Chromatographic separation is a pre-eminent downstream processing operation for the isolation of biological products, and has excellent resolution so is almost indispensable in the manufacturing of biopharmaceuticals for human diagnostic and therapeutic purposes. The complexity of chromatographic process dynamics, the large number of parameters involved, most of which depend on the processing materials, pose great challenges for the deriving of operating strategies for achieving maximum process efficiency. To date, the chromatographic process is based on experimentation and iterated to achieve the desired target. However, such trial and error approaches is time consuming and expensive and limits the number of variants which can be tested within the commonly short development time window. This paper uses mathematical modelling, computer simulation and optimisation in order to identify viable cost effective solutions. It allows the integration of process interactions, quantification of process trade-offs and rapid achievement of optimal strategies. A case-study is given based on the expanded bed hydrophobic interaction chromatographic separation of a liable protein from Sacchxiromyces cerevisiae cell homogenate. An overall process performance diagram is generated, representing the key process trade-offs that need to be considered during the design and operation of the chromatographic process. This novel approach overcomes the limitation of as experimentally based approach, and provides a powerful tool for the bioprocess engineer for the development of chromatographic separations