@inproceedings{LindowBaumHege2018, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Atomic Accessibility Radii for Molecular Dynamics Analysis}, booktitle = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data}, publisher = {The Eurographics Association}, isbn = {978-3-03868-061-1}, doi = {10.2312/molva.20181101}, year = {2018}, abstract = {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.}, language = {en} } @inproceedings{KuhnLindowGuentheretal.2013, author = {Kuhn, Alexander and Lindow, Norbert and G{\"u}nther, Tobias and Wiebel, Alexander and Theisel, Holger and Hege, Hans-Christian}, title = {Trajectory Density Projection for Vector Field Visualization}, booktitle = {EuroVis 2013, short papers. M. Hlawitschka, Tino Weinkauf (eds.)}, doi = {10.2312/PE.EuroVisShort.EuroVisShort2013.031-035}, pages = {31 -- 35}, year = {2013}, language = {en} } @inproceedings{LindowBaumBondaretal.2012, author = {Lindow, Norbert and Baum, Daniel and Bondar, Ana-Nicoleta and Hege, Hans-Christian}, title = {Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization}, booktitle = {Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12)}, doi = {10.1109/BioVis.2012.6378599}, pages = {99 -- 106}, year = {2012}, language = {en} } @inproceedings{ArltLindowBaumetal.2016, author = {Arlt, Tobias and Lindow, Norbert and Baum, Daniel and Hilger, Andre and Mahnke, Ingo and Hege, Hans-Christian and Lepper, Verena and Siopi, Tzulia and Mahnke, Heinz.Eberhard}, title = {Virtual Access to Hidden Texts - Study of Ancient Papyri}, booktitle = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, year = {2016}, abstract = {When physical unfolding/unrolling of papyri is not possible or too dangerous for preserving the precious object, tomographic approaches may be the ap- propriate alternative. Requirements are the resolution and the contrast to distinguish writing and substrate. The steps to be performed are the following: (1) Select the object of interest (archaeological arguments, cultural back- ground of the object, etc.). (2) Find the proper physical procedure, especially with respect to contrast, take the tomographic data, e.g. by absorption x-ray tomography. (3) Apply mathematical unfolding transformations to the tomographic data, in order to obtain a 2d-planar reconstruction of text.}, language = {en} } @inproceedings{KozlikovaKroneLindowetal.2015, author = {Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, title = {Visualization of Biomolecular Structures: State of the Art}, booktitle = {EuroVis 2015 STARS Proceedings}, doi = {10.2312/eurovisstar.20151112}, pages = {61 -- 81}, year = {2015}, abstract = {Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.}, language = {en} }