This book covers computational modeling of "biomolecular site dynamics". It also describes the use of rule-based modeling, in coordination with quantitative experimental approaches, to gain insights into site dynamics and to introduce the basic concepts and techniques of rule-based modeling. The book is divided into three parts. The first part covers the biological significance and physical chemistry of site dynamics. The second part provides an introduction to the essential methodology of rule-based modeling. The third part consists of examples of rule-based modeling capabilities.