37-Issue 3

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https://diglib.eg.org/handle/10.2312/2632394

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Browsing 37-Issue 3 by Subject "CCS Concepts Human"

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    Analyzing Residue Surface Proximity to Interpret Molecular Dynamics
    (The Eurographics Association and John Wiley & Sons Ltd., 2018) Lichtenberg, Nils; Menges, Raphael; Ageev, Vladimir; George, Ajay Abisheck Paul; Heimer, Pascal; Imhof, Diana; Lawonn, Kai; Jeffrey Heer and Heike Leitte and Timo Ropinski
    The surface of a molecule holds important information about the interaction behavior with other molecules. In dynamic folding or docking processes, residues of amino acids with different properties change their position within the molecule over time. The atoms of the residues that are accessible to the solvent can directly contribute to binding interactions, while residues buried within the molecular structure contribute to the stability of the molecule. Understanding patterns and causality of structural changes is important for experts in the pharmaceutical domain, e.g., in the process of drug design. We apply an iterative computation of the Solvent Accessible Surface in order to extract virtual layers of a molecule. The extraction allows to track the movement of residues in the body of the molecule, with respect to the distance of the residue to the surface or the core during dynamics simulations. We visualize the obtained layer information for the complete time span of the molecular dynamics simulation as a 2D-map and for individual time-steps as a 3D-representation of the molecule. The data acquisition has been implemented alongside with further analysis functionality in a prototypical application, which is available to the public domain. We underline the feasibility of our approach with a study from the pharmaceutical domain, where our approach has been used for novel insights into the folding behavior of μ-conotoxins.
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    An Approximate Parallel Vectors Operator for Multiple Vector Fields
    (The Eurographics Association and John Wiley & Sons Ltd., 2018) Gerrits, Tim; Rössl, Christian; Theisel, Holger; Jeffrey Heer and Heike Leitte and Timo Ropinski
    The Parallel Vectors (PV) Operator extracts the locations of points where two vector fields are parallel. In general, these features are line structures. The PV operator has been used successfully for a variety of problems, which include finding vortex-core lines or extremum lines. We present a new generic feature extraction method for multiple 3D vector fields: The Approximate Parallel Vectors (APV) Operator extracts lines where all fields are approximately parallel. The definition of the APV operator is based on the application of PV for two vector fields that are derived from the given set of fields. The APV operator enables the direct visualization of features of vector field ensembles without processing fields individually and without causing visual clutter. We give a theoretical analysis of the APV operator and demonstrate its utility for a number of ensemble data.
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    Core Lines in 3D Second-Order Tensor Fields
    (The Eurographics Association and John Wiley & Sons Ltd., 2018) Oster, Timo; Rössl, Christian; Theisel, Holger; Jeffrey Heer and Heike Leitte and Timo Ropinski
    Vortices are important features in vector fields that show a swirling behavior around a common core. The concept of a vortex core line describes the center of this swirling behavior. In this work, we examine the extension of this concept to 3D second-order tensor fields. Here, a behavior similar to vortices in vector fields can be observed for trajectories of the eigenvectors. Vortex core lines in vector fields were defined by Sujudi and Haimes to be the locations where stream lines are parallel to an eigenvector of the Jacobian. We show that a similar criterion applied to the eigenvector trajectories of a tensor field yields structurally stable lines that we call tensor core lines. We provide a formal definition of these structures and examine their mathematical properties. We also present a numerical algorithm for extracting tensor core lines in piecewise linear tensor fields. We find all intersections of tensor core lines with the faces of a dataset using a simple and robust root finding algorithm. Applying this algorithm to tensor fields obtained from structural mechanics simulations shows that it is able to effectively detect and visualize regions of rotational or hyperbolic behavior of eigenvector trajectories.
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    A General Illumination Model for Molecular Visualization
    (The Eurographics Association and John Wiley & Sons Ltd., 2018) Casajus, Pedro Hermosilla; Vázquez, Pere-Pau; Vinacua, Àlvar; Ropinski, Timo; Jeffrey Heer and Heike Leitte and Timo Ropinski
    Several visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom-based representations are the Space-filling, the Solvent Excluded Surface, the Balls-and-Sticks, and the Licorice models. While each of these representations has its individual benefits, when applied to large-scale models spatial arrangements can be difficult to interpret when employing current visualization techniques. In the past it has been shown that global illumination techniques improve the perception of molecular visualizations; unfortunately existing approaches are tailored towards a single visual representation. We propose a general illumination model for molecular visualization that is valid for different representations. With our illumination model, it becomes possible, for the first time, to achieve consistent illumination among all atom-based molecular representations. The proposed model can be further evaluated in real-time, as it employs an analytical solution to simulate diffuse light interactions between objects. To be able to derive such a solution for the rather complicated and diverse visual representations, we propose the use of regression analysis together with adapted parameter sampling strategies as well as shape parametrization guided sampling, which are applied to the geometric building blocks of the targeted visual representations. We will discuss the proposed sampling strategies, the derived illumination model, and demonstrate its capabilities when visualizing several dynamic molecules.
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    Maps and Globes in Virtual Reality
    (The Eurographics Association and John Wiley & Sons Ltd., 2018) Yang, Yalong; Jenny, Bernhard; Dwyer, Tim; Marriott, Kim; Chen, Haohui; Cordeil, Maxime; Jeffrey Heer and Heike Leitte and Timo Ropinski
    This paper explores different ways to render world-wide geographic maps in virtual reality (VR). We compare: (a) a 3D exocentric globe, where the user's viewpoint is outside the globe; (b) a flat map (rendered to a plane in VR); (c) an egocentric 3D globe, with the viewpoint inside the globe; and (d) a curved map, created by projecting the map onto a section of a sphere which curves around the user. In all four visualisations the geographic centre can be smoothly adjusted with a standard handheld VR controller and the user, through a head-tracked headset, can physically move around the visualisation. For distance comparison exocentric globe is more accurate than egocentric globe and flat map. For area comparison more time is required with exocentric and egocentric globes than with flat and curved maps. For direction estimation, the exocentric globe is more accurate and faster than the other visual presentations. Our study participants had a weak preference for the exocentric globe. Generally the curved map had benefits over the flat map. In almost all cases the egocentric globe was found to be the least effective visualisation. Overall, our results provide support for the use of exocentric globes for geographic visualisation in mixed-reality.
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    Spatio-Temporal Contours from Deep Volume Raycasting
    (The Eurographics Association and John Wiley & Sons Ltd., 2018) Frey, Steffen; Jeffrey Heer and Heike Leitte and Timo Ropinski
    We visualize contours for spatio-temporal processes to indicate where and when non-continuous changes occur or spatial bounds are encountered. All time steps are comprised densely in one visualization, with contours allowing to efficiently analyze processes in the data even in case of spatial or temporal overlap. Contours are determined on the basis of deep raycasting that collects samples across time and depth along each ray. For each sample along a ray, its closest neighbors from adjacent rays are identified, considering time, depth, and value in the process. Large distances are represented as contours in image space, using color to indicate temporal occurrence. This contour representation can easily be combined with volume rendering-based techniques, providing both full spatial detail for individual time steps and an outline of the whole time series in one view. Our view-dependent technique supports efficient progressive computation, and requires no prior assumptions regarding the shape or nature of processes in the data. We discuss and demonstrate the performance and utility of our approach via a variety of data sets, comparison and combination with an alternative technique, and feedback by a domain scientist.
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    Visualization of 4D Vector Field Topology
    (The Eurographics Association and John Wiley & Sons Ltd., 2018) Hofmann, Lutz; Rieck, Bastian; Sadlo, Filip; Jeffrey Heer and Heike Leitte and Timo Ropinski
    In this paper, we present an approach to the topological analysis of four-dimensional vector fields. In analogy to traditional 2D and 3D vector field topology, we provide a classification and visual representation of critical points, together with a technique for extracting their invariant manifolds. For effective exploration of the resulting four-dimensional structures, we present a 4D camera that provides concise representation by exploiting projection degeneracies, and a 4D clipping approach that avoids self-intersection in the 3D projection. We exemplify the properties and the utility of our approach using specific synthetic cases.