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The Athena++ adaptive mesh refinement framework: Design and magnetohydrodynamic solvers

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arXiv 2020年

作者： Stone, James M. Tomida, Kengo White, Christopher J. Felker, Kyle G. Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Earth and Space Science Osaka University Toyonaka Osaka560-0043 Japan Kavli Institute for Theoretical Physics University of California Santa Barbara Santa BarbaraCA93107 United States School of Natural Sciences Institute for Advanced Study PrincetonNJ08544 United States Astronomical Institute Tohoku University Sendai Miyagi980-8578 Japan Argonne National Laboratory LemontIL60439 United States

The design and implementation of a new framework for adaptive mesh refinement (AMR) calculations is described. It is intended primarily for applications in astrophysical fluid dynamics, but its flexible and modular design enables its use for a wide variety of physics. The framework works with both uniform and nonuniform grids in Cartesian and curvilinear coordinate systems. It adopts a dynamic execution model based on a simple design called a "task list" that improves parallel performance by overlapping communication and computation, simplifies the inclusion of a diverse range of physics, and even enables multiphysics models involving different physics in different regions of the calculation. We describe physics modules implemented in this framework for both non-relativistic and relativistic magnetohydrodynamics (MHD). These modules adopt mature and robust algorithms originally developed for the Athena MHD code and incorporate new extensions: support for curvilinear coordinates, higher-order time integrators, more realistic physics such as a general equation of state, and diffusion terms that can be integrated with super-time-stepping algorithms. The modules show excellent performance and scaling, with well over 80% parallel efficiency on over half a million threads. The source code has been made publicly available. Copyright © 2020, The Authors. All rights reserved.

关键词： Magnetohydrodynamics

Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

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Physical Review Letters 2018年第14期120卷 143001-143001页

作者： Linfeng Zhang Jiequn Han Han Wang Roberto Car Weinan E Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA and Center for Data Science Beijing International Center for Mathematical Research Peking University Beijing Institute of Big Data Research Beijing 100871 People’s Republic of China

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

关键词： Classical statistical mechanics Density functional theory First-principles calculations Interatomic & molecular potentials Learning Neuronal networks Potential energy surfaces Solid-state chemistry Thermal properties Van der Waals interaction Molecular dynamics

Retraction notice to "Hydrological and climate impacts on river characteristics of Pahang River Basin, Malaysia" [ Heliyon 9 2023 e21573]

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Heliyon 2025年第1期11卷 e41351页

作者： Mohd Khairul Amri Kamarudin Mohd Ekhwan Toriman Noorjima Abd Wahab Mohd Armi Abu Samah Khairul Nizam Abdul Maulud Firdaus Mohamad Hamzah Ahmad Shakir Mohd Saudi Sunardi Sunardi Faculty of Applied Social Science University Sultan Zainal Abidin Gong Badak Campus 21300 Terengganu Malaysia. East Coast Environmental Research Institute (ESERI) University Sultan Zainal Abidin Gong Badak Campus Nerus 21300 Kuala Malaysia. Faculty of Social Sciences and Humanities National University of Malaysia 43600 Bangi Selangor Malaysia. Kulliyyah of Science International Islamic University Malaysia 25200 Kuantan Pahang Malaysia. Earth Observation Center Institute of Climate Change National University of Malaysia 43600 Bangi Selangor Malaysia. Department of Mathematics Defense Base Center National Defence University of Malaysia Sungai Besi Camp 57000 Kuala Lumpur Malaysia. Department of Environmental Health Institute of Medical Science Technology Universiti Kuala Lumpur Kajang Selangor Malaysia. Graduate Program on Environmental Studies Postgraduate School Universitas Padjadjaran Jl. Dipati Ukur No. 35 Bandung 40132 Indonesia.

[This retracts the article DOI: 10.1016/***.2023.e21573.].

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DeePCG: Constructing coarse-grained models via deep neural networks

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arXiv 2018年

作者： Weinan, E. Zhang, Linfeng Han, Jiequn Wang, Han Car, Roberto Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China Caep Software Center for High Performance Numerical Simulation Huayuan Road 6 Beijing100088 China Program in Applied and Computational Mathematics Princeton Institute for Science and Technology of Materials Princeton University PrincetonNJ08544 United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Beijing Institute of Big Data Research Beijing100871 China

We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- A nd/or three-body contributions. The scheme, called Deep Coarse-Grained Potential (abbreviated DeePCG), exploits a carefully crafted neural network to construct a many-body coarse-grained potential. The network is trained with full atomistic data in a way that preserves the natural symmetries of the system. The resulting model is very accurate and can be used to sample the configurations of the coarse-grained variables in a much faster way than with the original atomistic model. As an application we consider liquid water and use the oxygen coordinates as the coarse-grained variables, starting from a full atomistic simulation of this system at the ab initio molecular dynamics level. We find that the two-body, three-body, and higher-order oxygen correlation functions produced by the coarse-grained and full atomistic models agree very well with each other, illustrating the effectiveness of the DeePCG model on a rather challenging task. Copyright © 2018, The Authors. All rights reserved.

关键词： Deep neural networks

KamLAND's search for correlated low-energy electron antineutrinos with astrophysical neutrinos from IceCube

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arXiv 2022年

作者： Abe, S. Asami, S. Eizuka, M. Futagi, S. Gando, A. Gando, Y. Gima, T. Goto, A. Hachiya, T. Hata, K. Hosokawa, K. Ichimura, K. Ieki, S. Ikeda, H. Inoue, K. Ishidoshiro, K. Kamei, Y. Kawada, N. Kishimoto, Y. Kinoshita, T. Koga, M. Kurasawa, M. Maemura, N. Mitsui, T. Miyake, H. Nakahata, T. Nakamura, K. Nakamura, K. Nakamura, R. Ozaki, H. Sakai, T. Sambonsugi, H. Shimizu, I. Shirai, J. Shiraishi, K. Suzuki, A. Suzuki, Y. Takeuchi, A. Tamae, K. Watanabe, H. Yoshida, Y. Obara, S. Ichikawa, A.K. Yoshida, S. Umehara, S. Fushimi, K. Kotera, K. Urano, Y. Berger, B.E. Fujikawa, B.K. Learned, J.G. Maricic, J. Axani, Spencer N. Smolsky, J. Lertprasertpong, J. Winslow, L.A. Fu, Z. Ouellet, J. Efremenko, Y. Karwowski, H.J. Markoff, D.M. Tornow, W. Li, A. Detwiler, J.A. Enomoto, S. Decowski, M.P. Grant, C. Song, H. O'Donnell, T. Dell'Oro, S. Research Center for Neutrino Science Tohoku University Sendai980-8578 Japan Frontier Research Institute for Interdisciplinary Sciences Tohoku University Sendai980-8578 Japan Graduate Program on Physics for the Universe Tohoku University Sendai980-8578 Japan Department of Physics Tohoku University Sendai980-8578 Japan Institute for the Physics and Mathematics of the Universe The University of Tokyo Kashiwa277-8568 Japan Graduate School of Science Osaka University Toyonaka560-0043 Japan Osaka University Osaka Ibaraki567-0047 Japan Graduate School of Advanced Technology and Science Tokushima University Tokushima770-8506 Japan Nuclear Science Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department of Physics and Astronomy University of Hawaii at Manoa HonoluluHI96822 United States Massachusetts Institute of Technology CambridgeMA02139 United States Boston University BostonMA02215 United States Department of Physics and Astronomy University of Tennessee KnoxvilleTN37996 United States Triangle Universities Nuclear Laboratory DurhamNC27708 United States The University of North Carolina at Chapel Hill Chapel HillNC27599 United States North Carolina Central University DurhamNC27701 United States Physics Department Duke University DurhamNC27705 United States Center for Experimental Nuclear Physics and Astrophysics University of Washington SeattleWA98195 United States Nikhef The University of Amsterdam Science Park Amsterdam Netherlands Center for Neutrino Physics Virginia Polytechnic Institute State University BlacksburgVA24061 United States

We report the results of a search for MeV-scale astrophysical neutrinos in KamLAND presented as an excess in the number of coincident neutrino interactions associated with the publicly available high-energy neutrino datasets from the IceCube Neutrino Observatory. We find no statistically significant excess in the number of observed low-energy electron antineutrinos in KamLAND, given a coincidence time window of ±500 s, ±1,000 s, ±3,600 s, and ±10,000 s around each of the IceCube neutrinos. We use this observation to present limits from 1.8 MeV to 100 MeV on the electron antineutrino fluence, assuming a mono-energetic flux. We then compare the results to several astrophysical measurements performed by IceCube and place a limit at the 90% confidence level on the electron antineutrino isotropic thermal luminosity from the TXS 0506+056 blazar. Copyright © 2022, The Authors. All rights reserved.

关键词： Electrons

Development of a do-it-yourself (D.I.Y.) gel electrophoresis apparatus for Grade-12 STEM general biology students

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Journal of Physics: Conference Series 2021年第1期1835卷

作者： Janne Noelle L. Gamale Dharel P. Acut Karla Marie Frances P. Niere Gwen Stephany S. Silagan Ethel P. Curaraton Guadalupe C. Latonio Rhett Anthony C. Latonio Joy R. Magsayo High School Department Sotero B. Cabahug FORUM for Literacy Consolacion Cebu 6001 Philippines Applied Physics Program National Institute of Physics College of Science University of the Philippines – Diliman Roxas Ave. Diliman Quezon City 1101 Philippines Science Education Program Graduate School College of Teacher Education Cebu Normal University Osmeña Blvd. Cebu City Cebu 6000 Philippines Department of Science and Mathematics Education College of Education Mindanao State University – Iligan Institute of Technology Iligan City 9200 Philippines

A hurdle to effective science education in schools is often the lack of teaching materials. Teaching science education in the 21st century requires direct visualization and manipulation with effective use and implementation for meaningful learning to occur, thus, unleashing students' potential towards the lesson, boosting their engagement in learning, and applying the knowledge into skills. This study was carried out to develop a do-it-yourself gel electrophoresis apparatus. This study was conducted in Cebu Normal University, Philippines with nineteen (19) teachers from the Methods of Teaching Science and Instructional Trends and Issues Class who evaluated the apparatus in terms of usability and functionality. The respondents tested the Gel Electrophoresis apparatus by conducting the experiment and they evaluated the apparatus' functionality and usability by using an evaluation sheet which is composed of eleven (11) usability questions, four (4) functionality questions. Suggestions were also asked to improve the said apparatus. After gathering data, the suggestions made by the respondents were incorporated which resulted to the improved D.I.Y. Gel Electrophoresis Apparatus. A manual with the procedures was also designed to further guide students and teachers on how to build the apparatus. With the findings and results obtained in the study, the respondents recommended the usage of the developed do-it-yourself gel electrophoresis apparatus in their respective classes and agreed that it is a good source of learning the concept of gel electrophoresis as a 21st century biological technique. The apparatus was easy to set-up and is of low-cost. During experimentation, the apparatus yielded with a positive result – the separation of food dyes which follows the principle of gel electrophoresis. Moreover, the experiment encourages creativity and it helps with the understanding of the nature of DNA and the concept of gel electrophoresis as a 21st century biological skills.

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Homogenization for Generalized Langevin Equations with Applications to Anomalous Diffusion

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arXiv 2019年

作者： Lim, Soon Hoe Wehr, Jan Lewenstein, Maciej Nordita KTH Royal Institute of Technology Stockholm University Roslagstullsbacken 23 StockholmSE-106 91 Sweden Department of Mathematics Program in Applied Mathematics University of Arizona TucsonAZ85721-0089 United States ICFO - Institut de Ciéncies Fotóniques Barcelona Institute of Science and Technology Av. Carl Friedrich Gauss 3 Castelldefels [Barcelona08860 Spain ICREA Pg. Lluis Companys 23 Barcelona08010 Spain

We study homogenization for a class of generalized Langevin equations (GLEs) with state-dependent coefficients and exhibiting multiple time scales. In addition to the small mass limit, we focus on homogenization limits, which involve taking to zero the inertial time scale and, possibly, some of the memory time scales and noise correlation time scales. The latter are meaningful limits for a class of GLEs modeling anomalous diffusion. We find that, in general, the limiting stochastic differential equations (SDEs) for the slow degrees of freedom contain non-trivial drift correction terms and are driven by non-Markov noise processes. These results follow from a general homogenization theorem stated and proven here. We illustrate them using stochastic models of particle diffusion. Copyright © 2019, The Authors. All rights reserved.

关键词： Time measurement

WITHDRAWN: Environmental dimensionality determines species coexistence

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Journal of Theoretical Biology 2021年 526卷

作者： Kalle Parvinen Johan A.J. Metz Ulf Dieckmann Department of Mathematics and Statistics University of Turku FI-20014 Finland Evolution and Ecology Program International Institute for Applied Systems Analysis (IIASA) Laxenburg A-2361 Austria Institute of Biology and Mathematical Institute Leiden University NL-2333BE the Netherlands Netherlands Centre for Biodiversity Naturalis Leiden NL-2333CR the Netherlands Department of Evolutionary Studies of Biosystems The Graduate University for Advanced Studies (Sokendai) Hayama Kanagawa 240-0193 Japan

This article has been withdrawn: please see Elsevier Policy on Article Withdrawal ( http://***/locate/withdrawalpolicy ). This article has been withdrawn at the request of the editor and publisher. The publisher regrets that an error occurred which led to the premature publication of this paper. This error bears no reflection on the article or its authors. The publisher apologizes to the authors and the readers for this unfortunate error.

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Metadata for the Flux Density Calibration of the April 2018 Event Horizon Telescope Data

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arXiv 2023年

作者： Koay, J.Y. Romero-Cañizales, C. Matthews, L.D. Janssen, M. Blackburn, L. Tilanus, R.P.J. Park, J. Asada, K. Matsushita, S. Baczko, A.-K. Bella, N. La Chan, C.-K. Crew, G.B. Fish, V. Patel, N. Ramakrishnan, V. Rottmann, H. Wagner, J. Wiik, K. Friberg, P. Goddi, C. Issaoun, S. Keating, G. Kim, J. Krichbaum, T.P. Marrone, D. Narayanan, G. Roy, A. Ruíz, I. Sánchez, S. Torne, P. Weintroub, J. Academia Sinica Institute of Astronomy and Astrophysics No.1 Sec. 4 Roosevelt Rd Taipei10617 Taiwan Massachusetts Institute of Technology Haystack Observatory 99 Millstone Road WestfordMA01886 United States Auf dem Hügel 69 Bonn53121 Germany Center for Astrophysics Harvard & Smithsonian 60 Garden St. CambridgeMA02138 United States Black Hole Initiative Harvard University 20 Garden Street CambridgeMA02138 United States Steward Observatory Department of Astronomy University of Arizona 933 N. Cherry Avenue TucsonAZ85721 United States Department of Astronomy and Space Science Kyung Hee University 1732 Deogyeong-daero Giheung-gu Gyeonggi-do Yongin-si17104 Korea Republic of Department of Astrophysics IMAPP Radboud University P.O. Box 9010 Nijmegen6500 GL Netherlands Data Science Institute University of Arizona 1230 N. Cherry Ave. TucsonAZ85721 United States Program in Applied Mathematics University of Arizona 617 N. Santa Rita TucsonAZ85721 United States Finnish Centre for Astronomy with ESO University of Turku FI-20014 Finland Aalto University Metsähovi Radio Observatory Metsähovintie 114 KylmäläFI-02540 Finland Tuorla Observatory Department of Physics and Astronomy University of Turku Finland East Asian Observatory 660 N. A’ohoku Place HiloHI96720 United States INAF - Osservatorio Astronomico di Cagliari Via della Scienza 5 CA Selargius09047 Italy California Institute of Technology 1200 East California Boulevard PasadenaCA91125 United States Department of Astronomy University of Massachusetts AmherstMA01003 United States Institut de Radioastronomie Millimétrique Avenida Divina Pastora 7 Local 20 GranadaE-18012 Spain

The Event Horizon Telescope (EHT) observations carried out in 2018 April at 1.3 mm wavelengths included 9 stations in the array, comprising 7 single-dish telescopes and 2 phased arrays. The metadata package for the 2018 EHT observing campaign contains calibration tables required for the a-priori amplitude calibration of the 2018 April visibility data. This memo is the official documentation accompanying the release of the 2018 EHT metadata package, providing an overview of the contents of the package. We describe how telescope sensitivities, gain curves and other relevant parameters for each station in the EHT array were collected, processed, and validated to produce the calibration tables. Copyright © 2023, The Authors. All rights reserved.

关键词： Telescopes