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Parallel computation of alpha complexes for biomolecules

Masood, TB and Ray, T and Natarajan, V (2020) Parallel computation of alpha complexes for biomolecules. In: Computational Geometry: Theory and Applications, 90 .

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Official URL: https://dx.doi.org/10.1016/j.comgeo.2020.101651


The alpha complex, a subset of the Delaunay triangulation, has been extensively used as the underlying representation for biomolecular structures. We propose a GPU-based parallel algorithm for the computation of the alpha complex, which exploits the knowledge of typical spatial distribution and sizes of atoms in a biomolecule. Unlike existing methods, this algorithm does not require prior construction of the Delaunay triangulation. The algorithm computes the alpha complex in two stages. The first stage proceeds in a bottom-up fashion and computes a superset of the edges, triangles, and tetrahedra belonging to the alpha complex. The false positives from this estimation stage are removed in a subsequent pruning stage to obtain the correct alpha complex. Computational experiments on several biomolecules demonstrate the superior performance of the algorithm, up to a factor of 50 when compared to existing methods that are optimized for biomolecules.

Item Type: Journal Article
Publication: Computational Geometry: Theory and Applications
Publisher: Elsevier B.V.
Additional Information: Copyright for this article belongs to Elsevier B.V.
Keywords: Triangulation, Biomolecular structures; Bottom-up fashion; Computational experiment; Delau-nay triangulations; False positive; Gpu-based; Parallel Computation, Biomolecules
Department/Centre: Division of Electrical Sciences > Computer Science & Automation
Date Deposited: 09 Jun 2020 06:04
Last Modified: 09 Jun 2020 06:04
URI: http://eprints.iisc.ac.in/id/eprint/65274

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