The Simmerling lab at Stony Brook University carries out research in the area of computational structural biology. In particular, the lab focuses on understanding how dynamic structural changes are involved in the behavior of biomolecules, such as proteins and nucleic acids. Recent advances in computer hardware and simulation algorithms have established computational methods as a robust and important component of biomolecular research. These simulations are highly complementary to experimental tools, and methods such as molecular dynamics simulation are able to provide a detailed description of the motions of individual atoms over short timescales that are typically inaccessible to experiment. Simulations are not limited to the averages over time and over large numbers of molecules that prevent crystallographic or NMR experiments from characterizing transiently populated conformations such as important intermediates in multi-step conformational changes. In additional to direct dynamics, treatment of simulation data using statistical mechanics can provide valuable thermodynamic properties such as binding affinities or the free energy profiles resulting from conformational changes.