This book is a definitive introduction to models of computation for the design of complex, heterogeneous systems. It has a particular focus on cyber-physical systems, which integrate computing, networking, and physical dynamics. The book captures more than twenty years of experience in the Ptolemy Project at UC Berkeley, which pioneered many design, modeling, and simulation techniques that are now in widespread use. All of the methods covered in the book are realized in the open source Ptolemy II modeling framework and are available for experimentation through links provided in the book.