The study of complex systems in a unified framework has become recognized in recent years as a new scientific discipline, the ultimate in the interdisciplinary fields. Breaking down the barriers between physics, chemistry, and biology and the so-called soft sciences of psychology, sociology, economics and anthropology, this text explores the universal physical and mathematical principles that govern the emergence of complex systems from simple components. Dynamics of Complex Systems is the first text describing the modern unified study of complex systems. It is designed for upper-undergraduate/beginning graduate level students, and covers a broad range of applications in a broad array of disciplines. A central goal of this text is to develop models and modeling techniques that are useful when applied to all complex systems. This is done by adopting both analytic tools, including statistical mechanics and stochastic dynamics, and computer simulation techniques, such as cellular automata and Monte Carlo. In four sets of paired, self-contained chapters, Yaneer Bar-Yam discusses complex systems in the context of neural networks, protein folding, living organisms, and finally, human civilization itself. He explores fundamental questions about the structure, dynamics, evolution, development and quantitative complexity that apply to all complex systems. In the first chapter, mathematical foundations such as iterative maps and chaos, probability theory and random walks, thermodynamics, information and computation theory, fractals and scaling, are reviewed to enable the text to be read by students and researchers with a variety of backgrounds.