Three-dimensional alpha shapes
ACM Transactions on Graphics (TOG)
Computing Smooth Molecular Surfaces
IEEE Computer Graphics and Applications
Interactive Visualization of Molecular Surface Dynamics
IEEE Transactions on Visualization and Computer Graphics
Interactive exploration of protein cavities
EuroVis'11 Proceedings of the 13th Eurographics / IEEE - VGTC conference on Visualization
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Molecular dynamics simulations are a principal tool in the study of molecules. The efficient investigation of the structure and dynamics of the simulated molecular systems benefits from interactive high-quality visualizations. Molecular surfaces are among the most common representations for visual analysis of the properties of these molecules, especially when studying proteins and other biomolecules. In this paper we evaluate the suitability of parallel graphics hardware (GPUs) for interactive computation and visualization of the Solvent Excluded Surface. This surface consists of spherical and toroidal geometric primitives, which can be rendered using ray casting on the GPU, thereby obtaining unsurpassed visual quality at interactive frame rates. The key, however, is the efficient calculation of the Reduced Surface that defines the occurrence and location of these primitives. The Reduced Surface can be computed quite efficient and allows for a partial update of the surface in regions where changes occur. However, the original algorithm to construct the Reduced Surface cannot be parallelized straightforward. We introduce a novel, parallel algorithm, leveraging programmable GPUs, for computing the Reduced Surface. This allows the high-quality rendering and interactive exploration of complex molecules and time-varying molecular datasets.