TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique.

Area of Science:

• Computational biology
• Molecular modeling
• Scientific computing

Background:

• Realistic mathematical modeling and numerical simulation of biomolecules are crucial, especially for implicit solvent modeling.
• Existing methods for molecular surface generation face challenges with large biomolecular systems.

Purpose of the Study:

• To introduce a novel and efficient method for generating molecular surface meshes.
• To address the limitations of current surface generation techniques for large biomolecules.

Main Methods:

• The tracing molecular surface for meshing (TMSmesh) method directly computes surface points by solving nonlinear equations.
• It employs a trace technique to connect surface points for polygonization, resulting in a triangulated mesh.
• The method exhibits linear complexity concerning the number of atoms.

Main Results:

• TMSmesh successfully generates meshes for biomolecules, including those with over one million atoms.
• The generated meshes are validated through boundary element solutions of the Poisson-Boltzmann equation.
• This enables simulations of electrostatic solvation for large-scale molecular systems.

Conclusions:

• TMSmesh provides an efficient and scalable solution for molecular surface meshing.
• The method facilitates advanced simulations, particularly in implicit solvent modeling and electrostatic analysis.
• The TMSmesh software and benchmark molecules are publicly available for research.