SMOPT

SMOPT refines triangular molecular surface meshes to improve mesh quality while preserving manifoldness for accurate boundary element simulations and body-fitted volume mesh generation.

Key Features:

• Redundancy Removal: Identifies and removes redundant points, specifically vertices with three- or four-valence, to simplify the mesh without compromising structure.
• Mesh Smoothing: Applies a modified Laplacian smoothing method that eliminates surface irregularities while preventing intersecting triangles.
• Preservation of Manifoldness: Maintains manifoldness throughout refinement to preserve valid surface topology required for downstream analyses.
• Integration with TMSmesh 2.0: The refinement procedure is integrated into the TMSmesh 2.0 triangular molecular surface mesh generator.
• Support for Tetgen: Supports generation of body-fitted volume meshes using Tetgen for finite element and volumetric analyses.
• Handling Complex Geometries: Designed to handle triangular biomolecular surface meshes with highly irregular or arbitrary complex geometries.
• Compatibility with Other Generators: Can be applied to meshes produced by other surface triangular mesh generators.

Scientific Applications:

• Biomolecular Surface Meshes: Improves irregular biomolecular surface meshes to enable more accurate modeling of molecular structures relevant to drug design and protein interaction studies.
• Boundary Element Simulations: Produces meshes suitable for boundary element method simulations, enhancing accuracy and numerical stability.
• Volume Mesh Generation: Facilitates body-fitted volume mesh generation via Tetgen for finite element analysis and other volumetric studies.

Methodology:

SMOPT employs two primary algorithms—a redundancy-removal algorithm for three- and four-valence vertices and a modified Laplacian smoothing algorithm—that operate in tandem to simplify and smooth meshes while preserving manifoldness and handling arbitrary complex geometries.