Transport across biological membranes is critical to survival in all kingdoms of life and is mediated by proteins inserted into the lipid bilayer membrane. The goal of our research is understand the fundamental physicochemical properties that underlie protein transport. Structural dynamics in the protein enable conformational changes that underlie functionality. These structural rearrangements are carefully orchestrated and are inherent to the protein structure, which have been fine-tuned over the course of evolution to perform a certain function. Protein function is therefore sensitive to mutations, which frequently lead to disease. In our research, we use molecular dynamics simulation to determine atomistic structural dynamics in membrane proteins. Several of our simulations are based on not yet published high-resolution structures determined by X-ray crystallography and cryo-electron microscopy provided by collaborators. We also use time-resolved low-resolution X-ray data to drive simulations. Development of such computational structural refinement protocols is critical to model low-resolution data.