CUDA-based triangulations of convolution molecular surfaces

Sérgio Dias, Kuldeep Bora, Abel Gomes
2010 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10  
Computing molecular surfaces is important to measure areas and volumes of molecules, as well as to infer useful information about interactions with other molecules. Over the years many algorithms have been developed to triangulate and to render molecular surfaces. However, triangulation algorithms usually are very expensive in terms of memory storage and time performance, and thus far from real-time performance. Fortunately, the massive computational power of the new generation of low-cost GPUs
more » ... opens up an opportunity window to solve these problems: real-time performance and cheap computing commodities. This paper just presents a GPU-based algorithm to speed up the triangulation and rendering of molecular surfaces using CUDA. Our triangulation algorithm for molecular surfaces is based on a multi-threaded, parallel version of the Marching Cubes (MC) algorithm. However, the input of our algorithm is not the volume dataset of a given molecule as usual for Marching Cubes, but the atom centers provided by the PDB file of such a molecule. We also carry out a study that compares a serial version (CPU) and a parallel version (GPU) of the MC algorithm in triangulating molecular surfaces as a way to understand how real-time rendering of molecular surfaces can be achieved in the future.
doi:10.1145/1851476.1851553 dblp:conf/hpdc/DiasBG10 fatcat:chkrgki3ljgxdjjzozsv5nbkda