Nano: Collaborative Research: EMT: Toward Universal Bottom-Up Nanofabrication with DNA

背景资料。生物有机体和人类技术的最大区别之一在于它们是如何构建的。动植物由内而外生长，通常是从单个细胞生长到包含数十亿个细胞的有机体，每个细胞都是由分子成分组成的，这些分子成分在细胞内以原子精度制造。相比之下，人类最伟大的工程奇迹，如飞机、摩天大楼和计算机，是从外到内组装在一起的，零部件是在工厂里制造并一件一件地组装起来的。这种区别通常被称为“自下而上”和“自上而下”组装。在生物“自下而上”方法中，组装过程由部件本身指导，而在工程“自上而下”方法中，概念上在被建造的对象上方有一个实体来监督和指导制造过程。人类工程学已经掌握了自上而下的方法来创造非常复杂的系统(但还没有将它们扩展到原子和分子尺度)，并利用自下而上的方法来合成各种分子、聚合物和晶体结构(但还没有创造出极其复杂的信息丰富的结构)。项目目标。我们的目标是展示自下而上的技术如何通过在分子内部嵌入信息和计算过程来创建复杂的原子定义结构，就像生物学所做的那样。在生物发育中，程序(基因组)使用生物化学来指导生长过程并确定有机体的最终形式。用计算机科学的话来说，一个可以编程来完成任何可以完成的任务的系统被称为“通用”系统。通用计算机可以被编程来执行任何计算，而通用构造函数可以被编程来执行任何施工任务。最近的工作从理论上证明了普遍的分子自组装是可能的，并在实验上证明了这种方法是有希望的，使用DNA作为构建材料来创造功能分子装置，即所谓的DNA纳米技术。在这项提议中，我们的目标是将DNA纳米技术带到这样一个点，即可以很好地实现通用的自下而上的自组装，从而能够展示直接的技术应用。明确的目标。我们的目标是在我们对复杂的自组装逻辑进行编程的能力以及我们将DNA结构与化学、光学和电子相关材料接口的能力方面取得重大进展。我们将重点关注四个主要目标，从长期的基础工作到近期的开发：(1)复杂分子级电子电路模板的自组装；(2)对分子行走马达的行为进行编程，以在纳米制造任务中传输组件；(3)连接碳纳米管线以创建小型纳米级电子电路；以及(4)通过在具有功能电接触的硅晶片上的目标位置放置和定向自组装组件，实现自下而上和自上而下的集成制造。独一无二的是，这项研究的目标需要同时开发两种新型计算系统：第一种受到生物自组装和发展的启发，在分子机器和生物化学水平上运行，并将被编程构建第二种，由组装成纳米级电路的碳纳米管组成，它像传统计算设备一样在电子水平上运行。该项目的一个重要方面将是培养能够跨越这项工作所涉及的跨学科学科的年轻科学家(本科生、研究生和博士后)。

Background. One of the greatest contrasts between the biological organisms and human technology lies in how they are constructed. Plants and animals grow from the inside out, often from a single cell to an organism containing billions of cells, each of which is built from molecular components that are manufactured with atomic precision within the cell. In contrast, mankind's greatest engineering marvels, such as airplanes and skyscrapers and computers, are put together from the outside in, with components being manufactured in factories and assembled piece by piece. This distinction is often referred to as "bottom-up" vs "top-down" assembly in the biological "bottom-up" approach, the assembly process is guided by the components themselves, while in the engineering "top-down" approach, there is an entity conceptually above the object being built that supervises and guides the manufacturing process. Human engineering has mastered top-down methods to create systems of great complexity (but has not extended them to the atomic and molecular scale) and has exploited bottom-up methods for the synthesis of diverse molecular, polymeric and crystalline structures (but has not created information-rich structures of great complexity). Project Goals. Our goal is to demonstrate how bottom-up techniques can create complex atomically-defined structures, as biology does, by embedding information and computational processes within the molecules themselves. In biological development, a program (the genome) uses biochemistry to guide the growth process and determine the ultimate form of the organism. In the parlance of computer science, a system that can be programmed to accomplish any task that can be accomplished is called a "universal" system. A universal computer can be programmed to perform any computation, while a universal constructor can be programmed to carry out any construction task. Recent work has theoretically shown that universal molecular self-assembly is possible and has experimentally demonstrated that the approach shows promise, using DNA as a construction material to create functional molecular devices so-called "DNA nanotechnology". In this proposal, we aim to bring DNA nanotechnology to the point where universal bottom-up self-assembly can be achieved well enough that immediate technological applications can be demonstrated. Specific Aims. We aim to make major advances both in our ability to program complex self-assembly logic and in our ability to interface the DNA structures to chemically-, optically-, and electronically-relevant materials. We will focus on four main goals, which span the range from long-term fundamental work to near-term development: (1) self-assembly of a template for a complex molecular-scale electronic circuit; (2) programming the behavior of molecular walking motors to transport components in nanofabrication tasks; (3) attaching carbon nanotube wires to create small nanoscale electronic circuits; and (4) integrating bottom-up and top-down fabrication by placing and orienting self-assembled components at target locations on silicon wafers with functional electrical contacts. Uniquely, the aims of this research require simultaneously development of two novel computing systems: the first, inspired by biological self-assembly and development, operates at the level of molecular machines and biochemistry, and will be programmed to construct the second, composed of carbon nanotubes assembled into nanoscale circuits, which operates at the electrical level like conventional computing devices.Broader Impact. An important aspect of this project will be the training of young scientists (undergraduates, graduate students, and postdocs) capable of spanning the interdisciplinary subjects involved in this work.