Two-dimensional (2D) simulation of capillary electrophoresis is developed to model affinity interaction and wall adsorption simultaneously.Finite difference schemes are used to evaluate the mass transfer equation in cylindrical coordinates.A Langmuir second-order kinetic law is applied to regulate the wall adsorption and desorption processes.Contributions from the simulation parameters are investigated extensively and parameters for accurate and efficient simulation are identified.With the 2D model, capillary zone electrophoresis and affimity capillary electrophoresis (ACE) in the presence of strong or weak wall adsorption are simulated to elucidate peak distortions.Finite sample injection length/amount and wall adsorption that lead to systematic errors in the estimated binding constants in ACE are quantified for the first time with both actual experiments and computer simulation.Methods for correcting the estimated binding constants are proposed to extend the usefulness of ACE.