My CV in pdf format.

My research interests include mesh generation, molecular graphics, visualization, computational geometry and topology and their applications in structural biology. My Ph.D study supervisor is Dr. Cheng Ho-lun, Alan.  My primary research focuses on the meshing of skin surfaces. 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, which would be useful for the applications such as molecular shape visualization and electrostatic potential computation. We also define and extract the cavities on the molecular skin surface for the application such as protein docking and similarity matching problem. Recently, I am working on the algorithm generating quality volumetric meshes for the macromolecules.

Skin Meshing Software

Skin 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.

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.

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.

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

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.