Minxin Chen

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Qualified, stable, and efficient molecular surface meshing appears to be necessitated by recent developments for realistic mathematical modeling and numerical simulation of biomolecules, especially in implicit solvent modeling (e.g., see a review in B. Z. Lu et al. Commun. Comput. Phys. 2008, 3, 973-1009). In this paper, we present a new method: tracing(More)
A parallel finite element simulator, ichannel, is developed for ion transport through three-dimensional ion channel systems that consist of protein and membrane. The coordinates of heavy atoms of the protein are taken from the Protein Data Bank and the membrane is represented as a slab. The simulator contains two components: a parallel adaptive finite(More)
The molecular Gaussian surface has been frequently used in the field of molecular modeling and simulation. Typically, the Gaussian surface is defined using two controlling parameters; the decay rate and isovalue. Currently, there is a lack of studies in which a systematic approach in the determination of optimal parameterization according to the geometric(More)
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