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Atom Simplification and Quality T-mesh Generation for Multi-resolution Biomolecular Surfaces

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Isogeometric Analysis and Applications 2014

Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 107))

Abstract

In this paper, we present an algorithm to simplify low-contributing atoms and generate quality T-meshes for multi-resolution biomolecular surfaces. The structure of biomolecules is first simplified using an error-bounded atom elimination method. An extended cross field-based parameterization method is then developed to adapt the parametric line spacings to different surface resolutions. Moreover, an anisotropy defined from an input scalar field can also be achieved. From the parameterization results, we extract adaptive and anisotropic T-meshes for the further T-spline surface construction. Finally, a gradient flow-based method is developed to improve the T-mesh quality, with the anisotropy preserved in the quadrilateral elements. The effectiveness of the presented algorithm has been verified using several large biomolecular complexes.

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Acknowledgements

T. Liao and Y. Zhang were supported in part by PECASE Award N00014-14-1-0234 and NSF CAREER Award OCI-1149591. G. Xu was supported in part by NSFC under the grants (11101401, 81173663), and NSFC Fund for Creative Research Groups of China (grant No. 11321061).

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Authors and Affiliations

  1. Department of Mechanical Engineering, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, 15213, USA

    Tao Liao, Guoliang Xu & Yongjie Jessica Zhang

  2. Institute of Computational Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China

    Tao Liao, Guoliang Xu & Yongjie Jessica Zhang

Authors
  1. Tao Liao
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  2. Guoliang Xu
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Correspondence to Yongjie Jessica Zhang .

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Editors and Affiliations

  1. Johannes Kepler Universität Linz Institut für Angewandte Geometrie, Linz, Austria

    Bert Jüttler

  2. Technische Universität Kaiserslautern Fachbereich Mathematik, Kaiserslautern, Germany

    Bernd Simeon

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Liao, T., Xu, G., Zhang, Y.J. (2015). Atom Simplification and Quality T-mesh Generation for Multi-resolution Biomolecular Surfaces. In: Jüttler, B., Simeon, B. (eds) Isogeometric Analysis and Applications 2014. Lecture Notes in Computational Science and Engineering, vol 107. Springer, Cham. https://doi.org/10.1007/978-3-319-23315-4_7

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