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Statistical wall shear stress maps of ruptured and unruptured middle cerebral artery aneurysms
(2012)
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.
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.
We present iCon.text, a kiosk platform for the iPad centered around artefacts, whose content and layout can be tailored without programming skills for specific museum exhibitions. The central metaphor to access information is a virtual postcard with one front and a customizable number of back sides that provide details about exhibits to museum visitors in textual and image form. Back sides can link to others cards. Access to these postcards is possible through one or more navigation views that can be navigated to from a navigation bar.
The entry point to the application is designed as a multitouch interactive pile of cards in a playful manner that allows visitors of any age an easy approach to the presentation and interaction metaphor. To directly access a certain postcard, a mosaic view can be uitilized to provide an overview about all available exhibits. A category view groups postcards into themes. Locating artefacts on a zoomable map or exhibition floor plan allows for conveying information about spatial contexts between different objects and their location. Furthermore, contexts can be illustrated with a two stage view comprising an overview and corresponding detail views to provide further insights into the spatial, temporal, and thematic contexts of artefacts. The application scaffolding allows the design of bilingual presentations to support exhibitions with an international audience. The logo of the presenting institution or exhibition can be incorporated to display the the kiosk's corporate design branding and to access an imprint or further informations. Usage is logged into files to provide a basis for extracting statistical information about the usage.
The details about the exhibits are presented as images and as such impose no limit to the design choices made by the content provider or exhibition designer.
The application (enhanced with a panoramic view) has been integrated successfully into a large special exhibition about the ancient city of Pergamon 2011/2012 at the Pergamon Museum Berlin within the interdisciplinary project "Berlin Sculpture Network".