Small: Collaborative Research: Programmed Cyclic Molecular Dancing on 2D Origami Lattices

分子间的相互作用可以看作是分子间的通信和信息交换。近年来，人们通过基于DNA的自下而上的自组装来探索对分子信息处理的理解。这些研究探索算法、可编程的分子相互作用，包括分子装置。在这项工作中，两个具有互补专业知识的PI，一个化学家和一个数学家，结合在一起，进一步实现编程的分子相互作用的可能性。这个高度跨学科的项目的目标是在DNA自组装过程中引入环境控制，这将以预先编程的方式指导分子相互作用。它引入了一个“时钟”(计算的基本部分)，它在预先设计的平台上控制不同分子物种的程控振荡连接/分离。拟议的项目将使来自同一组构建块的各种预先编程的分子形状能够自组装。这些形状可以作为纳米电子元件的支架，如果实现，将允许更小、更密集和更快的计算机硬件。此外，程序化的动态分子相互作用将是核酸机器人(Nubots)在平台上作用的第一个化身。几名本科生和至少两名博士生(每个机构一名)将通过这一奖项接受培训。该项目将使这些个体成为独特的跨学科研究科学家，能够从事需要广泛科学知识的研究。该项目的目标是在分子编程中引入对周期性动态分子排列的环境控制，开发一种在不同分子物种之间进行分子信号通信的方法，并使用这种方法来获得及时循环的分子排列。特别是，该项目将(1)通过激光照明开发环境控制的分子条件，允许两个不同的分子浮动瓦片物种之间的振荡平台附着/分离，以及(2)通过在二维DNA折纸阵列上模拟二维生命游戏般的动力学，引入两个分子物种之间具有振荡动力学的算法分子相互作用。该系统的平台由2D DNA折纸阵列和自由漂浮的瓷砖组成，前者的瓷砖具有信号线，后者能够附着在平台上各自的“身份”对等物体上，并将信号传输到邻近位置。阵列瓷砖以棋盘方式排列，使得在每个周期中，其中一种颜色接收浮动瓷砖并计算其他颜色瓷砖的下一周期瓷砖的身份。浮动瓷砖配备有纳米颗粒，其暴露在适当的激光波长下会增加局部温度，从而可以使这些浮动瓷砖与平台分离。

Molecular interactions can be seen as molecular communications and exchanges of information. In recent years the understanding of molecular information processing has been explored through DNA-based bottom-up self-assembly. These studies explore algorithmic, programmable molecular interactions including molecular devices. In this work, two PIs with complementary expertise, a chemist and a mathematician, join together to further the possibilities for programmed molecular interactions. The goal of this highly interdisciplinary project is to introduce environmental control within the DNA self-assembly process that will direct molecular interactions in a preprogrammed manner. It introduces a "clock" (an essential part of computation) that controls programmed oscillating attachments/detachments of different molecular species on a predesigned platform. The proposed project will enable self-assembly of a variety of preprogrammed molecular shapes from the same set of building blocks. These shapes could serve as scaffolds for nanoelectronic components, which if achieved, will allow for smaller, denser and faster computer hardware. Furthermore, programmed dynamical molecular interactions would be the first incarnation of nucleic acid robots (nubots) acting on a platform. Several undergraduates and at least two PhD graduate students (one in each institution) will receive training through this award. This project will prepare these individuals as unique interdisciplinary research scientists able to pursue studies that require broad scientific knowledge.The goal of this project is to introduce environmental control for periodic dynamical, molecular arrangements in molecular programming, to develop a method for molecular signal communication between different molecular species, and to use this method to obtain molecular arrangements that cycle in time. In particular the project will (1) develop molecular conditions for environmental control through laser illumination that will allow oscillating platform attachments/detachments between two different molecular floating tile species and (2) introduce algorithmic molecular interactions with oscillating dynamics between two molecular species by simulating a two-dimensional Game-of-Life-like dynamics on a two dimensional DNA origami array. The system has a platform consisting of a 2D DNA origami array whose tiles have signaling strands, and free floating tiles able to attach to their respective "identity" counterparts on the platform and to transmit signals to neighboring locations. The array tiles are arranged in a checker-board fashion such that in an alternate manner, at each cycle, one of the colors receives the floating tiles and computes the identity of the next cycle tiles of the other color tiles. The floating tiles are equipped with nano-particles whose exposure to appropriate laser wave length increases the local temperature and thereby can disassociate those floating tiles from the platform.