Triangulated manifold meshing method preserving molecular surface topology

Generation of manifold mesh is an urgent issue in mathematical simulations of biomolecule using boundary element methods (BEM) or finite element method (FEM). Defects, such as not closed mesh, intersection of elements and missing of small structures, exist in surface meshes generated by most of the current meshing method. Usually the molecular surface meshes produced by existing methods need to be revised carefully by third party software to ensure the surface represents a continuous manifold before being used in a BEM and FEM calculations. Based on the trace technique proposed in our previous work [1], in this paper, we present an improved meshing method to avoid intersections and preserve the topology of the molecular Gaussian surface. The new method divides the whole Gaussian surface into single valued pieces along each of x, y, z directions by tracing the extreme points along the fold curves on the surface. Numerical test results show that the surface meshes produced by the new method are manifolds and preserve surface topologies. The result surface mesh can also be directly used in surface conforming volume mesh generation for FEM type simulation.

The improved version of TMSmesh divides the molecular Gaussian surface into single valued pieces on each of x, y, z directions through a new technique of tracing along the fold curves. This makes the resulted mesh be a manifold mesh and preserve the topology of the molecular Gaussian surface, which is critical for BEM and FEM types of molecular modelling and simulation to produce convergent and reasonable results. Figure optionsDownload high-quality image (152 K)Download as PowerPoint slideHighlights
► A new technique of tracing along the fold curves on molecular surface is employed.
► The surface is divided into single valued pieces along each of x, y, z directions.
► The resulted meshes of our method are manifolds without intersections.
► Molecular surface structures smaller than grid space are found in our method.