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

Seeman、Winfree和Rothemund的开拓性工作提高了工程有用结构和设备的前景，这些结构和设备可以从分子成分中自主组装。发展这种能力将给医药、信息技术、制造业、能源生产和21世纪社会的其他企业带来变革性的好处。在这个项目中，一组具有自组装、软件工程、形式验证、编程语言、计算理论、生物化学和分子生物学专业知识的科学家将在纳米尺度上探索这种“物质编程”的能力和局限性。这个项目的中心论点是，软件工程师和理论计算机科学家为创建、控制和推理极其复杂的软件、硬件、网络和环境而开发的方法，将成为处理纳米技术将面临的更大挑战的重要起点。该项目将研究计算建模、算法随机性、需求工程、产品线、软件验证和软件安全在DNA瓦片组装、DNA折纸和DNA链位移反应中的应用。该项目将以一个清晰的评估结束——希望是一个令人信服的概念证明——软件工程方法在分子编程和纳米级自组装中的适用性和适应性。该项目将有助于为纳米级自组装的社会效益提供严格推理、验证和安全导向的方法。它将加强软件工程方法，使它们适应具有挑战性的新领域。它将加强爱荷华州立大学和附近的辛普森学院的跨学科科学教育，并将为其他地方的此类活动提供可上网的教育材料。

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.