In my Ph.D. research I have applied mechanical engineering knowledge and approaches to develop technologies for two topics: programmable matter and green energy through biofuels. Specifically, I have addressed the issues of 3D assembly in a fluid environment and gas exchange in photobioreactors. In the first part of this dissertation, I investigated a programmable matter system that consists of cm-scale building blocks which are agitated in a stochastic flow pattern and assembled using local fluid forces. The fundamental aspect of this approach that my research concentrated on was the problem of component alignment. Towards this end we developed a novel alignment strategy and characterized it using a combination of numerical simulations and experiments. In the second part of this dissertation, I demonstrate the optimal geometric and operational conditions for CO2 transport to planar cultures of photosynthetic organisms via hollow fiber membranes. Firstly, I examined the growth pattern of Synechococcus elongatus around individual hollow fiber membranes to determine the optimal spacing and conditions for maximizing photosynthetic activity. I expanded on this initial work and used the information from the single fiber experiments to design, fabricate, and characterize arrays of HFM fibers. By using this novel configuration of hollow fiber membranes, I was able to grow and sustain an organism culture with effectiveness comparable to state of the art methods while eliminating the need for media circulation and replenishment and allowing for integration into waveguide photobioreactors.