TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko JF - Advances in Physics: X N2 - Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending. Y1 - 2018 U6 - https://doi.org/10.1080/23746149.2017.1404436 VL - 3 IS - 1 SP - 1404436 ER - TY - JOUR A1 - Agudo Jácome, Leonardo A1 - Hege, Hans-Christian A1 - Paetsch, Olaf A1 - Pöthkow, Kai T1 - Three-dimensional reconstruction and quantification of dislocation substructures from transmission electron microscopy stereo pairs JF - Ultramicroscopy N2 - A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (>300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3% and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed. Y1 - 2018 U6 - https://doi.org/10.1016/j.ultramic.2018.08.015 VL - 195 SP - 157 EP - 170 ER - TY - CHAP A1 - Coconu, Liviu A1 - Ullmer, Brygg A1 - Paar, Philip A1 - Liu, Jing A1 - Konkel, Miriam A1 - Hege, Hans-Christian T1 - A smartphone-based tangible interaction approach for landscape visualization. T2 - PerDis ’18 Proceedings of the 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018 N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1145/3205873.3210707 SP - no. 23 PB - ACM CY - New York, NY, USA ER - TY - CHAP A1 - Ullmer, Brygg A1 - Paar, Philip A1 - Coconu, Liviu A1 - Liu, Jing A1 - Konkel, Miriam A1 - Hege, Hans-Christian T1 - An 1834 mediterranean garden in Berlin – engaged from 2004, 2018, 2032, and 2202 T2 - PerDis ’18 – 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018 N2 - In 2004, a team of researchers realized a semi-immersive interactive gallery installation, visualizing an 1834 Mediterranean garden, introduced as “italienisches Kunststück” (Italian legerdemain) by Peter Joseph Lenné. 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. Y1 - 2018 U6 - https://doi.org/10.1145/3205873.3205894 SP - no. 12 PB - ACM CY - New York, NY, USA ER - TY - GEN A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Atomic Accessibility Radii for Molecular Dynamics Analysis N2 - In molecular structure analysis and visualization, the molecule’s atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called atomic accessibility radius’, that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely. T3 - ZIB-Report - 18-18 KW - molecular dynamics KW - atomic radii KW - cavity analysis Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68468 SN - 1438-0064 ER - TY - CHAP A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Atomic Accessibility Radii for Molecular Dynamics Analysis T2 - Workshop on Molecular Graphics and Visual Analysis of Molecular Data N2 - In molecular structure analysis and visualization, the molecule’s atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called atomic accessibility radius’, that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely. Y1 - 2018 SN - 978-3-03868-061-1 U6 - https://doi.org/10.2312/molva.20181101 PB - The Eurographics Association ER - TY - GEN A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Leborgne, Morgan A1 - Hege, Hans-Christian T1 - Interactive Visualization of RNA and DNA Structures N2 - The analysis and visualization of nucleic acids (RNA and DNA) play an increasingly important role due to the growing number of known 3-dimensional structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. For the first time, we present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization. T3 - ZIB-Report - 18-33 KW - ribonucleic acids KW - DNA KW - RNA KW - secondary & tertiary structures KW - interactive rendering KW - ray casting KW - brushing & linking Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69704 SN - 1438-0064 ER - TY - GEN A1 - Agudo Jácome, Leonardo A1 - Hege, Hans-Christian A1 - Paetsch, Olaf A1 - Pöthkow, Kai T1 - Three-Dimensional Reconstruction and Quantification of Dislocation Substructures from Transmission Electron Microscopy Stereo-Pairs N2 - A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo-pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo-pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (> 300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo-pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3 % and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed. T3 - ZIB-Report - 18-50 KW - dislocation, diffraction contrast, scanning transmission electron microscopy, stereoscopy, visualization Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70339 SN - 1438-0064 ER - TY - GEN A1 - Nava-Yazdani, Esfandiar A1 - Hege, Hans-Christian A1 - von Tycowicz, Christoph A1 - Sullivan, T. J. T1 - A Shape Trajectories Approach to Longitudinal Statistical Analysis N2 - For Kendall’s shape space we determine analytically Jacobi fields and parallel transport, and compute geodesic regression. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and reduce the computational expense by several orders of magnitude. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As application example we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative. Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data only. T3 - ZIB-Report - 18-42 KW - shape space, shape trajectories, geodesic regression, longitudinal analysis, osteoarthritis Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69759 SN - 1438-0064 ER -