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  • 1
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    Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-08-29
    Description: Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    Observation of Attractive and Repulsive Polarons in a Bose-Einstein Condensate (2016)
    American Physical Society (APS)
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    Publication Date: 2016-07-29
    Description: Author(s): Nils B. Jørgensen, Lars Wacker, Kristoffer T. Skalmstang, Meera M. Parish, Jesper Levinsen, Rasmus S. Christensen, Georg M. Bruun, and Jan J. Arlt Researchers have used impurities within a Bose-Einstein condensate to simulate polarons—electron-phonon combinations in solid-state systems. [Phys. Rev. Lett. 117, 055302] Published Thu Jul 28, 2016
    Keywords: Condensed Matter: Structure, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    Generation of subsurface voids and a nanocrystalline surface layer in femtosecond laser irradiation of a single-crystal Ag target (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-01-13
    Description: Author(s): Chengping Wu, Martin S. Christensen, Juha-Matti Savolainen, Peter Balling, and Leonid V. Zhigilei Structural transformations in a shallow surface region of a bulk Ag (001) target irradiated by a femtosecond laser pulse are investigated in large-scale atomistic simulations and experiments. The simulations reveal a complex interplay of fast laser melting, rapid resolidification, and dynamic relaxa... [Phys. Rev. B 91, 035413] Published Mon Jan 12, 2015
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 4
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    Decoherence of Impurities in a Fermi Sea of Ultracold Atoms (2015)
    American Physical Society (APS)
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    Publication Date: 2015-09-24
    Description: Author(s): Marko Cetina, Michael Jag, Rianne S. Lous, Jook T. M. Walraven, Rudolf Grimm, Rasmus S. Christensen, and Georg M. Bruun The superposition of internal states of impurity atoms in a strongly interacting Fermi gas decohere an order of magnitude faster than predictions that assume this process occurs via quasiparticle scattering. [Phys. Rev. Lett. 115, 135302] Published Tue Sep 22, 2015
    Keywords: Condensed Matter: Structure, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Cataclysmic variables from the Catalina Real-time Transient Survey (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-06
    Description: We present 855 cataclysmic variable candidates detected by the Catalina Real-time Transient Survey (CRTS) of which at least 137 have been spectroscopically confirmed and 705 are new discoveries. The sources were identified from the analysis of five years of data, and come from an area covering three quarters of the sky. We study the amplitude distribution of the dwarf novae cataclysmic variables (CVs) discovered by CRTS during outburst, and find that in quiescence they are typically 2 mag fainter compared to the spectroscopic CV sample identified by the Sloan Digital Sky Survey. However, almost all CRTS CVs in the SDSS footprint have ugriz photometry. We analyse the spatial distribution of the CVs and find evidence that many of the systems lie at scale heights beyond those expected for a Galactic thin disc population. We compare the outburst rates of newly discovered CRTS CVs with the previously known CV population, and find no evidence for a difference between them. However, we find significant evidence for a systematic difference in orbital period distribution. We discuss the CVs found below the orbital period minimum and argue that many more are yet to be identified among the full CRTS CV sample. We cross-match the CVs with archival X-ray catalogues and find that most of the systems are dwarf novae rather than magnetic CVs.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    On the inference of stellar ages and convective-core properties in main-sequence solar-like pulsators (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-29
    Description: Particular diagnostic tools may isolate the signature left on the oscillation frequencies by the presence of a small convective core. Their frequency derivative is expected to provide information about convective core's properties and stellar age. The main goal of this work is to study the potential of the diagnostic tools with regard to the inference of stellar age and stellar core's properties. For that, we computed diagnostic tools and their frequency derivatives from the oscillation frequencies of main-sequence models with masses between 1.0 and 1.6 M and with different physics. We considered the dependence of the diagnostic tools on stellar age and on the size of the relative discontinuity in the squared sound speed at the edge of the convectively unstable region. We find that the absolute value of the frequency derivatives of the diagnostic tools increases as the star evolves on the main sequence. The fraction of stellar main-sequence evolution for models with masses 〉1.2 M may be estimated from the frequency derivatives of two of the diagnostic tools. For lower mass models, constraints on the convective core's overshoot can potentially be derived based on the analysis of the same derivatives. For at least 35 per cent of our sample of stellar models, the frequency derivative of the diagnostic tools takes its maximum absolute value on the frequency range where observed oscillations may be expected.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    Discovery of ~9000 new RR Lyrae in the southern Catalina surveys (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-27
    Description: We present the results of a deep, wide-area variability survey in the Southern hemisphere, the first of its kind. As part of the Catalina Sky Surveys, the Siding Spring Survey (SSS) has covered 14 800 deg 2 in the declination range of –75° ≤ ≤ –15°. To mine the enormous SSS data set efficiently, we have developed two algorithms: automatic period selection (APS) and automatic Fourier decomposition (AFD), which aim to sharpen the period estimation and produce robust light-curve models. Armed with the APS and AFD outputs, we classify 10 540 ab-type RR Lyrae (RRab) stars (~90 per cent of which are new) across the southern sky. As well as the positional information we supply photometric metallicities, and unreddened distances. For the RRab stars in the halo, a study of the photometric metallicity distribution reveals a nearly Gaussian shape with a mean metallicity of [Fe/H] = –1.4 dex and a dispersion of 0.3 dex. A spatial study of the RRab metallicities shows no significant radial gradient in the first ~7 kpc from the Galaxy centre. However, further out, a small negative gradient is clearly present. This is complemented by a very obvious correlation of the mean RR Lyrae metallicity with distance above the Galactic plane, z . We have also carried out an initial sub-structure search using the discovered RRab, and present the properties of the candidates with significance greater than 2. Most prominent among these is a southern extension of the Sagittarius dwarf galaxy's stream system, reaching down to declinations ~ -40 °.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Evolution of autoantibody responses via somatic hypermutation outside of germinal centers (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-09-21
    Description: Somatically mutated high-affinity autoantibodies are a hallmark of some autoimmune diseases, including systemic lupus erythematosus. It has long been presumed that germinal centers (GCs) are critical in autoantibody production, because they are the only sites currently believed to sustain a high rate of somatic hypermutation. Contrary to this idea, we found that splenic autoreactive B cells in autoimmune MRL.Fas(lpr) mice proliferated and underwent active somatic hypermutation at the T zone-red pulp border rather than in GCs. Our results implicate this region as an important site for hypermutation and the loss of B cell self-tolerance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉William, Jacqueline -- Euler, Chad -- Christensen, Sean -- Shlomchik, Mark J -- P01-A36529/PHS HHS/ -- New York, N.Y. -- Science. 2002 Sep 20;297(5589):2066-70.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Laboratory Medicine, Section of Immunobiology, Yale University School of Medicine, Box 208035, New Haven, CT 06520-8035, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12242446" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antibodies, Anti-Idiotypic/immunology ; Autoantibodies/*biosynthesis ; Autoimmune Diseases/immunology ; *Autoimmunity ; B-Lymphocytes/*immunology ; Base Sequence ; Dendritic Cells, Follicular/immunology ; Genes, Immunoglobulin ; Germinal Center/*immunology ; Immunoglobulin Variable Region/genetics ; Mice ; Mice, Inbred MRL lpr ; Mice, Transgenic ; Molecular Sequence Data ; Rheumatoid Factor/*biosynthesis ; Self Tolerance ; *Somatic Hypermutation, Immunoglobulin ; Spleen/*immunology ; T-Lymphocytes/immunology
    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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  • 9
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    Derivatives of erythropoietin that are tissue protective but not erythropoietic (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-13
    Description: Erythropoietin (EPO) is both hematopoietic and tissue protective, putatively through interaction with different receptors. We generated receptor subtype-selective ligands allowing the separation of EPO's bioactivities at the cellular level and in animals. Carbamylated EPO (CEPO) or certain EPO mutants did not bind to the classical EPO receptor (EPOR) and did not show any hematopoietic activity in human cell signaling assays or upon chronic dosing in different animal species. Nevertheless, CEPO and various nonhematopoietic mutants were cytoprotective in vitro and conferred neuroprotection against stroke, spinal cord compression, diabetic neuropathy, and experimental autoimmune encephalomyelitis at a potency and efficacy comparable to EPO.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leist, Marcel -- Ghezzi, Pietro -- Grasso, Giovanni -- Bianchi, Roberto -- Villa, Pia -- Fratelli, Maddalena -- Savino, Costanza -- Bianchi, Marina -- Nielsen, Jacob -- Gerwien, Jens -- Kallunki, Pekka -- Larsen, Anna Kirstine -- Helboe, Lone -- Christensen, Soren -- Pedersen, Lars O -- Nielsen, Mette -- Torup, Lars -- Sager, Thomas -- Sfacteria, Alessandra -- Erbayraktar, Serhat -- Erbayraktar, Zubeyde -- Gokmen, Necati -- Yilmaz, Osman -- Cerami-Hand, Carla -- Xie, Qiao-Wen -- Coleman, Thomas -- Cerami, Anthony -- Brines, Michael -- New York, N.Y. -- Science. 2004 Jul 9;305(5681):239-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉H. Lundbeck A/S, 2500 Valby, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15247477" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Binding Sites ; Cells, Cultured ; Diabetic Neuropathies/drug therapy ; Drug Design ; Encephalomyelitis, Autoimmune, Experimental/drug therapy ; Erythropoiesis ; Erythropoietin/*analogs & ; derivatives/chemistry/genetics/metabolism/pharmacology/*therapeutic use ; Female ; Hematocrit ; Humans ; Ligands ; Mice ; Mice, Inbred C3H ; Mutagenesis ; Nervous System Diseases/*drug therapy ; Neurons/metabolism ; Neuroprotective Agents/chemistry/metabolism/pharmacology/*therapeutic use ; Rats ; Rats, Sprague-Dawley ; Receptors, Erythropoietin/metabolism ; Recombinant Proteins ; Signal Transduction ; Spinal Cord Compression/drug therapy ; Stroke/drug therapy ; Structure-Activity Relationship
    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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  • 10
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    Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications (2016)
    American Chemical Society (ACS)
    Details
    Publication Date: 2016-04-14
    Description: Chemical Reviews DOI: 10.1021/acs.chemrev.5b00584
    Print ISSN: 0009-2665
    Electronic ISSN: 1520-6890
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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