Shi Xinwei (时新伟)
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Postdocotal ResearcherRoom 4337, Genome Center, GBSF 451 East Health Sciences Drive University of California Davis, CA 95616 Phone: (530) 754 9738 |
Biographical Information
2006 - present, Postdoctoral Researcher, Genome Center, University of California, Davis
2002 - 2005 PH.D, Computer Science Department, National University of Singapore
2000 - 2002, Software Engineer, Huawei Technology
1994 - 2000, B.S and M.S, Department of Computer Science and Engineering, Harbin Institute of Technology
Research
My research interests include mesh generation, molecular graphics, visualization, computational geometry and topology and their applications in structural biology. Recently, I am working on the computation of electrostatic potentials for proteins and RNAs. My primary research in my PH.D sudy focuses on the meshing of skin surfaces and their volumes. We use the skin surface as a surface model of macromolecules such as proteins and DNAs. We worked out efficient skin triangulation algorithms generating guaranteed quality surface triangulations and quality tetrahedral meshes for the macromolecules. We also define and extract the cavities on the molecular skin surface for the application ssuch as protein docking and similarity matching problem.
Software
Skin Meshing SoftwareSkin meshing software can construct quality surface meshes for the skin surfaces specified by a set of spheres. The input is the coordinates of the center and the radii of the spheres. The software can also import the PDB files downloaded from the protein data bank. The output is a triangular mesh with guaranteed quality of the skin surface specified by the spheres or the molecular skin model of the molecule in the pdb file. In the right figures, the skin model of a DNA molecule and a human faces modeled by skin are illustrated. The left column shows the union of the input spheres and the right column illustrates the rendering of the triangular mesh.The software is based on a Delaunay based meshing algorithm using restricted union of balls which is described in the papers in the publication part. Please refer to the software page for the usage and download. |
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Publications
Quality Mesh Generation for Molecular Skin Surfaces Using Restricted Union of Balls
With Ho-Lun Cheng
Accepted by IEEE Visualization 2005
Quality surface meshes for molecular models are desirable in the studies of protein shapes and functionalities. However, there is still no robust software that is capable to generate such meshes with good quality. In this paper, we present a Delaunay-based surface triangulation algorithm generating quality surface meshes for the molecular skin model. We expand the restricted union of balls along the surface and generate an $\varepsilon$-sampling of the skin surface incrementally. At the same time, a quality surface mesh is extracted from the Delaunay triangulation of the sample points. The algorithm supports robust and efficient implementation and guarantees the mesh quality and topology as well. Our results facilitate molecular visualization and have made a contribution towards generating quality volumetric tetrahedral meshes for the macromolecules.
Guaranteed Quality Triangulation of Molecular Skin Surfaces
With Ho-Lun, Cheng
IEEE Visualization 2004,
We present an efficient algorithm to mesh the macromolecules surface model represented by the skin surface defined by Edelsbrunner. Our algorithm overcomes several challenges residing in current surface meshing methods. First, we guarantee the mesh quality with a provable lower bound of 21◦ on its minimum angle. Second, we ensure the triangulation is homeomorphic to the original surface. Third, we improve the efficiency of constructing the Restricted Delaunay Triangulation(RDT) of smooth surfaces. We achieve this by constructing the RDT using the advancing front method without computing the Delaunay tetrahedrization of the sample points on the surfaces. The difficulty of handling the front collision problem is tackled by employing the Morse theory. In particular, we construct the Morse-Smale complex to simplify the topological changes of the front. Our implementation results suggest that the algorithm decrease the time of generating high quality homeomorphic skin mesh from hours to a few minutes.
Cavities on the Surfaces of Macromolecules
With Cheng Ho-Lun,
Japan Conference on Discrete and Computational Geometry (JCDCG) 2004
We present an approach to define and extract the cavities on the surfaces of macromolecules. Each cavity is represented by a triangular mesh enclosing a depression on a molecule such as a protein and a DNA. These surface patches would facilitate the study of ligand docking problem and similarity matching of proteins.
The application of camera-dependent-video in 3D-Scence Construction
With Guo Hengye and Liu Xin
International Conference on Image and Graphics 2000
In virtual environment, the integration of video images and computer graphics can produce a more convincing 3D-scene. This paper mainly discusses some key techniques about the application of camera-dependent-video as the background of real-time 3D-scene. We focus on the multi-layers windows display technology, camera-dependent-video playing, and control parameters passing. A framework of the realization and some experimental results are illustrated in the paper.