AF: SHF: Small: Algorithmic and Architectural Foundation for Next-Generation Collective DNA Robots

分子机器人是一种重要的自动执行纳米机械任务的人工分子机器。DNA是制造分子机器人的极好材料，因为它们的几何、热力学和动力学性质很容易理解，并且高度可编程。目前还没有系统的方法将高水平的机械任务转化为低水平的分子实现，也没有软件工具使具有不同背景的研究人员能够构建具有新功能的DNA机器人。为了实现这一目标，需要更简单的算法和更模块化的构建块来创建更广泛的集体行为，直到有足够的理解来开发一种将在实践中工作的分子机器人编程语言。该项目将为以下问题提供更好的答案：在多大程度上，简单的算法可以允许越来越复杂的纳米机械任务被编程并由DNA分子执行？DNA机器人的合作是否允许用更少的时间和精力完成更复杂的任务？当向通用DNA机器人工具箱中添加新的构建块时，会出现什么可组合性问题？什么样的设计原则可以让DNA机器人在日益复杂和多样化的操作环境中发挥良好的作用？科学的理解将被纳入公共在线软件工具，以辅助分子机器人的设计和构建，并将引入课堂。课程材料将在多个教育机构之间共享。公众参与将通过公开演讲、实验室参观、播客、新闻报道、YouTube视频和艺术作品来促进。该项目包括三个主要目标：开发一种新的构建模块，用于留下类似信息素的信号来标记机器人的位置；演示如何使用新的构建模块来构建DNA机器人，从而在任意迷宫中找到并修改从入口到出口的直接路径；开发软件工具，自动转换用户指定的机器人系统来设计图表、模拟、DNA序列和实验协议。DNA折纸技术将用于构建DNA机器人的测试场地，DNA链位移机制将用于对DNA机器人的行为进行编程。荧光光谱和原子力显微镜将用于定量分析DNA机器人的行为，在整体和单分子水平上。研究小组将研究调整DNA机器人行为的机制，如果它是定性的，但不是定量的，并了解DNA机器人的行为如何取决于其操作环境的具体配置。新的构建模块扩展了通用DNA机器人的工具箱，并允许执行涉及测量和标记未知环境的任务。解决迷宫的机器人可以用于高效的分子运输，在复杂的环境中，一组领导机器人用很少的能量标记出一条直接的路径，一组跟随机器人沿着标记的路径行走，只运输分子货物，而不花费任何时间在间接路线上。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

A molecular robot is an important type of artificial molecular machine that automatically carry out nanomechanical tasks. DNA is an excellent material for building molecular robots, because their geometric, thermodynamic and kinetic properties are well understood and highly programmable. There exist no systematic approaches for translating high-level mechanical tasks to low-level molecular implementations nor software tools that enable researchers with diverse backgrounds to build DNA robots with new functions. To accomplish that, more simple algorithms and more modular building blocks are needed to create a wider range of collective behaviors, until there is enough understanding for the development of a molecular robotics programming language that will work in practice. This project will provide better answers to the following questions: To what extent can simple algorithms allow increasingly complex nanomechanical tasks to be programmed and carried out by DNA molecules? Does cooperation in DNA robots allow more complex tasks to be accomplished with less time and less energy? What composability issues arise when new building blocks are added to the toolbox for general-purpose DNA robots? What design principles can allow DNA robots to function well in increasingly complex and diverse operating environments? The scientific understanding will be incorporate into public online software tools to assist the design and construction of molecular robots, which will be introduced into the classroom. Course materials will be shared among multiple educational institutions. Public engagement will be promoted through public talks, lab tours, podcasts, news stories, YouTube videos and artwork.The project involves three main goals: developing a new building block for leaving pheromone-like signals to mark where a robot has been, demonstrating how the new building block can be used to construct DNA robots that find and modify a direct path from the entrance to the exit in an arbitrary maze, and developing software tools that automatically convert user-specified robotics systems to design diagrams, simulations, DNA sequences and experimental protocols. DNA origami technique will be used to build testing grounds for DNA robots, while DNA strand displacement mechanism will be used to program the behavior of DNA robots. Fluorescence spectroscopy and atomic force microscopy will be used to quantitatively analyze the behavior of DNA robots, in bulk and at the single-molecule level. The team of investigators will study the mechanisms for tuning the behavior of DNA robots, if it is qualitatively but not quantitatively as designed, and understand how the behavior of DNA robots depends on the specific configuration of their operating environment. The new building block expands the toolbox for general-purpose DNA robots and allows tasks that involve surveying and marking an unknown environment. The maze-solving robots could be used to perform efficient molecular transportation where a group of leader robots mark a direct path in a complex environment using very little energy and a group of follower robots walk on marked path only to transport molecular cargos without spending any time on indirect routes.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.