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37th International Cosmic Ray Conference, ICRC 2021

作者： Saito, T. Delgado, C. Blanch, O. Artero, M. Barrio, J.A. Cassol, F. Diaz, C. Hadasch, D. Hoffmann, D. Houles, J. Inome, Y. Iori, M. Jouvin, L. Kerszberg, D. Kobayashi, Y. Kubo, H. Martinez, G. Mazin, D. Moretti, E. Nakamori, T. Nozaki, S. Oka, T. Okumura, A. Palatiello, M. Polo, M. Prast, J. Sakurai, S. Sunada, Y. Takahashi, M. Takeishi, R. Tejedor, L.A. Yamamoto, T. Yoshida, T. Abe, H. Aguasca, A. Agudo, I. Antonelli, L.A. Aramo, C. Armstrong, T. Asano, K. Ashkar, H. Aubert, P. Baktash, A. Bamba, A. Baquero Larriva, A. Baroncelli, L. Barres de Almeida, U. Batkovic, I. Becerra González, J. Bernardos, M.I. Berti, A. Biederbeck, N. Bigongiari, C. Bonnoli, G. Bordas, P. Bose, D. Bulgarelli, A. Burelli, I. Buscemi, M. Cardillo, M. Caroff, S. Carosi, A. Cerruti, M. Chai, Y. Cheng, K. Chikawa, M. Chytka, L. Contreras, J.L. Cortina, J. Costantini, H. Dalchenko, M. De Angelis, A. de Bony de Lavergne, M. Deleglise, G. Delgado Mengual, J. della Volpe, D. Depaoli, D. Di Pierro, F. Di Venere, L. Dominik, R.M. Dominis Prester, D. Donini, A. Dorner, D. Doro, M. Elsässer, D. Emery, G. Escudero, J. Fiasson, A. Foffano, L. Fonseca, M.V. Freixas Coromina, L. Fukami, S. Fukazawa, Y. Garcia, E. Garcia López, R. Giglietto, N. Giordano, F. Gliwny, P. Godinovic, N. Green, D. Grespan, P. Gunji, S. Hackfeld, J. Hahn, A. Hassan, T. Hayashi, K. Heckmann, L. Heller, M. Herrera Llorente, J. Hirotani, K. Horns, D. Hrabovsky, M. Hrupec, D. Hui, D. Hütten, M. Inada, T. Ishio, K. Iwamura, Y. Jacquemont, M. Jimenez Martinez, I. Jurysek, J. Kagaya, M. Karas, V. Katagiri, H. Kataoka, J. Kong, A. Kushida, J. Lamanna, G. Lamastra, A. Le Flour, T. Longo, F. López-Coto, R. López-Moya, M. López-Oramas, A. Luque-Escamilla, P.L. Majumdar, P. Makariev, M. Mandat, D. Manganaro, M. Mannheim, K. Mariotti, M. Marquez, P. Marsella, G. Martí, J. Martinez, O. Martínez, M. Marusevec, P. Mas, A. Maurin, G. Mestre Guillen, E. Micanovic, S. Miceli, D. Miener, T. Miranda, J.M. ICRR Institute for Cosmic Ray Research University of Tokyo 5-1-5 Kashiwa-no-ha Chiba Kashiwa277-8582 Japan CIEMAT Avda. Complutense 40 Madrid28040 Spain The Barcelona Institute of Science and Technology Bellaterra Campus UAB Barcelona08193 Spain EMFTEL Department IPARCOS Universidad Complutense de Madrid Madrid28040 Spain Aix-Marseille Université CNRS IN2P3 CPPM 163 Avenue de Luminy MarseilleCedex 09 13288 France INFN Sezione di Roma La Sapienza P.le Aldo Moro 2 Roma00185 Italy Division of Physics and Astronomy Graduate School of Science Kyoto University Sakyo-ku Kyoto606-8502 Japan Department of Physics Yamagata University Yamagata990-8560 Japan ISEE Nagoya University Chikusa-ku Nagoya464-8602 Japan Graduate School of Science and Engineering Saitama University 255 Simo-Ohkubo Sakura-ku Saitama338-8570 Japan CNRS Laboratoire d'Annecy de Physique des Particules IN2P3 Univ. Grenoble Alpes Univ. Savoie Mont Blanc Annecy74000 France Department of Physics Konan University Hyogo Kobe658-8501 Japan Faculty of Science Ibaraki University Ibaraki Mito310-8512 Japan Departament de Física Quàntica i Astrofísica Institut de Ciències del Cosmos Universitat de Barcelona IEEC-UB Spain Instituto de Astrofísica de Andalucía CSIC Spain INAF - Osservatorio Astronomico di Roma Italy INFN Sezione di Napoli Italy IRFU CEA Université Paris-Saclay France Universität Hamburg Institut für Experimentalphysik Germany Graduate School of Science University of Tokyo Japan INAF - Osservatorio di Astrofisica e Scienza dello Spazio di Bologna Italy Centro Brasileiro de Pesquisas Físicas Brazil INFN Sezione di Padova Università degli Studi di Padova Italy Instituto de Astrofísica de Canarias Departamento de Astrofísica Universidad de La Laguna Spain Max-Planck-Institut für Physik Germany Department of Physics TU Dortmund University Germany Saha Institute of Nuclear Physics India INFN Sezione di Trieste Università degli Studi di Udine Italy INFN Sezio

The first Large Size Telescope (LST-1) of the Cherenkov Telescope Array has been operational since October 2018 at La Palma, Spain. We report on the results obtained during the camera commissioning. The noise level of the readout is determined as a 0.2 p.e. level. The gain of PMTs are well equalized within 2% variation, using the calibration flash system. The effect of the night sky background on the signal readout noise as well as the PMT gain estimation are also well evaluated. Trigger thresholds are optimized for the lowest possible gamma-ray energy threshold and the trigger distribution synchronization has been achieved within 1 ns precision. Automatic rate control realizes the stable observation with 1.5% rate variation over 3 hours. The performance of the novel DAQ system demonstrates a less than 10% dead time for 15 kHz trigger rate even with sophisticated online data correction. © 2022 Sissa Medialab Srl. All rights reserved.

关键词： Cameras

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Current md forcefields fail to capture key features of protein structure and fluctuations: a case study of cyclophilin a and t4 lysozyme

arXiv

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arXiv 2020年

作者： Mei, Zhe Grigas, Alex T. Treado, John D. Corres, Gabriel Melendez Vuorte, Maisa Sammalkorpi, Maria Regan, Lynne Levine, Zachary A. O’Hern, Corey S. Department of Chemistry Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Biology UPR Humacao Puerto RicoHumacao00792 Puerto Rico Department of Chemistry and Materials Science School of Chemical Engineering Aalto University Aalto Finland Department of Bioproducts and Biosystems School of Chemical Engineering Aalto University Aalto Finland Institute of Quantitative Biology Biochemistry and Biotechnology Center for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Edinburgh United Kingdom Department of Pathology Yale School of Medicine New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways when they are solved by x-ray crystallography versus solution-based NMR spectroscopy. Given these discrepancies, it is unclear whether molecular dynamics (MD) simulations can accurately recapitulate protein conformations. We therefore perform extensive MD simulations across multiple force fields and sampling techniques to investigate the degree to which computer simulations can capture the ensemble of conformations observed in experiments. By analyzing fluctuations in the atomic coordinates and core packing, we show that conformations sampled in MD simulations both move away from and sample a larger conformational space than the ensemble of structures observed in NMR experiments. However, we find that adding inter-residue distance restraints that match those obtained via Nuclear Overhauser Effect measurements enables the MD simulations to sample more NMR-like conformations, though significant differences between the core packing features in restrained MD and the NMR ensemble remain. Given that the protein structures obtained from the MD simulations possess smaller and less dense protein cores compared to those solved by NMR, we suggest that future improvements to MD forcefields should aim to increase the packing of hydrophobic residues in protein cores. © 2020, CC BY.

关键词： Molecular dynamics

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Void distributions reveal structural link between jammed packings and protein cores

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physical Review E 2019年第2期99卷 022416-022416页

作者： John D. Treado Zhe Mei Lynne Regan Corey S. O'Hern Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical & Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Chemistry Yale University New Haven Connecticut 06520 USA Department of Molecular Biophysics & Biochemistry Yale University New Haven Connecticut 06520 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packing of amino-acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino-acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. We measure the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation. We find that the cluster size statistics are similar for void percolation in packings of amino-acid-shaped particles and randomly placed spheres, but different from that for void percolation in jammed sphere packings. We propose that the connected void regions are a defining structural feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino-acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations.

关键词： Jamming Protein structure Packing & jamming problems Proteins Crystal structures Finite-size scaling Molecular dynamics Percolation theory

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Physics Performance of the Large-Sized Telescope prototype of the Cherenkov Telescope Array 37

Physics Performance of the Large-Sized Telescope prototype o...

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37th International Cosmic Ray Conference, ICRC 2021

作者： Abe, H. Aguasca, A. Agudo, I. Antonelli, L.A. Aramo, C. Armstrong, T. Artero, M. Asano, K. Ashkar, H. Aubert, P. Baktash, A. Bamba, A. Baquero Larriva, A. Baroncelli, L. Barres de Almeida, U. Barrio, J.A. Batkovic, I. Becerra González, J. Bernardos, M.I. Berti, A. Biederbeck, N. Bigongiari, C. Blanch, O. Bonnoli, G. Bordas, P. Bose, D. Bulgarelli, A. Burelli, I. Buscemi, M. Cardillo, M. Caroff, S. Carosi, A. Cassol, F. Cerruti, M. Chai, Y. Cheng, K. Chikawa, M. Chytka, L. Contreras, J.L. Cortina, J. Costantini, H. Dalchenko, M. De Angelis, A. de Bony de Lavergne, M. Deleglise, G. Delgado, C. Delgado Mengual, J. della Volpe, D. Depaoli, D. Di Pierro, F. Di Venere, L. Díaz, C. Dominik, R.M. Dominis Prester, D. Donini, A. Dorner, D. Doro, M. Elsässer, D. Emery, G. Escudero, J. Fiasson, A. Foffano, L. Fonseca, M.V. Freixas Coromina, L. Fukami, S. Fukazawa, Y. Garcia, E. Garcia López, R. Giglietto, N. Giordano, F. Gliwny, P. Godinovic, N. Green, D. Grespan, P. Gunji, S. Hackfeld, J. Hadasch, D. Hahn, A. Hassan, T. Hayashi, K. Heckmann, L. Heller, M. Herrera Llorente, J. Hirotani, K. Hoffmann, D. Horns, D. Houles, J. Hrabovsky, M. Hrupec, D. Hui, D. Hütten, M. Inada, T. Inome, Y. Iori, M. Ishio, K. Iwamura, Y. Jacquemont, M. Jimenez Martinez, I. Jouvin, L. Jurysek, J. Kagaya, M. Karas, V. Katagiri, H. Kataoka, J. Kerszberg, D. Kobayashi, Y. Kong, A. Kubo, H. Kushida, J. Lamanna, G. Lamastra, A. Le Flour, T. Longo, F. López-Coto, R. López-Moya, M. López-Oramas, A. Luque-Escamilla, P.L. Majumdar, P. Makariev, M. Mandat, D. Manganaro, M. Mannheim, K. Mariotti, M. Marquez, P. Marsella, G. Martí, J. Martinez, O. Martínez, G. Martínez, M. Marusevec, P. Mas, A. Maurin, G. Mazin, D. Mestre Guillen, E. Micanovic, S. Miceli, D. Miener, T. Miranda, J.M. Miranda, L.D.M. Mirzoyan, R. Mizuno, T. Molina, E. Montaruli, T. Monteiro, I. Moralejo, A. Morcuende, D. Moretti, E. Morselli, A. Mrakovcic, K. Murase, K. Nagai, A. Nakamori, T. Nickel, L. Nieto, D. Institute for Cosmic Ray Research University of Tokyo 5-1-5 Kashiwa-no-ha Kashiwa Chiba277-8582 Japan Departament de Física Quàntica i Astrofísica Institut de Ciències del Cosmos Universitat de Barcelona IEEC-UB Spain Instituto de Astrofísica de Andalucía-CSIC Granada18080 Spain INAF Osservatorio Astronomico di Roma Italy INFN Sezione di Napoli Italy Aix Marseille Univ CNRS IN2P3 CPPM France 08193 Spain IRFU CEA Université Paris-Saclay France LAPP Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS-IN2P3 9 Chemin de Bellevue - BP 110 AnnecyCedex 74941 France Universität Hamburg Institut für Experimentalphysik Germany Graduate School of Science University of Tokyo Japan EMFTEL Department IPARCOS Universidad Complutense de Madrid MadridE-28040 Spain INAF Osservatorio di Astrofisica e Scienza Spazio di Bologna Italy Centro Brasileiro de Pesquisas Físicas Brazil INFN Sezione di Padova PadovaI-35131 Italy Università degli Studi di Padova Via Marzolo 8 Padova35131 Italy Instituto de Astrofísica de Canarias Departamento de Astrofísica Universidad de La Laguna Spain Max-Planck-Institut für Physik München80805 Germany Department of Physics TU Dortmund University Otto-Hahn-Str. 4 Dortmund44221 Germany Saha Institute of Nuclear Physics INFN Sezione di Trieste Università degli Studi di Udine Italy INFN Sezione di Catania Italy Italy University of Geneva Département de Physique Nucléaire et Corpusculaire Switzerland Palacky University Olomouc Faculty of Science Czech Republic CIEMAT Port d'Informació Científica Spain INFN Sezione di Torino via P. Giuria 1 Torino10125 Italy Dipartimento di Fisica Universitá degli Studi di Torino Italy INFN Sezione di Bari Università di Bari Italy University of Rijeka Department of Physics Croatia Institute for Theoretical Physics and Astrophysics Universität Würzburg Germany Physics Program Graduate School of Advanced Science and Engineering Hiroshima University Japan INFN Sezione di Bari Politecnico di B

The Large-Sized Telescope (LST) prototype of the future Cherenkov Telescope Array (CTA) is located at the Northern site of CTA, on the Canary Island of La Palma. It is designed to provide optimal performance in the lowest part of the energy range covered by CTA, observing gamma rays down to energies of tens of GeV. The LST prototype started performing astronomical observations in November 2019 during the commissioning of the telescope and it has been taking data since then. In this contribution, we will present the tuning of the characteristics of the telescope in the Monte Carlo (MC) simulations to describe the data obtained, the estimation of its angular and energy resolution, and an evaluation of its sensitivity, both with simulations and with observations of the Crab Nebula. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND 4.0)

关键词： Telescopes

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Revealing the Side-Chain-Dependent Ordering Transition of Highly Crystalline Double-Cable Conjugated Polymers

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Angewandte Chemie 2021年第48期133卷

作者： Guitao Feng Wenliang Tan Safakath Karuthedath Cheng Li Xuechen Jiao Amelia C. Y. Liu Hariprasad Venugopal Zheng Tang Long Ye Frédéric Laquai Christopher R. McNeill Weiwei Li Beijing Advanced Innovation Center for Soft Matter Science and Engineering & State Key Laboratory of Organic-Inorganic Composites Beijing University of Chemical Technology Beijing 100029 China Beijing National Laboratory for Molecular Sciences Key Laboratory of Organic Solids Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China Department of Materials Science and Engineering Monash University Wellington Road Clayton Victoria 3800 Australia King Abdullah University of Science and Technology (KAUST) KAUST Solar Center (KSC) Physical Sciences and Engineering Division (PSE) Material Science and Engineering Program (MSE) Thuwal 23955-6900 Kingdom of Saudi Arabia School of Physics and Astronomy Monash University Wellington Road Clayton Victoria 3800 Australia Ramaciotti Centre for Cryo-Electron Microscopy Monash University Clayton Victoria 3800 Australia Center for Advanced Low-dimension Materials College of Materials Science and Engineering Donghua University Shanghai 201620 P. R. China School of Materials Science and Engineering Tianjin Key Laboratory of Molecular Optoelectronic Science Tianjin University Tianjin 300350 P. R. China

We developed a series of highly crystalline double-cable conjugated polymers for application in single-component organic solar cells (SCOSCs). These polymers contain conjugated backbones as electron donor and pendant perylene bisimide units (PBIs) as electron acceptor. PBIs are connected to the backbone via alkyl units varying from hexyl (C 6 H 12 ) to eicosyl (C 20 H 40 ) as flexible linkers. For double-cable polymers with short linkers, the PBIs tend to stack in a head-to-head fashion, resulting in large d -spacings (e.g. 64 Å for the polymer P12 with C 12 H 24 linker) along the lamellar stacking direction. When the length of the linker groups is longer than a certain length, the PBIs instead adopt a more ordered packing likely via H -aggregation, resulting in short d -spacings (e.g. 50 Å for the polymer P16 with C 16 H 32 linker). This work highlights the importance of linker length on the molecular packing of the acceptor units and the influences on the photovoltaic performance of SCOSCs.

关键词： cryo-transmission electron microscopy double-cable conjugated polymers lamellar stacking single-component organic solar cells

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Numerical convergence of discrete exterior calculus on arbitrary surface meshes

arXiv

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arXiv 2018年

作者： Mohameda, Mamdouh S. Hiranib, Anil N. Samtaneya, Ravi Mechanical Engineering Physical Science and Engineering Division King Abdullah University Science and Technology Thuwal Saudi Arabia Department of Mathematics University of Illinois Urbana-ChampaignIL United States Department Mechanical Design Production Faculty of Engineering Cairo University Giza Egypt

Discrete exterior calculus (DEC) is a structure-preserving numerical framework for partial differential equations solution, particularly suitable for simplicial meshes. A longstanding and widespread assumption has been that DEC requires special (Delaunay) triangulations, which complicated the mesh generation process especially on curved surfaces. This paper presents numerical evidences demonstrating that this restriction is unnecessary. Convergence experiments are carried out for various physical problems using both Delaunay and non- Delaunay triangulations. Signed diagonal definition for the key DEC operator (Hodge star) is adopted. The errors converge as expected for all considered meshes and experiments. This relieves the DEC paradigm from unnecessary triangulation limitation. Copyright © 2018, arXiv, All rights reserved.

关键词： Poisson equation

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Mach number effect on the instability of a planar interface subjected to a rippled shock

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physical Review E 2018年第4期98卷 043105-043105页

作者： Wenbin Zhang Qiang Wu Liyong Zou Xianxu Zheng Xinzhu Li Xisheng Luo Juchun Ding Laboratory for Shock Wave and Detonation Physics Institute of Fluid Physics China Academy of Engineering Physics Mianyang Sichuan 621900 China Mechanical Engineering Physical Science and Engineering Division King Abdullah University of Science and Technology Thuwal 23955-6900 Saudi Arabia Advanced Propulsion Laboratory Department of Modern Mechanics University of Science and Technology of China Hefei 230026 China

The Richtmyer-Meshkov (RM) instability of a planar interface (N2−SF6) subjected to a sinusoidal rippled shock, as the variant of a sinusoidal interface impinged by a planar shock, is investigated through high-order compressible multicomponent hydrodynamic simulations. The rippled shock is generated by a planar shock penetrating through a single-mode interface (He−N2), and its propagation characteristic agrees reasonably with Bates' analytical solution. Evolution of the flat contact surface impacted by the rippled shock is found to be heavily dependent on the rippled shock phase, and it can be well explained by the impulsive perturbation and continuous perturbation regimes. Various rippled shocks with different Mach numbers ranging from 1.15 to 1.80 are considered. It is found that the influence of the shock strength on the instability growth behaves differently for rippled shocks at different phases. In the case that the shock-interface collision happens when the rippled shock amplitude vanishes for the first time, as the shock strength increases, the impulsive perturbation (i.e., amplitude growth caused by the impulsive shock impact) plays an increasingly more important role in the instability growth than the continuous perturbation (i.e., amplitude growth induced by the disturbed postshock pressure field). In contrast, in the case that the impingement occurs when the rippled shock amplitude becomes zero for the second time, the instability development contributed by the impulsive perturbation is a certain percentage of the total instability growth regardless of the shock strength. The role of the impulsive perturbation in the present nonstandard RM instability within the single-mode framework can be reasonably predicted by an empirical formula combined with the model of Ishizaki et al. [Phys. Rev. E 53, R5592 (1996)].

关键词： Flow instability Interfacial flows

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Quantum Simulation for High-Energy Physics

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PRX Quantum 2023年第2期4卷 027001-027001页

作者： Christian W. Bauer Zohreh Davoudi A. Baha Balantekin Tanmoy Bhattacharya Marcela Carena Wibe A. de Jong Patrick Draper Aida El-Khadra Nate Gemelke Masanori Hanada Dmitri Kharzeev Henry Lamm Ying-Ying Li Junyu Liu Mikhail Lukin Yannick Meurice Christopher Monroe Benjamin Nachman Guido Pagano John Preskill Enrico Rinaldi Alessandro Roggero David I. Santiago Martin J. Savage Irfan Siddiqi George Siopsis David Van Zanten Nathan Wiebe Yukari Yamauchi Kübra Yeter-Aydeniz Silvia Zorzetti Physics Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Department of Physics Maryland Center for Fundamental Physics and the NSF Institute for Robust Quantum Simulation University of Maryland College Park Maryland 20742 USA Department of Physics University of Wisconsin Madison Wisconsin 53706 USA T-2 Los Alamos National Laboratory Los Alamos New Mexico 87545 USA Fermi National Accelerator Laboratory Batavia Illinois 60510 USA Enrico Fermi Institute University of Chicago Chicago Illinois 60637 USA Kavli Institute for Cosmological Physics University of Chicago Chicago Illinois 60637 USA Department of Physics University of Chicago Chicago Illinois 60637 USA Department of Physics and Illinois Center for the Advanced Study of the Universe and Illinois Quantum Information Science and Technology Center University of Illinois Urbana Illinois 61801 USA QuEra Computing Inc Boston Massachusetts 02135 USA Department of Mathematics University of Surrey Guildford Surrey GU2 7XH United Kingdom Center for Nuclear Theory Department of Physics and Astronomy Stony Brook University New York 11794-3800 USA Department of Physics Brookhaven National Laboratory Upton New York 11973 USA Peng Huanwu Center for Fundamental Theory Hefei Anhui 230026 China Interdisciplinary Center for Theoretical Study University of Science and Technology of China Hefei Anhui 230026 China Pritzker School of Molecular Engineering Chicago Quantum Exchange and Kadanoff Center for Theoretical Physics University of Chicago Illinois 60637 USA qBraid Co. Harper Court 5235 Chicago Illinois 60615 USA Department of Physics Harvard University Cambridge Massachusetts 02138 USA Department of Physics and Astronomy University of Iowa Iowa City Iowa 52242 USA Duke Quantum Center Duke University Durham North Carolina 27701 USA Department of Electrical and Computer Engineering Duke University Durham North Carolina 27708 USA Department of Physics Duke University

It is for the first time that quantum simulation for high-energy physics (HEP) is studied in the U.S. decadal particle-physics community planning, and in fact until recently, this was not considered a mainstream topic in the community. This fact speaks of a remarkable rate of growth of this subfield over the past few years, stimulated by the impressive advancements in quantum information sciences (QIS) and associated technologies over the past decade, and the significant investment in this area by the government and private sectors in the U.S. and other countries. High-energy physicists have quickly identified problems of importance to our understanding of nature at the most fundamental level, from tiniest distances to cosmological extents, that are intractable with classical computers but may benefit from quantum advantage. They have initiated, and continue to carry out, a vigorous program in theory, algorithm, and hardware co-design for simulations of relevance to the HEP mission. This Roadmap is an attempt to bring this exciting and yet challenging area of research to the spotlight, and to elaborate on what the promises, requirements, challenges, and potential solutions are over the next decade and beyond.

关键词： Quantum simulation

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Using physical features of protein core packing to distinguish real proteins from decoys

arXiv

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arXiv 2020年

作者： Grigas, Alex T. Mei, Zhe Treado, John D. Levine, Zachary A. Regan, Lynne O'Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Pathology Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Institute of Quantitative Biology Biochemistry and Biotechnology Centre for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute signifficantly to their stability. As a dataset of decoys to compare with real protein structures, we studied submissions to the bi-annual CASP competition (speciffically CASP11, 12, and 13), in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence. Our analysis reveals that many of the submissions possess cores that do not recapitulate the features that define real proteins. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a deep learning method, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoys from the CASP competitions equally well, if not better than, state-of-the-art methods that incorporate many additional features. Copyright © 2020, The Authors. All rights reserved.

关键词： Proteins

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Universal research index: An inclusive metric to quantify scientific research output

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Journal of Academic Librarianship 2023年第3期49卷

作者： Keshavarz-Fathi, Mahsa Yazdanpanah, Niloufar Kolahchi, Sajad Ziaei, Heliya Darmstadt, Gary L. Dorigo, Tommaso Dochy, Filip Levin, Lisa Thongboonkerd, Visith Ogino, Shuji Chen, Wei-Hsin Perc, Matjaz Tremblay, Mark S. Olusanya, Bolajoko O. Rao, Idupulapati M. Hatziargyriou, Nikos Moradi-Lakeh, Maziar Bella, Federico Rosivall, Laszlo Gandomi, Amir H. Sorooshian, Armin Gupta, Manoj Gal, Ciprian Lozano, Andres M. Weaver, Connie Tanzer, Michael Poggi, Alessandro Sepanlou, Sadaf G. Weiskirchen, Ralf Jambrak, Anet Režek Torres, Pedro J. Capanoglu, Esra Barba, Francisco J. Ernest, Chua Kian Jon Sigman, Mariano Pluchino, Stefano Gharehpetian, Gevork B. Fereshtehnejad, Seyed-Mohammad Yang, Muh-Hwa Thomas, Sabu Cai, Wenju Comini, Elisabetta Scolding, Neil J. Myles, Paul S. Nieto, Juan J. Perry, George Sedikides, Constantine Rezaei, Nima School of Medicine Tehran University of Medical Sciences Tehran Iran Universal Scientific Education and Research Network (USERN) Iran Department of Pediatrics Stanford University School of Medicine Stanford CA United States Istituto Nazionale di Fisica Nucleare (INFN) Via Francesco Marzolo Sezione di Padova Italy High Impact Learning Academy Learning and Development Department Brussels Belgium Center for Marine Biodiversity and Conservation Integrative Oceanography Division Scripps Institution of Oceanography University of California San Diego San Diego CA United States Medical Proteomics Unit Office for Research and Development Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand Department of Epidemiology Harvard T.H. Chan School of Public Health Boston MA United States Program in MPE Molecular Pathological Epidemiology Department of Pathology Brigham and Women's Hospital and Harvard Medical School Boston MA United States Broad Institute of MIT and Harvard Cambridge MA United States Department of Aeronautics and Astronautics National Cheng Kung University Tainan Taiwan Research Center for Smart Sustainable Circular Economy Tunghai University Taichung 407 Taiwan Department of Mechanical Engineering National Chin-Yi University of Technology Taichung 411 Taiwan Faculty of Natural Sciences and Mathematics University of Maribor Maribor Slovenia Department of Medical Research China Medical University Hospital China Medical University Taichung Taiwan Complexity Science Hub Vienna Vienna Austria Alma Mater Europaea Maribor Slovenia Children's Hospital of Eastern Ontario Research Institute Department of Pediatrics University of Ottawa Ottawa ON Canada Centre for Healthy Start Initiative Ikoyi Lagos Nigeria Alliance of Bioversity International International Center for Tropical Agriculture Cali Colombia International Centre of Insect Physiology and Ecology (ICIPE) Nairobi Kenya School of Electrical and Computer Engineering Natio

Scientometrics and bibliometrics, the subfields of library and information science, deal with the quantity and quality of research outputs. Currently, various scientometric indices are being used to quantify and compare research outputs. The most widely known is the h-index. However, this index and its derivatives suffer from dependence on the mere count of a scholar's highly cited publications. To remedy this deficiency, we developed a novel index, the Universal Research Index (UR-Index) (https://***/UR-Index/) by which every single publication has its own impact on the total score. We developed this index by surveying international top 1 % cited scientists in various disciplines and included additional component variables such as publication type, leading role of a scholar, co-author count, and source metrics to this scientometric index. We acknowledge that unconscious biases built into the component variables included in the UR-Index might put research from specific groups at a disadvantage, thus continued efforts to improve equitable scholarly impact in science and academia are encouraged. © 2023 Elsevier Inc.

关键词： Citations CiteScore h-index Impact factor Leading author Research impact Scholarly impact Scholarly output Scientometrics UR-Index USERN

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