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One of the best illustrations of "Simulating Systems" is this video from the STAR Global Conference 2013, in which Scott D. Reynolds of M/E Engineering explores the use of CFD for studying the impact of wind on the built environment.
Asked to examine the influence of helicopter exhaust plumes on surrounding bulidings, M/E Engineering decided to simulate the whole system, including fully unsteady wind profiles (with gusts that vary in speed and direction), and the full complexity of the local urban landscape. Best of all, the simulation includes an actual moving helicopter that entrains gas from nearby building plumes as it takes off and lands.