We will show our continuum(or implicit solvent)finite element/boundary element molecular modeling approaches in computations of molecular surface mesh,Poisson-Boltzmann electrostatic solvation energy,ion transport property of ion channels/nanopores.In particular,one application is to study the ion current signals of a DNA-nanopore system which is a potential technology for next generation of gen sequencing.Another application is to study the effect of charged substrate and product species to their diffusion-controlled binging rate.