All living things rely on the efficient storage, transduction, and use of energy. For example, all free energy used by biological systems originates from solar energy stored by photosynthesis and its effective use relies on its transformation from one form to the other. In this volume, leaders in the fields of computational modeling of electron transfer, proton transfer, proton-couples electron transfer, and energy transduction present new methods for simulating bioenergetic processes and summarize applications to proteins, including the photosynthetic reaction center, bacteriorhodopsin, and cytochrome c.