High-fidelity geometric modeling for biomedical applications

  • Authors:

  • Zeyun Yu;Michael J. Holst;J. Andrew McCammon

  • Affiliations:

  • Department of Mathematics, University of California, San Diego, La Jolla, CA 92093, USA;Department of Mathematics, University of California, San Diego, La Jolla, CA 92093, USA;Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA and Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA

  • Venue:
  • Finite Elements in Analysis and Design
  • Year:
  • 2008

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Abstract

We describe a combination of algorithms for high-fidelity geometric modeling and mesh generation. Although our methods and implementations are application-neutral, our primary target application is multiscale biomedical models that range in scales across the molecular, cellular, and organ levels. Our software toolchain implementing these algorithms is general in the sense that it can take as input a molecule in PDB/PQR forms, a 3D scalar volume, or a user-defined triangular surface mesh that may have very low quality. The main goal of our work presented is to generate high quality and smooth surface triangulations from the aforementioned inputs, and to reduce the mesh sizes by mesh coarsening. Tetrahedral meshes are also generated for finite element analysis in biomedical applications. Experiments on a number of bio-structures are demonstrated, showing that our approach possesses several desirable properties: feature-preservation, local adaptivity, high quality, and smoothness (for surface meshes). The availability of this software toolchain will give researchers in computational biomedicine and other modeling areas access to higher-fidelity geometric models.