Voronoi Diagram Computation for a Molecule Using Graphics Hardware


The KIPS Transactions:PartA, Vol. 19, No. 4, pp. 169-174, Aug. 2012
10.3745/KIPSTA.2012.19.4.169,   PDF Download:

Abstract

We present an algorithm that computes a 3 dimensional Voronoi diagram for a protein molecule in this paper. The molecule is represented as a set of spheres with van der Waals radii. The Voronoi diagram is constructed in the 3D space by finding the voxels containing it. For the feasibility of the computation, we represent the molecule as a BVH (bounding volume hierarchy), and our system is accelerated by modern graphics hardware with CUDA programming support. Compared to single-core CPU implementations, experimental results show 323 times faster performance in the computation time, when the space is partitioned into 224 voxels.


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Cite this article
[IEEE Style]
K. J. Kim, J. E. Lee, N. H. Baek, "Voronoi Diagram Computation for a Molecule Using Graphics Hardware," The KIPS Transactions:PartA, vol. 19, no. 4, pp. 169-174, 2012. DOI: 10.3745/KIPSTA.2012.19.4.169.

[ACM Style]
Ku Jin Kim, Jung Eun Lee, and Nak Hoon Baek. 2012. Voronoi Diagram Computation for a Molecule Using Graphics Hardware. The KIPS Transactions:PartA, 19, 4, (2012), 169-174. DOI: 10.3745/KIPSTA.2012.19.4.169.