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18th International Workshop on Vision, Modeling and Visualization, VMV 2013

作者： Iglesias, J.A. Berkels, B. Rumpf, M. Scherzer, O. Computational Science Center University of Vienna Austria Institute for Numerical Simulation University of Bonn Germany Institute of Mathematics and Image Computing University of Lübeck Germany Radon Institute of Computational and Applied Mathematics Austrian Academy of Sciences Linz Austria

Frequently, one aims at the co-registration of geometries described implicitly by images as level sets. This paper proposes a novel shape sensitive approach for the matching of such implicit surfaces. Motivated by physical models of elastic shells a variational approach is proposed, which distinguishes two different types of energy contributions: a membrane energy measuring the rate of tangential distortion when deforming the reference surface into the template surface, and a bending energy reflecting the required amount of bending. The variational model is formulated via a narrow band approach. The built in tangential distortion energy leads to a suitable equidistribution of deformed length and area elements, under the optimal matching deformation, whereas the minimization of the bending energy fosters a proper matching of shape features such as crests, valleys or bumps. In the implementation, a spatial discretization via finite elements, a nonlinear conjugate gradient scheme with a Sobolev metric, and a cascadic multilevel optimization strategy are used. The features of the proposed method are discussed via applications both for synthetic and realistic examples. © The Eurographics Association 2013.

关键词： Bending (deformation)

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Proceedings of the Frontiers of Retrovirology Conference 2016

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Retrovirology 2016年第1期13卷 1-40页

作者： Irena Zurnic Sylvia Hütter Nicole Stanke Tobias Kern Fabian Lindel Gesche Gerresheim Martin Hamann Erik Müllers Dirk Lindemann Ute Lehmann Juliane Reh Paul Lesbats Peter Cherepanov Melanie Mann Erik Serrao Alan Engelman Claire Da Silva Santos Kevin Tartour Andrea Cimarelli Rya Burdick Jianbo Chen Jaya Sastri Wei-Shau Hu Vinay Pathak Oliver T. Keppler Patrícia de Sousa-Pereira Hanna-Mari Baldauf Marcel Stern Karine Pradeau Sylvia Eiler Nicolas Levy Marc Ruff Sarah Lennon Sarah Cianferani Stéphane Emiliani Vincent Parissi Sylvie Rato Miguel Munoz Angela Ciuffi Antonio Rausell Amalio Telenti Alexander Zhyvoloup Ian Anderson Chen- Hsuin Lee Ariberto Fassati Anat Melamed Delphine Planas Petronela Ancuta Yuwei Zhang Huicheng Chen Annie Bernier Annie Gosselin Janos Kriston-Vizi Robin Ketteler Andy Merritt Charles Bangham Jocelyn Turpin Anthony Rodari Benoit Van Driessche Mathilde Galais Nadége Delacourt Sylvain Fauquenoy Caroline Vanhulle Anna Kula Carine Van Lint Ernst J. Wolvetang Arsène Burny Olivier Rohr Thijs van Montfort Renee van der Sluis Ben Berkhout Dave Speijer Gang Wang Na Zhao Atze T. Das Mirte Scherpenisse Bo Meng Andrzej Rutkowski Lars Dölken Andrew Lever Neil Berry Claire Ham Neil Almond Hoi Ping Mok Nicholas Norton Axel Fun Jack Hirst Mark Wills Chris Hellmund Harriet Groom Thomas Schuster Benedikt Asbach Ralf Wagner Christine Gross Martina Kalmer Andrea K. Thoma-Kress Norbert Donhauser Sebastian Millen Sandra M. Müller-Schmucker Veit Wiesmann Thomas Wittenberg Jan Gettemans Minghua Li Shan-Lu Liu Eric O. Freed Janis Müller Jan Münch Simone Joas Clement Wesley Gnanadurai Edina Lump Christina M. Stürzel Daniel Sauter Frank Kirchhoff Katharina Mack Kathrin Starz Christina Stürzel Xaver Sewald Nasim Motamedi Pradeep Uchil Ruoxi Pi Christin Herrmann Walther Mothes Mark Ladinsky Pamela Bjorkman Jagadish Beloor Priti Kumar Thomas Murooka Thorsten Mempel Michael Brehm Dale Greiner Erica Parrish Nicholas F. Parrish Beatrice H. Hahn Frederic Bibollet-Ruche Ulrike Sauermann Katharina Töpfer Tina Schultheiss Chris Molecular Virology and Gene Therapy Molecular Medicine Leuven Belgium Molecular Virology Technical University Dresden Dresden Germany Center for Regenerative Therapies Dresden Dresden Germany Potsdam University Potsdam Germany The Francis Crick Institute London Great Britain Institute of Clinical and Molecular Virology Friedrich-Alexander-Universität Erlangen-Nuremberg Erlangen Germany Dana Farber Cancer Institute Boston MA United States CIRI Lyon France National Cancer Institute Frederick MD United States Virology Max von Pettenkofer-Institut LMU Munich Munich Germany Institute of Medical Virology University of Frankfurt Frankfurt a. M. Germany German Center for Infection Research Munich Germany Institute of Medical Virology University Hospital Frankfurt Frankfurt a. M. Germany CIBIO/InBIO University of Porto Vairão Portugal Faculty of Sciences University of Porto Porto Portugal Virology Max von Pettenkofer Institute LMU Munich Germany Institute for Medical Virology Frankfurt a. M. Germany Integrative structural Biology IGBMC Illkirch France Institut Pluridisciplinaire Hubert Curien Strasbourg France Institut Cochin Paris France CNRS UMR5234 MFP Lab Bordeaux France Associated International Laboratory (LIA) Microbiology and Immunology CNRS/Université de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology Bordeaux/Hamburg France Institute of Microbiology University Hospital Center and University of Lausanne Lausanne Switzerland Imagine Institute Paris Descartes University Paris France J. Craig Venter Institute La Jolla CA United States Infection University College London London Great Britain Medicine Imperial College London Great Britain Microbiology & Infection University of Montreal Montreal Great Britain CRCHUM Montreal Canada University College London LMCB London Great Britain MRC Technology Centre for Therapeutic Discovery London Great Britain Section of Virology Department of Medicine Imperial Co

Oral presentationsSession 1: Entry & uncoatingO1 Host cell polo-like kinases (PLKs) promote early prototype foamy virus (PFV) replicationIrena Zurnic, Sylvia Hütter, Ute Lehmann, Nicole Stanke, Juliane Re... 详细信息

Oral presentations

Session 1: Entry & uncoating

O1 Host cell polo-like kinases (PLKs) promote early prototype foamy virus (PFV) replication

Irena Zurnic, Sylvia Hütter, Ute Lehmann, Nicole Stanke, Juliane Reh, Tobias Kern, Fabian Lindel, Gesche Gerresheim, Martin Hamann, Erik Müllers, Paul Lesbats, Peter Cherepanov, Erik Serrao, Alan Engelman, Dirk Lindemann

O2 A novel entry/uncoating assay reveals the presence of at least two species of viral capsids during synchronized HIV-1 infection

Claire Da Silva Santos, Kevin Tartour, Andrea Cimarelli

O3 Dynamics of nuclear envelope association and nuclear import of HIV-1 complexes

Rya Burdick, Jianbo Chen, Jaya Sastri, Wei-Shau Hu, Vinay Pathak

O4 Human papillomavirus protein E4 potently enhances the susceptibility to HIV infection

Oliver T. Keppler

Session 2: Reverse transcription & integration

O5 Structure and function of HIV-1 integrase post translational modifications

Karine Pradeau, Sylvia Eiler, Nicolas Levy, Sarah Lennon, Sarah Cianferani, Stéphane Emiliani, Marc Ruff

O6 Regulation of retroviral integration by RNA polymerase II associated factors and chromatin structure

Vincent Parissi

Session 3: Transcription and latency

O7 A novel single-cell analysis pipeline to identify specific biomarkers of HIV permissiveness

Sylvie Rato, Antonio Rausell, Miguel Munoz, Amalio Telenti, Angela Ciuffi

O8 A capsid-dependent integration program linking T cell activation to HIV-1 gene expression

Alexander Zhyvoloup, Anat Melamed, Ian Anderson, Delphine Planas, Janos Kriston-Vizi, Robin Ketteler, Chen-Hsuin Lee, Andy Merritt, Petronela Ancuta, Charles Bangham, Ariberto Fassati

O9 Characterisation of new RNA polymerase III and RNA polymerase II transcriptional promoters in the Bovine Leukemia Virus genome

Anthony Rodari, Benoit Van Driessche, Mathilde Galais, Nadége Delacourt, Sylv

关键词： Human Immunodeficiency Virus Infection Simian Immunodeficiency Virus Feline Immunodeficiency Virus Bovine Leukemia Virus Prototype Foamy Virus

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Containment for double-integrator multi-agent systems in heterogeneous networks

Containment for double-integrator multi-agent systems in het...

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IEEE Annual Conference on Decision and Control

作者： Jiahu Qin Wei Xing Zheng Huijun Gao Qichao Ma University of Science and Technology of China Hefei China School of Computing Engineering and Mathematics University of Western Sydney Penrith NSW 2751 Australia Research Institute of Intelligent Control and Systems Harbin Institute of Technology Harbin 150080 Heilongjiang Province China Department of Automation University of Science and Technology of China Hefei China

ISBN: (纸本)9781467360890

This paper is concerned with the containment control for a group of double-integrator agents with multiple dynamic leaders communicating over heterogeneous networks, i.e., the position and velocity network topologies are modeled by different graphs. Different containment control algorithms are proposed and analyzed for the two cases that the leaders move with the same constant velocity and the same time-varying velocity, respectively. For the former case the sufficient conditions provided for guaranteeing the containment control are structural and thus easy to verify. Though the conditions proposed for the latter case that leaders move with time-varying velocity are algebraic, such algebraic conditions can be satisfied if the position and velocity network topologies among the follower agents are undirected.

关键词： Network topology Eigenvalues and eigenfunctions Educational institutions Symmetric matrices Heuristic algorithms Algorithm design and analysis Vectors

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Comprehensive, open-source resource usage measurement and analysis for HPC systems

Comprehensive, open-source resource usage measurement and an...

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作者： Browne, James C. Deleon, Robert L. Patra, Abani K. Barth, William L. Hammond, John Jones, Matthew D. Furlani, Thomas R. Schneider, Barry I. Gallo, Steven M. Ghadersohi, Amin Gentner, Ryan J. Palmer, Jeffrey T. Simakov, Nikolay Innus, Martins Bruno, Andrew E. White, Joseph P. Cornelius, Cynthia D. Yearke, Thomas Marcus, Kyle Von Laszewski, Gregor Wang, Fugang Department of Computer Science University of Texas Austin TX 78758 United States Center for Computational Research University at Buffalo State University of New York 701 Ellicott Street Buffalo NY 14203 United States Mechanical and Aerospace Engineering Department University at Buffalo State University of New York Amherst NY 14260 United States Texas Advanced Computing Center University of Texas Austin TX 78758 United States National Institute of Science and Technology Gaithersburg MD United States Pervasive Technology Institute Indiana University 2719 East 10th Street Bloomington IN 47408 United States

The important role high-performance computing (HPC) resources play in science and engineering research, coupled with its high cost (capital, power and manpower), short life and oversubscription, requires us to optimize its usage - an outcome that is only possible if adequate analytical data are collected and used to drive systems management at different granularities - job, application, user and system. This paper presents a method for comprehensive job, application and system-level resource use measurement, and analysis and its implementation. The steps in the method are system-wide collection of comprehensive resource use and performance statistics at the job and node levels in a uniform format across all resources, mapping and storage of the resultant job-wise data to a relational database, which enables further implementation and transformation of the data to the formats required by specific statistical and analytical algorithms. Analyses can be carried out at different levels of granularity: job, user, application or system-wide. Measurements are based on a new lightweight job-centric measurement tool 'TACC-Stats', which gathers a comprehensive set of resource use metrics on all compute nodes and data logged by the system scheduler. The data mapping and analysis tools are an extension of the XDMoD project. The method is illustrated with analyses of resource use for the Texas Advanced computing Center's Lonestar4, Ranger and Stampede supercomputers and the HPC cluster at the Center for computational Research. The illustrations are focused on resource use at the system, job and application levels and reveal many interesting insights into system usage patterns and also anomalous behavior due to failure/misuse. The method can be applied to any system that runs the TACC-Stats measurement tool and a tool to extract job execution environment data from the system scheduler. Copyright © 2014 John Wiley & Sons, Ltd.

关键词： Digital storage

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Accuracy of generalized gradient approximation functionals for density-functional perturbation theory calculations

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Physical Review B 2014年第6期89卷 064305-064305页

作者： Lianhua He Fang Liu Geoffroy Hautier Micael J. T. Oliveira Miguel A. L. Marques Fernando D. Vila J. J. Rehr G.-M. Rignanese Aihui Zhou LSEC Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China School of Applied Mathematics Central University of Finance and Economics Beijing 100081 China European Theoretical Spectroscopy Facility (ETSF) Institute of Condensed Matter and Nanosciences (IMCN) Université Catholique de Louvain Chemin des Étoiles 8 1348 Louvain-la-Neuve Belgium Center for Computational Physics University of Coimbra Rua Larga 3004-516 Coimbra Portugal Institut Lumière Matière UMR5306 Université Lyon 1-CNRS Université de Lyon F-69622 Villeurbanne Cedex France Department of Physics University of Washington Seattle Washington 98195 USA

We assess the validity of various exchange-correlation functionals for computing the structural, vibrational, dielectric, and thermodynamical properties of materials in the framework of density-functional perturbation theory (DFPT). We consider five generalized-gradient approximation (GGA) functionals (PBE, PBEsol, WC, AM05, and HTBS) as well as the local density approximation (LDA) functional. We investigate a wide variety of materials including a semiconductor (silicon), a metal (copper), and various insulators (SiO2 α-quartz and stishovite, ZrSiO4 zircon, and MgO periclase). For the structural properties, we find that PBEsol and WC are the closest to the experiments and AM05 performs only slightly worse. All three functionals actually improve over LDA and PBE in contrast with HTBS, which is shown to fail dramatically for α-quartz. For the vibrational and thermodynamical properties, LDA performs surprisingly very well. In the majority of the test cases, it outperforms PBE significantly and also the WC, PBEsol and AM05 functionals though by a smaller margin (and to the detriment of structural parameters). On the other hand, HTBS performs also poorly for vibrational quantities. For the dielectric properties, none of the functionals can be put forward. They all (i) fail to reproduce the electronic dielectric constant due to the well-known band gap problem and (ii) tend to overestimate the oscillator strengths (and hence the static dielectric constant).

关键词： PERTURBATION (Quantum dynamics) SILICON THERMODYNAMICS DIELECTRIC devices DIELECTRICS

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Coexistence of size-dependent and size-independent thermal conductivities in phosphorene

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Physical Review B 2014年第21期90卷 214302-214302页

作者： Liyan Zhu Gang Zhang Baowen Li Department of Physics Center for Computational Science and Engineering and Graphene Research Center National University of Singapore Singapore 117542 Republic of Singapore Institute of High Performance Computing Singapore 138632 Republic of Singapore NUS Graduate School for Integrative Sciences and Engineering National University of Singapore Singapore 117546 Republic of Singapore Center for Phononics and Thermal Energy Science School of Physics Sciences and Engineering Tongji University Shanghai 200092 People's Republic of China

Thermal conductivity of single layer phosphorene is investigated by combining density functional calculations and the Peierls-Boltzmann transport equation. Differing from isotropic and divergent thermal conductivities in two-dimensional graphene and MoS2, a compelling coexistence of size-dependent and size-independent thermal conductivities is discovered for single layer black phosphorus (BP) along zigzag (ZZ) and armchair (AM) directions, respectively. Additionally, thermal conductivities in single layer phosphorene are found to be highly anisotropic because of orientation dependent group velocities and phonon relaxation times; e.g., thermal conductivities at 300 K are 83.5 and 24.3 W/m K along ZZ and AM directions, respectively, for single layer BP with a size of 10μm.

关键词： THERMAL conductivity DENSITY functionals TRANSPORT theory (mathematics) GRAPHENE CHEMICAL relaxation PHONONS

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Faraday waves in collisionally inhomogeneous Bose-Einstein condensates

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Physical Review A 2014年第2期89卷 023609-023609页

作者： Antun Balaž Remus Paun Alexandru I. Nicolin Sudharsan Balasubramanian Radha Ramaswamy Scientific Computing Laboratory Institute of Physics Belgrade University of Belgrade Pregrevica 118 11080 Belgrade Serbia Department of Computational Physics and Information Technologies Horia Hulubei National Institute of Physics and Nuclear Engineering (IFIN-HH) P. O. Box MG-6 077125 Romania Centre for Nonlinear Science Post-Graduate and Research Department of Physics Government College for Women (Autonomous) Kumbakonam 612001 India

We study the emergence of Faraday waves in cigar-shaped collisionally inhomogeneous Bose-Einstein condensates subject to periodic modulation of the radial confinement. Considering a Gaussian-shaped radially inhomogeneous scattering length, we show through extensive numerical simulations and detailed variational treatment that the spatial period of the emerging Faraday waves increases as the inhomogeneity of the scattering length gets weaker, and that it saturates once the width of the radial inhomogeneity reaches the radial width of the condensate. In the regime of strongly inhomogeneous scattering lengths, the radial profile of the condensate is akin to that of a hollow cylinder, while in the weakly inhomogeneous case the condensate is cigar shaped and has a Thomas-Fermi radial density profile. Finally, we show that when the frequency of the modulation is close to the radial frequency of the trap, the condensate exhibits resonant waves which are accompanied by a clear excitation of collective modes, while for frequencies close to twice that of the radial frequency of the trap, the observed Faraday waves set in forcefully and quickly destabilize condensates with weakly inhomogeneous two-body interactions.

关键词： BOSE-Einstein condensation FARADAY effect COLLISIONS (Physics) THEORY of wave motion GAUSSIAN processes NUMERICAL analysis

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Forgeability of Wang-Zhu-Feng-Yau’s Attribute-Based Signature with Policy-and-Endorsement Mechanism

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Journal of Computer science & Technology 2013年第4期28卷 743-748页

作者：葛爱军黄欣沂陈成马传贵张锐 State Key Laboratory of Mathematical Engineering and Advanced Computing Zhengzhou Information Science and Technology Institute State Key Laboratory of Information Security Institute of Information Engineering Chinese Academy of Sciences Fujian Provincial Key Laboratory of Network Security and Cryptology School of Mathematics and Computer ScienceFujian Normal University Institute of Software Chinese Academy of Sciences

Recently, Wang et al. presented a new construction of attribute-based signature with policy-and-endorsement mechanism. The existential unforgeability of their scheme was claimed to be based on the strong Diffie-Hellman assumption in the random oracle model. Unfortunately, by carefully revisiting the design and security proof of Wang et alfs scheme, we show that their scheme cannot provide unforgeability, namely, a forger, whose attributes do not satisfy a given signing predicate, can also generate valid signatures. We also point out the flaws in Wang et al.＇s proof.

关键词： attribute-based signature existential unforgeability policy-and-endorsement

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Complex polarisabilities and hyperpolarisabilities of atoms

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Journal of Physics: Conference Series 2015年第9期635卷

作者： M W J Bromley S J Grunefeld J M Rossi J C Berengut L Y Tang J Jiang Yongjun Cheng J Mitroy School of Mathematics and Physics The University of Queensland Australia Computational Science Research Center San Diego State University U. S. A. School of Physics University of New South Wales Australia Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan P. R. China Northwest Normal University Langzhou P. R. China Harbin Institute of Technology Harbin P. R. China School of Engineering Charles Darwin University Australia

The complex dipole polarisabilities of alkali atoms are computed for low-lying eigenstates. We present a unified method of calculation of the real part of the polarisability as well as two different imaginary contributions to the polarisability. One imaginary polarisability is related to the resonant damping of the cross-section both below and above threshold, whilst the other imaginary polarisability describes the photoionisation cross-section above threshold. We also present preliminary calculations of the complex hyperpolarisabilities of atomic clocks and how they are impacted by the linear and non-linear photon-atom interactions.

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Synchronization in Time-varying Networks of Non-Introspective Agents without Exchange of Controller States

Synchronization in Time-varying Networks of Non-Introspectiv...

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American Control Conference

作者： Tao Yang Havard Fjaer Grip Ali Saberi Meirong Zhang Anton A. Stoorvogel ACCESS Linnaeus Centre Royal Institute of Technology (KTH) SE-100 44 Stockholm Sweden Department of Engineering Cybernetics Norwegian University of Science and Technology School of Electrical Engineering and Computer Science Washington State University Pullman WA 99164-2752 USA Department of Electrical Engineering Mathematics and Computing Science University of Twente P.O. Box 217 7500 AE Enschede The Netherlands

ISBN: (纸本)9781479932757

We consider two synchronization problems, namely, state synchronization for networks of identical linear agents, and regulated output synchronization for networks of non-identical linear agents, under a time-varying topology. Agents are assumed to be multiple-input multiple-output (MIMO), minimum-phase, right invertible and non-introspective (i.e., they only receive relative output information from their neighboring agents, but lack independent information about their own states or outputs). The time-varying topology is assumed to switch among a finite number of directed graphs containing a directed spanning tree with an arbitrarily a priori given non-vanishing dwell time. Moreover agents are unable to exchange of controller states with their neighboring agents. For solving each problem, we propose a distribute dynamic protocol based on a combination of low-gain and high-gain design techniques.

关键词： Synchronization Topology Switches Network topology Educational institutions Eigenvalues and eigenfunctions Trajectory

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