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In this paper, we introduce the air traffic operations and management simulator (ATOMS), which is an air traffic and airspace modeling and simulation system for the analysis of free-flight concepts. This paper describes the design, architecture, functionality, and applications of the ATOMS. It is an intent-based simulator that discretizes the airspace in equal-sized hyper-rectangular cells to maintain intent reference points. It can simulate end-to-end airspace operations and air navigation procedures for conventional air traffic, as well as for free flight. Atmospheric and wind data that are modeled in the ATOMS result in accurate trajectory predictions. The ATOMS uses a multiagent-based modeling paradigm for modular design and easy integration of various air traffic subsystems. A variety of advanced air traffic management (ATM) concepts that are envisioned in free flight are prototyped in the ATOMS, including airborne separation assurance (ASA), cockpit display of traffic information (CDTI), weather avoidance, and decision support systems (DSSs). Experimental results indicate that advanced ATM concepts make a sound case for free flight; however, there is a need to investigate and understand their complex interaction under nonnominal scenarios.