The objective of this research is the development of methods for the control of energy flow in buildings, as enabled by cyber infrastructure. The approach is inherently interdisciplinary, bringing together electrical and mechanical engineers alongside computer scientists to advance the state of the art in simulation, design, specification and control of buildings with multiple forms of energy systems, including generation and storage. A significant novelty of this project lies in a fundamental view of a building as a set of overlapping, interacting networks. These networks include the thermal network of the physical building, the energy distribution network, the sensing and control network, as well as the human network, which in the past have been considered only separately. This work thus seeks to develop methods for simulating, optimizing, modeling, and control of complex, heterogeneous networks, with specific application to energy efficient buildings. The advent of maturing distributed and renewable energy sources for on-site cooling, heating, and power production and the concomitant developments in the areas of cyberphysical and microgrid systems present an enormous opportunity to substantially increase energy efficiency and reduce energy-related emissions in the commercial building energy sector. In addition, there is a direct impact of the proposed work in training students with backgrounds in the unique blend of engineering and computer science that is needed for the study of cyber-enabled energy efficient management of structures, as well as planned interactions at the undergraduate and K-12 level.