This objective of this proposal is to improve the management of the air traffic system, a cyber-physical system where the need for a tight connection between the computational algorithms and the physical system is critical to safe, reliable and efficient performance. The approach is based on an adaptive multi-agent coordination algorithm with a particular emphasis on the systematic selection of the agents, their actions and the agents' reward functions. The intellectual merit lies in addressing the agent coordination problem in a physical setting by shifting the focus from ``how to learn" to ``what to learn." This paradigm shift allows a separation between the learning algorithms used by agents, and the reward functions used to tie those learning systems into system performance. By exploring agent reward functions that implicitly model agent interactions based on feedback from the real world, this work aims to build cyber-physical systems where an agent that learns to optimize its own reward leads to the optimization of the system objective function. The broader impact is in providing new air traffic flow management algorithms that will significantly reduce air traffic congestion. The potential impact cannot only be measured in currency ($41B loss in 2007) but in terms of improved experience by all travelers, providing a significant benefit to society. In addition, the PIs will use this project to train graduate and undergraduate students (i) by developing new courses in multi-agent learning for transportation systems; and (ii) by providing summer internship opportunities at NASA Ames Research Center.