TY - GEN A1 - Golas, Ulrike T1 - A General Attribution Concept for Models in M- adhesive Transformation Systems: Long Version N2 - Attributes are an important concept for modeling data in practical applications. Up to now there is no adequate way to define attributes for different kinds of models used in M-adhesive transformation systems, which are a special kind of graph transformation systems based on M-adhesive categories. Especially a proper representation and definition of attributes and their values as well as a suitable handling of the data does not fit well with other graph transformation formalisms. In this paper, we propose a new method to define attributes in a natural, but still formally precise and widely applicable way. We define a new kind of adhesive category, called W-adhesive, that can be used for transformations of attributes, while the underlying models are still M-adhesive ones. As a result, attributed models can be used as they are intended to be, but with a formal background and proven well-behavior. T3 - ZIB-Report - 12-22 KW - graph transformation KW - attribution KW - adhesive categories Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15547 SN - 1438-0064 ER - TY - THES A1 - Wende, Florian T1 - Dynamic Load Balancing on Massively Parallel Computer Architectures N2 - This thesis reports on using dynamic load balancing methods on massively parallel computers in the context of multithreaded computations. In particular we investigate the applicability of a randomized work stealing algorithm to ray tracing and breadth-first search as representatives of real-world applications with dynamic work creation. For our considerations we made use of current massively parallel hardware accelerators: Nvidia Tesla M2090, and Intel Xeon Phi. For both of the two we demonstrate the suitability of the work stealing scheme for the said real-world applications. Also the necessity of dynamic load balancing for irregular computations on such hardware is illustrated. N2 - Vorliegende Bachelorarbeit befasst sich mit Methoden der dynamischen Lastbalancierung auf massiv parallelen Computern im Rahmen von mehrprozess gestützten Ausführungen von Programmen. Im einzelnen wird die Eignung eines randomisierten Work-Stealing Algorithmus für die Ausführung realer Anwendungen mit dynamischer Arbeitserzeugung, wie Ray-Tracing und Breitensuche, untersucht. Für die entsprechenden Betrachtungen wer den aktuelle massiv parallele Hardwarebeschleuniger vom Typ Nvidia Tesla M2090 und Intel Xeon Phi verwendet. Für beide Beschleunigertypen konnte die Tauglichkeit des Work-Stealing Schemas für die genannten Anwendungen gezeigt werden. Ebenfalls wird die Notwendigkeit der Verwendung dynamischer Lastausgleichsmethoden für irreguläre Berechnungen auf der genannten Hardware verdeutlicht. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42166 ER - TY - GEN A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU N2 - Simulations of the critical Ising model by means of local update algorithms suffer from critical slowing down. One way to partially compensate for the influence of this phenomenon on the runtime of simulations is using increasingly faster and parallel computer hardware. Another approach is using algorithms that do not suffer from critical slowing down, such as cluster algorithms. This paper reports on the Swendsen-Wang multi-cluster algorithm on Intel Xeon Phi coprocessor 5110P, Nvidia Tesla M2090 GPU, and x86 multi-core CPU. We present shared memory versions of the said algorithm for the simulation of the two- and three-dimensional Ising model. We use a combination of local cluster search and global label reduction by means of atomic hardware primitives. Further, we describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im plementations of the Swendsen-Wang algorithm are demonstrated. T3 - ZIB-Report - 13-44 KW - Swendsen-Wang Multi-Cluster Algorithm KW - Ising Model KW - Xeon Phi KW - GPGPU KW - Connected Component Labeling Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42187 SN - 1438-0064 ER - TY - GEN A1 - Pyszkalski, Wolfgang T1 - Übersicht über die Datenhaltung im ZIB und die Möglichkeiten einer Nutzung durch Projekte N2 - Dieser Bericht beschreibt in allgemein verständlicher Form die Struktur der Datenhaltung im Zuse‐Institut Berlin (ZIB) und die aktuell verwendeten Strategien im Umgang mit immer stärker wachsenden Datenmengen, sowie der Herausforderung der Speicherung unwiederbringlicher Daten über im Grunde unbegrenzte Zeit. T3 - ZIB-Report - 13-16 KW - Langfristige Datenhaltung KW - Speichersysteme KW - Magnetband KW - Vertrauenswürdigkeit des Langzeitspeichers KW - Sicherstellung der Lesbarkeit des Bandmaterials Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42060 SN - 1438-0064 ER - TY - JOUR A1 - Delle Site, Luigi A1 - Krekeler, Christian A1 - Whittaker, John A1 - Agarwal, Animesh A1 - Klein, Rupert A1 - Höfling, Felix T1 - Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir JF - Advanced Theory and Simulations N2 - The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the reservoirs. Here, a combined, explicit reservoir is constructed by interfacing the atomistic region with regions of point-like, non-interacting particles (tracers) embedded in a thermodynamic mean field. The tracer molecules acquire atomistic resolution upon entering the atomistic region and equilibrate with this environment, while atomistic molecules become tracers governed by an effective mean-field potential after crossing the atomistic boundary. The approach is extensively tested on thermodynamic, structural, and dynamic properties of liquid water. Conceptual and numerical advantages of the procedure as well as new perspectives are highlighted and discussed. Y1 - 2019 U6 - https://doi.org/10.1002/adts.201900014 VL - 2 SP - 1900014 ER - TY - JOUR A1 - Stoop, Ralph L. A1 - Straube, Arthur A1 - Johansen, Tom H. A1 - Tierno, Pietro T1 - Collective directional locking of colloidal monolayers on a periodic substrate JF - Phys. Rev. Lett. N2 - We investigate the directional locking effects that arise when a monolayer of paramagnetic colloidal particles is driven across a triangular lattice of magnetic bubbles. We use an external rotating magnetic field to generate a two-dimensional traveling wave ratchet forcing the transport of particles along a direction that intersects two crystallographic axes of the lattice. We find that, while single particles show no preferred direction, collective effects induce transversal current and directional locking at high density via a spontaneous symmetry breaking. The colloidal current may be polarized via an additional bias field that makes one transport direction energetically preferred. Y1 - 2020 U6 - https://doi.org/10.1103/PhysRevLett.124.058002 VL - 124 SP - 058002 ER - TY - JOUR A1 - Abbott, Joshua L. A1 - Straube, Arthur A1 - Aarts, Dirk G. A. L. A1 - Dullens, Roel P. A. T1 - Transport of a colloidal particle driven across a temporally oscillating optical potential energy landscape JF - New J. Phys. N2 - A colloidal particle is driven across a temporally oscillating one-dimensional optical potential energy landscape and its particle motion is analysed. Different modes of dynamic mode locking are observed and are confirmed with the use of phase portraits. The effect of the oscillation frequency on the mode locked step width is addressed and the results are discussed in light of a high-frequency theory and compared to simulations. Furthermore, the influence of the coupling between the particle and the optical landscape on mode locking is probed by increasing the maximum depth of the optical landscape. Stronger coupling is seen to increase the width of mode locked steps. Finally, transport across the temporally oscillating landscape is studied by measuring the effective diffusion coefficient of a mobile particle, which is seen to be highly sensitive to the driving velocity and mode locking. Y1 - 2019 U6 - https://doi.org/10.1088/1367-2630/ab3765 VL - 21 SP - 083027 ER - TY - JOUR A1 - Straube, Arthur A1 - Pagès, Josep M. A1 - Tierno, Pietro A1 - Ignés-Mullol, Jordi A1 - Sagués, Francesc T1 - Collective dynamics and conformal ordering in electrophoretically driven nematic colloids JF - Phys. Rev. Research N2 - We present a theoretical framework to understand the collective dynamics of an ensemble of electrophoretically driven colloidal particles that are forced to assemble around a single topological defect in a nematic liquid crystal by an alternating current electric field. Our generic model combines phoretic propulsion with electrostatic interactions and liquid-crystal-mediated hydrodynamics, which are effectively cast into a long-range interparticle repulsion, while nematic elasticity plays a subdominant role. Simulations based on this model fully capture the collective organization process observed in the experiments and other striking effects as the emergence of conformal ordering and a nearly frequency-independent repulsive interaction above 10Hz. Our results demonstrate the importance of hydrodynamic interactions on the assembly of driven microscale matter in anisotropic media. Y1 - 2019 U6 - https://doi.org/10.1103/PhysRevResearch.1.022008 VL - 1 SP - 022008 ER - TY - CHAP A1 - Soboll, T. A1 - Golas, Ulrike ED - Filipe, J. ED - Fred, A. T1 - A Local-Global Model for Multiagent Systems - Sheaves on the Category MAS T2 - Proceedings of ICAART 2012 Y1 - 2012 VL - 2 SP - 331 EP - 334 PB - SciTePress ER - TY - JOUR A1 - Golas, Ulrike A1 - Lambers, L. A1 - Ehrig, Hartmut A1 - Orejas, Fernando T1 - Attributed Graph Transformation with Inheritance JF - Theoretical Computer Science Y1 - 2012 U6 - https://doi.org/10.1016/j.tcs.2012.01.032 VL - 424 SP - 46 EP - 68 ER - TY - CHAP A1 - Flik, T. A1 - Reinefeld, Alexander ED - Czichos, Horst ED - Hennecke, Manfred T1 - Rechnerorganisation T2 - Hütte – Das Ingenieurwissen Y1 - 2012 SP - J6 EP - J124 PB - Springer-Verlag Berlin ET - 34 ER - TY - CHAP A1 - Golas, Ulrike ED - Ehrig, Hartmut ED - Engels, G. ED - Kreowski, H.-J. ED - Rozenberg, G. T1 - A General Attribution Concept for Models in M-Adhesive Transformation Systems T2 - Proceedings of ICGT 2012 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-33654-6_13 VL - 7562 SP - 187 EP - 202 PB - Springer ER - TY - CHAP A1 - Golas, Ulrike A1 - Lambers, L. A1 - Ehrig, Hartmut A1 - Giese, H. ED - Ehrig, Hartmut ED - Engels, G. ED - Kreowski, H.-J. ED - Rozenberg, G. T1 - Towards Bridging the Gap between Formal Foundations and Current Practice for Triple Graph Grammars - Flexible Relations between Source and Target Elements T2 - Proceedings of ICGT 2012 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-33654-6_10 VL - 7562 SP - 141 EP - 155 PB - Springer ER - TY - CHAP A1 - Heckel, R. A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Hermann, Frank ED - Ehrig, Hartmut ED - Engels, G. ED - Kreowski, H.-J. ED - Rozenberg, G. T1 - Parallelism and Concurrency of Stochastic Graph Transformations T2 - Proceedings of ICGT 2012 Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-33654-6_7 VL - 7562 SP - 96 EP - 110 PB - Springer ER - TY - JOUR A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Habel, A. A1 - Lambers, L. A1 - Orejas, Fernando T1 - M-Adhesive Transformation Systems with Nested Application Conditions. Part 2 JF - Fundamenta Informaticae Y1 - 2012 U6 - https://doi.org/10.3233/FI-2012-705 VL - 118 IS - 1-2 SP - 35 EP - 63 ER - TY - GEN ED - Golas, Ulrike ED - Soboll, T. T1 - Proceedings of ACCAT 2012 T2 - Electronic Proceedings in Theoretical Computer Science 93 Y1 - 2012 U6 - https://doi.org/10.4204/EPTCS.93 ER - TY - CHAP A1 - Schäfer, Patrick A1 - Högqvist, Mikael T1 - SFA : a symbolic fourier approximation and index for similarity search in high dimensional datasets T2 - Proceedings of the 15th International Conference on Extending Database Technology Y1 - 2012 UR - http://doi.acm.org/10.1145/2247596.2247656 U6 - https://doi.org/10.1145/2247596.2247656 SP - 516 EP - 527 PB - ACM CY - New York, NY, USA ER - TY - CHAP A1 - Orejas, Fernando A1 - Boronat, Artur A1 - Golas, Ulrike A1 - Mylonakis, Nikos ED - Pfenning, Frank T1 - Checking Bisimilarity for Attributed Graph Transformation T2 - Foundations of Software Science and Computation Structures. Proceedings of FOSSACS 2013 Y1 - 2013 U6 - https://doi.org/10.1007/978-3-642-37075-5_8 VL - 7794 SP - 113 EP - 128 PB - Springer ER - TY - CHAP A1 - Schäfer, Patrick A1 - Dreßler, Sebastian T1 - Shooting Audio Recordings of Insects with SFA T2 - AmiBio Workshop, Bonn, Germany Y1 - 2013 ER - TY - THES A1 - Reinbacher, Uwe T1 - Implementierung und Evaluierung eines FPGA-basierten statischen Paketfilters Y1 - 2013 ER - TY - CHAP A1 - Ritter, Zully A1 - Baumann, Wolfgang A1 - Felsenberg, Dieter T1 - In vivo tibial compressive stiffness variations after HR-pQCT measurements of 60 days immobility during the Berlin bed rest study II using μfinite element analysis T2 - 6th World Congress of Biomechanics (WCB 2010), August 1-6, 2010 Singapore: In Conjunction with 14th International Conference on Biomedical Engineering (ICBME) and 5th Asia Pacific Conference on Biomechanics (APBiomech) KW - finite-element analysis KW - bone structure KW - compressive stiffness KW - bed rest KW - HR-pQCT measurement Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-14515-5_209 VL - 31 SP - 823 EP - 826 ER - TY - JOUR A1 - Kramer, Tobias A1 - Kreisbeck, Christoph A1 - Riha, Christian A1 - Chiatti, Olivio A1 - Buchholz, Sven A1 - Wieck, Andreas A1 - Reuter, Dirk A1 - Fischer, Saskia T1 - Thermal energy and charge currents in multi-terminal nanorings JF - AIP Advances N2 - We study in experiment and theory thermal energy and charge transfer close to the quantum limit in a ballistic nanodevice, consisting of multiply connected one-dimensional electron waveguides. The fabricated device is based on an AlGaAs/GaAs heterostructure and is covered by a global top-gate to steer the thermal energy and charge transfer in the presence of a temperature gradient, which is established by a heating current. The estimate of the heat transfer by means of thermal noise measurements shows the device acting as a switch for charge and thermal energy transfer. The wave-packet simulations are based on the multi-terminal Landauer-Büttiker approach and confirm the experimental finding of a mode-dependent redistribution of the thermal energy current, if a scatterer breaks the device symmetry. Y1 - 2016 U6 - https://doi.org/10.1063/1.4953812 VL - 6 SP - 065306 ER -