TY - JOUR A1 - Mahnke, Heinz-Eberhard A1 - Arlt, Tobias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Herter, Felix A1 - Lindow, Norbert A1 - Manke, Ingo A1 - Siopi, Tzulia A1 - Menei, Eve A1 - Etienne, Marc A1 - Lepper, Verena T1 - Virtual unfolding of folded papyri JF - Journal of Cultural Heritage N2 - The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Musée du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for “Lord”. Y1 - 2020 U6 - https://doi.org/10.1016/j.culher.2019.07.007 VL - 41 SP - 264 EP - 269 PB - Elsevier ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Accelerated Visualization of Dynamic Molecular Surfaces JF - Comput. Graph. Forum Y1 - 2010 U6 - https://doi.org/10.1111/j.1467-8659.2009.01693.x VL - 29 SP - 943 EP - 952 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Leborgne, Morgan A1 - Hege, Hans-Christian T1 - Interactive Visualization of RNA and DNA Structures JF - IEEE Transactions on Visualization and Computer Graphics N2 - The analysis and visualization of nucleic acids (RNA and DNA) is playing an increasingly important role due to their fundamental importance for all forms of life and the growing number of known 3D 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. We present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables for the first time 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. Y1 - 2019 U6 - https://doi.org/10.1109/TVCG.2018.2864507 VL - 25 IS - 1 SP - 967 EP - 976 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Ligand Excluded Surface: A New Type of Molecular Surface JF - IEEE Transactions on Visualization and Computer Graphics N2 - The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes – including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules. Y1 - 2014 U6 - https://doi.org/10.1109/TVCG.2014.2346404 VL - 20 IS - 12 SP - 2486 EP - 2495 ER - TY - GEN A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Ligand Excluded Surface: A New Type of Molecular Surface N2 - The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes – including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules. T3 - ZIB-Report - 14-27 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51194 SN - 1438-0064 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Voronoi-Based Extraction and Visualization of Molecular Paths JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2011 U6 - https://doi.org/10.1109/TVCG.2011.259 VL - 17 IS - 12 SP - 2025 EP - 2034 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Perceptually Linear Parameter Variations JF - Computer Graphics Forum Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03054.x target VL - 31 IS - 2 SP - 535 EP - 544 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Interactive Rendering of Materials and Biological Structures on Atomic and Nanoscopic Scale JF - Computer Graphics Forum Y1 - 2012 U6 - https://doi.org/10.1111/j.1467-8659.2012.03128.x target VL - 31 IS - 3 SP - 1325 EP - 1334 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 - Bondar, Ana-Nicoleta A1 - Hege, Hans-Christian T1 - Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization T2 - Proceedings of IEEE Symposium on Biological Data Visualization (biovis’12) Y1 - 2012 U6 - https://doi.org/10.1109/BioVis.2012.6378599 SP - 99 EP - 106 ER -