Within the past decade, novel gel materials with a modified internal morphology have been synthesized and are available for a wide range of applications including drug delivery and separation of biomolecules with relevance in clinical diagnostics, electroldnetic pumping, and sensors.(1-3) One way to achieve this internal modification is to embed nanoparticles into the polymer matrix so that when an electrical field is applied to the system, the presence of these particles can change the biomacromolecule transport through the gel, possibly altering the separation.(4) As a result, gaining a very deep understanding of the role that these nanoparticles can have in the separation efficiency in terms of electrophoresis techniques becomes very important. To the best of our knowledge, this contribution is the first effort that examines the role of morphology (in the form of an axially diverging microdomain) on the prediction of optimal separation times for two protein models when they are subjected to electrophoresis. The research conducted predicts that the optimal separation time of a short, straight pore yields the best resolution in this type of electrophoretic separation.