The KIPS Transactions:PartA (정보처리학회논문지A)

Korea Information Processing Society (한국정보처리학회)
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Voronoi Diagram Computation for a Molecule Using Graphics Hardware

그래픽 하드웨어를 이용한 분자용 보로노이 다이어그램 계산

  • 이정은 (경북대학교 전자전기컴퓨터학부) ;
  • 백낙훈 (경북대학교 컴퓨터학부) ;
  • 김구진 (경북대학교 컴퓨터학부)
  • Received : 2012.02.21
  • Accepted : 2012.03.27
  • Published : 2012.08.31
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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 $2^{24}$ voxels.

본 논문에서는 주어진 단백질 분자에 대해 3차원 보로노이 다이어그램을 계산하는 알고리즘을 제안한다. 분자는 반경이 서로 다른 구의 집합으로 표현되며, 각 구의 반경은 원자의 반데르바스 (van der Waals) 반경에 대응한다. 보로노이 다이어그램은 3차원 공간을 복셀(voxel)의 집합으로 분할한 뒤, 보로노이 다이어그램을 포함하는 복셀을 보수적으로 추출함으로써 구성된다. 분자의 계층적 성질을 이용하여 BVH(bounding volume hierarchy)를 구성하고, CUDA 프로그래밍을 통하여 그래픽 하드웨어 가속을 활용함으로써 계산 시간 효율성을 높인다. 공간이 최대 $2^{24}$개의 복셀로 분할될 경우, 단일 코어 CPU로 구현하는 알고리즘에 비해 계산 속도가 323배 가량 향상 되었다.

Keywords

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