In trauma, many injuries impact anatomical structures, which may in turn affect physiological processes--not only those processes within the structures, but ones occurring in physical proximity to them as well. Our goal is to endow a 3D anatomical model with physiological mechanisms to demonstrate such effects. Our approach couples deformable object simulation for organs with physiological modeling, in a way that supports three-dimensional animated simulation. We demonstrate our approach through our current model of respiratory mechanics in a virtual 3D environment. Anatomical models that can capture physiological and pathophysiological changes can serve as an infrastructure for more detailed modeling, as well as benefiting surgical planning, surgical training, and general medical education.