This book introduces an integrated experimental-computational approach to investigate the mechanisms responsible for microbubble-induced injury during mechanical ventilation of patients with Acute Lung Injury and Acute Respiratory Distress Syndrome. In this approach, a computational model was developed to account for a minimal level of complexity required, but with significantly complex dynamics such as fluid-structure interaction. Once validated, these quantitative models of respiratory physiology are then being used to interpret counter-intuitive experimental data, suggest new avenues of investigation and develop novel patient-specific therapies. The author discusses key concepts and principles, such as cellular engineering and biomechanics, respiratory system, epithelial cell injury, multi-scale computational modeling and molecular/cellular scale imaging and analysis. This textbook presents state-of-the-art analytical and computational approaches to problems in fluid-structure interaction and free surface flow. This book should be an important reference for any researcher interested in the fundamental science and simulation techniques for flow in the respiratory system.