@article{SchimunekSeidlElezetal.2024, author = {Schimunek, Johannes and Seidl, Philipp and Elez, Katarina and Hempel, Tim and Le, Tuan and No{\´e}, Frank and Olsson, Simon and Raich, Llu{\´i}s and Winter, Robin and Gokcan, Hatice and Gusev, Filipp and Gutkin, Evgeny M. and Isayev, Olexandr and Kurnikova, Maria G. and Narangoda, Chamali H. and Zubatyuk, Roman and Bosko, Ivan P. and Furs, Konstantin V. and Karpenko, Anna D. and Kornoushenko, Yury V. and Shuldau, Mikita and Yushkevich, Artsemi and Benabderrahmane, Mohammed B. and Bousquet-Melou, Patrick and Bureau, Ronan and Charton, Beatrice and Cirou, Bertrand C. and Gil, G{\´e}rard and Allen, William J. and Sirimulla, Suman and Watowich, Stanley and Antonopoulos, Nick and Epitropakis, Nikolaos and Krasoulis, Agamemnon and Itsikalis, Vassilis and Theodorakis, Stavros and Kozlovskii, Igor and Maliutin, Anton and Medvedev, Alexander and Popov, Petr and Zaretckii, Mark and Eghbal-Zadeh, Hamid and Halmich, Christina and Hochreiter, Sepp and Mayr, Andreas and Ruch, Peter and Widrich, Michael and Berenger, Francois and Kumar, Ashutosh and Yamanishi, Yoshihiro and Zhang, Kam Y. J. and Bengio, Emmanuel and Bengio, Yoshua and Jain, Moksh J. and Korablyov, Maksym and Liu, Cheng-Hao and Marcou, Gilles and Glaab, Enrico and Barnsley, Kelly and Iyengar, Suhasini M. and Ondrechen, Mary Jo and Haupt, V. Joachim and Kaiser, Florian and Schroeder, Michael and Pugliese, Luisa and Albani, Simone and Athanasiou, Christina and Beccari, Andrea and Carloni, Paolo and D'Arrigo, Giulia and Gianquinto, Eleonora and Goßen, Jonas and Hanke, Anton and Joseph, Benjamin P. and Kokh, Daria B. and Kovachka, Sandra and Manelfi, Candida and Mukherjee, Goutam and Mu{\~n}iz-Chicharro, Abraham and Musiani, Francesco and Nunes-Alves, Ariane and Paiardi, Giulia and Rossetti, Giulia and Sadiq, S. Kashif and Spyrakis, Francesca and Talarico, Carmine and Tsengenes, Alexandros and Wade, Rebecca C. and Copeland, Conner and Gaiser, Jeremiah and Olson, Daniel R. and Roy, Amitava and Venkatraman, Vishwesh and Wheeler, Travis J. and Arthanari, Haribabu and Blaschitz, Klara and Cespugli, Marco and Durmaz, Vedat and Fackeldey, Konstantin and Fischer, Patrick D. and Gorgulla, Christoph and Gruber, Christian and Gruber, Karl and Hetmann, Michael and Kinney, Jamie E. and Padmanabha Das, Krishna M. and Pandita, Shreya and Singh, Amit and Steinkellner, Georg and Tesseyre, Guilhem and Wagner, Gerhard and Wang, Zi-Fu and Yust, Ryan J. and Druzhilovskiy, Dmitry S. and Filimonov, Dmitry A. and Pogodin, Pavel V. and Poroikov, Vladimir and Rudik, Anastassia V. and Stolbov, Leonid A. and Veselovsky, Alexander V. and De Rosa, Maria and De Simone, Giada and Gulotta, Maria R. and Lombino, Jessica and Mekni, Nedra and Perricone, Ugo and Casini, Arturo and Embree, Amanda and Gordon, D. Benjamin and Lei, David and Pratt, Katelin and Voigt, Christopher A. and Chen, Kuang-Yu and Jacob, Yves and Krischuns, Tim and Lafaye, Pierre and Zettor, Agn{\`e}s and Rodr{\´i}guez, M. Luis and White, Kris M. and Fearon, Daren and Von Delft, Frank and Walsh, Martin A. and Horvath, Dragos and Brooks III, Charles L. and Falsafi, Babak and Ford, Bryan and Garc{\´i}a-Sastre, Adolfo and Yup Lee, Sang and Naffakh, Nadia and Varnek, Alexandre and Klambauer, G{\"u}nter and Hermans, Thomas M.}, title = {A community effort in SARS-CoV-2 drug discovery}, volume = {43}, journal = {Molecular Informatics}, number = {1}, doi = {https://doi.org/10.1002/minf.202300262}, pages = {e202300262}, year = {2024}, language = {en} } @article{GuerlerMollWeberetal.2008, author = {Guerler, A. and Moll, Sebastian and Weber, Marcus and Meyer, Holger and Cordes, Frank}, title = {Selection and flexible optimization of binding modes from conformation ensembles}, volume = {92}, journal = {Biosystems}, number = {1}, doi = {DOI: 10.1016/j.biosystems.2007.11.004}, pages = {42 -- 48}, year = {2008}, language = {en} } @article{GuerlerMollWeberetal.2007, author = {G{\"u}rler, A. and Moll, Sebastian and Weber, Marcus and Meyer, Holger and Cordes, Frank}, title = {Selection and flexible optimization of binding modes from conformation ensembles}, journal = {Biosystems}, year = {2007}, language = {en} } @article{FrankvonKleistKunzetal.2011, author = {Frank, M. and von Kleist, Max and Kunz, A. and Harms, G. and Sch{\"u}tte, Christof and Kloft, Ch.}, title = {Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1}, volume = {55}, journal = {Antimicrob. Agents Chemother.}, number = {12}, pages = {5529 -- 5540}, year = {2011}, language = {en} } @article{SenneTrendelkampSchroerMeyetal.2012, author = {Senne, M. and Trendelkamp-Schroer, B. and Mey, A. and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {EMMA - A software package for Markov model building and analysis}, volume = {8}, journal = {Journal of Chemical Theory and Computation}, doi = {10.1021/ct300274u}, pages = {2223 -- 2238}, year = {2012}, language = {en} } @article{FrankChiLauSzabo2008, author = {Frank, A. and Chi Lau, L. and Szab{\´o}, J{\´a}cint}, title = {A note on degree-constrained subgraphs}, volume = {308}, journal = {Discrete Mathematics}, number = {12}, publisher = {Elsevier}, pages = {2647 -- 2648}, year = {2008}, 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} } @article{AsadovaAchouriArjasetal.2025, author = {Asadova, Nigar and Achouri, Karim and Arjas, Kristian and Ajugui{\´e}, Baptiste and Aydin, Roland and Baron, Alexandre and Beutel, Dominik and Bodermann, Bernd and Boussaoud, Kaoutar and Burger, Sven and Choi, Minseok and Czajkowski, Krzysztof and Evlyukhin, Andrey B. and Fazel-Najafabadi, Atefeh and Fernandez-Corbaton, Ivan and Garg, Puneet and Globosits, David and Hohenester, Ulrich and Kim, Hongyoon and Kim, Seokwoo and Lalanne, Philippe and Le Ru, Eric C. and Meyer, J{\"o}rg and Mun, Jungho and Patelli, Lorenzo and Pflug, Lukas and Rockstuhl, Carsten and Rho, Junsuk and Rotter, Stefan and Stout, Brian and T{\"o}rm{\"a}, P{\"a}ivi and Trigo, Jorge Olmos and Tristram, Frank and Tsitsas, Nikolaos L. and Vall{\´e}e, Renaud and Vynck, Kevin and Weiss, Thomas and Wiecha, Peter and Wriedt, Thomas and Yannopapas, Vassilios and Yurkin, Maxim A. and Zouros, Grigorios P.}, title = {T-matrix representation of optical scattering response: Suggestion for a data format}, volume = {333}, journal = {J. Quant. Spectrosc. Radiat. Transf.}, arxiv = {http://arxiv.org/abs/2408.10727}, doi = {10.1016/j.jqsrt.2024.109310}, pages = {109310}, year = {2025}, language = {en} } @misc{EijkhofBodlaenderKoster2002, author = {Eijkhof, Frank van den and Bodlaender, Hans L. and Koster, Arie M.C.A.}, title = {Safe reduction rules for weighted treewidth}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7164}, number = {02-49}, year = {2002}, abstract = {Several sets of reductions rules are known for preprocessing a graph when computing its treewidth. In this paper, we give reduction rules for a weighted variant of treewidth, motivated by the analysis of algorithms for probabilistic networks. We present two general reduction rules that are safe for weighted treewidth. They generalise many of the existing reduction rules for treewidth. Experimental results show that these reduction rules can significantly reduce the problem size for several instances of real-life probabilistic networks.}, language = {en} } @misc{BodlaenderKosterEijkhofetal.2001, author = {Bodlaender, Hans L. and Koster, Arie M.C.A. and Eijkhof, Frank van den and Gaag, Linda C. van der}, title = {Pre-processing for Triangulation of Probabilistic Networks}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6655}, number = {01-39}, year = {2001}, abstract = {The currently most efficient algorithm for inference with a probabilistic network builds upon a triangulation of a network's graph. In this paper, we show that pre-processing can help in finding good triangulations for probabilistic networks, that is, triangulations with a minimal maximum clique size. We provide a set of rules for stepwise reducing a graph, without losing optimality. This reduction allows us to solve the triangulation problem on a smaller graph. From the smaller graph's triangulation, a triangulation of the original graph is obtained by reversing the reduction steps. Our experimental results show that the graphs of some well-known real-life probabilistic networks can be triangulated optimally just by preprocessing; for other networks, huge reductions in their graph's size are obtained.}, language = {en} }