EAGER: Collaborative Research: Modeling and Analysis of Molecular Programming and Nanoscale Self-Assembly

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Pioneering work of Seeman, Winfree, and Rothemund has raised the prospect of engineering useful structures and devices that autonomously assemble themselves from molecular components. Developing this capability will have transformative benefits for medicine, information technology, manufacturing, energy production, and other enterprises of twenty-first century society. In this project a team of scientists with expertise in self-assembly, software engineering, formal verification, programming languages, theory of computing, biochemistry, and molecular biology will explore the power and limitations of this "programming of matter" at the nanoscale.The central thesis of this project is that methods that software engineers and theoretical computer scientists have developed for creating, controlling, and reasoning about software, hardware, networks, and environments of immense complexity will be an essential starting point for dealing with the greater challenges that nanotechnology will confront. The project will investigate applications of computational modeling, algorithmic randomness, requirements engineering, product lines, software verification, and software safety to DNA tile assembly, DNA origami, and DNA strand-displacement reactions. The project will conclude with a clear assessment--hopefully a compelling proof of concept--of the applicability and adaptability of software engineering methods in molecular programming and nanoscale self-assembly.The project will contribute to a rigorously reasoned, verification- and safety-oriented approach to the social benefits of nanoscale self-assembly. It will strengthen software engineering methods as it adapts them to challenging new domains. It will enhance interdisciplinary science education at Iowa State University and nearby Simpson College, and it will provide web-accessible educational materials for such activities elsewhere.