To prepare for future air quality modeling needs and to reduce the duplication of effort in maintaining multiple modeling systems, the U.S. Environmental Protection Agency (EPA) is developing a third-generation comprehensive air quality modeling system, Models-3, employing an incremental prototyping strategy. The objective of the Models-3 air quality model prototyping effort is to test the following science and system concepts: (1) flexibility (i.e., the ability to address multiple air quality issues, such as regional- and urban-scale oxidant and acid deposition); (2) functional modularity and extensibility (i.e., modular and interchangeable science process implementation using a consistent input/output subsystem); (3) systematic and integrated sensitivity and uncertainty analysis; and (4) adaptation of key algorithms for high-performance computational platforms.