Synthetic Molecular Machines for Active Self-Assembly: Prototype Algorithms, Designs and Experimental Verification

The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology's numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules. 

In this thesis defense, we demonstrate the construction of algorithms and molecular prototypes in the context of this vision. For example, we show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the construction of a linear polymer that grows exponentially fast. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules.