Part I. Overcoming Uncertainty: 1. From Physical Processes to Theoretical Foundations of Cyber-Physical Systems Design and Optimization Paul Bogdan and Radu Marculescu; 2. Effective Uncertainty Evaluation in Large-Scale Systems Junfei Xie, Yan Wan, Yi Zhou, Kevin Mills, James J. Filliben and Yu Lei; 3. A Flexible Graph Partitioning Algorithm for Cyber-Physical Systems Rahul Dhal and Sandip Roy; Part II. Exploiting Structure for Control: 4. A Survey on Remote Estimation Problems Marcos M. Vasconcelos and Nuno Martins; 5. Joint Scheduling and Optimal Adaptive Event-triggered Control of Distributed Cyber-physical Systems Hao Xu, Avimanyu Sahoo, and S. Jagannathan; 6. Online Adaptive Network Design for Disturbance Rejection Airlie Chapman, Eric Schoof, and Mehran Mesbahi; 7. Meanings and Applications of Structure in Networks of Dynamic Systems Vasu Chetty and Sean Warnick; Part III. Privacy, Security, and Protection: 8. Preserving Confidentiality of Critical Energy Infrastructure Information Bernard Lesieutre, Alex Borden and Parameswaran Ramanathan; 9. A Framework for Cyber-Physical System Security Situation Awareness Wei Yu, Guobin Xu, Khanh Pham, Erik Blasch, Genshe Chen, Dan Shen, and Paul Moulema; 10. Security in the Cyber-Physical Electric Power Infrastructure Bruce McMillin, Ravi Akella, Gerry Howser, Thoshitha Gamage and Tom Roth; 11. Bio-Inspired Framework for Allocation of Protection Resources in Cyber-Physical Networks Victor M. Preciado, Michael Zargham, Chinwendu Enyioha, Cameron Nowzari, Shuo Han, Masaki Ogura, Ali Jadbabaie, and George Pappas; Part IV. Frameworks and Testbeds: 12. Resource Management in Cloud Assisted Cyber Physical Systems Brijesh Kashyap Chejerla, Sanjay Madria and Sajal K. Das; 13. Middleware for the Internet of Things Rahav Dor and Chenyang Lu; 14. In Silica and In Vitro Modeling Platforms for Stimulation of Emergent Processes in Neuronal Networks Sandip Roy, Patrick Corrigan and James Krueger; Part V. Conclusion: 15. Wide-Area Management of Cyber-Physical Infrastructures: A Call to Action Sandip Roy, Sajal K. Das, and Mengran Xue.