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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)
Generation of manifold mesh is an urgent issue in mathematical simulations of biomolecule using boundary element methods (BEM) or finite element method (FEM). Defects, such as not closed mesh, intersection of elements and missing of small structures, exist in surface meshes generated by most of the current meshing method. Usually the molecular surface(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)
OBJECTIVE To evaluate the role of nuclear factor-kappa B (NF-kappaB) and inhibitory kappaB alpha (IkappaBalpha) in hepatocellular cacinoma (HCC) SMMC7721 cells, the consequence of NF-kappaB inhibition in SMMC7721 cells transfected with mutated IkappaBalpha (mIkappaBalpha) plasmid and the effect of stable inhibition of NF-kappaB activity in combination with(More)
We present a numerical method to approximate the memory functions in the generalized Langevin models for the collective dynamics of macromolecules. We first derive the exact expressions of the memory functions, obtained from projection to subspaces that correspond to the selection of coarse-grain variables. In particular, the memory functions are expressed(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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