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Publisher Correction: Epithelial cell plasticity drives endoderm formation during gastrulation

Nature cell biology 2021年第8期23卷 925页

作者： Katharina Scheibner Silvia Schirge Ingo Burtscher Maren Büttner Michael Sterr Dapeng Yang Anika Böttcher Martin Irmler Johannes Beckers Filippo M Cernilogar Gunnar Schotta Fabian J Theis Heiko Lickert Institute of Diabetes and Regeneration Research Helmholtz Diabetes Center Helmholtz Zentrum München Munich Germany. Institute of Stem Cell Research Helmholtz Zentrum München Munich Germany. German Center for Diabetes Research (DZD) Munich Germany. Institute of Computational Biology Helmholtz Zentrum München Munich Germany. Developmental Biology Program Sloan Kettering Institute New York NY USA. Institute of Experimental Genetics Helmholtz Zentrum München Munich Germany. School of Life Sciences Weihenstephan Technische Universität München Freising Germany. Division of Molecular Biology Biomedical Center Faculty of Medicine Ludwig Maximilian University Munich Germany. Department of Mathematics Technische Universität München Munich Germany. Institute of Diabetes and Regeneration Research Helmholtz Diabetes Center Helmholtz Zentrum München Munich Germany. heiko.lickert@helmholtz-muenchen.de. Institute of Stem Cell Research Helmholtz Zentrum München Munich Germany. heiko.lickert@helmholtz-muenchen.de. German Center for Diabetes Research (DZD) Munich Germany. heiko.lickert@helmholtz-muenchen.de. School of Medicine Klinikum Rechts der Isar Technische Universität München Munich Germany. heiko.lickert@helmholtz-muenchen.de.

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Combining endogenous and exogenous variables in a special case of non-parametric time series forecasting model

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Moscow University computational mathematics and Cybernetics 2016年第2期40卷 71-78页

作者： Motrenko, A.P. Rudakov, K.V. Strijov, V.V. Department of Control and Applied Mathematics Moscow Institute of Physics and Technology (State University) Institutskii per. 9 Dolgoprudnyi Moscow oblast 141700 Russian Federation Department of Computational Mathematics and Cybernetics Moscow State University Moscow 119899 Russian Federation Dorodnicyn Computing Center Russian Academy of Sciences ul. Vavilova 40 GSP-1 Moscow 119333 Russian Federation

We address a problem of increasing quality of forecasting time series by taking into account the information about exogenous time series. We aim to improve a non-parametric forecasting algorithm that minimizes the convolution of a histogram of time series with the loss function. We propose to adjust the histogram, using mixtures of conditional histograms as a less sparse alternative to multidimensional histogram and in some cases demonstrate the decrease of loss compared to the basic forecasting algorithm. To the extent of our knowledge, such approach to combining endogenous and exogenous time series is original and has not been proposed yet. The suggested method is illustrated with the data from the Russian Railways. © 2016, Allerton Press, Inc.

关键词： exogenous time series forecasting hist algorithm mixture model time series

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Complex band structure and electronic transmission

arXiv

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arXiv 2017年

作者： Jensen, Anders Strange, Mikkel Smidstrup, Søren Stokbro, Kurt Solomon, Gemma C. Reuter, Matthew G. Nano-Science Center Department of Chemistry University of Copenhagen Copenhagen Ø2100 Denmark Department of Physics Technical University of Denmark Kongens Lyngby2800 Denmark QuantumWise A/S Fruebjergvej 3 Box 4 Copenhagen2100 Denmark Department of Applied Mathematics & Statistics Institute for Advanced Computational Science Stony Brook University Stony BrookNY11794 United States

The function of nano-scale devices critically depends on the choice of materials. For electron transport junctions it is natural to characterize the materials by their conductance length dependence, β. Theoretical estimations of β are made employing two primary theories: complex band structure and DFT-NEGF Landauer transport. Both reveal information on β of individual states;i.e. complex Bloch waves and transmission eigenchannels, respectively. However, it is unclear how the β-values of the two approaches compare. Here, we present calculations of decay constants for the two most conductive states as determined by complex band structure and standard DFT-NEGF transport calculations for two molecular and one semi-conductor junctions. Despite the different nature of the two methods, we find strong agreement of the calculated decay constants for the molecular junctions while the semi-conductor junction shows some discrepancies. The results presented here provide a template for studying the intrinsic, channel resolved length dependence of the junction through complex band structure of the central material in the heterogeneous nano-scale junction. Copyright © 2017, The Authors. All rights reserved.

关键词： Electron transport properties

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On the effect of non-Gaussian lensing deflections on CMB lensing measurements

arXiv

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arXiv 2018年

作者： Böhm, Vanessa Sherwin, Blake D. Liu, Jia Hill, J. Colin Schmittfull, Marcel Namikawa, Toshiya Berkeley Center for Cosmological Physics University of California BerkeleyCA94720 United States Lawrence Berkeley National Laboratory 1 Cyclotron Road BerkeleyCA93720 United States Department of Applied Mathematics and Theoretical Physics University of Cambridge Wilberforce Road CambridgeCB3 0WA United Kingdom Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States Center for Computational Astrophysics Flatiron Institute 162 5th Avenue 10010 New YorkNY United States Institute for Advanced Study Einstein Drive PrincetonNJ08540 United States Leung Center for Cosmology and Particle Astrophysics National Taiwan University Taipei10617 Taiwan

We investigate the impact of non-Gaussian lensing deflections on measurements of the CMB lensing power spectrum. We find that the false assumption of their Gaussianity significantly biases these measurements in current and future experiments at the percent level. The bias is detected by comparing CMB lensing reconstructions from simulated CMB data lensed with Gaussian deflection fields to reconstructions from simulations lensed with fully non-Gaussian deflection fields. The non-Gaussian deflections are produced by ray-tracing through snapshots of an N-body simulation and capture both the non-Gaussianity induced by non-linear structure formation and by multiple correlated deflections. We find that the amplitude of the measured bias is in agreement with analytical predictions by Böhm et al. 2016. The bias is largest in temperature-based measurements and we do not find evidence for it in measurements from a combination of polarization fields (EB,EB). We argue that the non-Gaussian bias should be even more important for measurements of cross-correlations of CMB lensing with low-redshift tracers of large-scale structure. Copyright © 2018, The Authors. All rights reserved.

关键词： Deflection (structures)

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Constraints on black-hole charges with the 2017 EHT observations of M87

arXiv

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arXiv 2021年

作者： Kocherlakota, Prashant Rezzolla, Luciano Falcke, Heino Fromm, Christian M. Kramer, Michael Mizuno, Yosuke Nathanail, Antonios Olivares, Héctor Younsi, Ziri Akiyama, Kazunori Alberdi, Antxon Alef, Walter Carlos Algaba, Juan Anantua, Richard Asada, Keiichi Azulay, Rebecca Baczko, Anne-Kathrin Ball, David Baloković, Mislav Barrett, John Benson, Bradford A. Bintley, Dan Blackburn, Lindy Blundell, Raymond Boland, Wilfred Bouman, Katherine L. Bower, Geoffrey C. Boyce, Hope Bremer, Michael Brinkerink, Christiaan D. Brissenden, Roger Britzen, Silke Broderick, Avery E. Broguiere, Dominique Bronzwaer, Thomas Byun, Do-Young Carlstrom, John E. Chael, Andrew Chan, Chi-Kwan Chatterjee, Shami Chatterjee, Koushik Chen, Ming-Tang Chen, Yongjun Chesler, Paul M. Cho, Ilje Christian, Pierre Conway, John E. Cordes, James M. Crawford, Thomas M. Crew, Geoffrey B. Cruz-Osorio, Alejandro Cui, Yuzhu Davelaar, Jordy de Laurentis, Mariafelicia Deane, Roger Dempsey, Jessica Desvignes, Gregory Doeleman, Sheperd S. Eatough, Ralph P. Farah, Joseph Fish, Vincent L. Fomalont, Ed Fraga-Encinas, Raquel Friberg, Per Alyson Ford, H. Fuentes, Antonio Galison, Peter Gammie, Charles F. García, Roberto Gentaz, Olivier Georgiev, Boris Goddi, Ciriaco Gold, Roman Gómez, José L. Gómez-Ruiz, Arturo I. Gu, Minfeng Gurwell, Mark Hada, Kazuhiro Haggard, Daryl Hecht, Michael H. Hesper, Ronald Ho, Luis C. Ho, Paul Honma, Mareki Huang, Chih-Wei L. Huang, Lei Hughes, David H. Ikeda, Shiro Inoue, Makoto Issaoun, Sara James, David J. Jannuzi, Buell T. Janssen, Michael Jeter, Britton Jiang, Wu Jimenez-Rosales, Alejandra Johnson, Michael D. Jorstad, Svetlana Jung, Taehyun Karami, Mansour Karuppusamy, Ramesh Kawashima, Tomohisa Keating, Garrett K. Kettenis, Mark Kim, Dong-Jin Kim, Jae-Young Kim, Jongsoo Kim, Junhan Kino, Motoki Yi Koay, Jun Kofuji, Yutaro Koch, Patrick M. Koyama, Shoko Kramer, Carsten Krichbaum, Thomas P. Kuo, Cheng-Yu Lauer, Tod R. Lee, Sang-Sung Levis, Aviad Li, Yan-Rong Li, Zhiyuan Lindqvist, Michael Lico, Rocco Lindahl, Greg Liu, Jun Liu, Kuo Liuzzo, Institut für Theoretische Physik Goethe-Universität Max-von-Laue-Str. 1 Frankfurt60438 Germany Frankfurt Institute for Advanced Studies Ruth-Moufang-Str. 1 Frankfurt60438 Germany School of Mathematics Trinity College Dublin 2 Ireland Radboud University P.O. Box 9010 Nijmegen6500 GL Netherlands Black Hole Initiative at Harvard University 20 Garden Street CambridgeMA02138 United States Center for Astrophysics — Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States Max-Planck-Institut für Radioastronomie Auf dem Hügel 69 BonnD-53121 Germany Tsung-Dao Lee Institute School of Physics and Astronomy Shanghai Jiao Tong University Shanghai200240 China Institut für Theoretische Physik Goethe-Universität Frankfurt Max-von-Laue-Straße 1 Frankfurt am MainD-60438 Germany Department of Physics National and Kapodistrian University of Athens Panepistimiopolis ZografosGR 15783 Greece Mullard Space Science Laboratory University College London Holmbury St. Mary Dorking SurreyRH5 6NT United Kingdom Massachusetts Institute of Technology Haystack Observatory 99 Millstone Road WestfordMA01886 United States National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n GranadaE-18008 Spain Department of Physics Faculty of Science University of Malaya Kuala Lumpur50603 Malaysia Center for Computational Astrophysics Flatiron Institute 162 Fifth Avenue New YorkNY10010 United States Institute of Astronomy and Astrophysics Academia Sinica 11F of Astronomy-Mathematics Building AS/NTU No. 1 Sec. 4 Roosevelt Rd Taipei10617 Taiwan Departament d’Astronomia i Astrofísica Universitat de València C. Dr. Moliner 50 Burjassot ValènciaE-46100 Spain Observatori Astronòmic Universitat de València C. Catedrático José Beltrán 2 PaternaValènciaE-46980 Spain Steward Observatory and Department of Astronomy University of Arizona 933 N. Cherry Ave. Tucson

Our understanding of strong gravity near supermassive compact objects has recently improved thanks to the measurements made by the Event Horizon Telescope (EHT). We use here the M87* shadow size to infer constraints on the physical charges of a large variety of nonrotating or rotating black holes. For example, we show that the quality of the measurements is already sufficient to rule out that M87* is a highly charged dilaton black hole. Similarly, when considering black holes with two physical and independent charges, we are able to exclude considerable regions of the space of parameters for the doubly-charged dilaton and the Sen black holes. Copyright © 2021, The Authors. All rights reserved.

关键词： Gravitation

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WannierTools: An open-source software package for novel topological materials

arXiv

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arXiv 2017年

作者： Wu, QuanSheng Zhang, ShengNan Song, Hai-Feng Troyer, Matthias Soluyanov, Alexey A. Theoretische Physik and Station Q Zurich ETH Zurich Zurich8093 Switzerland Institute of Physics Chinese Academy of Sciences Beijing100190 China Institute of Applied Physics and Computational Mathematics Beijing100094 China Department of Physics St. Petersburg State University St. Petersburg199034 Russia

We present an open-source software package WannierTools, a tool for investigation of novel topological materials. This code works in the tight-binding framework, which can be generated by another software package Wannier90 [1]. It can help to classify the topological phase of a given materials by calculating the Wilson loop, and can get the surface state spectrum which is detected by angle resolved photoemission (ARPES) and in scanning tunneling microscopy (STM) experiments. It also identifies positions of Weyl/Dirac points and nodal line structures, calculates the Berry phase around a closed momentum loop and Berry curvature in a part of the Brillouin zone(BZ). Copyright © 2017, The Authors. All rights reserved.

关键词： Scanning tunneling microscopy

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Topological crystalline antiferromagnetic state in tetragonal FeS

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Physical Review B 2017年第16期96卷 165102-165102页

作者： Ningning Hao Fawei Zheng Ping Zhang Shun-Qing Shen Anhui Province Key Laboratory of Condensed Matter Physics at Extreme Conditions High Magnetic Field Laboratory Chinese Academy of Sciences Hefei 230031 Anhui China Collaborative Innovation Center of Advanced Microstructures Nanjing University Jiangsu Province 210093 China Institute of Applied Physics and Computational Mathematics Beijing 100088 China Beijing Computational Science Research Center Beijing 100193 China Department of Physics The University of Hong Kong Pokfulam Road Hong Kong China

Integration between magnetism and topology is an exotic phenomenon in condensed-matter physics. Here, we propose an exotic phase named topological crystalline antiferromagnetic state, in which antiferromagnetism intrinsically integrates with nontrivial topology, and we suggest such a state can be realized in tetragonal FeS. A combination of first-principles calculations and symmetry analyses shows that the topological crystalline antiferromagnetic state arises from band reconstruction induced by pair checkerboard antiferromagnetic order together with band-gap opening induced by intrinsic spin-orbit coupling in tetragonal FeS. The topological crystalline antiferromagnetic state is protected by the product of fractional translation symmetry, mirror symmetry, and time-reversal symmetry, and presents some unique features. In contrast to strong topological insulators, the topological robustness is surface dependent. These findings indicate that nontrivial topological states could emerge in pure antiferromagnetic materials, which sheds new light on potential applications of topological properties in fast-developing antiferromagnetic spintronics.

关键词： Antiferromagnetism Superconductivity Topological materials Chalcogenides First-principles calculations

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A case study competition among methods for analyzing large spatial data

arXiv

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arXiv 2017年

作者： Heaton, Matthew J. Datta, Abhirup Finley, Andrew O. Furrer, Reinhard Guhaniyogi, Rajarshi Gerber, Florian Gramacy, Robert B. Guinness, Joseph Hammerling, Dorit Katzfuss, Matthias Lindgren, Finn Nychka, Douglas Sun, Furong Zammit-Mangion, Andrew Department of Statistics Brigham Young University 223 TMCB ProvoUT84602 United States Department of Biostatistics Johns Hopkins University 615 N. Wolfe Street BaltimoreMD21205 United States Department of Forestry and Geography Michigan State University 126 Natural Resources Building Each LansingMI48824 Department of Mathematics Department of Computational Science University of Zurich Switzerland Department of Applied Mathematics & Statistics University of California Santa Cruz 1156 High Street SOE2 Santa CruzCA95064 United States Department of Mathematics University of Zurich Switzerland Department of Statistics Virginia Tech Department of Statistics [MC0439 Hutcheson Hall 250 Drillfield Drive BlacksburgVA24061 United States Department of Statistics North Carolina State University Campus Box 8203 2311 Stinson Drive RaleighNC27695 Institute for Mathematics Applied to Geosciences National Center for Atmospheric Research BoulderCO80305 United States Department of Statistics Texas A&M University College StationTX77843 United States School of Mathematics University of Edinburgh EdinburghEH9 3FD United Kingdom Department of Statistics Virginia Tech Hutcheson Hall 250 Drillfield Drive BlacksburgVA24061 United States School of Mathematics and Applied Statistics University of Wollongong NSW2522 Australia

The Gaussian process is an indispensable tool for spatial data analysts. The onset of the "big data" era, however, has lead to the traditional Gaussian process being computationally infeasible for modern spatial data. As such, various alternatives to the full Gaussian process that are more amenable to handling big spatial data have been proposed. These modern methods often exploit low rank structures and/or multi-core and multi-threaded computing environments to facilitate computation. This study provides, first, an introductory overview of several methods for analyzing large spatial data. Second, this study describes the results of a predictive competition among the described methods as implemented by different groups with strong expertise in the methodology. Specifically, each research group was provided with two training datasets (one simulated and one observed) along with a set of prediction locations. Each group then wrote their own implementation of their method to produce predictions at the given location and each which was subsequently run on a common computing environment. The methods were then compared in terms of various predictive diagnostics. Supplementary materials regarding implementation details of the methods and code are available for this article online. Copyright © 2017, The Authors. All rights reserved.

关键词： Big data

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P-wave velocity prediction in porous medium with liquid-pocket patchy saturation

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applied mathematics and Mechanics(English Edition) 2015年第11期36卷 1427-1440页

作者： Jiawei LIU Weitao SUN Jing BA Zhou Pei-Yuan Center for Applied Mathematics Tsinghua University Department of Computational Geophysics Xi'an Jiaotong University

It becomes increasingly clear that non-uniform distribution of immiscible fluids in porous rock is particularly relevant to seismic wave dispersion. White proposed a patchy saturation model in 1975, in which spherical gas pockets were located at the center of a liquid saturated cube. For an extremely light and compressible inner gas, the physical properties can be approximated by a vacuum with White＇s model. The model successfully analyzes the dispersion phenomena of a P-wave velocity in gas-water- saturated rocks. In the case of liquid pocket saturation, e.g., an oil-pocket surrounded by a water saturated host matrix, the light fluid-pocket assumption is doubtful, and few works have been reported in White＇s framework. In this work, Poisson＇s ratio, the bulk modulus, and the effective density of a dual-liquid saturated medium are formulated for the heterogeneous porous rocks containing liquid-pockets. The analysis of the difference between the newly derived bulk modulus and that of White＇s model shows that the effects of liquid-pocket saturation do not disappear unless the porosity approaches zero. The inner pocket fluid can no longer be ignored. The improvements of the P-wave velocity predictions are illustrated with two examples taken from experiments, i.e., the P-wave velocity in the sandstone saturated by oil and brine and the P-wave velocity for heavy oils and stones at different temperatures.

关键词： White＇s model porous medium P-wave dispersion liquid pocket

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An energy-based equilibrium contact angle boundary condition on jagged surfaces for phase-field methods

arXiv

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arXiv 2017年

作者： Frank, Florian Liu, Chen Scanziani, Alessio Alpak, Faruk O. Riviere, Beatrice Rice University Department of Computational and Applied Mathematics 6100 Main Street HoustonTX77005 United States Shell Technology Center 3333 Highway 6 South HoustonTX77082 United States Imperial College London Department of Earth Science and Engineering LondonSW7 2AZ United Kingdom

We consider an energy-based boundary condition to impose an equilibrium wetting angle for the Cahn-Hilliard-Navier-Stokes phase-field model on voxel-set-type computational domains. These domains typically stem from the µCT imaging of porous rock and approximate a (on µm scale) smooth domain with a certain resolution. Planar surfaces that are perpendicular to the main axes are naturally approximated by a layer of voxels. However, planar surfaces in any other directions and curved surfaces yield a jagged / rough surface approximation by voxels. For the standard Cahn-Hilliard formulation, where the contact angle between the diffuse interface and the domain boundary (fluid-solid interface / wall) is 90◦, jagged surfaces have no impact on the contact angle. However, a prescribed contact angle smaller or larger than 90◦ on jagged voxel surfaces is amplified in either direction. As a remedy, we propose the introduction of surface energy correction factors for each fluid-solid voxel face that counterbalance the difference of the voxel-set surface area with the underlying smooth one. The discretization of the model equations is performed with the discontinuous Galerkin method, however, the presented semi-analytical approach of correcting the surface energy is equally applicable to other direct numerical methods such as finite elements, finite volumes, or finite differences, since the correction factors appear in the strong formulation of the model. Copyright © 2017, The Authors. All rights reserved.

关键词： Porous materials

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