Molecular Mesh Generation and Processing

Dr. Zeyun Yu
Department of Mathematics and Department of Chemistry/Biochemistry
UC San Diego


Molecular surface and volumetric meshes are important for molecular modeling and simulation. I'll talk about mesh generation using a so-called "soft-model" approach, meaning that each atom is treated as a smoothly decaying Gaussian function instead of a hard sphere, and the molecular surfaces are given as level sets of the summation of such functions from all atoms in a molecule. The mesh generation toolchain consists of several steps: (1) from molecules to 3D volumes; (2) from volumes to initial surface meshes; (3) surface mesh post-processing; and (4) volumetric mesh generation and smoothing. A number of examples on molecules taken from Protein Data Bank (PDB) will be demonstrated.