Many of the industrial processes, used by manufacturers to produce biologics, have not been significantly updated since their original design and conception. And thus, there is a great opportunity to update and optimize manufacturing processes. Downstream purification is often considered the bottleneck of the manufacturing process and when biologics are being purified for clinical applications, the final purity is paramount. As a result, pharmaceutical products are subjected to multiple concentration, conditioning, and chromatographic steps. The pharmaceutical industry is constantly and slowly evolving and is always looking to improve efficiency. Simulations and modeling are becoming more commonly used in the pharmaceutical industry as a tool to strategically design and test new production and separation processes developed at the research and development scale. In this thesis, computational fluid dynamics (CFD) modeling was used to develop more efficient bioseparation processes by (1) using a cuboid module geometry and (2) chromatographic medium with product-specific affinity ligands. The laterally-fed class of chromatography modules has a unique cuboidal geometry, with lateral feeding of the sample in the channel above the bed and lateral collection of permeate. CFD simulations and experimental results have shown that the laterally-fed class of chromatography devices can produce sharper elution peaks, have better peak resolution, and consequently purer product fractions than conventional membrane and resin-based chromatographic formats. The enhanced performance by the laterally-fed class of chromatography devices is attributed to improved system fluidics and narrow solute residence time distribution. One other approach to improving efficiency is to address the tradeoff between purity and recovered yield, due to the non-specific binding nature of many commercial resins and membranes. Purification using high-affinity biological ligands selected on specificity to the target molecule could be a feasible solution. A purification scheme for pertactin was developed with final eluate purity of 90% and approximately 100% recovery. / Thesis / Master of Applied Science (MASc)