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arXiv 2020年

作者： Berre, Inga Boon, Wietse M. Flemisch, Bernd Fumagalli, Alessio Gläser, Dennis Keilegavlen, Eirik Scotti, Anna Stefansson, Ivar Tatomir, Alexandru Brenner, Konstantin Burbulla, Samuel Devloo, Philippe Duran, Omar Favino, Marco Hennicker, Julian Lee, I-Hsien Lipnikov, Konstantin Masson, Roland Mosthaf, Klaus Chiara Nestola, Maria Giuseppina Ni, Chuen-Fa Nikitin, Kirill Schädle, Philipp Svyatskiy, Daniil Yanbarisov, Ruslan Zulianp, Patrick Department of Mathematics University of Bergen Allégaten 41 Bergen5007 Norway Department of Mathematics KTH Royal Institute of Technology Lindstedtsvägen 25 Stockholm11428 Sweden Department of Hydromechanics and Modelling of Hydrosystems University of Stuttgart Pfaffenwaldring 61 Stuttgart70569 Germany Laboratory for Modeling and Scientific Computing MOX Politecnico di Milano p.za Leonardo da Vinci 32 Milano20133 Italy Department of Applied Geology Geosciences Center University of Göttingen Goldschmidtstrasse 3 Göttingen37077 Germany Department of Earth Sciences Uppsala University Villavägen 16 UppsalaS-75236 Sweden University of Côte d’Azur CNRS INRIA LJAD Nice France Institute of Applied Analysis and Numerical Simulation University of Stuttgart Pfaffenwaldring 57 Stuttgart70569 Germany FEC Universidade Estadual de Campinas Cidade Universitária R. Josiah Willard Gibbs 85 Campinas-SPCEP 13083-839 Brazil Institute of Earth Sciences University of Lausanne Building Geopolis UNIL-Mouline Lausanne1015 Switzerland Section de Mathématiques Université de Genève 2-4 rue du Lièvre CP 64 Genève1211 Switzerland Graduate Institute of Applied Geology National Central University Taiwan Center for Environmental Studies National Central University Taiwan Los Alamos National Laboratory New Mexico United States Department of Environmental Engineering Technical University of Denmark Bygningstorvet Building 115 Kgs. Lyngby2800 Denmark Numerical Simulation in Science Medicine and Engineering Group Institute of Computational Science Università della Svizzera italiana. Via G. Buffi 13 Lugano Ticino6900 Switzerland Marchuk Institute of Numerical Mathematics of Russian Academy of Sciences Moscow Russia ETH Zürich Geothermal Energy and Geofluids Group Institute of Geophysics Zürich8092 Switzerland

Flow in fractured porous media occurs in the earth’s subsurface, in biological tissues, and in man-made materials. Fractures have a dominating influence on flow processes, and the last decade has seen an extensive development of models and numerical methods that explicitly account for their presence. To support these developments, we present a portfolio of four benchmark cases for single-phase flow in three-dimensional fractured porous media. The cases are specifically designed to test the methods’ capabilities in handling various complexities common to the geometrical structures of fracture networks. Based on an open call for participation, results obtained with 17 numerical methods were collected. This paper presents the underlying mathematical model, an overview of the features of the participating numerical methods, and their performance in solving the benchmark cases. Copyright © 2020, The Authors. All rights reserved.

关键词： Numerical methods

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Facile Anhydrous Proton Transport on Hydroxyl Functionalized Graphane

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Physical Review Letters 2017年第18期118卷 186101-186101页

作者： Abhishek Bagusetty Pabitra Choudhury Wissam A. Saidi Bridget Derksen Elizabeth Gatto J. Karl Johnson Computational Modeling and Simulation Program University of Pittsburgh Pittsburgh Pennsylvania 15260 USA Department of Chemical and Petroleum Engineering University of Pittsburgh Pittsburgh Pennsylvania 15261 USA Department of Chemical Engineering New Mexico Tech Socorro New Mexico 87801 USA Department of Mechanical and Materials Science University of Pittsburgh Pittsburgh Pennsylvania 15261 USA

Graphane functionalized with hydroxyl groups is shown to rapidly conduct protons under anhydrous conditions through a contiguous network of hydrogen bonds. Density functional theory calculations predict remarkably low barriers to diffusion of protons along a 1D chain of surface hydroxyls. Diffusion is controlled by the local rotation of hydroxyl groups, a mechanism that is very different from that found in 1D water wires in confined nanopores or in bulk water. The proton mean square displacement in the 1D chain was observed to follow Fickian diffusion rather than the expected single-file mobility. A charge analysis reveals that the charge on the proton is essentially equally shared by all hydrogens bound to oxygens, effectively delocalizing the proton.

关键词： Anomalous diffusion Graphene Membrane structures

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Regional Biomechanical Imaging of Liver Cancer Cells

SSRN

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SSRN 2018年

作者： Pei, Weiwei Chen, Jiayao Wang, Chao Qiu, Suhao Zeng, Jianfeng Gao, Mingyuan Zhou, Bin Li, Dan Sacks, Michael S. Han, Lin Shan, Hong Hu, Wentao Zhou, Guangmin Feng, Yuan Soochow University Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions Jiangsu Suzhou215123 China Soochow University Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions Jiangsu Suzhou215123 China Guangdong Provincial Engineering Research Center of Molecular Imaging Fifth Affiliated Hospital Sun Yat-sen University Guangdong Zhuhai519000 China School of Biomedical Engineering Science and Health Systems Drexel University PhiladelphiaPA19104 United States Institute for Medical Imaging Technology School of Biomedical Engineering Shanghai Jiao Tong University Shanghai200240 China Willerson Center for Cardiovascular Modeling and Simulation Institute for Computational Engineering & Sciences University of Texas at Austin TX78712 United States

Liver cancer is one of the leading cancers, especially in developing countries. Understanding the biomechanical properties of the liver cancer cells can not only help to elucidate the mechanisms behind the cancer progression, but also provide important information for diagnosis and treatment. At the cellular level, we used well-established atomic force microscopy (AFM) techniques to characterize the heterogeneity of mechanical properties of two different types of human liver cancer cells and a normal liver cell. Stiffness maps with a resolution of 128x128 were acquired for each cell. The distributions of the indentation moduli of the cells showed significant differences between cancerous cells and healthy controls. Significantly, the variability was even greater amongst different types of cancerous cells. Fitting of the histogram of the effective moduli using a normal distribution function showed the Bel7402 cells were stiffer than the normal cells while HepG2 cells were softer. Morphological analysis of the cell structures also showed a higher cytoskeleton content among the cancerous cells. Results provided a foundation for applying knowledge of cell stiffness heterogeneity to search for tissue-level, early-stage indicators of liver cancer. © 2018, The Authors. All rights reserved.

关键词： Cells

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SeeBridge information delivery manual (IDM) for next generation bridge inspection 33

SeeBridge information delivery manual (IDM) for next generat...

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33rd International Symposium on Automation and Robotics in Construction, ISARC 2016

作者： Sacks, Rafael Kedar, Amir Borrmann, André Ma, Ling Singer, Dominic Kattel, Uri Faculty of Civil and Environmental Engineering. Technion - Israel Institute of Technology Israel Kedmor Engineers Givatayim Israel Computational Modeling and Simulation Technical University Munich Germany National Building Research Institute Technion - Israel Institute of Technology Israel

Innovative solutions for rapid and intelligent survey and assessment methods are required in maintenance, repair, retrofit and rebuild of enormous numbers of bridges in service throughout the world. Motivated by this need, a next-generation integrated bridge inspection system named SeeBridge is proposed. To frame the system, an Information Delivery Manual (IDM) was compiled to specify the technical components, activities and information exchanges in the SeeBridge process. The IDM supports development of the system by rigorously defining the information and data repositories that structure bridge engineers' knowledge. The SeeBridge process is mapped, parts of the data repositories are presented and the future use of the IDM is discussed.

关键词： Remote sensing

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Using simulation games for teaching & learning discrete-event simulation

Using simulation games for teaching & learning discrete-even...

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2016 Winter simulation Conference, WSC 2016

作者： Padilla, Jose J. Lynch, Christopher J. Diallo, Saikou Y. Gore, Ross J. Barraco, Anthony Kavak, Hamdi Jenkins, Bakari Virginia Modeling Analysis and Simulation Center Old Dominion University 1030 University Blvd. SuffolkVA23435 United States Modeling Simulation and Visualization Engineering Dept. Old Dominion University 1300 Eng. and Computational Sciences Building NorfolkVA23529 United States Pruden Center for Industry and Technology 4169 Pruden Blvd. SuffolkVA23434 United States

ISBN: (纸本)9781509044863

Capturing and retaining the attention of students while learning complex topics like modeling and simulation is a critical task. In discrete-event simulation (DES), educators rely on examples like queueing systems in fast food restaurants or manufacturing organizations to provide the necessary context for learning. In many instances, these examples fall short in capturing the attention of students, especially at the middle and high school levels. One approach for learning complex topics, like creating simulations, is through gaming. This paper reports on the creative use of regular simulation tools to develop simulation games with entertainment content aimed towards engaging young learners. Two games are presented: one focuses on the use of decision nodes while the second focuses on the use of batch/separator nodes. As part of future work, we propose to use these games to evaluate how much knowledge transfers from an entertainment context to one using simulations for real-life situations. © 2016 IEEE.

关键词： Discrete event simulation

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Controlling the Error on Target Motion through Real-time Mesh Adaptation: Applications to Deep Brain Stimulation

arXiv

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arXiv 2017年

作者： Bui, Huu Phuoc Tomar, Satyendra Courtecuisse, Hadrien Audette, Michel Cotin, Stéphane Bordas, Stéphane P.A. Institute of Computational Engineering University of Luxembourg Faculty of Sciences Communication and Technology Luxembourg University of Strasbourg CNRS ICube Strasbourg France Department of Modeling Simulation and Visualization Engineering Old Dominion University Norfolk United States Inria Nancy-Grand Est Villers-lès-Nancy France Institute of Mechanics and Advanced Materials School of Engineering Cardiff University United Kingdom Intelligent Systems for Medicine Laboratory University of Western Australia Perth Australia

We present an error-controlled mesh refinement procedure for needle insertion simulation and apply it to the simulation of electrode implantation for deep brain stimulation, including brain shift. Our approach enables to control the error in the computation of the displacement and stress fields around the needle tip and needle shaft by suitably refining the mesh, whilst maintaining a coarser mesh in other parts of the domain. We demonstrate through academic and practical examples that our approach increases the accuracy of the displacement and stress fields around the needle without increasing the computational expense. This enables real-time simulations. The proposed methodology has direct implications to increase the accuracy and control the computational expense of the simulation of percutaneous procedures such as biopsy, brachytherapy, regional anesthesia, or cryotherapy and can be essential to the development of robotic guidance. Copyright © 2017, The Authors. All rights reserved.

关键词： Finite element method

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i-PI 2.0: A universal force engine for advanced molecular simulations

arXiv

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arXiv 2018年

作者： Kapil, Venkat Rossi, Mariana Marsalek, Ondrej Petraglia, Riccardo Litman, Yair Spura, Thomas Cheng, Bingqing Cuzzocrea, Alice Meißner, Robert H. Wilkins, David M. Juda, Przemyslaw Bienvenue, Sébastien P. Fang, Wei Kessler, Jan Poltavsky, Igor Vandenbrande, Steven Wieme, Jelle Corminboeuf, Clemence Kühne, Thomas D. Manolopoulos, David E. Markland, Thomas E. Richardson, Jeremy O. Tkatchenko, Alexandre Tribello, Gareth A. van Speybroeck, Veronique Ceriotti, Michele Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Fritz Haber Institute of the Max Planck Society Theory Department Faradayweg 4-6 Berlin14195 Germany Physics and Materials Science Research Unit University of Luxembourg L-1511 Luxembourg Department of Chemistry Stanford University StanfordCA94305 United States Atomistic Simulation Centre School of Mathematics and Physics Queen’s University Belfast BelfastBT7 1NN United Kingdom Department of Chemistry and Center for Sustainable Systems Design University of Paderborn Warburger Str. 100 PaderbornD-33098 Germany Laboratory of Physical Chemistry ETH Zurich Zurich8093 Switzerland Center for Molecular Modeling Ghent University Zwijnaarde9052 Belgium Physical and Theoretical Chemistry Laboratory South Parks Road OxfordOX1 3QZ United Kingdom Laboratory for Computational Molecular Design Institute of Chemical Sciences and Engineering École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Charles University Faculty of Mathematics and Physics Ke Karlovu 3 Prague 2121 16 Czech Republic

Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born-Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code[1] was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives. Copyright © 2018, The Authors. All rights reserved.

关键词： Molecular dynamics

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Optomechanical Control of Quantum Yield inTrans–CisUltrafast Photoisomerization of a Retinal Chromophore Model

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Angewandte Chemie 2017年第14期129卷

作者： Alessio Valentini Daniel Rivero Felipe Zapata Cristina García‐Iriepa Marco Marazzi Raúl Palmeiro Ignacio Fdez. Galván Diego Sampedro Massimo Olivucci Luis Manuel Frutos Department of Analytical Chemistry Physical Chemistry and Chemical Engineering University of Alcalá Ctra. A2 Km 33 6 28871 Alcalá de Henares Spain Department of Biotechnology Chemistry and Pharmacy University of Siena via A. Moro 2 53100 Siena Italy Departamento de Química Centro de Investigación en Síntesis Química (CISQ) University of La Rioja Madre de Dios 53 26006 Logroño Spain Theory-Modeling-Simulation SRSMC Université de Lorraine-Nancy Vandoeuvre-lès-Nancy Nancy France Theory-Modeling-Simulation SRSMC CNRS SRSMC Boulevard des Aiguillettes Vandoeuvre-lès-Nancy France Department of Chemistry-Ångström Uppsala Center for Computational Chemistry–UC3 Uppsala University Box 518 75120 Uppsala Sweden Department of Chemistry Bowling Green State University Bowling Green OH 43403 USA USIAS and Institut de Physique et Chimie des Matériaux de Strasbourg Université de Strasbourg-CNRS 67034 Strasbourg France

The quantum yield of a photochemical reaction is one of the most fundamental quantities in photochemistry, as it measures the efficiency of the transduction of light energy into chemical energy. Nature has evolved photoreceptors in which the reactivity of a chromophore is enhanced by its molecular environment to achieve high quantum yields. The retinal chromophore sterically constrained inside rhodopsin proteins represents an outstanding example of such a control. In a more general framework, mechanical forces acting on a molecular system can strongly modify its reactivity. Herein, we show that the exertion of tensile forces on a simplified retinal chromophore model provokes a substantial and regular increase in the trans ‐to‐ cis photoisomerization quantum yield in a counterintuitive way, as these extension forces facilitate the formation of the more compressed cis photoisomer. A rationale for the mechanochemical effect on this photoisomerization mechanism is also proposed.

关键词： Halbklassische Dynamik Mechanochemie Photoisomerisierung Quantenausbeute Retinal-Modelle

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26th Annual computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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An approach to describe arbitrary transition curves in an IFC-based alignment product data model

An approach to describe arbitrary transition curves in an IF...

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2014 International Conference on Computing in Civil and Building engineering

作者： Amann, J. Flurl, M. Jubierre, J.R. Borrmann, A. Department of Computational Modeling and Simulation Faculty of Civil Geo and Environmental Engineering Technische Universität München P.O. Box 80333 Munich Germany

ISBN: (纸本)9780784413616

Open standards for infrastructure based on Industry Foundation Classes (IFC) are mainly developed by the open INFRA initiative of the building Smart organization. Recently, several proposals for alignment models emerged with the development of the upcoming IFC 5 standard that, in particular, targets infrastructure projects such as roads, bridges and tunnel buildings. A common drawback of all of these proposals is their limited description of arbitrary transition curves. For instance, in all proposed alignment models, there are some missing types of transition curves or different parameters are suggested to describe a certain transition curve type. Designing a neutral data format that satisfies all stakeholders in an international context is, therefore, difficult. A novel approach to describe transition curves based on the Industry Foundation Classes Programming Language (IFCPL) is described and its integration into an IFC-based alignment model is shown to avoid these problems. © ASCE 2014.

关键词： TRANSITION CURVES INTERNAL FISSION COUNTER INFRASTRUCTURE Open Standard

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