Controlled mass transport of macromolecules is a complex problem with many applications in biomedicine. Modeling is an effective way to understand the influence of environmental factors on transport. Unfortunately, the time and length scales relevant to transport processes are prohibitive to observe with atomistic molecular dynamics. Coarse grained models of proteins, combined with the mesoscopic hydrodynamic method of lattice Boltzmann, allows us to run simulations on the order of microseconds and micrometers. We have validated that our highly simplified model behaves correctly and are actively testing various environmental conditions (pH, ionic strength, membrane geometry, pore decoration) to develop optimized mass transport systems.