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  • 1
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    Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression [Medical Sciences] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-02-01
    Description: Dominant mutations or DNA amplification of tyrosine kinases are rare among the oncogenic alterations implicated in prostate cancer. We demonstrate that castration-resistant prostate cancer (CRPC) in men exhibits increased tyrosine phosphorylation, raising the question of whether enhanced tyrosine kinase activity is observed in prostate cancer in the absence of specific tyrosine kinase mutation or DNA amplification. We generated a mouse model of prostate cancer progression using commonly perturbed non-tyrosine kinase oncogenes and pathways and detected a significant up-regulation of tyrosine phosphorylation at the carcinoma stage. Phosphotyrosine peptide enrichment and quantitative mass spectrometry identified oncogene-specific tyrosine kinase signatures, including activation of EGFR, ephrin type-A receptor 2 (EPHA2), and JAK2. Kinase:substrate relationship analysis of the phosphopeptides also revealed ABL1 and SRC tyrosine kinase activation. The observation of elevated tyrosine kinase signaling in advanced prostate cancer and identification of specific tyrosine kinase pathways from genetically defined tumor models point to unique therapeutic approaches using tyrosine kinase inhibitors for advanced prostate cancer.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share (2014)
    Kottyan, L. C., Zoller, E. E., Bene, J., Lu, X., Kelly, J. A., Rupert, A. M., Lessard, C. J., Vaughn, S. E., Marion, M., Weirauch, M. T., Namjou, B., Adler, A., Rasmussen, A., Glenn, S., Montgomery, C. G., Hirschfield, G. M., Xie, G., Coltescu, C., Amos, C., Li, H., Ice, J. A., Nath, S. K., Mariette, X., Bowman, S., for UK Primary Sjogren's Syndrome Registry, Rischmueller, M., Lester, S., Brun, J. G., Goransson, L. G., Harboe, E., Omdal, R., Cunninghame-Graham, D. S., Vyse, T., Miceli-Richard, C., Brennan, M. T., Lessard, J. A., Wahren-Herlenius, M., Kvarnstrom, M., Illei, G. G., Witte, T., Jonsson, R., Eriksson, P., Nordmark, G., Ng, W.-F., for UK Primary Sjogren's Syndrome Registry, Anaya, J.-M., Rhodus, N. L., Segal, B. M., Merrill, J. T., James, J. A., Guthridge, J. M., Hal Scofield, R., Alarcon-Riquelme, M., Bae, S.-C., Boackle, S. A., Criswell, L. A., Gilkeson, G., Kamen, D. L., Jacob, C. O., Kimberly, R., Brown, E., Edberg, J., Alarcon, G. S., Reveille, J. D., Vila, L. M., Petri, M., Ramsey-Goldman, R., Freedman, B. I., Niewold, T., Stevens, A. M., Tsao, B. P., Ying, J., Mayes, M. D., Gorlova, O. Y., Wakeland, W., Radstake, T., Martin, E., Martin, J., Siminovitch, K., Moser Sivils, K. L., Gaffney, P. M., Langefeld, C. D., Harley, J. B., Kaufman, K. M.
    Oxford University Press
    Details
    Publication Date: 2014-12-24
    Description: Exploiting genotyping, DNA sequencing, imputation and trans-ancestral mapping, we used Bayesian and frequentist approaches to model the IRF5 – TNPO3 locus association, now implicated in two immunotherapies and seven autoimmune diseases. Specifically, in systemic lupus erythematosus (SLE), we resolved separate associations in the IRF5 promoter (all ancestries) and with an extended European haplotype. We captured 3230 IRF5 – TNPO3 high-quality, common variants across 5 ethnicities in 8395 SLE cases and 7367 controls. The genetic effect from the IRF5 promoter can be explained by any one of four variants in 5.7 kb ( P -value meta = 6 x 10 –49 ; OR = 1.38–1.97). The second genetic effect spanned an 85.5-kb, 24-variant haplotype that included the genes IRF5 and TNPO3 ( P -values EU = 10 –27 –10 –32 , OR = 1.7–1.81). Many variants at the IRF5 locus with previously assigned biological function are not members of either final credible set of potential causal variants identified herein. In addition to the known biologically functional variants, we demonstrated that the risk allele of rs4728142, a variant in the promoter among the lowest frequentist probability and highest Bayesian posterior probability, was correlated with IRF5 expression and differentially binds the transcription factor ZBTB3. Our analytical strategy provides a novel framework for future studies aimed at dissecting etiological genetic effects. Finally, both SLE elements of the statistical model appear to operate in Sjögren's syndrome and systemic sclerosis whereas only the IRF5–TNPO3 gene-spanning haplotype is associated with primary biliary cirrhosis, demonstrating the nuance of similarity and difference in autoimmune disease risk mechanisms at IRF5 – TNPO3 .
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018-10-05
    Description: The use of potent therapies inhibiting critical oncogenic pathways active in epithelial cancers has led to multiple resistance mechanisms, including the development of highly aggressive, small cell neuroendocrine carcinoma (SCNC). SCNC patients have a dismal prognosis due in part to a limited understanding of the molecular mechanisms driving this malignancy and the lack of effective treatments. Here, we demonstrate that a common set of defined oncogenic drivers reproducibly reprograms normal human prostate and lung epithelial cells to small cell prostate cancer (SCPC) and small cell lung cancer (SCLC), respectively. We identify shared active transcription factor binding regions in the reprogrammed prostate and lung SCNCs by integrative analyses of epigenetic and transcriptional landscapes. These results suggest that neuroendocrine cancers arising from distinct epithelial tissues may share common vulnerabilities that could be exploited for the development of drugs targeting SCNCs.
    Keywords: Medicine, Diseases
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-07-08
    Description: Swi2/Snf2-type ATPases regulate genome-associated processes such as transcription, replication and repair by catalysing the disruption, assembly or remodelling of nucleosomes or other protein-DNA complexes. It has been suggested that ATP-driven motor activity along DNA disrupts target protein-DNA interactions in the remodelling reaction. However, the complex and highly specific remodelling reactions are poorly understood, mostly because of a lack of high-resolution structural information about how remodellers bind to their substrate proteins. Mot1 (modifier of transcription 1 in Saccharomyces cerevisiae, denoted BTAF1 in humans) is a Swi2/Snf2 enzyme that specifically displaces the TATA box binding protein (TBP) from the promoter DNA and regulates transcription globally by generating a highly dynamic TBP pool in the cell. As a Swi2/Snf2 enzyme that functions as a single polypeptide and interacts with a relatively simple substrate, Mot1 offers an ideal system from which to gain a better understanding of this important enzyme family. To reveal how Mot1 specifically disrupts TBP-DNA complexes, we combined crystal and electron microscopy structures of Mot1-TBP from Encephalitozoon cuniculi with biochemical studies. Here we show that Mot1 wraps around TBP and seems to act like a bottle opener: a spring-like array of 16 HEAT (huntingtin, elongation factor 3, protein phosphatase 2A and lipid kinase TOR) repeats grips the DNA-distal side of TBP via loop insertions, and the Swi2/Snf2 domain binds to upstream DNA, positioned to weaken the TBP-DNA interaction by DNA translocation. A 'latch' subsequently blocks the DNA-binding groove of TBP, acting as a chaperone to prevent DNA re-association and ensure efficient promoter clearance. This work shows how a remodelling enzyme can combine both motor and chaperone activities to achieve functional specificity using a conserved Swi2/Snf2 translocase.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276066/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276066/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wollmann, Petra -- Cui, Sheng -- Viswanathan, Ramya -- Berninghausen, Otto -- Wells, Melissa N -- Moldt, Manuela -- Witte, Gregor -- Butryn, Agata -- Wendler, Petra -- Beckmann, Roland -- Auble, David T -- Hopfner, Karl-Peter -- GM55763/GM/NIGMS NIH HHS/ -- R01 GM055763/GM/NIGMS NIH HHS/ -- R01 GM055763-13/GM/NIGMS NIH HHS/ -- England -- Nature. 2011 Jul 6;475(7356):403-7. doi: 10.1038/nature10215.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Ludwig-Maximilians University, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21734658" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/genetics/metabolism/ultrastructure ; Encephalitozoon cuniculi/*chemistry ; Fungal Proteins/*chemistry/*metabolism/ultrastructure ; Microscopy, Electron ; Models, Biological ; Models, Molecular ; Promoter Regions, Genetic/genetics ; Protein Conformation ; Protein Structure, Tertiary ; Structure-Activity Relationship ; Substrate Specificity ; TATA-Box Binding Protein/*chemistry/*metabolism/ultrastructure ; Transcription Factor TFIIB/chemistry/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    cGAS produces a 2'-5'-linked cyclic dinucleotide second messenger that activates STING (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-06-01
    Description: Detection of cytoplasmic DNA represents one of the most fundamental mechanisms of the innate immune system to sense the presence of microbial pathogens. Moreover, erroneous detection of endogenous DNA by the same sensing mechanisms has an important pathophysiological role in certain sterile inflammatory conditions. The endoplasmic-reticulum-resident protein STING is critically required for the initiation of type I interferon signalling upon detection of cytosolic DNA of both exogenous and endogenous origin. Next to its pivotal role in DNA sensing, STING also serves as a direct receptor for the detection of cyclic dinucleotides, which function as second messenger molecules in bacteria. DNA recognition, however, is triggered in an indirect fashion that depends on a recently characterized cytoplasmic nucleotidyl transferase, termed cGAMP synthase (cGAS), which upon interaction with DNA synthesizes a dinucleotide molecule that in turn binds to and activates STING. We here show in vivo and in vitro that the cGAS-catalysed reaction product is distinct from previously characterized cyclic dinucleotides. Using a combinatorial approach based on mass spectrometry, enzymatic digestion, NMR analysis and chemical synthesis we demonstrate that cGAS produces a cyclic GMP-AMP dinucleotide, which comprises a 2'-5' and a 3'-5' phosphodiester linkage 〉Gp(2'-5')Ap(3'-5')〉. We found that the presence of this 2'-5' linkage was required to exert potent activation of human STING. Moreover, we show that cGAS first catalyses the synthesis of a linear 2'-5'-linked dinucleotide, which is then subject to cGAS-dependent cyclization in a second step through a 3'-5' phosphodiester linkage. This 13-membered ring structure defines a novel class of second messenger molecules, extending the family of 2'-5'-linked antiviral biomolecules.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143541/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143541/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ablasser, Andrea -- Goldeck, Marion -- Cavlar, Taner -- Deimling, Tobias -- Witte, Gregor -- Rohl, Ingo -- Hopfner, Karl-Peter -- Ludwig, Janos -- Hornung, Veit -- 243046/European Research Council/International -- U19AI083025/AI/NIAID NIH HHS/ -- England -- Nature. 2013 Jun 20;498(7454):380-4. doi: 10.1038/nature12306. Epub 2013 May 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53127 Bonn, Germany. andrea.ablasser@uni-bonn.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23722158" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/chemistry ; Animals ; Biocatalysis ; Cell Line ; Cyclic GMP/chemistry ; Cyclization ; HEK293 Cells ; Humans ; Magnetic Resonance Spectroscopy ; Membrane Proteins/*metabolism ; Mice ; Models, Molecular ; Molecular Structure ; Nucleotidyltransferases/genetics/*metabolism ; Oligoribonucleotides/biosynthesis/chemistry/*metabolism ; Second Messenger Systems/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Structural mechanism of cytosolic DNA sensing by cGAS (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-06-01
    Description: Cytosolic DNA arising from intracellular bacterial or viral infections is a powerful pathogen-associated molecular pattern (PAMP) that leads to innate immune host defence by the production of type I interferon and inflammatory cytokines. Recognition of cytosolic DNA by the recently discovered cyclic-GMP-AMP (cGAMP) synthase (cGAS) induces the production of cGAMP to activate the stimulator of interferon genes (STING). Here we report the crystal structure of cGAS alone and in complex with DNA, ATP and GTP along with functional studies. Our results explain the broad DNA sensing specificity of cGAS, show how cGAS catalyses dinucleotide formation and indicate activation by a DNA-induced structural switch. cGAS possesses a remarkable structural similarity to the antiviral cytosolic double-stranded RNA sensor 2'-5'oligoadenylate synthase (OAS1), but contains a unique zinc thumb that recognizes B-form double-stranded DNA. Our results mechanistically unify dsRNA and dsDNA innate immune sensing by OAS1 and cGAS nucleotidyl transferases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768140/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768140/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Civril, Filiz -- Deimling, Tobias -- de Oliveira Mann, Carina C -- Ablasser, Andrea -- Moldt, Manuela -- Witte, Gregor -- Hornung, Veit -- Hopfner, Karl-Peter -- 243046/European Research Council/International -- U19 AI083025/AI/NIAID NIH HHS/ -- U19AI083025/AI/NIAID NIH HHS/ -- England -- Nature. 2013 Jun 20;498(7454):332-7. doi: 10.1038/nature12305. Epub 2013 May 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23722159" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/chemistry/metabolism ; Animals ; Base Sequence ; Catalytic Domain ; Crystallography, X-Ray ; *Cytosol ; DNA/chemistry/*metabolism/pharmacology ; Guanosine Triphosphate/chemistry/metabolism ; HEK293 Cells ; Humans ; Membrane Proteins/genetics/metabolism ; Mice ; Models, Biological ; Models, Molecular ; Mutation ; Nucleotidyltransferases/*chemistry/genetics/metabolism ; Protein Conformation/drug effects ; Structure-Activity Relationship ; Substrate Specificity ; Swine ; Uridine Triphosphate/chemistry/metabolism ; Zinc/chemistry/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Paramyxovirus V proteins disrupt the fold of the RNA sensor MDA5 to inhibit antiviral signaling (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-01-19
    Description: The retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) melanoma differentiation-associated protein 5 (MDA5) senses cytoplasmic viral RNA and activates antiviral innate immunity. To reveal how paramyxoviruses counteract this response, we determined the crystal structure of the MDA5 adenosine 5'-triphosphate (ATP)-hydrolysis domain in complex with the viral inhibitor V protein. The V protein unfolded the ATP-hydrolysis domain of MDA5 via a beta-hairpin motif and recognized a structural motif of MDA5 that is normally buried in the conserved helicase fold. This leads to disruption of the MDA5 ATP-hydrolysis site and prevention of RNA-bound MDA5 filament formation. The structure explains why V proteins inactivate MDA5, but not RIG-I, and mutating only two amino acids in RIG-I induces robust V protein binding. Our results suggest an inhibition mechanism of RLR signalosome formation by unfolding of receptor and inhibitor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Motz, Carina -- Schuhmann, Kerstin Monika -- Kirchhofer, Axel -- Moldt, Manuela -- Witte, Gregor -- Conzelmann, Karl-Klaus -- Hopfner, Karl-Peter -- U19AI083025/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 8;339(6120):690-3. doi: 10.1126/science.1230949. Epub 2013 Jan 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Gene Center, Ludwig-Maximilians-University, Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23328395" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; DEAD-box RNA Helicases/*chemistry/genetics/*metabolism ; HEK293 Cells ; Humans ; Hydrolysis ; Immunity, Innate ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutation ; *Parainfluenza Virus 5/immunology ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; RNA, Double-Stranded/*metabolism ; Signal Transduction ; Sus scrofa ; Viral Proteins/*chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Patient-specific kinase activity patterns in CRPC [Medical Sciences] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-12-04
    Description: In prostate cancer, multiple metastases from the same patient share similar copy number, mutational status, erythroblast transformation specific (ETS) rearrangements, and methylation patterns supporting their clonal origins. Whether actionable targets such as tyrosine kinases are also similarly expressed and activated in anatomically distinct metastatic lesions of the same patient is...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 9
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    Imaging quasiperiodic electronic states in a synthetic Penrose tiling (2017)
    Springer Nature
    Details
    Publication Date: 2017-06-23
    Description: Imaging quasiperiodic electronic states in a synthetic Penrose tiling Nature Communications, Published online: 22 June 2017; doi:10.1038/ncomms15961 Quasicrystals possess long-range order but lack translational symmetry. Here, the authors use atomic manipulation and scanning tunnelling microscopy to assemble a Penrose tiling quasicrystal and observe that its electronic density of states has a quasiperiodic order, linked to the quasicrystal topology.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 10
    Electronic Resource
    Electronic Resource
    CO overlayers on Ru(0001) studied by helium atom scattering: Structure, dynamics, and the influence of coadsorbed H and O (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 8262-8273 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Ordered phases of CO on a Ru(0001) surface have been characterized with regard to structural and dynamical properties using high resolution helium atom scattering. In the energy regime below 10 meV a vibrational mode corresponding to a frustrated translation parallel to the surface (FTx) could be identified, the energy amounts to 5.9 meV for isolated CO molecules and to 5.75 meV for the ((square root of 3)×(square root of 3))R30°CO structure. The formation of the more compressed (2(square root of 3)×2(square root of 3))R30°CO and (5(square root of 3)×5(square root of 3))R30°CO structures is accompanied by significant changes of the low energy external vibrations, in pronounced contrast to the gradual frequency increase of the CO internal ν1-vibration. Coadsorption of hydrogen or oxygen was found to result in substantially larger FTx energies. Implications of these findings on the character of the molecule-surface interaction will be discussed, as well as the connection between the FTx-dispersion and the strength and type of the adsorbate-adsorbate interaction. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.473828
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