@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{RettigHaasePletnyovetal.2019, author = {Rettig, Anika and Haase, Tobias and Pletnyov, Alexandr and Kohl, Benjamin and Ertel, Wolfgang and von Kleist, Max and Sunkara, Vikram}, title = {SLCV - A Supervised Learning - Computer Vision combined strategy for automated muscle fibre detection in cross sectional images}, journal = {PeerJ}, publisher = {PeerJ}, address = {PeerJ}, doi = {10.7717/peerj.7053}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72639}, year = {2019}, abstract = {Muscle fibre cross sectional area (CSA) is an important biomedical measure used to determine the structural composition of skeletal muscle, and it is relevant for tackling research questions in many different fields of research. To date, time consuming and tedious manual delineation of muscle fibres is often used to determine the CSA. Few methods are able to automatically detect muscle fibres in muscle fibre cross sections to quantify CSA due to challenges posed by variation of bright- ness and noise in the staining images. In this paper, we introduce SLCV, a robust semi-automatic pipeline for muscle fibre detection, which combines supervised learning (SL) with computer vision (CV). SLCV is adaptable to different staining methods and is quickly and intuitively tunable by the user. We are the first to perform an error analysis with respect to cell count and area, based on which we compare SLCV to the best purely CV-based pipeline in order to identify the contribution of SL and CV steps to muscle fibre detection. Our results obtained on 27 fluorescence-stained cross sectional images of varying staining quality suggest that combining SL and CV performs signifi- cantly better than both SL based and CV based methods with regards to both the cell separation- and the area reconstruction error. Furthermore, applying SLCV to our test set images yielded fibre detection results of very high quality, with average sensitivity values of 0.93 or higher on different cluster sizes and an average Dice Similarity Coefficient (DSC) of 0.9778.}, language = {en} } @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} } @misc{Niemann2019, type = {Master Thesis}, author = {Niemann, Jan-Hendrik}, title = {A Dynamic Memory Approach for Consensus Problems with Packet Loss}, pages = {64}, year = {2019}, language = {en} } @phdthesis{Reuter2018, author = {Reuter, Bernhard}, title = {Generalisierte Markov-Modellierung von Nichtgleichgewichtssystemen - Simulation und Modellierung der Amyloid-beta(1-40)-Konformationsdynamik unter Mikrowelleneinfluss}, year = {2018}, language = {de} } @article{Deuflhard2018, author = {Deuflhard, Peter}, title = {The Grand Four. Affine Invariant Globalizations of Newton's Method}, volume = {46}, journal = {Vietnam Journal of Mathematics}, number = {4}, doi = {10.1007/s10013-018-0301-3}, pages = {761 -- 777}, year = {2018}, language = {en} } @inproceedings{CoconuUllmerPaaretal.2018, author = {Coconu, Liviu and Ullmer, Brygg and Paar, Philip and Liu, Jing and Konkel, Miriam and Hege, Hans-Christian}, title = {A smartphone-based tangible interaction approach for landscape visualization.}, booktitle = {PerDis '18 Proceedings of the 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018}, publisher = {ACM}, address = {New York, NY, USA}, doi = {10.1145/3205873.3210707}, pages = {no. 23}, year = {2018}, abstract = {The use of tangible interfaces for navigation of landscape scenery - for example, lost places re-created in 3D - has been pursued and articulated as a promising, impactful application of interactive visualization. In this demonstration, we present a modern, low-cost implementation of a previously-realized multimodal gallery installation. Our demonstration centers upon the versatile usage of a smartphone for sensing, navigating, and (optionally) displaying element on a physical surface in tandem with a larger, more immersive display.}, language = {en} } @inproceedings{UllmerPaarCoconuetal.2018, author = {Ullmer, Brygg and Paar, Philip and Coconu, Liviu and Liu, Jing and Konkel, Miriam and Hege, Hans-Christian}, title = {An 1834 mediterranean garden in Berlin - engaged from 2004, 2018, 2032, and 2202}, booktitle = {PerDis '18 - 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018}, publisher = {ACM}, address = {New York, NY, USA}, doi = {10.1145/3205873.3205894}, pages = {no. 12}, year = {2018}, abstract = {In 2004, a team of researchers realized a semi-immersive interactive gallery installation, visualizing an 1834 Mediterranean garden, introduced as "italienisches Kunstst{\"u}ck" (Italian legerdemain) by Peter Joseph Lenn{\´e}. The park was originally realized on the grounds of Schloss Sanssouci in Potsdam, Germany. The installation centered on highly detailed renderings of hundreds of plants projected upon a panoramic display. Interactivity was expressed with a tangible interface which (while presently dated) we believe remains without near-precedent then or since. We present the installation (experienced by roughly 20,000 visitors), focusing on the interaction aspects. We introduce new book and table/door-format mockups. Drawing upon a heuristic of the scientist-philosopher Freeman Dyson, we consider grounded future prospect variations in the contexts of 2018, 2032, and 2202. We see this exercise as prospectively generalizing to a variety of similar and widely diverse application domains.}, language = {en} }