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.
are new areas of research under the more general notion of DNA computing. The basic idea behind DNA computing is quite simple, elegant and beautiful: Use DNA sequences to encode information and implement computational algorithms using biological and chemical operations. The main goal from Simpson's perspective was to develop relevant educational materials and expose our students, who are undergraduates, to this exciting field. We established an interdisciplinary group (Computer Science, Chemistry, Biology, Physics) of five faculty members and eight students. The group held weekly seminar meetings and discussed topics related to tile self-assembly, DNA strand displacement and DNA origami. Single stranded DNA sequences have the ability to combine together and form various nanostructures (DNA origami). A major topic of our study was how to manipulate DNA strands to obtain pre-determined shapes. We enhanced our "Introduction to Nanoscience" course to include analysis and characterization of DNA nanostructures using atomic force microscopy. The course was taught during the grant period and will be taught again in 2013. Two students majoring in Chemistry studied a DNA origami design with the capability of interfacing with cells in vitro, triggering programmed release of a molecular payload in response to cellular cues to stimulate intracellular signaling. Their research was focused on developing this model to yield a construct with high efficacy. They presented a poster "Drug delivery and DNA Origami: Rational design for targeted, intracellular delivery of molecular payloads" at the Simpson College Undergraduate Symposium (April 19, 2012). Four students majoring in Computer Science designed and implemented a distributed genetic algorithm for tile self-assembly optimization. They presented their work at the Midwest Instruction and Computing Symposium April 2012. One student worked in the summer on parameterized construction of a base-n counter in the abstract Tile Assembly Model at Iowa State University. He presented his work at Simpson’s Summer Research Symposium (September 26, 2012). We believe that exposing undergraduate students to this discipline and giving them the opportunity to be actively engaged in interdisciplinary research is essential in order to produce the next generation of scientists.
