INSPIRE: Robust Molecular Programming: Advances in the Design and Verification of Reliable Self-Assembling Nanosystems

INSPIRE奖的部分资金来自以下NSF单位：计算机和信息科学与工程局计算机和通信基础司的软件和硬件基础计划；计算机和信息科学与工程局计算机和通信基础司的生物计算基金；生物局分子和细胞生物科学部的网络和调节计划；计算机和信息科学与工程局和生物局计算机和通信基金会的生物和计算共享原则基金(BCSP)；以及刺激竞争研究的实验计划办公室(EPSCoR)。分子编程，也被称为DNA纳米技术，利用核酸的信息处理能力来设计纳米级的自组装、可编程的结构和设备。过去几年的研究已经展示了DNA瓷砖自组装如何实现算法；DNA链置换反应如何实现逻辑电路、神经网络和分子机器人；以及DNA折纸如何创建二维和三维结构，作为靶向药物递送装置或设备可以在指定位置连接的“纳米面包板”。简单地说，分子编程就是在分子尺度上为我们做的事情编程，它是字面上的计算机科学意义上的编程。这个项目将把分子生物学的方法与计算机科学特别是软件工程的方法结合起来，开始发展一门健壮的分子编程学科。这将是一个对DNA纳米系统进行编程的系统过程，尽管其环境的化学动力学存在概率变化，但它们将高度自信地完成应该做的事情。该项目将开发这种强大的分子编程方法，与DNA纳米技术中真实的、尖端的湿实验室研究相结合。由软件工程师开发的用于设计和验证可靠的、可扩展的异步系统的方法，以及由理论计算机科学家开发的将随机性与计算相结合的原理，将专门应用于创建更复杂但更健壮的DNA起源的全新方法，将该方法应用于可靠的生物传感器，以及用于在纳米尺度上模块化计算的新方法。该项目将软件工程方法直接应用于DNA纳米技术，对于使DNA纳米技术及其在21世纪社会的医药、信息技术、制造、能源生产和其他企业中的预期应用变得更有生产力、更可预测和更安全具有潜在的变革性好处。该项目还将加强爱荷华州立大学的跨学科STEM教育，并为爱荷华州中部正在发展的生物技术走廊做出贡献。

This INSPIRE award is partially funded by the following NSF units: the Software and Hardware Foundations Program in the Division of Computer and Communications Foundations of the Computer and Information Science and Engineering Directorate; the Bio Computing fund in the Division of Computer and Communications Foundations of the Computer and Information Science and Engineering Directorate; the Networks and Regulation Program in the Division of Molecular and Cellular Biosciences of the Biology Directorate; the fund for Biological and Computing Shared Principles (BCSP) in both the Computer and Communications Foundations of the Computer and Information Science and Engineering Directorate and the Biology Directorate; and the Office of Experimental Program to Stimulate Competitive Research (EPSCoR). Molecular programming, also known as DNA nanotechnology, exploits the information-processing capabilities of nucleic acids to design self-assembling, programmable structures and devices at the nanoscale. Research in the past few years has shown how DNA tile self-assembly can implement algorithms; how DNA strand displacement reactions can implement logic circuits, neural networks, and molecular robots; and how DNA origami can create two- and three-dimensional structures that can serve as targeted drug-delivery devices or "nano-breadboards" to which devices can be attached at specified locations. Simply stated, molecular programming is programming matter to do our bidding at molecular scales, and it is programming in the literal sense of computer science.This project will combine methods from molecular biology with methods from computer science, and especially software engineering, to begin the development of a discipline of robust molecular programming. This will be a systematic process for programming DNA nanosystems with a high level of confidence that they will do what they are supposed to do, despite the probabilistic vicissitudes of the chemical kinetics of their environments. The project will develop this robust approach to molecular programming in concert with real, cutting-edge wet-lab research in DNA nanotechnology. Methods developed by software engineers for designing and verifying reliable, asynchronous systems that scale and principles developed by theoretical computer scientists for integrating randomness with computation will be applied specifically to a fundamentally new approach to creating more complex yet more robust DNA origamis, to applications of this approach to reliable biosensors, and to a new method for modularizing computations at the nanoscale. This project's unconventional application of software engineering methods directly to DNA nanotechnology has potentially transformative benefits for making DNA nanotechnology and its anticipated applications to medicine, information technology, manufacturing, energy production, and other enterprises of twenty-first century society more productive, predictable, and safe. The project will also enhance interdisciplinary STEM education at Iowa State University and contribute to a developing biotech corridor in central Iowa.