One of the challenges for the future cyber-physical systems is the exploration of large design spaces. Evolutionary algorithms (EAs), which embody a simplified computational model of the mutation and selection mechanisms of natural evolution, are known to be effective for design optimization. However, the traditional formulations are limited to choosing values for a predetermined set of parameters within a given fixed architecture. This project explores techniques, based on the idea of hidden genes, which enable EAs to select a variable number of components, thereby expanding the explored design space to include selection of a system's architecture. Hidden genetic optimization algorithms have a broad range of potential applications in cyber-physical systems, including automated construction systems, transportation systems, micro-grid systems, and space systems. The project integrates education with research by involving students ranging from high school through graduate school in activities commensurate with their skills, and promotes dissemination of the research results through open source distribution of algorithm implementation code and participation in the worldwide Global Trajectory Optimization Competition. Instead of using a single layer of coding to represent the variables of the system in current EAs, this project investigates adding a second layer of coding to enable hiding some of the variables, as needed, during the search for the optimal system's architecture. This genetic hiding concept is found in nature and provides a natural way of handling system architectures covering a range of different sizes in the design space. In addition, the standard mutation and selection operations in EAs will be replaced by new operations that are intended to extract the full potential of the hidden gene model. Specific applications include space mission design, microgrid optimization, and traffic network signal coordinated planning.