30-Issue 3

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https://diglib.eg.org/handle/10.2312/163

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Browsing 30-Issue 3 by Subject "Computational Geometry and Object Modeling"

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    Interactive Exploration of Protein Cavities
    (The Eurographics Association and Blackwell Publishing Ltd., 2011) Krone, M.; Falk, M.; Rehm, S.; Pleiss, J.; Ertl, T.; H. Hauser, H. Pfister, and J. J. van Wijk
    We present a novel application for the interactive exploration of cavities within proteins in dynamic data sets. Inside a protein, cavities can often be found close to the active center. Therefore, when analyzing a molecular dynamics simulation trajectory it is of great interest to find these cavities and determine if such a cavity opens up to the environment, making the binding site accessible to the surrounding substrate. Our user-driven approach enables expert users to select a certain cavity and track its evolution over time. The user is supported by different visualizations of the extracted cavity to facilitate the analysis. The boundary of the protein and its cavities is obtained by means of volume ray casting, where the volume is computed in real-time for each frame, therefore allowing the examination of time-dependent data sets. A fast, partial segmentation of the volume is applied to obtain the selected cavity and trace it over time. Domain experts found our method useful when they applied it exemplarily on two trajectories of lipases from Rhizomucor miehei and Candida antarctica. In both data sets cavities near the active center were easily identified and tracked over time until they reached the surface and formed an open substrate channel.
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    Stable Morse Decompositions for Piecewise Constant Vector Fields on Surfaces
    (The Eurographics Association and Blackwell Publishing Ltd., 2011) Szymczak, Andrzej; H. Hauser, H. Pfister, and J. J. van Wijk
    Numerical simulations and experimental observations are inherently imprecise. Therefore, most vector fields of interest in scientific visualization are known only up to an error. In such cases, some topological features, especially those not stable enough, may be artifacts of the imprecision of the input. This paper introduces a technique to compute topological features of user-prescribed stability with respect to perturbation of the input vector field. In order to make our approach simple and efficient, we develop our algorithms for the case of piecewise constant (PC) vector fields. Our approach is based on a super-transition graph, a common graph representation of all PC vector fields whose vector value in a mesh triangle is contained in a convex set of vectors associated with that triangle. The graph is used to compute a Morse decomposition that is coarse enough to be correct for all vector fields satisfying the constraint. Apart from computing stable Morse decompositions, our technique can also be used to estimate the stability of Morse sets with respect to perturbation of the vector field or to compute topological features of continuous vector fields using the PC framework.