Volume 37 (2018)

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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.
Bladder Runner: Visual Analytics for the Exploration of RT-Induced Bladder Toxicity in a Cohort Study
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Raidou, Renata Georgia; Casares-Magaz, Oscar; Amirkhanov, Aleksandr; Moiseenko, Vitali; Muren, Ludvig P.; Einck, John P.; Vilanova, Anna; Gröller, Eduard; Jeffrey Heer and Heike Leitte and Timo Ropinski
We present the Bladder Runner, a novel tool to enable detailed visual exploration and analysis of the impact of bladder shape variation on the accuracy of dose delivery, during the course of prostate cancer radiotherapy (RT). Our tool enables the investigation of individual patients and cohorts through the entire treatment process, and it can give indications of RT-induced complications for the patient. In prostate cancer RT treatment, despite the design of an initial plan prior to dose administration, bladder toxicity remains very common. The main reason is that the dose is delivered in multiple fractions over a period of weeks, during which, the anatomical variation of the bladder - due to differences in urinary filling - causes deviations between planned and delivered doses. Clinical researchers want to correlate bladder shape variations to dose deviations and toxicity risk through cohort studies, to understand which specific bladder shape characteristics are more prone to side effects. This is currently done with Dose-Volume Histograms (DVHs), which provide limited, qualitative insight. The effect of bladder variation on dose delivery and the resulting toxicity cannot be currently examined with the DVHs. To address this need, we designed and implemented the Bladder Runner, which incorporates visualization strategies in a highly interactive environment with multiple linked views. Individual patients can be explored and analyzed through the entire treatment period, while inter-patient and temporal exploration, analysis and comparison are also supported. We demonstrate the applicability of our presented tool with a usage scenario, employing a dataset of 29 patients followed through the course of the treatment, across 13 time points. We conducted an evaluation with three clinical researchers working on the investigation of RT-induced bladder toxicity. All participants agreed that Bladder Runner provides better understanding and new opportunities for the exploration and analysis of the involved cohort data.
Curvature Continuity Conditions Between Adjacent Toric Surface Patches
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Sun, Lanyin; Zhu, Chungang; Fu, Hongbo and Ghosh, Abhijeet and Kopf, Johannes
Toric surface patch is the multi-sided generalization of classical Bézier surface patch. Geometric continuity of the parametric surface patches plays a crucial role in geometric modeling. In this paper, the necessary and sufficient conditions of curvature continuity between toric surface patches are illustrated with the theory of toric degeneration. Furthermore, some practical sufficient conditions of curvature continuity of toric surface patches are also developed.
DimSUM: Dimension and Scale Unifying Map for Visual Abstraction of DNA Origami Structures
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Miao, Haichao; Llano, Elisa De; Isenberg, Tobias; Gröller, Eduard; Barišic, Ivan; Viola, Ivan; Jeffrey Heer and Heike Leitte and Timo Ropinski
We present a novel visualization concept for DNA origami structures that integrates a multitude of representations into a Dimension and Scale Unifying Map (DimSUM). This novel abstraction map provides means to analyze, smoothly transition between, and interact with many visual representations of the DNA origami structures in an effective way that was not possible before. DNA origami structures are nanoscale objects, which are challenging to model in silico. In our holistic approach we seamlessly combine three-dimensional realistic shape models, two-dimensional diagrammatic representations, and ordered alignments in one-dimensional arrangements, with semantic transitions across many scales. To navigate through this large, two-dimensional abstraction map we highlight locations that users frequently visit for certain tasks and datasets. Particularly interesting viewpoints can be explicitly saved to optimize the workflow. We have developed DimSUM together with domain scientists specialized in DNA nanotechnology. In the paper we discuss our design decisions for both the visualization and the interaction techniques. We demonstrate two practical use cases in which our approach increases the specialists' understanding and improves their effectiveness in the analysis. Finally, we discuss the implications of our concept for the use of controlled abstraction in visualization in general.
Directing the Photography: Combining Cinematic Rules, Indirect Light Controls and Lighting-by-Example
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Galvane, Quentin; Lino, Christophe; Christie, Marc; Cozot, Rémi; Fu, Hongbo and Ghosh, Abhijeet and Kopf, Johannes
The placement of lights in a 3D scene is a technical and artistic task that requires time and trained skills. Most 3D modelling tools only provide a direct control of light sources, through the manipulation of parameters such as size, location, flux (the perceived power of light) or opening angle (the light frustum). Approaches have been relying on automated or semi-automated techniques to relieve users from such low-level manipulations at the expense of an important computational cost. In this paper, guided by discussions with experts in scene and object lighting, we propose an indirect control of area light sources. We first formalize the classical 3-point lighting design principle (key-light, fill-lights and back/rim-lights) in a parametric model. Given a key-light placed in the scene, we then provide a computational approach to (i) automatically compute the position and size of fill-lights and back/rim-lights by analyzing the geometry of 3D character, and (ii) automatically compute the flux and size of key, fill and back/rim lights, given a sample reference image in a computationally efficient way. Results demonstrate the benefits of the approach on the quick lighting of 3D characters, and further demonstrate the feasibility of interactive control of multiple lights through image features.
Light Optimization for Detail Highlighting
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Gkaravelis, Anastasios; Papaioannou, Georgios; Fu, Hongbo and Ghosh, Abhijeet and Kopf, Johannes
In this paper we propose an effective technique for the automatic arrangement of spot lights and other luminaires on or near user-provided arbitrary mounting surfaces in order to highlight the geometric details of complex objects. Since potential applications include the lighting design for exhibitions and similar installations, the method takes into account obstructing geometry and potential occlusion from visitors and other non-permanent blocking geometry. Our technique generates the most appropriate position and orientation for light sources based on a local contrast maximization near salient geometric features and a clustering mechanism, producing consistent and view-independent results, with minimal user intervention. We validate our method with realistic test cases including multiple and disjoint exhibits as well as high occlusion scenarios.
Sit & Relax: Interactive Design of Body-Supporting Surfaces
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Leimer, Kurt; Birsak, Michael; Rist, Florian; Musialski, Przemyslaw; Fu, Hongbo and Ghosh, Abhijeet and Kopf, Johannes
We propose a novel method for interactive design of well-fitting body-supporting surfaces that is driven by the pressure distribution on the body's surface. Our main contribution is an interactive modeling system that utilizes captured body poses and computes an importance field that is proportional to the pressure distribution on the body for a given pose. This distribution indicates where the body should be supported in order to easily hold a particular pose, which is one of the measures of comfortable sitting. Using our approximation, we propose the entire workflow for interactive design of C2 smooth surfaces which serve as seats, or generally, as body supporting furniture for comfortable sitting. Finally, we also provide a design tool for RHINOCEROS/GRASSHOPPER that allows for interactive creation of single designs or entire multi-person sitting scenarios. We also test the tool with design students and present several results. Our method aims at interactive design in order to help designers to create appropriate surfaces digitally without additional empirical design passes.
Subdivision Schemes With Optimal Bounded Curvature Near Extraordinary Vertices
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Ma, Yue; Ma, Weiyin; Fu, Hongbo and Ghosh, Abhijeet and Kopf, Johannes
We present a novel method to construct subdivision stencils near extraordinary vertices with limit surfaces having optimal bounded curvature at extraordinary positions. With the proposed method, subdivision stencils for newly inserted and updated vertices near extraordinary vertices are first constructed to ensure subdivision with G1 continuity and bounded curvature at extraordinary positions. The remaining degrees of freedom of the constructed subdivision stencils are further used to optimize the eigenbasis functions corresponding to the subsubdominant eigenvalues of the subdivision with respect to G2 continuity constraints. We demonstrate the method by replacing subdivision stencils near extraordinary vertices for Catmull-Clark subdivision and compare the results with the original Catmull-Clark subdivision and previous tuning schemes known with small curvature variation near extraordinary positions. The results show that the proposed method produces subdivision schemes with better or comparable curvature behavior around extraordinary vertices with comparatively simple subdivision stencils.
Watercolor Woodblock Printing with Image Analysis
(The Eurographics Association and John Wiley & Sons Ltd., 2018) Panotopoulou, Athina; Paris, Sylvain; Whiting, Emily; Gutierrez, Diego and Sheffer, Alla
Watercolor paintings have a unique look that mixes subtle color gradients and sophisticated diffusion patterns. This makes them immediately recognizable and gives them a unique appeal. Creating such paintings requires advanced skills that are beyond the reach of most people. Even for trained artists, producing several copies of a painting is a tedious task. One can resort to scanning an existing painting and printing replicas, but these are all identical and have lost an essential characteristic of a painting, its uniqueness. We address these two issues with a technique to fabricate woodblocks that we later use to create watercolor prints. The woodblocks can be reused to produce multiple copies but each print is unique due to the physical process that we introduce. We also design an image processing pipeline that helps users to create the woodblocks and describe a protocol that produces prints by carefully controlling the interplay between the paper, ink pigments, and water so that the final piece depicts the desired scene while exhibiting the distinctive features of watercolor. Our technique enables anyone with the resources to produce watercolor prints.

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Browsing Volume 37 (2018) by Subject "Applied computing"

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