Permanent charge (simplified mathematical model for protein structure) is the most important structure of an ion channel and is the major controller for properties of ionic flows through the ion channel. Another important factor for ionic flow specifics is the boundary conditions. In this talk, we will report our studies toward an understanding of effects of interplays between permanent charge and boundary conditions on ionic flow via a quasi-one-dimensional Poisson-Nernst-Planck (PNP) model.Permanent charges considered here are restricted to a special case of piecewise constant with one non-zero portion. For ionic mixtures with one cation (positively charged) species and one anion (negatively charged) species, a fairly rich behavior of permanent charge effects has been revealed from rigorous analyses based on a geometric framework for PNP and from numerical simulations guided by the analytical results. For ionic mixtures with three ion species: two cations and one anion, richer behavior is expected and our preliminary analysis and case studies identify, in concrete manner, a number of these, including some surprising ones.