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 "Applied computing"

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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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    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.
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    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.