We use molecular simulation and theory to understand multi-scale, hierarchical interactions in complex biomolecular systems, with a specific focus on proteins and peptides. In particular, our group develops general methods for predicting peptide structure and self-assembly behavior, and is designing new approaches for linking simulations and theories across multiple length and time scales in fundamental, rigorous ways. These efforts are used to understand (1) folding and design principles in proteins; (2) peptide structure, association, self-assembly, and aggregation; and (3) the role of water and the hydrophobic interaction in driving biological recognition and self-assembly processes.