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  • 1
    Publication Date: 2015-05-27
    Description: Author(s): Q. D. Gibson, L. M. Schoop, L. Muechler, L. S. Xie, M. Hirschberger, N. P. Ong, R. Car, and R. J. Cava Design principles and predictions of new three-dimensional (3D) Dirac semimetals are presented and placed in the context of currently known materials. Three different design principles are presented (cases I, II, and III), each of which yields predictions for new candidates. For case I, 3D Dirac sem... [Phys. Rev. B 91, 205128] Published Fri May 22, 2015
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 2
    Publication Date: 2003-05-06
    Description: We have used adenosine diphosphate analogs containing electron paramagnetic resonance (EPR) spin moieties and EPR spectroscopy to show that the nucleotide-binding site of kinesin-family motors closes when the motor.diphosphate complex binds to microtubules. Structural analyses demonstrate that a domain movement in the switch 1 region at the nucleotide site, homologous to domain movements in the switch 1 region in the G proteins [heterotrimeric guanine nucleotide-binding proteins], explains the EPR data. The switch movement primes the motor both for the free energy-yielding nucleotide hydrolysis reaction and for subsequent conformational changes that are crucial for the generation of force and directed motion along the microtubule.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Naber, Nariman -- Minehardt, Todd J -- Rice, Sarah -- Chen, Xiaoru -- Grammer, Jean -- Matuska, Marija -- Vale, Ronald D -- Kollman, Peter A -- Car, Roberto -- Yount, Ralph G -- Cooke, Roger -- Pate, Edward -- AR39643/AR/NIAMS NIH HHS/ -- AR42895/AR/NIAMS NIH HHS/ -- DK05915/DK/NIDDK NIH HHS/ -- GM29072/GM/NIGMS NIH HHS/ -- RR1081/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2003 May 2;300(5620):798-801.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of California, San Francisco, CA 94143, USA. naber@itsa.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12730601" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine Nucleotides/*metabolism ; Adenosine Diphosphate/analogs & derivatives/metabolism ; Adenosine Triphosphate/analogs & derivatives/metabolism ; Animals ; Binding Sites ; Computer Simulation ; Crystallography, X-Ray ; *Drosophila Proteins ; Drosophila melanogaster ; Electron Spin Resonance Spectroscopy ; Humans ; Hydrogen Bonding ; Hydrolysis ; Kinesin/*chemistry/*metabolism ; Microtubules/*metabolism ; Models, Molecular ; Molecular Motor Proteins/*chemistry/*metabolism ; Molecular Probes/metabolism ; Protein Conformation ; Spin Labels
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2001-02-07
    Description: We determined the structure of the hydrated Cu(II) complex by both neutron diffraction and first-principles molecular dynamics. In contrast with the generally accepted picture, which assumes an octahedrally solvated Cu(II) ion, our experimental and theoretical results favor fivefold coordination. The simulation reveals that the solvated complex undergoes frequent transformations between square pyramidal and trigonal bipyramidal configurations. We argue that this picture is also consistent with experimental data obtained previously by visible near-infrared absorption, x-ray absorption near-edge structure, and nuclear magnetic resonance methods. The preference of the Cu(II) ion for fivefold instead of sixfold coordination, which occurs for other cations of comparable charge and size, results from a Jahn-Teller destabilization of the octahedral complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pasquarello, A -- Petri, I -- Salmon, P S -- Parisel, O -- Car, R -- Toth, E -- Powell, D H -- Fischer, H E -- Helm, L -- Merbach, A -- New York, N.Y. -- Science. 2001 Feb 2;291(5505):856-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Romand de Recherche Numerique en Physique des Materiaux (IRRMA), PPH-Ecublens, CH-1015 Lausanne, Switzerland. Alfredo.Pasquarello@epfl.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11157161" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1990-12-14
    Description: Melting of diamond at high pressure and the properties of liquid carbon at pressures greater than 1 megabar were investigated with a first-principles molecular dynamics technique. The results indicate an increase of the diamond melting temperature with pressure, which is opposite to the behavior of silicon and germanium. This is contrary to long-held assumptions, but agrees with recent experiments, and has important implications for geology and astrophysics. As is the case for the solid phase of carbon at low temperature, which changes greatly with pressure from graphite to diamond, the structural and bonding properties of liquid carbon vary strongly with pressure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galli, G -- Martin, R M -- Car, R -- Parrinello, M -- New York, N.Y. -- Science. 1990 Dec 14;250(4987):1547-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17818281" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1997-03-28
    Description: The vibrational properties of amorphous SiO2 were studied within first-principles density functional theory. The calculated spectrum is in good agreement with neutron data, showing, in particular, a double peak in the high-frequency region. This doublet results from different local modes of the tetrahedral subunits and cannot be ascribed to a longitudinal-optic-transverse-optic (LO-TO) effect. This solves a long-standing controversy about the origin of the doublet in neutron spectra. A LO-TO splitting is recovered only when the long-wavelength limit is probed, as in optical experiments. These findings should be a general feature of tetrahedral AX2 amorphous networks.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarnthein -- Pasquarello -- Car -- New York, N.Y. -- Science. 1997 Mar 28;275(5308):1925-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉J. Sarnthein, Institut Romand de Recherche Numerique en Physique des Materiaux (IRRMA), IN-Ecublens, CH-1015 Lausanne, Switzerland. A. Pasquarello and R. Car, IRRMA, IN-Ecublens, CH-1015 Lausanne, Switzerland, and Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9072968" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1997-01-31
    Description: The uncatalyzed edge growth of carbon nanotubes was investigated by first-principles molecular dynamics simulations. At experimental temperatures the open end of single-walled nanotubes closed spontaneously into a graphitic dome, which may explain why these nanotubes do not grow in the absence of transition metal catalysts. On the other hand, chemical bonding between the edges of adjacent coaxial tubes ("lip-lip" interactions) trapped the end of a double-walled nanotube in a metastable energy minimum, thus preventing dome closure. These calculations show that this end geometry exhibits a high degree of chemical activity and easily accommodates incoming carbon fragments, supporting a model of growth by chemisorption from the vapor phase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Charlier -- De Vita A -- Blase -- Car -- New York, N.Y. -- Science. 1997 Jan 31;275(5300):646-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Romand de Recherche Numerique en Physique des Materiaux, Ecublens, CH-1015 Lausanne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9005846" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2002-03-30
    Description: Probing the lowest energy configuration of a complex system by quantum annealing was recently found to be more effective than its classical, thermal counterpart. By comparing classical and quantum Monte Carlo annealing protocols on the two-dimensional random Ising model (a prototype spin glass), we confirm the superiority of quantum annealing relative to classical annealing. We also propose a theory of quantum annealing based on a cascade of Landau-Zener tunneling events. For both classical and quantum annealing, the residual energy after annealing is inversely proportional to a power of the logarithm of the annealing time, but the quantum case has a larger power that makes it faster.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Santoro, Giuseppe E -- Martonak, Roman -- Tosatti, Erio -- Car, Roberto -- New York, N.Y. -- Science. 2002 Mar 29;295(5564):2427-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Scuola Internazionale Superiore di Studi Avanzati (SISSA) and Istituto Nazionale per la Fisica della Materia (INFM) (Unita di Ricerca SISSA), I-34014 Trieste, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11923532" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2014-06-20
    Description: Liquid water's isothermal compressibility and isobaric heat capacity, and the magnitude of its thermal expansion coefficient, increase sharply on cooling below the equilibrium freezing point. Many experimental, theoretical and computational studies have sought to understand the molecular origin and implications of this anomalous behaviour. Of the different theoretical scenarios put forward, one posits the existence of a first-order phase transition that involves two forms of liquid water and terminates at a critical point located at deeply supercooled conditions. Some experimental evidence is consistent with this hypothesis, but no definitive proof of a liquid-liquid transition in water has been obtained to date: rapid ice crystallization has so far prevented decisive measurements on deeply supercooled water, although this challenge has been overcome recently. Computer simulations are therefore crucial for exploring water's structure and behaviour in this regime, and have shown that some water models exhibit liquid-liquid transitions and others do not. However, recent work has argued that the liquid-liquid transition has been mistakenly interpreted, and is in fact a liquid-crystal transition in all atomistic models of water. Here we show, by studying the liquid-liquid transition in the ST2 model of water with the use of six advanced sampling methods to compute the free-energy surface, that two metastable liquid phases and a stable crystal phase exist at the same deeply supercooled thermodynamic condition, and that the transition between the two liquids satisfies the thermodynamic criteria of a first-order transition. We follow the rearrangement of water's coordination shell and topological ring structure along a thermodynamically reversible path from the low-density liquid to cubic ice. We also show that the system fluctuates freely between the two liquid phases rather than crystallizing. These findings provide unambiguous evidence for a liquid-liquid transition in the ST2 model of water, and point to the separation of time scales between crystallization and relaxation as being crucial for enabling it.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palmer, Jeremy C -- Martelli, Fausto -- Liu, Yang -- Car, Roberto -- Panagiotopoulos, Athanassios Z -- Debenedetti, Pablo G -- England -- Nature. 2014 Jun 19;510(7505):385-8. doi: 10.1038/nature13405.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA. ; Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA. ; 1] Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA [2] Air Products and Chemicals Inc., Allentown, Pennsylvania 18195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24943954" target="_blank"〉PubMed〈/a〉
    Keywords: *Models, Molecular ; Temperature ; Thermodynamics ; Water/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2016-03-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palmer, Jeremy C -- Martelli, Fausto -- Liu, Yang -- Car, Roberto -- Panagiotopoulos, Athanassios Z -- Debenedetti, Pablo G -- England -- Nature. 2016 Mar 10;531(7593):E2-3. doi: 10.1038/nature16540.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA. ; Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26961661" target="_blank"〉PubMed〈/a〉
    Keywords: *Models, Molecular ; Water/*chemistry
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
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