Molecular Surface Remeshing with Local Region Refinement.

Area of Science:

• Computational chemistry
• Biophysics
• Scientific computing

Background:

• Molecular surface mesh generation is crucial for implicit-solvent modeling using boundary element method (BEM) and finite element method (FEM).
• Existing molecular surface meshes often suffer from low-quality elements, small angles, and redundant vertices, hindering accurate biomolecular system simulations.
• Efficiently removing low-quality elements, particularly in complex molecular structures, remains a challenge for current methods.

Purpose of the Study:

• To develop and present an advanced mesh refinement technique for molecular surface meshes.
• To enhance mesh quality by smoothing, eliminating invalid regions, and improving minimal angles.
• To provide a robust solution for improving mesh quality in implicit-solvent modeling of biomolecular systems.

Main Methods:

• A novel mesh refinement method incorporating mesh smoothing and a cut-and-fill strategy for invalid region elimination.
• Focus on improving the minimal angle and overall element quality of molecular surface meshes.
• Comparative analysis against four state-of-the-art mesh refinement techniques.

Main Results:

• The proposed method demonstrated significant improvements in minimal angle and aspect ratio compared to existing methods.
• Achieved superior performance in various meshing quality measurements, including element regularity.
• Successfully preserved critical area and volume properties of the molecular surface meshes.

Conclusions:

• The developed mesh refinement method offers a substantial advancement for generating high-quality molecular surface meshes.
• This technique effectively addresses limitations of current methods in handling complex molecular structures.
• The improved mesh quality facilitates more accurate and efficient implicit-solvent modeling of biomolecular systems.