Molecular surface remeshing with local region refinement

Abstract

Molecular 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.