@article{LindowBaumHege2014, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Ligand Excluded Surface: A New Type of Molecular Surface}, series = {IEEE Transactions on Visualization and Computer Graphics}, volume = {20}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {12}, doi = {10.1109/TVCG.2014.2346404}, pages = {2486 -- 2495}, year = {2014}, abstract = {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.}, language = {en} } @misc{LindowBaumHege, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Ligand Excluded Surface: A New Type of Molecular Surface}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51194}, abstract = {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.}, language = {en} } @inproceedings{KlindtProhaskaBaumetal.2012, author = {Klindt, Marco and Prohaska, Steffen and Baum, Daniel and Hege, Hans-Christian}, title = {Conveying Archaeological Contexts to Museum Visitors: Case Study Pergamon Exhibition}, series = {VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers}, booktitle = {VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers}, editor = {Arnold, David and Kaminski, Jaime and Niccolucci, Franco and Stork, Andre}, publisher = {Eurographics Association}, address = {Brighton, UK}, doi = {10.2312/PE/VAST/VAST12S/025-028}, pages = {25 -- 28}, year = {2012}, language = {en} } @inproceedings{KlindtBaumProhaskaetal.2012, author = {Klindt, Marco and Baum, Daniel and Prohaska, Steffen and Hege, Hans-Christian}, title = {iCon.text - a customizable iPad app for kiosk applications in museum exhibitions}, series = {EVA 2012 Berlin}, booktitle = {EVA 2012 Berlin}, publisher = {Gesellschaft zur F{\"o}rderung angewandter Informatik e.V.}, address = {Volmerstraße 3, 12489 Berlin}, pages = {150 -- 155}, year = {2012}, 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}, series = {Proceedings of IEEE Symposium on Biological Data Visualization (biovis'12)}, 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{SchmidtEhrenbergBaumHege2002, author = {Schmidt-Ehrenberg, Johannes and Baum, Daniel and Hege, Hans-Christian}, title = {Visualizing Dynamic Molecular Conformations}, series = {Proceedings of IEEE Visualization 2002}, booktitle = {Proceedings of IEEE Visualization 2002}, editor = {J. Moorhead, Robert and Gross, Markus and I. Joy, Kenneth}, publisher = {IEEE Computer Society Press}, address = {Boston MA, USA}, doi = {10.1109/VISUAL.2002.1183780}, pages = {235 -- 242}, year = {2002}, language = {en} } @article{RigortGuentherHegerletal.2012, author = {Rigort, Alexander and G{\"u}nther, David and Hegerl, Reiner and Baum, Daniel and Weber, Britta and Prohaska, Steffen and Medalia, Ohad and Baumeister, Wolfgang and Hege, Hans-Christian}, title = {Automated segmentation of electron tomograms for a quantitative description of actin filament networks}, series = {Journal of Structural Biology}, volume = {177}, journal = {Journal of Structural Biology}, doi = {10.1016/j.jsb.2011.08.012}, pages = {135 -- 144}, year = {2012}, language = {en} } @article{SchmidtEhrenbergBaumHege2001, author = {Schmidt-Ehrenberg, Johannes and Baum, Daniel and Hege, Hans-Christian}, title = {Visually stunning - Molecular conformations}, series = {The Biochemist}, volume = {23}, journal = {The Biochemist}, number = {5}, pages = {22 -- 26}, year = {2001}, language = {en} } @article{WeberGreenanProhaskaetal.2012, author = {Weber, Britta and Greenan, Garrett and Prohaska, Steffen and Baum, Daniel and Hege, Hans-Christian and M{\"u}ller-Reichert, Thomas and Hyman, Anthony and Verbavatz, Jean-Marc}, title = {Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos}, series = {Journal of Structural Biology}, volume = {178}, journal = {Journal of Structural Biology}, number = {2}, doi = {10.1016/j.jsb.2011.12.004}, pages = {129 -- 138}, year = {2012}, language = {en} } @article{LindowBaumHege2011, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Voronoi-Based Extraction and Visualization of Molecular Paths}, series = {IEEE Transactions on Visualization and Computer Graphics}, volume = {17}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {12}, doi = {10.1109/TVCG.2011.259}, pages = {2025 -- 2034}, year = {2011}, language = {en} } @article{LindowBaumProhaskaetal.2010, author = {Lindow, Norbert and Baum, Daniel and Prohaska, Steffen and Hege, Hans-Christian}, title = {Accelerated Visualization of Dynamic Molecular Surfaces}, series = {Comput. Graph. Forum}, volume = {29}, journal = {Comput. Graph. Forum}, doi = {10.1111/j.1467-8659.2009.01693.x}, pages = {943 -- 952}, year = {2010}, language = {en} } @article{LindowBaumBondaretal.2013, author = {Lindow, Norbert and Baum, Daniel and Bondar, Ana-Nicoleta and Hege, Hans-Christian}, title = {Exploring cavity dynamics in biomolecular systems}, series = {BMC Bioinformatics}, volume = {14}, journal = {BMC Bioinformatics}, edition = {(Suppl 19):S5}, doi = {10.1186/1471-2105-14-S19-S5}, year = {2013}, language = {en} } @misc{HombergBaumWiebeletal.2014, author = {Homberg, Ulrike and Baum, Daniel and Wiebel, Alexander and Prohaska, Steffen and Hege, Hans-Christian}, title = {Definition, Extraction, and Validation of Pore Structures in Porous Materials}, series = {Topological Methods in Data Analysis and Visualization III}, journal = {Topological Methods in Data Analysis and Visualization III}, editor = {Bremer, Peer-Timo and Hotz, Ingrid and Pascucci, Valerio and Peikert, Ronald}, publisher = {Springer}, doi = {10.1007/978-3-319-04099-8_15}, pages = {235 -- 248}, year = {2014}, language = {en} } @article{CourniaAllenAndricioaeietal.2015, author = {Cournia, Zoe and Allen, Toby W. and Andricioaei, Ioan and Antonny, Bruno and Baum, Daniel and Brannigan, Grace and Buchete, Nicolae-Viorel and Deckman, Jason T. and Delemotte, Lucie and del Val, Coral and Friedman, Ran and Gkeka, Paraskevi and Hege, Hans-Christian and H{\´e}nin, J{\´e}r{\^o}me and Kasimova, Marina A. and Kolocouris, Antonios and Klein, Michael L. and Khalid, Syma and Lemieux, Joanne and Lindow, Norbert and Roy, Mahua and Selent, Jana and Tarek, Mounir and Tofoleanu, Florentina and Vanni, Stefano and Urban, Sinisa and Wales, David J. and Smith, Jeremy C. and Bondar, Ana-Nicoleta}, title = {Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory}, series = {Journal of Membrane Biology}, volume = {248}, journal = {Journal of Membrane Biology}, number = {4}, doi = {10.1007/s00232-015-9802-0}, pages = {611 -- 640}, year = {2015}, language = {en} } @misc{KozlikovaKroneFalketal., author = {Kozlikova, Barbora and Krone, Michael and Falk, Martin and Lindow, Norbert 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}, issn = {1438-0064}, doi = {10.2312/eurovisstar.20151112}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57217}, 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 survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.}, language = {en} } @misc{KroneKozlikovaLindowetal., author = {Krone, Michael and Kozlikova, Barbora and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Parulek, Julius and Hege, Hans-Christian and Viola, Ivan}, title = {Visual Analysis of Biomolecular Cavities: State of the Art}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60193}, abstract = {In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.}, language = {en} } @misc{HombergBaumWiebeletal., author = {Homberg, Ulrike and Baum, Daniel and Wiebel, Alexander and Prohaska, Steffen and Hege, Hans-Christian}, title = {Definition, Extraction, and Validation of Pore Structures in Porous Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42510}, abstract = {An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation.}, language = {en} } @inproceedings{BaumMahlowLameckeretal., author = {Baum, Daniel and Mahlow, Kristin and Lamecker, Hans and Zachow, Stefan and M{\"u}ller, Johannes and Hege, Hans-Christian}, title = {The Potential of Surface-based Geometric Morphometrics for Evolutionary Studies: An Example using Dwarf Snakes (Eirenis)}, series = {Abstract in DigitalSpecimen 2014}, booktitle = {Abstract in DigitalSpecimen 2014}, abstract = {Geometric morphometrics plays an important role in evolutionary studies. The state-of-the-art in this field are landmark-based methods. Since the landmarks usually need to be placed manually, only a limited number of landmarks are generally used to represent the shape of an anatomical structure. As a result, shape characteristics that cannot be properly represented by small sets of landmarks are disregarded. In this study, we present a method that is free of this limitation. The method takes into account the whole shape of an anatomical structure, which is represented as a surface, hence the term 'surface-based morphometrics'. Correspondence between two surfaces is established by defining a partitioning of the surfaces into homologous surface patches. The first step for the generation of a surface partitioning is to place landmarks on the surface. Subsequently, the landmarks are connected by curves lying on the surface. The curves, called 'surface paths', might either follow specific anatomical features or they can be geodesics, that is, shortest paths on the surface. One important requirement, however, is that the resulting surface path networks are topologically equivalent across all surfaces. Once the surface path networks have been defined, the surfaces are decomposed into patches according to the path networks. This approach has several advantages. One of them is that we can discretize the surface by as many points as desired. Thus, even fine shape details can be resolved if this is of interest for the study. Since a point discretization is used, another advantage is that well-established analysis methods for landmark-based morphometrics can be utilized. Finally, the shapes can be easily morphed into one another, thereby greatly supporting the understanding of shape changes across all considered specimens. To show the potential of the described method for evolutionary studies of biological specimens, we applied the method to the para-basisphenoid complex of the snake genus Eirenis. By using this anatomical structure as example, we present all the steps that are necessary for surface-based morphometrics, including the segmentation of the para-basisphenoid complex from micro-CT data sets. We also show some first results using statistical analysis as well as classification methods based on the presented technique.}, language = {en} } @inproceedings{ArltLindowBaumetal., 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}, series = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, booktitle = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, 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} } @misc{KramerNoackBaumetal.2017, author = {Kramer, Tobias and Noack, Matthias and Baum, Daniel and Hege, Hans-Christian and Heller, Eric J.}, title = {Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66338}, year = {2017}, abstract = {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.}, language = {en} }