Cyber-physical energy systems require the integration of a heterogeneous physical layers and decision control networks, mediated by decentralized and distributed local sensing/actuation structures backed by an information layer. With the North American Electric Reliability Corporation (NERC) Critical Infrastructure Protection (CIP) [1] requirements and president's visions of more secure, reliable and controllable cyber-physical system, a new paradigm for modeling and research investigation is needed. In this paper, we present common challenges and our vision of solutions to design advanced Cyber-physical energy systems with embedded security and distributed control. Finally, we present a survey of our research results in this domain.