During the last decade, we have witnessed a rapid penetration of autonomous systems technology into aerial, road, underwater, and sea vehicles. The autonomy assumed by these vehicles holds the potential to increase performance significantly, for instance, by reducing delays and increasing capacity, while enhancing safety, in a number of transportation systems. However, to exploit the full potential of these autonomy-enabled transportation systems, we must rethink transportation networks and control algorithms that coordinate autonomous vehicles operating on such networks. This project focuses on the design and operation of autonomy-enabled transportation networks that provide provable guarantees on achieving high performance and maintaining safety at all times. The foundational problems arising in this domain involve taking into account the physics governing the vehicles in order to coordinate them using cyber means. This research effort aims to advance the science of cyber-physical systems by following a unique and radical approach, drawing inspiration and techniques from non-equilibrium statistical mechanics and self-organizing systems, and blending this inspiration with the foundational tools of queueing theory, control theory, and optimization. This approach may allow orders of magnitude improvement in the servicing capabilities of various transportation networks for moving goods or people. The applications include the automation of warehouses, factory floors, sea ports, aircraft carrier decks, transportation networks involving driverless cars, drone-enabled delivery networks, air traffic management, and military logistics networks. The project also aims to start a new wave of classes and tutorials that will create trained engineers and a research community in the area of safe and efficient transportation networks enabled by autonomous cyber-physical systems.