FN Thomson Reuters Web of Science™ VR 1.0 PT S AU Voronov, DL Cambie, R Ahn, M Anderson, EH Chang, CH Gullikson, EM Heilmann, RK Salmassi, F Schattenburg, ML Yashchuk, VV Padmore, HA AF Voronov, D. L. Cambie, R. Ahn, M. Anderson, E. H. Chang, C. H. Gullikson, E. M. Heilmann, R. K. Salmassi, F. Schattenburg, M. L. Yashchuk, V. V. Padmore, H. A. BE Garrett, R Gentle, I Nugent, K Wilkins, S TI Ultra-high Resolution Optics for EUV and Soft X-ray Inelastic Scattering SO SRI 2009: THE 10TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION SE AIP Conference Proceedings LA English DT Proceedings Paper CT 10th International Conference on Synchrotron Radiation Instrumentation CY SEP 27-OCT 02, 2009 CL Australian Synchrotron, Melbourne, AUSTRALIA SP Australian Synchrotron, State Govt Victoria, Australian Govt, Dept Innovat, Ind Sci & Res, Elsevier, Int Atom Energy Agcy, Australian Res Council, Mol & Mat Struct Network, JJ X-Rray A/S, Lightsources HO Australian Synchrotron DE blazed gratings; multilayer EUV; soft x-rays; lithography; anisotropic etch ID EXTREME-ULTRAVIOLET; GRATINGS; FABRICATION; EFFICIENCY; SOLIDS AB We describe a revolutionary new approach to high spectral resolution soft x-ray optics. Conventionally in the soft x-ray energy range, high spectral resolution is obtained by use of a relatively low line density grating operated in 1(st) order with small slits. This severely limits throughput. This limitation can be removed by use of a grating either in very high order, or with very high line density, if one can maintain high diffraction efficiency. We have developed a new technology for achieving both of these goals which should allow high throughput spectroscopy, at resolving powers of up to 10(6) at 1 keV. Such optics should provide a revolutionary advance for high resolution lifetime free spectroscopy, such as RIXS, and for pulse compression of chirped beams. We report recent developmental fabrication and characterization of a prototype grating optimized for 14.2 nm EUV light. The prototype grating with a 200 nm period of the blazed grating substrate coated with 20 Mo/Si bilayers with a period of 7.1 nm demonstrates good dispersion in the third order (effective groove density of 15,000 lines per mm) with a diffraction efficiency of more than 33%. C1 [Voronov, D. L.; Cambie, R.; Anderson, E. H.; Gullikson, E. M.; Yashchuk, V. V.; Padmore, H. A.] Lawrence Berkeley Lab, Berkeley, CA 94720 USA. [Ahn, M.; Chang, C. H.; Heilmann, R. K.; Schattenburg, M. L.] MIT, Cambridge, MA 02139 USA. RP Voronov, DL (reprint author), Lawrence Berkeley Lab, Berkeley, CA 94720 USA. RI Heilmann, Ralf/D-4680-2009 NR 22 TC 0 Z9 0 U1 2 U2 7 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0782-4 J9 AIP CONF PROC PY 2010 VL 1234 BP 891 EP + DI 10.1063/1.3463360 PG 2 WC Physics, Applied SC Physics GA BRU32 UT WOS:000283705500204 ER PT S AU Xu, SL Makarov, O Benn, R Yoder, DW Stepanov, S Becker, M Corcoran, S Hilgart, M Nagarajan, V Ogata, CM Pothineni, S Sanishvili, R Smith, JL Fischetti, RF AF Xu, Shenglan Makarov, Oleg Benn, Rich Yoder, Derek W. Stepanov, Sergey Becker, Michael Corcoran, Stephen Hilgart, Mark Nagarajan, Venugopalan Ogata, Craig M. Pothineni, Sudhir Sanishvili, Ruslan Smith, Janet L. Fischetti, Robert F. BE Garrett, R Gentle, I Nugent, K Wilkins, S TI Micro-Crystallography Developments at GM/CA-CAT at the APS SO SRI 2009: THE 10TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION SE AIP Conference Proceedings LA English DT Proceedings Paper CT 10th International Conference on Synchrotron Radiation Instrumentation CY SEP 27-OCT 02, 2009 CL Australian Synchrotron, Melbourne, AUSTRALIA SP Australian Synchrotron, State Govt Victoria, Australian Govt, Dept Innovat, Ind Sci & Res, Elsevier, Int Atom Energy Agcy, Australian Res Council, Mol & Mat Struct Network, JJ X-Rray A/S, Lightsources HO Australian Synchrotron DE Mini beam; Mini Collimator; Goniostat; Active beam stop AB Recently, several important structures have been solved using micro-crystallographic techniques that previously could not have been solved with conventional crystallography. At GM/CA-CAT we continue to develop micro-crystallographic capabilities for difficult problems such as small crystals of large macromolecular complexes or membrane proteins grown in the lipidic cubic phase. This paper will describe three major upgrades to our arsenal of tools, "mini-beam" collimators, active beamstop, and an improved goniostat. Our "mini-beam" collimators have evolved to a new triple-collimator fabricated from molybdenum as a uni-body. This has significantly improved the robustness, ease of initial alignment, and reduction of background. More recently, two prototypes of a quad-collimator have been developed and fabricated to provide a selection of mini-beams of 5, 10, 20 mu m and a 300 mu m scatter-guard on a single body. The smaller beams and samples have increased the demand on the tolerances of our goniostat. To meet these challenges we have designed and implemented a goniostat with a 1-micron peak-to-peak sphere of confusion. This is a significant improvement over the previous 6 micron sphere of confusion of the commercially available air-bearing and XY stages. Finally, an "active beamstop" has been constructed. This will provide non-invasive, real time feedback at the sample during data collection. C1 [Xu, Shenglan; Makarov, Oleg; Benn, Rich; Yoder, Derek W.; Stepanov, Sergey; Becker, Michael; Corcoran, Stephen; Hilgart, Mark; Nagarajan, Venugopalan; Ogata, Craig M.; Pothineni, Sudhir; Sanishvili, Ruslan; Fischetti, Robert F.] Argonne Natl Lab, Biosci Div, 9700 S Cass Ave, Argonne, IL 60439 USA. [Smith, Janet L.] Univ Michigan, Ann Arbor, MI 48109 USA. RP Xu, SL (reprint author), Argonne Natl Lab, Biosci Div, 9700 S Cass Ave, Argonne, IL 60439 USA. NR 5 TC 7 Z9 7 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0782-4 J9 AIP CONF PROC PY 2010 VL 1234 BP 905 EP + PG 2 WC Physics, Applied SC Physics GA BRU32 UT WOS:000283705500207 ER PT S AU Borland, M AF Borland, M. BE Garrett, R Gentle, I Nugent, K Wilkins, S TI Concepts and performance for a next-generation storage ring hard x-ray source SO SRI 2009: THE 10TH INTERNATIONAL CONFERENCE ON SYNCHROTRON RADIATION INSTRUMENTATION SE AIP Conference Proceedings LA English DT Proceedings Paper CT 10th International Conference on Synchrotron Radiation Instrumentation CY SEP 27-OCT 02, 2009 CL Australian Synchrotron, Melbourne, AUSTRALIA SP Australian Synchrotron, State Govt Victoria, Australian Govt, Dept Innovat, Ind Sci & Res, Elsevier, Int Atom Energy Agcy, Australian Res Council, Mol & Mat Struct Network, JJ X ray A s, Lightsources HO Australian Synchrotron DE Radiation sources; Storage rings ID PULSES AB Among the possibilities for a next-generation hard x-ray source is a so-called "ultimate storage ring." This refers to a large, high-energy storage ring with very low emittance and high current. Such a ring has the potential to deliver significantly higher spectral brightness and transverse coherence than present third-generation rings. At the same time, it promises the stability and reliability that users have come to expect in a light source. In this paper, we present a design for a 7-GeV, 40-sector storage ring with a circumference of 3.1 km and an emittance of 15 pm in both planes. C1 Argonne Natl Lab, Argonne, IL 60439 USA. RP Borland, M (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. NR 18 TC 3 Z9 3 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0782-4 J9 AIP CONF PROC PY 2010 VL 1234 BP 911 EP 914 DI 10.1063/1.3463364 PG 4 WC Physics, Applied SC Physics GA BRU32 UT WOS:000283705500208 ER PT J AU Chang, YJ Pukall, R Saunders, E Lapidus, A Copeland, A Nolan, M Del Rio, TG Lucas, S Chen, F Tice, H Cheng, JF Han, C Detter, JC Bruce, D Goodwin, L Pitluck, S Mikhailova, N Liolios, K Pati, A Ivanova, N Mavromatis, K Chen, A Palaniappan, K Land, M Hauser, L Jeffries, CD Brettin, T Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Chang, Yun-Juan Pukall, Ruediger Saunders, Elizabeth Lapidus, Alla Copeland, Alex Nolan, Matt Del Rio, Tijana Glavina Lucas, Susan Chen, Feng Tice, Hope Cheng, Jan-Fang Han, Cliff Detter, John C. Bruce, David Goodwin, Lynne Pitluck, Sam Mikhailova, Natalia Liolios, Konstantinos Pati, Amrita Ivanova, Natalia Mavromatis, Konstantinos Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Jeffries, Cynthia D. Brettin, Thomas Rohde, Manfred Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Acidaminococcus fermentans type strain (VR4(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; mesophile; diplococcus; gastrointestinal tract; trans-aconitate degradation; glutamate fermentation; Acidaminococcaceae; Selenomonadales; Negativicutes; GEBA ID HUMAN CLINICAL-SAMPLES; 2-HYDROXYGLUTARYL-COA DEHYDRATASE; TRANS-ACONITATE; SP NOV.; BACTERIA; COMMUNITY; ARCHAEA; OPERON; CLASSIFICATION; IDENTIFICATION AB Acidaminococcus fermentans (Rogosa 1969) is the type species of the genus Acidaminococcus, and is of phylogenetic interest because of its isolated placement in a genomically little characterized region of the Firmicutes. A. fermentans is known for its habitation of the gastrointestinal tract and its ability to oxidize trans-aconitate. Its anaerobic fermentation of glutamate has been intensively studied and will now be complemented by the genomic basis. The strain described in this report is a nonsporulating, nonmotile, Gram-negative coccus, originally isolated from a pig alimentary tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Acidaminococcaceae, and the 2,329,769 bp long genome with its 2,101 protein-coding and 81 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Pukall, Ruediger; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chang, Yun-Juan; Lapidus, Alla; Copeland, Alex; Nolan, Matt; Del Rio, Tijana Glavina; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mikhailova, Natalia; Liolios, Konstantinos; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Brettin, Thomas; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Chang, Yun-Juan; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Brettin, Thomas] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Saunders, Elizabeth; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Gabriele Gehrich-Schroter for growing A. fermentans cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract No. DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 48 TC 7 Z9 19 U1 1 U2 11 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 1 BP 1 EP 14 DI 10.4056/sigs.1002553 PG 14 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DV UT WOS:000290221800001 PM 21304687 ER PT J AU Abt, B Foster, B Lapidus, A Clum, A Sun, H Pukall, R Lucas, S Del Rio, TG Nolan, M Tice, H Cheng, JF Pitluck, S Liolios, K Ivanova, N Mavromatis, K Ovchinnikova, G Pati, A Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Abt, Birte Foster, Brian Lapidus, Alla Clum, Alicia Sun, Hui Pukall, Ruediger Lucas, Susan Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Cellulomonas flavigena type strain (134(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE non-motile; non-sporulating; aerobic; mesophile; Gram-positive; cellulolytic; xylan degrader; Cellulomonadaceae; GEBA ID GENERA CELLULOMONAS; GENUS CELLULOMONAS; BACTERIAL NAMES; SP-NOV.; PROPOSAL; CLASSIFICATION; IDENTIFICATION; ARCHAEA; SYSTEM; ACTINOBACTERIA AB Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Abt, Birte; Pukall, Ruediger; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Foster, Brian; Lapidus, Alla; Clum, Alicia; Sun, Hui; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Lawrence Livermore Natl Lab, Livermore, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Gabriele Gehrich-Schroter for growing C. flavigena cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 52 TC 14 Z9 17 U1 1 U2 6 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 1 BP 15 EP 25 DI 10.4056/sigs.1012662 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DV UT WOS:000290221800002 PM 21304688 ER PT J AU Tindall, BJ Sikorski, J Lucas, S Goltsman, E Copeland, A Del Rio, TG Nolan, M Tice, H Cheng, JF Han, C Pitluck, S Liolios, K Ivanova, N Mavromatis, K Ovchinnikova, G Pati, A Fahnrich, R Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Tindall, Brian J. Sikorski, Johannes Lucas, Susan Goltsman, Eugene Copeland, Alex Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Cheng, Jan-Fang Han, Cliff Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Faehnrich, Regine Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Meiothermus ruber type strain (21(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE thermophilic; aerobic; non-motile; free-living; Gram-negative; Thermales; Deinococci; GEBA ID SP-NOV.; PHYLOGENETIC TREE; BACTERIAL NAMES; THERMUS-RUBER; ARCHAEA; NOMENCLATURE; RADIODURANS; SYSTEM; CHINA; TOOL AB Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus Meiothermus. This thermophilic genus is of special interest, as its members share relatively low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary lineage from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. The temperature related split is in accordance with the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the low-temperature group. This is the first completed genome sequence of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Lucas, Susan; Goltsman, Eugene; Copeland, Alex; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Tindall, Brian J.; Sikorski, Johannes; Faehnrich, Regine; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Lapidus, A (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle, and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and SI 1352/1-2. NR 46 TC 18 Z9 19 U1 1 U2 5 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 1 BP 26 EP 36 DI 10.4056/sigs.1032748 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DV UT WOS:000290221800003 PM 21304689 ER PT J AU Sikorski, J Tindall, BJ Lowry, S Lucas, S Nolan, M Copeland, A Del Rio, TG Tice, H Cheng, JF Han, C Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Sikorski, Johannes Tindall, Brian J. Lowry, Stephen Lucas, Susan Nolan, Matt Copeland, Alex Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Han, Cliff Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Meiothermus silvanus type strain (VI-R2(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE thermophilic; aerobic; biofouler; colored biofilm in paper industry; Gram-negative; Thermales; Deinococci; GEBA ID SP-NOV.; PHYLOGENETIC TREE; THERMUS-RUBER; BACTERIA; IDENTIFICATION; ARCHAEA; SYSTEM; GENUS; TOOL AB Meiothermus silvanus (Tenreiro et al. 1995) Nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16S rRNA gene sequence similarity. Meiothermus constitutes an evolutionary lineage separate from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. M. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biofouler. This is the second completed genome sequence of a member of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,721,669 bp long genome with its 3,667 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Lowry, Stephen; Lucas, Susan; Nolan, Matt; Copeland, Alex; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Tindall, Brian J.; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Lapidus, A (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Helga Pomrenke for growing M. silvanus cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and SI 1352/1-2. NR 43 TC 8 Z9 8 U1 1 U2 9 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 1 BP 37 EP 46 DI 10.4056/sigs.1042812 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DV UT WOS:000290221800004 PM 21304690 ER PT J AU LaButti, K Sikorski, J Schneider, S Nolan, M Lucas, S Del Rio, TG Tice, H Cheng, JF Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Tindall, BJ Rohde, M Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF LaButti, Kurt Sikorski, Johannes Schneider, Susanne Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Tindall, Brian J. Rohde, Manfred Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Planctomyces limnophilus type strain (Mu 290(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE stalk; multicellular rosettes; low salt tolerance; Gram-negative; Planctomycetales; Planctomycetes; GEBA ID 16S RIBOSOMAL-RNA; BUDDING BACTERIA; ORDER PLANCTOMYCETALES; SP-NOV; HORTOBAGYI 1965; ARCHAEA; CELL; IDENTIFICATION; PEPTIDOGLYCAN; PIRELLULA AB Planctomyces limnophilus Hirsch and Muller 1986 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. Besides Pirellula staleyi, this is the second completed genome sequence of the family Planctomycetaceae. P. limnophilus is of interest because it differs from Pirellula by the presence of a stalk and its structure of fibril bundles, its cell shape and size, the formation of multicellular rosettes, low salt tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304 protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [LaButti, Kurt; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Schneider, Susanne; Tindall, Brian J.; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Lapidus, A (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Helga Pomrenke (DSMZ) for growing cultures of P. limnophilus. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and SI 1352/1-2. NR 45 TC 17 Z9 20 U1 2 U2 9 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 1 BP 47 EP 56 DI 10.4056/sigs.1052813 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DV UT WOS:000290221800005 PM 21304691 ER PT J AU Sikorski, J Lapidus, A Chertkov, O Lucas, S Copeland, A Del Rio, TG Nolan, M Tice, H Cheng, JF Han, C Brambilla, E Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Bruce, D Detter, C Tapia, R Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Goker, M Spring, S Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Sikorski, Johannes Lapidus, Alla Chertkov, Olga Lucas, Susan Copeland, Alex Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Cheng, Jan-Fang Han, Cliff Brambilla, Evelyne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Bruce, David Detter, Chris Tapia, Roxanne Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Goeker, Markus Spring, Stefan Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobe; mesophile; halophile; chemolithotroph; methylotroph; organotroph; degradation of betaine; consumption of trimethylamine; homoacetogen; Clostridia; Halanaerobiales; GEBA ID CARBONIC-ANHYDRASE; ANAEROBIC-BACTERIA; SP-NOV; ARCHAEA; IDENTIFICATION; SYSTEM; GENUS; TOOL AB Acetohalobium arabaticum Zhilina and Zavarzin 1990 is of special interest because of its physiology and its participation in the anaerobic C-1-trophic chain in hypersaline environments. This is the first completed genome sequence of the family Halobacteroidaceae and only the second genome sequence in the order Halanaerobiales. The 2,469,596 bp long genome with its 2,353 protein-coding and 90 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Brambilla, Evelyne; Goeker, Markus; Spring, Stefan; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lapidus, Alla; Lucas, Susan; Copeland, Alex; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Bruce, David; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Han, Cliff; Bruce, David; Detter, Chris; Tapia, Roxanne; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growing cultures of A. arabaticum. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and SI 1352/1-2. NR 36 TC 5 Z9 6 U1 1 U2 11 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 1 BP 57 EP 65 DI 10.4056/sigs.1062906 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DV UT WOS:000290221800006 PM 21304692 ER PT J AU Goker, M Held, B Lapidus, A Nolan, M Spring, S Yasawong, M Lucas, S Del Rio, TG Tice, H Cheng, JF Goodwin, L Tapia, R Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Brambilla, E Land, M Hauser, L Chang, YJ Jeffries, CD Brettin, T Detter, JC Han, C Rohde, M Sikorski, J Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Goeker, Markus Held, Brittany Lapidus, Alla Nolan, Matt Spring, Stefan Yasawong, Montri Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Goodwin, Lynne Tapia, Roxanne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Brambilla, Evelyne Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brettin, Thomas Detter, John C. Han, Cliff Rohde, Manfred Sikorski, Johannes Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE hyperthermophile; obligately anaerobic; moderately acidophilic; fermentative; cocci-shaped; hot spring; Crenarchaeota; Desulfurococcaceae; GEBA ID NEW-ZEALAND; BACTERIA; ARCHAEA; IDENTIFICATION; PHYLOGENY; ROTORUA; SYSTEM; TOOL AB Ignisphaera aggregans Niederberger et al. 2006 is the type and sole species of genus Ignisphaera. This archaeal species is characterized by a coccoid-shape and is strictly anaerobic, moderately acidophilic, heterotrophic hyperthermophilic and fermentative. The type strain AQ1.S1(T) was isolated from a near neutral, boiling spring in Kuirau Park, Rotorua, New Zealand. This is the first completed genome sequence of the genus Ignisphaera and the fifth genome (fourth type strain) sequence in the family Desulfurococcaceae. The 1,875,953 bp long genome with its 2,009 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Goeker, Markus; Spring, Stefan; Brambilla, Evelyne; Sikorski, Johannes; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Held, Brittany; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Goodwin, Lynne; Tapia, Roxanne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Detter, John C.; Han, Cliff; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Yasawong, Montri; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Held, Brittany; Goodwin, Lynne; Tapia, Roxanne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2, SI 1352/12]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growth of I. aggregans and the help of Alexander Auch (Tubingen, Germany) in creating a local version of the GBDP software. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and SI 1352/12 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY. NR 38 TC 7 Z9 10 U1 1 U2 3 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 1 BP 66 EP 75 DI 10.4056/sigs.1072907 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DV UT WOS:000290221800007 PM 21304693 ER PT J AU Goker, M Held, B Lucas, S Nolan, M Yasawong, M Del Rio, TG Tice, H Cheng, JF Bruce, D Detter, JC Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Sikorski, J Pukall, R Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Goeker, Markus Held, Brittany Lucas, Susan Nolan, Matt Yasawong, Montri Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Bruce, David Detter, John C. Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Sikorski, Johannes Pukall, Ruediger Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Olsenella uli type strain (VPI D76D-27C(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE microaerotolerant anaerobe; human gingival crevices; primary endodontic infections; Coriobacteriaceae; GEBA ID ENDODONTIC INFECTIONS; EMENDED DESCRIPTIONS; LACTOBACILLUS-ULI; SP-NOV; BACTERIA; IDENTIFICATION; PROPOSAL; ARCHAEA; SYSTEM; ACTINOBACTERIA AB Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001 is the type species of the genus Olsenella, which belongs to the actinobacterial family Coriobacteriaceae. The species is of interest because it is frequently isolated from dental plaque in periodontitis patients and can cause primary endodontic infection. The species is a Gram-positive, non-motile and non-sporulating bacterium. The strain described in this study was isolated from human gingival crevices. This is the first completed sequence of the genus Olsenella and the fifth sequence from a member of the family Coriobacteriaceae. The 2,051,896 bp long genome with its 1,795 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Lucas, Susan; Nolan, Matt; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Goeker, Markus; Sikorski, Johannes; Pukall, Ruediger; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Held, Brittany; Bruce, David; Detter, John C.; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Yasawong, Montri; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Lapidus, A (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548] FX We would like to gratefully acknowledge the help of Gabriele Gehrich-Schroter to growing O. uli and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548' for MY. NR 39 TC 8 Z9 9 U1 1 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 1 BP 76 EP 84 DI 10.4056/sigs.1082860 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DV UT WOS:000290221800008 PM 21304694 ER PT J AU LaButti, K Mayilraj, S Clum, A Lucas, S Del Rio, TG Nolan, M Tice, H Cheng, JF Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Goodwin, L Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Spring, S Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF LaButti, Kurt Mayilraj, Shanmugam Clum, Alicia Lucas, Susan Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Goodwin, Lynne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Spring, Stefan Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; motile; vibrio-shaped; thiosulfate-reducing; H2S producing; peptide utilization; Synergistaceae; Synergistetes; GEBA ID BACTERIA; ARCHAEA; NOV; IDENTIFICATION; SYSTEM; TOOL AB Dethiosulfovibrio peptidovorans Magot et al. 1997 is the type species of the genus Dethiosulfovibrio of the family Synergistaceae in the recently created phylum Synergistetes. The strictly anaerobic, vibriod, thiosulfate-reducing bacterium utilizes peptides and amino acids, but neither sugars nor fatty acids. It was isolated from an offshore oil well where it was been reported to be involved in pitting corrosion of mild steel. Initially, this bacterium was described as a distant relative of the genus Thermoanaerobacter, but was not assigned to a genus, it was subsequently placed into the novel phylum Synergistetes. A large number of repeats in the genome sequence prevented an economically justifiable closure of the last gaps. This is only the third published genome from a member of the phylum Synergistetes. The 2,576,359 bp long genome consists of three contigs with 2,458 protein-coding and 59 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Mayilraj, Shanmugam; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [LaButti, Kurt; Clum, Alicia; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Mayilraj, Shanmugam] Inst Microbial Technol, Chandigarh, India. [Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Lawrence Livermore Natl Lab, Livermore, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2]; Indian Council of Scientific and Industrial Research FX We would like to gratefully acknowledge the help of Esther Schuler for growing D. peptidovorans and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. The Indian Council of Scientific and Industrial Research provided a Raman Research Fellowship to Shanmugam Mayilraj. NR 23 TC 6 Z9 6 U1 1 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 1 BP 85 EP 92 DI 10.4056/sigs.1092865 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DV UT WOS:000290221800009 PM 21304695 ER PT J AU Pitluck, S Yasawong, M Munk, C Nolan, M Lapidus, A Lucas, S Del Rio, TG Tice, H Cheng, JF Bruce, D Detter, C Tapia, R Han, C Goodwin, L Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Spring, S Sikorski, J Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Pitluck, Sam Yasawong, Montri Munk, Christine Nolan, Matt Lapidus, Alla Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Bruce, David Detter, Chris Tapia, Roxanne Han, Cliff Goodwin, Lynne Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Spring, Stefan Sikorski, Johannes Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE chemoorganotroph; anaerobe; thermophile; barophile; upwelling system; core sample; deep sea sediment; Thermoanaerobacterales; Firmicutes; GEBA ID BACTERIA; ARCHAEA; IDENTIFICATION; GRAPHS; SYSTEM; TOOL AB Thermosediminibacter oceani (Lee et al. 2006) is the type species of the genus Thermosediminibacter in the family Thermoanaerobacteraceae. The anaerobic, barophilic, chemoorganotrophic thermophile is characterized by straight to curved Gram-negative rods. The strain described in this study was isolated from a core sample of deep sea sediments of the Peruvian high productivity upwelling system. This is the first completed genome sequence of a member of the genus Thermosediminibacter and the seventh genome sequence in the family Thermoanaerobacteraceae. The 2,280,035 bp long genome with its 2,285 protein-coding and 63 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Spring, Stefan; Sikorski, Johannes; Goeker, Markus; Klenk, Hans-Peter] German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. [Pitluck, Sam; Munk, Christine; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Yasawong, Montri; Rohde, Manfred] Helmholtz Ctr Infect Res, HZI, Braunschweig, Germany. [Munk, Christine; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. RI Spring, Stefan/N-6933-2013; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2, SI 1352/1-2]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548]; UT-Battelle FX We would like to gratefully acknowledge the help of Maren Schroder for growing T. oceani cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and SI 1352/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY. NR 31 TC 7 Z9 9 U1 1 U2 10 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 108 EP 116 DI 10.4056/sigs.1133078 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300002 PM 21304740 ER PT J AU Mavromatis, K Sikorski, J Pabst, E Teshima, H Lapidus, A Lucas, S Nolan, M Del Rio, TG Cheng, JF Bruce, D Goodwin, L Pitluck, S Liolios, K Ivanova, N Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Spring, S Goker, M Wirth, R Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Mavromatis, Konstantinos Sikorski, Johannes Pabst, Elke Teshima, Hazuki Lapidus, Alla Lucas, Susan Nolan, Matt Del Rio, Tijana Glavina Cheng, Jan-Fang Bruce, David Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Spring, Stefan Goeker, Markus Wirth, Reinhard Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Vulcanisaeta distributa type strain (IC-017(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE hyperthermophilic; acidophilic; non-motile; microaerotolerant anaerobe; Thermoproteaceae; Crenarchaeota; GEBA ID PHYLOGENETIC ANALYSIS; ARCHAEA; BACTERIA; ARCHAEBACTERIA; SYSTEM AB Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Mavromatis, Konstantinos; Teshima, Hazuki; Lapidus, Alla; Lucas, Susan; Nolan, Matt; Del Rio, Tijana Glavina; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. [Pabst, Elke; Wirth, Reinhard] Univ Regensburg, Microbiol Archaeenzentrum, Regensburg, Germany. [Teshima, Hazuki; Bruce, David; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] Helmholtz Ctr Infect Res, HZI, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Kyrpides, NC (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Con-tract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 33 TC 7 Z9 8 U1 1 U2 5 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 117 EP 125 DI 10.4056/sigs.1113067 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300003 PM 21304741 ER PT J AU Yasawong, M Teshima, H Lapidus, A Nolan, M Lucas, S Del Rio, TG Tice, H Cheng, JF Bruce, D Detter, C Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Sikorski, J Pukall, R Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Yasawong, Montri Teshima, Hazuki Lapidus, Alla Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Bruce, David Detter, Chris Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Sikorski, Johannes Pukall, Ruediger Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Arcanobacterium haemolyticum type strain (11018(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE obligate parasite; human pathogen; pharyngeal lesions; skin lesions; facultative anaerobe; Actinomycetaceae; Actinobacteria; GEBA ID CORYNEBACTERIUM-HAEMOLYTICUM; BRAIN-ABSCESS; CLASSIFICATION; BACTERIA; PROPOSAL; ARCHAEA; SYSTEM; NOV; ACTINOBACTERIA; IDENTIFICATION AB Arcanobacterium haemolyticum (ex MacLean et al. 1946) Collins et al. 1983 is the type species of the genus Arcanobacterium, which belongs to the family Actinomycetaceae. The strain is of interest because it is an obligate parasite of the pharynx of humans and farm animal; occasionally, it causes pharyngeal or skin lesions. It is a Gram-positive, nonmotile and non-sporulating bacterium. The strain described in this study was isolated from infections amongst American soldiers of certain islands of the North and West Pacific. This is the first completed sequence of a member of the genus Arcanobacterium and the ninth type strain genome from the family Actinomycetaceae. The 1,986,154 bp long genome with its 1,821 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Pukall, Ruediger; Goeker, Markus; Klenk, Hans-Peter] German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. [Yasawong, Montri; Rohde, Manfred] Helmholtz Ctr Infect Res, HZI, Braunschweig, Germany. [Teshima, Hazuki; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Teshima, Hazuki; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548] FX We would like to gratefully acknowledge the help of Gabriele Gehrich-Schroter for growing A. haemolyticum cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY. NR 52 TC 4 Z9 6 U1 1 U2 4 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 126 EP 135 DI 10.4056/sigs.1123072 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300004 PM 21304742 ER PT J AU Mavromatis, K Yasawong, M Chertkov, O Lapidus, A Lucas, S Nolan, M Del Rio, TG Tice, H Cheng, JF Pitluck, S Liolios, K Ivanova, N Tapia, R Han, C Bruce, D Goodwin, L Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Rohde, M Brambilla, E Spring, S Goker, M Sikorski, J Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Mavromatis, Konstantinos Yasawong, Montri Chertkov, Olga Lapidus, Alla Lucas, Susan Nolan, Matt Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Tapia, Roxanne Han, Cliff Bruce, David Goodwin, Lynne Pati, Amrita Chen, Ami Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Rohde, Manfred Brambilla, Evelyne Spring, Stefan Goeker, Markus Sikorski, Johannes Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE spiral shaped; corkscrew-like motility; chemoorganotroph; strictly anaerobe; obligately halophile; rhodanese-like protein; Spirochaetaceae; GEBA ID ANAEROBIC SPIROCHETE; BACTERIAL NAMES; OIL-FIELD; SP NOV.; GENE; ARCHAEA; CLASSIFICATION; IDENTIFICATION; NOMENCLATURE; CALIFORNIA AB Spirochaeta smaragdinae Magot et al. 1998 belongs to the family Spirochaetaceae. The species is Gram-negative, motile, obligately halophilic and strictly anaerobic and is of interest because it is able to ferment numerous polysaccharides. S. smaragdinae is the only species of the family Spirochaetaceae known to reduce thiosulfate or element sulfur to sulfide. This is the first complete genome sequence in the family Spirochaetaceae. The 4,653,970 bp long genome with its 4,363 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Mavromatis, Konstantinos; Chertkov, Olga; Lapidus, Alla; Lucas, Susan; Nolan, Matt; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Tapia, Roxanne; Han, Cliff; Bruce, David; Goodwin, Lynne; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Yasawong, Montri; Rohde, Manfred] Helmholtz Ctr Infect Res, HZI, Braunschweig, Germany. [Chertkov, Olga; Tapia, Roxanne; Han, Cliff; Bruce, David; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Ami; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Brambilla, Evelyne; Spring, Stefan; Goeker, Markus; Sikorski, Johannes; Klenk, Hans-Peter] German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Kyrpides, NC (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Land, Miriam/A-6200-2011; Lapidus, Alla/I-4348-2013; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Hauser, Loren/H-3881-2012 OI Land, Miriam/0000-0001-7102-0031; Lapidus, Alla/0000-0003-0427-8731; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growing cultures of S. smarasgdinae. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY. NR 40 TC 14 Z9 15 U1 3 U2 9 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 136 EP 144 DI 10.4056/sigs.1143106 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300005 PM 21304743 ER PT J AU Kiss, H Cleland, D Lapidus, A Lucas, S Del Rio, TG Nolan, M Tice, H Han, C Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Lu, M Brettin, T Detter, JC Goker, M Tindall, BJ Beck, B McDermott, TR Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Cheng, JF AF Kiss, Hajnalka Cleland, David Lapidus, Alla Lucas, Susan Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Lu, Megan Brettin, Thomas Detter, John C. Goeker, Markus Tindall, Brian J. Beck, Brian McDermott, Timothy R. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Cheng, Jan-Fang TI Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE extreme thermal soil; thermoacidophile; Gram-positive; nonmotile; non-spore-forming; obligate aerobe; Incertae sedis; Chloroflexi; GEBA ID SP-NOV; SPHAEROBACTER-THERMOPHILUS; EMENDED DESCRIPTION; BACTERIA; PROPOSAL; ARCHAEA; THERMOMICROBIA; IDENTIFICATION; DATABASE; SYSTEM AB 'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Goeker, Markus; Tindall, Brian J.; Klenk, Hans-Peter] German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. [Kiss, Hajnalka; Han, Cliff; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Cleland, David; Beck, Brian] ATCC, Manassas, VA USA. [Lapidus, Alla; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Lu, Megan; Brettin, Thomas; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Cheng, Jan-Fang] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [McDermott, Timothy R.] Montana State Univ, Thermal Biol Inst, Bozeman, MT 59717 USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725. NR 30 TC 6 Z9 10 U1 1 U2 8 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 153 EP 162 DI 10.4056/sigs.1153107 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300007 PM 21304745 ER PT J AU Roeselers, G Newton, ILG Woyke, T Auchtung, TA Dilly, GF Dutton, RJ Fisher, MC Fontanez, KM Lau, E Stewart, FJ Richardson, PM Barry, KW Saunders, E Detter, JC Wu, DY Eisen, JA Cavanaugh, CM AF Roeselers, Guus Newton, Irene L. G. Woyke, Tanja Auchtung, Thomas A. Dilly, Geoffrey F. Dutton, Rachel J. Fisher, Meredith C. Fontanez, Kristina M. Lau, Evan Stewart, Frank J. Richardson, Paul M. Barry, Kerrie W. Saunders, Elizabeth Detter, John C. Wu, Dongying Eisen, Jonathan A. Cavanaugh, Colleen M. TI Complete genome sequence of Candidatus Ruthia magnifica SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Hydrotheral vent; Clam; sulfur; symbiosis; chemosynthesis, vesicomyidae ID HYDROTHERMAL VENT CLAM; CALYPTOGENA-MAGNIFICA; CHEMOAUTOTROPHIC BACTERIA; ESCHERICHIA-COLI; SYMBIONT; DATABASE AB The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Mollusca) is a member of the Vesicomyidae. Species within this family form symbioses with chemosynthetic Gammaproteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a rudimentary gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. The C. magnifica symbiont, Candidatus Ruthia magnifica, was the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced (Newton et al. 2007). Here we expand upon the original report and provide additional details complying with the emerging MIGS/MIMS standards. The complete genome exposed the genetic blueprint of the metabolic capabilities of the symbiont. Genes which were predicted to encode the proteins required for all the metabolic pathways typical of free-living chemoautotrophs were detected in the symbiont genome. These include major pathways including carbon fixation, sulfur oxidation, nitrogen assimilation, as well as amino acid and cofactor/vitamin biosynthesis. This genome sequence is invaluable in the study of these enigmatic associations and provides insights into the origin and evolution of autotrophic endosymbiosis. C1 [Roeselers, Guus; Newton, Irene L. G.; Auchtung, Thomas A.; Dilly, Geoffrey F.; Fisher, Meredith C.; Fontanez, Kristina M.; Lau, Evan; Stewart, Frank J.; Cavanaugh, Colleen M.] Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA. [Roeselers, Guus] Radboud Univ Nijmegen, Dept Microbiol, NL-6525 AJ Nijmegen, Netherlands. [Newton, Irene L. G.] Dept Biol Sci, Wellesley, MA 02482 USA. [Woyke, Tanja; Richardson, Paul M.; Barry, Kerrie W.; Saunders, Elizabeth; Detter, John C.] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA. [Dutton, Rachel J.] Harvard Univ, Sch Med, Dept Microbiol & Mol Genet, Boston, MA 02115 USA. [Wu, Dongying; Eisen, Jonathan A.] Univ Calif Davis, Davis Genome Ctr, Genome & Biomed Sci Facil, Davis, CA 95616 USA. RP Cavanaugh, CM (reprint author), Harvard Univ, Dept Organism & Evolutionary Biol, 16 Divin Ave,Biolabs 4080, Cambridge, MA 02138 USA. EM cavanaug@fas.harvard.edu RI Roeselers, Guus/J-2971-2012; OI Dilly, Geoffrey/0000-0003-2140-4955; Lau, Evan/0000-0002-7434-4362; Roeselers, Guus/0000-0002-4725-6105; Eisen, Jonathan A./0000-0002-0159-2197 FU Office of Science of the U.S. Department of Energy; Howard Hughes Medical Institute; Netherlands Organisation for Scientific Research (NWO); Office of Science of the U. S. Department of Energy [DE-AC02-05CH11231] FX This research was funded by a grant from the Office of Science of the U. S. Department of Energy to CMC and JAE, a Howard Hughes Medical Institute Predoctoral Fellowship to ILGN and a Rubicon grant from the Netherlands Organisation for Scientific Research (NWO) to GR. The work was conducted in part at the U.S. Department of Energy Joint Genome Institute, which is supported by the Office of Science of the U. S. Department of Energy under Contract No. DE-AC02-05CH11231. We thank Eddy Rubin and David Bruce for project management. NR 23 TC 2 Z9 2 U1 0 U2 2 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 163 EP 173 DI 10.4056/sigs.1103048 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300008 PM 21304746 ER PT J AU Nolan, M Sikorski, J Davenport, K Lucas, S Del Rio, TG Tice, H Cheng, JF Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Tapia, R Brettin, T Detter, JC Han, C Yasawong, M Rohde, M Tindall, BJ Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Nolan, Matt Sikorski, Johannes Davenport, Karen Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Tapia, Roxanne Brettin, Thomas Detter, John C. Han, Cliff Yasawong, Montri Rohde, Manfred Tindall, Brian J. Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Ferrimonas balearica type strain (PAT(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE chemoorganotroph; iron(III)-reducing bacterium; facultatively anaerobic; Ferrimonadaceae; Gammaproteobacteria; GEBA ID SP-NOV.; MARINE ALTEROMONAS; BACTERIA; ARCHAEA; IDENTIFICATION; PROPOSAL; SYSTEM; TOOL AB Ferrimonas balearica Rossello-Mora et al. 1996 is the type species of the genus Ferrimonas, which belongs to the family Ferrimonadaceae within the Gammaproteobacteria. The species is a Gram-negative, motile, facultatively anaerobic, non spore-forming bacterium, which is of special interest because it is a chemoorganotroph and has a strictly respiratory metabolism with oxygen, nitrate, Fe(III)-oxyhydroxide, Fe(III)-citrate, MnO2, selenate, selenite and thiosulfate as electron acceptors. This is the first completed genome sequence of a member of the genus Ferrimonas and also the first sequence from a member of the family Ferrimonadaceae. The 4,279,159 bp long genome with its 3,803 protein-coding and 144 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Tindall, Brian J.; Goeker, Markus; Klenk, Hans-Peter] German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. [Nolan, Matt; Davenport, Karen; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Tapia, Roxanne; Brettin, Thomas; Detter, John C.; Han, Cliff; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Davenport, Karen; Goodwin, Lynne; Tapia, Roxanne; Brettin, Thomas; Detter, John C.; Han, Cliff] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Yasawong, Montri; Rohde, Manfred] Helmholtz Ctr Infect Res, HZI, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548] FX We would like to gratefully acknowledge the help of Regine Fahnrich for growing F. balearica cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY. NR 36 TC 4 Z9 10 U1 2 U2 5 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 174 EP 182 DI 10.4056/sigs.1161239 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300009 PM 21304747 ER PT J AU Gilbert, JA Meyer, F Schriml, L Joint, IR Muhling, M Field, D AF Gilbert, Jack A. Meyer, Folker Schriml, Lynn Joint, Ian R. Muehling, Martin Field, Dawn TI Metagenomes and metatranscriptomes from the L4 long-term coastal monitoring station in the Western English Channel SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Marine; aerobic; surface water; coastal; temperate; metagenome; metatranscriptome; pyrosequencing; time-series; diel; seasonal ID MICROBIAL COMMUNITIES; SEQUENCES AB Both metagenomic data and metatranscriptomic data were collected from surface water (0-2m) of the L4 sampling station (50.2518 N, 4.2089 W), which is part of the Western Channel Observatory long-term coastal-marine monitoring station. We previously generated from this area a six-year time series of 16S rRNA V6 data, which demonstrated robust seasonal structure for the bacterial community, with diversity correlated with day length. Here we describe the features of these metagenomes and metatranscriptomes. We generated 8 metagenomes (4.5 million sequences, 1.9 Gbp, average read-length 350 bp) and 7 metatranscriptomes (392,632 putative mRNA-derived sequences, 159 Mbp, average read-length 272 bp) for eight time-points sampled in 2008. These time points represent three seasons (winter, spring, and summer) and include both day and night samples. These data demonstrate the major differences between genetic potential and actuality, whereby genomes follow general seasonal trends yet with surprisingly little change in the functional potential over time; transcripts tended to be far more structured by changes occurring between day and night. C1 [Gilbert, Jack A.; Joint, Ian R.] Plymouth Marine Lab, Plymouth PL1 3DH, Devon, England. [Gilbert, Jack A.; Meyer, Folker] Argonne Natl Lab, Argonne, IL 60439 USA. [Gilbert, Jack A.; Meyer, Folker] Univ Chicago, Chicago, IL 60637 USA. [Schriml, Lynn] Univ Maryland, Sch Med, Baltimore, MD 21201 USA. [Muehling, Martin] TU Bergakad Freiberg, IOZ Interdisciplinary Ctr Ecol, D-09599 Freiberg, Germany. [Field, Dawn] NERC, Ctr Ecol & Hydrol, Oxford OX1 3SR, England. RP Gilbert, JA (reprint author), Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England. EM gilbertjack@anl.gov OI Meyer, Folker/0000-0003-1112-2284; Schriml, Lynn/0000-0001-8910-9851 FU Natural Environmental Research Council [NERC - NE/F00138X/1]; Office of Advanced Scientific Computing Research, Office of Science, U. S. Department of Energy [DE-AC02-06CH11357]; U. S. Department of Energy Office of Science laboratory [DE-AC02-06CH11357] FX This work was funded by a grant from the Natural Environmental Research Council (NERC - NE/F00138X/1). The authors thank Neil Hall from the NERC / University of Liverpool Advanced Genomics Facility. This work was supported in part by the Office of Advanced Scientific Computing Research, Office of Science, U. S. Department of Energy, under Contract DE-AC02-06CH11357. The submitted manuscript has been created by UChicago Argonne, LLC, Operator of Argonne National Laboratory ("Argonne"). Argonne, a U. S. Department of Energy Office of Science laboratory, is operated under Contract No. DE-AC02-06CH11357. The U. S. Government retains for itself, and others acting on its behalf, a paid-up nonexclusive, irrevocable worldwide license in said article to reproduce, prepare derivative works, distribute copies to the public, and perform publicly and display publicly, by or on behalf of the Government. NR 15 TC 15 Z9 15 U1 3 U2 21 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 183 EP 193 DI 10.4056/sigs.1202536 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300010 PM 21304748 ER PT J AU Sikorski, J Munk, C Lapidus, A Djao, ODN Lucas, S Del Rio, TG Nolan, M Tice, H Han, C Cheng, JF Tapia, R Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Sims, D Meincke, L Brettin, T Detter, JC Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Lang, E Spring, S Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Sikorski, Johannes Munk, Christine Lapidus, Alla Djao, Olivier Duplex Ngatchou Lucas, Susan Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Han, Cliff Cheng, Jan-Fang Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Sims, David Meincke, Linda Brettin, Thomas Detter, John C. Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Lang, Elke Spring, Stefan Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Sulfurimonas autotrophica type strain (OK10(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE mesophilic; facultatively anaerobic; sulfur metabolism; deep-sea hydrothermal vents; spermidine; Gram-negative; Helicobacteriaceae; Epsilonproteobacteria; GEBA ID SP-NOV.; BACTERIA; ARCHAEA; SYSTEM; CHEMOLITHOAUTOTROPH; DENITRIFICANS; GRAPHS AB Sulfurimonas autotrophica Inagaki et al. 2003 is the type species of the genus Sulfurimonas. This genus is of interest because of its significant contribution to the global sulfur cycle as it oxidizes sulfur compounds to sulfate and by its apparent habitation of deep-sea hydrothermal and marine sulfidic environments as potential ecological niche. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second complete genome sequence of the genus Sulfurimonas and the 15(th) genome in the family Helicobacteraceae. The 2,153,198 bp long genome with its 2,165 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Lang, Elke; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. [Munk, Christine; Lapidus, Alla; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Han, Cliff; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Sims, David; Brettin, Thomas; Detter, John C.; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Munk, Christine; Tapia, Roxanne; Goodwin, Lynne; Meincke, Linda; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Djao, Olivier Duplex Ngatchou; Rohde, Manfred] Helmholtz Ctr Infect Res, HZI, Braunschweig, Germany. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Petra Aumann for growing S. autotrophica cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 36 TC 17 Z9 17 U1 1 U2 16 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 194 EP 202 DI 10.4056/sigs.1173118 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300011 PM 21304749 ER PT J AU Brambilla, E Djao, ODN Daligault, H Lapidus, A Lucas, S Hammon, N Nolan, M Tice, H Cheng, JF Han, C Tapia, R Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Spring, S Sikorski, J Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Brambilla, Evelyne Djao, Olivier Duplex Ngatchou Daligault, Hajnalka Lapidus, Alla Lucas, Susan Hammon, Nancy Nolan, Matt Tice, Hope Cheng, Jan-Fang Han, Cliff Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Spring, Stefan Sikorski, Johannes Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE obligately anaerobic; mesophilic; hydrogen; methane; Gram-negative; Methanomicrobiaceae; Euryarchaeota; GEBA ID SP-NOV; METHANOGENS; BACTERIA; HYDROGEN; ARCHAEA; COMPETITION; SYSTEM; GRAPHS AB Methanoplanus petrolearius Ollivier et al. 1998 is the type strain of the genus Methanoplanus. The strain was originally isolated from an offshore oil field from the Gulf of Guinea. Members of the genus Methanoplanus are of interest because they play an important role in the carbon cycle and also because of their significant contribution to the global warming by methane emission in the atmosphere. Like other archaea of the family Methanomicrobiales, the members of the genus Methanoplanus are able to use CO2 and H-2 as a source of carbon and energy; acetate is required for growth and probably also serves as carbon source. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Methanomicrobiaceae and the sixth complete genome sequence from the order Methanomicrobiales. The 2,843,290 bp long genome with its 2,824 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter] US DOE, Joint Genome Inst, Washington, DC 20585 USA. [Brambilla, Evelyne; Spring, Stefan; Sikorski, Johannes; Goeker, Markus] German Collect Microorganisms & Cell Cultures Gmb, DSMZ, Braunschweig, Germany. [Djao, Olivier Duplex Ngatchou; Rohde, Manfred] Helmholtz Ctr Infect Res, HZI, Braunschweig, Germany. [Daligault, Hajnalka; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), US DOE, Joint Genome Inst, Washington, DC 20585 USA. RI Spring, Stefan/N-6933-2013; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growing cultures of M. petrolearius. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 38 TC 7 Z9 10 U1 1 U2 8 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 2 BP 203 EP 211 DI 10.4056/sigs.1183143 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EA UT WOS:000290222300012 PM 21304750 ER PT J AU Gilbert, JA Meyer, F Jansson, J Gordon, J Pace, N Tiedje, J Ley, R Fierer, N Field, D Kyrpides, N Glockner, FO Klenk, HP Wommack, KE Glass, E Docherty, K Gallery, R Stevens, R Knight, R AF Gilbert, Jack A. Meyer, Folker Jansson, Janet Gordon, Jeff Pace, Norman Tiedje, James Ley, Ruth Fierer, Noah Field, Dawn Kyrpides, Nikos Gloeckner, Frank-Oliver Klenk, Hans-Peter Wommack, K. Eric Glass, Elizabeth Docherty, Kathryn Gallery, Rachel Stevens, Rick Knight, Rob TI The Earth Microbiome Project: Meeting report of the "1st EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6(th) 2010. SO STANDARDS IN GENOMIC SCIENCES LA English DT Article AB This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6(th) 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world. C1 [Gilbert, Jack A.; Meyer, Folker; Glass, Elizabeth; Stevens, Rick] Argonne Natl Lab, Argonne, IL 60439 USA. [Gilbert, Jack A.] Univ Chicago, Dept Ecol & Evolut, Chicago, IL 60637 USA. [Meyer, Folker] Univ Chicago, Computat Inst, Chicago, IL 60637 USA. [Jansson, Janet] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Earth Sci, Berkeley, CA 94720 USA. [Gordon, Jeff] Ctr Genome Sci & Syst Biol, St Louis, MO USA. [Pace, Norman; Fierer, Noah; Knight, Rob] UCB Boulder, Dept Chem & Biochem, Boulder, CO USA. [Tiedje, James] Michigan State Univ, Ctr Microbial Ecol, E Lansing, MI 48824 USA. [Ley, Ruth] Cornell Univ, Dept Microbiol, Ithaca, NY USA. [Field, Dawn] NERC Ctr Ecol & Hydrol, Oxford, England. [Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Gloeckner, Frank-Oliver] MPI Marine Microbiol, Bremen, Germany. [Klenk, Hans-Peter] DSMZ Deutsch Sammlung Mikroorganismen & Zellkultu, Braunschweig, Germany. [Wommack, K. Eric] Univ Delaware, Delaware Biotechnol Inst, Newark, DE USA. [Docherty, Kathryn; Gallery, Rachel] NEON, Boulder, CO USA. RP Gilbert, JA (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. RI Jansson, Janet/F-9951-2012; Ley, Ruth/M-8542-2014; Knight, Rob/D-1299-2010; Kyrpides, Nikos/A-6305-2014; OI Ley, Ruth/0000-0002-9087-1672; Kyrpides, Nikos/0000-0002-6131-0462; Meyer, Folker/0000-0003-1112-2284 FU U.S. Dept. of Energy [DE-AC02-06CH11357] FX We would like to thanks Argonne National Laboratory for hosting the meeting and Darlyn Mishur for organisation. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. NR 4 TC 76 Z9 78 U1 6 U2 41 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 3 BP 249 EP 253 DI 10.4056/sigs.1443528 PG 5 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EH UT WOS:000290223000002 PM 21304728 ER PT J AU Djao, ODN Zhang, XJ Lucas, S Lapidus, A Del Rio, TG Nolan, M Tice, H Cheng, JF Han, C Tapia, R Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Ovchinnikova, G Pati, A Brambilla, E Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Sikorski, J Spring, S Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Djao, Olivier Duplex Ngatchou Zhang, Xiaojing Lucas, Susan Lapidus, Alla Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Cheng, Jan-Fang Han, Cliff Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Ovchinnikova, Galina Pati, Amrita Brambilla, Evelyne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Sikorski, Johannes Spring, Stefan Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; motile; Gram-negative; syntrophism with methanogen; crotonate; butyrate; isobutyrate; Syntrophomonadaceae; GEBA ID SYNTROPHOMONAS-WOLFEI; SP-NOV; BACTERIA; ARCHAEA; DATABASE; SYSTEM; GRAPHS AB Syntrophothermus lipocalidus Sekiguchi et al. 2000 is the type species of the genus Syntrophothermus. The species is of interest because of its strictly anaerobic lifestyle, its participation in the primary step of the degradation of organic maters, and for releasing products which serve as substrates for other microorganisms. It also contributes significantly to maintain a regular pH in its environment by removing the fatty acids through beta-oxidation. The strain is able to metabolize isobutyrate and butyrate, which are the substrate and the product of degradation of the substrate, respectively. This is the first complete genome sequence of a member of the genus Syntrophothermus and the second in the family Syntrophomonadaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,405,559 bp long genome with its 2,385 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Brambilla, Evelyne; Sikorski, Johannes; Spring, Stefan; Goeker, Markus; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Djao, Olivier Duplex Ngatchou; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Zhang, Xiaojing; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne; Bristow, James; Eisen, Jonathan A.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Chang, Yun-Juan] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UTBattelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) in cultivation of the strain. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UTBattelle, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 36 TC 6 Z9 6 U1 1 U2 5 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 3 BP 267 EP 275 DI 10.4056/sigs.1233249 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EH UT WOS:000290223000003 PM 21304731 ER PT J AU Sun, H Spring, S Lapidus, A Davenport, K Del Rio, TG Tice, H Nolan, M Copeland, A Cheng, JF Lucas, S Tapia, R Goodwin, L Pitluck, S Ivanova, N Pagani, I Mavromatis, K Ovchinnikova, G Pati, A Chen, A Palaniappan, K Hauser, L Chang, YJ Jeffries, CD Detter, JC Han, C Rohde, M Brambilla, E Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Land, M AF Sun, Hui Spring, Stefan Lapidus, Alla Davenport, Karen Del Rio, Tijana Glavina Tice, Hope Nolan, Matt Copeland, Alex Cheng, Jan-Fang Lucas, Susan Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Pagani, Ionna Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Han, Cliff Rohde, Manfred Brambilla, Evelyne Goeker, Markus Woyke, Tanja Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Land, Miriam TI Complete genome sequence of Desulfarculus baarsii type strain (2st14(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE obligate anaerobic; sulfate reduction; Wood-Ljungdahl pathway; freshwater sediment; Deltaproteobacteria; Desulfarculaceae; GEBA ID SULFATE-REDUCING BACTERIA; CARBON-DIOXIDE; GENE; ARCHAEA; SYSTEM; CLASSIFICATION; IDENTIFICATION; GRAPHS; TOOL AB Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the genus Desulfarculus, which represents the family Desulfarculaceae and the order Desulfarculales. This species is a mesophilic sulfate-reducing bacterium with the capability to oxidize acetate and fatty acids of up to 18 carbon atoms completely to CO2. The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is used by this species for the complete oxidation of carbon sources and autotrophic growth on formate. The type strain 2st14(T) was isolated from a ditch sediment collected near the University of Konstanz, Germany. This is the first completed genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Spring, Stefan; Brambilla, Evelyne; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Sun, Hui; Lapidus, Alla; Davenport, Karen; Del Rio, Tijana Glavina; Tice, Hope; Nolan, Matt; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Pagani, Ionna; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Han, Cliff; Woyke, Tanja; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Land, Miriam] DOE Joint Genome Inst, Walnut Creek, CA USA. [Davenport, Karen; Tapia, Roxanne; Goodwin, Lynne; Detter, John C.; Han, Cliff] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Land, Miriam] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory; German Research Foundation (DFG) [INST 599/12] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growing cultures of D. baarsii. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract. German Research Foundation (DFG) supported DSMZ under INST 599/12. NR 39 TC 14 Z9 15 U1 0 U2 7 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 3 BP 276 EP 284 DI 10.4056/sigs.1243258 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EH UT WOS:000290223000004 PM 21304732 ER PT J AU Pitluck, S Yasawong, M Held, B Lapidus, A Nolan, M Copeland, A Lucas, S Del Rio, TG Tice, H Cheng, JF Chertkov, O Goodwin, L Tapia, R Han, C Liolios, K Ivanova, N Mavromatis, K Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Pukall, R Spring, S Rohde, M Sikorski, J Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Pitluck, Sam Yasawong, Montri Held, Brittany Lapidus, Alla Nolan, Matt Copeland, Alex Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Chertkov, Olga Goodwin, Lynne Tapia, Roxane Han, Cliff Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Pukall, Ruediger Spring, Stefan Rohde, Manfred Sikorski, Johannes Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; obligate amino-acid-degrading; Gram-negative; nonmotile; asaccharolytic; mesophilic; chemoorganotrophic; Synergistaceae; 'Synergistetes'; GEBA ID BACTERIA; ARCHAEA; IDENTIFICATION; DATABASE; GRAPHS; SYSTEM; TOOL AB Aminomonas paucivorans Baena et al. 1999 is the type species of the genus Aminomonas, which belongs to the family Synergistaceae. The species is of interest because it is an asac-charolytic chemoorganotrophic bacterium which ferments quite a number of amino acids. This is the first finished genome sequence ( with one gap in a rDNA region) of a member of the genus Aminomonas and the third sequence from the family Synergistaceae. The 2,630,120 bp long genome with its 2,433 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Pukall, Ruediger; Spring, Stefan; Sikorski, Johannes; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Pitluck, Sam; Held, Brittany; Lapidus, Alla; Nolan, Matt; Copeland, Alex; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Chertkov, Olga; Goodwin, Lynne; Tapia, Roxane; Han, Cliff; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Yasawong, Montri; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Held, Brittany; Chertkov, Olga; Goodwin, Lynne; Tapia, Roxane; Han, Cliff] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Spring, Stefan/N-6933-2013; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548] FX We would like to gratefully acknowledge the help of Katja Steenblock for growing A. paucivorans cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY. NR 26 TC 6 Z9 6 U1 1 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 3 BP 285 EP 293 DI 10.4056/sigs.1253298 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EH UT WOS:000290223000005 PM 21304733 ER PT J AU Del Rio, TG Chertkov, O Yasawong, M Lucas, S Deshpande, S Cheng, JF Detter, C Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Pukall, R Sikorski, J Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Del Rio, Tijana Glavina Chertkov, Olga Yasawong, Montri Lucas, Susan Deshpande, Shweta Cheng, Jan-Fang Detter, Chris Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Pukall, Ruediger Sikorski, Johannes Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Intrasporangium calvum type strain (7 KIPT) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE airborne; Gram-positive; non-motile; intercalary vesicles; nocardioform; Actinobacteria; Intrasporangiaceae; GEBA ID LL-DIAMINOPIMELIC ACID; CLASS ACTINOBACTERIA; BACTERIA; NOV; CLASSIFICATION; PROPOSAL; ARCHAEA; SYSTEM; ACTINOMYCETALES; IDENTIFICATION AB Intrasporangium calvum Kalakoutskii et al. 1967 is the type species of the genus Intrasporangium, which belongs to the actinobacterial family Intrasporangiaceae. The species is a Gram-positive bacterium that forms a branching mycelium, which tends to break into irregular fragments. The mycelium of this strain may bear intercalary vesicles but does not contain spores. The strain described in this study is an airborne organism that was isolated from a school dining room in 1967. One particularly interesting feature of I. calvum is that the type of its menaquinone is different from all other representatives of the family Intrasporangiaceae. This is the first completed genome sequence from a member of the genus Intrasporangium and also the first sequence from the family Intrasporangiaceae. The 4,024,382 bp long genome with its 3,653 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Del Rio, Tijana Glavina; Chertkov, Olga; Lucas, Susan; Deshpande, Shweta; Cheng, Jan-Fang; Detter, Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Detter, Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Yasawong, Montri; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Pukall, Ruediger; Sikorski, Johannes; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Lapidus, A (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2, SI 1352/1-2]; Thailand Research Fund Royal Golden Jubilee Ph.D. Program [PHD/0019/2548] FX We would like to gratefully acknowledge the help of Gabriele Gehrich-Schroter for growing I. calvum cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and SI 1352/1-2, and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548' for MY. NR 38 TC 1 Z9 3 U1 1 U2 1 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 3 BP 294 EP 303 DI 10.4056/sigs.1263355 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EH UT WOS:000290223000006 PM 21304734 ER PT J AU Sikorski, J Chertkov, O Lapidus, A Nolan, M Lucas, S Del Rio, TG Tice, H Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Brambilla, E Yasawong, M Rohde, M Pukall, R Spring, S Goeker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Sikorski, Johannes Chertkov, Olga Lapidus, Alla Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brambilla, Evelyne Yasawong, Montri Rohde, Manfred Pukall, Ruediger Spring, Stefan Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; none-motile; Gram-negative; 3-hydroxybutyrate; mesophilic; chemoorganotrophic; Fusobacteriaceae; GEBA ID SP-NOV; BACTERIA; ARCHAEA; IDENTIFICATION; FERMENTATION; DATABASE; SYSTEM; GRAPHS; TOOL AB Ilyobacter polytropus Stieb and Schink 1984 is the type species of the genus Ilyobacter, which belongs to the fusobacterial family Fusobacteriaceae. The species is of interest because its members are able to ferment quite a number of sugars and organic acids. I. polytropus has a broad versatility in using various fermentation pathways. Also, its members do not degrade poly-beta-hydroxybutyrate but only the monomeric 3-hydroxybutyrate. This is the first completed genome sequence of a member of the genus Ilyobacter and the second sequence from the family Fusobacteriaceae. The 3,132,314 bp long genome with its 2,934 protein-coding and 108 RNA genes consists of two chromosomes ( 2 and 1 Mbp long) and one plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Brambilla, Evelyne; Pukall, Ruediger; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chertkov, Olga; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Tapia, Roxane; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Yasawong, Montri; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Spring, Stefan/N-6933-2013; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2]; Thailand Research Fund Royal Golden Jubilee Ph. D. Program [PHD/0019/2548] FX We would like to gratefully acknowledge the help of Katja Steenblock (DSMZ) for growing I. polytropus cultures. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and Thailand Research Fund Royal Golden Jubilee Ph. D. Program No. PHD/0019/2548 for MY. NR 36 TC 5 Z9 8 U1 1 U2 3 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 3 BP 304 EP 314 DI 10.4056/sigs.1273360 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EH UT WOS:000290223000007 PM 21304735 ER PT J AU Anderson, I Djao, ODN Misra, M Chertkov, O Nolan, M Lucas, S Lapidus, A Del Rio, TG Tice, H Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Pati, A Brambilla, E Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Sikorski, J Spring, S Rohde, M Eichinger, K Huber, H Wirth, R Goker, M Detter, JC Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Anderson, Iain Djao, Olivier Duplex Ngatchou Misra, Monica Chertkov, Olga Nolan, Matt Lucas, Susan Lapidus, Alla Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Tapia, Roxanne Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Brambilla, Evelyne Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Sikorski, Johannes Spring, Stefan Rohde, Manfred Eichinger, Konrad Huber, Harald Wirth, Reinhard Goeker, Markus Detter, John C. Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Methanothermus fervidus type strain (V24S(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE hyperthermophile; strictly anaerobic; motile; Gram-positive; chemolithoautotroph; Methanothermaceae; Euryarchaeota; GEBA ID D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE; METHANOGENIC BACTERIA; SP-NOV; ARCHAEON; RNA; DATABASE; REVEALS; SYSTEM; GRAPHS AB Methanothermus fervidus Stetter 1982 is the type strain of the genus Methanothermus. This hyperthermophilic genus is of a thought to be endemic in Icelandic hot springs. M. fervidus was not only the first characterized organism with a maximal growth temperature ( 97 degrees C) close to the boiling point of water, but also the first archaeon in which a detailed functional analysis of its histone protein was reported and the first one in which the function of 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24S(T) is of interest because of its very low substrate ranges, it grows only on H-2 + CO2. This is the first completed genome sequence of the family Methanothermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,243,342 bp long genome with its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Anderson, Iain; Misra, Monica; Chertkov, Olga; Nolan, Matt; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Djao, Olivier Duplex Ngatchou; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Misra, Monica; Chertkov, Olga; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Brambilla, Evelyne; Sikorski, Johannes; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eichinger, Konrad; Huber, Harald; Wirth, Reinhard] Univ Regensburg, Archaeenzentrum, Regensburg, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Spring, Stefan/N-6933-2013; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1] FX This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1. NR 45 TC 6 Z9 24 U1 1 U2 9 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 3 BP 315 EP 324 DI 10.4056/sigs.1283367 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EH UT WOS:000290223000008 PM 21304736 ER PT J AU Sun, H Lapidus, A Nolan, M Lucas, S Del Rio, TG Tice, H Cheng, JF Tapia, R Han, C Goodwin, L Pitluck, S Pagani, I Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Djao, ODN Rohde, M Sikorski, J Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Sun, Hui Lapidus, Alla Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Tapia, Roxane Han, Cliff Goodwin, Lynne Pitluck, Sam Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Djao, Olivier Duplex Ngatchou Rohde, Manfred Sikorski, Johannes Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Gram-positive; aerobic; pathogen; mesophile; non alkaliphilic; zig-zag-shaped mycelium; actinomycetoma; conjunctivitis; cholangitis; Nocardiopsaceae; GEBA ID SP-NOV.; STREPTOMYCES-GRISEUS; BACTERIAL NAMES; APPROVED LISTS; SUBSP PRASINA; ACTINOMYCETE; PROPOSAL; CLASSIFICATION; IDENTIFICATION; ARCHAEA AB Nocardiopsis dassonvillei (Brocq-Rousseau 1904) Meyer 1976 is the type species of the genus Nocardiopsis, which in turn is the type genus of the family Nocardiopsaceae. This species is of interest because of its ecological versatility. Members of N. dassonvillei have been isolated from a large variety of natural habitats such as soil and marine sediments, from different plant and animal materials as well as from human patients. Moreover, representatives of the genus Nocardiopsis participate actively in biopolymer degradation. This is the first complete genome sequence in the family Nocardiopsaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,543,312 bp long genome consist of a 5.77 Mbp chromosome and a 0.78 Mbp plasmid and with its 5,570 protein-coding and 77 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Sun, Hui; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Tapia, Roxane; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Djao, Olivier Duplex Ngatchou; Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Marlen Jando for growing cultures of N. dassonvillei and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1. NR 56 TC 17 Z9 25 U1 0 U2 4 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 3 BP 325 EP 336 DI 10.4056/sigs.1363462 PG 12 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EH UT WOS:000290223000009 PM 21304737 ER PT J AU Han, C Gu, W Zhang, XJ Lapidus, A Nolan, M Copeland, A Lucas, S Del Rio, TG Tice, H Cheng, JF Tapia, R Goodwin, L Pitluck, S Pagani, I Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Schneider, S Rohde, M Goker, M Pukall, R Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Detter, JC AF Han, Cliff Gu, Wei Zhang, Xiaojing Lapidus, Alla Nolan, Matt Copeland, Alex Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Tapia, Roxane Goodwin, Lynne Pitluck, Sam Pagani, Ioanna Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Schneider, Susanne Rohde, Manfred Goeker, Markus Pukall, Ruediger Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Detter, John C. TI Complete genome sequence of Thermaerobacter marianensis type strain (7p75a(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly aerobic; none-motile; Gram-variable; thermophilic; chemoheterotrophic; deep-sea; family Incertae Sedis XVII; Clostridiales; GEBA ID THERMOPHILIC MARINE BACTERIUM; SP-NOV.; ARCHAEA; IDENTIFICATION; EUBACTERIA; PHYLOGENY; DATABASE; PROPOSAL; SYSTEM; GRAPHS AB Thermaerobacter marianensis Takai et al. 1999 is the type species of the genus Thermaerobacter, which belongs to the Clostridiales family Incertae Sedis XVII. The species is of special interest because T. marianensis is an aerobic, thermophilic marine bacterium, originally isolated from the deepest part in the western Pacific Ocean (Mariana Trench) at the depth of 10, 897 m. Interestingly, the taxonomic status of the genus has not been clarified until now. The genus Thermaerobacter may represent a very deep group within the Firmicutes or potentially a novel phylum. The 2,844,696 bp long genome with its 2,375 protein-coding and 60 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Schneider, Susanne; Goeker, Markus; Pukall, Ruediger; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Han, Cliff; Gu, Wei; Zhang, Xiaojing; Lapidus, Alla; Nolan, Matt; Copeland, Alex; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxane; Goodwin, Lynne; Pitluck, Sam; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Detter, John C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Han, Cliff; Gu, Wei; Zhang, Xiaojing; Tapia, Roxane; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Pagani, Ioanna/E-7390-2012; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle and Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Gabriele Gehrich-Schroter (DSMZ) for growing T. marianensis cultures. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 41 TC 5 Z9 6 U1 0 U2 10 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 3 IS 3 BP 337 EP 345 DI 10.4056/sigs.1373474 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759EH UT WOS:000290223000010 PM 21304738 ER PT J AU Foster, B Pukall, R Abt, B Nolan, M Del Rio, TG Chen, F Lucas, S Tice, H Pitluck, S Cheng, JF Chertkov, O Brettin, T Han, C Detter, JC Bruce, D Goodwin, L Ivanova, N Mavromatis, K Pati, A Mikhailova, N Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Chain, P Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Foster, Brian Pukall, Ruediger Abt, Birte Nolan, Matt Del Rio, Tijana Glavina Chen, Feng Lucas, Susan Tice, Hope Pitluck, Sam Cheng, Jan-Fang Chertkov, Olga Brettin, Thomas Han, Cliff Detter, John C. Bruce, David Goodwin, Lynne Ivanova, Natalia Mavromatis, Konstantinos Pati, Amrita Mikhailova, Natalia Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Chain, Patrick Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; Gram-positive; non-motile; cellulases; xylanases; Promicromonosporaceae; GEBA ID SYSTEM; BACTERIA; PROPOSAL; ARCHAEA AB Xylanimonas cellulosilytica Rivas et al. 2003 is the type species of the genus Xylanimonas of the actinobacterial family Promicromonosporaceae. The species X. cellulosilytica is of interest because of its ability to hydrolyze cellulose and xylan. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large family Promicromonosporaceae, and the 3,831,380 bp long genome (one chromosome plus an 88,604 bp long plasmid) with its 3485 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Foster, Brian; Nolan, Matt; Del Rio, Tijana Glavina; Chen, Feng; Lucas, Susan; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Brettin, Thomas; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Mikhailova, Natalia; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] DOE Joint Genome Inst, Walnut Creek, CA USA. [Pukall, Ruediger; Abt, Birte; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chertkov, Olga; Brettin, Thomas; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Chain, Patrick] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. RP Lapidus, A (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Chain, Patrick/0000-0003-3949-3634; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Gabriele Gehrich-Schroter for growing X. cellulosilytica cultures, and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. NR 16 TC 4 Z9 4 U1 1 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 1 EP 8 DI 10.4056/sigs.571102 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500001 PM 21304672 ER PT J AU Mavromatis, K Sikorski, J Lapidus, A Del Rio, TG Copeland, A Tice, H Cheng, JF Lucas, S Chen, F Nolan, M Bruce, D Goodwin, L Pitluck, S Ivanova, N Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Chain, P Meincke, L Sims, D Chertkov, O Han, C Brettin, T Detter, JC Wahrenburg, C Rohde, M Pukall, R Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Mavromatis, Konstantinos Sikorski, Johannes Lapidus, Alla Del Rio, Tijana Glavina Copeland, Alex Tice, Hope Cheng, Jan-Fang Lucas, Susan Chen, Feng Nolan, Matt Bruce, David Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Chain, Patrick Meincke, Linda Sims, David Chertkov, Olga Han, Cliff Brettin, Thomas Detter, John C. Wahrenburg, Claudia Rohde, Manfred Pukall, Ruediger Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE thermophile; acidophilic; aerobic; non-pathogenic; food spoilage; non-motile but encodes flagellar genes; GEBA ID POTASSIUM UPTAKE SYSTEM; BACILLUS-ACIDOCALDARIUS; FATTY-ACIDS; SP NOV.; FORMING BACTERIUM; ALPHA-AMYLASE; ORCHARD SOIL; SOUTH-AFRICA; PH; ACIDOTERRESTRIS AB Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family 'Alicyclobacillaceae'. A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family 'Alicyclobacillaceae'. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Mavromatis, Konstantinos; Lapidus, Alla; Del Rio, Tijana Glavina; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Meincke, Linda; Sims, David; Chertkov, Olga; Han, Cliff; Brettin, Thomas; Detter, John C.; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Wahrenburg, Claudia; Pukall, Ruediger; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Bruce, David; Goodwin, Lynne; Chain, Patrick; Meincke, Linda; Sims, David; Chertkov, Olga; Han, Cliff; Brettin, Thomas; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 53 TC 8 Z9 8 U1 1 U2 12 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 9 EP 18 DI 10.4056/sigs.591104 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500002 PM 21304673 ER PT J AU Ivanova, N Sikorski, J Jando, M Lapidus, A Nolan, M Lucas, S Del Rio, TG Tice, H Copeland, A Cheng, JF Chen, F Bruce, D Goodwin, L Pitluck, S Mavromatis, K Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Chain, P Saunders, E Han, C Detter, JC Brettin, T Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Ivanova, Natalia Sikorski, Johannes Jando, Marlen Lapidus, Alla Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Tice, Hope Copeland, Alex Cheng, Jan-Fang Chen, Feng Bruce, David Goodwin, Lynne Pitluck, Sam Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Chain, Patrick Saunders, Elizabeth Han, Cliff Detter, John C. Brettin, Thomas Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Gordonia bronchialis type strain (3410(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE obligate aerobic; human-pathogenic; endocarditis; Gram-positive; non-motile; Gordoniaceae; GEBA ID SP NOV.; GENUS RHODOCOCCUS; DESULFURIZING ACTINOMYCETE; RHODOCHROUS COMPLEX; PROPOSAL; CLASSIFICATION; SYSTEM; SOIL; ACTINOBACTERIA; ORGANISMS AB Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Ivanova, Natalia; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Saunders, Elizabeth; Han, Cliff; Detter, John C.; Brettin, Thomas; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Jando, Marlen; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Bruce, David; Goodwin, Lynne; Chain, Patrick; Saunders, Elizabeth; Han, Cliff; Detter, John C.; Brettin, Thomas] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. NR 48 TC 12 Z9 12 U1 1 U2 4 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 19 EP 28 DI 10.4056/sigs.611106 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500003 PM 21304674 ER PT J AU Nolan, M Sikorski, J Jando, M Lucas, S Lapidus, A Del Rio, TG Chen, F Tice, H Pitluck, S Cheng, JF Chertkov, O Sims, D Meincke, L Brettin, T Han, C Detter, JC Bruce, D Goodwin, L Land, M Hauser, L Chang, YJ Jeffries, CD Ivanova, N Mavromatis, K Mikhailova, N Chen, A Palaniappan, K Chain, P Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Nolan, Matt Sikorski, Johannes Jando, Marlen Lucas, Susan Lapidus, Alla Del Rio, Tijana Glavina Chen, Feng Tice, Hope Pitluck, Sam Cheng, Jan-Fang Chertkov, Olga Sims, David Meincke, Linda Brettin, Thomas Han, Cliff Detter, John C. Bruce, David Goodwin, Lynne Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Chen, Amy Palaniappan, Krishna Chain, Patrick Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Streptosporangium roseum type strain (NI 9100(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE sporangia; vegetative and aerial mycelia; aerobic; non-motile; non-motile spores; Gram-positive; Streptosporangiaceae; S. claviforme; GEBA ID GENUS STREPTOSPORANGIUM; COMB-NOV; PROPOSAL; SYSTEM; CLASSIFICATION; BACTERIA; ARCHAEA; SUBSP; SOIL AB Streptosporangium roseum Couch 1955 is the type strain of the species which is the type species of the genus Streptosporangium. The 'pinkish coiled Streptomyces-like organism with a spore case' was isolated from vegetable garden soil in 1955. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Streptosporangiaceae, and the second largest microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its 9,421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Jando, Marlen; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Nolan, Matt; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Sims, David; Meincke, Linda; Brettin, Thomas; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Chain, Patrick; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Sims, David; Meincke, Linda; Brettin, Thomas; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Chain, Patrick] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Chen, Amy; Palaniappan, Krishna; Chain, Patrick] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. NR 30 TC 14 Z9 26 U1 1 U2 9 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 29 EP 37 DI 10.4056/sigs.631049 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500004 PM 21304675 ER PT J AU Spring, S Nolan, M Lapidus, A Del Rio, TG Copeland, A Tice, H Cheng, JF Lucas, S Land, M Chen, F Bruce, D Goodwin, L Pitluck, S Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Hauser, L Chang, YJ Jeffries, CD Munk, C Kiss, H Chain, P Han, C Brettin, T Detter, JC Schuler, E Goker, M Rohde, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Spring, Stefan Nolan, Matt Lapidus, Alla Del Rio, Tijana Glavina Copeland, Alex Tice, Hope Cheng, Jan-Fang Lucas, Susan Land, Miriam Chen, Feng Bruce, David Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Munk, Christine Kiss, Hajnalka Chain, Patrick Han, Cliff Brettin, Thomas Detter, John C. Schueler, Esther Goeker, Markus Rohde, Manfred Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Desulfohalobium retbaense type strain (HR100T) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE sulfate-reducer; Gram-negative; mesophile; moderately halophilic; strictly anaerobic; hydrogen utilization; hypersaline lake; Desulfohalobiaceae; Deltaproteobacteria; Proteobacteria; GEBA ID SULFATE-REDUCING BACTERIUM; DESULFOVIBRIO-DESULFURICANS ATCC-27774; GREAT-SALT-LAKE; SP-NOV.; SYSTEM; OXIDOREDUCTASE; RESPIRATION; HALOPHILUS; ARCHAEA; BIOLOGY AB Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H-2 and a limited range of organic substrates, which are incompletely oxidized to acetate and CO2, for growth. The type strain HR100T was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Spring, Stefan; Schueler, Esther; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Nolan, Matt; Lapidus, Alla; Del Rio, Tijana Glavina; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Land, Miriam; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Munk, Christine; Kiss, Hajnalka; Chain, Patrick; Han, Cliff; Brettin, Thomas; Detter, John C.; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Bruce, David; Goodwin, Lynne; Munk, Christine; Kiss, Hajnalka; Chain, Patrick; Han, Cliff; Brettin, Thomas; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna] Lawrence Livermore Natl Lab, Livermore, CA USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Chain, Patrick/0000-0003-3949-3634; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory; German Research Foundation (DFG); DSMZ [INST 599/1-1] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract. German Research Foundation (DFG) supported DSMZ under INST 599/1-1. NR 35 TC 8 Z9 8 U1 1 U2 8 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 38 EP 48 DI 10.4056/sigs.581048 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500005 PM 21304676 ER PT J AU Pati, A LaButti, K Pukall, R Nolan, M Del Rio, TG Tice, H Cheng, JF Lucas, S Chen, F Copeland, A Ivanova, N Mavromatis, K Mikhailova, N Pitluck, S Bruce, D Goodwin, L Land, M Hauser, L Chang, YJ Jeffries, CD Chen, A Palaniappan, K Chain, P Brettin, T Sikorski, J Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lapidus, A AF Pati, Amrita LaButti, Kurt Pukall, Ruediger Nolan, Matt Del Rio, Tijana Glavina Tice, Hope Cheng, Jan-Fang Lucas, Susan Chen, Feng Copeland, Alex Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pitluck, Sam Bruce, David Goodwin, Lynne Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Chen, Amy Palaniappan, Krishna Chain, Patrick Brettin, Thomas Sikorski, Johannes Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lapidus, Alla TI Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Sphaerobacteridae; Thermomicrobia; thermophile; obligate aerobic; sewage sludge isolate; pleomorphic; non-motile; non-sporeforming; GEBA ID BACTERIA; SYSTEM; ACTINOBACTERIA; PROPOSAL; ARCHAEA; SLUDGE; NOV AB Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of the genus Sphaerobacter, which is the type genus of the family Sphaerobacteraceae, the order Sphaerobacterales and the subclass Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome of strain S 6022(T) is described which is an obligate aerobe that was originally isolated from an aerated laboratory-scale fermentor that was pulse fed with municipal sewage sludge. We describe the features of this organism, together with the complete genome and annotation. This is the first complete genome sequence of the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Pati, Amrita; LaButti, Kurt; Nolan, Matt; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Copeland, Alex; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pitluck, Sam; Bruce, David; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chen, Amy; Chain, Patrick; Brettin, Thomas; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lapidus, Alla] DOE Joint Genome Inst, Walnut Creek, CA USA. [Pukall, Ruediger; Sikorski, Johannes; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Bruce, David; Goodwin, Lynne; Chain, Patrick; Brettin, Thomas] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. RP Lapidus, A (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634; FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Gabriele Gehrich-Schroter for growing S. thermophilus cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. NR 23 TC 10 Z9 10 U1 1 U2 6 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 49 EP 56 DI 10.4056/sigs.601105 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500006 PM 21304677 ER PT J AU Gronow, S Welnitz, S Lapidus, A Nolan, M Ivanova, N Del Rio, TG Copeland, A Chen, F Tice, H Pitluck, S Cheng, JF Saunders, E Brettin, T Han, C Detter, JC Bruce, D Goodwin, L Land, M Hauser, L Chang, YJ Jeffries, CD Pati, A Mavromatis, K Mikhailova, N Chen, A Palaniappan, K Chain, P Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lucas, S AF Gronow, Sabine Welnitz, Sabine Lapidus, Alla Nolan, Matt Ivanova, Natalia Del Rio, Tijana Glavina Copeland, Alex Chen, Feng Tice, Hope Pitluck, Sam Cheng, Jan-Fang Saunders, Elizabeth Brettin, Thomas Han, Cliff Detter, John C. Bruce, David Goodwin, Lynne Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Pati, Amrita Mavromatis, Konstantinos Mikhailova, Natalia Chen, Amy Palaniappan, Krishna Chain, Patrick Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lucas, Susan TI Complete genome sequence of Veillonella parvula type strain (Te3(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE opportunistic infections; human oral microflora; dental plaque; intergeneric coaggregation; methylmalonyl-CoA decarboxylase; Veillonellaceae ID BACTERIA; SYSTEM; SELENOMONAS; DIVERSITY; ARCHAEA; NOV. AB Veillonella parvula (Veillon and Zuber 1898) Prevot 1933 is the type species of the genus Veillonella in the family Veillonellaceae within the order Clostridiales. The species V. parvula is of interest because it is frequently isolated from dental plaque in the human oral cavity and can cause opportunistic infections. The species is strictly anaerobic and grows as small cocci which usually occur in pairs. Veillonellae are characterized by their unusual metabolism which is centered on the activity of the enzyme methylmalonyl-CoA decarboxylase. Strain Te3(T), the type strain of the species, was isolated from the human intestinal tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large clostridial family Veillonellaceae, and the 2,132,142 bp long single replicon genome with its 1,859 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Lapidus, Alla; Nolan, Matt; Ivanova, Natalia; Del Rio, Tijana Glavina; Copeland, Alex; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Saunders, Elizabeth; Brettin, Thomas; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Pati, Amrita; Mavromatis, Konstantinos; Mikhailova, Natalia; Chain, Patrick; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lucas, Susan] DOE Joint Genome Inst, Walnut Creek, CA USA. [Gronow, Sabine; Welnitz, Sabine; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Saunders, Elizabeth; Brettin, Thomas; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Chain, Patrick] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Chen, Amy; Palaniappan, Krishna] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Chain, Patrick/0000-0003-3949-3634; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. NR 41 TC 7 Z9 7 U1 1 U2 7 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 57 EP 65 DI 10.4056/sigs.521107 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500007 PM 21304678 ER PT J AU Reeve, W O'Hara, G Chain, P Ardley, J Brau, L Nandesena, K Tiwari, R Malfatti, S Kiss, H Lapidus, A Copeland, A Nolan, M Land, M Ivanova, N Mavromatis, K Markowitz, V Kyrpides, N Melino, V Denton, M Yates, R Howieson, J AF Reeve, Wayne O'Hara, Graham Chain, Patrick Ardley, Julie Braeu, Lambert Nandesena, Kemanthi Tiwari, Ravi Malfatti, Stephanie Kiss, Hajnalka Lapidus, Alla Copeland, Alex Nolan, Matt Land, Miriam Ivanova, Natalia Mavromatis, Konstantinos Markowitz, Victor Kyrpides, Nikos Melino, Vanessa Denton, Matthew Yates, Ron Howieson, John TI Complete genome sequence of Rhizobium leguminosarum bv trifolii strain WSM2304, an effective microsymbiont of the South American clover Trifolium polymorphum SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE microsymbiont; non-pathogenic; aerobic; Gram-negative rod; root-nodule bacteria; nitrogen fixation; Alphaproteobacteria ID BIOVAR TRIFOLII; SELECTION; SPP.; NODULATION; SYMBIOSIS; REVISION; BACTERIA; SYSTEM; TOOL AB Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a diverse range of annual and perennial Trifolium (clover) species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative rod, isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont predominated in the perennial grasslands of Glencoe Research Station, in Uruguay, to competitively nodulate its host, and fix atmospheric nitrogen. Here we describe the basic features of WSM2304, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a nitrogen fixing microsymbiont of a clover species from the American center of origin. We reveal that its genome size is 6,872,702 bp encoding 6,643 protein-coding genes and 62 RNA only encoding genes. This multipartite genome was found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four circular plasmids of size 1,266,105 bp, 501,946 bp, 308,747 bp and 257,956 bp. C1 [Reeve, Wayne; O'Hara, Graham; Ardley, Julie; Braeu, Lambert; Nandesena, Kemanthi; Tiwari, Ravi; Melino, Vanessa; Yates, Ron; Howieson, John] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Chain, Patrick; Malfatti, Stephanie; Kiss, Hajnalka; Lapidus, Alla; Copeland, Alex; Nolan, Matt; Land, Miriam; Ivanova, Natalia; Mavromatis, Konstantinos; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chain, Patrick; Malfatti, Stephanie; Kiss, Hajnalka] Lawrence Livermore Natl Lab, Livermore, CA USA. [Land, Miriam] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. RI Denton, Matthew/D-9697-2011; Melino, Vanessa/B-1920-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; OI Melino, Vanessa/0000-0003-2742-5079; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Denton, Matthew/0000-0002-2804-0384; Ivanova, Natalia/0000-0002-5802-9485 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Crop and Plant Research Institute (CaPRI); Grains Research and Development Corporation (GRDC) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We thank Gordon Thompson (Murdoch University) for the preparation of SEM and TEM photos. We gratefully acknowledge the funding received from Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI), and the Grains Research and Development Corporation (GRDC), to support the National Rhizobium Program (NRP) and the Centre for Rhizobium Studies (CRS) at Murdoch University. NR 34 TC 20 Z9 20 U1 1 U2 17 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 66 EP 76 DI 10.4056/sigs.44642 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500008 PM 21304679 ER PT J AU Reeve, W Chain, P O'Hara, G Ardley, J Nandesena, K Breu, L Tiwari, R Malfatti, S Kiss, H Lapidus, A Copeland, A Nolan, M Land, M Hauser, L Chang, YJ Ivanova, N Mavromatis, K Markowitz, V Kyrpides, N Gollagher, M Yates, R Dilworth, M Howieson, J AF Reeve, Wayne Chain, Patrick O'Hara, Graham Ardley, Julie Nandesena, Kemanthi Braeu, Lambert Tiwari, Ravi Malfatti, Stephanie Kiss, Hajnalka Lapidus, Alla Copeland, Alex Nolan, Matt Land, Miriam Hauser, Loren Chang, Yun-Juan Ivanova, Natalia Mavromatis, Konstantinos Markowitz, Victor Kyrpides, Nikos Gollagher, Margaret Yates, Ron Dilworth, Michael Howieson, John TI Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419 SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE microsymbiont; non-pathogenic; aerobic; Gram-negative rod; root-nodule bacteria; nitrogen fixation; Alphaproteobacteria ID ADHAERENS CASIDA 1982; RHIZOBIUM-MELILOTI; ACID TOLERANCE; ROOT-NODULE; SP-NOV; GENE; TOOL; FIXATION; BACTERIA; PROPOSAL AB Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in Australia as an inoculant for annual medics during 1985 to 1993 due to its nitrogen fixation, saprophytic competence and acid tolerance properties. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first report of a complete genome sequence for a microsymbiont of the group of annual medic species adapted to acid soils. We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding genes and 81 RNA only encoding genes. The genome contains a chromosome of size 3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp. The smallest plasmid is a feature unique to this medic microsymbiont. C1 [Reeve, Wayne; O'Hara, Graham; Ardley, Julie; Nandesena, Kemanthi; Braeu, Lambert; Tiwari, Ravi; Yates, Ron; Dilworth, Michael; Howieson, John] Murdoch Univ, Ctr Rhizobium Studies, Perth, WA, Australia. [Chain, Patrick; Malfatti, Stephanie; Kiss, Hajnalka; Lapidus, Alla; Copeland, Alex; Nolan, Matt; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Ivanova, Natalia; Mavromatis, Konstantinos; Kyrpides, Nikos] DOE Joint Genome Inst, Walnut Creek, CA USA. [Chain, Patrick; Malfatti, Stephanie; Kiss, Hajnalka] Lawrence Livermore Natl Lab, Livermore, CA USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Gollagher, Margaret] Murdoch Univ, Inst Sustainabil & Technol Policy, Perth, WA, Australia. [Yates, Ron; Howieson, John] Dept Agr & Food, S Perth, WA, Australia. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Perth, WA, Australia. RI Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Crop and Plant Research Institute (CaPRI); Grains Research and Development Corporation (GRDC) FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We would like to gratefully acknowledge the funding received from Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI), and the Grains Research and Development Corporation (GRDC), to support the National Rhizobium Program (NRP) and the Centre for Rhizobium Studies (CRS) at Murdoch University. NR 48 TC 33 Z9 33 U1 1 U2 12 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 77 EP 86 DI 10.4506/sigs.43526 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500009 PM 21304680 ER PT J AU Del Rio, TG Abt, B Spring, S Lapidus, A Nolan, M Tice, H Copeland, A Cheng, JF Chen, F Bruce, D Goodwin, L Pitluck, S Ivanova, N Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Chain, P Saunders, E Detter, JC Brettin, T Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Lucas, S AF Del Rio, Tijana Glavina Abt, Birte Spring, Stefan Lapidus, Alla Nolan, Matt Tice, Hope Copeland, Alex Cheng, Jan-Fang Chen, Feng Bruce, David Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Chain, Patrick Saunders, Elizabeth Detter, John C. Brettin, Thomas Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Lucas, Susan TI Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE filamentous; gliding; myxospores; aerobic; mesophile; Gram-negative; biomass degrader; chitinolytic; 'Chitinophagaceae'; GEBA ID SP-NOV.; SOIL; BACTERIA; ARCHAEA; SYSTEM; GENUS AB Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is the type species of the rapidly growing genus Chitinophaga in the sphingobacterial family 'Chitinophagaceae'. Members of the genus Chitinophaga vary in shape between filaments and spherical bodies without the production of a fruiting body, produce myxospores, and are of special interest for their ability to degrade chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family 'Chitinophagaceae', and the 9,127,347 bp long single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Abt, Birte; Spring, Stefan; Chain, Patrick; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Del Rio, Tijana Glavina; Lapidus, Alla; Nolan, Matt; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Brettin, Thomas; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Lucas, Susan] DOE Joint Genome Inst, Walnut Creek, CA USA. [Bruce, David; Goodwin, Lynne; Chain, Patrick; Saunders, Elizabeth; Detter, John C.; Brettin, Thomas] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. Lawrence Livermore Natl Lab, Livermore, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Chain, Patrick/0000-0003-3949-3634 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Birgit Merkhoffer for growing C. pinensis cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. NR 24 TC 23 Z9 23 U1 1 U2 14 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 87 EP 95 DI 10.4056/sigs.661199 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500010 ER PT J AU Ivanova, N Daum, C Lang, E Abt, B Kopitz, M Saunders, E Lapidus, A Lucas, S Del Rio, TG Nolan, M Tice, H Copeland, A Cheng, JF Chen, F Bruce, D Goodwin, L Pitluck, S Mavromatis, K Pati, A Mikhailova, N Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Brettin, T Rohde, M Goker, M Bristow, J Markowitz, V Eisen, JA Hugenholtz, P Kyrpides, NC Klenk, HP AF Ivanova, Natalia Daum, Chris Lang, Elke Abt, Birte Kopitz, Markus Saunders, Elizabeth Lapidus, Alla Lucas, Susan Del Rio, Tijana Glavina Nolan, Matt Tice, Hope Copeland, Alex Cheng, Jan-Fang Chen, Feng Bruce, David Goodwin, Lynne Pitluck, Sam Mavromatis, Konstantinos Pati, Amrita Mikhailova, Natalia Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Brettin, Thomas Rohde, Manfred Goeker, Markus Bristow, Jim Markowitz, Victor Eisen, Jonathan A. Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Haliangium ochraceum type strain (SMP-2(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; gliding; myxobacteria; fruiting bodies; moderately halophilic; mesophile; Gram-negative; decomposition of bacterial and yeast cells; Myxococcales; GEBA ID GEN. NOV.; SORANGIUM-CELLULOSUM; MYXOBACTERIA; PATTERNS; BACTERIA; DOMAINS; ARCHAEA; SYSTEM; JAPAN AB Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family 'Haliangiaceae'. Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast cells as most myxobacteria do. The fruiting bodies contain particularly small coccoid myxospores. H. ochraceum encodes the first actin homologue identified in a bacterial genome. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Lang, Elke; Abt, Birte; Kopitz, Markus; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Ivanova, Natalia; Daum, Chris; Lapidus, Alla; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Pati, Amrita; Mikhailova, Natalia; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Brettin, Thomas; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Saunders, Elizabeth; Bruce, David; Goodwin, Lynne; Detter, John C.; Brettin, Thomas] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. NR 39 TC 24 Z9 29 U1 3 U2 17 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 96 EP 106 DI 10.4056/sigs.69.1277 PG 11 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500011 PM 21304682 ER PT J AU Saunders, E Tindall, BJ Fahnrich, R Lapidus, A Copeland, A Del Rio, TG Lucas, S Chen, F Tice, H Cheng, JF Han, C Detter, JC Bruce, D Goodwin, L Chain, P Pitluck, S Pati, A Ivanova, N Mavromatis, K Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Brettin, T Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Saunders, Elisabeth Tindall, Brian J. Faehnrich, Regine Lapidus, Alla Copeland, Alex Del Rio, Tijana Glavina Lucas, Susan Chen, Feng Tice, Hope Cheng, Jan-Fang Han, Cliff Detter, John C. Bruce, David Goodwin, Lynne Chain, Patrick Pitluck, Sam Pati, Amrita Ivanova, Natalia Mavromatis, Konstantinos Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brettin, Thomas Rohde, Manfred Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Haloterrigena turkmenica type strain (4k(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE extreme halophile; thermophile; free-living; aerobic; non-pathogenic; carotenoids-containing; Halobacteriaceae; GEBA ID RIBOSOMAL-RNA GENE; FAMILY HALOBACTERIACEAE; NATRONOBACTERIUM-PHARAONIS; NATRONOMONAS-PHARAONIS; HALOPHILIC ARCHAEA; SALT LAKE; SP-NOV.; NATRIALBA; BACTERIA; PROPOSAL AB Haloterrigena turkmenica (Zvyagintseva and Tarasov 1987) Ventosa et al. 1999, comb. nov. is the type species of the genus Haloterrigena in the euryarchaeal family Halobacteriaceae. It is of phylogenetic interest because of the yet unclear position of the genera Haloterrigena and Natrinema within the Halobacteriaceae, which created some taxonomic problems historically. H. turkmenica, was isolated from sulfate saline soil in Turkmenistan, is a relatively fast growing, chemoorganotrophic, carotenoid-containing, extreme halophile, requiring at least 2 M NaCl for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Haloterrigena, but the eighth genome sequence from a member of the family Halobacteriaceae. The 5,440,782 bp genome (including six plasmids) with its 5,287 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Saunders, Elisabeth; Lapidus, Alla; Copeland, Alex; Del Rio, Tijana Glavina; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Chain, Patrick; Pitluck, Sam; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] DOE Joint Genome Inst, Walnut Creek, CA USA. [Saunders, Elisabeth; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Chain, Patrick] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Tindall, Brian J.; Faehnrich, Regine; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Rohde, Manfred] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis Genome Ctr, Davis, CA USA. RP Kyrpides, NC (reprint author), DOE Joint Genome Inst, Walnut Creek, CA USA. RI chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Chain, Patrick/0000-0003-3949-3634; FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1. NR 37 TC 15 Z9 26 U1 1 U2 5 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 1 BP 107 EP 116 DI 10.4056/sigs.68923 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759CZ UT WOS:000290219500012 PM 21304683 ER PT J AU Sikorski, J Lapidus, A Copeland, A Del Rio, TG Nolan, M Lucas, S Chen, F Tice, H Cheng, JF Saunders, E Bruce, D Goodwin, L Pitluck, S Ovchinnikova, G Pati, A Ivanova, N Mavromatis, K Chen, A Palaniappan, K Chain, P Land, M Hauser, L Chang, YJ Jeffries, CD Brettin, T Detter, JC Han, C Rohde, M Lang, E Spring, S Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Sikorski, Johannes Lapidus, Alla Copeland, Alex Del Rio, Tijana Glavina Nolan, Matt Lucas, Susan Chen, Feng Tice, Hope Cheng, Jan-Fang Saunders, Elizabeth Bruce, David Goodwin, Lynne Pitluck, Sam Ovchinnikova, Galina Pati, Amrita Ivanova, Natalia Mavromatis, Konstantinos Chen, Amy Palaniappan, Krishna Chain, Patrick Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brettin, Thomas Detter, John C. Han, Cliff Rohde, Manfred Lang, Elke Spring, Stefan Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Sulfurospirillum deleyianum type strain (5175(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; microaerobic; sulfur reduction; dissimilatory nitrate reduction; Gram-negative; motile; Campylobacteraceae; GEBA ID C NITRITE REDUCTASE; MICROBIAL SULFUR RESPIRATION; SP NOV.; SPIRILLUM-5175; BACTERIUM; PURIFICATION; ORGANISMS; PROPOSAL; ARCHAEA; AMMONIA AB Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus Sulfurospirillum. S. deleyianum is a model organism for studying sulfur reduction and dissimilatory nitrate reduction as an energy source for growth. Also, it is a prominent model organism for studying the structural and functional characteristics of cytochrome c nitrite reductase. Here, we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the genus Sulfurospirillum. The 2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Lang, Elke; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lapidus, Alla; Copeland, Alex; Del Rio, Tijana Glavina; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Saunders, Elizabeth; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chain, Patrick; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Detter, John C.; Han, Cliff; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Bruce, David; Goodwin, Lynne; Brettin, Thomas; Detter, John C.; Han, Cliff] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Chain, Patrick] Lawrence Livermore Natl Lab, Livermore, CA USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California; Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Petra Aumann in cultivation of the strain and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 35 TC 15 Z9 15 U1 1 U2 11 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 2 BP 149 EP 157 DI 10.4056/sigs.671209 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DD UT WOS:000290219900001 PM 21304697 ER PT J AU Ivanova, N Sikorski, J Jando, M Munk, C Lapidus, A Del Rio, TG Copeland, A Tice, H Cheng, JF Lucas, S Chen, F Nolan, M Bruce, D Goodwin, L Pitluck, S Mavromatis, K Mikhailova, N Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Meincke, L Brettin, T Detter, JC Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Ivanova, Natalia Sikorski, Johannes Jando, Marlen Munk, Christine Lapidus, Alla Del Rio, Tijana Glavina Copeland, Alex Tice, Hope Cheng, Jan-Fang Lucas, Susan Chen, Feng Nolan, Matt Bruce, David Goodwin, Lynne Pitluck, Sam Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Meincke, Linda Brettin, Thomas Detter, John C. Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Geodermatophilus obscurus type strain (G-20(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; non-pathogenic; soil and rock varnish; morphogenetic growth cycle of C-form and R-form; Frankineae; Actinobacteria; GEBA ID PHYLOGENETIC ANALYSIS; FAMILY FRANKIACEAE; ROCK-VARNISH; BACTERIA; GENUS; IDENTIFICATION; SYSTEM; DERMATOPHILACEAE; BLASTOCOCCUS; MOUNTAINS AB Geodermatophilus obscurus Luedemann 1968 is the type species of the genus, which is the type genus of the family Geodermatophilaceae. G. obscurus is of interest as it has frequently been isolated from stressful environments such as rock varnish in deserts, and as it exhibits interesting phenotypes such as lytic capability of yeast cell walls, UV-C resistance, strong production of extracellular functional amyloid (FuBA) and manganese oxidation. This is the first completed genome sequence of the family Geodermatophilaceae. The 5,322,497 bp long genome with its 5,161 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Jando, Marlen; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Ivanova, Natalia; Lapidus, Alla; Del Rio, Tijana Glavina; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Meincke, Linda; Brettin, Thomas; Detter, John C.; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Munk, Christine; Bruce, David; Goodwin, Lynne; Meincke, Linda; Brettin, Thomas; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. Lawrence Livermore Natl Lab, Livermore, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California; Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 42 TC 35 Z9 36 U1 2 U2 16 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 2 BP 158 EP 167 DI 10.4056/sigs.711311 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DD UT WOS:000290219900002 PM 21304698 ER PT J AU Tice, H Mayilraj, S Sims, D Lapidus, A Nolan, M Lucas, S Del Rio, TG Copeland, A Cheng, JF Meincke, L Bruce, D Goodwin, L Pitluck, S Ivanova, N Mavromatis, K Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Brettin, T Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Chen, F AF Tice, Hope Mayilraj, Shanmugam Sims, David Lapidus, Alla Nolan, Matt Lucas, Susan Del Rio, Tijana Glavina Copeland, Alex Cheng, Jan-Fang Meincke, Linda Bruce, David Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Brettin, Thomas Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Chen, Feng TI Complete genome sequence of Nakamurella multipartita type strain (Y-104(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE polysaccharide-accumulating; septa-forming; nonmotile; Gram-positive; MK-8 (H-4); 'Microsphaeraceae'; Frankineae; GEBA ID PROPOSAL; SYSTEM; NOV; BACTERIA; ARCHAEA AB Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the monospecific genus Nakamurella in the actinobacterial suborder Frankineae. The nonmotile, coccus-shaped strain was isolated from activated sludge acclimated with sugar-containing synthetic wastewater, and is capable of accumulating large amounts of polysaccharides in its cells. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Mayilraj, Shanmugam; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Tice, Hope; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Copeland, Alex; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Brettin, Thomas; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Chen, Feng] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Mayilraj, Shanmugam] MTCC, Inst Microbial Technol, Chandigarh, India. [Sims, David; Meincke, Linda; Bruce, David; Goodwin, Lynne; Detter, John C.; Brettin, Thomas; Markowitz, Victor] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1]; Indian Council of Scientific and Industrial Research FX We would like to gratefully acknowledge the help of Marlen Jando for growing N. multipartita cells, and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and the Indian Council of Scientific and Industrial Research provided a Raman Research Fellow to Shanmugam Mayilraj. NR 24 TC 13 Z9 13 U1 5 U2 20 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 2 BP 168 EP 175 DI 10.4056/sigs.721316 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DD UT WOS:000290219900003 PM 21304699 ER PT J AU Lail, K Sikorski, J Saunders, E Lapidus, A Del Rio, TG Copeland, A Tice, H Cheng, JF Lucas, S Nolan, M Bruce, D Goodwin, L Pitluck, S Ivanova, N Mavromatis, K Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Chain, P Brettin, T Detter, JC Schutze, A Rohde, M Tindall, BJ Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klen, HP Chen, F AF Lail, Kathleen Sikorski, Johannes Saunders, Elizabeth Lapidus, Alla Del Rio, Tijana Glavina Copeland, Alex Tice, Hope Cheng, Jan-Fang Lucas, Susan Nolan, Matt Bruce, David Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Chain, Patrick Brettin, Thomas Detter, John C. Schuetze, Andrea Rohde, Manfred Tindall, Brian J. Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klen, Hans-Peter Chen, Feng TI Complete genome sequence of Spirosoma linguale type strain (1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE psychroactive; oligotrophic; aerobic; ringlike morphology; non-pathogenic; free-living; Cytophagaceae; GEBA ID SP NOV.; GENUS SPIROSOMA; BACTERIAL NAMES; FLECTOBACILLUS; PROPOSAL; ARCHAEA; SYSTEM; SOIL AB Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living and non-pathogenic organism, known for its peculiar ringlike and horseshoe-shaped cell morphology. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the third completed genome sequence of a member of the family Cytophagaceae. The 8,491,258 bp long genome with its eight plasmids, 7,069 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Lail, Kathleen; Lapidus, Alla; Del Rio, Tijana Glavina; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Brettin, Thomas; Detter, John C.; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Chen, Feng] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Schuetze, Andrea; Tindall, Brian J.; Goeker, Markus; Klen, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Saunders, Elizabeth; Bruce, David; Goodwin, Lynne; Brettin, Thomas; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Chain, Patrick] Lawrence Livermore Natl Lab, Livermore, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Kyrpides, NC (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 32 TC 11 Z9 11 U1 2 U2 7 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 2 BP 176 EP 185 DI 10.4056/sigs.741334 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DD UT WOS:000290219900004 PM 21304700 ER PT J AU Pukall, R Lapidus, A Del Rio, TG Copeland, A Tice, H Cheng, JF Lucas, S Chen, F Nolan, M LaButti, K Pati, A Ivanova, N Mavromatis, K Mikhailova, N Pitluck, S Bruce, D Goodwin, L Land, M Hauser, L Chang, YJ Jeffries, CD Chen, A Palaniappan, K Chain, P Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Brettin, T AF Pukall, Ruediger Lapidus, Alla Del Rio, Tijana Glavina Copeland, Alex Tice, Hope Cheng, Jan-Fang Lucas, Susan Chen, Feng Nolan, Matt LaButti, Kurt Pati, Amrita Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pitluck, Sam Bruce, David Goodwin, Lynne Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Chen, Amy Palaniappan, Krishna Chain, Patrick Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Brettin, Thomas TI Complete genome sequence of Kribbella flavida type strain (IFO 14399(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Actinobacteria; aerobic; soil; mycelia; LL-diaminopimelic acid; Propionibacterineae; Nocardioidaceae; GEBA ID SYSTEM; CLASSIFICATION; BACTERIA; PROPOSAL; ARCHAEA; NOV AB The genus Kribbella consists of 15 species, with Kribbella flavida (Park et al. 1999) as the type species. The name Kribbella was formed from the acronym of the Korea Research Institute of Bioscience and Biotechnology, KRIBB. Strains of the various Kribbella species were originally isolated from soil, potato, alum slate mine, patinas of catacombs or from horse racecourses. Here we describe the features of K. flavida together with the complete genome sequence and annotation. In addition to the 5.3 Mbp genome of Nocardioides sp. JS614, this is only the second completed genome sequence of the family Nocardioidaceae. The 7,579,488 bp long genome with its 7,086 protein-coding and 60 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Pukall, Ruediger; Goeker, Markus; Eisen, Jonathan A.; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lapidus, Alla; Del Rio, Tijana Glavina; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; LaButti, Kurt; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pitluck, Sam; Bruce, David; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Bristow, Jim; Hugenholtz, Philip; Kyrpides, Nikos C.; Brettin, Thomas] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Bruce, David; Goodwin, Lynne; Chain, Patrick; Brettin, Thomas] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Land, Miriam/A-6200-2011; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Kyrpides, Nikos/A-6305-2014 OI Chain, Patrick/0000-0003-3949-3634; Land, Miriam/0000-0001-7102-0031; Lapidus, Alla/0000-0003-0427-8731; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Katja Steenblock for growing K. flavida cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 20 TC 4 Z9 4 U1 1 U2 4 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 2 BP 186 EP 193 DI 10.4056/sigs.731321 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DD UT WOS:000290219900005 PM 21304701 ER PT J AU Wirth, R Sikorski, J Brambilla, E Misra, M Lapidus, A Copeland, A Nolan, M Lucas, S Chen, F Tice, H Cheng, JF Han, C Detter, JC Tapia, R Bruce, D Goodwin, L Pitluck, S Pati, A Anderson, I Ivanova, N Mavromatis, K Mikhailova, N Chen, A Palaniappan, K Bilek, Y Hader, T Land, M Hauser, L Chang, YJ Jeffries, CD Tindall, BJ Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Wirth, Reinhard Sikorski, Johannes Brambilla, Evelyne Misra, Monica Lapidus, Alla Copeland, Alex Nolan, Matt Lucas, Susan Chen, Feng Tice, Hope Cheng, Jan-Fang Han, Cliff Detter, John C. Tapia, Roxane Bruce, David Goodwin, Lynne Pitluck, Sam Pati, Amrita Anderson, Iain Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Chen, Amy Palaniappan, Krishna Bilek, Yvonne Hader, Thomas Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Tindall, Brian J. Rohde, Manfred Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Thermocrinis albus type strain (HI 11/12(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE microaerophilic; (hyper-)thermophile; chemolithoautotrophic; biogeochemistry; non-sporeforming; Gram-negative; flagellated; non-pathogen; Aquificaceae; GEBA ID HYDROGEN-OXIDIZING BACTERIUM; PHYLOGENETIC ANALYSIS; AQUIFEX-AEOLICUS; RIBOSOMAL-RNA; GEN. NOV.; AQUIFICALES; SYSTEM; ACID; 2-METHYLTHIO-1,4-NAPHTHOQUINONE; LIPOPOLYSACCHARIDE AB Thermocrinis albus Eder and Huber 2002 is one of three species in the genus Thermocrinis in the family Aquificaceae. Members of this family have become of significant interest because of their involvement in global biogeochemical cycles in high-temperature ecosystems. This interest had already spurred several genome sequencing projects for members of the family. We here report the first completed genome sequence a member of the genus Thermocrinis and the first type strain genome from a member of the family Aquificaceae. The 1,500,577 bp long genome with its 1,603 protein-coding and 47 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Brambilla, Evelyne; Tindall, Brian J.; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Wirth, Reinhard; Bilek, Yvonne; Hader, Thomas] Univ Regensburg, Archaeenzentrum, Regensburg, Germany. [Misra, Monica; Lapidus, Alla; Copeland, Alex; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Tapia, Roxane; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Pati, Amrita; Anderson, Iain; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Misra, Monica; Han, Cliff; Detter, John C.; Tapia, Roxane; Bruce, David; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 44 TC 9 Z9 10 U1 1 U2 5 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 2 BP 194 EP 202 DI 10.4056/sigs.761490 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DD UT WOS:000290219900006 PM 21304702 ER PT J AU Sikorski, J Lapidus, A Copeland, A Misra, M Del Rio, TG Nolan, M Lucas, S Chen, F Tice, H Cheng, JF Jando, M Schneider, S Bruce, D Goodwin, L Pitluck, S Liolios, K Mikhailova, N Pati, A Ivanova, N Mavromatis, K Chen, A Palaniappan, K Chertkov, O Land, M Hauser, L Chang, YJ Jeffries, CD Brettin, T Detter, JC Han, C Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Sikorski, Johannes Lapidus, Alla Copeland, Alex Misra, Monica Del Rio, Tijana Glavina Nolan, Matt Lucas, Susan Chen, Feng Tice, Hope Cheng, Jan-Fang Jando, Marlen Schneider, Susanne Bruce, David Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Mikhailova, Natalia Pati, Amrita Ivanova, Natalia Mavromatis, Konstantinos Chen, Amy Palaniappan, Krishna Chertkov, Olga Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brettin, Thomas Detter, John C. Han, Cliff Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Segniliparus rotundus type strain (CDC 1076(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; non-sporeforming; novel mycolic acid; opportunistic pathogen; Corynebacterineae; GEBA ID BACTERIA; RUGOSUS; SYSTEM; PROPOSAL; BIOLOGY; ARCHAEA; GRAPHS; TOOL; NOV AB Segniliparus rotundus Butler 2005 is the type species of the genus Segniliparus, which is currently the only genus in the corynebacterial family Segniliparaceae. This family is of large interest because of a novel late-emerging genus-specific mycolate pattern. The type strain has been isolated from human sputum and is probably an opportunistic pathogen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Segniliparaceae. The 3,157,527 bp long genome with its 3,081 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Jando, Marlen; Schneider, Susanne; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lapidus, Alla; Copeland, Alex; Misra, Monica; Del Rio, Tijana Glavina; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chertkov, Olga; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Detter, John C.; Han, Cliff; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Misra, Monica; Bruce, David; Goodwin, Lynne; Brettin, Thomas; Detter, John C.; Han, Cliff] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Chertkov, Olga] Lawrence Livermore Natl Lab, Livermore, CA USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 25 TC 6 Z9 11 U1 1 U2 8 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 2 BP 203 EP 211 DI 10.4056/sigs.791633 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DD UT WOS:000290219900007 PM 21304703 ER PT J AU Pukall, R Lapidus, A Del Rio, TG Copeland, A Tice, H Cheng, JF Lucas, S Chen, F Nolan, M Bruce, D Goodwin, L Pitluck, S Mavromatis, K Ivanova, N Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Chain, P Meincke, L Sims, D Brettin, T Detter, JC Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Kyrpides, NC Klenk, HP Hugenholtz, P AF Pukall, Ruediger Lapidus, Alla Del Rio, Tijana Glavina Copeland, Alex Tice, Hope Cheng, Jan-Fang Lucas, Susan Chen, Feng Nolan, Matt Bruce, David Goodwin, Lynne Pitluck, Sam Mavromatis, Konstantinos Ivanova, Natalia Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Chain, Patrick Meincke, Linda Sims, David Brettin, Thomas Detter, John C. Rohde, Manfred Goeker, Markus Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Kyrpides, Nikos C. Klenk, Hans-Peter Hugenholtz, Philip TI Complete genome sequence of Conexibacter woesei type strain (ID131577(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE aerobic; short rods; forest soil; Solirubrobacterales; Conexibacteraceae; GEBA ID BIOLOGICAL SOIL CRUSTS; SP-NOV.; PHYLOGENETIC ANALYSIS; CLASS ACTINOBACTERIA; GEN. NOV.; BACTERIA; PROPOSAL; IDENTIFICATION; COMMUNITY; SYSTEM AB The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of descent within the class Actinobacteria. Strain ID131577(T) was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous flagella. They may form aggregates after a longer period of growth and, then as a typical characteristic, an undulate structure is formed by self-aggregation of flagella with entangled bacterial cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Pukall, Ruediger; Goeker, Markus; Kyrpides, Nikos C.; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lapidus, Alla; Del Rio, Tijana Glavina; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Ivanova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C.; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Bruce, David; Goodwin, Lynne; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Chain, Patrick] Lawrence Livermore Natl Lab, Livermore, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Kyrpides, Nikos/A-6305-2014; Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of Califor-nia, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC5207NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Susanne Schneider for DNA extraction and quality analysis and Katja Steenblock for growing C. woesei cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of Califor-nia, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC5207NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1. NR 31 TC 5 Z9 5 U1 1 U2 14 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 2 BP 212 EP 219 DI 10.4056/sigs.751339 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DD UT WOS:000290219900008 PM 21304704 ER PT J AU Harmon-Smith, M Celia, L Chertkov, O Lapidus, A Copeland, A Del Rio, TG Nolan, M Lucas, S Tice, H Cheng, JF Han, C Detter, JC Bruce, D Goodwin, L Pitluck, S Pati, A Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Brettin, T Goker, M Beck, B Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Chen, F AF Harmon-Smith, Miranda Celia, Laura Chertkov, Olga Lapidus, Alla Copeland, Alex Del Rio, Tijana Glavina Nolan, Matt Lucas, Susan Tice, Hope Cheng, Jan-Fang Han, Cliff Detter, John C. Bruce, David Goodwin, Lynne Pitluck, Sam Pati, Amrita Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Brettin, Thomas Goeker, Markus Beck, Brian Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Chen, Feng TI Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE anaerobic; mesophile; nonmotile; non-sporeforming; Gram-negative; termite intestine; 'Fusobacteria'; 'Leptotrichiaceae'; GEBA ID BACTEROIDES; IDENTIFICATION; BACTERIA; ARCHAEA; SYSTEM; TOOL AB Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family 'Leptotrichiaceae'. The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean termites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA sequence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Chertkov, Olga; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Brettin, Thomas] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Celia, Laura; Beck, Brian] ATCC, Manassas, VA USA. [Harmon-Smith, Miranda; Lapidus, Alla; Copeland, Alex; Del Rio, Tijana Glavina; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Pati, Amrita; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Chen, Feng] US DOE, Joint Genome Inst, Walnut Creek, CA USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Lapidus, Alla/I-4348-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462 FU US Department of Energy's Office of Science, Biological and Environmental Research; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725] FX We would like to gratefully acknowledge the help of Janice Carr (Centers of Disease Control, Atlanta, Georgia) for providing the EM photo of S. thermitidis NCTC 11300T. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725 NR 27 TC 11 Z9 11 U1 1 U2 7 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 2 BP 220 EP 227 DI 10.4056/sigs.811799 PG 8 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DD UT WOS:000290219900009 PM 21304705 ER PT J AU Spring, S Rachel, R Lapidus, A Davenport, K Tice, H Copeland, A Cheng, JF Lucas, S Chen, F Nolan, M Bruce, D Goodwin, L Pitluck, S Ivanova, N Mavromatis, K Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CC Brettin, T Detter, JC Tapia, R Han, C Heimerl, T Weikl, F Brambilla, E Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Spring, Stefan Rachel, Reinhard Lapidus, Alla Davenport, Karen Tice, Hope Copeland, Alex Cheng, Jan-Fang Lucas, Susan Chen, Feng Nolan, Matt Bruce, David Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia C. Brettin, Thomas Detter, John C. Tapia, Roxanne Han, Cliff Heimerl, Thomas Weikl, Fabian Brambilla, Evelyne Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Thermosphaera aggregans type strain (M11TL(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE hyperthermophile; strictly fermentative metabolism; sulfur reduction; obligate anaerobic; hot solfataric spring; Desulfurococcaceae; Crenarchaeota; GEBA ID ARCHAEON PYROCOCCUS-FURIOSUS; HYPERTHERMOPHILIC ARCHAEON; DESULFUROCOCCUS-KAMCHATKENSIS; FERREDOXIN OXIDOREDUCTASE; ELEMENTAL SULFUR; HOT-SPRINGS; SYSTEM; ARCHAEBACTERIA; INSIGHTS; SYNTHASE AB Thermosphaera aggregans Huber et al. 1998 is the type species of the genus Thermosphaera, which comprises at the time of writing only one species. This species represents archaea with a hyperthermophilic, heterotrophic, strictly anaerobic and fermentative phenotype. The type strain M11TL(T) was isolated from a water-sediment sample of a hot terrestrial spring ( Obsidian Pool, Yellowstone National Park, Wyoming). Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,316,595 bp long single replicon genome with its 1,410 protein-coding and 47 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Spring, Stefan; Brambilla, Evelyne; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Rachel, Reinhard; Heimerl, Thomas; Weikl, Fabian] Univ Regensburg, Archaeenzentrum, Regensburg, Germany. [Lapidus, Alla; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia C.; Brettin, Thomas; Detter, John C.; Tapia, Roxanne; Han, Cliff; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Davenport, Karen; Bruce, David; Goodwin, Lynne; Tapia, Roxanne; Han, Cliff] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna] Lawrence Livermore Natl Lab, Livermore, CA USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia C.; Brettin, Thomas; Detter, John C.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. [Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy's Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory; German Research Foundation (DFG) [INST 599/1-1] FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract. German Research Foundation (DFG) supported DSMZ under INST 599/1-1. NR 52 TC 11 Z9 13 U1 1 U2 8 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 245 EP 259 DI 10.4056/sigs.821804 PG 15 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700001 PM 21304709 ER PT J AU Pati, A Sikorski, J Gronow, S Munk, C Lapidus, A Copeland, A Del Tio, TG Nolan, M Lucas, S Chen, F Tice, H Cheng, JF Han, C Detter, JC Bruce, D Tapia, R Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Mikhailova, N Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Spring, S Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Pati, Amrita Sikorski, Johannes Gronow, Sabine Munk, Christine Lapidus, Alla Copeland, Alex Del Tio, Tijana Glavina Nolan, Matt Lucas, Susan Chen, Feng Tice, Hope Cheng, Jan-Fang Han, Cliff Detter, John C. Bruce, David Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Spring, Stefan Rohde, Manfred Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Brachyspira murdochii type strain (56-150(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE host-associated; non-pathogenic; motile; anaerobic; Gram-negative; Brachyspiraceae; Spirochaetes; GEBA ID SERPULINA-MURDOCHII; GENUS BRACHYSPIRA; BACTERIAL NAMES; SP. NOV.; IDENTIFICATION; HYODYSENTERIAE; CHICKENS; RECLASSIFICATION; NOMENCLATURE; RECOGNITION AB Brachyspira murdochii Stanton et al. 1992 is a non-pathogenic host-associated spirochete of the family Brachyspiraceae. Initially isolated from the intestinal content of a healthy swine, the 'group B spirochaetes' were first described under as Serpulina murdochii. Members of the family Brachyspiraceae are of great phylogenetic interest because of the extremely isolated location of this family within the phylum 'Spirochaetes'. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a type strain of a member of the family Brachyspiraceae and only the second genome sequence from a member of the genus Brachyspira. The 3,241,804 bp long genome with its 2,893 protein-coding and 40 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Gronow, Sabine; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Pati, Amrita; Lapidus, Alla; Copeland, Alex; Del Tio, Tijana Glavina; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Munk, Christine; Han, Cliff; Detter, John C.; Bruce, David; Tapia, Roxanne; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Lapidus, Alla/I-4348-2013; Hauser, Loren/H-3881-2012; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013 OI Lapidus, Alla/0000-0003-0427-8731; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938 FU US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Sabine Welnitz for growing B. murdochii cells and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 44 TC 13 Z9 13 U1 1 U2 6 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 260 EP 269 DI 10.4056/sigs.831993 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700002 PM 21304710 ER PT J AU Kiss, H Lang, E Lapidus, A Copeland, A Nolan, M Del Rio, TG Chen, F Lucas, S Tice, H Cheng, JF Han, C Goodwin, L Pitluck, S Liolios, K Pati, A Ivanova, N Mavromatis, K Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Brettin, T Spring, S Rohde, M Goker, M Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Kiss, Hajnalka Lang, Elke Lapidus, Alla Copeland, Alex Nolan, Matt Del Rio, Tijana Glavina Chen, Feng Lucas, Susan Tice, Hope Cheng, Jan-Fang Han, Cliff Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Pati, Amrita Ivanova, Natalia Mavromatis, Konstantinos Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Brettin, Thomas Spring, Stefan Rohde, Manfred Goeker, Markus Woyke, Tanja Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE dissimilatory nitrate-reducer; mesophile; free-living; marine; obligately anaerobic; motile; Deferribacteraceae; Deferribacteres; GEBA ID RESERVOIR MODEL COLUMN; NITRATE; BACTERIA; NITRITE; ARCHAEA; INJECTION; SYSTEM; TOOL AB Denitrovibrio acetiphilus Myhr and Torsvik 2000 is the type species of the genus Denitrovibrio in the bacterial family Deferribacteraceae. It is of phylogenetic interest because there are only six genera described in the family Deferribacteraceae. D. acetiphilus was isolated as a representative of a population reducing nitrate to ammonia in a laboratory column simulating the conditions in off-shore oil recovery fields. When nitrate was added to this column undesirable hydrogen sulfide production was stopped because the sulfate reducing populations were superseded by these nitrate reducing bacteria. Here we describe the features of this marine, mesophilic, obligately anaerobic organism respiring by nitrate reduction, together with the complete genome sequence, and annotation. This is the second complete genome sequence of the order Deferribacterales and the class Deferribacteres, which is the sole class in the phylum Deferribacteres. The 3,222,077 bp genome with its 3,034 protein-coding and 51 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Lang, Elke; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Kiss, Hajnalka; Lapidus, Alla; Copeland, Alex; Nolan, Matt; Del Rio, Tijana Glavina; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Brettin, Thomas; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Kiss, Hajnalka; Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Brettin, Thomas] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy's Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Markus Kopitz for growing the D. acetiphilus cells, and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 29 TC 7 Z9 8 U1 5 U2 8 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 270 EP 279 DI 10.4056/sigs.892105 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700003 PM 21304711 ER PT J AU Chertkov, O Sikorski, J Brambilla, E Lapidus, A Copeland, A Del Rio, TG Nolan, M Lucas, S Tice, H Cheng, JF Han, C Detter, JC Bruce, D Tapia, R Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Ovchinnikova, G Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Spring, S Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF Chertkov, Olga Sikorski, Johannes Brambilla, Evelyne Lapidus, Alla Copeland, Alex Del Rio, Tijana Glavina Nolan, Matt Lucas, Susan Tice, Hope Cheng, Jan-Fang Han, Cliff Detter, John C. Bruce, David Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Spring, Stefan Rohde, Manfred Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Aminobacterium colombiense type strain (ALA-1(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE strictly anaerobic; fermentation of amino acids; Gram-negative staining; syntrophic organism; Synergistaceae; GEBA ID ACID-DEGRADING BACTERIUM; MOBILE SP NOV.; GEN. NOV.; EMENDED DESCRIPTION; ANAEROBIC SLUDGE; ARCHAEA; IDENTIFICATION; ANAEROBACULUM; SYSTEM; GRAPHS AB Aminobacterium colombiense Baena et al. 1999 is the type species of the genus Aminobacterium. This genus is of large interest because of its isolated phylogenetic location in the family Synergistaceae, its strictly anaerobic lifestyle, and its ability to grow by fermentation of a limited range of amino acids but not carbohydrates. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the family Synergistaceae and the first genome sequence of a member of the genus Aminobacterium. The 1,980,592 bp long genome with its 1,914 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Sikorski, Johannes; Brambilla, Evelyne; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chertkov, Olga; Lapidus, Alla; Copeland, Alex; Del Rio, Tijana Glavina; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Bruce, David; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Chertkov, Olga; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Han, Cliff; Detter, John C.; Bruce, David; Tapia, Roxanne; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy's Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Maren Schroder (DSMZ) for growing A. colombiense cells. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and UT-Battelle Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and SI 1352/1-2. NR 35 TC 13 Z9 15 U1 3 U2 12 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 280 EP 289 DI 10.4056/sigs.902116 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700004 PM 21304712 ER PT J AU Mavromatis, K Abt, B Brambilla, E Lapidus, A Copeland, A Deshpande, S Nolan, M Lucas, S Tice, H Cheng, JF Han, C Detter, JC Woyke, T Goodwin, L Pitluck, S Held, B Brettin, T Tapia, R Ivanova, N Mikhailova, N Pati, A Liolios, K Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Mavromatis, Konstantinos Abt, Birte Brambilla, Evelyne Lapidus, Alla Copeland, Alex Deshpande, Shweta Nolan, Matt Lucas, Susan Tice, Hope Cheng, Jan-Fang Han, Cliff Detter, John C. Woyke, Tanja Goodwin, Lynne Pitluck, Sam Held, Brittany Brettin, Thomas Tapia, Roxanne Ivanova, Natalia Mikhailova, Natalia Pati, Amrita Liolios, Konstantinos Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Rohde, Manfred Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE sphere-shaped; non-motile; non-spore-forming; aerobic; mesophile; Gram-negative; Puniceicoccaceae; Opitutae; GEBA ID RICE PADDY SOIL; SP-NOV.; PHYLUM VERRUCOMICROBIA; GEN. NOV.; FAMILY PUNICEICOCCACEAE; MARINE BACTERIUM; IDENTIFICATION; ARCHAEA; FUCOIDAN; DIVISION AB Coraliomargarita akajimensis Yoon et al. 2007 is the type species of the genus Coraliomargarita. C. akajimensis is an obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium that was isolated from seawater surrounding the hard coral Galaxea fascicularis. C. akajimensis is of special interest because of its phylogenetic position in a genomically under-studied area of the bacterial diversity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Puniceicoccaceae. The 3,750,771 bp long genome with its 3,137 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Mavromatis, Konstantinos; Lapidus, Alla; Copeland, Alex; Deshpande, Shweta; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Woyke, Tanja; Goodwin, Lynne; Pitluck, Sam; Held, Brittany; Brettin, Thomas; Tapia, Roxanne; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Liolios, Konstantinos; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Abt, Birte; Brambilla, Evelyne; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Han, Cliff; Detter, John C.; Goodwin, Lynne; Held, Brittany; Brettin, Thomas; Tapia, Roxanne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Lawrence Livermore Natl Lab, Livermore, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Kyrpides, NC (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy's Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1] FX We would like to gratefully acknowledge the help of Marlen Jando (DSMZ) for growing C. akajimensis cultures. This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1. NR 35 TC 9 Z9 9 U1 3 U2 10 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 290 EP 299 DI 10.4056/sigs.952166 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700005 PM 21304713 ER PT J AU Pati, A Gronow, S Lapidus, A Copeland, A Del Rio, TG Nolan, M Lucas, S Tice, H Cheng, JF Han, C Chertkov, O Bruce, D Tapia, R Goodwin, L Pitluck, S Liolios, K Ivanova, N Mavromatis, K Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Pati, Amrita Gronow, Sabine Lapidus, Alla Copeland, Alex Del Rio, Tijana Glavina Nolan, Matt Lucas, Susan Tice, Hope Cheng, Jan-Fang Han, Cliff Chertkov, Olga Bruce, David Tapia, Roxanne Goodwin, Lynne Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Rohde, Manfred Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Arcobacter nitrofigilis type strain (CIT) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE symbiotic; Spartina alterniflora Loisel; nitrogen fixation; micro-anaerophilic; motile; Campylobacteraceae; GEBA ID SPARTINA-ALTERNIFLORA LOISEL; CAMPYLOBACTER; BACTERIA; PROPOSAL; ARCHAEA; IDENTIFICATION; SYSTEM; GRAPHS; ROOTS; TOOL AB Arcobacter nitrofigilis (McClung et al. 1983) Vandamme et al. 1991 is the type species of the genus Arcobacter in the family Campylobacteraceae within the Epsilonproteobacteria. The species was first described in 1983 as Campylobacter nitrofigilis [1] after its detection as a free-living, nitrogen-fixing Campylobacter species associated with Spartina alterniflora Loisel roots [2]. It is of phylogenetic interest because of its lifestyle as a symbiotic organism in a marine environment in contrast to many other Arcobacter species which are associated with warm-blooded animals and tend to be pathogenic. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a type stain of the genus Arcobacter. The 3,192,235 bp genome with its 3,154 protein-coding and 70 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Pati, Amrita; Lapidus, Alla; Copeland, Alex; Del Rio, Tijana Glavina; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Chertkov, Olga; Bruce, David; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Han, Cliff; Chertkov, Olga; Bruce, David; Tapia, Roxanne; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Gronow, Sabine; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Kyrpides, NC (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Sabine Welnitz for growing the A. nitrofigilis cells, and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and UT-Battelle Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 35 TC 14 Z9 16 U1 2 U2 13 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 300 EP 308 DI 10.4056/sigs.912121 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700006 PM 21304714 ER PT J AU Liolios, K Sikorski, J Jando, M Lapidus, A Copeland, A Del Rio, TG Nolan, M Lucas, S Tice, H Cheng, JF Han, C Woyke, T Goodwin, L Pitluck, S Ivanova, N Mavromatis, K Mikhailova, N Chertkov, O Kuske, C Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Detter, JC Brettin, T Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Klenk, HP Kyrpides, NC AF Liolios, Konstantinos Sikorski, Johannes Jando, Marlen Lapidus, Alla Copeland, Alex Del Rio, Tijana Glavina Nolan, Matt Lucas, Susan Tice, Hope Cheng, Jan-Fang Han, Cliff Woyke, Tanja Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Chertkov, Olga Kuske, Cheryl Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Detter, John C. Brettin, Thomas Rohde, Manfred Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Klenk, Hans-Peter Kyrpides, Nikos C. TI Complete genome sequence of Thermobispora bispora type strain (R51(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE Two distinct 16S rRNA genes; strictly thermophilic; non-pathogenic; Streptosporangineae; GEBA ID GENUS MICROBISPORA; PROPOSAL; ACTINOBACTERIA; BACTERIA; ARCHAEA; SYSTEM; NOV; CLASSIFICATION; IDENTIFICATION; TOOL AB Thermobispora bispora (Henssen 1957) Wang et al. 1996 is the type species of the genus Thermobispora. This genus is of great interest because it is strictly thermophilic and because it has been shown for several of its members that the genome contains substantially distinct (6.4% sequence difference) and transcriptionally active 16S rRNA genes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member from the suborder Streptosporangineae and the first genome sequence of a member of the genus Thermobispora. The 4,189,976 bp long genome with its 3,596 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [Liolios, Konstantinos; Lapidus, Alla; Copeland, Alex; Del Rio, Tijana Glavina; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Woyke, Tanja; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Chertkov, Olga; Kuske, Cheryl; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Brettin, Thomas; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Jando, Marlen; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Han, Cliff; Goodwin, Lynne] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Brettin, Thomas] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Kyrpides, NC (reprint author), US DOE, Joint Genome Inst, Walnut Creek, CA USA. RI Hauser, Loren/H-3881-2012; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-1, SI 1352/1-2] FX We would like to gratefully acknowledge the help of Susanne Schneider (DSMZ) for DNA extraction and quality analysis. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2. NR 33 TC 13 Z9 13 U1 2 U2 13 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 318 EP 326 DI 10.4056/sigs.962171 PG 9 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700008 PM 21304716 ER PT J AU von Jan, M Lapidus, A Del Rio, TG Copeland, A Tice, H Cheng, JF Lucas, S Chen, F Nolan, M Goodwin, L Han, C Pitluck, S Liolios, K Ivanova, N Mavromatis, K Ovchinnikova, G Chertkov, O Pati, A Chen, A Palaniappan, K Land, M Hauser, L Chang, YJ Jeffries, CD Saunders, E Brettin, T Detter, JC Chain, P Eichinger, K Huber, H Spring, S Rohde, M Goker, M Wirth, R Woyke, T Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP AF von Jan, Mathias Lapidus, Alla Del Rio, Tijana Glavina Copeland, Alex Tice, Hope Cheng, Jan-Fang Lucas, Susan Chen, Feng Nolan, Matt Goodwin, Lynne Han, Cliff Pitluck, Sam Liolios, Konstantinos Ivanova, Natalia Mavromatis, Konstantinos Ovchinnikova, Galina Chertkov, Olga Pati, Amrita Chen, Amy Palaniappan, Krishna Land, Miriam Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D. Saunders, Elizabeth Brettin, Thomas Detter, John C. Chain, Patrick Eichinger, Konrad Huber, Harald Spring, Stefan Rohde, Manfred Goeker, Markus Wirth, Reinhard Woyke, Tanja Bristow, Jim Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter TI Complete genome sequence of Archaeoglobus profundus type strain (AV18(T)) SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE hyperthermophilic; marine; strictly anaerobic; sulfate respiration; hydrogen utilization; hydrothermal systems; Archaeoglobaceae; GEBA ID 16S RIBOSOMAL-RNA; SEA HYDROTHERMAL VENT; SITU GROWTH CHAMBER; MID-ATLANTIC RIDGE; B-DNA-POLYMERASES; IZU-BONIN ARC; SP-NOV; F420H2-QUINONE OXIDOREDUCTASE; SULFOLOBUS-SOLFATARICUS; HALORHABDUS-UTAHENSIS AB Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. All members were isolated from marine hydrothermal habitats and are obligate anaerobes. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the class Archaeoglobi. The 1,563,423 bp genome with its 1,858 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. C1 [von Jan, Mathias; Spring, Stefan; Goeker, Markus; Klenk, Hans-Peter] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Lapidus, Alla; Del Rio, Tijana Glavina; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Goodwin, Lynne; Han, Cliff; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Chertkov, Olga; Pati, Amrita; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Saunders, Elizabeth; Brettin, Thomas; Detter, John C.; Chain, Patrick; Woyke, Tanja; Bristow, Jim; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Goodwin, Lynne; Han, Cliff; Brettin, Thomas; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Chain, Patrick; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Eichinger, Konrad; Huber, Harald; Wirth, Reinhard] Univ Regensburg, Microbiol Archaeenzentrum, Regensburg, Germany. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RP Klenk, HP (reprint author), DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. RI Hauser, Loren/H-3881-2012; chain, patrick/B-9777-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Lapidus, Alla/I-4348-2013 OI Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; UT-Battelle Oak Ridge National Laboratory [DE-AC05-00OR22725]; German Research Foundation (DFG) [INST 599/1-2] FX We would like to gratefully acknowledge the help of Jrn Petersen (DSMZ) for retrieving information concerning the cryptic plasmid of A. profundus. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and UT-Battelle Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2. NR 99 TC 12 Z9 23 U1 1 U2 10 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 327 EP 346 DI 10.4056/sigs.942153 PG 20 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700009 PM 21304717 ER PT J AU Reeve, W O'Hara, G Chain, P Ardley, J Brau, L Nandesena, K Tiwari, R Copeland, A Nolan, M Han, C Brettin, T Land, M Ovchinikova, G Ivanova, N Mavromatis, K Markowitz, V Kyrpides, N Melino, V Denton, M Yates, R Howieson, J AF Reeve, Wayne O'Hara, Graham Chain, Patrick Ardley, Julie Braeu, Lambert Nandesena, Kemanthi Tiwari, Ravi Copeland, Alex Nolan, Matt Han, Cliff Brettin, Thomas Land, Miriam Ovchinikova, Galina Ivanova, Natalia Mavromatis, Konstantinos Markowitz, Victor Kyrpides, Nikos Melino, Vanessa Denton, Matthew Yates, Ron Howieson, John TI Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers SO STANDARDS IN GENOMIC SCIENCES LA English DT Article DE microsymbiont; non-pathogenic; aerobic; Gram-negative rod; root-nodule bacteria; nitrogen fixation; Alphaproteobacteria ID BIOVAR TRIFOLII; SELECTION; SPP.; NODULATION; SYMBIOSIS; BACTERIA; SYSTEM AB Rhizobium leguminosarum bv trifolii is a soil-inhabiting bacterium that has the capacity to be an effective nitrogen fixing microsymbiont of a diverse range of annual Trifolium (clover) species. Strain WSM1325 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from root nodules collected in 1993 from the Greek Island of Serifos. WSM1325 is produced commercially in Australia as an inoculant for a broad range of annual clovers of Mediterranean origin due to its superior attributes of saprophytic competence, nitrogen fixation and acid-tolerance. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a microsymbiont of annual clovers. We reveal that its genome size is 7,418,122 bp encoding 7,232 protein-coding genes and 61 RNA-only encoding genes. This multipartite genome contains 6 distinct replicons; a chromosome of size 4,767,043 bp and 5 plasmids of size 828,924 bp, 660,973 bp, 516,088 bp, 350,312 bp and 294,782 bp. C1 [Reeve, Wayne; O'Hara, Graham; Ardley, Julie; Braeu, Lambert; Nandesena, Kemanthi; Tiwari, Ravi; Melino, Vanessa; Yates, Ron; Howieson, John] Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. [Chain, Patrick; Copeland, Alex; Nolan, Matt; Han, Cliff; Land, Miriam; Ovchinikova, Galina; Ivanova, Natalia; Mavromatis, Konstantinos; Kyrpides, Nikos] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Chain, Patrick] Lawrence Livermore Natl Lab, Livermore, CA USA. [Han, Cliff] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Brettin, Thomas; Land, Miriam] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. RP Reeve, W (reprint author), Murdoch Univ, Ctr Rhizobium Studies, Murdoch, WA 6150, Australia. RI Denton, Matthew/D-9697-2011; Melino, Vanessa/B-1920-2012; chain, patrick/B-9777-2013; Land, Miriam/A-6200-2011; Kyrpides, Nikos/A-6305-2014; OI Melino, Vanessa/0000-0003-2742-5079; Land, Miriam/0000-0001-7102-0031; Kyrpides, Nikos/0000-0002-6131-0462; Denton, Matthew/0000-0002-2804-0384; Ivanova, Natalia/0000-0002-5802-9485 FU US Department of Energy's Office of Science; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Murdoch University through the Crop and Plant Research Institute (CaPRI); Grains Research and Development Corporation (GRDC); Centre for Rhizobium Studies (CRS) at Murdoch University FX This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We thank Gordon Thompson (Murdoch University) for the preparation of SEM and TEM photos. We gratefully acknowledge the funding received from Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI), and the Grains Research and Development Corporation (GRDC), to support the National Rhizobium Program (NRP) and the Centre for Rhizobium Studies (CRS) at Murdoch University. NR 31 TC 26 Z9 29 U1 2 U2 21 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 347 EP 356 DI 10.4056/sigs.852027 PG 10 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700010 PM 21304718 ER PT J AU Copeland, A Sikorski, J Lapidus, A Nolan, M Del Rio, TG Lucas, S Chen, F Tice, H Pitluck, S Cheng, JF Pukall, R Chertkov, O Brettin, T Han, C Kuske, C Bruce, D Goodwin, L Ivanova, N Mavromatis, K Mikhailova, N Chen, A Palaniappan, K Chain, P Rohde, M Goker, M Bristow, J Eisen, JA Markowitz, V Hugenholtz, P Kyrpides, NC Klenk, HP Detter, JC AF Copeland, Alex Sikorski, Johannes Lapidus, Alla Nolan, Matt Del Rio, Tijana Glavina Lucas, Susan Chen, Feng Tice, Hope Pitluck, Sam Cheng, Jan-Fang Pukall, Ruediger Chertkov, Olga Brettin, Thomas Han, Cliff Kuske, Cheryl Bruce, David Goodwin, Lynne Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Chen, Amy Palaniappan, Krishna Chain, Patrick Rohde, Manfred Goeker, Markus Bristow, James Eisen, Jonathan A. Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C. Klenk, Hans-Peter Detter, John C. TI Complete genome sequence of Atopobium parvulum type strain (IPP 1246(T)) (vol 1, pg 166, 2009) SO STANDARDS IN GENOMIC SCIENCES LA English DT Correction ID STREPTOCOCCUS-PARVULUS; NOV C1 [Copeland, Alex; Lapidus, Alla; Nolan, Matt; Del Rio, Tijana Glavina; Lucas, Susan; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Brettin, Thomas; Han, Cliff; Kuske, Cheryl; Bruce, David; Goodwin, Lynne; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Detter, John C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA. [Sikorski, Johannes; Pukall, Ruediger; Goeker, Markus] DSMZ German Collect Microorganisms & Cell Culture, Braunschweig, Germany. [Chertkov, Olga; Brettin, Thomas; Han, Cliff; Kuske, Cheryl; Bruce, David; Goodwin, Lynne; Detter, John C.] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM USA. [Chen, Amy; Palaniappan, Krishna; Markowitz, Victor] Univ Calif Berkeley, Lawrence Berkeley Lab, Biol Data Management & Technol Ctr, Berkeley, CA 94720 USA. [Chain, Patrick] Lawrence Livermore Natl Lab, Livermore, CA USA. [Rohde, Manfred] HZI Helmholtz Ctr Infect Res, Braunschweig, Germany. [Eisen, Jonathan A.] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA. RI chain, patrick/B-9777-2013; Kyrpides, Nikos/A-6305-2014; Lapidus, Alla/I-4348-2013 OI Kyrpides, Nikos/0000-0002-6131-0462; Lapidus, Alla/0000-0003-0427-8731 NR 4 TC 0 Z9 0 U1 1 U2 5 PU GENOMIC STAND CONSORT PI EAST LANSING PA MICHIGAN STATE UNIV, GEEO GARRITY, DEPT MICROBIOL, 6162 BIOMED & PHYS SCI BLDG, EAST LANSING, MI 48824 USA SN 1944-3277 J9 STAND GENOMIC SCI JI Stand. Genomic Sci. PY 2010 VL 2 IS 3 BP 361 EP 362 DI 10.4056/sigs.992408 PG 2 WC Genetics & Heredity; Microbiology SC Genetics & Heredity; Microbiology GA 759DL UT WOS:000290220700011 PM 21304720 ER PT J AU Daly, DS Anderson, KK Seurynck-Servoss, SL Gonzalez, RM White, AM Zangar, RC AF Daly, Don Simone Anderson, Kevin K. Seurynck-Servoss, Shannon L. Gonzalez, Rachel M. White, Amanda M. Zangar, Richard C. TI An Internal Calibration Method for Protein-Array Studies SO STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY LA English DT Article DE protein array; internal calibration ID NORMALIZATION METHODS; MICROARRAY DATA; QUALITY-CONTROL; VALIDATION AB Nuisance factors in a protein-array study add obfuscating variation to spot intensity measurements, diminishing the accuracy and precision of protein concentration predictions. The effects of nuisance factors may be reduced by design of experiments, and by estimating and then subtracting nuisance effects. Estimated nuisance effects also inform about the quality of the study and suggest refinements for future studies. We demonstrate a method to reduce nuisance effects by incorporating a non-interfering internal calibration in the study design and its complemental analysis of variance. We illustrate this method by applying a chip-level internal calibration in a biomarker discovery study. The variability of sample intensity estimates was reduced 16% to 92% with a median of 58%; confidence interval widths were reduced 8% to 70% with a median of 35%. Calibration diagnostics revealed processing nuisance trends potentially related to spot print order and chip location on a slide. The accuracy and precision of a protein-array study may be increased by incorporating a non-interfering internal calibration. Internal calibration modeling diagnostics improve confidence in study results and suggest process steps that may need refinement. Though developed for our protein-array studies, this internal calibration method is applicable to other targeted array-based studies. C1 [Daly, Don Simone; Anderson, Kevin K.; White, Amanda M.; Zangar, Richard C.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Seurynck-Servoss, Shannon L.] Univ Arkansas, Fayetteville, AR 72701 USA. [Gonzalez, Rachel M.] Univ Washington, Seattle, WA 98195 USA. RP Daly, DS (reprint author), Pacific NW Natl Lab, Richland, WA 99352 USA. EM ds.daly@pnl.gov; kevin.anderson@pnl.gov; sservoss@uark.edu; rmgher@myuw.net; amanda.white@pnl.gov; richard.zangar@pnl.gov OI Anderson, Kevin/0000-0001-5613-5893 FU Early Detection Research Network of the National Cancer Institute [CA117378]; National Institute of Biomedical Imaging and Bioengineering [EB006177]; Pacific Northwest National Laboratory [DE-AC06-76RL01830] FX The authors thank Dr. Steven Skates for his insightful comments and suggestions that greatly improved the interpretation of our results. This research was supported by grants CA117378 from the Early Detection Research Network of the National Cancer Institute and EB006177 from National Institute of Biomedical Imaging and Bioengineering. Additional support was provided by the Pacific Northwest National Laboratory operated by Battelle for the U. S. Department of Energy under Contract DE-AC06-76RL01830. NR 32 TC 6 Z9 6 U1 0 U2 3 PU BERKELEY ELECTRONIC PRESS PI BERKELEY PA 2809 TELEGRAPH AVENUE, STE 202, BERKELEY, CA 94705 USA SN 1544-6115 J9 STAT APPL GENET MOL JI Stat. Appl. Genet. Mol. Biol. PY 2010 VL 9 IS 1 AR 14 DI 10.2202/1544-6115.1506 PG 23 WC Biochemistry & Molecular Biology; Mathematical & Computational Biology; Statistics & Probability SC Biochemistry & Molecular Biology; Mathematical & Computational Biology; Mathematics GA 551HR UT WOS:000274198200009 ER PT B AU Lehoucq, RB Von Lilienfeld-Toal, A AF Lehoucq, Richard B. Von Lilienfeld-Toal, Anatole BE Fosdick, R Fried, E TI Translation of Walter Noll's "Derivation of the Fundamental Equations of Continuum Thermodynamics from Statistical Mechanics" SO STATISTICAL MECHANICS, MOLECULAR MODELING, AND THE NOTION OF STRESS: AN INVITED COLLECTION LA English DT Article; Book Chapter DE Continuum mechanical; Statistical mechanical AB This article represents a translation of the original impel, "Die Hi:Heating der Grundglerchungen der Thermomechanik der Kontinua aus der Statistischen Mechanik", which was written by Walter Noll and appeared in the Journal of Rational Mechanics and Analysis 4 (1955). 627-646 In the original paper, Noll addressed and analyzed the seminal paper of Irving & Kirkwood, published live years earlier. on "The statistical mechanical theory of transport processes IV The Equations of Hydrodynamics" Noll gave new interpretations and provided a firm setting for ideas advanced by Irving & Kirkwood that clearly and directly related to the basic principles of continuum mechanics This translation aims to expose the important contribution of Noll to a wider community of researchers at a tulle when the atomistic modeling of material behavior is being advanced Noll's use of elementary mathematics to discover physical effects, to explain physical concepts. and to draw conclusions of a physical nature is exhibited Noll's paper emerged from a report that he presented in a seminar at Indiana University in the summer of 1954 The seminar was organized by Clifford Truesdell. whose inspiration Noll gratefully acknowledged C1 [Lehoucq, Richard B.] Sandia Natl Labs, Appl Math & Applicat Dept, Albuquerque, NM 87185 USA. [Von Lilienfeld-Toal, Anatole] Sandia Natl Labs, Multiscale Dynam Mat Modeling Dept, Albuquerque, NM 87185 USA. RP Lehoucq, RB (reprint author), Sandia Natl Labs, Appl Math & Applicat Dept, POB 5800, Albuquerque, NM 87185 USA. NR 2 TC 0 Z9 0 U1 0 U2 0 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES BN 978-90-481-9777-4 PY 2010 BP 5 EP 24 DI 10.1007/s10659-010-9246-9 D2 10.1007/978-90-481-9778-1 PG 20 WC Engineering, Mechanical; Mathematics, Applied; Statistics & Probability SC Engineering; Mathematics GA BQX70 UT WOS:000282067900002 ER PT B AU Williams, BJ Santner, TJ Notz, WI Lehman, JS AF Williams, Brian J. Santner, Thomas J. Notz, William I. Lehman, Jeffrey S. BE Kneib, T Tutz, G TI Sequential Design of Computer Experiments for Constrained Optimization SO STATISTICAL MODELLING AND REGRESSION STRUCTURES: FESTSCHRIFT IN HONOUR OF LUDWIG FAHRMEIR LA English DT Article; Book Chapter ID PREDICTION AB This paper proposes a sequential method of designing computer or physical experiments when the goal is to optimize one integrated signal function subject to constraints on the integral of a second response function. Such problems occur, for example, in industrial problems where the computed responses depend on two types of inputs: manufacturing variables and noise variables. In industrial settings, manufacturing variables are determined by the product designer; noise variables represent field conditions which are modeled by specifying a probability distribution for these variables. The update scheme of the proposed method selects the control portion of the next input site to maximize a posterior expected "improvement" and the environmental portion of this next input is selected to minimize the mean square prediction error of the objective function at the new control site. The method allows for dependence between the objective and constraint functions. The efficacy of the algorithm relative to the single-stage design and relative to a design assuming independent responses is illustrated. Implementation issues for the deterministic and measurement error cases are discussed as are some generalizations of the method. C1 [Williams, Brian J.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Santner, Thomas J.; Notz, William I.] Ohio State Univ, Dept Stat, Columbus, OH 43210 USA. [Lehman, Jeffrey S.] JPMorganChase, Home Finance Mkt Analyt, Columbus, OH 43240 USA. RP Williams, BJ (reprint author), Los Alamos Natl Lab, POB 1663,MS F600, Los Alamos, NM 87545 USA. EM brianw@lanl.gov; tjs@stat.osu.edu; win@stat.osu.edu; lehman@bankone.com NR 19 TC 8 Z9 8 U1 0 U2 0 PU PHYSICA-VERLAG GMBH & CO PI HEIDELBERG PA TIERGARTENSTR 17, D-69121 HEIDELBERG, GERMANY BN 978-3-7908-2412-4 PY 2010 BP 449 EP 472 DI 10.1007/978-3-7908-2413-1_24 D2 10.1007/978-3-7908-2413-1 PG 24 WC Statistics & Probability SC Mathematics GA BNO56 UT WOS:000275129600024 ER PT S AU Kasiviswanathan, SP Rudelson, M Smith, A Ullman, J AF Kasiviswanathan, Shiva Prasad Rudelson, Mark Smith, Adam Ullman, Jonathan GP ACM TI The Price of Privately Releasing Contingency Tables and the Spectra of Random Matrices with Correlated Rows SO STOC 2010: PROCEEDINGS OF THE 2010 ACM SYMPOSIUM ON THEORY OF COMPUTING SE Annual ACM Symposium on Theory of Computing LA English DT Proceedings Paper CT 42nd ACM Symposium on Theory of Computing CY JUN 06-08, 2010 CL Cambridge, MA SP ACM SIGACT AB Marginal (contingency) tables are the method of choice for government agencies releasing statistical summaries of categorical data. In this paper, we derive lower bounds on how much distortion (noise) is necessary in these tables to ensure the privacy of sensitive data. We extend a line of recent work on impossibility results for private data analysis [9, 12, 13, 15] to a natural and important class of functionalities. Consider a database consisting of n rows (one per individual), each row comprising d binary attributes. For any subset of T attributes of size vertical bar T vertical bar = k, the marginal table for T has 2(k) entries; each entry counts how many times in the database a particular setting of these attributes occurs. We provide lower bounds for releasing all ((d)(k)) k-attribute marginal tables under several different notions of privacy. (1) We give efficient polynomial time attacks which allow an adversary to reconstruct sensitive information given insufficiently :perturbed marginal table releases. In particular, for a constant k, we obtain a tight bound of (Omega) over tilde (min{root n, root d(k-1)})(1) on the average distortion per entry for any mechanism that releases all k-attribute marginals while providing "attribute" :privacy (a weak notion implied by most privacy definitions). (2) Our reconstruction attacks require a new lower bound on the least singular value of a random matrix with correlated rows. Let M-(k) be a matrix with ((d)(k)) rows formed by taking all possible k-way entry-wise products of an underlying set of d random vectors from {0, 1}(n). For constant k, we show that the least singular value of M-(k) is (Omega) over tilde(root d(k)) with high probability (the same asymptotic bound as for independent rows). (3) We obtain stronger lower bounds for marginal tables satisfying differential privacy. We give a lower bound of (Omega) over tilde (min{root n, root d(k)}), which is tight for n = (Omega) over tilde (d(k)). We extend our analysis to obtain stronger results for mechanisms that add instance-independent noise and weaker results when k is super-constant. C1 [Kasiviswanathan, Shiva Prasad] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Kasiviswanathan, SP (reprint author), Los Alamos Natl Lab, CCS-3, Los Alamos, NM 87545 USA. EM kasivisw@gmail.com; rudelsonm@missouri.edu; asmith@cse.psu.edu; jullman@seas.harvard.edu NR 33 TC 16 Z9 16 U1 1 U2 2 PU ASSOC COMPUTING MACHINERY PI NEW YORK PA 1515 BROADWAY, NEW YORK, NY 10036-9998 USA SN 0737-8017 BN 978-1-60558-817-9 J9 ACM S THEORY COMPUT PY 2010 BP 775 EP 784 PG 10 WC Computer Science, Theory & Methods SC Computer Science GA BTH89 UT WOS:000286949900080 ER PT J AU Thomas, AW AF Thomas, A. W. BE Maeda, K Nakamura, SN Tamura, H Hashimoto, O TI IMPORTANCE OF STRANGE QUARKS IN HADRONS, NUCLEI AND DENSE MATTER SO STRANGENESS IN NUCLEAR AND HADRONIC SYSTEMS (SENDAI08) LA English DT Proceedings Paper CT Sendai International Symposium on Strangeness in Nuclear and Hadronic Systems CY DEC 15-18, 2008 CL Sendai, JAPAN DE Chiral symmetry; lattice QCD; strange quark; sigma commutator; strange sigma commutator; hypernuclei; dense matter; neutron star ID MESON COUPLING MODEL; HYPERNUCLEI; OBSERVABLES AB We review recent progress in our understanding of the role of strange quarks in the structure of the nucleon. For the contribution to its mass the result is remarkably small, an order of magnitude smaller than commonly assumed. This has profound consequences for the searches for dark matter which are currently underway. There has also been remarkable progress in the understanding of hypernuclei. In particular, there is a very natural explanation at the quark level of why Lambda-hypernuclei are bound whereas Sigma-hypernuclei are not. The consequences for dense matter, for example in neutron stars, are not yet fully understood but we know they are significant. C1 [Thomas, A. W.] Jefferson Lab, Suite 1,12000 Jefferson Ave, Newport News, VA 23606 USA. [Thomas, A. W.] Coll William & Mary, Williamsburg, VA 23187 USA. RP Thomas, AW (reprint author), Jefferson Lab, Suite 1,12000 Jefferson Ave, Newport News, VA 23606 USA. FU DOE [DE-AC05-06OR23177] FX This work was supported by DOE contract DE-AC05-06OR23177, under which Jefferson Science Associates, LLC, operates Jefferson Lab. NR 17 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4277-60-0 PY 2010 BP 1 EP 8 DI 10.1142/9789814277860_0001 PG 8 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BG9CS UT WOS:000393058900001 ER PT J AU Burkert, VD AF Burkert, Volker D. BE Maeda, K Nakamura, SN Tamura, H Hashimoto, O TI STRANGENESS PHYSICS WITH CLAS SO STRANGENESS IN NUCLEAR AND HADRONIC SYSTEMS (SENDAI08) LA English DT Proceedings Paper CT Sendai International Symposium on Strangeness in Nuclear and Hadronic Systems CY DEC 15-18, 2008 CL Sendai, JAPAN DE Hyperons; complete experiments; missing resonances ID PHOTOPRODUCTION AB A brief overview of strangeness physics with the CLAS detector at JLab is given, mainly covering the domain of nucleon resonances. Several excited states predicted by the symmetric constituent quark model may have significant couplings to the KA or KE channels. We will discuss data that are relevant in the search for such states in the strangeness channel, and give an outlook on the future prospects of the N* program at JLab with electromagnetic probes. C1 [Burkert, Volker D.] Jefferson Lab, Newport News, VA 23606 USA. RP Burkert, VD (reprint author), Jefferson Lab, Newport News, VA 23606 USA. EM burkert@jlab.org NR 14 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4277-60-0 PY 2010 BP 43 EP 50 DI 10.1142/9789814277860_0005 PG 8 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BG9CS UT WOS:000393058900005 ER PT J AU Smith, ES AF Smith, Elton S. CA CLAS Collaboration BE Maeda, K Nakamura, SN Tamura, H Hashimoto, O TI PRODUCTION AND SEARCHES FOR CASCADE BARYONS WITH CLAS SO STRANGENESS IN NUCLEAR AND HADRONIC SYSTEMS (SENDAI08) LA English DT Proceedings Paper CT Sendai International Symposium on Strangeness in Nuclear and Hadronic Systems CY DEC 15-18, 2008 CL Sendai, JAPAN DE Cascade resonances; hyperon photoproduction; cascade pentaquarks AB We present the results of photoproduction cross sections of the ground state cascade Xi(-) and the first excited state Xi*(-) (1530) measured with the CLAS detector. The photoproduction of the cascade resonances has been investigated in the reactions gamma p -> K+K+(X) and gamma p -> K+K+pi(-)(X). The differential and total cross sections of the E were determined for photon beam energies from 2.75 to 4.75 GeV and are consistent with a production mechanism of Y* -> K+ Xi(-) through a t-channel process. The cross-section of the Xi*(-) (1530) has been determined for photon beam energies from 3.35 to 4.75 GeV. The reaction gamma p -> K+K+pi(-)(Xi(0)) has also been investigated in the search for excited cascade resonances decaying to pi(-)Xi(0). No significant signal of excited cascade states other than the well-known Xi*(-) (1530) is observed. We also present the latest results of a search for the (Phi)(--) (1862) exotic pentaquark state in a photoproduction experiment on a deuterium target. A high-statistics sample of pi(-)Xi(-) events have been collected and analyzed. A preliminary invariant mass spectrum of the pi(-)Xi(-) system is presented, which is used to set upper limits on the photoproduction of the Phi(--) pentaquark state. C1 [Smith, Elton S.] Thomas Jefferson Natl Accelerator Facil, 12000 Jefferson Ave, Newport News, VA 23606 USA. RP Smith, ES (reprint author), Thomas Jefferson Natl Accelerator Facil, 12000 Jefferson Ave, Newport News, VA 23606 USA. EM elton@jlab.org FU U.S. Department of Energy [DE-AC05-06OR23177] FX This work was supported by the U.S. Department of Energy contract DE-AC05-06OR23177, under which Jefferson Science Associates, LLC operates the Thomas Jefferson National Accelerator Facility. I would like to especially thank L. Guo, for discussions regarding the cascade cross section measurements, and my colleagues from eg3, the search for cascade pentaquarks. NR 10 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4277-60-0 PY 2010 BP 118 EP 125 DI 10.1142/9789814277860_0015 PG 8 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BG9CS UT WOS:000393058900015 ER PT J AU Nemura, H Ishii, N Aoki, S Hatsuda, T AF Nemura, H. Ishii, N. Aoki, S. Hatsuda, T. BE Maeda, K Nakamura, SN Tamura, H Hashimoto, O TI STUDY OF HYPERON-NUCLEON POTENTIAL FROM LATTICE QCD SO STRANGENESS IN NUCLEAR AND HADRONIC SYSTEMS (SENDAI08) LA English DT Proceedings Paper CT Sendai International Symposium on Strangeness in Nuclear and Hadronic Systems CY DEC 15-18, 2008 CL Sendai, JAPAN DE Lattice QCD calculations; hyperon-nucleon interactions ID SCATTERING AB We study p Xi(0) and p Lambda forces by using quenched lattice QCD. The Bethe-Salpeter amplitude is calculated for the lowest scattering state of the systems. The numerical calculation is twofold: (i) For the p Xi(0), the potentials and scattering lengths are obtained by using 32(3) x 32 lattice with beta = 5.7, the lattice spacing of a = 0.1416(9) fm, and two kinds of ud quark mass corresponding to m(pi) similar or equal to 0.37 GeV and 0.51 GeV. The present results indicate that the p Xi(0) interactions are both attractive at S-1(0) and S-3(1) channels, and the interaction in the S-3(1) is more attractive than in the S-1(0). These attractive forces become stronger as the u, d quark mass decreases. (ii) For the p Lambda, the potentials are calculated by using the 32(3) x 48 lattice, and two kinds of ud quark mass corresponding to m pi similar or equal to 0.47 GeV and 0.51 GeV. The present preliminary result shows that the p Lambda interactions are both attractive at S-1(0) and S-3(1) channels. C1 [Nemura, H.] RIKEN, Nishina Ctr Accelerator Based Sci, Strangeness Nucl Phys Lab, Wako, Saitama 3510198, Japan. [Ishii, N.] Univ Tsukuba, Ctr Computat Sci, Tsukuba, Ibaraki 3058571, Japan. [Aoki, S.] Univ Tsukuba, Grad Sch Pure & Appl Sci, Tsukuba, Ibaraki 3058571, Japan. [Aoki, S.] Brookhaven Natl Lab, Riken BNL Res Ctr, Upton, NY 11973 USA. [Hatsuda, T.] Univ Tokyo, Dept Phys, Tokyo 1130033, Japan. RP Nemura, H (reprint author), RIKEN, Nishina Ctr Accelerator Based Sci, Strangeness Nucl Phys Lab, Wako, Saitama 3510198, Japan. EM nemura@riken.jp; ishii@rarfaxp.riken.jp; saoki@het.ph.tsukuba.ac.jp; hatsuda@phys.s.u-tokyo.ac.jp FU "Large scale simulation program" at KEK [08-19]; Ministry of Education, Science, Sports and Culture [18540253, 19540261, 20028013, 20340047] FX The authors would like to thank Dr. T. Izubuchi for providing a sample FFT code. The quenched QCD calculations have been done by using Blue Gene/L computer under the "Large scale simulation program" at KEK (No. 08-19). Part of numerical analysis has been done by using RIKEN super combined cluster system at RIKEN. This research was partly supported by the Ministry of Education, Science, Sports and Culture, Grant-in-Aid (Nos. 18540253, 19540261, 20028013, 20340047). NR 12 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4277-60-0 PY 2010 BP 150 EP 155 DI 10.1142/9789814277860_0019 PG 6 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BG9CS UT WOS:000393058900019 ER PT J AU Garibaldi, F Cisbani, E Cusanno, F Frullani, S Iodice, M Urciuoli, GM De Leo, R Lagamba, L Marrone, S LeRose, JJ de Jager, CW Feuerbach, RJ Higinbotham, DW Reitz, B Acha, A Markowitz, P Bydzovsky, P Sotona, M Chang, CC Millener, J AF Garibaldi, F. Cisbani, E. Cusanno, F. Frullani, S. Iodice, M. Urciuoli, G. M. De Leo, R. Lagamba, L. Marrone, S. LeRose, John J. de Jager, C. W. Feuerbach, R. J. Higinbotham, D. W. Reitz, B. Acha, A. Markowitz, P. Bydzovsky, P. Sotona, M. Chang, C. C. Millener, J. CA Hall Collaboration BE Maeda, K Nakamura, SN Tamura, H Hashimoto, O TI HIGH-RESOLUTION HYPERNUCLEAR SPECTROSCOPY ELECTRON SCATTERING AT JLab, HALL A SO STRANGENESS IN NUCLEAR AND HADRONIC SYSTEMS (SENDAI08) LA English DT Proceedings Paper CT Sendai International Symposium on Strangeness in Nuclear and Hadronic Systems CY DEC 15-18, 2008 CL Sendai, JAPAN ID ELECTROMAGNETIC PRODUCTION; JEFFERSON-LAB; STRANGENESS AB The characteristics of the Jefferson LAB electron beam, together with those of the experimental equipments, offer a unique opportunity to study hypernuclear spectroscopy via electromagnetic induced reactions. Experiment 94-107 started a systematic study on 1p-shell targets, C-12, Be-9 and O-16. We present the results from C-12, O-16 and very preliminary results from Be-9. For C-12 for the first time measurable strength in the core-excited part of the spectrum between the ground state and the p(Lambda) state was shown in B-12(Lambda) for the first time. A high-quality N-16(Lambda) spectrum was produced for the first time with sub-MeV Energy resolution. A very precise B-Lambda value for N-16(Lambda), calibrated against the elementary (e,e'K+) reaction on hydrogen, has also been obtained. Final data on Be-9 will be available soon. The missing energy resolution is the best ever obtained in hypernuclear production experiments. C1 [Garibaldi, F.; Cisbani, E.; Cusanno, F.; Frullani, S.; Iodice, M.; Urciuoli, G. M.] INFN Roma, Rome, Italy. [Garibaldi, F.; Cisbani, E.; Cusanno, F.; Frullani, S.; Iodice, M.; Urciuoli, G. M.] ISS, Rome, Italy. [De Leo, R.; Lagamba, L.; Marrone, S.] INFN, Bari, Italy. [LeRose, John J.; de Jager, C. W.; Feuerbach, R. J.; Higinbotham, D. W.; Reitz, B.] Jefferson Lab, Newport News, VA 23606 USA. [Acha, A.; Markowitz, P.] FIU, Miami, FL USA. [Bydzovsky, P.; Sotona, M.] Inst Nucl Phys, Rez, Czech Republic. [Chang, C. C.] Univ Maryland, College Pk, MD 20742 USA. [Millener, J.] BNL, Upton, NY USA. RP Garibaldi, F (reprint author), INFN Roma, Rome, Italy. EM franco.garibaldi@iss.infn.it FU US Department of Energy [DE-AC05-84ER40150, W-31-109-ENG-38, DE-FG02-99ER41110, DE-AC02-98-CH10886]; Southeastern Universities Research Association [M175]; Italian Istituto Nazionale di Fisica Nucleare (INFN); Grant Agency of the Czech Republic [202/05/2142] FX This work was supported by the US Department of Energy contract DE-AC05-84ER40150 Modification No. M175 under which the Southeastern Universities Research Association operates the Thomas Jefferson National Accelerator Facility, by the Italian Istituto Nazionale di Fisica Nucleare (INFN), by the US Department of Energy under contracts W-31-109-ENG-38, DE-FG02-99ER41110, and DE-AC02-98-CH10886, and No. 202/05/2142 of the Grant Agency of the Czech Republic. NR 10 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4277-60-0 PY 2010 BP 195 EP 204 DI 10.1142/9789814277860_0026 PG 10 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BG9CS UT WOS:000393058900026 ER PT J AU Tsushima, K Guichon, PAM Shyam, R Thomas, AW AF Tsushima, K. Guichon, P. A. M. Shyam, R. . Thomas, A. W. BE Maeda, K Nakamura, SN Tamura, H Hashimoto, O TI BINDING OF HYPERNUCLEI, AND PHOTOPRODUCTION OF Lambda-HYPERNUCLEI IN THE LATEST QUARK-MESON COUPLING MODEL SO STRANGENESS IN NUCLEAR AND HADRONIC SYSTEMS (SENDAI08) LA English DT Proceedings Paper CT Sendai International Symposium on Strangeness in Nuclear and Hadronic Systems CY DEC 15-18, 2008 CL Sendai, JAPAN DE Sigma hypernuclei; photoproduction; quark-based calculation ID KAON PHOTOPRODUCTION; NUCLEI AB We study the binding of hypernuclei based on the latest version of quark meson coupling model, and estimate the photoproduction cross sections for the C-12(gamma, K+)(Lambda 1)(2) B reaction using the bound Lambda spinors obtained in the model. C1 [Tsushima, K.; Shyam, R. .; Thomas, A. W.] Thomas Jefferson Lab, 12000 Jefferson Ave, Newport News, VA 23606 USA. [Guichon, P. A. M.] CEA Saclay, SPhN DAPNIA, F-91191 Gif Sur Yvette, France. [Shyam, R. .] Saha Inst Nucl Phys, Kolkata 70064, India. [Thomas, A. W.] Coll William & Mary, Williamsburg, VA 23187 USA. RP Tsushima, K (reprint author), Thomas Jefferson Lab, 12000 Jefferson Ave, Newport News, VA 23606 USA. FU Jefferson Science Associates, LLC under U.S. DOE [DE-AC05-06OR23177] FX K.T. would like to thank the organizers of SENDAI08, O. Hashimoto, H. Tamura, S. N. Nakamura and K. Maeda for a warm hospitality in entire period of the conference. Notice: Authored by Jefferson Science Associates, LLC under U.S. DOE Contract No. DE-AC05-06OR23177. The U.S. Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce this manuscript for U.S. Government purposes. NR 19 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4277-60-0 PY 2010 BP 254 EP 259 DI 10.1142/9789814277860_0033 PG 6 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BG9CS UT WOS:000393058900033 ER PT J AU Gibson, BF AF Gibson, B. F. BE Maeda, K Nakamura, SN Tamura, H Hashimoto, O TI A VIEW TOWARDS THE FUTURE OF STRANGENESS PHYSICS SO STRANGENESS IN NUCLEAR AND HADRONIC SYSTEMS (SENDAI08) LA English DT Proceedings Paper CT Sendai International Symposium on Strangeness in Nuclear and Hadronic Systems CY DEC 15-18, 2008 CL Sendai, JAPAN DE Strangeness physics; hypernuclei; hadronic physics AB These observations provide a personal perspective regarding the physics presented during this Sendai International Symposium on Strangeness in Nuclear and Hadronic Systems. No attempt has been made to summarize the oral presentations in the sense of a traditional summary talk. Many presentations covered physics from others than that of the speaker. Hopefully, the ideas discussed will outlive the rapporteurs who so ably brought them to life at SENDAI08. C1 [Gibson, B. F.] Los Alamos Natl Lab, Theoret Div, Los Alamos, NM 87545 USA. RP Gibson, BF (reprint author), Los Alamos Natl Lab, Theoret Div, Los Alamos, NM 87545 USA. EM bfgibson@lanl.gov FU National Nuclear Security Administration of the U.S. Department of Energy at Los Alamos National Laboratory [DE-AC52-06NA25396] FX This work was performed under the auspices of the National Nuclear Security Administration of the U.S. Department of Energy at Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396. NR 0 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4277-60-0 PY 2010 BP 379 EP 383 DI 10.1142/9789814277860_0052 PG 5 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BG9CS UT WOS:000393058900052 ER PT J AU Gubler, P Oka, M Jido, D Kojo, T Nishikawa, T AF Gubler, P. Oka, M. Jido, D. Kojo, T. Nishikawa, T. BE Maeda, K Nakamura, SN Tamura, H Hashimoto, O TI SPIN-3/2 PENTAQUARK IN QCD SUM RULES SO STRANGENESS IN NUCLEAR AND HADRONIC SYSTEMS (SENDAI08) LA English DT Proceedings Paper CT Sendai International Symposium on Strangeness in Nuclear and Hadronic Systems CY DEC 15-18, 2008 CL Sendai, JAPAN DE Pentaquark baryons; QCD sum rules AB The QCD sum rule method is applied to the Theta(+) pentaquark with quantum numbers IJ(P) = 03/2(+/-). It is found that the sum rule gives positive evidence for the 03/2(+) state, while we cannot extract any evidence for the 03/2(-) state. C1 [Gubler, P.; Oka, M.] Tokyo Inst Technol, Dept Phys, Meguro Ku, H-27, Tokyo 1528551, Japan. [Jido, D.] Kyoto Univ, Yukawa Inst Theoret Phys, Kyoto 6068502, Japan. [Kojo, T.] Brookhaven Natl Lab, RBRC, Upton, NY 11973 USA. [Nishikawa, T.] Juntendo Univ, Dept Phys, Chiba 2701695, Japan. RP Gubler, P (reprint author), Tokyo Inst Technol, Dept Phys, Meguro Ku, H-27, Tokyo 1528551, Japan. EM phil@th.phys.titech.ac.jp OI Gubler, Philipp/0000-0002-0991-8462 NR 2 TC 0 Z9 0 U1 0 U2 0 PU WORLD SCIENTIFIC PUBL CO PTE LTD PI SINGAPORE PA PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE BN 978-981-4277-60-0 PY 2010 BP 388 EP 389 DI 10.1142/9789814277860_0055 PG 2 WC Physics, Nuclear; Physics, Particles & Fields SC Physics GA BG9CS UT WOS:000393058900055 ER PT S AU Sheridan, MF Patra, AK Dalbey, K Hubbard, B AF Sheridan, Michael F. Patra, Abani K. Dalbey, Keith Hubbard, Bernard BE Groppelli, G ViereckGoette, L TI Probabilistic digital hazard maps for avalanches and massive pyroclastic flows using TITAN2D SO STRATIGRAPHY AND GEOLOGY OF VOLCANIC AREAS SE Geological Society of America Special Papers LA English DT Article; Book Chapter ID IRREGULAR 3-DIMENSIONAL TERRAIN; FLUIDIZED GRANULAR MASSES; DEBRIS FLOWS; EXPERIMENTAL TESTS; VOLCANO; MODEL; SIMULATIONS; MEXICO; COLIMA AB Geologists create volcanic hazard maps using scientific data to portray potential future geological events; the end users are principally public safety officials. Typical maps use a few simple polygons to outline areas of potential inundation or cover by a few categories of flows based on past frequency and size. Uncertainties in data regarding flow characteristics complicate the construction of accurate hazard maps. Generally, there are inadequate exposures of good sections, poorly known extents of units, and imprecise volumes for deposits. Crisis conditions limit the time available for field and laboratory work. Computer models can simulate possible scenarios, but the volumes, styles of emplacement, and source starting locations are poorly known in many cases. The large uncertainty in initial conditions is seldom taken into account in the construction of hazard maps, and these uncertainties are rarely passed on to the end users of the maps. TITAN2D is a computational model for volcanic block-and-ash flows and rock avalanches of various types and scales, and it forms the core of the TITAN toolkit for volcanic hazard analysis, which can integrate high-performance computing, database management, and visualization to a very sophisticated level. TITAN provides a solution to mapping problems by providing a probabilistic calculation of inundation depth that takes into account many of the critical uncertainties. C1 [Sheridan, Michael F.] SUNY Buffalo, Dept Geol, Buffalo, NY 14260 USA. [Patra, Abani K.] SUNY Buffalo, Dept Mech & Aerosp Engn, Buffalo, NY 14260 USA. [Dalbey, Keith] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Hubbard, Bernard] US Geol Survey, Reston, VA 20192 USA. RP Sheridan, MF (reprint author), SUNY Buffalo, Dept Geol, Buffalo, NY 14260 USA. RI Patra, Abani/F-8262-2016 NR 49 TC 7 Z9 8 U1 0 U2 4 PU GEOLOGICAL SOC AMER INC PI BOULDER PA 3300 PENROSE PL, PO BOX 9140, BOULDER, CO 80301 USA SN 0072-1077 BN 978-0-8137-2464-5 J9 GEOL SOC AM SPEC PAP PY 2010 VL 464 BP 281 EP 291 DI 10.1130/2010.2464(14) PG 11 WC Geology; Geosciences, Multidisciplinary SC Geology GA BTA56 UT WOS:000286214000015 ER PT J AU Park, G Park, CY Jun, SM Farrar, CR AF Park, G. Park, C. Y. Jun, S-M Farrar, C. R. BE Casciati, F Giordano, M TI Monitoring of Bolted Joints Using Piezoelectric Active-sensing for Aerospace Applications SO STRUCTURAL HEALTH MONITORING 2010 SE Structural Health Monitoring LA English DT Proceedings Paper CT 5th European Workshop on Structural Health Monitoring CY JUN 28-JUL 04, 2010 CL Naples, ITALY SP AleniaAeronautica, CIRA, DAppolonia S p A, US AF Off Sci Res, Univ Pavia, Natl Res Council, Inst Composite & Biomed Mat ID VALIDATION; SENSORS AB This paper is a report of an initial investigation into tracking and monitoring the integrity of bolted joints using piezoelectric active-sensors. The target application of this study is a fitting lug assembly of unmanned aerial vehicles (UAVs), where a composite wing is mounted to UAV fuselage. The SHM methods deployed in this study are impedance-based SHM techniques, time-series analysis, and high-frequency response functions measured by piezoelectric active-sensors. Different types of simulated damage are introduced into the structure, and the capability of each technique is examined and compared. Additional considerations encountered in this initial investigation are made to guide further thorough research required for the successful field deployment of this technology. C1 [Park, G.; Farrar, C. R.] Los Alamos Natl Lab, Engn Inst, Los Alamos, NM 87545 USA. RP Park, G (reprint author), Los Alamos Natl Lab, Engn Inst, MS T001, Los Alamos, NM 87545 USA. NR 9 TC 1 Z9 1 U1 0 U2 0 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-024-2 J9 STRUCT HLTH MONIT PY 2010 BP 131 EP 136 PG 6 WC Construction & Building Technology; Engineering, Civil SC Construction & Building Technology; Engineering GA BJG25 UT WOS:000328062600019 ER PT J AU Park, G Taylor, SG Farinholt, KM Farrar, CR AF Park, G. Taylor, S. G. Farinholt, K. M. Farrar, C. R. BE Casciati, F Giordano, M TI SHM of Wind Turbine Blades using Piezoelectric Active-Sensors SO STRUCTURAL HEALTH MONITORING 2010 SE Structural Health Monitoring LA English DT Proceedings Paper CT 5th European Workshop on Structural Health Monitoring CY JUN 28-JUL 04, 2010 CL Naples, ITALY SP AleniaAeronautica, CIRA, DAppolonia S p A, US AF Off Sci Res, Univ Pavia, Natl Res Council, Inst Composite & Biomed Mat AB This paper presents a variety of structural health monitoring (SHM) techniques, based on the use of piezoelectric active-sensors, used to determine the structural integrity of wind turbine blades, Specifically, Lamp wave propagations, frequency response functions, and time series based methods are utilized to estimate the condition of wind turbine blades. For experiments, a 1m section of a 9m CX100 blade is used. Overall, these three methods yielded a sufficient damage detection capability to warrant further investigation into field deployment. A full-scale fatigue test of a CX-100 wind turbine blade is also conducted. This paper summarizes considerations needed to design such SHM systems, experimental procedures and results, and practical implementation issues that can be used as guidelines for future investigations. C1 [Park, G.; Taylor, S. G.; Farinholt, K. M.; Farrar, C. R.] Los Alamos Natl Lab, Engn Inst, Los Alamos, NM 87545 USA. RP Park, G (reprint author), Los Alamos Natl Lab, Engn Inst, MS-T001, Los Alamos, NM 87545 USA. NR 4 TC 1 Z9 1 U1 1 U2 1 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-024-2 J9 STRUCT HLTH MONIT PY 2010 BP 321 EP 326 PG 6 WC Construction & Building Technology; Engineering, Civil SC Construction & Building Technology; Engineering GA BJG25 UT WOS:000328062600049 ER PT J AU Farrar, C Worden, K Park, G AF Farrar, C. Worden, K. Park, G. BE Casciati, F Giordano, M TI Complexity: A New Axiom for Structural Health Monitoring SO STRUCTURAL HEALTH MONITORING 2010 SE Structural Health Monitoring LA English DT Proceedings Paper CT 5th European Workshop on Structural Health Monitoring CY JUN 28-JUL 04, 2010 CL Naples, ITALY SP AleniaAeronautica, CIRA, DAppolonia S p A, US AF Off Sci Res, Univ Pavia, Natl Res Council, Inst Composite & Biomed Mat AB The basic purpose of the paper is simple; having proposed a set of axioms or 'basic truths' regarding Structural Health Monitoring (SHM) in a previous paper, the authors would like to extend the set by the proposal for a new axiom. This axiom relates to an observation that the presence of damage in a structure or system usually results in increased complexity of measured responses or features. It is argued that this observation could lead to principled means of selecting effective features for SHM. C1 [Farrar, C.; Park, G.] Los Alamos Natl Lab, Engn Inst, Los Alamos, NM 87545 USA. RP Farrar, C (reprint author), Los Alamos Natl Lab, Engn Inst, POB 1663, Los Alamos, NM 87545 USA. NR 6 TC 0 Z9 0 U1 0 U2 0 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA BN 978-1-60595-024-2 J9 STRUCT HLTH MONIT PY 2010 BP 882 EP 888 PG 7 WC Construction & Building Technology; Engineering, Civil SC Construction & Building Technology; Engineering GA BJG25 UT WOS:000328062600135 ER PT J AU Aytug, T Paranthaman, M Specht, ED Zhang, Y Kim, K Zuev, YL Cantoni, C Goyal, A Christen, DK Maroni, VA Chen, Y Selvamanickam, V AF Aytug, T. Paranthaman, M. Specht, E. D. Zhang, Y. Kim, K. Zuev, Y. L. Cantoni, C. Goyal, A. Christen, D. K. Maroni, V. A. Chen, Y. Selvamanickam, V. TI Enhanced flux pinning in MOCVD-YBCO films through Zr additions: systematic feasibility studies SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID SELF-ASSEMBLED NANODOTS; YBA2CU3O7-DELTA FILMS; COATED CONDUCTORS; CURRENT DENSITIES; NANORODS; DEPOSITION AB Systematic effects of Zr additions on the structural and flux pinning properties of YBa(2)Cu(3)O(7-delta) (YBCO) films deposited by metal-organic chemical vapor deposition (MOCVD) have been investigated. Detailed characterization, conducted by coordinated transport, x-ray diffraction, scanning and transmission electron microscopy analyses, and imaging Raman microscopy have revealed trends in the resulting property/performance correlations of these films with respect to varying mole percentages (mol%) of added Zr. For compositions <= 7.5 mol%, Zr additions lead to improved in-field critical current density, as well as extra correlated pinning along the c-axis direction of the YBCO films via the formation of columnar, self-assembled stacks of BaZrO(3) nanodots. C1 [Aytug, T.; Paranthaman, M.; Specht, E. D.; Zhang, Y.; Kim, K.; Zuev, Y. L.; Cantoni, C.; Goyal, A.; Christen, D. K.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Maroni, V. A.] Argonne Natl Lab, Argonne, IL 60439 USA. [Chen, Y.; Selvamanickam, V.] SuperPower Inc, Schenectady, NY 12304 USA. RP Aytug, T (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. EM aytugt@oml.gov RI Paranthaman, Mariappan/N-3866-2015; Cantoni, Claudia/G-3031-2013; Specht, Eliot/A-5654-2009 OI Paranthaman, Mariappan/0000-0003-3009-8531; Cantoni, Claudia/0000-0002-9731-2021; Specht, Eliot/0000-0002-3191-2163 FU US Department of Energy, Office of Electricity Delivery and Energy Reliability; LLC [DE-AC05-00OR22725]; [DEAC02-06CH11357] FX This work was done as part of the ORNL-SuperPower and the ANL-SuperPower CRADA and supported by the US Department of Energy, Office of Electricity Delivery and Energy Reliability. The research was performed at the Oak Ridge National Laboratory, managed by U.T.-Battelle, LLC for the USDOE under contract no. DE-AC05-00OR22725, and at Argonne National Laboratory under contract no. DEAC02-06CH11357 between UChicago Argonne, LLC and the USDOE. The imaging Raman microscopy was performed at the Argonne National Laboratory Center for Nanoscale Materials. NR 24 TC 28 Z9 29 U1 1 U2 15 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 014005 DI 10.1088/0953-2048/23/1/014005 PG 7 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400006 ER PT J AU Freyhardt, HC Lee, D Izumi, T AF Freyhardt, Herbert C. Lee, Dominic Izumi, Teruo TI Coated conductors and their applications SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Editorial Material C1 [Freyhardt, Herbert C.] Univ Houston, Houston, TX 77004 USA. [Lee, Dominic] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Izumi, Teruo] ISTEC, Tokyo, Japan. RP Freyhardt, HC (reprint author), Univ Houston, Houston, TX 77004 USA. NR 0 TC 0 Z9 0 U1 1 U2 3 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 010201 DI 10.1088/0953-2048/23/1/010201 PG 1 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400001 ER PT J AU Maroni, VA Kropf, AJ Aytug, T Paranthaman, M AF Maroni, V. A. Kropf, A. J. Aytug, T. Paranthaman, M. TI Raman and x-ray absorption spectroscopy characterization of Zr-doped MOCVD YBa2Cu3O6+delta SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID BENT SILICON CRYSTAL; COATED CONDUCTOR; LAUE GEOMETRY; FILMS; EXAFS; FLUORESCENCE; PARTICLES; IFEFFIT; SIZE AB Metal-organic chemical vapor deposited YBa2Cu3O6+delta (YBCO) films (about 0.9 mu m thick) containing varying amounts of added zirconium were examined by Raman microscopy and synchrotron x-ray absorption spectroscopy. The self-field and in-field (1 T, B parallel to c) J(c) performance of the YBCO films at 77 K (reported by the group at Oak Ridge National Laboratory that fabricated the samples) exhibited an increase on going from 0 mol% (m/o) Zr-added to 2.5 m/o Zr-added but then decreased sharply with increasing Zr content. Raman measurements on these films showed that the added Zr had little effect on YBCO cation disorder up to about 7.5 m/o Zr-added. Cation disorder increased while Ba-Cu-O content remained relatively constant for Zr additions >= 7.5 m/o. In the region of sharpest descent of J(c) with increasing Zr content (2.5-7.5 m/o Zr-added) neither the cation disorder nor the Ba-Cu-O content showed a systematic variation with J(c). Zirconium K edge x-ray absorption near-edge spectroscopy revealed that virtually all of the added Zr in each sample was present as a BaZrO3-like phase (BZO). The J(c) performance of the Zr-added films showed a high correlation with the variations in the next-nearest-neighbor Zr-M (M = Zr, Y) scattering path amplitude from the extended x-ray absorption fine structure (EXAFS) and the critical temperature over the full range of Zr additions and with cation disorder at the higher Zr- added levels (>7.5 m/o). There was no obvious correlation with the amount of residual barium cuprate or CuO. Approximate ranges for the BZO particle dimensions estimated from the EXAFS data indicated that the mean particle size gets larger with increasing Zr addition. C1 [Maroni, V. A.; Kropf, A. J.] Argonne Natl Lab, Argonne, IL 60439 USA. [Aytug, T.; Paranthaman, M.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Maroni, VA (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. EM maroni@anl.gov RI ID, MRCAT/G-7586-2011; Paranthaman, Mariappan/N-3866-2015 OI Paranthaman, Mariappan/0000-0003-3009-8531 FU US Department of Energy, Office of Electricity Delivery and Energy Reliability, Advanced Cables and Conductors; U TBattelle, LLC [DE-AC05-00OR22725]; UChicago Argonne, LLC and the USDOE [DE-AC02-06CH11357]; Department of Energy; MRCAT; US Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357] FX The assistance of Jon Hiller in adapting the milling procedure to our samples is gratefully acknowledged. The research described in this paper was supported by the US Department of Energy, Office of Electricity Delivery and Energy Reliability, Advanced Cables and Conductors. The work was performed at the Oak Ridge National Laboratory, managed by U TBattelle, LLC for the USDOE under Contract No DE-AC05-00OR22725, and at the Argonne National Laboratory under contract DE-AC02-06CH11357 between UChicago Argonne, LLC and the USDOE. MRCAT operations at the Advanced Photon Source are supported by the Department of Energy and the MRCAT member institutions. Use of the Advanced Photon Source and of Raman spectroscopy instrumentation at the Center for Nanoscale Materials was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract No. DE-AC02-06CH11357. NR 28 TC 7 Z9 7 U1 0 U2 12 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 014020 DI 10.1088/0953-2048/23/1/014020 PG 10 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400021 ER PT J AU Matias, V Rowley, EJ Coulter, Y Maiorov, B Holesinger, T Yung, C Glyantsev, V Moeckly, B AF Matias, Vladimir Rowley, E. John Coulter, Yates Maiorov, B. Holesinger, Terry Yung, Chris Glyantsev, Viktor Moeckly, Brian TI YBCO films grown by reactive co-evaporation on simplified IBAD-MgO coated conductor templates SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID BEAM-ASSISTED DEPOSITION; THIN-FILMS; YBA2CU3O7 FILMS; MICROWAVE; FABRICATION; EVAPORATION AB We demonstrate coated conductors fabricated by reactive co-evaporation of YBa(2)Cu(3)O(y) (YBCO) by cyclic deposition and reaction (RCE-CDR) on ion-beam-assisted-deposition-(IBAD-) textured templates simplified by the elimination of the epitaxial buffer layer. Hastelloy substrates, both polished and unpolished, were used as a starting material for the IBAD templates. Y(2)O(3) bed layers were then deposited followed by IBAD- textured MgO and a thin homoepitaxial MgO layer. The MgO-terminated templates were used for direct deposition of YBCO by RCE-CDR. Critical current densities obtained for the undoped YBCO material are comparable to the best values measured previously with the use of LaMnO(3) or SrTiO(3) epitaxial buffer layers and state-of-the-art coated conductor results. The structural characterization data indicate a well oriented YBCO film with a robust template. Electrical measurements also indicate no weak links and a typical magnetic field behavior of undoped YBCO, characterized by a low density of naturally occurring strong pinning centers and correlations along the ab direction. C1 [Matias, Vladimir; Rowley, E. John; Coulter, Yates; Maiorov, B.; Holesinger, Terry] Los Alamos Natl Lab, Superconduct Technol Ctr, Los Alamos, NM 87545 USA. [Yung, Chris; Glyantsev, Viktor; Moeckly, Brian] Superconductor Technol Inc, Santa Barbara, CA 93111 USA. RP Matias, V (reprint author), Los Alamos Natl Lab, Superconduct Technol Ctr, POB 1663, Los Alamos, NM 87545 USA. EM vlado@lanl.gov OI Maiorov, Boris/0000-0003-1885-0436 FU Department of Energy Office of Electricity Delivery and Energy Reliability FX We would like to thank Paul Dowden at LANL for his help in this work. The work at LANL is funded by the Department of Energy Office of Electricity Delivery and Energy Reliability. NR 18 TC 23 Z9 23 U1 3 U2 22 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 014018 DI 10.1088/0953-2048/23/1/014018 PG 5 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400019 ER PT J AU Pleva, EF Mehrotra, V Schwenterly, SW AF Pleva, E. F. Mehrotra, V. Schwenterly, S. W. TI Conductor requirements for high-temperature superconducting utility power transformers SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID HTS TRANSFORMER; WINDINGS; TESTS AB High-temperature superconducting (HTS) coated conductors in utility power transformers must satisfy a set of operating requirements that are driven by two major considerations-HTS transformers must be economically competitive with conventional units, and the conductor must be robust enough to be used in a commercial manufacturing environment. The transformer design and manufacturing process will be described in order to highlight the various requirements that it imposes on the HTS conductor. Spreadsheet estimates of HTS transformer costs allow estimates of the conductor cost required for an HTS transformer to be competitive with a similarly performing conventional unit. C1 [Pleva, E. F.; Mehrotra, V.] Waukesha Elect Syst, Waukesha, WI 53186 USA. [Schwenterly, S. W.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Pleva, EF (reprint author), Waukesha Elect Syst, Waukesha, WI 53186 USA. EM Ed.Pleva@Waukesha.spx.com NR 24 TC 10 Z9 10 U1 0 U2 3 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 014025 DI 10.1088/0953-2048/23/1/014025 PG 5 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400026 ER PT J AU Selvamanickam, V Guevara, A Zhang, Y Kesgin, I Xie, Y Carota, G Chen, Y Dackow, J Zhang, Y Zuev, Y Cantoni, C Goyal, A Coulter, J Civale, L AF Selvamanickam, V. Guevara, A. Zhang, Y. Kesgin, I. Xie, Y. Carota, G. Chen, Y. Dackow, J. Zhang, Y. Zuev, Y. Cantoni, C. Goyal, A. Coulter, J. Civale, L. TI Enhanced and uniform in-field performance in long (Gd, Y)-Ba-Cu-O tapes with zirconium doping fabricated by metal-organic chemical vapor deposition SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID COATED CONDUCTORS; IBAD MGO; FILMS AB The influence of Zr doping in (Gd, Y)-Ba-Cu-O ((Gd, Y)BCO) tapes made by metal-organic chemical vapor deposition has been studied with a specific objective of uniform and reproducible enhancement in in-field critical current (I(c)) over long lengths. 50 m long tapes with 7.5 and 10 at.% Zr doping in 1 mu m thick (Gd, Y) BCO films have been found to exhibit a sharply enhanced peak in I(c) in the orientation of field parallel to the c-axis and retain 28% of their self-field I(c) value at 77 K and 1 T. BaZrO(3) (BZO) nanocolumn density in the cross-sectional microstructure was found to increase with increasing Zr addition. The end segments of the 50 m long tapes were found to display nearly identical angular dependence of critical current at 77 K and 1 T, indicative of the uniformity in in-field performance over this length. A 610 m long tape was fabricated with 10% Zr doping and a 130 m segment showed a 3.2% uniformity in critical current measured every meter in the orientation of B parallel to c-axis. A retention factor of 36% of the zero-field I(c) value measured at 0.52 T over the 130 m is consistent with that obtained in short samples. C1 [Selvamanickam, V.; Guevara, A.; Zhang, Y.; Kesgin, I.] Univ Houston, Texas Ctr Superconduct, Houston, TX 77059 USA. [Selvamanickam, V.; Guevara, A.; Zhang, Y.; Kesgin, I.] Univ Houston, Dept Mech Engn, Houston, TX 77059 USA. [Xie, Y.; Carota, G.; Chen, Y.; Dackow, J.] SuperPower Inc, Schenectady, NY 12304 USA. [Zhang, Y.; Zuev, Y.; Cantoni, C.; Goyal, A.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Coulter, J.; Civale, L.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Selvamanickam, V (reprint author), Univ Houston, Texas Ctr Superconduct, Houston, TX 77059 USA. RI Kesgin, Ibrahim/A-4178-2012; Cantoni, Claudia/G-3031-2013; OI Cantoni, Claudia/0000-0002-9731-2021; Civale, Leonardo/0000-0003-0806-3113 FU US Department of Energy [DE-AC05-00OR22725] FX The work at the University of Houston and SuperPower was partially supported by the US Department of Energy through a contract with UT-Battelle. Research at ORNL was sponsored by the US Department of Energy, Office of Electricity Delivery and Energy Reliability-Superconductivity Program, under contract DE-AC05-00OR22725 with UT-Battelle, LLC managing contractor for Oak Ridge National Laboratory. NR 16 TC 34 Z9 35 U1 0 U2 11 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 014014 DI 10.1088/0953-2048/23/1/014014 PG 6 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400015 ER PT J AU Solovyov, VF Develos-Bagarinao, K Li, Q Qing, J Zhou, J AF Solovyov, Vyacheslav F. Develos-Bagarinao, Katherine Li, Qiang Qing, Jie Zhou, Juan TI Nature of Y1Ba2Cu3O7 nucleation centers on ceria buffers SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID YBCO COATED CONDUCTORS; TFA-MOD PROCESS; THIN-FILMS; GROWTH-MECHANISM; DEPOSITION; SUBSTRATE; PROGRESS; SURFACE; SIZE; MICROSTRUCTURE AB The purpose of this study is to enhance properties of the second-generation wires by increasing the density of Y1Ba2Cu3O7 (YBCO) nucleation centers on the surface of the ceria buffer. To identify the nature of the nucleation centers, we compare nucleation kinetics and performance of YBCO layers deposited by the metal-organic process on a standard RABiTS tape to YBCO on ceria buffers with well-controlled structure and surface morphology. The structure of the YBCO layer at the early stage of nucleation and growth is determined by high-flux synchrotron x-ray diffraction. It is shown that the best buffers exhibit high YBCO nucleation rates and produce YBCO nuclei with the least cation disorder. The high YBCO nucleation rate is associated with a high density of threading dislocation outcrops. A strategy for buffer optimization is identified. C1 [Solovyov, Vyacheslav F.; Li, Qiang; Qing, Jie; Zhou, Juan] Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. [Develos-Bagarinao, Katherine] AIST Tsukuba Cent 2, Natl Inst Adv Ind Sci & Technol, Tsukuba, Ibaraki 3058568, Japan. RP Solovyov, VF (reprint author), Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. RI Develos-Bagarinao, Katherine/C-6649-2011; Solovyov, Vyacheslav/A-7724-2009; OI Develos-Bagarinao, Katherine/0000-0001-6846-191X; Solovyov, Vyacheslav/0000-0003-1879-9802 FU Brookhaven Science Associates, LLC [DE-AC02-98CH10886]; US Department of Energy, Office of Basic Energy Sciences [DE-AC02-98CH10886] FX This paper has been authored by Brookhaven Science Associates, LLC under contract no. DE-AC02-98CH10886 with the US Department of Energy, Office of Electricity Delivery and Energy Reliability. Research was carried out in part at the Center for Functional Nanomaterials and National Synchrotron Light Source (Beamline X-18A), Brookhaven National Laboratory, which are supported by the US Department of Energy, Office of Basic Energy Sciences, under contract no. DE-AC02-98CH10886. We greatly appreciate support from Martin Rupich and Xiaoping Li from American Superconductor Corporation, who provided the RABiTS tape and the precursor films for the study. We are grateful to Steven Ehrlich of NSLS for assistance during the beamline experiments and Arnie Moodebaugh for comments and suggestions. NR 53 TC 19 Z9 21 U1 1 U2 19 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 014008 DI 10.1088/0953-2048/23/1/014008 PG 10 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400009 ER PT J AU Stan, L Chen, Y Xiong, X Holesinger, TG Maiorov, B Civale, L DePaula, RF Selvamanickam, V Jia, QX AF Stan, L. Chen, Y. Xiong, X. Holesinger, T. G. Maiorov, B. Civale, L. DePaula, R. F. Selvamanickam, V. Jia, Q. X. TI Investigation of (Y, Gd)Ba2Cu3O7-x grown by MOCVD on a simplified IBAD MgO template SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID YBCO-COATED CONDUCTORS; DEPOSITION; SUPERCONDUCTORS; PROGRESS AB We have used an ion beam sputtered Y2O3-Al2O3 (YALO) composite to simplify the architecture of high temperature superconducting (HTS) coated conductors (CCs) based on a IBAD MgO template. By implementing YALO, we have reduced the total non-superconducting layers between the polycrystalline metal substrate and the superconducting film from five ( the standard architecture) to four. Well textured (Y, Gd)Ba2Cu3O7-x ((Y, Gd)BCO) films have been successfully grown by MOCVD on this simplified template. The microstructural characterization revealed that all layers are continuous and uniform with sharp and clean interfaces. Additionally, the YALO maintained its amorphous nature after the deposition of the superconductive layer, which is a plus in terms of its efficiency as a diffusion barrier. The achievement of a self-field critical current of 230 A cm(-1) at 75.5 K is another proof of the effectiveness of YALO as a diffusion barrier and nucleation seed for the MgO. The transport properties under an applied magnetic field of MOCVD grown (Y, Gd) BCO on LMO buffered MgO/YALO/Ni-alloy are comparable with those of (Y, Gd) BCO on a standard architecture, thus demonstrating good compatibility between the simplified template with the MOCVD grown (Y, Gd)BCO. The use of a single composite YALO layer instead of individual layers of Y2O3 and Al2O3 for the large scale fabrication of HTS CCs based on IBAD MgO provides advantages such as potentially reduced cost due to the reduced number of fabrication steps. C1 [Stan, L.; Holesinger, T. G.; Maiorov, B.; Civale, L.; DePaula, R. F.; Jia, Q. X.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Chen, Y.] SuperPower Inc, Schenectady, NY 12304 USA. [Xiong, X.; Selvamanickam, V.] Univ Houston, Dept Mech Engn, Houston, TX 77204 USA. RP Stan, L (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. RI Jia, Q. X./C-5194-2008; OI Maiorov, Boris/0000-0003-1885-0436; Civale, Leonardo/0000-0003-0806-3113 NR 16 TC 5 Z9 5 U1 0 U2 16 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 014011 DI 10.1088/0953-2048/23/1/014011 PG 4 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400012 ER PT J AU Thompson, JR Sinclair, JW Christen, DK Zhang, YF Zuev, YL Cantoni, C Chen, YM Selvamanickam, V AF Thompson, J. R. Sinclair, J. W. Christen, D. K. Zhang, Yifei Zuev, Y. L. Cantoni, C. Chen, Yimin Selvamanickam, V. TI Field, temperature, and angle dependent critical current density J(c)(H, T, theta) in coated conductors obtained via contact-free methods SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID SUPERCONDUCTORS; MAGNETIZATION; FILMS AB Applications of coated conductors based on high-T-c superconductors often require detailed knowledge of their critical current density J(c) as a function of magnetic field orientation as well as field strength and temperature. This work demonstrates experimental methods for obtaining the angularly dependent J(c) using contact-free magnetic measurements, and qualifies those methods using several well defined conditions. The studies complement traditional transport techniques and are readily extended to conditions of field and temperature where the current density is very large and transport methods become difficult. Results on representative materials are presented. C1 [Thompson, J. R.; Christen, D. K.; Zhang, Yifei; Zuev, Y. L.; Cantoni, C.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. [Thompson, J. R.; Sinclair, J. W.] Univ Tennessee, Dept Phys, Knoxville, TN 37996 USA. [Chen, Yimin; Selvamanickam, V.] SuperPower Inc, Schenectady, NY 12304 USA. RP Thompson, JR (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. RI Sinclair, John/E-7692-2011; Cantoni, Claudia/G-3031-2013 OI Cantoni, Claudia/0000-0002-9731-2021 FU Division of Materials Sciences and Engineering, Office of Basic Energy Sciences, US Department of Energy; US Department of Energy, Office of Electricity Delivery and Energy Reliability [DE-AC05-00OR22725] FX We wish to thank F A List and S W Cook for assistance in preparing the samples. The work of JWS was supported by the Division of Materials Sciences and Engineering, Office of Basic Energy Sciences, US Department of Energy, and research at ORNL was sponsored by the US Department of Energy, Office of Electricity Delivery and Energy Reliability, Superconductivity Program for Electric Power Systems, under contract No. DE-AC05-00OR22725 with UT-Battelle, LLC. NR 18 TC 11 Z9 11 U1 1 U2 12 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 014002 DI 10.1088/0953-2048/23/1/014002 PG 6 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400003 ER PT J AU Wee, SH Shin, J Cantoni, C Zuev, YL Cook, S Goyal, A AF Wee, Sung Hun Shin, Junsoo Cantoni, Claudia Zuev, Yuri L. Cook, Sy Goyal, Amit TI Multifunctional, phase separated, BaTiO3 + CoFe2O4 cap buffer layers for improved flux-pinning in YBa2Cu3O7-delta based coated conductors SO SUPERCONDUCTOR SCIENCE & TECHNOLOGY LA English DT Article ID SELF-ASSEMBLED NANODOTS; YBA2CU3O7-DELTA FILMS; PERFORMANCE AB Phase separated, epitaxial, nanostructured film comprised of BaTiO3 (BTO) and CoFe2O4 (CFO) composite has been developed as a potential multifunctional cap buffer layer for improved flux-pinning in YBa2Cu3O7-delta (YBCO) films. All films were deposited by pulsed laser deposition on SrTiO3 (STO) (100) single crystal substrates. The CFO fraction and growth temperature were identified as key factors for determining the areal number density and mean diameter of the CFO nanocolumns. Compared to the reference sample grown on a pure BTO cap layer, the YBCO films grown on BTO + CFO cap layers show a remarkable improvement in isotropic flux-pinning and, consequently, J(c) over the entire field and angle ranges. Transmission electron microscopy analysis confirmed the presence of a very defective YBCO layer containing a high density of randomly distributed defects at the interface area, induced by nanostructural modulation on the surface of the BTO + CFO composite cap layer. C1 [Wee, Sung Hun; Shin, Junsoo; Cantoni, Claudia; Zuev, Yuri L.; Cook, Sy; Goyal, Amit] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Wee, Sung Hun] Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. [Zuev, Yuri L.] Univ Tennessee, Dept Phys, Knoxville, TN 37996 USA. RP Wee, SH (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RI Cantoni, Claudia/G-3031-2013 OI Cantoni, Claudia/0000-0002-9731-2021 FU US Department of Energy, Office of Electricity Delivery and Energy Reliability-Superconductivity Program [DE-AC05-00OR22725]; Oak Ridge National Laboratory (ORNL) FX Junsoo Shin would like to thank Oak Ridge Associated Universities for a postdoctoral fellowship. Sung Hun Wee would like to thank the support from the University of Tennessee, Knoxville. We would like to thank Clifford C Davisson for preparing the LMO + MgO target by powder mixing, compaction and sintering. Research was partially sponsored by the US Department of Energy, Office of Electricity Delivery and Energy Reliability-Superconductivity Program (under contract DE-AC05-00OR22725) and partially by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory (ORNL), managed by UT-Battelle, LLC for the US Department of Energy. NR 12 TC 11 Z9 11 U1 0 U2 10 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0953-2048 J9 SUPERCOND SCI TECH JI Supercond. Sci. Technol. PD JAN PY 2010 VL 23 IS 1 AR 014007 DI 10.1088/0953-2048/23/1/014007 PG 7 WC Physics, Applied; Physics, Condensed Matter SC Physics GA 530SA UT WOS:000272611400008 ER PT S AU Sanders, D Edwards, P Ramulu, M Grant, G AF Sanders, Daniel Edwards, Paul Ramulu, M. Grant, Glenn BE Sanders, DG TI Optimization of the Friction Stir Welding Process for Superplastic Forming and Improved Surface Texture for Titanium Aerospace Structures SO SUPERPLASTICITY IN ADVANCED MATERIALS SE Key Engineering Materials LA English DT Proceedings Paper CT 10th International Conference on Superplasticity in Advanced Materials CY JUN 29-JUL 02, 2009 CL Seattle, WA SP Univ Washington, Dept Mech Engn & Educ Outreach Program, ICSAM 2009 Comm DE friction stir welding; superplastic forming; superplasticity; surface texture; surface roughness; titanium; 6Al-4V; fine grain titanium; fatigue; aircraft structure; pin tool feed marks ID 6AL-4V AB In friction stir welding (FSW), the semi-circular shaped FSW pin tool feed marks that are left behind varied in depth and shape which are detrimental not only in fatigue performance but also in further processing such as superplastic forming (SPF). Experimental investigation was conducted to determine the effects of changes to the FSW process parameters on the surface roughness of the weld of fine grain 2 mm thick titanium alloy, Ti- 6Al-4V. In addition to optimizing the surface texture of the welds, the superplastic performance of the weld nugget was made to be equal to the superplasticity of the parent metal by altering the spindle speed and feed rate used during FSW to identify the quality in terms of cold weld or hot weld. FSW process conditions of spindle speed of 500 RPM and a feed rate of 150 mm/min was found to produce a uniform deformation in both weld and parent metal when the joint was superplastc formed. C1 [Sanders, Daniel; Edwards, Paul] Boeing Co, POB 3707,MS 5K-63, Seattle, WA 98124 USA. [Sanders, Daniel; Edwards, Paul; Ramulu, M.] Univ Washington, Dept Mech Engn, Seattle, WA 98195 USA. [Grant, Glenn] Pacific Northwest Natl Lab, Energy Mat & Mfg, Richland, WA 99352 USA. RP Sanders, D (reprint author), Boeing Co, POB 3707,MS 5K-63, Seattle, WA 98124 USA. EM daniel.g.sanders@boeing.com; paul.d.edwards2@boeing.com; ramulum@u.washington.edu; glenn.grant@pnl.gov NR 8 TC 3 Z9 3 U1 2 U2 14 PU TRANS TECH PUBLICATIONS LTD PI DURNTEN-ZURICH PA KREUZSTRASSE 10, 8635 DURNTEN-ZURICH, SWITZERLAND SN 1013-9826 J9 KEY ENG MATER PY 2010 VL 433 BP 153 EP + DI 10.4028/www.scientific.net/KEM.433.153 PG 3 WC Materials Science, Multidisciplinary SC Materials Science GA BPU10 UT WOS:000279945300018 ER PT J AU Moyer, BA Sloop, FV Fowler, CJ Haverlock, TJ Kang, HA Delmau, LH Bau, DM Hossain, MA Bowman-James, K Shriver, JA Bill, NL Gross, DE Marquez, M Lynch, VM Sessler, JL AF Moyer, Bruce A. Sloop, Frederick V., Jr. Fowler, Christopher J. Haverlock, Tamara J. Kang, Hyun-Ah Delmau, Laetitia H. Bau, Diadra M. Hossain, Md Alamgir Bowman-James, Kristin Shriver, James A. Bill, Nathan L. Gross, Dustin E. Marquez, Manuel Lynch, Vincent M. Sessler, Jonathan L. TI Enhanced liquid-liquid anion exchange using macrocyclic anion receptors: effect of receptor structure on sulphate-nitrate exchange selectivity SO SUPRAMOLECULAR CHEMISTRY LA English DT Article DE liquid-liquid anion exchange; anion binding; macrocycle; calixpyrrole; equilibrium model; extraction ID ION-PAIR RECEPTOR; SOLVENT-EXTRACTION; HOFMEISTER BIAS; QUATERNARY AMMONIUM; BINDING; CALIXPYRROLES; COMPLEXES; SALT; METHYLTRIOCTYLAMMONIUM; COORDINATION AB When certain macrocyclic anion receptors are added to a chloroform solution of the nitrate form of a lipophilic quaternary ammonium salt (methyltri-C8,10-ammonium nitrate, Aliquat 336N), the extraction of sulphate from an aqueous sodium nitrate solution via exchange with the organic-phase nitrate is significantly enhanced. Eight macrocycles were surveyed, including two derivatives of a tetraamide macrocycle, five derivatives of calix[4]pyrrole and -decafluorocalix[5]pyrrole. Under the hypothesis that the enhancement originates from sulphate binding by the anion receptors in the chloroform phase, it was possible to obtain reasonable fits to the sulphate distribution survey data based on the formation of 1:1 and 2:1 receptor:sulphate complexes in the chloroform phase. Apparent 1:1 sulphate-binding constants obtained from the model in this system fell in the range [image omitted]. Comparison of the results for the various anion receptors included in this study reveals that sulphate binding is sensitive to the nature of the substituents on the parent macrocycle scaffolds in a way that does not follow straightforwardly from simple chemical expectations, such as electron-withdrawing effects on hydrogen-bond donor strength. C1 [Moyer, Bruce A.; Sloop, Frederick V., Jr.; Fowler, Christopher J.; Haverlock, Tamara J.; Kang, Hyun-Ah; Delmau, Laetitia H.; Bau, Diadra M.] Oak Ridge Natl Lab, Div Chem Sci, Oak Ridge, TN 37831 USA. [Hossain, Md Alamgir; Bowman-James, Kristin] Univ Kansas, Dept Chem, Lawrence, KS 66045 USA. [Shriver, James A.; Bill, Nathan L.; Gross, Dustin E.; Marquez, Manuel; Lynch, Vincent M.; Sessler, Jonathan L.] Univ Texas Austin, Inst Cellular & Mol Biol, Dept Chem & Biochem, Austin, TX 78712 USA. RP Moyer, BA (reprint author), Oak Ridge Natl Lab, Div Chem Sci, POB 2008, Oak Ridge, TN 37831 USA. EM moyerba@ornl.gov; kbjames@ku.edu; sessler@mail.utexas.edu RI Gross, Dustin/B-4249-2011; Sloop, Jr., Frederick/J-2301-2016; Moyer, Bruce/L-2744-2016; OI Gross, Dustin/0000-0001-8668-3380; Sloop, Jr., Frederick/0000-0001-6473-9507; Moyer, Bruce/0000-0001-7484-6277; Bill, Nathan/0000-0001-9432-3182 FU Division of Chemical Sciences, Geosciences and Biosciences, Office Basic Energy Sciences, US Department of Energy; US Department of Energy [DE-FG02-04ER63741, DE-FG02-01ER15186, DE-FG02-04ER63745]; National Science Foundation [CHE-0316623]; University of Malaga (Junta de Andalucia) [P09-TEP-5369] FX Research at Oak Ridge National Laboratory (ORNL) was sponsored by the Division of Chemical Sciences, Geosciences and Biosciences, Office Basic Energy Sciences, US Department of Energy. Research at the University of Texas at Austin was supported by the US Department of Energy (Grant Nos DE-FG02-04ER63741 and DE-FG02-01ER15186 to J.L.S.). Work at the University of Kansas was supported by US Department of Energy (Grant No. DE-FG02-04ER63745 to K.B.-J.) and the National Science Foundation (Grant No. CHE-0316623 to K.B.-J.). M.M. gratefully acknowledges partial funding for this work from University of Malaga (Junta de Andalucia), Project P09-TEP-5369 in collaboration with Prof. Ignacio Loscertales. NR 68 TC 19 Z9 19 U1 2 U2 22 PU TAYLOR & FRANCIS LTD PI ABINGDON PA 4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND SN 1061-0278 J9 SUPRAMOL CHEM JI Supramol. Chem. PY 2010 VL 22 IS 11-12 SI SI BP 653 EP 671 AR PII 929556568 DI 10.1080/10610271003763263 PG 19 WC Chemistry, Multidisciplinary SC Chemistry GA 682QN UT WOS:000284418200003 ER PT B AU Vugrin, ED Warren, DE Ehlen, MA Camphouse, RC AF Vugrin, Eric D. Warren, Drake E. Ehlen, Mark A. Camphouse, R. Chris BE Gopalakrishnan, K Peeta, S TI A Framework for Assessing the Resilience of Infrastructure and Economic Systems SO SUSTAINABLE AND RESILIENT CRITICAL INFRASTRUCTURE SYSTEMS: SIMULATION, MODELING, AND INTELLIGENT ENGINEERING LA English DT Article; Book Chapter AB Recent U.S. national mandates are shilling the country's homeland security policy from one of asset-level critical infrastructure protection (CIP) to all-hazards critical infrastructure resilience, creating the need for a unifying framework for assessing the resilience of critical infrastructure systems and the economies that rely on them. Resilience has been defined and applied in many disciplines; consequently, many disparate approaches exist. We propose a general framework for assessing the resilience of infrastructure and economic systems. The framework consists of three primary components: (I) a definition of resilience that is specific to infrastructure systems; (2) a quantitative model for measuring the resilience of systems to disruptive events through the evaluation of both impacts to system performance and the cost of recovery; and (3) a qualitative method for assessing the system properties that inherently determine system resilience, providing insight and direction for potential improvements in these systems. C1 [Vugrin, Eric D.; Warren, Drake E.; Ehlen, Mark A.] Sandia Natl Labs, Infrastruct & Econ Syst Anal Dept, Albuquerque, NM 87185 USA. [Camphouse, R. Chris] Sandia Natl Labs, Performance Assessment & Decis Anal Dept, Carlsbad, NM USA. RP Vugrin, ED (reprint author), Sandia Natl Labs, Infrastruct & Econ Syst Anal Dept, POB 5800, Albuquerque, NM 87185 USA. EM edvugri@sandia.gov; dewarre@sandia.gov; maehlen@sandia.gov; rccamph@sandia.gov NR 33 TC 34 Z9 35 U1 0 U2 4 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY BN 978-3-642-11404-5 PY 2010 BP 77 EP 116 DI 10.1007/978-3-642-11405-2_3 D2 10.1007/978-3-642-11405-2 PG 40 WC Computer Science, Artificial Intelligence; Engineering, Civil SC Computer Science; Engineering GA BOV52 UT WOS:000277773800003 ER PT B AU Viamajala, S Donohoe, BS Decker, SR Vinzant, TB Selig, MJ Himmel, ME Tucker, MP AF Viamajala, Sridhar Donohoe, Bryon S. Decker, Stephen R. Vinzant, Todd B. Selig, Michael J. Himmel, Michael E. Tucker, Melvin P. BE Singh, OV Harvey, SP TI Heat and Mass Transport in Processing of Lignocellulosic Biomass for Fuels and Chemicals SO SUSTAINABLE BIOTECHNOLOGY: SOURCES OF RENEWABLE ENERGY LA English DT Article; Book Chapter DE Lignocellulose; Biomass; Biofuels; Heat transport; Mass transport ID ALKALINE PEROXIDE DELIGNIFICATION; SULFURIC-ACID PRETREATMENT; HIGH-SOLIDS CONCENTRATIONS; CELL-WALL POROSITY; CORN STOVER; ENZYMATIC-HYDROLYSIS; PHANEROCHAETE-CHRYSOSPORIUM; ETHANOL-PRODUCTION; BETA-GLUCOSIDASE; CATALYTIC MODULE AB Lignocellulosic biomass, a major feedstock for renewable biofuels and chemicals, is processed by various thermochemical and/or biochemical means. This multi-step processing often involves reactive transformations limited by heat and mass transport. These limitations are dictated by restrictions including (1) plant anatomy, (2) complex ultra-structure and chemical composition of plant cell walls., (3) process engineering requirements or, (4) a combination of these factors. The plant macro- and micro-structural features impose limitations on chemical and enzyme accessibility to carbohydrate containing polymers (cellulose and hemicellulose) which can limit conversion rates and extents. Multiphase systems containing insoluble substrates, soluble catalysts and, in some cases, gaseous steam can pose additional heat and mass transfer restrictions leading to non-uniform reactions. In this chapter, some of these transport challenges relevant to biochemical conversion are discussed in order to underscore the importance of a fundamental understanding of these processes for development of robust and cost-effective routes to fuels and products from lignocellulosic biomass. C1 [Viamajala, Sridhar] Univ Toledo, Dept Chem & Environm Engn, Toledo, OH 43606 USA. [Tucker, Melvin P.] Natl Renewable Energy Lab, Natl Bioenergy Ctr, Golden, CO 80401 USA. [Donohoe, Bryon S.; Decker, Stephen R.; Vinzant, Todd B.; Selig, Michael J.; Himmel, Michael E.] Natl Renewable Energy Lab, Chem & Biosci Ctr, Golden, CO 80401 USA. RP Viamajala, S (reprint author), Univ Toledo, Dept Chem & Environm Engn, 2801 W Bancroft St, Toledo, OH 43606 USA. EM sridhar.viamajala@utoledo.edu; Bryon.Donohoe@nrel.gov; Steve.Decker@nrel.gov; Todd.Vinzant@nrel.gov; Michael.Selig@nrel.gov; Mike.Himmel@nrel.gov; Melvin.Tucker@nrel.gov NR 65 TC 11 Z9 11 U1 0 U2 6 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES BN 978-90-481-3294-2 PY 2010 BP 1 EP 18 DI 10.1007/978-90-481-3295-9_1 D2 10.1007/978-90-481-3295-9 PG 18 WC Biotechnology & Applied Microbiology SC Biotechnology & Applied Microbiology GA BND55 UT WOS:000274229200001 ER PT J AU Clark, WW AF Clark, Woodrow W., II BE Clark, WW TI Sustainable Communities Design Handbook Green Engineering, Architecture, and Technology Introduction SO SUSTAINABLE COMMUNITIES DESIGN HANDBOOK: GREEN ENGINEERING, ARCHITECTURE, AND TECHNOLOGY LA English DT Editorial Material; Book Chapter C1 [Clark, Woodrow W., II] Lawrence Livermore Natl Lab, Livermore, CA USA. [Clark, Woodrow W., II] Clark Strateg Partners, Los Angeles, CA USA. RP Clark, WW (reprint author), Clark Strateg Partners, Los Angeles, CA USA. NR 5 TC 0 Z9 0 U1 0 U2 1 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS BN 978-0-08-096336-5 PY 2010 BP 1 EP 8 DI 10.1016/B978-1-85617-804-4.00001-X PG 8 WC Architecture; Construction & Building Technology; Engineering, Environmental; Engineering, Civil SC Architecture; Construction & Building Technology; Engineering GA BEQ85 UT WOS:000317755400003 ER PT B AU Clark, WW Cooke, G AF Clark, Woodrow W., II Cooke, Grant BE Clark, WW TI The Third Industrial Revolution SO SUSTAINABLE COMMUNITIES DESIGN HANDBOOK: GREEN ENGINEERING, ARCHITECTURE, AND TECHNOLOGY LA English DT Article; Book Chapter C1 [Clark, Woodrow W., II] Lawrence Livermore Natl Lab, Livermore, CA USA. [Clark, Woodrow W., II] Clark Strateg Partners, Los Angeles, CA USA. RP Clark, WW (reprint author), Clark Strateg Partners, Los Angeles, CA USA. NR 9 TC 0 Z9 0 U1 0 U2 0 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS BN 978-0-08-096336-5 PY 2010 BP 9 EP 22 DI 10.1016/B978-1-85617-804-4.00002-1 PG 14 WC Architecture; Construction & Building Technology; Engineering, Environmental; Engineering, Civil SC Architecture; Construction & Building Technology; Engineering GA BEQ85 UT WOS:000317755400004 ER PT B AU Clark, WW AF Clark, Woodrow W., II BE Clark, WW TI Sustainable Communities Design Handbook Green Engineering, Architecture, and Technology PREFACE SO SUSTAINABLE COMMUNITIES DESIGN HANDBOOK: GREEN ENGINEERING, ARCHITECTURE, AND TECHNOLOGY LA English DT Editorial Material; Book Chapter C1 [Clark, Woodrow W., II] Lawrence Livermore Natl Lab, Livermore, CA USA. [Clark, Woodrow W., II] Clark Strateg, Los Angeles, CA USA. RP Clark, WW (reprint author), Clark Strateg, Los Angeles, CA USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS BN 978-0-08-096336-5 PY 2010 BP XVII EP XVIII DI 10.1016/B978-1-85617-804-4.00017-3 PG 2 WC Architecture; Construction & Building Technology; Engineering, Environmental; Engineering, Civil SC Architecture; Construction & Building Technology; Engineering GA BEQ85 UT WOS:000317755400002 ER PT B AU Schultz, D Clark, WW Sowell, A AF Schultz, Don Clark, Woodrow W., II Sowell, Arnie BE Clark, WW TI Life-Cycle Analysis The Economic Analysis of Demand-Side Programs and Projects in California SO SUSTAINABLE COMMUNITIES DESIGN HANDBOOK: GREEN ENGINEERING, ARCHITECTURE, AND TECHNOLOGY LA English DT Article; Book Chapter C1 [Clark, Woodrow W., II] Lawrence Livermore Natl Lab, Livermore, CA USA. [Clark, Woodrow W., II] Clark Strateg Partners, Los Angeles, CA USA. NR 1 TC 0 Z9 0 U1 0 U2 0 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS BN 978-0-08-096336-5 PY 2010 BP 99 EP 137 DI 10.1016/B978-1-85617-804-4.00007-0 PG 39 WC Architecture; Construction & Building Technology; Engineering, Environmental; Engineering, Civil SC Architecture; Construction & Building Technology; Engineering GA BEQ85 UT WOS:000317755400009 ER PT B AU Clark, WW Sowell, A Schultz, D AF Clark, Woodrow W., II Sowell, Arnie Schultz, Don BE Clark, WW TI California Standard Practice Manual Economic Analysis of Demand-Side Programs and Projects SO SUSTAINABLE COMMUNITIES DESIGN HANDBOOK: GREEN ENGINEERING, ARCHITECTURE, AND TECHNOLOGY LA English DT Article; Book Chapter C1 [Clark, Woodrow W., II] Lawrence Livermore Natl Lab, Livermore, CA USA. [Clark, Woodrow W., II] Clark Strateg Partners, Los Angeles, CA USA. RP Clark, WW (reprint author), Clark Strateg Partners, Los Angeles, CA USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS BN 978-0-08-096336-5 PY 2010 BP 277 EP 312 DI 10.1016/B978-1-85617-804-4.00018-5 PG 36 WC Architecture; Construction & Building Technology; Engineering, Environmental; Engineering, Civil SC Architecture; Construction & Building Technology; Engineering GA BEQ85 UT WOS:000317755400017 ER PT B AU Clark, WW AF Clark, Woodrow W., II CA Los Angeles Community Coll Dist BE Clark, WW TI Request for Qualifications SO SUSTAINABLE COMMUNITIES DESIGN HANDBOOK: GREEN ENGINEERING, ARCHITECTURE, AND TECHNOLOGY LA English DT Article; Book Chapter C1 [Clark, Woodrow W., II] Lawrence Livermore Natl Lab, Livermore, CA USA. [Clark, Woodrow W., II] Clark Strateg Partners, Los Angeles, CA USA. RP Clark, WW (reprint author), Clark Strateg Partners, Los Angeles, CA USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA SARA BURGERHARTSTRAAT 25, PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS BN 978-0-08-096336-5 PY 2010 BP 313 EP 366 DI 10.1016/B978-1-85617-804-4.00022-7 PG 54 WC Architecture; Construction & Building Technology; Engineering, Environmental; Engineering, Civil SC Architecture; Construction & Building Technology; Engineering GA BEQ85 UT WOS:000317755400018 ER PT B AU Febrer, M Abberton, MT Jenkins, G Milbourne, D AF Febrer, Melanie Abberton, Michael T. Jenkins, Glyn Milbourne, Dan BE Huyghe, C TI Exploring the Potential for Translational Genomics Approaches in Forage Legumes: Regions of Highly Conserved Microsynteny Between White Clover and Medicago truncatula Revealed by BAC Sequencing SO SUSTAINABLE USE OF GENETIC DIVERSITY IN FORAGE AND TURF BREEDING LA English DT Proceedings Paper CT Conference of the Eucarpia Fodder and Amenity Species Section CY 2009 CL La Rochelle, FRANCE SP French Assoc Forage & Turf Breeders ID TRIFOLIUM-REPENS L. AB The model legume species Medicago truncatula is a potentially useful tool for gene discovery in white clover using translational genomics strategies. A prerequisite to the practical implementation of this approach is a good understanding of the extent of conservation of gene order between the species. Previous studies have demonstrated conservation at the macrosyntenic level, but no published information exists on the extent of conserved microsynteny between these species. In a previously published study, we reported the construction of a BAC library of white clover, the end sequencing of approximately 700 clover BACs, and the comparison of these BAC-end sequences to the M. truncatula genome. We found that 14 paired BAC-ends were shown to have the equivalent pairs of M. truncatula sequence on the same M. truncatula BAC clone or contig sequence within a span of 25-200 Kb, suggesting they represent orthologous regions in the two species. In this follow-up analysis, we have chosen five of these BACs, sequenced them to approximately six-fold coverage, and compared the resulting assembled contigs to their putatively equivalent regions of M. truncatula. Highly conserved gene content and almost complete conservation of gene order and orientation for all five sequences were found, suggesting that translational genomics approaches for gene discovery using Medicago could be successful. C1 [Milbourne, Dan] TEAGASC, Crops Res Ctr, Oak Pk, Carlow, Ireland. RP Milbourne, D (reprint author), TEAGASC, Crops Res Ctr, Oak Pk, Carlow, Ireland. EM dan.milbourne@teagasc.ie NR 3 TC 1 Z9 1 U1 0 U2 5 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY BN 978-90-481-8705-8 PY 2010 BP 415 EP + DI 10.1007/978-90-481-8706-5_60 PG 2 WC Agronomy; Plant Sciences SC Agriculture; Plant Sciences GA BPX09 UT WOS:000280198100060 ER PT S AU Lee, DM AF Lee, David M. BE Lulek, T Wal, A Lulek, B TI Probing the Big Bang at the Relativistic Heavy Ion Collider (RHIC) (or Probing the Big Bang 13.7 billion years later) SO SYMMETRY AND STRUCTURAL PROPERTIES OF CONDENSED MATTER SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 10th Conference of Summer School on Theoretical Physics CY SEP 02-09, 2009 CL Myczkowce, POLAND SP Nicolas C Metropolis Math Fdn ID SUPERDENSE MATTER AB The Relativistic Heavy Ion Collider (RHIC) at the Brookhaven National Laboratory in the USA is a variable energy proton-proton and ion-ion collider that is the first accelerator capable of colliding heavy ions. RHIC was designed to do experiments that provide important information about the Standard Model of particle physics, Quantum Chromodynamics (QCD). QCD predicts that in the early part of the Universe just after the Big Bang the world consisted of a Quark Gluon Plasma, a weakly interacting collection of quarks and gluons. At RHIC we can recreate the conditions of the early Universe by colliding heavy ions at 200 GeV. This paper will give a general overview of the physics motivation for studying the QGP, how our experiments are designed to study the QGP, what we have learned over the last 9 years, and what the future holds. C1 Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Lee, DM (reprint author), Los Alamos Natl Lab, H846,P-25, Los Alamos, NM 87545 USA. EM dlee@lanl.gov NR 14 TC 0 Z9 0 U1 0 U2 3 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2010 VL 213 AR 012012 DI 10.1088/1742-6596/213/1/012012 PG 13 WC Physics, Applied; Physics, Condensed Matter SC Physics GA BTK79 UT WOS:000287181400012 ER PT S AU Louck, JD AF Louck, James D. BE Lulek, T Wal, A Lulek, B TI Matrix Schur Functions, Permutation Matrices, and Young Operators as Inner Product Spaces SO SYMMETRY AND STRUCTURAL PROPERTIES OF CONDENSED MATTER SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 10th Conference of Summer School on Theoretical Physics CY SEP 02-09, 2009 CL Myczkowce, POLAND SP Nicolas C Metropolis Math Fdn AB An inner product is defined on the space of permutation matrices and the space of matrices dual to the permutation matrices is given. The relationship of permutation matrices to the expansion of matrices of fixed line-sum is discussed. This inner product carries over to the space of linear Young operators, as does the notion of the dual space. Motivation from physics for considering such algebraic structures is also given; in particular, the real, orthogonal, irreducible representations of the symmetric group originating from the matrix Schur functions are given. C1 Los Alamos Natl Lab, Santa Fe, NM 87506 USA. RP Louck, JD (reprint author), Los Alamos Natl Lab, 54 Wildflower Way, Santa Fe, NM 87506 USA. EM jimlouck@aol.com NR 22 TC 0 Z9 0 U1 0 U2 0 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2010 VL 213 AR 012010 DI 10.1088/1742-6596/213/1/012010 PG 15 WC Physics, Applied; Physics, Condensed Matter SC Physics GA BTK79 UT WOS:000287181400010 ER PT S AU Ade, H Wang, C Yan, HP AF Ade, Harald Wang, Cheng Yan, Hongping BA Bras, W Goossens, JGP Goderis, B BF Bras, W Goossens, JGP Goderis, B TI The case for soft X-rays: Improved compositional contrast for structure and morphology determination with real and reciprocal space methods SO SYNCHROTRON RADIATION IN POLYMER SCIENCE (SRPS 4) SE IOP Conference Series-Materials Science and Engineering LA English DT Proceedings Paper CT Conference on the Synchrotron Radiation in Polymer Science (SRPS 4) CY SEP 08-11, 2009 CL Kerkrade, NETHERLANDS ID POLYMER BLENDS; THIN-FILMS; POLY(METHYL METHACRYLATE); RESPONSIVE MICROGELS; BLOCK-COPOLYMER; HIGH-RESOLUTION; MICROSCOPY; SPECTROMICROSCOPY; SURFACE; REFLECTIVITY AB Although the interactions of soft x-rays and hard x-rays with polymers are fundamentally the same and are characterized by absorption and phase shifts, the relative and absolute strength of these interactions as a function of photon energy has profound practical implications. We delineate the basic physics of x-ray interactions with polymers as expressed in the optical constants of polymeric materials and exemplify the resulting advantages of soft x-rays over hard x-rays for real space and reciprocal space characterization methods in the context of a number of recent and ongoing applications. A perspective on future capabilities and applications will be provided. C1 [Ade, Harald; Yan, Hongping] NCSU, Dept Phys, Raleigh, NC 27596 USA. [Wang, Cheng] Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA. RP Ade, H (reprint author), NCSU, Dept Phys, Raleigh, NC 27596 USA. EM harald_ade@ncsu.edu RI Ade, Harald/E-7471-2011; YAN, HONGPING/N-7549-2013 OI YAN, HONGPING/0000-0001-6235-4523 FU US Department of Energy, Office of Science, Basic Energy Science, Division of Materials Science and Engineering [DE-FG02-98ER45737] FX We thank Ben Watts for providing the spectra for PFB and F8BT on which the optical constants and Figures 1, 2, and 5 are based. Samples for R-SoXR data and analysis displayed in Figure 5 were provided by A. Garcia (UCSB). Work at NCSU supported exclusively by the US Department of Energy, Office of Science, Basic Energy Science, Division of Materials Science and Engineering under contract DE-FG02-98ER45737. NR 63 TC 1 Z9 1 U1 0 U2 5 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1757-8981 J9 IOP CONF SER-MAT SCI PY 2010 VL 14 AR 012020 DI 10.1088/1757-899X/14/1/012020 PG 9 WC Materials Science, Multidisciplinary; Polymer Science SC Materials Science; Polymer Science GA BVE46 UT WOS:000291273200020 ER PT S AU Pavlopoulou, E Anastasiadis, SH Kortright, JB Bras, W Portale, G AF Pavlopoulou, E. Anastasiadis, S. H. Kortright, J. B. Bras, W. Portale, G. BA Bras, W Goossens, JGP Goderis, B BF Bras, W Goossens, JGP Goderis, B TI Investigation of the Micellization in Thin Films Using Resonant Soft X-Ray Scattering SO SYNCHROTRON RADIATION IN POLYMER SCIENCE (SRPS 4) SE IOP Conference Series-Materials Science and Engineering LA English DT Proceedings Paper CT Conference on the Synchrotron Radiation in Polymer Science (SRPS 4) CY SEP 08-11, 2009 CL Kerkrade, NETHERLANDS ID BLOCK-COPOLYMER MICELLES; DIBLOCK COPOLYMER/HOMOPOLYMER MIXTURES; HOMOPOLYMER BLENDS; POLYMER MICELLES; ORDER; ADSORPTION; BRUSHES; SOLVENT; SURFACE; MATRIX AB The use of Resonant Soft X-rays Scattering (RSOXS) for the investigation of block copolymer micelles within a thin homopolymer film is demonstrated in this work. Thin films of polystyrene-block-polyisoprene, PS-b-PI, copolymer within a high molecular weight polystyrene, PS, matrix were coated onto Si3N4 substrates. The formation of copolymer micelles with a polyisoprene core and a polystyrene corona was verified by the RSOXS measurements. The thin film samples are difficult to study with hard x-rays or neutrons, and well-suited to the RSOXS approach having stronger cross-sections. The core radius of the PS-b-PI micelles was estimated from the experimental data and was found to be in good agreement with measurements in the bulk and with that theoretically predicted. Increasing copolymer concentration resulted in an increase in the number density of micelles in the films; however, no ordering of the confined micelles was observed, even at high copolymer concentrations, possibly because of the segregation of significant fraction of the PS-b-PI copolymer chains to the air/polymer and polymer/substrate interfaces. In order to overcome this problem polystyrene-block-poly(methyl methacrylate), PS-b-PMMA, was utilized. A PS-b-PMMA/PS film of high copolymer concentration was spin-coated on a pre-treated Si3N4 substrate and RSOXS revealed the formation of dense micelle assemblies within the PS matrix. C1 [Pavlopoulou, E.; Anastasiadis, S. H.] Fdn Res & Technol Hellas, Inst Elect Struct & Laser, POB 1527, Iraklion 71110, Greece. [Pavlopoulou, E.] Univ Crete, Dept Mat Sci & Technol, Iraklion, Greece. [Anastasiadis, S. H.] Univ Crete, Dept Chem, Iraklion, Greece. [Kortright, J. B.] Lawrence Berkeley Natl Lab, Mat Sci Div, Berkeley, CA 94720 USA. [Bras, W.; Portale, G.] Netherlands Org Sci Res, DUBBLE CRG, European Synchrotron Radiat Facil, F-38043 Grenoble, France. RP Pavlopoulou, E (reprint author), Fdn Res & Technol Hellas, Inst Elect Struct & Laser, POB 1527, Iraklion 71110, Greece. EM portale@esrf.fr RI Pavlopoulou, Eleni/A-6224-2014 FU Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, of the U.S. Department of Energy [DE-AC02-05CH11231]; NATO Scientific Affairs Division (Science for Peace programme); Greek General Secretariat of Research and Technology (PENED 2003 programme) [03ED581] FX The authors would like to acknowledge Profs. N. Hadjichristidis and H. Iatrou for the synthesis and donation of the PS-b-PI copolymer, Dr. Y. Gallot for the synthesis and donation of the PS-b-PMMA copolymer and Dr. U. Jonas for providing the silane that was used, as well as for usefull discussions. Data were acquired at the beamline 6.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, which is supported by the Director, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Part of this project was sponsored by NATO Scientific Affairs Division (Science for Peace programme) and the Greek General Secretariat of Research and Technology (PENED 2003 programme, project 03ED581). NR 25 TC 3 Z9 3 U1 1 U2 8 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1757-8981 J9 IOP CONF SER-MAT SCI PY 2010 VL 14 AR 012017 DI 10.1088/1757-899X/14/1/012017 PG 7 WC Materials Science, Multidisciplinary; Polymer Science SC Materials Science; Polymer Science GA BVE46 UT WOS:000291273200017 ER PT S AU Wang, C Hexemer, A Nasiatka, J Chan, ER Young, AT Padmore, HA Schlotter, WF Luning, J Swaraj, S Watts, B Gann, E Yan, H Ade, H AF Wang, C. Hexemer, A. Nasiatka, J. Chan, E. R. Young, A. T. Padmore, H. A. Schlotter, W. F. Luening, J. Swaraj, S. Watts, B. Gann, E. Yan, H. Ade, H. BA Bras, W Goossens, JGP Goderis, B BF Bras, W Goossens, JGP Goderis, B TI Resonant Soft X-ray Scattering of Polymers with a 2D Detector: Initial Results and System Developments at the Advanced Light Source SO SYNCHROTRON RADIATION IN POLYMER SCIENCE (SRPS 4) SE IOP Conference Series-Materials Science and Engineering LA English DT Proceedings Paper CT Conference on the Synchrotron Radiation in Polymer Science (SRPS 4) CY SEP 08-11, 2009 CL Kerkrade, NETHERLANDS ID THIN-FILMS; REFLECTIVITY; MICROSCOPY; DIFFRACTION; CONTRAST; CELLS AB Most advanced applications of polymers rely on heterogeneous structures or specific interfacial properties to yield desired performance and functionalities. Rational design and application require that these structures be characterized. Recently, it has been demonstrated that soft x-ray scattering is a unique complementary technique to conventional hard x-ray and neutron scattering and an excellent tool for polymer structure determination with improved chemical sensitivity. Efforts to enhance the capabilities and efficiency of soft x-ray scattering through the use of a CCD detector will be delineated and first results presented. Development of a dedicated setup at beamline 11.0.1.2 of the Advanced Light Source will be described. This set-up has an elliptically polarized undulator as a source, which offers complete polarization control and hence unique capabilities. C1 [Wang, C.; Hexemer, A.; Nasiatka, J.; Chan, E. R.; Young, A. T.; Padmore, H. A.] Univ Calif Berkeley, Lawrence Berkeley Lab, Adv Light Source, Berkeley, CA 94720 USA. [Schlotter, W. F.; Luening, J.] Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA. [Swaraj, S.; Watts, B.; Gann, E.; Yan, H.; Ade, H.] North Carolina State Univ, Dept Phys, Raleigh, NC 27695 USA. RP Wang, C (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Adv Light Source, Berkeley, CA 94720 USA. EM cwang2@lbl.gov; ahexemer@lbl.gov; harald_ade@ncsu.edu RI Wang, Cheng /E-7399-2012; Swaraj, Sufal/E-4407-2010; Ade, Harald/E-7471-2011; YAN, HONGPING/N-7549-2013; Wang, Cheng/A-9815-2014; Gann, Eliot/A-5246-2014 OI Swaraj, Sufal/0000-0001-7351-2320; YAN, HONGPING/0000-0001-6235-4523; FU Laboratory Directed Research Development at LBNL; US Department of Energy, Office of Science, Basic Energy Science, Division of Materials Science and Engineering [DE-FG02-98ER45737] FX This work is supported by the Laboratory Directed Research Development at LBNL. Work at NCSU supported by the US Department of Energy, Office of Science, Basic Energy Science, Division of Materials Science and Engineering under contract DE-FG02-98ER45737. Portions of this research were carried out at the Stanford Synchrotron Radiation Lightsource, a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences. NR 27 TC 17 Z9 17 U1 4 U2 18 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1757-8981 J9 IOP CONF SER-MAT SCI PY 2010 VL 14 AR 012016 DI 10.1088/1757-899X/14/1/012016 PG 7 WC Materials Science, Multidisciplinary; Polymer Science SC Materials Science; Polymer Science GA BVE46 UT WOS:000291273200016 ER PT B AU Weiss, M Dale, L McNeil, M AF Weiss, Martin Dale, Larry McNeil, Michael BE Junginger, M VanSark, W Faaij, A TI Household appliances SO TECHNOLOGICAL LEARNING IN THE ENERGY SECTOR: LESSONS FOR POLICY, INDUSTRY AND SCIENCE LA English DT Article; Book Chapter C1 [Weiss, Martin] Univ Utrecht, Copernicus Inst, Utrecht, Netherlands. [Dale, Larry; McNeil, Michael] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. RP Weiss, M (reprint author), Univ Utrecht, Copernicus Inst, Utrecht, Netherlands. NR 0 TC 0 Z9 0 U1 0 U2 0 PU EDWARD ELGAR PUBLISHING LTD PI CHELTENHAM PA GLENSANDA HOUSE, MONTPELLIER PARADE, CHELTENHAM GL50 1UA, GLOS, ENGLAND BN 978-1-84844-834-6 PY 2010 BP 193 EP 205 PG 13 WC Economics; Public Administration SC Business & Economics; Public Administration GA BZF99 UT WOS:000301451900016 ER PT S AU Beimel, A Kasiviswanathan, SP Nissim, K AF Beimel, Amos Kasiviswanathan, Shiva Prasad Nissim, Kobbi BE Micciancio, D TI Bounds on the Sample Complexity for Private Learning and Private Data Release SO THEORY OF CRYPTOGRAPHY, PROCEEDINGS SE Lecture Notes in Computer Science LA English DT Proceedings Paper CT 7th Theory of Cryptography Conference CY FEB 09-11, 2010 CL ETH, Zurich, SWITZERLAND SP Int Assoc Cryptol Res, ETH, Informat Security & Cryptography Grp HO ETH ID EXAMPLES; NOISE AB Learning is a task that generalizes many of the analyses that are applied to collections of data, and in particular, collections of sensitive individual information. Hence, it is natural to ask what can be learned while preserving individual privacy. [Kasiviswanathan, Lee, Nissim, Raskhodnikova, and Smith; FOCS 2008] initiated such a discussion. They formalized the notion of private learning, as a combination of PAC learning and differential privacy, and investigated what concept classes can be learned privately. Somewhat surprisingly, they showed that, ignoring time complexity, every PAC learning task could be performed privately with polynomially many samples, and in many natural cases this could even be done in polynomial time. While these results seem to equate non-private and private learning, there is still a significant gap: the sample complexity of (non-private) PAC learning is crisply characterized in terms of the VC-dimension of the concept class, whereas this relationship is lost in the constructions of private learners, which exhibit, generally, a higher sample complexity. Looking into this gap, we examine several private learning tasks and give tight bounds on their sample complexity. In particular, we show strong separations between sample complexities of proper and improper private learners (such separation does not exist for non-private learners), and between sample complexities of efficient and inefficient proper private learners. Our results show that VC-dimension is not the right measure for characterizing the sample complexity of proper private learning. We also examine the task of private data release (as initiated by [Blum, Ligett, and Roth; STOC 2008]), and give new lower bounds on the sample complexity. Our results show that the logarithmic dependence on size of the instance space is essential for private data release. C1 [Beimel, Amos; Nissim, Kobbi] Ben Gurion Univ Negev, Dept Comp Sci, IL-84105 Beer Sheva, Israel. [Kasiviswanathan, Shiva Prasad] Los Alamos Natl Lab, CCS 3, Los Alamos, NM USA. [Nissim, Kobbi] Microsoft Audience Intelligence, Redwood City, CA USA. RP Beimel, A (reprint author), Ben Gurion Univ Negev, Dept Comp Sci, IL-84105 Beer Sheva, Israel. RI Nissim, Kobbi/F-1442-2012; Nissim, Kobbi/B-4912-2012; BEIMEL, AMOS/F-2033-2012 OI Nissim, Kobbi/0000-0002-6632-8645; FU Israel Science Foundation [938/09, 860/06]; Frankel Center for Computer Science FX Research partially supported by the Israel Science Foundation (grant No. 938/09) and by the Frankel Center for Computer Science. Research partly supported by the Israel Science Foundation (grant No. 860/06). NR 18 TC 9 Z9 9 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 0302-9743 BN 978-3-642-11798-5 J9 LECT NOTES COMPUT SC PY 2010 VL 5978 BP 437 EP + PG 3 WC Computer Science, Theory & Methods SC Computer Science GA BPZ99 UT WOS:000280461700026 ER PT S AU Bonfiglio, D Veranda, M Cappello, S Chacon, L Spizzo, G AF Bonfiglio, D. Veranda, M. Cappello, S. Chacon, L. Spizzo, G. BE Garbet, X Sauter, O TI Magnetic chaos healing in the helical reversed-field pinch: indications from the volume-preserving field line tracing code NEMATO SO THEORY OF FUSION PLASMAS: JOINT VARENNA-LAUSANNE INTERNATIONAL WORKSHOP SE Journal of Physics Conference Series LA English DT Proceedings Paper CT Joint Varenna-Lausanne Workshop on the Theory of Fusion Plasmas CY AUG 30-SEP 03, 2010 CL Varenna, ITALY ID MAGNETOHYDRODYNAMICS; BIFURCATION; SINGLE; STATES; MHD AB The emergence of a self-organized reversed-field pinch (RFP) helical regime, first shown by 3D MHD numerical simulations, has been highlighted in the RFX-mod experiment at high current operation (IP above 1 MA). In fact, a quasi-stationary helical configuration spontaneously appears, characterized by strong internal electron transport barriers. In such regime electron temperature and density become, to a very good approximation, functions of the helical flux coordinate related to the dominant helical magnetic component. In addition, this regime is diagnosed to be associated with the topological transition to a single-helical-axis (SHAx) state, achieved after the expulsion of the separatrix of the dominant mode's magnetic island. The SHAx state is theoretically predicted to be resilient to the magnetic chaos induced by secondary modes. In this paper, we present initial results of the volume-preserving field line tracing code nemato [Finn J M and Chacon L 2005 Phys. Plasmas 12 054503] applied to study the magnetic topology resulting from 3D MHD simulations of the RFP. First, a successful 2D verification test of the code is shown, then, initial application to a systematic study of chaos healing in the helical RFP is discussed. The separatrix disappearance is confirmed to play an essential role for chaos healing. The triggering effect of a reversed magnetic shear for the formation of ordered surfaces within magnetic chaos is also diagnosed. C1 [Bonfiglio, D.; Veranda, M.; Cappello, S.; Spizzo, G.] Euratom ENEA Assoc, Consorzio RFX, Padua, Italy. [Chacon, L.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Bonfiglio, D (reprint author), Euratom ENEA Assoc, Consorzio RFX, Padua, Italy. EM daniele.bonfiglio@igi.cnr.it RI Bonfiglio, Daniele/I-9398-2012; Spizzo, Gianluca/B-7075-2009; Cappello, Susanna/H-9968-2013 OI Bonfiglio, Daniele/0000-0003-2638-317X; Spizzo, Gianluca/0000-0001-8586-2168; Cappello, Susanna/0000-0002-2022-1113 FU European Communities; EURATOM/ENEA FX The authors would like to thank D. F. Escande and F. Sattin for helpful discussions in the course of this study. This work was supported by the European Communities under the Contract of Association between EURATOM/ENEA. NR 22 TC 12 Z9 12 U1 1 U2 7 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2010 VL 260 AR 012003 DI 10.1088/1742-6596/260/1/012003 PG 8 WC Physics, Fluids & Plasmas; Physics, Nuclear SC Physics GA BUR60 UT WOS:000290156400003 ER PT S AU Dinwiddie, RB Wang, H AF Dinwiddie, R. B. Wang, H. BE Gaal, DS Gaal, PS TI Imaging Heat SO THERMAL CONDUCTIVITY 30:THERMAL EXPANSION 18 SE THERMAL CONDUCTIVITY LA English DT Proceedings Paper CT 30th International Thermal Conductivity Conference/18th International Thermal Expansion Symposium CY AUG 29-SEP 02, 2009 CL Anter Corp, Pittsburgh, PA HO Anter Corp C1 [Dinwiddie, R. B.; Wang, H.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Dinwiddie, RB (reprint author), Oak Ridge Natl Lab, POB 2008,Bldg 4515,MS 6064, Oak Ridge, TN 37831 USA. RI Wang, Hsin/A-1942-2013 OI Wang, Hsin/0000-0003-2426-9867 NR 0 TC 0 Z9 0 U1 0 U2 2 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA SN 0163-9005 BN 978-1-60595-015-0 J9 THERM COND PY 2010 VL 30 BP 61 EP 62 PG 2 WC Thermodynamics; Energy & Fuels; Nuclear Science & Technology SC Thermodynamics; Energy & Fuels; Nuclear Science & Technology GA BWD72 UT WOS:000293683600007 ER PT S AU Kosny, J Stovall, T Yarbrough, D AF Kosny, J. Stovall, T. Yarbrough, D. BE Gaal, DS Gaal, PS TI Dynamic Heat Flow Measurements to Study the Distribution of Phase-Change Material in an Insulation Matrix SO THERMAL CONDUCTIVITY 30:THERMAL EXPANSION 18 SE THERMAL CONDUCTIVITY LA English DT Proceedings Paper CT 30th International Thermal Conductivity Conference/18th International Thermal Expansion Symposium CY AUG 29-SEP 02, 2009 CL Anter Corp, Pittsburgh, PA HO Anter Corp AB Phase change materials (PCMs) are used in building envelopes in many forms. The PCMs may be encased in discrete pouches or containers, or they may be distributed within another medium, such as in a board or within a loose-fill insulation product. In addition, most PCM products are blends containing fire retardants and chemical stabilizers. A combined experimental-analytical protocol involving these complex systems has been developed to determine the actual amount of phase-change energy available to provide useful thermal storage since currently used small scale testing of individual materials is shown to be inadequate. This paper presents this new methodology for performing dynamic heat flow analysis of complex PCM-enhanced building materials. The experimental analytical protocol uses a conventional heat-flow apparatus and three-dimensional (3-D), finite-difference modeling. Based upon results from this methodology, a simplified one-dimensional (1-D) model that can be easily used in whole-building simulations was developed. This paper describes this methodology as applied to an insulation assembly containing a complex array of PCM pouches. C1 [Kosny, J.; Stovall, T.; Yarbrough, D.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Kosny, J (reprint author), Oak Ridge Natl Lab, 1 Bethel Valley Rd, Oak Ridge, TN 37831 USA. NR 17 TC 0 Z9 0 U1 1 U2 2 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA SN 0163-9005 BN 978-1-60595-015-0 J9 THERM COND PY 2010 VL 30 BP 622 EP 631 PG 10 WC Thermodynamics; Energy & Fuels; Nuclear Science & Technology SC Thermodynamics; Energy & Fuels; Nuclear Science & Technology GA BWD72 UT WOS:000293683600062 ER PT S AU Kosny, J Kossecka, E Yarbrough, D AF Kosny, J. Kossecka, E. Yarbrough, D. BE Gaal, DS Gaal, PS TI Use of a Heat Flow Meter to Determine Active PCM Content in an Insulation SO THERMAL CONDUCTIVITY 30:THERMAL EXPANSION 18 SE THERMAL CONDUCTIVITY LA English DT Proceedings Paper CT 30th International Thermal Conductivity Conference/18th International Thermal Expansion Symposium CY AUG 29-SEP 02, 2009 CL Anter Corp, Pittsburgh, PA HO Anter Corp AB Residential and commercial roofs and walls are currently designed and tested using steady-state criteria. The resulting R-values, based on the apparent thermal conductivity, are used by building standards as an important measure of energy performance. Building envelope components, however, are subject to dynamic environmental conditions. This mismatch between the steady-state principles used in design and code requirements and their dynamic operation results in relatively low thermal efficiencies. Although several research centers have developed experimental methods for transient analysis of building envelopes, there are no standardized testing procedures available for screening materials and systems for which performance depends on dynamic response. For example, a full-scale dynamic evaluation of phase change materials (PCMs) is needed to assess their energy saving benefits. A nationally accepted small-scale (one to two foot size specimens) testing procedure is not available for the analysis of dynamic thermal characteristics of conventional thermal mass systems or PCM-enhanced materials. At the same time, data on these characteristics are necessary for whole-building simulations, energy analysis, and energy code work. The transient characteristics of PCM-enhanced products depend on the PCM content and quality. The only readily available method of thermal evaluation uses the differential scanning calorimeter. Unfortunately, this method requires small, relatively uniform test specimens. This requirement is unrealistic in the case of PCM-enhanced building envelope products such as PCM-cellulose, PCM-glass fiber, or PCM-gypsum blends. Small specimens are not representative of PCM-based blends, since these materials are not homogeneous. A procedure for making dynamic heat-flow measurements using existing instrumentation has been developed to analyze the benefits of thermal storage. This small-scale testing method is useful for thermal analysis and as a potential quality control method for producers of PCM-enhanced building materials. The research may provide the basis for consensus standard development. This paper uses as an example a dynamic testing process for PCM-enhanced cellulose insulation. C1 [Kosny, J.; Yarbrough, D.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Kosny, J (reprint author), Oak Ridge Natl Lab, POB 2008,MS 6070, Oak Ridge, TN 37831 USA. NR 12 TC 0 Z9 0 U1 0 U2 2 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA SN 0163-9005 BN 978-1-60595-015-0 J9 THERM COND PY 2010 VL 30 BP 642 EP 650 PG 9 WC Thermodynamics; Energy & Fuels; Nuclear Science & Technology SC Thermodynamics; Energy & Fuels; Nuclear Science & Technology GA BWD72 UT WOS:000293683600064 ER PT S AU Wang, H AF Wang, H. BE Gaal, DS Gaal, PS TI Thermal Conductivity of N-Type and P-Type Thermoelectrics from 300 K to 800 K SO THERMAL CONDUCTIVITY 30:THERMAL EXPANSION 18 SE THERMAL CONDUCTIVITY LA English DT Meeting Abstract CT 30th International Thermal Conductivity Conference/18th International Thermal Expansion Symposium CY AUG 29-SEP 02, 2009 CL Anter Corp, Pittsburgh, PA HO Anter Corp C1 [Wang, H.] Oak Ridge Natl Lab, Oak Ridge, TN USA. RI Wang, Hsin/A-1942-2013 OI Wang, Hsin/0000-0003-2426-9867 NR 0 TC 0 Z9 0 U1 0 U2 2 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA SN 0163-9005 BN 978-1-60595-015-0 J9 THERM COND PY 2010 VL 30 BP 933 EP 933 PG 1 WC Thermodynamics; Energy & Fuels; Nuclear Science & Technology SC Thermodynamics; Energy & Fuels; Nuclear Science & Technology GA BWD72 UT WOS:000293683600106 ER PT S AU Burkes, DE Kennedy, JR Hartmann, T Papesch, CA Hyde, TA AF Burkes, D. E. Kennedy, J. R. Hartmann, T. Papesch, C. A. Hyde, T. A. BE Gaal, DS Gaal, PS TI Thermal and Room Temperature Phase Characteristics of a U-20Pu-3Am-2Np-15Zr Metallic Alloy Containing Rare Earths SO THERMAL CONDUCTIVITY 30:THERMAL EXPANSION 18 SE THERMAL CONDUCTIVITY LA English DT Meeting Abstract CT 30th International Thermal Conductivity Conference/18th International Thermal Expansion Symposium CY AUG 29-SEP 02, 2009 CL Anter Corp, Pittsburgh, PA HO Anter Corp C1 [Papesch, C. A.] Idaho Natl Lab, Nucl Fuels & Mat Div, Idaho Falls, ID 83415 USA. NR 0 TC 0 Z9 0 U1 0 U2 0 PU DESTECH PUBLICATIONS, INC PI LANCASTER PA 439 DUKE STREET, LANCASTER, PA 17602-4967 USA SN 0163-9005 BN 978-1-60595-015-0 J9 THERM COND PY 2010 VL 30 BP 937 EP 937 PG 1 WC Thermodynamics; Energy & Fuels; Nuclear Science & Technology SC Thermodynamics; Energy & Fuels; Nuclear Science & Technology GA BWD72 UT WOS:000293683600110 ER PT S AU Sherby, OD Wadsworth, J Lesuer, DR Syn, CK AF Sherby, O. D. Wadsworth, J. Lesuer, D. R. Syn, C. K. BE Chandra, T Wanderka, N Reimers, W Ionescu, M TI STRUCTURE AND HARDNESS OF MARTENSITE IN QUENCHED Fe-C STEELS SO THERMEC 2009, PTS 1-4 SE Materials Science Forum LA English DT Proceedings Paper CT 6th International Conference on Processing and Manufacturing of Advanced Materials (THERMEC)/2nd Symposium Session on Multiscale Mechanical Modelling of Complex Materials and Engineering Applications CY AUG 25-29, 2009 CL Berlin, GERMANY SP Minerals, Met & Mat Soc (TMS) DE Lath martensite; electronic structure; hardness; transformation ID CARBON-STEELS; MICROSTRUCTURE; IRON AB The exceptional high hardness of lath martensite in quenched Fe-C steels is explained by the Engel-Brewer valence electron theory for crystal structures. The theory predicts the transformation sequence FCC-HCP-BCC with FCC iron as Fe-3v, HCP iron as Fe-2v, BCC iron as Fe-Iv and carbon as C-4v. Electronic compatibility requires transformation from FCC to HCP to form two separate components. Carbon-rich clusters of C-4v with 8 Fe-3v atoms are distributed uniformly in a carbon-free matrix of HCP Fe-2v atoms. The carbon-iron clusters are viewed as particle-like, calculated as 0.63 nm in size, and is responsible for the high strength of martensite. The carbon-free region experiences shear deformation during FCC to HCP transformation leading to work hardened fine grains Subsequent transformation to BCC iron maintains the same size carbon cluster with additional shearing deformation during HCP to BCC formation in the carbon-free region Tempering studies of quenched martensite are shown to support the carbon-iron cluster model. C1 [Sherby, O. D.] Stanford Univ, Stanford, CA 94305 USA. [Wadsworth, J.] Battelle Mem Inst, Columbus, OH 43201 USA. [Lesuer, D. R.; Syn, C. K.] Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. RP Sherby, OD (reprint author), Stanford Univ, Stanford, CA 94305 USA. EM bulatole@aol.com; wadsworthj@battelle.org; syn1@llnl.gov FU Lawrence Livermore National Laboratory FX The authors wish to thank Prof. Tara Chandra for his support and encouragement in their work and for organizing the THERMEC conferences, which have served as an effective forum for presentation and review of work on thermal mechanical processing of steels. The authors also acknowledge the support provided by Lawrence Livermore National Laboratory. NR 26 TC 1 Z9 1 U1 2 U2 16 PU TRANS TECH PUBLICATIONS LTD PI DURNTEN-ZURICH PA KREUZSTRASSE 10, 8635 DURNTEN-ZURICH, SWITZERLAND SN 0255-5476 J9 MATER SCI FORUM PY 2010 VL 638-642 BP 160 EP + DI 10.4028/www.scientific.net/MSF.638-642.160 PN 1-4 PG 3 WC Materials Science, Multidisciplinary; Materials Science, Biomaterials; Materials Science, Coatings & Films; Materials Science, Composites SC Materials Science GA BQH93 UT WOS:000281043800026 ER PT S AU Ionita, A Clements, BE Mas, EM AF Ionita, A. Clements, B. E. Mas, E. M. BE Chandra, T Wanderka, N Reimers, W Ionescu, M TI Modeling Aspects of the Dynamic Response of Heterogeneous Materials SO THERMEC 2009, PTS 1-4 SE Materials Science Forum LA English DT Proceedings Paper CT 6th International Conference on Processing and Manufacturing of Advanced Materials CY AUG 25-29, 2009 CL Berlin, GERMANY SP Minerals, Met & Mat Soc DE two-scale; finite element; heterogeneous AB In engineering applications, simulations involving heterogeneous materials where it is necessary to capture the local response coming from the heterogeneities is very difficult. The use of homogenization techniques can reduce the size of the problem but will miss the local effects. Homogenization can also be difficult if the constituents obey different constitutive laws. Additional complications arise if inelastic deformation occurs. In such cases a two-scale approach is preferred and this work addresses these issues in the context of a two-scale Finite Element Method (FEM). Examples of using two-scale FEM approaches are presented. C1 [Ionita, A.; Clements, B. E.; Mas, E. M.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Ionita, A (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. EM ionita@lanl.gov; hclements@lanl.gov; mas@lanl.gov OI Clements, Brad/0000-0002-9664-637X NR 5 TC 0 Z9 0 U1 0 U2 0 PU TRANS TECH PUBLICATIONS LTD PI STAFA-ZURICH PA LAUBLSRUTISTR 24, CH-8717 STAFA-ZURICH, SWITZERLAND SN 0255-5476 J9 MATER SCI FORUM PY 2010 VL 638-642 BP 1017 EP 1022 DI 10.4028/www.scientific.net/MSF.638-642.1017 PN 1-4 PG 6 WC Materials Science, Multidisciplinary; Materials Science, Biomaterials; Materials Science, Coatings & Films; Materials Science, Composites SC Materials Science GA BQH93 UT WOS:000281043800166 ER PT S AU Haruyama, O Wada, R Kohda, M Yokoyama, Y Nishiyama, N Egami, T AF Haruyama, O. Wada, R. Kohda, M. Yokoyama, Y. Nishiyama, N. Egami, T. BE Chandra, T Wanderka, N Reimers, W Ionescu, M TI Inhomogeneous Amorphous Structure Of Bulk Metallic Glasses Examined From Structural Relaxation Kinetics SO THERMEC 2009, PTS 1-4 SE Materials Science Forum LA English DT Proceedings Paper CT 6th International Conference on Processing and Manufacturing of Advanced Materials (THERMEC)/2nd Symposium Session on Multiscale Mechanical Modelling of Complex Materials and Engineering Applications CY AUG 25-29, 2009 CL Berlin, GERMANY SP Minerals, Met & Mat Soc (TMS) DE Bulk metallic glass; Structural relaxation; Volume relaxation; Structural inhomogeneity ID SUPERCOOLED LIQUID; FORMING ALLOY; TRANSITION; CRYSTALLIZATION; TRANSPORT AB The kinetics of structural relaxation in fragile glass former, Pd46Cu35 5P18 5 BMG, and strong glass former, Zr50Cu40Al10 BMG, was investigated by volume relaxation The former exhibited a relaxation phenomenon that is well understood by the local topological instability model, while the latter showed monotonous relaxation behavior over a wide range down to T-g-60 K. The discrepancy may be closely related to the difference in the fragility of both glasses C1 [Haruyama, O.; Wada, R.; Kohda, M.] Tokyo Univ Sci, Fac Sci & Technol, Noda, Chiba 2788510, Japan. [Yokoyama, Y.] Tohoku Univ, Inst Mat Res, Sendai, Miyagi 980, Japan. [Nishiyama, N.] R&D Inst Mat & Composites, ERATO Tohoku Univ Lab, Sendai, Miyagi 980, Japan. [Egami, T.] Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. [Egami, T.] Univ Tennessee, Dept Phys & Astron, Knoxville, TN 37996 USA. [Egami, T.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Haruyama, O (reprint author), Tokyo Univ Sci, Fac Sci & Technol, Noda, Chiba 2788510, Japan. NR 17 TC 0 Z9 0 U1 1 U2 8 PU TRANS TECH PUBLICATIONS LTD PI DURNTEN-ZURICH PA KREUZSTRASSE 10, 8635 DURNTEN-ZURICH, SWITZERLAND SN 0255-5476 J9 MATER SCI FORUM PY 2010 VL 638-642 BP 1632 EP + DI 10.4028/www.scientific.net/MSF.638-642.1632 PN 1-4 PG 2 WC Materials Science, Multidisciplinary; Materials Science, Biomaterials; Materials Science, Coatings & Films; Materials Science, Composites SC Materials Science GA BQH93 UT WOS:000281043800270 ER PT S AU Androulakis, J Todorov, I Chung, DY Ballikaya, S Wang, GY Uher, C Kanatzidis, M AF Androulakis, John Todorov, Ilyia Chung, Duck-Young Ballikaya, Sedat Wang, Guoyu Uher, Ctirad Kanatzidis, Mercouri BE Baniecki, JD Snyder, GJ Malen, JA Tuller, HL TI High thermoelectric efficiency in co-doped degenerate p-type PbTe SO THERMOELECTRIC MATERIALS 2010 - GROWTH, PROPERTIES, NOVEL CHARACTERIZATION METHODS AND APPLICATIONS SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium DD on Thermoelectric Materials -Growth, Properties, Novel Characterization Methods, and Applications at MRS Spring Meeting CY APR 05-09, 2010 CL San Francisco, CA ID VALENCE-BAND; FIGURE; MERIT AB We explored the effect of K and K-Na substitution for Pb atoms in the lattice of PbTe, in an effort to test a hypothesis for the development of a resonant state that may enhance the thermoelectric power. At 300K the data can adequately be explained by a combination of a single and two-band model for the valence band of PbTe depending on hole density that varies in the range 1-15 x 10(19) cm(-3). A change in scattering mechanism was observed in the temperature dependence of the electrical conductivity, s, for samples concurrently doped with K and Na which results in significantly enhanced s at elevated temperatures and hence power factors. Thermal conductivity data provide evidence of a strong interaction between the light-and the heavy-hole valence bands at least up to 500K. Figure of merits as high as 1.3 at 700K were measured as a result of the enhanced power factors. C1 [Androulakis, John; Kanatzidis, Mercouri] Northwestern Univ, Dept Chem, 2145 Sheridan Rd, Evanston, IL 60208 USA. [Todorov, Ilyia; Chung, Duck-Young; Kanatzidis, Mercouri] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. [Ballikaya, Sedat; Wang, Guoyu; Uher, Ctirad] Univ Michigan, Dept Phys, Ann Arbor, MI 48109 USA. RP Androulakis, J (reprint author), Northwestern Univ, Dept Chem, 2145 Sheridan Rd, Evanston, IL 60208 USA. FU ONR FX We acknowledge financial support from ONR. NR 12 TC 0 Z9 0 U1 0 U2 0 PU MATERIALS RESEARCH SOC PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 BN 978-1-107-40670-4; 978-1-60511-244-2 J9 MATER RES SOC SYMP P PY 2010 VL 1267 DI 10.1557/PROC-1267-DD04-03 PG 6 WC Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA BG9NS UT WOS:000393457200006 ER PT S AU Biswas, K He, JQ Zhang, QC Wang, GY Uher, C Dravid, VP Kanatzidis, MG AF Biswas, Kanishka He, Jiaqing Zhang, Qichun Wang, Guoyu Uher, Ctirad Dravid, Vinayak P. Kanatzidis, Mercouri G. BE Baniecki, JD Snyder, GJ Malen, JA Tuller, HL TI Investigation of the thermoelectric properties of the PbTe-SrTe system SO THERMOELECTRIC MATERIALS 2010 - GROWTH, PROPERTIES, NOVEL CHARACTERIZATION METHODS AND APPLICATIONS SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium DD on Thermoelectric Materials -Growth, Properties, Novel Characterization Methods, and Applications at MRS Spring Meeting CY APR 05-09, 2010 CL San Francisco, CA ID NANOSTRUCTURED THERMOELECTRICS; HIGH FIGURE; TELLURIDE; MERIT; PERFORMANCE; EFFICIENCY AB PbTe-based materials are promising for efficient heat energy to electricity conversion. We present studies of the thermoelectric properties of the PbTe-SrTe system. X-ray diffraction patterns reveal that all the samples crystallize in the rock salt structure without noticeable secondary phase. Na2Te doping of the PbTe-SrTe materials resulting in a positive sign Hall coefficient indicating p-type conduction. Lattice thermal conductivity is significantly decreased with the insertion of SrTe in PbTe lattice. The ZT similar to 1.3 of these materials is derived from their very low thermal conductivities and reasonably high power factor at 800 K. C1 [Biswas, Kanishka; He, Jiaqing; Zhang, Qichun; Kanatzidis, Mercouri G.] Northwestern Univ, Dept Chem, 2145 Sheridan Rd, Evanston, IL 60208 USA. [He, Jiaqing; Dravid, Vinayak P.] Northwestern Univ, Mat Sci & Engn, Evanston, IL 60208 USA. [Wang, Guoyu; Uher, Ctirad] Univ Michigan, Dept Phys, Ann Arbor, MI 48109 USA. [Kanatzidis, Mercouri G.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. RP Biswas, K (reprint author), Northwestern Univ, Dept Chem, 2145 Sheridan Rd, Evanston, IL 60208 USA. FU Office of Naval Research Grant [N00014-08-1-0613]; Revolutionary Materials for Solid State Energy Conversion, an Energy frontier Research Center -U.S. Department of Energy, Office of Basic Energy Sciences [DE-SC0001054] FX The authors acknowledge the financial assistance of the Office of Naval Research Grant N00014-08-1-0613. The work at the University of Michigan is supported as part of the Revolutionary Materials for Solid State Energy Conversion, an Energy frontier Research Center funded by the U. S. Department of Energy, Office of Basic Energy Sciences under Award Number DE-SC0001054. NR 17 TC 0 Z9 0 U1 0 U2 0 PU MATERIALS RESEARCH SOC PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 BN 978-1-107-40670-4; 978-1-60511-244-2 J9 MATER RES SOC SYMP P PY 2010 VL 1267 DI 10.1557/PROC-1267-DD06-05 PG 6 WC Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA BG9NS UT WOS:000393457200023 ER PT S AU Jie, Q Zhou, J Dimitrov, IK Li, CP Uher, C Wang, H Porter, WD Li, Q AF Jie, Qing Zhou, Juan Dimitrov, Ivo K. Li, Chang-Peng Uher, Ctirad Wang, Hsin Porter, Wallace D. Li, Qiang BE Baniecki, JD Snyder, GJ Malen, JA Tuller, HL TI Thermoelectric Properties of Non-equilibrium Synthesized Ce0.9Fe3CoSb12 Filled Skutterudites SO THERMOELECTRIC MATERIALS 2010 - GROWTH, PROPERTIES, NOVEL CHARACTERIZATION METHODS AND APPLICATIONS SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium DD on Thermoelectric Materials -Growth, Properties, Novel Characterization Methods, and Applications at MRS Spring Meeting CY APR 05-09, 2010 CL San Francisco, CA ID THERMAL-CONDUCTIVITY; TRANSPORT; ANTIMONIDES AB We report on the thermoelectric properties of the filled skutterudite Ce0.9Fe3CoSb12 prepared via non-equilibrium synthesis method. Melt-spun ribbons were directly converting into single phase polycrystalline pellets under pressure. For comparison, pellets with the same composition were also prepared using the conventional solid-state reaction followed by long term annealing. It was found that the non-equilibrium synthesized samples have higher power factors and lower thermal conductivity, leading to substantially higher figure of merit. C1 [Jie, Qing; Zhou, Juan; Dimitrov, Ivo K.; Li, Qiang] Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. [Li, Chang-Peng; Uher, Ctirad] Univ Michigan, Dept Phys, Ann Arbor, MI 48109 USA. [Wang, Hsin; Porter, Wallace D.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. RP Jie, Q (reprint author), Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. FU U.S. Department of Energy, Office of Basic Energy Science [DE-AC02-98CH10886]; University Research Corridor; U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program FX This work was primarily supported by the U.S. Department of Energy, Office of Basic Energy Science, under Contract No. DE-AC02-98CH10886. High temperature measurements at the University of Michigan were supported by a grant from the University Research Corridor. The research through the Oak Ridge National Laboratory's High Temperature Materials Laboratory User Program was sponsored by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program. NR 18 TC 0 Z9 0 U1 0 U2 0 PU MATERIALS RESEARCH SOC PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 BN 978-1-107-40670-4; 978-1-60511-244-2 J9 MATER RES SOC SYMP P PY 2010 VL 1267 DI 10.1557/PROC-1267-DD03-03 PG 6 WC Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA BG9NS UT WOS:000393457200003 ER PT S AU Johnsen, S Girard, SN Todorov, I Chung, DY Kanatzidis, MG AF Johnsen, Simon Girard, Steven N. Todorov, Iliya Chung, Duck Young Kanatzidis, Mercouri G. BE Baniecki, JD Snyder, GJ Malen, JA Tuller, HL TI Reduction of the lattice thermal conductivity in immiscible PbS-PbTe systems SO THERMOELECTRIC MATERIALS 2010 - GROWTH, PROPERTIES, NOVEL CHARACTERIZATION METHODS AND APPLICATIONS SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium DD on Thermoelectric Materials -Growth, Properties, Novel Characterization Methods, and Applications at MRS Spring Meeting CY APR 05-09, 2010 CL San Francisco, CA ID PERFORMANCE AB The synthesis and properties characterization of several PbS1-xTex x =0-0.16 samples are presented. Notably it is shown how a local minimum occurs in the thermal diffusivity for the PbS1-x Te-x samples at x similar to 0.03. The thermoelectric properties of doped PbS1-x Te-x with x = 0.03 are reported and the properties are compared to the pure PbS and PbTe end members. The electronic contribution to the total thermal conductivity is analyzed for PbS1-x Te-x x = 0.03 and it is shown how the lattice thermal conductivity is significantly lowered compared to single crystalline PbS. C1 [Johnsen, Simon; Girard, Steven N.; Kanatzidis, Mercouri G.] Northwestern Univ, Dept Chem, 2145 Sheridan Rd, Evanston, IL 60208 USA. [Todorov, Iliya; Chung, Duck Young; Kanatzidis, Mercouri G.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. RP Johnsen, S (reprint author), Northwestern Univ, Dept Chem, 2145 Sheridan Rd, Evanston, IL 60208 USA. FU Danish Research Council for Nature and Universe; Revolutionary Materials for Solid State Energy Conversion; Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-SC0001054] FX SJ would like to acknowledge the Danish Research Council for Nature and Universe for funding. This material is based upon work supported as part of the Revolutionary Materials for Solid State Energy Conversion, an Energy Frontier Research Center funded by the U.S.; Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001054. NR 15 TC 0 Z9 0 U1 0 U2 0 PU MATERIALS RESEARCH SOC PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 BN 978-1-107-40670-4; 978-1-60511-244-2 J9 MATER RES SOC SYMP P PY 2010 VL 1267 DI 10.1557/PROC-1267-DD06-03 PG 6 WC Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA BG9NS UT WOS:000393457200021 ER PT S AU Kwong, KS Smith, AE Subramanian, MA AF Kwong, Kyei-Sing Smith, Andrew E. Subramanian, M. A. BE Baniecki, JD Snyder, GJ Malen, JA Tuller, HL TI The Effect of Rh and Sr Substitution on the Thermoelectric Performance of LaCoO3 SO THERMOELECTRIC MATERIALS 2010 - GROWTH, PROPERTIES, NOVEL CHARACTERIZATION METHODS AND APPLICATIONS SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium DD on Thermoelectric Materials -Growth, Properties, Novel Characterization Methods, and Applications at MRS Spring Meeting CY APR 05-09, 2010 CL San Francisco, CA ID SYSTEM AB A series of LaCo1-xRhxO3 (x=0-1) samples and La1-ySryCo1-xRhxO3 (y=0.05, 0.15 and x =0.1-0.3) samples were prepared to study the effect of Rh substituion for Co in the four component system and Sr substitution for La in the five component system on the crystal structure and thermoelectric performance of the LaCoO3. At Rh substitution for Co of x=0.2 greater, the crystal structure shifts from rhombohederal (LaCoO3) to orthorhombic (LaRhO3). Thermoelectric evaluation revealed that Rh doped samples (0.3 < x < 1) show large positive seebeck coefficients indicating a P-type conduction in the temperature range of the tests (273 to 775K). Rh substitution for Co decreases thermal conductivity, increases Seebeck coefficient and consequently increases the theroelectric figure of merit ZT. Sr substitution for La increases thermal and electrical conductivity and consquenently negligiblely decreases the seebeck coefficient. A thermoelectric figure-of-merit (ZT) around 0.075 has been achieved for LaCo0.5Rh0.5O3 at 775 K, and is expected to be above 0.1 at 1000 K. Sr substitution improved the TE properties throughout the lower temperature range with a ZT=0.045 observed for La0.95Sr0.05Co0.9Rh0.1O3 at 425 K and ZT =0.05 for La0.85Sr0.15Co0.5Rh0.5O3 at 775 K. These findings provide new insight into thermoelectric perovskite oxides containing rhodium and strontium. C1 [Kwong, Kyei-Sing] Natl Energy Technol Lab, Albany, OR 97321 USA. [Smith, Andrew E.; Subramanian, M. A.] Oregon State Univ, Dept Chem, Corvallis, OR 97330 USA. RP Kwong, KS (reprint author), Natl Energy Technol Lab, Albany, OR 97321 USA. FU NETL under the RDS [DE-AC26-04NT41817]; NSF grant [DMR 0804167]; NSF-IGERT FX The technical effort at Oregon State University was performed in support of the NETL's on-going research on development of materials for energy applications under the RDS contract DE-AC26-04NT41817. The work performed at Oregon State University was also supported by NSF grant (DMR 0804167). A.E.S would like to thank NSF-IGERT for financial support. NR 16 TC 0 Z9 0 U1 0 U2 0 PU MATERIALS RESEARCH SOC PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 BN 978-1-107-40670-4; 978-1-60511-244-2 J9 MATER RES SOC SYMP P PY 2010 VL 1267 DI 10.1557/PROC-1267-DD11-0 PG 6 WC Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA BG9NS UT WOS:000393457200040 ER PT S AU Zhou, J Jie, Q Li, Q AF Zhou, Juan Jie, Qing Li, Qiang BE Baniecki, JD Snyder, GJ Malen, JA Tuller, HL TI Microstructure Investigation of Non-equilibrium Synthesized Filled Skutterudite CeFe4Sb12 SO THERMOELECTRIC MATERIALS 2010 - GROWTH, PROPERTIES, NOVEL CHARACTERIZATION METHODS AND APPLICATIONS SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium DD on Thermoelectric Materials -Growth, Properties, Novel Characterization Methods, and Applications at MRS Spring Meeting CY APR 05-09, 2010 CL San Francisco, CA ID THERMOELECTRIC-MATERIALS; GENERATION AB We have prepared a variety of filled skutterudites through non-equilibrium synthesis by converting melt-spun ribbons into single phase polycrystalline bulk under pressure. In general, better thermoelectric properties are found in these samples. In this work, we performed microstructure characterization of non-equilibrium synthesized p-type filled skutterudite CeFe4Sb12 by X-ray diffraction, scanning electron microscopy and transmission electron microscopy in order to understand the structural origin of the improved thermoelectric properties. It is found that the non-equilibrium synthesized samples have smaller grain size and cleaner grain boundaries when compared to the samples prepared by the conventional solid-state reaction plus long term annealing. While smaller grain size can help reduce the lattice thermal conductivity, cleaner grain boundaries ensure higher carrier mobility and subsequently, higher electrical conductivity at the application temperatures. C1 [Zhou, Juan; Jie, Qing; Li, Qiang] Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. RP Zhou, J (reprint author), Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. FU U.S. Department of Energy, Office of Basic Energy Sciences [DE-AC02-98CH10886]; Center for Functional Nanomaterials, Brookhaven National Laboratory FX This work was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886. We thank the Center for Functional Nanomaterials, Brookhaven National Laboratory for generous support in using its facilities. NR 9 TC 0 Z9 0 U1 0 U2 0 PU MATERIALS RESEARCH SOC PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 BN 978-1-107-40670-4; 978-1-60511-244-2 J9 MATER RES SOC SYMP P PY 2010 VL 1267 DI 10.1557/PROC-1267-DD05-25 PG 6 WC Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Materials Science; Physics GA BG9NS UT WOS:000393457200019 ER PT S AU Garrett, AJ Casterline, M Salvaggio, C AF Garrett, Alfred J. Casterline, May Salvaggio, Carl BE Dinwiddie, RB Safai, M TI Thermodynamics of Partially Frozen Cooling Lakes SO THERMOSENSE XXXII SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Thermosense XXXII CY APR 06-07, 2010 CL Orlando, FL SP SPIE DE power plant; cooling lake; thermal imagery; ice formation; heat transfer; snow insulation ID SEA-ICE; SIMULATIONS; IMAGERY; MODEL AB The Rochester Institute of Technology (RIT) collected visible, SWIR, MWIR and LWIR imagery of the Midland (Michigan) Cogeneration Ventures Plant from aircraft during the winter of 2008 - 2009. RIT also made ground-based measurements of lake water and ice temperatures, ice thickness and atmospheric variables. The Savannah River National Laboratory (SRNL) used the data collected by RIT and a 3-D hydrodynamic code to simulate the Midland cooling lake. The hydrodynamic code was able to reproduce the time distribution of ice coverage on the lake during the entire winter. The simulations and data show that the amount of ice coverage is almost linearly proportional to the rate at which heat is injected into the lake (Q). Very rapid melting of ice occurs when strong winds accelerate the movement of warm water underneath the ice. A snow layer on top of the ice acts as an insulator and decreases the rate of heat loss from the water below the ice to the atmosphere above. The simulated ice cover on the lake was not highly sensitive to the thickness of the snow layer. The simplicity of the relationship between ice cover and Q and the weak responses of ice cover to snow depth over the ice are probably attributable to the negative feedback loop that exists between ice cover and heat loss to the atmosphere. C1 [Garrett, Alfred J.] Savannah River Natl Lab, Aiken, SC USA. RP Garrett, AJ (reprint author), Savannah River Natl Lab, Highway 1, Aiken, SC USA. EM Alfred.garrett@srnl.doe.gov NR 11 TC 0 Z9 0 U1 0 U2 2 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8125-2 J9 PROC SPIE PY 2010 VL 7661 AR 766105 DI 10.1117/12.849349 PG 13 WC Thermodynamics; Optics SC Thermodynamics; Optics GA BSS33 UT WOS:000285625700003 ER PT S AU Bhattacharya, RN AF Bhattacharya, Raghu N. GP MRS BE Yamada, A Heske, C Contreras, MA Igalson, M Irvine, SJC TI Electrodeposited Cu-In-Ga-Se Thin Films for CIGS-Based Solar Cells SO THIN-FILM COMPOUND SEMICONDUCTOR VOLTAICS-2009 SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium on Thin-Film Compound Semiconductor Photovoltaics CY APR 13-17, 2009 CL San Francisco, CA AB Cyclic voltammogram studies were performed on H(2)SeO(3), CuSO(4) In(2)(SO(4))(3), GaCl(3), H(2)SeO(3) + CuSO(4)+ In(2)(SO(4))(3) and H(2)SeO(3) + CuSO(4) + In(2)(SO(4))(3) + GaCl(3) to understand the electrodeposition mechanism. The reduction potential from the cyclic voltammogram studies indicates that the first deposited layer is Cu from the Cu-In-Se and Cu-In-Ga-Se solution mixture. The subsequent deposition of the In and Ga layer is more favorable on the first-deposited Cu layer. C1 Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Bhattacharya, RN (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. NR 5 TC 0 Z9 0 U1 0 U2 2 PU MATERIALS RESEARCH SOCIETY PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 J9 MATER RES SOC SYMP P PY 2010 VL 1165 BP 37 EP 40 PG 4 WC Energy & Fuels; Materials Science, Multidisciplinary SC Energy & Fuels; Materials Science GA BSL62 UT WOS:000284867000006 ER PT S AU Dhere, RG Duenow, JN Duda, A Glynn, S Li, JA Metzger, WK Moutinho, H Gessert, TA AF Dhere, Ramesh G. Duenow, Joel N. Duda, Anna Glynn, Stephen Li, Jian Metzger, Wyatt K. Moutinho, Helio Gessert, Timothy A. GP MRS BE Yamada, A Heske, C Contreras, MA Igalson, M Irvine, SJC TI Recent Results for All-Dry-Processed CdTe/CdS Solar Cells SO THIN-FILM COMPOUND SEMICONDUCTOR VOLTAICS-2009 SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium on Thin-Film Compound Semiconductor Photovoltaics CY APR 13-17, 2009 CL San Francisco, CA AB Several wet-processing steps are used in fabricating high-efficiency CdTe/CdS solar cells. These steps can hinder in-line processing; thus, developing an all-dry processing option is attractive for a manufacturing-friendly process. In this study, we systematically modified the baseline process used in our laboratory to replace CdS deposited by chemical-bath deposition (CBD) with sputter-deposited CdS and Cu-doped graphite paste back-contact with Cu-doped ZnTe deposited by radio-frequency sputtering. In addition to CdTe deposited by close-spaced sublimation, we also used conventionally evaporated CdTe. The results show that replacing only CBD CdS with oxygenated CdS deposited by sputtering produces devices with performance comparable to baseline devices if the front bilayer SnO2 is replaced by a Cd2SnO4/ZnSnO alloy. Replacing the graphite paste back-contact with sputter-deposited Cu-doped ZnTe resulted in device performance comparable to baseline devices. Incorporating both dry processing steps gave performance comparable to the devices with sputtered CdS with a SnO2 front contact. We used capacitance-voltage and minority-carrier lifetime measurements to analyze the factors affecting device performance and we present the results here. C1 [Dhere, Ramesh G.; Duenow, Joel N.; Duda, Anna; Glynn, Stephen; Li, Jian; Metzger, Wyatt K.; Moutinho, Helio; Gessert, Timothy A.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Dhere, RG (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. NR 6 TC 0 Z9 0 U1 0 U2 3 PU MATERIALS RESEARCH SOC PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 J9 MATER RES SOC SYMP P PY 2010 VL 1165 BP 61 EP 66 PG 6 WC Energy & Fuels; Materials Science, Multidisciplinary SC Energy & Fuels; Materials Science GA BSL62 UT WOS:000284867000010 ER PT S AU Vora, N Repins, I Robbins, S Mann, J Castenada, H Armstrong, B Weber, D AF Vora, Nirav Repins, Ingrid Robbins, Steve Mann, Jonathan Castenada, Hector Armstrong, Brian Weber, Dominic GP MRS BE Yamada, A Heske, C Contreras, MA Igalson, M Irvine, SJC TI Large-Area Chemical Bath Deposition of CdS on Cu(In,Ga)Se-2 SO THIN-FILM COMPOUND SEMICONDUCTOR VOLTAICS-2009 SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium on Thin-Film Compound Semiconductor Photovoltaics CY APR 13-17, 2009 CL San Francisco, CA ID THIN-FILMS AB Chemical bath deposition (CBD) is a commonly used method of depositing cadmium sulfide (CdS) films for photovoltaic application. The method is based on decomposition of a sulfur source in an alkaline solution of a cadmium source on the surface of the Cu(In,Ga)Se-2 (CIGS) substrate. On the lab scale the CdS film is deposited by submerging a 1 '' square CIGS substrate in a heated beaker containing the chemical bath. This batch processing method is the one used for record-performing devices. There is an ongoing effort at the National Renewable Energy Laboratory to scale-up the CBD process to deposit CdS films on 6 '' square substrate. Efforts are focused at designing both batch and flow reactors for depositing uniform, device quality CdS films on larger substrates. Batch reactor designs involve reproducing the deposition process in the beaker on a bigger scale with minimal chemical waste, while flow reactors are designed for continuous processing, such as encountered in roll-to-roll manufacturing lines. C1 [Vora, Nirav; Repins, Ingrid; Robbins, Steve; Mann, Jonathan; Weber, Dominic] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Vora, N (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. NR 15 TC 0 Z9 0 U1 0 U2 2 PU MATERIALS RESEARCH SOC PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 J9 MATER RES SOC SYMP P PY 2010 VL 1165 BP 159 EP 164 PG 6 WC Energy & Fuels; Materials Science, Multidisciplinary SC Energy & Fuels; Materials Science GA BSL62 UT WOS:000284867000023 ER PT S AU Li, XN Pankow, J Yan, YF AF Li, Xiaonan Pankow, Joel Yan, Yanfa GP MRS BE Yamada, A Heske, C Contreras, MA Igalson, M Irvine, SJC TI Impurity Study of Optical Properties in Fluorine-Doped Tin Oxide for Thin-Film Solar Cells SO THIN-FILM COMPOUND SEMICONDUCTOR VOLTAICS-2009 SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium on Thin-Film Compound Semiconductor Photovoltaics CY APR 13-17, 2009 CL San Francisco, CA AB Tin oxide (SnO(2)) is a durable, inexpensive transparent conducting oxide (TCO) material used for thin-film photovoltaic devices. However, the optical properties of conducting SnO(2):F are generally not as good as in other conducting TCO materials such as ITO and ZnO:Al. Our previous analyses indicate that for thin-film solar cells, improving the optical properties of SnO(2)-coated glass could enhance photon collection and gain up to 10% additional photocurrent. Previously, we showed that some commercial SnO(2) samples could have much higher optical absorption than others [2]. In this work, we continue our study on causes that could contribute to the high optical absorption of SnO(2) films. The SnO(2):F samples are fabricated by low-pressure metal-organic chemical vapor deposition or atmospheric-pressure chemical vapor deposition with tin precursors that includes different amounts of chlorine. Optical, electrical, and compositional analyses were performed. In addition to the free-carrier-introduced optical absorption, the non-active dopant also impacts the optical absorption. Among the SnO2 films fabricated with different precursors, the optical properties show a relationship based on the level of chlorine in the precursors and films. With a low-optical-absorption SnO(2) layer, the solar cell could have better photon collection and a higher short-circuit current density. C1 [Li, Xiaonan; Pankow, Joel; Yan, Yanfa] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Li, XN (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. NR 6 TC 0 Z9 0 U1 0 U2 5 PU MATERIALS RESEARCH SOCIETY PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 J9 MATER RES SOC SYMP P PY 2010 VL 1165 BP 235 EP 240 PG 6 WC Energy & Fuels; Materials Science, Multidisciplinary SC Energy & Fuels; Materials Science GA BSL62 UT WOS:000284867000034 ER PT S AU Gessert, TA Yoshida, Y Fesenmaier, CC Duenow, JN Coutts, TJ AF Gessert, T. A. Yoshida, Y. Fesenmaier, C. C. Duenow, J. N. Coutts, T. J. GP MRS BE Yamada, A Heske, C Contreras, MA Igalson, M Irvine, SJC TI TCO Thin Films With Permittivity Control SO THIN-FILM COMPOUND SEMICONDUCTOR VOLTAICS-2009 SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium on Thin-Film Compound Semiconductor Photovoltaics CY APR 13-17, 2009 CL San Francisco, CA AB We have shown that variation in the real part of the dielectric permittivity of typical transparent conducting oxide (TCO) films can have a profound effect on the optical properties of the material. This has been demonstrated by adding small amounts of Zr to an ITO ceramic sputtering target and analyzing the resulting ITO and ITO:Zr (ITZO) films. Comparative electrical and optical analyses of the films show that, although the carrier concentration and mobility do not change appreciably by adding 1 wt.% ZrO(2) to the ITO sputtering target, the plasma wavelength increases significantly for the ITZO film. We believe that the underlying physics of these results can be exploited in designing future TCO films for photovoltaic (PV) applications especially those that embody industrial advantages but remain limited by low mobility. C1 [Gessert, T. A.; Yoshida, Y.; Fesenmaier, C. C.; Duenow, J. N.; Coutts, T. J.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Gessert, TA (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. NR 9 TC 0 Z9 0 U1 0 U2 3 PU MATERIALS RESEARCH SOCIETY PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 J9 MATER RES SOC SYMP P PY 2010 VL 1165 BP 247 EP 252 PG 6 WC Energy & Fuels; Materials Science, Multidisciplinary SC Energy & Fuels; Materials Science GA BSL62 UT WOS:000284867000036 ER PT S AU Moutinho, HR Dhere, RG Jiang, CS Al-Jassim, MM AF Moutinho, H. R. Dhere, R. G. Jiang, C. -S. Al-Jassim, M. M. GP MRS BE Yamada, A Heske, C Contreras, MA Igalson, M Irvine, SJC TI Scanning Kelvin Probe Microscopy of CdTe Solar Cells Measured Under Different Bias Conditions SO THIN-FILM COMPOUND SEMICONDUCTOR VOLTAICS-2009 SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium on Thin-Film Compound Semiconductor Photovoltaics CY APR 13-17, 2009 CL San Francisco, CA ID FORCE MICROSCOPY AB We have investigated different methods for preparing CdTe/CdS cross sections for electrical measurements, including the following: cleaving; using GaAs substrates; and sandwiching the structure between the substrate and a glass slide, and polishing with diamond discs and alumina suspension. The latter method proved to be the most reliable, with a success rate of over 90%. We investigated cross sections of CdTe/CdS samples with scanning Kelvin probe microscopy (SKPM) using two different methods: applying the alternate bias with a frequency equal to 18.5 kHz, or equal to the frequency of the second cantilever resonance peak. The results showed that using the second resonance frequency produced a smoother signal, allowing the calculation of the electric field inside the device using just the raw SKPM data. We were able to measure the distribution of the electrical potential inside working devices. Then, by taking the first derivative of the potential, we calculated the electric field and determined the location of the p-n junction. C1 [Moutinho, H. R.; Dhere, R. G.; Jiang, C. -S.; Al-Jassim, M. M.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Moutinho, HR (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. NR 10 TC 1 Z9 1 U1 1 U2 5 PU MATERIALS RESEARCH SOCIETY PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 J9 MATER RES SOC SYMP P PY 2010 VL 1165 BP 361 EP 366 PG 6 WC Energy & Fuels; Materials Science, Multidisciplinary SC Energy & Fuels; Materials Science GA BSL62 UT WOS:000284867000051 ER PT S AU Pern, FJ Jones, RA Gedvilas, LM Gessert, TA AF Pern, F. J. Jones, R. A. Gedvilas, L. M. Gessert, T. A. GP MRS BE Yamada, A Heske, C Contreras, MA Igalson, M Irvine, SJC TI Preliminary Evaluation of Conductive Adhesive Tapes as Potential Interleafing Connects for Flexible Thin-Film PV Applications SO THIN-FILM COMPOUND SEMICONDUCTOR VOLTAICS-2009 SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium on Thin-Film Compound Semiconductor Photovoltaics CY APR 13-17, 2009 CL San Francisco, CA AB Two types of commercial electrically conductive adhesive (CA) tapes, one isotropic and the other anisotropic, were investigated for their potential application as interleafing connects for flexible thin-film photovoltaic modules. The performance stability of their vacuum-laminated sample constructs between two 50-mu m stainless steel (SS) foils and between the SS foil and bilayer ZnO/Mo-coated SS foil was evaluated upon damp-heat and dry-heat exposure. Preliminary results indicated that the isotropic CA tape was more stable than the anisotropic tape. C1 [Pern, F. J.; Gedvilas, L. M.; Gessert, T. A.] Natl Renewable Energy Lab, Natl Ctr Photovolta, Golden, CO 80401 USA. RP Pern, FJ (reprint author), Natl Renewable Energy Lab, Natl Ctr Photovolta, Golden, CO 80401 USA. NR 8 TC 0 Z9 0 U1 0 U2 1 PU MATERIALS RESEARCH SOC PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 J9 MATER RES SOC SYMP P PY 2010 VL 1165 BP 399 EP 404 PG 6 WC Energy & Fuels; Materials Science, Multidisciplinary SC Energy & Fuels; Materials Science GA BSL62 UT WOS:000284867000056 ER PT S AU Duenow, JN Dhere, RG Li, JA Metzger, WK Duda, A Gessert, TA AF Duenow, Joel N. Dhere, Ramesh G. Li, Jian Metzger, Wyatt K. Duda, Anna Gessert, Timothy A. GP MRS BE Yamada, A Heske, C Contreras, MA Igalson, M Irvine, SJC TI Development of ZnTe Contacts for Cd(1-x)Mg(x)Te Thin-Film Solar Cells for Tandem Applications SO THIN-FILM COMPOUND SEMICONDUCTOR VOLTAICS-2009 SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium on Thin-Film Compound Semiconductor Photovoltaics CY APR 13-17, 2009 CL San Francisco, CA AB Polycrystalline Cd(1-x)Mg(x)Te (CMT) thin films are a potential absorber material for two-junction thin-film tandem solar cell applications because the desired top cell bandgap range of 1.6 to 1.8 eV is readily obtained using CMT with only small resultant changes in the lattice constant from that of CdTe. Tandem devices require the top cell to have a transparent back contact to transmit the sub-bandgap spectrum to the bottom cell. Sputtered Cu-doped ZnTe (ZnTe:Cu) thin films, which offer potential as a transparent back contact interface layer, have been used successfully in CdTe devices. We apply ZnTe:Cu back contacts to CMT devices to continue development toward a transparent top cell. We describe the effects of depositing ZnTe:Cu at different temperatures and with different Cu contents on the net acceptor concentration, minority carrier lifetime, and device performance. We present here the highest reported CMT device efficiency of 9.6% at a bandgap of 1.57 eV. C1 [Duenow, Joel N.; Dhere, Ramesh G.; Li, Jian; Metzger, Wyatt K.; Duda, Anna; Gessert, Timothy A.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Duenow, JN (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. NR 9 TC 2 Z9 2 U1 0 U2 3 PU MATERIALS RESEARCH SOCIETY PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 J9 MATER RES SOC SYMP P PY 2010 VL 1165 BP 405 EP 410 PG 6 WC Energy & Fuels; Materials Science, Multidisciplinary SC Energy & Fuels; Materials Science GA BSL62 UT WOS:000284867000057 ER PT S AU Romero, MJ Contreras, MA Repins, I Jiang, CS Al-Jassim, MM AF Romero, M. J. Contreras, M. A. Repins, I. Jiang, C. -S. Al-Jassim, M. M. GP MRS BE Yamada, A Heske, C Contreras, MA Igalson, M Irvine, SJC TI Recent Advances in the STM-Based Luminescence Microscopy of Cu(In,Ga)Se(2) Thin Films SO THIN-FILM COMPOUND SEMICONDUCTOR VOLTAICS-2009 SE Materials Research Society Symposium Proceedings LA English DT Proceedings Paper CT Symposium on Thin-Film Compound Semiconductor Photovoltaics CY APR 13-17, 2009 CL San Francisco, CA ID SOLAR-CELLS AB We report on recent advances in the development of a luminescence spectroscopy based on scanning tunneling microscopy (STM) and its application to fundamental aspects of Cu(In,Ga)Se(2) (CIGS) thin films. Relevant to our discussion is the specifics of the surface electronics. The CIGS shows pronounced stoichiometric deviations at the surface and, consequently, distinct surface electronics that has been shown to be critical in achieving high efficiency. Cathodoluminescence (CL), a luminescence spectrum imaging mode in scanning electron microscopy (SEM), provides a direct correlation between the Microstructure of the CIGS and its electronic properties. As such, cathodoluminescence can resolve the emission spectrum between grain boundaries and grain interiors or be used to investigate the influence of local orientation and stoichiometry on the electronic properties of the CIGS at the microscale. Cathodoluminescence is not a surface microscopy, however, and resolving the electronic structure of the CIGS surface remains elusive to all luminescence microscopies. With this motivation, we have developed a luminescence microscopy based on STM, in which tunneling electrons are responsible for the excitation of luminescence (scanning tunneling luminescence or STL). The hot-tunneling-electron excitation is confined to the surface and, consequently, the tunneling luminescence spectrum reveals the electronic states near the surface. The STM is integrated inside the SEM and, therefore, both CL and STL can be measured over the same location and compared. Using this setup, the transition from the grain interior to the surface can be investigated. We have improved the collection of our optics to a level in which tunneling luminescence spectrum imaging can be performed. Here we present a detailed account on our investigation of the surface electronics in CIGS deposited in the regime of selenium deficiency as defined by < Se >/(< Cu >> + < In > + < Ga >) = 1. C1 [Romero, M. J.; Contreras, M. A.; Repins, I.; Jiang, C. -S.; Al-Jassim, M. M.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Romero, MJ (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. NR 10 TC 0 Z9 0 U1 0 U2 6 PU MATERIALS RESEARCH SOCIETY PI WARRENDALE PA 506 KEYSTONE DRIVE, WARRENDALE, PA 15088-7563 USA SN 0272-9172 J9 MATER RES SOC SYMP P PY 2010 VL 1165 BP 419 EP 424 PG 6 WC Energy & Fuels; Materials Science, Multidisciplinary SC Energy & Fuels; Materials Science GA BSL62 UT WOS:000284867000059 ER PT B AU Fister, TT Fong, DD AF Fister, Tim T. Fong, Dillon D. BE Ramanathan, S TI In Situ Synchrotron Characterization of Complex Oxide Heterostructures SO THIN FILM METAL-OXIDES: FUNDAMENTALS AND APPLICATIONS IN ELECTRONICS AND ENERGY LA English DT Article; Book Chapter ID FERROELECTRIC THIN-FILMS; X-RAY-SCATTERING; TEMPERATURE DEFECT CHEMISTRY; MISFIT RELAXATION MECHANISMS; CHEMICAL-VAPOR-DEPOSITION; ABSORPTION FINE-STRUCTURE; PULSED-LASER DEPOSITION; SURFACE-STRUCTURE; DOMAIN CONFIGURATIONS; PHASE-TRANSFORMATION AB This chapter surveys the high temperature and oxygen partial pressure behavior of complex oxide heterostructures as determined by in situ synchrotron X-ray methods. We consider both growth and post-growth behavior, emphasizing C, the observation of structural and interfacial defects relevant to the size-dependent properties seen in these systems. C1 [Fister, Tim T.; Fong, Dillon D.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. RP Fister, TT (reprint author), Argonne Natl Lab, Div Mat Sci, 9700 S Cass Ave, Argonne, IL 60439 USA. EM fister@anl.gov; fong@anl.gov NR 195 TC 1 Z9 1 U1 0 U2 1 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES BN 978-1-4419-0663-2 PY 2010 BP 1 EP 49 DI 10.1007/978-1-4419-0664-9_1 D2 10.1007/978-1-4419-0664-9 PG 49 WC Engineering, Electrical & Electronic; Materials Science, Coatings & Films SC Engineering; Materials Science GA BMQ63 UT WOS:000273353000001 ER PT B AU Cantoni, C Goyal, A AF Cantoni, C. Goyal, A. BE Ramanathan, S TI High-T-c Superconducting Thin- and Thick-Film-Based Coated Conductors for Energy Applications SO THIN FILM METAL-OXIDES: FUNDAMENTALS AND APPLICATIONS IN ELECTRONICS AND ENERGY LA English DT Article; Book Chapter ID CRITICAL-CURRENT DENSITY; HIGH-TEMPERATURE SUPERCONDUCTORS; ANGLE GRAIN-BOUNDARIES; COLUMNAR DEFECTS; YBA2CU3O7-DELTA FILMS; PRECIPITATE FORMATION; CRITICAL CURRENTS; LASER DEPOSITION; SELF-FIELD; RABITS AB Although the first epitaxial films of YBCO with high T-c were grown nearly 20 years ago, the understanding and control of the nanostructures responsible for the dissipation-free electrical current transport in high temperature superconductors (HTS) is quite recent. In the last 6-7 years, major advances have occurred in the fundamental investigation of low angle grain boundaries, flux-pinning phenomena, growth mode, and atomic-level defect structures of FITS epitaxial films. As a consequence, it has been possible to map and even engineer to some extent the performance of HTS coatings in large regions of the operating H, T J phase space. With such progress, the future of high temperature superconducting wires looks increasingly promising despite the tremendous challenges offered by these brittle and anisotropic materials. Nevertheless, further performance improvements are necessary for the superconducting technology to become cost-competitive against copper wires and ultimately succeed in revolutionizing the transmission of electricity. This can be achieved by further diminishing the gap between theoretical and experimental values of the critical current density J(c), and/or increasing the thickness of the superconductive layer as much as possible without degrading performance. In addition, further progress in controlling extrinsic and/or intrinsic nano-sized defects within the films is necessary to significantly reduce the anisotropic response of HTS and obtain a nearly constant dependence of the critical current on the magnetic field orientation, which is considered important for power applications. This chapter is a review of the challenges still present in the area of superconducting film processing for HTS wires and the approaches currently employed to address them. C1 [Cantoni, C.; Goyal, A.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Cantoni, C (reprint author), Oak Ridge Natl Lab, POB 2008, Oak Ridge, TN 37831 USA. EM cantonic@ornl.gov NR 62 TC 0 Z9 0 U1 1 U2 3 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES BN 978-1-4419-0663-2 PY 2010 BP 233 EP 253 DI 10.1007/978-1-4419-0664-9_7 D2 10.1007/978-1-4419-0664-9 PG 21 WC Engineering, Electrical & Electronic; Materials Science, Coatings & Films SC Engineering; Materials Science GA BMQ63 UT WOS:000273353000007 ER PT B AU Quek, SY Kaxiras, E AF Quek, Su Ying Kaxiras, Efthimios BE Ramanathan, S TI Applications of Thin Film Oxides in Catalysis SO THIN FILM METAL-OXIDES: FUNDAMENTALS AND APPLICATIONS IN ELECTRONICS AND ENERGY LA English DT Article; Book Chapter ID SCANNING-TUNNELING-MICROSCOPY; CO OXIDATION; AU NANOPARTICLES; AU(111) SURFACE; AB-INITIO; GOLD; ADSORPTION; TITANIA; MOO3; DEFECTS AB Metal oxides are fundamentally important as heterogeneous catalysts either as stand-alone catalysts or in combination with other oxides and/or metals. In this chapter, we focus on how the use of thin film metal oxides, in lieu of bulk oxides, can potentially enhance catalytic activity. We illustrate this concept with two examples. In the first example, we discuss a molybdenum trioxide monolayered structure that can be grown on the gold (111) surface. In contrast to the bulk molybdenum trioxide that is composed of bilayers, this oxide monolayer is semimetallic and has distinct chemical properties. In the second example, we propose that ultrathin oxide layers can enable the coupling of structural distortions and charge transfer beyond that allowed in the bulk, and that ultrathin oxide supports can play a dynamic, active, role in promoting catalysis in supported metal catalysts. C1 [Quek, Su Ying] Univ Calif Berkeley, Lawrence Berkeley Lab, Mol Foundry, Berkeley, CA 94720 USA. [Kaxiras, Efthimios] Ecole Polytech Fed Lausanne, Sch Engn, Lausaunne, Switzerland. [Kaxiras, Efthimios] Harvard Univ, Sch Engn & Appl Sci, Dept Phys, Cambridge, MA 02138 USA. RP Quek, SY (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Mol Foundry, Berkeley, CA 94720 USA. EM squek@lbl.gov; efthimios.kaxiras@epfl.ch NR 70 TC 2 Z9 2 U1 1 U2 2 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES BN 978-1-4419-0663-2 PY 2010 BP 281 EP 301 DI 10.1007/978-1-4419-0664-9_9 D2 10.1007/978-1-4419-0664-9 PG 21 WC Engineering, Electrical & Electronic; Materials Science, Coatings & Films SC Engineering; Materials Science GA BMQ63 UT WOS:000273353000009 ER PT S AU Gennett, T Perkins, JD Repins, IL Sundaramoorthy, R Ginley, DS AF Gennett, Thomas Perkins, John D. Repins, Ingrid L. Sundaramoorthy, Rajalakshmi Ginley, David S. BE Delahoy, AE Eldada, LA TI The stability and performance of amorphous-InZnO within CIGS devices SO THIN FILM SOLAR TECHNOLOGY II SE Proceedings of SPIE-The International Society for Optical Engineering LA English DT Proceedings Paper CT Conference On Thin Film Solar Technology II CY AUG 01-04, 2010 CL San Diego, CA SP SPIE DE CIGS; InZnO; TCO AB NREL CIGS devices with up to 20% efficiency are prepared using a three-stage process for the CIGS layer with the last step of an intrinsic ZnO and conductive ZnO:Al bilayer. This work outlines the efficiency and performance parameters for these CIGs devices when this bilayer is replaced with indium zinc oxide (a-InZnO), an amorphous metal oxide. It is well known that metal oxides can serve a variety of important functions in thin film photovoltaics such as transparent electrical contacts (TCO's), antireflection coatings and chemical barriers. In the case of a-InZnO, we have reported on the determination of the relative roles of metals and oxygen stoichiometries on the opto-electronic properties of a-InZnO thin films as well as the stability of those films in damp heat. Since InZO has a tunable conductivity based on the amount of oxygen introduced during deposition, it can be used as both the intrinsic and TCO layers. We were able to establish preliminary metrics for an all InZnO bilayer whose performance was comparable to a common CIGs device. C1 [Gennett, Thomas; Perkins, John D.; Repins, Ingrid L.; Sundaramoorthy, Rajalakshmi; Ginley, David S.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Gennett, T (reprint author), Natl Renewable Energy Lab, 1617 Cole Blvd, Golden, CO 80401 USA. NR 5 TC 2 Z9 2 U1 0 U2 12 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8267-9 J9 P SOC PHOTO-OPT INS PY 2010 VL 7771 AR 77710O DI 10.1117/12.861043 PG 5 WC Energy & Fuels; Materials Science, Coatings & Films; Optics SC Energy & Fuels; Materials Science; Optics GA BSU61 UT WOS:000285830600012 ER PT S AU Reyes-Coronado, A Acosta, MF Merino, RI Orera, VM Kenanakis, G Katsarakis, N Kafesaki, M Soukoulis, CM AF Reyes-Coronado, A. Acosta, M. F. Merino, R. I. Orera, V. M. Kenanakis, G. Katsarakis, N. Kafesaki, M. Soukoulis, C. M. BE Chigrin, DN TI Electromagnetic response of anisotropic eutectic metamaterials in THz range SO THIRD INTERNATIONAL WORKSHOP ON THEORETICAL AND COMPUTATIONAL NANOPHOTONICS - TACONA-PHOTONICS 2010 SE AIP Conference Proceedings LA English DT Proceedings Paper CT 3rd International Workshop on Theoretical and Computational Nanophotonics (TaCoNa-Photonics 2010) CY NOV 03-05, 2010 CL Bad Honnef, GERMANY SP Karlsruhe Sch Opt & Photon, Univ Karlsruhe, European Off Aerosp Res & Dev (EOARD), Comp Simulat Technol AG, Wiley-VCH, Lumerical Solut Inc DE eutectic materials; effective medium; hyperbolic dispersion relation ID INDEX AB We study the electromagnetic (EM) response of anisotropic eutectic metamaterials, consisting in cylindrical polaritonic LiF rods embedded in a KCl host. The specular reflectance of the samples was measured at far infrared (3-12 THz). The sample reflection was simulated by modeling the eutectic structure and solving numerically Maxwell equations for the EM fields. The reflectance was also calculated from simple effective response functions models. A good agreement was obtained between experimental and calculated spectra. From the effective response functions calculations, we obtained a range of frequencies in which the system behaves as a homogeneous effective anisotropic media, with a hyperbolic dispersion relation, opening possibilities for negative refraction and focusing applications. C1 [Reyes-Coronado, A.; Kenanakis, G.; Katsarakis, N.; Kafesaki, M.; Soukoulis, C. M.] FORTH, IESL, POB 1385, Iraklion 71110, Crete, Greece. [Kafesaki, M.; Soukoulis, C. M.] Univ Crete, Dept Mat Sci & Technol, Iraklion 71003, Greece. [Acosta, M. F.; Merino, R. I.; Orera, V. M.] Univ Zaragoza, CSIC, Inst Ciencia Mat Aragon, E-50009 Zaragoza, Spain. [Katsarakis, N.] Technol Educ Inst Crete, Dept Sci, Iraklion, Greece. [Soukoulis, C. M.] Iowa State Univ, USDOE, Ames Lab, Ames, IA 50011 USA. [Soukoulis, C. M.] Iowa State Univ, Dept Phys & Astron, Ames, IA 50011 USA. RP Reyes-Coronado, A (reprint author), FORTH, IESL, POB 1385, Iraklion 71110, Crete, Greece. RI orera, Victor/A-4213-2011; Reyes-Coronado, Alejandro/G-5396-2013; Kenanakis, George/G-1283-2010; Merino, Rosa/K-4995-2012; OI Kenanakis, George/0000-0001-5843-3712; Merino, Rosa/0000-0003-0747-405X; Orera, Victor/0000-0001-9690-9064 FU The European Community through the ENSEMBLE FX The European Community through the ENSEMBLE project sponsored this work. NR 11 TC 2 Z9 2 U1 1 U2 3 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0846-3 J9 AIP CONF PROC PY 2010 VL 1291 BP 148 EP + DI 10.1063/1.3506106 PG 2 WC Engineering, Electrical & Electronic; Nanoscience & Nanotechnology; Optics; Physics, Applied SC Engineering; Science & Technology - Other Topics; Optics; Physics GA BTI55 UT WOS:000287019200051 ER PT S AU Davis, RW Aaron, JS Rempe, SL Timlin, JA AF Davis, Ryan W. Aaron, Jesse S. Rempe, Susan L. Timlin, Jerilyn A. BE Conchello, JA Cogswell, CJ Wilson, T Brown, TG TI Fluorescence Fluctuation Analysis of Mixed Chromophores from a Line-Scanning Hyperspectral Imaging System SO THREE-DIMENSIONAL AND MULTIDIMENSIONAL MICROSCOPY: IMAGE ACQUISITION AND PROCESSING XVII SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Three-Dimensional and Multidimensional Microscopy - Image Acquisition and Processing XVII CY JAN 25-28, 2010 CL San Francisco, CA SP SPIE DE Fluorescence correlation spectroscopy; hyperspectral imaging; spatiotemporal image correlation spectroscopy; fluorescence fluctuation; multivariate curve resolution; line-scan imaging; autofluorescence; photobleaching ID MULTIVARIATE CURVE RESOLUTION; CORRELATION SPECTROSCOPY; CELLS; SIZE AB Fluorescence fluctuation analysis of dilute biomolecules can provide a powerful method for fast and accurate determination of diffusion dynamics, local concentrations, and aggregation states in complex environments. However, spectral overlap among multiple exogenous and endogenous fluorescent species, photobleaching, and background inhomogeneities can compromise quantitative accuracy and constrain useful biological implementation of this analytical strategy in real systems. In order to better understand these limitations and expand the utility of fluctuation correlation methods, spatiotemporal fluorescence correlation analysis was performed on spectrally resolved line scanned images of modeled and real data from mixed fluorescent nanospheres in a synthetic gel matrix. It was found that collecting images at a pixel sampling regime optimal for spectral imaging provides a method for calibration and subsequent temporal correlation analysis which is insensitive to spectral mixing, spatial inhomogeneity, and photobleaching. In these analyses, preprocessing with multivariate curve resolution (MCR) provided the local concentrations of each spectral component in the images, thus facilitating correlation analysis of each component individually. This approach allowed quantitative removal of background signals and showed dramatically improved quantitative results compared to a hypothetical system employing idealized filters and multi-parameter fitting routines. C1 [Davis, Ryan W.] Sandia Natl Labs, Livermore, CA 94550 USA. RP Davis, RW (reprint author), Sandia Natl Labs, 7011 E Ave, Livermore, CA 94550 USA. EM rwdavis@sandia.gov RI Rempe, Susan/H-1979-2011; OI Timlin, Jerilyn/0000-0003-2953-1721 NR 26 TC 0 Z9 0 U1 0 U2 3 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-7966-2 J9 PROC SPIE PY 2010 VL 7570 AR 757002 DI 10.1117/12.842294 PG 11 WC Optics; Imaging Science & Photographic Technology SC Optics; Imaging Science & Photographic Technology GA BSL78 UT WOS:000284873500001 ER PT B AU Hsiung, LL Campbell, GH McNaney, JM AF Hsiung, Luke L. Campbell, Geoffrey H. McNaney, James M. GP TMS TI Transitions of Dislocation Glide to Twinning and Shear Transformation in Shock-Deformed Tantalum SO TMS 2010 139TH ANNUAL MEETING & EXHIBITION - SUPPLEMENTAL PROCEEDINGS, VOL 2: MATERIALS CHARACTERIZATION, COMPUTATION AND MODELING AND ENERGY LA English DT Proceedings Paper CT TMS 2010 Annual Meeting Supplemental Proceedings on Materials Processing and Properties CY FEB 14-18, 2010 CL Seattle, WA DE Shock deformation; dislocation structure; twinning; shear transformation ID TUNGSTEN ALLOYS C1 [Hsiung, Luke L.; Campbell, Geoffrey H.; McNaney, James M.] Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA 94551 USA. RP Hsiung, LL (reprint author), Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, POB 808,L-352, Livermore, CA 94551 USA. RI Campbell, Geoffrey/F-7681-2010; McNaney, James/F-5258-2013 NR 10 TC 0 Z9 0 U1 1 U2 11 PU MINERALS, METALS & MATERIALS SOC PI WARRENDALE PA 184 THORN HILL RD, WARRENDALE, PA 15086-7514 USA BN 978-0-87339-752-0 PY 2010 BP 25 EP 32 PG 8 WC Materials Science, Multidisciplinary; Materials Science, Characterization & Testing SC Materials Science GA BUB37 UT WOS:000288718300003 ER PT B AU Hsiung, LL Fluss, MJ Kuntz, JD El-Dasher, BS Choi, BW Tumey, SJ Kimura, A AF Hsiung, Luke L. Fluss, Michael J. Kuntz, Joshua D. El-Dasher, Bassem S. Choi, B. William Tumey, Scott J. Kimura, Akihiko GP TMS TI TEM Study of Oxide Nanoparticles in ODS Steels Developed for Radiation Tolerance SO TMS 2010 139TH ANNUAL MEETING & EXHIBITION - SUPPLEMENTAL PROCEEDINGS, VOL 2: MATERIALS CHARACTERIZATION, COMPUTATION AND MODELING AND ENERGY LA English DT Proceedings Paper CT TMS 2010 Annual Meeting Supplemental Proceedings on Materials Processing and Properties CY FEB 14-18, 2010 CL Seattle, WA DE HRTEM; ODS steels; oxide nanoparticles; interfaces; core/shell structure ID DISPERSION; PARTICLES; POWDER; DEFORMATION; BEHAVIOR C1 [Hsiung, Luke L.; Fluss, Michael J.; Kuntz, Joshua D.; El-Dasher, Bassem S.; Choi, B. William; Tumey, Scott J.] Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA USA. RP Hsiung, LL (reprint author), Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, L-352,POB 808, Livermore, CA USA. NR 14 TC 0 Z9 0 U1 1 U2 6 PU MINERALS, METALS & MATERIALS SOC PI WARRENDALE PA 184 THORN HILL RD, WARRENDALE, PA 15086-7514 USA BN 978-0-87339-752-0 PY 2010 BP 93 EP 100 PG 8 WC Materials Science, Multidisciplinary; Materials Science, Characterization & Testing SC Materials Science GA BUB37 UT WOS:000288718300012 ER PT B AU Caro, M DeMange, P Marian, J Caro, A AF Caro, M. DeMange, P. Marian, J. Caro, A. GP TMS TI Thermo-Mechanical Response of a TRISO Fuel Particle in a Fusion/Fission Engine for Incineration of Weapons Grade Plutonium SO TMS 2010 139TH ANNUAL MEETING & EXHIBITION - SUPPLEMENTAL PROCEEDINGS, VOL 2: MATERIALS CHARACTERIZATION, COMPUTATION AND MODELING AND ENERGY LA English DT Proceedings Paper CT TMS 2010 Annual Meeting Supplemental Proceedings on Materials Processing and Properties CY FEB 14-18, 2010 CL Seattle, WA AB The Laser Inertial Fusion-based (LIFE) engine is an advanced energy concept under development at Lawrence Livermore National Laboratory (LLNL). LIFE engine could be used to drive a subcritical fission blanket with fertile or fissile fuel. Current LIFE engine designs envisages fuel in pebble bed form with TRISO (tristructural isotropic) particles embedded in a graphite matrix, and pebbles flowing in molten salt Flibe (2LiF+BeF(2)) coolant at T-700C. Weapons-grade plutonium (WGPu) fuel is an attractive option for LIFE engine involving the achievement of high fractional burnups in a short lifetime frame. However, WGPu LIFE engine operating conditions of high neutron fast fluence, high radiation damage, and high Helium and Hydrogen production pose severe challenges for typical TRISO particles. The thermo-mechanical fuel performance code HUPPCO (High burn-Up fuel Pebble Performance COde) currently under development accounts for spatial and time dependence of the material elastic properties, temperature, and irradiation swelling and creep mechanisms. In this work, some aspects of the thermo-mechanical response of TRISO particles used for incineration of weapons grade fuel in LIFE engine are analyzed. Preliminary results show the importance of developing reliable high-fidelity models of the performance of these new fuel designs and the need of new experimental data relevant to WGPu LIFE conditions. C1 [Caro, M.; DeMange, P.; Marian, J.; Caro, A.] Lawrence Livermore Natl Lab, Livermore, CA USA. RP Caro, M (reprint author), Lawrence Livermore Natl Lab, 7000 E Ave, Livermore, CA USA. EM serranodecaro2@llnl.Rov NR 11 TC 0 Z9 0 U1 0 U2 2 PU MINERALS, METALS & MATERIALS SOC PI WARRENDALE PA 184 THORN HILL RD, WARRENDALE, PA 15086-7514 USA BN 978-0-87339-752-0 PY 2010 BP 101 EP 104 PG 4 WC Materials Science, Multidisciplinary; Materials Science, Characterization & Testing SC Materials Science GA BUB37 UT WOS:000288718300013 ER PT B AU Furlinger, K Wright, NJ Skinner, D AF Furlinger, Karl Wright, Nicholas J. Skinner, David BE Mueller, MS Resch, MM Schulz, A Nagel, WE TI Performance Analysis and Workload Characterization with IPM SO TOOLS FOR HIGH PERFORMANCE COMPUTING 2009 LA English DT Proceedings Paper CT 3rd International Workshop on Parallel Tools for High Performance Computing CY SEP 14-15, 2009 CL High Performance Comp Ctr Stuttgart, Dresden, GERMANY HO High Performance Comp Ctr Stuttgart AB IPM is a profiling and workload characterization tool for MPI applications. IPM achieves its goal of minimizing the monitoring overhead by recording performance data in a fixed-size hashtable resident in memory and by carefully optimizing time-critical operations. At the same time, IPM offers very detailed and user centric perfoituance metrics. IPM's performance data is delivered as an XML file that can subsequently be used to generate a detailed profiling report in HTML format, avoiding the need for custom GUI applications. Pairwise communication volume and communication topology between processes, communication time breakdown across ranks, MPI operation timings, and MPI message sizes (buffer lengths) are some of IPM's most widely used metrics. IPM is free and distributed under the LGPL license. C1 [Furlinger, Karl] Univ Calif Berkeley, Dept EECS, Div Comp Sci, Soda Hall 515, Berkeley, CA 94720 USA. [Wright, Nicholas J.; Skinner, David] Lawrence Berkeley Natl Lab, NERSC Ctr, Berkeley, CA 94720 USA. RP Furlinger, K (reprint author), Univ Calif Berkeley, Dept EECS, Div Comp Sci, Soda Hall 515, Berkeley, CA 94720 USA. EM fuerling@eecs.berkeley.edu; deskinner@lbl.gov; njwright@lbl.gov OI Furlinger, Karl/0000-0003-0398-4087 NR 8 TC 1 Z9 1 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY BN 978-3-642-11260-7 PY 2010 BP 31 EP 38 DI 10.1007/978-3-642-11261-4_3 PG 8 WC Computer Science, Theory & Methods SC Computer Science GA BH0GQ UT WOS:000394921900003 ER PT B AU Hilbrich, T Schulz, M de Supinski, BR Muller, MS AF Hilbrich, Tobias Schulz, Martin de Supinski, Bronis R. Mueller, Matthias S. BE Mueller, MS Resch, MM Schulz, A Nagel, WE TI MUST: A Scalable Approach to Runtime Error Detection in MPI Programs SO TOOLS FOR HIGH PERFORMANCE COMPUTING 2009 LA English DT Proceedings Paper CT 3rd International Workshop on Parallel Tools for High Performance Computing CY SEP 14-15, 2009 CL High Performance Comp Ctr Stuttgart, Dresden, GERMANY HO High Performance Comp Ctr Stuttgart AB The Message-Passing Interface (MPI) is large and complex. Therefore, programming MPI is error prone. Several MPI runtime correctness tools address classes of usage errors, such as deadlocks or non-portable constructs. To our knowledge none of these tools scales to more than about 100 processes. However, some of the current HPC systems use more than 100,000 cores and future systems are expected to use far more. Since errors often depend on the task count used, we need correctness tools that scale to the full system size. We present a novel framework for scalable MPI correctness tools to address this need. Our fine-grained, module-based approach supports rapid prototyping and allows correctness tools built upon it to adapt to different architectures and use cases. The design uses (PMPI)-M-n to instantiate a tool from a set of individual modules. We present an overview of our design, along with first performance results for a proof of concept implementation. C1 [Hilbrich, Tobias] GWT TUD GmbH, Chemnitzer Str 48b, D-01187 Dresden, Germany. [Schulz, Martin; de Supinski, Bronis R.] Lawrence Livermore Natl Lab, Livermore, CA 94551 USA. [Mueller, Matthias S.] Tech Univ Dresden, Ctr Informat Serv & High Performance Comp ZIH, D-01062 Dresden, Germany. RP Hilbrich, T (reprint author), GWT TUD GmbH, Chemnitzer Str 48b, D-01187 Dresden, Germany. EM tobias.hilbrich@zih.tu-dresden.de; schulzm@llnl.gov; bronis@llnl.gov; matthias.mueller@tu-dresden.de NR 13 TC 2 Z9 2 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY BN 978-3-642-11260-7 PY 2010 BP 53 EP 66 DI 10.1007/978-3-642-11261-4_5 PG 14 WC Computer Science, Theory & Methods SC Computer Science GA BH0GQ UT WOS:000394921900005 ER PT B AU Terpstra, D Jagode, H You, HH Dongarra, J AF Terpstra, Dan Jagode, Heike You, Haihang Dongarra, Jack BE Mueller, MS Resch, MM Schulz, A Nagel, WE TI Collecting Performance Data with PAPI-C SO TOOLS FOR HIGH PERFORMANCE COMPUTING 2009 LA English DT Proceedings Paper CT 3rd International Workshop on Parallel Tools for High Performance Computing CY SEP 14-15, 2009 CL High Performance Comp Ctr Stuttgart, Dresden, GERMANY HO High Performance Comp Ctr Stuttgart AB Modern high performance computer systems continue to increase in size and complexity. Tools to measure application performance in these increasingly complex environments must also increase the richness of their measurements to provide insights into the increasingly intricate ways in which software and hardware interact. PAPI (the Performance API) has provided consistent platform and operating system independent access to CPU hardware performance counters for nearly a decade. Recent trends toward massively parallel multi-core systems with often heterogeneous architectures present new challenges for the measurement of hardware performance information, which is now available not only on the CPU core itself, but scattered across the chip and system. We discuss the evolution of PAPI into Component PAPI, or PAPI-C, in which multiple sources of performance data can be measured simultaneously via a common software interface. Several examples of components and component data measurements are discussed. We explore the challenges to hardware performance measurement in existing multi -core architectures. We conclude with an exploration of future directions for the PAPI interface. C1 [Terpstra, Dan; Jagode, Heike; Dongarra, Jack] Univ Tennessee, Knoxville, TN 37996 USA. [Dongarra, Jack] Oak Ridge Natl Lab, Oak Ridge, TN USA. [You, Haihang] Natl Inst Computat Sci, Oak Ridge, TN USA. RP Terpstra, D (reprint author), Univ Tennessee, Knoxville, TN 37996 USA. EM terpstra@eecs.utk.edu; jagode@eecs.utk.edu; you@eecs.utk.edu; dongarra@eecs.utk.edu FU Office of Mathematical, Information, and Computational Sciences of the Office of Science (OoS), U.S. Department of Energy (DoE) [DE-AC05-00OR22725]; UT-Battelle, LLC; Office of Science of the Department of Energy [DE-AC05-00OR22725]; U.S. Department of Energy Office of Science [DE-FC02-06ER25761]; National Science Foundation, Software Development for Cyberinfrastructure (SDCI) [NSF OCI-0722072, 207401]; Department of Defense FX This research was sponsored in part by the Office of Mathematical, Information, and Computational Sciences of the Office of Science (OoS), U.S. Department of Energy (DoE), under Contract No. DE-AC05-00OR22725 with UT-Battelle, LLC. This work used resources of the National Center for Computational Sciences at Oak Ridge National Laboratory, which is supported by the Office of Science of the Department of Energy under Contract DE-AC05-00OR22725. These resources were made available via the Performance Evaluation and Analysis Consortium End Station, a Department of Energy INCITE project.; This work was also supported in part by the U.S. Department of Energy Office of Science under contract DE-FC02-06ER25761, by the National Science Foundation, Software Development for Cyberinfrastructure (SDCI) Grant No. NSF OCI-0722072 Subcontract No. 207401, and by the Department of Defense, using resources at the Extreme Scale Systems Center. NR 17 TC 15 Z9 15 U1 0 U2 0 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY BN 978-3-642-11260-7 PY 2010 BP 157 EP 173 DI 10.1007/978-3-642-11261-4_11 PG 17 WC Computer Science, Theory & Methods SC Computer Science GA BH0GQ UT WOS:000394921900011 ER PT S AU McKinsey, DN Akerib, D Bedikian, S Bernstein, A Bolozdynya, A Bradley, A Chapman, J Clark, K Classen, T Curioni, A Dahl, E Dazeley, S Dragowsky, M de Viveiros, L Druszkiewicz, E Fiorucci, S Gaitskell, R Hall, C Faham, CH Kastens, L Kazkaz, K Lander, R Leonard, D Malling, D Mannino, R Mei, D Mock, J Nikkel, JA Phelps, P Shutt, T Skulski, W Sorensen, P Spaans, J Stiegler, T Svoboda, R Sweany, M Tripathi, M Walsh, N Webb, R White, J Wolfs, F Woods, M Zhang, C AF McKinsey, D. N. Akerib, D. Bedikian, S. Bernstein, A. Bolozdynya, A. Bradley, A. Chapman, J. Clark, K. Classen, T. Curioni, A. Dahl, E. Dazeley, S. Dragowsky, M. de Viveiros, L. Druszkiewicz, E. Fiorucci, S. Gaitskell, R. Hall, C. Faham, C. Hernandez Kastens, L. Kazkaz, K. Lander, R. Leonard, D. Malling, D. Mannino, R. Mei, D. Mock, J. Nikkel, J. A. Phelps, P. Shutt, T. Skulski, W. Sorensen, P. Spaans, J. Stiegler, T. Svoboda, R. Sweany, M. Tripathi, M. Walsh, N. Webb, R. White, J. Wolfs, F. Woods, M. Zhang, C. BE Coccia, E Pandola, L Fornengo, N Aloisio, R TI The LUX Dark Matter Search SO TOPICS IN ASTROPARTICLE AND UNDERGROUND PHYSICS (TAUP2009) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 11th International Conference on Topics in Astroparticle and Underground Physics CY JUL 01-05, 2009 CL Rome, ITALY SP INFN Gran Sasso Natl Lab ID XENON AB The Large Underground Xenon (LUX) experiment is a liquid xenon time projection chamber designed for extremely low levels of radioactive background in its fiducial volume. The overall liquid xenon mass is 300 kg, with a 100 kg fiducial mass. LUX is currently under construction, and integration of the full detector will begin in Fall 2009 at the Sanford Underground Science and Engineering Laboratory in South Dakota. The LUX sensitivity to the WIMP-nucleon spin-independent scattering cross-section will be 7 x 10(-46) cm(2) at 100 GeV after 300 days of low-background operation. C1 [McKinsey, D. N.; Bedikian, S.; Curioni, A.; Kastens, L.; Nikkel, J. A.] Yale Univ, Dept Phys, 217 Prospect St, New Haven, CT 06511 USA. [Chapman, J.; Dahl, E.; de Viveiros, L.; Fiorucci, S.; Gaitskell, R.; Faham, C. Hernandez; Malling, D.] Brown Univ, Dept Phys, Providence, RI 02912 USA. [Akerib, D.; Bradley, A.; Clark, K.; Dragowsky, M.; Phelps, P.; Shutt, T.] Case Western Reserve Univ, Dept Phys, Cleveland, OH 44106 USA. [Bernstein, A.; Dazeley, S.; Kazkaz, K.; Sorensen, P.] Lawrence Livermore Natl Lab, Livermore, CA USA. [Bolozdynya, A.] Moscow Engn Phys Inst, Moscow 115409, Russia. [Mannino, R.; Stiegler, T.; Webb, R.; White, J.] Texas A&M Univ, Dept Phys, College Stn, TX 77843 USA. [Classen, T.; Lander, R.; Mock, J.; Svoboda, R.; Sweany, M.; Tripathi, M.; Walsh, N.] Univ Calif Davis, Dept Phys, Davis, CA 95616 USA. [Hall, C.; Leonard, D.] Univ Maryland, Dept Phys, College Pk, MD 20742 USA. [Druszkiewicz, E.; Wolfs, F.] Univ Rochester, Dept Elect & Comp Engn, Rochester, NY 14627 USA. [Skulski, W.] Univ Rochester, Dept Phys & Astron, Rochester, NY 14627 USA. [Mei, D.; Spaans, J.; Zhang, C.] Univ South Dakota, Dept Phys, Vermillion, SD 57069 USA. RP McKinsey, DN (reprint author), Yale Univ, Dept Phys, 217 Prospect St, New Haven, CT 06511 USA. EM daniel.mckinsey@yale.edu RI Fiorucci, Stefano/I-1251-2012; de Viveiros, Luiz/M-9205-2013 OI de Viveiros, Luiz/0000-0002-7038-2361 NR 6 TC 33 Z9 33 U1 0 U2 2 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2010 VL 203 AR 012026 DI 10.1088/1742-6596/203/1/012026 PG 3 WC Astronomy & Astrophysics; Physics, Particles & Fields SC Astronomy & Astrophysics; Physics GA BQA08 UT WOS:000280470400026 ER PT S AU Otsuki, K Burrows, A Martinez-Pinedo, G Typel, S Langanke, K Matos, M AF Otsuki, K. Burrows, A. Martinez-Pinedo, G. Typel, S. Langanke, K. Matos, M. BE Susa, H Utsunomiya, H Arnould, M Gales, S Motobayashi, T Scheidenberger, C TI r-process in Type II supernovae and the role of direct capture SO TOURS SYMPOSIUM ON NUCLEAR PHYSICS AND ASTROPHYSICS - VII SE AIP Conference Proceedings LA English DT Proceedings Paper CT Tours Symposium on Nuclear Physics and Astrophysics VII CY NOV 16-20, 2009 CL Kobe, JAPAN SP Grand Accelerateur Natl Ions Lourds, Helmholtzzentrum Schwerionenforschung Gmbh, Riken Nishina Ctr Accelerator Based Sci, Univ Libre Bruxelles, French Japanese Int Associated Lab, Inamori Fdn DE astrophysics; supernova; r-process ID NEUTRON; RATES AB We have calculated r-process nucleosynthesis based on acoustic wave driven supernova simulation. The environment includes extremely high entropy cases which has not been studied in previous studies. Plenty of actinide and third peak elements are formed in an averaged abundance, while elements around the first and second peaks are overproduced. We also studied the effect of direct capture in r-process. The direct capture furthers r-process and make freeze out earlier. It will change the final abundance drastically. We recalculated r-process nucleosynthesis of the simulation considering the direct capture reaction. While we could not see a significant difference in averaged abundances, significant differences appeared in several individual yields. C1 [Otsuki, K.] Hokkaido Univ, Kita Ku, N10W8, Sapporo, Hokkaido 0600810, Japan. [Burrows, A.] Princeton Univ, Princeton, NJ 08544 USA. [Martinez-Pinedo, G.; Typel, S.; Langanke, K.] GSI Planckstrasse 1, D-64291 Darmstadt, Germany. [Matos, M.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Otsuki, K (reprint author), Hokkaido Univ, Kita Ku, N10W8, Sapporo, Hokkaido 0600810, Japan. RI Martinez-Pinedo, Gabriel/A-1915-2013; OI Martinez-Pinedo, Gabriel/0000-0002-3825-0131; Typel, Stefan/0000-0003-3238-9973 NR 8 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0784-8 J9 AIP CONF PROC PY 2010 VL 1238 BP 240 EP + DI 10.1063/1.3455940 PG 2 WC Astronomy & Astrophysics; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BRL76 UT WOS:000283073300043 ER PT S AU Savajols, H Amthor, AM Boutin, D Drouart, A Payet, J Nolen, JN Manikonda, S AF Savajols, H. Amthor, A. M. Boutin, D. Drouart, A. Payet, J. Nolen, J. N. Manikonda, S. CA S3 Collaboration BE Susa, H Utsunomiya, H Arnould, M Gales, S Motobayashi, T Scheidenberger, C TI S-3: The Super Separator Spectrometer for SPIRAL2 stable beams SO TOURS SYMPOSIUM ON NUCLEAR PHYSICS AND ASTROPHYSICS - VII SE AIP Conference Proceedings LA English DT Proceedings Paper CT Tours Symposium on Nuclear Physics and Astrophysics VII CY NOV 16-20, 2009 CL Kobe, JAPAN SP Grand Accelerateur Natl Ions Lourds, Helmholtzzentrum Schwerionenforschung Gmbh, Riken Nishina Ctr Accelerator Based Sci, Univ Libre Bruxelles, French Japanese Int Associated Lab, Inamori Fdn DE separator; spectrometer; superheavy elements; Sn-100 AB S-3 (Super Separator Spectrometer) is a device designed for experiments with the very high intensity stable beams of LINAG, the superconducting linear accelerator of GANIL, which will be built in the framework of SPIRAL2. These beams, which will provide ions with A/Q = 3 in SPIRAL2 phase one, can reach intensities up to 1mA for light ions, A<50. These unprecedented intensities open new opportunities in several physics domains, e.g. super-heavy and very-heavy nuclei, spectroscopy at and beyond the drip line, isomers and ground state properties, multi-nucleon transfer and deep-inelastic reactions. An international collaboration has been formed to propose physics experiments and develop technical solutions for this new instrument. C1 [Savajols, H.; Amthor, A. M.] GANIL, BP 55027, F-14076 Caen 5, France. [Boutin, D.; Drouart, A.] CEA DSM Irfu SPhN, F-91191 Gif Sur Yvette, France. [Payet, J.] CEA DSM Irfu SCAM, F-91191 Gif Sur Yvette, France. [Nolen, J. N.; Manikonda, S.] Argonne Natl Lab, Argonne, IL 60439 USA. RP Savajols, H (reprint author), GANIL, BP 55027, F-14076 Caen 5, France. RI Manikonda, Shashikant/D-6936-2011 NR 5 TC 5 Z9 5 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0784-8 J9 AIP CONF PROC PY 2010 VL 1238 BP 251 EP + DI 10.1063/1.3455944 PG 2 WC Astronomy & Astrophysics; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BRL76 UT WOS:000283073300045 ER PT S AU Mase, T Adriani, O Bonechi, L Bongi, M Castellini, G D'Alessandro, R Faus, A Grandi, M Haguenauer, M Itow, Y Kasahara, K Kawade, K Macina, D Masuda, K Matsubara, Y Menjo, H Mitsuka, G Muraki, Y Nakai, M Papini, P Perrot, AL Ricciarini, S Sako, T Shimizu, Y Taki, K Tamura, T Torii, S Tricomi, A Turner, WC Velasco, J Viciani, A Yoshida, K AF Mase, T. Adriani, O. Bonechi, L. Bongi, M. Castellini, G. D'Alessandro, R. Faus, A. Grandi, M. Haguenauer, M. Itow, Y. Kasahara, K. Kawade, K. Macina, D. Masuda, K. Matsubara, Y. Menjo, H. Mitsuka, G. Muraki, Y. Nakai, M. Papini, P. Perrot, A-L. Ricciarini, S. Sako, T. Shimizu, Y. Taki, K. Tamura, T. Torii, S. Tricomi, A. Turner, W. C. Velasco, J. Viciani, A. Yoshida, K. BE Susa, H Utsunomiya, H Arnould, M Gales, S Motobayashi, T Scheidenberger, C TI LHCf: calibration of hadron interaction models for high energy cosmic-ray physics at the LHC energy SO TOURS SYMPOSIUM ON NUCLEAR PHYSICS AND ASTROPHYSICS - VII SE AIP Conference Proceedings LA English DT Proceedings Paper CT Tours Symposium on Nuclear Physics and Astrophysics VII CY NOV 16-20, 2009 CL Kobe, JAPAN SP Grand Accelerateur Natl Ions Lourds, Helmholtzzentrum Schwerionenforschung Gmbh, Riken Nishina Ctr Accelerator Based Sci, Univ Libre Bruxelles, French Japanese Int Associated Lab, Inamori Fdn DE high-energy cosmic-ray; hadron interaction model; LHC AB LHCf measures the energy and transverse momentum of neutral particles produced in the forward region of the LHC interaction point. In high energy cosmic ray measurements, the results strongly depend on the hadron interaction model which is used in the air shower simulation. LHCf will take data at root s= 0.9, 2.4, 7, 10 and 14 TeV collisions at LHC and provide crucial calibration points for the hadron interaction models. C1 [Mase, T.; Itow, Y.; Kawade, K.; Masuda, K.; Matsubara, Y.; Mitsuka, G.; Sako, T.; Taki, K.] Nagoya Univ, Solar Terr Environm Lab, Nagoya, Aichi 4648601, Japan. [Haguenauer, M.] Ecode Polytech, Palaiseau, France. [Turner, W. C.; Yoshida, K.] LBNL, Berkeley, CA USA. RP Mase, T (reprint author), Nagoya Univ, Solar Terr Environm Lab, Nagoya, Aichi 4648601, Japan. RI Bongi, Massimo/L-9417-2015; OI Bongi, Massimo/0000-0002-6050-1937; Ricciarini, Sergio Bruno/0000-0001-6176-3368; Castellini, Guido/0000-0002-0177-0643; Tricomi, Alessia Rita/0000-0002-5071-5501; Papini, Paolo/0000-0003-4718-2895 NR 3 TC 0 Z9 0 U1 1 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0784-8 J9 AIP CONF PROC PY 2010 VL 1238 BP 349 EP + DI 10.1063/1.3455964 PG 2 WC Astronomy & Astrophysics; Physics, Nuclear SC Astronomy & Astrophysics; Physics GA BRL76 UT WOS:000283073300064 ER PT S AU Thrall, KD AF Thrall, Karla D. BE Morris, JB Shusterman, DJ TI Vapor Dosimetry in the Nose and Upper Airways of Humans SO TOXICOLOGY OF THE NOSE AND UPPER AIRWAYS SE Target Organ Toxicology Series LA English DT Article; Book Chapter ID COMPUTATIONAL FLUID-DYNAMICS; UPPER RESPIRATORY-TRACT; RISK-ASSESSMENT; VINYL-ACETATE; PHARMACOKINETIC MODEL; NASAL; EXPOSURE; RAT; ACETONE C1 [Thrall, Karla D.] Pacific Northwest Natl Lab, Richland, WA 99352 USA. RP Thrall, KD (reprint author), Pacific Northwest Natl Lab, Richland, WA 99352 USA. NR 18 TC 0 Z9 0 U1 1 U2 1 PU INFORMA HEALTHCARE PI LONDON PA TELEPHONE HOUSE, 69-77 PAUL ST, LONDON, EC2A 4LQ, ENGLAND SN 1073-0842 BN 978-1-4200-8188-6; 978-1-4200-8187-9 J9 TARG ORG T PY 2010 BP 116 EP 121 PG 6 WC Otorhinolaryngology; Toxicology SC Otorhinolaryngology; Toxicology GA BF7BF UT WOS:000383903800008 ER PT J AU Geist, DR Deng, ZQ Mueller, RP Brink, SR Chandler, JA AF Geist, David R. Deng, Zhiqun Mueller, Robert P. Brink, Steven R. Chandler, James A. TI Survival and Growth of Juvenile Snake River Fall Chinook Salmon Exposed to Constant and Fluctuating Temperatures SO TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY LA English DT Article ID DETERMINING THERMAL TOLERANCE; BONNEVILLE CUTTHROAT TROUT; PARR-SMOLT TRANSFORMATION; CALIFORNIA CENTRAL VALLEY; WATER TEMPERATURE; STEELHEAD TROUT; ADENOSINE-TRIPHOSPHATASE; ONCORHYNCHUS-KISUTCH; PREDATOR AVOIDANCE; COHO SALMON AB The incipient lethal temperature (ILT) and critical thermal maximum (CTM) methods are used to set temperature limits for fish. However, the standard application of these methods does not always match the temperature regimes that fish experience in the wild. We used alternative methods to determine the thermal tolerance thresholds of juvenile fall-run Chinook salmon Oncorhynchus tshawytscha exposed to the temperature regimes that are common in the entrapment pools that form along the shoreline of the Snake River when flows are altered to meet electric power demand. A modified CTM test with a steady temperature rise (1.5 degrees C/h) showed that one-half the fish died when temperatures reached 27.4-27.9 degrees C and that survival at 25 degrees C was highly variable; the average time to the first death was 9.1 h, varying from 1.7 to 22.5 h. Over 30 d, 99.8% of the fish in the constant temperature regimes (14-22 degrees C) survived. In the fluctuating temperature regimes (which varied from 10-14 degrees C to 22-27.5 degrees C), overall survival was 97.3%; however, only 83.0% and 88.9% survived in the groups that reached daily maximums of 27 degrees C and 27.5 degrees C, respectively. Growth over 30 d in the constant thermal regimes was nearly twice as high as that in the fluctuating regimes, even when daily average temperatures were similar. The maximum growth was 1.9%/d in terms of fork length [FL] and 11.2%/d in terms of weight (WT) at a constant 20 degrees C. The lowest growth occurred in the two groups exposed to daily temperatures of 27 degrees C or more, namely, 0.7-0.8% (FL) and 2.7-3.4% (WT). The results of this study suggest that thermal tolerance tests that expose juvenile fall Chinook salmon to thermal regimes that match the field conditions in entrapment pools along the shoreline of the Snake River provide higher temperature criteria than the standard ILT and CTM methods. C1 [Geist, David R.; Deng, Zhiqun; Mueller, Robert P.] Battelle Pacific NW, Environm Sustainabil Div, Richland, WA 99352 USA. [Brink, Steven R.; Chandler, James A.] Idaho Power Co, Boise, ID 83707 USA. RP Geist, DR (reprint author), Battelle Pacific NW, Environm Sustainabil Div, POB 999, Richland, WA 99352 USA. EM david.geist@pnl.gov RI Deng, Daniel/A-9536-2011 OI Deng, Daniel/0000-0002-8300-8766 FU Idaho Power Company [54973A] FX The authors thank all the people who made this study successful, including Jennifer Monroe, Michelle Lester, Katie Murray, Kevin Kimble, and Valerie Cullinan as well as other staff too numerous to mention. Chuck Coutant provided consultation on the study design and reviewed the final report. Phil Groves reviewed earlier versions of the manuscript. Substantial improvements to the initial manuscript were made by W. Connor and two anonymous reviewers. This study was funded by Idaho Power Company under contract 54973A. The Pacific Northwest National Laboratory is owned by the U.S. Department of Energy and operated by Battelle Memorial Institute under contract DE-AC05-76RL01830. NR 61 TC 9 Z9 10 U1 2 U2 32 PU AMER FISHERIES SOC PI BETHESDA PA 5410 GROSVENOR LANE SUITE 110, BETHESDA, MD 20814-2199 USA SN 0002-8487 J9 T AM FISH SOC JI Trans. Am. Fish. Soc. PD JAN PY 2010 VL 139 IS 1 BP 92 EP 107 DI 10.1577/T09-003.1 PG 16 WC Fisheries SC Fisheries GA 589DE UT WOS:000277124800008 ER PT J AU Wang, P Liu, W Johnston, DB Rausch, KD Schmidt, SJ Tumbleson, ME Singh, V AF Wang, P. Liu, W. Johnston, D. B. Rausch, K. D. Schmidt, S. J. Tumbleson, M. E. Singh, V. TI EFFECT OF ENDOSPERM HARDNESS ON AN ETHANOL PROCESS USING A GRANULAR STARCH HYDROLYZING ENZYME SO TRANSACTIONS OF THE ASABE LA English DT Article DE Corn; Dry grind process; Endosperm; Endosperm hardness; Ethanol; Granular starch hydrolyzing enzyme; Protease; Urea ID CORN; MAIZE; FERMENTATION; GRAIN AB Granular starch hydrolyzing enzymes (GSHE) can hydrolyze starch at low temperature (32 degrees C). The dry grind process using GSHE (GSH process) has fewer unit operations and no changes in process conditions (pH 4.0 and 32 degrees C) compared to the conventional process because it dispenses with the cooking and liquefaction step. In this study, the effects of endosperm hardness, protease, urea, and GSHE levels on GSH process were evaluated. Ground corn, soft endosperm, and hard endosperm were processed using two GSHE levels (0.1 and 0.4 mL per 100 g ground material) and four treatments of protease and urea addition. Soft and hard endosperm materials were obtained by grinding and sifting flaking grits from a dry milling pilot plant; classifications were confirmed using scanning electron microscopy. During 72 h of simultaneous granular starch hydrolysis and fermentation (GSHF), ethanol and glucose profiles were determined using HPLC. Soft endosperm resulted in higher final ethanol concentrations compared to ground corn or hard endosperm. Addition of urea increased final ethanol concentrations for soft and hard endosperm. Protease addition increased ethanol concentrations and fermentation rates for soft endosperm, hard endosperm, and ground corn. The effect of protease addition on ethanol concentrations and fermentation rates was most predominant for soft endosperm, less for hard endosperm, and least for ground corn. Samples (soft endosperm, hard endosperm, or corn) with protease resulted in higher (1.0% to 10.5% v/v) ethanol concentration compared to samples with urea. The GSH process with protease requires little or no urea addition. For fermentation of soft endosperm, GSHE dose can be reduced. Due to nutrients (lipids, minerals, and soluble proteins) present in corn that enhance yeast growth, ground corn fermented faster at the beginning than hard and soft endosperm. C1 [Rausch, K. D.; Tumbleson, M. E.; Singh, V.] Univ Illinois, Dept Agr & Biol Engn, Urbana, IL 61801 USA. [Wang, P.] US DOE, Natl Energy Technol Lab, Morgantown, WV USA. [Johnston, D. B.] ARS, USDA, Eastern Reg Res Ctr, Wyndmoor, PA USA. [Schmidt, S. J.] Univ Illinois, Dept Food Sci & Human Nutr, Urbana, IL 61801 USA. RP Singh, V (reprint author), Univ Illinois, Dept Agr & Biol Engn, 360G AESB,1304 W Penn Ave, Urbana, IL 61801 USA. EM vsingh@illinois.edu NR 23 TC 4 Z9 4 U1 0 U2 2 PU AMER SOC AGRICULTURAL & BIOLOGICAL ENGINEERS PI ST JOSEPH PA 2950 NILES RD, ST JOSEPH, MI 49085-9659 USA SN 2151-0032 EI 2151-0040 J9 T ASABE JI Trans. ASABE PD JAN-FEB PY 2010 VL 53 IS 1 BP 307 EP 312 PG 6 WC Agricultural Engineering SC Agriculture GA 579LC UT WOS:000276370800031 ER PT J AU Densmore, JD McClarren, RG AF Densmore, Jeffery D. McClarren, Ryan G. TI MOMENT ANALYSIS OF ANGULAR APPROXIMATION METHODS FOR TIME-DEPENDENT RADIATION TRANSPORT SO TRANSPORT THEORY AND STATISTICAL PHYSICS LA English DT Article DE Time-dependent radiation transport; Moment analysis; Diffusion approximation; P(1/3) approximation; Simplified P(N) approximation ID EQUATIONS AB We extend moment analysis, a technique developed for investigating the accuracy of discrete-ordinates spatial discretization schemes, to time-dependent radiation transport and apply it to several angular approximation methods. Specifically, we examine the diffusion approximation, the P(1/3) approximation, and three time-dependent generalizations of the simplified P(N) approximation: the SP(2), SP(3), and SSP(3) approximations. We show that all of the these methods preserve the correct flux-weighted average of x but not the correct flux-weighted average of (x - x(a))(2), where x is the spatial variable and x(a) is an arbitrary point. We also demonstrate that, for general cross sections and large elapsed time, the error in the flux-weighted average of (x - x(a))(2) is smallest in magnitude for the SP(2) and SP(3) approximations. In addition, we present a simple improvement to the SP(2) approximation that allows this method to produce the correct flux-weighted average of (x - x(a))(2). We present numerical results that test this analysis. From these results, we find that the angular approximation methods with the most accurate solutions also have the most accurate values for the flux-weighted average of (x - x(a))(2). In particular, the SP(2) and SP(3) approximations are two of the most accurate methods at large elapsed times, while the improved SP(2) approximation is one of the most accurate methods at all times. We also observe, however, that an accurate value for the flux-weighted average of (x - x(a))(2) is not always accompanied by an accurate solution. Consequently, we conclude that an accurate flux-weighted average of (x - x(a))(2) is a necessary rather than sufficient condition for an overall accurate angular approximation method. C1 [Densmore, Jeffery D.] Los Alamos Natl Lab, Computat Phys & Methods Grp, Los Alamos, NM 87545 USA. [McClarren, Ryan G.] Texas A&M Univ, Dept Nucl Engn, College Stn, TX 77843 USA. RP Densmore, JD (reprint author), Los Alamos Natl Lab, Computat Phys & Methods Grp, POB 1663,MS D409, Los Alamos, NM 87545 USA. EM jdd@lanl.gov FU U.S. government [DE-AC52-06NA25396] FX The work of the first author (J.D.D.) was performed under U.S. government contract DE-AC52-06NA25396 for Los Alamos National Laboratory, which is operated by Los Alamos National Security, LLC, for the U.S. Department of Energy. NR 10 TC 4 Z9 4 U1 0 U2 0 PU TAYLOR & FRANCIS INC PI PHILADELPHIA PA 325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA SN 0041-1450 J9 TRANSPORT THEOR STAT JI Transport. Theor. Statist. Phys. PY 2010 VL 39 IS 2-4 BP 192 EP 233 DI 10.1080/00411450.2010.533742 PG 42 WC Mathematics, Applied; Physics, Mathematical SC Mathematics; Physics GA 731QT UT WOS:000288125100005 ER PT J AU Franzese, O Knee, HE Slezak, L AF Franzese, Oscar Knee, Helmut E. (Bill) Slezak, Lee TI Effect of Wide-Based Single Tires on Fuel Efficiency of Class 8 Combination Trucks SO TRANSPORTATION RESEARCH RECORD LA English DT Article AB In 2007 and 2008, the Oak Ridge National Laboratory, in collaboration with several industry partners, collected real-world performance and situational data for long-haul operations of Class 8 trucks from a fleet engaged in normal freight operations. Such data and information are useful to support Class 8 modeling of combination truck performance and technology evaluation efforts for energy efficiency and to provide a means of accounting for real-world driving performance within combination truck research and analyses. Some general statistics, including distribution of idling times during long-haul trucking operations, are presented. However, the main focus is on the analysis of some of the extensive real-world information collected in this project, specifically on the assessment of the effect that different types of tires [i.e., dual tires versus new generation wide-based single tires (NGWBSTs)] have on the fuel efficiency of Class 8 trucks. The tire effect is also evaluated as a function of the vehicle load level. In all cases analyzed, the statistical tests strongly suggest that fuel efficiencies achieved when all NGWBSTs or combinations of duals and NGWBSTs are used are higher than in the case of a truck equipped with all dual tires. The results show that the fuel efficiency improvement increases as the number of NGWBSTs on the truck increases, with observed improvements of around 6% when either the tractor or the trailer was equipped with NGWBSTs and more than 9% when both were mounted with these types of tires. C1 [Franzese, Oscar; Knee, Helmut E. (Bill)] Oak Ridge Natl Lab, Natl Transportat Res Ctr, Ctr Transportat Anal, Knoxville, TN 37932 USA. [Slezak, Lee] US DOE, Vehicle Technol Program, Washington, DC 20585 USA. RP Franzese, O (reprint author), Oak Ridge Natl Lab, Natl Transportat Res Ctr, Ctr Transportat Anal, 2360 Cherahala Blvd, Knoxville, TN 37932 USA. EM franzeseo@ornl.gov FU Office of Vehicle Technologies, U.S. Department of Energy FX This project was sponsored by the Office of Vehicle Technologies, U.S. Department of Energy. The authors thank that office for funding and supporting this project. The authors also recognize Schrader Trucking of Jefferson City, Tennessee, for making its trucks available to serve as test vehicles for this project. The company provided necessary access to vehicles for the smooth conduct of the test as well as fueling and routing information to the project team for incorporation into the test data. Finally, the authors thank the Michelin Americas Research Company in Greenville, South Carolina, for providing the tires for the test vehicles. NR 19 TC 1 Z9 1 U1 1 U2 1 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0361-1981 J9 TRANSP RES RECORD JI Transp. Res. Record PY 2010 IS 2191 BP 1 EP 7 DI 10.3141/2191-01 PG 7 WC Engineering, Civil; Transportation; Transportation Science & Technology SC Engineering; Transportation GA 725XH UT WOS:000287679700001 ER PT J AU Ha, J Chae, S Chou, KW Tyliszczak, T Monteiro, PJM AF Ha, J. Chae, S. Chou, K. W. Tyliszczak, T. Monteiro, P. J. M. TI Scanning Transmission X-Ray Microscopic Study of Carbonated Calcium Silicate Hydrate SO TRANSPORTATION RESEARCH RECORD LA English DT Article ID RADIOACTIVE WASTE-FORMS; CEMENT; LEACHABILITY; SPECTROSCOPY; DURABILITY; GEOPOLYMER; CORROSION; CONCRETE; DIOXIDE AB Calcium silicate hydrate (C-S-H) is the main hydration product of portland cement. Studying the structural and chemical decomposition of C-S-H after carbonation is critical for determining the durability and serviceability of concrete. Recent studies showed that the mechanical properties are likely to be enhanced when mineral admixtures and polymers are introduced. So far, no molecular-level studies have been conducted on carbonated C-S-H material to clarify these effects. In this research, scanning transmission X-ray microscopy (STXM) is used to study C-S-H modified with two organic polymers (hexadecyltrimethylammonium and polyethylene glycol 200) and exposed to different reaction times with CO(2). STXM uses light in the soft X-ray region where a number of atomic resonances are present. By tuning the X-ray energies to a certain absorption edge, elemental and chemical identification was performed. The energy of the X-rays was tuned to the C K-edge, Ca L(2,3)-edge, and Si K-edge. Detailed images were also recorded with a lateral resolution of 30 nm. Structural, elemental, and chemical heterogeneities were spatially identified. Significant differences were found in carbon spectra in the atmospheric and 48-h continuous CO(2)-carbonated C-S-H samples, suggesting that carbon-containing precipitates formed within a C-S-H matrix differ depending on the extent of carbonation. Si K-edge spectra suggest increased polymerization of silicates depending on the duration of CO(2) exposure. This study found that the degree of silicate polymerization and the coordination environment for carbon-containing mineral phases vary with the CO(2) exposure level. C1 [Ha, J.; Chae, S.; Monteiro, P. J. M.] Univ Calif Berkeley, Dept Civil & Environm Engn, Berkeley, CA 94720 USA. [Chou, K. W.; Tyliszczak, T.] Univ Calif Berkeley, Lawrence Berkeley Lab, Adv Light Source, Berkeley, CA 94720 USA. RP Ha, J (reprint author), Univ Calif Berkeley, Dept Civil & Environm Engn, Berkeley, CA 94720 USA. EM juyoung@berkeley.edu NR 20 TC 6 Z9 6 U1 0 U2 14 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0361-1981 J9 TRANSPORT RES REC JI Transp. Res. Record PY 2010 IS 2142 BP 83 EP 88 DI 10.3141/2142-12 PG 6 WC Engineering, Civil; Transportation; Transportation Science & Technology SC Engineering; Transportation GA 596GP UT WOS:000277673400013 ER PT J AU Das, S Peterson, B Chin, SM AF Das, Sujit Peterson, Bruce Chin, Shih-Miao TI Analysis of Fuel Ethanol Transportation Activity and Potential Distribution Constraints SO TRANSPORTATION RESEARCH RECORD LA English DT Article AB An analysis is provided of fuel ethanol transportation activity and potential distribution constraints if the total 36 billion gal of renewable fuel use by 2022 is mandated by the US Environmental Protection Agency (EPA) under the Energy Independence and Security Act of 2007 Ethanol transport by domestic truck, marine, and rail distribution systems from ethanol refineries to blending terminals is estimated with the Oak Ridge National Laboratory's North American infrastructure network model Most supply and demand data provided by EPA were geocoded, and the transportation infrastructure network was updated through use of available commercial sources. The percentage Increases in ton mile movements by rail, waterways, and highways m 2022 are estimated to be 2 8%, 0 6%, and 0 13%, respectively, compared with the corresponding 2005 total domestic flows by various modes Overall, a significantly higher level of future ethanol demand would have a minimal impact on the transportation infrastructure However, there will be spatial impacts, and a significant level of investment will be needed because of a considerable increase m rail traffic from refineries to ethanol distribution terminals C1 [Das, Sujit; Peterson, Bruce; Chin, Shih-Miao] Oak Ridge Natl Lab, Energy & Transportat Sci Div, Knoxville, TN 37923 USA. RP Das, S (reprint author), Oak Ridge Natl Lab, Energy & Transportat Sci Div, 2360 Cherahala Blvd, Knoxville, TN 37923 USA. NR 7 TC 0 Z9 0 U1 1 U2 4 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0361-1981 J9 TRANSP RES RECORD JI Transp. Res. Record PY 2010 IS 2168 BP 136 EP 145 DI 10.3141/2168.16 PG 10 WC Engineering, Civil; Transportation; Transportation Science & Technology SC Engineering; Transportation GA 694EF UT WOS:000285277100016 ER PT J AU Eksioglu, SD Li, S Zhang, S Sokhansanj, S Petrolia, D AF Eksioglu, Sandra D. Li, Song Zhang, Shu Sokhansanj, Shahabaddine Petrolia, Daniel TI Analyzing Impact of Intermodal Facilities on Design and Management of Biofuel Supply Chain SO TRANSPORTATION RESEARCH RECORD LA English DT Article ID LOCATION PROBLEM; BIOMASS; ALGORITHM AB The impact of an intermodal facility on location and transportation decisions for biofuel production plants is analyzed. Location decisions affect the management of the inbound and outbound logistics of a plant. This supply chain design and management problem is modeled as a mixed integer program. Input data for this model are location of intermodal facilities and available transportation modes, cost and cargo capacity for each transportation mode, geographical distribution of biomass feedstock and production yields, and biomass processing and inventory costs. Outputs from this model are the number, location, and capacity of biofuel production plants. For each plant, the transportation mode used, timing of shipments, shipment size, inventory size, and production schedule that minimize the delivery cost of biofuel are determined. The model proposed in this research can be used as a decision-making tool for investors in the biofuels industry since it estimates the real cost of the business. The state of Mississippi is considered as the testing grounds for the model. C1 [Eksioglu, Sandra D.; Li, Song; Zhang, Shu] Mississippi State Univ, Dept Ind & Syst Engn, Mississippi State, MS 39762 USA. [Petrolia, Daniel] Mississippi State Univ, Dept Agr Econ, Mississippi State, MS 39762 USA. [Sokhansanj, Shahabaddine] Oak Ridge Natl Lab, Bioenergy Resource & Engn Syst Environm Sci Div, Oak Ridge, TN 37830 USA. RP Eksioglu, SD (reprint author), Mississippi State Univ, Dept Ind & Syst Engn, POB 9542,McCain Engn Bldg, Mississippi State, MS 39762 USA. EM sde47@ise.msstate.edu RI Petrolia, Daniel/I-4221-2013; Eksioglu, Sandra/G-8623-2016 OI Petrolia, Daniel/0000-0003-2102-1612; Eksioglu, Sandra/0000-0002-6674-2133 NR 25 TC 34 Z9 34 U1 1 U2 18 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0361-1981 EI 2169-4052 J9 TRANSPORT RES REC JI Transp. Res. Record PY 2010 IS 2191 BP 144 EP 151 DI 10.3141/2191-18 PG 8 WC Engineering, Civil; Transportation; Transportation Science & Technology SC Engineering; Transportation GA 725XH UT WOS:000287679700018 ER PT S AU Grissino-Mayer, HD Miller, DL Mora, CI AF Grissino-Mayer, Henri D. Miller, Dana L. Mora, Claudia I. BE Stoffel, M Bollschweiler, M Butler, DR Luckman, BH TI Dendrotempestology and the Isotopic Record of Tropical Cyclones in Tree Rings of the Southeastern United States SO TREE RINGS AND NATURAL HAZARDS: A STATE-OF-THE-ART SE Advances in Global Change Research LA English DT Article; Book Chapter ID INDUCED BREAKDOWN SPECTROSCOPY; HURRICANE ACTIVITY; FOREST HISTORY; NEW-HAMPSHIRE; RATIOS; GROWTH; PINE; RECONSTRUCTION; HYDROLOGY; ALABAMA C1 [Grissino-Mayer, Henri D.] Univ Tennessee, Dept Geog, Lab Tree Ring Sci, Knoxville, TN 37996 USA. [Miller, Dana L.] Univ Tennessee, Dept Earth & Planetary Sci, Knoxville, TN 37996 USA. [Mora, Claudia I.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Grissino-Mayer, HD (reprint author), Univ Tennessee, Dept Geog, Lab Tree Ring Sci, Knoxville, TN 37996 USA. EM grissino@utk.edu RI Mora, Claudia/B-5511-2017; OI Mora, Claudia/0000-0003-2042-0208; Labotka, Dana/0000-0001-6640-3505; Grissino-Mayer, Henri/0000-0003-1088-2927 NR 56 TC 2 Z9 2 U1 1 U2 3 PU SPRINGER PI DORDRECHT PA PO BOX 17, 3300 AA DORDRECHT, NETHERLANDS SN 1574-0919 BN 978-90-481-8735-5 J9 ADV GLOB CHANGE RES JI Adv. Glob. Change Res. PY 2010 VL 41 BP 291 EP 303 DI 10.1007/978-90-481-8736-2_28 D2 10.1007/978-90-481-8736-2 PG 13 WC Environmental Sciences; Environmental Studies; Forestry SC Environmental Sciences & Ecology; Forestry GA BPC30 UT WOS:000278502000028 ER PT S AU Stoica, T Sutter, E Calarco, R AF Stoica, Toma Sutter, Eli Calarco, Raffaella BE Aldea, A Barsan, V TI GaN and InN Nanowires: Growth and Optoelectronic Properties SO TRENDS IN NANOPHYSICS: THEORY, EXPERIMENT AND TECHNOLOGY SE Engineering Materials LA English DT Article; Book Chapter ID MOLECULAR-BEAM EPITAXY; QUANTUM-DOT; OPTICAL-PROPERTIES; MAGNETIC-FIELD; MBE; TRANSISTORS; STATES; NANOCOLUMNS; NUCLEATION; DIFFUSION AB Self-assembled GaN and InN nanowires (NWs) were synthesized by radio frequency Plasma-Assisted Molecular Beam Epitaxy (PAMBE) without external catalyst. NWs of micrometers length and diameter in the range of 20-200 nm are fabricated using this method under N-rich conditions. Driving mechanisms of the NW nucleation and the growth are discussed. The NWs have been investigated using scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), atomic force microscopy (AFM), and photoluminescence (PL). Electric and photoelectric measurements on single wire devices have been performed as well. We establish that the dark, Ultraviolet (UV) photo-current and band-edge absorption tails in GaN NWs are strongly dependent on wire diameter. A model of surface Fermi level pinning and Franz-Keldysh effect in carrier depletion region at wire surface were used to explain the observed behaviors. InN NWs show infrared (IR) photoluminescence strongly dependent on the growth parameters. High electron concentration of 10(18) - 10(19) cm(-3) was evaluated from line shape analysis of PL spectra. The Fermi level pinning at the surface corresponds to a surface accumulation layer. To modify the surface of InN NWs, core-shell InN/GaN NWs were grown. In this paper we focus on the influence of surface effects on the growth and properties of GaN and InN nanowires. C1 [Stoica, Toma; Calarco, Raffaella] Forschungszentrum Julich, JARA FIT Julich Aachen Res Alliance, D-52425 Julich, Germany. [Stoica, Toma; Calarco, Raffaella] Forschungszentrum Julich, Inst Bio & Nanosyst IBN 1, D-52425 Julich, Germany. [Sutter, Eli] Brookhaven Natl Lab, Ctr Funct Nanomat, Upton, NY 11973 USA. RP Stoica, T (reprint author), Forschungszentrum Julich, JARA FIT Julich Aachen Res Alliance, D-52425 Julich, Germany. EM istoica@fz-juelich.de; esutter@bnl.gov; R.Calarco@fz-juelich.de NR 62 TC 0 Z9 0 U1 1 U2 7 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 1612-1317 BN 978-3-642-12069-5 J9 ENG MATER PY 2010 BP 73 EP 96 DI 10.1007/978-3-642-12070-1_4 D2 10.1007/978-3-642-12070-1 PG 24 WC Nanoscience & Nanotechnology; Physics, Applied SC Science & Technology - Other Topics; Physics GA BQN05 UT WOS:000281353400004 ER PT J AU Calfapietra, C Ainsworth, EA Beier, C De Angelis, P Ellsworth, DS Godbold, DL Hendrey, GR Hickler, T Hoosbeek, MR Karnosky, DF King, J Korner, C Leakey, ADB Lewin, KF Liberloo, M Long, SP Lukac, M Matyssek, R Miglietta, F Nagy, J Norby, RJ Oren, R Percy, KE Rogers, A Mugnozza, GS Stitt, M Taylor, G Ceulemans, R AF Calfapietra, Carlo Ainsworth, Elizabeth A. Beier, Claus De Angelis, Paolo Ellsworth, David S. Godbold, Douglas L. Hendrey, George R. Hickler, Thomas Hoosbeek, Marcel R. Karnosky, David F. King, John Korner, Christian Leakey, Andrew D. B. Lewin, Keith F. Liberloo, Marion Long, Stephen P. Lukac, Martin Matyssek, Rainer Miglietta, Franco Nagy, John Norby, Richard J. Oren, Ram Percy, Kevin E. Rogers, Alistair Mugnozza, Giuseppe Scarascia Stitt, Mark Taylor, Gail Ceulemans, Reinhart CA ESF-Forest Face Grp TI Challenges in elevated CO2 experiments on forests SO TRENDS IN PLANT SCIENCE LA English DT Review ID ATMOSPHERIC CO2; CARBON-DIOXIDE; CLIMATE-CHANGE; ECOSYSTEM RESPONSES; ENRICHMENT SYSTEM; GROWTH DYNAMICS; AIR FUMIGATION; DESIGN; SPRUCE; OZONE AB Current forest Free Air CO2 Enrichment (FACE) experiments are reaching completion. Therefore, it is time to define the scientific goals and priorities of future experimental facilities. In this opinion article, we discuss the following three overarching issues (i) What are the most urgent scientific questions and how can they be addressed? (ii) What forest ecosystems should be investigated? (iii) Which other climate change factors should be coupled with elevated CO2 concentrations in future experiments to better predict the effects of climate change? Plantations and natural forests can have conflicting purposes for high productivity and environmental protection. However, in both cases the assessment of carbon balance and how this will be affected by elevated CO2 concentrations and the interacting climate change factors is the most pressing priority for future experiments. C1 [Calfapietra, Carlo] IBAF NR Monterotondo Scalo Roma, Rome, Italy. [Ainsworth, Elizabeth A.] USDA, Urbana, IL USA. [Ainsworth, Elizabeth A.; Leakey, Andrew D. B.; Long, Stephen P.; Rogers, Alistair] Univ Illinois, Urbana, IL 61801 USA. [Beier, Claus] Tech Univ Denmark, Roskilde, Denmark. [De Angelis, Paolo] Univ Tuscia, Viterbo, Italy. [Ellsworth, David S.] Univ Western Sydney, Penrith, NSW, Australia. [Godbold, Douglas L.] Bangor Univ, Bangor, Gwynedd, Wales. [Hendrey, George R.] CUNY, Queens Coll, New York, NY USA. [Hickler, Thomas] Lund Univ, Lund, Sweden. [Hoosbeek, Marcel R.] Wageningen Univ, Wageningen, Netherlands. [Karnosky, David F.] Michigan Technol Univ, Houghton, MI 49931 USA. [King, John] N Carolina State Univ, Raleigh, NC 27695 USA. [Korner, Christian] Univ Basel, Basel, Switzerland. [Lewin, Keith F.] Brookhaven Natl Lab, Upton, NY 11973 USA. [Liberloo, Marion; Ceulemans, Reinhart] Univ Antwerp, Antwerp, Belgium. [Lukac, Martin] Univ London Imperial Coll Sci Technol & Med, Ascot, Berks, England. [Matyssek, Rainer] Tech Univ Munich, D-8050 Freising Weihenstephan, Germany. [Miglietta, Franco] IBIMET CNR, Florence, Italy. [Norby, Richard J.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Oren, Ram] Duke Univ, Durham, NC USA. [Percy, Kevin E.] KE Percy Air Qual Effects Consulting Ltd, Ft McMurray, AB, Canada. [Mugnozza, Giuseppe Scarascia] Forestry & Land Use CRA, Dept Agron, Rome, Italy. [Stitt, Mark] Max Planck Inst Mol Plant Physiol, Golm, Germany. [Taylor, Gail] Univ Southampton, Southampton, Hants, England. RP Calfapietra, C (reprint author), IBAF NR Monterotondo Scalo Roma, Rome, Italy. EM carlo.calfapietra@ibaf.cnr.it RI Leakey, Andrew/Q-9889-2016; Miglietta, Franco/A-1257-2009; Hickler, Thomas/S-6287-2016; De Angelis, Paolo/A-6863-2012; Rogers, Alistair/E-1177-2011; Norby, Richard/C-1773-2012; Lukac, Martin/A-4379-2013; Beier, Claus/E-6288-2013; Korner, Christian/B-6592-2014; Calfapietra, Carlo/E-2269-2015; Beier, Claus/C-1789-2016; Ceulemans, Reinhart/F-2109-2016 OI Leakey, Andrew/0000-0001-6251-024X; Miglietta, Franco/0000-0003-1474-8143; Hickler, Thomas/0000-0002-4668-7552; Ellsworth, David/0000-0002-9699-2272; De Angelis, Paolo/0000-0001-8310-8831; Rogers, Alistair/0000-0001-9262-7430; Norby, Richard/0000-0002-0238-9828; Lukac, Martin/0000-0002-8535-6334; Beier, Claus/0000-0003-0348-7179; FU European Science Foundation (ESF) FX This paper was produced at an Interdisciplinary New Initiative Fund (INIF) workshop 'FACEing the Future: Planning the Next Generation of Elevated CO2 Experiments on Crops and Ecosystems', which was financed by the European Science Foundation (ESF). This paper is dedicated to our friend and colleague Dr. David F. Karnosky, who passed away suddenly on October 24, 2008. NR 37 TC 20 Z9 20 U1 1 U2 50 PU ELSEVIER SCIENCE LONDON PI LONDON PA 84 THEOBALDS RD, LONDON WC1X 8RR, ENGLAND SN 1360-1385 J9 TRENDS PLANT SCI JI Trends Plant Sci. PD JAN PY 2010 VL 15 IS 1 BP 5 EP 10 DI 10.1016/j.tplants.2009.11.001 PG 6 WC Plant Sciences SC Plant Sciences GA 553OU UT WOS:000274377500002 ER PT J AU Wang, W Hadfield, M Wereszczak, AA AF Wang, Wei Hadfield, Mark Wereszczak, Andrew A. TI Surface strength of silicon nitride in relation to rolling contact performance measured on ball-on-rod and modified four-ball tests SO TRIBOLOGY INTERNATIONAL LA English DT Article; Proceedings Paper CT 34th Leeds-Lyon Symposium on Tribology CY SEP 04-07, 2007 CL Inst Natl Sci Appliquees, Lyon, FRANCE HO Inst Natl Sci Appliquees DE Rolling contact fatigue; Silicon nitride; Surface strength AB Silicon nitride (Si(3)N(4)) has been used in various rolling contact applications in turbomachinery. automotive and power industry. It is favoured to replace conventional steel due to its low density, low friction, corrosion resistance and good performance under extreme condition. However, a major limitation of its wider application is its high material and machining cost, especially the cost associated with the finishing process. In the present study, a low cost sintered and reaction bonded silicon nitride (SRBSN) is used to study the surface machining effects on its rolling contact performance. Attempt has been made to link the surface strengths of Si(3)N(4) derived from half-rod and C-sphere flexure strength specimens to the rolling contact lifetimes of Si(3)N(4) rod and ball specimens. The rolling contact fatigue tests are carried out on ball-on-rod and modified four ball machines. Three types of surfaces with coarse, fine and conventional finishing conditions are examined. Flexure strength tests on half-rod and C-sphere show an increasing surface strength from specimens with coarse, fine to conventionally machined conditions. During rolling contact fatigue test of as-machined specimens, there are no failures observed on both ball-on-rod and four ball tests after 100 million stress cycles. However, there is a trend of decreasing wear volumes measured on the contact path of rods and balls with coarse, fine and conventional conditions. In four ball test, spall failures are observed on pre-crack specimens. There is a trend of increasing rolling contact fatigue lifetime from pre-cracked specimens with coarse, fine to conventional machining conditions. (c) 2009 Elsevier Ltd. All rights reserved. C1 [Wang, Wei; Hadfield, Mark] Bournemouth Univ, Sch Design Engn & Comp, Poole BH12 5BB, Dorset, England. [Wereszczak, Andrew A.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. RP Hadfield, M (reprint author), Bournemouth Univ, Sch Design Engn & Comp, Poole BH12 5BB, Dorset, England. EM mhadfield@bournemouth.ac.uk RI Wereszczak, Andrew/I-7310-2016 OI Wereszczak, Andrew/0000-0002-8344-092X NR 10 TC 3 Z9 4 U1 1 U2 4 PU ELSEVIER SCI LTD PI OXFORD PA THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND SN 0301-679X J9 TRIBOL INT JI Tribol. Int. PD JAN-FEB PY 2010 VL 43 IS 1-2 BP 423 EP 432 DI 10.1016/j.triboint.2009.07.005 PG 10 WC Engineering, Mechanical SC Engineering GA 519OJ UT WOS:000271776100052 ER PT S AU Milne, E Cerri, CEP Carvalho, JLN AF Milne, Eleanor Cerri, Carlos Eduardo P. Nunes Carvalho, Joao Luis BE Tscharntke, T Leuschner, C Veldkamp, E Faust, H Guhardja, E Bidin, A TI Agricultural expansion in the Brazilian state of Mato Grosso; implications for C stocks and greenhouse gas emissions SO TROPICAL RAINFORESTS AND AGROFORESTS UNDER GLOBAL CHANGE: ECOLOGICAL AND SOCIO-ECONOMIC VALUATIONS SE Environmental Science and Engineering BS Environmental Engineering LA English DT Article; Book Chapter DE Brazil; Mato Grosso; Rondonia; agricultural expansion; deforestation ID ORGANIC-CARBON STOCKS; MODELING SYSTEM; DEFORESTATION; AMAZON; MATTER AB The states of Rondonia and Mato Grosso in Brazil together make up the world's largest agricultural frontier. Between 2001 and 2004, deforestation, to provide land for highly mechanized agriculture in this area, reached unprecedented rates. The environmental consequences of this include increased greenhouse gas (GHG) emissions from above and below ground sources. In this area where agriculture is a relatively new activity, land use and management practices change rapidly as farmers react to market pressures but also use trial and error to increase productivity/reduce losses. Farmers routinely make use of the latest technologies making agricultural expansion very different from historical examples. The fact that systems are in a state of flux has implications for sustainability and the ability of scientists to produce local and national GHG inventories and project future GHG emissions and carbon stock changes. Such projections are necessary to assess the full environmental impacts of such large scale native vegetation loss and to inform policy makers accordingly. A pilot study of farmer interviews around the town of Sinop, Mato Grosso, found that land management methods have varied over time, with a recent trend emerging to move from monoculture systems to integrated crop/livestock systems. The interviews also revealed that management practices employed by the small (<500 ha) farms differed markedly from those employed by medium (>500 ha) and large (>10,000 ha) farms. Wider studies carried out in the neighbouring state of Rondonia have shown soil C stocks and GHG emissions to be highly dependent on agricultural management. We discuss the implications of rapidly changing management practices in the agricultural frontier region of Mato Grosso and Rondonia on past regional estimates of C stocks and GHG fluxes and future projections. The future outlook is discussed in the context of possibility of REDD being included in a successor to the Kyoto Protocol. C1 [Milne, Eleanor] Macaulay Inst, Aberdeen AB15 8QH, Scotland. [Milne, Eleanor] Colorado State Univ, NREL, Ft Collins, CO 80523 USA. [Cerri, Carlos Eduardo P.; Nunes Carvalho, Joao Luis] Univ Sao Paulo, Ctr Nucl Energy Agr, BR-13400970 Piracicaba, SP, Brazil. RP Milne, E (reprint author), Macaulay Inst, Aberdeen AB15 8QH, Scotland. EM eleanor.milne@colostate.edu NR 24 TC 0 Z9 1 U1 0 U2 9 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES SN 1863-5520 BN 978-3-642-00492-6 J9 ENVIRON SCI ENG JI Environ. Sci. Eng. PY 2010 BP 447 EP 460 DI 10.1007/978-3-642-00493-3_21 D2 10.1007/978-3-642-00493-3 PG 14 WC Ecology; Engineering, Environmental; Environmental Sciences; Forestry SC Environmental Sciences & Ecology; Engineering; Forestry GA BOB63 UT WOS:000276107400021 ER PT B AU Chandler, DW Stolte, S AF Chandler, David W. Stolte, Steven BE Brouard, M Vallance, C TI Elastic and Inelastic Scattering: Energy Transfer in Collisions SO TUTORIALS IN MOLECULAR REACTION DYNAMICS LA English DT Article; Book Chapter C1 [Chandler, David W.] Sandia Natl Labs, Combust Res Facil, Livermore, CA USA. [Stolte, Steven] Vrije Univ Amsterdam, Dept Phys Chem, Ctr Laser, Amsterdam, Netherlands. [Stolte, Steven] Jilin Univ, Inst Atom & Mol Phys, Changchun 130023, Peoples R China. RP Chandler, DW (reprint author), Sandia Natl Labs, Combust Res Facil, Livermore, CA USA. NR 0 TC 1 Z9 1 U1 0 U2 0 PU ROYAL SOC CHEMISTRY PI CAMBRIDGE PA THOMAS GRAHAM HOUSE, SCIENCE PARK, CAMBRIDGE CB4 4WF, CAMBS, ENGLAND BN 978-0-85404-158-9 PY 2010 BP 116 EP 166 PG 51 WC Chemistry, Physical SC Chemistry GA BSY41 UT WOS:000286130900005 ER PT S AU Podesta, JJ AF Podesta, J. J. BE Maksimovic, M Issautier, K MeyerVernet, N Moncuquet, M Pantellini, F TI Theory of solar wind turbulence with scale-dependent alignment, anisotropy, and cross-helicity SO TWELFTH INTERNATIONAL SOLAR WIND CONFERENCE SE AIP Conference Proceedings LA English DT Proceedings Paper CT 12th International Solar Wind Conference CY JUN 21-26, 2009 CL St Milo, FRANCE SP LESIA, Paris Observ, CNRS, CNES, French Natl Sun Earth Connect Program, European Space Agcy, NASA DE magnetohydrodynamics; turbulence; solar wind ID MAGNETOHYDRODYNAMIC TURBULENCE; FLUCTUATIONS; VELOCITY AB A theory of incompressible MHD turbulence with nonvanishing cross-helicity is derived based on two new observations from the Wind spacecraft. The first is the observation that the normalized cross-helicity sigma(c), is approximately scale-invariant throughout the inertial range. The second is the observation that the probabilities p and q for velocity and magnetic field fluctuations to be positively or negatively aligned are also approximately scale-invariant. The theory extends the theory of Boldyrev (2006) to turbulence with nonvanishing cross-helicity assuming that the cascades of the two Elsasser energies are both in a state of critical balance. C1 Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Podesta, JJ (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. EM jpodesta@solar.stanford.edu NR 16 TC 2 Z9 2 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0759-6 J9 AIP CONF PROC PY 2010 VL 1216 BP 115 EP 119 DI 10.1063/1.3395814 PG 5 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA BQO19 UT WOS:000281438100027 ER PT S AU Podesta, JJ AF Podesta, J. J. BE Maksimovic, M Issautier, K MeyerVernet, N Moncuquet, M Pantellini, F TI Spectral anisotropy of solar wind turbulence in the inertial range and dissipation range SO TWELFTH INTERNATIONAL SOLAR WIND CONFERENCE SE AIP Conference Proceedings LA English DT Proceedings Paper CT 12th International Solar Wind Conference CY JUN 21-26, 2009 CL St Milo, FRANCE SP LESIA, Paris Observ, CNRS, CNES, French Natl Sun Earth Connect Program, European Space Agcy, NASA DE solar wind; turbulence; wavelet analysis ID MAGNETIC-FIELD; POWER SPECTRA AB Wavelet analysis is a tool that can simultaneously analyze spacecraft data in both time and frequency. This enables the magnetic energy spectrum (trace spectrum) to be measured for different angles between the local mean magnetic field B(0) and the direction of the mean flow within a single data set. Examples obtained around solar minimum using Ulysses data at high latitudes and Stereo data for high-speed streams in the ecliptic plane show that the spectral exponent in the inertial range varies nearly monotonically from approximately 1.6 when B(0) is perpendicular to the flow to 2.0 when B(0) is parallel to the flow, roughly consistent with anisotropic theories of incompressible MHD turbulence. This and other new information about the 3D wavector spectrum of solar wind fluctuations in the inertial range and the dissipation range are briefly discussed. C1 Los Alamos Natl Lab, Los Alamos, NM 87544 USA. RP Podesta, JJ (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87544 USA. EM jpodesta@solar.stanford.edu NR 17 TC 4 Z9 4 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0759-6 J9 AIP CONF PROC PY 2010 VL 1216 BP 128 EP 131 DI 10.1063/1.3395817 PG 4 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA BQO19 UT WOS:000281438100030 ER PT S AU Vinas, AF Gurgiolo, C Nieves-Chinchilla, T Gary, SP Goldstein, ML AF Vinas, A. F. Gurgiolo, C. Nieves-Chinchilla, T. Gary, S. P. Goldstein, M. L. BE Maksimovic, M Issautier, K MeyerVernet, N Moncuquet, M Pantellini, F TI Whistler Waves Driven by Anisotropic Strahl Velocity Distributions: Cluster Observations SO TWELFTH INTERNATIONAL SOLAR WIND CONFERENCE SE AIP Conference Proceedings LA English DT Proceedings Paper CT 12th International Solar Wind Conference CY JUN 21-26, 2009 CL St Milo, FRANCE SP LESIA, Paris Observ, CNRS, CNES, French Natl Sun Earth Connect Program, European Space Agcy, NASA DE solar wind; strahl; whistler waves ID ELECTRON-DISTRIBUTION FUNCTIONS; HELIOS PLASMA-EXPERIMENT; SOLAR-WIND; INSTABILITY; FIELD; HALO AB Observed properties of the strahl using high resolution 3D electron velocity distribution data obtained from the Cluster/PEACE experiment are used to investigate its linear stability. An automated method to isolate the strata is used to allow its moments to be computed independent of the solar wind core+halo. Results show that the strahl can have a high temperature anisotropy (T-perpendicular to/T-parallel to greater than or similar to 2). This anisotropy is shown to be an important free energy source for the excitation of high frequency whistler waves. The analysis suggests that the resultant whistler waves are strong enough to regulate the electron velocity distributions in the solar wind through pitch-angle scattering. C1 [Vinas, A. F.; Gurgiolo, C.; Goldstein, M. L.] NASA, Goddard Space Flight Ctr, Geospace Phys Lab, Code 673, Greenbelt, MD 88004 USA. [Gurgiolo, C.] Bitterroot Basic Res, Hamilton, MT USA. [Gary, S. P.] Los Alamos Natl Lab, Los Alamos, NM USA. RP Vinas, AF (reprint author), NASA, Goddard Space Flight Ctr, Geospace Phys Lab, Code 673, Greenbelt, MD 88004 USA. EM adolfo.vinas@nasa.gov; pgary@lanl.gov RI Goldstein, Melvyn/B-1724-2008; Nieves-Chinchilla, Teresa/F-3482-2016 OI Nieves-Chinchilla, Teresa/0000-0003-0565-4890 FU NASA Post-doctoral program FX We would like to thank the PEACE, FGM, CIS and EFW teams for use of their data. We also acknowledge the Cluster Active Archive as a source of some of the data used. AFV and MLG would like to acknowledge the support of NASA headquarters to the Cluster mission and the PEACE experiment. TNC would like to thank ORAU for her support through the NASA Post-doctoral program. AFV would like to thank John Dorelli for his comments and pleasant discussions. NR 23 TC 6 Z9 6 U1 0 U2 3 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0759-6 J9 AIP CONF PROC PY 2010 VL 1216 BP 265 EP + PG 2 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA BQO19 UT WOS:000281438100063 ER PT S AU Foullon, C Lavraud, B Owen, CJ Fazakerley, AN Skoug, RM AF Foullon, C. Lavraud, B. Owen, C. J. Fazakerley, A. N. Skoug, R. M. BE Maksimovic, M Issautier, K MeyerVernet, N Moncuquet, M Pantellini, F TI Heliospheric Current Sheet Distortions from Adjacent Outflowing Transients: Multi-spacecraft Observations SO TWELFTH INTERNATIONAL SOLAR WIND CONFERENCE SE AIP Conference Proceedings LA English DT Proceedings Paper CT 12th International Solar Wind Conference CY JUN 21-26, 2009 CL St Milo, FRANCE SP LESIA, Paris Observ, CNRS, CNES, French Natl Sun Earth Connect Program, European Space Agcy, NASA DE Heliospheric Current Sheet; Solar wind/magnetosphere interactions ID WIND; MAGNETOPAUSE; SURFACE; SHAPE AB The heliospheric current sheet (HCS) is a permanent solar wind feature, with well predicted Earth passages, but it can be structured and its main orientation can be highly distorted. We report new observations from 2 spacecraft in the solar wind (supported by observations from 3 spacecraft in the nightside magnetosheath), showing an evolution across the Sun-Earth line of large field reversals adjacent to the HCS. Contrary to a previously reported multi-spacecraft event, this case shows that the field inversion structure cannot be assumed to be well preserved and close to planar on the scale of the magnetospheric cross-section. However, both cases indicate the presence of field reversals in an away sector that is connected to the southern solar magnetic hemisphere but lies unexpectedly above a toward sector. Following the interpretation of the reversals as transient outflowing loops, associated initial flow deviations can be envisaged to account for the HCS deformations. C1 [Foullon, C.] Univ Warwick, Dept Phys, CFSA, Coventry CV4 7AL, W Midlands, England. [Foullon, C.; Owen, C. J.; Fazakerley, A. N.] Univ Coll London, MSSL, Surrey RH56NT, England. [Lavraud, B.] Univ Toulouse 1 UPS, CESR, CNRS, UMR 5187, Toulouse, France. [Skoug, R. M.] Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. RP Foullon, C (reprint author), Univ Warwick, Dept Phys, CFSA, Coventry CV4 7AL, W Midlands, England. EM Claire.Foullon@warwick.ac.uk; lavraud@cesr.fr; cjo@mssl.ucl.ac.uk RI Owen, Christopher/C-2999-2008; Foullon, Claire/A-3539-2009 OI Owen, Christopher/0000-0002-5982-4667; Foullon, Claire/0000-0002-2532-9684 NR 12 TC 4 Z9 4 U1 0 U2 3 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0759-6 J9 AIP CONF PROC PY 2010 VL 1216 BP 367 EP + DI 10.1063/1.3395876 PG 2 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA BQO19 UT WOS:000281438100086 ER PT S AU Chollet, E Skoug, R Steinberg, J Crooker, N Giacalone, J AF Chollet, Eileen Skoug, Ruth Steinberg, John Crooker, Nancy Giacalone, Joe BE Maksimovic, M Issautier, K MeyerVernet, N Moncuquet, M Pantellini, F TI Reconnection and Disconnection: Observations of Suprathermal Electron Heat Flux Dropouts SO TWELFTH INTERNATIONAL SOLAR WIND CONFERENCE SE AIP Conference Proceedings LA English DT Proceedings Paper CT 12th International Solar Wind Conference CY JUN 21-26, 2009 CL St Milo, FRANCE SP LESIA, Paris Observ, CNRS, CNES, French Natl Sun Earth Connect Program, European Space Agcy, NASA DE Particle emission; Solar Wind; Solar activity ID ADVANCED COMPOSITION EXPLORER; MAGNETIC-FIELD; SOLAR-WIND; PARTICLES; PROTON AB Suprathermal electron heat flux dropouts (HFD) serve as a sensitive test of the magnetic topology of the inner heliosphere. Since the heat flux electron strahl always flows away from the Sun, a heat flux dropout should indicate either that the magnetic field line is completely disconnected from the Sun or that the heat flux strahl is scattered into other pitch angles. We present observations of two suprathermal electron heat flux dropout events observed by the Advanced Composition Explorer (ACE) spacecraft which occur simultaneously with impulsive energetic ion events. Since suprathermal electrons encompass the same velocity range as ions with energies of a few MeV/nucleon, the similarities and differences between them as observed at 1 AU probes the sources and transport of these two species. We compare the two events to show the difference between the signatures of a simple disconnection and a more complicated reconnection scenario. Comparing suprathermal electron modulations with energetic ion modulations is a powerful technique for determining the magnetic topology between particle injection at the Sun and observation at 1 AU. C1 [Chollet, Eileen] CALTECH, Pasadena, CA 91125 USA. [Skoug, Ruth; Steinberg, John] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Crooker, Nancy] Boston Univ, Boston, MA 02215 USA. [Giacalone, Joe] Univ Arizona, Tucson, AZ 85721 USA. RP Chollet, E (reprint author), CALTECH, Pasadena, CA 91125 USA. EM echollet@srl.caltech.edu; giacalon@lpl.arizona.edu NR 11 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0759-6 J9 AIP CONF PROC PY 2010 VL 1216 BP 600 EP + DI 10.1063/1.3395937 PG 2 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA BQO19 UT WOS:000281438100140 ER PT J AU Parish, CM Brewer, LN AF Parish, Chad M. Brewer, Luke N. TI Multivariate statistics applications in phase analysis of STEM-EDS spectrum images SO ULTRAMICROSCOPY LA English DT Article DE STEM; X-ray microanalysis; Spectrum imaging; Spectral imaging; Quantification; Multivariate statistical analysis; Principal component analysis; PCA ID LEAD-ZIRCONATE-TITANATE; TRANSMISSION ELECTRON-MICROSCOPY; PLZT THIN-FILMS; QUANTITATIVE-ANALYSIS; MICROANALYSIS; ACQUISITION; SPECIMENS; TIME AB Spectrum imaging (SI) methods are displacing traditional spot analyses as the predominant paradigm for spectroscopic analysis with electron beam instrumentation. The multivariate nature of SI provides clear advantages for qualitative analysis of multiphase specimens relative to traditional gray-scale images acquired with non-spectroscopic signals, where different phases with similar average atomic number may exhibit the same intensity. However, with the improvement in qualitative analysis with the SI paradigm has come a decline in the quantitative analysis of the phases thus identified, since the spectra from individual pixels typically have insufficient counting statistics for proper quantification. The present paper outlines a methodology for quantitative analysis within the spectral imaging paradigm, which is illustrated through X-ray energy-dispersive spectroscopy (EDS) of a multiphase (Pb,La)(Zr,Ti)O(3) ceramic in scanning transmission electron microscopy (STEM). Statistical analysis of STEM-EDS Sl is shown to identify the number of distinct phases in the analyzed specimen and to provide better segmentation than the STEM high-angle annular dark-field (HAADF) signal. Representative spectra for the identified phases are extracted from the segmented images with and without exclusion of pixels that exhibit spectral contributions from multiple phases, and subsequently quantified using Cliff-Lorimer sensitivity factors. The phase compositions extracted with the method while excluding pixels from multiple phases are found to be in good agreement with those extracted from user-selected regions of interest, while providing improved confidence intervals. Without exclusion of multiphase pixels, the extracted composition is found to be in poor statistical agreement with the other results because of systematic errors arising from the cross-phase spectral contamination. The proposed method allows quantification to be performed in the presence of discontinuous phase distributions and overlapping phases, challenges that are typical of many nanoscale analyses performed by STEM-EDS. (C) 2009 Elsevier B.V. All rights reserved. C1 [Parish, Chad M.; Brewer, Luke N.] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Parish, CM (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. EM parishcm@ornl.gov RI Parish, Chad/J-8381-2013 FU United States Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX Sandia is a multiprogram laboratory operated by Sandia Corporation, a LockheedMartin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. Bruce Tuttle and Pat Mahoney provided the PLZT samples. Mike Keenan, Paul Kotula, Chris Stork, Blythe Clark, and Khalid Hattar provided comments and discussion. NR 43 TC 17 Z9 17 U1 0 U2 28 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0304-3991 J9 ULTRAMICROSCOPY JI Ultramicroscopy PD JAN PY 2010 VL 110 IS 2 BP 134 EP 143 DI 10.1016/j.ultramic.2009.10.011 PG 10 WC Microscopy SC Microscopy GA 555EF UT WOS:000274490100006 PM 19897301 ER PT J AU Erni, R Rossell, MD Nakashima, PNH AF Erni, Rolf Rossell, Marta D. Nakashima, Philip N. H. TI Optimization of exit-plane waves restored from HRTEM through-focal series SO ULTRAMICROSCOPY LA English DT Article DE HRTEM; Through-focal series reconstruction; Exit-plane wave; Aberration correction; Modulation transfer function ID TRANSMISSION ELECTRON-MICROSCOPY; SCAN CCD CAMERA; HIGH-RESOLUTION TEM; ABERRATION CORRECTION; IMAGE-RESTORATION; PHASE-RETRIEVAL; FOCUS-VARIATION; RECONSTRUCTION; MICROGRAPHS; SIMULATIONS AB Atomic-resolution transmission electron microscopy has largely benefited from the implementation of aberration correctors in the imaging part of the microscope. Though the dominant geometrical axial aberrations can in principle be corrected or suitably adjusted, the impact of higher-order aberrations, which are mainly due to the implementation of non-round electron optical elements, on the imaging process remains unclear. Based on a semi-empirical criterion, we analyze the impact of residual aperture aberrations on the quality of exit-plane waves that are retrieved from through-focal series recorded using an aberration-corrected and monochromated instrument which was operated at 300 kV and enabled for an information transfer of similar to 0.05 nm. We show that the impact of some of the higher-order aberrations in retrieved exit-plane waves can be balanced by a suitable adjustment of symmetry equivalent lower-order aberrations. We find that proper compensation and correction of 1st and 2nd order aberrations is critical, and that the required accuracy is difficult to achieve. This results in an apparent insensitivity towards residual higher-order aberrations. We also investigate the influence of the detector characteristics on the image contrast. We find that correction for the modulation transfer function results in a contrast gain of up to 40%. (C) 2009 Elsevier B.V. All rights reserved. C1 [Erni, Rolf] Swiss Fed Labs Mat Testing & Res Empa, Ctr Electron Microscopy, CH-8600 Dubendorf, Switzerland. [Erni, Rolf; Rossell, Marta D.] Univ Calif Berkeley, Lawrence Berkeley Lab, Natl Ctr Electron Microscopy, Berkeley, CA 94704 USA. [Rossell, Marta D.] ETH, Dept Mat, Lab Multifunct Mat, CH-8093 Zurich, Switzerland. [Nakashima, Philip N. H.] Monash Univ, ARC Ctr Excellence Design Light Met, Clayton, Vic 3800, Australia. RP Erni, R (reprint author), Swiss Fed Labs Mat Testing & Res Empa, Ctr Electron Microscopy, Uberlandstr 129, CH-8600 Dubendorf, Switzerland. EM rolf.erni@empa.ch RI Erni, Rolf/P-7435-2014; Nakashima, Philip/B-1357-2008; Rossell, Marta/E-9785-2017 OI Erni, Rolf/0000-0003-2391-5943; Nakashima, Philip/0000-0002-7495-1349; FU Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy [DE-AC02-05CH11231] FX Part of this work was performed at NCEM, which is supported by the Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. PN is grateful to the Monash Centre for Electron Microscopy for providing computing resources used in the MTF calculations. NR 44 TC 8 Z9 8 U1 0 U2 24 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0304-3991 EI 1879-2723 J9 ULTRAMICROSCOPY JI Ultramicroscopy PD JAN PY 2010 VL 110 IS 2 BP 151 EP 161 DI 10.1016/j.ultramic.2009.10.015 PG 11 WC Microscopy SC Microscopy GA 555EF UT WOS:000274490100008 PM 19931286 ER PT J AU Mishra, SK Deymier, PA Muralidharan, K Frantziskonis, G Pannala, S Simunovic, S AF Mishra, Sudib K. Deymier, P. A. Muralidharan, Krishna Frantziskonis, G. Pannala, Sreekanth Simunovic, Srdjan TI Modeling the coupling of reaction kinetics and hydrodynamics in a collapsing cavity SO ULTRASONICS SONOCHEMISTRY LA English DT Article DE Cavitation; Reaction; Multiphase; Lattice Boltzmann Model; Stochastic ID GAS-VAPOR BUBBLE; MICROSPHERES; SONOCHEMISTRY; CAVITATION; FLOWS AB We introduce a model of cavitation based on the multiphase Lattice Boltzmann method (LBM) that allows for coupling between the hydrodynamics of a collapsing cavity and supported solute chemical species. We demonstrate that this model can also be coupled to deterministic or stochastic chemical reactions. In a two-species model of chemical reactions (with a major and a minor species). the major difference observed between the deterministic and stochastic reactions takes the form of random fluctuations in concentration of the minor species. We demonstrate that advection associated with the hydrodynamics of a collapsing cavity leads to highly inhomogeneous concentration of solutes. In turn these inhomogeneities in concentration may lead to significant increase in concentration-dependent reaction rates and can result in a local enhancement in the production of minor species. Published by Elsevier B.V. C1 [Mishra, Sudib K.; Frantziskonis, G.] Univ Calif Irvine, Dept Mech & Aerosp Engn, Irvine, CA 92697 USA. [Deymier, P. A.; Muralidharan, Krishna; Frantziskonis, G.] Univ Arizona, Dept Mat Sci & Engn, Tucson, AZ 85721 USA. [Pannala, Sreekanth; Simunovic, Srdjan] Oak Ridge Natl Lab, Comp Sci & Math Div, Oak Ridge, TN 37831 USA. RP Mishra, SK (reprint author), Univ Calif Irvine, Dept Mech & Aerosp Engn, Irvine, CA 92697 USA. EM mishras@uci.edu RI Pannala, Sreekanth/F-9507-2010 FU Mathematical, Information, and Computational Sciences Division; Office of Advanced Scientific Computing Research; US Department of Energy FX This research was supported by the Mathematical, Information, and Computational Sciences Division, Office of Advanced Scientific Computing Research, US Department of Energy. NR 26 TC 13 Z9 13 U1 1 U2 10 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 1350-4177 J9 ULTRASON SONOCHEM JI Ultrason. Sonochem. PD JAN PY 2010 VL 17 IS 1 BP 258 EP 265 DI 10.1016/j.ultsonch.2009.05.014 PG 8 WC Acoustics; Chemistry, Multidisciplinary SC Acoustics; Chemistry GA 548AD UT WOS:000273930300046 PM 19520598 ER PT S AU Hunter, SR Patton, JF Sepaniak, MJ Datskos, PG Smith, DB AF Hunter, Scott R. Patton, James F. Sepaniak, Michael J. Datskos, Panos G. Smith, D. Barton BE Carapezza, EM TI Distributed optical microsensors for hydrogen leak detection and related applications SO UNATTENDED GROUND, SEA, AND AIR SENSOR TECHNOLOGIES AND APPLICATIONS XII SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Unattended Ground, Sea, and Air Sensor Technologies and Applications XII CY APR 05-08, 2010 CL Orlando, FL SP SPIE DE optical; microsensor; networked; array; hydrogen; palladium; microcantilever ID MICROCANTILEVER SENSORS; MICROMECHANICAL SENSORS; THIN-FILM; FIBER; CANTILEVER; PALLADIUM; PERFORMANCE; ARRAYS; OXYGEN AB Significant advances have recently been made to develop optically interrogated microsensor based chemical sensors with specific application to hydrogen vapor sensing and leak detection in the hydrogen economy. We have developed functionalized polymer-film and palladium/silver alloy coated microcantilever arrays with nanomechanical sensing for this application. The uniqueness of this approach is in the use of independent component analysis (ICA) and the classification techniques of neural networks to analyze the signals produced by an array of microcantilever sensors. This analysis identifies and quantifies the amount of hydrogen and other trace gases physisorbed on the arrays. Selectivity is achieved by using arrays of functionalized sensors with a moderate distribution of specificity among the sensing elements. The device consists of an array of beam-shaped transducers with molecular recognition phases (MRPs) applied to one surface of the transducers. Bending moments on the individual transducers can be detected by illuminating them with a laser or an LED and then reading the reflected light with an optical position sensitive detector (PSD) such as a CCD. Judicious selection of MRPs for the array provides multiple isolated interaction surfaces for sensing the environment. When a particular chemical agent binds to a transducer, the effective surface stresses of its modified and uncoated sides change unequally and the transducer begins to bend. The extent of bending depends upon the specific interactions between the microcantilever's MRP and the analyte. Thus, the readout of a multi-MRP array is a complex multidimensional signal that can be analyzed to deconvolve a multicomponent gas mixture. The use of this sensing and analysis technique in unattended networked arrays of sensors for various monitoring and surveillance applications is discussed. C1 [Hunter, Scott R.; Datskos, Panos G.; Smith, D. Barton] Oak Ridge Natl Lab, Measurement Sci & Syst Engn Div, Oak Ridge, TN 37831 USA. RP Hunter, SR (reprint author), Oak Ridge Natl Lab, Measurement Sci & Syst Engn Div, POB 2008, Oak Ridge, TN 37831 USA. EM huntersr@ornl.gov NR 40 TC 0 Z9 0 U1 2 U2 4 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8157-3 J9 PROC SPIE PY 2010 VL 7693 AR 769307 DI 10.1117/12.852700 PG 12 WC Engineering, Electrical & Electronic; Optics SC Engineering; Optics GA BSN18 UT WOS:000284996500002 ER PT S AU Koch, MW Nguyen, HD AF Koch, Mark W. Nguyen, Hung D. BE Carapezza, EM TI Learning a Detection Map for a Network of Unattended Ground Sensors SO UNATTENDED GROUND, SEA, AND AIR SENSOR TECHNOLOGIES AND APPLICATIONS XII SE Proceedings of SPIE LA English DT Proceedings Paper CT Conference on Unattended Ground, Sea, and Air Sensor Technologies and Applications XII CY APR 05-08, 2010 CL Orlando, FL SP SPIE DE Probability of detection map; sensor probability of detection function; sensor fusion; variable bandwidth 2D Parzen kernel; anisotropic; vulnerability analysis; networked seismic sensors; footstep detection ID DENSITY-FUNCTION AB We have developed algorithms to automatically learn a detection map of a deployed sensor field for a virtual presence and extended defense (VPED) system without apriori knowledge of the local terrain. The VPED system is an unattended network of sensor pods, with each pod containing acoustic and seismic sensors. Each pod has the ability to detect and classify moving targets at a limited range. By using a network of pods we can form a virtual perimeter with each pod responsible for a certain section of the perimeter. The site's geography and soil conditions can affect the detection performance of the pods. Thus, a network in the field may not have the same performance as a network designed in the lab. To solve this problem we automatically estimate a network's detection performance as it is being installed at a site by a mobile deployment unit (MDU). The MDU will wear a GPS unit, so the system not only knows when it can detect the MDU, but also the MDU's location. In this paper, we demonstrate how to handle anisotropic sensor-configurations, geography, and soil conditions. C1 [Koch, Mark W.; Nguyen, Hung D.] Sandia Natl Labs, Albuquerque, NM 87158 USA. RP Koch, MW (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87158 USA. NR 10 TC 0 Z9 0 U1 0 U2 0 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8157-3 J9 PROC SPIE PY 2010 VL 7693 AR 76930N DI 10.1117/12.849454 PG 10 WC Engineering, Electrical & Electronic; Optics SC Engineering; Optics GA BSN18 UT WOS:000284996500010 ER PT J AU Picker, RC AF Picker, Randal C. TI Easterbrook on Copyright SO UNIVERSITY OF CHICAGO LAW REVIEW LA English DT Article C1 [Picker, Randal C.] Univ Chicago, Sch Law, Chicago, IL 60637 USA. [Picker, Randal C.] Univ Chicago, Computat Inst, Chicago, IL 60637 USA. [Picker, Randal C.] Argonne Natl Lab, Argonne, IL 60439 USA. RP Picker, RC (reprint author), Univ Chicago, Sch Law, Chicago, IL 60637 USA. NR 16 TC 3 Z9 3 U1 2 U2 2 PU UNIV CHICAGO LAW SCH PI CHICAGO PA 1111 E 60TH ST, CHICAGO, IL 60637 USA SN 0041-9494 J9 U CHICAGO LAW REV JI Univ. Chic. Law Rev. PY 2010 VL 77 SI SI BP 1165 EP 1179 PG 15 WC Law SC Government & Law GA 687RG UT WOS:000284795000011 ER PT S AU Grahame, TJ AF Grahame, Thomas J. BE Zereini, F Wiseman, CLS TI Distinguishing Health Effects Among Different PM(2.5) Components SO URBAN AIRBORNE PARTICULATE MATTER: ORIGIN, CHEMISTRY, FATE AND HEALTH IMPACTS SE Environmental Science and Engineering BS Environmental Engineering LA English DT Article; Book Chapter ID PARTICULATE AIR-POLLUTION; CONCENTRATED AMBIENT PARTICLES; POSITIVE MATRIX FACTORIZATION; HEART-RATE-VARIABILITY; EMERGENCY-DEPARTMENT VISITS; EXPOSURE MEASUREMENT ERROR; SHORT-TERM EXPOSURE; SOURCE-APPORTIONMENT; OXIDATIVE STRESS; DIESEL EXHAUST C1 US DOE, Washington, DC 20585 USA. RP Grahame, TJ (reprint author), US DOE, 1000 Independence Ave SW, Washington, DC 20585 USA. EM thomas.grahame@hq.doe.gov NR 68 TC 0 Z9 0 U1 1 U2 4 PU SPRINGER PI NEW YORK PA 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES SN 1863-5520 BN 978-3-642-12277-4 J9 ENVIRON SCI ENG JI Environ. Sci. Eng. PY 2010 BP 575 EP 597 DI 10.1007/978-3-642-12278-1_29 PG 23 WC Environmental Sciences; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Meteorology & Atmospheric Sciences GA BSQ69 UT WOS:000285483900029 ER PT B AU Sullivan, JH Pope, LC Sutherland, BM Bennett, PV Blum, JE Stapleton, AE Gitz, DC AF Sullivan, Joseph H. Pope, Linda C. Sutherland, Betsy M. Bennett, Paula V. Blum, James E. Stapleton, Aim E. Gitz, Dennis C., III BA Gao, W Schmoldt, DL Slusser, JR BF Gao, W Schmoldt, DL Slusser, JR TI Assessment of DNA Damage as a Tool to Measure UV-B Tolerance in Soybean Lines Differing in Foliar Flavonoid Composition SO UV RADIATION IN GLOBAL CLIMATE CHANGE: MEASUREMENTS, MODELING AND EFFECTS ON ECOSYSTEMS LA English DT Article; Book Chapter DE Glycine max; soybean; DNA damage; pyrimidine dimers; UV-B radiation; stratospheric ozone depletion ID SOLAR ULTRAVIOLET-B; BARLEY PRIMARY LEAVES; PYRIMIDINE DIMERS; LEAF EXPANSION; EPIDERMAL-TRANSMITTANCE; LIQUIDAMBAR STYRACIFLUA; SCREENING EFFECTIVENESS; ELEVATIONAL GRADIENT; BALANCING DAMAGE; MOLECULAR LENGTH AB Damage to DNA, in the form of cyclobutane pyrimidine dimers (CPD), may occur in soybean (Glycine max (L.) Men) plants when they are exposed to increasing levels of ultraviolet-B (UV-B) radiation. Flavonoids and other phenolics accumulate in the epidermal layer of leaves and may provide protection for sensitive tissues including DNA molecules. We evaluated the steady state levels of accumulated damage and the protection afforded by flavonoids in two soybean isolines: Clark producing high levels of flavonoids, and Clark-magenta producing extremely low flavonoid levels. Both cultivars were grown in the field under ambient and supplemental UV-B radiation. Leaf tissue was harvested in a diurnal sequence, and the samples were analyzed. Two methods of analysis were used in order to develop a common reference point between the two. In one method, DNA was isolated and treated with UV endonuclease, and the DNA fragments were separated using unidirectional pulsed field electrophoresis and quantified through electronic imaging. In the alternate method, a western blotting procedure, immobilized DNA was reacted with monoclonal antibodies specific to CPD DNA damage. Results were similar in both techniques and show lesion frequency to be low in both isolines. However significant differences were found between cultivars, UV treatments, time of day collected, and levels of PAR. The average level of dimers per megabase for the isoline Clark was similar to 4 (with or without supplemental UV), and for Clark-magenta, similar to 4 for samples with no supplemental UV and similar to 6 for those exposed to supplemental UV radiation. Diurnally, dimer levels were frequently higher in the Clark-magenta isoline, especially when exposed to supplemental UV-B. Both isolines appear to be either well-protected from DNA damage, or repair is efficient enough to minimize biologically significant accumulation of DNA damage. This suggests that protection mechanisms, other than flavonoids alone, contribute to maintenance of DNA integrity in soybean. C1 [Sullivan, Joseph H.] Univ Maryland, Dept Plant Sci & Landscape Architecture, College Pk, MD 20742 USA. [Sutherland, Betsy M.; Bennett, Paula V.] Brookhaven Natl Lab, Upton, NY 11973 USA. [Blum, James E.] Univ N Carolina, Dept Math & Stat, Wilmington, NC 28403 USA. [Stapleton, Aim E.] Univ N Carolina, Dept Biol & Marine Biol, Wilmington, NC 28403 USA. [Gitz, Dennis C., III] ARS, USDA, Lubbock, TX 79415 USA. RP Sullivan, JH (reprint author), Univ Maryland, Dept Plant Sci & Landscape Architecture, 2122 Plant Sci Bldg, College Pk, MD 20742 USA. EM jsull@umd.edu; bms@bnl.gov; blumj@uncw.edu; stapletona@uncw.edu NR 70 TC 2 Z9 2 U1 1 U2 3 PU TSINGHUA UNIVERSITY PRESS PI BEIJING PA TSINGHUA UNIVERSITY HAIDIANQU, BEIJING 100084, PEOPLES R CHINA BN 978-7-302-20360-5 PY 2010 BP 437 EP 457 DI 10.1007/978-3-642-03313-1_15 D2 10.1007/978-3-642-03313-1 PG 21 WC Ecology; Environmental Sciences; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Meteorology & Atmospheric Sciences GA BOX64 UT WOS:000277962100015 ER PT J AU Liu, Y Sundberg, JP Das, S Carpenter, D Cain, KT Michaud, EJ Voy, BH AF Liu, Y. Sundberg, J. P. Das, S. Carpenter, D. Cain, K. T. Michaud, E. J. Voy, B. H. TI Molecular Basis for Hair Loss in Mice Carrying a Novel Nonsense Mutation (Hrrh-R) in the Hairless Gene (Hr) SO VETERINARY PATHOLOGY LA English DT Article DE alopecia; hair follicle; hairless mice; microarray analysis ID VITAMIN-D-RECEPTOR; PAPULAR LESIONS; TRANSCRIPTION FACTORS; CELL-DIFFERENTIATION; AP-1 PROTEINS; MESSENGER-RNA; STEM-CELLS; MOUSE; SKIN; EXPRESSION AB Animal models carrying mutations in the hairless (Hr) gene provide a rich resource for study of hair follicle biology. A spontaneous mouse mutant with a phenotype strikingly similar to rhino mutants of Hr arose spontaneously in the mouse facility at Oak Ridge National Laboratory. Sequence analysis of Hr in these mutants uncovered a nonsense mutation in exon 12, designated as Hr(rh-R) (rhino, Oak Ridge). The mutation led to significant reduction in Hr mRNA levels, predicted to be due to nonsense-mediated decay. Histological analysis indicated dilated hair follicle infundibula at 14 days of age that rapidly became filled with cornified material. Microarray analyses revealed that expression levels of many genes involved in keratinocyte differentiation, epidermal regeneration, and wound healing were significantly upregulated before morphological detection of the phenotype, suggesting their role in onset of the Hr(rh-R) phenotype. Identification of this new Hr allele and the underlying molecular alterations allows further understanding of the role of Hr in hair follicle biology. C1 [Liu, Y.; Das, S.; Carpenter, D.; Cain, K. T.; Michaud, E. J.; Voy, B. H.] Oak Ridge Natl Lab, Div Life Sci, Oak Ridge, TN USA. [Sundberg, J. P.] Jackson Lab, Bar Harbor, ME 04609 USA. RP Voy, BH (reprint author), POB 2008, Oak Ridge, TN 37831 USA. EM voybh@ornl.gov FU US Department of Energy [DE-AC05-00OR22725] FX Funding for this research was provided by the Office of Biological and Environmental Research, US Department of Energy, under contract DE-AC05-00OR22725 with UT-Battelle LLC, the managing organization of ORNL for the U.S. DOE. NR 72 TC 4 Z9 5 U1 0 U2 1 PU AMER COLL VET PATHOLOGIST PI LAWRENCE PA 810 EAST 10TH STREET, LAWRENCE, KS 66044 USA SN 0300-9858 J9 VET PATHOL JI Vet. Pathol. PD JAN PY 2010 VL 47 IS 1 SI SI BP 167 EP 175 DI 10.1177/0300985809352970 PG 9 WC Pathology; Veterinary Sciences SC Pathology; Veterinary Sciences GA 551OJ UT WOS:000274218600023 PM 20080498 ER PT S AU Figueira, JM Deibel, CM Niello, JOF Greene, J Jiang, CL Lee, HY Marley, ST Pardo, RC Patel, N Paul, M Rehm, KE Ugalde, C Zinkann, G AF Figueira, J. M. Deibel, C. M. Fernandez Niello, J. O. Greene, J. Jiang, C. L. Lee, H. Y. Marley, S. T. Pardo, R. C. Patel, N. Paul, M. Rehm, K. E. Ugalde, C. Zinkann, G. BE Alarcon, R Arellano, HF Cole, PL Kreiner, AJ TI Study of the P-30(alpha,p)S-33 reaction using a gas-filled magnetic spectrograph SO VIII LATIN AMERICAN SYMPOSIUM ON NUCLEAR PHYSICS AND APPLICATIONS SE AIP Conference Proceedings LA English DT Proceedings Paper CT 8th Latin American Symposium on Nuclear Physics and Applications CY DEC 15-19, 2009 CL Univ Chile, Santiago, CHILE SP Univ Chile, Univ Concepcion, Chilean Nucl Energy Commiss, Phys Latin Amer Ctr HO Univ Chile DE charged-particle spectroscopy; gas-filled magnetic spectrograph; X-ray bursts; (alpha,p) reactions AB We have developed a technique using a gas-filled magnetic spectrograph which enables us to study (alpha,p) transfer reactions of astrophysical interest in inverse kinematics and by means of the time-inverse reactions. We present preliminary experimental results of the reaction P-30(alpha,p)S-33 which confirm that the technique permits the study of these kinds of transfer reactions. C1 [Figueira, J. M.; Fernandez Niello, J. O.] Comis Nacl Energia Atom, Lab TANDAR, B1650KNA San Martin, RA-1429 Buenos Aires, DF, Argentina. [Figueira, J. M.] Consejo Nacl Invest Cient & Tecn, Buenos Aires, DF, Argentina. [Deibel, C. M.] Michigan State Univ, Joint Inst Nucl Astrophys, E Lansing, MI 48824 USA. [Fernandez Niello, J. O.] Univ Nacl Gen San Martin, Buenos Aires, DF, Argentina. [Marley, S. T.] Western Michigan Univ, Dept Phys, Kalamazoo, MI 49008 USA. [Patel, N.] Colorado Sch Mines, Dept Phys, Golden, CO 80401 USA. [Paul, M.] Hebrew Univ Jerusalem, Racah Inst Phys, Jerusalem, Israel. [Deibel, C. M.; Greene, J.; Jiang, C. L.; Lee, H. Y.; Marley, S. T.; Pardo, R. C.; Patel, N.; Rehm, K. E.; Ugalde, C.; Zinkann, G.] Argonne Natl Lab, Div Phys, Argonne, IL 60439 USA. RP Figueira, JM (reprint author), Comis Nacl Energia Atom, Lab TANDAR, B1650KNA San Martin, RA-1429 Buenos Aires, DF, Argentina. FU US Department of Energy; Office of Nuclear Physics [DE-AC02-06CH11357]; CONICET (Argentina) FX This work was supported by the US Department of Energy, Office of Nuclear Physics under contract No. DE-AC02-06CH11357 and the CONICET (Argentina). NR 3 TC 1 Z9 1 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0814-2 J9 AIP CONF PROC PY 2010 VL 1265 BP 174 EP + DI 10.1063/1.3480159 PG 2 WC Physics, Applied; Physics, Nuclear SC Physics GA BTK35 UT WOS:000287164800036 ER PT S AU Cole, PL Burkert, VD Gothe, RW Joo, K Mokeev, VI Stoler, P AF Cole, Philip L. Burkert, Volker D. Gothe, Ralf W. Joo, Kyungseon Mokeev, Victor I. Stoler, Paul CA CLAS Collaboration BE Alarcon, R Arellano, HF Cole, PL Kreiner, AJ TI Electroproduction of Excited Baryons with the CLAS Detector in Hall B of Jefferson Lab SO VIII LATIN AMERICAN SYMPOSIUM ON NUCLEAR PHYSICS AND APPLICATIONS SE AIP Conference Proceedings LA English DT Proceedings Paper CT 8th Latin American Symposium on Nuclear Physics and Applications CY DEC 15-19, 2009 CL Univ Chile, Santiago, CHILE SP Univ Chile, Univ Concepcion, Chilean Nucl Energy Commiss, Phys Latin Amer Ctr HO Univ Chile DE baryon resonances; electromagnetic form factors; Jefferson Lab AB Recent results from Jefferson Lab (JLab) on the extraction of single- and double-polarization observables in both the 1 pi- and 2 pi-channel show their high sensitivity to resonant production amplitudes and therefore their importance for the extraction of resonance parameters. The CEBAF Large Acceptance Spectrometer (CLAS) has access to the baryon resonance (N*) form factors at high Q(2), which is advantageous for the study of the dynamical properties of nucleon resonances. In anticipation of the 12 GeV energy upgrade to JLab, our group plans to extract the electromagnetic transition form factors (electrocouplings) for many well-established excited nucleon states in the unexplored domain of Q(2) > 5 GeV2. The expected data on resonance electrocouplings will allow us to systematically explore how in the strong interaction regime of QCD bare quarks are dressed with gluons and how quark cores of the various N* states emerge from QCD. C1 [Cole, Philip L.] Idaho State Univ, Dept Phys, Pocatello, ID 83209 USA. [Burkert, Volker D.; Mokeev, Victor I.] Jefferson Lab, Newport News, VA 23606 USA. [Gothe, Ralf W.] Univ South Carolina, Dept Phys & Astron, Columbia, SC 29208 USA. [Joo, Kyungseon] Univ Connecticut, Dept Phys, Storrs, CT 06269 USA. [CLAS Collaboration] Rensselaer Polytech Inst, Dept Phys, Troy, NY 12181 USA. [Mokeev, Victor I.] Moscow MV Lomonosov State Univ, Skobeltsyn Nucl Phys Inst, Moscow 119899, Russia. RP Cole, PL (reprint author), Idaho State Univ, Dept Phys, Pocatello, ID 83209 USA. EM colephil@isu.edu FU NSF [085561] FX The presenting author, PLC, greatfully acknowledges the great work the organizations did in making this conference (VIII LASNPA) so successful. In particular, PLC wishes to thank Ricardo Alarcon for doing an exemplary job in putting together this conference. NSF grant 085561 made this work possible. NR 25 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0814-2 J9 AIP CONF PROC PY 2010 VL 1265 BP 213 EP + DI 10.1063/1.3480168 PG 2 WC Physics, Applied; Physics, Nuclear SC Physics GA BTK35 UT WOS:000287164800043 ER PT S AU Hennings-Yeomans, R Cooper, M Currie, SA Makela, MF Ramsey, JC Tajima, S Womack, TL Long, JC Stanislaus, S AF Hennings-Yeomans, R. Cooper, M. Currie, S. A. Makela, M. F. Ramsey, J. C. Tajima, S. Womack, T. L. Long, J. C. Stanislaus, S. BE Alarcon, R Arellano, HF Cole, PL Kreiner, AJ TI Sensitivity Reach of the Neutron EDM Experiment: The Electric Field Strength SO VIII LATIN AMERICAN SYMPOSIUM ON NUCLEAR PHYSICS AND APPLICATIONS SE AIP Conference Proceedings LA English DT Proceedings Paper CT 8th Latin American Symposium on Nuclear Physics and Applications CY DEC 15-19, 2009 CL Univ Chile, Santiago, CHILE SP Univ Chile, Univ Concepcion, Chilean Nucl Energy Commiss, Phys Latin Amer Ctr HO Univ Chile DE Liquid helium; Superfluid helium (He-II); Dielectric properties; Instrumentation ID CP CONSERVATION AB The search for an electric dipole moment of the neutron tests physics beyond the Standard Model such as new sources of CP-violation and Supersymmetry. The nEDM experiment aims to improve the sensitivity on the current limit of the electric dipole moment of the neutron to <10(-27) e.cm. The experiment will use a flux of Ultra Cold Neutrons (UCNs) produced and stored in a bath of superfluid He-II. A change in precession frequency is expected for a non-zero EDM when an electric field is applied parallel and antiparallel to a magnetic field across the neutron storage cell. A dominant parameter in terms of reducing the statistical uncertainty of this measurement is the strength of the applied electric field. An experiment to measure if superfluid He-II can sustain up to 50 kV/cm for a volume and electrode spacings comparable to the nEDM experiment has been constructed at Los Alamos National Laboratory. It consists in a large-area parallel plate capacitor immersed in a 200 liter central volume inside a suitable cryostat that in turn is connected to a dilution refrigerator unit. A description of test runs and the status of the experiment is presented. C1 [Hennings-Yeomans, R.; Cooper, M.; Currie, S. A.; Makela, M. F.; Ramsey, J. C.; Tajima, S.; Womack, T. L.] Los Alamos Natl Lab, Div Phys, Los Alamos, NM 87545 USA. [Long, J. C.] Indiana Univ, Dept Phys, Bloomington, IN 47405 USA. [Stanislaus, S.] Valparaiso Univ, Dept Phys & Astron, Valparaiso, IN 46383 USA. RP Hennings-Yeomans, R (reprint author), Los Alamos Natl Lab, Div Phys, Los Alamos, NM 87545 USA. OI Makela, Mark/0000-0003-0592-3683; Currie, Scott/0000-0002-6164-7321 NR 13 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0814-2 J9 AIP CONF PROC PY 2010 VL 1265 BP 334 EP + DI 10.1063/1.3480197 PG 2 WC Physics, Applied; Physics, Nuclear SC Physics GA BTK35 UT WOS:000287164800065 ER PT S AU Milazzo, PM Abbondanno, U Aerts, G Alvarez, H Alvarez-Velarde, F Andriamonje, S Andrzejewski, J Assimakopoulos, P Audouin, L Badurek, G Baumann, P Becvar, F Belloni, F Berthoumieux, E Calvino, F Calviani, M Cano-Ott, D Capote, R Carrapico, C Cennini, P Chepel, V Chiaveri, E Colonna, N Cortes, G Couture, A Cox, J Dahlfors, M David, S Dillman, I Domingo-Pardo, C Dridi, W Duran, I Eleftheriadis, C Embid-Segura, M Ferrant, L Ferrari, A Ferreira-Marques, R Fujii, K Furman, W Goncalves, I Gonzalez-Romero, E Gramegna, F Guerrero, C Gunsing, F Heil, M Herrera-Martinez, A Jericha, E Kappeler, F Kadi, Y Karadimos, D Karamanis, D Kerveno, M Koehler, P Kossionides, E Krticka, M Lamboudis, C Leeb, H Lindote, A Lopes, I Lozano, M Lukic, S Marganiec, J Marrone, S Martinez, T Massimi, C Mastinu, P Mengoni, A Mosconi, M Neves, F Oberhummer, H O'Brien, S Pancin, J Papachristodoulou, C Paradela, C Patronis, N Pavlik, A Pavlopoulos, P Perrot, L Plag, R Plukis, A Poch, A Praena, J Pretel, C Quesada, J Reifarth, R Rubbia, C Rudolf, G Salgado, J Santos, C Sarchiapone, L Savvidis, I Stephan, C Tagliente, G Tain, JL Tassan-Got, L Tavora, L Terlizzi, R Vannini, G Vaz, P Ventura, A Villamarin, D Vincente, MC Vlachoudis, V Vlastou, R Voss, F Walter, S Wiescher, M Wisshak, K AF Milazzo, P. M. Abbondanno, U. Aerts, G. Alvarez, H. Alvarez-Velarde, F. Andriamonje, S. Andrzejewski, J. Assimakopoulos, P. Audouin, L. Badurek, G. Baumann, P. Becvar, F. Belloni, F. Berthoumieux, E. Calvino, F. Calviani, M. Cano-Ott, D. Capote, R. Carrapico, C. Cennini, P. Chepel, V. Chiaveri, E. Colonna, N. Cortes, G. Couture, A. Cox, J. Dahlfors, M. David, S. Dillman, I. Domingo-Pardo, C. Dridi, W. Duran, I. Eleftheriadis, C. Embid-Segura, M. Ferrant, L. Ferrari, A. Ferreira-Marques, R. Fujii, K. Furman, W. Goncalves, I. Gonzalez-Romero, E. Gramegna, F. Guerrero, C. Gunsing, F. Heil, M. Herrera-Martinez, A. Jericha, E. Kaeppeler, F. Kadi, Y. Karadimos, D. Karamanis, D. Kerveno, M. Koehler, P. Kossionides, E. Krticka, M. Lamboudis, C. Leeb, H. Lindote, A. Lopes, I. Lozano, M. Lukic, S. Marganiec, J. Marrone, S. Martinez, T. Massimi, C. Mastinu, P. Mengoni, A. Mosconi, M. Neves, F. Oberhummer, H. O'Brien, S. Pancin, J. Papachristodoulou, C. Paradela, C. Patronis, N. Pavlik, A. Pavlopoulos, P. Perrot, L. Plag, R. Plukis, A. Poch, A. Praena, J. Pretel, C. Quesada, J. Reifarth, R. Rubbia, C. Rudolf, G. Salgado, J. Santos, C. Sarchiapone, L. Savvidis, I. Stephan, C. Tagliente, G. Tain, J. L. Tassan-Got, L. Tavora, L. Terlizzi, R. Vannini, G. Vaz, P. Ventura, A. Villamarin, D. Vincente, M. C. Vlachoudis, V. Vlastou, R. Voss, F. Walter, S. Wiescher, M. Wisshak, K. BE Alarcon, R Arellano, HF Cole, PL Kreiner, AJ TI Study of Neutron-Induced Fission Cross Sections of U, Am, and Cm at n_TOF SO VIII LATIN AMERICAN SYMPOSIUM ON NUCLEAR PHYSICS AND APPLICATIONS SE AIP Conference Proceedings LA English DT Proceedings Paper CT 8th Latin American Symposium on Nuclear Physics and Applications CY DEC 15-19, 2009 CL Univ Chile, Santiago, CHILE SP Univ Chile, Univ Concepcion, Chilean Nucl Energy Commiss, Phys Latin Amer Ctr HO Univ Chile DE Neutron cross section; neutron-induced fission reactions; n_TOF ID CERN AB Neutron induced fission cross sections of several isotopes have been measured at the CERN n_TOF spallation neutron facility. Between them some measurements involve isotopes ((233)u, (241)-Am, Am-243, (245)cm) relevant for applications to nuclear technologies. The n_TOF facility delivers neutrons with high instantaneous flux and in a wide energy range, from thermal up to 250 MeV. The experimental apparatus consists of an ionization chamber that discriminates fission fragments and a particles coming from natural radioactivity of the samples. All the measurements were performed referring to the standard cross section of U-235. C1 [Milazzo, P. M.; Abbondanno, U.; Belloni, F.; Fujii, K.] Ist Nazl Fis Nucl, Trieste, Italy. [Aerts, G.; Andriamonje, S.; Berthoumieux, E.; Ferrant, L.; Gunsing, F.; Pancin, J.; Perrot, L.; Plukis, A.; Stephan, C.; Tassan-Got, L.] CNRS, IN2P3 IPN, Orsay, France. [Alvarez, H.; Duran, I.; Paradela, C.] Univ Santiago de Compostela, Santiago De Compostela, Spain. [Alvarez-Velarde, F.; Cano-Ott, D.; Embid-Segura, M.; Gonzalez-Romero, E.; Guerrero, C.; Martinez, T.; Vincente, M. C.] CIEMAT, Madrid, Spain. [Andrzejewski, J.; Marganiec, J.] Univ Lodz, Lodz, Poland. [Assimakopoulos, P.; Herrera-Martinez, A.; Karadimos, D.; Karamanis, D.; Papachristodoulou, C.; Patronis, N.] Univ Loannina, Loannina, Greece. [Audouin, L.; Dillman, I.; Heil, M.; Kaeppeler, F.; Mosconi, M.; Plag, R.; Reifarth, R.; Voss, F.; Walter, S.; Wisshak, K.] Forschungszentrum Karlsruhe, Karlsruhe, Germany. [Baumann, P.; Jericha, E.; Leeb, H.; Oberhummer, H.] Osterreichischen Univ Tech, Inst Atom, Vienna, Austria. [Becvar, F.; Kerveno, M.; Krticka, M.; Rudolf, G.] CNRS, IN2P3 IReS, Strasbourg, France. [Calvino, F.; Cortes, G.; Poch, A.; Pretel, C.] Univ Politecn Cataluna, Barcelona, Spain. [Calviani, M.; Gramegna, F.; Mastinu, P.; Praena, J.] Ist Nazl Fis Nucl, Lab Nazl Legnaro, Legnaro, Italy. [Capote, R.; Mengoni, A.; Quesada, J.] IAEA, Vienna, Austria. [Capote, R.; Lozano, M.] Univ Seville, Seville, Spain. [Carrapico, C.; Salgado, J.; Santos, C.; Tavora, L.; Vaz, P.] ITN, Lisbon, Portugal. [Cennini, P.; Chiaveri, E.; Dahlfors, M.; Ferrari, A.; Goncalves, I.; Kadi, Y.; Sarchiapone, L.; Vlachoudis, V.] CERN, Geneva, Switzerland. [Chepel, V.; Ferreira-Marques, R.; Lindote, A.; Lopes, I.; Neves, F.] Univ Coimbra, LIP, Coimbra, Portugal. [Colonna, N.; Marrone, S.; Tagliente, G.; Terlizzi, R.] Ist Nazl Fis Nucl, Bari, Italy. [Couture, A.; Cox, J.; O'Brien, S.; Wiescher, M.] Notre Dame Univ, Notre Dame, IN 46556 USA. [Domingo-Pardo, C.; Tain, J. L.] Univ Valencia, CSIC, Valencia, Spain. [Eleftheriadis, C.; Lamboudis, C.; Savvidis, I.] Aristotle Univ Thessaloniki, Thessaloniki, Greece. [Furman, W.] Joint Inst Nucl Res Dubna, Dubna, Russia. [Koehler, P.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. [Kossionides, E.; Vlastou, R.] NSCR, Athens, Greece. [Massimi, C.; Vannini, G.] Univ Bologna, Ist Nazl Fis Nucl, Bologna, Italy. [Pavlik, A.] Univ Vienna, Inst Phys, Fac Phys, Vienna, Austria. [Pavlopoulos, P.] Pole Univ Leonard Vinci, Paris, France. [Rubbia, C.] Univ Pavia, Pavia, Italy. [Ventura, A.] ENEA, Bologna, Italy. RP Milazzo, PM (reprint author), Ist Nazl Fis Nucl, Trieste, Italy. RI Lopes, Isabel/A-1806-2014; Gonzalez Romero, Enrique/L-7561-2014; Pretel Sanchez, Carme/L-8287-2014; Martinez, Trinitario/K-6785-2014; Capote Noy, Roberto/M-1245-2014; Massimi, Cristian/B-2401-2015; Alvarez Pol, Hector/F-1930-2011; Paradela, Carlos/J-1492-2012; Gramegna, Fabiana/B-1377-2012; Calvino, Francisco/K-5743-2014; Massimi, Cristian/K-2008-2015; Jericha, Erwin/A-4094-2011; Becvar, Frantisek/D-3824-2012; Chepel, Vitaly/H-4538-2012; Quesada Molina, Jose Manuel/K-5267-2014; Lindote, Alexandre/H-4437-2013; Neves, Francisco/H-4744-2013; Goncalves, Isabel/J-6954-2013; Vaz, Pedro/K-2464-2013; Cortes, Guillem/B-6869-2014; Tain, Jose L./K-2492-2014; Cano Ott, Daniel/K-4945-2014 OI Marques, Rui/0000-0003-3549-8198; Paradela Dobarro, Carlos/0000-0003-0175-8334; Lopes, Isabel/0000-0003-0419-903X; Chepel, Vitaly/0000-0003-0675-4586; Lozano Leyva, Manuel Luis/0000-0003-2853-4103; Koehler, Paul/0000-0002-6717-0771; Domingo-Pardo, Cesar/0000-0002-2915-5466; Mengoni, Alberto/0000-0002-2537-0038; Gonzalez Romero, Enrique/0000-0003-2376-8920; Martinez, Trinitario/0000-0002-0683-5506; Capote Noy, Roberto/0000-0002-1799-3438; Massimi, Cristian/0000-0001-9792-3722; Alvarez Pol, Hector/0000-0001-9643-6252; Gramegna, Fabiana/0000-0001-6112-0602; Calvino, Francisco/0000-0002-7198-4639; Massimi, Cristian/0000-0003-2499-5586; Pavlik, Andreas/0000-0001-7526-3372; Goncalves, Isabel/0000-0002-1997-955X; Jericha, Erwin/0000-0002-8663-0526; Quesada Molina, Jose Manuel/0000-0002-2038-2814; Lindote, Alexandre/0000-0002-7965-807X; Neves, Francisco/0000-0003-3635-1083; Vaz, Pedro/0000-0002-7186-2359; Cano Ott, Daniel/0000-0002-9568-7508 FU EC [FIKW-CT-2000-00107] FX This work was supported by the EC under Contract FIKW-CT-2000-00107 and by the funding agencies of the participating institutes. NR 21 TC 0 Z9 0 U1 1 U2 7 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0814-2 J9 AIP CONF PROC PY 2010 VL 1265 BP 477 EP + DI 10.1063/1.3480244 PG 3 WC Physics, Applied; Physics, Nuclear SC Physics GA BTK35 UT WOS:000287164800099 ER PT B AU Hess-Flores, M Duchaineau, MA Goldman, MJ Joy, KI AF Hess-Flores, Mauricio Duchaineau, Mark A. Goldman, Michael J. Joy, Kenneth I. BE Richard, P Braz, J TI ITERATIVE DENSE CORRESPONDENCE CORRECTION THROUGH BUNDLE ADJUSTMENT FEEDBACK-BASED ERROR DETECTION SO VISAPP 2010: PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON COMPUTER VISION THEORY AND APPLICATIONS, VOL 1 LA English DT Proceedings Paper CT 5th International Conference on Computer Vision Theory and Applications (VISAPP 2010) CY MAY 17-21, 2010 CL Univ Angers, Angers, FRANCE SP Inst Syst & Technol Informat Control & Commun, Workflow Management Coalit, Ecole Ingn Univ Angers, Lab Ingn Syst Automatises, Univ Angers HO Univ Angers DE Dense correspondences; Pose estimation; Scene reconstruction; Bundle adjustment; Resolution pyramid; Error analysis AB A novel method to detect and correct inaccuracies in a set of unconstrained dense correspondences between two images is presented. Starting with a robust, general-purpose dense correspondence algorithm, an initial pose estimate and dense 3D scene reconstruction are obtained and bundle-adjusted. Reprojection errors are then computed for each correspondence pair, which is used as a metric to distinguish high and low-error correspondences. An affine neighborhood-based coarse-to-fine iterative search algorithm is then applied only on the high-error correspondences to correct their positions. Such an error detection and correction mechanism is novel for unconstrained dense correspondences, for example not obtained through epipolar geometry-based guided matching. Results indicate that correspondences in regions With issues such as occlusions, repetitive patterns and moving objects can be identified and corrected, such that a more accurate set of dense correspondences results from the feedback-based process, as proven by more accurate pose and structure estimates. C1 [Hess-Flores, Mauricio; Joy, Kenneth I.] Univ Calif Davis, Inst Data Anal & Visualizat, Davis, CA 95616 USA. [Duchaineau, Mark A.; Goldman, Michael J.] Lawrence Livermore Natl Lab, Livermore, CA USA. RP Hess-Flores, M (reprint author), Univ Calif Davis, Inst Data Anal & Visualizat, Davis, CA 95616 USA. EM mhessf@ucdavis.edu; duchaine@llnl.gov; goldman21@llnl.gov; kijoy@ucdavis.edu NR 10 TC 0 Z9 0 U1 0 U2 0 PU INSTICC-INST SYST TECHNOLOGIES INFORMATION CONTROL & COMMUNICATION PI SETUBAL PA AVENIDA D MANUEL L, 27A 2 ESQUERDO, SETUBAL, 2910-595, PORTUGAL BN 978-989-674-028-3 PY 2010 BP 400 EP 405 PG 6 WC Computer Science, Artificial Intelligence; Engineering, Electrical & Electronic SC Computer Science; Engineering GA BG9BQ UT WOS:000393008200061 ER PT S AU Harvey, NR Porter, R Theiler, J AF Harvey, Neal R. Porter, Reid Theiler, James BE Rahman, Z Reichenbach, SE Neifeld, MA TI Ship Detection in Satellite Imagery Using Rank-Order Grayscale Hit-or-Miss Transforms SO VISUAL INFORMATION PROCESSING XIX SE Proceedings of SPIE-The International Society for Optical Engineering LA English DT Proceedings Paper CT Conference on Visual Information Processing XIX CY APR 06-07, 2010 CL Orlando, FL SP SPIE DE ship detection; panchromatic image; mathematical morphology; hit-or-miss transform; grayscale; rank-order AB Ship detection from satellite imagery is something that has great utility in various communities. Knowing where ships are and their types provides useful intelligence information. However, detecting and recognizing ships is a difficult problem. Existing techniques suffer from too many false-alarms. We describe approaches we have taken in trying to build ship detection algorithms that have reduced false alarms. Our approach uses a version of the grayscale morphological Hit-or-Miss transform. While this is well known and used in its standard form, we use a version in which we use a rank-order selection for the dilation and erosion parts of the transform, instead of the standard maximum and minimum operators. This provides some slack in the fitting that the algorithm employs and provides a method for tuning the algorithm's performance for particular detection problems. We describe our algorithms, show the effect of the rank-order parameter on the algorithm's performance and illustrate the use of this approach for real ship detection problems with panchromatic satellite imagery. C1 [Harvey, Neal R.; Porter, Reid; Theiler, James] Los Alamos Natl Lab, Space & Remote Sensing Sci Grp, Los Alamos, NM 87545 USA. RP Harvey, NR (reprint author), Los Alamos Natl Lab, Space & Remote Sensing Sci Grp, POB 1663, Los Alamos, NM 87545 USA. EM harve@lanl.gov NR 12 TC 0 Z9 1 U1 0 U2 1 PU SPIE-INT SOC OPTICAL ENGINEERING PI BELLINGHAM PA 1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98227-0010 USA SN 0277-786X BN 978-0-8194-8165-8 J9 P SOC PHOTO-OPT INS PY 2010 VL 7701 AR 770102 DI 10.1117/12.850886 PG 12 WC Engineering, Electrical & Electronic; Optics SC Engineering; Optics GA BSO07 UT WOS:000285051200001 ER PT B AU Ramachandran, S Tang, H Gutenkunst, RN Bustamante, CD AF Ramachandran, Sohini Tang, Hua Gutenkunst, Ryan N. Bustamante, Carlos D. BE Speicher, MR Antonarakis, SE Motulsky, AG TI Genetics and Genomics of Human Population Structure SO VOGEL AND MOTULSKY'S HUMAN GENETICS, FOURTH EDITION: PROBLEMS AND APPROACHES LA English DT Article; Book Chapter ID ALLELE FREQUENCY-SPECTRUM; RECENT POSITIVE SELECTION; MULTILOCUS GENOTYPE DATA; SPURIOUS SIGNATURES; EUROPEAN AMERICANS; HUMAN-EVOLUTION; WIDE PATTERNS; HAPLOTYPE MAP; LINKED LOCI; ASSOCIATION AB Recent developments in sequencing technology have created a flood of new data on human genetic variation, and this data has yielded new insights into human population structure. Here we review what both early and more recent studies have taught us about human population structure and history. Early studies showed that most human genetic variation occurs within populations rather than between them, and that genetically related populations often cluster geographically. Recent Studies based on much larger data sets have recapitulated these observations, but have also demonstrated that high-density genotyping allows individuals to be reliably assigned to their population of origin. In fact, for admixed individuals, even the ancestry Of Particular genomic regions can often be reliably inferred. Recent studies have also offered detailed information about the composition of specific populations from around the world, revealing how history has shaped their genetic makeup. We also briefly review quantitative models of human genetic history, including the role natural selection has played in shaping human genetic variation. C1 [Ramachandran, Sohini] Harvard Univ, Soc Fellows, Cambridge, MA 02138 USA. [Tang, Hua] Stanford Med Sch, Dept Genet, Stanford, CA USA. [Gutenkunst, Ryan N.] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA. [Bustamante, Carlos D.] Cornell Univ, Dept Biol Stat & Computat Biol, Ithaca, NY USA. [Ramachandran, Sohini] Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA. RP Ramachandran, S (reprint author), Harvard Univ, Soc Fellows, 78 Mt Auburn St, Cambridge, MA 02138 USA. EM sramach@fas.harvard.edu; huatang@stanford.edu; ryano@lanl.gov; cdb28@cornell.edu NR 75 TC 1 Z9 1 U1 0 U2 1 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY BN 978-3-540-37653-8 PY 2010 BP 589 EP 615 DI 10.1007/978-3-540-37654-5_20 D2 10.1007/978-3-540-37654-5 PG 27 WC Genetics & Heredity SC Genetics & Heredity GA BNM20 UT WOS:000274935100022 ER PT B AU Predota, M Wesolowski, DJ Machesky, ML Cummings, PT AF Predota, M. Wesolowski, D. J. Machesky, M. L. Cummings, P. T. BE Birkle, P TorresAlvarado, IS TI Molecular dynamics simulations of rutile/aqueous solution interface SO WATER-ROCK INTERACTION (WRI-13) LA English DT Proceedings Paper CT 13th International Symposium on Water-Rock Interaction (WRI) CY AUG 16-20, 2010 CL Guanajuato, MEXICO SP Consejo Nacl Ciencia & Tecnologia, Centro Investigac Cientifica Educac Super Ensenada, Int Assoc GeoChemistry, WRI 7 USGS, Inst Mexicano Tecnologia Agua, Schlumberger Water Serv, Univ Guanajuato, Deutsche Gesell Tech Zusammenarbeit, Deutscher Akademischer Austauschdienst ID ELECTRIC DOUBLE-LAYER; RUTILE 110 SURFACE; WATER INTERFACE; MUSIC MODEL; ADSORPTION; 250-DEGREES-C; PROTONATION; POTENTIALS; METAL; TIO2 AB Computer simulations of (110) rutile surface interacting with aqueous solution were carried out as part of a multidisciplinary team effort to characterize metal-oxide interfaces. The purpose of these simulations is twofold (i) provide results which can be linked with experimental observations and help in interpreting them, (ii) advance the methodology of computer simulations and extend their possibilities in determining new properties. So far, we were able to provide information from simulation on the structure and space-dependent diffusivity of water and ions at the interface, strength of hydrogen bonds at the interface, space dependent viscosity of water and the temperature effect on these properties. In this work we have identified the temperature and surface charge (related to pH of solution) effect on the adsorption of Rb+ and Na+ ions. While the temperature effect on Rb+ adsorption is weak, increasing temperature leads to shift of Na+ ions closer to the surface. C1 [Predota, M.] Univ South Bohemia, Fac Sci, Ceske Budejovice, Czech Republic. [Wesolowski, D. J.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Machesky, M. L.] Illinois State Water Survey, Champaign, IL 61820 USA. [Cummings, P. T.] Vanderbilt Univ, Nashville, TN 37235 USA. NR 19 TC 0 Z9 0 U1 0 U2 0 PU CRC PRESS-TAYLOR & FRANCIS GROUP PI BOCA RATON PA 6000 BROKEN SOUND PARKWAY NW, STE 300, BOCA RATON, FL 33487-2742 USA BN 978-1-4398-6299-5; 978-0-415-60426-0 PY 2010 BP 815 EP 818 PG 4 WC Geology; Water Resources SC Geology; Water Resources GA BG7YG UT WOS:000392008600193 ER PT B AU Gherardi, F Pruess, K Xu, T AF Gherardi, F. Pruess, K. Xu, T. BE Birkle, P TorresAlvarado, IS TI Modeling gas-water-rock interactions at Mt. Amiata geothermal field (Italy) SO WATER-ROCK INTERACTION (WRI-13) LA English DT Proceedings Paper CT 13th International Symposium on Water-Rock Interaction (WRI) CY AUG 16-20, 2010 CL Guanajuato, MEXICO SP Consejo Nacl Ciencia & Tecnologia, Centro Investigac Cientifica Educac Super Ensenada, Int Assoc GeoChemistry, WRI 7 USGS, Inst Mexicano Tecnologia Agua, Schlumberger Water Serv, Univ Guanajuato, Deutsche Gesell Tech Zusammenarbeit, Deutscher Akademischer Austauschdienst ID FLUID; CO2 AB A novel concept for enhanced geothermal systems (EGS) was proposed recently that would use supercritical CO2 (sc-CO2) instead of water as heat transmission fluid. Modeling studies have indicated that sc-CO2 has very favorable properties (low viscosity and large expansivity) for heat extraction and transmission to the land surface. The present paper considers the CO2-rich geothermal system at Mt. Amiata in Tuscany (Central Italy) as a potential analogue for studying geochemical changes in the peripheral and outer zones of an EGS operated with sc-CO2 (CO2-EGS). Field observations of mineral alteration and fluid chemistry are used to constrain reactive chemical transport simulations, and to obtain insights into rock-fluid interactions in a CO2-EGS system. C1 [Gherardi, F.] CNR, Ist Geosci & Georisorse, Pisa, Italy. [Pruess, K.; Xu, T.] Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA USA. FU Assistant Secretary for Energy Efficiency and Renewable Energy, Office of Geothermal Technologies, U.S. Department of Energy [DE-AC02-05CH11231]; LBNL FX This paper was partly supported by the Assistant Secretary for Energy Efficiency and Renewable Energy, Office of Geothermal Technologies, U.S. Department of Energy, Contract DE-AC02-05CH11231 with LBNL. NR 11 TC 0 Z9 0 U1 0 U2 0 PU CRC PRESS-TAYLOR & FRANCIS GROUP PI BOCA RATON PA 6000 BROKEN SOUND PARKWAY NW, STE 300, BOCA RATON, FL 33487-2742 USA BN 978-1-4398-6299-5; 978-0-415-60426-0 PY 2010 BP 859 EP 862 PG 4 WC Geology; Water Resources SC Geology; Water Resources GA BG7YG UT WOS:000392008600203 ER PT B AU Kharaka, YK Thordsen, JJ Bullen, TD Cole, DR Phelps, TJ Birkholzer, JT Hovorka, SD AF Kharaka, Y. K. Thordsen, J. J. Bullen, T. D. Cole, D. R. Phelps, T. J. Birkholzer, J. T. Hovorka, S. D. BE Birkle, P TorresAlvarado, IS TI Near surface and deep subsurface monitoring for successful geologic sequestration of CO2 SO WATER-ROCK INTERACTION (WRI-13) LA English DT Proceedings Paper CT 13th International Symposium on Water-Rock Interaction (WRI) CY AUG 16-20, 2010 CL Guanajuato, MEXICO SP Consejo Nacl Ciencia & Tecnologia, Centro Investigac Cientifica Educac Super Ensenada, Int Assoc GeoChemistry, WRI 7 USGS, Inst Mexicano Tecnologia Agua, Schlumberger Water Serv, Univ Guanajuato, Deutsche Gesell Tech Zusammenarbeit, Deutscher Akademischer Austauschdienst ID WATER-ROCK INTERACTIONS; SALINE AQUIFERS; STORAGE; USA AB Geochemical results from Multi-laboratory Frio Brine Pilot I-II (Texas) proved powerful in: 1-Tracking the flow of CO2 into the Frio sandstones; 2-showing that some CO2 was detected in the overlying B sandstone that is separated by 15 m of shale; and 3-showing mobilization of metals, organics, and major changes in chemical and isotopic compositions of brine, including calculated pH lowering (6.3-3.0) and increases in alkalinity. Geochemical modeling, chemical data and Fe isotopes indicate rapid dissolution of minerals, especially calcite and Fe-oxyhydroxides, and that portions of metal increases were caused by corrosion of well pipe. Similar isotopic and chemical changes were also observed in samples obtained from shallow (1.5 m) potable groundwater following CO2 injection in the ZERT site, Montana. Results from both the deep and shallow tests show highly sensitive chemical and isotopic tracers that can monitor injection performance and provide early detection of CO2 and brine leakages at CO2 injection sites. C1 [Kharaka, Y. K.; Thordsen, J. J.; Bullen, T. D.] US Geol Survey, 345 Middlefield Rd, Menlo Pk, CA 94025 USA. [Cole, D. R.; Phelps, T. J.] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Birkholzer, J. T.] Lawrence Berkeley Natl Lab, Berkeley, CA USA. [Hovorka, S. D.] Univ Texas Austin, Bur Econ Geol, Austin, TX USA. FU DOE-NETL; EPRI; EPA; DOE; LBNL; USGS FX The Frio Brine Pilot was directed by Susan Hovorka, TBEG, Austin, TX, managed by Sandia Technologies, LLC, and funded by DOE-NETL. The ZERT project is directed by Lee Spangler and managed by Laura Dobeck, MSU, Bozeman, MT; it was funded primarily by EPRI, but also by EPA, DOE, LBNL and USGS. NR 13 TC 0 Z9 0 U1 0 U2 0 PU CRC PRESS-TAYLOR & FRANCIS GROUP PI BOCA RATON PA 6000 BROKEN SOUND PARKWAY NW, STE 300, BOCA RATON, FL 33487-2742 USA BN 978-1-4398-6299-5; 978-0-415-60426-0 PY 2010 BP 867 EP 870 PG 4 WC Geology; Water Resources SC Geology; Water Resources GA BG7YG UT WOS:000392008600205 ER PT B AU Zheng, LG Spycher, N Apps, J Birkholzer, J AF Zheng, Liange Spycher, Nicolas Apps, John Birkholzer, Jens BE Birkle, P TorresAlvarado, IS TI Potential impacts of CO2 leakage on the quality of fresh water aquifers SO WATER-ROCK INTERACTION (WRI-13) LA English DT Proceedings Paper CT 13th International Symposium on Water-Rock Interaction (WRI) CY AUG 16-20, 2010 CL Guanajuato, MEXICO SP Consejo Nacl Ciencia & Tecnologia, Centro Investigac Cientifica Educac Super Ensenada, Int Assoc GeoChemistry, WRI 7 USGS, Inst Mexicano Tecnologia Agua, Schlumberger Water Serv, Univ Guanajuato, Deutsche Gesell Tech Zusammenarbeit, Deutscher Akademischer Austauschdienst ID ROCK INTERACTIONS; MINERAL TRAP; FERRIC IRON; GAS; INJECTION; SEQUESTRATION; SEDIMENTS; STORAGE; SOILS; FIELD AB CO2 sequestration in deep subsurface reservoirs must ensure the protection of overlying potable groundwater aquifers. Questions exist whether potable water could become contaminated by leakage and upward migration of CO2, possibly containing co-injected H2S and/or organic compounds mobilized at depth by supercritical CO2. Some recent investigations on these various issues are summarized. The potential increase in the concentrations of trace metals in groundwater due to the release of CO2 is discussed. Simulations of benzene mobilization by supercritical CO2 and the effect of co-injected H2S are also reported. CO2 dissolution into groundwater leads to a pH decrease and an increase in dissolved carbonate content, which can trigger the dissolution/precipitation of minerals and sorption/exchange reactions, possibly mobilizing trace elements. Modeling results show that the leakage of co-injected H2S into groundwater could exacerbate potential impacts and benzene potentially present at depth could be dissolved by supercritical CO2 and mobilized to shallower groundwater. C1 [Zheng, Liange; Spycher, Nicolas; Apps, John; Birkholzer, Jens] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. NR 22 TC 0 Z9 0 U1 0 U2 0 PU CRC PRESS-TAYLOR & FRANCIS GROUP PI BOCA RATON PA 6000 BROKEN SOUND PARKWAY NW, STE 300, BOCA RATON, FL 33487-2742 USA BN 978-1-4398-6299-5; 978-0-415-60426-0 PY 2010 BP 903 EP 906 PG 4 WC Geology; Water Resources SC Geology; Water Resources GA BG7YG UT WOS:000392008600214 ER PT S AU Xu, XW Zhu, LM Kannengiesser, U Liu, Y AF Xu, Xiwei Zhu, Liming Kannengiesser, Udo Liu, Yan BE Chen, L Triantafillou, P Suel, T TI An Architectural Style for Process-Intensive Web Information Systems SO WEB INFORMATION SYSTEM ENGINEERING-WISE 2010 SE Lecture Notes in Computer Science LA English DT Proceedings Paper CT 11th International Conference on Web Information Systems Engineering CY DEC 12-14, 2010 CL Hong Kong, PEOPLES R CHINA SP Croucher Fdn, KC Wong Educ Fdn DE REST; Resource-Oriented; Process-Intensive; Business Process AB REpresentational State Transfer (REST) is the architecture style behind the World Wide Web (WWW), allowing for many desirable quality attributes such as adaptability and interoperability. However, as many process-intensive Web information systems do not make use of REST, they often do not achieve these qualities. This paper addresses this issue by proposing RESTful Business Processes (RESTfulBP), an architectural style that adapts REST principles to Web-based business processes. RESTfulBP views processes and activities as transferrable resources by representing them as process fragments associated with a set of standard operations. Distributed process fragments interoperate by adhering to these operations and exchanging process information. The process information contains basic workflow patterns that are used for dynamic process coordination at runtime. We validate our approach through an industry case study. C1 [Xu, Xiwei; Zhu, Liming; Kannengiesser, Udo] NICTA, Australian Technol Pk, Eveleigh, Australia. Pacific Northwest Natl Lab, Richland, WA USA. [Xu, Xiwei; Zhu, Liming; Kannengiesser, Udo; Liu, Yan] Univ New South Wales, Sch Comp Sci & Engn, Sydney, NSW 2052, Australia. RP Xu, XW (reprint author), NICTA, Australian Technol Pk, Eveleigh, Australia. EM xiwei.xu@nicta.com.au; liming.zhu@nicta.com.au; udo.kannengiesser@nicta.com.au; yan.liu@pnl.gov FU Australian Government; Department of Broadband, Communications; Digital Economy; Australian Research Council through the ICT Centre of Excellence program FX NICTA is funded by the Australian Government as represented by the Department of Broadband, Communications and the Digital Economy and the Australian Research Council through the ICT Centre of Excellence program. NR 23 TC 6 Z9 6 U1 0 U2 1 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 0302-9743 BN 978-3-642-17615-9 J9 LECT NOTES COMPUT SC PY 2010 VL 6488 BP 534 EP + PG 3 WC Computer Science, Information Systems; Computer Science, Theory & Methods SC Computer Science GA BTC71 UT WOS:000286484400047 ER PT J AU Babu, SS Sonnenberg, G Schwenk, C Goldak, J Porzner, H Khurana, SP Zhang, W Gayler, JL AF Babu, Sudarsanam Suresh Sonnenberg, Garrett Schwenk, Christopher Goldak, John Porzner, Harald Khurana, Shuchi P. Zhang, Wei Gayler, John L. TI How Can Computational Weld Mechanics Help Industry? SO WELDING JOURNAL LA English DT Editorial Material C1 [Babu, Sudarsanam Suresh] Ohio State Univ, Columbus, OH 43210 USA. [Schwenk, Christopher] BAM Fed Inst Mat Res & Testing, Berlin, Germany. [Goldak, John] Carleton Univ, Ottawa, ON K1S 5B6, Canada. [Porzner, Harald] ESI N Amer, Welding & Heat Treatment Ctr Excellence, Bloomfield Hills, MI USA. [Khurana, Shuchi P.] Edison Welding Inst, Columbus, OH 43212 USA. [Zhang, Wei] Oak Ridge Natl Lab, Oak Ridge, TN USA. [Gayler, John L.] Amer Welding Soc, Miami, FL 33126 USA. [Sonnenberg, Garrett] Northrop Grumman Shipbldg, Newport News, VA USA. RP Babu, SS (reprint author), Ohio State Univ, Columbus, OH 43210 USA. EM babu.13@osu.edu RI Babu, Sudarsanam/D-1694-2010; Schwenk, Christopher/A-4769-2010 OI Babu, Sudarsanam/0000-0002-3531-2579; NR 7 TC 8 Z9 8 U1 0 U2 7 PU AMER WELDING SOC PI MIAMI PA 550 N W LEJEUNE RD, MIAMI, FL 33126 USA SN 0043-2296 J9 WELD J JI Weld. J. PD JAN PY 2010 VL 89 IS 1 BP 40 EP 45 PG 6 WC Metallurgy & Metallurgical Engineering SC Metallurgy & Metallurgical Engineering GA 541RU UT WOS:000273438300007 ER PT S AU Veers, PS AF Veers, P. S. BE Sorensen, JD Sorensen, JN TI Fatigue loading of wind turbines SO WIND ENERGY SYSTEMS: OPTIMISING DESIGN AND CONSTRUCTION FOR SAFE AND RELIABLE OPERATION SE Woodhead Publishing Series in Energy LA English DT Article; Book Chapter DE wind turbine; safety; reliability; fatigue; damage; Miner's Rule; loading; materials; stochastic; safety factors; structures; design criteria; standards ID DESIGN AB Wind turbine structures need to be designed with careful consideration of the fatigue strength and loading on critical load-bearing components. Each material in the various components of a wind turbine will potentially use different damage models to map the cyclic fatigue loadings into progressive deterioration of the material. In most cases, linear damage models using a Miner's Rule type approach are prevalent in design. The loadings of a particular turbine can be described as a function of the inflow conditions, which are considered to be weakly stationary for short periods, typically 10 minutes. These characteristic response statistics of the turbine are aggregated into a long-term distribution of loads using the theory of random variables and probability distribution functions. The long-term distribution is applied to the damage model to produce an estimate of fatigue lifetime. The design criteria require that the estimated stresses be amplified by safety factors to account for unfavourable deviations of action and material properties, as well as modeling uncertainties. C1 Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Veers, PS (reprint author), Sandia Natl Labs, POB 5800, Albuquerque, NM 87185 USA. EM psveers@sandia.gov NR 43 TC 0 Z9 0 U1 0 U2 0 PU WOODHEAD PUBL LTD PI CAMBRIDGE PA ABINGTON HALL ABINGTON, CAMBRIDGE CB1 6AH, CAMBS, ENGLAND SN 2044-9364 BN 978-1-84569-580-4 J9 WOODHEAD PUBL SER EN PY 2010 IS 10 BP 130 EP 158 PG 29 WC Energy & Fuels; Engineering, Mechanical SC Energy & Fuels; Engineering GA BVB33 UT WOS:000290952800005 ER PT S AU Vernoud, L Bechtel, HA Borondics, F Martin, MC AF Vernoud, Laetitia Bechtel, Hans A. Borondics, Ferenc Martin, Michael C. BE PredoiCross, A Billinghurst, BE TI Reconciling FTIR Spectroscopy with Top-off Operations at the Advanced Light Source SO WIRMS 2009: 5TH INTERNATIONAL WORKSHOP ON INFRARED MICROSCOPY AND SPECTROSCOPY WITH ACCELERATOR BASED SOURCES SE AIP Conference Proceedings LA English DT Proceedings Paper CT 5th International Workshop on Infrared Microscopy and Spectroscopy with Accelerator Based Sources CY SEP 13-17, 2009 CL Banff Conference Ctr, Banff, CANADA SP Canadian Light Source Inc, CanmetENERGY, Bruker AXS, Varian, Blue Sky Spectroscopy, Canadian Inst Synchrotron Radiat, Adv Design Consulting Inc, Int Union Pure & Appl Chem HO Banff Conference Ctr DE FTIR; synchrotron; infrared radiation; microspectroscopy ID SYNCHROTRON-RADIATION AB Top-off operations is a quasi-continuous injection mode that increases the flux and brightness of a synchrotron source and improves thermal stability of optical components by maintaining a constant current in the storage ring. Although the increased and constant flux is advantageous for FTIR measurements, the frequent injections (about one every 30 seconds in the ALS case) introduce artifacts into the spectrum by creating spikes in the interferogram data. These spikes are caused by brief beam motion during the injection event. Here, we describe our efforts to minimize the effects of top-off generated interferogram spikes on several FTIR spectrometers. They include using a fast feedback mirror system to correct for beam motion and a gating signal to inhibit interferogram collection during a top-off injection. C1 [Vernoud, Laetitia; Bechtel, Hans A.; Borondics, Ferenc; Martin, Michael C.] Lawrence Berkeley Natl Lab, Adv Light Source Div, Berkeley, CA 94720 USA. RP Vernoud, L (reprint author), Lawrence Berkeley Natl Lab, Adv Light Source Div, 1 Cyclotron Rd, Berkeley, CA 94720 USA. RI Borondics, Ferenc/A-7616-2008 NR 5 TC 6 Z9 5 U1 0 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0757-2 J9 AIP CONF PROC PY 2010 VL 1214 BP 36 EP 38 DI 10.1063/1.3326342 PG 3 WC Spectroscopy SC Spectroscopy GA BTK37 UT WOS:000287165600010 ER PT S AU Bechtel, HA Martin, MC May, TE Lerch, P AF Bechtel, Hans A. Martin, Michael C. May, T. E. Lerch, Philippe BE PredoiCross, A Billinghurst, BE TI Improved Spatial Resolution For Reflection Mode Infrared Spectromicroscopy SO WIRMS 2009: 5TH INTERNATIONAL WORKSHOP ON INFRARED MICROSCOPY AND SPECTROSCOPY WITH ACCELERATOR BASED SOURCES SE AIP Conference Proceedings LA English DT Proceedings Paper CT 5th International Workshop on Infrared Microscopy and Spectroscopy with Accelerator Based Sources CY SEP 13-17, 2009 CL Banff Conference Ctr, Banff, CANADA SP Canadian Light Source Inc, CanmetENERGY, Bruker AXS, Varian, Blue Sky Spectroscopy, Canadian Inst Synchrotron Radiat, Adv Design Consulting Inc, Int Union Pure & Appl Chem (IUPAC) HO Banff Conference Ctr DE FTIR; microscopy; synchrotron; resolution ID SYNCHROTRON-RADIATION; PERFORMANCE; LIMITS AB Standard commercial infrared microscopes operating in reflection mode use a mirror to direct the reflected light from the sample to the detector. This mirror blocks about half of the incident light, however, and thus degrades the spatial resolution by reducing the numerical aperture of the objective. Here, we replace the mirror with a 50% beamsplitter to allow full illumination of the objective and retain a way to direct the reflected light to the detector. The improved spatial resolution is demonstrated using a microscope coupled to a synchrotron source. C1 [Bechtel, Hans A.; Martin, Michael C.] Lawrence Berkeley Natl Lab, Adv Light Source Div, 1 Cyclotron Rd, Berkeley, CA 94720 USA. [May, T. E.] Univ Saskatchewan, Canadian Light Source Inc, Saskatoon, SK S7N 0X4, Canada. [Lerch, Philippe] Paul Scherrer Inst, Swiss Light Source, Villigen 5232, Switzerland. RP Bechtel, HA (reprint author), Lawrence Berkeley Natl Lab, Adv Light Source Div, 1 Cyclotron Rd, Berkeley, CA 94720 USA. FU Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231] FX The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 8 TC 0 Z9 0 U1 0 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0757-2 J9 AIP CONF PROC PY 2010 VL 1214 BP 51 EP + DI 10.1063/1.3326347 PG 2 WC Spectroscopy SC Spectroscopy GA BTK37 UT WOS:000287165600014 ER PT B AU Vineyard, CM Taylor, SE Bernard, ML Verzi, SJ Caudell, TP Heileman, GL Watson, P AF Vineyard, Craig M. Taylor, Shawn E. Bernard, Michael L. Verzi, Stephen J. Caudell, Thomas P. Heileman, Greg L. Watson, Patrick BE Callaos, N Eshraghian, K Imai, M Lesso, W Zinn, CD TI A Cortical-Hippocampal Neural Architecture for Episodic Memory with Information Theoretic Model Analysis SO WMSCI 2010: 14TH WORLD MULTI-CONFERENCE ON SYSTEMICS, CYBERNETICS AND INFORMATICS, VOL I LA English DT Proceedings Paper CT 14th World Multi-Conference on Systemics, Cybernetics and Informatics CY JUN 29-JUL 02, 2010 CL Orlando, FL SP Int Inst Informat & Syst DE Artificial neural network; hippocampus; information theory; computational neural architecture AB Extensive neuroscience research on the hippocampus has identified its crucial role in memory formation and recall. Specifically, associative binding of the components comprising an episodic memory has been identified as one of the functions performed by the hippocampus. Based upon neuroanatomical function we have devised a computational cortical-hippocampal architecture using variants of adaptive resonance theory (ART) artificial neural networks. This computational model is capable of processing multi-modal sensory inputs and capturing qualitative memory phenomena such as auto-association and recall. Model performance is assessed both qualitatively and quantitatively. From a quantitative standpoint, we have applied the mathematics of information theory to quantify the similarity between recalled images yielded by the model and the unaltered original inputs. Thus in this paper we present a neurologically plausible computational architecture as well as a quantitative assessment of model performance. C1 [Vineyard, Craig M.; Taylor, Shawn E.; Bernard, Michael L.; Verzi, Stephen J.] Sandia Natl Labs, POB 5800,Mail Stop 1188, Albuquerque, NM 87185 USA. [Caudell, Thomas P.; Heileman, Greg L.] Univ New Mexico, Dept Elect & Comp Engn, Albuquerque, NM 87131 USA. [Watson, Patrick] Univ Illinois, Beckman Inst, Urbana, IL 61801 USA. RP Vineyard, CM (reprint author), Sandia Natl Labs, POB 5800,Mail Stop 1188, Albuquerque, NM 87185 USA. NR 8 TC 1 Z9 1 U1 0 U2 0 PU INT INST INFORMATICS & SYSTEMICS PI ORLANDO PA 14269 LORD BARCLAY DR, ORLANDO, FL 32837 USA BN 978-1-934272-98-5 PY 2010 BP 281 EP 285 PG 5 WC Computer Science, Cybernetics; Computer Science, Theory & Methods SC Computer Science GA BG7LF UT WOS:000391420000054 ER PT B AU Gelston, G AF Gelston, Gariann BE Baralt, J Callaos, N Chu, HW Jastroch, N Lesso, W TI Live Operation Data Collection Optimization and Communication for the Domestic Nuclear Detection Office's Rail Test Center SO WMSCI 2010: 14TH WORLD MULTI-CONFERENCE ON SYSTEMICS, CYBERNETICS AND INFORMATICS, VOL III LA English DT Proceedings Paper CT 14th World Multi-Conference on Systemics, Cybernetics and Informatics CY JUN 29-JUL 02, 2010 CL Orlando, FL SP Int Inst Informat & Syst DE Data Collection; DCS; Field Studies; Testing; Decision Support; DSS AB For the Domestic Nuclear Detection Office's Rail Test Center (DNDO's RTC), port operation knowledge with flexible collection tools and technique are essential in both technology testing design and implementation intended for live operational settings. Increased contextual data, flexibility in procedures, and rapid availability and targeted communication of information are keys to addressing the challenges of optimization, validation, analysis, and decision-making in data collection within a live operational setting for technology evaluation. These collection and communication concepts need to be integrated into technology testing strategies, designs, data collection methods, validation, and analysis processes. A modified data collection technique is proposed for providing information within the operational context to improve communication and understanding through a two-phased live operation test method. C1 [Gelston, Gariann] Pacific Northwest Natl Lab, POB 999,MSIN K6-52, Richland, WA 99352 USA. RP Gelston, G (reprint author), Pacific Northwest Natl Lab, POB 999,MSIN K6-52, Richland, WA 99352 USA. NR 15 TC 0 Z9 0 U1 0 U2 0 PU INT INST INFORMATICS & SYSTEMICS PI ORLANDO PA 14269 LORD BARCLAY DR, ORLANDO, FL 32837 USA BN 978-1-936338-00-9 PY 2010 BP 84 EP 87 PG 4 WC Computer Science, Cybernetics; Computer Science, Theory & Methods SC Computer Science GA BG7LA UT WOS:000391417500016 ER PT B AU Barrows, A Kucik, P Skimmyhorn, W Straigis, J AF Barrows, Anne Kucik, Paul Skimmyhorn, William Straigis, John BE Baralt, J Callaos, N Chu, HW Jastroch, N Lesso, W TI A Systems Analysis of the AQ Khan Network SO WMSCI 2010: 14TH WORLD MULTI-CONFERENCE ON SYSTEMICS, CYBERNETICS AND INFORMATICS, VOL III LA English DT Proceedings Paper CT 14th World Multi-Conference on Systemics, Cybernetics and Informatics CY JUN 29-JUL 02, 2010 CL Orlando, FL SP Int Inst Informat & Syst AB In this study, we apply the methods of engineering risk analysis to understand the structure of a nuclear proliferation network in order to defeat it. These methods are typically applied to engineering systems in order to assess the weaknesses in a system and determine the most cost-effective way to improve that system; instead, this analysis turns risk analysis on its head, as we seek to understand the uncertainties, dependencies, and redundancies that exist in the system in order to induce failure (or degradation). In order to accomplish this goal, our team modeled the A.Q. Khan network as a supply chain in order to determine its weak points and possible ways to defeat the network. We then attempted to generalize our findings in order to apply them to future networks. Our report is based completely on our analysis of open source information. C1 [Barrows, Anne] Sandia Natl Labs, Adv Syst Deployments, Livermore, CA 94550 USA. [Kucik, Paul] US Mil Acad, Ctr Operat Res, West Point, NY 10996 USA. [Skimmyhorn, William] US Mil Acad, Dept Social Sci, West Point, NY 10996 USA. [Straigis, John] Lockheed Martin Space Syst, Syst Engn, Sunnyvale, CA 94085 USA. RP Barrows, A (reprint author), Sandia Natl Labs, Adv Syst Deployments, Livermore, CA 94550 USA. NR 9 TC 0 Z9 0 U1 0 U2 0 PU INT INST INFORMATICS & SYSTEMICS PI ORLANDO PA 14269 LORD BARCLAY DR, ORLANDO, FL 32837 USA BN 978-1-936338-00-9 PY 2010 BP 306 EP 309 PG 4 WC Computer Science, Cybernetics; Computer Science, Theory & Methods SC Computer Science GA BG7LA UT WOS:000391417500057 ER PT S AU Frank, AJ AF Frank, Arthur J. BE Yam, VWW TI Recent Advances in Sensitized Solar Cells SO WOLEDS AND ORGANIC PHOTOVOLTAICS: RECENT ADVANCES AND APPLICATIONS SE Green Energy and Technology LA English DT Proceedings Paper CT WOLEDs and Organic Photovoltaics Workshop CY JAN 08-10, 2009 CL Univ Hong Kong, Hong Kong, PEOPLES R CHINA SP Strateg Res Theme Mol Mat, Initiat Clean Energy & Environm HO Univ Hong Kong ID TIO2 NANOTUBE ARRAYS; BAND-EDGE MOVEMENT; ELECTRON-TRANSPORT; CONVERSION EFFICIENCY; ENERGY-CONVERSION; LIGHT-SCATTERING; RECOMBINATION; ANATASE; PHOTOCARRIERS; NANOCRYSTALS AB Understanding the principal physical and chemical factors that govern or limit cell performance is critical for underpinning the development of next-generation sensitized solar cells. Recent studies of dye-sensitized solar cells (DSSCs) covering nanoporous (pore diameter <100 nm) one-dimensional TiO2 nanostructured arrays and molecular voltage enhancers are discussed. Films constructed of oriented one-dimensional nanostructures, such as nanotube arrays, which are aligned perpendicularly to the charge-collecting substrate, could potentially improve the charge-collection efficiency by promoting faster transport and/or slower recombination. The extent to which transport or recombination could be affected by an oriented architecture is expected to depend on the influence of other mechanistic factors, such as the density and location of defects, crystallinity, and film uniformity. Orientational disorder within the nanotube array could also influence the transport and recombination kinetics. Such architectural disorder in titanium dioxide films is shown to have a strong influence on the transport, recombination, and light-harvesting properties of DSSCs. The mechanism by which molecular adsorbents alter the photovoltage of DSSCs is dependent on the properties of the adsorbent. In principle, an adsorbent could affect the photovoltage by either altering the recombination rate of photoelectrons in TiO2 with oxidized redox species in the electrolyte or inducing band-edge movement. The net effect of altering the band positions and recombination kinetics can either improve or diminish cell performance. The mechanisms by which several molecular adsorbents increase the photovoltage of DSSCs are discussed. C1 Natl Renewable Energy Lab, Chem & Mat Sci Ctr, Golden, CO 80401 USA. RP Frank, AJ (reprint author), Natl Renewable Energy Lab, Chem & Mat Sci Ctr, Golden, CO 80401 USA. EM Arthur.Frank@nrel.gov RI Yam, Vivian/D-3150-2009 NR 49 TC 0 Z9 0 U1 1 U2 4 PU SPRINGER-VERLAG BERLIN PI BERLIN PA HEIDELBERGER PLATZ 3, D-14197 BERLIN, GERMANY SN 1865-3529 BN 978-3-642-14934-4 J9 GREEN ENERGY TECHNOL PY 2010 BP 153 EP 168 DI 10.1007/978-3-642-14935-1_6 PG 16 WC Energy & Fuels; Materials Science, Multidisciplinary; Physics, Applied SC Energy & Fuels; Materials Science; Physics GA BGC91 UT WOS:000322347000007 ER PT S AU Anderson, J Attenkofer, K Delagnes, E Frisch, H Genat, JF Grabas, H Heintz, MK May, E Meehan, S Oberla, E Ruckman, LL Tang, F Varner, G Va'Vra, J Wetstein, M AF Anderson, John Attenkofer, Klaus Delagnes, Eric Frisch, Henry Genat, Jean-Francois Grabas, Herve Heintz, Mary K. May, Edward Meehan, Samuel Oberla, Eric Ruckman, Larry L. Tang, Fukun Varner, Gary Va'Vra, Jaroslav Wetstein, Matthew BE Chwastowski, J Royon, C TI CONSIDERATIONS ABOUT LARGE AREA-LOW COST FAST IMAGING PHOTO-DETECTORS SO WORKSHOP ON TIMING DETECTORS: ELECTRONICS, MEDICAL AND PARTICLE PHYSICS APPLICATIONS SE Acta Physica Polonica B Proceedings Supplement LA English DT Proceedings Paper CT Workshop on Timing Detectors - Electronics, Medical and Particle Physics Applications CY NOV 29-DEC 01, 2010 CL Krakow, POLAND SP Polish Acad Arts & Sci, T Kosciuszko Cracow Univ Technol, H Niewodniczanski Inst Nucl Phys PAN, AGH Univ Sci & Technol AB The Large Area Picosecond Photodetectors described in this contribution incorporate a photocathode and a borosilicate glass capillary Micro-Channel Plate (MCP) pair functionalised by atomic layer deposition (ALD) of separate resistive and secondary emission materials. Initial testing with matched pairs of small glass capillary test disks has demonstrated gains of the order of 10(5)-10(6). Compared to other fast imaging devices, these photodetectors are expected to provide timing resolutions in the 10-100 ps range, and two-dimension position in the sub-millimeter range. If daisy chained, large detectors read at both ends with fast digitising integrated electronics providing zero-suppressed calibrated data should be produced at relatively low cost in large quantities. C1 [Anderson, John; Attenkofer, Klaus; May, Edward; Meehan, Samuel; Oberla, Eric; Wetstein, Matthew] Argonne Natl Lab, Argonne, IL 60439 USA. RP Anderson, J (reprint author), Argonne Natl Lab, 9700 S Cass Ave, Argonne, IL 60439 USA. RI delagnes, eric/G-8782-2011 NR 4 TC 0 Z9 0 U1 0 U2 2 PU JAGIELLONIAN UNIV PI CRACOW PA GOLEBIA 24, 31-007 CRACOW, POLAND SN 1899-2358 J9 ACTA PHYS POL B PR S PY 2010 VL 4 IS 1 BP 13 EP 19 DI 10.5506/APhysPolBSupp.4.13 PG 7 WC Instruments & Instrumentation; Physics, Applied; Physics, Particles & Fields SC Instruments & Instrumentation; Physics GA BVT32 UT WOS:000292709300002 ER PT S AU Ramberg, E Ronzhin, A Albrow, M Los, S Pranko, A Malik, S Zatserklyaniy, A AF Ramberg, E. Ronzhin, A. Albrow, M. Los, S. Pranko, A. Malik, S. Zatserklyaniy, A. BE Chwastowski, J Royon, C TI PHOTODETECTOR TIMING RESEARCH AT FERMILAB SO WORKSHOP ON TIMING DETECTORS: ELECTRONICS, MEDICAL AND PARTICLE PHYSICS APPLICATIONS SE Acta Physica Polonica B Proceedings Supplement LA English DT Proceedings Paper CT Workshop on Timing Detectors - Electronics, Medical and Particle Physics Applications CY NOV 29-DEC 01, 2010 CL Krakow, POLAND SP Polish Acad Arts & Sci, T Kosciuszko Cracow Univ Technol, H Niewodniczanski Inst Nucl Phys PAN, AGH, Univ Sci Technol AB We describe here the outlines of research undertaken by Fermi lab into timing characteristics of photodetectors. We describe our experimental method and give benchtop results on the timing resolution of micro-channel plate photomultipliers (MCP-PMT) and silicon photomultipliers (SiPM). In addition, we describe results of various configurations of these detectors, along with quartz radiators, in particle test beams at Fermi lab. Results for timing of scintillator light using the DRS4 high speed digitizer are also presented. C1 [Ramberg, E.; Ronzhin, A.; Albrow, M.; Los, S.; Pranko, A.] Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. RP Ramberg, E (reprint author), Fermilab Natl Accelerator Lab, POB 500, Batavia, IL 60510 USA. NR 5 TC 1 Z9 1 U1 0 U2 1 PU JAGIELLONIAN UNIV PI CRACOW PA GOLEBIA 24, 31-007 CRACOW, POLAND SN 1899-2358 J9 ACTA PHYS POL B PR S PY 2010 VL 4 IS 1 BP 29 EP 34 DI 10.5506/APhysPolBSupp.4.29 PG 6 WC Instruments & Instrumentation; Physics, Applied; Physics, Particles & Fields SC Instruments & Instrumentation; Physics GA BVT32 UT WOS:000292709300004 ER PT S AU Albrow, M AF Albrow, Michael BE Chwastowski, J Royon, C TI FAST TIMING DETECTORS FOR FORWARD PROTONS AT THE LHC SO WORKSHOP ON TIMING DETECTORS: ELECTRONICS, MEDICAL AND PARTICLE PHYSICS APPLICATIONS SE Acta Physica Polonica B Proceedings Supplement LA English DT Proceedings Paper CT Workshop on Timing Detectors - Electronics, Medical and Particle Physics Applications CY NOV 29-DEC 01, 2010 CL Krakow, POLAND SP Polish Acad Arts & Sci, T Kosciuszko Cracow Univ Technol, H Niewodniczanski Inst Nucl Phys PAN, AGH, Univ Sci Technol AB I discuss the development of high precision timing detectors for high momentum protons at the LHC, and their application in studying exclusive Higgs boson production. C1 Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. RP Albrow, M (reprint author), Fermilab Natl Accelerator Lab, POB 500, Batavia, IL 60510 USA. NR 4 TC 2 Z9 2 U1 0 U2 0 PU JAGIELLONIAN UNIV PI CRACOW PA GOLEBIA 24, 31-007 CRACOW, POLAND SN 1899-2358 J9 ACTA PHYS POL B PR S PY 2010 VL 4 IS 1 BP 65 EP 70 DI 10.5506/APhysPolBSupp.4.65 PG 6 WC Instruments & Instrumentation; Physics, Applied; Physics, Particles & Fields SC Instruments & Instrumentation; Physics GA BVT32 UT WOS:000292709300009 ER PT S AU Ulmer, MP Adami, C Durret, F Neto, GL Ilbert, O Covone, G Cypriano, E Mahoney, W Gavazzi, R Allam, S Kron, R AF Ulmer, M. P. Adami, C. Durret, F. Lima Neto, G. Ilbert, O. Covone, G. Cypriano, E. Mahoney, W. Gavazzi, R. Allam, S. Kron, R. BE Comastri, A Cappi, M Angelini, L TI Observations of a z similar to 0.9 cluster of galaxies SO X-RAY ASTRONOMY-2009: PRESENT STATUS, MULTI-WAVELENGTH APPROACH AND FUTURE PERSPECTIVES, PROCEEDINGS SE AIP Conference Proceedings LA English DT Proceedings Paper CT International Conference on X-Ray Astronomy-2009: Present Status, Multi-Wavelength Approach and Future Perspectives CY SEP 07-11, 2009 CL Bologna, ITALY SP NASA, European Space Agcy, Italian Natl Inst Astrophys, Univ Bologna, Astron Dept DE Clusters; Galaxies; X-rays; High Redshift; Infrared AB We present a multi-wavelength study on a z similar to 0.9, CI 1257+4738. The cluster CI 1257+4738 was found by comparing a ROSAT image with red ground based images, taken to determine if the red galaxies were young dusty ones or old early type galaxies. This adds another cluster to the handful of clusters with z larger than about 0.9. Each one provides new insights as to the relationship between the evolution of galaxies and the ICM. We acquired Chandra, XMM-Newton, Spitzer IRAC plus MIPS 24 data to study this relationship between galaxies and the ICM. The Chandra plus Spitzer and ground-based data gave us the unique opportunity to find candidate galaxies and AGNs that could be at redshifts from 3 up to as high as 10. C1 [Ulmer, M. P.] Northwestern Univ, Evanston, IL 60208 USA. [Ulmer, M. P.; Adami, C.; Ilbert, O.] Lab dAstrophys, Marseille, France. [Durret, F.; Gavazzi, R.] Inst dAstrophys Paris, Paris, France. [Lima Neto, G.] Inst Astron Geofisico, Sao Paulo, Brazil. [Covone, G.] Univ Napoli Federico 2, Naples, Italy. [Cypriano, E.] UCL, London, England. [Mahoney, W.] CALTECH, Pasadena, CA 91125 USA. [Allam, S.] Fermilab Natl Accelerator Lab, Batavia, IL USA. [Kron, R.] Univ Chicago, Chicago, IL USA. RP Ulmer, MP (reprint author), Northwestern Univ, Evanston, IL 60208 USA. RI Covone, Giovanni/J-6040-2012 OI Covone, Giovanni/0000-0002-2553-096X NR 2 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0795-4 J9 AIP CONF PROC PY 2010 VL 1248 BP 302 EP + DI 10.1063/1.3475242 PG 2 WC Astronomy & Astrophysics; Physics, Applied SC Astronomy & Astrophysics; Physics GA BSA02 UT WOS:000284017700100 ER PT S AU Ryan, CG Siddons, DP Kirkham, R Dunn, PA Kuczewski, A Moorhead, G De Geronimo, G Paterson, DJ de Jonge, MD Hough, RM Lintern, MJ Howard, DL Kappen, P Cleverley, J AF Ryan, C. G. Siddons, D. P. Kirkham, R. Dunn, P. A. Kuczewski, A. Moorhead, G. De Geronimo, G. Paterson, D. J. de Jonge, M. D. Hough, R. M. Lintern, M. J. Howard, D. L. Kappen, P. Cleverley, J. BE Denecke, MA Walker, CT TI The New Maia Detector System: Methods For High Definition Trace Element Imaging Of Natural Material SO X-RAY OPTICS AND MICROANALYSIS, PROCEEDINGS SE AIP Conference Proceedings LA English DT Proceedings Paper CT 20th International Congress on X-Ray Optics and Microanalysis CY SEP 15-18, 2009 CL Karlsruhe, GERMANY SP Res Ctr Karlsruhe Program NUCLEAR, European Joint Res Ctr Inst Transuranium Elements, Deutsch Forschungsgemeinsch, European Microbeam Anal Soc DE SXRF; Dynamic Analysis; X-ray microprobe; silicon detector; trace element imaging; real-time processing ID QUANTITATIVE PIXE MICROANALYSIS; PROTON MICROPROBE; X-RAY; NUCLEAR MICROPROBE; EXAFS EXPERIMENTS; DYNAMIC-ANALYSIS; SYNCHROTRON AB Motivated by the need for megapixel high definition trace element imaging to capture intricate detail in natural material, together with faster acquisition and improved counting statistics in elemental imaging, a large energy-dispersive detector array called Maia has been developed by CSIRO and BNL for SXRF imaging on the XFM beamline at the Australian Synchrotron. A 96 detector prototype demonstrated the capacity of the system for real-time deconvolution of complex spectral data using an embedded implementation of the Dynamic Analysis method and acquiring highly detailed images up to 77M pixels spanning large areas of complex mineral sample sections. C1 [Ryan, C. G.; Kirkham, R.; Dunn, P. A.; Moorhead, G.; Hough, R. M.; Lintern, M. J.; Cleverley, J.] CSIRO, Bayview Ave, Clayton, Vic 3168, Australia. [Siddons, D. P.; Kuczewski, A.] Brookhaven Natl Lab, Natl Synchrotron Light Source, Brookhaven, NY USA. [De Geronimo, G.] Brookhaven Natl Lab, Instrumentat Div, Brookhaven, NY USA. [Paterson, D. J.; de Jonge, M. D.; Howard, D. L.] Australian Synchrotron, Clayton, Vic, Australia. [Ryan, C. G.; Moorhead, G.] Univ Melbourne, Sch Phys, Melbourne, Vic 3010, Australia. [Ryan, C. G.] Univ Tasmania, CODES Ctr Excellence, Hobart, Tas, Australia. [Kappen, P.] La Trobe Univ, Dept Phys, Bundoora, Vic, Australia. RP Ryan, CG (reprint author), CSIRO, Bayview Ave, Clayton, Vic 3168, Australia. RI Ryan, Chris/A-6032-2011; Kirkham, Robin/C-9786-2010; Cleverley, James/C-3829-2011; Dunn, Paul/D-6721-2012; Moorhead, Gareth/B-6634-2009; de Jonge, Martin/C-3400-2011; Lintern, Melvyn/M-6809-2013 OI Ryan, Chris/0000-0003-2891-3912; Kirkham, Robin/0000-0003-1012-3496; Moorhead, Gareth/0000-0002-9299-9549; Lintern, Melvyn/0000-0002-4436-6165 FU US Department of EnergyBasic Energy Sciences; NSERC; US Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357]; University of Washington, Simon Fraser University; Advanced Photon Source FX The authors wish to thank Dr Jules Dubrawski (Iluka Resources Ltd., Western Australia) for provision of the concentrate sample, Dr Asaf Raza (University of Melbourne) for sample preparation and Dr Robert Gordon (APS) for his guidance at PNC/XOR, pizzas and classic Sunday breakfasts. PNC/XOR facilities at the Advanced Photon Source, and research at these facilities, are supported by the US Department of EnergyBasic Energy Sciences, a major facilities access grant from NSERC, the University of Washington, Simon Fraser University and the Advanced Photon Source. Use of the Advanced Photon Source is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract DE-AC02-06CH11357. NR 22 TC 52 Z9 52 U1 0 U2 15 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0764-0 J9 AIP CONF PROC PY 2010 VL 1221 BP 9 EP + DI 10.1063/1.3399266 PG 2 WC Nanoscience & Nanotechnology; Optics; Physics, Applied SC Science & Technology - Other Topics; Optics; Physics GA BPC75 UT WOS:000278534600002 ER PT S AU Campbell, SI Miller, SD Bilheux, JC Reuter, MA Peterson, PF Kohl, JA Trater, JR Vazhkudai, SS Lynch, VE Green, ML AF Campbell, Stuart I. Miller, Stephen D. Bilheux, Jean-Christophe Reuter, Michael A. Peterson, Peter F. Kohl, James A. Trater, James R. Vazhkudai, Sudharshan S. Lynch, Vickie E. Green, Mark L. BE Ungar, G TI The SNS/HFIR Web Portal System for SANS SO XIV INTERNATIONAL CONFERENCE ON SMALL-ANGLE SCATTERING (SAS09) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 14th International Conference on Small-Angle Scattering (SAS09) CY SEP 13-18, 2009 CL Oxford, ENGLAND SP Int Union Crystallography Comm SAS AB The new generation of neutron scattering instruments being built are higher resolution and produce one or more orders of magnitude larger data than the previous generation of instruments. For instance, we have grown out of being able to perform some important tasks with our laptops. The data sizes are too big and the computational time would be too long. These large datasets can be problematic as facility users now begin to struggle with many of the same issues faced by more established computing communities. These issues include data access, management, and movement, data format standards, distributed computing, and collaboration with others. The Neutron Science Portal has been designed, and implemented to provide users with an easy-to-use interface for managing and processing data, while also keeping an eye on meeting modern computer security requirements that are currently being imposed on institutions. Users can browse or search for data which they are allowed to see, run data reduction and analysis applications, perform sample activation calculations and perform McStas simulations. Collaboration is facilitated by providing users a read/writeable common area, shared across all experiment team members. The portal currently has over 370 registered users; almost 7TB of experiment and user data, approximately 1,000,000 files cataloged, and had almost 10,000 unique visits last year. Future directions for enhancing portal robustness include examining how to mirror data and portal services, better facilitation of collaborations via virtual organizations, enhancing disconnected service via "thick client" applications, and better inter-facility connectivity to support cross-cutting research. C1 [Campbell, Stuart I.; Miller, Stephen D.; Bilheux, Jean-Christophe; Reuter, Michael A.; Peterson, Peter F.; Kohl, James A.; Trater, James R.; Vazhkudai, Sudharshan S.; Lynch, Vickie E.] Oak Ridge Natl Lab, Oak Ridge, TN USA. RP Campbell, SI (reprint author), Oak Ridge Natl Lab, Oak Ridge, TN USA. EM campbellsi@ornl.gov RI Campbell, Stuart/A-8485-2010; Lynch, Vickie/J-4647-2012; Bilheux, Jean/A-2823-2016; Peterson, Peter/L-2496-2013 OI Campbell, Stuart/0000-0001-7079-0878; Lynch, Vickie/0000-0002-5836-7636; Bilheux, Jean/0000-0003-2172-6487; Peterson, Peter/0000-0002-1353-0348 NR 27 TC 0 Z9 0 U1 0 U2 9 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2010 VL 247 AR 012013 DI 10.1088/1742-6596/247/1/012013 PG 9 WC Crystallography; Instruments & Instrumentation; Materials Science, Multidisciplinary SC Crystallography; Instruments & Instrumentation; Materials Science GA BVS59 UT WOS:000292653200013 ER PT S AU Hexemer, A Bras, W Glossinger, J Schaible, E Gann, E Kirian, R MacDowell, A Church, M Rude, B Padmore, H AF Hexemer, Alexander Bras, Wim Glossinger, James Schaible, Eric Gann, Eliot Kirian, Rick MacDowell, Alastair Church, Matthew Rude, Bruce Padmore, Howard BE Ungar, G TI A SAXS/WAXS/GISAXS Beamline with Multilayer Monochromator SO XIV INTERNATIONAL CONFERENCE ON SMALL-ANGLE SCATTERING (SAS09) SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 14th International Conference on Small-Angle Scattering (SAS09) CY SEP 13-18, 2009 CL Oxford, ENGLAND SP Int Union Crystallog Comm SAS ID BLOCK-COPOLYMER ELECTROLYTES; X-RAY-SCATTERING; SMALL-ANGLE; CONDUCTIVITY; DIFFRACTION; CRYSTALLIZATION; ORDER; SAXS; ESRF AB We discuss the construction of a new SAXS/WAXS beamline at the Advanced Light Source at Lawrence Berkeley Laboratory. The beamline is equipped with a multilayer monochromator in order to obtain a high X-ray flux. The detrimental effects that the increased bandwidth transmitted by this monochromator could have on the data quality of the SAXS and WAXS patterns is shown to be negligible for the experimental program intended to be operated on this beamline. C1 [Hexemer, Alexander; Glossinger, James; Schaible, Eric; Gann, Eliot; Kirian, Rick; MacDowell, Alastair; Church, Matthew; Rude, Bruce; Padmore, Howard] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. RP Hexemer, A (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, 1 Cyclotron Rd, Berkeley, CA 94720 USA. RI MacDowell, Alastair/K-4211-2012; Gann, Eliot/A-5246-2014; OI Kirian, Richard/0000-0001-7197-3086 NR 26 TC 135 Z9 135 U1 3 U2 27 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2010 VL 247 AR 012007 DI 10.1088/1742-6596/247/1/012007 PG 11 WC Crystallography; Instruments & Instrumentation; Materials Science, Multidisciplinary SC Crystallography; Instruments & Instrumentation; Materials Science GA BVS59 UT WOS:000292653200007 ER PT S AU Rainovski, G Pietralla, N Leske, J Ahn, T Coquard, L Bauer, C Moler, T Gladnishki, K Danchev, M Damyanova, A Karagyozov, D Topchiyska, R Lister, CJ Janssens, RVF Carpenter, MP Zhu, S AF Rainovski, G. Pietralla, N. Leske, J. Ahn, T. Coquard, L. Bauer, C. Moeler, Th Gladnishki, K. Danchev, M. Damyanova, A. Karagyozov, D. Topchiyska, R. Lister, C. J. Janssens, R. V. F. Carpenter, M. P. Zhu, S. BE Stoyanov, C Janeca, N TI Experimental studies of proton-neutron mixed symmetry states in the mass A approximate to 130 region SO XVIII INTERNATIONAL SCHOOL ON NUCLEAR PHYSICS, NEUTRON PHYSICS AND APPLICATIONS SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 18th International School on Nuclear Physics, Neutron Physics and Applications CY SEP 21-27, 2009 CL Varna, BULGARIA SP Inst Nucl Res & Nucl Energy ID TRANSITION-PROBABILITY; SCATTERING; NUCLEI; BA-134; SHELL; MODE AB Considerable progress has been achieved recently in the experimental investigation of quadrupole-collective isovector excitations in the valence shell, the so called mixed-symmetry states (MSSs), in the mass A approximate to 130 region. This is due to a new experimental technique for study MSSs which is based on the observation of low-multiplicity gamma-ray events from inverse kinematics Coulomb excitation with the large 4 pi spectrometer, such as Gammasphere. The obtained experimental information for the MSSs of stable N = 80 isotones indicates that for low-collective vibrational nuclei the underlying single-particle structure can be the most important factor for preserving or fragmenting the MSSs through the mechanism of shell stabilization. The evolution of the MSSs from Xe-134 to Ce-138 is also used to determine the local strength of the proton-neutron interaction derived for first time from states with symmetric and antisymmetric nature. C1 [Rainovski, G.; Gladnishki, K.; Danchev, M.; Damyanova, A.; Karagyozov, D.; Topchiyska, R.] Sofia Univ St Kliment Ohridski, Fac Phys, Sofia 1164, Bulgaria. [Pietralla, N.; Leske, J.; Ahn, T.; Coquard, L.; Bauer, C.; Moeler, Th] Tech Univ Darmstadt, Inst Kernphys, D-64289 Darmstadt, Germany. [Lister, C. J.; Janssens, R. V. F.; Carpenter, M. P.; Zhu, S.] Argonne Natl Lab, Argonne, IL 60439 USA. RP Rainovski, G (reprint author), Sofia Univ St Kliment Ohridski, Fac Phys, Sofia 1164, Bulgaria. EM rig@phys.uni-sofia.bg RI Gladnishki, Kalin/A-6462-2009; Carpenter, Michael/E-4287-2015; Ahn, Tan/C-9158-2016; Rainovski, Georgi/A-3450-2008 OI Carpenter, Michael/0000-0002-3237-5734; Ahn, Tan/0000-0003-2249-7399; Rainovski, Georgi/0000-0002-1729-0249 FU US NSF [PHY-0245018]; US Department of Energy, Office of Nuclear Physics [DE-AC02-06CH11357, DE- FG02-04ER41334]; SU NSF [249/09]; BG NSF [DO 02-219]; German-Bulgarian exchange program [D/06/05918, DAAD-09]; DFG [SFB 634, Pi 393/2-1] FX This work is supported by the US NSF within contract PHY-0245018, by the US Department of Energy, Office of Nuclear Physics, under contract DE-AC02-06CH11357 and under grant DE- FG02-04ER41334, by the SU NSF within contract 249/09, by the BG NSF within contract DO 02-219, by the German-Bulgarian exchange program under grants D/06/05918 and DAAD-09, and by the DFG under grants SFB 634 and Pi 393/2-1. NR 26 TC 0 Z9 0 U1 0 U2 1 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2010 VL 205 AR 012039 DI 10.1088/1742-6596/205/1/012039 PG 6 WC Physics, Nuclear SC Physics GA BQA09 UT WOS:000280470600039 ER PT S AU Duque, JG Chen, H Kilina, S Tretiak, S Shreve, A Tu, XM Zheng, M Swan, A Doorn, SK AF Duque, Juan G. Chen, Hang Kilina, Svetlana Tretiak, Sergei Shreve, Andy Tu, Xiaomin Zheng, Ming Swan, Anna Doorn, Stephen K. BE Champion, PM Ziegler, LD TI Resonant Raman Spectroscopy of Chirality-Enriched Semiconducting Single Walled Carbon Nanotubes SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt C1 [Duque, Juan G.; Kilina, Svetlana; Tretiak, Sergei; Shreve, Andy; Doorn, Stephen K.] Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. [Chen, Hang; Swan, Anna] Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA. [Tu, Xiaomin; Zheng, Ming] Natl Inst Stand & Technol, Div Polymer, Gaithersburg, MD 20899 USA. RP Duque, JG (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. RI Duque, Juan/G-2657-2010; Tretiak, Sergei/B-5556-2009 OI Tretiak, Sergei/0000-0001-5547-3647 FU LANL-LDRD funding; LANL-LDRD Director's Postdoc Fellowship FX The authors will like to thank Andrea Ferrari for helpful discussion. This work was supported by LANL-LDRD funding. JGD thanks the LANL-LDRD Directors Postdoc Fellowship. NR 2 TC 0 Z9 0 U1 1 U2 6 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 79 EP + DI 10.1063/1.3482819 PG 2 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900042 ER PT S AU Tretiak, S Fernandez-Alberti, S Roitberg, A AF Tretiak, Sergei Fernandez-Alberti, Sebastian Roitberg, Adrian BE Champion, PM Ziegler, LD TI Modeling of Non-Adiabatic Photoinduced Dynamics and Energy Transfer in Conjugated Molecules SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt C1 [Tretiak, Sergei] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Tretiak, S (reprint author), Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RI Tretiak, Sergei/B-5556-2009 OI Tretiak, Sergei/0000-0001-5547-3647 NR 0 TC 0 Z9 0 U1 0 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 182 EP 182 DI 10.1063/1.3482454 PG 1 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900100 ER PT S AU Gupta, S Saxena, A AF Gupta, Sanju Saxena, Avadh BE Champion, PM Ziegler, LD TI Curved Nanocarbons: Probing the Curvature and Topology Effects Using Phonon Spectra SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt ID CARBON NANOTUBES C1 [Gupta, Sanju] Univ Penn, Biophys & Chem, 3301 Spruce St, Philadelphia, PA 19104 USA. [Saxena, Avadh] Los Alamos Natl Lab, Div Theoret, POB 1663, Los Alamos, NM 87544 USA. RP Gupta, S (reprint author), Univ Penn, Biophys & Chem, 3301 Spruce St, Philadelphia, PA 19104 USA. FU U.S. Department of Energy; CINT-LANL gateway FX This work was supported by the U.S. Department of Energy (A.S.) and CINT-LANL gateway (S.G.). The authors are indebted to Prof. H. Kuzmany (U. Wien, Austria) for providing the Raman spectra of peapods and double-walled nanotubes and Prof. Y. Gogotsi (U. Drexel) for the visible Raman spectra of micro-graphite and graphite nanocones used in the present work. The authors are also thankful to Dr. S. Hayashi (Kobe University, Japan) for the onion-like carbon samples prepared in Moscow, Russia. NR 5 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 200 EP + DI 10.1063/1.3482465 PG 2 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900110 ER PT S AU Lu, X Venugopalan, S Kim, H Grimsditch, M Rodriguez, S Ramdas, AK AF Lu, X. Venugopalan, S. Kim, Hyunjung Grimsditch, M. Rodriguez, S. Ramdas, A. K. BE Champion, PM Ziegler, LD TI Doubly Resonant Raman-EPR Spectrum of Ruby (Al2O3:Cr3+) SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt C1 [Lu, X.; Rodriguez, S.; Ramdas, A. K.] Purdue Univ, Dept Phys, W Lafayette, IN 47907 USA. [Venugopalan, S.] SUNY Binghamton, Dept Phys, Binghamton, NY 13902 USA. [Kim, Hyunjung] Sogang Univ, Dept Phys, Seoul 121742, South Korea. [Grimsditch, M.] Argonne Natl Lab, Argonne, IL 60439 USA. RP Lu, X (reprint author), Purdue Univ, Dept Phys, W Lafayette, IN 47907 USA. FU US National Science Foundation [DMR 0705793] FX Work supported by the US National Science Foundation (DMR 0705793). NR 1 TC 0 Z9 0 U1 0 U2 4 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 249 EP + DI 10.1063/1.3482495 PG 2 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900137 ER PT S AU Sepaniak, M Wells, S Bhandari, D Lavrik, N AF Sepaniak, Michael Wells, Sabrina Bhandari, Deepak Lavrik, Nickolay BE Champion, PM Ziegler, LD TI Nanofabrication of Disc on Pillar Substrates for Surface Enhanced Raman Spectroscopy SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt C1 [Sepaniak, Michael; Wells, Sabrina; Bhandari, Deepak] Univ Tennessee, Dept Chem, Knoxville, TN 37996 USA. [Lavrik, Nickolay] Ctr Nanophase Mat Sci, Oak Ridge Natl Lab, Oak Ridge, TN 37830 USA. RP Sepaniak, M (reprint author), Univ Tennessee, Dept Chem, Knoxville, TN 37996 USA. FU US Environmental Protection Agency STAR Program [EPA-83274001] FX A portion of this research at Oak Ridge National Laboratory's Center for Nanophase Materials Sciences was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. This research was also supported by the US Environmental Protection Agency STAR Program under grant EPA-83274001 with the University of Tennessee. NR 3 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 273 EP + DI 10.1063/1.3482508 PG 2 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900150 ER PT S AU Olejniczak, I Wolak, J Barszcz, B Schlueter, JA Manson, JL AF Olejniczak, I. Wolak, J. Barszcz, B. Schlueter, J. A. Manson, J. L. BE Champion, PM Ziegler, LD TI CuF2 Structural Changes in Two-Dimensional Quantum Magnet (H2O)(2)(pyz) Under Pressure: Raman Study SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt ID PYRAZINE C1 [Olejniczak, I.; Wolak, J.; Barszcz, B.] Polish Acad Sci, Inst Mol Phys, Ul Smoluchowskiego 17, PL-60179 Poznan, Poland. [Schlueter, J. A.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. [Manson, J. L.] Eastern Washington Univ, Dept Chem & Biochem, Cheney, WA 99037 USA. RP Olejniczak, I (reprint author), Polish Acad Sci, Inst Mol Phys, Ul Smoluchowskiego 17, PL-60179 Poznan, Poland. RI Barszcz, Boleslaw/N-3927-2014 FU Ministry of Science and Higher Education (Poland) FX This work was supported by the Ministry of Science and Higher Education (Poland) as the research project in the Years 2008-2010. NR 3 TC 0 Z9 0 U1 0 U2 2 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 597 EP + DI 10.1063/1.3482697 PG 2 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900317 ER PT S AU Sage, JT Barabanschikov, A Kubo, M Champion, PM Zhao, J Sturhahn, W Alp, EE AF Sage, J. T. Barabanschikov, A. Kubo, M. Champion, P. M. Zhao, J. Sturhahn, W. Alp, E. E. BE Champion, PM Ziegler, LD TI Comprehensive Description of Heme Iron Dynamics From X-ray Vibrational Spectroscopy SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt C1 [Sage, J. T.; Barabanschikov, A.; Champion, P. M.] Northeastern Univ, NDept Phys, Boston, MA 02115 USA. [Kubo, M.] Univ Hyogo, Dept Chem, Kobe, Hyogo, Japan. [Zhao, J.; Sturhahn, W.; Alp, E. E.] Argonne Natl Lab, Dept Adv Photon Source, Argonne, IL 60439 USA. RP Sage, JT (reprint author), Northeastern Univ, NDept Phys, Boston, MA 02115 USA. RI Barabanschikov, Alexander/L-3048-2013 NR 0 TC 0 Z9 0 U1 0 U2 1 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 645 EP 645 DI 10.1063/1.3482726 PG 1 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900341 ER PT S AU Iberi, VO Camden, JP Guiton, BS AF Iberi, Vighter O. Camden, Jon P. Guiton, Beth S. BE Champion, PM Ziegler, LD TI Imaging Plasmon Modes in Metallic Nanostructures with Correlated Optical and Electron Microscopy SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt ID NANOPARTICLES C1 [Iberi, Vighter O.; Camden, Jon P.] Univ Tennessee, Dept Chem, Knoxville, TN 37996 USA. [Guiton, Beth S.] Oak Ridge Natl Lab, Mat Sci & Technol Div, Oak Ridge, TN 37831 USA. RP Iberi, VO (reprint author), Univ Tennessee, Dept Chem, Knoxville, TN 37996 USA. NR 4 TC 0 Z9 0 U1 0 U2 9 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 1004 EP 1004 DI 10.1063/1.3482260 PG 1 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900528 ER PT S AU Nowak-Lovato, KL Rector, KD AF Nowak-Lovato, K. L. Rector, K. D. BE Champion, PM Ziegler, LD TI Targeted SERS Nanosensors for Time-Lapse Microscopy of Live Cell Response to Drug-Based Stimuli SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt C1 [Nowak-Lovato, K. L.] Los Alamos Natl Lab, Biosci Div, MS M888, Los Alamos, NM 87567 USA. [Rector, K. D.] Los Alamos Natl Lab, Div Chem, Los Alamos, NM 87567 USA. RP Nowak-Lovato, KL (reprint author), Los Alamos Natl Lab, Biosci Div, MS M888, Los Alamos, NM 87567 USA. RI Rector, Kirk/C-3584-2011 FU Los Alamos National Security [DE-RP52-05NA25396]; U.S. Department of Energy; Los Alamos National Laboratory; Laboratory Directed Research and Development [20080001DR] FX This manuscript has been authored by Los Alamos National Security under Contract No. DE-RP52-05NA25396 with the U.S. Department of Energy. The authors wish to acknowledge the Los Alamos National Laboratory, Laboratory Directed Research and Development grant 20080001DR for support of this project. NR 2 TC 0 Z9 0 U1 0 U2 0 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 1085 EP + DI 10.1063/1.3482310 PG 2 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900572 ER PT S AU Lascola, R McWhorter, S Murph, SH AF Lascola, Robert McWhorter, Scott Murph, Simona Hunyadi BE Champion, PM Ziegler, LD TI Advanced Gas Sensors Using SERS-Activated Waveguides SO XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY SE AIP Conference Proceedings LA English DT Proceedings Paper CT 22nd International Conference on Raman Spectroscopy CY AUG 08-13, 2010 CL Boston, MA SP NE Univ, Boston Univ & Photon Ctr, Horiba Sci, Thermo Sci, Bruker Opt ID ENHANCED RAMAN-SCATTERING; CAPILLARY CELL; NANOPARTICLES AB This contribution describes progress towards the development and testing of a functionalized capillary that will provide detection of low-concentration gas-phase analytes through SERS. Measurement inside a waveguide allows interrogation of a large surface area, potentially overcoming the short distance dependence of the SERS effect. C1 [Lascola, Robert; McWhorter, Scott; Murph, Simona Hunyadi] Savannah River Natl Lab, Analyt Dev Directorate, Aiken, SC 29808 USA. RP Lascola, R (reprint author), Savannah River Natl Lab, Analyt Dev Directorate, Aiken, SC 29808 USA. OI Lascola, Robert/0000-0002-6784-5644 NR 8 TC 0 Z9 0 U1 1 U2 6 PU AMER INST PHYSICS PI MELVILLE PA 2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA SN 0094-243X BN 978-0-7354-0818-0 J9 AIP CONF PROC PY 2010 VL 1267 BP 1095 EP 1096 DI 10.1063/1.3482315 PG 2 WC Physics, Applied SC Physics GA BQK65 UT WOS:000281210900577 ER PT S AU Cizewski, JA Jones, KL Kozub, RL Pain, SD AF Cizewski, J. A. Jones, K. L. Kozub, R. L. Pain, S. D. CA ORRUBA RIBENS Collaboration BE BarronPalos, L Bijker, R Fossion, R Lizcano, D TI Single-particle structure of neutron-rich nuclei SO XXXIII SYMPOSIUM ON NUCLEAR PHYSICS SE Journal of Physics Conference Series LA English DT Proceedings Paper CT 33rd Symposium on Nuclear Physics CY JAN 05-08, 2010 CL Morelos, MEXICO ID STATE AB Neutron transfer (d,p) reactions have been measured with rare isotope beams of (132)sn, (130)sn and Te-134 accelerated to approximate to 4.5 MeV/u interacting with CD2 targets. Reaction protons were detected in an early implementation of the ORRUBA array of position-sensitive silicon strip detectors. Neutron excitations in the 2f(7/2), 3p(3/2), 3p(1/2) and 2f(5/2) orbitals were populated. C1 [Cizewski, J. A.; Jones, K. L.; Pain, S. D.] Rutgers State Univ, Dept Phys & Astron, New Brunswick, NJ 08903 USA. [Jones, K. L.] Univ Tennessee, Dept Phys & Astron, Knoxville, TN 37996 USA. [Kozub, R. L.] Tennessee Technol Univ, Dept Phys, Cookeville, TN 38505 USA. [Pain, S. D.] Oak Ridge Natl Lab, Div Phys, Oak Ridge, TN 37831 USA. RP Cizewski, JA (reprint author), Rutgers State Univ, Dept Phys & Astron, New Brunswick, NJ 08903 USA. EM cizewski@rutgers.edu RI Pain, Steven/E-1188-2011; Jones, Katherine/B-8487-2011 OI Pain, Steven/0000-0003-3081-688X; Jones, Katherine/0000-0001-7335-1379 FU U.S. Department of Energy [DE-FG52-08NA28552, DE-AC05-00OR22725, DE-FG02-96ER40955, DE-FG02-96ER40990, DE-FG03-93-ER40789, DE-FG03-93ER40789]; National Science Foundation; LDRD program of ORNL FX This work was supported in part by the U.S. Department of Energy under contract numbers DE-FG52-08NA28552 (Rutgers, ORAU), DE-AC05-00OR22725 (ORNL), DE-FG02-96ER40955 (TTU), DE-FG02-96ER40990 (TTU), DE-FG03-93-ER40789 (UTK), DE-FG03-93ER40789 (Mines); the National Science Foundation; and the LDRD program of ORNL. NR 15 TC 4 Z9 4 U1 1 U2 2 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1742-6588 J9 J PHYS CONF SER PY 2010 VL 239 AR UNSP 012007 DI 10.1088/1742-6596/239/1/012007 PG 4 WC Physics, Nuclear SC Physics GA BTQ55 UT WOS:000287788100007 ER PT J AU Kim, SJ Miller, GJ Corbett, JD AF Kim, Sung-Jin Miller, Gordon J. Corbett, John D. TI Zigzag Chains of Alternating Atoms in A(2)AuBi (A = Na, K) and K2AuSb. Synthesis, Structure, and Bonding SO ZEITSCHRIFT FUR ANORGANISCHE UND ALLGEMEINE CHEMIE LA English DT Article DE Intermetallic phases; Bonding; Electronic structure; Gold; Bismuth ID CLOSED-SHELL INTERACTIONS; CRYSTAL-STRUCTURE; INTERMETALLIC PHASES; ELECTRONIC-STRUCTURE; ZINTL PHASES; GOLD; METALS; CHEMISTRY; SYSTEMS AB The polar intermetallic phases A(2)AuBi (A = Na (I), K (II)), and K2AuSb (III) were obtained by direct reaction of the elements at elevated temperatures in niobium ampoules. The three isotypic compounds extend the prominent A(2)MP(n) (M = transition metal; P-n = group 15) structure family. Single-crystal X-ray diffraction experiments show that these phases (I / II / III) crystallize in the orthorlionibic space group Cnicin (No. 63), with a = 9.447(2) / 10.632(2) / 10.450(2) angstrom; b = 7.700(2) 7.918(2) / 7.857(2) angstrom; c = 5.849(1) / 6.597(1) / 6.501 (1) angstrom; V = 425.4(2) / 555.4(2) / 533.8(2) angstrom(3), respectively, and Z = 4 The simple structures, which contain zigzag chains of linear two-bonded gold atoms and acute angles (64 to 76 degrees) at two-bonded antimony or bismuth, can readily be rationalized with the Zintl-Klemm concept. TB-LMTO calculations Show distinct band gaps at E-F, and analyses of DOS and COHP curves show optimized Au-Pn bonding, appreciable Au-Au interactions across the chains. aid covalent interactions between A and Pn atoms. The observed structural preference over an isoelectronic NaTl type structure, the cation influences. and site coloring were investigated with VASP and EHTB calculations. C1 [Kim, Sung-Jin; Miller, Gordon J.; Corbett, John D.] US DOE, Ames Lab, Ames, IA 50011 USA. [Kim, Sung-Jin; Miller, Gordon J.; Corbett, John D.] Iowa State Univ, Dept Chem, Ames, IA 50011 USA. RP Miller, GJ (reprint author), US DOE, Ames Lab, Ames, IA 50011 USA. EM gmiller@iastate.edu; jcorbett@iastate.edu FU Office of the Basic Energy Sciences. Materials Sciences Division, U.S. Department of Energy (DOE); Iowa State Univetsity [DE-AC02-07CH11358] FX This research was supported by the Office of the Basic Energy Sciences. Materials Sciences Division, U.S. Department of Energy (DOE) and was carried out in the facilities of Ames Laboratory. The Ames Laboratory is operated for DOE by Iowa State Univetsity under contract No. DE-AC02-07CH11358. NR 61 TC 7 Z9 7 U1 1 U2 13 PU WILEY-BLACKWELL PI MALDEN PA COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA SN 0044-2313 J9 Z ANORG ALLG CHEM JI Z. Anorg. Allg. Chem. PY 2010 VL 636 IS 1 BP 67 EP 73 DI 10.1002/zaac.200900417 PG 7 WC Chemistry, Inorganic & Nuclear SC Chemistry GA 555BH UT WOS:000274481500012 ER PT J AU Minch, R Peters, L Ehm, L Knorr, K Siidra, OI Prakapenka, V Dera, P Depmeier, W AF Minch, Robert Peters, Lars Ehm, Lars Knorr, Karsten Siidra, Oleg I. Prakapenka, Vitali Dera, Przemyslaw Depmeier, Wulf TI Evidence for the existence of a PbCO3-II phase from high pressure X-ray measurements SO ZEITSCHRIFT FUR KRISTALLOGRAPHIE LA English DT Article DE High pressure; X-ray diffraction; Phase transition; Lead carbonate ID POST-ARAGONITE PHASE; SINGLE-CRYSTAL; RIETVELD REFINEMENT; CERUSSITE; STRONTIANITE; TEMPERATURE; DIFFRACTION; CARBONATES; TRANSITION; WITHERITE AB The high-pressure room temperature behavior of PbCO3 was investigated by angle-dispersive synchrotron powder diffraction up to 16.16(5) GPa. A phase transition to a high-pressure polymorph II of lead carbonate was observed at a pressure of approximately p(c) = 8.7 GPa. Thereby, the symmetry is reduced from orthorhombic Pmcn to monoclinic P12(1)/c1. The cell parameters at p = 8.90(5) GPa are a = 5.101(1) angstrom, b = 8.303(3) angstrom, c = 5.602(2) angstrom, beta = 89.51(4)degrees, Z = 4. The transformation is supposed to be of 2(nd) order. C1 [Minch, Robert; Peters, Lars; Depmeier, Wulf] Univ Kiel, Inst Geowissensch, D-24118 Kiel, Germany. [Ehm, Lars] SUNY Stony Brook, Inst Mineral Phys, Stony Brook, NY 11794 USA. [Ehm, Lars] Brookhaven Natl Lab, Natl Synchrotron Light Source, Upton, NY 11973 USA. [Knorr, Karsten] BrukerAXS GmbH, D-76187 Karlsruhe, Germany. [Siidra, Oleg I.] St Petersburg State Univ, Dept Crystallog, St Petersburg 199034, Russia. [Prakapenka, Vitali; Dera, Przemyslaw] Univ Chicago, GSECARS, Chicago, IL 60637 USA. RP Minch, R (reprint author), Univ Kiel, Inst Geowissensch, Olshaussenstr 40, D-24118 Kiel, Germany. EM robert@min.uni-kiel.de RI Dera, Przemyslaw/F-6483-2013; Siidra, Oleg/H-2975-2013 OI Siidra, Oleg/0000-0003-1908-3152 FU Deutsche Forschungsgemeinschaft [KN 507/5-1]; National Science Foundation - Earth Sciences [EAR-0622171]; Department of Energy - Geosciences [DE-FG02-94ER14466]; U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-AC02-06CH11357]; RF programme [02.740.11.0326] FX This research was supported by the Deutsche Forschungsgemeinschaft under project number KN 507/5-1 in the framework of the priority program: "Synthesis, 'in situ' characterization and quantum mechanical modeling of Earth Materials, oxides, carbides and nitrides at extremely high pressures and temperatures". This work was performed at GeoSoilEnviroCARS (Sector 13), Advanced Photon Source (APS), Argonne National Laboratory. GeoSoilEnviroCARS is supported by the National Science Foundation - Earth Sciences (EAR-0622171) and Department of Energy - Geosciences (DE-FG02-94ER14466). Use of the Advanced Photon Source was supported by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. RF programme state contract # 02.740.11.0326. Special thanks go to anonymous reviewer for very helpful comments. NR 30 TC 4 Z9 4 U1 1 U2 16 PU OLDENBOURG VERLAG PI MUNICH PA LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY SN 0044-2968 J9 Z KRISTALLOGR JI Z. Kristall. PY 2010 VL 225 IS 4 BP 146 EP 152 DI 10.1524/zkri.2010.1194 PG 7 WC Crystallography SC Crystallography GA 598ID UT WOS:000277828100003 ER PT J AU Shi, XW Xiong, G Huang, XJ Harder, R Robinson, I AF Shi, Xiaowen Xiong, Gang Huang, Xiaojing Harder, Ross Robinson, Ian TI Structural inhomogeneity in Silicon-On-Insulator probed with coherent X-ray diffraction SO ZEITSCHRIFT FUR KRISTALLOGRAPHIE LA English DT Article DE Coherent; Inhomogeneity; X-ray diffractive imaging; Silicon-On-Insulator ID STRAIN CHARACTERIZATION; WAFERS; SI AB We report our research on X-ray micro-beam diffraction and coherent X-ray diffractive imaging techniques to study structural inhomogeneities in Silicon-On-Insulator continuous plain wafers. Inhomogeneities were measured quantitatively and attributed to limitations of the manufacturing process. 3-dimensional image reconstructions were performed by using our Error-Reduction and Hybrid-Input-Output iterative algorithms. These revealed images of the focussed X-ray beam passing through the active layer of the wafer. C1 [Shi, Xiaowen; Xiong, Gang; Huang, Xiaojing; Robinson, Ian] UCL, London Ctr Nanotechnol, London WC1E 6BT, England. [Shi, Xiaowen; Xiong, Gang; Huang, Xiaojing; Robinson, Ian] UCL, Dept Phys & Astron, London WC1E 6BT, England. [Huang, Xiaojing; Harder, Ross] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Shi, XW (reprint author), UCL, London Ctr Nanotechnol, Mortimer St, London WC1E 6BT, England. EM xiaowen.shi.09@ucl.ac.uk RI Huang, Xiaojing/K-3075-2012 OI Huang, Xiaojing/0000-0001-6034-5893 NR 20 TC 3 Z9 3 U1 0 U2 3 PU OLDENBOURG VERLAG PI MUNICH PA LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY SN 0044-2968 J9 Z KRISTALLOGR JI Z. Kristall. PY 2010 VL 225 IS 12 BP 610 EP 615 DI 10.1524/zkri.2010.1354 PG 6 WC Crystallography SC Crystallography GA 704TM UT WOS:000286075900011 ER PT J AU Frick, B Mamontov, E van Eijck, L Seydel, T AF Frick, Bernhard Mamontov, Eugene van Eijck, Lambert Seydel, Tilo TI Recent Backscattering Instrument Developments at the ILL and SNS SO ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS LA English DT Article DE Neutron Spectroscopy; Backscattering; Instrumentation ID ELASTIC NEUTRON-SCATTERING; HIGH-RESOLUTION; SPECTROMETER; ANALYZERS; DYNAMICS; IN16; IRIS AB We present new developments in neutron backscattering spectroscopy from two major neutron scattering centers. The first example is the reactor backscattering project IN16B, which is under construction at the Institut Laue-Langevin (ILL), Grenoble, France, the second is the spallation source near-backscattering spectrometer BASIS at the spallation neutron source SNS, Oak Ridge National Laboratory, USA, in operation since 2007. After explaining the energy resolution contributions to neutron backscattering and presenting the current status, we describe the layout, performance and the complementarity of the two most advanced backscattering projects. A few examples should illustrate the status and new experimental possibilities. C1 [Frick, Bernhard; van Eijck, Lambert; Seydel, Tilo] Inst Laue Langevin, F-38042 Grenoble, France. [Mamontov, Eugene] Oak Ridge Natl Lab, Spallat Neutron Source, Oak Ridge, TN 37831 USA. RP Frick, B (reprint author), Inst Laue Langevin, BP 156,6 Rue Jules Horowitz, F-38042 Grenoble, France. EM frick@ill.eu RI Frick, Bernhard/C-2756-2011; Mamontov, Eugene/Q-1003-2015 OI Mamontov, Eugene/0000-0002-5684-2675 NR 29 TC 15 Z9 15 U1 0 U2 13 PU WALTER DE GRUYTER GMBH PI BERLIN PA GENTHINER STRASSE 13, D-10785 BERLIN, GERMANY SN 0942-9352 J9 Z PHYS CHEM JI Z. Phys. Chemie-Int. J. Res. Phys. Chem. Chem. Phys. PY 2010 VL 224 IS 1-2 BP 33 EP 60 DI 10.1524/zpch.2010.6091 PG 28 WC Chemistry, Physical SC Chemistry GA 565FP UT WOS:000275275000003 ER PT J AU Dreuw, A Plotner, J Wormit, M Head-Gordon, M Dutoi, AD AF Dreuw, Andreas Ploetner, Juergen Wormit, Michael Head-Gordon, Martin Dutoi, Anthony Dean TI An Additive Long-range Potential to Correct for the Charge-transfer Failure of Time-dependent Density Functional Theory SO ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS LA English DT Article DE Excited States; Time Dependent Density Functional Theory; Charge Transfer; Long-range Corrected Potential; Hartree-Fock Exchange ID TRANSFER EXCITED-STATES; TRANSFER EXCITATIONS; CORRELATION ENERGIES; ASYMPTOTIC-BEHAVIOR; EXACT EXCHANGE; PI-SYSTEMS; APPROXIMATION; COMPLEXES; MOLECULES AB Time-dependent density functional theory is one of the most widely used methods for the calculation of excited states of large molecules. However, it exhibits substantial problems with charge-transfer excited states when conventional exchange-correlation functionals are employed. Here, we introduce an additive long-range potential that can, in principle, be directly employed with any existing local, GGA or hybrid-functional, without re-fitting of the original functionals. The additive potential shifts the excitation energies to higher values and corrects for the wrong asymptotic behavior of their potential energy surfaces with respect to charge-separating coordinates. First examples of its successful application are shown. C1 [Dreuw, Andreas; Ploetner, Juergen; Wormit, Michael] Goethe Univ Frankfurt, Inst Phys & Theoret Chem, D-60438 Frankfurt, Germany. [Head-Gordon, Martin] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Head-Gordon, Martin] Univ Calif Berkeley, Lawrence Berkeley Lab, Chem Sci & Phys Biosci Div, Berkeley, CA 94720 USA. [Dutoi, Anthony Dean] Univ Heidelberg, Inst Phys & Theoret Chem, D-69120 Heidelberg, Germany. RP Dreuw, A (reprint author), Goethe Univ Frankfurt, Inst Phys & Theoret Chem, Max von Laue Str 7, D-60438 Frankfurt, Germany. EM andreas.dreuw@theochem.uni-frankfurt.de RI Fachbereich14, Dekanat/C-8553-2015 FU Deutsche Forschungsgemeinschaft [SPP 1145]; Office of Basic Energy Sciences, Chemical Sciences Division of the US Department of Energy [DE-AC03-76SF0098] FX This work has been supported by the Deutsche Forschungsgemeinschaft within the Priority Programme SPP 1145 "First Principle Methods". AD holds a Heisenberg-Professorship funded by the Deutsche Forschungsgemeinschaft. ADD is a fellow of the Humboldt foundation. Financial support from the Director of the Office of Basic Energy Sciences, Chemical Sciences Division of the US Department of Energy, under Contract DE-AC03-76SF0098 is gratefully acknowledged. NR 54 TC 7 Z9 7 U1 4 U2 11 PU OLDENBOURG VERLAG PI MUNICH PA LEKTORAT MINT, POSTFACH 80 13 60, D-81613 MUNICH, GERMANY SN 0942-9352 J9 Z PHYS CHEM JI Z. Phys. Chemie-Int. J. Res. Phys. Chem. Chem. Phys. PY 2010 VL 224 IS 3-4 SI SI BP 311 EP 324 DI 10.1524/zpch.2010.6107 PG 14 WC Chemistry, Physical SC Chemistry GA 641KR UT WOS:000281124800003 ER PT J AU Small, W Gjersing, E Herberg, JL Wilson, TS Maitland, DJ AF Small, Ward, IV Gjersing, Erica Herberg, Julie L. Wilson, Thomas S. Maitland, Duncan J. TI Magnetic resonance flow velocity and temperature mapping of a shape memory polymer foam device SO BIOMEDICAL ENGINEERING ONLINE LA English DT Article ID IN-VITRO; POLYURETHANE; STENT AB Background: Interventional medical devices based on thermally responsive shape memory polymer (SMP) are under development to treat stroke victims. The goals of these catheter-delivered devices include re-establishing blood flow in occluded arteries and preventing aneurysm rupture. Because these devices alter the hemodynamics and dissipate thermal energy during the therapeutic procedure, a first step in the device development process is to investigate fluid velocity and temperature changes following device deployment. Methods: A laser-heated SMP foam device was deployed in a simplified in vitro vascular model. Magnetic resonance imaging (MRI) techniques were used to assess the fluid dynamics and thermal changes associated with device deployment. Results: Spatial maps of the steady-state fluid velocity and temperature change inside and outside the laser-heated SMP foam device were acquired. Conclusions: Though non-physiological conditions were used in this initial study, the utility of MRI in the development of a thermally-activated SMP foam device has been demonstrated. C1 [Small, Ward, IV; Herberg, Julie L.; Wilson, Thomas S.; Maitland, Duncan J.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Gjersing, Erica] Univ Calif Davis, Dept Chem Engn & Mat Sci, Davis, CA 95616 USA. [Maitland, Duncan J.] Texas A&M Univ, Dept Biomed Engn, College Stn, TX 77843 USA. RP Maitland, DJ (reprint author), Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. EM small3@llnl.gov; elgjersing@ucdavis.edu; herberg1@llnl.gov; wilson97@llnl.gov; djmaitland@tamu.edu FU U. S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; National Institutes of Health, National Institute of Biomedical Imaging and Bioengineering [R01EB000462]; Lawrence Livermore National Laboratory Directed Research and Development [04-ERD-093] FX We would like to thank Robert S. Maxwell and Sarah C. Chinn for their support. This work was performed under the auspices of the U. S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and supported by the National Institutes of Health, National Institute of Biomedical Imaging and Bioengineering, Grant R01EB000462, and Lawrence Livermore National Laboratory Directed Research and Development, Grant 04-ERD-093. NR 22 TC 4 Z9 4 U1 2 U2 17 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1475-925X J9 BIOMED ENG ONLINE JI Biomed. Eng. Online PD DEC 31 PY 2009 VL 8 AR 42 DI 10.1186/1475-925X-8-42 PG 7 WC Engineering, Biomedical SC Engineering GA 542WR UT WOS:000273530400001 PM 20043833 ER PT J AU Gary, SP Smith, CW AF Gary, S. Peter Smith, Charles W. TI Short-wavelength turbulence in the solar wind: Linear theory of whistler and kinetic Alfven fluctuations SO JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS LA English DT Article ID ELECTRON MAGNETOHYDRODYNAMIC TURBULENCE; MAGNETIC-FIELD; DISSIPATION RANGE; ENERGY CASCADE; POWER SPECTRA; ANISOTROPY; DEPENDENCE; WAVES; AU AB There is a debate as to the identity of the fluctuations which constitute the relatively high-frequency plasma turbulence observed in the solar wind. One school holds that these modes are kinetic Alfven waves, whereas another opinion is that they are whistler modes. Here linear kinetic theory for electromagnetic fluctuations in homogeneous, collisionless, magnetized plasmas is used to compute two dimensionless transport ratios, the electron compressibility C(e) and the magnetic compressibility C(parallel to) for these two modes. The former is a measure of the amplitude of density fluctuations, and the latter indicates the relative energy in magnetic fluctuations in the component parallel to the background magnetic field B(o). For beta(e) << 1, [C(parallel to)](Alfven) << [C(parallel to)](whistler), and the latter quantity is of order 0.5 at whistler propagation strongly oblique to B(o). Such values of C(parallel to) are sometimes measured at relatively high frequencies and beta(e) << 1 in the solar wind; thus, it is concluded that such observations correspond to whistler mode turbulence. But other solar wind observations indicate that kinetic Alfven fluctuations also contribute to relatively high-frequency solar wind turbulence. C1 [Gary, S. Peter] Los Alamos Natl Lab, Grp ISR 1, Los Alamos, NM 87545 USA. [Smith, Charles W.] Univ New Hampshire, Ctr Space Sci, Durham, NH 03824 USA. RP Gary, SP (reprint author), Los Alamos Natl Lab, Grp ISR 1, MS D466, Los Alamos, NM 87545 USA. EM pgary@lanl.gov; chuck@briaxa.sr.unh.edu FU Laboratory Directed Research and Development Program; Solar and Heliospheric Physics SRT; Heliophysics Guest Investigators Programs; National Aeronautics and Space Administration FX The Los Alamos portion of this work was performed under the auspices of the U.S. Department of Energy (DOE). It was supported by the Magnetic Turbulence and Kinetic Dissipation Project of the Laboratory Directed Research and Development Program at Los Alamos, and by the Solar and Heliospheric Physics SR&T and the Heliophysics Guest Investigators Programs as well as by Cluster/PEACE data analysis funding of the National Aeronautics and Space Administration. NR 42 TC 64 Z9 64 U1 0 U2 4 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0148-0227 J9 J GEOPHYS RES-SPACE JI J. Geophys. Res-Space Phys. PD DEC 31 PY 2009 VL 114 AR A12105 DI 10.1029/2009JA014525 PG 7 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 539MP UT WOS:000273259100004 ER PT J AU Kostko, O Kim, SK Leone, SR Ahmed, M AF Kostko, Oleg Kim, Sang Kyu Leone, Stephen R. Ahmed, Musahid TI Mass-Analyzed Threshold Ionization (MATI) Spectroscopy of Atoms and Molecules Using VUV Synchrotron Radiation SO JOURNAL OF PHYSICAL CHEMISTRY A LA English DT Article ID HIGH-RESOLUTION THRESHOLD; ENERGY PHOTOELECTRON-SPECTRUM; ROTATIONALLY RESOLVED PHOTOIONIZATION; RYDBERG STATES; WATER CLUSTERS; DYNAMICS; NITROGEN; IONS; BENZENE; ARGON AB Mass-analyzed threshold ionization (MATI) spectroscopy using synchrotron radiation (Advanced Light Source, Lawrence Berkeley National Laboratory) has been performed for Ar, N(2), O(2), N(2)O, H(2)O, C(2)H(2) and C(6)H(6). MATI allows for a better determination of ionization energies compared to those derived from photoionization efficiency curves traditionally used in synchrotron photoionization mass spectrometry. The separation of the long-lived Rydberg state from the directly formed prompt ion, essential for a meaningful MATI spectrum, has been accomplished by employing an arrangement of ion optics coupled to unique electric field pulsing schemes. For Ar, a number of resolved bands below the ionization energy are observed, and these are ascribed to high-n,l Rydberg states prepared in the MATI scheme. The first vibrational state resolved MATI spectra of N(2) and O(2) are reported, and spectral characteristics are discussed in comparison with previously reported threshold photoelectron spectroscopic studies. Although MATI pet-formed with synchrotron radiation is intrinsically less sensitive compared to laser-based sources, this work demonstrates that MATI spectroscopy performed with widely tunable vacuum ultraviolet (VUV) radiation is a complementary technique for studying the ionization spectroscopy of polyatomic molecules. C1 [Kostko, Oleg; Kim, Sang Kyu; Leone, Stephen R.; Ahmed, Musahid] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Chem Sci, Berkeley, CA 94720 USA. [Leone, Stephen R.] Univ Calif Berkeley, Dept Chem & Phys, Berkeley, CA 94720 USA. RP Ahmed, M (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Div Chem Sci, 1 Cyclotron Rd, Berkeley, CA 94720 USA. EM MAhmed@lbl.gov RI Ahmed, Musahid/A-8733-2009; Kostko, Oleg/B-3822-2009; Kostko, Oleg/A-3693-2010; Kim, Sang Kyu/C-1613-2011 OI Kostko, Oleg/0000-0003-2068-4991; FU U.S. Department of Energy [DE-AC02-05CH 11231]; SBS Foundation, Air Force Office of Scientific Research [FA9550-04-1-0242] FX This work was Supported by the Director, Office of Energy Research, Office of Basic Energy Sciences, and Chemical Sciences Division of the U.S. Department of Energy under contract no. DE-AC02-05CH 11231. S.K.K. thanks the SBS Foundation and was partly supported by a MURI program (S.R.L.) from the Air Force Office of Scientific Research, contract no. FA9550-04-1-0242. S.R.L. gratefully acknowledges the support of a Morris Belkin Visiting Professorship at the Weizmann Institute of Science. Leonid Belau and Lynelle Takahashi are acknowledged for their help during the initial attempts to implement MATI at the synchrotron. NR 40 TC 18 Z9 18 U1 3 U2 30 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1089-5639 J9 J PHYS CHEM A JI J. Phys. Chem. A PD DEC 31 PY 2009 VL 113 IS 52 BP 14206 EP 14211 DI 10.1021/jp9008338 PG 6 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 539OF UT WOS:000273263700003 PM 19476362 ER PT J AU Garand, E Buchachenko, AA Yacovitch, TI Szczesniak, MM Chalasinski, G Neumark, DM AF Garand, Etienne Buchachenko, Alexei A. Yacovitch, Tara I. Szczesniak, Malgorzata M. Chalasinski, Grzegorz Neumark, Daniel M. TI Study of KrO- and KrO via Slow Photoelectron Velocity-Map Imaging Spectroscopy and ab Initio Calculations SO JOURNAL OF PHYSICAL CHEMISTRY A LA English DT Article ID KINETIC-ENERGY SPECTROSCOPY; RARE-GAS OXIDES; CORRELATED MOLECULAR CALCULATIONS; GAUSSIAN-BASIS SETS; QUANTUM-MECHANICAL TREATMENT; LYING ELECTRONIC STATES; LOWEST EXCITED-STATES; OPEN-SHELL ATOMS; NEGATIVE-IONS; PHOTODETACHMENT SPECTROSCOPY AB The high-resolution photoelectron spectrum of KrO- was obtained using slow electron velocity-map imaging (SEVI). The SEVI spectrum reveals numerous vibronic transitions between multiple electronic states of KrO- and KrO, both of which are open-shell species. Detailed assignments are made by comparison with theoretical simulations based on high level ab initio calculations and an atoms-in-molecule model that accounts for spin-orbit coupling in the anion and neutral. Several KrO- and KrO vibrational frequencies and excited-state term energies are accurately determined from the analysis of the experimental spectra and are found to be in good agreement with the calculated values. C1 [Buchachenko, Alexei A.] Moscow MV Lomonosov State Univ, Dept Chem, Lab Mol Struct & Quantum Mech, Moscow 119991, Russia. [Garand, Etienne; Yacovitch, Tara I.; Neumark, Daniel M.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Szczesniak, Malgorzata M.; Chalasinski, Grzegorz] Oakland Univ, Dept Chem, Rochester, MI 48309 USA. [Chalasinski, Grzegorz] Univ Warsaw, Fac Chem, PL-02093 Warsaw, Poland. [Neumark, Daniel M.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Chem Sci, Berkeley, CA 94720 USA. RP Buchachenko, AA (reprint author), Moscow MV Lomonosov State Univ, Dept Chem, Lab Mol Struct & Quantum Mech, Moscow 119991, Russia. EM alexei@classic.chem.msu.su; dneumark@berkeley.edu RI Buchachenko, Alexei/C-8452-2012; Neumark, Daniel/B-9551-2009; OI Buchachenko, Alexei/0000-0003-0701-5531; Neumark, Daniel/0000-0002-3762-9473; Garand, Etienne/0000-0001-5062-5453 FU Air Force Office of Scientific Research [FA9550-09-10343]; National Science Foundation [CHE-0719260]; Russian Basic Research Fund [08-03-00414]; National Science and Engineering Research Council of Canada (NSERC); Fonds Quebecois de la Recherche sur la Nature et les Technologies (FQRNT) FX This work was supported by the Air Force Office of Scientific Research under Grant No. FA9550-09-10343(DMN), the National Science Foundation under Grant No. CHE-0719260 (MMS and GC), and the Russian Basic Research Fund under Project No. 08-03-00414 (AAB). EG thanks the National Science and Engineering Research Council of Canada (NSERC) for a post graduate scholarship and TY thanks the Fonds Quebecois de la Recherche sur la Nature et les Technologies (FQRNT) for a master's scholarship. NR 44 TC 3 Z9 3 U1 0 U2 7 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1089-5639 J9 J PHYS CHEM A JI J. Phys. Chem. A PD DEC 31 PY 2009 VL 113 IS 52 BP 14439 EP 14446 DI 10.1021/jp903819m PG 8 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 539OF UT WOS:000273263700034 PM 19569654 ER PT J AU Kay, JJ van de Meerakker, SYT Wade, EA Strecker, KE Chandler, DW AF Kay, Jeffrey J. van de Meerakker, Sebastiaan Y. T. Wade, Elisabeth A. Strecker, Kevin E. Chandler, David W. TI Differential Cross Sections for Rotational Excitation of ND3 by Ne SO JOURNAL OF PHYSICAL CHEMISTRY A LA English DT Article ID BEAM SCATTERING; STATE; COLLISIONS; AR; PHOTOELECTRON; MOLECULES; DYNAMICS; ARGON; GAS; HCL AB We report the first measured differential cross sections for rotationally inelastic collisions between ND3 and Ne, obtained using velocity-mapped ion imaging. In these experiments, ND3 molecules initially in the J = 0, K = 0 and J = 1, K = 1 quantum states collide with Ne atoms at a center-of-mass collision energy of 65 meV, leading to rotational excitation of ND3. Differential cross sections are then determined from images of the rotationally excited scattered molecules using an iterative extraction method. These measurements complement and compare well with previous measurements of differential cross sections for the ammonia-rare gas system (Meyer, H. J. Chem. Phys. 1994, 101, 6697.; Meyer, H. J. Phys. Chem. 1995, 99, 1101.) and are also relevant to the production of cold ND3 molecules by crossed-beam scattering (Kay, J. J.; van de Meerakker, S. Y. T.; Strecker, K. E.; Chandler, D. W. Faraday Discuss. 2009, DOI: 10.1039/B819256C). C1 [Kay, Jeffrey J.; Strecker, Kevin E.; Chandler, David W.] Sandia Natl Labs, Livermore, CA 94550 USA. [van de Meerakker, Sebastiaan Y. T.] Max Planck Gesell, Fritz Haber Inst, D-14195 Berlin, Germany. [Wade, Elisabeth A.] Mills Coll, Dept Chem & Phys, Oakland, CA 94613 USA. RP Strecker, KE (reprint author), Sandia Natl Labs, Livermore, CA 94550 USA. EM kstreck@sandia.gov; chand@sandia.gov RI van de Meerakker, Sebastiaan/D-4581-2012 FU U.S. Department of Energy, Office of Basic Energy Science FX We acknowledge Mr. Mark Jaska for technical support. Funding for this work was provided by the U.S. Department of Energy, Office of Basic Energy Science. Sandia is a multiprogram laboratory operated by Sandia Corportation, a Lockheed Martin Co., for the U.S. Department of Energy. NR 21 TC 9 Z9 9 U1 1 U2 16 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1089-5639 EI 1520-5215 J9 J PHYS CHEM A JI J. Phys. Chem. A PD DEC 31 PY 2009 VL 113 IS 52 BP 14800 EP 14806 DI 10.1021/jp904983w PG 7 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 539OF UT WOS:000273263700078 PM 19694449 ER PT J AU de Miranda, MP Kendrick, BK AF de Miranda, Marcelo P. Kendrick, Brian K. TI Single-Parameter Quantification of the Sensitivity of a Molecular Collision to Molecular Polarization SO JOURNAL OF PHYSICAL CHEMISTRY A LA English DT Article ID QUANTUM REACTIVE SCATTERING; ROTATIONALLY INELASTIC-COLLISIONS; ELEMENTARY CHEMICAL-REACTIONS; DIFFERENTIAL CROSS-SECTIONS; HYDROGEN-EXCHANGE REACTION; WAVE PACKET FORMULATION; HYPERQUANTIZATION ALGORITHM; GLORY SCATTERING; MATHEMATICAL-THEORY; STATISTICAL-THEORY AB This article introduces the concept of intrinsic entropy, S, of a molecular collision. Defined in rigorously quantum mechanical terms as the von Neumann entropy of the intrinsic density matrices of reagents and products, the intrinsic entropy is a dimensionless number in the 0 <= S <= 1 range. Its limits are associated with situations where the collision cross section is due to a single combination of reagent and product polarizations (S = 0) or where there is absolutely no selectivity with respect to the molecular polarizations (S = 1). The usefulness of the intrinsic entropy as a quantifier of the sensitivity of a molecular collision to molecular polarizations is demonstrated with examples for the benchmark H + D-2 reaction. C1 [de Miranda, Marcelo P.] Univ Leeds, Sch Chem, Leeds LS2 9JT, W Yorkshire, England. [Kendrick, Brian K.] Los Alamos Natl Lab, Theoret Div T 1 MS B268, Los Alamos, NM 87545 USA. RP de Miranda, MP (reprint author), Univ Leeds, Sch Chem, Leeds LS2 9JT, W Yorkshire, England. EM m.miranda@leeds.ac.uk FU U.S. Department of Energy [20020015ER, AC52-06NA25396] FX B.K.K. acknowledges that part of this work was done under the auspices of the U.S. Department of Energy under Project No. 20020015ER of the Laboratory Directed Research and Development program at Los Alamos National Laboratory. Los Alamos National Laboratory is operated by Los Alamos National Security, LLC, for the National Nuclear Security Administration of the U.S. Department of Energy under contract No. DE-AC52-06NA25396. NR 74 TC 3 Z9 3 U1 0 U2 5 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1089-5639 J9 J PHYS CHEM A JI J. Phys. Chem. A PD DEC 31 PY 2009 VL 113 IS 52 BP 14943 EP 14951 DI 10.1021/jp9050275 PG 9 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 539OF UT WOS:000273263700096 PM 20028174 ER PT J AU Ramanathan, A Agarwal, PK AF Ramanathan, Arvind Agarwal, Pratul K. TI Computational Identification of Slow Conformational Fluctuations in Proteins SO JOURNAL OF PHYSICAL CHEMISTRY B LA English DT Article ID NORMAL-MODE ANALYSIS; MOLECULAR-DYNAMICS SIMULATIONS; HIV-1 CAPSID PROTEIN; ENZYME CATALYSIS; DIHYDROFOLATE-REDUCTASE; CYCLOPHILIN-A; CIS/TRANS ISOMERIZATION; PRINCIPAL COMPONENTS; TRYPSIN-INHIBITOR; HUMAN UBIQUITIN AB Conformational flexibility of proteins has been linked to their designated functions. Slow conformational fluctuations occurring at the microsecond to millisecond time scale, in particular, have recently attracted considerable interest in connection to the mechanism of enzyme catalysis. Computational methods are providing valuable insights into the connection between protein structure, flexibility, and function. In this report, we present Studies oil identification and characterization of microsecond flexibility of ubiquitin, based on quasi-harmonic analysis (QHA) and normal-mode analysis (NMA). The results indicate that the slowest 10 QHA modes, Computed from the 0.5 us molecular dynamics ensemble, contribute over 78% of all motions. The identified slow movements show over 75% similarity with the conformational fluctuations observed in nuclear magnetic resonance ensemble and also agree with displacements in the set of X-ray structures. The slowest modes show high flexibility in the beta 1-beta 2, alpha 1-beta 3, and beta 3-beta 4 loop regions, with functional implications in the mechanism of binding other proteins. NMA Of ubiquitin structures was not able to reproduce the long time scale fluctuations, as they were found to strongly depend on the reference structures. Further, conformational fluctuations Coupled to the cis/trans isomerization reaction catalyzed by the enzyme cyclophilin A (CypA), occurring at the microsecond to millisecond time scale, have also been identified and characterized oil the basis of QHA of conformations sampled along the reaction pathway. The results indicate that QHA covers the same conformational landscape as the experimentally observed CypA flexibility. Overall, the identified slow conformational fluctuations ill ubiquitin and CypA indicate that the intrinsic flexibility of these proteins is closely linked to their designated functions. C1 [Ramanathan, Arvind; Agarwal, Pratul K.] Oak Ridge Natl Lab, Computat Biol Inst, Oak Ridge, TN 37831 USA. [Ramanathan, Arvind; Agarwal, Pratul K.] Oak Ridge Natl Lab, Div Math & Comp Sci, Oak Ridge, TN 37831 USA. [Ramanathan, Arvind] Carnegie Mellon Univ, Sch Comp Sci, Lane Ctr Computat Biol, Joint Carnegie Mellon Univ Univ Pittsburgh PhD Pr, Pittsburgh, PA 15213 USA. RP Agarwal, PK (reprint author), Oak Ridge Natl Lab, Computat Biol Inst, POB 2008,MS 6016, Oak Ridge, TN 37831 USA. EM agarwalpk@ornl.gov RI Ramanathan, Arvind/E-5388-2010 FU National Institutes of Health [R21GM083946]; ORISE; National Center For Computational Sciences ORNL [BIP003]; U.S. Department of Energy [DE-AC05-000R22725] FX P.K.A. acknowledges the financial Support by ORNL's LDRD fund and the National Institutes of Health (R21GM083946). A.R. acknowledges the Advanced Short-Term Research Opportunity (from ORISE) program, This research used resources of the National Center For Computational Sciences ORNL under the Director's Discretionary allocation (project: BIP003), which is supported by the Office of Science of the U.S. Department of Energy tinder Contract No. DE-AC05-000R22725. NR 80 TC 20 Z9 20 U1 2 U2 11 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1520-6106 J9 J PHYS CHEM B JI J. Phys. Chem. B PD DEC 31 PY 2009 VL 113 IS 52 BP 16669 EP 16680 DI 10.1021/jp9077213 PG 12 WC Chemistry, Physical SC Chemistry GA 534ZS UT WOS:000272936900026 PM 19908896 ER PT J AU Loebick, CZ Derrouiche, S Marinkovic, N Wang, C Hennrich, F Kappes, MM Haller, GL Pfefferle, LD AF Loebick, Codruta Zoican Derrouiche, Salim Marinkovic, Nebojsa Wang, Chuan Hennrich, Frank Kappes, Manfred M. Haller, Gary L. Pfefferle, Lisa D. TI Effect of Manganese Addition to the Co-MCM-41 Catalyst in the Selective Synthesis of Single Wall Carbon Nanotubes SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID CO DISPROPORTIONATION; BIMETALLIC CATALYSTS; INCORPORATED MCM-41; AQUEOUS SUSPENSION; RAMAN-SPECTROSCOPY; PURITY EVALUATION; REDOX PROPERTIES; GROWTH; MECHANISM; DECOMPOSITION AB The effect of manganese addition to the Co-MCM-41 catalyst on the synthesis of single wall carbon nanotubes (SWNT) by CO disproportionation was characterized. The ratio between the two metals in the MCM-41 framework was varied, and its effect on the resultant SWNT distribution was studied and compared with the results obtained for the monometallic Co-MCM-41 catalyst. Methods including temperature-programmed reduction, X-ray absorption fine structure, thermogravimetric analysis, TEM imaging, and Raman and fluorescence spectroscopy were employed to characterize the behavior of the catalysts under the SWNT synthesis conditions and the diameter and Structure distribution of the resultant nanotubes. We found that addition of Mn to the Co-MCM-41 catalyst promotes the growth of SWNT, leading to synthesis of high yield, small diameter SWNT. Manganese does not act in the nucleation of SWNT but acts as an anchoring site for cobalt particles formed during the synthesis process as shown by X-ray absorption. C1 [Loebick, Codruta Zoican; Derrouiche, Salim; Wang, Chuan; Haller, Gary L.; Pfefferle, Lisa D.] Yale Univ, Dept Chem Engn, New Haven, CT 06520 USA. [Marinkovic, Nebojsa] Univ Delaware, Brookhaven Natl Lab, Natl Synchrotron Light Source, Newark, DE 19716 USA. [Hennrich, Frank; Kappes, Manfred M.] Univ Karlsruhe, Nanotechnol Inst, Karlsruhe, Germany. RP Pfefferle, LD (reprint author), Yale Univ, Dept Chem Engn, New Haven, CT 06520 USA. EM lisa.pfefferle@yale.edu RI Marinkovic, Nebojsa/A-1137-2016 OI Marinkovic, Nebojsa/0000-0003-3579-3453 FU U.S. Department of Energy, Office of Basic Energy Science [DE-FG02-06ER46322]; NanoHoldings LLC; NSLS beamlines [X18B, X23A2] FX The authors gratefully acknowledge the financial support from the U.S. Department of Energy, Office of Basic Energy Science, Grant No. DE-FG02-06ER46322, and NanoHoldings LLC. We thank the NSLS beamlines X18B and X23A2, Brookhaven Laboratory for use of their facilities. NR 51 TC 15 Z9 15 U1 3 U2 17 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 31 PY 2009 VL 113 IS 52 BP 21611 EP 21620 DI 10.1021/jp908262u PG 10 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 534ZN UT WOS:000272936400025 ER PT J AU Titov, A Zapol, P Kral, P Liu, DJ Iddir, H Baishya, K Curtiss, LA AF Titov, Alexey Zapol, Peter Kral, Petr Liu, Di-Jia Iddir, Hakim Baishya, Kopinjol Curtiss, Larry A. TI Catalytic Fe-xN Sites in Carbon Nanotubes SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID OXYGEN REDUCTION REACTION; ABSORPTION FINE-STRUCTURE; CELL CATHODE CATALYST; ELECTROLYTE FUEL-CELL; O-2 REDUCTION; ACTIVE-SITES; NITROGEN; ELECTROCATALYSTS; ELECTROREDUCTION; SURFACE AB To reduce fuel cell cost, durable and inexpensive electrode catalysts need to be developed to replace precious metal materials, particularly for the electrocatalytic oxygen reduction at cathodes. In this study, we explored the structure and the energetics of Fe-xN (x = 2,4) incorporated into carbon nanotubes and graphene using density functional theory to show that these structures are more stable than iron atoms on nanotubes and that pyridinic structures of Fe-4N are more favorable than pyrrolic structures. EXAFS spectra simulated from the optimized structures show good agreement with results of measurements obtained oil arrays of aligned nanotubes doped with iron and nitrogen, which have demonstrated activity toward oxygen-reduction reactions. C1 [Zapol, Peter; Iddir, Hakim; Curtiss, Larry A.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. [Titov, Alexey; Kral, Petr] Univ Illinois, Dept Chem, Chicago, IL 60607 USA. [Liu, Di-Jia] Argonne Natl Lab, Chem Sci & Engn Div, Argonne, IL 60439 USA. [Baishya, Kopinjol] Univ Illinois, Dept Phys, Chicago, IL 60607 USA. [Curtiss, Larry A.] Argonne Natl Lab, Ctr Nanoscale Mat, Argonne, IL 60439 USA. RP Zapol, P (reprint author), Argonne Natl Lab, Div Mat Sci, 9700 S Cass Ave, Argonne, IL 60439 USA. EM zapol@anl.gov; pkral@uic.edu RI Zapol, Peter/G-1810-2012 OI Zapol, Peter/0000-0003-0570-9169 FU DOE BES [DE-AC02-06CH11357] FX The authors acknowledge the use of Argonne LCRC computer resources. Computational resources for this project have been provided in part by Molecular Science Computing Facility located at Pacific Northwest National Laboratory. A.T. acknowledges the UIC Office of Research for partial support. This work was supported by the DOE BES under Contract No. DE-AC02-06CH11357. NR 52 TC 56 Z9 56 U1 4 U2 51 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 31 PY 2009 VL 113 IS 52 BP 21629 EP 21634 DI 10.1021/jp810792d PG 6 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 534ZN UT WOS:000272936400027 ER PT J AU Mehmood, F Greeley, J Curtiss, LA AF Mehmood, F. Greeley, J. Curtiss, L. A. TI Density Functional Studies of Methanol Decomposition on Subnanometer Pd Clusters SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID INITIO MOLECULAR-DYNAMICS; TOTAL-ENERGY CALCULATIONS; O BOND SCISSION; WAVE BASIS-SET; CARBON-MONOXIDE; DIMETHYL ETHER; PALLADIUM CATALYSTS; CO ADSORPTION; SURFACES; PD(111) AB A density functional theory Study of the decomposition of methanol on subnanometer palladium Clusters (primarily Pd-4) is presented. Methanol dehydrogenation through C-H bond breaking to form hydroxymethyl (CH2OH) as the initial step, followed by steps involving formation of hydroxymethylene (CHOH), formyl (CHO), and carbon monoxide (CO), is found to be the most favorable reaction pathway. A competing dehydrogenation pathway with O-H bond breaking as the first step, followed by formation of methoxy (CH3O) and formaldehyde (CH2O), is slightly less favorable. In contrast, pathways involving C-O bond cleavage are much less energetically favorable, and no feasible pathways involving C-O bond formation to yield dimethyl ether (CH3OCH3) are found. Comparisons of the results are made with methanol decomposition products adsorbed on more extended Pd Surfaces; all reaction intermediates are found to bind slightly more strongly to the clusters than to the surfaces. C1 [Mehmood, F.; Curtiss, L. A.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. [Greeley, J.; Curtiss, L. A.] Argonne Natl Lab, Ctr Nanoscale Mat, Argonne, IL 60439 USA. RP Curtiss, LA (reprint author), Argonne Natl Lab, Div Mat Sci, 9700 S Cass Ave, Argonne, IL 60439 USA. FU U.S. Department of Energy [DE-AC0206CH11357]; Pacific Northwest National Laboratory; ANL Laboratory Computing Resource Center (LCRC) FX Work, including use of the Center for Nanoscale Materials, is Supported by the U.S. Department of Energy under Contract DE-AC0206CH11357. We acknowledge grants of computer time from EMSL, a national scientific user facility located at Pacific Northwest National Laboratory and the ANL Laboratory Computing Resource Center (LCRC). NR 68 TC 24 Z9 24 U1 7 U2 26 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 31 PY 2009 VL 113 IS 52 BP 21789 EP 21796 DI 10.1021/jp907772c PG 8 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 534ZN UT WOS:000272936400046 ER PT J AU Wong, BM AF Wong, Bryan M. TI Optoelectronic Properties of Carbon Nanorings: Excitonic Effects from Time-Dependent Density Functional Theory SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID CONJUGATED MOLECULES; ELECTRONIC-STRUCTURE; NANOTUBES; MACROCYCLES; EXCITATIONS; STATES; BELTS AB The electronic structure and size-scaling of optoelectronic properties in cycloparaphenylene carbon nanorings are investigated using time-dependent density functional theory (TDDFT). The TDDFT calculations on these molecular nanostructures indicate that the lowest excitation energy surprisingly becomes larger as the carbon nanoring size is increased, in contradiction with typical quantum confinement effects. In order to understand their unusual electronic properties, I performed an extensive investigation of excitonic effects by analyzing electron-hole transition density matrices and exciton binding energies as a function of size in these nanoring systems. The transition density matrices allow a global view of electronic coherence during an electronic excitation, and the exciton binding energies give a quantitative measure of electron-hole interaction energies in the nanorings. Based oil overall trends in exciton binding energies and their spatial delocalization, I find that excitonic effects play a vital role in understanding the unique photoinduced dynamics in these carbon nanoring systems. C1 Sandia Natl Labs, Dept Chem Mat, Livermore, CA 94551 USA. RP Wong, BM (reprint author), Sandia Natl Labs, Dept Chem Mat, Livermore, CA 94551 USA. EM bmwong@sandia.gov RI Wong, Bryan/B-1663-2009 OI Wong, Bryan/0000-0002-3477-8043 FU National Science Foundation [TG-CHE080076N]; United States Department of Energy's National Nuclear Security Administration [DE-AC04-94AL85000] FX This research was supported, in part, by the National Science Foundation through TeraGrid resources (Grant No. TG-CHE080076N) provided by the National Center for Supercomputing Applications. Funding for this effort was provided by the Readiness in Technical Base and Facilities (RTBF) program at Sandia National Laboratories, a multiprogram laboratory operated by Sandia Corporation, it Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract No. DE-AC04-94AL85000. NR 42 TC 75 Z9 75 U1 1 U2 22 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 31 PY 2009 VL 113 IS 52 BP 21921 EP 21927 DI 10.1021/jp9074674 PG 7 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 534ZN UT WOS:000272936400063 ER PT J AU Han, WQ Wen, W Hanson, JC Teng, XW Marinkovic, N Rodriguez, JA AF Han, Wei-Qiang Wen, Wen Hanson, Jonathan C. Teng, Xiaowei Marinkovic, Nebojsa Rodriguez, Jose A. TI One-Dimensional Ceria as Catalyst for the Low-Temperature Water-Gas Shift Reaction SO JOURNAL OF PHYSICAL CHEMISTRY C LA English DT Article ID OXYGEN STORAGE CAPACITY; OXIDE NANOPARTICLES; HYDROGEN-PRODUCTION; CEO2; GOLD; SPECTROSCOPY; REDUCTION; NANOTUBES; BEHAVIOR; HYDRIDE AB Synchrotron-based in Situ time-resolved X-ray diffraction and X-ray absorption spectroscopy were used to study pure ceria and Pd-loaded ceria nanotubes and nanorods (1D-ceria) as catalysts for the water-gas shift (WGS) reaction. While bulk ceria is very poor as WGS catalysts, pure I D-ceria displayed catalytic activity at a temperature as low as 300 degrees C. The reduction of the pure ID-ceria in pure hydrogen started at 150 degrees C, which is a much lower temperature than those previously reported for the reduction of 3D ceria nanoparticles. This low reduction temperature reflects the novel morphology of the oxide systems and may be responsible for the low-temperature WGS catalytic activity seen for the 1D-ceria. Pd-loaded 1D ceria displayed significant WGS activity starting at 200 degrees C. During pretreatment in H(2), the ceria lattice parameter increased significantly around 60 degrees C, which indicates that Pd-oxygen interactions may facilitate the reduction of Pd-loaded 1D-ceria. Pd and ceria both participate in the formation of the active sites for the catalytic reactions. The low-temperature hydrogen pretreatment results in higher WGS activity for Pd-loaded 1D-ceria. C1 [Han, Wei-Qiang; Wen, Wen; Teng, Xiaowei] Brookhaven Natl Lab, Ctr Funct Nanomat, Upton, NY 11973 USA. [Hanson, Jonathan C.; Rodriguez, Jose A.] Brookhaven Natl Lab, Dept Chem, Upton, NY 11973 USA. [Marinkovic, Nebojsa] Univ Delaware, Dept Chem Engn, Newark, DE 19716 USA. RP Han, WQ (reprint author), Brookhaven Natl Lab, Ctr Funct Nanomat, Upton, NY 11973 USA. EM whan@bnl.gov RI Han, WQ/E-2818-2013; Marinkovic, Nebojsa/A-1137-2016; Hanson, jonathan/E-3517-2010 OI Marinkovic, Nebojsa/0000-0003-3579-3453; FU U.S. DOE [DE-AC02-98CH10886]; DOE [DE-FG05-89ER45384, DE-AC02-76CH00016] FX This work is supported by the U.S. DOE under Contract DE-AC02-98CH10886 and Laboratory Directed Research and Development Fund of Brookhaven National Laboratory. This research is carried Out at X7B, X18B, and X19A of the National Synchrotron Light Source, which is supported and maintained by DOE under the Contracts DE-FG05-89ER45384 and DE-AC02-76CH00016. NR 47 TC 40 Z9 43 U1 2 U2 44 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1932-7447 J9 J PHYS CHEM C JI J. Phys. Chem. C PD DEC 31 PY 2009 VL 113 IS 52 BP 21949 EP 21955 DI 10.1021/jp9066444 PG 7 WC Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary SC Chemistry; Science & Technology - Other Topics; Materials Science GA 534ZN UT WOS:000272936400067 ER PT J AU Adamson, P Andreopoulos, C Arms, KE Armstrong, R Auty, DJ Ayres, DS Backhouse, C Barnes, PD Barr, G Barrett, WL Becker, BR Belias, A Bernstein, RH Betancourt, M Bhattacharya, D Bishai, M Blake, A Bock, GJ Boehm, J Boehnlein, DJ Bogert, D Bower, C Cavanaugh, S Chapman, JD Cherdack, D Childress, S Choudhary, BC Cobb, JH Coelho, JAB Coleman, SJ Cronin-Hennessy, D Culling, AJ Danko, IZ de Jong, JK Devenish, NE Diwan, MV Dorman, M Erwin, AR Escobar, CO Evans, JJ Falk, E Feldman, GJ Frohne, MV Gallagher, HR Godley, A Goodman, MC Gouffon, P Gran, R Grashorn, EW Grzelak, K Habig, A Harris, D Harris, PG Hartnell, J Hatcher, R Heller, K Himmel, A Holin, A Howcroft, C Huang, X Hylen, J Irwin, GM Isvan, Z Jaffe, DE James, C Jensen, D Kafka, T Kasahara, SMS Koizumi, G Kopp, S Kordosky, M Koskinen, DJ Krahn, Z Kreymer, A Lang, K Ling, J Litchfield, PJ Litchfield, RP Loiacono, L Lucas, P Ma, J Mann, WA Marshak, ML Marshall, JS Mayer, N McGowan, AM Mehdiyev, R Meier, JR Messier, MD Metelko, CJ Michael, DG Miller, WH Mishra, SR Mitchell, J Moore, CD Morfin, J Mualem, L Mufson, S Musser, J Naples, D Nelson, JK Newman, HB Nichol, RJ Nicholls, TC Ochoa-Ricoux, JP Oliver, WP Ospanov, R Paley, J Para, A Patterson, RB Patzak, T Pavlovic, Z Pawloski, G Pearce, GF Petyt, DA Pittam, R Plunkett, RK Rahaman, A Rameika, RA Raufer, TM Rebel, B Reichenbacher, J Rodrigues, PA Rosenfeld, C Rubin, HA Ryabov, VA Sanchez, MC Saoulidou, N Schneps, J Schreiner, P Shanahan, P Smart, W Smith, C Sousa, A Speakman, B Stamoulis, P Strait, M Tagg, N Talaga, RL Thomas, J Thomson, MA Thron, JL Tinti, G Toner, R Tsarev, VA Tzanakos, G Urheim, J Vahle, P Viren, B Ward, DR Watabe, M Weber, A Webb, RC West, N White, C Whitehead, L Wojcicki, SG Wright, DM Yang, T Zhang, K Zheng, H Zois, M Zwaska, R AF Adamson, P. Andreopoulos, C. Arms, K. E. Armstrong, R. Auty, D. J. Ayres, D. S. Backhouse, C. Barnes, P. D., Jr. Barr, G. Barrett, W. L. Becker, B. R. Belias, A. Bernstein, R. H. Betancourt, M. Bhattacharya, D. Bishai, M. Blake, A. Bock, G. J. Boehm, J. Boehnlein, D. J. Bogert, D. Bower, C. Cavanaugh, S. Chapman, J. D. Cherdack, D. Childress, S. Choudhary, B. C. Cobb, J. H. Coelho, J. A. B. Coleman, S. J. Cronin-Hennessy, D. Culling, A. J. Danko, I. Z. de Jong, J. K. Devenish, N. E. Diwan, M. V. Dorman, M. Erwin, A. R. Escobar, C. O. Evans, J. J. Falk, E. Feldman, G. J. Frohne, M. V. Gallagher, H. R. Godley, A. Goodman, M. C. Gouffon, P. Gran, R. Grashorn, E. W. Grzelak, K. Habig, A. Harris, D. Harris, P. G. Hartnell, J. Hatcher, R. Heller, K. Himmel, A. Holin, A. Howcroft, C. Huang, X. Hylen, J. Irwin, G. M. Isvan, Z. Jaffe, D. E. James, C. Jensen, D. Kafka, T. Kasahara, S. M. S. Koizumi, G. Kopp, S. Kordosky, M. Koskinen, D. J. Krahn, Z. Kreymer, A. Lang, K. Ling, J. Litchfield, P. J. Litchfield, R. P. Loiacono, L. Lucas, P. Ma, J. Mann, W. A. Marshak, M. L. Marshall, J. S. Mayer, N. McGowan, A. M. Mehdiyev, R. Meier, J. R. Messier, M. D. Metelko, C. J. Michael, D. G. Miller, W. H. Mishra, S. R. Mitchell, J. Moore, C. D. Morfin, J. Mualem, L. Mufson, S. Musser, J. Naples, D. Nelson, J. K. Newman, H. B. Nichol, R. J. Nicholls, T. C. Ochoa-Ricoux, J. P. Oliver, W. P. Ospanov, R. Paley, J. Para, A. Patterson, R. B. Patzak, T. Pavlovic, Z. Pawloski, G. Pearce, G. F. Petyt, D. A. Pittam, R. Plunkett, R. K. Rahaman, A. Rameika, R. A. Raufer, T. M. Rebel, B. Reichenbacher, J. Rodrigues, P. A. Rosenfeld, C. Rubin, H. A. Ryabov, V. A. Sanchez, M. C. Saoulidou, N. Schneps, J. Schreiner, P. Shanahan, P. Smart, W. Smith, C. Sousa, A. Speakman, B. Stamoulis, P. Strait, M. Tagg, N. Talaga, R. L. Thomas, J. Thomson, M. A. Thron, J. L. Tinti, G. Toner, R. Tsarev, V. A. Tzanakos, G. Urheim, J. Vahle, P. Viren, B. Ward, D. R. Watabe, M. Weber, A. Webb, R. C. West, N. White, C. Whitehead, L. Wojcicki, S. G. Wright, D. M. Yang, T. Zhang, K. Zheng, H. Zois, M. Zwaska, R. CA MINOS Collaboration TI Search for Muon-Neutrino to Electron-Neutrino Transitions in MINOS SO PHYSICAL REVIEW LETTERS LA English DT Article ID GLOBAL ANALYSIS; LEPTON CHARGE; OSCILLATIONS; DETECTOR AB This Letter reports on a search for nu(mu)->nu(e) transitions by the MINOS experiment based on a 3.14x10(20) protons-on-target exposure in the Fermilab NuMI beam. We observe 35 events in the Far Detector with a background of 27 +/- 5(stat)+/- 2(syst) events predicted by the measurements in the Near Detector. If interpreted in terms of nu(mu)->nu(e) oscillations, this 1.5 sigma excess of events is consistent with sin(2)(2 theta(13)) comparable to the CHOOZ limit when |Delta m(2)|=2.43x10(-3) eV(2) and sin(2)(2 theta(23))=1.0 are assumed. C1 [Adamson, P.; Bernstein, R. H.; Bock, G. J.; Boehnlein, D. J.; Bogert, D.; Childress, S.; Choudhary, B. C.; Harris, D.; Hatcher, R.; Hylen, J.; James, C.; Jensen, D.; Koizumi, G.; Kreymer, A.; Lucas, P.; Moore, C. D.; Morfin, J.; Para, A.; Plunkett, R. K.; Rameika, R. A.; Rebel, B.; Saoulidou, N.; Shanahan, P.; Smart, W.; Zwaska, R.] Fermilab Natl Accelerator Lab, Batavia, IL 60510 USA. [Frohne, M. V.; Schreiner, P.] Benedictine Univ, Dept Phys, Lisle, IL 60532 USA. [Bishai, M.; Diwan, M. V.; Jaffe, D. E.; Viren, B.; Whitehead, L.; Zhang, K.] Brookhaven Natl Lab, Upton, NY 11973 USA. [Himmel, A.; Howcroft, C.; Michael, D. G.; Mualem, L.; Newman, H. B.; Ochoa-Ricoux, J. P.; Patterson, R. B.; Zheng, H.] CALTECH, Lauritsen Lab, Pasadena, CA 91125 USA. [Ayres, D. S.; Goodman, M. C.; Huang, X.; McGowan, A. M.; Reichenbacher, J.; Sanchez, M. C.; Talaga, R. L.; Thron, J. L.] Argonne Natl Lab, Argonne, IL 60439 USA. [Stamoulis, P.; Tzanakos, G.; Zois, M.] Univ Athens, Dept Phys, GR-15771 Athens, Greece. [Blake, A.; Chapman, J. D.; Culling, A. J.; Marshall, J. S.; Mitchell, J.; Thomson, M. A.; Toner, R.; Ward, D. R.] Univ Cambridge, Cavendish Lab, Cambridge CB3 0HE, England. [Coelho, J. A. B.; Escobar, C. O.] Univ Estadual Campinas, IFGW UNICAMP, BR-13083970 Campinas, SP, Brazil. [Patzak, T.] Univ Paris 07, APC, F-75205 Paris 13, France. [Boehm, J.; Cavanaugh, S.; Feldman, G. J.; Sanchez, M. C.; Sousa, A.] Harvard Univ, Dept Phys, Cambridge, MA 02138 USA. [Frohne, M. V.] Coll Holy Cross, Notre Dame, IN 46556 USA. [de Jong, J. K.; Rubin, H. A.; White, C.] IIT, Div Phys, Chicago, IL 60616 USA. [Armstrong, R.; Bower, C.; Mayer, N.; Messier, M. D.; Mufson, S.; Musser, J.; Paley, J.; Urheim, J.] Indiana Univ, Bloomington, IN 47405 USA. [Sanchez, M. C.] Iowa State Univ, Dept Phys & Astron, Ames, IA 50011 USA. [Ryabov, V. A.; Tsarev, V. A.] PN Lebedev Phys Inst, Dept Nucl Phys, Moscow 119991, Russia. [Barnes, P. D., Jr.; Wright, D. M.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Dorman, M.; Evans, J. J.; Holin, A.; Kordosky, M.; Koskinen, D. J.; Nichol, R. J.; Smith, C.; Thomas, J.; Vahle, P.] UCL, Dept Phys & Astron, London WC1E 6BT, England. [Arms, K. E.; Becker, B. R.; Betancourt, M.; Cronin-Hennessy, D.; Grashorn, E. W.; Heller, K.; Kasahara, S. M. S.; Krahn, Z.; Litchfield, P. J.; Marshak, M. L.; McGowan, A. M.; Meier, J. R.; Miller, W. H.; Petyt, D. A.; Speakman, B.; Strait, M.] Univ Minnesota, Minneapolis, MN 55455 USA. [Gran, R.; Habig, A.] Univ Minnesota, Dept Phys, Duluth, MN 55812 USA. [Tagg, N.] Otterbein Coll, Westerville, OH 43081 USA. [Backhouse, C.; Barr, G.; Cobb, J. H.; de Jong, J. K.; Evans, J. J.; Grzelak, K.; Litchfield, R. P.; Pittam, R.; Rodrigues, P. A.; Sousa, A.; Tinti, G.; Weber, A.; West, N.] Univ Oxford, Subdept Particle Phys, Oxford OX1 3RH, England. [Bhattacharya, D.; Danko, I. Z.; Isvan, Z.; Naples, D.] Univ Pittsburgh, Dept Phys & Astron, Pittsburgh, PA 15260 USA. [Andreopoulos, C.; Belias, A.; Dorman, M.; Hartnell, J.; Metelko, C. J.; Nicholls, T. C.; Pearce, G. F.; Raufer, T. M.] Rutherford Appleton Lab, Sci & Technol Facil Council, Didcot OX11 0QX, Oxon, England. [Gouffon, P.] Univ Sao Paulo, Inst Fis, BR-05315970 Sao Paulo, Brazil. [Godley, A.; Ling, J.; Mishra, S. R.; Rahaman, A.; Rosenfeld, C.] Univ S Carolina, Dept Phys & Astron, Columbia, SC 29208 USA. [Irwin, G. M.; Pawloski, G.; Wojcicki, S. G.; Yang, T.] Stanford Univ, Dept Phys, Stanford, CA 94305 USA. [Auty, D. J.; Devenish, N. E.; Falk, E.; Harris, P. G.; Hartnell, J.] Univ Sussex, Dept Phys & Astron, Brighton BN1 9QH, E Sussex, England. [Watabe, M.; Webb, R. C.] Texas A&M Univ, Dept Phys, College Stn, TX 77843 USA. [Kopp, S.; Lang, K.; Loiacono, L.; Ma, J.; Mehdiyev, R.; Ospanov, R.; Pavlovic, Z.] Univ Texas Austin, Dept Phys, Austin, TX 78712 USA. [Cherdack, D.; Gallagher, H. R.; Kafka, T.; Mann, W. A.; Oliver, W. P.; Schneps, J.; Tagg, N.] Tufts Univ, Dept Phys, Medford, MA 02155 USA. [Grzelak, K.] Univ Warsaw, Dept Phys, PL-00681 Warsaw, Poland. [Barrett, W. L.] Western Washington Univ, Dept Phys, Bellingham, WA 98225 USA. [Coleman, S. J.; Kordosky, M.; Nelson, J. K.; Vahle, P.] Coll William & Mary, Dept Phys, Williamsburg, VA 23187 USA. [Erwin, A. R.] Univ Wisconsin, Dept Phys, Madison, WI 53706 USA. RP Adamson, P (reprint author), Fermilab Natl Accelerator Lab, POB 500, Batavia, IL 60510 USA. RI Nichol, Ryan/C-1645-2008; Harris, Philip/I-7419-2012; Coelho, Joao/D-3546-2013; Tinti, Gemma/I-5886-2013; Ryabov, Vladimir/E-1281-2014; Koskinen, David/G-3236-2014; Evans, Justin/P-4981-2014; Gouffon, Philippe/I-4549-2012; Ling, Jiajie/I-9173-2014; Inst. of Physics, Gleb Wataghin/A-9780-2017; OI Hartnell, Jeffrey/0000-0002-1744-7955; Bernstein, Robert/0000-0002-7610-950X; Cherdack, Daniel/0000-0002-3829-728X; Weber, Alfons/0000-0002-8222-6681; Ochoa-Ricoux, Juan Pedro/0000-0001-7376-5555; Harris, Philip/0000-0003-4369-3874; Koskinen, David/0000-0002-0514-5917; Evans, Justin/0000-0003-4697-3337; Gouffon, Philippe/0000-0001-7511-4115; Ling, Jiajie/0000-0003-2982-0670; COLEMAN, STEPHEN/0000-0002-4621-9169 FU US DOE; UK STFC; US NSF; State and University of Minnesota; University of Athens, Greece; Brazil's FAPESP; CNPq FX This work was supported by the US DOE; the UK STFC; the US NSF; the State and University of Minnesota; the University of Athens, Greece; and Brazil's FAPESP and CNPq. We are grateful to the Minnesota Department of Natural Resources, the crew of the Soudan Underground Laboratory, and the staff of Fermilab for their contribution to this effort. NR 31 TC 41 Z9 41 U1 0 U2 18 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 31 PY 2009 VL 103 IS 26 AR 261802 DI 10.1103/PhysRevLett.103.261802 PG 5 WC Physics, Multidisciplinary SC Physics GA 539CY UT WOS:000273232200009 PM 20366304 ER PT J AU Asakawa, M Ejiri, S Kitazawa, M AF Asakawa, Masayuki Ejiri, Shinji Kitazawa, Masakiyo TI Third Moments of Conserved Charges as Probes of QCD Phase Structure SO PHYSICAL REVIEW LETTERS LA English DT Article ID QUARK-GLUON PLASMA; FLUCTUATIONS; COLLABORATION; PERSPECTIVE; COLLISIONS AB The third moments of conserved charges, the baryon and electric charge numbers, and energy, as well as their mixed moments, carry more information on the state around the QCD phase boundary than previously proposed fluctuation observables and higher order moments. In particular, their signs give plenty of information on the location of the state created in relativistic heavy ion collisions in the temperature and baryon chemical potential plane. We demonstrate this with an effective model. C1 [Asakawa, Masayuki; Kitazawa, Masakiyo] Osaka Univ, Dept Phys, Osaka 5600043, Japan. [Ejiri, Shinji] Brookhaven Natl Lab, Dept Phys, Upton, NY 11973 USA. RP Asakawa, M (reprint author), Osaka Univ, Dept Phys, Osaka 5600043, Japan. EM yuki@phys.sci.osaka-u.ac.jp; ejiri@quark.phy.bnl.gov; kitazawa@phys.sci.osaka-u.ac.jp FU Monbu-Kagakusyo of Japan [19840037, 20540268]; U.S. Department of Energy [DE-AC02-98CH10886] FX This work is supported in part by a Grant-in-Aid for Scientific Research by Monbu-Kagakusyo of Japan (No. 19840037 and 20540268) and the U.S. Department of Energy (No. DE-AC02-98CH10886). NR 29 TC 95 Z9 95 U1 0 U2 1 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 31 PY 2009 VL 103 IS 26 AR 262301 DI 10.1103/PhysRevLett.103.262301 PG 4 WC Physics, Multidisciplinary SC Physics GA 539CY UT WOS:000273232200012 PM 20366307 ER PT J AU Bai, Y Carena, M Lykken, J AF Bai, Yang Carena, Marcela Lykken, Joseph TI Dilaton-Assisted Dark Matter SO PHYSICAL REVIEW LETTERS LA English DT Article AB A dilaton could be the dominant messenger between standard model fields and dark matter. The measured dark matter relic abundance relates the dark matter mass and spin to the conformal breaking scale. The dark matter-nucleon spin-independent cross section is predicted in terms of the dilaton mass. We compute the current constraints on the dilaton from LEP and Tevatron experiments, and the gamma-ray signal from dark matter annihilation to dilatons that could be observed by Fermi Large Area Telescope. C1 [Bai, Yang; Carena, Marcela; Lykken, Joseph] Dept Theoret Phys, Fermilab, Batavia, IL 60510 USA. [Carena, Marcela] Univ Chicago, Enrico Fermi Inst, Chicago, IL 60637 USA. RP Bai, Y (reprint author), Dept Theoret Phys, Fermilab, Batavia, IL 60510 USA. FU U.S. Department of Energy [DE-AC02-07CH11359] FX We thank Tom Appelquist, Bill Bardeen, and Paddy Fox for interesting discussions. We also thank the Aspen Center for Physics where part of this work was finished. Fermilab is operated by Fermi Research Alliance, LLC under Contract no. DE-AC02-07CH11359 with the U.S. Department of Energy. NR 22 TC 22 Z9 22 U1 1 U2 1 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 EI 1079-7114 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 31 PY 2009 VL 103 IS 26 AR 261803 DI 10.1103/PhysRevLett.103.261803 PG 4 WC Physics, Multidisciplinary SC Physics GA 539CY UT WOS:000273232200010 PM 20366305 ER PT J AU Dudek, JJ Edwards, RG Peardon, MJ Richards, DG Thomas, CE AF Dudek, Jozef J. Edwards, Robert G. Peardon, Michael J. Richards, David G. Thomas, Christopher E. CA Hadron Spectrum Collaboration TI Highly Excited and Exotic Meson Spectrum from Dynamical Lattice QCD SO PHYSICAL REVIEW LETTERS LA English DT Article AB Using a new quark-field construction algorithm and a large variational basis of operators, we extract a highly excited isovector meson spectrum on dynamical anisotropic lattices. We show how carefully constructed operators can be used to reliably identify the continuum spin of extracted states, overcoming the reduced cubic symmetry of the lattice. Using this method we extract, with confidence, excited states, states with exotic quantum numbers (0(+-), 1(-+), and 2(+-)), and states of high spin, including, for the first time in lattice QCD, spin-four states. C1 [Dudek, Jozef J.; Edwards, Robert G.; Richards, David G.; Thomas, Christopher E.] Jefferson Lab, Newport News, VA 23606 USA. [Dudek, Jozef J.] Old Dominion Univ, Dept Phys, Norfolk, VA 23529 USA. [Peardon, Michael J.] Trinity Coll Dublin, Sch Math, Dublin 2, Ireland. RP Dudek, JJ (reprint author), Jefferson Lab, 12000 Jefferson Ave, Newport News, VA 23606 USA. EM dudek@jlab.org OI Peardon, Michael/0000-0002-4199-6284 FU U.S. DOE [DE-AC05-06OR23177] FX We thank our colleagues within the Hadron Spectrum Collaboration. The CHROMA software suite [9] was used to perform this work on clusters at Jefferson Laboratory using time awarded under the USQCD Initiative. Authored by Jefferson Science Associates, LLC under U.S. DOE Contract No. DE-AC05-06OR23177. NR 9 TC 94 Z9 94 U1 0 U2 5 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 31 PY 2009 VL 103 IS 26 AR 262001 DI 10.1103/PhysRevLett.103.262001 PG 4 WC Physics, Multidisciplinary SC Physics GA 539CY UT WOS:000273232200011 PM 20366306 ER PT J AU Giovannetti, G Kumar, S Stroppa, A van den Brink, J Picozzi, S AF Giovannetti, Gianluca Kumar, Sanjeev Stroppa, Alessandro van den Brink, Jeroen Picozzi, Silvia TI Multiferroicity in TTF-CA Organic Molecular Crystals Predicted through Ab Initio Calculations SO PHYSICAL REVIEW LETTERS LA English DT Article ID IONIC PHASE-TRANSITION; TOTAL-ENERGY CALCULATIONS; WAVE BASIS-SET; HUBBARD-MODEL; TETRATHIAFULVALENE-CHLORANIL; DENSITY FUNCTIONALS; DIELECTRIC RESPONSE; COULOMB INTERACTION; CHARGE; SYSTEMS AB We show by means of ab initio calculations that the organic molecular crystal TTF-CA is multiferroic: it has an instability to develop spontaneously both ferroelectric and magnetic ordering. Ferroelectricity is driven by a Peierls transition of the TTF-CA in its ionic state. Subsequent antiferromagnetic ordering strongly enhances the opposing electronic contribution to the polarization. It is so large that it switches the direction of the total ferroelectric moment. Within an extended Hubbard model, we capture the essence of the electronic interactions in TTF-CA, confirm the presence of a multiferroic groundstate, and clarify how this state develops microscopically. C1 [Giovannetti, Gianluca; Stroppa, Alessandro; Picozzi, Silvia] CNR, INFM, CASTI Reg Lab, I-67100 Laquila, Italy. [Kumar, Sanjeev] Univ Twente, Fac Sci & Technol, NL-7500 AE Enschede, Netherlands. [Kumar, Sanjeev] Univ Twente, MESA Res Inst, NL-7500 AE Enschede, Netherlands. [Kumar, Sanjeev; van den Brink, Jeroen] Leiden Univ, Inst Lorentz Theoret Phys, Leiden, Netherlands. [van den Brink, Jeroen] Stanford Univ, Stanford Inst Mat & Energy Sci, Menlo Pk, CA USA. [van den Brink, Jeroen] SLAC, Menlo Pk, CA USA. [van den Brink, Jeroen] Radboud Univ Nijmegen, Inst Mol & Mat, NL-6525 ED Nijmegen, Netherlands. [van den Brink, Jeroen] Leibniz Inst Solid State & Mat Res Dresden, D-01171 Dresden, Germany. RP Giovannetti, G (reprint author), CNR, INFM, CASTI Reg Lab, I-67100 Laquila, Italy. RI van den Brink, Jeroen/E-5670-2011; Stroppa, Alessandro/E-7702-2010; Picozzi, Silvia/E-2374-2011; Giovannetti, Gianluca/L-4339-2013 OI van den Brink, Jeroen/0000-0001-6594-9610; Stroppa, Alessandro/0000-0003-1000-4745; Picozzi, Silvia/0000-0002-3232-788X; FU European Research Council under the European Community [FP7/2007-2013)/ERC,]; NanoNed [203523]; FOM FX The research leading to part of these results has received funding from the European Research Council under the European Community 7th Framework Program (FP7/2007-2013)/ERC, Grant Agreement No. 203523, from NanoNed and FOM. The authors acknowledge G. Kresse for carefully reading the manuscript. NR 51 TC 49 Z9 49 U1 2 U2 30 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 31 PY 2009 VL 103 IS 26 AR 266401 DI 10.1103/PhysRevLett.103.266401 PG 4 WC Physics, Multidisciplinary SC Physics GA 539CY UT WOS:000273232200030 ER PT J AU Lee, CC Yin, WG Ku, W AF Lee, Chi-Cheng Yin, Wei-Guo Ku, Wei TI Ferro-Orbital Order and Strong Magnetic Anisotropy in the Parent Compounds of Iron-Pnictide Superconductors SO PHYSICAL REVIEW LETTERS LA English DT Article AB The puzzling nature of magnetic and lattice phase transitions of iron pnictides is investigated via a first-principles Wannier function analysis of representative parent compound LaOFeAs. A rare ferro-orbital ordering is found to give rise to the recently observed highly anisotropic magnetic coupling, and drive both phase transitions-without resorting to widely employed frustration or nesting picture. The revealed necessity of the additional orbital physics leads to a correlated electronic structure fundamentally distinct from that of the cuprates. In particular, the strong coupling to the magnons advocates active roles of light orbitons in spin dynamics and electron pairing in iron pnictides. C1 [Lee, Chi-Cheng; Yin, Wei-Guo; Ku, Wei] Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. [Ku, Wei] SUNY Stony Brook, Dept Phys, Stony Brook, NY 11790 USA. RP Lee, CC (reprint author), Brookhaven Natl Lab, Condensed Matter Phys & Mat Sci Dept, Upton, NY 11973 USA. RI Yin, Weiguo/A-9671-2014; Lee, Chi-Cheng/F-5057-2015 OI Yin, Weiguo/0000-0002-4965-5329; Lee, Chi-Cheng/0000-0002-3895-9802 FU U.S. Department of Energy, Office of Basic Energy Science [DE-AC02-98CH10886]; DOE-CMSN FX This work was supported by the U.S. Department of Energy, Office of Basic Energy Science, under Contract No. DE-AC02-98CH10886, and DOE-CMSN. NR 29 TC 256 Z9 256 U1 5 U2 48 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 31 PY 2009 VL 103 IS 26 AR 267001 DI 10.1103/PhysRevLett.103.267001 PG 4 WC Physics, Multidisciplinary SC Physics GA 539CY UT WOS:000273232200041 PM 20366336 ER PT J AU Waite, WF Santamarina, JC Cortes, DD Dugan, B Espinoza, DN Germaine, J Jang, J Jung, JW Kneafsey, TJ Shin, H Soga, K Winters, WJ Yun, TS AF Waite, W. F. Santamarina, J. C. Cortes, D. D. Dugan, B. Espinoza, D. N. Germaine, J. Jang, J. Jung, J. W. Kneafsey, T. J. Shin, H. Soga, K. Winters, W. J. Yun, T-S. TI PHYSICAL PROPERTIES OF HYDRATE-BEARING SEDIMENTS SO REVIEWS OF GEOPHYSICS LA English DT Review ID GULF-OF-MEXICO; BOTTOM-SIMULATING REFLECTOR; RAY COMPUTED-TOMOGRAPHY; CARBON-DIOXIDE HYDRATE; HEAT-FLOW CALORIMETER; 2L-38 RESEARCH WELL; SI METHANE HYDRATE; GAS-HYDRATE; SEA-FLOOR; THERMAL-CONDUCTIVITY AB Methane gas hydrates, crystalline inclusion compounds formed from methane and water, are found in marine continental margin and permafrost sediments worldwide. This article reviews the current understanding of phenomena involved in gas hydrate formation and the physical properties of hydrate-bearing sediments. Formation phenomena include pore-scale habit, solubility, spatial variability, and host sediment aggregate properties. Physical properties include thermal properties, permeability, electrical conductivity and permittivity, small-strain elastic P and S wave velocities, shear strength, and volume changes resulting from hydrate dissociation. The magnitudes and interdependencies of these properties are critically important for predicting and quantifying macroscale responses of hydrate-bearing sediments to changes in mechanical, thermal, or chemical boundary conditions. These predictions are vital for mitigating borehole, local, and regional slope stability hazards; optimizing recovery techniques for extracting methane from hydrate-bearing sediments or sequestering carbon dioxide in gas hydrate; and evaluating the role of gas hydrate in the global carbon cycle. C1 [Waite, W. F.; Winters, W. J.] US Geol Survey, Woods Hole, MA 02543 USA. [Santamarina, J. C.; Cortes, D. D.; Espinoza, D. N.; Jang, J.; Jung, J. W.; Shin, H.] Georgia Inst Technol, Sch Civil & Environm Engn, Atlanta, GA 30332 USA. [Dugan, B.] Rice Univ, Dept Earth Sci, Houston, TX 77005 USA. [Germaine, J.] MIT, Dept Civil & Environm Engn, Cambridge, MA 02139 USA. [Kneafsey, T. J.] Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA. [Soga, K.] Univ Cambridge, Dept Engn, Cambridge CB2 1PZ, England. [Yun, T-S.] Yonsei Univ, Sch Civil & Environm Engn, Seoul 120749, South Korea. RP Waite, WF (reprint author), US Geol Survey, 384 Woods Hole Rd, Woods Hole, MA 02543 USA. EM wwaite@usgs.gov RI Dugan, Brandon/A-2651-2011; Yun, Tae Sup/G-7988-2012; Cortes, Douglas/A-7879-2013; Kneafsey, Timothy/H-7412-2014; Espinoza, D. Nicolas/E-3764-2016; OI Dugan, Brandon/0000-0002-2555-6430; Kneafsey, Timothy/0000-0002-3926-8587; Espinoza, D. Nicolas/0000-0002-3418-0180; Waite, William/0000-0002-9436-4109; Jang, Jaewon/0000-0002-9749-4072 NR 326 TC 157 Z9 172 U1 16 U2 104 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 8755-1209 EI 1944-9208 J9 REV GEOPHYS JI Rev. Geophys. PD DEC 31 PY 2009 VL 47 AR RG4003 DI 10.1029/2008RG000279 PG 38 WC Geochemistry & Geophysics SC Geochemistry & Geophysics GA 539MT UT WOS:000273259500001 ER PT J AU Jain, R Srivastava, R AF Jain, Rishi Srivastava, Ranjan TI Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli SO BMC SYSTEMS BIOLOGY LA English DT Article ID GENOME-SCALE; DRUG DISCOVERY; OBJECTIVE FUNCTIONS; RNA BACTERIOPHAGE; PROTEIN SYNTHESIS; PARTICLES; PHAGE; GROWTH; MS2; RECONSTRUCTION AB Background: RNA viruses are responsible for a variety of illnesses among people, including but not limited to the common cold, the flu, HIV, and ebola. Developing new drugs and new strategies for treating diseases caused by these viruses can be an expensive and time-consuming process. Mathematical modeling may be used to elucidate host-pathogen interactions and highlight potential targets for drug development, as well providing the basis for optimizing patient treatment strategies. The purpose of this work was to determine whether a genome-scale modeling approach could be used to understand how metabolism is impacted by the host-pathogen interaction during a viral infection. Escherichia coli/MS2 was used as the host-pathogen model system as MS2 is easy to work with, harmless to humans, but shares many features with eukaryotic viruses. In addition, the genome-scale metabolic model of E. coli is the most comprehensive model at this time. Results: Employing a metabolic modeling strategy known as "flux balance analysis" coupled with experimental studies, we were able to predict how viral infection would alter bacterial metabolism. Based on our simulations, we predicted that cell growth and biosynthesis of the cell wall would be halted. Furthermore, we predicted a substantial increase in metabolic activity of the pentose phosphate pathway as a means to enhance viral biosynthesis, while a break down in the citric acid cycle was predicted. Also, no changes were predicted in the glycolytic pathway. Conclusions: Through our approach, we have developed a technique of modeling virus-infected host metabolism and have investigated the metabolic effects of viral infection. These studies may provide insight into how to design better drugs. They also illustrate the potential of extending such metabolic analysis to higher order organisms, including humans. C1 [Jain, Rishi; Srivastava, Ranjan] Univ Connecticut, Dept Chem Mat & Biomol Engn, Storrs, CT 06269 USA. [Jain, Rishi] Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA. RP Srivastava, R (reprint author), Univ Connecticut, Dept Chem Mat & Biomol Engn, Storrs, CT 06269 USA. EM jainr@ornl.gov; srivasta@engr.uconn.edu FU NIH [1R03LM009753-01] FX Support for this work was provided by NIH Grant 1R03LM009753-01. NR 35 TC 12 Z9 12 U1 0 U2 12 PU BIOMED CENTRAL LTD PI LONDON PA 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND SN 1752-0509 J9 BMC SYST BIOL JI BMC Syst. Biol. PD DEC 30 PY 2009 VL 3 AR 121 DI 10.1186/1752-0509-3-121 PG 11 WC Mathematical & Computational Biology SC Mathematical & Computational Biology GA 549TR UT WOS:000274077700001 PM 20042079 ER PT J AU Huang, D Johnson, K Liu, Y Wiscombe, W AF Huang, Dong Johnson, Karen Liu, Yangang Wiscombe, Warren TI High resolution retrieval of liquid water vertical distributions using collocated Ka-band and W-band cloud radars SO GEOPHYSICAL RESEARCH LETTERS LA English DT Article ID DUAL-WAVELENGTH RADAR; MICROWAVE RADIOMETER; STRATUS CLOUD AB The retrieval of cloud water content using dualfrequency radar attenuation is very sensitive to error in radar reflectivity. Either a long radar dwell time or an average over many range gates is needed to reduce random noise in radar data and thus to obtain accurate retrievals but at the cost of poorer temporal and spatial resolution. In this letter we have shown that, by using advanced mathematical inversion techniques like total variation regularization, vertically resolved liquid water content can be retrieved at an accuracy of about 0.15 gm(-3) at 40 m resolution. This is demonstrated using the co-located Ka-band and W-band cloud radars operated by the Atmospheric Radiation Measurement program. The liquid water path calculated from the radars agrees closely with that from a microwave radiometer, with a mean difference of 70 gm(-2). Comparison with lidar observations reveals that the dual-frequency retrieval also reasonably captures the cloud base height of drizzling clouds-something that is very difficult to determine from radar reflectivity alone. Citation: Huang, D., K. Johnson, Y. Liu, and W. Wiscombe (2009), High resolution retrieval of liquid water vertical distributions using collocated Ka-band and W-band cloud radars, Geophys. Res. Lett., 36, L24807, doi:10.1029/2009GL041364. C1 [Huang, Dong; Johnson, Karen; Liu, Yangang; Wiscombe, Warren] Brookhaven Natl Lab, Upton, NY 11973 USA. [Wiscombe, Warren] NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA. RP Huang, D (reprint author), Brookhaven Natl Lab, 75 Rutherford Dr, Upton, NY 11973 USA. EM dhuang@bnl.gov RI Liu, Yangang/H-6154-2011; Wiscombe, Warren/D-4665-2012; Huang, Dong/H-7318-2014 OI Wiscombe, Warren/0000-0001-6844-9849; Huang, Dong/0000-0001-9715-6922 FU DOE [DE- AC0298CH10886] FX This work is supported by the DOE Atmosphere Radiation Measurement program under contract DE- AC0298CH10886. We thank Robin Hogan, Pavlos Kollias, and Michael Jensen for insightful discussions. We are grateful to Virendra Ghate for providing the non- precipitating cloud cases. NR 25 TC 4 Z9 4 U1 3 U2 7 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0094-8276 J9 GEOPHYS RES LETT JI Geophys. Res. Lett. PD DEC 30 PY 2009 VL 36 AR L24807 DI 10.1029/2009GL041364 PG 6 WC Geosciences, Multidisciplinary SC Geology GA 539LB UT WOS:000273254700002 ER PT J AU Jain, A Yang, XJ Kheshgi, H McGuire, AD Post, W Kicklighter, D AF Jain, Atul Yang, Xiaojuan Kheshgi, Haroon McGuire, A. David Post, Wilfred Kicklighter, David TI Nitrogen attenuation of terrestrial carbon cycle response to global environmental factors SO GLOBAL BIOGEOCHEMICAL CYCLES LA English DT Article ID NET PRIMARY PRODUCTIVITY; LAND-USE; CLIMATE-CHANGE; ELEVATED CO2; MODEL; ECOSYSTEMS; DEPOSITION; SOIL; BIOSPHERE; PATTERNS AB Nitrogen cycle dynamics have the capacity to attenuate the magnitude of global terrestrial carbon sinks and sources driven by CO2 fertilization and changes in climate. In this study, two versions of the terrestrial carbon and nitrogen cycle components of the Integrated Science Assessment Model (ISAM) are used to evaluate how variation in nitrogen availability influences terrestrial carbon sinks and sources in response to changes over the 20th century in global environmental factors including atmospheric CO2 concentration, nitrogen inputs, temperature, precipitation and land use. The two versions of ISAM vary in their treatment of nitrogen availability: ISAM-NC has a terrestrial carbon cycle model coupled to a fully dynamic nitrogen cycle while ISAM-C has an identical carbon cycle model but nitrogen availability is always in sufficient supply. Overall, the two versions of the model estimate approximately the same amount of global mean carbon uptake over the 20th century. However, comparisons of results of ISAM-NC relative to ISAM-C reveal that nitrogen dynamics: (1) reduced the 1990s carbon sink associated with increasing atmospheric CO2 by 0.53 PgC yr(-1) (1 Pg = 10(15) g), (2) reduced the 1990s carbon source associated with changes in temperature and precipitation of 0.34 PgC yr(-1) in the 1990s, (3) an enhanced sink associated with nitrogen inputs by 0.26 PgC yr(-1), and (4) enhanced the 1990s carbon source associated with changes in land use by 0.08 PgC yr(-1) in the 1990s. These effects of nitrogen limitation influenced the spatial distribution of the estimated exchange of CO2 with greater sink activity in high latitudes associated with climate effects and a smaller sink of CO2 in the southeastern United States caused by N limitation associated with both CO2 fertilization and forest regrowth. These results indicate that the dynamics of nitrogen availability are important to consider in assessing the spatial distribution and temporal dynamics of terrestrial carbon sources and sinks. C1 [Jain, Atul; Yang, Xiaojuan] Univ Illinois, Dept Atmospher Sci, Urbana, IL 61801 USA. [Kheshgi, Haroon] ExxonMobil Res & Engn Co, Annandale, NJ 08801 USA. [Kicklighter, David] Marine Biol Lab, Woods Hole, MA 02543 USA. [McGuire, A. David] Univ Alaska Fairbanks, US Geol Survey, Alaska Cooperat Fish & Wildlife Res Unit, Fairbanks, AK 99775 USA. [Post, Wilfred] Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA. RP Jain, A (reprint author), Univ Illinois, Dept Atmospher Sci, 105 S Gregory Ave, Urbana, IL 61801 USA. EM jain1@uiuc.edu RI Post, Wilfred/B-8959-2012; Yang, Xiaojuan/I-3643-2016; Jain, Atul/D-2851-2016 OI Yang, Xiaojuan/0000-0002-2686-745X; Jain, Atul/0000-0002-4051-3228 FU National Aeronautics and Space Administration Land Cover and Land Use Change Program [NNX08AK75G] FX We acknowledge Victoria Wittig and Daniel Hayes whose comments led to significant improvements in this manuscript. We thank F. Dentener for providing us the N deposition data. We also acknowledge the financial support of the National Aeronautics and Space Administration Land Cover and Land Use Change Program(NNX08AK75G). NR 60 TC 56 Z9 57 U1 1 U2 33 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0886-6236 J9 GLOBAL BIOGEOCHEM CY JI Glob. Biogeochem. Cycle PD DEC 30 PY 2009 VL 23 AR GB4028 DI 10.1029/2009GB003519 PG 13 WC Environmental Sciences; Geosciences, Multidisciplinary; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Geology; Meteorology & Atmospheric Sciences GA 539LG UT WOS:000273255300003 ER PT J AU Yang, XJ Wittig, V Jain, AK Post, W AF Yang, Xiaojuan Wittig, Victoria Jain, Atul K. Post, Wilfred TI Integration of nitrogen cycle dynamics into the Integrated Science Assessment Model for the study of terrestrial ecosystem responses to global change SO GLOBAL BIOGEOCHEMICAL CYCLES LA English DT Article ID ATMOSPHERIC CARBON-DIOXIDE; NET PRIMARY PRODUCTIVITY; ELEVATED CO2; CLIMATE-CHANGE; LITTER DECOMPOSITION; ORGANIC-CARBON; TEMPERATE FOREST; FACE EXPERIMENTS; SOIL CARBON; LEAF-LITTER AB A comprehensive model of terrestrial N dynamics has been developed and coupled with the geographically explicit terrestrial C cycle component of the Integrated Science Assessment Model (ISAM). The coupled C-N cycle model represents all the major processes in the N cycle and all major interactions between C and N that affect plant productivity and soil and litter decomposition. Observations from the LIDET data set were compiled for calibration and evaluation of the decomposition submodel within ISAM. For aboveground decomposition, the calibration is accomplished by optimizing parameters related to four processes: the partitioning of leaf litter between metabolic and structural material, the effect of lignin on decomposition, the climate control on decomposition and N mineralization and immobilization. For belowground decomposition, the calibrated processes include the partitioning of root litter between decomposable and resistant material as a function of litter quality, N mineralization and immobilization. The calibrated model successfully captured both the C and N dynamics during decomposition for all major biomes and a wide range of climate conditions. Model results show that net N immobilization and mineralization during litter decomposition are dominantly controlled by initial N concentration of litter and the mass remaining during decomposition. The highest and lowest soil organic N storage are in tundra (1.24 Kg N m(-2)) and desert soil (0.06 Kg N m(-2)). The vegetation N storage is highest in tropical forests (0.5 Kg N m(-2)), and lowest in tundra and desert (<0.03 Kg N m(-2)). N uptake by vegetation is highest in warm and moist regions, and lowest in cold and dry regions. Higher rates of N leaching are found in tropical regions and subtropical regions where soil moisture is higher. The global patterns of vegetation and soil N, N uptake and N leaching estimated with ISAM are consistent with measurements and previous modeling studies. This gives us confidence that ISAM framework can predict plant N availability and subsequent plant productivity at regional and global scales and furthermore how they can be affected by factors that alter the rate of decomposition, such as increasing atmospheric [CO(2)], climate changes, litter quality, soil microbial activity and/or increased N. C1 [Yang, Xiaojuan; Wittig, Victoria; Jain, Atul K.] Univ Illinois, Dept Atmospher Sci, Urbana, IL 61801 USA. [Post, Wilfred] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Yang, XJ (reprint author), Univ Illinois, Dept Atmospher Sci, 105 S Gregory Ave, Urbana, IL 61801 USA. EM jain1@uiuc.edu RI Post, Wilfred/B-8959-2012; Yang, Xiaojuan/I-3643-2016; Jain, Atul/D-2851-2016 OI Yang, Xiaojuan/0000-0002-2686-745X; Jain, Atul/0000-0002-4051-3228 FU U.S. National Aeronautics and Space Administration Land Cover and Land Use Change Program [NNX08AK75G]; Office of Science, U.S. Department of Energy [DOE DE-FG02-06ER64195]; Energy Biosciences Institute, University of Illinois FX This research is supported in part by the U.S. National Aeronautics and Space Administration Land Cover and Land Use Change Program (NNX08AK75G), the Office of Science, U.S. Department of Energy (DOE DE-FG02-06ER64195), and Energy Biosciences Institute, University of Illinois. NR 97 TC 41 Z9 44 U1 3 U2 33 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0886-6236 J9 GLOBAL BIOGEOCHEM CY JI Glob. Biogeochem. Cycle PD DEC 30 PY 2009 VL 23 AR GB4029 DI 10.1029/2009GB003474 PG 18 WC Environmental Sciences; Geosciences, Multidisciplinary; Meteorology & Atmospheric Sciences SC Environmental Sciences & Ecology; Geology; Meteorology & Atmospheric Sciences GA 539LG UT WOS:000273255300002 ER PT J AU Anick, DJ Leung, K AF Anick, David J. Leung, Kevin TI Transition states for hydride-water (H-)(H2O)n clusters, n=2-6, 20 SO JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM LA English DT Article DE Hydride; Water cluster; Dodecahedral cage; AIMD; Laage-Hynes move ID TERAHERTZ LASER SPECTROSCOPY; 1ST PRINCIPLES SIMULATIONS; DENSITY-FUNCTIONAL THEORY; AUGMENTED-WAVE METHOD; AB-INITIO; LITHIUM HYDRIDE; ISOTOPIC EXCHANGE; DIHYDROGEN BONDS; PROTON-TRANSFER; REACTION PATHS AB Hydride anion (H-) reacts quickly in aqueous solution to form molecular hydrogen (H-2) and hydroxide ion (OH-), but (H-)(H2O) clusters have many PES local minima in which the hydride is solvated by two or more water molecules making dihydrogen bonds. Using ab initio methods applied to (H-)(H2O), clusters for n <= 6 and for n = 20, we explored these clusters' reaction pathways and transition states. At the B3LYP/6-311++G** level of theory, all of the small (2 <= n <= 6) clusters are unstable or barely stable at 0 K: all activation barriers for reaction to form H-2 are under 0.5 kcal/mol, all but one are under 0.2 kcal/mol, and most are negative. In some instances the lowest-barrier reaction pathway is multi-step, requiring H-bond rearrangements first, and those rearrangements are consistent with improving the "presolvation" of the emerging (OH-) in accordance with a "solvation hierarchy." The arrangements explored for n = 20 consist of (H-) encapsulated by a dodecahedral cage with coordination of 3, 4, 5, or 6 at the hydride anion. The lowest-energy (H-)(H2O)(20) cluster found has 4 H-bonds to the anion. Of several reaction pathways explored, the lowest barrier height is 3,68 kcal/mol at 0 K, suggesting that a low-temperature stable solvated hydride can exist. For the (H-)(H2O)(20) Clusters at their transition states to H-2 formation, the H--H distances are at or below the van der Waals cutoff for covalent H-H bonding (92 pm). In all, 21 transition states to (H-2)(OH-)(H2O)(n-1) and eight H-bond rearranging transition states are presented. During a 25 ps AND simulation of H- in a box of 32 H2O's at 300 K, reaction to form H-2 did not occur, the hydride ion spent 95% of the time being 4-coordinated, and two first-shell exchanges were observed. This and other calculations suggest the mean survival time of (H-) in bulk water at 300 K is likely between 20 and 100 ps. (C) 2009 Elsevier B.V. All rights reserved. C1 [Anick, David J.] Harvard Univ, Sch Med, Belmont, MA 02478 USA. [Leung, Kevin] Sandia Natl Labs, Albuquerque, NM 87185 USA. RP Anick, DJ (reprint author), Harvard Univ, Sch Med, 115 Mill St, Belmont, MA 02478 USA. EM david.anick@rcn.com FU Department of Energy [DE-AC04-94AL85000]; U.S. Department of Energy FX Kevin Leung was supported by the Department of Energy under Contract DE-AC04-94AL85000. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the U.S. Department of Energy. NR 66 TC 2 Z9 2 U1 2 U2 8 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0166-1280 J9 J MOL STRUC-THEOCHEM JI Theochem-J. Mol. Struct. PD DEC 30 PY 2009 VL 916 IS 1-3 BP 61 EP 71 DI 10.1016/j.theochem.2009.09.012 PG 11 WC Chemistry, Physical SC Chemistry GA 526AH UT WOS:000272259400010 ER PT J AU Feng, ZX Kim, CY Elam, JW Ma, Q Zhang, Z Bedzyk, MJ AF Feng, Zhenxing Kim, Chang-Yong Elam, Jeffrey W. Ma, Qing Zhang, Zhan Bedzyk, Michael J. TI Direct Atomic-Scale Observation of Redox-Induced Cation Dynamics in an Oxide-Supported Monolayer Catalyst: WOx/alpha-Fe2O3(0001) SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID RAY STANDING WAVES; SURFACE AB For the case of one-third of a monolayer of tungsten grown by atomic layer deposition on a hematite alpha-Fe2O3(0001) surface, we report direct atomic-scale observations of the structural and chemical changes that occur as this model interfacial system evolves from the as-deposited state to the oxidized state, then to the reduced state, and finally back to the oxidized state. In situ X-ray standing-wave atomic images relative to the hematite lattice show dramatic (but redox-reversible) changes to the W cation locations with respect to the occupied and unoccupied Fe surface sites. These structural changes are concurrent with X-ray photoelectron spectroscopy chemical shift changes, where W is observed to go from the 6+ to 5+ oxidation state. These novel observations of redox-induced cation dynamics in an oxide-supported catalyst are explained by models that account for W incorporation at the interface in Fe sites with various coordination schemes. Our proposed structure models are supported by our X-ray absorption fine structure measurements. C1 [Feng, Zhenxing; Bedzyk, Michael J.] Northwestern Univ, Inst Catalysis Energy Proc, Dept Mat Sci & Engn, Evanston, IL 60208 USA. [Ma, Qing] Northwestern Univ, Synchrotron Res Ctr, DND CAT, Evanston, IL 60208 USA. [Kim, Chang-Yong] Canadian Light Source Inc, Saskatoon, SK S7N 0X4, Canada. [Elam, Jeffrey W.] Argonne Natl Lab, Div Energy Syst, Argonne, IL 60439 USA. [Zhang, Zhan] Argonne Natl Lab, Xray Sci Div, Argonne, IL 60439 USA. [Bedzyk, Michael J.] Argonne Natl Lab, Div Mat Sci, Argonne, IL 60439 USA. RP Bedzyk, MJ (reprint author), Northwestern Univ, Inst Catalysis Energy Proc, Dept Mat Sci & Engn, Evanston, IL 60208 USA. EM bedzyk@northwestern.edu RI Bedzyk, Michael/B-7503-2009; Bedzyk, Michael/K-6903-2013; Kim, Chang-Yong/I-3136-2014; Feng, Zhenxing/J-7457-2013; Zhang, Zhan/A-9830-2008 OI Kim, Chang-Yong/0000-0002-1280-9718; Feng, Zhenxing/0000-0001-7598-5076; Zhang, Zhan/0000-0002-7618-6134 FU Institute for Catalysis in Energy Processes (U.S. DOE) [DE-FG02-03ER15457]; MRSEC (NSF) [DMR-0520513] FX This work was supported by the Institute for Catalysis in Energy Processes (U.S. DOE Grant DE-FG02-03ER15457) and MRSEC (NSF Grant DMR-0520513). X-ray measurements were performed at Argonne National Laboratory (U.S. DOE Grant DE-AC02-06CH11357), APS stations 5ID-C, 5BM-D, 12ID-C, and 33ID-D. NR 15 TC 13 Z9 14 U1 0 U2 16 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 30 PY 2009 VL 131 IS 51 BP 18200 EP + DI 10.1021/ja906816y PG 4 WC Chemistry, Multidisciplinary SC Chemistry GA 543YA UT WOS:000273615800005 PM 20028144 ER PT J AU Leung, K Nielsen, IMB Criscenti, LJ AF Leung, Kevin Nielsen, Ida M. B. Criscenti, Louise J. TI Elucidating the Bimodal Acid-Base Behavior of the Water-Silica Interface from First Principles SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID FREQUENCY VIBRATIONAL SPECTROSCOPY; OPTICAL 2ND-HARMONIC GENERATION; MOLECULAR-DYNAMICS SIMULATIONS; DENSITY-FUNCTIONAL THEORY; ATOMIC-FORCE MICROSCOPY; LIQUID WATER; AB-INITIO; AMORPHOUS SILICA; AQUEOUS-SOLUTION; SILANOL GROUPS AB Understanding the acid-base behavior of silica surfaces is critical for many nanoscience and bionano interface applications. Silanol groups (SiOH) on silica surfaces exhibit two acidity constants-one as acidic as vinegar-but their structural basis remains controversial. The atomic details of the more acidic silanol site govern not just the overall surface charge density at near neutral solution pH but also how ions and biomolecules interact with and bind to silica immersed in water. Using ab initio molecular dynamics simulations and multiple representative crystalline silica surfaces, we determine the deprotonation free energies of silanol groups with different structural motifs. We show that previously proposed motifs related to chemical connectivity or intersilanol hydrogen bonds do not yield high acidity. Instead, a plausible candiate for pK(a) = 4.5 silanol groups may be found in locally strained or defected regions with sparse silanol coverage. In the process, irreversible ring-opening reactions of strained silica trimer rings in contact with liquid water are observed. C1 [Leung, Kevin; Criscenti, Louise J.] Sandia Natl Labs, Albuquerque, NM 87185 USA. [Nielsen, Ida M. B.] Sandia Natl Labs, Livermore, CA 94551 USA. RP Leung, K (reprint author), Sandia Natl Labs, MS 1415 & 1322, Albuquerque, NM 87185 USA. EM kleung@sandia.gov FU Department of Energy [DE-AC04-94AL85000] FX We thank Ron Shen, Stephen Garofalini, Susan Rempe, Jeff Brinker, Dave Tallant, Ying-Bing Jiang, and Franz Geiger for discussions. This work was supported by the Department of Energy under Contract DE-AC04-94AL85000. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the U.S. Department of Energy. L.J.C. acknowledges support from the U.S. DOE Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. NR 89 TC 86 Z9 87 U1 6 U2 69 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 30 PY 2009 VL 131 IS 51 BP 18358 EP 18365 DI 10.1021/ja906190t PG 8 WC Chemistry, Multidisciplinary SC Chemistry GA 543YA UT WOS:000273615800047 PM 19947602 ER PT J AU Killian, CE Metzler, RA Gong, YUT Olson, IC Aizenberg, J Politi, Y Wilt, FH Scholl, A Young, A Doran, A Kunz, M Tamura, N Coppersmith, SN Gilbert, PUPA AF Killian, Christopher E. Metzler, Rebecca A. Gong, Y. U. T. Olson, Ian C. Aizenberg, Joanna Politi, Yael Wilt, Fred H. Scholl, Andreas Young, Anthony Doran, Andrew Kunz, Martin Tamura, Nobumichi Coppersmith, Susan N. Gilbert, P. U. P. A. TI Mechanism of Calcite Co-Orientation in the Sea Urchin Tooth SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID CRYSTAL-GROWTH; SINGLE-CRYSTALS; PRECURSOR PHASE; LARVAL SPICULE; CARBONATE; TEETH; ECHINODERMATA; ECHINOIDEA; DESIGN; BIOMINERALIZATION AB Sea urchin teeth are remarkable and complex calcite structures, continuously growing at the forming end and self-sharpening at the mature grinding tip. The calcite (CaCO(3)) crystals of tooth components, plates, fibers, and a high-Mg polycrystalline matrix, have highly co-oriented crystallographic axes. This ability to co-orient calcite in a mineralized structure is shared by all echinoderms. However, the physicochemical mechanism by which calcite crystals become co-oriented in echinoderms remains enigmatic. Here, we show differences in calcite c-axis orientations in the tooth of the purple sea urchin (Strongylocentrotus purpuratus), using high-resolution X-ray photoelectron emission spectromicroscopy (X-PEEM) and microbeam X-ray diffraction (mu XRD). All plates share one crystal orientation, propagated through pillar bridges, while fibers and polycrystalline matrix share another orientation. Furthermore, in the forming end of the tooth, we observe that CaCO(3) is present as amorphous calcium carbonate (ACC). We demonstrate that co-orientation of the nanoparticles in the polycrystalline matrix occurs via solid-state secondary nucleation, propagating out from the previously formed fibers and plates, into the amorphous precursor nanoparticles. Because amorphous precursors were observed in diverse biominerals, solid-state secondary nucleation is likely to be a general mechanism for the co-orientation of biomineral components in organisms from different phyla. C1 [Killian, Christopher E.; Metzler, Rebecca A.; Gong, Y. U. T.; Olson, Ian C.; Coppersmith, Susan N.; Gilbert, P. U. P. A.] Univ Wisconsin, Dept Phys, Madison, WI 53706 USA. [Killian, Christopher E.; Wilt, Fred H.] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA. [Aizenberg, Joanna] Harvard Univ, Sch Engn & Appl Sci, Cambridge, MA 02138 USA. [Politi, Yael] Weizmann Inst Sci, Dept Biol Struct, IL-76100 Rehovot, Israel. [Scholl, Andreas; Young, Anthony; Doran, Andrew; Kunz, Martin; Tamura, Nobumichi] Univ Calif Berkeley, Lawrence Berkeley Lab, Adv Light Source, Berkeley, CA 94720 USA. RP Gilbert, PUPA (reprint author), Univ Wisconsin, Dept Phys, 1150 Univ Ave, Madison, WI 53706 USA. EM pupa@physics.wisc.edu RI Kunz, Martin/K-4491-2012; Scholl, Andreas/K-4876-2012; Gilbert, Pupa/A-6299-2010; OI Kunz, Martin/0000-0001-9769-9900; Gilbert, Pupa/0000-0002-0139-2099; Doran, Andrew/0000-0001-5158-4569 FU DOE [DE-FG02-07ER15899, DE-AC02-05CH11231]; NSF [CHE-0613972]; UW-Vilas Award; Hamel Award FX We thank Lia Addadi and Steve Weiner for discussions and comments about the manuscript. We also thank Paul Voyles for tripod polishing. This work was supported by DOE award DE-FG02-07ER15899, NSF award CHE-0613972, and UW-Vilas and Hamel Awards to PUPAG. The experiments were performed at the ALS, supported by DOE under contract DE-AC02-05CH11231. NR 36 TC 93 Z9 94 U1 9 U2 88 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 30 PY 2009 VL 131 IS 51 BP 18404 EP 18409 DI 10.1021/ja907063z PG 6 WC Chemistry, Multidisciplinary SC Chemistry GA 543YA UT WOS:000273615800052 PM 19954232 ER PT J AU Tatarkhanov, M Ogletree, DF Rose, F Mitsui, T Fomin, E Maier, S Rose, M Cerda, JI Salmeron, M AF Tatarkhanov, Mous Ogletree, D. Frank Rose, Franck Mitsui, Toshiyuki Fomin, Evgeny Maier, Sabine Rose, Mark Cerda, Jorge I. Salmeron, Miquel TI Metal- and Hydrogen-Bonding Competition during Water Adsorption on Pd(111) and Ru(0001) SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID SCANNING TUNNELING MICROSCOPE; PARTIAL DISSOCIATION; EFFICIENT METHOD; STM IMAGES; AB-INITIO; ICE; SIMULATION; SURFACES; DIFFUSION; BILAYER AB The initial stages of water adsorption on the Pd(111) and Ru(0001) surfaces have been investigated experimentally by scanning tunneling microscopy in the temperature range between 40 and 130 K, and theoretically with density functional theory (DFT) total energy calculations and scanning tunneling microscopy (STM) image simulations. Below 125 K, water dissociation does not occur at any appreciable rate, and only molecular films are formed. Film growth starts by the formation of flat hexamer clusters where the molecules bind to the metal substrate through the O-lone pair while making H-bonds with neighboring molecules. As coverage increases, larger networks of linked hexagons are formed with a honeycomb structure, which requires a fraction of the water molecules to have their molecular plane perpendicular to the metal surface with reduced water-metal interaction. Energy minimization favors the growth of networks with limited width. As additional water molecules adsorb on the surface, they attach to the periphery of existing islands, where they interact only weakly with the metal substrate. These molecules hop along the periphery of the clusters at intermediate temperatures. At higher temperatures, they bind to the metal to continue the honeycomb growth. The water-Ru interaction is significantly stronger than the water-Pd interaction, which is consistent with the greater degree of hydrogen-bonded network formation and reduced water-metal bonding observed on Pd relative to Ru. C1 [Tatarkhanov, Mous; Ogletree, D. Frank; Rose, Franck; Mitsui, Toshiyuki; Fomin, Evgeny; Maier, Sabine; Rose, Mark; Salmeron, Miquel] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Tatarkhanov, Mous; Fomin, Evgeny; Rose, Mark] Univ Calif Berkeley, Dept Phys, Berkeley, CA 94720 USA. [Cerda, Jorge I.] CSIC, ICMM, E-28049 Madrid, Spain. [Salmeron, Miquel] Univ Calif Berkeley, Dept Mat Sci & Engn, Berkeley, CA 94720 USA. RP Salmeron, M (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. EM mbsalmeron@lbl.gov RI Cerda, Jorge/F-4043-2010; Maier, Sabine/B-5917-2008; Ogletree, D Frank/D-9833-2016 OI Cerda, Jorge/0000-0001-6176-0191; Maier, Sabine/0000-0001-9589-6855; Ogletree, D Frank/0000-0002-8159-0182 FU U.S. Department of Energy [DE-AC02-05CH11231]; Spanish Ministry of Science and Technology [MAT2007-66719-C03-02] FX This work was supported by the Director, Office of Energy Research, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. J.I.C. was supported by the Spanish Ministry of Science and Technology under Project No. MAT2007-66719-C03-02. D.F.O. was supported by the Molecular Foundry, Lawrence Berkeley National Laboratory, under the Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. NR 43 TC 44 Z9 44 U1 4 U2 60 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 30 PY 2009 VL 131 IS 51 BP 18425 EP 18434 DI 10.1021/ja907468m PG 10 WC Chemistry, Multidisciplinary SC Chemistry GA 543YA UT WOS:000273615800055 PM 19947628 ER PT J AU Hartshorne, RS Reardon, CL Ross, D Nuester, J Clarke, TA Gates, AJ Mills, PC Fredrickson, JK Zachara, JM Shi, L Beliaev, AS Marshall, MJ Tien, M Brantley, S Butt, JN Richardson, DJ AF Hartshorne, Robert S. Reardon, Catherine L. Ross, Daniel Nuester, Jochen Clarke, Thomas A. Gates, Andrew J. Mills, Paul C. Fredrickson, Jim K. Zachara, John M. Shi, Liang Beliaev, Alex S. Marshall, Matthew J. Tien, Ming Brantley, Susan Butt, Julea N. Richardson, David J. TI Characterization of an electron conduit between bacteria and the extracellular environment SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE cytochrome-c; iron respiration; protein film voltammetry; electron paramagnetic resonance; Shewanella ID SHEWANELLA-PUTREFACIENS MR-1; OUTER-MEMBRANE CYTOCHROMES; C-TYPE CYTOCHROME; ONEIDENSIS MR-1; ESCHERICHIA-COLI; REDUCTION; MTRC; RESPIRATION; TRANSPORT; FE(III) AB A number of species of Gram-negative bacteria can use insoluble minerals of Fe(III) and Mn(IV) as extracellular respiratory electron acceptors. In some species of Shewanella, deca-heme electron transfer proteins lie at the extracellular face of the outer membrane (OM), where they can interact with insoluble substrates. To reduce extracellular substrates, these redox proteins must be charged by the inner membrane/periplasmic electron transfer system. Here, we present a spectro-potentiometric characterization of a trans-OM icosa-heme complex, MtrCAB, and demonstrate its capacity to move electrons across a lipid bilayer after incorporation into proteoliposomes. We also show that a stable MtrAB subcomplex can assemble in the absence of MtrC; an MtrBC subcomplex is not assembled in the absence of MtrA; and MtrA is only associated to the membrane in cells when MtrB is present. We propose a model for the modular organization of the MtrCAB complex in which MtrC is an extracellular element that mediates electron transfer to extracellular substrates and MtrB is a trans-OM spanning beta-barrel protein that serves as a sheath, within which MtrA and MtrC exchange electrons. We have identified the MtrAB module in a range of bacterial phyla, suggesting that it is widely used in electron exchange with the extracellular environment. C1 [Hartshorne, Robert S.; Clarke, Thomas A.; Gates, Andrew J.; Mills, Paul C.; Butt, Julea N.; Richardson, David J.] Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England. [Reardon, Catherine L.; Fredrickson, Jim K.; Zachara, John M.; Shi, Liang; Beliaev, Alex S.; Marshall, Matthew J.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Ross, Daniel; Tien, Ming] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA. [Nuester, Jochen; Brantley, Susan] Penn State Univ, Dept Geosci, University Pk, PA 16802 USA. RP Richardson, DJ (reprint author), Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England. EM d.richardson@uea.ac.uk RI Richardson, David/E-2275-2011; Gates, Andrew/F-8218-2011; clarke, tom/D-1837-2009; Beliaev, Alexander/E-8798-2016; Butt, Julea/E-2133-2011; OI Gates, Andrew/0000-0002-4594-5038; clarke, tom/0000-0002-6234-1914; Beliaev, Alexander/0000-0002-6766-4632; Butt, Julea/0000-0002-9624-5226; Ross, Daniel/0000-0002-8272-1877 FU Department of Energy's Office of Biological and Environmental Research, at Pacific Northwest National Laboratory (PNNL); National Science Foundation [EAR 05-19144]; Center for Environmental Kinetics Analysis (NSF) [CHE-0431328]; U.S. Department of Energy, Biological and Environmental Research; Royal Society Wolfson Foundation FX We thank the reviewers and editor of the article for helpful comments during the revision process. The EMSL Scientific Grand Challenge was performed in part at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the Department of Energy by Battelle. J. N. and S. B. were supported by the National Science Foundation (Grant EAR 05-19144). M.T., J.N., and D.R. were supported by the Center for Environmental Kinetics Analysis (NSF CHE-0431328 and the U.S. Department of Energy, Biological and Environmental Research). D.J.R. is a Royal Society Wolfson Foundation Merit Award holder. NR 24 TC 162 Z9 168 U1 10 U2 93 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 29 PY 2009 VL 106 IS 52 BP 22169 EP 22174 DI 10.1073/pnas.0900086106 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 538IV UT WOS:000273178700026 PM 20018742 ER PT J AU Tsuruma, Y Al-Mahboob, A Ikeda, S Sadowski, JT Yoshikawa, G Fujikawa, Y Sakurai, T Saiki, K AF Tsuruma, Yuki Al-Mahboob, Abdullah Ikeda, Susumu Sadowski, Jerzy T. Yoshikawa, Genki Fujikawa, Yasunori Sakurai, Toshio Saiki, Koichiro TI Real-Time Observation and Control of Pentacene Film Growth on an Artificially Structured Substrate SO ADVANCED MATERIALS LA English DT Article ID SELF-ASSEMBLED MONOLAYERS; FIELD-EFFECT TRANSISTORS; CONJUGATED MOLECULES; ORGANIC ELECTRONICS; PERFORMANCE; DIFFUSION; ENERGY AB Suppression of nucleation around a gold electrode during pentacene growth on a SiO(2) channel is found by photoemission electron microscopy. Mass flow is driven by the difference between the molecular orientations on SiO(2) and gold. The poor connectivity at the channel/electrode boundary causes degradation in the performance of a field-effect transistor, which is found to be improved by self-assembled monolayer treatment on the electrode (see figure; thickness in monolayers (ML)). C1 [Tsuruma, Yuki; Ikeda, Susumu; Saiki, Koichiro] Univ Tokyo, Dept Complex Sci & Engn, Kashiwa, Chiba 2778561, Japan. [Al-Mahboob, Abdullah; Sadowski, Jerzy T.; Yoshikawa, Genki; Fujikawa, Yasunori; Sakurai, Toshio] Tohoku Univ, Inst Mat Res, Aoba Ku, Sendai, Miyagi 9808577, Japan. [Sadowski, Jerzy T.] Brookhaven Natl Lab, Ctr Funct Nanomat, Upton, NY 11973 USA. [Yoshikawa, Genki] Natl Inst Mat Sci, World Premier Int Ctr Mat Nanoarchitecton MANA, Tsukuba, Ibaraki 3050044, Japan. RP Saiki, K (reprint author), Univ Tokyo, Dept Complex Sci & Engn, 5-1-5 Kashiwanoha, Kashiwa, Chiba 2778561, Japan. EM saiki@k.u-tokyo.ac.jp RI Fujikawa, Yasunori/A-6527-2009; YOSHIKAWA, Genki/B-1372-2010; Saiki, Koichiro/E-4496-2011; Ikeda, Susumu/C-2452-2011; Al-Mahboob, Abdullah/B-9529-2011 OI Ikeda, Susumu/0000-0003-3962-8367; Sadowski, Jerzy/0000-0002-4365-7796; FU Ministry of Education, Culture, Sports, Science, and Technology; Japan Society for the Promotion of Science; Institute for Materials Research, Tohoku University FX This work was supported by Grant-in-Aids for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology. Y.T is grateful to a Grant-in-Aid for JSPS Fellows from the Japan Society for the Promotion of Science. This work was partly performed under the Inter-university Cooperative Research Program of the Institute for Materials Research, Tohoku University. Supporting Information is available online from Wiley InterScience or from the author. NR 39 TC 15 Z9 15 U1 4 U2 32 PU WILEY-V C H VERLAG GMBH PI WEINHEIM PA PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY SN 0935-9648 J9 ADV MATER JI Adv. Mater. PD DEC 28 PY 2009 VL 21 IS 48 BP 4996 EP + DI 10.1002/adma.200901436 PG 6 WC Chemistry, Multidisciplinary; Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Chemistry; Science & Technology - Other Topics; Materials Science; Physics GA 540SL UT WOS:000273359300020 PM 25376650 ER PT J AU Cheng, S Zhao, YH Guo, YZ Li, Y Wei, QM Wang, XL Ren, Y Liaw, PK Choo, H Lavernia, EJ AF Cheng, Sheng Zhao, Yonghao Guo, Yazhou Li, Ying Wei, Qiuming Wang, Xun-Li Ren, Yang Liaw, Peter K. Choo, Hahn Lavernia, Enrique J. TI High Plasticity and Substantial Deformation in Nanocrystalline NiFe Alloys Under Dynamic Loading SO ADVANCED MATERIALS LA English DT Article ID ULTRAFINE-GRAINED METALS; NANOSTRUCTURED METALS; MECHANICAL-PROPERTIES; TENSILE DUCTILITY; STRENGTH; OPTIMIZATION; TEMPERATURE; MAXIMUM; COPPER; NICKEL AB A nanocrystalline (NC) NiFe alloy is presented, in which both highly improved plasticity and strength are achieved by the dynamic-loading-induced deformation mechanisms of de-twinning (that is, reduction of twin density) and significant grain coarsening (see figure). This work highlights potential ingenious avenues to exploit the superior behavior of NC materials under extreme conditions. C1 [Cheng, Sheng; Liaw, Peter K.; Choo, Hahn] Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. [Zhao, Yonghao; Li, Ying; Lavernia, Enrique J.] Univ Calif Davis, Dept Chem Engn & Mat Sci, Davis, CA 95616 USA. [Guo, Yazhou; Wei, Qiuming] Univ N Carolina, Dept Mech Engn, Charlotte, NC 28223 USA. [Wang, Xun-Li] Oak Ridge Natl Lab, Neutron Scattering Sci Div, Oak Ridge, TN 37831 USA. [Ren, Yang] Argonne Natl Lab, Adv Photon Source, Argonne, IL 60439 USA. RP Cheng, S (reprint author), Univ Tennessee, Dept Mat Sci & Engn, Knoxville, TN 37996 USA. EM scheng1@utk.edu RI Choo, Hahn/A-5494-2009; Lavernia, Enrique/I-6472-2013; Guo, Yazhou/E-3318-2016; Li, Ying/G-3908-2010; Wei, Qiuming/B-7579-2008; Wei, Qiangmin/D-3931-2011; Zhao, Yonghao/A-8521-2009; Wang, Xun-Li/C-9636-2010; Cheng, Sheng/D-9153-2013 OI Choo, Hahn/0000-0002-8006-8907; Lavernia, Enrique/0000-0003-2124-8964; Li, Ying/0000-0003-3738-9307; Wang, Xun-Li/0000-0003-4060-8777; Cheng, Sheng/0000-0003-1137-1926 FU NSF [DMR-0231320, DMR-0421219]; Office of Naval Research [ONR N00014-08-1-0405]; US Department of Energy [DE-AC05-00OR22725, DE-AC02-06CH11357] FX S.C. and Y.Z. contributed equally to this work. S.C. and P.K.L. acknowledge financial support by the NSF International Materials Institutes program (DMR-0231320) and NSF Major Research instrumentation Program (DMR-0421219). Y.Z. and E.J.L. acknowledge support by the Office of Naval Research (Grant number ONR N00014-08-1-0405). X-L.W. acknowledges support by US Department of Energy (DE-AC05-00OR22725 and DE-AC02-06CH11357) with UT-Battelle, LLC. Supporting Information is available online from Wiley InterScience or from the authors. NR 27 TC 24 Z9 24 U1 6 U2 68 PU WILEY-V C H VERLAG GMBH PI WEINHEIM PA PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY SN 0935-9648 J9 ADV MATER JI Adv. Mater. PD DEC 28 PY 2009 VL 21 IS 48 BP 5001 EP + DI 10.1002/adma.200901991 PG 5 WC Chemistry, Multidisciplinary; Chemistry, Physical; Nanoscience & Nanotechnology; Materials Science, Multidisciplinary; Physics, Applied; Physics, Condensed Matter SC Chemistry; Science & Technology - Other Topics; Materials Science; Physics GA 540SL UT WOS:000273359300021 PM 25378188 ER PT J AU Campbell, IH Crone, BK AF Campbell, I. H. Crone, B. K. TI A near infrared organic photodiode with gain at low bias voltage SO APPLIED PHYSICS LETTERS LA English DT Article DE absorption coefficients; organic semiconductors; photoconductivity; photodiodes ID SOLAR-CELLS; PHOTODETECTORS; EFFICIENCY; FILM AB We demonstrate an organic photodiode with near infrared optical response out to about 1100 nm with a gain of similar to 10 at 1000 nm under 5 V reverse bias. The diodes employ a soluble naphthalocyanine with a peak absorption coefficient of similar to 10(5) cm(-1) at 1000 nm. In contrast to most organic photodiodes, no exciton dissociating material is used. At zero bias, the diodes are inefficient with an external quantum efficiency of similar to 10(-2). In reverse bias, large gain occurs and is linear with bias voltage above 4 V. The observed gain is consistent with a photoconductive gain mechanism. C1 [Campbell, I. H.; Crone, B. K.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. RP Campbell, IH (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. EM campbell@lanl.gov FU Los Alamos National Laboratory [LDRD X9T9] FX This work was funded by the Los Alamos National Laboratory LDRD X9T9 program. NR 18 TC 27 Z9 27 U1 2 U2 19 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 28 PY 2009 VL 95 IS 26 AR 263302 DI 10.1063/1.3279133 PG 3 WC Physics, Applied SC Physics GA 538XF UT WOS:000273216900058 ER PT J AU Nazaretski, E Thibodaux, JP Vekhter, I Civale, L Thompson, JD Movshovich, R AF Nazaretski, E. Thibodaux, J. P. Vekhter, I. Civale, L. Thompson, J. D. Movshovich, R. TI Direct measurements of the penetration depth in a superconducting film using magnetic force microscopy SO APPLIED PHYSICS LETTERS LA English DT Article DE magnetic force microscopy; magnetisation; metallic thin films; niobium; penetration depth (superconductivity); superconducting materials; superconducting thin films ID TEMPERATURE-DEPENDENCE; GAP FUNCTION; VORTICES; YBA2CU3O6.95; NODES; LINES AB We report the local measurements of the magnetic penetration depth lambda in a superconducting Nb film using magnetic force microscopy (MFM). We developed a method for quantitative extraction of the penetration depth from single-parameter simultaneous fits to the lateral and height profiles of the MFM signal, and demonstrate that the obtained value is in excellent agreement with that obtained from the bulk magnetization measurements. C1 [Nazaretski, E.; Civale, L.; Thompson, J. D.; Movshovich, R.] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Nazaretski, E.] Brookhaven Natl Lab, Upton, NY 11973 USA. [Thibodaux, J. P.; Vekhter, I.] Louisiana State Univ, Dept Phys & Astron, Baton Rouge, LA 70803 USA. RP Nazaretski, E (reprint author), Los Alamos Natl Lab, POB 1663, Los Alamos, NM 87545 USA. EM enazaretski@bnl.gov RI Vekhter, Ilya/M-1780-2013; OI Civale, Leonardo/0000-0003-0806-3113 FU U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering [DE-FG02-08ER46492]; Louisiana Board of Regents FX We acknowledge help of Dr. P. Goodwin at LANL with AFM imaging of the film and technical assistance of J. K. Baldwin with fabrication of Nb films. This work was supported by the US DOE at LANL and BNL, by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering (L.C.) and via Grant No. DE-FG02-08ER46492 (I. V. and J. P. T.), by the Louisiana Board of Regents (J. P. T.) NR 26 TC 6 Z9 6 U1 1 U2 7 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 28 PY 2009 VL 95 IS 26 AR 262502 DI 10.1063/1.3276563 PG 3 WC Physics, Applied SC Physics GA 538XF UT WOS:000273216900038 ER PT J AU Rumaiz, AK Woicik, JC Cockayne, E Lin, HY Jaffari, GH Shah, SI AF Rumaiz, Abdul K. Woicik, J. C. Cockayne, E. Lin, H. Y. Jaffari, G. Hassnain Shah, S. I. TI Oxygen vacancies in N doped anatase TiO2: Experiment and first-principles calculations SO APPLIED PHYSICS LETTERS LA English DT Article DE catalysis; density functional theory; electronic structure; nitrogen; semiconductor doping; semiconductor materials; titanium compounds; vacancies (crystal); X-ray photoelectron spectra ID AUGMENTED-WAVE METHOD; RESONANT PHOTOEMISSION; TITANIUM; PHOTOCATALYSIS; FERROMAGNETISM; DEPENDENCE; SURFACES; FILMS AB We have determined the electronic and atomic structure of N doped TiO2 using a combination of hard x-ray photoelectron spectroscopy and first-principles density functional theory calculations. Our results reveal that N doping of TiO2 leads to the formation of oxygen vacancies and the combination of both N impurity and oxygen vacancies accounts for the observed visible light catalytic behavior of N doped TiO2. C1 [Rumaiz, Abdul K.] Brookhaven Natl Lab, Natl Synchrotron Light Source, Upton, NY 11973 USA. Natl Inst Stand & Technol, Gaithersburg, MD 20899 USA. [Lin, H. Y.; Shah, S. I.] Univ Delaware, Dept Mat Sci & Engn, Newark, DE 19716 USA. [Jaffari, G. Hassnain; Shah, S. I.] Univ Delaware, Dept Phys & Astron, Newark, DE 19716 USA. RP Rumaiz, AK (reprint author), Brookhaven Natl Lab, Natl Synchrotron Light Source, Upton, NY 11973 USA. EM rumaiz@bnl.gov RI Rumaiz, Abdul/J-5084-2012 FU U.S. Department of Energy FX A. K. R would like to acknowledge P. D. Siddons (NSLS) for support. This work was performed at the National Synchrotron Light Source, which is supported by the U.S. Department of Energy. NR 27 TC 61 Z9 61 U1 11 U2 71 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 28 PY 2009 VL 95 IS 26 AR 262111 DI 10.1063/1.3272272 PG 3 WC Physics, Applied SC Physics GA 538XF UT WOS:000273216900034 ER PT J AU Tsetseris, L Pantelides, ST AF Tsetseris, L. Pantelides, S. T. TI Morphology and defect properties of the Ge-GeO2 interface SO APPLIED PHYSICS LETTERS LA English DT Article DE ab initio calculations; dangling bonds; defect states; elemental semiconductors; germanium; germanium compounds; interface roughness; interface states; passivation; semiconductor-insulator boundaries ID AUGMENTED-WAVE METHOD; MOS DEVICES; HYDROGEN; MOSFETS AB Ge-based devices, currently being pursued as replacement of their Si counterparts, typically contain a germanium oxide layer next to the substrate. Here we show using first-principles calculations that, in contrast to Si technology, hydrogenation and fluorination are not effective ways of passivating Ge-GeO2 interfacial P-b centers with a Ge dangling bond (DB). Moreover, we identify DB geometries that differ from the P-b structures and we find that the Ge-GeO2 boundary has a higher atomic-scale roughness than the Si-SiO2 interface. These key differences in interface morphology and defect properties are consistent with experimental data. C1 [Tsetseris, L.] Natl Tech Univ Athens, Dept Phys, GR-15780 Athens, Greece. [Tsetseris, L.] Aristotle Univ Thessaloniki, Dept Phys, GR-54124 Thessaloniki, Greece. [Tsetseris, L.; Pantelides, S. T.] Vanderbilt Univ, Dept Phys & Astron, Nashville, TN 37235 USA. [Pantelides, S. T.] Oak Ridge Natl Lab, Oak Ridge, TN 37831 USA. RP Tsetseris, L (reprint author), Natl Tech Univ Athens, Dept Phys, GR-15780 Athens, Greece. EM leonidas.tsetseris@vanderbilt.edu FU AFOSR [NFA9550-05-1-0306]; McMinn Endowment at Vanderbilt University FX The work was supported by the AFOSR (MURI Grant No. NFA9550-05-1-0306) and the McMinn Endowment at Vanderbilt University. The calculations were performed at EORNL's Center for Computational Sciences. NR 28 TC 33 Z9 33 U1 2 U2 68 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 28 PY 2009 VL 95 IS 26 AR 262107 DI 10.1063/1.3280385 PG 3 WC Physics, Applied SC Physics GA 538XF UT WOS:000273216900030 ER PT J AU Wang, WM Lin, AS Phillips, JD Metzger, WK AF Wang, Weiming Lin, Albert S. Phillips, Jamie D. Metzger, Wyatt K. TI Generation and recombination rates at ZnTe:O intermediate band states SO APPLIED PHYSICS LETTERS LA English DT Article DE carrier lifetime; conduction bands; doping profiles; electron-hole recombination; II-VI semiconductors; multiphoton processes; oxygen; photoluminescence; semiconductor doping; semiconductor thin films; solar cells; time resolved spectra; valence bands; zinc compounds ID SOLAR-CELLS; EFFICIENCY; SEMICONDUCTORS; TRANSITIONS; CIRCUIT; ALLOYS; GAAS AB Carrier generation and recombination processes of ZnTeO thin films are studied by time-resolved photoluminescence, where carrier lifetimes at oxygen states and the conduction band are inferred to be >1 mu s and < 100 ps, respectively. The radiative recombination coefficient for optical transitions from oxygen states to the valence band is extracted to be 1.2x10(-10) cm(3) sec(-1) based on the excitation dependence of decay time constants. Rate equation analysis further suggests an increase in electron lifetime at the conduction band as oxygen states occupation is critical in achieving high conversion efficiency for solar cells based on multiphoton processes in these materials. C1 [Wang, Weiming; Lin, Albert S.; Phillips, Jamie D.] Univ Michigan, Dept Elect Engn & Comp Sci, Ann Arbor, MI 48109 USA. [Metzger, Wyatt K.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Wang, WM (reprint author), Univ Michigan, Dept Elect Engn & Comp Sci, Ann Arbor, MI 48109 USA. EM umwwm@umich.edu RI Phillips, Jamie/E-9394-2010 FU American Chemical Society; Center for Solar and Thermal Energy Conversion; U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences [DE-SC0000957] FX Material growth was supported by the donors of the American Chemical Society Petroleum Research fund, and optical measurements and analysis at UM were supported by part of the Center for Solar and Thermal Energy Conversion in Complex Materials, an Energy Frontier Research Center funded by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award No. DE-SC0000957. NR 23 TC 31 Z9 32 U1 3 U2 31 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 28 PY 2009 VL 95 IS 26 AR 261107 DI 10.1063/1.3274131 PG 3 WC Physics, Applied SC Physics GA 538XF UT WOS:000273216900007 ER PT J AU Odell, A Delin, A Johansson, B Bock, N Challacombe, M Niklasson, AMN AF Odell, Anders Delin, Anna Johansson, Borje Bock, Nicolas Challacombe, Matt Niklasson, Anders M. N. TI Higher-order symplectic integration in Born-Oppenheimer molecular dynamics SO JOURNAL OF CHEMICAL PHYSICS LA English DT Article DE ab initio calculations; molecular dynamics method; potential energy surfaces; SCF calculations ID MATRIX; TRAJECTORIES; ORBITALS AB The extended Lagrangian formulation of time-reversible Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, C. J. Tymczak, and M. Challacombe, Phys. Rev. Lett. 100, 123004 (2008); Phys. Rev. Lett. 97, 123001 (2006)] enables the use of geometric integrators in the propagation of both the nuclear and the electronic degrees of freedom on the Born-Oppenheimer potential energy surface. Different symplectic integrators up to the sixth order have been adapted and optimized in the framework of ab initio self-consistent-field theory. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular, for the case of very high accuracy requirements. C1 [Odell, Anders; Delin, Anna; Johansson, Borje; Niklasson, Anders M. N.] Royal Inst Technol, Dept Mat Sci & Engn, SE-10044 Stockholm, Sweden. [Bock, Nicolas; Challacombe, Matt; Niklasson, Anders M. N.] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. RP Odell, A (reprint author), Royal Inst Technol, Dept Mat Sci & Engn, SE-10044 Stockholm, Sweden. EM odell@mse.kth.se; amn@lanl.gov RI Delin, Anna/P-2100-2014 OI Delin, Anna/0000-0001-7788-6127 FU U. S. Department of Energy [DE-AC5206NA25396]; Vetenskapsradet; Jernkontoret; Stiftelsen for Strategisk Forskning; Kungliga Vetenskapsakademien; ERC FX We gratefully acknowledge the support of the U. S. Department of Energy under Contract No. DE-AC5206NA25396 through the LANL LDRD/ER program for this work. We also gratefully acknowledge Vetenskapsradet, Jernkontoret, Stiftelsen for Strategisk Forskning, Kungliga Vetenskapsakademien and ERC for support. We thank SNIC for computer resources and NSC for computer support. A special thanks goes to the T-Division Ten bar Cafe at Los Alamos National Laboratory for facilitating stimulating discussions, and to Travis Peery for his generosity and expertise. Error amplitude NR 34 TC 17 Z9 17 U1 2 U2 10 PU AMER INST PHYSICS PI MELVILLE PA 1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USA SN 0021-9606 EI 1089-7690 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 28 PY 2009 VL 131 IS 24 AR 244106 DI 10.1063/1.3268338 PG 10 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 538XG UT WOS:000273217000011 PM 20059053 ER PT J AU Rodgers, JM Weeks, JD AF Rodgers, Jocelyn M. Weeks, John D. TI Accurate thermodynamics for short-ranged truncations of Coulomb interactions in site-site molecular models SO JOURNAL OF CHEMICAL PHYSICS LA English DT Article DE liquid mixtures; thermodynamics; water ID FIELD THEORY; SIMULATION; FLUIDS; WATER; LIQUIDS; SYSTEMS; ELECTROLYTES; POTENTIALS; MECHANICS; PROTEINS AB Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple analytical corrections for the thermodynamics of uniform truncated systems are possible. In particular, results for the simple point charge/extended (SPC/E) water model treated with spherically truncated Coulomb interactions suggested by local molecular field theory [J. M. Rodgers and J. D. Weeks, Proc. Natl. Acad. Sci. U.S.A. 105, 19136 (2008)] are presented. We extend the results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] so that we may treat the thermodynamics of mixtures of flexible charged and uncharged molecules simulated with spherical truncations. We show that the energy and pressure of spherically truncated bulk SPC/E water are easily corrected using exact second-moment-like conditions on long-ranged structure. Furthermore, applying the pressure correction as an external pressure removes the density errors observed by other research groups in NPT simulations of spherically truncated bulk species. C1 [Rodgers, Jocelyn M.; Weeks, John D.] Univ Maryland, Inst Phys Sci & Technol, College Pk, MD 20742 USA. [Rodgers, Jocelyn M.] Univ Maryland, Chem Phys Program, College Pk, MD 20742 USA. [Weeks, John D.] Univ Maryland, Dept Chem & Biochem, College Pk, MD 20742 USA. RP Rodgers, JM (reprint author), Lawrence Berkeley Natl Lab, Div Mat Sci, Berkeley, CA 94720 USA. EM jdw@ipst.umd.edu NR 34 TC 13 Z9 13 U1 1 U2 18 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0021-9606 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 28 PY 2009 VL 131 IS 24 AR 244108 DI 10.1063/1.3276729 PG 8 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 538XG UT WOS:000273217000013 PM 20059055 ER PT J AU Xu, LJ Mei, DH Henkelman, G AF Xu, Lijun Mei, Donghai Henkelman, Graeme TI Adaptive kinetic Monte Carlo simulation of methanol decomposition on Cu(100) SO JOURNAL OF CHEMICAL PHYSICS LA English DT Article DE adsorption; bonds (chemical); catalysis; copper; density functional theory; dissociation; Monte Carlo methods; organic compounds; potential energy surfaces; reaction kinetics theory; surface chemistry ID FINDING SADDLE-POINTS; DENSITY-FUNCTIONAL THEORY; POTENTIAL-ENERGY SURFACE; ELASTIC BAND METHOD; PARTIAL OXIDATION; 1ST-PRINCIPLES CALCULATIONS; INFRARED-SPECTROSCOPY; CHEMICAL-REACTIONS; TIME-SCALE; CU(111) AB The adaptive kinetic Monte Carlo method was used to calculate the decomposition dynamics of a methanol molecule on Cu(100) at room temperature over a time scale of minutes. Mechanisms of reaction were found using minimum mode following saddle point searches based on forces and energies from density functional theory. Rates of reaction were calculated with harmonic transition state theory. The dynamics followed a pathway from CH3OH, CH3O, CH2O, HCO, and finally to CO. Our calculations confirm that methanol decomposition starts with breaking the O-H bond followed by breaking C-H bonds in the dehydrogenated intermediates until CO is produced. The bridge site on the Cu(100) surface is the active site for scissoring chemical bonds. Reaction intermediates are mobile on the surface which allows them to find this active reaction site. This study illustrates how the adaptive kinetic Monte Carlo method can model the dynamics of surface chemistry from first principles. C1 [Xu, Lijun; Henkelman, Graeme] Univ Texas Austin, Dept Chem & Biochem, Austin, TX 78712 USA. [Mei, Donghai] Pacific NW Natl Lab, Inst Interfacial Catalysis, Richland, WA 99352 USA. RP Xu, LJ (reprint author), Univ Texas Austin, Dept Chem & Biochem, Austin, TX 78712 USA. EM henkelman@mail.utexas.edu RI Mei, Donghai/D-3251-2011; Henkelman, Graeme/A-9301-2008; Mei, Donghai/A-2115-2012 OI Henkelman, Graeme/0000-0002-0336-7153; Mei, Donghai/0000-0002-0286-4182 FU National Science Foundation [CHE-0645497]; Robert A. Welch Foundation [F-1601]; Laboratory Directed Research and Development (LDRD) project at Pacific Northwest National Laboratory (PNNL); Science Theme Project [ST25428] FX This work was supported by the National Science Foundation (Grant No. CHE-0645497) and the Robert A. Welch Foundation under Grant No. F-1601. D.M. was supported by a Laboratory Directed Research and Development (LDRD) project at Pacific Northwest National Laboratory (PNNL). The authors used the resources in the Texas Advanced Computing Center and computing time granted by the Science Theme Project (Grant No. ST25428) using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy national scientific user facility located at PNNL. NR 67 TC 23 Z9 24 U1 5 U2 42 PU AMER INST PHYSICS PI MELVILLE PA 1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USA SN 0021-9606 EI 1089-7690 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 28 PY 2009 VL 131 IS 24 AR 244520 DI 10.1063/1.3281688 PG 8 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 538XG UT WOS:000273217000050 PM 20059092 ER PT J AU Wei, F Xu, YY Guo, Y Liu, SL Wang, HF AF Wei, Feng Xu, Yan-yan Guo, Yuan Liu, Shi-lin Wang, Hong-fei TI Quantitative Surface Chirality Detection with Sum Frequency Generation Vibrational Spectroscopy: Twin Polarization Angle Approach SO CHINESE JOURNAL OF CHEMICAL PHYSICS LA English DT Article DE Sum-frequency generation vibrational spectroscopy; Twin polarization angle approach; Surface; Chirality; Limonene ID 2ND HARMONIC-GENERATION; NONLINEAR-OPTICAL SPECTROSCOPY; 2ND-HARMONIC GENERATION; AIR/WATER INTERFACE; MOLECULAR CHIRALITY; ACTIVE MOLECULES; RAMAN-SCATTERING; SFG-VS; ORIENTATION; MONOLAYER AB Here we report a novel twin polarization angle (TPA) approach in the quantitative chirality detection with the surface sum-frequency generation vibrational spectroscopy (SFG-VS). Generally, the achiral contribution dominates the surface SFG-VS signal, and the pure chiral signal is usually two or three orders of magnitude smaller. Therefore, it has been difficult to make quantitative detection and analysis of the chiral contributions to the surface SFG-VS signal. In the TPA method, by varying together the polarization angles of the incoming visible light and the sum frequency signal at fixed s or p polarization of the incoming infrared beam, the polarization dependent SFG signal can give not only direct signature of the chiral contribution in the total SFG-VS signal, but also the accurate measurement of the chiral and achiral components in the surface SFG signal. The general description of the TPA method is presented and the experiment test of the TPA approach is also presented for the SFG-VS from the S- and R-limonene chiral liquid surfaces. The most accurate degree of chiral excess values thus obtained for the 2878 cm(-1) spectral peak of the S- and R-limonene liquid surfaces are (23.7 +/- 0.4)% and (-25.4 +/- 1.3)%, respectively. C1 [Xu, Yan-yan] Chinese Acad Sci, Grad Univ, Beijing 100190, Peoples R China. [Wei, Feng; Liu, Shi-lin] Univ Sci & Technol China, Dept Chem Phys, Hefei Natl Lab Phys Sci Microscale, Hefei 230026, Anhui, Peoples R China. [Xu, Yan-yan; Guo, Yuan; Wang, Hong-fei] Chinese Acad Sci, Inst Chem, Lab Mol React Dynam, Beijing Natl Lab Mol Sci, Beijing 100190, Peoples R China. RP Wang, HF (reprint author), Pacific NW Natl Lab, Environm Mol Sci Lab, 902 Battelle Blvd,POB 999,MSIN K8-91, Richland, WA 99352 USA. EM hongfei.wang@pnl.gov RI Wang, Hongfei/B-1263-2010; Liu, Shilin/F-1997-2010 OI Wang, Hongfei/0000-0001-8238-1641; FU Natural Science Foundation of China (NSFC) [20373076, 20425309, 20533070, 20673122]; Ministry of Science and Technology of China (MOST) [2007CB815205, 2007CB815204] FX Hong-fei Wang thanks the support by the Natural Science Foundation of China (NSFC) (No.20373076, No.20425309, and No.20533070) and the Ministry of Science and Technology of China (MOST) (No.2007CB815205). Shi-lin Liu thanks the support by the NSFC (No.20533070) and the MOST (No.2007CB815204). Yuan Guo thanks the support by the NSFC (No.20673122) and the MOST (No.2007CB815205). NR 52 TC 15 Z9 15 U1 7 U2 45 PU CHINESE PHYSICAL SOC PI BEIJING PA P O BOX 603, BEIJING 100080, PEOPLES R CHINA SN 1674-0068 J9 CHINESE J CHEM PHYS JI Chin. J. Chem. Phys. PD DEC 27 PY 2009 VL 22 IS 6 BP 592 EP 600 DI 10.1088/1674-0068/22/06/592-600 PG 9 WC Physics, Atomic, Molecular & Chemical SC Physics GA 542BP UT WOS:000273466600007 ER PT J AU Chen, BW Lei, CH Shin, YS Liu, J AF Chen, Baowei Lei, Chenghong Shin, Yongsoon Liu, Jun TI Probing mechanisms for enzymatic activity enhancement of organophosphorus hydrolase in functionalized mesoporous silica SO BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS LA English DT Article DE Organophosphorus hydrolase; Mesoporous silica; Enzyme activity; Conformational change; Spectroscopic methods ID 3-DIMENSIONAL STRUCTURE; MOLECULAR-SIEVES; IMMOBILIZED ENZYMES; SECONDARY STRUCTURE; NANOPOROUS SUPPORT; CATALYTIC ACTIVITY; CONFINED SPACES; PHOSPHOTRIESTERASE; STABILIZATION; COPOLYMER AB We have previously reported that organophosphorus hydrolase (OPH) can be spontaneously entrapped in functionalized mesoporous silica (FMS) with HOOC- as the functional groups and the entrapped OPH in HOOC-FMS showed enhanced enzyme specific activity. This work is to study the mechanisms that why OPH entrapped in FMS displayed the enhanced activity in views of OPH-FMS interactions using spectroscopic methods. The circular dichroism (CD) spectra show that, comparing to the secondary structure of OPH free in solution, OPH in HOOC-FMS displayed increased alpha-helix/beta-strand transition of OPH with increased OPH loading density. The fluorescence emission spectra of Trp residues were used to assess the tertiary structural changes of the enzyme. There was a 42% increase in fluorescence. This is in agreement with the fact that the fluorescence intensity of OPH was increased accompanying with the increased OPH activity when decreasing urea concentrations in solution. The steady-state anisotropy was increased after OPH entrapping in HOOC-FMS comparing to the free OPH in solution, indicating that protein mobility was reduced upon entrapment. The solvent accessibility of Trp residues of OPH was probed by using acrylamide as a collisional quencher. Trp residues of OPH-FMS had less solvent exposure comparing with free OPH in solution due to its electrostatical binding to HOOC-FMS thereby displaying the increased fluorescence intensity. These results suggest the interactions of OPH with HOOC-FMS resulted in the protein immobilization and a favorable conformational change for OPH in the crowded confinement space and accordingly the enhanced activity. (C) 2009 Elsevier Inc. All rights reserved. C1 [Chen, Baowei; Lei, Chenghong; Shin, Yongsoon; Liu, Jun] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Lei, CH (reprint author), Pacific NW Natl Lab, Mail Stop P7-56,POB 999, Richland, WA 99352 USA. EM Chenghong.Lei@pnl.gov FU NIH National Institute of General Medical Sciences [R01GM080987] FX This work was supported by the NIH National Institute of General Medical Sciences (Grant No. R01GM080987). Pacific Northwest National Laboratory (PNNL) is operated for US Department of Energy by Battelle under Contract DE-AC06-RLO1830. A portion of the research described in this paper was performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at PNNL. NR 31 TC 17 Z9 18 U1 1 U2 14 PU ACADEMIC PRESS INC ELSEVIER SCIENCE PI SAN DIEGO PA 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA SN 0006-291X J9 BIOCHEM BIOPH RES CO JI Biochem. Biophys. Res. Commun. PD DEC 25 PY 2009 VL 390 IS 4 BP 1177 EP 1181 DI 10.1016/j.bbrc.2009.10.112 PG 5 WC Biochemistry & Molecular Biology; Biophysics SC Biochemistry & Molecular Biology; Biophysics GA 531GB UT WOS:000272650800019 PM 19874798 ER PT J AU Miller, MB Chen, DL Xie, HB Luebke, DR Johnson, JK Enick, RM AF Miller, Matthew B. Chen, De-Li Xie, Hong-Bin Luebke, David R. Johnson, J. Karl Enick, Robert M. TI Solubility of CO2 in CO2-philic oligomers; COSMOtherm predictions and experimental results SO FLUID PHASE EQUILIBRIA LA English DT Article DE Carbon dioxide; Solubility; Poly propylene glycol di-methyl ether; Poly ethylene glycol di-methyl ether; Poly di-methyl siloxane; Perfluoro poly ether; COSMO-RS; COSMOtherm ID SUPERCRITICAL CARBON-DIOXIDE; VAPOR-LIQUID-EQUILIBRIUM; BASIS-SETS; MODEL; ENERGY; APPROXIMATION; TEMPERATURE; PRESSURES; CHEMISTRY; MIXTURES AB We report the solubility of carbon dioxide in four physical solvents and compare our data to predicted phase behavior using the conductor-like screening model for real solvents (COSMO-RS) formalism. The solubility data are presented in pressure-composition (Px) diagrams as well as Henry's law coefficients on a wt% basis at 298.15 K. The oligomers presented in this study are poly ethylene glycol di-methyl ether (PEGDME), perfluoro polyether (PFPE), poly di-methyl siloxane (PDMS), and poly propylene glycol di-methyl ether (PPGDME), which is a new solvent designed for this application by our group. These oligomers had 2-5 repeat units. We assess these four oligomers for capturing CO2 from high-pressure streams. The COSMO-RS formalism is able to qualitatively and to some extent quantitatively describe solubilities Of CO2 in each of the oligomers. (C) 2009 Elsevier B.V. All rights reserved. C1 [Miller, Matthew B.] Univ Pittsburgh, Swanson Sch Engn, Dept Chem Engn, Pittsburgh, PA 15261 USA. [Miller, Matthew B.; Chen, De-Li; Xie, Hong-Bin; Luebke, David R.; Johnson, J. Karl; Enick, Robert M.] US DOE, Natl Energy Technol Lab, Pittsburgh, PA 15236 USA. RP Miller, MB (reprint author), Univ Pittsburgh, Swanson Sch Engn, Dept Chem Engn, Pittsburgh, PA 15261 USA. EM mbm35@pitt.edu; karlj@pitt.edu; rme@pitt.edu RI Chen, De-Li/H-6867-2012; Johnson, Karl/E-9733-2013; Xie, Hong-Bin /N-9886-2016 OI Johnson, Karl/0000-0002-3608-8003; FU National Energy Technology Laboratory [DE-AC26-04NT41817] FX This work was performed in support of the National Energy Technology Laboratory's ongoing research in the area of carbon management under the RDS contract DE-AC26-04NT41817. NR 34 TC 38 Z9 38 U1 1 U2 34 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0378-3812 J9 FLUID PHASE EQUILIBR JI Fluid Phase Equilib. PD DEC 25 PY 2009 VL 287 IS 1 BP 26 EP 32 DI 10.1016/j.fluid.2009.08.022 PG 7 WC Thermodynamics; Chemistry, Physical; Engineering, Chemical SC Thermodynamics; Chemistry; Engineering GA 532ZI UT WOS:000272790000005 ER PT J AU Tan, KM Clancy, S Borovilos, M Zhou, M Horer, S Moy, S Volkart, LL Sassoon, J Baumann, U Joachimiak, A AF Tan, Kemin Clancy, Shonda Borovilos, Maria Zhou, Min Hoerer, Stefan Moy, Shiu Volkart, Lour L. Sassoon, Judyth Baumann, Ulrich Joachimiak, Andrzej TI The Mannitol Operon Repressor MtlR Belongs to a New Class of Transcription Regulators in Bacteria SO JOURNAL OF BIOLOGICAL CHEMISTRY LA English DT Article ID COMPLETE GENOME SEQUENCE; ESCHERICHIA-COLI; PHOSPHOTRANSFERASE SYSTEM; BACILLUS-STEAROTHERMOPHILUS; NUCLEOTIDE-SEQUENCE; PROTEIN-STRUCTURE; HIGH-THROUGHPUT; BINDING-SITES; LARGE-SCALE; ENZYME-II AB Many bacteria express phosphoenolpyruvate-dependent phosphotransferase systems (PTS). The mannitol-specific PTS catalyze the uptake and phosphorylation of D-mannitol. The uptake system comprises several genes encoded in the single operon. The expression of the mannitol operon is regulated by a proposed transcriptional factor, mannitol operon repressor (MtlR) that was first studied in Escherichia coli. Here we report the first crystal structures of MtlR from Vibrio parahemeolyticus (Vp-MtlR) and its homolog YggD protein from Shigella flexneri (Sf-YggD). MtlR and YggD belong to the same protein family (Pfam05068). Although Vp-MtlR and Sf-YggD share low sequence identity (22%), their overall structures are very similar, representing a novel all alpha-helical fold, and indicate similar function. However, their lack of any known DNA-binding structural motifs and their unfavorable electrostatic properties imply that MtlR/YggD are unlikely to bind a specific DNA operator directly as proposed earlier. This structural observation is further corroborated by in vitro DNA-binding studies of E. coli MtlR (Ec-MtlR), which detected no interaction of Ec-MtlR with the well characterized mannitol operator/promoter region. Therefore, MtlR/YggD belongs to a new class of transcription factors in bacteria that may regulate gene expression indirectly as a part of a larger transcriptional complex. C1 [Tan, Kemin; Clancy, Shonda; Borovilos, Maria; Zhou, Min; Moy, Shiu; Volkart, Lour L.; Joachimiak, Andrzej] Argonne Natl Lab, Biosci Div, Midwest Ctr Struct Genom, Argonne, IL 60439 USA. [Tan, Kemin; Clancy, Shonda; Borovilos, Maria; Zhou, Min; Moy, Shiu; Volkart, Lour L.; Joachimiak, Andrzej] Argonne Natl Lab, Biosci Div, Struct Biol Ctr, Argonne, IL 60439 USA. [Hoerer, Stefan; Sassoon, Judyth; Baumann, Ulrich] Univ Bern, Dept Chem & Biochem, CH-3012 Bern, Switzerland. RP Joachimiak, A (reprint author), Argonne Natl Lab, Biosci Div, Midwest Ctr Struct Genom, 9700 S Cass Ave, Argonne, IL 60439 USA. EM andrzejj@anl.gov FU National Institutes of Health [GM074942]; United States Department of Energy, Office of Biological and Environmental Research [DE-AC02-06CH11357] FX This work was supported, in whole or in part, by National Institutes of Health Grant GM074942. This work was also supported by the United States Department of Energy, Office of Biological and Environmental Research, under Contract DE-AC02-06CH11357. This work was created by UChicago Argonne, LLC, Operator of Argonne National Laboratory. NR 51 TC 7 Z9 7 U1 1 U2 8 PU AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC PI BETHESDA PA 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USA SN 0021-9258 J9 J BIOL CHEM JI J. Biol. Chem. PD DEC 25 PY 2009 VL 284 IS 52 BP 36670 EP 36679 DI 10.1074/jbc.M109.062679 PG 10 WC Biochemistry & Molecular Biology SC Biochemistry & Molecular Biology GA 535LT UT WOS:000272970500067 PM 19840941 ER PT J AU Rapaka, S Pawar, RJ Stauffer, PH Zhang, DX Chen, SY AF Rapaka, Saikiran Pawar, Rajesh J. Stauffer, Philip H. Zhang, Dongxiao Chen, Shiyi TI Onset of convection over a transient base-state in anisotropic and layered porous media SO JOURNAL OF FLUID MECHANICS LA English DT Article DE absolute/convective; instability; porous media ID GENERALIZED STABILITY THEORY; EFFECTIVE RAYLEIGH NUMBER; NATURAL-CONVECTION; THERMAL-CONVECTION; FLUID; HETEROGENEITY; FLOW; OPERATORS AB The topic of density-driven convection in porous media has been the focus of many recent studies due to its relevance as a long-term trapping mechanism during geological sequestration of carbon dioxide. Most of these studies have addressed the problem in homogeneous and anisotropic permeability fields using linear-stability analysis, and relatively little attention has been paid to the analysis for heterogeneous systems. Previous investigators have reduced the governing equations to an initial-value problem and have analysed it either with a quasi-steady-state approximation model or using numerical integration with arbitrary initial perturbations. Recently, Rapaka et al. (J. Fluid Mech., vol. 609, 2008, pp. 285-303) used the idea of non-modal stability analysis to compute the maximum amplification of perturbations in this system, optimized over the entire space of initial perturbations. This technique is a mathematically rigorous extension of the traditional normal-mode analysis to non-normal and time-dependent problems. In this work, we extend this analysis to the important cases of anisotropic and layered porous media with a permeability variation in the vertical direction. The governing equations are linearized and reduced to a set of coupled ordinary differential equations of the initial-value type using the Galerkin technique. Non-modal stability analysis is used to compute the maximum growth of perturbations along with the optimal wavenumber leading to this growth. We show that unlike the solution of the initial-value problem, results obtained using non-modal analysis are insensitive to the choice of bottom boundary condition. For the anisotropic problem, the dependence of critical time and wavenumber on the anisotropy ratio was found to be in good agreement with theoretical scalings proposed by Ennis-King et al. (Phys. Fluids, vol. 17, 2005, paper no. 084107). For heterogeneous systems, we show that uncertainty in the permeability field at low wavenumbers can influence the growth of perturbations. We use a Monte Carlo approach to compute the mean and standard deviation of the critical time for a sample permeability field. The results from theory are also compared with finite-volume simulations of the governing equations using fully heterogeneous porous media with strong layering. We show that the results from non-modal stability analysis match extremely well with those obtained from the simulations as long as the assumption of strong layering remains valid. C1 [Rapaka, Saikiran; Chen, Shiyi] Johns Hopkins Univ, Dept Mech Engn, Baltimore, MD 21218 USA. [Chen, Shiyi] Peking Univ, Coll Engn, SKLTCS & CAPT, Beijing 100871, Peoples R China. [Pawar, Rajesh J.; Stauffer, Philip H.] Los Alamos Natl Lab, EES 6, Los Alamos, NM 87544 USA. [Zhang, Dongxiao] Univ So Calif, Dept Civil & Environm Engn, Los Angeles, CA 90089 USA. RP Rapaka, S (reprint author), Johns Hopkins Univ, Dept Mech Engn, Baltimore, MD 21218 USA. EM saikiran@jhu.edu RI Zhang, Dongxiao/D-5289-2009; Stauffer, Philip/A-1384-2009; Chen, Shiyi/A-3234-2010; Rapaka, Saikiran/J-9501-2012; OI Zhang, Dongxiao/0000-0001-6930-5994; Rapaka, Saikiran/0000-0001-6527-0974; Stauffer, Philip/0000-0002-6976-221X FU NSF [CBET-0320907, AST-0428325] FX The authors would like to thank Professor Gregory Eyink and Professor Andrea Prosperetti for valuable discussions. Saikiran Rapaka would like to thank Professor Robert McKibbin and Professor Peder Tyvand for comments on the relation between anisotropy and horizontal layering. The simulations were performed on a computational cluster supported by the NSF under grant nos CBET-0320907 and AST-0428325. NR 46 TC 38 Z9 38 U1 0 U2 10 PU CAMBRIDGE UNIV PRESS PI NEW YORK PA 32 AVENUE OF THE AMERICAS, NEW YORK, NY 10013-2473 USA SN 0022-1120 J9 J FLUID MECH JI J. Fluid Mech. PD DEC 25 PY 2009 VL 641 BP 227 EP 244 DI 10.1017/S0022112009991479 PG 18 WC Mechanics; Physics, Fluids & Plasmas SC Mechanics; Physics GA 543OV UT WOS:000273588900012 ER PT J AU Bates, BL Wang, YQ Zhang, Y Pint, BA AF Bates, B. L. Wang, Y. Q. Zhang, Y. Pint, B. A. TI Formation and oxidation performance of low-temperature pack aluminide coatings on ferritic-martensitic steels SO SURFACE & COATINGS TECHNOLOGY LA English DT Article; Proceedings Paper CT 36th International Conference on Metallurgical Coatings and Thin Films CY APR 27-MAY 01, 2009 CL San Diego, CA SP Amer Vacuum Soc, Adv Surface Engn Div DE Aluminide coatings; Pack cementation; Al(2)O(3); Water vapor; Oxidation; Steels ID CHEMICAL-VAPOR-DEPOSITION; STEAM-TURBINE COMPONENTS; FE-BASE ALLOYS; WATER-VAPOR; DIFFUSION COATINGS; AL ALLOYS; BEHAVIOR; ENVIRONMENTS AB A pack cementation process was developed to coat commercial 9% Cr ferritic-martensitic steel T91 at temperatures below its normal tempering temperature to avoid any potential detrimental effect on the mechanical properties of the coated alloy. In order to prevent the formation of Fe(2)Al(5) coatings, the Al activity in the pack cementation process was reduced by substituting the pure Al masteralloy with binary Cr-Al masterailloys containing either 15 or 25 wt.% Al. When the Cr-25Al masteralloy was used, a duplex coating was formed at 700 degrees C, consisting of a thin Fe(2)Al(5) outer layer and an inner layer of FeAl. With the Cr-15Al masteralloy, an FeAl coating of similar to 12 mu m thick was achieved at 700 degrees C. The pack aluminicle coatings fabricated at 700 degrees C are being evaluated in air + 10 vol.% H(2)O at 650 degrees C and 700 degrees C to determine their long-term oxidation performance. (C) 2009 Elsevier B.V. All rights reserved. C1 [Bates, B. L.; Wang, Y. Q.; Zhang, Y.] Tennessee Technol Univ, Dept Mech Engn, Cookeville, TN 38505 USA. [Pint, B. A.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. RP Zhang, Y (reprint author), Tennessee Technol Univ, Dept Mech Engn, Cookeville, TN 38505 USA. EM yzhang@tntech.edu RI Pint, Bruce/A-8435-2008 OI Pint, Bruce/0000-0002-9165-3335 NR 26 TC 19 Z9 20 U1 1 U2 5 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0257-8972 J9 SURF COAT TECH JI Surf. Coat. Technol. PD DEC 25 PY 2009 VL 204 IS 6-7 BP 766 EP 770 DI 10.1016/j.surfcoat.2009.09.063 PG 5 WC Materials Science, Coatings & Films; Physics, Applied SC Materials Science; Physics GA 533XO UT WOS:000272859500005 ER PT J AU Helminiak, MA Yanar, NM Pettit, FS Taylor, TA Meier, GH AF Helminiak, M. A. Yanar, N. M. Pettit, F. S. Taylor, T. A. Meier, G. H. TI The behavior of high-purity, low-density air plasma sprayed thermal barrier coatings SO SURFACE & COATINGS TECHNOLOGY LA English DT Article; Proceedings Paper CT 36th International Conference on Metallurgical Coatings and Thin Films CY APR 27-MAY 01, 2009 CL San Diego, CA SP Amer Vacuum Soc, Adv Surface Engn Div DE APS TBC; Thermal conductivity; CTE mismatch; Sintering; Thermal resistance ID SUPERALLOYS; EXPANSION; ZIRCONIA; SYSTEM AB Research on the behavior of high-purity, low-density (85%) air plasma sprayed (APS) thermal barrier coatings (TBC) with NiCoCrAlY bond coats deposited by argon-shrouded plasma spraying is described. The microstructure of the APS topcoats is one variable in this study intended to maximize the coating thicknesses that can be applied without spallation and to minimize the thermal conduction through the YSZ layer. The specimens were evaluated using cyclic oxidation tests and important properties of the TBCs, such as resistance to sintering and phase transformation, were determined. The high purity resulted in top coats which are highly resistant to sintering and transformation from the metastable tetragonal phase to the equilibrium mixture of monoclinic and cubic phases. The porous topcoat microstructure also resulted in significant durability during thermal cycling. The actual failure mechanisms of the APS coatings were found to depend on topcoat thickness, CTE of the superalloy substrate and the nature of the thermal exposure. (C) 2009 Elsevier B.V. All rights reserved. C1 [Helminiak, M. A.; Yanar, N. M.; Pettit, F. S.; Meier, G. H.] Natl Energy Technol Lab, Pittsburgh, PA 15236 USA. [Helminiak, M. A.; Yanar, N. M.; Pettit, F. S.; Meier, G. H.] Univ Pittsburgh, Dept Mech Engn & Mat Sci, Pittsburgh, PA 15261 USA. [Taylor, T. A.] Praxair Surface Technol Inc, Indianapolis, IN 46224 USA. RP Yanar, NM (reprint author), Natl Energy Technol Lab, Pittsburgh, PA 15236 USA. EM nmy4@pitt.edu NR 14 TC 16 Z9 16 U1 0 U2 16 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0257-8972 J9 SURF COAT TECH JI Surf. Coat. Technol. PD DEC 25 PY 2009 VL 204 IS 6-7 BP 793 EP 796 DI 10.1016/j.surfcoat.2009.09.065 PG 4 WC Materials Science, Coatings & Films; Physics, Applied SC Materials Science; Physics GA 533XO UT WOS:000272859500010 ER PT J AU Haynes, JA Pint, BA Zhang, Y Wright, IG AF Haynes, J. A. Pint, B. A. Zhang, Y. Wright, I. G. TI Comparison of the oxidation behavior of beta and gamma-gamma ' NiPtAl coatings SO SURFACE & COATINGS TECHNOLOGY LA English DT Article; Proceedings Paper CT 36th International Conference on Metallurgical Coatings and Thin Films CY APR 27-MAY 01, 2009 CL San Diego, CA SP Amer Vacuum Soc, Adv Surface Engn Div DE Aluminide coatings; Bond coatings; High temperature oxidation; Platinum; Gamma prime; TBC ID CHEMICAL-VAPOR-DEPOSITION; THERMALLY GROWN OXIDE; NI-BASED SUPERALLOYS; SUBSTRATE COMPOSITION; CYCLIC OXIDATION; TBC SYSTEMS; BOND COATS; PLATINUM; PERFORMANCE; ADHESION AB This study compared the oxidation behaviors of gamma-gamma ' NiPtAl coatings and traditional beta-phase NiPtAl bond coatings. Both types of NiPtAl coatings were fabricated on two different single-crystal Ni-base superalloys using the same source of electroplated Pt. Characterization of the coating composition and alumina scale morphology after cyclic oxidation in dry oxygen at 1150 degrees C indicated that the addition of Ti in one superalloy had affected the scale microstructure and had degraded scale adhesion on the gamma-gamma' coating. In general, the alumina scale formed was thicker on the gamma-gamma'-coated substrates, and those coatings contained a larger number of pores, thought likely to be primarily due to a Kirkendall-type effect. (C) 2009 Elsevier B.V. All rights reserved. C1 [Haynes, J. A.; Pint, B. A.; Wright, I. G.] Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. [Zhang, Y.] Tennessee Technol Univ, Dept Mech Engn, Cookeville, TN 38505 USA. RP Haynes, JA (reprint author), Oak Ridge Natl Lab, Div Mat Sci & Technol, Oak Ridge, TN 37831 USA. EM z15@ornl.gov RI Pint, Bruce/A-8435-2008 OI Pint, Bruce/0000-0002-9165-3335 NR 26 TC 17 Z9 17 U1 2 U2 25 PU ELSEVIER SCIENCE SA PI LAUSANNE PA PO BOX 564, 1001 LAUSANNE, SWITZERLAND SN 0257-8972 J9 SURF COAT TECH JI Surf. Coat. Technol. PD DEC 25 PY 2009 VL 204 IS 6-7 BP 816 EP 819 DI 10.1016/j.surfcoat.2009.09.071 PG 4 WC Materials Science, Coatings & Films; Physics, Applied SC Materials Science; Physics GA 533XO UT WOS:000272859500015 ER PT J AU Maeda, Y Uchiyama, Y Bamba, A Kosugi, H Tsunemi, H Helder, EA Vink, J Kodaka, N Terada, Y Fukazawa, Y Hiraga, J Hughes, JP Kokubun, M Kouzu, T Matsumoto, H Miyata, E Nakamura, R Okada, S Someya, K Tamagawa, T Tamura, K Totsuka, K Tsuboi, Y Ezoe, Y Holt, SS Ishida, M Kamae, T Petre, R Takahashi, T AF Maeda, Yoshitomo Uchiyama, Yasunobu Bamba, Aya Kosugi, Hiroko Tsunemi, Hiroshi Helder, Eveline A. Vink, Jacco Kodaka, Natsuki Terada, Yukikatsu Fukazawa, Yasushi Hiraga, Junko Hughes, John P. Kokubun, Motohide Kouzu, Tomomi Matsumoto, Hironori Miyata, Emi Nakamura, Ryoko Okada, Shunsaku Someya, Kentaro Tamagawa, Toru Tamura, Keisuke Totsuka, Kohta Tsuboi, Yohko Ezoe, Yuichiro Holt, Stephen S. Ishida, Manabu Kamae, Tsuneyoshi Petre, Robert Takahashi, Tadayuki TI Suzaku X-Ray Imaging and Spectroscopy of Cassiopeia A SO PUBLICATIONS OF THE ASTRONOMICAL SOCIETY OF JAPAN LA English DT Article DE ISM: cosmic rays; ISM: individual (Cassiopeia A); ISM: supernova remnants ID SUPERNOVA REMNANT W49B; BOARD SUZAKU; PARTICLE-ACCELERATION; MAGNETIC-FIELD; LINE EMISSION; ENERGY; SPECTRUM; CHANDRA; ELECTRONS; SHELL AB Suzaku X-ray observations of a young supernova remnant, Cassiopeia A, were carried out. K-shell transition lines from highly ionized ions of various elements were detected, including Chromium (Cr-K alpha at 5.61 keV). The X-ray continuum spectra were modeled in the 3.4-40keV band, summed over the entire remnant, and were fitted with a simplest combination of the thermal bremsstrahlung and the non-thermal cut-off power-law models. The spectral fits with this assumption indicate that the continuum emission is likely to be dominated by non-thermal emission with a cut-off energy at > 1 keV. The thermal-to-non thermal fraction of the continuum flux in the 4-10 keV band is best estimated as similar to 0.1. Non-thermal-dominated continuum images in the 4-14 keV band were made. The peak of the non-thermal X-rays appears at the western part. The peak position of the TeV gamma-rays measured with HEGRA and MAGIC is also shifted at the western part with the I-sigma confidence. Since the location of the X-ray continuum emission was known to be presumably identified with the reverse shock region, the possible keV-TeV correlations give a hint that the accelerated multi-TeV hadrons in Cassiopeia A are dominated by heavy elements in the reverse shock region. C1 [Maeda, Yoshitomo; Uchiyama, Yasunobu; Bamba, Aya; Kokubun, Motohide; Nakamura, Ryoko; Okada, Shunsaku; Someya, Kentaro; Tamura, Keisuke; Ishida, Manabu; Takahashi, Tadayuki] Japan Aerosp Explorat Agcy JAXA, Dept High Energy Astrophys, ISAS, Kanagawa 2298510, Japan. [Uchiyama, Yasunobu; Kamae, Tsuneyoshi] Stanford Linear Accelerator Ctr, Kavli Inst Cosmol & Particle Astrophys, Menlo Pk, CA 94025 USA. [Kosugi, Hiroko; Tsunemi, Hiroshi; Miyata, Emi] Osaka Univ, Dept Earth & Space Sci, Grad Sch Sci, Osaka 5600043, Japan. [Helder, Eveline A.; Vink, Jacco] Univ Utrecht, Astron Inst Utrecht, NL-3508 TA Utrecht, Netherlands. [Kodaka, Natsuki; Terada, Yukikatsu; Kouzu, Tomomi] Saitama Univ, Dept Phys, Sakura, Ibaraki 3388570, Japan. [Fukazawa, Yasushi] Hiroshima Univ, Dept Phys Sci, Hiroshima 7398526, Japan. [Hiraga, Junko; Tamagawa, Toru] RIKEN, Cosm Radiat Lab, Wako, Saitama 3510198, Japan. [Hughes, John P.] Rutgers State Univ, Dept Phys & Astron, Piscataway, NJ 08854 USA. [Matsumoto, Hironori] Kyoto Univ, Dept Phys, Grad Sch Sci, Sakyo Ku, Kyoto 6068502, Japan. [Totsuka, Kohta; Tsuboi, Yohko] Chuo Univ, Dept Phys, Bunkyo Ku, Tokyo 1128551, Japan. [Ezoe, Yuichiro] Tokyo Metropolitan Univ, Dept Phys, Tokyo 1920397, Japan. [Holt, Stephen S.] FW Olin Coll Engn Needham, Needham, MA 02492 USA. [Petre, Robert] NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA. RP Maeda, Y (reprint author), Japan Aerosp Explorat Agcy JAXA, Dept High Energy Astrophys, ISAS, 3-1-1 Yoshinodai, Kanagawa 2298510, Japan. EM ymaeda@astro.isas.jaxa.jp RI Terada, Yukikatsu/A-5879-2013; XRAY, SUZAKU/A-1808-2009 OI Terada, Yukikatsu/0000-0002-2359-1857; FU Netherlands Organization for Scientific Research (NWO); Ministry of Education, Culture, Sports, Science and Technology [21018009, 16002004] FX We would like to express our sincere thanks to Prof. Gerd Puhlhofer for his insightful comments. We thank Dr. Javier Rico and his MAGIC Collaborators, who kindly provided TeV data, and technically guided us concerning how to handle it. Prof. Katsuji Koyama provided very useful comments on line analysis. We also thank all members of the Suzaku team. EH and JV are supported by the Vidi grant of JV from the Netherlands Organization for Scientific Research (NWO). This work is partly supported by a Grant-in-Aid for Scientific Research by the Ministry of Education, Culture, Sports, Science and Technology (21018009 & 16002004). NR 49 TC 24 Z9 24 U1 0 U2 1 PU OXFORD UNIV PRESS PI OXFORD PA GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND SN 0004-6264 EI 2053-051X J9 PUBL ASTRON SOC JPN JI Publ. Astron. Soc. Jpn. PD DEC 25 PY 2009 VL 61 IS 6 BP 1217 EP 1228 DI 10.1093/pasj/61.6.1217 PG 12 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 540BT UT WOS:000273306300004 ER PT J AU Pagel, JM Gooley, TA Rajendran, J Fisher, DR Wilson, WA Sandmaier, BM Matthews, DC Deeg, HJ Gopal, AK Martin, PJ Storb, RF Press, OW Appelbaum, FR AF Pagel, John M. Gooley, Theodore A. Rajendran, Joseph Fisher, Darrell R. Wilson, Wendy A. Sandmaier, Brenda M. Matthews, Dana C. Deeg, H. Joachim Gopal, Ajay K. Martin, Paul J. Storb, Rainer F. Press, Oliver W. Appelbaum, Frederick R. TI Allogeneic hematopoietic cell transplantation after conditioning with I-131-anti-CD45 antibody plus fludarabine and low-dose total body irradiation for elderly patients with advanced acute myeloid leukemia or high-risk myelodysplastic syndrome SO BLOOD LA English DT Article ID ACUTE MYELOGENOUS LEUKEMIA; BONE-MARROW-TRANSPLANTATION; VERSUS-HOST-DISEASE; UNRELATED DONORS; PHASE-I; HEMATOLOGIC MALIGNANCIES; MONOCLONAL-ANTIBODIES; ANTI-CD45 ANTIBODY; RANDOMIZED-TRIAL; 1ST REMISSION AB We conducted a study to estimate the maximum tolerated dose (MTD) of I-131-anti-CD45 antibody (Ab; BC8) that can be combined with a standard reduced-intensity conditioning regimen before allogeneic hematopoietic cell transplantation. Fifty-eight patients older than 50 years with advanced acute myeloid leukemia (AML) or high-risk myelodysplastic syndrome (MDS) were treated with I-131-BC8 Ab and fludarabine plus 2 Gy total body irradiation. Eighty-six percent of patients had AML or MDS with greater than 5% marrow blasts at the time of transplantation. Treatment produced a complete remission in all patients, and all had 100% donor-derived CD3(+) and CD33(+) cells in the blood by day 28 after the transplantation. The MTD of I-131-BC8 Ab delivered to liver was estimated to be 24 Gy. Seven patients (12%) died of nonrelapse causes by day 100. The estimated probability of recurrent malignancy at 1 year is 40%, and the 1-year survival estimate is 41%. These results show that CD45-targeted radiotherapy can be safely combined with a reduced-intensity conditioning regimen to yield encouraging overall survival for older, high-risk patients with AML or MDS. This study was registered at www.clinicaltrials.govas # NCT00008177. (Blood. 2009; 114: 5444-5453) C1 [Pagel, John M.; Gooley, Theodore A.; Wilson, Wendy A.; Sandmaier, Brenda M.; Matthews, Dana C.; Deeg, H. Joachim; Gopal, Ajay K.; Martin, Paul J.; Storb, Rainer F.; Press, Oliver W.; Appelbaum, Frederick R.] Fred Hutchinson Canc Res Ctr, Div Clin Res, Seattle, WA 98109 USA. [Pagel, John M.; Sandmaier, Brenda M.; Deeg, H. Joachim; Gopal, Ajay K.; Martin, Paul J.; Storb, Rainer F.; Press, Oliver W.; Appelbaum, Frederick R.] Univ Washington, Dept Med, Seattle, WA USA. [Rajendran, Joseph] Univ Washington, Dept Nucl Med, Seattle, WA 98195 USA. [Fisher, Darrell R.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Matthews, Dana C.] Univ Washington, Dept Pediat, Seattle, WA 98195 USA. RP Pagel, JM (reprint author), Fred Hutchinson Canc Res Ctr, Div Clin Res, 1100 Fairview Ave N,M-S D5-380, Seattle, WA 98109 USA. EM jpagel@fhcrc.org FU NCI NIH HHS [K08 CA095448, P01 CA018029, P01 CA044991, P01 CA078902, P30 CA015704, R01 CA109663] NR 57 TC 66 Z9 67 U1 0 U2 1 PU AMER SOC HEMATOLOGY PI WASHINGTON PA 2021 L ST NW, SUITE 900, WASHINGTON, DC 20036 USA SN 0006-4971 EI 1528-0020 J9 BLOOD JI Blood PD DEC 24 PY 2009 VL 114 IS 27 BP 5444 EP 5453 DI 10.1182/blood-2009-03-213298 PG 10 WC Hematology SC Hematology GA 536UD UT WOS:000273068400008 PM 19786617 ER PT J AU Calhoun, TR Ginsberg, NS Schlau-Cohen, GS Cheng, YC Ballottari, M Bassi, R Fleming, GR AF Calhoun, Tessa R. Ginsberg, Naomi S. Schlau-Cohen, Gabriela S. Cheng, Yuan-Chung Ballottari, Matteo Bassi, Roberto Fleming, Graham R. TI Quantum Coherence Enabled Determination of the Energy Landscape in Light-Harvesting Complex II SO JOURNAL OF PHYSICAL CHEMISTRY B LA English DT Article ID 2-DIMENSIONAL ELECTRONIC SPECTROSCOPY; ANTENNA PROTEIN; HIGHER-PLANTS; PHOTOSYNTHESIS; DYNAMICS; DISSIPATION; MECHANISM; COUPLINGS; SPECTRA; DENSITY AB The near-unity efficiency of energy transfer in photosynthesis makes photosynthetic light-harvesting complexes a promising avenue for developing new renewable energy technologies. Knowledge of the energy landscape of these complexes is essential in understanding their function, but its experimental determination has proven elusive. Here, the observation of quantum coherence using two-dimensional electronic spectroscopy is employed to directly measure the 14 lowest electronic energy levels in light-harvesting complex II (LHCII), the most abundant antenna complex in plants containing approximately 50% of the world's chlorophyll, We observe that the electronically excited states are relatively evenly distributed, highlighting an important design principle of photosynthetic complexes that explains the observed ultrafast intracomplex energy transfer in LHCII. C1 [Calhoun, Tessa R.; Ginsberg, Naomi S.; Schlau-Cohen, Gabriela S.; Cheng, Yuan-Chung; Fleming, Graham R.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Calhoun, Tessa R.; Ginsberg, Naomi S.; Schlau-Cohen, Gabriela S.; Cheng, Yuan-Chung; Fleming, Graham R.] Univ Calif Berkeley, Inst QB3, Berkeley, CA 94720 USA. [Calhoun, Tessa R.; Ginsberg, Naomi S.; Schlau-Cohen, Gabriela S.; Cheng, Yuan-Chung; Fleming, Graham R.] Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Ballottari, Matteo; Bassi, Roberto] Univ Verona, Dept Biotechnol, I-37134 Verona, Italy. RP Fleming, GR (reprint author), Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. EM GRFleming@lbl.gov RI Cheng, Yuan-Chung/A-6566-2008; OI Cheng, Yuan-Chung/0000-0003-0125-4267; Ballottari, Matteo/0000-0001-8410-3397; bassi, roberto/0000-0002-4140-8446 FU Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC0205CH11231]; Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energy [DE-AC03-76SF000098]; Italian Basic Research Foundation [IRB RBLA0345SF002]; FISR IDROBIO (University of Verona); LBNL Glenn T. Seaborg FX The authors thank Rienk van Grondelle for valuable discussions. This work was Supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract DE-AC0205CH11231 and the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energy through Grant DE-AC03-76SF000098 (at LBNL and UC Berkeley) and by the Italian Basic Research Foundation Contracts FIRB RBLA0345SF002 (Solanacee) and FISR IDROBIO (University of Verona). N.S.G. thanks the LBNL Glenn T. Seaborg postdoctoral fellowship for Support. NR 29 TC 169 Z9 170 U1 4 U2 42 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1520-6106 J9 J PHYS CHEM B JI J. Phys. Chem. B PD DEC 24 PY 2009 VL 113 IS 51 BP 16291 EP 16295 DI 10.1021/jp908300c PG 5 WC Chemistry, Physical SC Chemistry GA 531ZR UT WOS:000272713000002 PM 20014871 ER PT J AU Cardoso, MB Smolensky, D Heller, WT O'Neill, H AF Cardoso, Mateus B. Smolensky, Dmitriy Heller, William T. O'Neill, Hugh TI Insight into the Structure of Light-Harvesting Complex II and Its Stabilization in Detergent Solution SO JOURNAL OF PHYSICAL CHEMISTRY B LA English DT Article ID ANGLE NEUTRON-SCATTERING; X-RAY-SCATTERING; A/B PROTEIN COMPLEX; TIME-RESOLVED FLUORESCENCE; OCTYL-BETA-GLUCOSIDE; MEMBRANE-PROTEINS; LHC-II; CONTRAST VARIATION; PHOTOSYSTEM-II; RHODOPSEUDOMONAS-ACIDOPHILA AB The structure of spinach light-harvesting complex II (LHC II), stabilized in a solution of the detergent n-octyl-beta-D-glucoside (BOG), was investigated by small-angle neutron scattering (SANS). Physicochemical characterization of the isolated complex indicated that it was pure (>95%) and also in its native trimeric state. SANS with contrast variation was used to investigate the properties of the protein-detergent complex at three different H(2)O/D(2)O contrast match points, enabling the scattering properties of the protein and detergent to be investigated independently. The topological shape of LHC 11, determined using ab initio shape restoration methods from the SANS data at the contrast match point of BOG, was consistent with the X-ray crystallographic structure of LHC 11 (Liu et al. Nature 2004 428, 287-292). The interactions of the protein and detergent were investigated at the contrast match point for the protein and also in 100% D(2)O. The data suggested that BOG micelle structure was altered by its interaction with LHC 11, but large aggregate structures were not Formed. Indirect Fourier transform analysis of the LHC II/BOG scattering curves showed that the increase in the maximum dimension of the protein-detergent complex was consistent with the presence of a monolayer of detergent Surrounding the protein. A model of the LHC II/BOG complex was generated to interpret the measurements made in 100% D(2)O. This model adequately reproduced the overall size of the LHC II/BOG complex, but demonstrated that the detergent does not have a highly regular shape that surrounds the hydrophobic periphery of LHC II. In addition to demonstrating that natively Structured LHC 11 can be produced for functional characterization and for use in artificial solar energy applications, the analysis and modeling approaches described here can be used for characterizing detergent-associated alpha-helical transmembrane proteins. C1 [Cardoso, Mateus B.; Smolensky, Dmitriy; Heller, William T.; O'Neill, Hugh] Oak Ridge Natl Lab, Div Chem Sci, Ctr Struct Mol Biol, Oak Ridge, TN 37831 USA. RP Heller, WT (reprint author), Oak Ridge Natl Lab, Div Chem Sci, Ctr Struct Mol Biol, Oak Ridge, TN 37831 USA. EM hellerwt@ornl.gov; oneillhm@ornl.gov RI Cardoso, Mateus/A-7926-2015; OI Cardoso, Mateus/0000-0003-2102-1225; O'Neill, Hugh/0000-0003-2966-5527 FU Capes-Brazil; ORNL Laboratory; Office of Biological and Environmental Research, U.S. Department of Energy [DE-AC05-00OR22725] FX M.B.C. thanks Capes-Brazil for the support. This work was Supported by the ORNL Laboratory Director's Research Development Program. This research at Oak Ridge National Laboratory's Center for Structural Molecular Biology (CSMB) was supported by the Office of Biological and Environmental Research, using facilities Supported by the U.S. Department of Energy, managed by UT-Battelle, LLC, under Contract No.DE-AC05-00OR22725. NR 67 TC 16 Z9 16 U1 1 U2 17 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 1520-6106 J9 J PHYS CHEM B JI J. Phys. Chem. B PD DEC 24 PY 2009 VL 113 IS 51 BP 16377 EP 16383 DI 10.1021/jp905050b PG 7 WC Chemistry, Physical SC Chemistry GA 531ZR UT WOS:000272713000012 PM 19954150 ER PT J AU Wu, DY Hugenholtz, P Mavromatis, K Pukall, R Dalin, E Ivanova, NN Kunin, V Goodwin, L Wu, M Tindall, BJ Hooper, SD Pati, A Lykidis, A Spring, S Anderson, IJ D'haeseleer, P Zemla, A Singer, M Lapidus, A Nolan, M Copeland, A Han, C Chen, F Cheng, JF Lucas, S Kerfeld, C Lang, E Gronow, S Chain, P Bruce, D Rubin, EM Kyrpides, NC Klenk, HP Eisen, JA AF Wu, Dongying Hugenholtz, Philip Mavromatis, Konstantinos Pukall, Ruediger Dalin, Eileen Ivanova, Natalia N. Kunin, Victor Goodwin, Lynne Wu, Martin Tindall, Brian J. Hooper, Sean D. Pati, Amrita Lykidis, Athanasios Spring, Stefan Anderson, Iain J. D'haeseleer, Patrik Zemla, Adam Singer, Mitchell Lapidus, Alla Nolan, Matt Copeland, Alex Han, Cliff Chen, Feng Cheng, Jan-Fang Lucas, Susan Kerfeld, Cheryl Lang, Elke Gronow, Sabine Chain, Patrick Bruce, David Rubin, Edward M. Kyrpides, Nikos C. Klenk, Hans-Peter Eisen, Jonathan A. TI A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea SO NATURE LA English DT Article ID MICROBIAL DIVERSITY; PROTEIN FAMILIES; DATABASE GOLD; PROJECTS; SEQUENCE AB Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms(1). There are now nearly 1,000 completed bacterial and archaeal genomes available(2), most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution(3-5). To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits ( compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic 'phylogenomic' efforts to compile a phylogeny-driven 'Genomic Encyclopedia of Bacteria and Archaea' in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come. C1 [Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos; Dalin, Eileen; Ivanova, Natalia N.; Kunin, Victor; Hooper, Sean D.; Pati, Amrita; Lykidis, Athanasios; Anderson, Iain J.; D'haeseleer, Patrik; Lapidus, Alla; Nolan, Matt; Copeland, Alex; Chen, Feng; Cheng, Jan-Fang; Lucas, Susan; Kerfeld, Cheryl; Chain, Patrick; Rubin, Edward M.; Kyrpides, Nikos C.; Eisen, Jonathan A.] DOE Joint Genome Inst, Walnut Creek, CA 94598 USA. [Wu, Dongying; Singer, Mitchell; Eisen, Jonathan A.] Univ Calif Davis, Davis, CA 95616 USA. [Pukall, Ruediger; Tindall, Brian J.; Spring, Stefan; Lang, Elke; Gronow, Sabine; Klenk, Hans-Peter] Deutsch Sammlung Mikroorganism Zellkultur GmbH, German Collect Microorganisms & Cell Cultures, D-38124 Braunschweig, Germany. [Goodwin, Lynne; Han, Cliff; Chain, Patrick; Bruce, David] Los Alamos Natl Lab, DOE Joint Genome Inst, Los Alamos, NM 87545 USA. [D'haeseleer, Patrik; Zemla, Adam] Univ Virginia, Charlottesville, VA 22904 USA. [Wu, Martin] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. RP Eisen, JA (reprint author), DOE Joint Genome Inst, Walnut Creek, CA 94598 USA. EM jaeisen@ucdavis.edu RI Hugenholtz, Philip/G-9608-2011; chain, patrick/B-9777-2013; Kyrpides, Nikos/A-6305-2014; Spring, Stefan/N-6933-2013; Lapidus, Alla/I-4348-2013 OI Eisen, Jonathan A./0000-0002-0159-2197; Chain, Patrick/0000-0003-3949-3634; Kyrpides, Nikos/0000-0002-6131-0462; Spring, Stefan/0000-0001-6247-0938; Lapidus, Alla/0000-0003-0427-8731 FU US Department of Energy's Office of Science, Biological and Environmental Research Program; University of California, Lawrence Berkeley National Laboratory [DE-AC02-05CH11231]; Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Los Alamos National Laboratory [DE-AC02-06NA25396]; Gordon and Betty Moore Foundation [1660]; DFG INST [599/1-1] FX We thank the following people for assistance in aspects of the project including planning and discussions ( R. Stevens, G. Olsen, R. Edwards, J. Bristow, N. Ward, S. Baker, T. Lowe, J. Tiedje, G. Garrity, A. Darling, S. Giovannoni), analysis of genomes whose work could not be included in this report ( B. Henrissat, G. Xie, J. Kinney, I. Paulsen, N. Rawlings, M. Huntemann), project management ( M. Miller, M. Fenner, M. McGowen, A. Greiner), sequencing and finishing ( K. Ikeda, M. Chovatia, P. Richardson, T. Glavinadelrio, C. Detter), culture growth, DNA extraction, and metadata ( D. Gleim, E. Brambilla, S. Schneider, M. Schroder, M. Jando, G. Gehrich-Schroter, C. Wahrenburg, K. Steenblock, S. Welnitz, M. Kopitz, R. Fahnrich,H. Pomrenke, A. Schutze, M. Rohde, M. Goker), and manuscript editing ( M. Youle). This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract no. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract no. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract no. DE-AC02-06NA25396. Support for J. A. E., D. W. and M. W. was provided by the Gordon and Betty Moore Foundation Grant no. 1660 to J. A. E. Support for work at DSMZ was provided under DFG INST 599/1-1. NR 30 TC 555 Z9 562 U1 7 U2 102 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 0028-0836 J9 NATURE JI Nature PD DEC 24 PY 2009 VL 462 IS 7276 BP 1056 EP 1060 DI 10.1038/nature08656 PG 5 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 535UB UT WOS:000272996000047 PM 20033048 ER PT J AU Yeung, N Lin, YW Gao, YG Zhao, X Russell, BS Lei, LY Miner, KD Robinson, H Lu, Y AF Yeung, Natasha Lin, Ying-Wu Gao, Yi-Gui Zhao, Xuan Russell, Brandy S. Lei, Lanyu Miner, Kyle D. Robinson, Howard Lu, Yi TI Rational design of a structural and functional nitric oxide reductase SO NATURE LA English DT Article ID HEME-COPPER OXIDASE; DE-NOVO DESIGN; 4-HELIX BUNDLE PROTEIN; CU-B CENTER; PARACOCCUS-DENITRIFICANS; COMPUTATIONAL DESIGN; MOLECULAR-DYNAMICS; METAL-IONS; MYOGLOBIN; SITE AB Protein design provides a rigorous test of our knowledge about proteins and allows the creation of novel enzymes for biotechnological applications. Whereas progress has been made in designing proteins that mimic native proteins structurally(1-3), it is more difficult to design functional proteins(4-8). In comparison to recent successes in designing non-metalloproteins(4,6,7,9,10), it is even more challenging to rationally design metalloproteins that reproduce both the structure and function of native metalloenzymes(5,8,11-20). This is because protein metal-binding sites are much more varied than non-metal-containing sites, in terms of different metal ion oxidation states, preferred geometry and metal ion ligand donor sets. Because of their variability, it has been difficult to predict metal-binding site properties in silico, as many of the parameters, such as force fields, are ill-defined. Therefore, the successful design of a structural and functional metalloprotein would greatly advance the field of protein design and our understanding of enzymes. Here we report a successful, rational design of a structural and functional model of a metalloprotein, nitric oxide reductase (NOR), by introducing three histidines and one glutamate, predicted as ligands in the active site of NOR, into the distal pocket of myoglobin. A crystal structure of the designed protein confirms that the minimized computer model contains a haem/non-haem Fe(B) centre that is remarkably similar to that in the crystal structure. This designed protein also exhibits NO reduction activity, and so models both the structure and function of NOR, offering insight that the active site glutamate is required for both iron binding and activity. These results show that structural and functional metalloproteins can be rationally designed in silico. C1 [Yeung, Natasha; Lin, Ying-Wu; Zhao, Xuan; Russell, Brandy S.; Lei, Lanyu; Lu, Yi] Univ Illinois, Dept Chem, Urbana, IL 61801 USA. [Gao, Yi-Gui] Univ Illinois, George L Clark Xray Facil, Urbana, IL 61801 USA. [Gao, Yi-Gui] Univ Illinois, Mat Lab 3M, Urbana, IL 61801 USA. [Miner, Kyle D.; Lu, Yi] Univ Illinois, Dept Biochem, Urbana, IL 61801 USA. [Robinson, Howard] Brookhaven Natl Lab, Dept Biol, Upton, NY 11973 USA. RP Lu, Y (reprint author), Univ Illinois, Dept Chem, 1209 W Calif St, Urbana, IL 61801 USA. EM yi-lu@illinois.edu RI Lu, Yi/B-5461-2010; OI Lu, Yi/0000-0003-1221-6709; Miner, Kyle/0000-0001-9562-2459 FU US National Institutes of Health [GM062211] FX We thank M. J. Nilges for help with EPR analysis, S. L. Mullen and F. Sun for aiding in GC/MS data collection, E. Lee for help with computational modelling, N. M. Marshall for providing Azurin protein, J. R. Askim for help in FeBMb expression and purification, and T. Hayashi and P. Moenne-Loccoz for suggestions regarding N2O detection in solution. This work was supported by the US National Institutes of Health (GM062211). NR 41 TC 121 Z9 121 U1 4 U2 78 PU NATURE PUBLISHING GROUP PI LONDON PA MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND SN 0028-0836 J9 NATURE JI Nature PD DEC 24 PY 2009 VL 462 IS 7276 BP 1079 EP U144 DI 10.1038/nature08620 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 535UB UT WOS:000272996000052 PM 19940850 ER PT J AU Kim, W Silby, MW Purvine, SO Nicoll, JS Hixson, KK Monroe, M Nicora, CD Lipton, MS Levy, SB AF Kim, Wook Silby, Mark W. Purvine, Sam O. Nicoll, Julie S. Hixson, Kim K. Monroe, Matt Nicora, Carrie D. Lipton, Mary S. Levy, Stuart B. TI Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1 SO PLOS ONE LA English DT Article ID ESCHERICHIA-COLI; OVERLAPPING GENES; BACILLUS-SUBTILIS; SHIGELLA-FLEXNERI; IN-VIVO; EXPRESSION; GENOMES; SOIL; INITIATION; DISCOVERY AB Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of possible functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations that predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes that were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologs in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization. C1 [Kim, Wook; Silby, Mark W.; Nicoll, Julie S.; Levy, Stuart B.] Tufts Univ, Sch Med, Ctr Adaptat Genet & Drug Resistance, Boston, MA 02111 USA. [Kim, Wook; Silby, Mark W.; Nicoll, Julie S.; Levy, Stuart B.] Tufts Univ, Sch Med, Dept Mol Biol & Microbiol, Boston, MA 02111 USA. [Purvine, Sam O.; Hixson, Kim K.; Monroe, Matt; Nicora, Carrie D.; Lipton, Mary S.] Pacific NW Natl Lab, Richland, WA 99352 USA. RP Kim, W (reprint author), Harvard Univ, Ctr Syst Biol, Cambridge, MA 02138 USA. EM Stuart.Levy@tufts.edu FU US Department of Energy, Office of Biological and Environmental Research [43488, DE-AC05-76RL01830]; United States Department of Agriculture [2006-35604-16673]; Natural Sciences and Engineering Research Council of Canada FX Portions of this research were conducted at the Environmental Molecular Sciences Laboratory (EMSL), U. S. Department of Energy ( DOE) national scientific user facility located at the Pacific Northwest National Laboratory in Richland, Washington. This work was supported by the US Department of Energy, Office of Biological and Environmental Research ( project 43488), and the United States Department of Agriculture ( grant 2006-35604-16673 to SBL). PNNL is a multi-program national laboratory operated by Battelle Memorial Institute for the DOE under Contract DE-AC05-76RL01830. W.K. was supported in part by a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. NR 42 TC 20 Z9 20 U1 1 U2 6 PU PUBLIC LIBRARY SCIENCE PI SAN FRANCISCO PA 185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA SN 1932-6203 J9 PLOS ONE JI PLoS One PD DEC 24 PY 2009 VL 4 IS 12 AR e8455 DI 10.1371/journal.pone.0008455 PG 7 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 537HN UT WOS:000273104000017 PM 20041161 ER PT J AU Meyer, MM Wang, XB Reed, CA Wang, LS Kass, SR AF Meyer, Matthew M. Wang, Xue-Bin Reed, Christopher A. Wang, Lai-Sheng Kass, Steven R. TI Investigating the Weak to Evaluate the Strong: An Experimental Determination of the Electron Binding Energy of Carborane Anions and the Gas phase Acidity of Carborane Acids SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID NEUTRAL BRONSTED ACIDS; PROTON-TRANSFER; SUPERACIDS; CHEMISTRY; DENSITY AB Five CHB(11)X(6)Y(5)(-) carborane anions from the series X = Br, Cl, I and Y = H, Cl, CH(3) were generated by electrospray ionization, and their reactivity with a series of Bronsted acids and electron transfer reagents were examined in the gas phase. The undecachlorocarborane acid, H(CHB(11)Cl(11)), was found to be far more acidic than the former record holder, (1-C(4)F(9)SO(2))(2)NH (i.e., Delta H degrees(acid) = 241 +/- 29 vs 291.1 +/- 2.2 kcal mol(-1)) and bridges the gas-phase acidity and basicity scales for the first time. Its conjugate base, CHB(11)Cl(11)(-), was found by photoelectron spectroscopy to have a remarkably large electron binding energy (6.35 +/- 0.02 eV) but the value for the (1-C(4)F(9)SO(2))(2)N(-) anion is even larger (6.5 +/- 0.1 eV). Consequently, it is the weak H-(CHB(11)Cl(11)) BDE (70.0 kcal mol(-1), G3(MP2)) compared to the strong BDE of (1-C(4)F(9)SO(2))(2)N-H (127.4 +/- 3.2 kcal mol(-1)) that accounts for the greater acidity of carborane acids. C1 [Reed, Christopher A.] Univ Calif Riverside, Dept Chem, Riverside, CA 92521 USA. [Meyer, Matthew M.; Kass, Steven R.] Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA. [Wang, Xue-Bin; Wang, Lai-Sheng] Washington State Univ, Dept Phys, Richland, WA 99354 USA. [Wang, Xue-Bin; Wang, Lai-Sheng] Pacific NW Natl Lab, Div Chem & Mat Sci, Richland, WA 99352 USA. RP Reed, CA (reprint author), Univ Calif Riverside, Dept Chem, Riverside, CA 92521 USA. EM chris.reed@ucr.edu; Lai-Sheng_Wang@Brown.edu; kass@umn.edu FU National Science Foundation; Minnesota Supercomputer Institute for Advanced Computational Research; U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences FX We are grateful to the National Science Foundation for support of this research to SRK, CAR, and LSW as well as the Minnesota Supercomputer Institute for Advanced Computational Research. The photoelectron spectra work was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. We thank Irina Stoyanova for carborane anion synthesis and Dr. M. Juhasz for helpful discussions. NR 23 TC 17 Z9 17 U1 0 U2 22 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 23 PY 2009 VL 131 IS 50 BP 18050 EP + DI 10.1021/ja908964h PG 3 WC Chemistry, Multidisciplinary SC Chemistry GA 543XY UT WOS:000273615400020 PM 19950932 ER PT J AU Wood, DL Chlistunoff, J Majewski, J Borup, RL AF Wood, David L., III Chlistunoff, Jerzy Majewski, Jaroslaw Borup, Rodney L. TI Nafion Structural Phenomena at Platinum and Carbon Interfaces SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID PEM FUEL-CELLS; RESOLUTION NEUTRON-RADIOGRAPHY; OXYGEN REDUCTION KINETICS; SINGLE-CRYSTAL SURFACES; PERFLUORINATED IONOMER; LOADING ELECTRODES; IMAGING TECHNIQUE; IMPURITY CATIONS; WATER TRANSPORT; ULTRA-LOW AB Neutron reflectometry was used to examine the interactions of polymer electrolyte fuel cell (PEFC) materials that comprise the triple-phase interface. Smooth, idealized layers of Nafion on glassy carbon (GC) and Pt surfaces were used to experimentally model the PEFC electrode interfaces. Different multilayer structures of Nafion were found in contact with the Pt or GC surfaces. These structures showed separate hydrophobic and hydrophilic domains formed within the Nafion layer when equilibrated with saturated D(2)O vapor. A hydrophobic Nafion region was formed adjacent to a Pt film. However, when Nafion was in contact with a PtO surface, the Nafion at the Pt interface became hydrophilic. The adsorbed oxide layer caused a long-range restructuring of the perfluorosulfonic acid polymer chains that comprise Nafion. The thicknesses of the hydrophobic and hydrophilic domains changed to the same magnitude when the oxide layer was present compared to a thin hydrophobic domain in contact with Pt. A three-layer Nafion structure was formed when Nafion was in direct contact with GC. The findings in this research are direct experimental evidence that both the interfacial and long-range structural properties of Nafion are affected by the material with which it is in contact. Evidence of physical changes of aged Nafion films was obtained, and the results showed a permanent increase in the thickness of the Nafion film and a decrease in the scattering length density (SLID), which are attributed to irreversible swelling of the Nafion film. The aging also resulted in a decrease in the SLID of the GC substrate, which is likely due to either an increase in surface oxidation of the carbon or loss of carbon mass at the GC surface. C1 [Wood, David L., III; Chlistunoff, Jerzy; Borup, Rodney L.] Los Alamos Natl Lab, Mat Phys & Applicat Div, Sensors & Electrochem Devices Grp, Los Alamos, NM 87545 USA. [Majewski, Jaroslaw] Los Alamos Natl Lab, Jr Neutron Scattering Ctr, LANSCE LC, Los Alamos, NM 87545 USA. RP Wood, DL (reprint author), Oak Ridge Natl Lab, Mat Sci & Technol Div, Mat Proc Grp, POB 2008,MS 6083, Oak Ridge, TN 37831 USA. EM wooddl@ornl.gov RI Lujan Center, LANL/G-4896-2012; OI Wood, David/0000-0002-2471-4214 FU U.S. Department of Energy (DOE); Los Alamos National Laboratory under DOE [W7405-ENG-36]; DOE Office of Basic Energy Sciences [DE-FG02-04ER46173]; Los Alamos Neutron Science Center (LANSCE) Nano-Engineering Program Advisory Committee FX The financial support of this work was provided in part by the U.S. Department of Energy (DOE) Fuel Cell Technologies Program (Program Manager Nancy Garland). This work was also supported by Los Alamos National Laboratory under DOE Contract W7405-ENG-36 and a grant from the DOE Office of Basic Energy Sciences under Award Number DE-FG02-04ER46173. We thank the Los Alamos Neutron Science Center (LANSCE) Nano-Engineering Program Advisory Committee for granting three consecutive beam-time awards on the SPEAR instrument. We thank Erik Watkins and Dhaval Doshi of the Manuel Lujan, Jr. Neutron Scattering Center for providing helpful suggestions, technical guidance, and raw-data analysis. We thank Roger Lujan for preparing the Pt-sputtered films. NR 47 TC 47 Z9 47 U1 3 U2 66 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 23 PY 2009 VL 131 IS 50 BP 18096 EP 18104 DI 10.1021/ja9033928 PG 9 WC Chemistry, Multidisciplinary SC Chemistry GA 543XY UT WOS:000273615400032 PM 19924901 ER PT J AU Thukral, L Smith, JC Daidone, I AF Thukral, Lipi Smith, Jeremy C. Daidone, Isabella TI Common Folding Mechanism of a beta-Hairpin Peptide via Non-native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations SO JOURNAL OF THE AMERICAN CHEMICAL SOCIETY LA English DT Article ID REPLICA EXCHANGE SIMULATIONS; PROTEIN-G; POTENTIAL FUNCTIONS; AQUEOUS-SOLUTION; CHEMICAL-SHIFTS; KINETICS; PATHWAYS; CONFORMATION; FRAGMENT; SOLVENT AB The folding of a 15-residue beta-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics (MD) simulations. Fifteen independent MD trajectories, each 2.5 mu s-long for a total of 37.5 mu s, are performed of the peptide in explicit solvent, at room temperature, and without the use of enhanced sampling techniques. The computed folding time of 1-1.5 mu s obtained from the simulations is in good agreement with experiment [Xu, Y.; et al. J. Am. Chem. Soc. 2003, 125, 15388-15394]. A common folding mechanism is observed, in which the turn is always found to be the major determinant in initiating the folding process, followed by cooperative formation of the interstrand hydrogen bonds and the side-chain packing. Furthermore, direct transition to the folded state from fully unstructured conformations does not take place. Instead, the peptide is always observed to form partially structured conformations involving a non-native (ESYI) turn from which the native (NPDG) turn forms, triggering the folding to the beta-hairpin. C1 [Thukral, Lipi; Smith, Jeremy C.] Univ Heidelberg, Interdisciplinary Ctr Sci Comp, D-69120 Heidelberg, Germany. [Smith, Jeremy C.] Univ Tennessee, Oak Ridge Natl Lab, Ctr Biophys Mol, Oak Ridge, TN 37831 USA. [Daidone, Isabella] Univ Aquila, Dipartimento Chim Ingn Chim & Mat, I-67010 Coppito, AQ, Italy. RP Smith, JC (reprint author), Univ Heidelberg, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 368, D-69120 Heidelberg, Germany. EM smithjc@ornl.gov; daidone@caspur.it RI smith, jeremy/B-7287-2012; OI smith, jeremy/0000-0002-2978-3227; Thukral, Lipi/0000-0002-1961-039X FU Deutsche Forschungsgemeinschaft (DFG) [SM 63/12-1]; United States Department of Energy FX We acknowledge the Deutsche Forschungsgemeinschaft (DFG) for financial support under Grant SM 63/12-1 and the United States Department of Energy for a Laboratory-Directed Research and Development Grant to J.C.S. at ORNL. We thank Hannes Neuweiler and Soren Doose for helpful discussions. We acknowledge-the NSF Teragrid for computational resources. We are also thankful to M. Angeles Jimenez for kindly providing us the NMR structure of Peptide 1. NR 58 TC 27 Z9 27 U1 1 U2 12 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0002-7863 J9 J AM CHEM SOC JI J. Am. Chem. Soc. PD DEC 23 PY 2009 VL 131 IS 50 BP 18147 EP 18152 DI 10.1021/ja9064365 PG 6 WC Chemistry, Multidisciplinary SC Chemistry GA 543XY UT WOS:000273615400038 PM 19919102 ER PT J AU Haranczyk, M Sethian, JA AF Haranczyk, M. Sethian, J. A. TI Navigating molecular worms inside chemical labyrinths SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE fast marching methods; robotic navigation; accessible volume ID FAST MARCHING METHODS; SHAPE SELECTIVITY; ALGORITHMS; ZEOLITES; CRACKING; ALKANES AB Predicting whether a molecule can traverse chemical labyrinths of channels, tunnels, and buried cavities usually requires performing computationally intensive molecular dynamics simulations. Often one wants to screen molecules to identify ones that can pass through a given chemical labyrinth or screen chemical labyrinths to identify those that allow a given molecule to pass. Because it is impractical to test each molecule/ labyrinth pair using computationally expensive methods, faster, approximate methods are used to prune possibilities, "triaging" the ability of a proposed molecule to pass through the given chemical labyrinth. Most pruning methods estimate chemical accessibility solely on geometry, treating atoms or groups of atoms as hard spheres with appropriate radii. Here, we explore geometric configurations for a moving "molecular worm," which replaces spherical probes and is assembled from solid blocks connected by flexible links. The key is to extend the fast marching method, which is an ordered upwind one-pass Dijkstra-like method to compute optimal paths by efficiently solving an associated Eikonal equation for the cost function. First, we build a suitable cost function associated with each possible configuration, and second, we construct an algorithm that works in ensuing high-dimensional configuration space: at least seven dimensions are required to account for translational, rotational, and internal degrees of freedom. We demonstrate the algorithm to study shortest paths, compute accessible volume, and derive information on topology of the accessible part of a chemical labyrinth. As a model example, we consider an alkane molecule in a porous material, which is relevant to designing catalysts for oil processing. C1 [Sethian, J. A.] Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA. [Haranczyk, M.] Univ Calif Berkeley, Lawrence Berkeley Lab, Computat Res Div, Berkeley, CA 94720 USA. RP Sethian, JA (reprint author), Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA. EM sethian@math.berkeley.edu RI Haranczyk, Maciej/A-6380-2014 OI Haranczyk, Maciej/0000-0001-7146-9568 FU U.S. Department of Energy [DE-AC02-05CH11231, DE-AC03-76SF00098]; Division of Mathematical Sciences of the National Science Foundation FX We thank Berend Smit and Jenny Suckale for many valuable conversations. M. H. is a 2008 Glenn T. Seaborg Fellow at Lawrence Berkeley National Laboratory. M. H. was supported by the U.S. Department of Energy under Contract DE-AC02-05CH11231. J.A.S. was supported by the Applied Mathematical Sciences subprogram of the Office of Energy Research, U.S. Department of Energy, under Contract DE-AC03-76SF00098, and the Division of Mathematical Sciences of the National Science Foundation. NR 17 TC 18 Z9 18 U1 1 U2 11 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 22 PY 2009 VL 106 IS 51 BP 21472 EP 21477 DI 10.1073/pnas.0910016106 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 535TM UT WOS:000272994200004 PM 20018716 ER PT J AU Wang, DB Wallace, AF De Yoreo, JJ Dove, PM AF Wang, Dongbo Wallace, Adam F. De Yoreo, James J. Dove, Patricia M. TI Carboxylated molecules regulate magnesium content of amorphous calcium carbonates during calcification SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE biomineralization; dolomite; calcite; signatures; proteins ID URCHIN LARVAL SPICULE; DOLOMITE PRECIPITATION; CRYSTAL-GROWTH; PRECURSOR PHASE; ASPARTIC-ACID; ARAGONITE; CRYSTALLIZATION; PROTEINS; SKELETAL; WATER AB With the realization that many calcified skeletons form by processes involving a precursor phase of amorphous calcium carbonate (ACC), a new paradigm for mineralization is emerging. There is evidence the Mg content in biogenic ACC is regulated by carboxylated (acidic) proteins and other macromolecules, but the physical basis for such a process is unknown. We test the hypothesis that ACC compositions express a systematic relationship to the chemistry of carboxyl-rich biomolecules. A series of inorganic control experiments were conducted to establish the dependence of Mg/Ca ratios in ACC on solution composition. We then determined the influence of a suite of simple carboxylated organic acids on Mg content. Molecules with a strong affinity for binding Ca compared with Mg promote the formation of Mg-enriched ACC that is compositionally equivalent to high-magnesium calcites and dolomite. Measurements show Mg/Ca ratios are controlled by a predictable dependence upon the binding properties of the organic molecules. The trend appears rooted in the conformation and electrostatic potential topology of each molecule, but dynamic factors also may be involved. The dependence suggests a physical basis for reports that specific sequences of calcifying proteins are critical to modulating mineralization. Insights from this study may provide a plausible explanation for why some biogenic carbonates and carbonaceous cements often contain higher Mg signatures than those that are possible by classical crystal growth processes. The findings reiterate the controls of microenvironment on mineralization and suggest an origin of compositional offsets, or vital effects, long recognized by the paleoclimate community. C1 [Wang, Dongbo; Wallace, Adam F.; Dove, Patricia M.] Virginia Polytech Inst & State Univ, Dept Geosci, Blacksburg, VA 24061 USA. [De Yoreo, James J.] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. RP Dove, PM (reprint author), Virginia Polytech Inst & State Univ, Dept Geosci, Blacksburg, VA 24061 USA. EM dove@vt.edu RI Dove, Patricia/A-7911-2010; Wallace, Adam/A-9976-2012 FU U.S. Department of Energy [FG02-00ER15112, DE-AC02-05CH1123]; National Science Foundation [OCE-052667] FX We thank Prof. J.D. Rimstidt for thoughtful discussions; Prof. D.L. Popham and J. Smiley for HPLC analysis; and H. Motegi, N. Dixit, and Prof. R.B. Moore for assistance with thermogravimetric analysis. The research was supported by U.S. Department of Energy Grant FG02-00ER15112 and National Science Foundation Grant OCE-052667 (to P. M. D.). J.J.D. was supported by the Office of Science, Office of Basic Energy Sciences of the U.S. Department of Energy under Contract DE-AC02-05CH1123. NR 52 TC 89 Z9 90 U1 2 U2 60 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 22 PY 2009 VL 106 IS 51 BP 21511 EP 21516 DI 10.1073/pnas.0906741106 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 535TM UT WOS:000272994200011 PM 19955417 ER PT J AU Fernhoff, NB Derbyshire, ER Marletta, MA AF Fernhoff, Nathaniel B. Derbyshire, Emily R. Marletta, Michael A. TI A nitric oxide/cysteine interaction mediates the activation of soluble guanylate cyclase SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE thiol; TC-1; cGMP; S-nitrosation; redox ID S-NITROSYLATION; SULFHYDRYL-GROUP; OXIDE RECEPTOR; BOVINE LUNG; IN-VIVO; HEME; CELLS; OXIDATION; YC-1; DESENSITIZATION AB Nitric oxide (NO) regulates a number of essential physiological processes by activating soluble guanylate cyclase (sGC) to produce the second messenger cGMP. The mechanism of NO sensing was previously thought to result exclusively from NO binding to the sGC heme; however, recent studies indicate that heme-bound NO only partially activates sGC and additional NO is involved in the mechanism of maximal NO activation. Furthermore, thiol oxidation of sGC cysteines results in the loss of enzyme activity. Herein the role of cysteines in NO-stimulated sGC activity investigated. We find that the thiol modifying reagent methyl methanethiosulfonate specifically inhibits NO activation of sGC by blocking a non-heme site, which defines a role for sGC cysteine(s) in mediating NO binding. The nature of the NO/cysteine interaction was probed by examining the effects of redox active reagents on NO-stimulated activity. These results show that NO binding to, and dissociation from, the critical cysteine(s) does not involve a change in the thiol redox state. Evidence is provided for non-heme NO in the physiological activation of sGC in context of a primary cell culture of human umbilical vein endothelial cells. These findings have relevance to diseases involving the NO/cGMP signaling pathway. C1 [Marletta, Michael A.] Univ Calif Berkeley, Dept Mol & Cell Biol, Inst QB3, Berkeley, CA 94720 USA. [Marletta, Michael A.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. [Marletta, Michael A.] Univ Calif Berkeley, Lawrence Berkeley Lab, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA. [Marletta, Michael A.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Phys Biosci, Berkeley, CA 94720 USA. RP Marletta, MA (reprint author), Univ Calif Berkeley, Dept Mol & Cell Biol, Inst QB3, 570 Stanley Hall, Berkeley, CA 94720 USA. EM marletta@berkeley.edu FU National Institutes of Health [GM077365] FX We thank Dr. Arnie Falick, Dr. David King, Dr. Tony Iavarone, and Dr. Lori Kohlstaedt forMShelp and advice; Dr. Stephen Cary and Dr. Jonathan Winger for critical input; Dr. Joshua Woodward for helpful discussions; Sarah Deng for technical assistance; and Dr. Arnie Falick ( University of California, Berkeley) for acquiring the MALDI-TOF/TOF spectra. This study was funded by National Institutes of Health Grant GM077365 ( to M. A. M.). NR 41 TC 60 Z9 63 U1 0 U2 8 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 22 PY 2009 VL 106 IS 51 BP 21602 EP 21607 DI 10.1073/pnas.0911083106 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 535TM UT WOS:000272994200027 PM 20007374 ER PT J AU Jura, N Shan, YB Cao, XX Shaw, DE Kuriyan, J AF Jura, Natalia Shan, Yibing Cao, Xiaoxian Shaw, David E. Kuriyan, John TI Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3 SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE EGFR; human epidermal growth factor receptor 3; human epidermal growth factor receptor4; receptor oligomerization ID EPIDERMAL-GROWTH-FACTOR; CRYSTAL-STRUCTURE; BINDING; PROTEIN; ACTIVATION; MECHANISM; HER3; FAMILY; CONFORMATION; INHIBITION AB The kinase domain of human epidermal growth factor receptor (HER) 3/ErbB3, a member of the EGF receptor (EGFR) family, lacks several residues that are critical for catalysis. Because catalytic activity in EGFR family members is switched on by an allosteric interaction between kinase domains in an asymmetric kinase domain dimer, HER3 might be specialized to serve as an activator of other EGFR family members. We have determined the crystal structure of the HER3 kinase domain and show that it appears to be locked into an inactive conformation that resembles that of EGFR and HER4. Although the crystal structure shows that the HER3 kinase domain binds ATP, we confirm that it is catalytically inactive but can serve as an activator of the EGFR kinase domain. The HER3 kinase domain forms a dimer in the crystal, mediated by hydrophobic contacts between the N-terminal lobes of the kinase domains. This N-lobe dimer closely resembles a dimer formed by inactive HER4 kinase domains in crystal structures determined previously, and molecular dynamics simulations suggest that the HER3 and HER4 N-lobe dimers are stable. The kinase domains of HER3 and HER4 form similar chains in their respective crystal lattices, in which N-lobe dimers are linked together by reciprocal exchange of C-terminal tails. The conservation of this tiling pattern in HER3 and HER4, which is the closest evolutionary homolog of HER3, might represent a general mechanism by which this branch of the HER receptors restricts ligand-independent formation of active heterodimers with other members of the EGFR family. C1 [Jura, Natalia; Cao, Xiaoxian; Kuriyan, John] Univ Calif Berkeley, Howard Hughes Med Inst, Dept Mol & Cell Biol, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA. [Kuriyan, John] Univ Calif Berkeley, Howard Hughes Med Inst, Dept Chem, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA. [Kuriyan, John] Univ Calif Berkeley, Lawrence Berkeley Lab, Phys Biosci Div, Berkeley, CA 94720 USA. [Shan, Yibing; Shaw, David E.] DE Shaw Res, New York, NY 10036 USA. [Shaw, David E.] Columbia Univ, Ctr Computat Biol & Bioinformat, New York, NY 10032 USA. RP Kuriyan, J (reprint author), Univ Calif Berkeley, Howard Hughes Med Inst, Dept Mol & Cell Biol, Calif Inst Quantitat Biosci, Berkeley, CA 94720 USA. EM kuriyan@berkeley.edu FU National Cancer Institute [RO1 CA96504-06]; Susan G. KomenBreast Cancer Foundation; U.S. Department of Energy at the Lawrence Berkeley National Laboratory [DE-AC03-76SF00098] FX We thank Chang Wang for technical help and Xuewu Zhang for the HER3 cDNA construct. We also thank Mark Moasser, Xuewu Zhang, and members of the Kuriyan laboratory for helpful discussions. This work was supported in part by Grant RO1 CA96504-06 from the National Cancer Institute (to J.K.) and by the Susan G. KomenBreast Cancer Foundation. We thank the staff at the Advanced Light Source, which is supported by the U.S. Department of Energy under Contract DE-AC03-76SF00098 at the Lawrence Berkeley National Laboratory. NR 39 TC 142 Z9 143 U1 2 U2 17 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 22 PY 2009 VL 106 IS 51 BP 21608 EP 21613 DI 10.1073/pnas.0912101106 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 535TM UT WOS:000272994200028 PM 20007378 ER PT J AU Fleissner, MR Brustad, EM Kalai, T Altenbach, C Cascio, D Peters, FB Hideg, K Peuker, S Schultz, PG Hubbell, WL AF Fleissner, Mark R. Brustad, Eric M. Kalai, Tamas Altenbach, Christian Cascio, Duilio Peters, Francis B. Hideg, Kalman Peuker, Sebastian Schultz, Peter G. Hubbell, Wayne L. TI Site-directed spin labeling of a genetically encoded unnatural amino acid SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE EPR; nitroxides; T4 lysozyme ID SIDE-CHAIN STRUCTURE; T4 LYSOZYME; ESCHERICHIA-COLI; NITROXIDE MOTION; STRUCTURAL DETERMINANTS; PROTEIN-STRUCTURE; EPR-SPECTRA; DYNAMICS; CODE; RESONANCE AB The traditional site-directed spin labeling (SDSL) method, which utilizes cysteine residues and sulfhydryl-reactive nitroxide reagents, can be challenging for proteins that contain functionally important native cysteine residues or disulfide bonds. To make SDSL amenable to any protein, we introduce an orthogonal labeling strategy, i.e., one that does not rely on any of the functional groups found in the common 20 amino acids. In this method, the genetically encoded unnatural amino acid p-acetyl-L-phenylalanine (p-AcPhe) is reacted with a hydroxylamine reagent to generate a nitroxide side chain (K1). The utility of this scheme was demonstrated with seven mutants of T4 lysozyme, each containing a single p-AcPhe at a solvent-exposed helix site; the mutants were expressed in amounts qualitatively similar to the wild-type protein. In general, the EPR spectra of the resulting K1 mutants reflect higher nitroxide mobilities than the spectra of analogous mutants containing the more constrained disulfide-linked side chain (R1) commonly used in SDSL. Despite this increased flexibility, site dependence of the EPR spectra suggests that K1 will be a useful sensor of local structure and of conformational changes in solution. Distance measurements between pairs of K1 residues using double electron electron resonance (DEER) spectroscopy indicate that K1 will also be useful for distance mapping. C1 [Brustad, Eric M.; Peters, Francis B.; Schultz, Peter G.] Scripps Res Inst, Dept Chem, La Jolla, CA 92037 USA. [Brustad, Eric M.; Peters, Francis B.; Schultz, Peter G.] Scripps Res Inst, Skaggs Inst Chem Biol, La Jolla, CA 92037 USA. [Fleissner, Mark R.; Altenbach, Christian; Hubbell, Wayne L.] Univ Calif Los Angeles, Jules Stein Eye Inst, Los Angeles, CA 90095 USA. [Fleissner, Mark R.; Altenbach, Christian; Hubbell, Wayne L.] Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA 90095 USA. [Kalai, Tamas; Hideg, Kalman] Univ Pecs, Inst Organ & Med Chem, H-7624 Pecs, Hungary. [Cascio, Duilio] Univ Calif Los Angeles, UCLA DOE Inst Genom & Prote, Los Angeles, CA 90095 USA. [Peuker, Sebastian] Center of Advanced European Studies and Research, D-53175 Bonn, Germany. RP Schultz, PG (reprint author), Scripps Res Inst, Dept Chem, La Jolla, CA 92037 USA. EM schultz@scripps.edu; hubbellw@jsei.ucla.edu FU U.S. Department of Energy [DE-FC02-02ER63421]; National Institutes of Health [R01EY05216, RT32EY007026, R01GM062159]; Jules Stein Professor Endowment; Hungarian National Research Funds [OTKA T048334, OTKA-NKTH K67597] FX We thank Evan K. Brooks (University of California, Los Angeles) for excellent technical assistance, Dr. Joe Horwitz for assistance with the CD spectropolarimetry experiments, Sebastian Peuker for assistance with the p-methoxyaniline catalyzed reaction, and the UCLA DOE X-Ray Crystallography Core Facility, which was supported by U.S. Department of Energy Grant DE-FC02-02ER63421. This work was supported by National Institutes of Health Grants R01EY05216 (to W.L.H), RT32EY007026 (to M.R.F.), R01GM062159 (to P.G.S.), and the Jules Stein Professor Endowment (W.L.H.). Synthesis of new spin label reagents was supported by Hungarian National Research Funds OTKA T048334 and OTKA-NKTH K67597 (to K.H. and T.K.). NR 46 TC 101 Z9 102 U1 5 U2 44 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 22 PY 2009 VL 106 IS 51 BP 21637 EP 21642 DI 10.1073/pnas.0912009106 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 535TM UT WOS:000272994200033 PM 19995976 ER PT J AU Zawadzka, AM Kim, Y Maltseva, N Nichiporuk, R Fan, Y Joachimiak, A Raymond, KN AF Zawadzka, Anna M. Kim, Youngchang Maltseva, Natalia Nichiporuk, Rita Fan, Yao Joachimiak, Andrzej Raymond, Kenneth N. TI Characterization of a Bacillus subtilis transporter for petrobactin, an anthrax stealth siderophore SO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LA English DT Article DE crystal structure; substrate-binding protein; Gram-positive bacteria; iron ID MEDIATED IRON TRANSPORT; BINDING-PROTEIN; FUR REGULON; BACILLIBACTIN; ACQUISITION; CEREUS; IDENTIFICATION; BIOSYNTHESIS; MACROPHAGES; STARVATION AB Iron deprivation activates the expression of components of the siderophore-mediated iron acquisition systems in Bacillus subtilis, including not only the synthesis and uptake of its siderophore bacillibactin but also expression of multiple ABC transporters for iron scavenging using xenosiderophores. The yclNOPQ operon is shown to encode the complete transporter for petrobactin (PB), a photoreactive 3,4-catecholate siderophore produced by many members of the B. cereus group, including B. anthracis. Isogenic disruption mutants in the yclNOPQ transporter, including permease YclN, ATPase YclP, and a substrate-binding protein YclQ, are unable to use either PB or the photoproduct of FePB (FePB(nu)) for iron delivery and growth, in contrast to the wild-type B. subtilis. Complementation of the mutations with the copies of the respective genes restores this capability. The YclQ receptor binds selectively iron-free and ferric PB, the PB precursor, 3,4-dihydroxybenzoic acid (3,4-DHB), and FePB(nu) with high affinity; the ferric complexes are seen in ESI-MS, implying strong electrostatic interaction between the protein-binding pocket and siderophore. The first structure of a Gram-positive siderophore receptor is presented. The 1.75-angstrom crystal structure of YclQ reveals a bilobal periplasmic binding protein (PBP) fold consisting of two alpha/beta/gamma sandwich domains connected by a long alpha-helix with the binding pocket containing conserved positively charged and aromatic residues and large enough to accommodate FePB. Orthologs of the B. subtilis PB-transporter YclNOPQ in PB-producing Bacilli are likely contributors to the pathogenicity of these species and provide a potential target for antibacterial strategies. C1 [Kim, Youngchang; Maltseva, Natalia; Fan, Yao; Joachimiak, Andrzej] Argonne Natl Lab, Biosci Div, Midwest Ctr Struct Genom, Argonne, IL 60439 USA. [Zawadzka, Anna M.; Nichiporuk, Rita; Raymond, Kenneth N.] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. RP Kim, Y (reprint author), Argonne Natl Lab, Biosci Div, Midwest Ctr Struct Genom, 9700 S Cass Ave, Argonne, IL 60439 USA. EM ykim@anl.gov RI Fan, Yao/C-7910-2014 FU National Institutes of Health [AI11744, GM074942, 1S10RR022393-01]; U.S. Department of Energy, Office of Biological and Environmental Research [DE-AC02-06CH11357] FX We acknowledge helpful discussions on data analysis with Dr. Ulla Andersen and Dr. Petr Kuzmic. Dr. William Eschenfeldt advised on YclQ cloning for crystallization. We thank members of the Structural Biology Center at Argonne National Laboratory for their help with data collection at the 19ID beamline. We acknowledge Dr. Ahmad Gaballa for advice on B. subtilis transformation, and thank Drs. Rebecca Abergel and Trisha Hoette for advice and help with manuscript editing. Crude extract of PB was obtained from Prof. B. Rowe Byers (Univ of Mississippi Medical Center, Jackson, MS) and the B. subtilis yclNd, yclPd, and yclQd strains were received from Dr. Etienne Dervyn (Institut National de la Recherche Agronomique, Paris). This work was supported by National Institutes of Health Grants AI11744 (to K.N.R.), GM074942 (to A.J.), and 1S10RR022393-01 for the acquisition of the Q-TOF MS, and by the U.S. Department of Energy, Office of Biological and Environmental Research Contract DE-AC02-06CH11357. NR 48 TC 34 Z9 34 U1 2 U2 8 PU NATL ACAD SCIENCES PI WASHINGTON PA 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA SN 0027-8424 J9 P NATL ACAD SCI USA JI Proc. Natl. Acad. Sci. U. S. A. PD DEC 22 PY 2009 VL 106 IS 51 BP 21854 EP 21859 DI 10.1073/pnas.0904793106 PG 6 WC Multidisciplinary Sciences SC Science & Technology - Other Topics GA 535TM UT WOS:000272994200071 PM 19955416 ER PT J AU Dabney, MS Parilla, PA Gedvilas, LM Mahan, AH Ginley, DS AF Dabney, M. S. Parilla, P. A. Gedvilas, L. M. Mahan, A. H. Ginley, D. S. TI Altering the nucleation of thermally annealed hydrogenated amorphous silicon with laser processing SO APPLIED PHYSICS LETTERS LA English DT Article ID POLYCRYSTALLINE SILICON; EXCIMER-LASER; CRYSTALLIZATION; FILMS; DEPOSITION; GROWTH; GLASS AB We demonstrate the use of laser processing to affect the nucleation of crystallites in thermally annealed hydrogenated amorphous silicon (a-Si:H) thin films. The influence of film H content and subcrystallization threshold laser fluence are investigated by x-ray diffraction measurements during in situ thermal annealing at 600 degrees C. All laser-treated films show a reduced incubation time for crystallization compared to as-grown films, with the largest differences exhibited for samples with higher film H and higher laser fluences. These results are consistent with multivacancy annihilation by laser processing, based upon a recently developed model for a nucleation center in a-Si: H. (C) 2009 American Institute of Physics. [doi:10.1063/1.3259654] C1 [Dabney, M. S.; Parilla, P. A.; Gedvilas, L. M.; Mahan, A. H.; Ginley, D. S.] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Dabney, MS (reprint author), Natl Renewable Energy Lab, Golden, CO 80401 USA. EM Matthew_Dabney@nrel.gov FU U.S. Department of Energy [DE-AC39-98-GO10337] FX This work was supported by the U.S. Department of Energy under Contract No. DE-AC39-98-GO10337. NR 13 TC 3 Z9 3 U1 0 U2 2 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 21 PY 2009 VL 95 IS 25 AR 251902 DI 10.1063/1.3259654 PG 3 WC Physics, Applied SC Physics GA 536II UT WOS:000273037700015 ER PT J AU Stehr, D Morris, CM Talbayev, D Wagner, M Kim, HC Taylor, AJ Schneider, H Petroff, PM Sherwin, MS AF Stehr, D. Morris, C. M. Talbayev, D. Wagner, M. Kim, H. C. Taylor, A. J. Schneider, H. Petroff, P. M. Sherwin, M. S. TI Ultrafast carrier capture in InGaAs quantum posts SO APPLIED PHYSICS LETTERS LA English DT Article ID OPTICAL-PROPERTIES; DOTS; RELAXATION; GAAS; SPECTROSCOPY; GROWTH AB To explore the capture dynamics of photoexcited carriers in semiconductor quantum posts, optical pump terahertz (THz) probe and time-resolved photoluminescence spectroscopy were performed. The results of the THz experiment show that after ultrafast excitation, electrons relax within a few picoseconds into the quantum posts, which act as efficient traps. The saturation of the quantum post states, probed by photoluminescence, was reached at approximately ten times the quantum post density in the samples. The results imply that quantum posts are highly attractive nanostructures for future device applications. (C) 2009 American Institute of Physics. [doi:10.1063/1.3275666] C1 [Stehr, D.; Morris, C. M.; Sherwin, M. S.] Univ Calif Santa Barbara, Inst Terahertz Sci & Technol, Santa Barbara, CA 93106 USA. [Talbayev, D.; Taylor, A. J.] Los Alamos Natl Lab, Ctr Integrated Nanotechnol, Los Alamos, NM 87545 USA. [Wagner, M.; Schneider, H.] Forschungszentrum Dresden Rossendorf, Inst Ion Beam Phys & Mat Res, D-01314 Dresden, Germany. [Kim, H. C.; Petroff, P. M.] Univ Calif Santa Barbara, Dept Mat, Santa Barbara, CA 93106 USA. [Sherwin, M. S.] Univ Calif Santa Barbara, Dept Phys, Santa Barbara, CA 93106 USA. RP Stehr, D (reprint author), Univ Calif Santa Barbara, Inst Terahertz Sci & Technol, Santa Barbara, CA 93106 USA. EM stehr@itst.ucsb.edu RI Schneider, Harald/B-8648-2009; Talbayev, Diyar/C-5525-2009; Morris, Christopher/J-9874-2012 OI Schneider, Harald/0000-0002-8060-8504; Talbayev, Diyar/0000-0003-3537-1656; FU NSF [CCF0507295]; Alexander-von-Humboldt Foundation; Center for Integrated Nanotechnologies; IMMS FX The authors acknowledge support through NSF via Nanoscale Interdisciplinary Research Team Grant CCF0507295, M. Helm for carefully reading the manuscript and H.J. Krenner for critical discussions. D.S. thanks the Alexander-von-Humboldt Foundation for financial support. This research at LANL was supported by the Center for Integrated Nanotechnologies and the IMMS. NR 18 TC 8 Z9 8 U1 1 U2 9 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0003-6951 J9 APPL PHYS LETT JI Appl. Phys. Lett. PD DEC 21 PY 2009 VL 95 IS 25 AR 251105 DI 10.1063/1.3275666 PG 3 WC Physics, Applied SC Physics GA 536II UT WOS:000273037700005 ER PT J AU Weitering, HH AF Weitering, Hanno H. TI The World's Thinnest Superconductor SO CHEMPHYSCHEM LA English DT Editorial Material DE lead; scanning probe microscopy; silicon; superconductors; thin films ID 2-DIMENSIONAL LIMIT; FILMS; METAL C1 [Weitering, Hanno H.] Univ Tennessee, Dept Phys & Astron, Knoxville, TN 37996 USA. [Weitering, Hanno H.] Oak Ridge Natl Lab, Mat Sci & Technol Div, Oak Ridge, TN 37831 USA. RP Weitering, HH (reprint author), Univ Tennessee, Dept Phys & Astron, Knoxville, TN 37996 USA. EM hanno@utk.edu NR 24 TC 3 Z9 3 U1 2 U2 11 PU WILEY-V C H VERLAG GMBH PI WEINHEIM PA PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY SN 1439-4235 J9 CHEMPHYSCHEM JI ChemPhysChem PD DEC 21 PY 2009 VL 10 IS 18 BP 3183 EP 3185 DI 10.1002/cphc.200900663 PG 3 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 541JH UT WOS:000273410600004 PM 19790204 ER PT J AU Kose, ME Graf, P Kopidakis, N Shaheen, SE Kim, K Rumbles, G AF Kose, Muhammet E. Graf, Peter Kopidakis, Nikos Shaheen, Sean E. Kim, Kwiseon Rumbles, Garry TI Exciton Migration in Conjugated Dendrimers: A Joint Experimental and Theoretical Study SO CHEMPHYSCHEM LA English DT Article DE dendrimers; density functional calculations; diffusion; electronic structure; excitons ID EXCITATION-ENERGY TRANSFER; ORGANIC SOLAR-CELLS; PHOTOVOLTAIC CELLS; DIFFUSION LENGTH; POLYMERS; HETEROJUNCTION; OLIGOTHIOPHENE; TRANSPORT; DYNAMICS; POLYTHIOPHENE AB We report a joint experimental and theoretical investigation of exciton diffusion in phenyl-cored thiophene dendrimers. Experimental exciton diffusion lengths of the dendrimers vary between 8 and 17 nm, increasing with the size of the dendrimer. A theoretical methodology is developed to estimate exciton diffusion lengths for conjugated small molecules in a simulated amorphous film. The theoretical approach exploits Fermi's Golden Rule to estimate the energy transfer rates for a large ensemble of bimolecular complexes in random relative orientations. Utilization of Poisson's equation in the evaluation of the Coulomb integral leads to very efficient calculation of excitonic couplings between the donor and the acceptor chromophores. Electronic coupling calculations with delocalized transition densities revealed efficient coupling pathways in the bulk of the material, but do not result in strong couplings between the chromophores which are calculated for more localized transition densities. The molecular structures of dendrimers seem to be playing a significant role in the magnitude of electronic coupling between chromophores. Simulated diffusion lengths correlate well with the experimental data. The chemical structure of the chromophore, the shape of the transition densities and the exciton lifetime are found to be the most important factors in determining the size of the exciton diffusion length in amorphous films of conjugated materials. C1 [Kose, Muhammet E.] N Dakota State Univ, Dept Chem & Mol Biol, Fargo, ND 58108 USA. [Graf, Peter; Kopidakis, Nikos; Kim, Kwiseon; Rumbles, Garry] Natl Renewable Energy Lab, Golden, CO 80401 USA. [Shaheen, Sean E.] Univ Denver, Dept Phys & Astron, Denver, CO 80208 USA. RP Kose, ME (reprint author), N Dakota State Univ, Dept Chem & Mol Biol, Fargo, ND 58108 USA. EM muhammet.kose@ndsu.edu RI Kose, Muhammet/C-7167-2012; Shaheen, Sean/M-7893-2013; Kopidakis, Nikos/N-4777-2015; OI Rumbles, Garry/0000-0003-0776-1462 FU Xcel Energy Renewable Development Fund [RD-107] FX We greatly acknowledge Xcel Energy Renewable Development Fund RD-107 program for support of this work. MIX thanks Brian A. Gregg for the work performed in his laboratory. NR 48 TC 20 Z9 20 U1 0 U2 27 PU WILEY-V C H VERLAG GMBH PI WEINHEIM PA PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY SN 1439-4235 J9 CHEMPHYSCHEM JI ChemPhysChem PD DEC 21 PY 2009 VL 10 IS 18 BP 3285 EP 3294 DI 10.1002/cphc.200900386 PG 10 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 541JH UT WOS:000273410600020 PM 19806627 ER PT J AU Szigethy, G Raymond, KN AF Szigethy, Geza Raymond, Kenneth N. TI Designing the Ideal Uranyl Ligand: a Sterically Induced Speciation Change in Complexes with Thiophene-Bridged Bis(3-hydroxy-N-methylpyridin-2-one) SO INORGANIC CHEMISTRY LA English DT Article ID SEQUESTERING AGENTS; COORDINATION AB Structural characterization of a mononuclear uranyl complex with a tetradentate, thiophene-linked bis(3-hydroxy-N-methylpyridin-2-one) ligand reveals the most planar coordination geometry yet observed with this ligand class. The introduction of ethylsulfanyl groups onto the thiophene linker disrupts this planar, conjugated ligand arrangement, resulting in the formation of dimeric (UO(2))(2)L(2) species in which each ligand spans two uranyl centers. Relative energy calculations reveal that this tendency toward dimer formation is the result of steric interference between ethylsulfanyl substitutents and linking amides. C1 [Raymond, Kenneth N.] LBNL, Glenn T Seaborg Ctr, Div Chem Sci, Berkeley, CA 94720 USA. Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA. RP Raymond, KN (reprint author), LBNL, Glenn T Seaborg Ctr, Div Chem Sci, Berkeley, CA 94720 USA. FU Director, Office of Science, Office of Basic Energy Sciences (OBES); U.S. Departrnent of Energy at LBNL [De-AC02-05CH11231] FX This research is supported by the Director, Office of Science, Office of Basic Energy Sciences (OBES), and the OBES Division of Chemical Sciences, Geosciences and Biosciences of the U.S. Departrnent of Energy at LBNL under Contract De-AC02-05CH11231. NR 16 TC 16 Z9 16 U1 4 U2 16 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0020-1669 J9 INORG CHEM JI Inorg. Chem. PD DEC 21 PY 2009 VL 48 IS 24 BP 11489 EP 11491 DI 10.1021/ic901815b PG 3 WC Chemistry, Inorganic & Nuclear SC Chemistry GA 529YY UT WOS:000272556700003 PM 19928845 ER PT J AU Fukushima, T Fujita, E Muckerman, JT Polyansky, DE Wada, T Tanaka, K AF Fukushima, Takashi Fujita, Etsuko Muckerman, James T. Polyansky, Dmitry E. Wada, Tohru Tanaka, Koji TI Photochemical Stereospecific Hydrogenation of a Ru Complex with an NAD(+)/NADH-Type Ligand SO INORGANIC CHEMISTRY LA English DT Article ID NAD(+) MODEL LIGAND; AQUEOUS-SOLUTION; RUTHENIUM(II) COMPLEXES; ASYMMETRIC INDUCTION; EXCITED-STATES; HYDRIDE DONOR; 2,2-BIPYRIDINE; 2,2-BIPYRAZINE; RADIOLYSIS; REDUCTION AB A polypyridylruthenium complex with an NAD(+)/NADH model ligand, [Ru(bpy)(2)(pbn)](2+) [bpy = 2,2'-bipyridine, pbn = 2-(2-pyridyl)benzo[b]-1,5-naphthyridine] in a D2O/CH3CN/triethylamine solution, undergoes stereospecific hydrogenation to give Delta-(S)- and Lambda-(R)- [Ru(bpy)(2)(pbnDD)](2+) [pbnDD = 5,10-dideutero-2-(2-pyridyl)benzo[b]-1,5-naphthyridine] upon visible-light irradiation. This result clearly indicates the pathway via the pi-stacked dimer of the deuterated one-electron-reduced species. The reduction of [Ru(bpy)(2)(pbn)](2+) with Na2S2O4 in D2O did not afford any stereospecific products. Furthermore, the more sterically crowded Ru complex, [Ru(dmb)(2)(pbn)](2+) (dmb = 6,6'-dimethyl-2,2'-bipyridine), did not produce the corresponding pbnDD species upon irradiation. C1 [Fukushima, Takashi; Wada, Tohru; Tanaka, Koji] IMS, Aichi 4448787, Japan. [Fujita, Etsuko; Muckerman, James T.; Polyansky, Dmitry E.] Brookhaven Natl Lab, Dept Chem, Upton, NY 11973 USA. RP Tanaka, K (reprint author), IMS, 5-1 Higashiyama, Aichi 4448787, Japan. RI Muckerman, James/D-8752-2013; Fujita, Etsuko/D-8814-2013; Polyansky, Dmitry/C-1993-2009 OI Polyansky, Dmitry/0000-0002-0824-2296 FU Ministry of Education, Culture, Sports, Science, and Technology of Japan [20002005]; U.S. Department of Energy (DOE) [DE-AC02-98CH10886] FX The work at IMS is supported by a Grand-in-Aid for Specially Promoted Research (Grant 20002005) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan. The work at BNL is funded under Contract DE-AC02-98CH10886 with the U.S. Department of Energy (DOE) and supported by its Division of Chemical Sciences, Geosciences, & Biosciences, Office of Basic Energy Sciences (BES) E.F. and J.T.M also thank the U.S. DOE for funding under the BES Solar Energy Utilization Initiative. NR 13 TC 30 Z9 30 U1 7 U2 37 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0020-1669 J9 INORG CHEM JI Inorg. Chem. PD DEC 21 PY 2009 VL 48 IS 24 BP 11510 EP 11512 DI 10.1021/ic901935u PG 3 WC Chemistry, Inorganic & Nuclear SC Chemistry GA 529YY UT WOS:000272556700010 PM 19928751 ER PT J AU Wells, DM Jin, GB Skanthakumar, S Haire, RG Soderholm, L Ibers, JA AF Wells, Daniel M. Jin, Geng Bang Skanthakumar, S. Haire, Richard G. Soderholm, L. Ibers, James A. TI Quaternary Neptunium Compounds: Syntheses and Characterization of KCuNpS3, RbCuNpS3, CsCuNpS3, KAgNpS3, and CsAgNpS3 SO INORGANIC CHEMISTRY LA English DT Article ID MAGNETIC-PROPERTIES; PHYSICAL-PROPERTIES; CRYSTAL-STRUCTURES; RARE-EARTH; BAND-GAPS; = S; LN; CHALCOGENIDES; GD; METAL AB The five quaternary neptunium compounds KCuNpS3, RbCuNpS3, CsCuNpS3, KAgNpS3, and CsAgNpS3 (AMNpS(3)) have been synthesized by the reaction of Np, Cu or Ag, S, and K2S or Rb2S3 or Cs2S3 at 793 K (Rb) or 873 K These isostructural compounds crystallize as black rectangular plates in the KCuZrS3 structure type in space group Cmcm of the orthorhombic system. The structure comprises MS4 (M = Cu or Ag) tetrahedra and NpS6 octahedra that edge share to form (2)(infinity)[MNpS3-] layers. These layers are separated by the alkali-metal cations. The Np-S bond lengths vary from 2.681(2) to 2.754(1) angstrom. When compared to the corresponding isostructural Th and U compounds these bond distances obey the expected actinide contraction. As the structure contains no S-S bonds, formal oxidation states of +1/+1/+4/-2 may 4 be assigned to A/M/Np/S, respectively. From these results a value of 2.57 for the bond-valence parameter r(0) for Np4+-S2- has been derived and applied to the estimation of the formal oxidation states of Np in the binary NpxSy compounds whose structures are known. C1 [Wells, Daniel M.; Jin, Geng Bang; Ibers, James A.] Northwestern Univ, Dept Chem, Evanston, IL 60208 USA. [Skanthakumar, S.; Soderholm, L.] Argonne Natl Lab, Chem Sci & Engn Div, Argonne, IL 60439 USA. [Haire, Richard G.] Oak Ridge Natl Lab, Dept Chem Sci, Oak Ridge, TN 37831 USA. RP Ibers, JA (reprint author), Northwestern Univ, Dept Chem, 2145 Sheridan Rd, Evanston, IL 60208 USA. FU U.S. Department of Energy, Basic Energy Sciences [ER-15522]; U.S. Department of Energy, OBES, Chemical Science and Engineering Division [DEAC02-06CH11357]; National Science Foundation [DMR-0520513] FX This research was supported at Northwestern University by the U.S. Department of Energy, Basic Energy Sciences Grant ER-15522 and at Argonne National Laboratory by the U.S. Department of Energy, OBES, Chemical Science and Engineering Division, under contract DEAC02-06CH11357. D M W. wishes to thank the MRSEC program of the National Science Foundation (DMR-0520513) for Support. NR 48 TC 15 Z9 15 U1 2 U2 10 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0020-1669 J9 INORG CHEM JI Inorg. Chem. PD DEC 21 PY 2009 VL 48 IS 24 BP 11513 EP 11517 DI 10.1021/ic901229d PG 5 WC Chemistry, Inorganic & Nuclear SC Chemistry GA 529YY UT WOS:000272556700011 PM 19705856 ER PT J AU Spencer, LP Yang, P Scott, BL Batista, ER Boncella, JM AF Spencer, Liam P. Yang, Ping Scott, Brian L. Batista, Enrique R. Boncella, James M. TI Oxidative Addition to U(V)-U(V) Dimers: Facile Routes to Uranium(VI) Bis(imido) Complexes SO INORGANIC CHEMISTRY LA English DT Article ID ELECTRON-TRANSFER REACTIONS; URANYL ARYLOXIDE COMPLEXES; FUNCTIONAL THEORY ANALYSIS; PENTAVALENT URANIUM; TRIVALENT URANIUM; F-ELEMENT; CRYSTAL-STRUCTURES; IMIDO ANALOGS; REACTIVITY; CHEMISTRY AB The ability of dimeric bis(imido) uranium(V) complexes with the general formula [U(N(t)Bu)(2)(Y)((t)Bu(2)bpy)](2) (Y = I (1), SPh (2); (t)Bu(2)bpy = 4,4'-di-tert-butyl-2,2'-bipyridyl) to behave as two-electron reducing agents was examined with I(2), AgX (X = Cl, Br), PhEEPh (E = S, Se, Te), and chalcogen (O, S, Se) atom transfer reagents. The addition of I(2) and AgX to 1 leads to the formation of uranium(VI) dihalide complexes with the general formula U(N(t)Bu)(2)(I)(X)((t)Bu(2)bpy) (X = I (3), Cl (4), Br (5)). Complexes 1 and 2 can also reduce PhEEPh to generate uranium(VI) complexes with the general formula U(N(t)Bu)(2)(X)(EPh)((t)Bu(2)bpy) (X = I, E = S (6), Se (8), Te (10); X = SPh, E = S (7), Se (12)). These unsymmetrical complexes appear to be in equilibrium with the uranium(VI) complexes U(N(t)Bu)(2)(X)(2)((t)Bu(2)bpy) and U((t)'Bu)(2)(EPh)(2)((t)Bu(2)bpy) (E = Se (9), Te (11)) and suggest that both U-I and U-E bonds possess a labile nature in bis(imido) uranium(VI) complexes. Complex 1 also reacts as a two-electron reductant toward chalcogen atom transfer reagents such as 4-methylmorpholine N-oxide, S(8), and Se to produce dimeric bis(imido) uranium(VI) complexes with the general formula [U(N(t)Bu)(2)(I)((t)Bu(2)bpy)](2)(mu-E) (E = O (13), S (14), Se (15)) and [U(N(t)Bu)(2)(I)((t)Bu(2)bpy)](2)(mu-eta(2):eta(2-)E(4)) (E = S (16), Se (17)). Density functional theory studies performed on a model complex of 13 indicate the presence of multiple bonding in the bridging U-O bond. C1 [Spencer, Liam P.; Scott, Brian L.; Boncella, James M.] Los Alamos Natl Lab, Mat Phys & Applicat Div, Los Alamos, NM 87545 USA. [Yang, Ping; Batista, Enrique R.] Los Alamos Natl Lab, Div Theoret, Los Alamos, NM 87545 USA. RP Boncella, JM (reprint author), Los Alamos Natl Lab, Mat Phys & Applicat Div, MS J514, Los Alamos, NM 87545 USA. EM boncella@lanl.gov RI Yang, Ping/E-5355-2011; Scott, Brian/D-8995-2017; OI Scott, Brian/0000-0003-0468-5396; Boncella, James/0000-0001-8393-392X; Yang, Ping/0000-0003-4726-2860 FU U.S. Department of Energy; U.S. D.O.E [DEAC52-06NA25396] FX P Y. and L P.S thank the Seaborg Institute For their postdoctoral Fellowships E.RB was partially supported by the Division of Chemical Sciences. Office of Basic Energy Sciences, U.S. Department of Energy under the Heavy Element Chemistry program at LANL. We thank the Center for Integrated Nanotechnology at LANL for computing support. LANL is operated by Los Alamos National Security, LLC, for the National Nuclear Security Administration of the U.S. D.O.E under contract DEAC52-06NA25396. NR 59 TC 44 Z9 44 U1 2 U2 23 PU AMER CHEMICAL SOC PI WASHINGTON PA 1155 16TH ST, NW, WASHINGTON, DC 20036 USA SN 0020-1669 J9 INORG CHEM JI Inorg. Chem. PD DEC 21 PY 2009 VL 48 IS 24 BP 11615 EP 11623 DI 10.1021/ic901581r PG 9 WC Chemistry, Inorganic & Nuclear SC Chemistry GA 529YY UT WOS:000272556700024 PM 19947591 ER PT J AU Franck, JM Demas, V Martin, RW Bouchard, LS Pines, A AF Franck, John M. Demas, Vasiliki Martin, Rachel W. Bouchard, Louis-S. Pines, Alexander TI Shimmed matching pulses: Simultaneous control of rf and static gradients for inhomogeneity correction SO JOURNAL OF CHEMICAL PHYSICS LA English DT Article DE magnetic fields; NMR spectroscopy; radiofrequency spectroscopy ID RESOLUTION NMR-SPECTRA; COHERENCE TRANSFER ECHOES; EX-SITU NMR; ADIABATIC PULSES; MAGNETIC-FIELDS; SPIN DYNAMICS; SPECTROSCOPY; ACQUISITION; SEQUENCES; DESIGN AB Portable NMR systems generally suffer from poor field homogeneity and are therefore used more commonly for imaging and relaxation measurements rather than for spectroscopy. In recent years, various approaches have been proposed to increase the sample volume that is usable for spectroscopy. These include approaches based on manual shimming and those based on clever combinations of modulated radio frequency and gradient fields. However, this volume remains small and, therefore, of limited utility. We present improved pulses designed to correct for inhomogeneous dispersion across wide ranges of frequency offsets without eliminating chemical shift or spatial encoding. This method, based on the adiabatic double passage, combines the relatively larger corrections available from spatially matched rf gradients [C. Meriles , J. Magn. Reson. 164, 177 (2003)]. with the adjustable corrections available from time-modulated static field gradients [D. Topgaard , Proc. Natl. Acad. Sci. U.S.A. 101, 17576 (2004)]. We explain the origins of these corrections with a theoretical model that simplifies and expedites the design of the pulse waveforms. We also present a generalized method for evaluating and comparing pulses designed for inhomogeneity correction. Experiments validate this method and support simulations that offer new possibilities for significantly enhanced performance in portable environments. C1 [Franck, John M.] Univ Calif Santa Barbara, Dept Chem & Biochem, Santa Barbara, CA 93106 USA. [Franck, John M.; Demas, Vasiliki; Martin, Rachel W.; Bouchard, Louis-S.; Pines, Alexander] Univ Calif Berkeley, Coll Chem, Berkeley, CA 94720 USA. [Franck, John M.; Pines, Alexander] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Demas, Vasiliki] T2 Biosyst, Cambridge, MA 02141 USA. [Martin, Rachel W.] Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA. [Bouchard, Louis-S.] Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA 90095 USA. RP Franck, JM (reprint author), Univ Calif Santa Barbara, Dept Chem & Biochem, Santa Barbara, CA 93106 USA. EM johnfranck@gmail.com OI Franck, John/0000-0002-5432-4823 NR 30 TC 7 Z9 8 U1 0 U2 10 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0021-9606 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 21 PY 2009 VL 131 IS 23 AR 234506 DI 10.1063/1.3243850 PG 16 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 536HU UT WOS:000273036300030 PM 20025334 ER PT J AU Fu, L Bienenstock, A Brennan, S AF Fu, Ling Bienenstock, Arthur Brennan, Sean TI X-ray study of the structure of liquid water SO JOURNAL OF CHEMICAL PHYSICS LA English DT Article DE Compton effect; intermolecular mechanics; liquid structure; water; X-ray scattering ID RADIAL-DISTRIBUTION FUNCTION; SCATTERING EXPERIMENTS; TEMPERATURE; DIFFRACTION; INTENSITIES; PRESSURE; MODEL AB The radial distribution function (RDF) of liquid water has been determined by x-ray scattering. Using a free-standing water jet and a diffracted beam analyzer to separate the Compton from the elastic scattering experimentally, several significant sources of error have been eliminated in the experiment. These have enabled the collection of quality data out to 19.7 A degrees(-1). Data were collected both at 278 K and at 296 K. Our RDF presents fine structure, particularly, a distinct peak at 3.4 A degrees and a peak split at 4.5 A degrees. These features cannot be interpreted by a simple tetrahedral configuration suggested by continuum models. The uncertainties due to the truncation effects and the choice of scattering factors are found to have little influence on the RDF at intermolecular distances. C1 [Fu, Ling; Bienenstock, Arthur] Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA. [Fu, Ling; Bienenstock, Arthur; Brennan, Sean] Stanford Linear Accelerator Ctr, Stanford Synchrotron Radiat Lab, Menlo Pk, CA 94025 USA. RP Fu, L (reprint author), Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA. EM ling.fu@gmail.com FU U. S. Department of Energy, Office of Basic Energy Sciences FX The authors thank A. K. Soper, G. Hura, T. HeadGordon, and A. Habenschuss for kindly sending us the data used for comparison in the article. We also thank A. Nilsson and T. Hufnagel for helpful discussions and M. L. Saboungi for a valuable e-mail exchange. This research was carried out at the SSRL, a national user facility operated by Stanford University on behalf of the U. S. Department of Energy, Office of Basic Energy Sciences. We thank the staff of SSRL for their help with the experiment. NR 37 TC 35 Z9 38 U1 0 U2 20 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0021-9606 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 21 PY 2009 VL 131 IS 23 AR 234702 DI 10.1063/1.3273874 PG 10 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 536HU UT WOS:000273036300033 PM 20025337 ER PT J AU Huang, W Bulusu, S Pal, R Zeng, XC Wang, LS AF Huang, Wei Bulusu, Satya Pal, Rhitankar Zeng, Xiao Cheng Wang, Lai-Sheng TI CO chemisorption on the surfaces of the golden cages SO JOURNAL OF CHEMICAL PHYSICS LA English DT Article DE adsorption; carbon compounds; chemisorption; gold; metal clusters; photoelectron spectra; solid-state phase transformations; spin-orbit interactions; surface chemistry ID CARBON-MONOXIDE ADSORPTION; CLUSTER ANIONS; AU CLUSTERS; PHOTOELECTRON-SPECTROSCOPY; VIBRATIONAL SPECTROSCOPY; SATURATED ADSORPTION; MOLECULAR-OXYGEN; OXIDATION; SIZE; O-2 AB We report a joint experimental and theoretical study of CO chemisorption on the golden cages. We find that the Au(17)- cage is highly robust and retains its cage structure in Au(17)(CO)(-). On the other hand, the Au(16)- cage is transformed to a structure similar to Au(17)- upon the adsorption of CO. Au(18)- is known to consist of two nearly degenerate structures, i.e., a cage and a pyramidal isomer, which coexist in the cluster beam. However, upon CO chemisorption only the cage isomer is observed while the pyramidal isomer no longer exists due to its less favorable interaction with CO, compared to the cage isomer. We find that inclusion of the spin-orbit effects is critical in yielding simulated spectra in quantitative agreement with the experimental data and providing unequivocal structural information and molecular insights into the chemical interactions between CO and the golden cages. C1 [Bulusu, Satya; Pal, Rhitankar; Zeng, Xiao Cheng] Univ Nebraska, Dept Chem, Lincoln, NE 68588 USA. [Bulusu, Satya; Pal, Rhitankar; Zeng, Xiao Cheng] Univ Nebraska, Ctr Mat & Nanosci, Lincoln, NE 68588 USA. [Huang, Wei] Washington State Univ, Dept Phys, Richland, WA 99354 USA. [Huang, Wei] Pacific NW Natl Lab, Chem & Mat Sci Div, Richland, WA 99352 USA. [Wang, Lai-Sheng] Brown Univ, Dept Chem, Providence, RI 02912 USA. RP Zeng, XC (reprint author), Univ Nebraska, Dept Chem, Lincoln, NE 68588 USA. EM xczeng@phase2.unl.edu; lai-sheng_wang@brown.edu FU National Science Foundation [CHE-0749496, CHE-0427746, DMR-0820521]; Nebraska Research Initiative; University of Nebraska Holland Computing Center FX W. H. would like to thank Dr. Niranjan Govind for invaluable discussions of spin-orbit DFT calculations in NWCHEM. The experimental work and NWChem calculations done at Washington were supported by the National Science Foundation (Grant No. CHE-0749496), and was performed at the EMSL, a national scientific user facility sponsored by the DOE's Office of Biological and Environmental Research and located at the Pacific Northwest National Laboratory, operated for DOE by Battelle. The theoretical work done at Nebraska was supported by grants from the National Science Foundation (Grant Nos. CHE-0427746 and DMR-0820521), the Nebraska Research Initiative, and the University of Nebraska Holland Computing Center. NR 65 TC 25 Z9 25 U1 1 U2 21 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0021-9606 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 21 PY 2009 VL 131 IS 23 AR 234305 DI 10.1063/1.3273326 PG 6 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 536HU UT WOS:000273036300023 PM 20025327 ER PT J AU Kowalski, K Valiev, M AF Kowalski, Karol Valiev, Marat TI Extensive regularization of the coupled cluster methods based on the generating functional formalism: Application to gas-phase benchmarks and to the S(N)2 reaction of CHCl3 and OH- in water SO JOURNAL OF CHEMICAL PHYSICS LA English DT Review DE coupled cluster calculations; ion-molecule reactions; negative ions; organic compounds; oxygen compounds; reaction kinetics theory; water ID MOLECULAR ELECTRONIC-STRUCTURE; GAUSSIAN-BASIS SETS; FULL CCSDT MODEL; NONITERATIVE ENERGY CORRECTIONS; REDUCED MULTIREFERENCE CCSD; BODY PERTURBATION THEORIES; OPEN-SHELL SYSTEMS; DOUBLE-ZETA BASIS; N-2 TRIPLE BOND; CONFIGURATION-INTERACTION AB The recently introduced energy expansion based on the use of generating functional (GF) [K. Kowalski and P. D. Fan, J. Chem. Phys. 130, 084112 (2009)] provides a way of constructing size-consistent noniterative coupled cluster (CC) corrections in terms of moments of the CC equations. To take advantage of this expansion in a strongly interacting regime, the regularization of the cluster amplitudes is required in order to counteract the effect of excessive growth of the norm of the CC wave function. Although proven to be efficient, the previously discussed form of the regularization does not lead to rigorously size-consistent corrections. In this paper we address the issue of size-consistent regularization of the GF expansion by redefining the equations for the cluster amplitudes. The performance and basic features of proposed methodology are illustrated on several gas-phase benchmark systems. Moreover, the regularized GF approaches are combined with quantum mechanical molecular mechanics module and applied to describe the S(N)2 reaction of CHCl3 and OH- in aqueous solution. C1 [Kowalski, Karol; Valiev, Marat] Pacific NW Natl Lab, William R Wiley Environm Mol Sci Lab, Richland, WA 99352 USA. RP Kowalski, K (reprint author), Pacific NW Natl Lab, William R Wiley Environm Mol Sci Lab, K8-91 Battelle,POB 999, Richland, WA 99352 USA. EM karol.kowalski@pnl.gov FU Extreme Scale Computing Initiative; Pacific Northwest National Laboratory; Office of Naval Research and the Division of Chemical Sciences, Office of Basic Energy, DOE [DE-AC06-76RLO-1830] FX The work related to the development of the Reg-GF approaches and their pilot parallel implementations (K. K.) and the merger of the regularized methods with the QM/MM module (M. V.) was partially supported by the Extreme Scale Computing Initiative (K. K), a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory. M. V. would like to acknowledge the support from Office of Naval Research and the Division of Chemical Sciences, Office of Basic Energy, DOE. All calculations have been performed using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific tional Laboratory is funded by the Office of Biological and Environmental Research in the U.S. Department of Energy. The Pacific Northwest National Laboratory is operated for the U.S. Department of Energy by the Battelle Memorial Institute under Contract No. DE-AC06-76RLO-1830.Northwest National Laboratory. The William R. Wiley Environmental Molecular Sciences Laboratory at the Pacific Northwest Na NR 135 TC 4 Z9 4 U1 1 U2 13 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0021-9606 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 21 PY 2009 VL 131 IS 23 AR 234107 DI 10.1063/1.3270957 PG 12 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 536HU UT WOS:000273036300010 PM 20025314 ER PT J AU Munsky, B Nemenman, I Bel, G AF Munsky, Brian Nemenman, Ilya Bel, Golan TI Specificity and completion time distributions of biochemical processes SO JOURNAL OF CHEMICAL PHYSICS LA English DT Article DE biochemistry; Laplace transforms; master equation; molecular biophysics; reaction kinetics; stochastic processes ID T-CELL-ACTIVATION; SIGNAL-TRANSDUCTION; ACID POLYMERASE; RATE CONSTANTS; DISCRIMINATION; MECHANISM; ACCURACY; NETWORKS; SYSTEMS; MODEL AB In order to produce specific complex structures from a large set of similar biochemical building blocks, many biochemical systems require high sensitivity to small molecular differences. The first and most common model used to explain this high specificity is kinetic proofreading, which has been extended to a variety of systems from detection of DNA mismatch to cell signaling processes. While the specification properties of kinetic proofreading models are well known and were studied in various contexts, very little is known about their temporal behavior. In this work, we study the dynamical properties of discrete stochastic two-branch kinetic proofreading schemes. Using the Laplace transform of the corresponding chemical master equation, we obtain an analytical solution for the completion time distribution. In particular we provide expressions for the specificity as well as the mean and variance of the process completion times. We also show that, for a wide range of parameters, a process distinguishing between two different products can be reduced to a much simpler three-point process. Our results allow for the systematic study of the interplay between specificity and completion times, as well as testing the validity of the kinetic proofreading model in biological systems. C1 [Munsky, Brian; Nemenman, Ilya; Bel, Golan] Los Alamos Natl Lab, Ctr Nonlinear Studies & Comp, Computat & Stat Sci Div, Los Alamos, NM 87545 USA. [Nemenman, Ilya] Emory Univ, Dept Phys, Dept Biol, Atlanta, GA 30322 USA. [Nemenman, Ilya] Emory Univ, Computat & Life Sci Strateg Initiat, Atlanta, GA 30322 USA. RP Munsky, B (reprint author), Los Alamos Natl Lab, Ctr Nonlinear Studies & Comp, Computat & Stat Sci Div, Los Alamos, NM 87545 USA. EM golanbel@gmail.com RI Bel, Golan/C-6528-2008; BEL, GOLAN/F-1573-2012; Munsky, Brian/A-1947-2016; OI Bel, Golan/0000-0002-3307-9478; BEL, GOLAN/0000-0002-3307-9478; Munsky, Brian/0000-0001-6147-7329; Nemenman, Ilya/0000-0003-3024-4244 FU LANL LDRD program FX thank N. Hengartner, J. Hopfield, and N. Sinitsyn for discussions during early stages of this work. We also thank B. Goldstein, R. Gutenkunst, M. Monine, and especially M. Savageau for helpful comments regarding this work. This work was partially funded by LANL LDRD program. NR 42 TC 11 Z9 11 U1 0 U2 9 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0021-9606 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 21 PY 2009 VL 131 IS 23 AR 235103 DI 10.1063/1.3274803 PG 10 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 536HU UT WOS:000273036300047 PM 20025351 ER PT J AU Wen, HD Huse, N Schoenlein, RW Lindenberg, AM AF Wen, Haidan Huse, Nils Schoenlein, Robert W. Lindenberg, Aaron M. TI Ultrafast conversions between hydrogen bonded structures in liquid water observed by femtosecond x-ray spectroscopy SO JOURNAL OF CHEMICAL PHYSICS LA English DT Article DE high-pressure effects; high-speed optical techniques; hydrogen bonds; liquid structure; water; X-ray absorption spectra ID ABSORPTION FINE-STRUCTURE; VIBRATIONAL-RELAXATION; TEMPERATURE-DEPENDENCE; INFRARED-SPECTROSCOPY; DYNAMICS; H2O; NETWORK; ENERGY; EXCITATIONS; PULSES AB We present the first femtosecond soft x-ray spectroscopy in liquids, enabling the observation of changes in hydrogen bond structures in water via core-hole excitation. The oxygen K-edge of vibrationally excited water is probed with femtosecond soft x-ray pulses, exploiting the relation between different water structures and distinct x-ray spectral features. After excitation of the intramolecular OH stretching vibration, characteristic x-ray absorption changes monitor the conversion of strongly hydrogen-bonded water structures to more disordered structures with weaker hydrogen-bonding described by a single subpicosecond time constant. The latter describes the thermalization time of vibrational excitations and defines the characteristic maximum rate with which nonequilibrium populations of more strongly hydrogen-bonded water structures convert to less-bonded ones. On short time scales, the relaxation of vibrational excitations leads to a transient high-pressure state and a transient absorption spectrum different from that of statically heated water. C1 [Huse, Nils; Schoenlein, Robert W.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Chem Sci, Ultrafast Xray Sci Lab, Berkeley, CA 94720 USA. [Wen, Haidan; Lindenberg, Aaron M.] SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA. [Schoenlein, Robert W.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Lindenberg, Aaron M.] Stanford Univ, Dept Mat Sci & Engn, Stanford, CA 94305 USA. RP Huse, N (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Div Chem Sci, Ultrafast Xray Sci Lab, Berkeley, CA 94720 USA. EM nhuse@lbl.gov; aaronl@stanford.edu RI WEN, HAIDAN/B-5258-2009; Schoenlein, Robert/D-1301-2014; Huse, Nils/A-5712-2017 OI Schoenlein, Robert/0000-0002-6066-7566; Huse, Nils/0000-0002-3281-7600 FU Office of Science, Office of Basic Energy Sciences, the Chemical Sciences, Geosciences, and Biosciences Division [DE-AC02-05CH11231]; Department of Energy through the Stanford PULSE Institute; National Science Foundation (NSF) [CHE-0518637] FX This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, the Chemical Sciences, Geosciences, and Biosciences Division under the Department of Energy Contract No. DE-AC02-05CH11231 (LBNL-Ultrafast X-ray Science Laboratory), by the Department of Energy through the Stanford PULSE Institute, and by the National Science Foundation (NSF) Contract No. CHE-0518637. NR 39 TC 24 Z9 24 U1 4 U2 25 PU AMER INST PHYSICS PI MELVILLE PA CIRCULATION & FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA SN 0021-9606 J9 J CHEM PHYS JI J. Chem. Phys. PD DEC 21 PY 2009 VL 131 IS 23 AR 234505 DI 10.1063/1.3273204 PG 5 WC Chemistry, Physical; Physics, Atomic, Molecular & Chemical SC Chemistry; Physics GA 536HU UT WOS:000273036300029 PM 20025333 ER PT J AU Luo, JW Bester, G Zunger, A AF Luo, Jun-Wei Bester, Gabriel Zunger, Alex TI Long- and short-range electron-hole exchange interaction in different types of quantum dots SO NEW JOURNAL OF PHYSICS LA English DT Article ID FINE-STRUCTURE; EXCITONS; SEMICONDUCTORS; NANOCRYSTALS; STATES; INP AB The electron-hole (e-h) exchange interaction leads to the splitting of the exciton into a pair of bright and a pair of dark states. This bright-dark-or singlet-triplet-exciton splitting was historically calculated as the sum of a longrange (LR) and a short-range (SR) component. Using a numerical atomistic approach, we are able to calculate the exchange integrals as a function of the e-h range of interaction S, revealing the 'internal' structure of the integrals. We apply this procedure to thickness-fluctuation GaAs/AlGaAs quantum dots (QDs), self-assembled InAs/GaAs QDs and colloidal InAs QDs. We find a heterogeneous situation, where the SR component contributes similar to 10, similar to 20-30 and similar to 20-50% to the total e-h exchange splitting, which is in the range of 10, 100 and 10 000 mu eV, for the three types of QDs, respectively. The balance between SR and LR is found to depend critically on the size, shape and type of structure. For all types of QDs we find, surprisingly, a range of interaction, close to the physical dimension of the structures, contributing to a reduction of the integral's magnitude. These results highlight the complexity of the exchange interaction, warning against simplified models, and establish the basic features of the nature and origin of dark-bright excitonic splitting in QDs. C1 [Bester, Gabriel] Max Planck Inst Solid State Res, D-70569 Stuttgart, Germany. [Luo, Jun-Wei; Zunger, Alex] Natl Renewable Energy Lab, Golden, CO 80401 USA. RP Bester, G (reprint author), Max Planck Inst Solid State Res, D-70569 Stuttgart, Germany. EM g.bester@fkf.mpg.de RI LUO, JUN-WEI/A-8491-2010; Bester, Gabriel/I-4414-2012; Zunger, Alex/A-6733-2013; LUO, JUNWEI/B-6545-2013 OI Bester, Gabriel/0000-0003-2304-0817; FU US Department of Energy; Office of Science; Basic Energy Science; Materials Sciences and Engineering Division [DE-AC36-08GO28308] FX Work at NREL was funded by the US Department of Energy, Office of Science, Basic Energy Science, Materials Sciences and Engineering Division, under Contract No. DE-AC36-08GO28308 to NREL. NR 27 TC 9 Z9 9 U1 0 U2 27 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 1367-2630 J9 NEW J PHYS JI New J. Phys. PD DEC 21 PY 2009 VL 11 AR 123024 DI 10.1088/1367-2630/11/12/123024 PG 12 WC Physics, Multidisciplinary SC Physics GA 537AW UT WOS:000273086200004 ER PT J AU Anthony, PL Delayen, JR Fryberger, D Goree, WS Mammosser, J Szalata, ZM Weisend, JG AF Anthony, P. L. Delayen, J. R. Fryberger, D. Goree, W. S. Mammosser, J. Szalata, Z. M. Weisend, J. G., II TI Experimental studies of light emission phenomena in superconducting RF cavities SO NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT LA English DT Article DE Field emission; Cavity lights; Ball lightning AB Experimental studies of light emission phenomena in superconducting RF cavities, which we categorize under the general heading of cavity lights, are described. The cavity lights data, which were obtained using a small CCD video camera, were collected in a series of nine experimental runs ranging from similar to 1/2 to similar to 2 h in duration. The video data were recorded on a standard VHS tape. As the runs progressed, additional instrumentation was added. For the last three runs a LabVIEW-controlled data acquisition system was included. These runs furnish evidence for several, possibly related, light emission phenomena. The most intriguing of these is what appear to be small luminous objects <= 1.5 mm in size, freely moving about in the vacuum space, generally without wall contact, as verified by reflections of the tracks in the cavity walls. In addition, on a number of occasions, these objects were observed to bounce off of the cavity walls. The wall-bounce aspect of most of these events was clearly confirmed by pre-bounce and post-bounce reflections concurrent with the tracks. In one of the later runs a mode of, behavior was observed that was qualitatively different from anything observed in the earlier runs. Perhaps the most perplexing aspect of this new mode was the observation of as many as seven luminous objects arrayed in what might be described as a macromolecular formation, coherently moving about in the interior of the cavity for extended periods of time, evidently without any wall contact. It is suggested that these mobile luminous objects are without explanation within the realm of established physics. Some remarks about more exotic theoretical possibilities are made, and future plans are discussed. (C) 2009 Elsevier B.V. All rights reserved. C1 [Anthony, P. L.; Fryberger, D.; Szalata, Z. M.; Weisend, J. G., II] SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA. [Delayen, J. R.; Mammosser, J.] TJNAF, Newport News, VA 23606 USA. [Goree, W. S.] 2G Enterprises, Pacific Grove, CA 93950 USA. [Delayen, J. R.] Old Dominion Univ, Ctr Accelerator Sci, Norfolk, VA 23529 USA. RP Fryberger, D (reprint author), SLAC Natl Accelerator Lab, Menlo Pk, CA 94025 USA. EM fryberger@slac.stanford.edu FU Department of Energy [DE-AC02-76SF-00515, DE-AC05-84ER40150] FX Supported by the Department of Energy Contracts DE-AC02-76SF-00515 and DE-AC05-84ER40150. NR 31 TC 3 Z9 3 U1 0 U2 2 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-9002 J9 NUCL INSTRUM METH A JI Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. PD DEC 21 PY 2009 VL 612 IS 1 BP 1 EP 45 DI 10.1016/j.nima.2009.08.084 PG 45 WC Instruments & Instrumentation; Nuclear Science & Technology; Physics, Nuclear; Physics, Particles & Fields SC Instruments & Instrumentation; Nuclear Science & Technology; Physics GA 537GN UT WOS:000273101300001 ER PT J AU Martel, P Clinton, E McWilliams, R Lawrence, D Miskimen, R Ahmidouch, A Ambrozewicz, P Asratyan, A Baker, K Benton, L Bernstein, A Cole, P Collins, P Dale, D Danagoulian, S Davidenko, G Demirchyan, R Deur, A Dolgolenko, A Dzyubenko, G Evdokimov, A Feng, J Gabrielyan, M Gan, L Gasparian, A Glamazdin, O Goryachev, V Gyurjyan, V Hardy, K Ito, M Khandaker, M Kingsberry, P Kolarkar, A Konchatnyi, M Korchin, O Korsch, W Kowalski, S Kubantsev, M Kubarovsky, V Larin, I Matveev, V McNulty, D Milbrath, B Minehart, R Mochalov, V Mtingwa, S Nakagawa, I Overby, S Pasyuk, E Payen, M Pedroni, R Prok, Y Ritchie, B Salgado, C Sitnikov, A Sober, D Stephens, W Teymurazyan, A Underwood, J Vasiliev, A Verebryusov, V Vishnyakov, V Wood, M AF Martel, P. Clinton, E. McWilliams, R. Lawrence, D. Miskimen, R. Ahmidouch, A. Ambrozewicz, P. Asratyan, A. Baker, K. Benton, L. Bernstein, A. Cole, P. Collins, P. Dale, D. Danagoulian, S. Davidenko, G. Demirchyan, R. Deur, A. Dolgolenko, A. Dzyubenko, G. Evdokimov, A. Feng, J. Gabrielyan, M. Gan, L. Gasparian, A. Glamazdin, O. Goryachev, V. Gyurjyan, V. Hardy, K. Ito, M. Khandaker, M. Kingsberry, P. Kolarkar, A. Konchatnyi, M. Korchin, O. Korsch, W. Kowalski, S. Kubantsev, M. Kubarovsky, V. Larin, I. Matveev, V. McNulty, D. Milbrath, B. Minehart, R. Mochalov, V. Mtingwa, S. Nakagawa, I. Overby, S. Pasyuk, E. Payen, M. Pedroni, R. Prok, Y. Ritchie, B. Salgado, C. Sitnikov, A. Sober, D. Stephens, W. Teymurazyan, A. Underwood, J. Vasiliev, A. Verebryusov, V. Vishnyakov, V. Wood, M. TI Nuclear targets for a precision measurement of the neutral pion radiative width SO NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT LA English DT Article DE Solid nuclear targets; Area density; X-ray attenuation AB A technique is presented for precision measurements of the area densities, rho T, of approximately 5% radiation length carbon and (208)Pb targets used in an experiment at Jefferson Laboratory to measure the neutral pion radiative width. The precision obtained in the area density for the carbon target is +/- 0.050%, and that obtained for the lead target through an X-ray attenuation technique is +/- 0.43%. (C) 2009 Elsevier B.V. All rights reserved. C1 [Miskimen, R.] Univ Massachusetts, Dept Phys, Amherst, MA 01003 USA. [Collins, P.; Pasyuk, E.; Ritchie, B.] Arizona State Univ, Tempe, AZ 85287 USA. [Sober, D.] Catholic Univ, Washington, DC USA. [Baker, K.] Hampton Univ, Hampton, VA 23668 USA. [Cole, P.; Dale, D.] Idaho State Univ, Pocatello, ID 83209 USA. [Gabrielyan, M.; Kolarkar, A.; Korsch, W.; Nakagawa, I.; Teymurazyan, A.] Univ Kentucky, Lexington, KY 40506 USA. [Glamazdin, O.; Konchatnyi, M.; Korchin, O.] Kharkov Phys & Technol Inst, Kharkov, Ukraine. [Bernstein, A.; Kowalski, S.; McNulty, D.; Prok, Y.] MIT, Cambridge, MA 02139 USA. [Khandaker, M.; Kingsberry, P.; Salgado, C.] Norfolk State Univ, Norfolk, VA USA. [Ahmidouch, A.; Ambrozewicz, P.; Benton, L.; Danagoulian, S.; Demirchyan, R.; Gasparian, A.; Hardy, K.; Mtingwa, S.; Overby, S.; Payen, M.; Pedroni, R.; Underwood, J.] N Carolina Agr & Tech State Univ, Greensboro, NC USA. [Feng, J.; Gan, L.] Univ N Carolina, Wilmington, NC USA. [Kubantsev, M.] Northwestern Univ, Evanston, IL 60208 USA. [Milbrath, B.] Pacific NW Natl Lab, Richland, WA 99352 USA. [Mochalov, V.; Vasiliev, A.] Inst High Energy Phys, Protvino, Russia. [Minehart, R.; Stephens, W.] Univ Virginia, Charlottesville, VA 22903 USA. RP Miskimen, R (reprint author), Univ Massachusetts, Dept Phys, 710 N Pleasant St, Amherst, MA 01003 USA. EM miskimen@physics.umass.edu RI McWilliams, R./J-4358-2016; Korchin, Alexander/J-4910-2016; OI Korchin, Alexander/0000-0001-7947-170X; Glamazdin, Alexander/0000-0002-4172-7324 NR 16 TC 2 Z9 2 U1 0 U2 2 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-9002 J9 NUCL INSTRUM METH A JI Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. PD DEC 21 PY 2009 VL 612 IS 1 BP 46 EP 49 DI 10.1016/j.nima.2009.09.063 PG 4 WC Instruments & Instrumentation; Nuclear Science & Technology; Physics, Nuclear; Physics, Particles & Fields SC Instruments & Instrumentation; Nuclear Science & Technology; Physics GA 537GN UT WOS:000273101300002 ER PT J AU Urciuoli, GM Cisbani, E Cusanno, F De Leo, R Di Bari, D Frullani, S Garibaldi, F Iodice, M Lagamba, L LeRose, JJ Markowitz, P Marrone, S Reitz, B AF Urciuoli, G. M. Cisbani, E. Cusanno, F. De Leo, R. Di Bari, D. Frullani, S. Garibaldi, F. Iodice, M. Lagamba, L. LeRose, J. J. Markowitz, P. Marrone, S. Reitz, B. TI A chi(2) test used for particle identification with the Hall A RICH detector at JLab SO NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT LA English DT Article DE RICH; Particle identification; Reconstruction algorithm; Cochran's theorem ID PROXIMITY FOCUSING RICH; JEFFERSON-LAB; PATTERN-RECOGNITION; CHERENKOV RINGS; KAON PHYSICS; PERFORMANCE; LHCB AB An algorithm, based on the chi(2) test, employed for particle identification by RICH detectors, is described. This algorithm is independent and complementary to the traditional algorithm based on the comparison between the average of the measured Cherenkov angles and the expected Cherenkov angles of the photons generated in the RICH by the particle to be identified. On the other hand it is much simpler and faster than a full likelihood analysis of the full event pattern. The particle rejection ratios achievable with the combined use of this algorithm and the algorithm based on the comparison between the average and the expected Cherenkov angles are very high. The algorithm also allows one to identify noise easily. The application of the algorithm is shown for the Hall A RICH detector in the E94-107 experiment at JLab. In this experiment an enormous background made up of pions and protons is 30 000 times bigger than the signal and had to be identified and rejected in order to extract the kaons from the electroproduction of hypernuclei. (C) 2009 Elsevier B.V. All rights reserved. C1 [Urciuoli, G. M.] Ist Nazl Fis Nucl, Sez Roma, I-00185 Rome, Italy. [Cisbani, E.; Cusanno, F.; Frullani, S.; Garibaldi, F.] Ist Nazl Fis Nucl, Grp Collegato Sanita, I-00161 Rome, Italy. [Cisbani, E.; Cusanno, F.; Frullani, S.; Garibaldi, F.] Ist Super Sanita, I-00161 Rome, Italy. [De Leo, R.; Di Bari, D.; Lagamba, L.; Marrone, S.] Univ Bari, I-70125 Bari, Italy. [De Leo, R.; Di Bari, D.; Lagamba, L.; Marrone, S.] Ist Nazl Fis Nucl, Sez Bari, I-70125 Bari, Italy. [Iodice, M.] Ist Nazl Fis Nucl, Sez Roma3, I-00146 Rome, Italy. [LeRose, J. J.; Reitz, B.] Thomas Jefferson Natl Accelerator Facil, Newport News, VA 23606 USA. [Markowitz, P.] Florida Int Univ, Miami, FL 33199 USA. RP Urciuoli, GM (reprint author), Ist Nazl Fis Nucl, Sez Roma, I-00185 Rome, Italy. EM guido.maria.urciuoli@roma1.infn.it RI Cisbani, Evaristo/C-9249-2011; OI Cisbani, Evaristo/0000-0002-6774-8473; Di Bari, Domenico/0000-0002-5559-8906 FU U.S. DOE [DE-AC05-84ER40150] FX Authored and supported by The Italian Istituto Nazionale di Fisica Nucleate and The Southeastern Universities Research Association, Inc. under U.S. DOE Contract No. DE-AC05-84ER40150. The U.S. Government retains a nonexclusive, paid-up, irrevocable, world-wide license to publish or reproduce this manuscript for U.S. Government purposes. NR 16 TC 3 Z9 3 U1 0 U2 2 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-9002 J9 NUCL INSTRUM METH A JI Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. PD DEC 21 PY 2009 VL 612 IS 1 BP 56 EP 68 DI 10.1016/j.nima.2009.09.061 PG 13 WC Instruments & Instrumentation; Nuclear Science & Technology; Physics, Nuclear; Physics, Particles & Fields SC Instruments & Instrumentation; Nuclear Science & Technology; Physics GA 537GN UT WOS:000273101300004 ER PT J AU Bourret-Courchesne, ED Bizarri, G Borade, R Yan, Z Hanrahan, SM Gundiah, G Chaudhry, A Canning, A Derenzo, SE AF Bourret-Courchesne, E. D. Bizarri, G. Borade, R. Yan, Z. Hanrahan, S. M. Gundiah, G. Chaudhry, A. Canning, A. Derenzo, S. E. TI Eu2+-doped Ba(2)Csl(5), a new high-performance scintillator SO NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT LA English DT Article DE Scintillator; Halides; Europium; Energy resolution; Luminescence; Gamma-ray detection ID COMMON INORGANIC SCINTILLATORS; LIGHT YIELD AB The crystal growth and scintillation properties of Ba(2)Csl(5):Eu2+ are reported. Crystals were produced by the vertical Bridgman technique in a sealed quartz ampoule. Ba(2)Csl(5):Eu2+ presents excellent scintillation properties. An estimated light yield of 97,000 +/- 5,000 photons per MeV (ph/MeV) of absorbed gamma-ray energy was measured. An energy resolution (FWHM over peak position) of 3.8 +/- 0.3% was observed for the 662 keV full absorption peak. Pulsed X-ray luminescence measurements show a relatively complex time response with four exponential decay components of 48,383, 1500 and 9900 ns with a contribution to the total light output of 1%, 26%, 68% and 25%, respectively. Under X-ray and UV excitation, the emission corresponds to a broadband centered at 2.85 eV. First principles calculations show strong localization of the excited state on the Eu site. Ba(2)Csl(5):Eu2+ has a density of about 5 g/cm(3). These first reported scintillation properties make Ba(2)Csl(5):Eu2+ a very high-performance scintillator. Published by Elsevier B.V. C1 [Bourret-Courchesne, E. D.; Yan, Z.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, Berkeley, CA 94720 USA. [Bizarri, G.; Borade, R.; Hanrahan, S. M.; Gundiah, G.; Chaudhry, A.; Derenzo, S. E.] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Life Sci, Berkeley, CA 94720 USA. [Chaudhry, A.] Univ Calif Davis, Dept Elect & Comp Engn, Davis, CA 95616 USA. [Canning, A.] Univ Calif Berkeley, Lawrence Berkeley Lab, Computat Res Div, Berkeley, CA 94720 USA. RP Bourret-Courchesne, ED (reprint author), Univ Calif Berkeley, Lawrence Berkeley Lab, Div Mat Sci, 1 Cyclotron Rd,Mailstop 55R0121, Berkeley, CA 94720 USA. EM EDBourret@lbl.gov FU US Department of Homeland Security/DNDO; US Department of Energy/NNSA/NA22; Lawrence Berkeley National Laboratory [AC02-05CH11231] FX This work was supported by the US Department of Homeland Security/DNDO and the US Department of Energy/NNSA/NA22 and carried out at Lawrence Berkeley National Laboratory under Contract no. AC02-05CH11231. NR 22 TC 72 Z9 73 U1 1 U2 11 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-9002 J9 NUCL INSTRUM METH A JI Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. PD DEC 21 PY 2009 VL 612 IS 1 BP 138 EP 142 DI 10.1016/j.nima.2009.10.146 PG 5 WC Instruments & Instrumentation; Nuclear Science & Technology; Physics, Nuclear; Physics, Particles & Fields SC Instruments & Instrumentation; Nuclear Science & Technology; Physics GA 537GN UT WOS:000273101300013 ER PT J AU Doumas, A Smith, GC AF Doumas, A. Smith, G. C. TI A Monte Carlo simulation comparing hydrocarbons as stopping gases for position sensitive neutron detectors SO NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT LA English DT Article DE Thermal neutron; Gas detector; Position resolution; Proton triton range ID THERMAL-NEUTRONS AB Various neutron detectors are being developed for the next generation user facilities, which incorporate new as well as existing approaches for the detection of thermal neutrons. Improvements in neutron detector efficiency, detector size and position resolution have occurred over the last three decades and further advances are expected in the next ten years. Since gas detectors are expected to continue in a key role for future thermal neutron experiments, it is advantageous to review some of the criteria for the choice of proton/triton stopping gases for gas-based detectors. Monte Carlo simulations, using the group of programs "Stopping and Range of Ions in Matter", have been run to determine key performance characteristics for neutron detectors which utilize the reaction (3)He(n,p)t. This paper will focus on investigating the use of three common hydrocarbons and CF(4) as stopping gases for thermal neutron detectors. A discussion of these gases will include their behavior in terms of proton and triton range, ion distribution and straggle. (C) 2009 Elsevier B.V. All rights reserved. C1 [Smith, G. C.] Brookhaven Natl Lab, Instrumentat Div, Upton, NY 11973 USA. [Doumas, A.] US Merchant Marine Acad, Kings Point, NY 11024 USA. RP Smith, GC (reprint author), Brookhaven Natl Lab, Instrumentat Div, Upton, NY 11973 USA. EM gsmith@bnl.gov FU US Department of Energy [DE-AC02-98CH10886] FX This work was supported in part by the US Department of Energy under Contract no. DE-AC02-98CH10886. NR 10 TC 3 Z9 4 U1 0 U2 1 PU ELSEVIER SCIENCE BV PI AMSTERDAM PA PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS SN 0168-9002 J9 NUCL INSTRUM METH A JI Nucl. Instrum. Methods Phys. Res. Sect. A-Accel. Spectrom. Dect. Assoc. Equip. PD DEC 21 PY 2009 VL 612 IS 1 BP 149 EP 154 DI 10.1016/j.nima.2009.09.050 PG 6 WC Instruments & Instrumentation; Nuclear Science & Technology; Physics, Nuclear; Physics, Particles & Fields SC Instruments & Instrumentation; Nuclear Science & Technology; Physics GA 537GN UT WOS:000273101300015 ER PT J AU Martz, DH Nguyen, HT Patel, D Britten, JA Alessi, D Krous, E Wang, Y Larotonda, MA George, J Knollenberg, B Luther, BM Rocca, JJ Menoni, CS AF Martz, D. H. Nguyen, H. T. Patel, D. Britten, J. A. Alessi, D. Krous, E. Wang, Y. Larotonda, M. A. George, J. Knollenberg, B. Luther, B. M. Rocca, J. J. Menoni, C. S. TI Large area high efficiency broad bandwidth 800 nm dielectric gratings for high energy laser pulse compression SO OPTICS EXPRESS LA English DT Article ID DIFFRACTION GRATINGS; DAMAGE THRESHOLD; PETAWATT LASER AB We have demonstrated broad bandwidth large area (229 mm x 114 mm) multilayer dielectric diffraction gratings for the efficient compression of high energy 800 nm laser pulses at high average power. The gratings are etched in the top layers of an aperiodic (Nb0.5Ta0.5)(2)O-5-SiO2 multilayer coating deposited by ion beam sputtering. The mean efficiency of the grating across the area is better than 97% at the center wavelength and remains above 96% at wavelengths between 820 nm and 780 nm. The gratings were used to compress 5.5 J pulses from a Ti:sapphire laser with an efficiency above 80 percent. (C) 2009 Optical Society of America C1 [Martz, D. H.; Patel, D.; Alessi, D.; Krous, E.; Wang, Y.; Larotonda, M. A.; Luther, B. M.; Rocca, J. J.; Menoni, C. S.] Colorado State Univ, NSF ERC Extreme Ultraviolet Sci & Technol, Ft Collins, CO 80523 USA. [Nguyen, H. T.; Britten, J. A.] Lawrence Livermore Natl Lab, Natl Ignit Facil Programs Directorate, Photon Sci & Applicat Program, Livermore, CA 94550 USA. [George, J.; Knollenberg, B.] Veeco Proc Equipment Inc, Ft Collins, CO 80525 USA. RP Martz, DH (reprint author), Colorado State Univ, NSF ERC Extreme Ultraviolet Sci & Technol, Ft Collins, CO 80523 USA. EM Dale.Martz@rams.colostate.edu RI Martz, Dale/A-9693-2012; Menoni, Carmen/B-4989-2011 FU NSF [EEC-0310717]; United States Department of Energy by the Lawrence Livermore National Laboratory [DE-AC52-07NA27344] FX This work was supported by the NSF Center for Extreme Ultraviolet Science and Technology under NSF Award Number EEC-0310717 and the United States Department of Energy by the Lawrence Livermore National Laboratory under contract number DE-AC52-07NA27344. NR 14 TC 32 Z9 34 U1 4 U2 18 PU OPTICAL SOC AMER PI WASHINGTON PA 2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036 USA SN 1094-4087 J9 OPT EXPRESS JI Opt. Express PD DEC 21 PY 2009 VL 17 IS 26 BP 23809 EP 23816 DI 10.1364/OE.17.023809 PG 8 WC Optics SC Optics GA 538AO UT WOS:000273156200049 PM 20052091 ER PT J AU Filippi, AM Archibald, R Bhaduri, BL Bright, EA AF Filippi, Anthony M. Archibald, Rick Bhaduri, Budhendra L. Bright, Edward A. TI Hyperspectral agricultural mapping using Support Vector Machine-Based Endmember Extraction (SVM-BEE) SO OPTICS EXPRESS LA English DT Article ID SPECTRAL MIXTURE ANALYSIS; CANOPY REFLECTANCE; CLASSIFICATION; ALGORITHM; VARIABILITY; IMAGERY; MODELS; VALIDATION; VEGETATION AB Extracting endmembers from remotely-sensed images of vegetated areas can present difficulties. In this research, we applied a recently-developed endmember-extraction algorithm based on Support Vector Machines to the problem of semi-autonomous estimation of vegetation endmembers from a hyperspectral image. This algorithm, referred to as Support Vector Machine-Based Endmember Extraction (SVM-BEE), accurately and rapidly yields a computed representation of hyperspectral data that can accommodate multiple distributions. The number of distributions is identified without prior knowledge, based upon this representation. Prior work established that SVM-BEE is robustly noise-tolerant and can semi-automatically estimate endmembers; synthetic data and a geologic scene were previously analyzed. Here we compared the efficacies of SVM-BEE, N-FINDR, and SMACC algorithms in extracting endmembers from a real, predominantly-agricultural scene. SVM-BEE estimated vegetation and other endmembers for all classes in the image, which N-FINDR and SMACC failed to do. SVM-BEE was consistent in the endmembers that it estimated across replicate trials. Spectral angle mapper (SAM) classifications based on SVM-BEE-estimated endmembers were significantly more accurate compared with those based on N-FINDR- and (in general) SMACC-endmembers. Linear spectral unmixing accrued overall accuracies similar to those of SAM. (C) 2009 Optical Society of America C1 [Filippi, Anthony M.] Texas A&M Univ, Dept Geog, College Stn, TX 77843 USA. [Archibald, Rick] Oak Ridge Natl Lab, Math Informat & Computat Sci Div, Oak Ridge, TN 37831 USA. [Bhaduri, Budhendra L.; Bright, Edward A.] Oak Ridge Natl Lab, Computat Sci & Engn Div, Oak Ridge, TN 37831 USA. RP Filippi, AM (reprint author), Texas A&M Univ, Dept Geog, College Stn, TX 77843 USA. EM filippi@tamu.edu RI Archibald, Rick/I-6238-2016 OI Archibald, Rick/0000-0002-4538-9780 FU U.S. Department of Energy (DOE) Higher Education Research Experiences (HERE) for Faculty at the Oak Ridge National Laboratory (ORNL); Mathematical, Information, and Computational Sciences Division; Office of Advanced Scientific Computing Research; U.S. Department of Energy [DE-AC05-00OR22725] FX A.M. Filippi acknowledges that this research was supported in part by an appointment to the U.S. Department of Energy (DOE) Higher Education Research Experiences ( HERE) for Faculty at the Oak Ridge National Laboratory (ORNL) administered by the Oak Ridge Institute for Science and Education. R. Archibald would like to thank the Householder fellowship that is supported under the Mathematical, Information, and Computational Sciences Division; Office of Advanced Scientific Computing Research; U.S. Department of Energy (DE-AC05-00OR22725). Prepared by Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6285, managed by UT-Battelle, LLC for the U.S. Department of Energy. This manuscript has been authored by employees of UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the U.S. Department of Energy. Accordingly, the United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. We thank M. Winter for providing an evaluation version of the N-FINDR algorithm. AVIRIS and ground-reference data were provided by D. Landgrebe and L. Biehl, Purdue University (http://cobweb.ecn.purdue.edu/similar to biehl/MultiSpec/). We are grateful for the useful comments of the anonymous reviewers, which improved the quality of this article. NR 51 TC 10 Z9 10 U1 0 U2 8 PU OPTICAL SOC AMER PI WASHINGTON PA 2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036 USA SN 1094-4087 J9 OPT EXPRESS JI Opt. Express PD DEC 21 PY 2009 VL 17 IS 26 BP 23823 EP 23842 DI 10.1364/OE.17.023823 PG 20 WC Optics SC Optics GA 538AO UT WOS:000273156200051 PM 20052093 ER PT J AU Sutton, EJ Boddington, SE Nedopil, AJ Henning, TD Demos, SG Baehner, R Sennino, B Lu, Y Daldrup-Link, HE AF Sutton, Elizabeth J. Boddington, Sophie E. Nedopil, Alexander J. Henning, Tobias D. Demos, Stavros G. Baehner, Rick Sennino, Barbara Lu, Ying Daldrup-Link, Heike E. TI An optical imaging method to monitor stem cell migration in a model of immune-mediated arthritis SO OPTICS EXPRESS LA English DT Article ID IN-VIVO TRACKING; NEAR-INFRARED FLUORESCENCE; COLLAGEN-INDUCED ARTHRITIS; GENE-THERAPY; MESENCHYMAL CELLS; TRANSPLANTATION; SURVIVAL; BONE; MYOCARDIUM; PATHOLOGY AB The objective of this work is to establish an optical imaging technique that would enable monitoring of the integration of mesenchymal stem cells (MSC) in arthritic joints. Our approach is based on first developing a labeling technique of MSC with the fluorescent dye DiD followed by tracking the cell migration kinetics from the spatial distribution of the DiD fluorescence in optical images (OI). The experimental approach involves first the in vitro OI of MSC labeled with DiD accompanied by fluorescence microscopy measurements to establish localization of the signal within the cells. Thereafter, DiD-labeled MSC were injected into polyarthritic, athymic rats and the signal localization within the experimental animals was monitored over several days. The experimental results indicate that DiD integrated into the cell membrane. DiD-labeled MSC localization in the arthritic ankle joints was observed with OI indicating that this method can be applied to monitor MSC in arthritic joints. (C) 2009 Optical Society of America C1 [Sutton, Elizabeth J.; Boddington, Sophie E.; Nedopil, Alexander J.; Henning, Tobias D.; Lu, Ying; Daldrup-Link, Heike E.] Univ Calif San Francisco, Dept Radiol, San Francisco, CA 94107 USA. [Sutton, Elizabeth J.] Harvard Univ, Mt Auburn Hosp, Dept Radiol, Cambridge, MA 02138 USA. [Demos, Stavros G.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Baehner, Rick] Univ Calif San Francisco, Dept Pathol, San Francisco, CA 94143 USA. [Sennino, Barbara] Univ Calif San Francisco, Dept Anat, San Francisco, CA 94143 USA. [Sennino, Barbara] Univ Calif San Francisco, Cardiovasc Res Inst, San Francisco, CA 94143 USA. [Lu, Ying] Univ Calif San Francisco, Biostat Core Facil, Ctr Comprehens Canc, San Francisco, CA 94143 USA. RP Sutton, EJ (reprint author), Univ Calif San Francisco, Dept Radiol, 185 Berry St,Suite 350, San Francisco, CA 94107 USA. EM Sophie.Boddington@radiology.ucsf.edu RI Daldrup-Link, Heike/D-9829-2012; OI Daldrup-Link, Heike/0000-0002-4929-819X; Sutton, Elizabeth/0000-0002-1407-7012 FU UCSF Department of Radiology; National Institute of Arthritis and Musculoskeletal and Skin Diseases [R01AR054458] FX This study was funded, in part, by a Seed grant from the UCSF Department of Radiology and in part by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (Award Number R01AR054458). This work performed in part under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE0-AC52-07NA27344. NR 40 TC 10 Z9 10 U1 0 U2 2 PU OPTICAL SOC AMER PI WASHINGTON PA 2010 MASSACHUSETTS AVE NW, WASHINGTON, DC 20036 USA SN 1094-4087 J9 OPT EXPRESS JI Opt. Express PD DEC 21 PY 2009 VL 17 IS 26 BP 24403 EP 24413 DI 10.1364/OE.17.024403 PG 11 WC Optics SC Optics GA 538AO UT WOS:000273156200107 PM 20052149 ER PT J AU Belczynski, K Ziolkowski, J AF Belczynski, Krzysztof Ziolkowski, Janusz TI ON THE APPARENT LACK OF Be X-RAY BINARIES WITH BLACK HOLES SO ASTROPHYSICAL JOURNAL LA English DT Article DE binaries: close; black hole physics; stars: evolution; stars: neutron ID STAR ENVELOPES; PHYSICAL-PROPERTIES; CLOSE BINARIES; NEUTRON-STARS; WHITE-DWARFS; MASS; EVOLUTION; POPULATION; EMISSION; CATALOG AB In our Galaxy there are 64 Be X-ray binaries known to date. Out of these, 42 host a neutron star (NS), and for the remainder the nature of the companion is unknown. None, so far, are known to host a black hole (BH). There seems to be no apparent mechanism that would prevent formation or detection of Be stars with BHs. This disparity is referred to as a missing Be-BH X-ray binary problem. We point out that current evolutionary scenarios that lead to the formation of Be X-ray binaries predict that the ratio of binaries with NSs to the ones with BHs is rather high, F-NStoBH similar to 10-50, with the more likely formation models providing the values at the high end. The ratio is a natural outcome of (1) the stellar initialmass function that produces more NSs than BHs and (2) common envelope evolution (i.e., a major mechanism involved in the formation of interacting binaries) that naturally selects progenitors of Be X-ray binaries with NSs (binaries with comparable mass components have more likely survival probabilities) over ones with BHs (which are much more likely to be common envelope mergers). A comparison of this ratio (i.e., F-NStoBH similar to 30) with the number of confirmed Be-NS X-ray binaries (42) indicates that the expected number of Be-BH X-ray binaries is of the order of only similar to 0-2. This is entirely consistent with the observed Galactic sample. C1 [Belczynski, Krzysztof] Los Alamos Natl Lab, Los Alamos, NM 87545 USA. [Belczynski, Krzysztof] Warsaw Univ, Astron Observ, PL-00478 Warsaw, Poland. [Ziolkowski, Janusz] Nicolaus Copernicus Astron Ctr, PL-00716 Warsaw, Poland. RP Belczynski, K (reprint author), Los Alamos Natl Lab, POB 1663,MS 466, Los Alamos, NM 87545 USA. EM kbelczyn@nmsu.edu; jz@camk.edu.pl FU Polish Ministry of Science and Higher Education (MSHE) [2009-2012]; MSHE [N N203 302835] FX We thank the anonymous referee, Duncan Lorimer, and Thomas Maccarone and Andrzej Zdziarski for a number of useful comments on this study. Additionally, K. B. is indebted to Karolina Tarczynska for her unceasing physical rehabilitation support that made thework over the course of this study possible. J. Z. acknowledges support from the Polish Ministry of Science and Higher Education (MSHE) project 362/1/N-INTEGRAL (2009-2012) and K. B. acknowledges the support from MSHE grant N N203 302835 (2008-2011). NR 66 TC 29 Z9 29 U1 0 U2 6 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0004-637X EI 1538-4357 J9 ASTROPHYS J JI Astrophys. J. PD DEC 20 PY 2009 VL 707 IS 2 BP 870 EP 877 DI 10.1088/0004-637X/707/2/870 PG 8 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 528RW UT WOS:000272465400003 ER PT J AU Maness, HL Kalas, P Peek, KMG Chiang, EI Scherer, K Fitzgerald, MP Graham, JR Hines, DC Schneider, G Metchev, SA AF Maness, H. L. Kalas, P. Peek, K. M. G. Chiang, E. I. Scherer, K. Fitzgerald, M. P. Graham, James R. Hines, D. C. Schneider, G. Metchev, S. A. TI HUBBLE SPACE TELESCOPE OPTICAL IMAGING OF THE ERODING DEBRIS DISK HD 61005 SO ASTROPHYSICAL JOURNAL LA English DT Article DE circumstellar matter; planetary systems: formation; planetary systems: protoplanetary disks; stars: individual (HD 61005) ID DIFFUSE INTERSTELLAR-MEDIUM; COLD NEARBY CLOUD; AU MICROSCOPII; RADIATION PRESSURE; PLANETARY SYSTEMS; BETA-PICTORIS; LOCAL BUBBLE; NA-I; DUST; STARS AB We present Hubble Space Telescope optical coronagraphic polarization imaging observations of the dusty debris disk HD 61005. The scattered light intensity image and polarization structure reveal a highly inclined disk with a clear asymmetric, swept back component, suggestive of significant interaction with the ambient interstellar medium (ISM). The combination of our new data with the published 1.1 mu m discovery image shows that the grains are blue scattering with no strong color gradient as a function of radius, implying predominantly submicron- sized grains. We investigate possible explanations that could account for the observed swept back, asymmetric morphology. Previous work has suggested that HD 61005 may be interacting with a cold, unusually dense interstellar cloud. However, limits on the intervening interstellar gas column density from an optical spectrum of HD 61005 in the Na I D lines render this possibility unlikely. Instead, HD 61005 may be embedded in a more typical warm, low-density cloud that introduces secular perturbations to dust grain orbits. This mechanism can significantly distort the ensemble disk structure within a typical cloud crossing time. For a counterintuitive relative flow direction-parallel to the disk midplane-we find that the structures generated by these distortions can very roughly approximate the HD 61005 morphology. Future observational studies constraining the direction of the relative ISM flow will thus provide an important constraint for future modeling. Independent of the interpretation for HD 61005, we expect that interstellar gas drag likely plays a role in producing asymmetries observed in other debris disk systems, such as HD 15115 and delta Velorum. C1 [Maness, H. L.; Kalas, P.; Peek, K. M. G.; Chiang, E. I.; Graham, James R.] Univ Calif Berkeley, Dept Astron, Berkeley, CA 94720 USA. [Scherer, K.] Ruhr Univ Bochum, Inst Theoret Phys 4, D-44780 Bochum, Germany. [Fitzgerald, M. P.] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Hines, D. C.] Space Sci Inst, Boulder, CO 80301 USA. [Schneider, G.] Univ Arizona, Steward Observ, Tucson, AZ 85721 USA. [Metchev, S. A.] SUNY Stony Brook, Dept Phys & Astron, Stony Brook, NY 11794 USA. RP Maness, HL (reprint author), Univ Calif Berkeley, Dept Astron, 601 Campbell Hall, Berkeley, CA 94720 USA. RI Fitzgerald, Michael/C-2642-2009 OI Fitzgerald, Michael/0000-0002-0176-8973 NR 74 TC 27 Z9 27 U1 0 U2 8 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 0004-637X J9 ASTROPHYS J JI Astrophys. J. PD DEC 20 PY 2009 VL 707 IS 2 BP 1098 EP 1114 DI 10.1088/0004-637X/707/2/1098 PG 17 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 528RW UT WOS:000272465400023 ER PT J AU Caputi, KI Lilly, SJ Aussel, H Le Floc'h, E Sanders, D Maier, C Frayer, D Carollo, CM Contini, T Kneib, JP Le Fevre, O Mainieri, V Renzini, A Scodeggio, M Scoville, N Zamorani, G Bardelli, S Bolzonella, M Bongiorno, A Coppa, G Cucciati, O de la Torre, S de Ravel, L Franzetti, P Garilli, B Ilbert, O Iovino, A Kampczyk, P Kartaltepe, J Knobel, C Kovac, K Lamareille, F Le Borgne, JF Le Brun, V Mignoli, M Peng, Y Perez-Montero, E Ricciardelli, E Salvato, M Silverman, J Surace, J Tanaka, M Tasca, L Tresse, L Vergani, D Zucca, E Abbas, U Bottini, D Capak, P Cappi, A Cassata, P Cimatti, A Elvis, M Hasinger, G Koekemoer, AM Leauthaud, A Maccagni, D Marinoni, C McCracken, H Memeo, P Meneux, B Oesch, P Pello, R Porciani, C Pozzetti, L Scaramella, R Scarlata, C Schiminovich, D Taniguchi, Y Zamojski, M AF Caputi, K. I. Lilly, S. J. Aussel, H. Le Floc'h, E. Sanders, D. Maier, C. Frayer, D. Carollo, C. M. Contini, T. Kneib, J. -P. Le Fevre, O. Mainieri, V. Renzini, A. Scodeggio, M. Scoville, N. Zamorani, G. Bardelli, S. Bolzonella, M. Bongiorno, A. Coppa, G. Cucciati, O. de la Torre, S. de Ravel, L. Franzetti, P. Garilli, B. Ilbert, O. Iovino, A. Kampczyk, P. Kartaltepe, J. Knobel, C. Kovac, K. Lamareille, F. Le Borgne, J. -F. Le Brun, V. Mignoli, M. Peng, Y. Perez-Montero, E. Ricciardelli, E. Salvato, M. Silverman, J. Surace, J. Tanaka, M. Tasca, L. Tresse, L. Vergani, D. Zucca, E. Abbas, U. Bottini, D. Capak, P. Cappi, A. Cassata, P. Cimatti, A. Elvis, M. Hasinger, G. Koekemoer, A. M. Leauthaud, A. Maccagni, D. Marinoni, C. McCracken, H. Memeo, P. Meneux, B. Oesch, P. Pello, R. Porciani, C. Pozzetti, L. Scaramella, R. Scarlata, C. Schiminovich, D. Taniguchi, Y. Zamojski, M. TI THE OPTICAL SPECTRA OF SPITZER 24 mu m GALAXIES IN THE COSMIC EVOLUTION SURVEY FIELD. II. FAINT INFRARED SOURCES IN THE zCOSMOS-BRIGHT 10k CATALOG SO ASTROPHYSICAL JOURNAL LA English DT Article DE galaxies: abundances; galaxies: active; galaxies: evolution; galaxies: starburst; infrared: galaxies ID MASS-METALLICITY RELATION; STAR-FORMING GALAXIES; ACTIVE GALACTIC NUCLEI; DIGITAL SKY SURVEY; SPACE-TELESCOPE; ENERGY-DISTRIBUTIONS; STARBURST GALAXIES; REDSHIFT SURVEY; INTERSTELLAR EXTINCTION; LUMINOSITY FUNCTION AB We have used the zCOSMOS-bright 10k sample to identify 3244 Spitzer/MIPS 24 mu m-selected galaxies with 0.06 mJy < S-24 mu m less than or similar to 0.50 mJy and I-AB < 22.5, over 1.5 deg(2) of the COSMOS field, and studied different spectral properties, depending on redshift. At 0.2 < z < 0.3, we found that different reddening laws of common use in the literature explain the dust extinction properties of similar to 80% of our infrared (IR) sources, within the error bars. For up to 16% of objects, instead, the H alpha lambda 6563/H beta lambda 4861 ratios are too high for their IR/UV attenuations, which is probably a consequence of inhomogeneous dust distributions. In only a few of our galaxies at 0.2 < z < 0.3, the IR emission could be mainly produced by dust heated by old rather than young stars. Besides, the line ratios of similar to 22% of our galaxies suggest that they might be star-formation/nuclear-activity composite systems. At 0.5 < z < 0.7, we estimated galaxy metallicities for 301 galaxies: at least 12% of them are securely below the upper-branch mass-metallicity trend, which is consistent with the local relation. Finally, we performed a combined analysis of the H-delta equivalent width versus D-n (4000) diagram for 1722 faint and bright 24 mu m galaxies at 0.6 < z < 1.0, spanning two decades in mid-IR luminosity. We found that, while secondary bursts of star formation are necessary to explain the position of the most luminous IR galaxies in that diagram, quiescent, exponentially declining star formation histories can well reproduce the spectral properties of similar to 40% of the less luminous sources. Our results suggest a transition in the possible modes of star formation at total IR luminosities L-TIR approximate to (3 +/- 2) x 10(11) L-circle dot. C1 [Caputi, K. I.; Lilly, S. J.; Maier, C.; Carollo, C. M.; Kampczyk, P.; Knobel, C.; Kovac, K.; Peng, Y.; Silverman, J.; Oesch, P.] ETH, Swiss Fed Inst Technol, Inst Astron, CH-8093 Zurich, Switzerland. [Aussel, H.; Le Floc'h, E.] Univ Paris Diderot, CEA DSM CNRS, DAPNIA SAp, F-91191 Gif Sur Yvette, France. [Sanders, D.; Kartaltepe, J.] Univ Hawaii, Inst Astron, Honolulu, HI USA. [Frayer, D.; Surace, J.; Scarlata, C.; Zamojski, M.] CALTECH, Spitzer Sci Ctr, Pasadena, CA 91125 USA. [Contini, T.; Lamareille, F.; Le Borgne, J. -F.; Pello, R.] Univ Toulouse, Lab Astrophys Toulouse Tarbes, Toulouse, France. [Kneib, J. -P.; Le Fevre, O.; Cucciati, O.; de la Torre, S.; de Ravel, L.; Ilbert, O.; Le Brun, V.; Tasca, L.; Tresse, L.; Abbas, U.; Cassata, P.; Meneux, B.] Lab Astrophys Marseille, Marseille, France. [Mainieri, V.; Perez-Montero, E.; Tanaka, M.] European So Observ, D-85748 Garching, Germany. [Renzini, A.; Ricciardelli, E.] Univ Padua, Dipartimento Astron, I-35122 Padua, Italy. [Scodeggio, M.; Franzetti, P.; Garilli, B.; Bottini, D.; Maccagni, D.; Memeo, P.] INAF IASF Milano, I-20133 Milan, Italy. [Zamorani, G.; Bardelli, S.; Bolzonella, M.; Coppa, G.; Mignoli, M.; Vergani, D.; Zucca, E.; Cappi, A.; Cimatti, A.; Pozzetti, L.] Osservatorio Astron Bologna, INAF, Bologna, Italy. [Bongiorno, A.; Hasinger, G.] Max Planck Inst Extraterr Phys, D-37075 Garching, Germany. [Iovino, A.] Osserv Astron Brera, INAF, I-20121 Milan, Italy. [Elvis, M.] Harvard Smithsonian Ctr Astrophys, Cambridge, MA 02138 USA. [Koekemoer, A. M.] Space Telescope Sci Inst, Baltimore, MD 21218 USA. [Leauthaud, A.] Univ Calif, Lawrence Berkeley Natl Lab, Berkeley Lab, Berkeley, CA USA. [Leauthaud, A.] Univ Calif, Berkeley Ctr Cosmol Phys, Berkeley, CA USA. [Marinoni, C.] Ctr Phys Theor, Marseille, France. [McCracken, H.] Univ Paris 06, Inst Astrophys Paris, UMR 7095, CNRS, F-75014 Paris, France. [Porciani, C.] Argelander Inst Astron, Bonn, Germany. [Scaramella, R.] Osserv Astron Roma, INAF, Monte Porzio Catone, RM, Italy. [Schiminovich, D.] Columbia Univ, Dept Astron, New York, NY 10027 USA. [Taniguchi, Y.] Ehime Univ, Matsuyama, Ehime 7908577, Japan. RP Caputi, KI (reprint author), Univ Edinburgh, Royal Observ, SUPA Inst Astron, Edinburgh EH9 3HJ, Midlothian, Scotland. EM kic@roe.ac.uk RI Pello, Roser/G-4754-2010; Le Fevre, Olivier/G-7389-2011; Kneib, Jean-Paul/A-7919-2015; Cappi, Alberto/O-9391-2015; Zucca, Elena/O-9396-2015; Bolzonella, Micol/O-9495-2015; Bardelli, Sandro/O-9369-2015; Mignoli, Marco/O-9426-2015; OI Franzetti, Paolo/0000-0002-6986-0127; Vergani, Daniela/0000-0003-0898-2216; Bongiorno, Angela/0000-0002-0101-6624; Kneib, Jean-Paul/0000-0002-4616-4989; Cappi, Alberto/0000-0002-9200-7167; Zucca, Elena/0000-0002-5845-8132; Bolzonella, Micol/0000-0003-3278-4607; Bardelli, Sandro/0000-0002-8900-0298; Mignoli, Marco/0000-0002-9087-2835; Iovino, Angela/0000-0001-6958-0304; bottini, dario/0000-0001-6917-041X; Pozzetti, Lucia/0000-0001-7085-0412; Scodeggio, Marco/0000-0002-2282-5850; Scaramella, Roberto/0000-0003-2229-193X; Koekemoer, Anton/0000-0002-6610-2048 FU European Southern Observatory (ESO) [175.A-0839]; Jet Propulsion Laboratory; California Institute of Technology; NASA [1407] FX This paper is based on observations made with the VIMOS spectrograph on the Melipal-VLT telescope, undertaken at the European Southern Observatory (ESO) under Large Program 175.A-0839. This paper is also based on observations made with the Spitzer Observatory, which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under NASA contract 1407. We thank the anonymous referee for a constructive report of this paper. NR 98 TC 10 Z9 10 U1 0 U2 5 PU IOP PUBLISHING LTD PI BRISTOL PA TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND SN 0004-637X EI 1538-4357 J9 ASTROPHYS J JI Astrophys. J. PD DEC 20 PY 2009 VL 707 IS 2 BP 1387 EP 1403 DI 10.1088/0004-637X/707/2/1387 PG 17 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 528RW UT WOS:000272465400043 ER PT J AU Drory, N Bundy, K Leauthaud, A Scoville, N Capak, P Ilbert, O Kartaltepe, JS Kneib, JP McCracken, HJ Salvato, M Sanders, DB Thompson, D Willott, CJ AF Drory, N. Bundy, K. Leauthaud, A. Scoville, N. Capak, P. Ilbert, O. Kartaltepe, J. S. Kneib, J. P. McCracken, H. J. Salvato, M. Sanders, D. B. Thompson, D. Willott, C. J. TI THE BIMODAL GALAXY STELLAR MASS FUNCTION IN THE COSMOS SURVEY TO z similar to 1: A STEEP FAINT END AND A NEW GALAXY DICHOTOMY SO ASTROPHYSICAL JOURNAL LA English DT Review DE cosmology: observations; galaxies: evolution; galaxies: luminosity function; mass function surveys ID STAR-FORMATION HISTORIES; TULLY-FISHER RELATION; DIGITAL SKY SURVEY; OPTICAL LUMINOSITY DENSITY; INFRARED CLUSTER SURVEY; LOW-REDSHIFT UNIVERSE; DARK-MATTER HALOES; GOODS-MUSIC SAMPLE; VLT DEEP SURVEY; DWARF GALAXIES AB We present a new analysis of stellar mass functions in the COSMOS field to fainter limits than has been previously probed at z <= 1. The increase in dynamic range reveals features in the shape of the stellar mass function that deviate from a single Schechter function. Neither the total nor the red (passive) or blue (star-forming) galaxy stellar mass functions can be well fitted with a single Schechter function once the mass completeness limit of the sample probes below similar to 3 x 10(9) M(circle dot). We observe a dip or plateau at masses similar to 10(10) M(circle dot), just below the traditional M*, and an upturn toward a steep faint-end slope of alpha similar to -1.7 at lower mass at all redshifts <= 1. This bimodal nature of the mass function is not solely a result of the blue/red dichotomy. Indeed, the blue mass function is by itself bimodal at z similar to 1. This suggests a new dichotomy in galaxy formation that predates the appearance of the red sequence. We propose two interpretations for this bimodal distribution. If the gas fraction increases toward lower mass, galaxies with M(baryon) similar to 10(10) M(circle dot) would shift to lower stellar masses, creating the observed dip. This would indicate a change in star formation efficiency, perhaps linked to supernovae feedback becoming much more efficient below similar to 10(10) M(circle dot). Therefore, we investigate whether the dip is present in the baryonic (stars+gas) mass function. Alternatively, the dip could be created by an enhancement of the galaxy assembly rate at similar to 10(11) M(circle dot), a phenomenon that naturally arises if the baryon fraction peaks at M(halo) similar to 10(12) M(circle dot). In this scenario, galaxies occupying the bump around M(*) would be identified with central galaxies and the second fainter component of the mass function having a steep faint-end slope with satellite galaxies. The low-mass end of the blue and total mass functions exhibit a steeper slope than has been detected in previous work that may increasingly approach the halo mass function value of -2. While the dip feature is apparent in the total mass function at all redshifts, it appears to shift from the blue to the red population, likely as a result of transforming high-mass blue galaxies into red ones. At the same time, we detect a drastic upturn in the number of low-mass red galaxies. Their increase with time seems to reflect a decrease in the number of blue systems and so we tentatively associate them with satellite dwarf (spheroidal) galaxies that have undergone quenching due to environmental processes. C1 [Drory, N.] Max Planck Inst Extraterr Phys, D-85748 Garching, Germany. [Leauthaud, A.] Univ Calif Berkeley, Lawrence Berkeley Lab, Berkeley, CA 94720 USA. [Leauthaud, A.] Univ Calif Berkeley, Berkeley Ctr Cosmol Phys, Berkeley, CA 94720 USA. [Capak, P.] CALTECH, Spitzer Sci Ctr, Pasadena, CA 91125 USA. [Ilbert, O.; Kneib, J. P.] Univ Aix Marseille 1, CNRS, UMR 6110, Lab Astrophys Marseille, F-13376 Marseille 12, France. [Kartaltepe, J. S.] Natl Opt Astron Observ, Tucson, AZ 85719 USA. [McCracken, H. J.] Univ Paris 06, CNRS, UMR7095, Inst Astrophys Paris, F-75014 Paris, France. [Salvato, M.] Max Planck Inst Plasma Phys, D-85748 Garching, Germany. [Sanders, D. B.] Univ Hawaii, Inst Astron, Honolulu, HI 96822 USA. [Thompson, D.] Univ Arizona, LBT Observ, Tucson, AZ 85721 USA. [Willott, C. J.] Natl Res Council Canada, Herzberg Inst Astrophys, Victoria, BC V9E 2E7, Canada. RP Drory, N (reprint author), Max Planck Inst Extraterr Phys, Giessenbachstr, D-85748 Garching, Germany. EM drory@mpe.mpg.de RI Kneib, Jean-Paul/A-7919-2015 OI Kneib, Jean-Paul/0000-0002-4616-4989 FU Chamberlain Fellowship; ANR [ANR-07-BLAN-0228] FX We thank R. Angulo, R. Bender, R. Ellis, P. F. Hopkins, S. Khochfar, and J. Tinker for stimulating discussions. We also thank P. F. Hopkins for providing gas mass fractions in electronic form. We thank the COSMOS collaboration for granting us access to their catalogs; and we gratefully acknowledge the contributions of the entire COSMOS team that have made this work possible. More information on the COSMOS survey is available at http://www.astro.caltech.edu/cosmos. A. L. acknowledges support from the Chamberlain Fellowship at LBNL and from the Berkeley Center for Cosmological Physics. H. J. McC. is supported by ANR grant "ANR-07-BLAN-0228." NR 123 TC 82 Z9 82 U1 0 U2 5 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 0004-637X J9 ASTROPHYS J JI Astrophys. J. PD DEC 20 PY 2009 VL 707 IS 2 BP 1595 EP 1609 DI 10.1088/0004-637X/707/2/1595 PG 15 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 528RW UT WOS:000272465400061 ER PT J AU Camarda, KD Anninos, P Fragile, PC Font, JA AF Camarda, Karen D. Anninos, Peter Fragile, P. Chris Font, Jose A. TI DYNAMICAL BAR-MODE INSTABILITY IN DIFFERENTIALLY ROTATING MAGNETIZED NEUTRON STARS SO ASTROPHYSICAL JOURNAL LA English DT Article DE gravitation; hydrodynamics; instabilities; stars: neutron; stars: rotation ID GRAVITATIONAL-RADIATION; RELATIVISTIC MAGNETOHYDRODYNAMICS; EQUATIONS; HYDRODYNAMICS; SIMULATIONS; PROFILES; BIRTH; STATE; CODE AB This paper presents a numerical study over a wide parameter space of the likelihood of dynamical bar-mode instability in differentially rotating magnetized neutron stars. The innovative aspect of this study is the incorporation of magnetic fields in such a context, which have thus far been neglected in the purely hydrodynamical simulations available in the literature. The investigation uses the Cosmos++ code which allows us to perform three-dimensional simulations on a cylindrical grid at high resolution. A sample of Newtonian magnetohydrodynamical simulations starting from a set of models previously analyzed by other authors without magnetic fields has been performed, providing estimates of the effects of magnetic fields on the dynamical bar-mode deformation of rotating neutron stars. Overall, our results suggest that the effect of magnetic fields is not likely to be very significant in realistic configurations. Only in the most extreme cases are the magnetic fields able to suppress growth of the bar mode. C1 [Camarda, Karen D.] Washburn Univ, Dept Phys & Astron, Topeka, KS 66621 USA. [Anninos, Peter] Lawrence Livermore Natl Lab, Livermore, CA 94550 USA. [Fragile, P. Chris] Coll Charleston, Dept Phys & Astron, Charleston, SC 29424 USA. [Font, Jose A.] Univ Valencia, Dept Astron & Astrofis, E-46100 Valencia, Spain. RP Camarda, KD (reprint author), Washburn Univ, Dept Phys & Astron, Topeka, KS 66621 USA. FU Barcelona Supercomputing Center (BSC) [AECT-2007-3-0002]; Lawrence Livermore National Laboratory (LLNL); College of Charleston (CoC); High Performance Academic Computing Environment at Washburn University (HiPACE); U.S. Department of Energy by Lawrence Livermore National Laboratory [DE-AC52-07NA27344]; Spanish Ministry of Education and Science [AYA 2007-67626-C03-01] FX Computations were performed at the Barcelona Supercomputing Center (BSC) under activity AECT-2007-3-0002, the Lawrence Livermore National Laboratory (LLNL), the College of Charleston (CoC), and at the High Performance Academic Computing Environment at Washburn University (HiPACE). This work was performed in part under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract No. DE-AC52-07NA27344. P. C. F. gratefully acknowledges the support of the College of Charleston 4th Century Initiative and the South Carolina Space Grant Consortium. J. A. F. acknowledges financial support from the Spanish Ministry of Education and Science (AYA 2007-67626-C03-01). NR 28 TC 9 Z9 10 U1 0 U2 4 PU IOP PUBLISHING LTD PI BRISTOL PA DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND SN 0004-637X J9 ASTROPHYS J JI Astrophys. J. PD DEC 20 PY 2009 VL 707 IS 2 BP 1610 EP 1622 DI 10.1088/0004-637X/707/2/1610 PG 13 WC Astronomy & Astrophysics SC Astronomy & Astrophysics GA 528RW UT WOS:000272465400062 ER PT J AU Park, H Nourgaliev, RR Martineau, RC Knoll, DA AF Park, HyeongKae Nourgaliev, Robert R. Martineau, Richard C. Knoll, Dana A. TI On physics-based preconditioning of the Navier-Stokes equations SO JOURNAL OF COMPUTATIONAL PHYSICS LA English DT Article DE Jacobian-free Newton-Krylov; Navier-Stokes equations; Physics-based preconditioning ID LOW MACH NUMBER; LARGE TEMPERATURE DIFFERENCES; NATURAL-CONVECTION FLOWS; NEWTON-KRYLOV METHODS; BENCHMARK PROBLEM; FLUID-DYNAMICS; SYSTEMS; SPEEDS; ALGORITHM; SOLVERS AB We develop a fully implicit scheme for the Navier-Stokes equations, in conservative form, for low to intermediate Mach number flows. Simulations in this range of flow regime produce stiff wave systems in which slow dynamical (advective) modes coexist with fast acoustic modes. Viscous and thermal diffusion effects in refined boundary layers can also produce stiffness. Implicit schemes allow one to step over the fast wave phenomena (or unresolved viscous time scales), while resolving advective time scales. In this study we employ the Jacobian-free Newton-Krylov (JFNK) method and develop a new physics-based preconditioner. To aid in overcoming numerical stiffness caused by the disparity between acoustic and advective modes, the governing equations are transformed into the primitive-variable form in a preconditioning step. The physics-based preconditioning incorporates traditional semi-implicit and physics-based splitting approaches without a loss of consistency between the original and preconditioned systems. The resulting algorithm is capable of solving low-speed natural circulation problems (M similar to 10(-4)) with significant heat flux as well as intermediate speed (M similar to 1) flows efficiently by following dynamical (advective) time scales of the problem. (C) 2009 Elsevier Inc. All rights reserved C1 [Park, HyeongKae; Nourgaliev, Robert R.; Martineau, Richard C.; Knoll, Dana A.] Idaho Natl Lab, Multiphys Methods Grp, Idaho Falls, ID 83415 USA. RP Park, H (reprint author), Idaho Natl Lab, Multiphys Methods Grp, 2525 N Fremont Ave, Idaho Falls, ID 83415 USA. EM Ryosuke.Park@inl.gov FU US Government [DE-AC05-00OR22725, DE-AC07-05ID14517] FX The submitted manuscript has been authored by a contractor of the US Government under Contract Nos. DE-AC05-00OR22725 and DE-AC07-05ID14517 (INL/JOU-08-15190). Accordingly, the US Government retains a non-exclusive, royalty-free license to publish or reproduce the published form of this contribution, or allow others to do so, for US Government purposes. The authors wish to thank Dr. Rick Rauenzahn (LANL) for useful discussion about Rhie-Chow based interpolation. NR 35 TC 9 Z9 10 U1 0 U2 9 PU ACADEMIC PRESS INC ELSEVIER SCIENCE PI SAN DIEGO PA 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA SN 0021-9991 J9 J COMPUT PHYS JI J. Comput. Phys. PD DEC 20 PY 2009 VL 228 IS 24 BP 9131 EP 9146 DI 10.1016/j.jcp.2009.09.015 PG 16 WC Computer Science, Interdisciplinary Applications; Physics, Mathematical SC Computer Science; Physics GA 519TF UT WOS:000271790600011 ER PT J AU Grocholski, B Shim, SH Sturhahn, W Zhao, J Xiao, Y Chow, PC AF Grocholski, B. Shim, S. -H. Sturhahn, W. Zhao, J. Xiao, Y. Chow, P. C. TI Spin and valence states of iron in (Mg0.8Fe0.2)SiO3 perovskite SO GEOPHYSICAL RESEARCH LETTERS LA English DT Article ID RAY-EMISSION SPECTROSCOPY; LOWER-MANTLE PEROVSKITE; EARTHS LOWER MANTLE; MOSSBAUER-SPECTROSCOPY; (MG,FE)SIO3 PEROVSKITE; (MG,FE)(SI,AL)O-3 PEROVSKITE; SYNCHROTRON MOSSBAUER; FERROUS IRON; PRESSURE; TRANSITIONS AB The spin and valence states of iron in (Mg0.8Fe0.2) SiO3 perovskite were measured between 0 and 65 GPa using synchrotron Mossbauer spectroscopy. Samples were synthesized in situ in the laser-heated diamond cell under reducing conditions. The dominant spin state of iron in perovskite is high spin at pressures below 50 GPa. Above 50 GPa, the spectra shows severe changes which can be explained by appearance of two distinct iron sites with similar site weightings. One site has Mossbauer parameters consistent with high spin Fe2+, while the other has the parameters previously interpreted as intermediate spin. The latter intermediate-spin assignment is not unique, as similar Mossbauer parameters have been reported for high spin Fe2+ in almandine at ambient pressure. However, our data do not rule out the existence of low-spin iron, which may exist with a smaller fraction and explain the observation of lower spin moments in the X-ray emission spectroscopy of perovskite at high pressure. From these considerations, our preferred interpretation is that iron in perovskite is mixed or high spin to at least 2000 km depths in the mantle, consistent with computational results. Our study also reveals that reducing conditions do not inhibit the formation of Fe3+ in perovskite at deep-mantle pressures. Citation: Grocholski, B., S.-H. Shim, W. Sturhahn, J. Zhao, Y. Xiao, and P. C. Chow (2009), Spin and valence states of iron in (Mg0.8Fe0.2) SiO3 perovskite, Geophys. Res. Lett., 36, L24303, doi: 10.1029/2009GL041262. C1 [Grocholski, B.; Shim, S. -H.] MIT, Dept Earth Atmospher & Planetary Sci, Cambridge, MA 02139 USA. [Xiao, Y.; Chow, P. C.] Argonne Natl Lab, HPCAT, Adv Photon Source, Argonne, IL 60439 USA. [Sturhahn, W.; Zhao, J.] Argonne Natl Lab, Sector 3, Adv Photon Source, Argonne, IL 60439 USA. RP Grocholski, B (reprint author), MIT, Dept Earth Atmospher & Planetary Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA. EM b.grocholski@gmail.com OI Shim, Sang-Heon/0000-0001-5203-6038 FU DOE-BES [DE-AC02-06CH11357]; DOE-NNSA; NSF [EAR0738655]; W. M. Keck Foundation FX The authors would like to thank J. Barr and T. Grove for help synthesizing the starting material and acknowledge S. Speakman, K. Catalli, and V. Prakapenka for experimental assistance. We would like to thank the editor, anonymous reviewers, D. Morgan, A. Bengtson, and R. Jeanloz for helpful comments. Use of Sector 3 was partially supported by COMPRES. Portions of this work were performed at HPCAT (Sector 16), Advanced Photon Source (APS), Argonne National Laboratory. HPCAT is supported by DOE-BES, DOE-NNSA, NSF, and the W. M. Keck Foundation. APS is supported by DOE-BES, under contract DE-AC02-06CH11357. This work was supported by NSF to S.-H. S. (EAR0738655). NR 33 TC 19 Z9 19 U1 0 U2 10 PU AMER GEOPHYSICAL UNION PI WASHINGTON PA 2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA SN 0094-8276 EI 1944-8007 J9 GEOPHYS RES LETT JI Geophys. Res. Lett. PD DEC 18 PY 2009 VL 36 AR L24303 DI 10.1029/2009GL041262 PG 5 WC Geosciences, Multidisciplinary SC Geology GA 535BO UT WOS:000272941800004 ER PT J AU Abelev, BI Aggarwal, MM Ahammed, Z Alakhverdyants, AV Anderson, BD Arkhipkin, D Averichev, GS Balewski, J Barannikova, O Barnby, LS Baumgart, S Beavis, DR Bellwied, R Benedosso, F Betancourt, MJ Betts, RR Bhasin, A Bhati, AK Bichsel, H Bielcik, J Bielcikova, J Biritz, B Bland, LC Bnzarov, I Bonner, BE Bouchet, J Braidot, E Brandin, AV Bridgeman, A Bruna, E Bueltmann, S Burton, TP Cai, XZ Caines, H Sanchez, MCD Catu, O Cebra, D Cendejas, R Cervantes, MC Chajecki, Z Chaloupka, P Chattopadhyay, S Chen, HF Chen, JH Chen, JY Cheng, J Cherney, M Chikanian, A Choi, KE Christie, W Chung, P Clarke, RF Codrington, MJM Corliss, R Cormier, TM Cosentino, MR Cramer, JG Crawford, HJ Das, D Dash, S Daugherity, M De Silva, LC Dedovich, TG DePhillips, M Derevschikov, AA de Souza, RD Didenko, L Djawotho, P Dzhordzhadze, V Dogra, SM Dong, X Drachenberg, JL Draper, JE Dunlop, JC Mazumdar, MRD Efimov, LG Elhalhuli, E Elnimr, M Engelage, J Eppley, G Erazmus, B Estienne, M Eun, L Fachini, P Fatemi, R Fedorisin, J Feng, A Filip, P Finch, E Fine, V Fisyak, Y Gagliardi, CA Gangadharan, DR Ganti, MS Garcia-Solis, EJ Geromitsos, A Geurts, F Ghazikhanian, V Ghosh, P Gorbunov, YN Gordon, A Grebenyuk, O Grosnick, D Grube, B Guertin, SM Guimaraes, KSFF Gupta, A Gupta, N Guryn, W Haag, B Hallman, TJ Hamed, A Harris, JW Heinz, M Heppelmann, S Hirsch, A Hjort, E Hoffman, AM Hoffmann, GW Hofman, DJ Hollis, RS Huang, HZ Humanic, TJ Huo, L Igo, G Iordanova, A Jacobs, P Jacobs, WW Jakl, P Jena, C Jin, F Jones, CL Jones, PG Joseph, J Judd, EG Kabana, S Kajimoto, K Kang, K Kapitan, J Kauder, K Keane, D Kechechyan, A Kettler, D Khodyrev, VY Kikola, DP Kiryluk, J Kisiel, A Klein, SR Knospe, AG Kocoloski, A Koetke, DD Konzer, J Kopytine, M Koralt, I Korsch, W Kotchenda, L Kouchpil, V Kravtsov, P Kravtsov, VI Krueger, K Krus, M Kumar, L Kurnadi, P Lamont, MAC Landgraf, JM LaPointe, S Lauret, J Lebedev, A Lednicky, R Lee, CH Lee, JH Leight, W LeVine, MJ Li, C Li, N Li, Y Lin, G Lindenbaum, SJ Lisa, MA Liu, F Liu, H Liu, J Liu, L Ljubicic, T Llope, WJ Longacre, RS Love, WA Lu, Y Ludlam, T Ma, GL Ma, YG Mahapatra, DP Majka, R Mall, OI Mangotra, LK Manweiler, R Margetis, S Markert, C Masui, H Matis, HS Matulenko, YA McDonald, D McShane, TS Meschanin, A Milner, R Minaev, NG Mioduszewski, S Mischke, A Mohanty, B Morozov, DA Munhoz, MG Nandi, BK Nattrass, C Nayak, TK Nelson, JM Netrakanti, PK Ng, MJ Nogach, LV Nurushev, SB Odyniec, G Ogawa, A Okada, H Okorokov, V Olson, D Pachr, M Page, BS Pal, SK Pandit, Y Panebratsev, Y Pawlak, T Peitzmann, T Perevoztchikov, V Perkins, C Peryt, W Phatak, SC Pile, P Planinic, M Ploskon, MA Pluta, J Plyku, D Poljak, N Poskanzer, AM Potukuchi, BVKS Prindle, D Pruneau, C Pruthi, NK Pujahari, PR Putschke, J Raniwala, R Raniwala, S Ray, RL Redwine, R Reed, R Ridiger, A Ritter, HG Roberts, JB Rogachevskiy, OV Romero, JL Rose, A Roy, C Ruan, L Russcher, MJ Sahoo, R Sakai, S Sakrejda, I Sakuma, T Salur, S Sandweiss, J Schambach, J Scharenberg, RP Schmitz, N Seele, J Seger, J Selyuzhenkov, I Semertzidis, Y Seyboth, P Shahaliev, E Shao, M Sharma, M Shi, SS Shi, XH Sichtermann, EP Simon, F Singaraju, RN Skoby, MJ Smirnov, N Sorensen, P Sowinski, J Spinka, HM Srivastava, B Stanislaus, TDS Staszak, D Strikhanov, M Stringfellow, B Suaide, AAP Suarez, MC Subba, NL Sumbera, M Sun, XM Sun, Y Sun, Z Surrow, B Symons, TJM de Toledo, A Takahashi, J Tang, AH Tang, Z Tarini, LH Tarnowsky, T Thein, D Thomas, JH Tian, J Timmins, AR Timoshenko, S Tlusty, D Tokarev, M Tram, VN Trentalange, S Tribble, RE Tsai, OD Ulery, J Ullrich, T Underwood, DG Van Buren, G van Nieuwenhuizen, G Vanfossen, JA Varma, R Vasconcelos, GMS Vasiliev, AN Videbaek, F Viyogi, YP Vokal, S Voloshin, SA Wada, M Walker, M Wang, F Wang, G Wang, H Wang, JS Wang, Q Wang, X Wang, XL Wang, Y Webb, G Webb, JC Westfall, GD Whitten, C Wieman, H Wissink, SW Witt, R Wu, Y Xie, W Xu, N Xu, QH Xu, Y Xu, Z Yang, Y Yepes, P Yip, K Yoo, IK Yue, Q Zawisza, M Zbroszczyk, H Zhan, W Zhang, S Zhang, WM Zhang, XP Zhang, Y Zhang, ZP Zhao, Y Zhong, C Zhou, J Zhu, X Zoulkarneev, R Zoulkarneeva, Y Zuo, JX AF Abelev, B. I. Aggarwal, M. M. Ahammed, Z. Alakhverdyants, A. V. Anderson, B. D. Arkhipkin, D. Averichev, G. S. Balewski, J. Barannikova, O. Barnby, L. S. Baumgart, S. Beavis, D. R. Bellwied, R. Benedosso, F. Betancourt, M. J. Betts, R. R. Bhasin, A. Bhati, A. K. Bichsel, H. Bielcik, J. Bielcikova, J. Biritz, B. Bland, L. C. Bnzarov, I. Bonner, B. E. Bouchet, J. Braidot, E. Brandin, A. V. Bridgeman, A. Bruna, E. Bueltmann, S. Burton, T. P. Cai, X. Z. Caines, H. Sanchez, M. Calderon de la Barca Catu, O. Cebra, D. Cendejas, R. Cervantes, M. C. Chajecki, Z. Chaloupka, P. Chattopadhyay, S. Chen, H. F. Chen, J. H. Chen, J. Y. Cheng, J. Cherney, M. Chikanian, A. Choi, K. E. Christie, W. Chung, P. Clarke, R. F. Codrington, M. J. M. Corliss, R. Cormier, T. M. Cosentino, M. R. Cramer, J. G. Crawford, H. J. Das, D. Dash, S. Daugherity, M. De Silva, L. C. Dedovich, T. G. DePhillips, M. Derevschikov, A. A. de Souza, R. Derradi Didenko, L. Djawotho, P. Dzhordzhadze, V. Dogra, S. M. Dong, X. Drachenberg, J. L. Draper, J. E. Dunlop, J. C. Mazumdar, M. R. Dutta Efimov, L. G. Elhalhuli, E. Elnimr, M. Engelage, J. Eppley, G. Erazmus, B. Estienne, M. Eun, L. Fachini, P. Fatemi, R. Fedorisin, J. Feng, A. Filip, P. Finch, E. Fine, V. Fisyak, Y. Gagliardi, C. A. Gangadharan, D. R. Ganti, M. S. Garcia-Solis, E. J. Geromitsos, A. Geurts, F. Ghazikhanian, V. Ghosh, P. Gorbunov, Y. N. Gordon, A. Grebenyuk, O. Grosnick, D. Grube, B. Guertin, S. M. Guimaraes, K. S. F. F. Gupta, A. Gupta, N. Guryn, W. Haag, B. Hallman, T. J. Hamed, A. Harris, J. W. Heinz, M. Heppelmann, S. Hirsch, A. Hjort, E. Hoffman, A. M. Hoffmann, G. W. Hofman, D. J. Hollis, R. S. Huang, H. Z. Humanic, T. J. Huo, L. Igo, G. Iordanova, A. Jacobs, P. Jacobs, W. W. Jakl, P. Jena, C. Jin, F. Jones, C. L. Jones, P. G. Joseph, J. Judd, E. G. Kabana, S. Kajimoto, K. Kang, K. Kapitan, J. Kauder, K. Keane, D. Kechechyan, A. Kettler, D. Khodyrev, V. Yu. Kikola, D. P. Kiryluk, J. Kisiel, A. Klein, S. R. Knospe, A. G. Kocoloski, A. Koetke, D. D. Konzer, J. Kopytine, M. Koralt, I. Korsch, W. Kotchenda, L. Kouchpil, V. Kravtsov, P. Kravtsov, V. I. Krueger, K. Krus, M. Kumar, L. Kurnadi, P. Lamont, M. A. C. Landgraf, J. M. LaPointe, S. Lauret, J. Lebedev, A. Lednicky, R. Lee, C-H. Lee, J. H. Leight, W. LeVine, M. J. Li, C. Li, N. Li, Y. Lin, G. Lindenbaum, S. J. Lisa, M. A. Liu, F. Liu, H. Liu, J. Liu, L. Ljubicic, T. Llope, W. J. Longacre, R. S. Love, W. A. Lu, Y. Ludlam, T. Ma, G. L. Ma, Y. G. Mahapatra, D. P. Majka, R. Mall, O. I. Mangotra, L. K. Manweiler, R. Margetis, S. Markert, C. Masui, H. Matis, H. S. Matulenko, Yu. A. McDonald, D. McShane, T. S. Meschanin, A. Milner, R. Minaev, N. G. Mioduszewski, S. Mischke, A. Mohanty, B. Morozov, D. A. Munhoz, M. G. Nandi, B. K. Nattrass, C. Nayak, T. K. Nelson, J. M. Netrakanti, P. K. Ng, M. J. Nogach, L. V. Nurushev, S. B. Odyniec, G. Ogawa, A. Okada, H. Okorokov, V. Olson, D. Pachr, M. Page, B. S. Pal, S. K. Pandit, Y. Panebratsev, Y. Pawlak, T. Peitzmann, T. Perevoztchikov, V. Perkins, C. Peryt, W. Phatak, S. C. Pile, P. Planinic, M. Ploskon, M. A. Pluta, J. Plyku, D. Poljak, N. Poskanzer, A. M. Potukuchi, B. V. K. S. Prindle, D. Pruneau, C. Pruthi, N. K. Pujahari, P. R. Putschke, J. Raniwala, R. Raniwala, S. Ray, R. L. Redwine, R. Reed, R. Ridiger, A. Ritter, H. G. Roberts, J. B. Rogachevskiy, O. V. Romero, J. L. Rose, A. Roy, C. Ruan, L. Russcher, M. J. Sahoo, R. Sakai, S. Sakrejda, I. Sakuma, T. Salur, S. Sandweiss, J. Schambach, J. Scharenberg, R. P. Schmitz, N. Seele, J. Seger, J. Selyuzhenkov, I. Semertzidis, Y. Seyboth, P. Shahaliev, E. Shao, M. Sharma, M. Shi, S. S. Shi, X-H. Sichtermann, E. P. Simon, F. Singaraju, R. N. Skoby, M. J. Smirnov, N. Sorensen, P. Sowinski, J. Spinka, H. M. Srivastava, B. Stanislaus, T. D. S. Staszak, D. Strikhanov, M. Stringfellow, B. Suaide, A. A. P. Suarez, M. C. Subba, N. L. Sumbera, M. Sun, X. M. Sun, Y. Sun, Z. Surrow, B. Symons, T. J. M. de Toledo, A. Szanto Takahashi, J. Tang, A. H. Tang, Z. Tarini, L. H. Tarnowsky, T. Thein, D. Thomas, J. H. Tian, J. Timmins, A. R. Timoshenko, S. Tlusty, D. Tokarev, M. Tram, V. N. Trentalange, S. Tribble, R. E. Tsai, O. D. Ulery, J. Ullrich, T. Underwood, D. G. Van Buren, G. van Nieuwenhuizen, G. Vanfossen, J. A., Jr. Varma, R. Vasconcelos, G. M. S. Vasiliev, A. N. Videbaek, F. Viyogi, Y. P. Vokal, S. Voloshin, S. A. Wada, M. Walker, M. Wang, F. Wang, G. Wang, H. Wang, J. S. Wang, Q. Wang, X. Wang, X. L. Wang, Y. Webb, G. Webb, J. C. Westfall, G. D. Whitten, C., Jr. Wieman, H. Wissink, S. W. Witt, R. Wu, Y. Xie, W. Xu, N. Xu, Q. H. Xu, Y. Xu, Z. Yang, Y. Yepes, P. Yip, K. Yoo, I-K. Yue, Q. Zawisza, M. Zbroszczyk, H. Zhan, W. Zhang, S. Zhang, W. M. Zhang, X. P. Zhang, Y. Zhang, Z. P. Zhao, Y. Zhong, C. Zhou, J. Zhu, X. Zoulkarneev, R. Zoulkarneeva, Y. Zuo, J. X. CA STAR Collaboration TI Azimuthal Charged-Particle Correlations and Possible Local Strong Parity Violation SO PHYSICAL REVIEW LETTERS LA English DT Article ID HEAVY-ION COLLISIONS; NUCLEAR COLLISIONS; HOT QCD AB Parity-odd domains, corresponding to nontrivial topological solutions of the QCD vacuum, might be created during relativistic heavy-ion collisions. These domains are predicted to lead to charge separation of quarks along the system's orbital momentum axis. We investigate a three-particle azimuthal correlator which is a P even observable, but directly sensitive to the charge separation effect. We report measurements of charged hadrons near center-of-mass rapidity with this observable in Au+Au and Cu+Cu collisions at s(NN)=200 GeV using the STAR detector. A signal consistent with several expectations from the theory is detected. We discuss possible contributions from other effects that are not related to parity violation. C1 [Abelev, B. 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Y.; Feng, A.; Li, N.; Liu, F.; Liu, L.; Shi, S. S.; Wu, Y.] CCNU HZNU, Inst Particle Phys, Wuhan 430079, Peoples R China. [Baumgart, S.; Bruna, E.; Caines, H.; Catu, O.; Chikanian, A.; Finch, E.; Harris, J. W.; Heinz, M.; Knospe, A. G.; Lin, G.; Majka, R.; Nattrass, C.; Putschke, J.; Sandweiss, J.; Smirnov, N.] Yale Univ, New Haven, CT 06520 USA. [Planinic, M.; Poljak, N.] Univ Zagreb, HR-10002 Zagreb, Croatia. RP Abelev, BI (reprint author), Univ Illinois, Chicago, IL 60607 USA. RI Barnby, Lee/G-2135-2010; Mischke, Andre/D-3614-2011; Takahashi, Jun/B-2946-2012; Planinic, Mirko/E-8085-2012; Yoo, In-Kwon/J-6222-2012; Peitzmann, Thomas/K-2206-2012; Witt, Richard/H-3560-2012; Yip, Kin/D-6860-2013; Voloshin, Sergei/I-4122-2013; Pandit, Yadav/I-2170-2013; Lednicky, Richard/K-4164-2013; Semertzidis, Yannis K./N-1002-2013; Yang, Yanyun/B-9485-2014; Cosentino, Mauro/L-2418-2014; Sumbera, Michal/O-7497-2014; Strikhanov, Mikhail/P-7393-2014; Dogra, Sunil /B-5330-2013; Fornazier Guimaraes, Karin Silvia/H-4587-2016; Chaloupka, Petr/E-5965-2012; Nattrass, Christine/J-6752-2016; Derradi de Souza, Rafael/M-4791-2013; Suaide, Alexandre/L-6239-2016; Inst. of Physics, Gleb Wataghin/A-9780-2017; Okorokov, Vitaly/C-4800-2017; Ma, Yu-Gang/M-8122-2013; OI Barnby, Lee/0000-0001-7357-9904; Takahashi, Jun/0000-0002-4091-1779; Peitzmann, Thomas/0000-0002-7116-899X; Yip, Kin/0000-0002-8576-4311; Pandit, Yadav/0000-0003-2809-7943; Yang, Yanyun/0000-0002-5982-1706; Cosentino, Mauro/0000-0002-7880-8611; Sumbera, Michal/0000-0002-0639-7323; Strikhanov, Mikhail/0000-0003-2586-0405; Fornazier Guimaraes, Karin Silvia/0000-0003-0578-9533; Nattrass, Christine/0000-0002-8768-6468; Derradi de Souza, Rafael/0000-0002-2084-7001; Suaide, Alexandre/0000-0003-2847-6556; Okorokov, Vitaly/0000-0002-7162-5345; Ma, Yu-Gang/0000-0002-0233-9900; Fisyak, Yuri/0000-0002-3151-8377; Bhasin, Anju/0000-0002-3687-8179; Sorensen, Paul/0000-0001-5056-9391; Thomas, James/0000-0002-6256-4536 FU Offices of NP and HEP within the U.S. DOE Office of Science; U.S. NSF; Sloan Foundation; DFG cluster of excellence; CNRS/IN2P3; STFC and EPSRC of the United Kingdom; FAPESP CNPq of Brazil; Ministry of Ed. and Sci. of the Russian Federation; NNSFC; CAS; MoST; MoE of China; GA and MSMT of the Czech Republic; FOM and NOW of the Netherlands; DAE; DST; CSIR of India; Polish Ministry of Sci. and Higher Ed.; Korea Research Foundation; Ministry of Sci., Ed. and Sports of the Rep. Of Croatia; Russian Ministry of Sci. and Tech; RosAtom of Russia FX We thank D. Kharzeev for many helpful discussions. We thank the RHIC Operations Group and RCF at BNL, the NERSC Center at LBNL and the Open Science Grid consortium for providing resources and support. This work was supported in part by the Offices of NP and HEP within the U.S. DOE Office of Science, the U.S. NSF, the Sloan Foundation, the DFG cluster of excellence "Origin and Structure of the Universe'', CNRS/IN2P3, STFC and EPSRC of the United Kingdom, FAPESP CNPq of Brazil, Ministry of Ed. and Sci. of the Russian Federation, NNSFC, CAS, MoST, and MoE of China, GA and MSMT of the Czech Republic, FOM and NOW of the Netherlands, DAE, DST, and CSIR of India, Polish Ministry of Sci. and Higher Ed., Korea Research Foundation, Ministry of Sci., Ed. and Sports of the Rep. Of Croatia, Russian Ministry of Sci. and Tech, and RosAtom of Russia. NR 24 TC 239 Z9 240 U1 3 U2 53 PU AMER PHYSICAL SOC PI COLLEGE PK PA ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA SN 0031-9007 EI 1079-7114 J9 PHYS REV LETT JI Phys. Rev. Lett. PD DEC 18 PY 2009 VL 103 IS 25 AR 251601 DI 10.1103/PhysRevLett.103.251601 PG 7 WC Physics, Multidisciplinary SC Physics GA 535HP UT WOS:000272958300007 PM 20366248 ER PT J AU Aubert, B Karyotakis, Y Lees, JP Poireau, V Prencipe, E Prudent, X Tisserand, V Tico, JG Grauges, E Martinelli, M Palano, A Pappagallo, M Eigen, G Stugu, B Sun, L Battaglia, M Brown, DN Hooberman, B Kerth, LT Kolomensky, YG Lynch, G Osipenkov, IL Tackmann, K Tanabe, T Hawkes, CM Soni, N Watson, AT Koch, H Schroeder, T Asgeirsson, DJ Hearty, C Mattison, TS McKenna, JA Barrett, M Khan, A Randle-Conde, A Blinov, VE Bukin, AD Buzykaev, AR Druzhinin, VP Golubev, VB Onuchin, AP Serednyakov, SI Skovpen, YI Solodov, EP Todyshev, KY Bondioli, M Curry, S Eschrich, I Kirkby, D Lankford, AJ Lund, P Mandelkern, M Martin, EC Stoker, DP Atmacan, H Gary, JW Liu, F Long, O Vitug, GM Yasin, Z Sharma, V Campagnari, C Hong, TM Kovalskyi, D Mazur, MA Richman, JD Beck, TW Eisner, AM Heusch, CA Kroseberg, J Lockman, WS Martinez, AJ Schalk, T Schumm, BA Seiden, A Wang, L Winstrom, LO Cheng, CH Doll, DA Echenard, B Fang, F Hitlin, DG Narsky, I Ongmongkolkul, P Piatenko, T Porter, FC Andreassen, R Mancinelli, G Meadows, BT Mishra, K Sokoloff, MD Bloom, PC Ford, WT Gaz, A Hirschauer, JF Nagel, M Nauenberg, U Smith, JG Wagner, SR Ayad, R Toki, WH Wilson, RJ Feltresi, E Hauke, A Jasper, H Karbach, TM Merkel, J Petzold, A Spaan, B Wacker, K Kobel, MJ Nogowski, R Schubert, KR Schwierz, R Bernard, D Latour, E Verderi, M Clark, PJ Playfer, S Watson, JE Andreotti, M Bettoni, D Bozzi, C Calabrese, R Cecchi, A Cibinetto, G Fioravanti, E Franchini, P Luppi, E Munerato, M Negrini, M Petrella, A Piemontese, L Santoro, V Baldini-Ferroli, R Calcaterra, A de Sangro, R Finocchiaro, G Pacetti, S Patteri, P Peruzzi, IM Piccolo, M Rama, M Zallo, A Contri, R Guido, E Lo Vetere, M Monge, MR Passaggio, S Patrignani, C Robutti, E Tosi, S Chaisanguanthum, KS Morii, M Adametz, A Marks, J Schenk, S Uwer, U Bernlochner, FU Klose, V Lacker, HM Lueck, T Volk, A Bard, DJ Dauncey, PD Tibbetts, M Behera, PK Charles, MJ Mallik, U Cochran, J Crawley, HB Dong, L Eyges, V Meyer, WT Prell, S Rosenberg, EI Rubin, AE Gao, YY Gritsan, AV Guo, ZJ Arnaud, N Bequilleux, J D'Orazio, A Davier, M Derkach, D da Costa, JF Grosdidier, G Le Diberder, F Lepeltier, V Lutz, AM Malaescu, B Pruvot, S Roudeau, P Schune, MH Serrano, J Sordini, V Stocchi, A Wormser, G Lange, DJ Wright, DM Bingham, I Burke, JP Chavez, CA Fry, JR Gabathuler, E Gamet, R Hutchcroft, DE Payne, DJ Touramanis, C Bevan, AJ Clarke, CK Di Lodovico, F Sacco, R Sigamani, M Cowan, G Paramesvaran, S Wren, AC Brown, DN Davis, CL Denig, AG Fritsch, M Gradl, W Hafner, A Alwyn, KE Bailey, D Barlow, RJ Jackson, G Lafferty, GD West, TJ Yi, JI Anderson, J Chen, C Jawahery, A Roberts, DA Simi, G Tuggle, JM Dallapiccola, C Salvati, E Cowan, R Dujmic, D Fisher, PH Henderson, SW Sciolla, G Spitznagel, M Yamamoto, RK Zhao, M Patel, PM Robertson, SH Schram, M Biassoni, P Lazzaro, A Lombardo, V Palombo, F Stracka, S Cremaldi, L Godang, R Kroeger, R Sonnek, P Summers, DJ Zhao, HW Simard, M Taras, P Nicholson, H De Nardo, G Lista, L Monorchio, D Onorato, G Sciacca, C Raven, G Snoek, HL Jessop, CP Knoepfel, KJ LoSecco, JM Wang, WF Corwin, LA Honscheid, K Kagan, H Kass, R Morris, JP Rahimi, AM Sekula, SJ Wong, QK Blount, NL Brau, J Frey, R Igonkina, O Kolb, JA Lu, M Rahmat, R Sinev, NB Strom, D Strube, J Torrence, E Castelli, G Gagliardi, N Margoni, M Morandin, M Posocco, M Rotondo, M Simonetto, F Stroili, R Voci, C Sanchez, PD Ben-Haim, E Bonneaud, GR Briand, H Chauveau, J Hamon, O Leruste, P Marchiori, G Ocariz, J Perez, A Prendki, J Sitt, S Gladney, L Biasini, M Manoni, E Angelini, C Batignani, G Bettarini, S Calderini, G Carpinelli, M Cervelli, A Forti, F Giorgi, MA Lusiani, A Morganti, M Neri, N Paoloni, E Rizzo, G Walsh, JJ Pegna, DL Lu, C Olsen, J Smith, AJS Telnov, AV Anulli, F Baracchini, E Cavoto, G Faccini, R Ferrarotto, F Ferroni, F Gaspero, M Jackson, PD Gioi, LL Mazzoni, MA Morganti, S Piredda, G Renga, F Voena, C Ebert, M Hartmann, T Schroder, H Waldi, R Adye, T Franek, B Olaiya, EO Wilson, FF Emery, S Esteve, L de Monchenault, GH Kozanecki, W Vasseur, G Yeche, C Zito, M Allen, MT Aston, D Bartoldus, R Benitez, JF Cenci, R Coleman, JP Convery, MR Dingfelder, JC Dorfan, J Dubois-Felsmann, GP Dunwoodie, W Field, RC Sevilla, MF Fulsom, BG Gabareen, AM Graham, MT Grenier, P Hast, C Innes, WR Kaminski, J Kelsey, MH Kim, H Kim, P Kocian, ML Leith, DWGS Li, S Lindquist, B Luitz, S Luth, V Lynch, HL MacFarlane, DB Marsiske, H Messner, R Muller, DR Neal, H Nelson, S O'Grady, CP Ofte, I Perl, M Ratcliff, BN Roodman, A Salnikov, AA Schindler, RH Schwiening, J Snyder, A Su, D Sullivan, MK Suzuki, K Swain, SK Thompson, JM Va'vra, J Wagner, AP Weaver, M West, CA Wisniewski, WJ Wittgen, M Wright, DH Wulsin, HW Yarritu, AK Young, CC Ziegler, V Chen