TY - GEN A1 - Schmidt, Heiko A1 - Oevermann, Michael A1 - Bastiaans, Rob J.M. A1 - Kerstein, Alan R. T1 - A Priori Tabulation of Turbulent Flame Speeds via a Combination of a Stochastic Mixing Model and Flamelet Generated Manifolds, Extended to Incorporate Strain Effects N2 - In this paper we revisit the a priori turbulent flame speed tabulation (TFST) technique for a given parameter space within the region of flamelet combustion-regimes. It can be used as a subgrid-scale (SGS) model in Large Eddy Simulation (LES). In a first step, stationary laminar flamelets are computed and stored over the progress variable following the ideas of flamelet generated manifolds (FGM). In a second step, the incompressible one-dimensional Navier-Stokes equations supplemented by the equation for the progress variable are solved on a grid that resolves all turbulent scales. Additionally, turbulent transport is implemented via the linear eddy model (LEM). The turbulent flame structures are solved until a statistically stationary mean value of the turbulent flame speed has been reached. The results are stored in a table that could be used by large scale premixed combustion models, e.g. front tracking schemes. First results are compared quantitatively with direct numerical simulations (DNS) taken from literature. Then it is illustrated in one example how the new method could help to fix constants in algebraic models for turbulent flame speeds. Further it is shown how the technique can be extended to incorporate turbulent strain effects. Finally we investigate the effect of the use of detailed and tabulated chemistry under unsteady conditions. T3 - ZIB-Report - 09-09 KW - Turbulente Verbrennung KW - Flammenstrukturen KW - Linear Eddy Model KW - FGM KW - Turbulente Brenngeschwindigkeit KW - Streckungseffekte KW - turbulent premixed combustion KW - flame structures KW - linear eddy model KW - flamelet generated manifolds KW - turbulent flame speed tabulation KW - strain effects Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11214 SN - 1438-0064 ER - TY - GEN A1 - Schmidt, Heiko A1 - Oevermann, Michael A1 - Bastiaans, Rob J.M. A1 - Kerstein, Alan R. T1 - A priori Tabulation of Turbulent Flame Speeds via a Combination of a Stochastic Mixing Model and Flamelet Generated Manifolds N2 - In this paper we propose a technique for a priori turbulent flame speed tabulation (TFST) for a given parameter space in standard combustion-regime diagrams. It can be used as a subgrid-scale (SGS) model in Large Eddy Simulation (LES). In a first step, stationary laminar flamelets are computed and stored over the progress variable following the ideas of flamelet generated manifolds (FGM). In a second step, the incompressible one-dimensional Navier-Stokes equations supplemented by the equation for the progress variable are solved on a grid that resolves all turbulent scales. Additionally, turbulent transport is implemented via the linear eddy model (LEM). The turbulent flame structures are solved until a statistically stationary mean value of the turbulent flame speed has been reached. The results are stored in a table that could be used by large scale premixed combustion models, e.g. front tracking schemes. Results are compared to an algebraic model and to direct numerical simulations (DNS). T3 - ZIB-Report - 08-02 KW - Verbrennung KW - Flammenstrukturen KW - stochastisches Turbulenzmodell KW - FGM KW - turbulente Brenngeschwindigkeiten KW - turbulent premixed combustion KW - flame structures KW - linear eddy model KW - flamelet generated manifolds KW - turbulent flame speeds Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10532 SN - 1438-0064 ER - TY - GEN A1 - Borndörfer, Ralf A1 - Dittbrenner, Bastian A1 - Langenhan, Andreas A1 - Seidl, Stephan A1 - Weider, Steffen T1 - Integrierte Dienst- und Dienstreihenfolgeplanung zur Erhöhung der Fahrerzufriedenheit N2 - Wir stellen einen mathematischen Optimierungsansatz zur integrierten Dienst- und Dienstreihenfolgeplanung im öffentlichen Nahverkehr vor, mit dem sich bei konstanten Personalkosten die Fahrerzufriedenheit deutlich steigern lässt. T3 - ZIB-Report - 14-02 KW - duty scheduling KW - duty rostering KW - integrated scheduling KW - Benders' decomposition Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50270 SN - 1438-0064 ER - TY - GEN A1 - Wiebel, Alexander A1 - Vos, Frans M. A1 - Hege, Hans-Christian T1 - Perception-Oriented Picking of Structures in Direct Volumetric Renderings N2 - Radiologists from all application areas are trained to read slice-based visualizations of 3D medical image data. Despite the numerous examples of sophisticated three-dimensional renderings, especially all variants of direct volume rendering, such methods are often considered not very useful by radiologists who prefer slice-based visualization. Just recently there have been attempts to bridge this gap between 2D and 3D renderings. These attempts include specialized techniques for volume picking that result in repositioning slices. In this paper, we present a new volume picking technique that, in contrast to previous work, does not require pre-segmented data or metadata. The positions picked by our method are solely based on the data itself, the transfer function and, most importantly, on the way the volumetric rendering is perceived by viewers. To demonstrate the usefulness of the proposed method we apply it for automatically repositioning slices in an abdominal MRI scan, a data set from a flow simulation and a number of other volumetric scalar fields. Furthermore we discuss how the method can be implemented in combination with various different volumetric rendering techniques. T3 - ZIB-Report - 11-45 KW - DVR KW - picking KW - pointing KW - direct volume rendering Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14343 SN - 1438-0064 ER - TY - GEN A1 - Allalen, Mohammed A1 - Brehm, Matthias A1 - Stüben, Hinnerk T1 - Performance of Quantum Chromodynamics (QCD) Simulations on the SGI Altix N2 - We study performance and scaling of the Berlin Quantum Chromodynamics Program (BQCD) on the SGI Altix 4700 at Leibniz Supercomputing Centre (LRZ). We employ different communication methods (MPI, MPI with two OpenMP threads per process, as well as the shmem library) and run the MPI version on the two types of nodes of that machine. For comparison with other machines we made performance measurements on an IBM p690 cluster and a Cray XT4. T3 - ZIB-Report - 08-54 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11086 SN - 1438-0064 ER - TY - GEN A1 - Helling, Christiane A1 - Klein, Rupert A1 - Woitke, Peter A1 - Nowak, Ulrich A1 - Sedlmayr, Erwin T1 - Dust in Brown Dwarfs IV. Dust formation and driven turbulence on mesoscopic scales N2 - Dust formation {in brown dwarf atmospheres} is studied by utilizing a model for driven turbulence in the mesoscopic scale regime. We apply a pseudo-spectral method where waves are created and superimposed {within} a {limited} wavenumber interval. The turbulent kinetic energy distribution follows the Kolmogoroff spectrum which is assumed to be the most likely value. Such superimposed, stochastic waves may occur in a convectively active environment. They cause nucleation fronts and nucleation events and thereby initiate the dust formation process which { continues until} all condensible material is consumed. Small disturbances {are found to} have a large impact on the dust forming system. An initially dust-hostile region, which may originally be optically thin, becomes optically thick in a patchy way showing considerable variations in the dust properties during the formation process. The dust appears in lanes and curls as a result of the interaction with waves, i.e. turbulence, which form larger and larger structures with time. Aiming on a physical understanding of the variability of brown dwarfs, related to structure formation in substellar atmospheres, we work out first necessary criteria for small-scale closure models to be applied in macroscopic simulations of dust forming astrophysical systems. T3 - ZIB-Report - 03-33 KW - substellar atmospheres KW - dust formation KW - turbulence Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7555 ER - TY - GEN A1 - Schmidt-Ehrenberg, Johannes A1 - Hege, Hans-Christian T1 - Visualizing Quantum Mechanical Phenomena N2 - In this paper we discuss several ways to visualize stationary and non-stationary quantum mechanical systems. We demonstrate an approach for the quantitative interpretation of probability density isovalues which yields a reasonable correlation between isosurfaces for different timesteps. As an intuitive quantity for visualizing the momentum of a quantum system we propose the probability flow density which can be treated by vector field visualization techniques. Finally, we discuss the visualization of non-stationary systems by a sequence of single timestep images. T3 - ZIB-Report - SC-99-39 KW - quantum dynamics KW - isosurfaces KW - probability flow KW - animation Y1 - 1999 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4287 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 - Helling, Christiane A1 - Klein, Rupert A1 - Sedlmayr, Erwin T1 - The multi-scale dust formation in substellar atmospheres N2 - Substellar atmospheres are observed to be irregularly variable for which the formation of dust clouds is the most promising candidate explanation. The atmospheric gas is convectively unstable and, last but not least, colliding convective cells are seen as cause for a turbulent fluid field. Since dust formation depends on the local properties of the fluid, turbulence influences the dust formation process and may even allow the dust formation in an initially dust-hostile gas. A regime-wise investigation of dust forming substellar atmospheric situations reveals that the largest scales are determined by the interplay between gravitational settling and convective replenishment which results in a dust-stratified atmosphere. The regime of small scales is determined by the interaction of turbulent fluctuations. Resulting lane-like and curled dust distributions combine to larger and larger structures. We compile necessary criteria for a subgrid model in the frame of large scale simulations as result of our study on small scale turbulence in dust forming gases. T3 - ZIB-Report - 03-34 KW - dust formation KW - turbuelnce KW - multi-scale problem KW - substellar atmosphere Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-7567 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, 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 -