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Molecular Surface Remeshing with Local Region Refinement
Khan, Dawar1,2; Yan, Dong-Ming1,2; Gui, Sheng2,3; Lu, Benzhuo2,3; Zhang, Xiaopeng1,2; Dong-Ming Yan
AbstractMolecular surface mesh generation is a prerequisite for using the boundary element method (BEM) and finite element method (FEM) in implicit-solvent modeling. Molecular surface meshes typically have small angles, redundant vertices, and low-quality elements. In the implicit-solvent modeling of biomolecular systems it is usually required to improve the mesh quality and eliminate low-quality elements. Existing methods often fail to efficiently remove low-quality elements, especially in complex molecular meshes. In this paper, we propose a mesh refinement method that smooths the meshes, eliminates invalid regions in a cut-and-fill strategy, and improves the minimal angle. We compared our method with four different state-of-the-art methods and found that our method showed a significant improvement over state-of-the-art methods in minimal angle, aspect ratio, and other meshing quality measurements. In addition, our method showed satisfactory results in terms of the ratio of regular vertices and the preservation of area and volume.
KeywordMolecular Surface Mesh Molecular Simulation Meshing Quality Finite Element Method
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine ; Physical Sciences
Indexed BySCI
Funding OrganizationScience Challenge Program(TZ2016003) ; National Key Research and Development Program of Ministry of Science and Technology(2016YFB0201304) ; National Natural Science Foundation of China(61772523 ; Chinese Government Scholarship ; 21573274 ; 11771435 ; 61620106003 ; 61331018)
WOS Research AreaBiochemistry & Molecular Biology ; Chemistry
WOS SubjectBiochemistry & Molecular Biology ; Chemistry, Multidisciplinary
WOS IDWOS:000435297000119
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Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Corresponding AuthorDong-Ming Yan
Affiliation1.Chinese Acad Sci, Inst Automat, Natl Lab Pattern Recognit, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
3.Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, State Key Lab Sci & Engn Comp, Acad Math & Syst Sci, Beijing 100190, Peoples R China
First Author AffilicationChinese Acad Sci, Inst Automat, Natl Lab Pattern Recognit, Beijing 100190, Peoples R China
Recommended Citation
GB/T 7714
Khan, Dawar,Yan, Dong-Ming,Gui, Sheng,et al. Molecular Surface Remeshing with Local Region Refinement[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2018,19(5):20.
APA Khan, Dawar,Yan, Dong-Ming,Gui, Sheng,Lu, Benzhuo,Zhang, Xiaopeng,&Dong-Ming Yan.(2018).Molecular Surface Remeshing with Local Region Refinement.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,19(5),20.
MLA Khan, Dawar,et al."Molecular Surface Remeshing with Local Region Refinement".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 19.5(2018):20.
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