By providing expositions to modeling principles, theories, computational solutions, and open problems, this reference presents a full scope on relevant biological phenomena, modeling frameworks, technical challenges, and algorithms. • Up-to-date developments of structures of biomolecules, systems biology, advanced models, and algorithms • Sampling techniques for estimating evolutionary rates and generating molecular structures • Accurate computation of probability landscape of stochastic networks, solving discrete chemical master equations • End-of-chapter exercises.