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Parallel Computation of Alpha Complexes for Biomolecules

Authors: Talha Bin Masood, Tathagata Ray, and Vijay Natarajan

Published in: LIPIcs, Volume 164, 36th International Symposium on Computational Geometry (SoCG 2020)


Abstract
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.

Cite as

Talha Bin Masood, Tathagata Ray, and Vijay Natarajan. Parallel Computation of Alpha Complexes for Biomolecules. In 36th International Symposium on Computational Geometry (SoCG 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 164, pp. 17:1-17:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)


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@InProceedings{masood_et_al:LIPIcs.SoCG.2020.17,
  author =	{Masood, Talha Bin and Ray, Tathagata and Natarajan, Vijay},
  title =	{{Parallel Computation of Alpha Complexes for Biomolecules}},
  booktitle =	{36th International Symposium on Computational Geometry (SoCG 2020)},
  pages =	{17:1--17:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-143-6},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{164},
  editor =	{Cabello, Sergio and Chen, Danny Z.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2020.17},
  URN =		{urn:nbn:de:0030-drops-121758},
  doi =		{10.4230/LIPIcs.SoCG.2020.17},
  annote =	{Keywords: Delaunay triangulation, parallel algorithms, biomolecules, GPU}
}
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