a novel boundary element method -- "node patch" BEM
finite element menthod
fast multipole method
Mesh generation for molecular systems, surface triangular mesh and volume tetrahedral mesh for purposes of mathematical modeling and numerical simulation (such as boundary element/finite element computation) of biomolecular systems besides of for usual visualization and structural geometric analysis.
Electrostatics, density distribution, diffusion-reaction processes described by the Poisson-Boltzmann equation, the Poisson-Nernst-Planck equations, and their modified forms.
Cellular network modeling of calcium signaling in myocyte and virus DNA/RND trafficking.
Prediction of solution structure (ions, water, and biomolecules), theory and computation of hydration, hydrophobicity, and associated entropy and free energy.
Synergistic binding in protein kinase.
Structural fluctuation and rate regulation in biomolecule.
Entropy and free energy calculations in binding and docking.
Developed a reduced Hessian method to direct calculation of entropy loss due to reduced translational and rotational motions upon molecular binding. And continue to extend this method as a domain-based coarse normal mode analysis for large conformational change prediction of supermolecule system.