GPGPU-based Contour Surfaces

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Parallel Contour-Buildup algorithm for the molecular surface

We propose an optimization of the Contour-Buildup algorithm for the Solvent Excluded Surface (SES) to remedy this issue. An optimized subdivision of calculation tasks of the original algorithm allows for full utilization of massive parallel processing hardware. Our approach is especially well suited for modern graphics hardware employing the CUDA programming language. As we do not rely on any pre-computations our method is intrinsically applicable to time-dependent data with arbitrarily long trajectories. We are able to visualize the SES for molecules with up to ten thousand atoms interactively on standard consumer graphics cards.

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Institution: Visualization Research Center (VISUS) University of Stuttgart, Visualization and Interactive Systems Institute (VIS) University of Stuttgart

The simulation data sets were provided by the project partners from the Institute of Technical Bio-chemistry, University of Stuttgart. This work is partially funded by German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) as part of projects D.3 and D.4 of the Collaborative Research Centre (SFB) 716.