@misc{MuellerBartholmeiFischeretal.2014, author = {M{\"u}ller, Anja and Bartholmei, Stephan and Fischer, Barbara and Hahn, Helene}, title = {Der GLAM-Hackathon "Coding da Vinci"}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54566}, year = {2014}, abstract = {Coding da Vinci, der erste deutsche Kultur-Hackathon, wurde gemeinsam von der Open Knowledge Foundation Deutschland, der Servicestelle Digitalisierung Berlin, Wikimedia Deutschland und der Deutschen Digitalen Bibliothek veranstaltet. Zwischen Ende April und Anfang Juli haben 150 Teilnehmer (Coder, Webdesigner, Kulturinteressierte u.a.) an Webseiten, mobilen Apps,Spielen, Hardwareprojekten und anderen Anwendungen offener Daten gearbeitet. Die Daten wurden von 16 Kultur-Einrichtungen bereitgestellt. Im Verlauf des Hackathons wurden daraus 17 funktionsf{\"a}hige Prototypen entwickelt, {\"o}ffentlich pr{\"a}sentiert und f{\"u}nf davon auch pr{\"a}miert.Doch was genau ist ein Hackathon? Wie kommen Kulturinstitutionen und Hacker zusammen? Wie gelangt eine Kulturinstitution zu offenen Daten? Welche Herausforderungen und Chancen bietet ein Hackathon f{\"u}r den Kulturbereich? Welche neue Qualit{\"a}t erw{\"a}chst aus einem partizipativen Zugang zum digitalen Kulturerbe und der M{\"o}glichkeit mit Daten zu arbeiten? Was bleibt zu tun,um die Ergebnisse nachhaltig zu sichern? Diese Fragen sollen anhand der Ergebnisse von CdV diskutiert werden. Unter dem Motto „lessons learned" wagen wir den Ausblick auf Coding da Vinci 2015.}, language = {de} } @inproceedings{SkibinaBockFischeretal.2013, author = {Skibina, Julia and Bock, Martin and Fischer, Dorit and Grunwald, R{\"u}diger and Steinmeyer, G{\"u}nter and Wedell, Reiner and Bretschneider, Mario and Burger, Sven and Beloglazov, Valentin}, title = {10-fs fiber based pulse delivery}, booktitle = {Conference on Lasers, Applications, and Technologies (LAT)}, pages = {LWF5}, year = {2013}, language = {en} } @article{HeinzeDipankarHenkenetal.2017, author = {Heinze, Rieke and Dipankar, Anurag and Henken, Cintia Carbajal and Moseley, Christopher and Sourdeval, Odran and Tr{\"o}mel, Silke and Xie, Xinxin and Adamidis, Panos and Ament, Felix and Baars, Holger and Barthlott, Christian and Behrendt, Andreas and Blahak, Ulrich and Bley, Sebastian and Brdar, Slavko and Brueck, Matthias and Crewell, Susanne and Deneke, Hartwig and Di Girolamo, Paolo and Evaristo, Raquel and Fischer, J{\"u}rgen and Frank, Christopher and Friederichs, Petra and G{\"o}cke, Tobias and Gorges, Ksenia and Hande, Luke and Hanke, Moritz and Hansen, Akio and Hege, Hans-Christian and Hose, Corinna and Jahns, Thomas and Kalthoff, Norbert and Klocke, Daniel and Kneifel, Stefan and Knippertz, Peter and Kuhn, Alexander and van Laar, Thriza and Macke, Andreas and Maurer, Vera and Mayer, Bernhard and Meyer, Catrin I. and Muppa, Shravan K. and Neggers, Roeland A. J. and Orlandi, Emiliano and Pantillon, Florian and Pospichal, Bernhard and R{\"o}ber, Niklas and Scheck, Leonhard and Seifert, Axel and Seifert, Patric and Senf, Fabian and Siligam, Pavan and Simmer, Clemens and Steinke, Sandra and Stevens, Bjorn and Wapler, Kathrin and Weniger, Michael and Wulfmeyer, Volker and Z{\"a}ngl, G{\"u}nther and Zhang, Dan and Quaas, Johannes}, title = {Large-eddy simulations over Germany using ICON: a comprehensive evaluation}, volume = {143}, journal = {Quarterly Journal of the Royal Meteorological Society}, number = {702}, doi = {10.1002/qj.2947}, pages = {69 -- 100}, year = {2017}, abstract = {Large-eddy simulations (LES) with the new ICOsahedral Non-hydrostatic atmosphere model (ICON) covering Germany are evaluated for four days in spring 2013 using observational data from various sources. Reference simulations with the established Consortium for Small-scale Modelling (COSMO) numerical weather prediction model and further standard LES codes are performed and used as a reference. This comprehensive evaluation approach covers multiple parameters and scales, focusing on boundary-layer variables, clouds and precipitation. The evaluation points to the need to work on parametrizations influencing the surface energy balance, and possibly on ice cloud microphysics. The central purpose for the development and application of ICON in the LES configuration is the use of simulation results to improve the understanding of moist processes, as well as their parametrization in climate models. The evaluation thus aims at building confidence in the model's ability to simulate small- to mesoscale variability in turbulence, clouds and precipitation. The results are encouraging: the high-resolution model matches the observed variability much better at small- to mesoscales than the coarser resolved reference model. In its highest grid resolution, the simulated turbulence profiles are realistic and column water vapour matches the observed temporal variability at short time-scales. Despite being somewhat too large and too frequent, small cumulus clouds are well represented in comparison with satellite data, as is the shape of the cloud size spectrum. Variability of cloud water matches the satellite observations much better in ICON than in the reference model. In this sense, it is concluded that the model is fit for the purpose of using its output for parametrization development, despite the potential to improve further some important aspects of processes that are also parametrized in the high-resolution model.}, language = {en} } @misc{FischerGoetschelWeiser2017, author = {Fischer, Lisa and G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Lossy data compression reduces communication time in hybrid time-parallel integrators}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63961}, year = {2017}, abstract = {Parallel in time methods for solving initial value problems are a means to increase the parallelism of numerical simulations. Hybrid parareal schemes interleaving the parallel in time iteration with an iterative solution of the individual time steps are among the most efficient methods for general nonlinear problems. Despite the hiding of communication time behind computation, communication has in certain situations a significant impact on the total runtime. Here we present strict, yet no sharp, error bounds for hybrid parareal methods with inexact communication due to lossy data compression, and derive theoretical estimates of the impact of compression on parallel efficiency of the algorithms. These and some computational experiments suggest that compression is a viable method to make hybrid parareal schemes robust with respect to low bandwidth setups.}, language = {en} } @article{FischerGoetschelWeiser2018, author = {Fischer, Lisa and G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Lossy data compression reduces communication time in hybrid time-parallel integrators}, volume = {19}, journal = {Comput. Vis. Sci.}, number = {1}, doi = {10.1007/s00791-018-0293-2}, pages = {19 -- 30}, year = {2018}, abstract = {Parallel in time methods for solving initial value problems are a means to increase the parallelism of numerical simulations. Hybrid parareal schemes interleaving the parallel in time iteration with an iterative solution of the individual time steps are among the most efficient methods for general nonlinear problems. Despite the hiding of communication time behind computation, communication has in certain situations a significant impact on the total runtime. Here we present strict, yet no sharp, error bounds for hybrid parareal methods with inexact communication due to lossy data compression, and derive theoretical estimates of the impact of compression on parallel efficiency of the algorithms. These and some computational experiments suggest that compression is a viable method to make hybrid parareal schemes robust with respect to low bandwidth setups.}, language = {en} } @misc{Fischer2017, type = {Master Thesis}, author = {Fischer, Lisa}, title = {On the convergence of inexact time parallel time integration}, pages = {61}, year = {2017}, language = {en} } @masterthesis{Fischer2014, type = {Bachelor Thesis}, author = {Fischer, Jens V.}, title = {A Gossiping Framework for Scalaris}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50685}, year = {2014}, language = {en} } @misc{FischerSchuetteDeuflhardetal.2001, author = {Fischer, Alexander and Sch{\"u}tte, Christof and Deuflhard, Peter and Cordes, Frank}, title = {Hierarchical Uncoupling-Coupling of Metastable Conformations}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6296}, number = {01-03}, year = {2001}, abstract = {Uncoupling-coupling Monte Carlo (UCMC) combines uncoupling techniques for finite Markov chains with Markov chain Monte Carlo methodology. UCMC aims at avoiding the typical metastable or trapping behavior of Monte Carlo techniques. From the viewpoint of Monte Carlo, a slowly converging long-time Markov chain is replaced by a limited number of rapidly mixing short-time ones. Therefore, the state space of the chain has to be hierarchically decomposed into its metastable conformations. This is done by means of combining the technique of conformation analysis as recently introduced by the authors, and appropriate annealing strategies. We present a detailed examination of the uncoupling-coupling procedure which uncovers its theoretical background, and illustrates the hierarchical algorithmic approach. Furthermore, application of the UCMC algorithm to the \$n\$-pentane molecule allows us to discuss the effect of its crucial steps in a typical molecular scenario.}, language = {en} } @article{GarciaSantiagoHammerschmidtSachsetal.2022, author = {Garcia Santiago, Xavier and Hammerschmidt, Martin and Sachs, Johannes and Burger, Sven and Kwon, Hyunah and Kn{\"o}ller, Marvin and Arens, Tilo and Fischer, Peer and Fernandez-Corbaton, Ivan and Rockstuhl, Carsten}, title = {Toward maximally electromagnetically chiral scatterers at optical frequencies}, volume = {9}, journal = {ACS Photonics}, arxiv = {http://arxiv.org/abs/2112.04422}, doi = {10.1021/acsphotonics.1c01887}, pages = {1954}, year = {2022}, language = {en} } @article{GorgullaCınaroğluFischeretal.2021, author = {Gorgulla, Christoph and {\c{C}}{\i}naroğlu, S{\"u}leyman and Fischer, Patrick D. and Fackeldey, Konstantin and Wagner, Gerhard and Arthanari, Haribabu}, title = {VirtualFlow Ants—Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization}, volume = {22}, journal = {Special Issue Artificial Intelligence \& Deep Learning Approaches for Structural Bioinformatics}, number = {11}, doi = {https://doi.org/10.3390/ijms22115807}, pages = {5807}, year = {2021}, abstract = {The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery.}, language = {en} }