Molecular Mesh Generation and Processing
Dr. Zeyun Yu
Department of Mathematics
and Department of Chemistry/Biochemistry
UC San Diego
Abstract
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.