High-Fidelity Mesh Generation and Applications in Bio-Modeling

GAMER: A Mesh Generation Toolchain We have developed a set of efficient algorithms dealing with surface and volumetric mesh generation from a variety of inputs, including molecules in standard forms of PDB or PQR, digitalized 3D scalar volumes, and user-specified surface meshes with arbitrarily low quality. The toolchain, having the capability of generating smooth, adaptive, high quality, and feature-preserving meshes, has been coded into a stand-alone software package, called GAMER (or Geometry-preserving Adaptive MeshER). The availability of our software toolchain will give researchers in molecular and cellular modeling and simulation areas easy access to high-fidelity geometric models. GAMER in Molecular Modeling GAMER has been successfully applied to modeling a number of bio-molecular systems. One such example is the mouse acetylcholinesterase (mAChE) molecule as shown in (A) in the figure on the right. The corresponding surface and tetrahedral meshes are generated using GAMER, as demonstrated in (B) and (C) respectively. The active site has been colored in yellow, in contrast to the non-active sites (in cyan). The picture in (D) depicts the Ach concentration at the steady-state Smoluchowski diffusion at 0.15M ionic strength. The red and blue represent the high to low concentration of AChs