM from coastal ocean waters using the MODIS-Aqua and SeaWiFS satellite sensors with mean absolute percent differences from field measurements of < 9 %for DOC, 20% for a(sub cdom)(355)1,6 % for a(sub cdom)(443), and 12% for the CDOM spectral slope. To our knowledge, the algorithms presented here represent the first validated algorithms for satellite retrieval of a(sub cdom) DOC, and CDOM spectral slope in the coastal ocean. The satellite-derived DOC and a(sub cdom) products demonstrate the seasonal net ecosystem production of DOC and photooxidation of CDOM from spring to fall. With accurate satellite retrievals of CDOM and DOC, we will be able to apply satellite observations to investigate interannual and decadal-scale variability in surface CDOM and DOC within continental margins and monitor impacts of climate change and anthropogenic activities on coastal ecosystems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robertson, R.M.; Barnes, V.E.; Carmony, D.D.

The multiplicity-cross-section differences ..delta..sigma/sub n/ between p-barp and pp interactions are determined and are compared with measured annihilations and ..delta..sigma/sub n/ at other energies. To the extent that these cross-section differences measure the values of sigma/sup A//sub n/, the topological cross sections for annihilations, we present evidence for a decided break from a single-cluster-model prediction for the parameter f/sup A/--/sub 2/. Alternatively, a picture of precocious Koba-Nielsen-Olesen scaling in p-barp annihilations leads to a reasonably good representation of f/sup A/--/sub 2/ vs over the whole measured range. We find =7.57 +- 0.31, D/sup A/=2.77 +- 0.10, f/sup A/--/sub 2/=-1.86 +-more » 0.20, and /D=2.73 +- 0.15. Finally we observe a remarkable agreement with theoretical prediction for R/sup asterisk//sub n/=..delta..sigma/sub n//sigma/sub n/+2( pp), an experimental ratio based on a strict application of the counting rules for quark duality diagrams, and we thereby find evidence that in the topological-cross-section difference ..delta..sigma/sub n/ the small nonannihilation contribution becomes progressively more negligible as n increases.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goudeau, Danielle; Nath, Nandita; Ciobanu, Doina

Our approach to prokaryotic single-cell Whole Genome Amplification at the JGI continues to evolve. To increase both the quality and number of single-cell genomes produced, we explore all aspects of the process from cell sorting to sequencing. For example, we now utilize specialized reagents, acoustic liquid handling, and reduced reaction volumes eliminate non-target DNA contamination in WGA reactions. More specifically, we use a cleaner commercial WGA kit from Qiagen that employs a UV decontamination procedure initially developed at the JGI, and we use the Labcyte Echo for tip-less liquid transfer to set up 2uL reactions. Acoustic liquid handling also dramaticallymore » reduces reagent costs. In addition, we are exploring new cell lysis methods including treatment with Proteinase K, lysozyme, and other detergents, in order to complement standard alkaline lysis and allow for more efficient disruption of a wider range of cells. Incomplete lysis represents a major hurdle for WGA on some environmental samples, especially rhizosphere, peatland, and other soils. Finding effective lysis strategies that are also compatible with WGA is challenging, and we are currently assessing the impact of various strategies on genome recovery.« less

Generation of Parametric Equivalent-Area Targets for Design of Low-Boom Supersonic Concepts

NASA Technical Reports Server (NTRS)

Li, Wu; Shields, Elwood

2011-01-01

A tool with an Excel visual interface is developed to generate equivalent-area (A(sub e)) targets that satisfy the volume constraints for a low-boom supersonic configuration. The new parametric Ae target explorer allows users to interactively study the tradeoffs between the aircraft volume constraints and the low-boom characteristics (e.g., loudness) of the ground signature. Moreover, numerical optimization can be used to generate the optimal A(sub e) target for given A(sub e) volume constraints. A case study is used to demonstrate how a generated low-boom Ae target can be matched by a supersonic configuration that includes a fuselage, wing, nacelle, pylon, aft pod, horizontal tail, and vertical tail. The low-boom configuration is verified by sonic-boom analysis with an off-body pressure distribution at three body lengths below the configuration

D1((2)B2g) to D0((2)Au) Fluorescence from the Matrix-Isolated Perylene Cation Following Laser Excitation into the D5(2)B3g) and D2 ((2)B3g) Electronic States

NASA Technical Reports Server (NTRS)

Chillier, Xavier D. F.; Stone, Bradley M.; Joblin, Christine; Salama, Farid; Allamandola, Louis J.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

Fluorescence spectra of the perylene cation, pumped by direct laser excitation via the D(sub 2)((2)B(sub 3g)) (left arrow) D(sub 0)((2)A(sub u)) and D(sub 5)(2)B(sub 3g)) (left arrow) D(sub 0)((2)A(sub u)) transitions, are presented. Direct excitation into the D5 or D2 states is followed by rapid non-radiative relaxation to D1 that, in turn,relaxes radiatively. Excitation spectroscopy across the D(sub 2)((2)B(sub 3g)) (left arrow) D(sub 0)((2)A(sub u)) transition near 730 nm shows that site splitting plays little or no role in determining the spectral substructure in the ion spectra. Tentative assignments for ground state vibrational frequencies are made by comparison of spectral intervals with calculated normal mode frequencies.

Model-independent description of quartet nd scattering at low energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grinyuk, B.E.; Simenog, I.V.; Sitnichenko, A.I.

1984-02-01

Asymptotic expansions are obtained for the scattering length a/sub 3//sub ///sub 2/ and the effective range r/sub 3//sub ///sub 2/ for the quartet state of three nucleons in the form of series in powers of the two-nucleon triplet effective range r/sub 0t/. This allows a model-independent description of these parameters and of the quartet phase shift of nd scattering in the effective-range approximation. Correlations between the parameters of three- and two-nucleon scattering are proposed and explained; these correlations allow the systematization of numerical calculations of a/sub 3//sub ///sub 2/ and r/sub 3//sub ///sub 2/ for different forms of interaction potentials.more » The influence of the energy dependence of the interaction on a/sub 3//sub ///sub 2/ is also considered.« less

SPRUCE Deep Peat Heat (DPH) Metagenomes for Peat Samples Collected June 2015

DOE Data Explorer

Klumber, Laurel A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Yang, Zamin K. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Schadt, Christopher W. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.

2015-01-01

This data set provides links to the results of metagenomic analyses of 38 peat core samples collected on 16 June 2015 from SPRUCE experiment treatment plots after approximately one year of belowground heating. These metagenomes are archived in the U.S. Department of Energy Joint Genome Institute (DOE JGI) Integrated Microbial Genomes (IMG) system and are available at the accession numbers provided in the accompanying inventory file.

Spectroscopic and dielectric response of zinc bismuth phosphate glasses as a function of chromium content

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, P. Srinivasa; Babu, P. Ramesh; Vijay, R.

2014-09-15

Graphical abstract: 20ZnF{sub 2}–(20 − x)Bi{sub 2}O{sub 3}–60P{sub 2}O{sub 5}:xCr{sub 2}O{sub 3} (0 ≤ x ≤2 mol%) glasses are prepared by melt quenching technique. The optical absorption spectra of present glasses are analyzed as a function of chromium content. The absorption bands are assigned to {sup 4}A{sub 2g}(F) ⟶ {sup 4}T{sub 1g}(F), {sup 4}A{sub 2g}(F) ⟶ {sup 4}T{sub 2g}(F), {sup 4}A{sub 2g}(F) ⟶ {sup 2}T{sub 1g}(G) and {sup 4}A{sub 2g}(F) ⟶ {sup 2}E{sub g}(G) transitions of Cr{sup 3+} ions. - Highlights: • ZnF{sub 2}–Bi{sub 2}O{sub 3}–P{sub 2}O{sub 5}:Cr{sub 2}O{sub 3} glasses were prepared by melt quenching and annealing. • Spectroscopicmore » and dielectric properties of chromium ions were investigated. • ESR and optical absorption spectra indicate the co-existence of Cr{sup 6+} ions with Cr{sup 5+} ions and Cr{sup 3+} ions. • Cr{sup 3+} ions act as modifiers and influence the semiconducting nature of the glass system. - Abstract: 20ZnF{sub 2}–(20 − x)Bi{sub 2}O{sub 3}–60P{sub 2}O{sub 5}:xCr{sub 2}O{sub 3} (0 ≤ x ≤2 mol%) glasses are prepared by melt quenching technique. Amorphous nature of these samples is confirmed by X-ray diffraction (XRD) analysis. FTIR study reveals bands due to CrO{sub 6}(o{sub d}) and CrO{sub 4}{sup 2−}(T{sub d}) units along with conventional phosphate groups. The optical absorption and ESR studies of present glasses are analyzed as a function of chromium content. The absorption bands are assigned to {sup 4}A{sub 2g}(F) ⟶ {sup 4}T{sub 1g}(F), {sup 4}A{sub 2g}(F) ⟶ {sup 4}T{sub 2g}(F), {sup 4}A{sub 2g}(F) ⟶ {sup 2}T{sub 1g}(G) and {sup 4}A{sub 2g}(F) ⟶ {sup 2}E{sub g}(G) transitions of Cr{sup 3+} ions. The highest concentration of Cr{sup 3+} ions (in octahedral sites, with network modifying positions) is found in the sample with 2.0 mol% of Cr{sub 2}O{sub 3}. The analysis of dielectric properties indicates a gradual increase in semiconducting character with increase in the

THE MID-INFRARED EXTINCTION LAW AND ITS VARIATION IN THE COALSACK NEBULA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang Shu; Gao Jian; Jiang, B. W.

In recent years, the wavelength dependence of interstellar extinction from the ultraviolet (UV) to the near- and mid-infrared (IR) has been studied extensively. Although it is well established that the UV/optical extinction law varies significantly among the different lines of sight, it is not clear how IR extinction varies among various environments. In this work, using the color-excess method and taking red giants as the extinction tracer, we determine interstellar extinction A{sub {lambda}} in the four Spitzer/IRAC bands in [3.6], [4.5], [5.8], [8.0] {mu}m (relative to A{sub K{sub s}}, extinction in the Two Micron All Sky Survey (2MASS) K{sub s}more » band at 2.16 {mu}m) of the Coalsack nebula, a nearby starless dark cloud, based on the data obtained from the 2MASS and Spitzer/GLIMPSE surveys. We select five individual regions across the nebula that span a wide variety of physical conditions ranging from diffuse and translucent to dense environments, as traced by the visual extinction, the Spitzer/MIPS 24 {mu}m emission, and CO emission. We find that A{sub {lambda}}/A{sub K{sub s}}, mid-IR extinction relative to A{sub K{sub s}}, decreases from diffuse to dense environments, which may be explained in terms of ineffective dust growth in dense regions. The mean extinction (relative to A{sub K{sub s}}) is calculated for the four IRAC bands as well and exhibits a flat mid-IR extinction law consistent with previous determinations for other regions. Extinction in the IRAC 4.5 {mu}m band is anomalously high, much higher than that of the other three IRAC bands, and cannot be explained in terms of CO and CO{sub 2} ice. Mid-IR extinction in the four IRAC bands has also been derived for four representative regions in the Coalsack Globule 2, which respectively exhibit strong ice absorption, moderate or weak ice absorption, and very weak or no ice absorption. The derived mid-IR extinction curves are all flat, with A{sub {lambda}}/A{sub K{sub s}} increasing with the decrease

Reproducibility of Tumor Motion Probability Distribution Function in Stereotactic Body Radiation Therapy of Lung Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang Fan; Medical Physics Graduate Program, Duke University, Durham, North Carolina; Hu Jing

2012-11-01

Purpose: To evaluate the reproducibility of tumor motion probability distribution function (PDF) in stereotactic body radiation therapy (SBRT) of lung cancer using cine megavoltage (MV) images. Methods and Materials: Cine MV images of 20 patients acquired during three-dimensional conformal (6-11 beams) SBRT treatments were retrospectively analyzed to extract tumor motion trajectories. For each patient, tumor motion PDFs were generated per fraction (PDF{sub n}) using three selected 'usable' beams. Patients without at least three usable beams were excluded from the study. Fractional PDF reproducibility (R{sub n}) was calculated as the Dice similarity coefficient between PDF{sub n} to a 'ground-truth' PDF (PDF{submore » g}), which was generated using the selected beams of all fractions. The mean of R{sub n}, labeled as R{sub m}, was calculated for each patient and correlated to the patient's mean tumor motion rang (A{sub m}). Change of R{sub m} during the course of SBRT treatments was also evaluated. Intra- and intersubject coefficient of variation (CV) of R{sub m} and A{sub m} were determined. Results: Thirteen patients had at least three usable beams and were analyzed. The mean of R{sub m} was 0.87 (range, 0.84-0.95). The mean of A{sub m} was 3.18 mm (range, 0.46-7.80 mm). R{sub m} was found to decrease as A{sub m} increases following an equation of R{sub m} = 0.17e{sup -0.9Am} + 0.84. R{sub m} also decreased slightly throughout the course of treatments. Intersubject CV of R{sub m} (0.05) was comparable to intrasubject CV of R{sub m} (range, 0.02-0.09); intersubject CV of A{sub m} (0.73) was significantly greater than intrasubject CV of A{sub m} (range, 0.09-0.24). Conclusions: Tumor motion PDF can be determined using cine MV images acquired during the treatments. The reproducibility of lung tumor motion PDF decreased exponentially as the tumor motion range increased and decreased slightly throughout the course of the treatments.« less

Involvement of MAPKs, NF-{kappa}B and p300 co-activator in IL-1{beta}-induced cytosolic phospholipase A{sub 2} expression in canine tracheal smooth muscle cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, S.-F.; Lin, C.-C.; Chen, H.-C.

2008-11-01

Cytosolic phospholipase A{sub 2} (cPLA{sub 2}) plays a pivotal role in mediating agonist-induced arachidonic acid release for prostaglandin (PG) synthesis during stimulation with interleukin-1{beta} (IL-1{beta}). However, the mechanisms underlying IL-1{beta}-induced cPLA{sub 2} expression and PGE{sub 2} synthesis by canine tracheal smooth muscle cells (CTSMCs) have not been defined. IL-1{beta} induced cPLA{sub 2} protein and mRNA expression, PGE{sub 2} production, and phosphorylation of p42/p44 MAPK, p38 MAPK (ATF{sub 2}), and JNK (c-Jun) in a time- and concentration-dependent manner, determined by Western blotting, RT-PCR, and ELISA, which was attenuated by the inhibitors of MEK1/2 (U0126), p38 MAPK (SB202190), and JNK (SP600125), ormore » transfection with dominant negative mutants of MEK1/2, p38, and JNK, respectively. Furthermore, IL-1{beta}-induced cPLA{sub 2} expression and PGE{sub 2} synthesis was inhibited by a selective NF-{kappa}B inhibitor (helenalin) or transfection with dominant negative mutants of NF-{kappa}B inducing kinase (NIK), I{kappa}B kinase (IKK)-{alpha}, and IKK-{beta}. Consistently, IL-1{beta} stimulated both I{kappa}B-{alpha} degradation and NF-{kappa}B translocation into nucleus in these cells. NF-{kappa}B translocation was blocked by helenalin, but not by U0126, SB202190, and SP600125. MAPKs together with NF-{kappa}B-activated p300 recruited to cPLA{sub 2} promoter thus facilitating the binding of NF-{kappa}B to cPLA{sub 2} promoter region and expression of cPLA{sub 2} mRNA. IL-1{beta}-induced cPLA{sub 2} expression and PGE{sub 2} production was inhibited by actinomycin D and cycloheximide, indicating the involvement of transcriptional and translational events in these responses. These results suggest that in CTSMCs, IL-1{beta}-induced cPLA{sub 2} expression and PGE{sub 2} synthesis was independently mediated through activation of MAPKs and NF-{kappa}B pathways and was connected to p300 recruitment and activation.« less

Representations of S{sub {infinity}} admissible with respect to Young subgroups

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nessonov, Nikolai I

2012-03-31

Let N be the set of positive integers and S{sub {infinity}} the set of finite permutations of N. For a partition {Pi} of the set N into infinite parts A{sub 1},A{sub 2},... we denote by S{sub {Pi}} the subgroup of S{sub {infinity}} whose elements leave invariant each of the sets A{sub j}. We set S{sub {infinity}}{sup (N)}={l_brace}s element of S{sub {infinity}:} s(i)=i for any i=1,2,...,N{r_brace}. A factor representation T of the group S{sub {infinity}} is said to be {Pi}-admissible if for some N it contains a nontrivial identity subrepresentation of the subgroup S{sub {Pi}} intersection S{sub {infinity}}{sup (N)}. In themore » paper, we obtain a classification of the {Pi}-admissible factor representations of S{sub {infinity}}. Bibliography: 14 titles.« less

In vivo dynamics of GFRα1-positive spermatogonia stimulated by GDNF signals using a bead transplantation assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uchida, Aya; Kishi, Kasane; Aiyama, Yoshimi

In mouse testes, spermatogonial stem cells (SSCs), a subpopulation of GFRα1 (GDNF family receptor-α1)-positive spermatogonia, are widely distributed along the convoluted seminiferous tubules. The proliferation and differentiation of the SSCs are regulated in part by local expression of GDNF (glial cell-derived neurotorphic factor), one of major niche factors for SSCs. However, the in vivo dynamics of the GDNF-stimulated GFRα1-positive spermatogonia remains unclear. Here, we developed a simple method for transplanting DiI-labeled and GDNF-soaked beads into the mouse testicular interstitium. By using this method, we examined the dynamics of GFRα1-positive spermatogonia in the tubular walls close to the transplanted GDNF-soaked beads. Themore » bead-derived GDNF signals were able to induce the stratified aggregate formation of GFRα1-positive undifferentiated spermatogonia by day 3 post-transplantation. Each aggregate consisted of tightly compacted A{sub single} and marginal A{sub paired}–A{sub aligned} GFRα1-positive spermatogonia and was surrounded by A{sub aligned} GFRα1-negative spermatogonia at more advanced stages. These data not only provide in vivo evidence for the inductive roles of GDNF in forming a rapid aggregation of GFRα1-positive spermatogonia but also indicate the usefulness of this in vivo assay system of various growth factors for the stem/progenitor spermatogonia in mammalian spermatogenesis. - Highlights: • A novel bead transplantation assay was developed to examine the in vivo effects of growth factors on spermatogonia. • A rapid aggregation of GFRα1-positive spermatogonia was induced by the transplanted GDNF-soaked beads. • Tightly-compacted A{sub single} and marginal A{sub paired}–A{sub aligned} spermatogonia were formed in each GFRα1-positive aggregate.« less

Conversion of 3-imidazoline-3-oxide nitroxyl radicals into nitronylnitroxyl radicals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigor'ev, I.A.; Shchukin, G.I.; Khramtsov, V.V.

1986-04-20

Continuing the studies of the effect of the pH of the medium on the EPR spectra of nitroxyl radicals (NR) containing acid-base functional groups at a distance of 2-3 sigma-bonds from the radical center, they have examined the EPR spectra of NR, which contain OH groups in the 2-position of the heterocycle. It is assumed that deprotonation of the OH group is accompanied by changes in the hfc constant a/sub N//sup 1/ and the g-factor. At pH values greater than or equal to 12, however, the EPR spectra of aqueous solutions of radicals undergo irreversible changes from a triplet tomore » a more complex multiplet, similar to the spectra of nitronylnitroxyl radicals. The EPR spectra of these solutions remain unchanged over periods of several days. The spectra have a quintet structure, with further splitting into four or three components. When similar experiments are carried out in D/sub 2/O, the additional hfs disappear as a result of deuterium exchange in the CH/sub 2/ and CH/sub 3/ groups of the radicals. A simulation of the EPR spectra was carried out, assuming splitting into two N nuclei (a/sub N//sup 1/ and a/sub N//sup 3/), with three or two equivalent H. This resulted in complete agreement between the calculated and experimental spectra. In order to assign the nitrogen hfc constants, they synthesized radicals containing the N/sup 15/ isotope in the 3-position of the imidazole ring. Comparison of the results of simulations of the EPR spectra enabled unambiguous assignments of the hfc constants a/sub N//sup 1/ and a/sub N//sup 3/ to be made.« less

Attenuation-based estimation of patient size for the purpose of size specific dose estimation in CT. Part II. Implementation on abdomen and thorax phantoms using cross sectional CT images and scanned projection radiograph images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang Jia; Christner, Jodie A.; Duan Xinhui

2012-11-15

Purpose: To estimate attenuation using cross sectional CT images and scanned projection radiograph (SPR) images in a series of thorax and abdomen phantoms. Methods: Attenuation was quantified in terms of a water cylinder with cross sectional area of A{sub w} from both the CT and SPR images of abdomen and thorax phantoms, where A{sub w} is the area of a water cylinder that would absorb the same dose as the specified phantom. SPR and axial CT images were acquired using a dual-source CT scanner operated at 120 kV in single-source mode. To use the SPR image for estimating A{sub w},more » the pixel values of a SPR image were calibrated to physical water attenuation using a series of water phantoms. A{sub w} and the corresponding diameter D{sub w} were calculated using the derived attenuation-based methods (from either CT or SPR image). A{sub w} was also calculated using only geometrical dimensions of the phantoms (anterior-posterior and lateral dimensions or cross sectional area). Results: For abdomen phantoms, the geometry-based and attenuation-based methods gave similar results for D{sub w}. Using only geometric parameters, an overestimation of D{sub w} ranging from 4.3% to 21.5% was found for thorax phantoms. Results for D{sub w} using the CT image and SPR based methods agreed with each other within 4% on average in both thorax and abdomen phantoms. Conclusions: Either the cross sectional CT or SPR images can be used to estimate patient attenuation in CT. Both are more accurate than use of only geometrical information for the task of quantifying patient attenuation. The SPR based method requires calibration of SPR pixel values to physical water attenuation and this calibration would be best performed by the scanner manufacturer.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fritz, T. K.; Gillessen, S.; Dodds-Eden, K.

We derive the extinction curve toward the Galactic center (GC) from 1 to 19 {mu}m. We use hydrogen emission lines of the minispiral observed by ISO-SWS and SINFONI. The extinction-free flux reference is the 2 cm continuum emission observed by the Very Large Array. Toward the inner 14'' x 20'', we find an extinction of A{sub 2.166{mu}m} = 2.62 {+-} 0.11, with a power-law slope of {alpha} = -2.11 {+-} 0.06 shortward of 2.8 {mu}m, consistent with the average near-infrared slope from the recent literature. At longer wavelengths, however, we find that the extinction is grayer than shortward of 2.8more » {mu}m. We find that it is not possible to fit the observed extinction curve with a dust model consisting of pure carbonaceous and silicate grains only, and the addition of composite particles, including ices, is needed to explain the observations. Combining a distance-dependent extinction with our distance-independent extinction, we derive the distance to the GC to be R{sub 0} = 7.94 {+-} 0.65 kpc. Toward Sgr A* (r < 0.''5), we obtain A{sub H} = 4.21 {+-} 0.10, A{sub Ks} = 2.42 {+-} 0.10, and A{sub L'} = 1.09 {+-} 0.13.« less

Gradient changes in structural condition of the B2 phase of NiTi surface layers after electron-beam treatments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meisner, Ludmila L., E-mail: llm@ispms.tsc.ru, E-mail: egu@ispms.tsc.ru; Gudimova, Ekaterina Yu., E-mail: llm@ispms.tsc.ru, E-mail: egu@ispms.tsc.ru; Ostapenko, Marina G., E-mail: artifact@ispms.tsc.ru

2014-11-14

Structural conditions of the B2 phase of the Ti{sub 49.5}Ni{sub 50.5} alloy surface layers before and after electron-beam treatments (pulse duration τ = 150 μs, number of pulses n = 5, beam energy density E ≤ 20 J/cm{sup 2}) were studied by X-ray diffraction analysis. Analysis of the X-ray patterns demonstrates that surface layers modified by electron beam treatment contain phase with B2{sup surf} structure. It is revealed that the lattice parameter of the B2{sup surf} phase in the surface (modified) layer is also higher than the lattice parameter of the B2 phase in the underlying layer (a{sub B2} = 3.0159±0.0005). Themore » values of lattice parameter of phase B2{sup surf} amounted a{sub B2}{sup surf} = 3.0316±0.0005 Å and a{sub B2}{sup surf} = 3.0252±0.0005 Å, for the specimens after electron-beam treatment at E{sub 1} = 15 J/cm{sup 2} and E{sub 2} = 20 J/cm{sup 2}, respectively. Inflated lattice parameters a{sub B2}{sup surf} are associated with changes in the chemical composition and the presence of residual stresses in the surface region of the samples after electron-beam treatments.« less

Structural characterization of synthetic and protein-bound porphyrins in terms of the lowest-frequency normal coordinates of the macrocycle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jentzen, W.; Song, X.Z.; Shelnutt, J.A.

1997-02-27

The X-ray crystal structures of synthetic and protein-bound metalloporphyrins are analyzed using a new normal structural decomposition method for classifying and quantifying their out-of-plane and in-plane distortions. These distortions are characterized in terms of equivalent displacements along the normal coordinates of the D{sub 4h}-symmetric porphyrin macrocycle (normal deformations). It is shown that the macrocyclic structure is, even in highly distorted porphyrins, accurately represented by displacements along only the lowest-frequency normal coordinates. Accordingly, the macrocyclic structure obtained from just the out-of-plane normal deformations of the saddling (sad, B{sub 2u})-, ruffling (ruf, B{sub 1u})-, doming (dom, A{sub 2u})-, waving [wav(x), wav(y); E{submore » g}]-, and propellering (pro, A{sub 1u})-type essentially simulates the out-of-plane distortion of the X-ray crystal structure. Similarly, the observed in-plane distortions are decomposed into in-plane normal deformations corresponding to the lowest-frequency vibrational modes including macrocycle stretching in the direction of the meso-carbon atoms (meso-str, B{sub 2g}), stretching in the direction of the nitrogen atoms (N-str, B{sub 1g}), x and y pyrrole translations [trn(x), trn(y); E{sub u}], macrocycle breathing (bre, A{sub 1g}), and pyrrole rotation (rot, A{sub 2g}). 71 refs., 9 figs., 4 tabs.« less

Parity Nonconservation in Proton-water Scattering at 800 MeV

DOE R&D Accomplishments Database

Nagle, D. E.; Bowman, J. D.; Carlini, R.; Mischke, R. E.; Frauenfelder, H.; Harper, R. W.; Yuan, V.; McDonald, A. B.; Talaga, R.

1982-01-01

A search has been made for parity nonconservation in the scattering of 800 MeV polarized protons from an unpolarized water target. The result is for the longitudinal asymmetry, A{sub L} = +(6.6 +- 3.2) x 10{sup -7}. Control runs with Pb, using a thickness which gave equivalent beam broadening from Coulomb multiple scattering, but a factor of ten less nuclear interactions than the water target, gave A{sub L} = -(0.5 +- 6.0) x 10{sup -7}.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konobeevski, E. S., E-mail: konobeev@inr.ru; Burmistrov, Yu. M.; Zuyev, S. V.

The first results are obtained in a kinematically complete experiment devoted to measuring the n + d {sup {yields}}p + n + n reaction yield at energies in the range E{sub n} = 40-60 MeV and various angles of divergence of two neutrons ({Delta}{theta} = 4{sup o}, 6{sup o}, and 8{sup o}) in the geometry of neutron-neutron final-state interaction. The {sup 1}S{sub 0} neutron-neutron scattering length a{sub nn} is determined by comparing the experimental energy dependence of the reaction yield with the results of a simulation in the Watson-Migdal approximation, which depend on a{sub nn}. For E{sub n} = 40more » MeV and {Delta}{theta} = 6{sup o} (the best statistics in the experiment), the value a{sub nn} = -17.9 {+-} 1.0 fm was obtained. A further improvement of the experimental accuracy will make it possible to remove the existing disagreement of the results from different experiments.« less

Dependence of ion density in the wake of the AE-C satellite on the ratio of body size to Debye length in an (O/sup +/)-dominated plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samir, U.; Kaufman, Y.J.; Brace, L.H.

Measurements of electron temperature, satellite potential, ion density and ion composition from the cylindrical electrostatic probe and the Bennett ion mass spectrometer on board the AE-C satellite were used to investigate the influence of the body size parameter R/sub D/=R/sub 0//lambda/sub D/ (where R/sub 0/ is the satellite radius and lambda/sub D/ is the ambient Debye length) on ion distribution in the very near wake. The investigation focused on (O/sup +/) plasmas. It was found that the ratio (..beta..) of density in the wake to ambient density varies with R/sub D/ and that the variation can be described by amore » simple exponential relationship of the form ..beta..=a/sub 0/ exp (a/sub 1/R/sub D/) for 37< or =R/sub D/< or =247 and a/sub 0/=0.006, a/sub 1/=-0.009. the present study extends that of Samir et al. (1979a).« less

Fueling Future with Algal Genomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigoriev, Igor

Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils ofmore » secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antonova, A. O., E-mail: anna-antonova-08@mail.ru; Reznik, S. N., E-mail: s.reznik@voliacable.com; Todorov, M. D., E-mail: mtod@tu-sofia.bg

We study dynamics of the Goodwin nonlinear accelerator business cycle model with periodic forced autonomous investment I{sub a}(t) = a(1 – cos ωt), where a and ω are the amplitude and the frequency of investment. We give examples of the parameters a and ω when the chaotic oscillations of income are possible. We find the critical values of amplitude a{sub cr} (ω): if a > a{sub cr} (ω) the period of the income equals to the driving period T=2π/ω.

An in situ estimation of anisotropic elastic moduli for a submarine shale

NASA Astrophysics Data System (ADS)

Miller, Douglas E.; Leaney, Scott; Borland, William H.

1994-11-01

Direct arrival times and slownesses from wide-aperture walkaway vertical seismic profile data acquired in a layered anisotropic medium can be processed to give direct estimate of the phase slowness surface associated with the medium at the depth of the receivers. This slowness surface can, in turn, be fit by an estimated transversely isotropic medium with a vertical symmetry axis (a 'TIV' medium). While the method requires that the medium between the receivers and the surface be horizontally stratified, no further measurement or knowledge of that medium is required. When applied to data acquired in a compacting shale sequence (here termed the 'Petronas shale') encountered by a well in the South China Sea, the method yields an estimated TIV medium that fits the data extremely well over 180 deg of propagation angles sampled by 201 source positions. The medium is strongly anisotropic. The anisotropy is significantly anelliptic and implies that the quasi-shear mode should be triplicated for off-axis propagation. Estimated density-normalized moduli (in units of sq km/sq s) for the Petronas shale are A(sub 11) = 6.99 +/- 0.21, A(sub 33) = 5.53 +/- 0.17, A(sub 55) = 0.91 +/- 0.05, and A(sub 13) = 2.64 +/- 0.26. Densities in the logged zone just below the survey lie in the range between 2200 and 2400 kg/cu m with an average value close to 2300 kg/cu m.

Implementing a Nitrogen-Based Model for Autotrophic Respiration Using Satellite and Field Observations

NASA Technical Reports Server (NTRS)

Choudhury, Bhaskar J.; Houser, Paul (Technical Monitor)

2001-01-01

The rate of carbon accumulation by terrestrial plant communities in a process-level, mechanistic modeling is the difference of the rate of gross photosynthesis by a canopy (A(sub g)) and autotrophic respiration (R) of the stand. Observations for different biomes often show that R to be a large and variable fraction of A(sub g), ca. 35% to 75%, although other studies suggest the ratio of R and A(sub g) to be less variable. Here, R has been calculated according to the two compartment model as being the sum of maintenance and growth components. The maintenance respiration of foliage and living fine roots for different biomes has been determined objectively from observed nitrogen content of these organs. The sapwood maintenance respiration is based on pipe theory, and checked against an independently derived equation considering sapwood biomass and its maintenance coefficient. The growth respiration has been calculated from the difference of A(sub g) and maintenance respiration. The A(sub g) is obtained as the product of biome-specific radiation use efficiency for gross photosynthesis under unstressed conditions and intercepted photosynthetically active radiation, and adjusted for stress. Calculations have been done using satellite and ground observations for 36 consecutive months (1987-1989) over large contiguous areas (ca. 10(exp 5) sq km) of boreal forests, crop land, temperate deciduous forest, temperate grassland, tropical deciduous forest, tropical evergreen forest, tropical savanna, and tundra. The ratio of annual respiration and gross photosynthesis, (R/A(sub g)), is found to be 0.5-0.6 for temperate and cold adopted biome areas, but somewhat higher for tropical biome areas (0.6-0.7). Interannual variation of the fluxes is found to be generally less than 15%. Calculated fluxes are compared with observations and several previous estimates. Results of sensitivity analysis are presented for uncertainties in parameterization and input data. It is found that

MEETING: Chlamydomonas Annotation Jamboree - October 2003

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grossman, Arthur R

2007-04-13

Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) ormore » individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

NUMERICAL SIMULATIONS OF THERMOHALINE CONVECTION: IMPLICATIONS FOR EXTRA-MIXING IN LOW-MASS RGB STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Denissenkov, Pavel A., E-mail: pavel.denisenkov@gmail.co

2010-11-01

Low-mass stars are known to experience extra-mixing in their radiative zones on the red giant branch (RGB) above the bump luminosity. To determine if the salt-fingering transport of chemical composition driven by {sup 3}He burning is efficient enough to produce RGB extra-mixing, two-dimensional numerical simulations of thermohaline convection for physical conditions corresponding to the RGB case have been carried out. We have found that the effective ratio of a salt finger's length to its diameter a{sub eff} {approx}< 0.5 is more than 10 times smaller than the value needed to reproduce observations (a{sub obs} {approx}> 7). On the other hand,more » using the thermohaline diffusion coefficient from linear stability analysis together with a = a{sub obs} is able to describe the RGB extra-mixing at all metallicities so well that it is tempting to believe that it may represent the true mechanism. In view of these results, follow-up three-dimensional numerical simulations of thermohaline convection for the RGB case are clearly needed.« less

Stimulation by Hyphopichia burtonii and Bacillus amyloliquefaciens of aflatoxin production by Aspergillus flavus in irradiated maize and rice grains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cuero, R.G.; Smith, J.E.; Lacey, J.

Aspergillus flavus was grown on maize and rice extract agars and on irradiated viable cracked maize and rice grains, either in pure culture or in dual culture with wild strains of either Hyphopichia burtonii or Bacillus amyloliquefaciens. Aflatoxin production by A. flavus and its growth and interactions with the other microorganisms were studied at three water activities (a/sub w/) (0.98, 0.95, and 0.90) and two temperatures (25 and 16/sup 0/C). Both H. burtonii and B. amyloliquefaciens markedly stimulated growth and aflotoxin production by A. flavus on cracked maize, especially at 25/sup 0/C and 0.95 and 0.98 a/sub w/. No aflatoxinmore » was detected in pure cultures of A. flavus on cracked rice after 12 days of incubation at 25/sup 0/C, but some was produced by mixed cultures at 16/sup 0/C and 0.98 a/sub w/. The morphological interactions among A. flavus, H. burtonii, and B. amyloliquefaciens were also examined on maize and rice extract agars under similar controlled conditions.« less

Defining Genome Project Standards in a New Era of Sequencing (GSC8 Meeting)

ScienceCinema

Chain, Patrick

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego.

Measurement of CP--violating asymmetries in $$D^0\\to\\pi^+\\pi^-$$ and $$D^0\\to K^+K^-$$ decays at CDF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaltonen, T.; /Helsinki Inst. of Phys.; Alvarez Gonzalez, B.

2011-11-01

We report on a measurement of CP-violating asymmetries (A{sub CP}) in the Cabibbo-suppressed D{sup 0} {yields} {pi}{sup +}{pi}{sup -} and D{sup 0} {yields} K{sup +}K{sup -} decays reconstructed in a data sample corresponding to 5.9 fb{sup -1} of integrated luminosity collected by the upgraded Collider Detector at Fermilab. We use the strong decay D*{sup +} {yields} D{sup 0}{pi}{sup +} to identify the flavor of the charmed meson at production and exploit CP-conserving strong c{bar c} pair-production in p{bar p} collisions. High-statistics samples of Cabibbo-favored D{sup 0} {yields} K{sup -}{pi}{sup +} decays with and without a D*{sup {+-}} tag are usedmore » to correct for instrumental effects and significantly reduce systematic uncertainties. We measure A{sub CP}(D{sup 0} {yields} {pi}{sup +}{pi}{sup -}) = (+0.22 {+-} 0.24(stat) {+-} 0.11 (syst))% and A{sub CP}(D{sup 0} {yields} K{sup +}K{sup -}) = (-0.24 {+-} 0.22 (stat) {+-} 0.09 (syst))%, in agreement with CP conservation. These are the most precise determinations from a single experiment to date. Under the assumption of negligible direct CP violation in D{sup 0} {yields} {pi}{sup +}{pi}{sup -} and D{sup 0} {yields} K{sup +}K{sup -} decays, the results provide an upper limit to the CP-violating asymmetry in D{sup 0} mixing, |A{sub CP}{sup ind}(D{sup 0})| < 0.13% at the 90% confidence level.« less

Structural and phase transformation of A{sup III}B{sup V}(100) semiconductor surface in interaction with selenium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bezryadin, N. N.; Kotov, G. I., E-mail: giktv@mail.ru; Kuzubov, S. V., E-mail: kuzub@land.ru

2015-03-15

Surfaces of GaAs(100), InAs(100), and GaP(100) substrates thermally treated in selenium vapor have been investigated by transmission electron microscopy and electron probe X-ray microanalysis. Some specific features and regularities of the formation of A{sub 3}{sup III}B{sub 4}{sup VI} (100)c(2 × 2) surface phases and thin layers of gallium or indium selenides A{sub 2}{sup III}B{sub 3}{sup VI} (100) on surfaces of different A{sup III}B{sup V}(100) semiconductors are discussed within the vacancy model of surface atomic structure.

Meson production in relativistic heavy-ion collisions at AGS energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steadman, S.G.; E802 Collaboration

1993-07-01

Single particle inclusive spectra are presented for pion and kaon production in Si+Au reactions at an incident momentum of 14.6 A {center_dot} GeV/c and Au+Au reactions at an incident momentum of 11.6 A {center_dot} GeV/c. A simple geometric scaling of the pion production for central collisions as A{sub proj}{sup 1/3} and A{sub targ}{sup 2/3} results from the observed production of about one pion per participant. Kaon yields are shown to be proportional to the number of excited participants and consistent with RQMD and ARC calculations.

Meson production in relativistic heavy-ion collisions at AGS energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steadman, S.G.

1993-01-01

Single particle inclusive spectra are presented for pion and kaon production in Si + Au reactions at an incident momentum of 14.6 A [center dot] GeV/c and Au + Au reactions at an incident momentum of 11.6 A [center dot] GeV/c. A simple geometric scaling of the pion production for central collisions as A[sub proj][sup 1/3] and A[sub targ][sup 2/3] results from the observed production of about one pion per participant. Kaon yields are shown to be proportional to the number of excited participants and consistent with RQMD and ARC calculations.

Tests of conformal field theory at the Yang-Lee singularity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wydro, Tomasz; McCabe, John F.

2009-12-14

This paper studies the Yang-Lee edge singularity of 2-dimensional (2D) Ising model based on a quantum spin chain and transfer matrix measurements on the cylinder. Based on finite-size scaling, the low-lying excitation spectrum is found at the Yang-Lee edge singularity. Based on transfer matrix techniques, the single structure constant is evaluated at the Yang-Lee edge singularity. The results of both types of measurements are found to be fully consistent with the predictions for the (A{sub 4}, A{sub 1}) minimal conformal field theory, which was previously identified with this critical point.

Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

ScienceCinema

Tringe, Susannah

2018-02-14

Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shepherd, R.E.; Myser, T.K.; Elliott, M.G.

The kinetics of the reaction of O/sub 2/ and Fe/sub 2/(ttha)/sup 2/minus// (ttha/sup 6/minus// = triethylenetetraminehexaacetate) are reported. The mechanism of oxidation is discussed in terms of the equilibrium binding of O/sub 2/ forming an ((Fe/sup III/O/sub 2//sup /minus//)ttha(Fe/sup II/)) intermediate in an open-chain configuration. When Fe/sub 2/(ttha)/sup 2/minus// is oxidized by H/sub 2/O/sub 2/, the HODMPO/sup /center dot// (DMPO = 5,5-dimethyl-1-pyrrolis-N-oxide) adduct is readily detected by its characteristic four-line 1:2:2:1 pattern (a/sub N/ = a/sub H/ = 15.0 G) in its ESR spectrum. The bound O/sub 2//sup /minus// intermediate in the Fe/sub 2/(ttha)/sup 2/minus// autoxidation scheme will extract anmore » H atom from C/sub 2/H/sub 5/OH in its solvent cage; the DMPO adduct of CH/sub 3/CHOH is trapped, giving a pattern of six equal lines (a/sub N/ = 16.0 G, a/sub H/ = 22.8 G). A maximum of 6% of the pathway results in a carbon-centered radial; the remainder of the reduction events produce Fe/sub 2/O(ttha)/sup 2/minus// by rapid reduction of the (Fe/sup III//sub 2/(O/sub 2//sup 2/minus//)(ttha))/sup 2/minus// intermediate. The Fe/sub 2/O(ttha)/sup 2/minus// ion was precipitated as its Me/sub 2/Dabco/sup 2+/ salt. This compound was shown to have ferric ions in an /sup 6/A/sub 1/ state; the Moessbauer spectrum yielded 0.63 mm/s for the isomer shift and 1.56 mm/s for the quadrupole splitting parameter vs sodium nitroprusside. The solid exhibited an Fe-O-Fe asymmetric stretch at 833 cm/sup /minus/1/ for /sup 16/O and 846 cm/sup /minus/1/ for the /sup 18/O-labeled complex. The uv-visible spectrum is very similar to that of the Fe/sub 2/(hedta)/sub 2//sup 2/minus// complex. 62 references, 7 figures, 3 tables.« less

Time-resolved photoelectron spectroscopy of a dinuclear Pt(II) complex: Tunneling autodetachment from both singlet and triplet excited states of a molecular dianion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winghart, Marc-Oliver, E-mail: marc-oliver.winghart@kit.edu; Unterreiner, Andreas-Neil; Yang, Ji-Ping

2016-02-07

Time-resolved pump-probe photoelectron spectroscopy has been used to study the relaxation dynamics of gaseous [Pt{sub 2}(μ-P{sub 2}O{sub 5}H{sub 2}){sub 4} + 2H]{sup 2−} after population of its first singlet excited state by 388 nm femtosecond laser irradiation. In contrast to the fluorescence and phosphorescence observed in condensed phase, a significant fraction of the photoexcited isolated dianions decays by electron loss to form the corresponding monoanions. Our transient photoelectron data reveal an ultrafast decay of the initially excited singlet {sup 1}A{sub 2u} state and concomitant rise in population of the triplet {sup 3}A{sub 2u} state, via sub-picosecond intersystem crossing (ISC). Wemore » find that both of the electronically excited states are metastably bound behind a repulsive Coulomb barrier and can decay via delayed autodetachment to yield electrons with characteristic kinetic energies. While excited state tunneling detachment (ESETD) from the singlet {sup 1}A{sub 2u} state takes only a few picoseconds, ESETD from the triplet {sup 3}A{sub 2u} state is much slower and proceeds on a time scale of hundreds of nanoseconds. The ISC rate in the gas phase is significantly higher than in solution, which can be rationalized in terms of changes to the energy dissipation mechanism in the absence of solvent molecules. [Pt{sub 2}(μ-P{sub 2}O{sub 5}H{sub 2}){sub 4} + 2H]{sup 2−} is the first example of a photoexcited multianion for which ESETD has been observed following ISC.« less

The Influence of Preoperative Aneurysmal Thrombus Quantity and Distribution on the Development of Type II Endoleaks with Aneurysm Sac Enlargement After EVAR of AAA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Müller-Wille, R., E-mail: rene.mueller-wille@ukr.de; Güntner, O., E-mail: oliverguentner@yahoo.de; Zeman, F., E-mail: florian.zeman@ukr.de

PurposeTo determine the influence of preoperative aneurysmal thrombus quantity and distribution on the development of type II endoleak with aneurysm sac enlargement after endovascular aneurysm repair (EVAR).Materials and MethodsWe retrospectively analyzed the pre- and postoperatively performed CT scans of 118 patients who had follow-up imaging for at least 1 year after EVAR available. We assessed preoperative thrombus perimeter (T{sub Peri}), diameter (T{sub Dia}), cross-sectional area (T{sub CSA}), and volume (T{sub Vol}). The preoperative thrombus distribution was classified into no thrombus, semilunar-shaped (anterior, right side, left side, posterior) thrombus, and circumferential type thrombus. The number of preoperative patent aortic side branches (ASB)more » was identified. Endpoint was type II endoleak with aneurysm volume (A{sub Vol}) increase of ≥5 % during follow-up.ResultsDuring follow-up (2 years, range 1–9 years), 17 patients with type II endoleak had significant A{sub Vol} increase. Less preoperative T{sub Peri}, T{sub Dia}, T{sub CSA}, and T{sub Vol} were associated with A{sub Vol} increase. A circumferential thrombus distribution significantly protected against aneurysm enlargement (p = 0.028). The variables with the strongest significance for A{sub Vol} increase were preoperative T{sub Vol}/A{sub Vol} ratio (OR 0.95; p = 0.037) and number of patent ASB (OR 3.52; p < 0.001).ConclusionA low preoperative T{sub Vol}/A{sub Vol} ratio and a high number of patent ASB were associated with aneurysm sac enlargement after EVAR.« less

Electron momentum spectroscopy of dimethyl ether taking account of nuclear dynamics in the electronic ground state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morini, Filippo; Deleuze, Michael Simon, E-mail: michael.deleuze@uhasselt.be; Watanabe, Noboru

The influence of nuclear dynamics in the electronic ground state on the (e,2e) momentum profiles of dimethyl ether has been analyzed using the harmonic analytical quantum mechanical and Born-Oppenheimer molecular dynamics approaches. In spite of fundamental methodological differences, results obtained with both approaches consistently demonstrate that molecular vibrations in the electronic ground state have a most appreciable influence on the momentum profiles associated to the 2b{sub 1}, 6a{sub 1}, 4b{sub 2}, and 1a{sub 2} orbitals. Taking this influence into account considerably improves the agreement between theoretical and newly obtained experimental momentum profiles, with improved statistical accuracy. Both approaches point outmore » in particular the most appreciable role which is played by a few specific molecular vibrations of A{sub 1}, B{sub 1}, and B{sub 2} symmetries, which correspond to C–H stretching and H–C–H bending modes. In line with the Herzberg-Teller principle, the influence of these molecular vibrations on the computed momentum profiles can be unraveled from considerations on the symmetry characteristics of orbitals and their energy spacing.« less

Rheological properties of molten Kilauea Iki basalt containing suspended crystals. Revision 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weed, H.C.; Ryerson, F.J.; Piwinskii, A.J.

1984-01-01

In order to model the flow behavior of molten silicate suspensions, such as magmas and slags, the rheological behavior must be known as a function of the concentration of suspended crystals, melt composition, and external conditions. We have determined the viscosity and crystallization sequence for a Kilauea Iki basalt between 1250/sup 0/C and 1149/sup 0/C at 100 kPa total pressure and fO/sub 2/ corresponding to the quartz-fayalite-magnetite buffer in an iron-saturated Pt30Rh rotating cup viscometer of the Couette type. The apparent viscosity varies from 9 to 879 Pa.s. The concentration of suspended cyrstals varies from 18 volume percent at 1250/supmore » 0/C to 59 volume percent at 1149/sup 0/C. The molten silicate suspension shows power-law behavior: log tau yx = A/sub 0/ + A/sub 1/ log du/dx, where tau/sub yx/ is the shear stress and (du/dx) the shear rate. Since A/sub 1/ less than or equal to 1, the apparent viscosity decreases with increasing shear rate and the system is pseudoplastic. 15 refs., 4 figs., 5 tabs.« less

Determination of the S-Wave Pi Pi Scattering Lengths From a Study of K - to Pi - Pi0 Pi0 Decays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Batley, J.R.; Culling, A.J.; Kalmus, G.

We report the results from a study of the full sample of {approx}6.031 x 10{sup 7} K{sup {+-}} {yields} {pi}{sup {+-}}{pi}{sup 0}{pi}{sup 0} decays recorded by the NA48/2 experiment at the CERN SPS. As first observed in this experiment, the {pi}{sup 0}{pi}{sup 0} invariant mass (M{sub 00}) distribution shows a cusp-like anomaly in the region around M{sub 00} = 2m{sub +}, where m{sub +} is the charged pion mass. This anomaly has been interpreted as an effect due mainly to the final state charge exchange scattering process {pi}{sup +}{pi}{sup -} {yields} {pi}{sup 0}{pi}{sup 0} in K{sup {+-}} {yields} {pi}{sup {+-}}{pi}{supmore » +}{pi}{sup -} decay. Fits to the M{sub 00} distribution using two different theoretical formulations provide the presently most precise determination of a{sub 0} - a{sub 2}, the difference between the {pi}{pi} S-wave scattering lengths in the isospin I = 0 and I = 2 states. Higher-order {pi}{pi} rescattering terms, included in the two formulations, allow also an independent, though less precise, determination of a{sub 2}.« less

On Measurements of the Electrons and Holes Impact-Ionization Coefficients in 4H–SiC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kyuregyan, A. S., E-mail: semlab@yandex.ru

All published results of measurements (at 300 K) of the impact ionization coefficients for electrons α{sub n} and holes α{sub p} in 4H–SiC are analyzed. It is shown that the most plausible approximations of dependences of α{sub n,} {sub p} on electric-field strength E have the usual form α{sub n,} {sub p} = a{sub n,p} exp(–E{sub n,} {sub p}/E) at fitting-parameter values of a{sub n} = 38.6 × 106 cm{sup –1}, E{sub n} = 25.6 MV/cm, a{sub p} = 5.31 × 106 cm{sup –1}, and E{sub p} = 13.1 MV/cm. These dependences α{sub n,} {sub p}(E) are used to calculatemore » the highest field strength E{sub b} and thickness w{sub b} of the space-charge region at the breakdown voltage U{sub b}. A number of new formulas for calculating α{sub n,} {sub p}(E) are obtained from the results of measuring the avalanche-multiplication coefficients and the excess-noise factors under the single-sided illumination of photodiodes with stepped doping.« less

Precise measurement of the left-right cross section asymmetry in Z boson production by electron-positron collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frey, R.E.

1994-12-01

A precise measurement of the left-right cross section asymmetry (A{sub LR}) for Z boson production by e{sup +}e{sup {minus}} collisions has been attained at the SLAC Linear Collider with the SLD detector. The author describes this measurement for the 1993 data run, emphasizing the significant improvements in polarized beam operation which took place for this run, where the luminosity-weighted electron beam polarization averaged 62.6 {+-} 1.2%. Preliminary 1993 results for A{sub LR} are presented. When combined with the (less precise) 1992 result, the preliminary result for the effective weak mixing angle is sin{sup 2}{theta}{sub W}{sup eff} = 0.2290 {+-} 0.0010.

Models of Hematopoietic Dynamics Following Burn for Use in Combined Injury Simulations

DTIC Science & Technology

2015-04-28

distribution is unlimited. 13. SUPPLEMENTARY NOTES 14. ABSTRACT The effects of thermal injury were incorporated into previously developed models that...per kilogram (C kg–1) absorbed dose (rad) 1 × 10–2 joule per kilogram (J kg–1§) equivalent and effective dose (rem) 1 × 10–2 joule per kilogram (J...Gy = 1 J kg–1). **The special name for the SI unit of equivalent and effective dose is the sievert (Sv). (1 Sv = 1 J kg–1). Table of Contents Table

Magnetic spectral signatures in the Earth's magnetosheath and plasma depletion layer

NASA Technical Reports Server (NTRS)

Anderson, Brian J.; Fuselier, Stephen A.; Gary, S. Peter; Denton, Richard E.

1994-01-01

Correlations between plasma properties and magnetic fluctuations in the sub-solar magnetosheath downstream of a quasi-perpendicular shock have been found and indicate that mirror and ion cyclotronlike fluctuations correlate with the magnetosheath proper and plasma depletion layer, respectively (Anderson and Fueselier, 1993). We explore the entire range of magnetic spectral signatures observed from the Active Magnetospheric Particle Tracer Explorers/Charge Composition Explorer (AMPTE/CCE)spacecraft in the magnetosheath downstream of a quasi-perpendicular shock. The magnetic spectral signatures typically progress from predominantly compressional fluctuations,delta B(sub parallel)/delta B perpendicular to approximately 3, with F/F (sub p) less than 0.2 (F and F (sub p) are the wave frequency and proton gyrofrequency, respectively) to predominantly transverse fluctuations, delta B(sub parallel)/delta B perpendicular to approximately 0.3, extending up to F(sub p). The compressional fluctuations are characterized by anticorrelation between the field magnitude and electron density, n(sub e), and by a small compressibility, C(sub e) identically equal to (delta n(sub e)/n(sub e)) (exp 2) (B/delta B(sub parallel)) (exp 2) approximately 0.13, indicative of mirror waves. The spectral characteristics of the transverse fluctuations are in agreement with predictions of linear Vlasov theory for the H(+) and He(2+) cyclotron modes. The power spectra and local plasma parameters are found to vary in concert: mirror waves occur for beta(s ub parallel p) (beta (sub parallel p) identically = 2 mu(sub zero) n(sub p) kT (sub parallel p) / B(exp 2) approximately = 2, A(sub p) indentically = T(sub perpendicular to p)/T(sub parallel p) - 1 approximately = 0.4, whereas cyclotron waves occur for beta (sub parallel p) approximately = 0.2 and A(sub p) approximately = 2. The transition from mirror to cyclotron modes is predicted by linear theory. The spectral characteristics overlap for

Hope or Hype? What is Next for Biofuels? (LBNL Science at the Theater)

ScienceCinema

Keasling, Jay; Bristow, Jim; Tringe, Susannah Green

2017-12-09

Science at the Theater: From the sun to your gas tank: A new breed of biofuels may help solve the global energy challenge and reduce the impact of fossil fuels on global warming. KTVU Channel 2 health and science editor John Fowler will moderate a panel of Lawrence Berkeley National Laboratory scientists who are developing ways to convert the solar energy stored in plants into liquid fuels. Jay Keasling is one of the foremost authorities in the field of synthetic biology. He is applying this research toward the production of advanced carbon-neutral biofuels that can replace gasoline on a gallon-for-gallon basis. Keasling is Berkeley Labs Acting Deputy Director and the Chief Executive Officer of the U.S. Department of Energys Joint BioEnergy Institute. Jim Bristow is deputy director of programs for the U.S. Department of Energy Joint Genome Institute (JGI), a national user facility in Walnut Creek, CA. He developed and implemented JGIs Community Sequencing Program, which provides large-scale DNA sequencing and analysis to advance genomics related to bioenergy and environmental characterization and cleanup. Susanna Green Tringe is a computational biologist with the U.S. Department of Energy Joint Genome Institute (JGI). She helped pioneer the field of metagenomics, a new strategy for isolating, sequencing, and characterizing DNA extracted directly from environmental samples, such as the contents of the termite gut, which yielded enzymes responsible for breakdown of wood into fuel.

Development of a general method for obtaining the geometry of microfluidic networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Razavi, Mohammad Sayed, E-mail: m.sayedrazavi@gmail.com; Salimpour, M. R.; Shirani, Ebrahim

2014-01-15

In the present study, a general method for geometry of fluidic networks is developed with emphasis on pressure-driven flows in the microfluidic applications. The design method is based on general features of network's geometry such as cross-sectional area and length of channels. Also, the method is applicable to various cross-sectional shapes such as circular, rectangular, triangular, and trapezoidal cross sections. Using constructal theory, the flow resistance, energy loss and performance of the network are optimized. Also, by this method, practical design strategies for the fabrication of microfluidic networks can be improved. The design method enables rapid prediction of fluid flowmore » in the complex network of channels and is very useful for improving proper miniaturization and integration of microfluidic networks. Minimization of flow resistance of the network of channels leads to universal constants for consecutive cross-sectional areas and lengths. For a Y-shaped network, the optimal ratios of consecutive cross-section areas (A{sub i+1}/A{sub i}) and lengths (L{sub i+1}/L{sub i}) are obtained as A{sub i+1}/A{sub i} = 2{sup −2/3} and L{sub i+1}/L{sub i} = 2{sup −1/3}, respectively. It is shown that energy loss in the network is proportional to the volume of network. It is also seen when the number of channels is increased both the hydraulic resistance and the volume occupied by the network are increased in a similar manner. Furthermore, the method offers that fabrication of multi-depth and multi-width microchannels should be considered as an integral part of designing procedures. Finally, numerical simulations for the fluid flow in the network have been performed and results show very good agreement with analytic results.« less

On Pulsating and Cellular Forms of Hydrodynamic Instability in Liquid-Propellant Combustion

NASA Technical Reports Server (NTRS)

Margolis, Stephen B.; Sacksteder, Kurt (Technical Monitor)

1998-01-01

An extended Landau-Levich model of liquid-propellant combustion, one that allows for a local dependence of the burning rate on the (gas) pressure at the liquid-gas interface, exhibits not only the classical hydrodynamic cellular instability attributed to Landau but also a pulsating hydrodynamic instability associated with sufficiently negative pressure sensitivities. Exploiting the realistic limit of small values of the gas-to-liquid density ratio p, analytical formulas for both neutral stability boundaries may be obtained by expanding all quantities in appropriate powers of p in each of three distinguished wave-number regimes. In particular, composite analytical expressions are derived for the neutral stability boundaries A(sub p)(k), where A, is the pressure sensitivity of the burning rate and k is the wave number of the disturbance. For the cellular boundary, the results demonstrate explicitly the stabilizing effect of gravity on long-wave disturbances, the stabilizing effect of viscosity (both liquid and gas) and surface tension on short-wave perturbations, and the instability associated with intermediate wave numbers for negative values of A(sub p), which is characteristic of many hydroxylammonium nitrate-based liquid propellants over certain pressure ranges. In contrast, the pulsating hydrodynamic stability boundary is insensitive to gravitational and surface-tension effects but is more sensitive to the effects of liquid viscosity because, for typical nonzero values of the latter, the pulsating boundary decreases to larger negative values of A(sub p) as k increases through O(l) values. Thus, liquid-propellant combustion is predicted to be stable (that is, steady and planar) only for a range of negative pressure sensitivities that lie below the cellular boundary that exists for sufficiently small negative values of A(sub p) and above the pulsating boundary that exists for larger negative values of this parameter.

Transformation process for production of ultrahigh carbon steels and new alloys

DOEpatents

Strum, M.J.; Goldberg, A.; Sherby, O.D.; Landingham, R.L.

1995-08-29

Ultrahigh carbon steels with superplastic properties are produced by heating a steel containing ferrite and carbide phases to a soaking temperature approximately 50 C above the A{sub 1} transformation temperature, soaking the steel above the A{sub 1} temperature for a sufficient time that the major portion of the carbides dissolve into the austenite matrix, and then cooling the steel in a controlled manner within predetermined limits of cooling rate or transformation temperature, to obtain a steel having substantially spheroidal carbides. New alloy compositions contain aluminum and solute additions which promote the formation of a fine grain size and improve the resistance of the carbides to coarsening at the forming temperature. 9 figs.

Transformation process for production of ultrahigh carbon steels and new alloys

DOEpatents

Strum, Michael J.; Goldberg, Alfred; Sherby, Oleg D.; Landingham, Richard L.

1995-01-01

Ultrahigh carbon steels with superplastic properties are produced by heating a steel containing ferrite and carbide phases to a soaking temperature approximately 50.degree. C. above the A.sub.1 transformation temperature, soaking the steel above the A.sub.1 temperature for a sufficient time that the major portion of the carbides dissolve into the austenite matrix, and then cooling the steel in a controlled manner within predetermined limits of cooling rate or transformation temperature, to obtain a steel having substantially spheroidal carbides. New alloy compositions contain aluminum and solute additions which promote the formation of a fine grain size and improve the resistance of the carbides to coarsening at the forming temperature.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xin, Qiaoling, E-mail: xinqiaoling0923@163.com; Jiang, Lining, E-mail: jianglining@bit.edu.cn

Let G be a finite group and H a normal subgroup. D(H; G) is the crossed product of C(H) and CG which is only a subalgebra of D(G), the double algebra of G. One can construct a C*-subalgebra F{sub H} of the field algebra F of G-spin models, so that F{sub H} is a D(H; G)-module algebra, whereas F is not. Then the observable algebra A{sub (H,G)} is obtained as the D(H; G)-invariant subalgebra of F{sub H}, and there exists a unique C*-representation of D(H; G) such that D(H; G) and A{sub (H,G)} are commutants with each other.

Complete genome sequence of Staphylothermus hellenicus P8T

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Iain; Wirth, Reinhard; Lucas, Susan

2011-01-01

Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phy- lum Crenarchaeota. Strain P8T is the type strain of the species and was isolated from a shal- low hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the com- plete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein- coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) La- boratory Sequencing Program (LSP) project.

Subsurface Microbes Expanding the Tree of Life

ScienceCinema

Banfield, Jillian

2018-02-14

Jillian Banfield, Ph.D., UC Berkeley Professor and Berkeley Lab Earth Sciences Division staff scientist and long-time user of the DOE Joint Genome Institute’s resources shares her perspective on how the DOE JGI helps advance her research addressing knowledge gaps related to the roles of subsurface microbial communities in biogeochemical cycling. The video was filmed near the town of Rifle, Colorado at the primary field site for Phase I of the Subsurface Systems Scientific Focus Area 2.0 sponsored by the DOE Office of Biological and Environmental Research.

Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

DOE PAGES

Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex; ...

2017-09-21

Dethiobacter alkaliphilus strain AHT1 T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is thus a Gram-positive bacterium with low GC content, within the phylum Firmicutes. We report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1 T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.

Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex

Dethiobacter alkaliphilus strain AHT1 T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is thus a Gram-positive bacterium with low GC content, within the phylum Firmicutes. We report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1 T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.

Recent Improvements in Estimating Convective and Stratiform Rainfall in Amazonia

NASA Technical Reports Server (NTRS)

Negri, Andrew J.

1999-01-01

In this paper we present results from the application of a satellite infrared (IR) technique for estimating rainfall over northern South America. Our main objectives are to examine the diurnal variability of rainfall and to investigate the relative contributions from the convective and stratiform components. We apply the technique of Anagnostou et al (1999). In simple functional form, the estimated rain area A(sub rain) may be expressed as: A(sub rain) = f(A(sub mode),T(sub mode)), where T(sub mode) is the mode temperature of a cloud defined by 253 K, and A(sub mode) is the area encompassed by T(sub mode). The technique was trained by a regression between coincident microwave estimates from the Goddard Profiling (GPROF) algorithm (Kummerow et al, 1996) applied to SSM/I data and GOES IR (11 microns) observations. The apportionment of the rainfall into convective and stratiform components is based on the microwave technique described by Anagnostou and Kummerow (1997). The convective area from this technique was regressed against an IR structure parameter (the Convective Index) defined by Anagnostou et al (1999). Finally, rainrates are assigned to the Am.de proportional to (253-temperature), with different rates for the convective and stratiform

Conductive lithium storage electrode

DOEpatents

Chiang, Yet-Ming; Chung, Sung-Yoon; Bloking, Jason T; Andersson, Anna M

2014-10-07

A compound comprising a composition A.sub.x(M'.sub.1-aM''.sub.a).sub.y(XD.sub.4).sub.z, A.sub.x(M'.sub.1-aM''.sub.a).sub.y(DXD.sub.4).sub.z, or A.sub.x(M'.sub.1-aM''.sub.a).sub.y(X.sub.2D.sub.7).sub.z, (A.sub.1-aM''.sub.a).sub.xM'.sub.y(XD.sub.4).sub.z, (A.sub.1-aM''.sub.a).sub.xM'.sub.y(DXD.sub.4).sub.z, or (A.sub.1-aM''.sub.a).sub.xM'.sub.y(X.sub.2D.sub.7).sub.z. In the compound, A is at least one of an alkali metal and hydrogen, M' is a first-row transition metal, X is at least one of phosphorus, sulfur, arsenic, molybdenum, and tungsten, M'' any of a Group IIA, IIIA, IVA, VA, VIA, VIIA, VIIIA, IB, IIB, IIIB, IVB, VB, and VIB metal, D is at least one of oxygen, nitrogen, carbon, or a halogen, 0.0001

Nanoscale modulations in (KLa)(CaW)O-6 and (NaLa)(CaW)O-6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Licurse, Mark; Borisevich, Albina Y; Davies, Peter

2012-01-01

Complex nanoscale modulations are identified in two new A-site ordered perovskites, (KLa)(CaW)O{sub 6} and (NaLa)(CaW)O{sub 6}. In (KLa)(CaW)O{sub 6}, selected-area electron diffraction (SAED) and high-resolution transmission electron microscopy (HRTEM) show an incommensurate nanocheckerboard modulation with {approx}9.4 x 9.4 a{sub p} periodicity (a{sub p} {approx} 4 {angstrom} for the cubic perovskite aristotype). For (NaLa)(CaW)O{sub 6} a one-dimensional modulation is observed with a {approx}16(1 1 0)a{sub p} repeat; the <1 1 0> orientation of the nanostripes is different from the <1 0 0> stripes observed in other mixed A-site systems. Studies using high temperature x-ray diffraction suggest the formation of the complexmore » modulations is associated with small deviations from the ideal 1:1:1:1 stoichiometry of the (A{sup +}La{sup 3+})(CaW)O{sub 6} phases. Z-contrast images acquired on an aberration-corrected microscope provide evidence for deviations from stoichiometry with a {approx}1:15 periodic arrangement of La{sub 4/3}(CaW)O{sub 6}:(NaLa)(CaW)O{sub 6} nano-phases.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novales-Sanchez, H.; Toscano, J. J.

A five-dimensional pure Yang-Mills theory, with the fifth coordinate compactified on the orbifold S{sup 1}/Z{sub 2} of radius R, leads to a four-dimensional theory which is governed by two types of infinitesimal gauge transformations, namely, the well-known standard gauge transformations (SGT) dictated by the SU{sub 4}(N) group under which the zero Fourier modes A{sub {mu}}{sup (0)a} transform as gauge fields, and a set of nonstandard gauge transformations (NSGT) determining the gauge nature of the Kaluza-Klein (KK) excitations A{sub {mu}}{sup (m)a}. By using a SGT-covariant gauge-fixing procedure for removing the degeneration associated with the NSGT, we integrate out the KK excitationsmore » and obtain a low-energy effective Lagrangian expansion involving all of the independent canonical-dimension-six operators that are invariant under the SGT of the SU{sub 4}(N) group and that are constituted by light gauge fields, A{sub {mu}}{sup (0)a}, exclusively. It is shown that this effective Lagrangian is invariant under the SGT, but it depends on the gauge-fixing of the gauge KK excitations. Our result shows explicitly that the one-loop contributions of the KK excitations to light (standard) Green's functions are renormalizable.« less

Full dimensional Franck-Condon factors for the acetylene A{sup ~} {sup 1}A{sub u}—X{sup ~1}Σ{sub g}{sup +} transition. II. Vibrational overlap factors for levels involving excitation in ungerade modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, G. Barratt, E-mail: barratt@mit.edu; Baraban, Joshua H.; Field, Robert W.

2014-10-07

A full-dimensional Franck-Condon calculation has been applied to the A{sup ~} {sup 1}A{sub u}—X{sup ~1}Σ{sub g}{sup +} transition in acetylene in the harmonic normal mode basis. Details of the calculation are discussed in Part I of this series. To our knowledge, this is the first full-dimensional Franck-Condon calculation on a tetra-atomic molecule undergoing a linear-to-bent geometry change. In the current work, the vibrational intensity factors for levels involving excitation in ungerade vibrational modes are evaluated. Because the Franck-Condon integral accumulates away from the linear geometry, we have been able to treat the out-of-plane component of trans bend (ν{sub 4}{sup ′′}) in themore » linear X{sup ~} state in the rotational part of the problem, restoring the χ Euler angle and the a-axis Eckart conditions. A consequence of the Eckart conditions is that the out-of-plane component of ν{sub 4}{sup ′′} does not participate in the vibrational overlap integral. This affects the structure of the coordinate transformation and the symmetry of the vibrational wavefunctions used in the overlap integral, and results in propensity rules involving the bending modes of the X{sup ~} state that were not previously understood. We explain the origin of some of the unexpected propensities observed in IR-UV laser-induced fluorescence spectra, and we calculate emission intensities from bending levels of the A{sup ~} state into bending levels of the X{sup ~} state, using normal bending mode and local bending mode basis sets. Our calculations also reveal Franck-Condon propensities for the Cartesian components of the cis bend (ν{sub 5}{sup ′′}), and we predict that the best A{sup ~}-state vibrational levels for populating X{sup ~}-state levels with large amplitude bending motion localized in a single C–H bond (the acetylene↔vinylidene isomerization coordinate) involve a high degree of excitation in ν{sub 6}{sup ′} (cis-bend). Mode ν{sub 4}{sup �

Isolation, enzyme-bound structure and antibacterial activity of platencin A[subscript 1] from Streptomyces platensis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Sheo B.; Ondeyka, John G.; Herath, Kithsiri B.

Natural products continue to serve as one of the best sources for discovery of antibacterial agents as exemplified by the recent discoveries of platensimycin and platencin. Chemical modifications as well as discovery of congeners are the main sources for gaining knowledge of structure-activity relationship of natural products. Screening for congeners in the extracts of the fermentation broths of Streptomyces platensis led to the isolation of platencin A{sub 1}, a hydroxy congener of platencin. The hydroxylation of the tricyclic enone moiety negatively affected the antibacterial activity and appears to be consistent with the hydrophobic binding pocket of the FabF. Isolation, structure,more » enzyme-bound structure and activity of platencin A{sub 1} and two other congeners have been described.« less

Production of High Harmonic X-ray Radiation from Non-linear Thomson Scattering at LLNL PLEIADES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lim, J; Doyuran, A; Frigola, P

2005-05-17

We describe an experiment for production of high harmonic x-ray radiation from Thomson backscattering of an ultra-short high power density laser by a relativistic electron beam at the PLEIADES facility at LLNL. In this scenario, electrons execute a ''figure-8'' motion under the influence of the high-intensity laser field, where the constant characterizing the field strength is expected to exceed unity: a{sub L} = eE{sub L}/m{sub e}cw{sub L} {ge} 1. With large a{sub L} this motion produces high harmonic x-ray radiation and significant broadening of the spectral peaks. This paper is intended to give a layout of the PLEIADES experiment, alongmore » with progress towards experimental goals.« less

Recent Results of TMD Measurements from Jefferson Lab Hall A

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Xiaodong

2013-10-01

This slide-show presents results on transverse momentum distributions. The presentation covers: target single-spin asymmetry (SSA) (in parity conserving interactions); • Results of JLab Hall A polarized {sup 3}He target TMD measurement; • Semi-­inclusive deep-inelastic scattering channels (E06-010); • Target single-spin asymmetry A{sub UT}, Collins and Sivers SSA on neutron; • Double-spin asymmetry A{sub LT}, extract TMD g{sub 1T} on neutron; • Inclusive channels SSA (E06-010, E05-015, E07-013) • Target SSA: inclusive {sup 3}He(e,e’) quasi-elastic scattering; • Target SSA: inclusive {sup 3}He(e,e’) deep inelastic-elastic scattering; • New SIDIS experiments planned in Hall-A for JLab-12 GeV.

Nonclassical Smoothening of Nanoscale Surface Corrugations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erlebacher, Jonah; Aziz, Michael J.; Chason, Eric

2000-06-19

We report the first experimental observation of nonclassical morphological equilibration of a corrugated crystalline surface. Periodic rippled structures with wavelengths of 290-550 nm were made on Si(001) by sputter rippling and then annealed at 650-750 degree sign C . In contrast to the classical exponential decay with time, the ripple amplitude A{sub {lambda}}(t) followed an inverse linear decay, A{sub {lambda}}(t)=A{sub {lambda}}( 0)/(1+k{sub {lambda}}t) , agreeing with a prediction of Ozdemir and Zangwill. We measure the activation energy for surface relaxation to be 1.6{+-}0.2 eV , consistent with the fundamental energies of creation and migration on Si(001). (c) 2000 The Americanmore » Physical Society.« less

Analysis of correlation functions in Toda theory and the Alday-Gaiotto-Tachikawa-Wyllard relation for SU(3) quiver

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kanno, Shoichi; Matsuo, Yutaka; Shiba, Shotaro

We give some evidences of the Alday-Gaiotto-Tachikawa-Wyllard relation between SU(3) quiver gauge theories and A{sub 2} Toda theory. In particular, we derive the explicit form of 5-point correlation functions in the lower orders and confirm the agreement with Nekrasov's partition function for SU(3)xSU(3) quiver gauge theory. The algorithm to derive the correlation functions can be applied to a general n-point function in A{sub 2} Toda theory, which will be useful to establish the relation for more generic quivers. Partial analysis is also given for the SU(3)xSU(2) case, and we comment on some technical issues that need clarification before establishing themore » relation.« less

A homologue of the defender against the apoptotic death gene (dad1 )in UV-exposed Chlamydomonas cells is downregulated with the onset of programmed cell death.

PubMed

Moharikar, Swati; D'Souza, Jacinta S; Rao, Basuthkar J

2007-03-01

We report here the isolation of a homologue of the potential anti-apoptotic gene, defender against apoptotic death (dad1 )from Chlamydomonas reinhardtii cells.Using polymerase chain reaction (PCR),we investigated its expression in the execution process of programmed cell death (PCD)in UV-C exposed dying C.reinhardtii cells.Reverse- transcriptase (RT)-PCR showed that C.reinhardtii dad1 amplification was drastically reduced in UV-C exposed dying C.reinhardtii cells.We connect the downregulation of dad1 with the upregulation of apoptosis protease activating factor-1 (APAF-1)and the physiological changes that occur in C.reinhardtii cells upon exposure to 12 J/m 2 UV-C in order to show a reciprocal relationship between proapoptotic and inhibitor of apoptosis factors.The temporal changes indicate a correlation between the onset of cell death and dad1 downregulation.The sequence of the PCR product of the cDNA encoding the dad1 homologue was aligned with the annotated dad1 (C_20215)from the Chlamydomonas database (http://genome.jgi-psf.org:8080/annotator/servlet/jgi.annotation.Annotation?pDb=chlre2); Annotation?pDb=chlre2 );this sequence was found to show 100% identity,both at the nucleotide and amino acid level. The 327 bp transcript showed an open reading frame of 87 amino acid residues.The deduced amino acid sequence of the putative C.reinhardtii DAD1 homologue showed 54% identity with Oryza sativa, 56 identity with Drosophila melanogaster, 66% identity with Xenopus laevis, and 64% identity with Homo sapiens,Sus scrofa,Gallus gallus,Rattus norvegicus and Mus musculus.

A Polynomial Time, Numerically Stable Integer Relation Algorithm

NASA Technical Reports Server (NTRS)

Ferguson, Helaman R. P.; Bailey, Daivd H.; Kutler, Paul (Technical Monitor)

1998-01-01

Let x = (x1, x2...,xn be a vector of real numbers. X is said to possess an integer relation if there exist integers a(sub i) not all zero such that a1x1 + a2x2 + ... a(sub n)Xn = 0. Beginning in 1977 several algorithms (with proofs) have been discovered to recover the a(sub i) given x. The most efficient of these existing integer relation algorithms (in terms of run time and the precision required of the input) has the drawback of being very unstable numerically. It often requires a numeric precision level in the thousands of digits to reliably recover relations in modest-sized test problems. We present here a new algorithm for finding integer relations, which we have named the "PSLQ" algorithm. It is proved in this paper that the PSLQ algorithm terminates with a relation in a number of iterations that is bounded by a polynomial in it. Because this algorithm employs a numerically stable matrix reduction procedure, it is free from the numerical difficulties, that plague other integer relation algorithms. Furthermore, its stability admits an efficient implementation with lower run times oil average than other algorithms currently in Use. Finally, this stability can be used to prove that relation bounds obtained from computer runs using this algorithm are numerically accurate.

Influence of chemical bonds on the lifetime of the molecular-field-split 2p levels in H{sub 2}S

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bueno, Andre Machado; Brito, Arnaldo Naves de; Fink, Reinhold F.

Different lifetime broadenings in molecular-field-split 2p core levels in H{sub 2}S are predicted theoretically and are identified in an experimental investigation of the S 2p Auger electron spectrum. The measurements were performed for the transition to the vibrationally resolved X{sup 1}A{sub 1} ground state of H{sub 2}S{sup 2+}. The lifetimes of the 3e{sub 1/2} and 5e{sub 1/2} levels of the 2p ionized molecule are found to be 64 and 74 meV, respectively. This unambiguous determination of the lifetime difference of 10{+-}1 meV is only possible as the 4e{sub 1/2}{yields}X{sup 1}A{sub 1}(2b{sub 1}{sup -2}) decay channel that overlaps the 5e{sub 1/2}{yields}X{supmore » 1}A{sub 1}(2b{sub 1}{sup -2}) channel is practically suppressed in Auger decay in H{sub 2}S. The lifetime difference is confirmed by ab initio calculations. A theoretical analysis shows that it results from the mutual orientation of the core hole in the intermediate states and the valence electron density in the sulfur 3p orbitals. Both are strongly influenced by the chemical bond. Thus the observed effect is the direct result of a fundamental property of molecular electronic structure.« less

THE ALBEDOS OF KEPLER'S CLOSE-IN SUPER-EARTHS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demory, Brice-Olivier, E-mail: bod21@cam.ac.uk

Exoplanet research focusing on the characterization of super-Earths is currently limited to the handful of targets orbiting bright stars that are amenable to detailed study. This Letter proposes to look at alternative avenues to probe the surface and atmospheric properties of this category of planets, known to be ubiquitous in our galaxy. I conduct Markov Chain Monte Carlo light-curves analyses for 97 Kepler close-in R{sub P} ≲ 2.0 R {sub ⊕} super-Earth candidates with the aim of detecting their occultations at visible wavelengths. Brightness temperatures and geometric albedos in the Kepler bandpass are constrained for 27 super-Earth candidates. A hierarchicalmore » Bayesian modeling approach is then employed to characterize the population-level reflective properties of these close-in super-Earths. I find median geometric albedos A{sub g} in the Kepler bandpass ranging between 0.16 and 0.30, once decontaminated from thermal emission. These super-Earth geometric albedos are statistically larger than for hot Jupiters, which have medians A{sub g} ranging between 0.06 and 0.11. A subset of objects, including Kepler-10b, exhibit significantly larger albedos (A{sub g} ≳ 0.4). I argue that a better understanding of the incidence of stellar irradation on planetary surface and atmospheric processes is key to explain the diversity in albedos observed for close-in super-Earths.« less

The integrated microbial genome resource of analysis.

PubMed

Checcucci, Alice; Mengoni, Alessio

2015-01-01

Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.

Complete genome sequence of the plant-associated Serratia plymuthica strain AS13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neupane, Saraswoti; Finlay, Roger D.; Kyrpides, Nikos C

2012-01-01

Serratia plymuthica AS13 is a plant-associated Gammaproteobacteria, isolated from rapeseed roots. It is of special interest because of its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The complete genome of S. plymuthica AS13 consists of a 5,442,549 bp circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced as part of the project enti- tled Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens within the 2010 DOE-JGI Community Sequencing Program (CSP2010).

Complete genome sequence of Serratia plymuthica strain AS12

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neupane, Saraswoti; Finlay, Roger D.; Alstrom, Sadhna

2012-01-01

A plant associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest due to its plant growth promoting and plant pathogen inhibiting ability. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled 'Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens'.

Light response of phytoplankton in the South Atlantic Ocean: Interpretation of observations and application to remote sensing

NASA Technical Reports Server (NTRS)

Hood, Raleigh R.

1995-01-01

A simplified, nonspectral derivation of a classical theory in plant physiology is presented and used to derive an absorption-based primary productivity algorithm. Field observations from a meridional transect (4 deg N to 42 deg S) in the Atlantic Ocean are then described and interpreted in this theoretical context. The observations include photosynthesis-irradiance curve parameters (alpha and P(sub max)), chlorophyll a and phaeopigment concentration, and estimated phytoplankton absorption coefficients at wavelength = 440 nm (a(sub ph)(440)). Observations near the top (50% I(sub 0)) and bottom (6% I(sub 0)) of the euphotic zone are contrasted. At both light levels, alpha, P(sub max), a(sub ph)(440), and pigment concentration varied similarly along the transect: values were highest at the equator and at the southern end of the transect and lowest in the central South Atlantic. It is concluded that this pattern was related to increased nutrient availability due to equatorial upwelling in the north, and increased wind mixing in the south. At the 50% light level, alpha increased relative to a(sub ph) at the southern end of the transect. This result appears to reflect a large-scale meridional (southward) increase in the average quantum efficiency of the photosynthetic units of the phytoplankton. A correlation analysis of the data reveals that at the 50% light level, variations in P(sub max) were more closely related to a(sub ph)(440) than chlorophyll concentration and that phytoplankton absorption explains 90% of the variability in P(sub max). In theory, this shows that the ratio of the average quantum efficiency of the photosynthetic units of the phytoplankton to the product of their average absorption cross section and turnover time is relatively constant. This result is used to simplify the absorption-based primary productivity algorithm derived previously. The feasibility of using this model to estimate production rate from satellite ocean color observations is

Complete basis set extrapolations for low-lying triplet electronic states of acetylene and vinylidene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sherrill, C. David; Byrd, Edward F. C.; Head-Gordon, Martin

2000-07-22

A recent study by Ahmed, Peterka, and Suits [J. Chem. Phys. 110, 4248 (1999)] has presented the first experimentally derived estimate of the singlet-triplet gap in the simplest alkyne, acetylene. Their value, T{sub 0}(a(tilde sign) {sup 3}B{sub 2})=28 900 cm{sup -1}, does not agree with previous theoretical predictions using the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] method and a triple-{zeta} plus double polarization plus f-function basis set (TZ2P f ), which yields 30 500{+-}1000 cm{sup -1}. This discrepancy has prompted us to investigate possible deficiencies in this usually-accurate theoretical approach. Employing extrapolations to the complete basis set limit alongmore » with corrections for full connected triple excitations, core correlation, and even relativistic effects, we obtain a value of 30 900 cm-1 (estimated uncertainty {+-}230 cm-1), demonstrating that the experimental value is underestimated. To assist in the interpretation of anticipated future experiments, we also present highly accurate excitation energies for the other three low-lying triplet states of acetylene, a(tilde sign) {sup 3}B{sub u}(33 570{+-}230 cm{sup -1}), b(tilde sign) {sup 3}A{sub u}(36 040{+-}260 cm{sup -1}), and b(tilde sign) {sup 3}A{sub 2}(38 380{+-}260 cm{sup -1}), and the three lowest-lying states of vinylidene, X(tilde sign) {sup 1}A{sub 1}(15 150{+-}230 cm{sup -1}), a(tilde sign) {sup 3}B{sub 2}(31 870{+-}230 cm{sup -1}), and b(tilde sign) {sup 3}A{sub 2}(36 840{+-}350 cm{sup -1}). Finally, we assess the ability of density functional theory (DFT) and the Gaussian-3 method to match our benchmark results for adiabatic excitation energies of C{sub 2}H{sub 2}. (c) 2000 American Institute of Physics.« less

Omega-3 fatty acid oxidation products prevent vascular endothelial cell activation by coplanar polychlorinated biphenyls

DOE Office of Scientific and Technical Information (OSTI.GOV)

Majkova, Zuzana; Layne, Joseph; Sunkara, Manjula

Coplanar polychlorinated biphenyls (PCBs) may facilitate development of atherosclerosis by stimulating pro-inflammatory pathways in the vascular endothelium. Nutrition, including fish oil-derived long-chain omega-3 fatty acids, such as docosahexaenoic acid (DHA, 22:6{omega}-3), can reduce inflammation and thus the risk of atherosclerosis. We tested the hypothesis that cyclopentenone metabolites produced by oxidation of DHA can protect against PCB-induced endothelial cell dysfunction. Oxidized DHA (oxDHA) was prepared by incubation of the fatty acid with the free radical generator 2,2-azo-bis(2-amidinopropane) dihydrochloride (AAPH). Cellular pretreatment with oxDHA prevented production of superoxide induced by PCB77, and subsequent activation of nuclear factor-{kappa}B (NF-{kappa}B). A{sub 4}/J{sub 4}-neuroprostanes (NPs)more » were identified and quantitated using HPLC ESI tandem mass spectrometry. Levels of these NPs were markedly increased after DHA oxidation with AAPH. The protective actions of oxDHA were reversed by treatment with sodium borohydride (NaBH{sub 4}), which concurrently abrogated A{sub 4}/J{sub 4}-NP formation. Up-regulation of monocyte chemoattractant protein-1 (MCP-1) by PCB77 was markedly reduced by oxDHA, but not by un-oxidized DHA. These protective effects were proportional to the abundance of A{sub 4}/J{sub 4} NPs in the oxidized DHA sample. Treatment of cells with oxidized eicosapentaenoic acid (EPA, 20:5{omega}-3) also reduced MCP-1 expression, but less than oxDHA. Treatment with DHA-derived cyclopentenones also increased DNA binding of NF-E2-related factor-2 (Nrf2) and downstream expression of NAD(P)H:quinone oxidoreductase (NQO1), similarly to the Nrf-2 activator sulforaphane. Furthermore, sulforaphane prevented PCB77-induced MCP-1 expression, suggesting that activation of Nrf-2 mediates the observed protection against PCB77 toxicity. Our data implicate A{sub 4}/J{sub 4}-NPs as mediators of omega-3 fatty acid-mediated protection

THE DARKEST SHADOWS: DEEP MID-INFRARED EXTINCTION MAPPING OF A MASSIVE PROTOCLUSTER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butler, Michael J.; Tan, Jonathan C.; Kainulainen, Jouni

We use deep 8 μm Spitzer-IRAC imaging of massive Infrared Dark Cloud (IRDC) G028.37+00.07 to construct a mid-infrared (MIR) extinction map that probes mass surface densities up to Σ ∼ 1 g cm{sup –2} (A{sub V} ∼ 200 mag), amongst the highest values yet probed by extinction mapping. Merging with an NIR extinction map of the region creates a high dynamic range map that reveals structures down to A{sub V} ∼ 1 mag. We utilize the map to: (1) measure a cloud mass ∼7 × 10{sup 4} M {sub ☉} within a radius of ∼8 pc. {sup 13}CO kinematics indicate thatmore » the cloud is gravitationally bound. It thus has the potential to form one of the most massive young star clusters known in the Galaxy. (2) Characterize the structures of 16 massive cores within the IRDC, finding they can be fit by singular polytropic spheres with ρ∝r{sup −k{sub ρ}} and k {sub ρ} = 1.3 ± 0.3. They have Σ-bar ≃0.1--0.4 g cm{sup −2}—relatively low values that, along with their measured cold temperatures, suggest that magnetic fields, rather than accretion-powered radiative heating, are important for controlling fragmentation of these cores. (3) Determine the Σ (equivalently column density or A{sub V} ) probability distribution function (PDF) for a region that is nearly complete for A{sub V} > 3 mag. The PDF is well fit by a single log-normal with mean A-bar {sub V}≃9 mag, high compared to other known clouds. It does not exhibit a separate high-end power law tail, which has been claimed to indicate the importance of self-gravity. However, we suggest that the PDF does result from a self-similar, self-gravitating hierarchy of structures present over a wide range of scales in the cloud.« less

FORMULATION OF NON-STEADY-STATE DUST FORMATION PROCESS IN ASTROPHYSICAL ENVIRONMENTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nozawa, Takaya; Kozasa, Takashi, E-mail: takaya.nozawa@ipmu.jp

2013-10-10

The non-steady-state formation of small clusters and the growth of grains accompanied by chemical reactions are formulated under the consideration that the collision of key gas species (key molecule) controls the kinetics of dust formation process. The formula allows us to evaluate the size distribution and condensation efficiency of dust formed in astrophysical environments. We apply the formulation to the formation of C and MgSiO{sub 3} grains in the ejecta of supernovae, as an example, to investigate how the non-steady effect influences the formation process, condensation efficiency f{sub con,{sub ∞}}, and average radius a{sub ave,{sub ∞}} of newly formed grainsmore » in comparison with the results calculated with the steady-state nucleation rate. We show that the steady-state nucleation rate is a good approximation if the collision timescale of key molecule τ{sub coll} is much smaller than the timescale τ{sub sat} with which the supersaturation ratio increases; otherwise the effect of the non-steady state becomes remarkable, leading to a lower f{sub con,{sub ∞}} and a larger a{sub ave,{sub ∞}}. Examining the results of calculations, we reveal that the steady-state nucleation rate is applicable if the cooling gas satisfies Λ ≡ τ{sub sat}/τ{sub coll} ∼> 30 during the formation of dust, and find that f{sub con,{sub ∞}} and a{sub ave,{sub ∞}} are uniquely determined by Λ{sub on} at the onset time t{sub on} of dust formation. The approximation formulae for f{sub con,{sub ∞}} and a{sub ave,{sub ∞}} as a function of Λ{sub on} could be useful in estimating the mass and typical size of newly formed grains from observed or model-predicted physical properties not only in supernova ejecta but also in mass-loss winds from evolved stars.« less

Cyclic stretch induces cyclooxygenase-2 gene expression in vascular endothelial cells via activation of nuclear factor kappa-{beta}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Haige; Hiroi, Toyoko; Hansen, Baranda S.

2009-11-27

Vascular endothelial cells respond to biomechanical forces, such as cyclic stretch and shear stress, by altering gene expression. Since endothelial-derived prostanoids, such as prostacyclin and thromboxane A{sub 2}, are key mediators of endothelial function, we investigated the effects of cyclic stretch on the expression of genes in human umbilical vein endothelial cells controlling prostanoid synthesis: cyclooxygenase-1 (COX-1), cyclooxygenase-2 (COX-2), prostacyclin synthase (PGIS) and thromboxane A{sub 2} synthase (TXAS). COX-2 and TXAS mRNAs were upregulated by cyclic stretch for 24 h. In contrast, PGIS mRNA was decreased and stretch had no effect on COX-1 mRNA expression. We further show that stretch-inducedmore » upregulation of COX-2 is mediated by activation of the NF-{kappa}{beta} signaling pathway.« less

Micro-Raman study on the softening and stiffening of phonons in rutile titanium dioxide film: Competing effects of structural defects, crystallite size, and lattice strain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gautam, Subodh K.; Singh, Fouran, E-mail: fouran@gmail.com; Sulania, I.

2014-04-14

Softening and stiffening of phonons in rutile titanium dioxide films are investigated by in situ micro-Raman studies during energetic ion irradiation. The in situ study minimized other possible mechanisms of phonon dynamics. Initial softening and broadening of Raman shift are attributed to the phonon confinement by structural defects and loss of stoichiometry. The stiffening of A{sub 1g} mode is ascribed to large distortion of TiO{sub 6} octahedra under the influence of lattice strain in the (110) plane, which gives rise to lengthening of equatorial Ti-O bond and shortening of apical Ti-O bond. The shortening of apical Ti-O bond induces stiffeningmore » of A{sub 1g} mode in the framework of the bond-order-length-strength correlation mechanism.« less

Six mode selective fiber optic spatial multiplexer.

PubMed

Velazquez-Benitez, A M; Alvarado, J C; Lopez-Galmiche, G; Antonio-Lopez, J E; Hernández-Cordero, J; Sanchez-Mondragon, J; Sillard, P; Okonkwo, C M; Amezcua-Correa, R

2015-04-15

Low-loss all-fiber photonic lantern (PL) mode multiplexers (MUXs) capable of selectively exciting the first six fiber modes of a multimode fiber (LP₀₁, LP_{11a>, LP11b, LP21a>, LP21b, and LP02) are demonstrated. Fabrication of the spatial mode multiplexers was successfully achieved employing a combination of either six step or six graded index fibers of four different core sizes. Insertion losses of 0.2-0.3 dB and mode purities above 9 dB are achieved. Moreover, it is demonstrated that the use of graded index fibers in a PL eases the length requirements of the adiabatic tapered transition and could enable scaling to large numbers.}

Efficient algorithms for computing a strong rank-revealing QR factorization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gu, M.; Eisenstat, S.C.

1996-07-01

Given an m x n matrix M with m {ge} n, it is shown that there exists a permutation {Pi} and an integer k such that the QR factorization given by equation (1) reveals the numerical rank of M: the k x k upper-triangular matrix A{sub k} is well conditioned, norm of (C{sub k}){sub 2} is small, and B{sub k} is linearly dependent on A{sub k} with coefficients bounded by a low-degree polynomial in n. Existing rank-revealing QR (RRQR) algorithms are related to such factorizations and two algorithms are presented for computing them. The new algorithms are nearly as efficientmore » as QR with column pivoting for most problems and take O(mn{sup 2}) floating-point operations in the worst case.« less

Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of [alpha]- and PPII-helices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, Matthew R.; Rajashankar, Kanagalaghatta R.; Patel, Manisha H.

2010-08-18

Streptococcus mutans antigen I/II (AgI/II) is a cell surface-localized protein adhesin that interacts with salivary components within the salivary pellicle. AgI/II contributes to virulence and has been studied as an immunological and structural target, but a fundamental understanding of its underlying architecture has been lacking. Here we report a high-resolution (1.8 {angstrom}) crystal structure of the A{sub 3}VP{sub 1} fragment of S. mutans AgI/II that demonstrates a unique fibrillar form (155 {angstrom}) through the interaction of two noncontiguous regions in the primary sequence. The A{sub 3} repeat of the alanine-rich domain adopts an extended {alpha}-helix that intertwines with the P{submore » 1} repeat polyproline type II (PPII) helix to form a highly extended stalk-like structure heretofore unseen in prokaryotic or eukaryotic protein structures. Velocity sedimentation studies indicate that full-length AgI/II that contains three A/P repeats extends over 50 nanometers in length. Isothermal titration calorimetry revealed that the high-affinity association between the A{sub 3} and P{sub 1} helices is enthalpically driven. Two distinct binding sites on AgI/II to the host receptor salivary agglutinin (SAG) were identified by surface plasmon resonance (SPR). The current crystal structure reveals that AgI/II family proteins are extended fibrillar structures with the number of alanine- and proline-rich repeats determining their length.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Itagaki, Masafumi; Miyoshi, Yoshinori; Hirose, Hideyuki

A procedure is presented for the determination of geometric buckling for regular polygons. A new computation technique, the multiple reciprocity boundary element method (MRBEM), has been applied to solve the one-group neutron diffusion equation. The main difficulty in applying the ordinary boundary element method (BEM) to neutron diffusion problems has been the need to compute a domain integral, resulting from the fission source. The MRBEM has been developed for transforming this type of domain integral into an equivalent boundary integral. The basic idea of the MRBEM is to apply repeatedly the reciprocity theorem (Green's second formula) using a sequence ofmore » higher order fundamental solutions. The MRBEM requires discretization of the boundary only rather than of the domain. This advantage is useful for extensive survey analyses of buckling for complex geometries. The results of survey analyses have indicated that the general form of geometric buckling is B[sub g][sup 2] = (a[sub n]/R[sub c])[sup 2], where R[sub c] represents the radius of the circumscribed circle of the regular polygon under consideration. The geometric constant A[sub n] depends on the type of regular polygon and takes the value of [pi] for a square and 2.405 for a circle, an extreme case that has an infinite number of sides. Values of a[sub n] for a triangle, pentagon, hexagon, and octagon have been calculated as 4.190, 2.281, 2.675, and 2.547, respectively.« less

Estimating Net Primary Productivity Using Satellite and Ancillary Data

NASA Technical Reports Server (NTRS)

Choudhury, Bhaskar J.

2002-01-01

The net primary productivity (C) or the annual rate of carbon accumulation per unit ground area by terrestrial plant communities is the difference of gross photosynthesis (A(sub g)) and respiration (R) per unit ground area. Available field observations show that R is a large and variable fraction of A(sub g), although it is generally recognized that there are considerable difficulties in determining these fluxes, and thus pose challenge in assessing the accuracy. Further uncertainties arise in extrapolating field measurements (which are acquired over a hectare or so area) to regional scale. Here, an approach is presented for determining these fluxes using satellite and ancillary data to be representative of regional scale and allow assessment of interannual variation. A, has been expressed as the product of radiation use efficiency for gross photosynthesis by an unstressed canopy and intercepted photosynthetically active radiation, which is then adjusted for stresses due to soil water shortage and temperature away from optimum. R has been calculated as the sum of growth and maintenance components (respectively, R(sub g) and R(sub m)).The R(sub m) has been determined from nitrogen content of plant tissue per unit ground area, while R(sub g) has been obtained as a fraction of the difference of A(sub g) and R(sub m). Results for five consecutive years (1986-1990) are presented for the Amazon-Tocontins, Mississippi, and Ob River basins.

A simple relation between the gamma N -> N(1535) helicity amplitudes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilberto Ramalho, Kazuo Tsushima

2011-09-01

It is shown that the helicity amplitudes A{sub 1/2} and S{sub 1/2} in the {gamma}N {yields} N(1535) reaction, can be well related by S{sub 1/2} = {radical}1+{tau}/{radical}2 M{sub S}{sup 2}-M{sup 2}/2M{sub S}Q A{sub 1/2} in the region Q{sup 2} > 2 GeV{sup 2}, where M and M{sub S} are the nucleon and N(1535) masses, q{sup 2} = -Q{sup 2} the four-momentum transfer squared, and {tau} = Q{sup 2}/(M{sub S} + M){sup 2}. This follows from the fact that the Pauli-type transition form factor F*{sub 2} extracted from the experimental data, turns up to show F*{sub 2} {approx_equal} 0 for Q{supmore » 2} > 1.5 GeV{sup 2}. The observed relation is tested by the experimental data and the MAID parametrization. A direct consequence of the relation is that the assumption,|A{sub 1/2}| >> |S{sub 1/2}|, is not valid for high Q{sup 2}. Instead, both amplitudes A{sub 1/2} and S{sub 1/2} have the same Q{sup 2} dependence in the high Q{sup 2} region, aside from that S{sub 1/2} has an extra factor, - 1/{radical} M{sub S}-M/2M{sub s}. The origin of this relation is interpreted in a perspective of a quark model.« less

Effect of thermodynamic disequilibrium on critical liquid-vapor flow conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bilicki, Z.; Kestin, J.

1989-01-01

In this lecture we characterize the effect of absence of unconstrained thermodynamic equilibrium and onset of a metastable state on the adiabatic flow of a mixture of liquid and its vapor through a convergent-divergent nozzle. We study steady-state flows and emphasize the relations that are present when the flow is choked. In such cases, there exists a cross-section in which the flow is critical and in which the adiabatic wave of small amplitude is stationary. More precisely, the relaxation process which results from the lack of equilibrium causes the system to be dispersive. In such circumstances, the critical velocity ismore » equal to the frozen speed of sound, a/sub f/ corresponding to /omega/ /yields/ /infinity/. The relaxation process displaces the critical cross-section quite far downstream from the throat and places it in the divergent portion of the channel. We present the topological portrait of solutions in a suitably defined state-velocity space and discuss the potential appearance of normal and dispersed shock waves. In extreme cases, the singular point (usually a saddle) which enables the flow to become supercritical is displaced so far that it is located outside the exit. Then, the flow velocity is everywhere subcritical (w < a/sub f/) even though it may exceed the equilibrium speed of sound (w /approx gt/ a/sub e/) beyond a certain cross-section, and in spite of the presence of a throat. 10 refs., 4 figs.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elkabbani, Ossama; Chang, Chonghwan; Tiede, D.

Photosynthetic reaction centers (RCs) from the photosynthetic bacteria Rhodobacter sphaeroides and Rhodopseudomonas viridis are protein complexes closely related in both structure and function. The structure of the Rps. viridis RC was used to determine the structure of the RC from Rb. sphaeroides. Small but meaningful differences between the positions of the helices and the cofactors in the two complexes were identified. The distances between helices A{sub L} adn A{sub M}, between B{sub L} and B{sub M}, and between bacteriopheophytins BP{sub L} and BP{sub M} are significantly shorter in Rps. viridis than they are in Rb. sphaeroides RCs. There are amore » number of differences in the amino acid residues that surround the cofactors; some of these residues form hydrogen bonds with the cofactors. Differences in chemical properties of the two RCs.« less

Modified many-body wave function for BCS-BEC crossover in Fermi gases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Shina; Levin, K.

2006-10-15

We present a many-body formalism for BCS-BEC crossover, which represents a modification of the Bardeen-Cooper-Schrieffer-Leggett ground state to include four-fermion and higher correlations. In the Bose-Einstein condensate regime, we show how our approach contains the four-fermion behavior of Petrov et al. and associated scattering length a{sub dd} at short distances and, second, reduces to composite-boson Bogoliubov physics at long distances. It reproduces the Lee-Yang term, whose numerical value is also fixed by a{sub dd}. We have also examined the next term beyond the Lee-Yang correction in a phenomenological fashion, building on cloud size data and collective mode experiments, although onemore » has to view this phenomenological analysis with some caution since experiments are in a state of flux and are performed close to unitarity.« less

Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steindorff, Andrei S.; Noronha, Elilane F.; Ulhoa, Cirano J.

2015-03-17

Biological control is a complex process which requires many mechanisms and a high diversity of biochemical pathways. The species of Trichoderma harzianum are well known for their biocontrol activity against many plant pathogens. To gain new insights into the biocontrol mechanism used by T. harzianum, we sequenced the isolate TR274 genome using Illumina. The assembly was performed using AllPaths-LG with a maximum coverage of 100x. The assembly resulted in 2282 contigs with a N50 of 37033bp. The genome size generated was 40.8 Mb and the GC content was 47.7%, similar to other Trichoderma genomes. Using the JGI Annotation Pipeline wemore » predicted 13,932 genes with a high transcriptome support. CEGMA tests suggested 100% genome completeness and 97.9% of RNA-SEQ reads were mapped to the genome. The phylogenetic comparison using orthologous proteins with all Trichoderma genomes sequenced at JGI, corroborates the Trichoderma (T. asperellum and T. atroviride), Longibrachiatum (T. reesei and T. longibrachiatum) and Pachibasium (T. harzianum and T. virens) section division described previously. The comparison between two Trichoderma harzianum species suggests a high genome similarity but some strain-specific expansions. Analyses of the secondary metabolites, CAZymes, transporters, proteases, transcription factors were performed. The Pachybasium section expanded virtually all categories analyzed compared with the other sections, specially Longibrachiatum section, that shows a clear contraction. These results suggests that these proteins families have an important role in their respective phenotypes. Future analysis will improve the understanding of this complex genus and give some insights about its lifestyle and the interactions with the environment.« less

Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuo, Alan; Grigoriev, Igor

2009-04-17

Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentousmore » ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.« less

Comparative genome analysis in the integrated microbial genomes (IMG) system.

PubMed

Markowitz, Victor M; Kyrpides, Nikos C

2007-01-01

Comparative genome analysis is critical for the effective exploration of a rapidly growing number of complete and draft sequences for microbial genomes. The Integrated Microbial Genomes (IMG) system (img.jgi.doe.gov) has been developed as a community resource that provides support for comparative analysis of microbial genomes in an integrated context. IMG allows users to navigate the multidimensional microbial genome data space and focus their analysis on a subset of genes, genomes, and functions of interest. IMG provides graphical viewers, summaries, and occurrence profile tools for comparing genes, pathways, and functions (terms) across specific genomes. Genes can be further examined using gene neighborhoods and compared with sequence alignment tools.

Layering of inertial confinement fusion targets in microgravity environments

NASA Astrophysics Data System (ADS)

Parks, P. B.; Fagaly, R. L.

1995-02-01

A critical concern in the fabrication of targets for inertial confinement fusion is ensuring that the hydrogenic (D2 or DT) fuel layer maintains spherical symmetry. Because of gravitationally induced sagging of the liquid prior to freezing, only relatively thin (less than 10 micrometers) layers of solid fuel can be produced by fast refreeze methods. One method to reduce the effective gravitational field environment is free-fall insertion into the target chamber. Another method to counterbalance the gravitational force is to use an applied magnetic field combined with a gradient field to induce a magnetic dipole force (F(sub m)) on the liquid fuel layer. For liquid deuterium, the required B dot product del(vector differential operator) B product to counterbalance the gravitational force (F(sub g)) is approximately 10 T(exp 2)/cm. In this paper, we examine the time-dependent dynamics of the liquid fuel layer in a reduced gravitational field environment. We employ an energy method which takes into account the sum of the free energy associated with the surface tension forces, net vertical force (F = F(sub m) - F(sub g) (in the case of magnetic field-assisted microgravity) or F(sub D) (the drag force in the case of free fall)), London-van der Waals forces, the kinetic energy of motion and viscous dissipation. By assuming that the motions are incompressible and irrotational, the volume integrals of the free energies over the deformed liquid fuel layer may be converted to surface integrals. With the surface expressed as the sum of Legendre polynomials, r(sub surface) = a + Sigma a(sub l)(t)P(sub l)(mu), the perturbed amplitude of the individual modes, a(sub l)(t) can be obtained. We show that the l = 1 vertical shift mode takes the longest to damp out, and may be problematic for free-fall insertion even for thin approximately 1 micrometer overfilled foam targets. For a given liquid fuel layer thickness delta, the equilibrium value of a(sub 1)/a (the concentricity of the

Satellite Sounder-Based OLR-, Cloud- and Atmospheric Temperature Climatologies for Climate Analyses

NASA Technical Reports Server (NTRS)

Molnar, Gyula I.; Susskind, Joel

2006-01-01

Global energy balance of the Earth-atmosphere system may change due to natural and man-made climate variations. For example, changes in the outgoing longwave radiation (OLR) can be regarded as a crucial indicator of climate variations. Clouds play an important role -still insufficiently assessed in the global energy balance on all spatial and temporal scales, and satellites provide an ideal platform to measure cloud and large-scale atmospheric variables simultaneously. The TOVS series of satellites were the first to provide this type of information since 1979. OLR [Mehta and Susskind], cloud cover and cloud top pressure [Susskind et al] are among the key climatic parameters computed by the TOVS Pathfinder Path-A algorithm using mainly the retrieved temperature and moisture profiles. AIRS, regarded as the new and improved TOVS , has a much higher spectral resolution and greater S/N ratio, retrieving climatic parameters with higher accuracy. First we present encouraging agreements between MODIS and AIRS cloud top pressure (C(sub tp) and effective (A(sub eff), a product of infrared emissivity at 11 microns and physical cloud cover or A(sub c)) cloud fraction seasonal and interannual variabilities for selected months. Next we present validation efforts and preliminary trend analyses of TOVS-retrieved C(sub tp) and A(sub eff). For example, decadal global trends of the TOVS Path-A and ISCCP-D2 P(sub c), and A(sub eff)/A(sub c), values are similar. Furthermore, the TOVS Path-A and ISCCP-AVHRR [available since 19831 cloud fractions correlate even more strongly, including regional trends. We also present TOVS and AIRS OLR validation effort results and (for the longer-term TOVS Pathfinder Path-A dataset) trend analyses. OLR interannual spatial variabilities from the available state-of-the-art CERES measurements and both from the AIRS [Susskind et al] and TOVS OLR computations are in remarkably good agreement. Global monthly mean CERES and TOVS OLR time series show very good

High Spectral Resolution MODIS Algorithms for Ocean Chlorophyll in Case II Waters

NASA Technical Reports Server (NTRS)

Carder, Kendall L.

2004-01-01

The Case 2 chlorophyll a algorithm is based on a semi-analytical, bio-optical model of remote sensing reflectance, R(sub rs)(lambda), where R(sub rs)(lambda) is defined as the water-leaving radiance, L(sub w)(lambda), divided by the downwelling irradiance just above the sea surface, E(sub d)(lambda,0(+)). The R(sub rs)(lambda) model (Section 3) has two free variables, the absorption coefficient due to phytoplankton at 675 nm, a(sub phi)(675), and the absorption coefficient due to colored dissolved organic matter (CDOM) or gelbstoff at 400 nm, a(sub g)(400). The R(rs) model has several parameters that are fixed or can be specified based on the region and season of the MODIS scene. These control the spectral shapes of the optical constituents of the model. R(sub rs)(lambda(sub i)) values from the MODIS data processing system are placed into the model, the model is inverted, and a(sub phi)(675), a(sub g)(400) (MOD24), and chlorophyll a (MOD21, Chlor_a_3) are computed. Algorithm development is initially focused on tropical, subtropical, and summer temperate environments, and the model is parameterized in Section 4 for three different bio-optical domains: (1) high ratios of photoprotective pigments to chlorophyll and low self-shading, which for brevity, we designate as 'unpackaged'; (2) low ratios and high self-shading, which we designate as 'packaged'; and (3) a transitional or global-average type. These domains can be identified from space by comparing sea-surface temperature to nitrogen-depletion temperatures for each domain (Section 5). Algorithm errors of more than 45% are reduced to errors of less than 30% with this approach, with the greatest effect occurring at the eastern and polar boundaries of the basins. Section 6 provides an expansion of bio-optical domains into high-latitude waters. The 'fully packaged' pigment domain is introduced in this section along with a revised strategy for implementing these variable packaging domains. Chlor_a_3 values derived semi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mueller, M. H.; Brun, T. O.; Hitterman, R. L.

Recent resistivity and neutron diffraction measurements have provided evidence for ordering of D(H) atoms on the octahedral interstitial sites of PdD/sub 1-x/. This order--disorder transition is responsible for the 50 K anomaly which has been reported in many of the physical properties. Neutron diffraction measurements on a PdD/sub 0/ /sub 76/ single crystal revealed satellite reflection at (4/5,2/5,0) and equivalent positions. These satellites can be accounted for by a multi-domained tetragonal unit cell with a/sub t/ = a/sub c/ root 5/2 and c/sub t/ = c/sub a/. This ordered state can be described as a deuteron density wave along amore » < 420 > cubic direction. This density is modulated such that four fully occupied planes (Pd and D) are followed by a vacant plane (Pd only).« less

A precise measurement of the left-right cross section asymmetry in Z boson production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lath, A.

1994-09-01

The thesis presents a measurement of the left-right asymmetry, A{sub LR}, n the production cross section of Z Bosons produced by e{sup +}e{sup -} annihilations, using polarized electrons, at a center of mass energy of 91.26 Gev. The data presented was recorded by the SLD detector at the SLAC Linear Collider during the 1993 run. The mean luminosity-weighted polarization of the electron beam was {rho}{sup lum} = (63.0{+-}1.1)%. Using a sample of 49,392 Z events, we measure A{sub LR} to be 0.1626{+-}0.0071(stat){+-}0.0030(sys.), which determined the effective weak mixing angle to be sin{sup 2} {theta}{sub W}{sup eff} = 0.2292{+-}0.0009(stat.){+-}0.0004(sys.). This resultmore » differs from that expected by the Standard Model of Particles and Fields by 2.5 standard deviations.« less

Parity Nonconservation in Proton-Proton and Proton-Water Scattering at 1.5 GeV/c

DOE R&D Accomplishments Database

Mischke, R. E.; Bowman, J. D.; Carlini, R.; MacArthur, D.; Nagle, D. E.; Frauenfelder, H.; Harper, R. W.; Yuan, V.; McDonald, A. B.; Talaga, R. L.

1984-07-01

Experiments searching for parity nonconservation in the scattering of 1.5 GeV/c (800 MeV) polarized protons from an unpolarized water target and a liquid hydrogen target are described. The intensity of the incident proton beam was measured upstream and downstream of the target by a pair of ionization detectors. The beam helicity was reversed at a 30-Hz rate. Auxiliary detectors monitored beam properties that could give rise to false effects. The result for the longitudinal asymmetry from the water is A{sub L} = (1.7 +- 3.3 +- 1.4) x 10{sup -7}, where the first error is statistical and the second is an estimate of systematic effects. The hydrogen data yield a preliminary result of A{sub L} = (1.0 +- 1.6) x 10{sup -7}. The systematic errors for p-p are expected to be < 1 x 10{sup -7}.

Calculation of the {pi}{sup +}{Sigma}{sup +} and {pi}{sup +}{Xi}{sup 0} Scattering Lengths in Lattice QCD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Torok, Aaron

The {pi}{sup +}{Sigma}{sup +} and {pi}{sup +}{Xi}{sup 0} scattering lengths were calculated in mixed-action Lattice QCD with domain-wall valence quarks on the asqtad-improved coarse MILC configurations at four light-quark masses, and at two light-quark masses on the fine MILC configurations. Heavy Baryon Chiral Perturbation Theory with two and three flavors of light quarks was used to perform the chiral extrapolations. To NNLO in the three-flavor chiral expansion, the kaon-baryon processes that were investigated show no signs of convergence. Using the two-flavor chiral expansion for extrapolation, the pion-hyperon scattering lengths are found to be a{sub {pi}}{sup +}{sub {Sigma}}{sup +} = -0.197{+-}0.017more » fm, and a{sub {pi}}{sup +}{sub {Xi}}{sup 0} = -0.098{+-}0.017 fm, where the comprehensive error includes statistical and systematic uncertainties.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Savich, A. I., E-mail: office@geodyn.ru; Burdina, N. A., E-mail: nina-burdina@mail.ru

Analysis of published data on the fundamental parameters of actual accelerograms of strong earthquakes having peak ground acceleration A{sub max}, predominant period T{sub pr}, and duration τ{sub 0.5} at 0.5A{sub max} determined that, for earthquakes of intensity greater than 6.5 – 7.0, the relationship between these quantities is sufficiently well described by the parameters B = ATτ and C = AτT{sup −1.338}, the former of which depends little on earthquake intensity I and is almost completely determined by the earthquake magnitude, while the latter, on the contrary, weakly depends on magnitude and is determined principally by the quantity I. Methodsmore » are proposed for using the parameters B and C to improve the reliability of determining parameters of accelerograms used to calculate the seismic resistance of hydraulic engineering facilities.« less

The production of premixed flame surface area in turbulent shear flow

NASA Technical Reports Server (NTRS)

Trouve, A.

1993-01-01

In the present work, we use three-dimensional Direct Numerical Simulation (DNS) of premixed flames in turbulent shear flow to characterize the effect of a mean shear motion on flame surface production. The shear is uniform in the unburnt gas, and simulations are performed for different values of the mean shear rate, S. The data base is then used to estimate and compare the different terms appearing in the Sigma-equation as a function of S. The analysis gives in particular the relative weights f the turbulent flow and mean flow components, a(sub T) and A(sub T), of the flame surface production term. This comparison indicates whether the dominant effects of a mean flow velocity gradient on flame surface area are implicit and scale with the modified turbulent flow parameters, kappa and epsilon, or explicit and scale directly with the rate of deformation.

Laser-saturated fluorescence of nitric oxide and chemiluminescence measurements in premixed ethanol flames

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marques, Carla S.T.; Barreta, Luiz G.; Sbampato, Maria E.

In this study, nitric oxide laser-saturated fluorescence (LSF) measurements were acquired from premixed ethanol flames at atmospheric pressure in a burner. NO-LSF experimental profiles for fuel-rich premixed ethanol flames ({phi} = 1.34 and {phi} = 1.66) were determined through the excitation/detection scheme of the Q{sub 2}(26.5) rotational line in the A{sup 2}{sigma}{sup +} - X{sup 2}{pi} (0,0) vibronic band and {gamma}(0,1) emission band. A calibration procedure by NO doping into the flame was applied to establish the NO concentration profiles in these flames. Chemiluminescent emission measurements in the (0, 0) vibronic emission bands of the OH{sup *} (A{sup 2}{sigma}{sup +}more » - X{sup 2}{pi}) and CH{sup *}(A{sup 2}{delta} - X{sup 2}{pi}) radicals were also obtained with high spatial and spectral resolution for fuel-rich premixed ethanol flames to correlate them with NO concentrations. Experimental chemiluminescence profiles and the ratios of the integrated areas under emission spectra (A{sub CH*}/A{sub CH*}(max.) and A{sub CH*}/A{sub OH*}) were determined. The relationships between chemiluminescence and NO concentrations were established along the premixed ethanol flames. There was a strong connection between CH{sup *} radical chemiluminescence and NO formation and the prompt-NO was identified as the governing mechanism for NO production. The results suggest the optimum ratio of the chemiluminescence of two radicals (A{sub CH*}/A{sub OH*}) for NO diagnostic purposes. (author)« less

Excited state non-adiabatic dynamics of pyrrole: A time-resolved photoelectron spectroscopy and quantum dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Guorong; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023; Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026

The dynamics of pyrrole excited at wavelengths in the range 242-217 nm are studied using a combination of time-resolved photoelectron spectroscopy and wavepacket propagations performed using the multi-configurational time-dependent Hartree method. Excitation close to the origin of pyrrole’s electronic spectrum, at 242 and 236 nm, is found to result in an ultrafast decay of the system from the ionization window on a single timescale of less than 20 fs. This behaviour is explained fully by assuming the system to be excited to the A{sub 2}(πσ{sup ∗}) state, in accord with previous experimental and theoretical studies. Excitation at shorter wavelengths hasmore » previously been assumed to result predominantly in population of the bright A{sub 1}(ππ{sup ∗}) and B{sub 2}(ππ{sup ∗}) states. We here present time-resolved photoelectron spectra at a pump wavelength of 217 nm alongside detailed quantum dynamics calculations that, together with a recent reinterpretation of pyrrole’s electronic spectrum [S. P. Neville and G. A. Worth, J. Chem. Phys. 140, 034317 (2014)], suggest that population of the B{sub 1}(πσ{sup ∗}) state (hitherto assumed to be optically dark) may occur directly when pyrrole is excited at energies in the near UV part of its electronic spectrum. The B{sub 1}(πσ{sup ∗}) state is found to decay on a timescale of less than 20 fs by both N-H dissociation and internal conversion to the A{sub 2}(πσ{sup ∗}) state.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaur, Ramanpreet; Kaper, Lex; Ellerbroek, Lucas E.

We present the optical to near-infrared spectrum of MAXI J1659-152 during the onset of its 2010 X-ray outburst. The spectrum was obtained with X-shooter on the ESO Very Large Telescope early in the outburst simultaneous with high-quality observations at both shorter and longer wavelengths. At the time of the observations, the source was in the low-hard state. The X-shooter spectrum includes many broad ({approx}2000 km s{sup -1}), double-peaked emission profiles of H, He I, and He II, characteristic signatures of a low-mass X-ray binary during outburst. We detect no spectral signatures of the low-mass companion star. The strength of themore » diffuse interstellar bands results in a lower limit to the total interstellar extinction of A{sub V} {approx_equal} 0.4 mag. Using the neutral hydrogen column density obtained from the X-ray spectrum we estimate A{sub V} {approx_equal} 1 mag. The radial velocity structure of the interstellar Na I D and Ca II H and K lines results in a lower limit to the distance of {approx}4 {+-} 1 kpc, consistent with previous estimates. With this distance and A{sub V} , the dereddened spectral energy distribution represents a flat disk spectrum. The two 10 minute X-shooter spectra show significant variability in the red wing of the emission-line profiles, indicating a global change in the density structure of the disk, though on a timescale much shorter than the typical viscous timescale of the disk.« less

Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon is a powerful experimental model for the grasses with a large and growing collection of genomic and experimental resources. We have added to these resources by greatly expanding the number of sequence-indexed T-DNA lines. We sequenced 21,165 T-DNA lines, 15,569 of which were ...

Computerized Analysis of MR and Ultrasound Images of Breast Lesions

DTIC Science & Technology

2001-07-01

Although general rules for the differentiation between benign and malignant mammographically identified breast lesions exist, considerable...round-robin runs yielded A(sub z) values of 0.94 and 0.87 in the task of distinguishing between benign and malignant lesions in the entire database

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

PubMed

Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

2012-01-01

The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

Electron spin echo envelope modulation studies of the Cu(II)-substituted derivative of isopenicillin N synthase: A structural and spectroscopic model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng Jiang; Peisach, J.; Lijune Ming

Electron spin echo envelope modulation spectroscopy (ESEEM) was used to study the active site structure of isopenicillin N synthase (IPNS) from Cephalosporium acremonium with Cu(II) as a spectroscopic probe. Fourier transform of the simulated electron spin-echo envelope for the Cu(II)-substituted enzyme, Cu(II)IPNS, revealed two nearly magnetically equivalent, equatorially coordinated His imidazoles. The superhyperfine coupling constant, A{sub iso}, for the remote {sup 14}N of each imidazole was 1.65 MHz. The binding of substrate to the enzyme altered the magnetic coupling so that A{sub iso} is 1.30 MHz for one nitrogen and 2.16 MHz for the other. From a comparison of themore » ESSEM of Cu(II)IPNS in D{sub 2}O and H{sub 2}O, it is suggested that water is a ligand of Cu(II) and this is displaced upon the addition of substrate.« less

Duality-symmetric supersymmetric Yang-Mills theory in three dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishino, Hitoshi; Rajpoot, Subhash

We formulate a duality-symmetric N=1 supersymmetric Yang-Mills theory in three dimensions. Our field content is (A{sub {mu}}{sup I},{lambda}{sup I},{phi}{sup I}), where the index I is for the adjoint representation of an arbitrary gauge group G. Our Hodge duality symmetry is F{sub {mu}{nu}}{sup I}=+{epsilon}{sub {mu}{nu}}{sup {rho}D}{sub {rho}{phi}}{sup I}. Because of this relationship, the presence of two physical fields A{sub {mu}}{sup I} and {phi}{sup I} within the same N=1 supermultiplet poses no problem. We can couple this multiplet to another vector multiplet (C{sub {mu}}{sup I},{chi}{sup I};B{sub {mu}{nu}}{sup I}) with 1+1 physical degrees of freedom modulo dim G. Thanks to peculiar couplings andmore » supersymmetry, the usual problem with an extra vector field in a nontrivial representation does not arise in our system.« less

Balanced Orifice Plate

NASA Technical Reports Server (NTRS)

Kelley, Anthony R. (Inventor); Buskirk, Paul D. (Inventor)

2006-01-01

An orifice plate for use in a conduit through which fluid flows is defined by a central circular region having a radius R, and a ring-shaped region surrounding the central circular region. The ring-shaped region has holes formed therethrough with those holes centered at each radius R thereof satisfying a relationship A(sub R)=al(X(sub R)V(sub R)(sup b)) where A(sub R) is a sum of areas of those holes having centers at radius R, X(sub R) is a flow coefficient at radius R, V(sub R) is a velocity of the fluid that is to flow through the conduit at radius R, b is a constant selected to make at least one process variable (associated with the fluid that is to flow through the conduit) approximately equal at each radius R, and a is a constant that is equal to (X(sub R)A(sub R)V(sub R)(sup b)) at each radius R.

Iron-based perovskite cathodes for solid oxide fuel cells

DOEpatents

Ralph, James M.; Rossignol, Cecile C.R.; Vaughey, John T.

2007-01-02

An A and/or A' site deficient perovskite of general formula of (A.sub.1-xA'.sub.x).sub.1-yFeO.sub.3-.delta. or of general formula A.sub.1-x-yA'.sub.xFeO.sub.3-67, wherein A is La alone or with one or more of the rare earth metals or a rare earth metal other than Ce alone or a combination of rare earth metals and X is in the range of from 0 to about 1; A' is Sr or Ca or mixtures thereof and Y is in the range of from about 0.01 to about 0.3; .delta. represents the amount of compensating oxygen loss. If either A or A' is zero the remaining A or A' is deficient. A fuel cell incorporating the inventive perovskite as a cathode is disclosed as well as an oxygen separation membrane. The inventive perovskite is preferably single phase.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pellicer-Porres, J., E-mail: Julio.Pellicer@uv.es; Segura, A.; Santamaría-Pérez, D.

We have measured high pressure α-quartz reflectance spectra in the mid infrared. We used single crystals, taking full profit of polarization. The quality of the spectra allows fitting the reflectance spectra. We have characterized the pressure evolution of E and A{sub 2} modes with increased precision, even in the spectral regions where they overlap. In addition, we have determined the TO-LO splitting of each mode. Some of the A{sub 2} modes show dramatic pressure variations of the LO-TO splitting, which cannot be explained only by changes in length and ionicity of individual bonds, requiring a new mechanism. We suggest thatmore » rotation of the SiO{sub 4} tetrahedra plays a fundamental role. We have also determined the evolution of the electronic dielectric constant under high pressure. We find that its pressure increment is mainly a volume effect, although the small increase in birefringence points to secondary changes associated to the electronic resonances.« less

SCBUCKLE user's manual: Buckling analysis program for simple supported and clamped panels

NASA Technical Reports Server (NTRS)

Cruz, Juan R.

1993-01-01

The program SCBUCKLE calculates the buckling loads and mode shapes of cylindrically curved, rectangular panels. The panel is assumed to have no imperfections. SCBUCKLE is capable of analyzing specially orthotropic symmetric panels (i.e., A(sub 16) = A(sub 26) = 0.0, D(sub 16) = D(sub 26) = 0.0, B(sub ij) = 0.0). The analysis includes first-order transverse shear theory and is capable of modeling sandwich panels. The analysis supports two types of boundary conditions: either simply supported or clamped on all four edges. The panel can be subjected to linearly varying normal loads N(sub x) and N(sub y) in addition to a constant shear load N(sub xy). The applied loads can be divided into two parts: a preload component; and a variable (eigenvalue-dependent) component. The analysis is based on the modified Donnell's equations for shallow shells. The governing equations are solved by Galerkin's method.

Atomic layer deposition of two dimensional MoS{sub 2} on 150 mm substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valdivia, Arturo; Conley, John F., E-mail: jconley@eecs.oregonstate.edu; Tweet, Douglas J.

2016-03-15

Low temperature atomic layer deposition (ALD) of monolayer to few layer MoS{sub 2} uniformly across 150 mm diameter SiO{sub 2}/Si and quartz substrates is demonstrated. Purge separated cycles of MoCl{sub 5} and H{sub 2}S precursors are used at reactor temperatures of up to 475 °C. Raman scattering studies show clearly the in-plane (E{sup 1}{sub 2g}) and out-of-plane (A{sub 1g}) modes of MoS{sub 2}. The separation of the E{sup 1}{sub 2g} and A{sub 1g} peaks is a function of the number of ALD cycles, shifting closer together with fewer layers. X-ray photoelectron spectroscopy indicates that stoichiometry is improved by postdeposition annealing in amore » sulfur ambient. High resolution transmission electron microscopy confirms the atomic spacing of monolayer MoS{sub 2} thin films.« less

Preparation and X-Ray diffraction studies of curium hydrides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibson, J.K.; Maire, R.G.

Curium hydrides were prepared by reaction of curium-248 metal with hydrogen and characterized by X-ray powder diffraction. Several of the syntheses resulted in a hexagonal compound with average lattice parameters of a/sub 0/ = 0.3769(8) nm and c/sub 0/ = 0.6732(12) nm. These products are considere to be CmH/sub 3//sup -//sub 8/ by analogy with the behavior of lanthanide-hydrogen and lighter actinide-hydrogen systems. Face-centered cubic products with an average lattice parameter of a/sub 0/ = 0.5322(4) nm were obtained from other curium hydride preparations. This parameter is slightly smaller than that reported previously for cubic curium dihydride, CmH /SUB 2-x/more » (B.M. Bansal and D. Damien. Inorg. Nucl. Chem. Lett. 6 603, 1970). The present results established a continuation of typical heavy trivalent lanthanidelike behavior of the transuranium actinide-hydrogen systems through curium.« less

Characterisation of iron inclusion during the formation of calcium sulfoaluminate phase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Idrissi, M., E-mail: mari_idrissi@yahoo.f; Diouri, A.; Damidot, D.

The iron distribution among the sulfoaluminate clinker phases and its ability to enter the calcium sulfoaluminate lattice in solid solution can have a significant influence on manufacturing process and reactivity of calcium sulfoaluminate (CSA) cements. X-ray diffraction (XRD) analysis, Moessbauer spectroscopy, scanning electron microscopy (SEM) equipped with an energy dispersive X-ray analysis system (EDAX) and infrared spectroscopy were used to identify the mineralogical conditions of iron inclusion during the formation of calcium sulfoaluminate (C{sub 4}A{sub 3}S) phase from different mixtures in the CaO-Al{sub 2}O{sub 3}-Fe{sub 2}O{sub 3}-SO{sub 3} system. The mixtures, heated in a laboratory electric oven, contained stoichiometric amountsmore » of reagent grade CaCO{sub 3}, Al{sub 2}O{sub 3}, Fe{sub 2}O{sub 3} and CaSO{sub 4.2}H{sub 2}O for the synthesis of Ca{sub 4}Al{sub (6-2x)}Fe{sub 2x}SO{sub 16}, where x, comprised between 0 and 3, is the mole number of Al{sub 2}O{sub 3} substituted by Fe{sub 2}O{sub 3}. With x increasing from 0 to 1.5, both the iron content of C{sub 4}A{sub 3}S phase and the amounts of side components such as C{sub 2}F and CS increased. For x values included in the range of 1.5-3.0, at temperatures higher than 1200 {sup o}C, melting phenomena were observed and, instead of the C{sub 4}A{sub 3}S solid solution, ferritic phases and anhydrite were formed.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Qiannan; Zhu, Ding; Zhou, Wanhai

Highlights: • Effects of four different preparation processes were studied at 20/60 °C. • All NS + HT, RS and RS + HT processes can optimize the thermodynamic performance. • The HT process can provoke the precipitation of A{sub 2}B{sub 7} and leads to a poor cycling life. • Al exhibits the most remarkable dissolution for all the alloys, especially at 60 °C. - Abstract: In order to optimize the microstructure and high temperature electrochemical performances of low-cost AB{sub 5}-type Ml(NiMnAl){sub 4.2}Co{sub 0.3}Fe{sub 0.5} hydrogen storage electrode alloys, four different preparation methods including normal solidification (NS), normal solidification and 900more » °C heat treatment (NS + HT), rapid solidification (RS), rapid solidification and 900 °C heat treatment (RS + HT) were adopted in this work. All alloys exhibit CaCu{sub 5} type hexagonal structure and there is a small amount of A{sub 2}B{sub 7} phase in NS + HT and RS + HT alloys. It is found the using of HT process can decrease the hydrogen equilibrium plateau pressure, the plateau slope and hysteresis at 40, 60 and 80 °C. The NS + HT and RS + HT alloys also possess better activation, high rate discharge performance, larger discharge capacity, but poor cycling performance due to the existence of A{sub 2}B{sub 7} phase which can accelerate dissolution of Ni, Mn and Fe elements in KOH alkaline electrolyte. The RS process can make alloy exhibit the best cycling performance especially at 60 °C.« less

MORFOMETRYKA—A NEW WAY OF ESTABLISHING MORPHOLOGICAL CLASSIFICATION OF GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferrari, F.; Carvalho, R. R. de; Trevisan, M., E-mail: fabricio@ferrari.pro.br

We present an extended morphometric system to automatically classify galaxies from astronomical images. The new system includes the original and modified versions of the CASGM coefficients (Concentration C{sub 1}, Asymmetry A{sub 3}, and Smoothness S{sub 3}), and the new parameters entropy, H, and spirality σ{sub ψ}. The new parameters A{sub 3}, S{sub 3}, and H are better to discriminate galaxy classes than A{sub 1}, S{sub 1}, and G, respectively. The new parameter σ{sub ψ} captures the amount of non-radial pattern on the image and is almost linearly dependent on T-type. Using a sample of spiral and elliptical galaxies from themore » Galaxy Zoo project as a training set, we employed the Linear Discriminant Analysis (LDA) technique to classify EFIGI (Baillard et al. 4458 galaxies), Nair and Abraham (14,123 galaxies), and SDSS Legacy (779,235 galaxies) samples. The cross-validation test shows that we can achieve an accuracy of more than 90% with our classification scheme. Therefore, we are able to define a plane in the morphometric parameter space that separates the elliptical and spiral classes with a mismatch between classes smaller than 10%. We use the distance to this plane as a morphometric index (M{sub i}) and we show that it follows the human based T-type index very closely. We calculate morphometric index M{sub i} for ∼780k galaxies from SDSS Legacy Survey–DR7. We discuss how M{sub i} correlates with stellar population parameters obtained using the spectra available from SDSS–DR7.« less

Estimating Net Primary Productivity Using Satellite and Ancillary Data

NASA Technical Reports Server (NTRS)

Choudhury, B. J.; Houser, Paul (Technical Monitor)

2001-01-01

The net primary productivity (C) or annual rate of carbon accumulation per unit ground area by terrestrial plant communities is the difference of the rate of gross photosynthesis (A(sub g)) and autotrophic respiration (R) per unit ground area. Although available observations show that R is a large and variable fraction of A(sub g), viz., 0.3 to 0.7, it is generally recognized that much uncertainties exist in this fraction due to difficulties associated with the needed measurements. Additional uncertainties arise when these measurements are extrapolated to regional or global land surface using empirical equations, for example, using regression equations relating C to mean annual precipitation and air temperature. Here, a process-based approach has been taken to calculate A(sub g) and R using satellite and ancillary data. A(sub g) has been expressed as a product of radiation use efficiency, magnitude of intercepted photosynthetically active radiation (PAR), and normalized by stresses due to soil water shortage and air temperature away from the optimum range. A biophysical model has been used to determine the radiation use efficiency from the maximum rate of carbon assimilation by a leaf, foliage temperature, and the fraction of diffuse PAR incident on a canopy. All meteorological data (PAR, air temperature, precipitation, etc.) needed for the calculation are derived from satellite observations, while a land use, land cover data (based on satellite and ground measurements) have been used to assess the maximum rate of carbon assimilation by a leaf of varied cover type based on field measurements. R has been calculated as the sum of maintenance and growth components. The maintenance respiration of foliage and live fine roots at a standard temperature of different land cover has been determined from their nitrogen content using field and satellite measurements, while that of living fraction of woody stem (viz., sapwood) from the seasonal maximum leaf area index as

Optical pattern recognition architecture implementing the mean-square error correlation algorithm

DOEpatents

Molley, Perry A.

1991-01-01

An optical architecture implementing the mean-square error correlation algorithm, MSE=.SIGMA.[I-R].sup.2 for discriminating the presence of a reference image R in an input image scene I by computing the mean-square-error between a time-varying reference image signal s.sub.1 (t) and a time-varying input image signal s.sub.2 (t) includes a laser diode light source which is temporally modulated by a double-sideband suppressed-carrier source modulation signal I.sub.1 (t) having the form I.sub.1 (t)=A.sub.1 [1+.sqroot.2m.sub.1 s.sub.1 (t)cos (2.pi.f.sub.o t)] and the modulated light output from the laser diode source is diffracted by an acousto-optic deflector. The resultant intensity of the +1 diffracted order from the acousto-optic device is given by: I.sub.2 (t)=A.sub.2 [+2m.sub.2.sup.2 s.sub.2.sup.2 (t)-2.sqroot.2m.sub.2 (t) cos (2.pi.f.sub.o t] The time integration of the two signals I.sub.1 (t) and I.sub.2 (t) on the CCD deflector plane produces the result R(.tau.) of the mean-square error having the form: R(.tau.)=A.sub.1 A.sub.2 {[T]+[2m.sub.2.sup.2.multidot..intg.s.sub.2.sup.2 (t-.tau.)dt]-[2m.sub.1 m.sub.2 cos (2.tau.f.sub.o .tau.).multidot..intg.s.sub.1 (t)s.sub.2 (t-.tau.)dt]} where: s.sub.1 (t) is the signal input to the diode modulation source: s.sub.2 (t) is the signal input to the AOD modulation source; A.sub.1 is the light intensity; A.sub.2 is the diffraction efficiency; m.sub.1 and m.sub.2 are constants that determine the signal-to-bias ratio; f.sub.o is the frequency offset between the oscillator at f.sub.c and the modulation at f.sub.c +f.sub.o ; and a.sub.o and a.sub.1 are constant chosen to bias the diode source and the acousto-optic deflector into their respective linear operating regions so that the diode source exhibits a linear intensity characteristic and the AOD exhibits a linear amplitude characteristic.

Perovskite catalysts for oxidative coupling

DOEpatents

Campbell, K.D.

1991-06-25

Perovskites of the structure A[sub 2]B[sub 2]C[sub 3]O[sub 10] are useful as catalysts for the oxidative coupling of lower alkane to heavier hydrocarbons. A is alkali metal; B is lanthanide or lanthanum, cerium, neodymium, samarium, praseodymium, gadolinium or dysprosium; and C is titanium.

Perovskite catalysts for oxidative coupling

DOEpatents

Campbell, Kenneth D.

1991-01-01

Perovskites of the structure A.sub.2 B.sub.2 C.sub.3 O.sub.10 are useful as catalysts for the oxidative coupling of lower alkane to heavier hydrocarbons. A is alkali metal; B is lanthanide or lanthanum, cerium, neodymium, samarium, praseodymium, gadolinium or dysprosium; and C is titanium.

IMG-ABC: An Atlas of Biosynthetic Gene Clusters to Fuel the Discovery of Novel Secondary Metabolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, I-Min; Chu, Ken; Ratner, Anna

2014-10-28

In the discovery of secondary metabolites (SMs), large-scale analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of relevant computational resources. We present IMG-ABC (https://img.jgi.doe.gov/abc/) -- An Atlas of Biosynthetic gene Clusters within the Integrated Microbial Genomes (IMG) system1. IMG-ABC is a rich repository of both validated and predicted biosynthetic clusters (BCs) in cultured isolates, single-cells and metagenomes linked with the SM chemicals they produce and enhanced with focused analysis tools within IMG. The underlying scalable framework enables traversal of phylogenetic dark matter and chemical structure space -- serving as a doorwaymore » to a new era in the discovery of novel molecules.« less

Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neupane, Saraswoti; Hogberg, Nils; Alstrom, Sadhna

2012-01-01

Serratia plymuthica are plant-associated, plant beneficial species belonging to the family Enterobacteriaceae. The members of the genus Serratia are ubiquitous in nature and their life style varies from endophytic to free-living. S. plymuthica AS9 is of special interest for its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The genome of S. plymuthica AS9 comprises a 5,442,880 bp long circular chromosome that consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome is part of the project entitled Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogensmore » awarded through the 2010 DOE-JGI Community Sequencing Program (CSP2010).« less

Hydrodynamic Instability and Thermal Coupling in a Dynamic Model of Liquid-Propellant Combustion

NASA Technical Reports Server (NTRS)

Margolis, S. B.

1999-01-01

For liquid-propellant combustion, the Landau/Levich hydrodynamic models have been combined and extended to account for a dynamic dependence of the burning rate on the local pressure and temperature fields. Analysis of these extended models is greatly facilitated by exploiting the realistic smallness of the gas-to-liquid density ratio rho. Neglecting thermal coupling effects, an asymptotic expression was then derived for the cellular stability boundary A(sub p)(k) where A(sub p) is the pressure sensitivity of the burning rate and k is the disturbance wavenumber. The results explicitly indicate the stabilizing effects of gravity on long-wave disturbances, and those of viscosity and surface tension on short-wave perturbations, and the instability associated with intermediate wavenumbers for critical negative values of A(sub p). In the limit of weak gravity, hydrodynamic instability in liquid-propellant combustion becomes a long-wave, instability phenomenon, whereas at normal gravity, this instability is first manifested through O(1) wavenumbers. In addition, surface tension and viscosity (both liquid and gas) each produce comparable effects in the large-wavenumber regime, thereby providing important modifications to the previous analyses in which one or more of these effects was neglected. For A(sub p)= O, the Landau/Levich results are recovered in appropriate limiting cases, although this typically corresponds to a hydrodynamically unstable parameter regime for p << 1. In addition to the classical cellular form of hydrodynamic stability, there exists a pulsating form corresponding to the loss of stability of steady, planar burning to time-dependent perturbations. This occurs for negative values of the parameter A(sub p), and is thus absent from the original Landau/Levich models. In the extended model, however, there exists a stable band of negative pressure sensitivities bounded above by the Landau type of instability, and below by this pulsating form of hydrodynamic

Localization of excitons by molecular layer formation in a polymer film

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chattopadhyay, S.; Datta, A.

2005-10-15

Spin coated films of atactic polystyrene of two different molecular weights have been studied with uv spectroscopy and x-ray reflectivity, the film thickness (d) varying from {approx}2R{sub g} to {approx}12R{sub g} where R{sub g} is the unperturbed radius of gyration of the polymer. uv extinction due to the pure electronic singlet {sup 1}A{sub 1g}{yields}{sup 1}E{sub 1u} is seen to increase with d{sup -1} for 4R{sub g}{<=}d{<=}12R{sub g} (region 1). This suggests excitonic interaction along d. The variation of total exciton energy (E) of the A{sub 1g}{yields}E{sub 1u} singlet with d in region 1 can be well explained by formation ofmore » linear J-aggregates of polystyrene molecules, in a lattice with spacing 'a' (in A) R{sub g}

Microstructural evolution of diamond films from CH{sub 4}/H{sub 2}/N{sub 2} plasma and their enhanced electrical properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sankaran, K. J.; Tai, N. H., E-mail: nhtai@mx.nthu.edu.tw; Lin, I. N., E-mail: inanlin@mail.tku.edu.tw

2015-02-21

The influence of N{sub 2} concentration in CH{sub 4}/H{sub 2}/N{sub 2} plasma on microstructural evolution and electrical properties of diamond films is systematically investigated. While the diamond films grown in CH{sub 4}/H{sub 2} plasma contain large diamond grains, for the diamond films grown using CH{sub 4}/H{sub 2}/(4%)N{sub 2} plasma, the microstructure drastically changed, resulting in ultra-nanosized diamond grains with Fd3m structure and a{sub 0} = 0.356 nm, along with the formation of n-diamond (n-D), a metastable form of diamond with space group Fm3m and a{sub 0} = 0.356 nm, and i-carbon (i-C) clusters, the bcc structured carbon with a{sub 0} = 0.432 nm. In addition, these films contain widemore » grain boundaries containing amorphous carbon (a-C). The electron field emission (EFE) studies show the best EFE behavior for 4% N{sub 2} films among the CH{sub 4}/H{sub 2}/N{sub 2} grown diamond films. They possess the lowest turn-on field value of 14.3 V/μm and the highest EFE current density value of 0.37 mA/cm{sup 2} at an applied field of 25.4 V/μm. The optical emission spectroscopy studies confirm that CN species are the major criterion to judge the changes in the microstructure of the films. It seems that the grain boundaries can provide electron conduction networks to transport efficiently the electrons to emission sites for field emission, as long as they have sufficient thickness. Whether the matrix nano-sized grains are 3C-diamond, n-D or i-C is immaterial.« less

Heat Transfer Through Turbulent Friction Layers

NASA Technical Reports Server (NTRS)

Reichardt, H.

1943-01-01

The "general Prandtl number" Pr(exp 1) - A(sub q)/A Pr, aside from the Reynolds number determines the ratio of turbulent to molecular heat transfer, and the temperature distribution in turbulent friction layers. A(sub q) = exchange coefficient for heat; A = exchange coefficient for momentum transfer. A formula is derived from the equation defining the general Prandtl number which describes the temperature as a function of the velocity. For fully developed thermal boundary layers all questions relating to heat transfer to and from incompressible fluids can be treated in a simple manner if the ratio of the turbulent shear stress to the total stress T(sub t)/T in the layers near the wall is known, and if the A(sub q)/A can be regarded as independent of the distance from the wall. The velocity distribution across a flat smooth channel and deep into the laminar sublayer was measured for isothermal flow to establish the shear stress ratio T(sub t)/T and to extend the universal wall friction law. The values of T(sub t)/T which resulted from these measurements can be approximately represented by a linear function of the velocity in the laminar-turbulent transition zone. The effect of the temperature relationship of the material values on the flow near the wall is briefly analyzed. It was found that the velocity at the laminar boundary (in contrast to the thickness of the laminar layer) is approximately independent of the temperature distribution. The temperature gradient at the wall and the distribution of temperature and heat flow in the turbulent friction layers were calculated on the basis of the data under two equations. The derived formulas and the figures reveal the effects of the Prandtl number, the Reynolds number, the exchange quantities and the temperature relationship of the material values.

The Chemistry and Excitation of Water in Molecular Clouds

NASA Technical Reports Server (NTRS)

Hollenbach, David

2003-01-01

We model the chemistry and thermal balance of opaque molecular clouds exposed to an external flux of ultraviolet photons. We include the processes of gas phase and grain surface chemical reactions; in particular we examine closely the freezing of atoms and molecules onto grain surfaces and the desorption of molecules from grain surfaces as a function of depth into a molecular cloud. We find that on the surface of a molecular cloud the gas phase water abundances are low because of photodissociation, and the grain phase water (ice) abundance is low because of photodesorption of water from the grain surfaces. Deeper into the cloud, at A(sub v) less than or approximately 2-8 depending on the strength of the external ultraviolet flux, the gas phase water abundance increases with depth as the photodissociation rates decline due to dust attenuation of the ultraviolet field. However, beyond A(sub v) less than or approximately 2-8 the gas phase water abundance declines because the water freezes as water ice on the grains, and photodesorption is no longer effective in clearing the ice. A peak water abundance of about 10(exp -6) to 10(exp -7) occurs at about A(sub v) approximately 2-8, relatively independent of the gas density and the ultraviolet field. We show that such a model matches very closely the observations of the Submillimeter Wave Astronomical Satellite (SWAS), a NASA Small Explorer Mission. The model elucidates several mechanisms that have been recently invoked to understand gas phase chemistry in clouds, including-the freeze-out of molecules onto grain surface, the desorption of these molecules from the surfaces, and the abundance gradients of molecules as functions of depth into molecular clouds.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jewitt, David; Li Jing, E-mail: jewitt@ucla.ed, E-mail: jli@igpp.ucla.ed

The asteroid (3200) Phaethon is widely recognized as the parent of the Geminid meteoroid stream. However, it has never shown evidence for ongoing mass loss or for any form of comet-like activity that would indicate the continued replenishment of the stream. Following an alert by Battams and Watson, we used NASA's STEREO-A spacecraft to image Phaethon near perihelion, in the period UT 2009 June 17-22, when the heliocentric distance was near 0.14 AU. The resulting photometry shows an unexpected brightening, by a factor of two, starting UT 2009 June 20.2 {+-} 0.2, which we interpret as an impulsive release ofmore » dust particles from Phaethon. If the density is near 2500 kg m{sup -3}, then the emitted dust particles must have a combined mass of {approx}2.5 x 10{sup 8} a{sub 1} kg, where a{sub 1} is the particle radius in millimeters. Assuming a{sub 1} = 1, this is approximately 10{sup -4} of the Geminid stream mass and to replenish the stream in steady state within its estimated {approx}10{sup 3} yr lifetime would require {approx}10 events like the one observed, per orbit. Alternatively, ongoing mass loss may be unrelated to the event which produced the Phaethon-Geminid complex. An impact origin of the dust is highly unlikely. Phaethon is too hot for water ice to survive, rendering the possibility that dust is ejected through gas drag from sublimated ice unlikely. Instead, we suggest that Phaethon is essentially a rock comet, in which the small perihelion distance leads both to the production of dust (through thermal fracture and decomposition cracking of hydrated minerals) and to its ejection into interplanetary space (through radiation pressure sweeping and other effects).« less

Applied quantum chemistry: Spectroscopic detection and characterization of the F{sub 2}BS and Cl{sub 2}BS free radicals in the gas phase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Bing; Clouthier, Dennis J., E-mail: dclaser@uky.edu; Sheridan, Phillip M.

2015-03-28

In this and previous work [D. J. Clouthier, J. Chem. Phys. 141, 244309 (2014)], the spectroscopic signatures of the X{sub 2}BY (X = H, halogen, Y = O, S) free radicals have been predicted using high level ab initio theory. The theoretical results have been used to calculate the electronic absorption and single vibronic level (SVL) emission spectra of the radicals under typical jet-cooled conditions. Using these diagnostic predictions, the previously unknown F{sub 2}BS and Cl{sub 2}BS free radicals have been identified and characterized. The radicals were prepared in a free jet expansion by subjecting precursor mixtures of BF{sub 3}more » or BCl{sub 3} and CS{sub 2} vapor to an electric discharge at the exit of a pulsed molecular beam valve. The B{sup ~2}A{sub 1}–X{sup ~} {sup 2}B{sub 2} laser-induced fluorescence spectra were found within 150 cm{sup −1} of their theoretically predicted positions with vibronic structure consistent with our Franck-Condon simulations. The B{sup ~2}A{sub 1} state emits down to the ground state and to the low-lying A{sup ~2}B{sub 1} excited state and the correspondence between the observed and theoretically derived SVL emission Franck-Condon profiles was used to positively identify the radicals and make assignments. Excited state Coriolis coupling effects complicate the emission spectra of both radicals. In addition, a forbidden component of the electronically allowed B{sup ~}–X{sup ~} band system of Cl{sub 2}BS is evident, as signaled by the activity in the b{sub 2} modes in the spectrum. Symmetry arguments indicate that this component gains intensity due to a vibronic interaction of the B{sup ~2}A{sub 1} state with a nearby electronic state of {sup 2}B{sub 2} symmetry.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagpure, I. M., E-mail: indrajitnagpure@gmail.com; Painuly, Deepshikha; Rabanal, Maria Eugenia

The various composition of ZnAlQ{sub 5} such as Zn{sub 1.5}A{sub 10.5}Q{sub 5}, Zn{sub 1}Al{sub 1}Q{sub 5}, Zn{sub 0.5}Al{sub 1.5}Q{sub 5} organic phosphors were prepared via simple cost effective co-precipitation method. The FTIR, SEM, photoluminescence analysis of the prepared phosphors were reported. ZnQ{sub 2} and AlQ{sub 3} were also prepared by similar method and their properties were compared with different composition of ZnAlQ{sub 5}. The structural elucidation in the form of stretching frequencies of chemical bonds of the prepared phosphor was carried out using Fourier Transform Infrared Spectroscopy (FTIR). The stretching frequency analysis confirms the formation of prepared phosphor materials. Themore » SEM analysis shows the surface morphological behavior of prepared phosphor materials. Greenish photoluminescence were observed at 505 to 510 nm for the different composition of ZnAlQ{sub 5},in which Zn{sub 1.5}Al{sub 0.5}Q{sub 5} shows maximum luminescence intensity at 505 nm. PL emission of ZnQ{sub 2} was observed at 515 nm, while for AlQ{sub 3} at 520 nm. The blue shift of 10 nm was observed in Zn{sub 1.5}A{sub 10.5}Q{sub 5} due to modification of energy level due to presence of Zn{sup 2+} and Al{sup 3+}. The enhancement in PL intensity was observed in Zn{sub 1.5}A{sub 10.5}Q{sub 5} compared to the other composition due to transfer of energy between Zn{sup 2+} and quinolate complex. Optical properties of the prepared materials were evaluated for possible applications in organic light emitting devices (OLED).« less

Weak values and weak coupling maximizing the output of weak measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Di Lorenzo, Antonio, E-mail: dilorenzo.antonio@gmail.com

2014-06-15

In a weak measurement, the average output 〈o〉 of a probe that measures an observable A{sup -hat} of a quantum system undergoing both a preparation in a state ρ{sub i} and a postselection in a state E{sub f} is, to a good approximation, a function of the weak value A{sub w}=Tr[E{sub f}A{sup -hat} ρ{sub i}]/Tr[E{sub f}ρ{sub i}], a complex number. For a fixed coupling λ, when the overlap Tr[E{sub f}ρ{sub i}] is very small, A{sub w} diverges, but 〈o〉 stays finite, often tending to zero for symmetry reasons. This paper answers the questions: what is the weak value that maximizesmore » the output for a fixed coupling? What is the coupling that maximizes the output for a fixed weak value? We derive equations for the optimal values of A{sub w} and λ, and provide the solutions. The results are independent of the dimensionality of the system, and they apply to a probe having a Hilbert space of arbitrary dimension. Using the Schrödinger–Robertson uncertainty relation, we demonstrate that, in an important case, the amplification 〈o〉 cannot exceed the initial uncertainty σ{sub o} in the observable o{sup -hat}, we provide an upper limit for the more general case, and a strategy to obtain 〈o〉≫σ{sub o}. - Highlights: •We have provided a general framework to find the extremal values of a weak measurement. •We have derived the location of the extremal values in terms of preparation and postselection. •We have devised a maximization strategy going beyond the limit of the Schrödinger–Robertson relation.« less

Spectroscopic studies of Cr{sup 3+} ions doped in poly(vinylalcohol) complexed polyethylene glycol polymer films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, T. Rajavardhana; Raju, Ch. Linga, E-mail: drchlraj-phy@yahoo.com; Brahmam, K. Veera

2015-05-15

Polymer films of Poly(vinylalcohol) (PVA) complexed with Polyethylene glycol (PEG) with different dopant concentrations of Cr{sup 3+} ions are prepared by solution cast technique. Electron paramagnetic resonance (EPR), Optical absorption and FT-IR studies have been carried out on the polymer films. The EPR spectra of the entire samples exhibit resonance signal at g ≈1.97 which is attributed to the isolated Cr{sup 3+} pairs. The temperature variation EPR studies show that the population of spin-levels participating in the resonance decreases with an increase in temperature, which is in accordance with the Boltzmann Law. The paramagnetic susceptibilities (X) have been calculated frommore » the EPR data at different temperatures. The linewidth of the g ≈1.97 resonance signal has been found to be decreasing with an increase in temperature, which confirms the pairing mechanism between Cr{sup 3+} ions. The Optical absorption spectrum of chromium ions in (PVA+PEG) polymer films exhibits three bands, corresponding to the d-d transitions {sup 4}A{sub 2g}(F)→{sup 4}T{sub 1g}(F), {sup 4}A{sub 2g}(F)→{sup 4}T{sub 2g}(F) and {sup 4}A{sub 2g}(F)→{sup 2}T{sub 1g}(G), in the order of decreasing energy. The crystal field parameter Dq and the Racah interelectronic repulsion parameters B and C have been evaluated. From the ultraviolet absorption edges, Optical band gap (E{sub opt}) and Urbach (ΔE) energies are evaluated. FT-IR spectrum exhibits few bands which are attributed to O-H, CH, C=C and C=O groups of stretching and bending vibrations.« less

Temperature Sensing Above 1000 C Using Cr-Doped GdAlO3 Spin-Allowed Broadband Luminescence

NASA Technical Reports Server (NTRS)

Eldridge, Jeffrey I.; Chambers, Matthew D.

2012-01-01

Cr-doped GdAlO3 (Cr:GdAlO3) is shown to produce remarkably high-intensity spin-allowed broadband luminescence with sufficiently long decay times to make effective luminescence-decay-time based temperature measurements above 1000 C. This phosphor is therefore an attractive alternative to the much lower luminescence intensity rare-earth-doped thermographic phosphors that are typically utilized at these elevated temperatures. In particular, Cr:GdAlO3 will be preferred over rare-earth-doped phosphors, such as Dy:YAG, at temperatures up to 1200 C for intensity-starved situations when the much lower emission intensity from rare-earth-doped phosphors is insufficient for accurate temperature measurements in the presence of significant radiation background. While transition-metal-doped phosphors such as Cr:Al2O3 (ruby) are known to exhibit high luminescence intensity at low dopant concentrations, quenching due to nonradiative decay pathways competing with the (sup 2)E to (sup 4)A(sub 2) radiative transition (R line) has typically restricted their use for temperature sensing to below 600 C. Thermal quenching of the broadband (sup 4)T(sub 2) to (sup 4)A(sub 2) radiative transition from Cr:GdAlO3, however, is delayed until much higher temperatures (above 1000 C). This spin-allowed broadband emission persists to high temperatures because the lower-lying (sup 2)E energy level acts as a reservoir to thermally populate the higher shorter-lived (sup 4)T(sub 2) energy level and because the activation energy for nonradiative crossover relaxation from the (sup 4)T(sub 2) level to the (sup 4)A(sub 2) ground state is high. The strong crystal field associated with the tight bonding of the AlO6 octahedra in the GdAlO3 perovskite structure is responsible for this behavior.

Hydrodynamic Instability in an Extended Landau/Levich Model of Liquid-Propellant Combustion at Normal and Reduced Gravity

NASA Technical Reports Server (NTRS)

Margolis, Stephen B.

1998-01-01

The classical Landau/Levich models of liquid-propellant combustion, despite their relative simplicity, serve as seminal examples that correctly describe the onset of hydrodynamic instability in reactive systems. Recently, these two separate models have been combined and extended to account for a dynamic dependence, absent in the original formulations, of the local burning rate on the local pressure and temperature fields. The resulting model admits an extremely rich variety of both hydrodynamic and reactive/diffusive instabilities that can be analyzed either numerically or analytically in various limiting parameter regimes. In the present work, a formal asymptotic analysis, based on the realistic smallness of the gas-to-liquid density ratio, is developed to investigate the combined effects of gravity and other parameters on the hydrodynamic instability of the propagating liquid/gas interface. In particular, an analytical expression is derived for the neutral stability boundary A(sub p)(k), where A(sub p) is the pressure sensitivity of the burning rate and k is the wavenumber of the disturbance. The results demonstrate explicitly the stabilizing effect of gravity on long-wave disturbances, the stabilizing effect of viscosity (both liquid and gas) and surface tension on short-wave perturbations, and the instability associated with intermediate wavenumbers for critical negative values of A(sub p). In the limiting case of weak gravity, it is shown that hydrodynamic instability in liquid-propellant combustion is a long-wave instability phenomenon, whereas at normal gravity, this instability is first manifested through O(1) wavenumber disturbances. It is also demonstrated that, in general, surface tension and the viscosity of both the liquid and gas phases each produce comparable stabilizing effects in the large-wavenumber regime, thereby providing important modifications to previous analyses in which one or more of these effects were neglected.

Magnetic Field Orientation Effects on the Standoff Distance of Earth's Bow Shock

NASA Technical Reports Server (NTRS)

Cairns, Iver H.; Lyon, J. G.

1996-01-01

Three-dimensional, global MHD simulations of solar wind flow onto a prescribed magnetopause obstacle are used to show that a bow shock's nose location a(sub s), and the relative subsolar magnetosheath thickness Delta(sub ms)/a(sub mp) are strong functions of the IMF cone angle theta (between v(sub sw) and B(sub sw)) and the Alfven Mach number M(sub A). For a given M(sub A) the shock is more distant for higher theta (restricted to the interval 0-90deg by symmetries), while a(sub s)/a(sub mp) and Delta(sub ms/a(sub mp) increase with decreasing M(sub A) for theta greater than or approximately 20deg but decrease with decreasing M(sub A) for theta approximately Odeg. Large differences in Delta(sub ms/a(sub mp) are predicted between theta = Odeg and 90deg at low M(sub A), with smaller differences remaining even at M(sub A) approximately 10. The theta = Odeg results confirm and extend the previous work of Spreiter and Rizzi [1974]. The simulations show that successful models for the subsolar shock location cannot subsume the dependences on M(sub A) and theta into a sole dependence on M(ms). Instead, they confirm a recent prediction [Cairns and Grabbe, 1994] that a(sub s)/a(sub mp) and Delta(sub ms)/a(sub mp) should depend strongly on theta and M(sub A) for M(sub A) less than or approximately 10 (as well as on other MHD variables). Detailed comparisons between theory and data remain to be done. However, preliminary comparisons show good agreement, with distant shock locations found for low M(sub A) and large theta greater than or approximately 45deg and closer locations found for theta less than or approximately 20deg even at M/A approximately 8.

THE ASTROPHYSICAL IMPLICATIONS OF DUST FORMATION DURING THE ERUPTIONS OF HOT, MASSIVE STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kochanek, C. S.

2011-12-10

Dust formation in the winds of hot stars is inextricably linked to the classic eruptive state of luminous blue variables because it requires very high mass-loss rates, M-dot {approx}>10{sup -2.5} M{sub sun} year{sup -1}, for grains to grow and for the non-dust optical depth of the wind to shield the dust formation region from the true stellar photosphere. Thus, dusty shells around hot stars trace the history of 'great' eruptions, and the statistics of such shells in the Galaxy indicate that these eruptions are likely the dominant mass-loss mechanism for evolved, M{sub ZAMS} {approx}> 40 M{sub Sun} stars. Dust formationmore » at such high M-dot also explains why very large grains (a{sub max} {approx}> 1 {mu}m) are frequently found in these shells, since a{sub max}{proportional_to} M-dot . The statistics of these shells (numbers, ages, masses, and grain properties such as a{sub max}) provide an archaeological record of this mass-loss process. In particular, the velocities v{sub shell}, transient durations (where known), and ejected masses M{sub shell} of the Galactic shells and the supernova (SN) 'impostors' proposed as their extragalactic counterparts are very different. While much of the difference is a selection effect created by shell lifetimes {proportional_to}(v{sub shell}{radical}(M{sub shell})){sup -1}, more complete Galactic and extragalactic surveys are needed to demonstrate that the two phenomena share a common origin given that their observed properties are essentially disjoint. If even small fractions (1%) of SNe show interactions with such dense shells of ejecta, as is currently believed, then the driving mechanism of the eruptions must be associated with the very final phases of stellar evolution, suggestive of some underlying nuclear burning instability.« less

A dynamic subgrid-scale model for LES of the G-equation

NASA Technical Reports Server (NTRS)

Bourlioux, A.; Im, H. G.; Ferziger, J. H.

1996-01-01

Turbulent combustion is a difficult subject as it must deal with all of the issues found in both turbulence and combustion. (We consider only premixed flames in this paper, but some of the ideas can be applied to the non-premixed case.) As in many other fields, there are two limiting cases that are easier to deal with than the general case. These are the situations in which the chemical time scale is either much shorter or much longer than the time scale associated with the turbulence. We deal with the former case. In this limit, the flame is thin compared to the turbulence length scales and can be idealized as an infinitely thin sheet. This is commonly called the flamelet regime; it has been the subject of many papers and the basis for many models (see, e.g., Linan & Williams 1993). In the flamelet model, the local flame structure is assumed to be identical to the laminar flame structure; thus the flame propagates normal to itself at the laminar flame speed, S(sub L). This allows the use of simple approximations. For example, one expects the rate of consumption of fuel to be proportional to the area of the flame surface. This idea allowed Damkohler (1940) to propose that the wrinkled flame could be replaced by a smooth one which travels at the turbulent flame speed, S(sub T), defined by S(sub T)/S(sub L) = A(sub L) /A(sub P) where A(sub L) is the total flame surface area and AP is the area projected onto the mean direction of propagation. This relation can be expected to be valid when the flame structure is modified only slightly by the turbulence. More recent approaches have attempted to relate the turbulent flame speed to turbulence intensity, u(sub '), which presumably, characterizes the wrinkling of the flame.

New possibilities for Cr/sup 3 +/ ions as activators of the active media of solid-state lasers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zharikov, E.V.; Lavrishchev, S.V.; Laptev, V.V.

An analysis is made of the relationship between the excited-state lifetime of chromium and the ratio of the luminescence intensities in the /sup 4/T/sub 2/--/sup 4/A/sub 2/ and /sup 2/E--/sup 4/A/sub 2/ channels, on one hand, and the Cr/sup 3 +/..-->..acceptor energy transfer efficiency, on the other. A method is proposed for determination of the energy gap ..delta..E between the /sup 2/E and /sup 4/T/sub 2/ levels of Cr/sup 3 +/ from the temperature dependence of the Cr/sup 3 +/..-->..acceptor nonradiative transfer efficiency. Two independent methods were used to determine ..delta..E for gadolinium gallium garnet (GGG) crystals doped with chromiummore » and with chromium and neodymium. The probabilities of Cr/sup 3 +/ intracenter relaxation and typical parameters of the Cr/sup 3 +/--Nd/sup 3 +/ energy transfer process were also determined. It was found that the values of ..delta..E in gadolinium scandium gallium (GdScGaG) and lanthanum lutetium gallium garnet crystals are comparable with the values of kT at liquid helium temperature. It is shown that the high efficiency of the Cr/sup 3 +/..-->..Nd/sup 3 +/ nonradiative transfer in GGG and GdScGaG crystals doped with chromium and neodymium at room temperature is due to the relatively low value of ..delta..E. It is noted that there are many crystals having the garnet structure and low values of ..delta..E that are potentially suitable for developing lasers utilizing the /sup 4/T/sub 2/--/sup 4/A/sub 2/ electronic--vibrational transition in Cr/sup 3 +/ and having an emission frequency continuously tunable over a wide spectral range.« less

ELEVEN NEW HEAVILY REDDENED FIELD WOLF-RAYET STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, J. D. T.; Cushing, Michael; Barletta, Anthony

We report the results of a medium-narrowband 2 {mu}m line survey covering 5.8 deg{sup 2} near the Galactic plane. We confirm 11 new field Wolf-Rayet stars along three lines of sight probing the inner Galaxy, demonstrating the capability to uncover distant and highly reddened populations of Galactic wind-borne emission-line stars suffering extinction as high as A{sub V} {approx} 40 and as distant as 9 kpc down to modest magnitude limits of K{sub s} {approx} 12.5. All stars are of subtype WC7-8, with median distance d = 6 kpc and median extinction A{sub K{sub s}} = 2.5. Over the fields surveyed,more » the density of Wolf-Rayet stars to limiting magnitude K{sub s} {approx} 12.5 was found to be 1.9 deg{sup -2}. We compare this to models which predict their distribution within the Galaxy and find that, even neglecting survey and subtype incompleteness, they consistently underpredict the number of newly discovered stars along the surveyed lines of sight.« less

Orthorhombic YBaCo{sub 4}O{sub 8.4} crystals as a result of saturation of hexagonal YBaCo{sub 4}O{sub 7} crystals with oxygen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podberezskaya, N. V., E-mail: podberez@niic.nsc.ru; Bolotina, N. B., E-mail: nb-bolotina@mail.ru; Komarov, V. Yu., E-mail: komarov-v-y@niic.nsc.ru

Hexagonal YBaCo{sub 4}O{sub 7} crystals (sp. gr. P6{sub 3}mc, a{sub h} = 6.3058(4) Å, c{sub h} = 10.2442(7) Å, Z = 2) are saturated with oxygen to the YBaCo{sub 4}O{sub 8.4} composition and studied by X-ray diffraction (XRD) analysis. The saturation is completed by a structural first-order phase transition to orthorhombic crystals (sp. gr. Pbc2{sub 1}, a{sub o} = 31.8419(2) Å, b{sub o} = 10.9239(5) Å, c{sub o} = 10.0960(5) Å, Z = 20). The connection of two lattices is expressed in terms of the action of matrix (500/120/001) on the hexagonal basis. Five structural fragments of the same typemore » but with different degrees of order alternate along the long axis of the oxygen-saturated orthorhombic structure. The XRD data on single crystals differ from the results obtained by other researchers on ceramic samples; possible causes of these differences are discussed.« less

The motion near L{sub 4} equilibrium point under non-point mass primaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huda, I. N., E-mail: ibnu.nurul@students.itb.ac.id; Utama, J. A.; Madley, D.

2015-09-30

The Circular Restricted Three-Body Problem (CRTBP) possesses five equilibrium points, that comprise three collinear (L{sub 1}, L{sub 2}, and L{sub 3}) and two triangular points (L{sub 4} and L{sub 5}). The classical study (with the primaries are point mass) suggests that the equilibrium points may cause the velocity of infinitesimal object relatively becomes zero and reveals the zero velocity curve. We study the motion of infinitesimal object near triangular equilibrium point (L{sub 4}) and determine its zero velocity curve. We extend the study by taking into account the effects of radiation of the bigger primary (q{sub 1} ≠ 1, q{submore » 2} = 1) and oblateness of the smaller primary (A{sub 1} = 0, A{sub 2} ≠ 0). The location of L{sub 4} is analytically derived then the stability of L{sub 4} and its zero velocity curves are studied numerically. Our study suggests that the oblateness and the radiation of primaries may affect the stability and zero velocity curve around L{sub 4}.« less

Generation of various radicals in nitrogen plasma and their behavior in media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uhm, Han S., E-mail: hsuhm@kw.ac.kr

2015-12-15

Research on the generation of radicals in nitrogen plasma shows that the most dominant radicals are excited nitrogen molecules in the metastable state of N{sub 2}(A{sub 3}∑{sub u}{sup +}). Hydroxyl molecules are generated from the dissociation of water molecules upon contact with excited nitrogen molecules. The estimated densities of various radicals in nitrogen plasma with an electron temperature of 1 eV are presented in this study. The behavior of these radicals in media is also investigated. Excited nitrogen molecules in the N{sub 2}(A{sub 3}∑{sub u}{sup +}) state from a plasma jet are injected into water, after which the molecules disappear instantaneouslymore » within a few tens of nm, producing hydroxyl molecules. Hydrogen peroxide, hydrogen dioxide, and nitrogen monoxide molecules can diffuse much deeper into water, implying the possibility that a chemical reaction between hydrogen dioxide and nitrogen monoxide molecules produces hydroxyl molecules in deep water, even though density in this case may not be very high.« less

The Search for Exotic Mesons in gamma p -> pi+pi+pi-n with CLAS at Jefferson Lab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Craig Bookwalter

2011-12-01

The {pi}{sub 1}(1600), a J{sup PC} = 1{sup {-+}} exotic meson has been observed by experiments using pion beams. Theorists predict that photon beams could produce gluonic hybrid mesons, of which the {pi}{sub 1}(1600) is a candidate, at enhanced levels relative to pion beams. The g12 rungroup at Jefferson Lab's CEBAF Large Acceptance Spectrometer (CLAS) has recently acquired a large photoproduction dataset, using a liquid hydrogen target and tagged photons from a 5.71 GeV electron beam. A partial-wave analysis of 502K {gamma}p {yields} {pi}{sup +}{pi}{sup +}{pi}{sup -}n events selected from the g12 dataset has been performed, and preliminary fit resultsmore » show strong evidence for well-known states such as the a{sub 1}(1260), a{sub 2}(1320), and {pi}{sub 2}(1670). However, we observe no evidence for the production of the {pi}{sub 1}(1600) in either the partial-wave intensities or the relative complex phase between the 1{sup {-+}} and the 2{sup {-+}} (corresponding to the {pi}{sub 2}) partial waves.« less

Damping of High-temperature Shape Memory Alloys

NASA Technical Reports Server (NTRS)

Duffy, Kirsten P.; Padula, Santo A., II; Scheiman, Daniel A.

2008-01-01

Researchers at NASA Glenn Research Center have been investigating high temperature shape memory alloys as potential damping materials for turbomachinery rotor blades. Analysis shows that a thin layer of SMA with a loss factor of 0.04 or more would be effective at reducing the resonant response of a titanium alloy beam. Two NiTiHf shape memory alloy compositions were tested to determine their loss factors at frequencies from 0.1 to 100 Hz, at temperatures from room temperature to 300 C, and at alternating strain levels of 34-35x10(exp -6). Elevated damping was demonstrated between the M(sub s) and M(sub f) phase transformation temperatures and between the A(sub s) and A(sub f) temperatures. The highest damping occurred at the lowest frequencies, with a loss factor of 0.2-0.26 at 0.1 Hz. However, the peak damping decreased with increasing frequency, and showed significant temperature hysteresis in heating and cooling. Keywords: High-temperature, shape memory alloy, damping, aircraft engine blades, NiTiHf

Influence of Ni on Martensitic Phase Transformations in NiTi Shape Memory Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frenzel, J.; George, Easo P; Dlouhy, A.

High-precision data on phase transformation temperatures in NiTi, including numerical expressions for the effect of Ni on M{sub S}, M{sub F}, A{sub S}, A{sub F} and T{sub 0}, are obtained, and the reasons for the large experimental scatter observed in previous studies are discussed. Clear experimental evidence is provided confirming the predictions of Tang et al. 1999 regarding deviations from a linear relation between the thermodynamic equilibrium temperature and Ni concentration. In addition to affecting the phase transition temperatures, increasing Ni contents are found to decrease the width of thermal hysteresis and the heat of transformation. These findings are rationalizedmore » on the basis of the crystallographic data of Prokoshkin et al. 2004 and the theory of Ball and James. The results show that it is important to document carefully the details of the arc-melting procedure used to make shape memory alloys and that, if the effects of processing are properly accounted for, precise values for the Ni concentration of the NiTi matrix can be obtained.« less

Measurement of the azimuthal angle distribution of leptons from W boson decays as a function of the W transverse momentum in pp collisions at {radical}(s)=1.8 TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acosta, D.; Field, R.D.; Klimenko, S.

We present the first measurement of the A{sub 2} and A{sub 3} angular coefficients of the W boson produced in proton-antiproton collisions. We study W{yields}e{nu}{sub e} and W{yields}{mu}{nu}{sub {mu}} candidate events produced in association with at least one jet at CDF, during Run Ia and Run Ib of the Tevatron at {radical}(s)=1.8 TeV. The corresponding integrated luminosity was 110 pb{sup -1}. The jet balances the transverse momentum of the W and introduces QCD effects in W boson production. The extraction of the angular coefficients is achieved through the direct measurement of the azimuthal angle of the charged lepton in themore » Collins-Soper rest-frame of the W boson. The angular coefficients are measured as a function of the transverse momentum of the W boson. The electron, muon, and combined results are in good agreement with the standard model prediction, up to order {alpha}{sub s}{sup 2} in QCD.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mijnheer, J.

Let (X(t): O{le}t{le}{infinity} be a stable subordinator with {alpha} {element_of}). For increasing sequences t{sub k} we give normalizing constants a{sub k} such that lim inf{sub k{le}{infinity}} a {sup {minus}1}{sub k} X(t{sub k}) is a.s. constant. We also derive a.s. upper bounds.

Gradient free energy in the axially anisotropic superfluid phases of /sup 3/He in the BCS approximation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brand, H.; Doerfle, M.

1981-02-01

We present the gradient free energy in the BCS approximation for the A phase in high magnetic fields and the A/sub 1/ phase. The A phase without external magnetic field, which has been considered previously by Blount and Cross, emerges as a special case of the result for the A phase in high magnetic fields.

A multiparametric analysis of the Einstein sample of early-type galaxies. 2: Galaxy formation history and properties of the interstellar medium

NASA Technical Reports Server (NTRS)

Eskridge, Paul B.; Fabbiano, Giuseppina; Kim, Dong-Woo

1995-01-01

We have conducted bivariate and multivariate statistical analysis of data measuring the integrated luminosity, shape, and potential depth of the Einstein sample of early-type galaxies (presented by Fabbiano et al. 1992). We find significant correlations between the X-ray properties and the axial ratios (a/b) of our sample, such that the roundest systems tend to have the highest L(sub x) and L(sub x)/L(sub B). The most radio-loud objects are also the roundest. We confirm the assertion of Bender et al. (1989) that galaxies with high L(sub x) are boxy (have negative a(sub 4)). Both a/b and a(sub 4) are correlated with L(sub B), but not with IRAS 12 um and 100 um luminosities. There are strong correlations between L(sub x), Mg(sub 2), and sigma(sub nu) in the sense that those systems with the deepest potential wells have the highest L(sub x) and Mg(sub 2). Thus the depth of the potential well appears to govern both the ability to reatin an ISM at the present epoch and to retain the enriched ejecta of early star formation bursts. Both L(sub x)/L(sub B) and L(sub 6) (the 6 cm radio luminosity) show threshold effects with sigma(sub nu) exhibiting sharp increases at log sigma(sub nu) approximately = 2.2. Finally, there is clearly an interrelationship between the various stellar and structural parameters: The scatter in the bivariate relationships between the shape parameters (a/b and a(sub 4)) and the depth parameter sigma(sub nu) is a function of abundance in the sense that, for a given a(sub 4) or a/b, the systems with the highest sigma(sub nu) also have the highest Mg(sub 2). Furthermore, for a constant sigma(sun nu), disky galaxies tend to have higher Mg(sub 2) than boxy ones. Alternatively, for a given abundance, boxy ellipticals tend to be more massive than disky ellipticals. One possibility is that early-type galaxies of a given mass, originating from mergers (boxy ellipticals), have lower abundances than 'primordial' (disky) early-type galaxies. Another is that

The WRKY transcription factor family in Brachypodium distachyon.

PubMed

Tripathi, Prateek; Rabara, Roel C; Langum, Tanner J; Boken, Ashley K; Rushton, Deena L; Boomsma, Darius D; Rinerson, Charles I; Rabara, Jennifer; Reese, R Neil; Chen, Xianfeng; Rohila, Jai S; Rushton, Paul J

2012-06-22

A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. The description of the WRKY transcription factor

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria.

PubMed

Sagova-Mareckova, Marketa; Ulanova, Dana; Sanderova, Petra; Omelka, Marek; Kamenik, Zdenek; Olsovska, Jana; Kopecky, Jan

2015-04-01

Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite

Proton--H/sub 2/ scattering on an ab initio CI potential energy surface. II. Combined vibrational--rotational excitation at 4. 67 and 6 eV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schinke, R.

1980-04-01

Infinite-order-sudden calculations have been performed at 4.67 and 6 eV on the ab initio CI potential energy surface determined recently by Schinke, Dupuis, and Lester. The vibrational degree of freedom has been treated exactly by solving vibrationally coupled radial equations. The rotationally summed differential cross sections for vibrational excitation are in good agreement with the measurements of Schmidt, Hermann, and Linder. It is shown that the rotational excitation cross sections in the vibrational ground state near the rainbow angle are almost exclusively determined by the potential between 2.5a/sub 0/ and 5a/sub 0/ proton--H/sub 2/ separations. In this region only themore » V/sub 2/ term of an expansion into Legendre polynomials is nonvanishing and is a factor of approx.3 smaller for the new surface than for the Giese and Gentry analytic potential. These differences result in a dramatic decrease of the rotational excitation cross sections in the rainbow region so that the present theoretical transition probabilities are in much better agreement with the experiments than our previous sudden vib--rotor calculations utilizing Giese and Gentry's surface.« less

In-situ observations of flux ropes formed in association with a pair of spiral nulls in magnetotail plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Ruilong; Xie, Lun; He, Jiansen

Signatures of secondary islands are frequently observed in the magnetic reconnection regions of magnetotail plasmas. In this paper, magnetic structures with the secondary-island signatures observed by Cluster are reassembled by a fitting-reconstruction method. The results show three-dimensionally that a secondary island event can manifest the flux rope formed with an A{sub s}-type null and a B{sub s}-type null paired via their spines. We call this A{sub s}-spine-B{sub s}-like configuration the helically wrapped spine model. The reconstructed field lines wrap around the spine to form the flux rope, and an O-type topology is therefore seen on the plane perpendicular to themore » spine. Magnetized electrons are found to rotate on and cross the fan surface, suggesting that both the torsional-spine and the spine-fan reconnection take place in the configuration. Furthermore, detailed analysis implies that the spiral nulls and flux ropes were locally generated nearby the spacecraft in the reconnection outflow region, indicating that secondary reconnection may occur in the exhaust away from the primary reconnection site.« less

An anomalous extinction law in the Cep OB3b young cluster: Evidence for dust processing during gas dispersal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, Thomas S.; Prchlik, Jakub J.; Megeath, S. Thomas

We determine the extinction law through Cep OB3b, a young cluster of 3000 stars undergoing gas dispersal. The extinction is measured toward 76 background K giants identified with MMT/Hectospec spectra. Color excess ratios were determined toward each of the giants using V and R photometry from the literature, g, r, i, and z photometry from the Sloan Digital Sky Survey and J, H, and K{sub s} photometry from the Two Micron All Sky Survey. These color excess ratios were then used to construct the extinction law through the dusty material associated with Cep OB3b. The extinction law through Cep OB3bmore » is intermediate between the R{sub V} = 3.1 and R{sub V} = 5 laws commonly used for the diffuse atomic interstellar medium and dense molecular clouds, respectively. The dependence of the extinction law on line-of-sight A{sub V} is investigated and we find the extinction law becomes shallower for regions with A{sub V} > 2.5 mag. We speculate that the intermediate dust law results from dust processing during the dispersal of the molecular cloud by the cluster.« less

Revisiting the relaxation dynamics of isolated pyrrole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montero, Raúl; Ovejas, Virginia; Fernández-Fernández, Marta

Herein, the interpretation of the femtosecond-scale temporal evolution of the pyrrole ion signal, after excitation in the 267–217 nm interval, recently published by our group [R. Montero, A. Peralta Conde, V. Ovejas, M. Fernández-Fernández, F. Castaño, J. R. Vázquez de Aldana, and A. Longarte, J. Chem. Phys.137, 064317 (2012)] is re-visited. The observation of a shift in the pyrrole{sup +} transient respect to zero delay reference, initially attributed to ultrafast dynamics on the πσ{sup *} type state (3s a{sub 1} ← π 1a{sub 2}), is demonstrated to be caused by the existence of pump + probe populated states, along themore » ionization process. The influence of these resonances in pump-prone ionization experiments, when multi-photon probes are used, and the significance of a proper zero-time reference, is discussed. The possibility of preparing the πσ{sup *} state by direct excitation is investigated by collecting 1 + 1 photoelectron spectra, at excitation wavelengths ranging from 255 to 219 nm. No conclusive evidences of ionization through this state are found.« less

Acceleration of polarized protons to 22 GeV/c and the measurement of spin-spin effects in p/sub up-arrow/+p/sub up-arrow/. -->. p+p

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khiari, F.Z.; Cameron, P.R.; Court, G.R.

1989-01-01

Accelerating polarized protons to 22 GeV/c at the Brookhaven Alternating Gradient Synchro- tron required both extensive hardware modifications and a difficult commissioning process. We had to overcome 45 strong depolarizing resonances to maintain polarization up to 22 GeV/c in this strong-focusing synchrotron. At 18.5 GeV/c we measured the analyzing power A and the spin-spin correlation parameter A/sub n//sub n/ in large- P/sub perpendicular//sup 2/ proton-proton elastic scattering, using the polarized proton beam and a polarized proton target. We also obtained a high-precision measurement of A at P/sub perpendicular//sup 2/ = 0.3 (GeV/c)/sup 2/ at 13.3 GeV/c. At 18.5 GeV/c wemore » found that A/sub n//sub n/ = (-2 +- 16)% at P/sub perpendicular//sup 2/ = 4.7 (GeV/c)/sup 2/, where it was about 60% near 12 GeV at the Argonne Zero Gradient Synchrotron. This sharp change suggests that spin-spin forces may have a strong and unexpected energy dependence at high P/sub perpendicular//sup 2/.« less

Cosmological parameter estimation from CMB and X-ray cluster after Planck

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jian-Wei; Cai, Rong-Gen; Guo, Zong-Kuan

We investigate constraints on cosmological parameters in three 8-parameter models with the summed neutrino mass as a free parameter, by a joint analysis of CCCP X-ray cluster data, the newly released Planck CMB data as well as some external data sets including baryon acoustic oscillation measurements from the 6dFGS, SDSS DR7 and BOSS DR9 surveys, and Hubble Space Telescope H{sub 0} measurement. We find that the combined data strongly favor a non-zero neutrino masses at more than 3σ confidence level in these non-vanilla models. Allowing the CMB lensing amplitude A{sub L} to vary, we find A{sub L} > 1 atmore » 3σ confidence level. For dark energy with a constant equation of state w, we obtain w < −1 at 3σ confidence level. The estimate of the matter power spectrum amplitude σ{sub 8} is discrepant with the Planck value at 2σ confidence level, which reflects some tension between X-ray cluster data and Planck data in these non-vanilla models. The tension can be alleviated by adding a 9% systematic shift in the cluster mass function.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patsha, Avinash, E-mail: avinash.phy@gmail.com, E-mail: dhara@igcar.gov.in; Dhara, Sandip; Tyagi, A. K.

The localized effect of impurities in single GaN nanowires in the sub-diffraction limit is reported using the study of lattice vibrational modes in the evanescent field of Au nanoparticle assisted tip enhanced Raman spectroscopy (TERS). GaN nanowires with the O impurity and the Mg dopants were grown by the chemical vapor deposition technique in the catalyst assisted vapor-liquid-solid process. Symmetry allowed Raman modes of wurtzite GaN are observed for undoped and doped nanowires. Unusually very strong intensity of the non-zone center zone boundary mode is observed for the TERS studies of both the undoped and the Mg doped GaN singlemore » nanowires. Surface optical mode of A{sub 1} symmetry is also observed for both the undoped and the Mg doped GaN samples. A strong coupling of longitudinal optical (LO) phonons with free electrons, however, is reported only in the O rich single nanowires with the asymmetric A{sub 1}(LO) mode. Study of the local vibration mode shows the presence of Mg as dopant in the single GaN nanowires.« less

Pressure-magnetic field induced phase transformation in Ni{sub 46}Mn{sub 41}In{sub 13} Heusler alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rama Rao, N. V., E-mail: nvrrao@dmrl.drdo.in; Manivel Raja, M.; Pandian, S.

2014-12-14

The effect of hydrostatic pressure and magnetic field on the magnetic properties and phase transformation in Ni{sub 46}Mn{sub 41}In{sub 13} Heusler alloy was investigated. Pressure (P)-magnetic field (H)-temperature (T) phase diagram has been constructed from experimental results. In the P–T contour of the phase diagram, the slope of the austenite-martensite phase boundary line appears positive (dT/dP > 0), while it appears negative (dT/dH < 0) in the H–T contour. The results revealed that pressure and magnetic field have opposite effect on phase stabilization. The combined effect of pressure and magnetic field on martensitic transition has led to two important findings: (i) pressure dependent shiftmore » of austenite start temperature (A{sub s}) is higher when larger field is applied, and (ii) field dependent shift of A{sub s} is lowered when a higher pressure is applied. The pressure and magnetic field dependent shift observed in the martensitic transformation has been explained on the basis of thermodynamic calculations. Curie temperature of the phases was found to increase with pressure at a rate of 0.6 K/kbar.« less

Preliminary results on heavy flavor physics at SLD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Usher, T.

1994-12-01

The author reports on preliminary heavy flavor physics results from the SLD detector at the SLAC Linear Collider. Efficient tagging of b{bar b} events is achieved with an impact parameter technique that takes advantage of the small and stable interaction point of the SLC and all charged tracks in Z{sup 0} decays. This technique is applied to samples of Z{sup 0} events collected during the 1992 and 1993 physics runs. Preliminary measurements of the ratio R{sub b} = {Gamma}(Z{sup 0} {yields} b{bar b})/{Gamma}(Z{sup 0} {yields} hadrons) and the average B hadron lifetime <{tau}{sub B}> are reported. In a sample ofmore » 27K Z{sup 0} events, values of R{sub b} = 0.235 {+-} 0.006(stat.) {+-} 0.018(syst.) and <{tau}{sub B}> = 1.53 {+-} 0.006(stat.) {+-} 0.018(syst.) are obtained. In addition, the first measurement of the left-right asymmetry A{sub b} is reported. Using a sample of 38K Z{sup 0} events with a luminosity weighted electron polarization of 62%, the author obtains a preliminary value of A{sub b} = 0.94 {+-} 0.006(stat.) {+-} 0.018(syst.).« less

Model-Dependent Constraint on Quark Total Angular Momentum Based on the Transverse Target-spin Asymmetry Measured in Deeply Virtual Compton Scattering at HERMES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nowak, Wolf-Dieter

Results are reported on the transverse target-spin asymmetry (TTSA) associated with deeply virtual Compton scattering on the proton. The data have been accumulated in the years 2002-2004 by the HERMES experiment at DESY, in which the HERA 27.6 GeV e+ beam scattered on a transversely polarized hydrogen target. Two azimuthal amplitudes of the TTSA appearing to LO in 1/Q and {alpha}s, A{sub UT}{sup sin({phi}-{phi}{sub S})cos{phi}} and A{sub UT}{sup cos({phi} -{phi}{sub S})sin{phi}}, are given as a function of -t,xB,Q2 in the kinematic range |t| < 0.7 GeV2, 0.03 < xB < 0.35 and 1 < Q2 < 10 GeV2. The firstmore » amplitude is found to be sensitive to the generalized parton distribution (GPD) E of the proton, which can be parameterized in a GPD model through quark total angular momentum Jq(q = u, d). Within the context of this model, a constraint in the (Ju,Jd) plane is obtained from HERMES TTSA data.« less

Coherence lengths for three-dimensional superconductors in the BCS-Bose picture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carter, R.M.; Casas, M.; Getino, J.M.

1995-12-01

Following an approach similar to that of Miyake or Randeria, Duan, and Shieh in two dimensions, we study a three-dimensional many-fermion gas at zero temperature interacting via some short-ranged two-body potential. To accommodate a possible singularity (e.g., the Coulomb repulsion) in the interaction, the potential is eliminated in favor of the two-body scattering {ital t}-matrix, the low-energy form of which is expressible in terms of the {ital s}-wave scattering length {ital a}{sub {ital s}}. The BCS gap equation for {ital s}-wave pairing is then solved simultaneously with the number equation in order to self-consistently obtain the zero-temperature BCS gap {Delta}more » as well as the chemical potential {mu} as functions of the dimensionless coupling variable {lambda}{equivalent_to}{ital k}{sub {ital F}}{ital a}{sub {ital s}}, where {ital k}{sub {ital F}} is the Fermi momentum. Results are valid for arbitrary coupling strength, and in the weak coupling limit reproduce the standard BCS results. Finally, root-mean-square pair sizes are obtained as a function of {lambda} and compared with experimental values.« less

Design and fabrication of elliptical-core few-mode fiber for MIMO-less data transmission.

PubMed

Liang, Junpeng; Mo, Qi; Fu, Songnian; Tang, Ming; Shum, P; Liu, Deming

2016-07-01

We propose a design strategy of elliptical core few-mode fiber (e-FMF) that supports three spatial modes with enhanced mode spacing between LP_{11a> and LP11b, to suppress intra-mode coupling during mode-division multiplexing (MDM) transmission. Our theoretical investigations show that there exist two optimization regimes for the e-FMF, as a comparison with traditional circular core FMF(c-FMF). At the regime of three-mode operation, there occurs a trade-off between mode spacing and bending-induced loss. Meanwhile, in terms of five-mode regime, a trade-off between mode spacing and high-order mode crosstalk happens. Finally, we fabricate 7.94 km e-FMF with the optimal parameters, based on the commercial fiber manufacture facility. The primary characterizations at 1550 nm show that three spatial modes of e-FMF can be transmitted with a loss less than 0.3 dB/km. Meanwhile, -22.44  dB crosstalk between LP11a> and LP11b is observed, even when the 2 km e-FMF is under stress-induced strong perturbation.}

Parity Violation in Proton-Proton Scattering at Intermediate Energies

DOE R&D Accomplishments Database

Yuan, V.; Frauenfelder, H.; Harper, R. W.; Bowman, J. D.; Carlini, R.; MacArthur, D. W.; Mischke, R. E.; Nagle, D. E.; Talaga, R. L.; McDonald, A. B.

1986-05-01

Results of a measurement of parity nonconservation in the anti p-p total cross sections at 800-MeV are presented. The dependence of transmission on beam properties and correction for systematic errors are discussed. The measured longitudinal asymmetry is A{sub L} = (+2.4 +- 1.1(statistical) +- 0.1(systematic)) x 10{sup -7}. A proposed experiment at 230 MeV is discussed.

Measurement of the Z0 → $$s\\bar{s}$$ Coupling at the SLD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Staengle, Hermann

1999-11-24

This dissertation presents a direct measurement of the parity-violating coupling of the Z{sup 0} to strange quarks, A{sub s}, derived from e{sup +}e{sup -} collision data containing approximately 550,000 hadronic decays of polarized Z{sup 0} bosons. Data were recorded with the SLC Large Detector (SLD) at the SLAC Linear Collider (SLC) between 1993 and 1998 with an average electron beam polarization of 73% and 74% during the 1993-5 and 1996-8 run periods, respectively. Making use of several unique features of the SLC and SLD, this measurement relies on a new generation particle identification system, the Cherenkov Ring Imaging Detector, tomore » test the Standard Model prediction of universality in the coupling of the Z{sup 0} to down-type quarks. Polarized Z{sup 0} --> s anti-s events are tagged by the presence in each event hemisphere of a high-momentum K {+-}, K{sub s}{sup 0} or Lambda{sup 0}/ anti-Lambda{sup 0} identified using particle identification and/or a mass tag. The background from heavy flavor events is suppressed with the CCD-based vertex detector. The event thrust axis is signed with the strangeness of the tagged particle to point in the direction of the initial s quark. The coupling A{sub s} is derived from a maximum likelihood fit to the polar angle distributions of the tagged s quark measured with left- and right-handed electron beams. To reduce the model dependence of the measurement, the background from u anti-u and d anti-d events as well as the analyzing power of the method for s anti-s events are constrained from the data. We obtain A{sub s} = 0.86 {+-} 0.08(stat.) {+-} 0.05(syst.). The result is consistent with both the Standard Model prediction and previous bottom quark coupling mA{sub b}, measurements performed by SLD and LEP, and therefore supports the predicted universality of the Z{sup 0} to down-type quark couplings.« less

Properties and Potential of Two (ni,pt)ti Alloys for Use as High-temperature Actuator Materials

NASA Technical Reports Server (NTRS)

Noebe, Ronald; Gaydosh, Darrell; Padula, Santo, II.; Garg, Anita; Biles, Tiffany; Nathal, Michael

2005-01-01

The microstructure, transformation temperatures, basic tensile properties, shape memory behavior, and work output for two (Ni,Ti)Pt high-temperature shape memory alloys have been characterized. One was a Ni30Pt20Ti50 alloy (referred to as 20Pt) with transformation temperatures above 230 C and the other was a Ni20Pt30Ti50 alloy (30Pt) with transformation temperatures about 530 C. Both materials displayed shape memory behavior and were capable of 100% (no-load) strain recovery for strain levels up to their fracture limit (3-4%) when deformed at room temperature. For the 20Pt alloy, the tensile strength, modulus, and ductility dramatically increased when the material was tested just about the austenite finish (A(sub f)) temperature. For the 30Pt alloy, a similar change in yield behavior at temperatures above the A(sub f) was not observed. In this case the strength of the austentite phase was at best comparable and generally much weaker than the martensite phase. A ductility minimum was also observed just below the A(sub s) temperature in this alloy. As a result of these differences in tensile behavior, the two alloys performed completely different when thermally cycled under constant load. The 20Pt alloy behaved similar to conventional binary NiTi alloys with work output due to the martensite-to-austenite transformation initially increasing with applied stress. The maximum work output measured in the 20Pt alloy was nearly 9 J/cu cm and was limited by the tensile ductility of the material. In contrast, the martensite-to-austenite transformation in the 30Pt alloy was not capable of performing work against any bias load. The reason for this behavior was traced back to its basic mechanical properties, where the yield strength of the austenite phase was similar to or lower than that of the martensite phase, depending on temperature. Hence, the recovery or transformation strain for the 30Pt alloy under load was essentially zero, resulting in zero work output.

Kinetics of calcium sulfoaluminate formation from tricalcium aluminate, calcium sulfate and calcium oxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xuerun, E-mail: xuerunli@163.com; Zhang, Yu; Shen, Xiaodong, E-mail: xdshen@njut.edu.cn

The formation kinetics of tricalcium aluminate (C{sub 3}A) and calcium sulfate yielding calcium sulfoaluminate (C{sub 4}A{sub 3}more » $$) and the decomposition kinetics of calcium sulfoaluminate were investigated by sintering a mixture of synthetic C{sub 3}A and gypsum. The quantitative analysis of the phase composition was performed by X-ray powder diffraction analysis using the Rietveld method. The results showed that the formation reaction 3Ca{sub 3}Al{sub 2}O{sub 6} + CaSO{sub 4} → Ca{sub 4}Al{sub 6}O{sub 12}(SO{sub 4}) + 6CaO was the primary reaction < 1350 °C with and activation energy of 231 ± 42 kJ/mol; while the decomposition reaction 2Ca{sub 4}Al{sub 6}O{sub 12}(SO{sub 4}) + 10CaO → 6Ca{sub 3}Al{sub 2}O{sub 6} + 2SO{sub 2} ↑ + O{sub 2} ↑ primarily occurred beyond 1350 °C with an activation energy of 792 ± 64 kJ/mol. The optimal formation region for C{sub 4}A{sub 3}$$ was from 1150 °C to 1350 °C and from 6 h to 1 h, which could provide useful information on the formation of C{sub 4}A{sub 3}$ containing clinkers. The Jander diffusion model was feasible for the formation and decomposition of calcium sulfoaluminate. Ca{sup 2+} and SO{sub 4}{sup 2−} were the diffusive species in both the formation and decomposition reactions. -- Highlights: •Formation and decomposition of calcium sulphoaluminate were studied. •Decomposition of calcium sulphoaluminate combined CaO and yielded C{sub 3}A. •Activation energy for formation was 231 ± 42 kJ/mol. •Activation energy for decomposition was 792 ± 64 kJ/mol. •Both the formation and decomposition were controlled by diffusion.« less

FORMING HABITABLE PLANETS AROUND DWARF STARS: APPLICATION TO OGLE-06-109L

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang Su; Zhou Jilin, E-mail: suwang@nju.edu.cn, E-mail: zhoujl@nju.edu.cn

2011-02-01

Dwarf stars are believed to have a small protostar disk where planets may grow up. During the planet formation stage, embryos undergoing type I migration are expected to be stalled at an inner edge of the magnetically inactive disk (a{sub crit} {approx} 0.2-0.3 AU). This mechanism makes the location around a{sub crit} a 'sweet spot' for forming planets. In dwarf stars with masses {approx}0.5 M{sub sun}, a{sub crit} is roughly inside the habitable zone of the system. In this paper, we study the formation of habitable planets due to this mechanism using model system OGLE-06-109L, which has a 0.51 M{submore » sun} dwarf star with two giant planets in 2.3 and 4.6 AU observed by microlensing. We model the embryos undergoing type I migration in the gas disk with a constant disk-accretion rate ( M-dot ). Giant planets in outside orbits affect the formation of habitable planets through secular perturbations at the early stage and secular resonance at the late stage. We find that the existence and the masses of the habitable planets in the OGLE-06-109L system depend on both M-dot and the speed of type I migration. If planets are formed earlier, so that M-dot is larger ({approx}10{sup -7} M{sub sun} yr{sup -1}), terrestrial planets cannot survive unless the type I migration rate is an order of magnitude less. If planets are formed later, so that M-dot is smaller ({approx}10{sup -8} M{sub sun} yr{sup -1}), single and high-mass terrestrial planets with high water contents ({approx}5%) will be formed by inward migration of outer planet cores. A slower-speed migration will result in several planets via collisions of embryos, and thus their water contents will be low ({approx}2%). Mean motion resonances or apsidal resonances among planets may be observed if multiple planets survive in the inner system.« less

Phase transitions and photoinduced transformations at high pressure in the molecular donor-acceptor fullerene complex (Cd(dedtc){sub 2}){sub 2} · C{sub 60}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meletov, K. P., E-mail: mele@issp.ac.ru; Konarev, D. V.; Tolstikova, A. O.

2015-06-15

The Raman spectra of crystals of C{sub 60} fullerene-cadmium diethyldithiocarbamate molecular donor-acceptor complexes (Cd(dedtc){sub 2}){sub 2} · C{sub 60} were measured at pressures of up to 17 GPa, and the crystal lattice parameters of these complexes were determined at pressures of up to 6 GPa. An increase in pressure up to ∼2 GPa leads to changes in the Raman spectra, which are manifested by splitting of the intramolecular H{sub g}(1)-H{sub g}(8) phonon modes and by softening of the A{sub g}(2) mode of the C{sub 60} molecule. A further increase in pressure up to 17 GPa does not induce significant newmore » changes to the Raman spectra, while a decrease is accompanied by the reverse transformation at a pressure of about 2 GPa. The pressure dependence of the lattice parameters also exhibits a reversible feature at 2 GPa related to a jumplike decrease in compressibility. All these data are indicative of a phase transition in the vicinity of 2 GPa related to the formation of covalent bonds between C{sub 60} molecules and, probably, the appearance of C{sub 120} dimers in fullerene layers. It was also found that, in the pressure interval from 2 to 6.3 GPa, the Raman spectra of complexes exhibit photoinduced transformations under prolonged exposure to laser radiation with a wavelength of λ = 532 nm and power density up to 5000 W/cm{sup 2}. These changes are manifested by splitting and softening of the A{sub g}(2) mode and resemble analogous changes accompanying the photopolymerization of C{sub 60} fullerene. The intensity of new bands exhibits exponential growth with increasing exposure time. The photopolymer yield depends on both the laser radiation power and external pressure. The A{sub g}(2) mode splitting under irradiation can be related to the formation of photo-oligomers with various numbers of intermolecular covalent bonds per C{sub 60} molecule.« less

Hot-wire calibration in subsonic/transonic flow regimes

NASA Technical Reports Server (NTRS)

Nagabushana, K. A.; Ash, Robert L.

1995-01-01

A different approach for calibrating hot-wires, which simplifies the calibration procedure and reduces the tunnel run-time by an order of magnitude was sought. In general, it is accepted that the directly measurable quantities in any flow are velocity, density, and total temperature. Very few facilities have the capability of varying the total temperature over an adequate range. However, if the overheat temperature parameter, a(sub w), is used to calibrate the hot-wire then the directly measurable quantity, voltage, will be a function of the flow variables and the overheat parameter i.e., E = f(u,p,a(sub w), T(sub w)) where a(sub w) will contain the needed total temperature information. In this report, various methods of evaluating sensitivities with different dependent and independent variables to calibrate a 3-Wire hot-wire probe using a constant temperature anemometer (CTA) in subsonic/transonic flow regimes is presented. The advantage of using a(sub w) as the independent variable instead of total temperature, t(sub o), or overheat temperature parameter, tau, is that while running a calibration test it is not necessary to know the recovery factor, the coefficients in a wire resistance to temperature relationship for a given probe. It was deduced that the method employing the relationship E = f (u,p,a(sub w)) should result in the most accurate calibration of hot wire probes. Any other method would require additional measurements. Also this method will allow calibration and determination of accurate temperature fluctuation information even in atmospheric wind tunnels where there is no ability to obtain any temperature sensitivity information at present. This technique greatly simplifies the calibration process for hot-wires, provides the required calibration information needed in obtaining temperature fluctuations, and reduces both the tunnel run-time and the test matrix required to calibrate hotwires. Some of the results using the above techniques are presented

A CROSSED MOLECULAR BEAM, LOW-TEMPERATURE KINETICS, AND THEORETICAL INVESTIGATION OF THE REACTION OF THE CYANO RADICAL (CN) WITH 1,3-BUTADIENE (C{sub 4}H{sub 6}). A ROUTE TO COMPLEX NITROGEN-BEARING MOLECULES IN LOW-TEMPERATURE EXTRATERRESTRIAL ENVIRONMENTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morales, Sebastien B.; Bennett, Christopher J.; Le Picard, Sebastien D.

2011-11-20

We present a joint crossed molecular beam and kinetics investigation combined with electronic structure and statistical calculations on the reaction of the ground-state cyano radical, CN(X {sup 2}{Sigma}{sup +}), with the 1,3-butadiene molecule, H{sub 2}CCHCHCH{sub 2}(X {sup 1} A{sub g}), and its partially deuterated counterparts, H{sub 2}CCDCDCH{sub 2}(X {sup 1} A{sub g}) and D{sub 2}CCHCHCD{sub 2}(X {sup 1} A{sub g}). The crossed beam studies indicate that the reaction proceeds via a long-lived C{sub 5}H{sub 6}N complex, yielding C{sub 5}H{sub 5}N isomer(s) plus atomic hydrogen under single collision conditions as the nascent product(s). Experiments with the partially deuterated 1,3-butadienes indicate thatmore » the atomic hydrogen loss originates from one of the terminal carbon atoms of 1,3-butadiene. A combination of the experimental data with electronic structure calculations suggests that the thermodynamically less favorable 1-cyano-1,3-butadiene isomer represents the dominant reaction product; possible minor contributions of less than a few percent from the aromatic pyridine molecule might be feasible. Low-temperature kinetics studies demonstrate that the overall reaction is very fast from room temperature down to 23 K with rate coefficients close to the gas kinetic limit. This finding, combined with theoretical calculations, indicates that the reaction proceeds on an entrance barrier-less potential energy surface (PES). This combined experimental and theoretical approach represents an important step toward a systematic understanding of the formation of complex, nitrogen-bearing molecules-here on the C{sub 5}H{sub 6}N PES-in low-temperature extraterrestrial environments. These results are compared to the reaction dynamics of D1-ethynyl radicals (C{sub 2}D; X {sup 2}{Sigma}{sup +}) with 1,3-butadiene accessing the isoelectronic C{sub 6}H{sub 7} surface as tackled earlier in our laboratories.« less

Measurement of CP observables in B{sup {+-}{yields}D}{sub CP}K{sup {+-}}decays and constraints on the CKM angle {gamma}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amo Sanchez, P. del; Lees, J. P.; Poireau, V.

Using the entire sample of 467x10{sup 6} {Upsilon}(4S){yields}BB decays collected with the BABAR detector at the PEP-II asymmetric-energy B factory at the SLAC National Accelerator Laboratory, we perform an analysis of B{sup {+-}}{yields}DK{sup {+-}}decays, using decay modes in which the neutral D meson decays to either CP-eigenstates or non-CP-eigenstates. We measure the partial decay rate charge asymmetries for CP-even and CP-odd D final states to be A{sub CP+}=0.25{+-}0.06{+-}0.02 and A{sub CP-}=-0.09{+-}0.07{+-}0.02, respectively, where the first error is the statistical and the second is the systematic uncertainty. The parameter A{sub CP+} is different from zero with a significance of 3.6 standardmore » deviations, constituting evidence for direct CP violation. We also measure the ratios of the charged-averaged B partial decay rates in CP and non-CP decays, R{sub CP+}=1.18{+-}0.09{+-}0.05 and R{sub CP-}=1.07{+-}0.08{+-}0.04. We infer frequentist confidence intervals for the angle {gamma} of the unitarity triangle, for the strong phase difference {delta}{sub B}, and for the amplitude ratio r{sub B}, which are related to the B{sup -}{yields}DK{sup -} decay amplitude by r{sub B}e{sup i({delta}{sub B}-{gamma})}=A(B{sup -}{yields}D{sup 0}K{sup -})/A(B{sup -}{yields}D{sup 0}K{sup -}). Including statistical and systematic uncertainties, we obtain 0.24

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palmer, Michael H., E-mail: m.h.palmer@ed.ac.uk; Ridley, Trevor, E-mail: tr01@staffmail.ed.ac.uk, E-mail: vronning@phys.au.dk, E-mail: nykj@phys.au.dk, E-mail: marcello.coreno@elettra.eu, E-mail: desimone@iom.cnr.it, E-mail: malgorzata.biczysko@shu.edu.cn, E-mail: alberto.baiardi@sns.it, E-mail: kipeters@wsu.edu; Vrønning Hoffmann, Søren, E-mail: tr01@staffmail.ed.ac.uk, E-mail: vronning@phys.au.dk, E-mail: nykj@phys.au.dk, E-mail: marcello.coreno@elettra.eu, E-mail: desimone@iom.cnr.it, E-mail: malgorzata.biczysko@shu.edu.cn, E-mail: alberto.baiardi@sns.it, E-mail: kipeters@wsu.edu

New photoelectron (PE) and ultra violet (UV) and vacuum UV (VUV) spectra have been obtained for chlorobenzene by synchrotron study with higher sensitivity and resolution than previous work and are subjected to detailed analysis. In addition, we report on the mass-resolved (2 + 1) resonance enhanced multiphoton ionization (REMPI) spectra of a jet-cooled sample. Both the VUV and REMPI spectra have enabled identification of a considerable number of Rydberg states for the first time. The use of ab initio calculations, which include both multi-reference multi-root doubles and singles configuration interaction (MRD-CI) and time dependent density functional theoretical (TDDFT) methods, hasmore » led to major advances in interpretation of the vibrational structure of the ionic and electronically excited states. Franck-Condon (FC) analyses of the PE spectra, including both hot and cold bands, indicate much more complex envelopes than previously thought. The sequence of ionic states can be best interpreted by our multi-configuration self-consistent field computations and also by comparison of the calculated vibrational structure of the B and C ionic states with experiment; these conclusions suggest that the leading sequence is the same as that of iodobenzene and bromobenzene, namely: X{sup 2}B{sub 1}(3b{sub 1}{sup −1}) < A{sup 2}A{sub 2}(1a{sub 2}{sup −1}) < B{sup 2}B{sub 2}(6b{sub 2}{sup −1}) < C{sup 2}B{sub 1}(2b{sub 1}{sup −1}). The absorption onset near 4.6 eV has been investigated using MRD-CI and TDDFT calculations; the principal component of this band is {sup 1}B{sub 2} and an interpretation based on the superposition of FC and Herzberg-Teller contributions has been performed. The other low-lying absorption band near 5.8 eV is dominated by a {sup 1}A{sub 1} state, but an underlying weak {sup 1}B{sub 1} state (πσ{sup ∗}) is also found. The strongest band in the VUV spectrum near 6.7 eV is poorly resolved and is analyzed in terms of two ππ{sup �

Investigation of Intravenous Hydroxocobalamin Compared to Hextend for Resuscitation in a Swine Model of Uncontrolled Hemorrhagic Shock: A Preliminary Report

DTIC Science & Technology

2017-06-16

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Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

DOE PAGES

Whitman, William B.; Woyke, Tanja; Klenk, Hans-Peter; ...

2015-05-17

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Here in this paper, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while theymore » are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity« less

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

PubMed Central

2015-01-01

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Herein, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity. PMID:26203337

The DOE Bioenergy Research Centers: History, Operations, and Scientific Output

DOE PAGES

Slater, Steven C.; Simmons, Blake A.; Rogers, Tamara S.; ...

2015-08-20

Over the past 7 years, the US Department of Energy's Office of Biological and Environmental Research has funded three Bioenergy Research Centers (BRCs). These centers have developed complementary and collaborative research portfolios that address the key technical and economic challenges in biofuel production from lignocellulosic biomass. All three centers have established a close, productive relationship with DOE's Joint Genome Institute (JGI). This special issue of Bioenergy Research samples the breadth of basic science and engineering work required to underpin a diverse, sustainable, and robust biofuel industry. In this report, which was collaboratively produced by all three BRCs, we discuss themore » BRC contributions over their first 7 years to the development of renewable transportation fuels. In additon, we also highlight the BRC research published in the current issue and discuss technical challenges in light of recent progress.« less

The Chlamydomonas genome project: a decade on

PubMed Central

Blaby, Ian K.; Blaby-Haas, Crysten; Tourasse, Nicolas; Hom, Erik F. Y.; Lopez, David; Aksoy, Munevver; Grossman, Arthur; Umen, James; Dutcher, Susan; Porter, Mary; King, Stephen; Witman, George; Stanke, Mario; Harris, Elizabeth H.; Goodstein, David; Grimwood, Jane; Schmutz, Jeremy; Vallon, Olivier; Merchant, Sabeeha S.; Prochnik, Simon

2014-01-01

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis and micronutrient homeostasis. Ten years since its genome project was initiated, an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the “omics” era. Housed at Phytozome, the Joint Genome Institute’s (JGI) plant genomics portal, the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of RNA-Seq data. Here, we present the past, present and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes. PMID:24950814

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitman, William B.; Woyke, Tanja; Klenk, Hans-Peter

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Here in this paper, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while theymore » are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity« less

Fuel cell oxygen electrode

DOEpatents

Shanks, H.R.; Bevolo, A.J.; Danielson, G.C.; Weber, M.F.

An oxygen electrode for a fuel cell utilizing an acid electrolyte has a substrate of an alkali metal tungsten bronze of the formula: A/sub x/WO/sub 3/ where A is an alkali metal and x is at least 0.2, which is covered with a thin layer of platinum tungsten bronze of the formula: Pt/sub y/WO/sub 3/ where y is at least 0.8.

Perovskite-like fluorides and oxyfluorides: Phase transitions and caloric effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Flerov, I. N., E-mail: flerov@iph.krasn.ru; Gorev, M. V., E-mail: gorev@iph.krasn.ru; Tressaud, A.

2011-01-15

An analysis of the effect that chemical and hydrostatic pressures have on the thermodynamic properties of perovskite-like fluorine-oxygen compounds A{sub 2}A Prime MeO{sub x}F{sub 6-x} has revealed that materials under-going order-disorder transitions and having significant external-pressure compliance have the highest caloric efficiency. Some of the fluorides and oxyfluorides under study can be considered promising solid coolants.

Singularities, swallowtails and Dirac points. An analysis for families of Hamiltonians and applications to wire networks, especially the Gyroid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaufmann, Ralph M., E-mail: rkaufman@math.purdue.edu; Khlebnikov, Sergei, E-mail: skhleb@physics.purdue.edu; Wehefritz-Kaufmann, Birgit, E-mail: ebkaufma@math.purdue.edu

2012-11-15

Motivated by the Double Gyroid nanowire network we develop methods to detect Dirac points and classify level crossings, aka. singularities in the spectrum of a family of Hamiltonians. The approach we use is singularity theory. Using this language, we obtain a characterization of Dirac points and also show that the branching behavior of the level crossings is given by an unfolding of A{sub n} type singularities. Which type of singularity occurs can be read off a characteristic region inside the miniversal unfolding of an A{sub k} singularity. We then apply these methods in the setting of families of graph Hamiltonians,more » such as those for wire networks. In the particular case of the Double Gyroid we analytically classify its singularities and show that it has Dirac points. This indicates that nanowire systems of this type should have very special physical properties. - Highlights: Black-Right-Pointing-Pointer New method for analytically finding Dirac points. Black-Right-Pointing-Pointer Novel relation of level crossings to singularity theory. Black-Right-Pointing-Pointer More precise version of the von-Neumann-Wigner theorem for arbitrary smooth families of Hamiltonians of fixed size. Black-Right-Pointing-Pointer Analytical proof of the existence of Dirac points for the Gyroid wire network.« less

All the nonadiabatic (J=0) bound states of NO{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salzgeber, R.F.; Mandelshtam, V.A.; Schlier, C.

1999-02-01

We calculated all 3170 A{sub 1} and B{sub 2} (J=0) vibronic bound states of the coupled electronic ground ({tilde X}&hthinsp;{sup 2}A{sub 1}) and the first excited ({tilde A}&hthinsp;{sup 2}B{sub 2}) surfaces of NO{sub 2}, using a modification of the {ital ab initio} potentials of Leonardi {ital et al.} [J. Chem. Phys. {bold 105}, 9051 (1996)]. The calculation was performed by harmonic inversion of the Chebyshev correlation function generated from a DVR Hamiltonian in Radau coordinates. The rms error of the eigenenergies is about 2.5 cm{sup {minus}1}, corresponding to a relative error of 10{sup {minus}4} near the dissociation energy. The resultsmore » are compared with the adiabatic and diabatic levels calculated from the same surfaces, with experimental data, and with some approximations for the number of states function N(E). The experimental levels are reproduced fairly well up to an energy of 12&hthinsp;000 cm{sup {minus}1} above the potential minimum while the total number of bound levels agrees to within 2{percent} with that calculated from the phase space volume. {copyright} {ital 1999 American Institute of Physics.}« less

Long-run growth rate in a random multiplicative model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pirjol, Dan

2014-08-01

We consider the long-run growth rate of the average value of a random multiplicative process x{sub i+1} = a{sub i}x{sub i} where the multipliers a{sub i}=1+ρexp(σW{sub i}₋1/2 σ²t{sub i}) have Markovian dependence given by the exponential of a standard Brownian motion W{sub i}. The average value (x{sub n}) is given by the grand partition function of a one-dimensional lattice gas with two-body linear attractive interactions placed in a uniform field. We study the Lyapunov exponent λ=lim{sub n→∞}1/n log(x{sub n}), at fixed β=1/2 σ²t{sub n}n, and show that it is given by the equation of state of the lattice gas inmore » thermodynamical equilibrium. The Lyapunov exponent has discontinuous partial derivatives along a curve in the (ρ, β) plane ending at a critical point (ρ{sub C}, β{sub C}) which is related to a phase transition in the equivalent lattice gas. Using the equivalence of the lattice gas with a bosonic system, we obtain the exact solution for the equation of state in the thermodynamical limit n → ∞.« less

Backward-propagating MeV electrons in ultra-intense laser interactions: Standing wave acceleration and coupling to the reflected laser pulse

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orban, Chris, E-mail: orban@physics.osu.edu; Feister, Scott; Innovative Scientific Solutions, Inc., Dayton, Ohio 45459

Laser-accelerated electron beams have been created at a kHz repetition rate from the reflection of intense (∼10{sup 18 }W/cm{sup 2}), ∼40 fs laser pulses focused on a continuous water-jet in an experiment at the Air Force Research Laboratory. This paper investigates Particle-in-Cell simulations of the laser-target interaction to identify the physical mechanisms of electron acceleration in this experiment. We find that the standing-wave pattern created by the overlap of the incident and reflected laser is particularly important because this standing wave can “inject” electrons into the reflected laser pulse where the electrons are further accelerated. We identify two regimes of standingmore » wave acceleration: a highly relativistic case (a{sub 0} ≥ 1), and a moderately relativistic case (a{sub 0} ∼ 0.5) which operates over a larger fraction of the laser period. In previous studies, other groups have investigated the highly relativistic case for its usefulness in launching electrons in the forward direction. We extend this by investigating electron acceleration in the specular (back reflection) direction and over a wide range of intensities (10{sup 17}–10{sup 19 }W cm{sup −2})« less

Further identification of endogenous gibberellins in the shoots of pea, line G2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halinska, A.; Davies, P.J.; Lee, J.W.

1989-12-01

To interpret the metabolism of radiolabeled gibberellins A{sub 12}-aldehyde and A{sub 12} in shoots of pea (Pisum sativum L.), the identity of the radiolabeled peaks has to be determined and the endogenous presence of the gibberellins demonstrated. High specific activity ({sup 14}C)GA{sub 12} and ({sup 14}C)GA{sub 12}-aldehyde were synthesized using a pumpkin endosperm enzyme preparation, and purified by high performance liquid chromatography (HPLC). ({sup 14}C)GA{sub 12} was supplied to upper shoots of pea, line G2, to produce radiolabeled metabolites on the 13-OH pathway. Endogenous compounds copurifying with the ({sup 14}C)GAs on HPLC were analyzed by gas chromatography-mass spectrometry. The endogenousmore » presence of GA{sub 53}, GA{sub 44}, GA{sub 19} and GA{sub 20} was demonstrated and their HPLC peak identity ascertained. The {sup 14}C was progressively diluted in GAs further down the pathway, proportional to the levels found in the tissue and inversely proportional to the speed of metabolism, ranging from 63% in GA{sub 53} to 4% in GA{sub 20}. Calculated levels of GA{sub 20}, GA{sub 19}, GA{sub 44}, and GA{sub 53} were 42, 8, 10, and 0.5 nanograms/gram, respectively.« less

Communication: Effect of accidental mode degeneracy on Raman intensity in 2D materials: Hybrid functional study of bilayer phosphorene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Yi-Yang; Zhang, Shengbai

2016-07-14

Bulk black phosphorus has two optical phonon modes labeled as A{sub g}{sup 2} and B{sub 2u}, respectively, that are nearly degenerate in frequency. However, density functional theory calculations using local or semi-local functionals cannot reproduce this degeneracy. Here, we propose a hybrid functional approach aided by van der Waals (vdW) force fields, which can accurately describe the lattice dynamic and electronic properties of both bulk and few-layer black phosphorus (phosphorene). Using this approach we show that in bilayer phosphorene, the two Raman modes derived from the B{sub 2u} and A{sub g}{sup 2} modes could exhibit strong resonance as a resultmore » of the accidental degeneracy so that both modes could be observed in Raman experiment. Without the mode degeneracy, however, the Raman intensity of the B{sub 2u}-derived mode would be too weak to be observed. We further show that the accidental degeneracy is correlated to the applied strain, which enables Raman spectroscopy to be a powerful tool for characterizing built-in strains in 2D materials, e.g., due to the interaction with substrates, which has emerged as an important issue in vdW epitaxy.« less

Iron alteration minerals in the visible and near-infrared spectra of low-albedo asteroids

NASA Technical Reports Server (NTRS)

Vilas, Faith; Jarvis, Kandy S.; Gaffey, Michael J.

1994-01-01

Absorption features centered near 0.60-0.65 and 0.80-0.90 micrometers have been identified in the spectra of five low-albedo main-belt and outer-belt asteroids. These absorption features are attributed respectively to the (6)A(sub 1) goes to (4)T(sub 2)(G) and (6)A(sub 1) goes to (4)T(sub 1)(G) charge transfer transitions in minerals such as goethite, hematite, and jarosite that are products of the aqueous alteration of anhydrous silicates. A shoulder near 0.63 micrometers has also been identified in the absorption feature centered near 0.7 micrometers attributed to oxidized iron in phyllosilicates found predominantly in C- and G-class asteroids reflectance spectra. The coexistence of iron oxides with phyllosilicates in asteroids believed to have undergone aqueous alteration would be expected based upon analogy with terrestrial aqueous alteration and the observed mineralogy of carbonaceous chondrites. The number of low-albedo asteroids having only iron alteration absorption features compared to the number of low-albedo asteroids having spectral characteristics indicative of phyllosilicates is small. Either the conditions under which these asteroids formed are rare, or the iron alteration minerals could be formed in the interiors of objects where phyllosilicates dominate the surface mineralogy.

New precision orbits of bright double-lined spectroscopic binaries. IX. HD 54371, HR 2692, and 16 ursa majoris

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fekel, Francis C.; Williamson, Michael H.; Muterspaugh, Matthew W.

2015-02-01

With extensive sets of new radial velocities we have determined orbital elements for three previously known spectroscopic binaries, HD 54371, HR 2692, and 16 UMa. All three systems have had the lines of their secondaries detected for the first time. The orbital periods range from 16.24 to 113.23 days, and the three binaries have modestly or moderately eccentric orbits. The secondary to primary mass ratios range from 0.50 to 0.64. The orbital dimensions (a{sub 1} sin i and a{sub 2} sin i) and minimum masses (m{sub 1} sin{sup 3} i and m{sub 2} sin{sup 3} i) of the binary componentsmore » all have accuracies of ⩽1%. With our spectroscopic results and the Hipparcos data, we also have determined astrometric orbits for two of the three systems, HR 2692 and 16 UMa. The primaries of HD 54371 and 16 UMa are solar-type stars, and their secondaries are likely K or M dwarfs. The primary of HR 2692 is a late-type subgiant and its secondary is a G or K dwarf. The primaries of both HR 2692 and 16 UMa may be pseudosynchronously rotating, while that of HD 54371 is rotating faster than its pseudosynchronous velocity.« less

Mammalian Ste20-like protein kinase 3 mediates trophoblast apoptosis in spontaneous delivery.

PubMed

Wu, Hung-Yi; Lin, Chia-Ying; Lin, Tze-Yi; Chen, Tai-Chang; Yuan, Chiun-Jye

2008-02-01

The placenta is essential in transferring gases and nutrients from the mother to the developing fetus. Trophoblast apoptosis may cause labor or other pregnancy-related disorders. This study demonstrated the essential role of Mst3, a human Ste20-like protein kinase, in the oxidative stress-induced apoptosis of trophoblasts of term placenta in normal spontaneous delivery. Oxidative stress, but not hormones released during labor such as prostaglandin E1, oxytocin or angiotensin II, induces the expression of Mst3 and apoptosis of human term placenta after elective Cesarean section without labor pain. The role of Mst3 in oxidative stress-induced apoptosis was further demonstrated in the 3A-sub-E, a human trophoblast cell line. The H2O2-induced apoptosis of 3A-sub-E cells was largely suppressed by overexpressed Mst3KR, the kinase-dead mutant or by selective knockdown of endogenous Mst3. Further studies showed that Jun N-terminal kinase (JNK) may participate in the signaling pathway of H2O2-induced apoptosis by mediating the level of Mst3. Subsequently, caspase 3 and other downstream apoptotic components may be activated by Mst3 and trigger the apoptotic process in human trophoblasts.

The WRKY transcription factor family in Brachypodium distachyon

PubMed Central

2012-01-01

Background A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. Results We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. Conclusions The description

Excited-state decay processes of binuclear rhodium(I) isocyanide complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miskowski, V.M.; Rice, S.F.; Gray, H.B.

1993-04-29

Emission lifetimes, quantum yields, and polarized excitation spectra of Rh[sub 2]b[sub 4][sup 2+] and Rh[sub 2](TMB)[sub 4][sup 2+] (b = 1,3-diisocyanopropane; TMB = 2,5-diisocyano-2,5-dimethylhexane) have been determined. The singlet and triplet d[sigma]* [yields] p[sigma]([sup 1,3]A[sub 2u]) excited states are luminescent with radiative rates of ca. 10[sup 8] and 10[sup 4] s[sup [minus

Integrability of the Kruskal--Zabusky Discrete Equation by Multiscale Expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levi, Decio; Scimiterna, Christian

2010-03-08

In 1965 Kruskal and Zabusky in a very famous article in Physical Review Letters introduced the notion of 'soliton' to describe the interaction of solitary waves solutions of the Korteweg de Vries equation (KdV). To do so they introduced a discrete approximation to the KdV, the Kruskal-Zabusky equation (KZ). Here we analyze the KZ equation using the multiscale expansion and show that the equation is only A{sub 2} integrable.

The Chlamydomonas genome project: a decade on.

PubMed

Blaby, Ian K; Blaby-Haas, Crysten E; Tourasse, Nicolas; Hom, Erik F Y; Lopez, David; Aksoy, Munevver; Grossman, Arthur; Umen, James; Dutcher, Susan; Porter, Mary; King, Stephen; Witman, George B; Stanke, Mario; Harris, Elizabeth H; Goodstein, David; Grimwood, Jane; Schmutz, Jeremy; Vallon, Olivier; Merchant, Sabeeha S; Prochnik, Simon

2014-10-01

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Improving Microbial Genome Annotations in an Integrated Database Context

PubMed Central

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Anderson, Iain; Mavromatis, Konstantinos; Kyrpides, Nikos C.; Ivanova, Natalia N.

2013-01-01

Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. PMID:23424620

Bimetric MOND gravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milgrom, Mordehai

2009-12-15

A new relativistic formulation of MOND is advanced, involving two metrics as independent degrees of freedom: the MOND metric g{sub {mu}}{sub {nu}}, to which alone matter couples, and an auxiliary metric g-circumflex{sub {mu}}{sub {nu}}. The main idea hinges on the fact that we can form tensors from the difference of the Levi-Civita connections of the two metrics, C{sub {beta}}{sub {gamma}}{sup {alpha}}={gamma}{sub {beta}}{sub {gamma}}{sup {alpha}}-{gamma}-circumflex{sub {beta}}{sub {gamma}}{sup {alpha}}, and these act like gravitational accelerations. In the context of MOND, we can form dimensionless 'acceleration' scalars and functions thereof (containing only first derivatives) from contractions of a{sub 0}{sup -1}C{sub {beta}}{sub {gamma}}{sup {alpha}}.more » I look at a subclass of bimetric MOND theories governed by the action I=-(16{pi}G){sup -1}{integral}[{beta}g{sup 1/2}R+{alpha}g-circumflex{sup 1/2}R-circumflex-2(gg-circumflex){sup 1/4}f({kappa})a{sub 0}{sup 2} M({upsilon}-tilde/a{sub 0}{sup 2})]d{sup 4}x+I{sub M}(g{sub {mu}}{sub {nu}},{psi}{sub i})+I-circumflex{sub M}(g-circumflex{sub {mu}}{sub {nu}},{chi}{sub i}), with {upsilon}-tilde as a scalar quadratic in the C{sub {beta}}{sub {gamma}}{sup {alpha}}, {kappa}=(g/g-circumflex){sup 1/4}, I{sub M} as the matter action, and allow for the existence of twin matter that couples to g-circumflex{sub {mu}}{sub {nu}} alone. Thus, gravity is modified not by modifying the elasticity of the space-time in which matter lives, but by the interaction between that space-time and the auxiliary one. In particular, I concentrate on the interesting and simple choice {upsilon}-tilde{proportional_to}g{sup {mu}}{sup {nu}}(C{sub {mu}}{sub {lambda}}{sup {gamma}}C{sub {nu}}{sub {gamma}}{sup {lambda}}-C{sub {mu}}{sub {nu}}{sup {gamma}}C{sub {lambda}}{sub {gamma}}{sup {lambda}}). This theory introduces only one new constant, a{sub 0}; it tends simply to general relativity (GR) in the limit a{sub 0}{yields}0 and to a

Inflation of the early cold Universe filled with a nonlinear scalar field and a nonideal relativistic Fermi gas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pashitskii, E. A., E-mail: pashitsk@iop.kiev.ua; Pentegov, V. I., E-mail: pentegov@iop.kiev.ua

We consider a possible scenario for the evolution of the early cold Universe born from a fairly large quantum fluctuation in a vacuum with a size a{sub 0} ≫ l{sub P} (where l{sub P} is the Planck length) and filled with both a nonlinear scalar field φ, whose potential energy density U(φ) determines the vacuum energy density λ, and a nonideal Fermi gas with short-range repulsion between particles, whose equation of state is characterized by the ratio of pressure P(n{sub F}) to energy density ε(n{sub F}) dependent on the number density of fermions n{sub F}. As the early Universe expands,more » the dimensionless quantity ν(n{sub F}) = P(n{sub F})/ε(n{sub F}) decreases with decreasing n{sub F} from its maximum value ν{sub max} = 1 for n{sub F} → ∞ to zero for n{sub F} → 0. The interaction of the scalar and gravitational fields, which is characterized by a dimensionless constant ξ, is proportional to the scalar curvature of four-dimensional space R = κ[3P(n{sub F})–ε(n{sub F})–4λ] (where κ is Einstein’s gravitational constant), and contains terms both quadratic and linear in φ. As a result, the expanding early Universe reaches the point of first-order phase transition in a finite time interval at critical values of the scalar curvature R = R{sub c} =–μ{sup 2}/ξ and radius a{sub c} ≫ a{sub 0}. Thereafter, the early closed Universe “rolls down” from the flat inflection point of the potential U(φ) to the zero potential minimum in a finite time. The release of the total potential energy of the scalar field in the entire volume of the expanding Universe as it “rolls down” must be accompanied by the production of a large number of massive particles and antiparticles of various kinds, whose annihilation plays the role of the Big Bang. We also discuss the fundamental nature of Newton’ gravitational constant G{sub N}.« less

THE PROPERTIES OF THE 2175 A EXTINCTION FEATURE DISCOVERED IN GRB AFTERGLOWS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zafar, Tayyaba; Watson, Darach; Eliasdottir, Ardis

The unequivocal, spectroscopic detection of the 2175 A bump in extinction curves outside the Local Group is rare. To date, the properties of the bump have been examined in only two gamma-ray burst (GRB) afterglows (GRB 070802 and GRB 080607). In this work, we analyze in detail the detections of the 2175 Angstrom-Sign extinction bump in the optical spectra of two further GRB afterglows: GRB 080605 and 080805. We gather all available optical/near-infrared photometric, spectroscopic, and X-ray data to construct multi-epoch spectral energy distributions (SEDs) for both GRB afterglows. We fit the SEDs with the Fitzpatrick and Massa model withmore » a single or broken power law. We also fit a sample of 38 GRB afterglows, known to prefer a Small Magellanic Cloud (SMC)-type extinction curve, with the same model. We find that the SEDs of GRB 080605 and GRB 080805 at two epochs are fit well with a single power law with a derived extinction of A{sub V} = 0.52{sup +0.13}{sub -0.16} and 0.50{sup +0.13}{sub -0.10}, and 2.1{sup +0.7}{sub -0.6} and 1.5 {+-} 0.2, respectively. While the slope of the extinction curve of GRB 080805 is not well constrained, the extinction curve of GRB 080605 has an unusual very steep far-UV rise together with the 2175 A bump. Such an extinction curve has previously been found in only a small handful of sightlines in the Milky Way. One possible explanation of such an extinction curve may be dust arising from two different regions with two separate grain populations, however we cannot distinguish the origin of the curve. We finally compare the four 2175 A bump sightlines to the larger GRB afterglow sample and to Local Group sightlines. We find that while the width and central positions of the bumps are consistent with what is observed in the Local Group, the relative strength of the detected bump (A{sub bump}) for GRB afterglows is weaker for a given A{sub V} than for almost any Local Group sightline. Such dilution of the bump strength may offer

Hydrodynamic Instability in an Extended Landau/Levich Model of Liquid-Propellant Combustion

NASA Technical Reports Server (NTRS)

Margolis, Stephen B.; Sackesteder, Kurt (Technical Monitor)

1998-01-01

The classical Landau/Levich models of liquid propellant combustion, which serve as seminal examples of hydrodynamic instability in reactive systems, have been combined and extended to account for a dynamic dependence, absent in the original formulations, of the local burning rate on the local pressure and/or temperature fields. The resulting model admits an extremely rich variety of both hydrodynamic and reactive/diffusive instabilities that can be analyzed in various limiting parameter regimes. In the present work, a formal asymptotic analysis, based on the realistic smallness of the gas-to-liquid density ratio, is developed to investigate the combined effects of gravity, surface tension and viscosity on the hydrodynamic instability of the propagating liquid/gas interface. In particular, a composite asymptotic expression, spanning three distinguished wavenumber regimes, is derived for both cellular and pulsating hydrodynamic neutral stability boundaries A(sub p)(k), where A(sub p) is the pressure sensitivity of the burning rate and k is the disturbance wavenumber. For the case of cellular (Landau) instability, the results demonstrate explicitly the stabilizing effect of gravity on long-wave disturbances, the stabilizing effect of viscosity and surface tension on short-wave perturbations, and the instability associated with intermediate wavenumbers for critical negative values of A(sub p). In the limiting case of weak gravity, it is shown that cellular hydrodynamic instability in this context is a long-wave instability phenomenon, whereas at normal gravity, this instability is first manifested through O(l) wavenumber disturbances. It is also demonstrated that, in the large wavenumber regime, surface tension and both liquid and gas viscosity all produce comparable stabilizing effects in the large-wavenumber regime, thereby providing significant modifications to previous analyses of Landau instability in which one or more of these effects were neglected. In contrast

Chloro-, methyl-, and (tetrahydroborato)tris((hexamethyldisilyl)amido)thorium(IV) and -uranium(IV). Crystal structure of (tetrahydroborato)tris((hexamethyldisilyl)amido)thorium(IV)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turner, H.W.; Andersen, R.A.; Zalkin, A.

1979-05-01

Reaction of sodium (hexamethyldisilyl)amide with thorium tetrachloride or uranium tetrachloride yields chlorotris-((hexamethyldisilyl)amido)thorium(IV) or -uranium(IV), respectively. The chloroamides of thorium or uranium react with dimethylmagnesium or methyllithium yielding the methyl derivatives MeTh(N(SiMe/sub 3/)/sub 2/)/sub 3/ or MeU(N(SiMe/sub 3/)/sub 2/)/sub 3/, respectively. The chloro compounds yield BH/sub 4/M(N(SiMe/sub 3/)/sub 2/)/sub 3/ upon reaction with lithium tetrahydroborate, where M is thorium or uranium. Infrared spectra of the tetrahydroborate derivatives suggest that BH/sub 4/ is bonded in a tridentate fashion in both compounds, the metal atoms being six-coordinate. Single-crystal X-ray analysis of the thorium borohydride confirms the infrared result. The white BH/sub 4/Th(N(Si(CH/sub 3/))/submore » 2/)/sub 3/ crystals are rhombohedral with cell dimensions a/sub r/ = 11.137 A and ..cap alpha../sub r/ = 113.61/sup 0/; the triply primitive hexagonal cell has a/sub h/ = 18.640 (3) A c/sub h/ = 8.604 (1) A, V = 2489 A/sup 3/, Z = 3, and D/sub x/ = 1.40 g/cm/sup 3/, space group R3m. The structure was refined by full-matrix least squares to a conventional R factor of 0.031 for 1014 data. The Th atom is on a threefold axis 2.32 A from three nitrogen atoms and 2.61 A from the boron atom, a distance which represents a triple bridge bond between Th and B. The three (dimethylsilyl)amide ligands are disordered by a mirror plane parallel to the threefold axis. CH/sub 3/Th(N(Si(CH/sub 3/)/sub 3/)/sub 2/)/sub 3/ is isomorphous with BH/sub 4/Th(N(Si(CH/sub 3/)/sub 3/)/sub 2/)/sub 3/ with cell dimensions a/sub h/ = 18.68 (1) A and c/sub h/ = 8.537 (6) A. The diffraction data yielded integral'' = 12.16 +- 0.33 e for the imaginary scattering term for Th with Cu K..cap alpha.. radiation.« less

The First Neptune Analog or Super-Earth with a Neptune-Like Orbit: MOA-2013-BLG-605Lb

NASA Technical Reports Server (NTRS)

Sumi, T.; Bennett, D. P.; Udalski, A.; Gould, A.; Poleski, R.; Bond, I. A.; Skowron, J.; Rattenbury, N.; Pogge, R. W.; Bensby, T.

2016-01-01

We present the discovery of the first Neptune analog exoplanet or super-Earth with a Neptune-like orbit, MOA- 2013-BLG-605Lb. This planet has a mass similar to that of Neptune or a super-Earth and it orbits at 9 approximately 14 times the expected position of the snow line, a(sub snow), which is similar to Neptune's separation of 11 a(sub snow) from the Sun. The planet/host-star mass ratio is q = (3.6 +/- 0.7) × 10(exp -4) and the projected separation normalized by the Einstein radius is s = 2.39 +/- 0.05. There are three degenerate physical solutions and two of these are due to a new type of degeneracy in the microlensing parallax parameters, which we designate "the wide degeneracy." The three models have (i) a Neptune-mass planet with a mass of M(sub p) = 21(+6/-7)(M) orbiting a low-mass M-dwarf with a mass of M(sub h) = 0.19(+0.05/-0.06 (solar mass)), (ii) a mini-Neptune with M(sub p) = 7.9(+1.8/-1.5)(M)) orbiting a brown dwarf host with M(sub h) = 0.068(+0.019/-0.011(solar mass)), and (iii) a super-Earth with M(sub p) = 3.2(+0.5/-0.3(M)) orbiting a low-mass brown dwarf host with M(sub h) = 0.025(+0.005/-0.004)(solar mass)), which is slightly favored. The 3D planet-host separations are 4.6(+4.7/-1.2)au, 2.1(+1.0/-0.2)au, and 0.94(+0.67/-0.02)au, which are 8.9(+10.5/-1.4)m 12(+7/-1), or 14(+11/-1) times larger than a(sub snow) for these models, respectively. Keck adaptive optics observations confirm that the lens is faint. This discovery suggests that low-mass planets with Neptune-like orbits are common. Therefore processes similar to the one that formed Neptune in our own solar system or cold super-Earths may be common in other solar systems.

Low cytoplasmic pH reduces ER-Golgi trafficking and induces disassembly of the Golgi apparatus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soonthornsit, Jeerawat; Yamaguchi, Yoko; Tamura, Daisuke

The Golgi apparatus was dramatically disassembled when cells were incubated in a low pH medium. The cis-Golgi disassembled quickly, extended tubules and spread to the periphery of cells within 30 min. In contrast, medial- and trans-Golgi were fragmented in significantly larger structures of smaller numbers at a slower rate and remained largely in structures distinct from the cis-Golgi. Electron microscopy revealed the complete disassembly of the Golgi stack in low pH treated cells. The effect of low pH was reversible; the Golgi apparatus reassembled to form a normal ribbon-like structure within 1–2 h after the addition of a control medium.more » The anterograde ER to Golgi transport and retrograde Golgi to ER transport were both reduced under low pH. Phospholipase A{sub 2} inhibitors (ONO, BEL) effectively suppressed the Golgi disassembly, suggesting that the phospholipase A{sub 2} was involved in the Golgi disassembly. Over-expression of Rab1, 2, 30, 33 and 41 also suppressed the Golgi disassembly under low pH, suggesting that they have protective role against Golgi disassembly. Low pH treatment reduced cytoplasmic pH, but not the luminal pH of the Golgi apparatus, strongly suggesting that reduction of the cytoplasmic pH triggered the Golgi disassembly. Because a lower cytoplasmic pH is induced in physiological or pathological conditions, disassembly of the Golgi apparatus and reduction of vesicular transport through the Golgi apparatus may play important roles in cell physiology and pathology. Furthermore, our findings indicated that low pH treatment can serve as an important tool to analyze the molecular mechanisms that support the structure and function of the Golgi apparatus. - Highlights: • The Golgi apparatus reversibly disassembles by low pH treatment. • The cis-Golgi disassembles quickly generating tubular structures. • Both anterograde and retrograde transport between the ER and the Golgi apparatus are reduced. • Phospholipase A{sub 2

MID-INFRARED SPECTROPHOTOMETRIC OBSERVATIONS OF FRAGMENTS B AND C OF COMET 73P/SCHWASSMANN-WACHMANN 3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harker, David E.; Woodward, Charles E.; Kelley, Michael S.

2011-01-15

We present mid-infrared spectra and images from the Gemini-N (+ Michelle) observations of fragments SW3-[B] and SW3-[C] of the ecliptic (Jupiter family) comet 73P/Schwassmann-Wachmann 3 pre-perihelion. We observed fragment B soon after an outburst event (between 2006 April 16-26 UT) and detected crystalline silicates. The mineralogy of both fragments was dominated by amorphous carbon and amorphous pyroxene. The grain size distribution (assuming a Hanner-modified power law) for fragment SW3-[B] has a peak grain radius of a{sub p} {approx} 0.5 {mu}m, and for fragment SW3-[C], a{sub p} {approx} 0.3 {mu}m; both values are larger than the peak grain radius of themore » size distribution for the dust ejected from ecliptic comet 9P/Tempel 1 during the Deep Impact event (a{sub p} = 0.2 {mu}m). The silicate-to-carbon ratio and the silicate crystalline mass fraction for the submicron to micron-sized portion of the grain size distribution on the nucleus of fragment SW3-[B] were 1.341{sup +0.250}{sub -0.253} and 0.335{sup +0.089}{sub -0.112}, respectively, while on the nucleus of fragment SW3-[C] they were 0.671{sup +0.076}{sub -0.076} and 0.257{sup +0.039}{sub -0.043}, respectively. The similarity in mineralogy and grain properties between the two fragments implies that 73P/Schwassmann-Wachmann 3 is homogeneous in composition. The slight differences in grain size distribution and silicate-to-carbon ratio between the two fragments likely arise because SW3-[B] was actively fragmenting throughout its passage while the activity in SW3-[C] was primarily driven by jets. The lack of diverse mineralogy in the fragments SW3-[B] and SW3-[C] of 73P/Schwassmann-Wachmann 3 along with the relatively larger peak in the coma grain size distribution suggests that the parent body of this comet may have formed in a region of the solar nebula with different environmental properties than the natal sites where comet C/1995 O1 (Hale-Bopp) and 9P/Tempel 1 nuclei aggregated.« less

Interstellar Extinction in the Vicinity of the Galactic Center

NASA Technical Reports Server (NTRS)

Cotera, Angela S.; Simpson, Janet P.; Erickson, Edwin F.; Colgan, Sean W. J.; Burton, Michael G.; Allen, David A.

2000-01-01

We present J (1.2 microns), H (1-6 microns), K' (2.11 microns) and Br(gamma) (2.166 microns) images from four large regions within the central 40 pc of the Galaxy. Localized variations in the extinction, as determined by observations of the stellar population, are examined using the median H-K' color as a function of position within each region. As the value of the derived extinction from the stars is dependent upon the intrinsic magnitude of the assumed stellar type, the J-H vs. H-K' diagrams are first used to investigate the distribution of stellar types in the four regions. We find that there is a distinct OB population, contrary to earlier assumptions, with the ratio of K and M giants and supergiants to OB stars approximately twice that of the solar neighborhood. Although the on the scale of approx. l' fluctuations in the extinction are on the order of A(sub V) approx. 2, throughout the entire region the extinction varies from A(sub V) approx. greater than 25 to A(sub V) approx. less than 40. We also examine whether there is any variation in the extinction and stellar number density relative to the usual radio features in these regions and do not find a significant correlation. Spectral imaging in Br(gamma) 2.166 microns emission shows a strong morphological correspondence between the 6 cm radio images and the diffuse Br(gamma) emission. By comparing the theoretical Br(gamma) flux derived from the radio flux using recombination theory, with our measured Br(gamma) flux, we obtain a second, independent, estimate of the extinction. We compare the two data sets and find that the extinction as derived from the stars is consistently greater, sometimes by a factor of two, than the value of the extinction derived from the Br(gamma) images. The derived extinction in various regions, however, is insufficient for any of these regions-to be located behind the molecular clouds as previously observed in the Galactic Center, consistent with the theory that the observed radio

Interstellar Extinction in the Vicinity of the Galactic Center

NASA Technical Reports Server (NTRS)

Cotera, Angela S.; Simpson, Janet P.; Erickson, Edwin F.; Colgan, Sean W. J.

1998-01-01

We present J (1.2 microns) H (1-6 microns) K' (2.11 microns) and Br(gamma) (2.166 microns) images from four large regions within the central 40 pc of the Galaxy. Localized variations in the extinction, as determined by observations of the stellar population, are examined using the median H-K' color as a function of position within each region. As the value of the derived extinction from the stars is dependent upon the intrinsic magnitude of the assumed stellar type, the J-H vs. H-K' diagrams are first used to investigate the distribution of stellar types in the four regions. We find that there is a distinct OB population, contrary to earlier assumptions, with the ratio of K and M giants and supergiants to OB stars approximately twice that of the solar neighborhood. Although the on the scale of approx. 1 min. fluctuations in the extinction are on the order of A(sub V) approx. greater than 2, throughout the entire region the extinction varies from A(sub V) approx. greater than 25 to A(sub V) approx. less than 40. We also examine whether there is any variation in the extinction and stellar number density relative to the unusual radio features in these regions and do not find a significant correlation. Spectral imaging in Br(gamma) 2.166 microns emission shows a strong morphological correspondence between the 6 cm radio images and the diffuse Br(gamma) emission. By comparing the theoretical Br(gamma) flux derived from the radio flux using recombination theory, with our measured Br(gamma) flux, we obtain a second, independent, estimate of the extinction. We compare the two data sets and find that the extinction as derived from the stars is consistently greater, sometimes by a factor of two, than the value of the extinction derived from the Br(gamma) images. The derived extinction in various regions, however, is insufficient for any of these regions to be located behind the molecular clouds as previously observed in the Galactic Center, consistent with the theory that

Shear Thinning Near the Critical Point of Xenon

NASA Technical Reports Server (NTRS)

Zimmerli, Gregory A.; Berg, Robert F.; Moldover, Michael R.; Yao, Minwu

2008-01-01

We measured shear thinning, a viscosity decrease ordinarily associated with complex liquids, near the critical point of xenon. The data span a wide range of reduced shear rate: 10(exp -3) < gamma-dot tau < 700, where gamma-dot tau is the shear rate scaled by the relaxation time tau of critical fluctuations. The measurements had a temperature resolution of 0.01 mK and were conducted in microgravity aboard the Space Shuttle Columbia to avoid the density stratification caused by Earth's gravity. The viscometer measured the drag on a delicate nickel screen as it oscillated in the xenon at amplitudes 3 mu,m < chi (sub 0) >430 mu, and frequencies 1 Hz < omega/2 pi < 5 Hz. To separate shear thinning from other nonlinearities, we computed the ratio of the viscous force on the screen at gamma-dot tau to the force at gamma-dot tau approximates 0: C(sub gamma) is identical with F(chi(sub 0), omega tau, gamma-dot tau )/F)(chi(sub 0, omega tau, 0). At low frequencies, (omega tau)(exp 2) < gamma-dot tau, C(sub gamma) depends only on gamma-dot tau, as predicted by dynamic critical scaling. At high frequencies, (omega tau)(exp 2) > gamma-dot tau, C(sub gamma) depends also on both x(sub 0) and omega. The data were compared with numerical calculations based on the Carreau-Yasuda relation for complex fluids: eta(gamma-dot)/eta(0)=[1+A(sub gamma)|gamma-dot tau|](exp - chi(sub eta)/3+chi(sub eta)), where chi(sub eta) =0.069 is the critical exponent for viscosity and mode-coupling theory predicts A(sub gamma) =0.121. For xenon we find A(sub gamma) =0.137 +/- 0.029, in agreement with the mode coupling value. Remarkably, the xenon data close to the critical temperature T(sub c) were independent of the cooling rate (both above and below T(sub c) and these data were symmetric about T(sub c) to within a temperature scale factor. The scale factors for the magnitude of the oscillator s response differed from those for the oscillator's phase; this suggests that the surface tension of the two

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novales-Sanchez, H.; Toscano, J. J.; Rosado, A.

In this paper, we review the search of possible physics effects beyond the standard model on the electromagnetic charge and anapole form factors, f{sub Q}(q{sup 2}) and f{sub A}(q{sup 2}), for a no massive Dirac neutrino, when these quantities are calculated in the frame of an effective electroweak Yang-Mills theory, which induces the most general SU{sub L}(2)-invariant Lorentz tensor structure of nonrenormalizable type for the WW{gamma} vertex. We found that in this frame, besides the standard model contribution, the additional contribution to f{sub Q}(q{sup 2}) and f{sub A}(q{sup 2}) (f{sub Q}{sup O{sub W}}(q{sup 2}) and f{sub A}{sup O{sub W}}(q{sup 2}),more » respectively) are gauge independent and finite functions of q{sup 2} after adopting a renormalization scheme. These form factors, f{sub Q}{sup O{sub W}}(q{sup 2}) and f{sub A}{sup O{sub W}}(q{sup 2}), get contribution at the one loop level only from the proper neutrino electromagnetic vertex. Besides, the relation f{sub Q}{sup eff}(q{sup 2}) = q{sup 2}f{sub A}{sup eff}(q{sup 2})(f{sub Q}{sup eff}(q{sup 2}) = f{sub Q}{sup SM}(q{sup 2})+f{sub Q}{sup O{sub W}}(q{sup 2}),f{sub A}{sup eff}(q{sup 2}) = f{sub A}{sup SM}(q{sup 2})+f{sub A}{sup O{sub W}}(q{sup 2})) is still fulfilled and hence the relation a{sub v}{sup eff} = {sup eff}/6(a{sub v}{sup eff} = a{sub v}{sup SM}+a{sub v}{sup O{sub W}},{sup eff} = {sup SM}+{sup O{sub W}}) is obtained, just as in the SM. Using the experimental constraint on the anomalous WW{gamma} vertex, a value for the additional contribution to the charge radius of Double-Vertical-Line {sup O{sub W}} Double-Vertical-Line Less-Than-Or-Equivalent-To 10{sup -34} cm{sup 2} is gotten, which is one order of magnitude lower than the SM value.« less

Chemical solution seed layer for rabits tapes

DOEpatents

Goyal, Amit; Paranthaman, Mariappan; Wee, Sung-Hun

2014-06-10

A method for making a superconducting article includes the steps of providing a biaxially textured substrate. A seed layer is then deposited. The seed layer includes a double perovskite of the formula A.sub.2B'B''O.sub.6, where A is rare earth or alkaline earth metal and B' and B'' are different rare earth or transition metal cations. A superconductor layer is grown epitaxially such that the superconductor layer is supported by the seed layer.

Design of Style-V -- A Translator to Convert Standard VHDL into a Stylized Form for Automated Microcode Generation

DTIC Science & Technology

1991-12-01

effort (Krieg-Brckner, 1984:299). Given two languages Alang and Blang, if the language concepts of the sublanguages, Asublang (the sublanguage for a...language Alang ) and Bsublang (the sublanguage for a lan- guage Blang), correspond in a one-to-one manner, then Asub- lang and Bsublang are said to be...then Aotherlang is said to be indirectly compati- ble with Bsublang. If Asublang is complete in the sense that all concepts of Alang can be mapped into

$eta$ production at high Q^2

DOE Office of Scientific and Technical Information (OSTI.GOV)

M.K. Jones

2012-04-01

The differential cross-sections for the p(e,e'p){eta} reaction have been measured in Hall C at Jefferson Lab at Q{sup 2} = 5.7 and 7.0 (GeV/c){sup 2} for center-of-mass energies from threshold to 1.8 GeV, encompassing the S{sub 11}(1535) resonance, which dominates the reaction. From fits to the data, the S{sub 11}(1535) helicity conserving photo-coupling amplitude, A{sub 1/2}, was extracted.

Electronic emission spectrum of methylnitrene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carrick, P.G.; Engelking, P.C.

The A /sup 3/E--X /sup 3/A/sub 2/ultraviolet emission spectrum of methylnitrene (CH/sub 3/N) was obtained in two ways: (1) by reacting methylazide (CH/sub 3/N/sub 3/) with metastable N/sub 2/ in a flowing afterglow; and (2) by discharging a mixture of methylazide (CH/sub 3/N/sub 3/) and helium in a corona excited supersonic expansion (CESE). The origin appears at T/sub 0/ = 31 811 cm/sup -1/. Several vibrational progressions were observed leading to the determination of a number of vibrational frequencies: v/sup double-prime//sub 1/ = 2938 , v/sup X//sub 2/ = 1350, v/sup double-prime//sub 3/ = 1039, v/sup X//sub 4/ = 3065,more » and v/sup double-prime//sub 6/ = 902 cm/sup -1/. Deuterium substitution confirmed the assignments of the vibrational frequencies. The X /sup 3/A/sub 2/ state is a normal, bound local minimum on the triplet electronic potential surface, and the upper A /sup 3/E state is able to support at least one quantum of vibration, assigned to v/sup //sub 3/, predominantly a C--N stretch. A comparison of flowing afterglow hollow cathode discharge sources and corona excited supersonic expansion sources shows the advantage of the CESE method of radical production for spectroscopy.« less

Novel 6xHis tagged foot-and-mouth disease virus vaccine bound to nanolipoprotein adjuvant via metal ions provides antigenic distinction and effective protective immunity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rai, Devendra K.; Segundo, Fayna Diaz-San; Department of Pathobiology and Veterinary Science, CANR, University of Connecticut, Storrs, CT 06269

Here, we engineered two FMD viruses with histidine residues inserted into or fused to the FMDV capsid. Both 6xHis viruses exhibited growth kinetics, plaque morphologies and antigenic characteristics similar to wild-type virus. The 6xHis tag allowed one-step purification of the mutant virions by Co{sup 2+} affinity columns. Electron microscopy and biochemical assays showed that the 6xHis FMDVs readily assembled into antigen: adjuvant complexes in solution, by conjugating with Ni{sup 2+}-chelated nanolipoprotein and monophosphoryl lipid A adjuvant (MPLA:NiNLP). Animals Immunized with the inactivated 6xHis-FMDV:MPLA:NiNLP vaccine acquired enhanced protective immunity against FMDV challenge compared to virions alone. Induction of anti-6xHis and anti-FMDVmore » neutralizing antibodies in the immunized animals could be exploited in the differentiation of vaccinated from infected animals needed for the improvement of FMD control measures. The novel marker vaccine/nanolipid technology described here has broad applications for the development of distinctive and effective immune responses to other pathogens of importance. - Highlights: • 6xHis-tags in A{sub 24} FMDV enable purification and biding to adjuvants via metal ions. • 6xHis A{sub 24} FMDV:MPLA:NiNLP vaccine enhanced protective immunity against FMDV. • Surface exposed capsid tags allow distinction of infected from vaccinated animals.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakhidov, A.A.; Yoshino, K.

Composites of fullerene C{sub 60} with conjugated polymers (CP) like polyalkylthiophene (PAT) and polyphenylene vinylene derivative (OO-PPV) have earlier demonstrated intensive charge transfer upon photoexcitation. Doping of CP/C{sub 60} composites by A metal vapors (A=K,Rb) is aimed at C{sub 60} induced SC, in which electrons of CP chains may participate in SC pairing, induced via hybridization with C{sub 60} molecules. We have found an SC phase experimentally both in PAT. (C{sub 60}) {sub y}K{sub x} and OO.PPV (C{sub 60}){sub y}K{sub x} by a sensitive method of low field microwave absorption (LFMA), and proved by SQUID. The SCT{sub c} ranges frommore » 12 to 17 K, depending on y and x. This SC phase shows a granular behavior in LFMA, and thus originates from SC A{sub 3}C{sub 60} clusters weakly linked by Josephson junctions. True C{sub 60} induced SC might be masked by granular A{sub 3}C{sub 60}. Anomalous LFMA and paramagnetic Meissner effects observed in SQUID, indicate the existence of Josephson {pi}-junctions. CP is apparently involved in SC via spin carrying polarons P in CP chains, which play a role of {pi}-junctions. Strategies for further search of C{sub 60} induced SC are discussed.« less

DISCOVERY OF METHYL ACETATE AND GAUCHE ETHYL FORMATE IN ORION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tercero, B.; Cernicharo, J.; Lopez, A.

2013-06-10

We report on the discovery of methyl acetate, CH{sub 3}COOCH{sub 3}, through the detection of a large number of rotational lines from each one of the spin states of the molecule: AA species (A{sub 1} or A{sub 2}), EA species (E{sub 1}), AE species (E{sub 2}), and EE species (E{sub 3} or E{sub 4}). We also report, for the first time in space, the detection of the gauche conformer of ethyl formate, CH{sub 3}CH{sub 2}OCOH, in the same source. The trans conformer is also detected for the first time outside the Galactic center source SgrB2. From the derived velocity ofmore » the emission of methyl acetate, we conclude that it arises mainly from the compact ridge region with a total column density of (4.2 {+-} 0.5) Multiplication-Sign 10{sup 15} cm{sup -2}. The derived rotational temperature is 150 K. The column density for each conformer of ethyl formate, trans and gauche, is (4.5 {+-} 1.0) Multiplication-Sign 10{sup 14} cm{sup -2}. Their abundance ratio indicates a kinetic temperature of 135 K for the emitting gas and suggests that gas-phase reactions could participate efficiently in the formation of both conformers in addition to cold ice mantle reactions on the surface of dust grains.« less

PDR MODEL MAPPING OF OBSCURED H{sub 2} EMISSION AND THE LINE-OF-SIGHT STRUCTURE OF M17-SW

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheffer, Y.; Wolfire, M. G.

2013-09-01

We observed H{sub 2} line emission with Spitzer-IRS toward M17-SW and modeled the data with our photon-dominated region (PDR) code. Derived gas density values of up to few times 10{sup 7} cm{sup -3} indicate that H{sub 2} emission originates in high-density clumps. We discover that the PDR code can be utilized to map the amount of intervening extinction obscuring the H{sub 2} emission layers, and thus we obtain the radial profile of A{sub V} relative to the central ionizing cluster NGC 6618. The extinction has a positive radial gradient, varying between 15-47 mag over the projected distance of 0.9-2.5 pcmore » from the primary ionizer, CEN 1. These high extinction values are in good agreement with previous studies of A{sub V} toward stellar targets in M17-SW. The ratio of data to PDR model values is used to infer the global line-of-sight structure of the PDR surface, which is revealed to resemble a concave surface relative to NGC 6618. Such a configuration confirms that this PDR can be described as a bowl-shaped boundary of the central H II region in M17. The derived structure and physical conditions are important for interpreting the fine-structure and rotational line emission from the PDR.« less

Studies on the metabolism of astaxanthin in the rainbow trout (Salmo gairdneri)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Al-Khalifah, A.S.

Racemic astaxanthin was fed to rainbow trout (Salmo gairdneri) for 2, 4, and 6 weeks. The fish showed a bright pink coloration of the skin and flesh; the highest amount of astaxanthin was found in the skin of fish fed the test diet for six weeks. Lutein, 3-epilutein, and zeaxanthin were also detected in the flesh and skin; it was concluded that astaxanthin was converted to zeaxanthin in the skin. The mean vitamin A content of the liver was determined; the ratio of vitamin A/sub 1/:vitamin A/sub 2/ was approximately 1:3. Retinol and 3,4-dehydroretinol were extracted from the intestine ofmore » rainbow trout low in vitamin A, after force feeding with astaxanthin using a feeding tube. Antibiotic-treated fish had no marked difference in vitamin A content compared with a control group that received no antibiotic. This proves that astaxanthin was converted to vitamin A in fish depleted of vitamin A, that microorganisms were not involved in the conversion, and that conversion occurred in the intestine. An in vitro study using /sup 3/H 3S, 3S'-astaxanthin incubated with duodenal and ileal segments of the intestine provided HLPC and radioisotope data, which showed that rainbow trout were able to bioconvert astaxanthin to vitamin A.« less

Are Hyperion and Phoebe Linked to Iapetus?

NASA Technical Reports Server (NTRS)

Jarvis, Kandy S.; Vilas, Faith; Larson, Stephen M.; Gaffey, Michael J.

1999-01-01

Narrowband reflectance spectra of the Saturnian satellites S VII Hyperion and S IX Phoebe were obtained across the 0.4 - 0.8 micron spectral region. The spectrum of Phoebe is similar to the spectrum of a C-class asteroid, with an absorption feature centered near 0.43 micron superimposed on the UV/blue intervalence charge transfer transition present in the spectrum. The spectrum of Hyperion shows the strong spectral slope apparent in spectra of many outer Solar System materials and attributed to organics. We use a linear mixing model to separate the reflectance spectrum of the dark material on Hyperion from the icy material. A distinct absorption feature centered at 0.67 micron is present. A slight inflection near 0.4 - 0.6 micron and change in slope near 0.73 micron suggesting the lower wavelength edge of an absorption are also present. These absorptions are very similar to those identified in the spectrum of the dark material on the surface of Iapetus, suggesting that the dark material on these two satellites is compositionally similar and has a similar origin. These absorption features are attributed to the (6)A(sub 1) yields (4)T(sub 2)(G) and (6)A(sub 1) yields (4)T(sub 1)(G) ferric charge transfer transitions in iron alteration minerals such as goethite and hematite that are products of the aqueous alteration of anhydrous silicates.

Effects of substitution, pressure, and temperature on the phonon mode in layered-rocksalt-type Li{sub (1−x)/2}Ga{sub (1−x)/2}Zn{sub x}O (x = 0.036–0.515) alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Lijie; Hu, Qiwei; Lei, Li, E-mail: lei@scu.edu.cn

2015-11-14

ZnO-based semiconductor alloys, Li{sub (1−x)/2}Ga{sub (1−x)/2}Zn{sub x}O (x = 0.036–0.515) with a layered-rocksalt-type structure, have been prepared under high pressure. The composition, pressure, and temperature dependence of phonons have been studied by Raman spectroscopy. We observe two disorder-activated Raman (DAR) modes when the Zn composition x increases: a broad Raman peak at ca. 400 cm{sup −1} and a left-shoulder peak at ca. 530 cm{sup −1} on the low-frequency side of A{sub 1g} mode at ca. 580 cm{sup −1}, which can be explained by reference to the phonon density of states for rocksalt-type ZnO. With the increase of the pressure and temperature, the left-shoulder DAR modemore » induced by substitution does not change at the same pace with the A{sub 1g} mode at Brillouin-zone center. We find that ion substitution can be seen as a kind of chemical pressure, and the chemical pressure caused by internal substitution and the physical pressure caused by external compression have equivalent effects on the shortening of correlation length, the distortion of crystal lattice, and the change of atomic occupation.« less

Causes and consequences of variation in conifer leaf life-span

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reich, P.B.; Koike, T.; Gower, S.T.

1995-07-01

Species with mutually supporting traits, such as high N{sub mass}, SLA, and A{sub mass}, and short leaf life-span, tend to inhabit either generally resource-rich environments or spatial and/or temporal microhabitats that are resource-rich in otherwise more limited habitats (e.g., {open_quotes}precipitation{close_quotes} ephemerals in warm deserts or spring ephemerals in the understory of temperate deciduous forests). In contrast, species with long leaf life-span often support foliage with low SLA, N{sub mass}, and A{sub mass}, and often grow in low-temperature limited, dry, and/or nutrient-poor environments. The contrast between evergreen and deciduous species, and the implications that emerge from such comparisons, can be consideredmore » a paradigm of modern ecological theory. However, based on the results of Reich et al. (1992) and Gower et al. (1993), coniferous species with foliage that persists for 9-10 years are likely to assimilate and allocate carbon and nutrients differently than other evergreen conifers that retain foliage for 2-3 years. Thus, attempts to contrast ecophysiological or ecosystem characteristics of evergreen versus deciduous life forms may be misleading, and pronounced differences among evergreen conifers may be ignored. Clearly, the deciduous-evergreen contrast, although useful in several ways, should be viewed from the broader perspective of a gradient in leaf life-span.« less

Metastable bcc mischmetal-magnesium alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sabariz, A.L.R.

1989-02-01

The bcc phase in the MM-Mg system can be metastably retained at room temperature for magnesium composition within the range 16 at.% - 20 at.%. The retention of a lower composition was restricted by quenching rate and at higher concentrations by intermetallic compound precipitation. The lattice parameter for the pure bcc mischmetal phase was determined by extrapolation. The value obtained (a/sub E/ = 4.131 /angstrom/) was in good agreement with the theoretical value (a/sub t/ = 4.156 /angstrom/). Magnetic susceptibility data suggested that bcc mischmetal-magnesium alloys underwent a change from paramagnetic to antiferromagnetic behavior on cooling at /approximately/20 K, independentmore » of magnesium composition. The value found for the magnetic effective moment per gram-atom-magnetic-rare earth of each bcc MM-Mg alloy examined (MM - 16 Mg, MM - 18 Mg and MM - 20 Mg) was found to be constant (p/sub eff/ approx. 1.62 ..mu../sub B/), independent of the magnesium composition. The observed Curie-Weiss temperature values decreasing with the magnesium content increasing were due to magnetic dilution. The equilibrium reaction bcc ..-->.. dhcp + MMMg presented an undercooling effect of /approximately/40/degree/C around the eutectoid composition (/approximately/17 at.% Mg). The sluggish character of this reaction was considered the strongest effect for the bcc structure retention in the mischmetal-magnesium system. 16 refs., 27 figs.« less

Compositional investigation of ∼2 μm luminescence of Ho{sup 3+}-doped lead silicate glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Xueqiang; Huang, Feifei; Gao, Song

2015-11-15

Graphical abstract: Ho{sup 3+}-doped lead silicate glass with lowest maximum phonon energy possesses highest ∼2 μm luminescence intensity. - Highlights: • With increment of lead oxide, maximum phonon energy in lead silicate glass decreased. • ∼2 μm luminescent intensity of Ho{sup 3+} increased with increment of lead oxide. • Lowest lead oxide content glass possesses highest quantum efficiency due to low maximum phonon energy. - Abstract: Lead silicate glass samples with varying lead oxide content were prepared in this study, and their luminescent properties were examined and analyzed. It was found that with increasing lead oxide content, the maximum phononmore » energies of the glass samples decreased, while their spontaneous transition probabilities first increased and then decreased. The influence of the spontaneous transition rate, A{sub 10}, and the multi-phonon relaxation rate, W{sub 10}, on the sample luminescent properties was analyzed using rate equations. As a result, it was found that with increasing lead oxide content, W{sub 10}/A{sub 10} decreased, while the quantum efficiency increased. Thus, the luminescent intensity at ∼2 μm increased in the glass samples with increased lead oxide content. The high luminescent intensity and long lifetime indicate that silicate glasses containing high levels of lead oxide could potentially be used in ∼2 μm lasers.« less

Comparative biochemistry and physiology of iron-respiring bacteria from acidic and neutral-pH environments: Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Magnuson, T S

2009-04-07

Acidophilic dissimilatory iron-reducing bacteria (DIRB) are now being detected in a variety of ‘extreme’ low-pH, radionuclide- and heavy-metal contaminated habitats where Fe(III) reduction is taking place, and may represent a significant proportion of metal-transforming organisms in these environments. Acidiphilium cryptum is our model organism, a facultative iron-respiring Alphaproteobacterium. Major findings of this project have been 1) Discovery of novel outer-membrane and periplasmic cytochromes c in acidophiles that are reactive with Fe and Cr, 2) Discovery of Cr(VI) reduction mechanisms in acidophiles, mediated by c-type cytochromes and other reductase activity, 3) Development of enzyme detection methods specific for Cr-reducing enzymes, 4)more » Characterization of biofilm formation in A. cryptum, and 5) Annotation of the Acidiphilium cryptum genome (Magnuson, Kusel, and Cummings, DOE-JGI 2005-2006). Two manuscripts and one book chapter have been published, and several more mauscripts are prepared for submission.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klenk, Hans-Peter; Held, Brittany; Lucas, Susan

Saccharomonospora azurea Runmao et al. 1987 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonosoras are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist and over-heated grain, where they might play a role in the primary degradation of plant material by attacking hemicellulose. They are Gram-negative staining organisms classified among the usually Gram-positive actinomycetes. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for with a completely sequenced type strain genome willmore » be published. Here we describe the features of this organism, together with the complete genome sequence with project status 'permanent draft', and annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).« less

Genome Neighborhood Network Reveals Insights into Enediyne Biosynthesis and Facilitates Prediction and Prioritization for Discovery

PubMed Central

Rudolf, Jeffrey D.; Yan, Xiaohui; Shen, Ben

2015-01-01

The enediynes are one of the most fascinating families of bacterial natural products given their unprecedented molecular architecture and extraordinary cytotoxicity. Enediynes are rare with only 11 structurally characterized members and four additional members isolated in their cycloaromatized form. Recent advances in DNA sequencing have resulted in an explosion of microbial genomes. A virtual survey of the GenBank and JGI genome databases revealed 87 enediyne biosynthetic gene clusters from 78 bacteria strains, implying enediynes are more common than previously thought. Here we report the construction and analysis of an enediyne genome neighborhood network (GNN) as a high-throughput approach to analyze secondary metabolite gene clusters. Analysis of the enediyne GNN facilitated rapid gene cluster annotation, revealed genetic trends in enediyne biosynthetic gene clusters resulting in a simple prediction scheme to determine 9- vs 10-membered enediyne gene clusters, and supported a genomic-based strain prioritization method for enediyne discovery. PMID:26318027

Sorbitol dehydrogenase of Aspergillus niger, SdhA, is part of the oxido-reductive D-galactose pathway and essential for D-sorbitol catabolism.

PubMed

Koivistoinen, Outi M; Richard, Peter; Penttilä, Merja; Ruohonen, Laura; Mojzita, Dominik

2012-02-17

In filamentous fungi D-galactose can be catabolised through the oxido-reductive and/or the Leloir pathway. In the oxido-reductive pathway D-galactose is converted to d-fructose in a series of steps where the last step is the oxidation of d-sorbitol by an NAD-dependent dehydrogenase. We identified a sorbitol dehydrogenase gene, sdhA (JGI53356), in Aspergillus niger encoding a medium chain dehydrogenase which is involved in D-galactose and D-sorbitol catabolism. The gene is upregulated in the presence of D-galactose, galactitol and D-sorbitol. An sdhA deletion strain showed reduced growth on galactitol and growth on D-sorbitol was completely abolished. The purified enzyme converted D-sorbitol to D-fructose with K(m) of 50±5 mM and v(max) of 80±10 U/mg. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Soliton configurations in generalized Mie electrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rybakov, Yu. P., E-mail: soliton4@mail.ru

2011-07-15

The generalization of the Mie electrodynamics within the scope of the effective 8-spinor field model is suggested, with the Lagrangian including Higgs-like potential and higher degrees of the invariant A{sub Micro-Sign }A{sup Micro-Sign }. Using special Brioschi 8-spinor identity, we show that the model includes the Skyrme and the Faddeev models as particular cases. We investigate the large-distance asymptotic of static solutions and estimate the electromagnetic contribution to the energy of the localized charged configuration.

Endohedral Metallofullerene Derivatives

NASA Technical Reports Server (NTRS)

Dorn, Harry C. (Inventor); Iezzi, Erick B. (Inventor); Duchamp, James (Inventor)

2008-01-01

Trimetallic nitride endohedral metallofullerene derivatives and their preparation are described. The trimetallic nitride endohedral metallofullerene derivatives have the general formula A(sub 3-n)X(sub n)@C(sub m)(R) where n ranges from 0 to 3, A and X may be trivalent metals and may be either rare earth metal or group IIIB metals, m is between about 60 and about 200, and R is preferably an organic group. Derivatives where the R group forms cyclized derivatives with the fullerene cage are also described.

Structural and spectroscopic study of mechanically synthesized SnO{sub 2} nanostructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vij, Ankush, E-mail: vij-anx@yahoo.com; Kumar, Ravi; Presently at Beant College of Engineering and Technology, Gurdaspur-143521

2016-05-23

We report the single step synthesis of SnO{sub 2} nanostructures using high energy mechanical attrition method. X-ray diffraction (XRD) pattern reveals the single phase rutile structure with appreciable broadening of diffraction peaks, which is a signature of nanostructure formation. The average crystallite size of SnO{sub 2} nanostructures has been calculated to be ~15 nm. The micro-Raman study reveals the shifting of A{sub 1g} Raman mode towards lower wave number, which is correlated with the nanostructure formation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karp, Peter D.

Pathway Tools is a systems-biology software package written by SRI International (SRI) that produces Pathway/Genome Databases (PGDBs) for organisms with a sequenced genome. Pathway Tools also provides a wide range of capabilities for analyzing predicted metabolic networks and user-generated omics data. More than 5,000 academic, industrial, and government groups have licensed Pathway Tools. This user community includes researchers at all three DOE bioenergy centers, as well as academic and industrial metabolic engineering (ME) groups. An integral part of the Pathway Tools software is MetaCyc, a large, multiorganism database of metabolic pathways and enzymes that SRI and its academic collaborators manuallymore » curate. This project included two main goals: I. Enhance the MetaCyc content of bioenergy-related enzymes and pathways. II. Develop computational tools for engineering metabolic pathways that satisfy specified design goals, in particular for bioenergy-related pathways. In part I, SRI proposed to significantly expand the coverage of bioenergy-related metabolic information in MetaCyc, followed by the generation of organism-specific PGDBs for all energy-relevant organisms sequenced at the DOE Joint Genome Institute (JGI). Part I objectives included: 1: Expand the content of MetaCyc to include bioenergy-related enzymes and pathways. 2: Enhance the Pathway Tools software to enable display of complex polymer degradation processes. 3: Create new PGDBs for the energy-related organisms sequenced by JGI, update existing PGDBs with new MetaCyc content, and make these data available to JBEI via the BioCyc website. In part II, SRI proposed to develop an efficient computational tool for the engineering of metabolic pathways. Part II objectives included: 4: Develop computational tools for generating metabolic pathways that satisfy specified design goals, enabling users to specify parameters such as starting and ending compounds, and preferred or disallowed intermediate

Final technical report for: Insertional Mutagenesis of Brachypodium distachyon DE-AI02-07ER64452

DOE Office of Scientific and Technical Information (OSTI.GOV)

John, Vogel P.

Several bioenergy grasses are poised to become a major source of energy in the United States. Despite their increasing importance, we know little about the basic biology underlying the traits that control the utility of grasses as energy crops. Better knowledge of grass biology (e.g. identification of the genes that control cell wall composition, plant architecture, cell size, cell division, reproduction, nutrient uptake, carbon flux, etc.) could be used to design rational strategies for crop improvement and shorten the time required to domesticate these species. The use of an appropriate model system is an efficient way to gain this knowledge.more » Brachypodium distachyon is a small annual grass with all the attributes needed to be a modern model organism including simple growth requirements, fast generation time, small stature, small genome size and self-fertility. These attributes led to the recommendation in the DOE’s “Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda” report to propose developing and using B. distachyon as a model for energy crops to accelerate their domestication. Strategic investments (e.g. genome sequencing) in B. distachyon by the DOE are now bearing fruit and B. distachyon is being used as a model grass by hundreds of laboratories worldwide. Sequence indexed insertional mutants are an extremely powerful tool for both forward and reverse genetics. They allow researchers to order mutants in any gene tagged in the collection by simply emailing a request. The goal of this project was to create a collection of sequence indexed insertional mutants (T-DNA lines) for the model grass Brachypodium distachyon in order to facilitate research by the scientific community. During the course of this grant we created a collection of 23,649 B. distachyon T-DNA lines and identified 26,112 unique insertion sites. The collection can be queried through the project website (http://jgi

Ultrafast measurements of chlorine dioxide photochemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ludowise, P.D.

Time-resolved mass spectrometry and time-resolved photoelectron spectroscopy are used to study the ultrafast photodissociation dynamics of chlorine dioxide, an important constituent in stratospheric ozone depletion. Chapter 1 introduces these pump/probe techniques, in which a femtosecond pump pulse excites a molecule to a dissociative state. At a later time, a second femtosecond probe pulse ionizes the molecule. The resulting mass and photoelectron spectra are acquired as a function of the delay between the pump and probe pulses, which follows the evolution of the molecule on the excited state. A comparison to other techniques used to study reaction dynamics is discussed. Chaptermore » 2 includes a detailed description of the design and construction of the experimental apparatus, which consists of a femtosecond laser system, a molecular beam time-of-flight spectrometer, and a data acquisition system. The time-of-flight spectrometer is specifically designed to have a short flight distance to maximize the photoelectron collection efficiency without degrading the resolution, which is limited by the bandwidth of the femtosecond laser system. Typical performance of the apparatus is demonstrated in a study of the time-resolved photoelectron spectroscopy of nitric oxide. The results of the time-resolved mass spectrometry experiments of chlorine dioxide are presented in Chapter 3. Upon excitation to the A {sup 2}A{sub 2} state near 3.2 eV, the molecule dissociates through an indirect two-step mechanism. The direct dissociation channel has been predicted to be open, but is not observed. A quantum beat is observed in the OClO{sup +} species, which is described as a vibrational coherence of the optically prepared A {sup 2}A{sub 2} state. Chapter 4 presents the results of the time-resolved photoelectron experiments of chlorine dioxide. At short delay time, the quantum beat of the OClO{sup +} species is observed in the X {sup 1}A{sub 1} state of the ion. At infinite delay

Conductive lithium storage electrode

DOEpatents

Chiang, Yet-Ming [Framingham, MA; Chung, Sung-Yoon [Incheon, KR; Bloking, Jason T [Mountain View, CA; Andersson, Anna M [Vasteras, SE

2012-04-03

A compound comprising a composition A.sub.x(M'.sub.1-aM''.sub.a).sub.y(XD.sub.4).sub.z, A.sub.x(M'.sub.1-aM''.sub.a).sub.y(DXD.sub.4).sub.z, or A.sub.x(M'.sub.1-aM''.sub.a).sub.y(X.sub.2D.sub.7).sub.z, and have values such that x, plus y(1-a) times a formal valence or valences of M', plus ya times a formal valence or valence of M'', is equal to z times a formal valence of the XD.sub.4, X.sub.2D.sub.7, or DXD.sub.4 group; or a compound comprising a composition (A.sub.1-aM''.sub.a).sub.xM'.sub.y(XD.sub.4).sub.z, (A.sub.1-aM''.sub.a).sub.xM'.sub.y(DXD.sub.4).sub.z (A.sub.1-aM''.sub.a).sub.xM'.sub.y(X.sub.2D.sub.7).sub.z and have values such that (1-a).sub.x plus the quantity ax times the formal valence or valences of M'' plus y times the formal valence or valences of M' is equal to z times the formal valence of the XD.sub.4, X.sub.2D.sub.7 or DXD.sub.4 group. In the compound, A is at least one of an alkali metal and hydrogen, M' is a first-row transition metal, X is at least one of phosphorus, sulfur, arsenic, molybdenum, and tungsten, M'' any of a Group IIA, IIIA, IVA, VA, VIA, VIIA, VIIIA, IB, IIB, IIIB, IVB, VB, and VIB metal, D is at least one of oxygen, nitrogen, carbon, or a halogen, 0.0001

Study of CP Symmetry Violation in the Charmonium-K*(892) Channel By a Complete Time Dependent Angular Analysis (BaBar Experiment) (in French)

DOE Office of Scientific and Technical Information (OSTI.GOV)

T'Jampens, Stephane; /Orsay

2006-09-18

This thesis presents the full-angular time-dependent analysis of the vector-vector channel B{sub d}{sup 0} {yields} J/{psi}(K{sub S}{sup 0}{pi}{sup 0})*{sup 0}. After a review of the CP violation in the B meson system, the phenomenology of the charmonium-K*(892) channels is exposed. The method for the measurement of the transversity amplitudes of the B {yields} J/{psi}K*(892), based on a pseudo-likelihood method, is then exposed. The results from a 81.9 fb{sup -1} of collected data by the BABAR detector at the {Upsilon}(4S) resonance peak are |A{sub 0}|{sup 2} = 0.565 {+-} 0.011 {+-} 0.004, |A{sub {parallel}}|{sup 2} = 0.206 {+-} 0.016 {+-} 0.007,more » |A{sub {perpendicular}}|{sup 2} = 0.228 {+-} 0.016 {+-} 0.007, {delta}{sub {parallel}} = -2.766 {+-} 0.105 {+-} 0.040 and {delta}{sub {perpendicular}} = 2.935 {+-} 0.067 {+-} 0.040. Note that ({delta}{sub {parallel}}, {delta}{sub {perpendicular}}) {yields} (-{delta}{sub {parallel}}, {pi} - {delta}{sub {perpendicular}}) is also a solution. The strong phases {delta}{sub {parallel}} and {delta}{sub {perpendicular}} are at {approx}> 3{sigma} from {+-}{pi}, signing the presence of final state interactions and the breakdown of the factorization hypothesis. The forward-backward analysis of the K{pi} mass spectrum revealed the presence of a coherent S-wave interfering with the K*(892). It is the first evidence of this wave in the K{pi} system coming from a B meson. The particularity of the B{sub d}{sup 0} {yields} J/{psi}(K{sub S}{sup 0}{pi}{sup 0})*{sup 0} channel is to have a time-dependent but also an angular distribution which allows to measure sin 2{beta} but also cos2{beta}. The results from an unbinned maximum likelihood fit are sin 2{beta} = -0.10 {+-} 0.57 {+-} 0.14 and cos 2{beta} = 3.32{sub -0.96}{sup +0.76} {+-} 0.27 with the transversity amplitudes fixed to the values given above. The other solution for the strong phases flips the sign of cos 2{beta}. Theoretical considerations based on the s-quark helicity

Luminescence of the (O{sub 2}(a{sup 1}Δ{sub g})){sub 2} collisional complex in the temperature range of 90-315 K: Experiment and theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zagidullin, M. V., E-mail: marsel@fian.smr.ru; Pershin, A. A., E-mail: anchizh93@gmail.com; Azyazov, V. N., E-mail: azyazov@ssau.ru

Experimental and theoretical studies of collision induced emission of singlet oxygen molecules O{sub 2}(a{sup 1}Δ{sub g}) in the visible range have been performed. The rate constants, half-widths, and position of peaks for the emission bands of the (O{sub 2}(a{sup 1}Δ{sub g})){sub 2} collisional complex centered around 634 nm (2) and 703 nm (3) have been measured in the temperature range of 90–315 K using a flow-tube apparatus that utilized a gas-liquid chemical singlet oxygen generator. The absolute values of the spontaneous emission rate constants k{sub 2} and k{sub 3} are found to be similar, with the k{sub 3}/k{sub 2} ratiomore » monotonically decreasing from 1.1 at 300 K to 0.96 at 90 K. k{sub 2} slowly decreases with decreasing temperature but a sharp increase in its values is measured below 100 K. The experimental results were rationalized in terms of ab initio calculations of the ground and excited potential energy and transition dipole moment surfaces of singlet electronic states of the (O{sub 2}){sub 2} dimole, which were utilized to compute rate constants k{sub 2} and k{sub 3} within a statistical model. The best theoretical results reproduced experimental rate constants with the accuracy of under 40% and correctly described the observed temperature dependence. The main contribution to emission process (2), which does not involve vibrational excitation of O{sub 2} molecules at the ground electronic level, comes from the spin- and symmetry-allowed 1{sup 1}A{sub g}←{sup 1}B{sub 3u} transition in the rectangular H configuration of the dimole. Alternatively, emission process (3), in which one of the monomers becomes vibrationally excited in the ground electronic state, is found to be predominantly due to the vibronically allowed 1{sup 1}A{sub g}←2{sup 1}A{sub g} transition induced by the asymmetric O–O stretch vibration in the collisional complex. The strong vibronic coupling between nearly degenerate excited singlet states of the dimole makes

Potassium and magnesium succinatouranilates – Synthesis and crystal structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novikov, S.A., E-mail: serg.alex.novikov@gmail.com; Grigoriev, M.S.; Serezhkina, L.B.

2017-04-15

Single crystal X-ray diffraction has been applied to determine the structures of two new uranyl coordination polymers: K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}] [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), where C{sub 4}H{sub 4}O{sub 4}{sup 2-} is succinate anion. Crystals of 1 and 2 contain polymeric complex anions [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} with the same A{sub 2}Q{sup 02}{sub 3} crystallochemical formula (A=UO{sub 2}{sup 2+}, Q{sup 02}=C{sub 4}O{sub 4}H{sub 4}{sup 2-}), and have layered (1) or chain (2) structure. It has been found, that conformation of succinate ionsmore » is one of the factors, which affects the structure of [(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]{sup 2-} anions. IR spectra of these new compounds are in good agreement with crystallographic data. Topological analysis of the uranium dicarboxylates with A{sub 2}Q{sup 02}{sub 3} crystallochemical formula has shown the presence of five isomers which differ from each other in coordination sequences and / or dimensionality. - Graphical abstract: Crystal structures of two new uranium(VI) coordination polymers with succinate linkers, namely K{sub 2}[(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}] (1) and [Mg(H{sub 2}O){sub 6}][(UO{sub 2}){sub 2}(C{sub 4}H{sub 4}O{sub 4}){sub 3}]·2H{sub 2}O (2), were determined by single-crystal XRD. Crystals of studied compounds are based on 2D or 1D structural units with the same composition and crystallochemical formula. Topological isomerism in A{sub 2}Q{sup 02}{sub 3} crystallochemical group and conformations of succinate anions in uranyl complexes are under discussion. - Highlights: • Two new uranium coordination polymers were synthesized. • Their structural units have the same composition and crystallochemical formula. • In spite the same composition and CCF dimensionality of units is different. • Structural features of

IRAS images of nearby dark clouds

NASA Technical Reports Server (NTRS)

Wood, Douglas O. S.; Myers, Philip C.; Daugherty, Debra A.

1994-01-01

We have investigated approximately 100 nearby molecular clouds using the extensive, all-sky database of IRAS. The clouds in this study cover a wide range of physical properties including visual extinction, size, mass, degree of isolation, homogeneity and morphology. IRAS 100 and 60 micron co-added images were used to calculate the 100 micron optical depth of dust in the clouds. These images of dust optical depth compare very well with (12)CO and (13)CO observations, and can be related to H2 column density. From the optical depth images we locate the edges of dark clouds and the dense cores inside them. We have identified a total of 43 `IRAS clouds' (regions with A(sub v) greater than 2) which contain a total of 255 `IRAS cores' (regions with A(sub v) greater than 4) and we catalog their physical properties. We find that the clouds are remarkably filamentary, and that the cores within the clouds are often distributed along the filaments. The largest cores are usually connected to other large cores by filaments. We have developed selection criteria to search the IRAS Point Source Catalog for stars that are likely to be associated with the clouds and we catalog the IRAS sources in each cloud or core. Optically visible stars associated with the clouds have been identified from the Herbig and Bell catalog. From these data we characterize the physical properties of the clouds including their star-formation efficiency.

Detecting anomalies in CMB maps: a new method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neelakanta, Jayanth T., E-mail: jayanthtn@gmail.com

2015-10-01

Ever since WMAP announced its first results, different analyses have shown that there is weak evidence for several large-scale anomalies in the CMB data. While the evidence for each anomaly appears to be weak, the fact that there are multiple seemingly unrelated anomalies makes it difficult to account for them via a single statistical fluke. So, one is led to considering a combination of these anomalies. But, if we ''hand-pick'' the anomalies (test statistics) to consider, we are making an a posteriori choice. In this article, we propose two statistics that do not suffer from this problem. The statistics aremore » linear and quadratic combinations of the a{sub ℓ m}'s with random co-efficients, and they test the null hypothesis that the a{sub ℓ m}'s are independent, normally-distributed, zero-mean random variables with an m-independent variance. The motivation for considering multiple modes is this: because most physical models that lead to large-scale anomalies result in coupling multiple ℓ and m modes, the ''coherence'' of this coupling should get enhanced if a combination of different modes is considered. In this sense, the statistics are thus much more generic than those that have been hitherto considered in literature. Using fiducial data, we demonstrate that the method works and discuss how it can be used with actual CMB data to make quite general statements about the incompatibility of the data with the null hypothesis.« less

Communication: Cosolvency and cononsolvency explained in terms of a Flory-Huggins type theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dudowicz, Jacek, E-mail: dudowicz@jfi.uchicago.edu; Freed, Karl F.; Douglas, Jack F.

2015-10-07

Standard Flory-Huggins (FH) theory is utilized to describe the enigmatic cosolvency and cononsolvency phenomena for systems of polymers dissolved in mixed solvents. In particular, phase boundaries (specifically upper critical solution temperature spinodals) are calculated for solutions of homopolymers B in pure solvents and in binary mixtures of small molecule liquids A and C. The miscibility (or immiscibility) patterns for the ternary systems are classified in terms of the FH binary interaction parameters (χ{sub αβ}) and the ratio r = ϕ{sub A}/ϕ{sub C} of the concentrations ϕ{sub A} and ϕ{sub C} of the two solvents. The trends in miscibility are comparedmore » to those observed for blends of random copolymers (A{sub x}C{sub 1−x}) with homopolymers (B) and to those deduced for A/B/C solutions of polymers B in liquid mixtures of small molecules A and C that associate into polymeric clusters (A{sub p}C{sub q}){sub i}, (i = 1, 2, …, ∞). Although the classic FH theory is able to explain cosolvency and cononsolvency phenomena, the theory does not include a consideration of the mutual association of the solvent molecules and the competitive association between the solvent molecules and the polymer. These interactions can be incorporated in refinements of the FH theory, and the present paper provides a foundation for such extensions for modeling the rich thermodynamics of polymers in mixed solvents.« less

Challenges for MSSM Higgs searches at hadron colliders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carena, Marcela S.; /Fermilab; Menon, A.

2007-04-01

In this article we analyze the impact of B-physics and Higgs physics at LEP on standard and non-standard Higgs bosons searches at the Tevatron and the LHC, within the framework of minimal flavor violating supersymmetric models. The B-physics constraints we consider come from the experimental measurements of the rare B-decays b {yields} s{gamma} and B{sub u} {yields} {tau}{nu} and the experimental limit on the B{sub s} {yields} {mu}{sup +}{mu}{sup -} branching ratio. We show that these constraints are severe for large values of the trilinear soft breaking parameter A{sub t}, rendering the non-standard Higgs searches at hadron colliders less promising.more » On the contrary these bounds are relaxed for small values of A{sub t} and large values of the Higgsino mass parameter {mu}, enhancing the prospects for the direct detection of non-standard Higgs bosons at both colliders. We also consider the available ATLAS and CMS projected sensitivities in the standard model Higgs search channels, and we discuss the LHC's ability in probing the whole MSSM parameter space. In addition we also consider the expected Tevatron collider sensitivities in the standard model Higgs h {yields} b{bar b} channel to show that it may be able to find 3 {sigma} evidence in the B-physics allowed regions for small or moderate values of the stop mixing parameter.« less

NEW PRECISION ORBITS OF BRIGHT DOUBLE-LINED SPECTROSCOPIC BINARIES. V. THE AM STARS HD 434 AND 41 SEXTANTIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fekel, Francis C.; Williamson, Michael H., E-mail: fekel@evans.tsuniv.ed

We have detected the secondary component in two previously known spectroscopic binaries, HD 434 and 41 Sex, and for the first time determined double-lined orbits for them. Despite the relatively long period of 34.26 days and a moderate eccentricity of 0.32, combined with the components' rotationally broadened lines, measurement of the primary and secondary radial velocities of HD 434 has enabled us to obtain significantly improved orbital elements. While the 41 Sex system has a much shorter period of 6.167 days and a circular orbit, the estimated V mag difference of 3.2 between its components also makes this a challengingmore » system. The new orbital dimensions (a{sub 1} sin i and a{sub 2} sin i) and minimum masses (m{sub 1} sin{sup 3} i and m{sub 2} sin{sup 3} i) of HD 434 have accuracies of 0.8% or better, while the same quantities for 41 Sex are good to 0.5% or better. Both components of HD 434 are Am stars while the Am star primary of 41 Sex has a late-F or early-G companion. All four stars are on the main sequence. The two components of HD 434 are rotating much faster than their predicted pseudosynchronous velocities, while both components of 41 Sex are synchronously rotating. For the primary of 41 Sex, the spectrum line depth changes noted by Sreedhar Rao et al. were not detected.« less

Locality of correlation in density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burke, Kieron; Cancio, Antonio; Gould, Tim

The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that E{sub C} → −A{sub C} ZlnZ +more » B{sub C}Z as Z → ∞, where Z is the atomic number, A{sub C} is known, and we estimate B{sub C} to be about 37 mhartree. The local density approximation yields A{sub C} exactly, but a very incorrect value for B{sub C}, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with B{sub C} a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rizal, Umesh, E-mail: umeshrizal680@gmail.com; Swain, Bibhu P., E-mail: bibhu.s@smit.smu.edu.in; Swain, Bhabani S., E-mail: bsswain@kookmin.ac.kr

Gallium nitride nanowires (GaN-NWs) of diameters ranging from 20 to 80 nm were grown on the p-type Si substrate by Thermal Chemical Vapor Deposition (TCVD) using Iron (Fe) catalyst via VLS mechanism. Raman and FTIR spectra reveal the presence of broad transverse optic (TO) and longitudinal optic (LO) phonon peak spreads over 500-600 cm{sup −1} and 720 cm{sup −1} respectively. The detail deconvolution of integrated transverse and longitudinal phonon analysis reveals phonon confinement brought out by incorporation of hydrogen atom. The red shifts of TO and LO phonon peak position indicates nanosized effect. I{sub A1(LO)}/I{sub A1(TO)} increases from 0.073 to 1.0 and theirmore » respective fwhm{sub A1(LO)}/fwhm{sub A1(TO)} also increases from 0.71 to 1.31 with increasing H{sub 2} flow rate. E{sub 1}(LO) - E{sub 1}(TO) and A{sub 1}(LO) - A{sub 1}(TO) increases from 173.83 to 190.73 and 184.89 to 193.22 respectively. Apart from this usual TO and LO phonon, we have found Surface Optic (SO) phonon at 671 cm{sup −1} in FTIR spectra. The intensity of PL peak increases with increasing H{sub 2} dilution reveals efficient passivation of defect centre at surface of GaN-NWs.« less

Microstructure, texture, and mechanical properties of friction stir welded commercial brass alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heidarzadeh, A., E-mail: ak.hz62@gmail.com

Microstructural evolution during friction stir welding of single-phase brass and corresponding mechanical properties were investigated. For this purpose, 2 mm thick brass plate was friction stir welded at a rotational speed of 450 rpm and traverse speed of 100 mm/min. The microstructure of the joint was studied using optical microscopy, scanning electron microscopy equipped with electron back scattered diffraction system, and scanning transmission electron microscopy. The mechanical properties were measured using hardness and tensile tests. The formation of subgrains and their transformation into new grains in conjunction with existence of A{sub 1}{sup ⁎}, A{sub 2}{sup ⁎} and C texture componentsmore » revealed that the continuous dynamic recrystallization plays a dominant role in the microstructural evolution. However, grain boundary bulging, along with the formation of twin boundaries, and presence of the G texture component showed that the discontinues dynamic recrystallization may participate in the new grain formation. Furthermore, the different strengthening mechanisms, which caused the higher strength of the joint, were discussed. - Highlights: •Microstructural evolution during FSW of a single phase brass was investigated. •CDRX and DDRX were the main mechanisms of the grain structure formation during FSW. •GDRX and SRX were not contributed in grain structure formation. •The lamellas TBs were formed in the SZ of the joints. •Grain boundary, dislocation, and texture effects resulted in higher strength.« less

Transition form factors of the N*(1535) as a dynamically generated resonance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jido, D.; Doering, M.; Oset, E.

2008-06-15

We discuss how electromagnetic properties provide useful tests of the nature of resonances, and we study these properties for the N*(1535) that appears dynamically generated from the strong interaction of mesons and baryons. Within this coupled-channels chiral unitary approach, we evaluate the A{sub 1/2} and S{sub 1/2} helicity amplitudes as a function of Q{sup 2} for the electromagnetic N*(1535){yields}{gamma}*N transition. Within the same formalism we evaluate the cross section for the reactions {gamma}N{yields}{eta}N. We find a fair agreement for the absolute values of the transition amplitudes, as well as for the Q{sup 2} dependence of the amplitudes, within theoretical andmore » experimental uncertainties discussed in the article. The ratios obtained between the S{sub 1/2} and A{sub 1/2} for the neutron or proton states of the N*(1535) are in qualitative agreement with experiment and there is agreement on the signs. The same occurs for the ratio of cross sections for the {eta} photoproduction on neutron and proton targets in the vicinity of the N*(1535) energy. The global results support the idea of this resonance as being dynamically generated, hence, largely built up from meson baryon components. However, the details of the model indicate that an admixture with a genuine quark state is also demanded that could help obtain a better agreement with experimental data.« less

Non-Abelian Yang-Mills analogue of classical electromagnetic duality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan, Hong-Mo; Faridani, J.; Tsun, T.S.

The classic question of non-Abelian Yang-Mills analogue to electromagnetic duality is examined here in a minimalist fashion at the strictly four-dimensional, classical field, and point charge level. A generalization of the Abelian Hodge star duality is found which, though not yet known to give dual symmetry, reproduces analogues to many dual properties of the Abelian theory. For example, there is a dual potential, but it is a two-indexed tensor {ital T}{sub {mu}{nu}} of the Freedman-Townsend-type. Though not itself functioning as such, {ital T}{sub {mu}{nu}} gives rise to a dual parallel transport {ital {tilde A}}{sub {mu}} for the phase of themore » wave function of the color magnetic charge, this last being a monopole of the Yang-Mills field but a source of the dual field. The standard color (electric) charge itself is found to be a monpole of {ital {tilde A}}{sub {mu}}. At the same time, the gauge symmetry is found doubled from say SU({ital N}) to SU({ital N}){times}SU({ital N}). A novel feature is that all equations of motion, including the standard Yang-Mills and Wong equations, are here derived from a ``universal`` principle, namely, the Wu-Yang criterion for monpoles, where interactions arise purely as a consequence of the topological definition of the monopole charge. The technique used is the loop space formulation of Polyakov.« less

8-Spinors and structure of solitons in generalized Mie electrodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rybakov, Yu. P., E-mail: soliton4@mail.ru

2013-02-15

A generalization of Mie electrodynamics is considered. It includes a 8-spinor field and higher powers of the Mie invariant A{sub {mu}}A{sup {mu}}. Particular topological properties of 8-spinors are indicated and are associated with the existence of the remarkable Brioschi identity of eight squares, which permits deriving a natural 8-spinor unification of the Skyrme model of baryons and the Faddeev model of leptons, these particles being treated as topological solitons. Two types of soliton configurations admitted by the model are constructed. These are charged static and neutral lightlike (luxons) ones.

Buffer layers for REBCO films for use in superconducting devices

DOEpatents

Goyal, Amit; Wee, Sung-Hun

2014-06-10

A superconducting article includes a substrate having a biaxially textured surface. A biaxially textured buffer layer, which can be a cap layer, is supported by the substrate. The buffer layer includes a double perovskite of the formula A.sub.2B'B''O.sub.6, where A is rare earth or alkaline earth metal and B' and B'' are different transition metal cations. A biaxially textured superconductor layer is deposited so as to be supported by the buffer layer. A method of making a superconducting article is also disclosed.

Out-of-plane quasielastic scattering from deuterium using polarized electrons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dolfini, S.; Alarcon, R.; Arenhoevel, H.

1995-06-01

We have measured the coincidence {ital d}({ital {rvec e}},{ital e}{prime}{ital p}) reaction in quasielastic scattering, detecting the proton in a noncoplanar geometry. The electron helicity asymmetry {ital A}{sub {ital e}} and the imaginary part of the longitudinal-transverse interference structure function {ital f}{sub {ital L}{ital T}}{sup {prime}} have been determined at a four-momentum transfer {ital Q}{sup 2}=3.3 fm{sup {minus}2}. The results are compared with theoretical calculations which use realistic potentials for the {ital NN} interaction.

N*(1535) electroproduction at high Q2

DOE Office of Scientific and Technical Information (OSTI.GOV)

G. Ramalho, M.T. Pena, K. Tsushima

2012-04-01

A covariant spectator quark model is applied to study the {gamma}N {yields} N*(1535) reaction in the large Q{sup 2} region. Starting from the relation between the nucleon and N*(1535) systems, the N*(1535) valence quark wave function is determined without the addition of any parameters. The model is then used to calculate the {gamma}N {yields} N*(1535) transition form factors. A very interesting, useful relation between the A{sub 1/2} and S{sub 1/2} helicity amplitudes for Q{sup 2} > GeV{sup 2}, is also derived.

On the thermopower and thermomagnetic properties of Er{sub x}Sn{sub 1–x}Se solid solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huseynov, J. I., E-mail: cih-58@mail.ru; Murguzov, M. I.; Ismayilov, Sh. S.

2017-02-15

The Er{sub x}Sn{sub 1–x}Se system is characterized by a significant deviation of the temperature dependence of the differential thermopower from linearity at temperatures below room temperature and a change in the sign of the thermomagnetic coefficient. The deviation of the thermopower of Er{sub x}Sn{sub 1–x}Se samples in the nonequilibrium state from linearity is found to be caused mainly by the entrainment of charge carriers by phonons α{sub ph}. The statistical forces of electronic entrainment, A{sub ph}(ε), are estimated.

Genomics of Climate Resilience (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bermingham, Eldredge

2013-03-27

Eldredge Bermingham of the Smithsonian Tropical Research Institute-Panama on "Genomics of climate resilience" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Rieseberg, Loren

2018-02-06

Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

Genomics of Climate Resilience (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

ScienceCinema

Bermingham, Eldredge

2018-02-13

Eldredge Bermingham of the Smithsonian Tropical Research Institute-Panama on "Genomics of climate resilience" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

PMI: Plant-Microbe Interfaces (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schadt, Christopher

2013-03-01

Christopher Schadt of Oak Ridge National Laboratory on Plant-Microbe Interactions in the context of poplar trees at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 held in Walnut Creek, CA.

Erratum to: The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

DOE PAGES

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; ...

2016-03-21

After publication of this study [1], we noticed that the Strain ID summary was not removed from the PDF due to a copyediting error. The original version of this article was corrected. The publisher apologizes for any inconvenience caused.

Charmless hadronic B decays into a tensor meson

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Hai-Yang; C. N. Yang Institute for Theoretical Physics, State University of New York Stony Brook, Stony Brook, New York 11794; Yang, Kwei-Chou

2011-02-01

observation that f{sub T}/f{sub L}<<1 for B{yields}K{sub 2}*(1430){phi}, whereas f{sub T}/f{sub L}{approx}1 for B{yields}K{sub 2}*(1430){omega} with f{sub T} being the transverse polarization fraction, can be accommodated in QCDF, but it cannot be dynamically explained at first place. For penguin-dominated B{yields}TV decays, we find f{sub L}(K{sub 2}*{rho}){approx}f{sub L}(K{sub 2}*{omega}){approx}0.65, whereas f{sub L}(K*f{sub 2}){approx}0.93. It will be of great interest to measure f{sub L} for these modes to test QCDF. Theoretically, transverse polarization is expected to be small in tree-dominated B{yields}TV decays except for the a{sub 2}{sup -}{rho}{sup 0}, a{sub 2}{sup -}{rho}{sup +}, K{sub 2}*{sup 0}K*{sup -} and K{sub 2}*{sup 0}K*{sup 0} modes. (vi) For tree-dominated decays, their rates are usually very small except for the a{sub 2}{sup 0}({pi}{sup -},{rho}{sup -}), a{sub 2}{sup +}({pi}{sup -},{rho}{sup -}) and f{sub 2}({pi}{sup -},{rho}{sup -}) modes with branching fractions of order 10{sup -6} or even larger.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klenk, Hans-Peter; Lu, Megan; Lucas, Susan

Saccharomonospora marina Liu et al. 2010 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they might play a role in the primary degradation of plant material by attacking hemicellulose. Organisms belonging to the genus are usually Gram-positive staining, non-acid fast, and classify among the actinomycetes. Next to S. viridis and S. azurea, S. marina is the third member in the genus Saccharomonosporamore » for with a completely sequenced (permanent draft status) type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 5,965,593 bp long chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).« less

DUK - A Fast and Efficient Kmer Based Sequence Matching Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mingkun; Copeland, Alex; Han, James

2011-03-21

A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmermore » hashing method to index reference sequences and Poisson model to calculate p-value. DUK is carefully implemented in C++ in object oriented design. The resulted classes can also be used to develop other tools quickly. DUK have been widely used in JGI for a wide range of applications such as contaminant removal, organelle genome separation, and assembly refinement. Many real applications and simulated dataset demonstrate its power.« less

A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mockler, Todd

Brachypodium distachyon is the premier experimental model grass platform and is related to candidate feedstock crops for bioethanol production. Based on the DOE-JGI Brachypodium Bd21 genome sequence and annotation we designed a whole genome DNA microarray platform. The quality of this array platform is unprecedented due to the exceptional quality of the Brachypodium genome assembly and annotation and the stringent probe selection criteria employed in the design. We worked with members of the international community and the bioinformatics/design team at Affymetrix at all stages in the development of the array. We used the Brachypodium arrays to interrogate the transcriptomes ofmore » plants grown in a variety of environmental conditions including diurnal and circadian light/temperature conditions and under a variety of environmental conditions. We examined the transciptional responses of Brachypodium seedlings subjected to various abiotic stresses including heat, cold, salt, and high intensity light. We generated a gene expression atlas representing various organs and developmental stages. The results of these efforts including all microarray datasets are published and available at online public databases.« less

Gene context analysis in the Integrated Microbial Genomes (IMG) data management system.

PubMed

Mavromatis, Konstantinos; Chu, Ken; Ivanova, Natalia; Hooper, Sean D; Markowitz, Victor M; Kyrpides, Nikos C

2009-11-24

Computational methods for determining the function of genes in newly sequenced genomes have been traditionally based on sequence similarity to genes whose function has been identified experimentally. Function prediction methods can be extended using gene context analysis approaches such as examining the conservation of chromosomal gene clusters, gene fusion events and co-occurrence profiles across genomes. Context analysis is based on the observation that functionally related genes are often having similar gene context and relies on the identification of such events across phylogenetically diverse collection of genomes. We have used the data management system of the Integrated Microbial Genomes (IMG) as the framework to implement and explore the power of gene context analysis methods because it provides one of the largest available genome integrations. Visualization and search tools to facilitate gene context analysis have been developed and applied across all publicly available archaeal and bacterial genomes in IMG. These computations are now maintained as part of IMG's regular genome content update cycle. IMG is available at: http://img.jgi.doe.gov.

Few-body resonances of unequal-mass systems with infinite interspecies two-body s-wave scattering length

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blume, D.; Daily, K. M.

Two-component Fermi and Bose gases with infinitely large interspecies s-wave scattering length a{sub s} exhibit a variety of intriguing properties. Among these are the scale invariance of two-component Fermi gases with equal masses, and the favorable scaling of Efimov features for two-component Bose gases and Bose-Fermi mixtures with unequal masses. This paper builds on our earlier work [Phys. Rev. Lett. 105, 170403 (2010)] and presents a detailed discussion of our studies of small unequal-mass two-component systems with infinite a{sub s} in the regime where three-body Efimov physics is absent. We report on nonuniversal few-body resonances. Just like with two-body systemsmore » on resonance, few-body systems have a zero-energy bound state in free space and a diverging generalized scattering length. Our calculations are performed within a nonperturbative microscopic framework and investigate the energetics and structural properties of small unequal-mass two-component systems as functions of the mass ratio {kappa}, and the numbers N{sub 1} and N{sub 2} of heavy and light atoms. For purely attractive Gaussian two-body interactions, we find that the (N{sub 1},N{sub 2})=(2,1) and (3,1) systems exhibit three-body and four-body resonances at mass ratios {kappa}=12.314(2) and 10.4(2), respectively. The three- and four-particle systems on resonance are found to be large. It seems feasible that the features discussed in this paper can be probed experimentally with present-day technology.« less

Development, Validation, and Potential Enhancements to the Second-Generation Operational Aerosol Product at the National Environmental Satellite, Data, and Information Service of the National Oceanic and Atmospheric Administration

NASA Technical Reports Server (NTRS)

Stowe, Larry L.; Ignatov, Alexander M.; Singh, Ramdas R.

1997-01-01

A revised (phase 2) single-channel algorithm for aerosol optical thickness, tau(sup A)(sub SAT), retrieval over oceans from radiances in channel 1 (0.63 microns) of the Advanced Very High Resolution Radiometer (AVHRR) has been implemented at the National Oceanic and Atmospheric Administration's National Environmental Satellite Data and Information Service for the NOAA 14 satellite launched December 30, 1994. It is based on careful validation of its operational predecessor (phase 1 algorithm), implemented for NOAA 14 in 1989. Both algorithms scale the upward satellite radiances in cloud-free conditions to aerosol optical thickness using an updated radiative transfer model of the ocean and atmosphere. Application of the phase 2 algorithm to three matchup Sun-photometer and satellite data sets, one with NOAA 9 in 1988 and two with NOAA 11 in 1989 and 1991, respectively, show systematic error is less than 10%, with a random error of sigma(sub tau) approx. equal 0.04. First results of tau(sup A)(sub SAT) retrievals from NOAA 14 using the phase 2 algorithm, and from checking its internal consistency, are presented. The potential two-channel (phase 3) algorithm for the retrieval of an aerosol size parameter, such as the Junge size distribution exponent, by adding either channel 2 (0.83 microns) from the current AVHRR instrument, or a 1.6-microns channel to be available on the Tropical Rainfall Measurement Mission and the NOAA-KLM satellites by 1997 is under investigation. The possibility of using this additional information in the retrieval of a more accurate estimate of aerosol optical thickness is being explored.

Structural and relaxor-like dielectric properties of unfilled tungsten bronzes Ba{sub 5−5x}Sm{sub 5x}Ti{sub 5x}Nb{sub 10−5x}O{sub 30}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, T., E-mail: weitong.nju@gmail.com, E-mail: weitong-nju@163.com; Dong, Z.; Zhou, Q. J.

2016-03-28

New unfilled tetragonal tungsten bronze (TTB) oxides, Ba{sub 5−5x}Sm{sub 5x}Ti{sub 5x}Nb{sub 10−5x}O{sub 30} (BSTN-x), where 0.10 ≤ x ≤ 0.35, have been synthesized in this work. Their crystal structure was determined and analyzed based on Rietveld structural refinement. It is found that single TTB phase can be formed in a particular x range (i.e., 0.15 ≤ x ≤ 0.3) due to the competition interaction between tolerance factor and electronegativity difference. Furthermore, dielectric and ferroelectric results indicate that phase transitions and ferroelectric states are sensitive to x. Referring to the local chemistry, we suggest that the raise of vacancies at the A{sub 2}-site compared with that of A{sub 1}-sitemore » will intensely depress the normal ferroelectric phase and is in favor of relaxor ferroelectric state. Macroscopically, previous A-site size difference standpoint on fill TTB compounds cannot give a reasonable explanation about the variation of dielectric maximum temperature (T{sub m}) for present BSTN-x compounds. Alternatively, tetragonality (c/a) is adopted which can well describe the variation of T{sub m} in whole x range. In addition, one by one correspondence between tetragonality and electrical features can be found, and the compositions involving high c/a are usually stabilized in normal ferroelectric phase. It is believed that c/a is a more appropriate parameter to illustrate the variation of ferroelectric properties for unfilled TTB system.« less

X-ray Reflected Spectra from Accretion Disk Models. III. A Complete Grid of Ionized Reflection Calculations

NASA Technical Reports Server (NTRS)

Garcia, J.; Dauser, T.; Reynolds, C. S.; Kallman, T. R.; McClintock, J. E.; Wilms, J.; Ekmann, W.

2013-01-01

We present a new and complete library of synthetic spectra for modeling the component of emission that is reflected from an illuminated accretion disk. The spectra were computed using an updated version of our code xillver that incorporates new routines and a richer atomic data base. We offer in the form of a table model an extensive grid of reflection models that cover a wide range of parameters. Each individual model is characterized by the photon index Gamma of the illuminating radiation, the ionization parameter zeta at the surface of the disk (i.e., the ratio of the X-ray flux to the gas density), and the iron abundance A(sub Fe) relative to the solar value. The ranges of the parameters covered are: 1.2 <= Gamma <= 3.4, 1 <= zeta <= 104, and 0.5 <= A(sub Fe) <= 10. These ranges capture the physical conditions typically inferred from observations of active galactic nuclei, and also stellar-mass black holes in the hard state. This library is intended for use when the thermal disk flux is faint compared to the incident power-law flux. The models are expected to provide an accurate description of the Fe K emission line, which is the crucial spectral feature used to measure black hole spin. A total of 720 reflection spectra are provided in a single FITS file suitable for the analysis of X-ray observations via the atable model in xspec. Detailed comparisons with previous reflection models illustrate the improvements incorporated in this version of xillver.

Electron spin resonance investigations of /sup 11/B/sup 12/C, /sup 11/B/sup 13/C, and /sup 10/B/sup 12/C in neon, argon, and krypton matrices at 4 K: Comparison with theoretical results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knight L.B. Jr.; Cobranchi, S.T.; Petty, J.T.

1989-01-15

The first spectroscopic study of the diatomic radical BC is reported which confirms previous theoretical predictions of a /sup 4/summation/sup -/ electronic ground state. The nuclear hyperfine interactions (A tensors) obtained for /sup 11/B, /sup 10/B, and /sup 13/C from the electron spin resonance (ESR) measurements are compared with extensive ab initio CI calculations. The BC molecule is one of the first examples of a small high spin radical for such an in-depth experimental--theoretical comparison. The electronic structure of BC obtained from an analysis of the nuclear hyperfine interaction (hfi) is compared to that obtained from a Mulliken-type population analysismore » conducted on a CI wave function which yields A/sub iso/ and A/sub dip/ results in good agreement with the observed values. The BC radical was generated by the laser vaporization of a boron--carbon mixture and trapped in neon, argon, and krypton matrices at 4 K for a complete ESR characterization. The magnetic parameters (MHz) obtained for /sup 11/B/sup 13/C in solid neon are: g/sub parallel/ = 2.0015(3); g/sub perpendicular/ = 2.0020(3); D(zfs) = 1701(2); /sup 11/B: chemically bondA/sub parallel/chemically bond = 100(1); chemically bondA/sub perpendicular/chemically bond = 79(1); /sup 13/C: chemically bondA/sub parallel/chemically bond = 5(2) and chemically bondA/sub perpendicular/chemically bond = 15(1). Based on comparison with the theoretical results, the most likely choice of signs is that all A values are positive.« less

Synthesis, crystal structure and magnetic properties of a new B-site ordered double perovskite Sr{sub 2}CuIrO{sub 6}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vasala, Sami; Yamauchi, Hisao; Karppinen, Maarit, E-mail: maarit.karppinen@aalto.fi

2014-12-15

Here we synthesize and characterize a new double-perovskite oxide Sr{sub 2}CuIrO{sub 6}. The synthesis requires the use of high oxygen pressure to stabilize the VI oxidation state of iridium. The compound has a tetragonally-distorted crystal structure due to the Jahn–Teller active Cu{sup II} ion, and a high degree of B-site cation order. Magnetic transition is apparent at 15 K, but the zero-field-cooled and field-cooled susceptibilities diverge below this temperature. The high degree of cation order would exclude the possibility of a typical spin-glass, indicating that the divergence is probably due to a frustration of the magnetic interactions between Cu andmore » Ir, with a high frustration factor of f≈25. - Graphical abstract: A new member of the A{sub 2}B′B″O{sub 6} double-perovskite family with JT-active Cu{sup II} at the B′ site and Ir{sup VI} at the B″ site is synthesized through high pressure synthesis and characterized for the structural and magnetic properties. - Highlights: • New member of the A{sub 2}CuB″O{sub 6} double-perovskite family is synthesized with B″=Ir. • Stabilization of Ir{sup VI} requires the use of high oxygen pressure synthesis. • Crystal structure is tetragonally distorted due to JT-active Cu{sup II}. • Divergence of ZFC and FC curves is seen below the T{sub N} of 15 K. • This is presumably due to a frustration effect.« less

Stimulated polariton scattering in an intracavity RbTiOPO₄ crystal generating frequency-tunable THz output.

PubMed

Ortega, Tiago A; Pask, Helen M; Spence, David J; Lee, Andrew J

2016-05-16

A high power, frequency-tunable THz source based on intracavity stimulated polariton scattering (SPS) in RbTiOPO₄ (RTP) is demonstrated for the first time. Frequency tunable THz output was obtained from 3.10 to 4.15 THz, with a gap at 3.17 to 3.49 THz, arising from the 104 cm^-1 A>1 mode in RTP. A maximum average output power of 16.2 µW was detected at 3.8 THz. This is the highest average output power ever reported for an intracavity polariton laser.

Perturbative Aspects of Low-Dimensional Quantum Field Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wardaya, Asep Y.; Theoretical Physics Laboratory, Theoretical High Energy Physics and Instrumentation Research Group, FMIPA, Institut Teknologi Bandung, Jl. Ganesha 10 Bandung 40132; Zen, Freddy P.

We investigate the low-dimensional applications of Quantum Field Theory (QFT), namely Chern-Simons-Witten Theory (CSWT) and Affine Toda Field Theory (ATFT) in 3- and 2- dimensions. We discuss the perturbative aspects of both theories and compare the results to the exact solutions obtained nonperturbatively. For the three dimensions CSWT case, the perturbative term agree with the nonperturbative polynomial invariants up to third order of the coupling constant 1/k. In the two dimensions ATFT, we investigate the perturbative aspect of S-matrices for A{sub 1}{sup (1)} case in eighth order of the coupling constant {beta}.