Membranes organize much of the cell and host a great deal of molecular machinery required to integrate signals from the outside, regulate the surrounding matrix, change shape, move, and grow. Understanding how a dense forest of proteins, sugars, and biomarkers modulates the shape of the cell is necessary to produce more detailed, accurate predictions of cell behavior, particularly in the studies of cell signaling processes that lead to oncogenesis. In this dissertation, I will present a series of molecular models which, when combined with continuum models and both in vitro and in vivo experiments, describe the molecular basis for membrane morphology changes. In particular, we investigate the mechanisms by which proteins assemble on a bilayer undergoing thermal fluctuations. This work serves to quantify and explain a series of biophysical experiments in molecular detail, and contributes to the development of multiscale models for predicting cell fate.