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In interdisciplinary fields such as systems biology, good communication between experimentalists and theorists is crucial for the success of a project. Theoretical modeling in physiology usually describes complex systems with many interdependencies. On one hand, these models have to be grounded on experimental data. On the other hand, experimenters must be able to understand the interdependent complexities of the theoretical model in order to interpret the model’s results in the physiological context. We promote interactive, visual simulations as an engaging way to present theoretical models in physiology and to make complex processes tangible. Based on a requirements analysis, we developed a new model for gas exchange in the human alveolus in combination with an interactive simulation software named  Alvin .  Alvin  exceeds the current standard with its spatio-temporal resolution and a combination of visual and quantitative feedback. In  Alvin , the course of the simulation can be traced in a three-dimensional rendering of an alveolus and dynamic plots. The user can interact by configuring essential model parameters.  Alvin  allows to run and compare multiple simulation instances simultaneously. We exemplified the use of  Alvin  for research by identifying unknown dependencies in published experimental data. Employing a detailed questionnaire, we showed the benefits of  Alvin  for education. We postulate that interactive, visual simulation of theoretical models, as we have implemented with  Alvin  on respiratory processes in the alveolus, can be of great help for communication between specialists and thereby advancing research.

Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus