In our research work we deals with the analysis and control of complex dynamics arising in network controlled systems and uncertain dynamical systems. The development of theoretical methods and tools are motivated by various applied problems that arise in electrical power grid, building systems, and aerospace applications. In particular, in our current research we are developing a unified framework based on unification of tools from system theory, stochastic dynamics and optimization for the design of a secure and resilient power grid that is robust to cyber-attacks and outages. We have discovered operator theoretic methods for the design of energy efficient building systems through real-time feedback control and development of optimal strategies for the placement of actuators and sensors. In collaboration with local company through DoD STTR program, we have contributed to the improvement of health and safety of fluid structure interaction systems such as aircraft wing, by developing a modeling and analysis framework based on system theoretic tools for the prediction of flutter instabilities. Similarly, data-driven operator theoretic methods were developed for real-time fault diagnosis of wind turbine blades. Many of these projects are collaborative and involving both theoretic development as well as practical implementation in the form of test-bed development or experimental validation. The successful application to a wide range of problems is made possible because of the key theoretical contributions made in the areas of applied dynamical systems and control theory. In particular, we have proposed novel operator theoretic methods for the stability analysis and control of complex dynamics and discovered fundamental limitations results for the estimation and control of nonlinear systems over uncertain networks.