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arXiv 2020年

作者： Anzt, Hartwig Bach, Felix Druskat, Stephan Löffler, Frank Loewe, Axel Renard, Bernhard Y. Seemann, Gunnar Struck, Alexander Achhammer, Elke Aggarwal, Piush Appel, Franziska Bader, Michael Brusch, Lutz Busse, Christian Chourdakis, Gerasimos Dabrowski, Piotr W. Ebert, Peter Flemisch, Bernd Friedl, Sven Fritzsch, Bernadette Funk, Maximilian D. Gast, Volker Goth, Florian Grad, Jean-Noël Hermann, Sibylle Hohmann, Florian Janosch, Stephan Kutra, Dominik Linxweiler, Jan Muth, Thilo Peters-Kottig, Wolfgang Rack, Fabian Raters, Fabian H.C. Rave, Stephan Reina, Guido Reißig, Malte Ropinski, Timo Schaarschmidt, Joerg Seibold, Heidi Thiele, Jan P. Uekerman, Benjamin Unger, Stefan Weeber, Rudolf Germany Innovative Computing Lab University of Tennessee KnoxvilleTN United States Department of English Studies Friedrich Schiller University Jena Germany Germany Department of Computer Science Humboldt-Universität zu Berlin Germany Heinz Nixdorf Chair for Distributed Information Systems Friedrich Schiller University Jena Germany Michael Stifel Center Jena Germany Center for Computation and Technology Louisiana State University Baton Rouge United States Germany Robert Koch Institute Berlin Germany Hasso Plattner Institute Faculty of Digital Engineering University of Potsdam Germany Institute for Experimental Cardiovascular Medicine University Heart Centre Freiburg Bad Krozingen Germany Faculty of Medicine University of Freiburg Freiburg Germany Matters of Activity. Image Space Material. Cluster of Excellence at Humboldt-Universität zu Berlin Germany Technische Universität München Germany Language Technology Lab Universität Duisburg-Essen Germany Germany Department of Informatics Technical University of Munich Germany Technische Universität Dresden Germany Deutsches Krebsforschungszentrum Heidelberg Germany Scientific Computing in Computer Science Technical University Munich Germany School of Computing Communication and Business Hochschule für Technik und Wirtschaft Berlin Germany Center for Bioinformatics Saar Saarland Informatics Campus Germany Institute for Modelling Hydraulic and Environmental Systems University of Stuttgart Germany Berlin Institute of Health Germany Scientific Computing Alfred Wegener Institute Helmholtz Center for Polar and Marine Research Bremerhaven Germany Max-Planck-Gesellschaft e.V. Institut für Theoretische Physik und Astrophysik Universität Würzburg Germany Institut für Computerphysik University of Stuttgart Germany University Library University of Stuttgart Germany Universität Bremen Germany Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany European Molecular Biology Laboratory Heidelb

Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin. Copyright © 2020, The Authors. All rights reserved.

关键词： Software design

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STABILITY ANALYSIS FOR NONLINEAR SCHRODINGER EQUATIONS WITH NONLINEAR ABSORBING BOUNDARY CONDITIONS

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Journal of Computational mathematics 2017年第1期35卷 1-18页

作者： Jiwei Zhang Zhenli Xu Xiaonan Wu Desheng Wang Applied and Computational Mathematics Division Beijing Computational Science Research Center China Department of Mathematics Institute of Natural Sciences and MOE Key Lab of Scientific and Engineering Computing Shanghai Jiao Tong University Shanghai 200240 China Department of Mathematics Hong Kong Baptist University Kowloon Hong Kong China Division of Mathematical Sciences School of Physical and Mathematical Sciences Nanyang Technological University Singapore 637371 Singapore

Local absorbing boundary conditions （labCs） for nonlinear Schr6dinger equations have been constructed in papers [PRE 78（2008） 026709; and PRE 79 （2009） 046711] using the so-called unified approach. In this paper, we present stability analysis for the reduced problem with labCs on the bounded computational domain by the energy estimate, and discuss a class of modified versions of labCs. To prove the stability analysis of the re- duced problem, we turn to the technique of some auxiliary variables which reduces the higher-order derivatives in labCs into a family of equations with lower-order derivatives. Furthermore, we extend the strategy to the stability analysis of two-dimensional problems by carefully dealing with the labCs at corners. Numerical examples are given to demon- strate the effectiveness of our boundary conditions and validate the theoretical analysis.

关键词： Nonlinear SchrSdinger equations Energy estimates Absorbing boundaryconditions.

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Corrigendum to: A convergent adaptive finite element method for elliptic Dirichlet boundary control problems

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IMA Journal of Numerical Analysis 2020年第1期40卷 800-800页

作者： Gong, Wei Liu, Wenbin Tan, Zhiyu Yan, Ningning National Center for Mathematics and Interdisciplinary Sciences Chinese Academy of Sciences Beijing China The State Key Laboratory of Scientific and Engineering Computing Chinese Academy of Sciences Beijing China Institute of Computational Mathematics Chinese Academy of Sciences Beijing China Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing China Kent Business School University of Kent Kent UK Department of Mathematics Hong Kong Baptist University Kowloon Tong Hong Kong SAR NCMIS Chinese Academy of Sciences Beijing China LSEC Chinese Academy of Sciences Beijing China Institute of Systems Science Chinese Academy of Sciences Beijing China

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A decoupling two-grid method for the time-dependent poisson-nernst-planck equations

arXiv

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arXiv 2018年

作者： Shen, Ruigang Shu, Shi Yang, Ying Lu, Benzhuo School of Mathematics and Computational Science Xiangtan University Xiangtan Hunan411105 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan411105 China School of Mathematics and Computational Science Guangxi Colleges Universities Key Laboratory of Data Analysis and Computation Guangxi Key Laboratory of Cryptography and information Security Guilin University of Electronic Technology Guilin Guangxi541004 China Institute of Computational Mathematics and Scientific/Engineering Computing National Center for Mathematics and Interdisciplinary Sciences Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China

We study a two-grid strategy for decoupling the time-dependent Poisson-Nernst-Planck equations describing the mass concentration of ions and the electrostatic potential. The computational system is decoupled to smaller systems by using coarse space solutions at each time level, which can speed up the solution process compared with the finite element method combined with the Gummel iteration. We derive the optimal error estimates in L2 norm for both semi- and fully discrete finite element approximations. Based on the a priori error estimates, the error estimates in H1 norm are presented for the two-grid algorithm. The theoretical results indicate this decoupling method can retain the same accuracy as the finite element method. Numerical experiments including the Poisson-Nernst-Planck equations for an ion channel show the efficiency and effectiveness of the decoupling two-grid method. Copyright © 2018, The Authors. All rights reserved.

关键词： Finite element method

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Analysis of the Mean Field Free Energy Functional of Electrolyte Solution with Non-zero Boundary Conditions and the Generalized PB/PNP Equations with Inhomogeneous Dielectric Permittivity

arXiv

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arXiv 2017年

作者： Liu, Xuejiao Qiao, Yu Lu, Benzhuo State Key Laboratory of Scientific and Engineering Computing National Center for Mathematics and Interdisciplinary Sciences Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China

The energy functional, the governing partial differential equation(s) (PDE), and the boundary conditions need to be consistent with each other in a modeling system. In electrolyte solution study, people usually use a free energy form of an infinite domain system (with vanishing potential boundary condition) and the derived PDE(s) for analysis and computing. However, in many real systems and/or numerical computing, the objective domain is finite, and people still use the similar energy form, PDE(s) but with different boundary conditions, which may cause inconsistency. In this work, (1) we present a mean field free energy functional for electrolyte solution within a finite domain with either physical or numerically required artificial boundary. Apart from the conventional energy components (electrostatic potential energy, ideal gas entropy term and chemical potential term), new boundary interaction terms are added for both Neumann and Dirichlet boundary conditions. These new terms count for physical interactions with the boundary (for real boundary) or the environment influence on the computational domain system (for non-physical but numerically designed boundary). (2) The traditional physical-based Poisson-Boltzmann (PB) equation and Poisson-Nernst-Planck (PNP) equations are proved to be consistent with the new free energy form, and different boundary conditions can be applied. (3) In particular, for inhomogeneous electrolyte with ionic concentration-dependent dielectric permittivity, we derive the generalized Boltzmann distribution (thereby the generalized PB equation) for equilibrium case, and the generalized PNP equations for non-equilibrium case, under different boundary conditions. Numerical tests are performed to demonstrate the different consequences resulted from different energy forms and their derived PDE(s). Copyright © 2017, The Authors. All rights reserved.

关键词： Poisson equation

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Incorporating Born solvation energy into the three-dimensional Poisson-Nernst-Planck model to study ion selectivity in KcsA K+ channels

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Physical Review E 2017年第6期96卷 062416-062416页

作者： Xuejiao Liu Benzhuo Lu State Key Laboratory of Scientific and Engineering Computing National Center for Mathematics and Interdisciplinary Sciences Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China and School of Mathematical Sciences University of Chinese Academy of Sciences Beijing 100049 China

Potassium channels are much more permeable to potassium than sodium ions, although potassium ions are larger and both carry the same positive charge. This puzzle cannot be solved based on the traditional Poisson-Nernst-Planck (PNP) theory of electrodiffusion because the PNP model treats all ions as point charges, does not incorporate ion size information, and therefore cannot discriminate potassium from sodium ions. The PNP model can qualitatively capture some macroscopic properties of certain channel systems such as current-voltage characteristics, conductance rectification, and inverse membrane potential. However, the traditional PNP model is a continuum mean-field model and has no or underestimates the discrete ion effects, in particular the ion solvation or self-energy (which can be described by Born model). It is known that the dehydration effect (closely related to ion size) is crucial to selective permeation in potassium channels. Therefore, we incorporated Born solvation energy into the PNP model to account for ion hydration and dehydration effects when passing through inhomogeneous dielectric channel environments. A variational approach was adopted to derive a Born-energy-modified PNP (BPNP) model. The model was applied to study a cylindrical nanopore and a realistic KcsA channel, and three-dimensional finite element simulations were performed. The BPNP model can distinguish different ion species by ion radius and predict selectivity for K+ over Na+ in KcsA channels. Furthermore, ion current rectification in the KcsA channel was observed by both the PNP and BPNP models. The I−V curve of the BPNP model for the KcsA channel indicated an inward rectifier effect for K+ (rectification ratio of ∼3/2) but indicated an outward rectifier effect for Na+ (rectification ratio of ∼1/6).

关键词： Electrostatic interactions Biomolecules Finite-element method

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An efficient sweep-based solver for the SN equations on high-order meshes

arXiv

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arXiv 2018年

作者： Haut, T.S. Maginot, P.G. Tomov, V.Z. Southworth, B.S. Brunner, T.A. Bailey, T.S. Center for Applied Scientific Computing Lawrence Livermore National Lab P. O. Box 7000 LivermoreCA94551 United States Design Physics Division Lawrence Livermore National Lab P. O. Box 7000 LivermoreCA94551 United States Department of Applied Mathematics University of Colorado Engineering Center ECOT 225 526 UCB BoulderCO80309-0526 United States

We propose a graph-based sweep algorithm for solving the steady state, mono-energetic discrete ordinates on meshes of high-order curved mesh elements. Our spatial discretization consists of arbitrarily high-order discontinuous Galerkin finite elements using upwinding at mesh element faces. To determine mesh element sweep ordering, we define a directed, weighted graph whose vertices correspond to mesh elements, and whose edges correspond to mesh element upwind dependencies. This graph is made acyclic by removing select edges in a way that approximately minimizes the sum of removed edge weights. Once the set of removed edges is determined, transport sweeps are performed by lagging the upwind dependency associated with the removed edges. The proposed algorithm is tested on several 2D and 3D meshes composed of high-order curved mesh elements. Copyright © 2018, The Authors. All rights reserved.

关键词： Mesh generation

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Bayesian inference for estimating model discrepancy of an electric motor

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PAMM 2018年第1期18卷

作者： David John Michael Schick Vincent Heuveline Corporate Research Robert Bosch GmbH Germany Engineering Mathematics and Computing Lab (EMCL) Interdisciplinary Center for Scientific Computing (IWR) Heidelberg University Germany Data Mining and Uncertainty Quantification Group (DMQ) Heidelberg Institute for Theoretical Studies (HITS) GmbH Germany

Uncertainty Quantification (UQ) is highly requested in computational modeling and simulation, especially in an industrial context. A main challenge is related to the fact that computational models are rarely able to represent the true physics perfectly and demonstrate a discrepancy compared to measurement data. Further, an accurate knowledge of considered model parameters is usually not available. E.g. fluctuations in manufacturing processes of hardware components introduce uncertainties which must be quantified in an appropriate way. Mathematically, such UQ tasks are posed as inverse problems, requiring efficient methods for their solution. We address this challenge by investigating the influence of model discrepancies onto the calibration of model parameters and further consider a Bayesian inference framework including an attempt to correct for model discrepancy by an additional term. A Markov Chain Monte Carlo (MCMC) method is utilized to approximate the posterior distribution. Synthetic measurement data from an electric motor model and an artificial model error are used to evaluate the framework. The application shows a promising perspective of the framework by good approximation of discrepancy and parameters.

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Learning from learning machines: A new generation of AI technology to meet the needs of science

arXiv

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arXiv 2021年

作者： Pion-Tonachini, Luca Bouchard, Kristofer Martin, Hector Garcia Peisert, Sean Holtz, W. Bradley Aswani, Anil Dwivedi, Dipankar Wainwright, Haruko Pilania, Ghanshyam Nachman, Benjamin Marrone, Babetta L. Falco, Nicola Prabhat Arnold, Daniel Wolf-Yadlin, Alejandro Powers, Sarah Climer, Sharlee Jackson, Quinn Carlson, Ty Sohn, Michael Zwart, Petrus Kumar, Neeraj Justice, Amy Tomlin, Claire Jacobson, Daniel Micklem, Gos Gkoutos, Georgios V. Bickel, Peter J. Cazier, Jean-Baptiste Müller, Juliane Webb-Robertson, Bobbie-Jo Stevens, Rick Anderson, Mark Kreutz-Delgado, Ken Mahoney, Michael W. Brown, James B. Pattern Computer Inc. Friday HarborWA98250 United States Biosciences Area Lawrence Berkeley National Lab BerkeleyCA94803 United States Computational Research Division Lawrence Berkeley National Lab BerkeleyCA94720 United States Helen Wils Neuroscience Institute Redwood Center for Theoretical Neuroscience Uc Berkeley BerkeleyCA94720 United States Doe Agile BioFoundry Lawrence Berkeley National Laboratory BerkeleyCA94803 United States Joint BioEnergy Institute Lawrence Berkeley National Laboratory BerkeleyCA94803 United States Bcam Basque Center for Applied Mathematics Bilbao48009 Spain Computer Science University of California Davis DavisCA95616 United States Cenic La MiradaCA90638 United States Health Informatics University of California Davis School of Medicine SacramentoCA95817 United States Berkeley Institute for Data Science University of California Berkeley BerkeleyCA94720 United States Industrial Engineering and Operations Research University of California Berkeley BerkeleyCA94720 United States Environmental & Earth Sciences Area Lawrence Berkeley National Laboratory BerkeleyCA94803 United States Nuclear Engineering University of California Berkeley BerkeleyCA94720 United States Materials Science and Technology Division Los Alamos National Laboratory Los AlamosNM87545 United States Physics Division Lawrence Berkeley National Lab BerkeleyCA94720 United States Bioscience Division Los Alamos National Laboratory Los AlamosNM87545 United States Earth and Environmental Sciences Area Lawrence Berkeley National Lab BerkeleyCA94803 United States Energy Technologies Area Lawrence Berkeley National Lab BerkeleyCA94803 United States Computing and Computational Sciences Oak Ridge National Laboratory Oak RidgeTN37831 United States Industrial & Systems Engineering The University of Tennessee KnoxvilleTN37996 United States Department of Computer Science University of Missouri-Saint Louis St. LouisMO63121 United

We outline emerging opportunities and challenges to enhance the utility of AI for scientific discovery. The distinct goals of AI for industry versus the goals of AI for science create tension between identifying patterns in data versus discovering patterns in the world from data. If we address the fundamental challenges associated with "bridging the gap" between domain-driven scientific models and data-driven AI learning machines, then we expect that these AI models can transform hypothesis generation, scientific discovery, and the scientific process itself. © 2021, CC BY.

关键词： Learning systems

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INTRODUCTION

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Bulletin of the American Meteorological Society 2024年第8期105卷 S1-S11页

作者： Boyer, T. Blunden, J. Dunn, R.J.H. NOAA/NESDIS National Centers for Environmental Information Silver Spring Maryland NOAA/NESDIS National Centers for Environmental Information Asheville North Carolina Met Office Hadley Centre Exeter United Kingdom European Centre for Medium-Range Weather Forecasts Reading United Kingdom University of Maryland College Park Maryland Scripps Institution of Oceanography University of California San Diego La Jolla California NOAA/NWS National Centers for Environmental Prediction Climate Prediction Center College Park Maryland Brandenburg University of Technology (BTU) Cottbus-Senftenberg Germany Servicio Meteorológico Nacional Buenos Aires Argentina NOAA/OAR Physical Sciences Laboratory Boulder Colorado European Centre for Medium-Range Weather Forecasts Bonn Germany Center for Geophysical Research and School of Physics University of Costa Rica San José Costa Rica Department of Meteorology and National Centre for Earth Observation University of Reading Reading United Kingdom Centro Nacional de Monitoramento e Alertas de Desastres Naturais CEMADEN São Paulo Brazil Université Grenoble Alpes Institut des Géosciences de l’Environnement IRD CNRS Grenoble INP Grenoble France Hampton University Hampton Virginia Seychelles Meteorological Authority Mahe Seychelles Section for Glaciers Ice and Snow Norwegian Water Resources and Energy Directorate Oslo Norway National Research Institute for Agriculture Food and Environment (INRAE) CARRTEL Université Savoie Mont Blanc Thonon les Bains France Graduate School of Agriculture Osaka Metropolitan University Sakai Japan Science Faculty Universidad Nacional de Colombia Bogotá Colombia University of Bremen Bremen Germany NOAA Global Monitoring Laboratory Boulder Colorado Servicio Nacional de Meteorología e Hidrología del Perú Lima Perú Centro de Investigaciones sobre Desertificación – Spanish National Research Council (CSIC-UV-GVA) Valencia Spain Hydro-Climate Extremes Lab (H-CEL) Ghent University Ghent Belgium Department o

In 2023, La Niña conditions that generally prevailed in the eastern Pacific Ocean from mid-2020 into early 2023 gave way to a strong El Niño by October. Atmospheric concentrations of Earth’s major greenhouse gases—carbon dioxide, methane, and nitrous oxide—all increased to record-high levels. The annual global average carbon dioxide concentration in the atmosphere rose to 419.3±0.1 ppm, which is 50% greater than the pre-industrial level. The growth from 2022 to 2023 was 2.8 ppm, the fourth highest in the record since the 1960s. The combined short-term effects of El Niño and the long-term effects of increasing levels of heat-trapping gases in the atmosphere contributed to new records for many essential climate variables reported here. The annual global temperature across land and oceans was the highest in records dating as far back as 1850, with the last seven months (June–December) having each been record warm. Over land, the globally averaged temperature was also record high. Dozens of countries reported record or near-record warmth for the year, including China and continental Europe as a whole (warmest on record), India and Russia (second warmest), and Canada (third warmest). Intense and widespread heatwaves were reported around the world. In Vietnam, an all-time national maximum temperature record of 44.2°C was observed at Tuong Duong on 7 May, surpassing the previous record of 43.4°C at Huong Khe on 20 April 2019. In Brazil, the air temperature reached 44.8°C in Araçuaí in Minas Gerais on 20 November, potentially a new national record and 12.8°C above normal. The effect of rising temperatures was apparent in the cryosphere, where snow cover extent by June 2023 was the smallest in the 56-year record for North America and seventh smallest for the Northern Hemisphere overall. Heatwaves contributed to the greatest average mass balance loss for Alpine glaciers around the world since the start of the record in 1970. Due to rapid volume loss beginning in 2021, St. A

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