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Feature-preserving adaptive mesh generation for molecular shape modeling and simulation.

Zeyun Yu¹, Michael J Holst, Yuhui Cheng

¹Department of Mathematics, University of California, San Diego, La Jolla, CA 92093, United States. zeyun.yu@gmail.com

Journal of Molecular Graphics & Modelling

|March 14, 2008

Summary

This summary is machine-generated.

We developed algorithms to generate molecular surface and volumetric meshes from atomic data. These high-quality meshes enable accurate molecular shape modeling and simulations.

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Area of Science:

Computational chemistry
Computer-aided molecular design
Scientific visualization

Background:

Molecular modeling and simulation require accurate geometric representations.
Existing meshing techniques may lack feature preservation or adaptivity for complex molecules.

Purpose of the Study:

To present a novel chain of algorithms for generating high-quality molecular surface and volumetric meshes.
To enable improved molecular shape modeling and simulations using generated meshes.

Main Methods:

Input: atomic centers and radii.
Output: triangular (surface) and tetrahedral (volumetric) meshes.
Algorithms designed for feature-preservation, local adaptivity, high quality, and smoothness.

Main Results:

Demonstrated successful mesh generation for various molecules.
Generated meshes exhibit desirable properties: feature-preservation, adaptivity, quality, and smoothness.
Successfully performed finite element method (FEM) molecular simulation using generated meshes.

Conclusions:

The developed algorithms provide a robust method for molecular mesh generation.
The approach is versatile and applicable to other 3D data, including scalar volumes and low-quality surface meshes.
This work facilitates advancements in molecular modeling, simulation, and broader meshing applications.