TY - GEN A1 - Kratz, Andrea A1 - Meyer, Björn A1 - Hotz, Ingrid T1 - A Visual Approach to Analysis of Stress Tensor Fields N2 - We present a visual approach for the exploration of stress tensor fields. Therefore, we introduce the idea of multiple linked views to tensor visualization. In contrast to common tensor visualization methods that only provide a single view to the tensor field, we pursue the idea of providing various perspectives onto the data in attribute and object space. Especially in the context of stress tensors, advanced tensor visualization methods have a young tradition. Thus, we propose a combination of visualization techniques domain experts are used to with statistical views of tensor attributes. The application of this concept to tensor fields was achieved by extending the notion of shape space. It provides an intuitive way of finding tensor invariants that represent relevant physical properties. Using brushing techniques, the user can select features in attribute space, which are mapped to displayable entities in a three-dimensional hybrid visualization in object space. Volume rendering serves as context, while glyphs encode the whole tensor information in focus regions. Tensorlines can be included to emphasize directionally coherent features in the tensor field. We show that the benefit of such a multi-perspective approach is manifold. Foremost, it provides easy access to the complexity of tensor data. Moreover, including wellknown analysis tools, such as Mohr diagrams, users can familiarize themselves gradually with novel visualization methods. Finally, by employing a focus-driven hybrid rendering, we significantly reduce clutter, which was a major problem of other three-dimensional tensor visualization methods. T3 - ZIB-Report - 10-26 KW - Visualisierung KW - Datenanalyse KW - Tensorfelder Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11915 ER - TY - GEN A1 - Meyer, Christian A1 - Panizzi, Lucia A1 - Schiela, Anton T1 - Uniqueness criteria for solutions of the adjoint equation in state-constrained optimal control N2 - The paper considers linear elliptic equations with regular Borel measures as inhomogeneity. Such equations frequently appear in state-constrained optimal control problems. By a counter-example of Serrin, it is known that, in the presence of non-smooth data, a standard weak formulation does not ensure uniqueness for such equations. Therefore several notions of solution have been developed that guarantee uniqueness. In this note, we compare different definitions of solutions, namely the ones of Stampacchia and the two notions of solutions of Casas and Alibert-Raymond, and show that they are the same. As side results, we reformulate the solution in the sense of Stampacchia, and prove the existence and uniqueness of solutions in in case of mixed boundary conditions. T3 - ZIB-Report - 10-28 KW - optimal control KW - elliptic partial differential equations KW - state constraints KW - measure right hand sides Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11933 ER - TY - JOUR A1 - Guerler, A. A1 - Moll, Sebastian A1 - Weber, Marcus A1 - Meyer, Holger A1 - Cordes, Frank T1 - Selection and flexible optimization of binding modes from conformation ensembles JF - Biosystems Y1 - 2008 UR - http://www.sciencedirect.com/science/article/pii/S0303264707001670 U6 - https://doi.org/DOI: 10.1016/j.biosystems.2007.11.004 VL - 92 IS - 1 SP - 42 EP - 48 ER - TY - JOUR A1 - Gürler, A. A1 - Moll, Sebastian A1 - Weber, Marcus A1 - Meyer, Holger A1 - Cordes, Frank T1 - Selection and flexible optimization of binding modes from conformation ensembles JF - Biosystems Y1 - 2007 ER - TY - JOUR A1 - Meyer, Christian A1 - Prüfert, Uwe A1 - Tröltzsch, Fredi T1 - On two numerical methods for state-constrained elliptic control problems JF - Optimization Methods and Software Y1 - 2007 UR - http://www.math.tu-berlin.de/~pruefert/Publicat/index_en.html UR - /homes/numerik/pruefert/WWW/Publicat/on2numerical.pdf VL - 22 IS - 6 SP - 871 EP - 899 ER - TY - JOUR A1 - Siefke, Thomas A1 - Hurtado, Carol A1 - Dickmann, Johannes A1 - Dickmann, Walter A1 - Käseberg, Tim A1 - Meyer, Jan A1 - Burger, Sven A1 - Zeitner, Uwe A1 - Bodermann, Bernd A1 - Kroker, Stefanie T1 - Quasi-bound states in the continuum for deep subwavelength structural information retrieval for DUV nano-optical polarizers JF - Opt. Express Y1 - 2020 U6 - https://doi.org/10.1364/OE.396044 VL - 28 SP - 23122 ER - TY - GEN A1 - Weber, Marcus A1 - Meyer, Holger T1 - ZIBgridfree - Adaptive Conformation Analysis with qualified Support of Transition States and Thermodynamic Weights N2 - This paper introduces a new algorithm of conformational analysis based on mesh-free methods as described in [M. Weber. Mehless methods in Conformation Dynamics.(2005)]. The adaptive decomposition of the conformational space by softly limiting functions avoids trapping effects and allows adaptive refinement strategies. These properties of the algorithm makes ZIBgridfree particularly suitable for the complete exploration of high-dimensional conformational space. The adaptive control of the algorithm benefits from the tight integration of molecular simulation and conformational analysis. An emphasized part of the analysis is the Robust Perron Cluster Analysis (PCCA+) based on the work of Peter Deuflhard and Marcus Weber. PCCA+ supports an almost-characteristic cluster definition with an outstanding mapping of transition states. The outcome is expressed by the metastable sets of conformations, their thermodynamic weights and flexibility. T3 - ZIB-Report - 05-17 KW - Molecular Dynamics KW - Meshfree Methods KW - Conformation Analysis KW - Quality Functions Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8514 ER - TY - GEN A1 - Meyer, Michael T1 - Ab Initio Study of Flavonoids N2 - Flavone and the flavylium ion have been studied at Hartree-Fock, M{\o}ller-Plesset and B3LYP hybrid density functional level to determine the structures and barriers to internal rotation. Both molecules have a high perpendicular barrier about the single bond connecting the phenyl ring with the benzopyrone and benzopyrylium ring, respectively. In contrast to biphenyl both molecules have low coplanar barriers. B3LYP overestimates the perpendicular barrier heights compared to other methods. The dependence of the population and orbital energies on the torsion has been investigated and the structures of both flavonoids have been estimated by means of a reaction field model. T3 - ZIB-Report - SC-99-23 KW - flavonol KW - conformation KW - reaction field KW - structure Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4110 ER - TY - JOUR A1 - Meyer, Michael A1 - Steinke, Thomas A1 - Sühnel, Jürgen T1 - Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions JF - Journal of Molecular Modeling Y1 - 2007 UR - http://dx.doi.org/10.1007/s00894-006-0148-5 VL - 13 IS - 2 SP - 335 EP - 345 PB - Springer Berlin / Heidelberg ER - TY - CHAP A1 - May, Patrick A1 - Steinke, Thomas A1 - Meyer, Michael T1 - THESEUS: A Parallel Threading Core T2 - Procs. 12th Internat. Conf. on Intelligent Systems for Mol. Bio. (ISMB) and 3rd European Conf. on Comp. Bio. (ECCB), Glasgow Y1 - 2004 SP - 199 ER - TY - JOUR A1 - Kleinfeld, David A1 - Bharioke, Arjun A1 - Blinder, Pablo A1 - Bock, David A1 - Briggman, Kevin A1 - Chklovskii, Dmitri A1 - Denk, Winfried A1 - Helmstaedter, Moritz A1 - Kaufhold, John A1 - Lee, Wei-Chung A1 - Meyer, Hanno A1 - Micheva, Kristina A1 - Oberlaender, Marcel A1 - Prohaska, Steffen A1 - Reid, R. A1 - Smith, Stephen A1 - Takemura, Shinya A1 - Tsai, Philbert A1 - Sakmann, Bert T1 - Large-scale automated histology in the pursuit of connectomes JF - Journal of Neuroscience Y1 - 2011 UR - http://www.zib.de/prohaska/docs/Kleinfeld_JNS_Connectomes_2011.pdf U6 - https://doi.org/10.1523/JNEUROSCI.4077-11.2011 VL - 31 IS - 45 SP - 16125 EP - 16138 ER - TY - JOUR A1 - Oberlaender, Marcel A1 - de Kock, Christiaan P. J. A1 - Bruno, Randy M. A1 - Ramirez, Alejandro A1 - Meyer, Hanno A1 - Dercksen, Vincent J. A1 - Helmstaedter, Moritz A1 - Sakmann, Bert T1 - Cell Type-Specific Three-Dimensional Structure of Thalamocortical Circuits in a Column of Rat Vibrissal Cortex JF - Cerebral Cortex Y1 - 2012 U6 - https://doi.org/doi:10.1093/cercor/bhr317 VL - 22 IS - 10 SP - 2375 EP - 2391 ER - TY - JOUR A1 - Kuß, Anja A1 - Gensel, Maria A1 - Meyer, Björn A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen T1 - Effective Techniques to Visualize Filament-Surface Relationships JF - Comput. Graph. Forum Y1 - 2010 VL - 29 SP - 1003 EP - 1012 ER - TY - GEN A1 - Kratz, Andrea A1 - Meyer, Björn A1 - Hotz, Ingrid ED - Hagen, Hans T1 - A Visual Approach to Analysis of Stress Tensor Fields T2 - Scientific Visualization: Interactions, Features, Metaphors Y1 - 2011 UR - http://drops.dagstuhl.de/opus/volltexte/2011/3296 U6 - https://doi.org/10.4230/DFU.Vol2.SciViz.2011.188 VL - 2 SP - 188 EP - 211 PB - Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik CY - Dagstuhl, Germany ER - TY - GEN A1 - Oberlaender, Marcel A1 - Bruno, Randy M. A1 - de Kock, Christiaan P. J. A1 - Meyer, Hanno A1 - Dercksen, Vincent J. A1 - Sakmann, Bert T1 - 3D distribution and sub-cellular organization of thalamocortical VPM synapses for individual excitatory neuronal cell types in rat barrel cortex T2 - Conference Abstract No. 173.19/Y35, 39th Annual Meeting of the Society for Neuroscience (SfN) Y1 - 2009 ER - TY - JOUR A1 - Diederichs, Gerd A1 - Seim, Heiko A1 - Meyer, Henning A1 - Issever, Ahi A1 - M. Link, Thomas A1 - J. Schröder, Ralf A1 - Scheibel, Markus T1 - CT-based patient-specific modeling of glenoid rim defects: A feasibility study JF - AJR Am J Roentgenol Y1 - 2008 U6 - https://doi.org/10.2214/AJR.08.1091 VL - 191 IS - 5 SP - 1406 EP - 1411 ER - TY - CHAP A1 - Kuß, Anja A1 - Prohaska, Steffen A1 - Meyer, Björn A1 - Rybak, Jürgen A1 - Hege, Hans-Christian T1 - Ontology-Based Visualization of Hierarchical Neuroanatomical Structures T2 - Proceedings of the Eurographics Workshop on Visual Computing for Biomedicine VCBM 2008 Y1 - 2008 SP - 177 EP - 184 ER - TY - JOUR A1 - Durmaz, Vedat A1 - Weber, Marcus A1 - Meyer, A1 - Mückter, T1 - Computergestützte Simulationen zur Abschätzung gesundheitlicher Risiken durch anthropogene Spurenstoffe der Wassermatrix JF - KA Korrespondenz Abwasser, Abfall Y1 - 2015 VL - 3/15 SP - 264 EP - 267 ER - TY - JOUR A1 - Heinze, Rieke A1 - Dipankar, Anurag A1 - Henken, Cintia Carbajal A1 - Moseley, Christopher A1 - Sourdeval, Odran A1 - Trömel, Silke A1 - Xie, Xinxin A1 - Adamidis, Panos A1 - Ament, Felix A1 - Baars, Holger A1 - Barthlott, Christian A1 - Behrendt, Andreas A1 - Blahak, Ulrich A1 - Bley, Sebastian A1 - Brdar, Slavko A1 - Brueck, Matthias A1 - Crewell, Susanne A1 - Deneke, Hartwig A1 - Di Girolamo, Paolo A1 - Evaristo, Raquel A1 - Fischer, Jürgen A1 - Frank, Christopher A1 - Friederichs, Petra A1 - Göcke, Tobias A1 - Gorges, Ksenia A1 - Hande, Luke A1 - Hanke, Moritz A1 - Hansen, Akio A1 - Hege, Hans-Christian A1 - Hose, Corinna A1 - Jahns, Thomas A1 - Kalthoff, Norbert A1 - Klocke, Daniel A1 - Kneifel, Stefan A1 - Knippertz, Peter A1 - Kuhn, Alexander A1 - van Laar, Thriza A1 - Macke, Andreas A1 - Maurer, Vera A1 - Mayer, Bernhard A1 - Meyer, Catrin I. A1 - Muppa, Shravan K. A1 - Neggers, Roeland A. J. A1 - Orlandi, Emiliano A1 - Pantillon, Florian A1 - Pospichal, Bernhard A1 - Röber, Niklas A1 - Scheck, Leonhard A1 - Seifert, Axel A1 - Seifert, Patric A1 - Senf, Fabian A1 - Siligam, Pavan A1 - Simmer, Clemens A1 - Steinke, Sandra A1 - Stevens, Bjorn A1 - Wapler, Kathrin A1 - Weniger, Michael A1 - Wulfmeyer, Volker A1 - Zängl, Günther A1 - Zhang, Dan A1 - Quaas, Johannes T1 - Large-eddy simulations over Germany using ICON: a comprehensive evaluation JF - Quarterly Journal of the Royal Meteorological Society N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1002/qj.2947 VL - 143 IS - 702 SP - 69 EP - 100 ER - TY - GEN A1 - Meyer, Michael A1 - Steinke, Thomas A1 - Brandl, Maria A1 - Sühnel, Jürgen T1 - Density functional study of guanine and uracil quartets and of guanine quartet metal/ion complexes N2 - The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density functional calculations. The total interaction energy $\Delta$E$^{T}$ of the $\it{C}$$_{4h}$-symmetric guanine quartet consisting of Hoogsteen type base pairs with two hydrogen bonds between two neighbour bases is -66.07 kcal/mol at the highest level. The uracil quartet with C6-H6...O4 interactions between the individual bases has only a small interaction energy of -20.92 kcal/mol and the interaction energy of -24.63 kcal/mol for the alternative structure with N3-H3...O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10 and 25 \% to all interaction energies. Complexes of metal ions with G-quartets can be classified into different structure types. The one with Ca$^{2+}$ in the central cavity adopts a $\it{C}$$_{4h}$-symmetric structure with coplanar bases, whereas the energies of the planar and non-planar Na$^{+}$ complexes are almost identical. The small ions Li$^{+}$, Be$^{2+}$, Cu$^{+}$ and Zn$^{2+}$ prefer a non-planar $\it{S}$$_{4}$-symmetric structure. The lack of co-planarity prevents probably a stacking of these base quartets. The central cavity is too small for K$^{+}$ ions and therefore this ion favours in contrast to all other investigated ions a $\it{C}$$_{4}$-symmetric complex, which is 4.73 kcal/mol more stable than the $\it{C}$$_{4h}$-symmetric one. The distance 1.665 {\AA} between K$^{+}$ and the root mean squares plane of the guanine bases is approximately half of the distance between two stacked G-quartets. The total interaction energy of alkaline earth ion complexes exceeds the ones with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen-bonded biological systems. Compared with the before mentioned methods the HCTH functional leads to longer hydrogen bonds and different relative energies for two U-quartets. Finally we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C-H...O contacts in the uracil quartet. In the G-quartet the MMFF94 hydrogen bond distances N2-H22...N7 are shorter than the DFT distances, whereas the N1-H1...O6 distances are longer. T3 - ZIB-Report - 00-16 KW - density functional theory KW - effective core potential KW - hydrogen bond KW - guanine KW - uracil KW - metal ion KW - C-H...O interaction Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5842 ER - TY - GEN A1 - Meyer, Michael A1 - Schnurre, Rüdiger A1 - Reissbrodt, Rolf A1 - Trowitzsch-Kienast, Wolfram T1 - Computer-aided design of novel siderophores: Pyridinochelin N2 - Pyridinochelin, a novel catecholate type siderophore, has been designed on the basis of the active analog enterobactin. Growth promotion tests indicate that this synthetic siderophore feeds various pathogenic bacteria effectively with iron even though it lacks one catecholate group compared to enterobactin. The superposition of the siderophore structures suggests that the structure of the skeleton connecting the catecholate groups might be an important factor for the iron transport. T3 - ZIB-Report - 00-20 KW - bioorganic chemistry KW - drug design KW - molecular modeling KW - iron transport KW - siderophore Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5887 ER - TY - GEN A1 - Meyer, Holger A1 - Moll, Sebastian A1 - Cordes, Frank A1 - Weber, Marcus T1 - ConFlow? A new space-based Application for complete Conformational Analysis of Molecules N2 - Biochemical interactions are determined by the 3D-structure of the involved components - thus the identification of conformations is a key for many applications in rational drug design. {\sf ConFlow} is a new multilevel approach to conformational analysis with main focus on completeness in investigation of conformational space. In contrast to known conformational analysis, the starting point for design is a space-based description of conformational areas. A tight integration of sampling and analysis leads to an identification of conformational areas simultaneously during sampling. An incremental decomposition of high-dimensional conformational space is used to guide the analysis. A new concept for the description of conformations and their path connected components based on convex hulls and {\em Hypercubes}is developed. The first results of the {\sf ConFlow} application constitute a 'proof of concept' and are further more highly encouraging. In comparison to conventional industrial applications, {\sf ConFlow} achieves higher accuracy and a specified degree of completeness with comparable effort. T3 - ZIB-Report - 06-31 KW - conformational-analysis in-silico-screening drug-design Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9258 ER - TY - JOUR A1 - Asadova, Nigar A1 - Achouri, Karim A1 - Arjas, Kristian A1 - Ajuguié, Baptiste A1 - Aydin, Roland A1 - Baron, Alexandre A1 - Beutel, Dominik A1 - Bodermann, Bernd A1 - Boussaoud, Kaoutar A1 - Burger, Sven A1 - Choi, Minseok A1 - Czajkowski, Krzysztof A1 - Evlyukhin, Andrey B. A1 - Fazel-Najafabadi, Atefeh A1 - Fernandez-Corbaton, Ivan A1 - Garg, Puneet A1 - Globosits, David A1 - Hohenester, Ulrich A1 - Kim, Hongyoon A1 - Kim, Seokwoo A1 - Lalanne, Philippe A1 - Le Ru, Eric C. A1 - Meyer, Jörg A1 - Mun, Jungho A1 - Patelli, Lorenzo A1 - Pflug, Lukas A1 - Rockstuhl, Carsten A1 - Rho, Junsuk A1 - Rotter, Stefan A1 - Stout, Brian A1 - Törmä, Päivi A1 - Trigo, Jorge Olmos A1 - Tristram, Frank A1 - Tsitsas, Nikolaos L. A1 - Vallée, Renaud A1 - Vynck, Kevin A1 - Weiss, Thomas A1 - Wiecha, Peter A1 - Wriedt, Thomas A1 - Yannopapas, Vassilios A1 - Yurkin, Maxim A. A1 - Zouros, Grigorios P. T1 - T-matrix representation of optical scattering response: Suggestion for a data format JF - J. Quant. Spectrosc. Radiat. Transf. Y1 - 2025 U6 - https://doi.org/10.1016/j.jqsrt.2024.109310 VL - 333 SP - 109310 ER -