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Automated Parallel and Body-Fitted Mesh Generation in Finite Element Simulation of Macromolecular Systems

Part of:Physiological, cellular and medical topicsComputer aspects of numerical algorithmsPartial differential equations, boundary value problems

Published online by Cambridge University Press:  16 March 2016

Yan Xie,
Tiantian Liu,
Bin Tu,
Benzhuo Lu and
Linbo Zhang
Yan Xie
Affiliation:
State Key Laboratory of Scientific and Engineering Computing, Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
Tiantian Liu
Affiliation:
State Key Laboratory of Scientific and Engineering Computing, Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
Bin Tu
Affiliation:
National Center for NanoScience and Technology, Chinese Academy of Sciences, Beijing 100190, China
Benzhuo Lu*
Affiliation:
State Key Laboratory of Scientific and Engineering Computing, Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
Linbo Zhang*
Affiliation:
State Key Laboratory of Scientific and Engineering Computing, Institute of Computational Mathematics and Scientific/Engineering Computing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
*
*Corresponding author. Email addresses:xieyan@lsec.cc.ac.cn (Y. Xie), liutt@lsec.cc.ac.cn (T. Liu), tubin@lsec.cc.ac.cn (B. Tu), bzlu@lsec.cc.ac.cn (B. Lu), zlb@lsec.cc.ac.cn (L. Zhang)
*Corresponding author. Email addresses:xieyan@lsec.cc.ac.cn (Y. Xie), liutt@lsec.cc.ac.cn (T. Liu), tubin@lsec.cc.ac.cn (B. Tu), bzlu@lsec.cc.ac.cn (B. Lu), zlb@lsec.cc.ac.cn (L. Zhang)

Abstract

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Mesh generation is a bottleneck for finite element simulations of biomolecules. A robust and efficient approach, based on the immersed boundary method proposed in [8], has been developed and implemented to generate large-scale mesh body-fitted to molecular shape for general parallel finite element simulations. The molecular Gaussian surface is adopted to represent the molecular surface, and is finally approximated by piecewise planes via the tool phgSurfaceCut in PHG [43], which is improved and can reliably handle complicated molecular surfaces, through mesh refinement steps. A coarse background mesh is imported first and then is distributed into each process using a mesh partitioning algorithm such as space filling curve [5] or METIS [22]. A bisection method is used for the mesh refinements according to the molecular PDB or PQR file which describes the biomolecular region. After mesh refinements, the mesh is optionally repartitioned and redistributed for load balancing. For finite element simulations, the modification of region mark and boundary types is done in parallel. Our parallel mesh generation method has been successfully applied to a sphere cavity model, a DNA fragment, a gramicidin A channel and a huge Dengue virus system. The results of numerical experiments show good parallel efficiency. Computations of electrostatic potential and solvation energy also validate the method. Moreover, the meshing process and adaptive finite element computation can be integrated as one PHG project to avoid the mesh importing and exporting costs, and improve the convenience of application as well.

Keywords

Parallel mesh generationbody-fittedPHGbiomoleculesfinite element simulation

MSC classification

Secondary:65N50: Mesh generation and refinement65Y05: Parallel computation92C40: Biochemistry, molecular biology65N30: Finite elements, Rayleigh-Ritz and Galerkin methods, finite methods

Information

Type
Research Article
Information
Communications in Computational Physics , Volume 19 , Issue 3 , March 2016, pp. 582 - 602
Copyright
Copyright © Global-Science Press 2016 

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