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arXiv 2024年

作者： Evans, Matthew L. Bergsma, Johan Merkys, Andrius Andersen, Casper W. Andersson, Oskar B. Beltrán, Daniel Blokhin, Evgeny Boland, Tara M. Balderas, Rubén Castañeda Choudhary, Kamal Díaz, Alberto Díaz García, Rodrigo Domínguez Eckert, Hagen Eimre, Kristjan Montero, María Elena Fuentes Krajewski, Adam M. Mortensen, Jens Jørgen Duarte, José Manuel Nápoles Pietryga, Jacob Qi, Ji de Jesús Trejo Carrillo, Felipe Vaitkus, Antanas Yu, Jusong Zettel, Adam de Castro, Pedro Baptista Carlsson, Johan Cerqueira, Tiago F.T. Divilov, Simon Hajiyani, Hamidreza Hanke, Felix Jose, Kevin Oses, Corey Riebesell, Janosh Schmidt, Jonathan Winston, Donald Xie, Christen Yang, Xiaoyu Bonella, Sara Botti, Silvana Curtarolo, Stefano Draxl, Claudia Cobas, Luis Edmundo Fuentes Hospital, Adam Liu, Zi-Kui Marques, Miguel A.L. Marzari, Nicola Morris, Andrew J. Ong, Shyue Ping Orozco, Modesto Persson, Kristin A. Thygesen, Kristian S. Wolverton, Chris Scheidgen, Markus Toher, Cormac Conduit, Gareth J. Pizzi, Giovanni Gražulis, Saulius Rignanese, Gian-Marco Armiento, Rickard Chemin des Étoiles 8 Louvain-la-Neuve1348 Belgium Matgenix SRL 185 Rue Armand Bury Gozée6534 Belgium École Polytechnique Fédérale de Lausanne Avenue de Forel 3 Lausanne1015 Switzerland Institute of Biotechnology Life Sciences Center Vilnius University Sauletekio av. 7 VilniusLT-10257 Lithuania SINTEF P.O. Box 4760 Torgarden TrondheimNO-7465 Norway Materials Design and Informatics unit Department of Physics Chemistry and Biology Linköping University Sweden Baldiri i Reixac 10-12 Barcelona08028 Spain Tilde Materials Informatics Straßmannstraße 25 Berlin10249 Germany Materials Platform for Data Science Sepapaja 6 Tallinn15551 Estonia Computational Atomic-Scale Materials Design Technical University of Denmark Kgs. Lyngby Denmark Av. Miguel de Cervantes 120 Complejo Industrial Chihuahua Chihuahua Chih. 31136 Mexico Material Measurement Laboratory National Institute of Standards and Technology GaithersburgMD20899 United States Department of Mechanical Engineering and Materials Science Duke University DurhamNC27708 United States Center for Extreme Materials Duke University DurhamNC27708 United States École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Universidad Autónoma de Chihuahua Facultad de Ciencias Quimicas Chihuahua31125 Mexico Department of Materials Science and Engineering The Pennsylvania State University University ParkPA16802 United States Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Department of NanoEngineering University of California 9500 Gilman Drive La Jolla San DiegoCA92093-0448 United States National Institute for Materials Science 1-2-1 Sengen Ibaraki Tsukuba305-0047 Japan Dassault Systèmes Germany GmbH Am Kabellager 11-13 Cologne51063 Germany CFisUC Department of Physics University of Coimbra Rua Larga Coimbra3004-516 Portugal Dassault Systèmes 22 Science Park CB4 0FJ United Kingdom Theory of Condensed Matter Cavendis

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. Since the first release of the OPTIMADE specification (v1.0), the API has undergone significant development, leading to the v1.2 release, and has underpinned multiple scientific studies. In this work, we highlight the latest features of the API format, accompanying software tools, and provide an update on the implementation of OPTIMADE in contributing materials databases. We end by providing several use cases that demonstrate the utility of the OPTIMADE API in materials research that continue to drive its ongoing development. © 2024, CC BY.

关键词： Electronic data interchange

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Localization transition in three-dimensional stealthy hyperuniform disordered systems

arXiv

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arXiv 2021年

作者： Sgrignuoli, F. Torquato, S. Dal Negro, L. Department of Electrical and Computer Engineering & Photonics Center Boston University 8 Saint Mary’s Street BostonMA02215 United States Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Division of Material Science and Engineering Boston University 15 Saint Mary’s Street BrooklineMA02446 United States Department of Physics Boston University 590 Commonwealth Avenue BostonMA02215 United States

The purpose of this work is to understand the fundamental connection between structural correlations and light localization in three-dimensional (3D) open scattering systems of finite size. We numerically investigate the transport of vector electromagnetic waves scattered by resonant electric dipoles spatially arranged in 3D space by stealthy hyperuniform disordered point patterns. Three-dimensional stealthy hyperuniform disordered systems (3D-SHDS) are engineered with different structural correlation properties determined by their degree of stealthiness χ. Such fine control of exotic states of amorphous matter enables the systematic design of optical media that interpolate in a tunable fashion between uncorrelated random structures and crystalline materials. By solving the electromagnetic multiple scattering problem using Green’s matrix spectral method, we establish a transport phase diagram that demonstrates a clear delocalization-localization transition beyond a critical scattering density that depends on χ. The transition is characterized by studying the Thouless number and the spectral statistics of the scattering resonances. In particular, by tuning the χ parameter, we demonstrate large spectral gaps and suppressed sub-radiant proximity resonances, facilitating light localization. Moreover, consistently with previous studies, our results show a region of the transport phase diagram where the investigated scattering systems become transparent. Our work provides a systematic description of the transport and localization properties of light in stealthy hyperuniform structures and motivates the engineering of novel photonic systems with enhanced light-matter interactions for applications to both classical and quantum devices. Copyright © 2021, The Authors. All rights reserved.

关键词： Phase diagrams

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Genomic medicine year in review: 2024

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American journal of human genetics 2024年第12期111卷 2585-2588页

作者： Teri A Manolio Jahnavi Narula Alauna Rupert Carol J Bult Rex L Chisholm Geoffrey S Ginsburg Eric D Green Gillian Hooker Gail P Jarvik George A Mensah Erin M Ramos Dan M Roden Robb Rowley Casey Overby Taylor Marc S Williams National Human Genome Research Institute National Institutes of Health Bethesda MD 20892 USA. Electronic address: manolio@nih.gov. National Human Genome Research Institute National Institutes of Health Bethesda MD 20892 USA. The Jackson Laboratory for Mammalian Genetics Bar Harbor ME 04609 USA. Center for Genetic Medicine Feinberg School of Medicine Northwestern University Chicago IL 60611 USA. All of Us Research Program National Institutes of Health Bethesda MD 20892 USA. Concert Nashville TN 37201 USA. Departments of Medicine (Medical Genetics) and Genome Sciences University of Washington Seattle WA 98195 USA. Center for Translation Research and Implementation Science National Heart Lung and Blood Institute National Institutes of Health Bethesda MD 20892 USA. Departments of Medicine Pharmacology and Biomedical Informatics Vanderbilt University Medical Center Nashville TN 37232 USA. Departments of Medicine and Biomedical Engineering Johns Hopkins University School of Medicine Baltimore MD 21218 USA. Department of Genomic Health Geisinger Danville PA 17822 USA.

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The structure of the stellar halo of the Andromeda galaxy explored with the NB515 for Subaru/HSC. I.: New insights on the stellar halo up to 120 kpc

arXiv

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arXiv 2024年

作者： Ogami, Itsuki Tanaka, Mikito Komiyama, Yutaka Chiba, Masashi Guhathakurta, Puragra Kirby, Evan N. Wyse, Rosemary F.G. Filion, Carrie Gilbert, Karoline M. Escala, Ivanna Mori, Masao Kirihara, Takanobu Tanaka, Masayuki Ishigaki, Miho N. Hayashi, Kohei Lee, Myung Gyoon Sharma, Sanjib Kalirai, Jason S. Lupton, Robert H. 2-21-1 Osawa Mitaka Tokyo181-8588 Japan National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Department of Advanced Sciences Faculty of Science and Engineering Hosei University 3-7-2 Kajino-cho Koganei Tokyo184-8584 Japan Astronomical Institute Tohoku University Aoba-ku Miyagi Sendai980-8578 Japan Department of Astronomy and Astrophysics University of California Santa Cruz University of California Observatories 1156 High Street Santa CruzCA95064 United States Department of Physics and Astronomy University of Notre Dame Notre DameIN46556 United States Department of Physics and Astronomy Johns Hopkins University BaltimoreMD21218 United States Center for Computational Astrophysics Flatiron Institute New YorkNY10010 United States John Hopkins Applied Physics Laboratory 11100 Johns Hopkins Road LaurelMD20723 United States Space Telescope Science Institute 3700 San Martin Dr. BaltimoreMD21218 United States The Observatories of the Carnegie Institution for Science 813 Santa Barbara Street PasadenaCA91101 United States Faculty of Pure and Applied Physics University of Tsukuba Tennodai 1-1-1 Ibaraki Tsukuba305-8577 Japan Center for Computational Sciences University of Tsukuba Tennodai 1-1-1 Ibaraki Tsukuba305-8577 Japan Kitami Institute of Technology 165 Koen-cho Hokkaido Kitami090-8507 Japan National Institute of Technology Sendai College Miyagi Natori981-1239 Japan Astronomy Program Department of Physics and Astronomy SNU Astronomy Research Center Seoul National University 1 Gwanak-ro Gwanak-gu Seoul08826 Korea Republic of Department of Astrophysical Sciences Princeton University 4 Ivy Lane PrincetonNJ08544 United States

We analyse the M31 halo and its substructure within a projected radius of 120 kpc using a combination of Subaru/HSC NB515 and CFHT/MegaCam g- & i-bands. We succeed in separating M31’s halo stars from foreground contamination with ∼ 90 % accuracy by using the surface gravity sensitive NB515 filter. Based on the selected M31 halo stars, we discover three new substructures, which associate with the Giant Southern Stream (GSS) based on their photometric metallicity estimates. We also produce the distance and photometric metallicity estimates for the known substructures. While these quantities for the GSS are reproduced in our study, we find that the North-Western stream shows a steeper distance gradient than found in an earlier study, suggesting that it is likely to have formed in an orbit closer to the Milky Way. For two streams in the eastern halo (Stream C and D), we identify distance gradients that had not been resolved. Finally, we investigate the global halo photometric metallicity distribution and surface brightness profile using the NB515-selected halo stars. We find that the surface brightness of the metal-poor and metal-rich halo populations, and the all population can be fitted to a power-law profile with an index of α = −1.65 ± 0.02, −2.82 ± 0.01, and −2.44 ± 0.01, respectively. In contrast to the relative smoothness of the halo profile, its photometric metallicity distribution appears to be spatially non-uniform with nonmonotonic trends with radius, suggesting that the halo population had insufficient time to dynamically homogenize the accreted populations. Copyright © 2024, The Authors. All rights reserved.

关键词： Luminance

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Characterizing the Directionality of Gravitational Wave Emission from Matter Motions within Core-collapse Supernovae

arXiv

引用

arXiv 2023年

作者： Pajkos, Michael A. Vancamp, Steven J. Pan, Kuo-Chuan Vartanyan, David Deppe, Nils Couch, Sean M. TAPIR Mailcode 350-17 California Institute of Technology PasadenaCA91125 United States Department of Physics and Astronomy Michigan State University East LansingMI48824 United States Department of Physics National Tsing Hua University Hsinchu30013 Taiwan Institute of Astronomy National Tsing Hua University Hsinchu30013 Taiwan Center for Informatics and Computation National Tsing Hua University Hsinchu30013 Taiwan National Center for Theoretical Sciences National Tsing Hua University Hsinchu30013 Taiwan Carnegie Observatories 813 Santa Barbara St PasadenaCA91101 United States Department of Physics Cornell University IthacaNY14853 United States Cornell Center for Astrophysics and Planetary Science Cornell University IthacaNY14853 United States Department of Computational Mathematics Science and Engineering Michigan State University East LansingMI48824 United States Facility for Rare Isotope Beams Michigan State University East LansingMI48824 United States

We analyze the directional dependence of the gravitational wave (GW) emission from 15 3D neutrino radiation hydrodynamic simulations of core-collapse supernovae. Using spin weighted spherical harmonics, we develop a new analytic technique to quantify the evolution of the distribution of GW emission over all angles. We construct a physics-informed toy model that can be used to approximate GW distributions for general ellipsoid-like systems, and use it to provide closed form expressions for the distribution of GWs for different CCSN phases. Using these toy models, we approximate the PNS dynamics during multiple CCSN stages and obtain similar GW distributions to simulation outputs. When considering all viewing angles, we apply this new technique to quantify the evolution of preferred directions of GW emission. For nonrotating cases, this dominant viewing angle drifts isotropically throughout the supernova, set by the dynamical timescale of the protoneutron star. For rotating cases, during core bounce and the following tens of ms, the strongest GW signal is observed along the equator. During the accretion phase, comparable-if not stronger-GW amplitudes are generated along the axis of rotation, which can be enhanced by the low T/|W| instability. We show two dominant factors influencing the directionality of GW emission are the degree of initial rotation and explosion morphology. Lastly, looking forward, we note the sensitive interplay between GW detector site and supernova orientation, along with its effect on detecting individual polarization modes. Copyright © 2023, The Authors. All rights reserved.

关键词： Gravity waves

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Multigoal-oriented error estimation and mesh adaptivity for fluid-structure interaction

arXiv

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arXiv 2021年

作者： Ahuja, K. Endtmayer, B. Steinbach, M.C. Wick, Thomas Discipline of Computer Science and Engineering Indian Institute of Technology Indore India Leibniz Universität Hannover Institut für Angewandte Mathematik Welfengarten 1 Hannover30167 Germany Leibniz Universität Hannover Germany Université Paris-Saclay ENS Paris-Saclay LMT - Laboratoire de Mécanique et Technologie Gif-sur-Yvette91190 France Johannes Kepler University Linz Doctoral Program on Computational Mathematics Altenbergerstr. 69 LinzA-4040 Austria Austrian Academy of Sciences Johann Radon Institute for Computational and Applied Mathematics Altenbergerstr. 69 LinzA-4040 Austria

In this work, we consider multigoal-oriented error estimation for stationary fluid-structure interaction. The problem is formulated within a variational-monolithic setting using arbitrary Lagrangian-Eulerian coordinates. Employing the dual-weighted residual method for goal-oriented a posteriori error estimation, adjoint sensitivities are required. For multigoal-oriented error estimation, a combined functional is formulated such that several quantities of interest are controlled simultaneously. As localization technique for mesh refinement we employ a partition-of-unity. Our algorithmic developments are substantiated with several numerical tests such as an elastic lid-driven cavity with two goal functionals, an elastic bar in a chamber with two goal functionals, and the FSI-1 benchmark with three goal *** Codes 65N30, 65N50, 74F10 © 2021, CC BY-NC-ND.

关键词： Fluid structure interaction

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Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics

引用

Quantitative Biology 2020年第3期8卷 228-237页

作者： Naoki Matsuda Ken-ichi Hironaka Masashi Fujii Takumi Wada Katsuyuki Kunida Haruki Inoue Miki Eto Daisuke Hoshino Yasuro Furuichi Yasuko Manabe Nobuharu LFujii Hiroyuki Noji Hiromi Imamura Shinya Kuroda Department of Biological Sciences Graduate School of ScienceUniversity of TokyoTokyo 113-0033Japan Molecular Genetics Research Laboratory Graduate School of ScienceUniversity of TokyoTokyo 113-0033Japan Department of Mathematical and Life Sciences Graduate School of Integrated Sciences for LifeHiroshima UniversityHiroshima 739-8526Japan Laboratory of Computati onal Biology Graduate School of Biological SciencesNara Institute of Science and Tech no logyNara 630-0192Japan Department of Computational Biology and Medical Sciences Graduate School of Frontier SciencesUniversity of TokyoTokyo 113-0033Japan Department of Engineering Science Graduate School of Informatics and EngineeringUniversity of Electro-CommunicationsTokyo 182-8585Japan Department of Health Promotion Sciences Graduate School of Human Health SciencesTokyo Metropolitan UniversityTokyo 192-0397Japan Department of Applied Chemistry Graduate School of EngineeringUniversity of TokyoTokyo 113-8656Japan Department of Functional Biology Graduate School of BiostudiesKyoto UniversityKyoto 606-8501Japan CREST Japan Science and Technology CorporationTokyo 113-0033Japan

Backgrounds ATP is the major energy source for myotube contraction,and is quickly produced to compensate ATP consumption and to maintain sufficient ATP *** is consumed mainly in cytoplasm and produced in mitochondria during myotube *** understand the mechanism of ATP homeostasis during myotube contraction,it is essential to monitor mitochondrial ATP at single-cell level,and examine how ATP is produced and consumed in ***:We established C2C12 cell line stably expressing fluorescent probe of mitochondrial ATP,and induced differentiation into myotubes・We gave electric pulse stimulation to the differentiated myotubes,and measured mitochondrial *** constructed mathematical model of mitochondrial ATP at single-cell level,and analyzed kinetic parameters of ATP production and ***:We performed hierarchical clustering analysis of time course of mitochondrial ATP,which resulted in two *** 1 showed strong transient increase,whereas cluster 2 showed weak transient *** modeling at single-cell level revealed that the ATP production rate of cluster 1 was larger than that of cluster 2,and that both regulatory pathways of ATP production and consumption of cluster 1 were faster than those of cluster *** 1 showed larger mitochondrial mass than cluster 2,suggesting that cluster 1 shows the similar property of slow muscle fibers,and cluster 2 shows the similar property of fast muscle *** Cluster 1 showed the stronger mitochondrial ATP increase by larger ATP production rate,but not smaller *** 1 might reflect the larger oxidative capacity of slow muscle fiber.

关键词： mitocondrial ATP production ATP consumption single-cell analysis mathematical modeling

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Big Data Governance for Building A Smart Cities 10

Big Data Governance for Building A Smart Cities

引用

10th International Conference on ICT for Smart Society, ICISS 2019

作者： Zulkarnain, Novan Kosala, Raymond Ranti, Benny Supangkat, Suhono Harso Bina Nusantara University Computer Science Department BINUS Graduate Program Doctor of Computer Science Information Systems Department Jakarta11480 Indonesia Universitas Indonesia Computer Science Department Depok16424 Indonesia Institute of Technology Bandung School of Electrical and Informatics Engineering Bandung40132 Indonesia

ISBN: (纸本)9781728148809

There have been many studies conducted related to Smart City, IT Governance and Big Data. In this study aims to find out how the relationship between the three and how to form a framework to explain it. The methodology used is qualitative by looking for some literature on smart city framework, IT Governance framework, and a Big Data framework. From these results, an overall picture of the relationship between the three is concluded, where Big Data has a role in IT Governance. and also the relationship of IT Governance to the realization of Smart City. And the final results of this study produce a framework to explain the relationship between Smart City, IT Governance and Big Data. © 2019 IEEE.

关键词： Big data

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Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

arXiv

引用

arXiv 2023年

作者： Takaba, Kenichiro Pulido, Iván Behara, Pavan Kumar Cavender, Chapin E. Friedman, Anika J. Henry, Michael M. MacDermott-Opeskin, Hugo Iacovella, Christopher R. Nagle, Arnav M. Payne, Alexander Matthew Shirts, Michael R. Mobley, David L. Chodera, John D. Wang, Yuanqing Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Pharmaceuticals Research Center Advanced Drug Discovery Asahi Kasei Pharma Corporation Shizuoka410-2321 Japan Center for Neurotherapeutics Department of Pathology and Laboratory Medicine University of California IrvineCA92697 United States Skaggs School of Pharmacy and Pharmaceutical Sciences University of California 9500 Gilman Drive La Jolla San DiegoCA92093 United States Department of Chemical and Biological Engineering University of Colorado Boulder BoulderCO80309 United States Open Molecular Software Foundation DavisCA95618 United States Department of Bioengineering University of California Berkeley BerkeleyCA94720 United States Department of Pharmaceutical Sciences University of California IrvineCA92697 United States Tri-Institutional Ph.D. Program in Chemical Biology Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University New YorkNY10004 United States

The development of reliable and extensible molecular mechanics (MM) force fields—fast, empirical models characterizing the potential energy surface of molecular systems—is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest. © 2023, CC BY.

关键词： Quantum chemistry

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Isotope effects on molecular structures and electronic properties of liquid water via deep potential molecular dynamics based on SCAN functional

arXiv

引用

arXiv 2020年

作者： Xu, Jianhang Zhang, Chunyi Zhang, Linfeng Chen, Mohan Santra, Biswajit Wu, Xifan Department of Physics Temple University PhiladelphiaPA19122 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States CAPT HEDPS College of Engineering Peking University Beijing100871 China Institute for Computational Molecular Science Temple University PhiladelphiaPA19122 United States

Feynman path-integral deep potential molecular dynamics (PI-DPMD) calculations have been employed to study both light (H2O) and heavy water (D2O) within the isothermal–isobaric ensemble. In particular, the deep neural network is trained based on ab initio data obtained from the strongly constrained and appropriately normed (SCAN) exchange-correlation functional. Because of the lighter mass of hydrogen than deuteron, the properties of light water is more influenced by nuclear quantum effect than those of heavy water. Clear isotope effects are observed and analyzed in terms of hydrogen-bond structure and electronic properties of water that are closely associated with experimental observables. The molecular structures of both liquid H2O and D2O agree well with the data extracted from scattering experiments. The delicate isotope effects on radial distribution functions and angular distribution functions are well reproduced as well. Our approach demonstrates that deep neural network combined with SCAN functional based ab initio molecular dynamics provides an accurate theoretical tool for modeling water and its isotope effects. Copyright © 2020, The Authors. All rights reserved.

关键词： Electronic properties

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