@misc{Golas2012, author = {Golas, Ulrike}, title = {A General Attribution Concept for Models in M- adhesive Transformation Systems: Long Version}, issn = {1438-0064}, doi = {10.1007/978-3-642-33654-6_13}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-15547}, year = {2012}, abstract = {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.}, language = {en} } @masterthesis{Wende2013, type = {Bachelor Thesis}, author = {Wende, Florian}, title = {Dynamic Load Balancing on Massively Parallel Computer Architectures}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42166}, school = {Zuse Institute Berlin (ZIB)}, pages = {100}, year = {2013}, abstract = {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.}, language = {en} } @misc{WendeSteinke2013, author = {Wende, Florian and Steinke, Thomas}, title = {Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU}, issn = {1438-0064}, doi = {10.1145/2503210.2503254}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42187}, year = {2013}, abstract = {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.}, language = {en} } @misc{Pyszkalski2013, author = {Pyszkalski, Wolfgang}, title = {{\"U}bersicht {\"u}ber die Datenhaltung im ZIB und die M{\"o}glichkeiten einer Nutzung durch Projekte}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42060}, year = {2013}, abstract = {Dieser Bericht beschreibt in allgemein verst{\"a}ndlicher Form die Struktur der Datenhaltung im Zuse-Institut Berlin (ZIB) und die aktuell verwendeten Strategien im Umgang mit immer st{\"a}rker wachsenden Datenmengen, sowie der Herausforderung der Speicherung unwiederbringlicher Daten {\"u}ber im Grunde unbegrenzte Zeit.}, language = {de} } @article{DelleSiteKrekelerWhittakeretal.2019, author = {Delle Site, Luigi and Krekeler, Christian and Whittaker, John and Agarwal, Animesh and Klein, Rupert and H{\"o}fling, Felix}, title = {Molecular Dynamics of Open Systems: Construction of a Mean-Field Particle Reservoir}, volume = {2}, journal = {Advanced Theory and Simulations}, arxiv = {http://arxiv.org/abs/1902.07067}, doi = {10.1002/adts.201900014}, pages = {1900014}, year = {2019}, abstract = {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.}, language = {en} } @article{StoopStraubeJohansenetal.2020, author = {Stoop, Ralph L. and Straube, Arthur and Johansen, Tom H. and Tierno, Pietro}, title = {Collective directional locking of colloidal monolayers on a periodic substrate}, volume = {124}, journal = {Phys. Rev. Lett.}, doi = {10.1103/PhysRevLett.124.058002}, pages = {058002}, year = {2020}, abstract = {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.}, language = {en} } @article{AbbottStraubeAartsetal.2019, author = {Abbott, Joshua L. and Straube, Arthur and Aarts, Dirk G. A. L. and Dullens, Roel P. A.}, title = {Transport of a colloidal particle driven across a temporally oscillating optical potential energy landscape}, volume = {21}, journal = {New J. Phys.}, doi = {10.1088/1367-2630/ab3765}, pages = {083027}, year = {2019}, abstract = {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.}, language = {en} } @article{StraubePagesTiernoetal.2019, author = {Straube, Arthur and Pag{\`e}s, Josep M. and Tierno, Pietro and Ign{\´e}s-Mullol, Jordi and Sagu{\´e}s, Francesc}, title = {Collective dynamics and conformal ordering in electrophoretically driven nematic colloids}, volume = {1}, journal = {Phys. Rev. Research}, doi = {10.1103/PhysRevResearch.1.022008}, pages = {022008}, year = {2019}, abstract = {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.}, language = {en} } @inproceedings{SobollGolas2012, author = {Soboll, T. and Golas, Ulrike}, title = {A Local-Global Model for Multiagent Systems - Sheaves on the Category MAS}, volume = {2}, booktitle = {Proceedings of ICAART 2012}, editor = {Filipe, J. and Fred, A.}, publisher = {SciTePress}, pages = {331 -- 334}, year = {2012}, language = {en} } @article{GolasLambersEhrigetal.2012, author = {Golas, Ulrike and Lambers, L. and Ehrig, Hartmut and Orejas, Fernando}, title = {Attributed Graph Transformation with Inheritance}, volume = {424}, journal = {Theoretical Computer Science}, doi = {10.1016/j.tcs.2012.01.032}, pages = {46 -- 68}, year = {2012}, language = {en} } @incollection{FlikReinefeld2012, author = {Flik, T. and Reinefeld, Alexander}, title = {Rechnerorganisation}, booktitle = {H{\"u}tte - Das Ingenieurwissen}, editor = {Czichos, Horst and Hennecke, Manfred}, edition = {34}, publisher = {Springer-Verlag Berlin}, pages = {J6 -- J124}, year = {2012}, language = {en} } @inproceedings{Golas2012, author = {Golas, Ulrike}, title = {A General Attribution Concept for Models in M-Adhesive Transformation Systems}, volume = {7562}, booktitle = {Proceedings of ICGT 2012}, editor = {Ehrig, Hartmut and Engels, G. and Kreowski, H.-J. and Rozenberg, G.}, publisher = {Springer}, doi = {10.1007/978-3-642-33654-6_13}, pages = {187 -- 202}, year = {2012}, language = {en} } @inproceedings{GolasLambersEhrigetal.2012, author = {Golas, Ulrike and Lambers, L. and Ehrig, Hartmut and Giese, H.}, title = {Towards Bridging the Gap between Formal Foundations and Current Practice for Triple Graph Grammars - Flexible Relations between Source and Target Elements}, volume = {7562}, booktitle = {Proceedings of ICGT 2012}, editor = {Ehrig, Hartmut and Engels, G. and Kreowski, H.-J. and Rozenberg, G.}, publisher = {Springer}, doi = {10.1007/978-3-642-33654-6_10}, pages = {141 -- 155}, year = {2012}, language = {en} } @inproceedings{HeckelEhrigGolasetal.2012, author = {Heckel, R. and Ehrig, Hartmut and Golas, Ulrike and Hermann, Frank}, title = {Parallelism and Concurrency of Stochastic Graph Transformations}, volume = {7562}, booktitle = {Proceedings of ICGT 2012}, editor = {Ehrig, Hartmut and Engels, G. and Kreowski, H.-J. and Rozenberg, G.}, publisher = {Springer}, doi = {10.1007/978-3-642-33654-6_7}, pages = {96 -- 110}, year = {2012}, language = {en} } @article{EhrigGolasHabeletal.2012, author = {Ehrig, Hartmut and Golas, Ulrike and Habel, A. and Lambers, L. and Orejas, Fernando}, title = {M-Adhesive Transformation Systems with Nested Application Conditions. Part 2}, volume = {118}, journal = {Fundamenta Informaticae}, number = {1-2}, doi = {10.3233/FI-2012-705}, pages = {35 -- 63}, year = {2012}, language = {en} } @misc{OPUS4-3402, title = {Proceedings of ACCAT 2012}, journal = {Electronic Proceedings in Theoretical Computer Science 93}, editor = {Golas, Ulrike and Soboll, T.}, doi = {10.4204/EPTCS.93}, year = {2012}, language = {en} } @inproceedings{SchaeferHoegqvist2012, author = {Sch{\"a}fer, Patrick and H{\"o}gqvist, Mikael}, title = {SFA : a symbolic fourier approximation and index for similarity search in high dimensional datasets}, booktitle = {Proceedings of the 15th International Conference on Extending Database Technology}, publisher = {ACM}, address = {New York, NY, USA}, doi = {10.1145/2247596.2247656}, pages = {516 -- 527}, year = {2012}, language = {en} } @inproceedings{OrejasBoronatGolasetal.2013, author = {Orejas, Fernando and Boronat, Artur and Golas, Ulrike and Mylonakis, Nikos}, title = {Checking Bisimilarity for Attributed Graph Transformation}, volume = {7794}, booktitle = {Foundations of Software Science and Computation Structures. Proceedings of FOSSACS 2013}, editor = {Pfenning, Frank}, publisher = {Springer}, doi = {10.1007/978-3-642-37075-5_8}, pages = {113 -- 128}, year = {2013}, language = {en} } @inproceedings{SchaeferDressler2013, author = {Sch{\"a}fer, Patrick and Dreßler, Sebastian}, title = {Shooting Audio Recordings of Insects with SFA}, booktitle = {AmiBio Workshop, Bonn, Germany}, year = {2013}, language = {en} } @misc{Reinbacher2013, type = {Master Thesis}, author = {Reinbacher, Uwe}, title = {Implementierung und Evaluierung eines FPGA-basierten statischen Paketfilters}, year = {2013}, language = {de} } @inproceedings{RitterBaumannFelsenberg2010, author = {Ritter, Zully and Baumann, Wolfgang and Felsenberg, Dieter}, title = {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}, volume = {31}, booktitle = {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)}, doi = {10.1007/978-3-642-14515-5_209}, pages = {823 -- 826}, year = {2010}, language = {en} } @article{KramerKreisbeckRihaetal.2016, author = {Kramer, Tobias and Kreisbeck, Christoph and Riha, Christian and Chiatti, Olivio and Buchholz, Sven and Wieck, Andreas and Reuter, Dirk and Fischer, Saskia}, title = {Thermal energy and charge currents in multi-terminal nanorings}, volume = {6}, journal = {AIP Advances}, doi = {10.1063/1.4953812}, pages = {065306}, year = {2016}, abstract = {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-B{\"u}ttiker approach and confirm the experimental finding of a mode-dependent redistribution of the thermal energy current, if a scatterer breaks the device symmetry.}, language = {en} }