This paper demonstrates a methodology for using Aspen Chromatography to simulate and compare several operational modes and their combinations in simulated moving bed (SMB) chromatography. After discussing briefly the basic SMB concepts, we introduce two bioprocesses, a binary chiral separation of Troger's base enantiomers and a ternary separation of amino acid mixture. We accomplish the binary separation in a 4-zone column, and the ternary separation in a 5-zone column. We simulate both separation systems under several SMB operational modes and their combinations. The specific operational modes include the asynchronous shifting of inlet/outlet ports (Varicol), varying feed flow rates (PowerFeed and Partial Feeding), and varying feed concentrations (ModiCon) within the switching interval, together with their combinations. We compare the simulation results in terms of purities and recoveries of both extract and raffinate products, along with other performance indices. Concentration profiles within the column provide a basis for comparison between operational modes, and give physical insights that explain why a given operational mode performs better or worse than the basic SMB. Our goal is to improve the performance of the basic SMB cases and expand the feasible separation regions of these systems by applying different operational modes. We propose guidelines for improving the performance of the operational modes of the studied systems, and present the improved separation regions where certain purity and recovery thresholds are met for various operational modes. For both binary and ternary separations, we can improve the separation performance with any of the investigated operational modes. Varicol improves the performance of the basic SMB, but is limited by its ability to fully increase all the component purities in both cases. PowerFeed gives only small improvements over the base case. ModiCon is the best overall single operation mode that is easy to operate and obtains much improved separation performance. The combined PowerFeed and ModiCon (PF&MC) is the best operational mode for both cases, yielding large improvements in product purity, recovery, and other performance indices. Adding Varicol to the PF&MC is not significant enough to recommend one over the others, and the slight improvement is not likely to be worth the increased complexity. To validate these observations further, we apply our recently developed Powell optimizer for dynamic simulations for use with Aspen Chromatography. We compare the improvements from operational modes in both 4-zone and 5-zone systems with smaller separation factors. Significantly, the qualitative rankings of the different operational mode improvement remain identical across the different performance indices between our heuristic improvement and Pareto optimization.