title: Feature-preserving adaptive mesh generation for molecular shape modeling and simulation.
abstract: We describe a chain of algorithms for molecular surface and volumetric mesh generation. We take as inputs the centers and radii of all atoms of a molecule and the toolchain outputs both triangular and tetrahedral meshes that can be used for molecular shape modeling and simulation. Experiments on a number of molecules are demonstrated, showing that our methods possess several desirable properties: feature-preservation, local adaptivity, high quality, and smoothness (for surface meshes). We also demonstrate an example of molecular simulation using the finite element method and the meshes generated by our method. The approaches presented and their implementations are also applicable to other types of inputs such as 3D scalar volumes and triangular surface meshes with low quality, and hence can be used for generation/improvement of meshes in a broad range of applications.
authors.affiliation: Department of Mathematics, University of California, San Diego, La Jolla, CA 92093, United States. zeyun.yu@gmail.com
authors.forename: Zeyun
authors.initials: Z
authors.lastname: Yu
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Holst
authors.forename: Yuhui
authors.initials: Y
authors.lastname: Cheng
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D000110:Acetylcholinesterase / Q000737:chemistry; D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D020342:Finite Element Analysis; D051379:Mice; D008958:Models, Molecular
chemical_list: D000110:Acetylcholinesterase