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

背景。生物有机体和人类技术之间最大的差异之一在于它们的构造方式。植物和动物是由内而外生长的，通常是从单个细胞到包含数十亿个细胞的有机体，每个细胞都是由细胞内以原子精度制造的分子成分构成的。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，都是由外到内组装而成的，零部件是在工厂里制造出来，一块一块地组装起来的。这种区别通常被称为“自底向上”与“自顶向下”组装，在生物学的“自底向上”方法中，组装过程由组件本身指导，而在工程的“自顶向下”方法中，在被构建对象的概念上有一个实体，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），并利用了自下而上的方法来合成各种分子、聚合物和晶体结构（但还没有创造出非常复杂的信息丰富的结构）。项目的目标。我们的目标是演示自下而上的技术如何通过在分子本身中嵌入信息和计算过程来创建复杂的原子定义结构，就像生物学一样。在生物发育中，一个程序（基因组）利用生物化学来指导生长过程并决定生物体的最终形态。用计算机科学的说法，一个可以通过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，而通用构造器可以被编程来执行任何构造任务。最近的研究从理论上表明，普遍的分子自组装是可能的，并且通过实验证明，这种方法是有希望的，使用DNA作为建筑材料来创造功能性的分子装置，即所谓的“DNA纳米技术”。在这个提议中，我们的目标是将DNA纳米技术带到一个点，在这个点上，普遍的自下而上的自组装可以很好地实现，从而可以证明直接的技术应用。具体的目标。我们的目标是在编程复杂自组装逻辑的能力以及将DNA结构与化学、光学和电子相关材料连接的能力方面取得重大进展。我们将专注于从长期基础工作到近期发展的四个主要目标：(1)复杂分子尺度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运输组件；(3)连接碳纳米管导线，形成小纳米级电子电路；(4)通过在具有功能电触点的硅片上的目标位置放置和定向自组装组件，集成自下而上和自上而下的制造。独特的是，这项研究的目标需要同时开发两个新的计算系统：第一个系统，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；第二个系统将被编程来构建，由碳纳米管组装成纳米级电路，在电子水平上运行，就像传统的计算设备一样。更广泛的影响。这个项目的一个重要方面是培养年轻科学家（本科生、研究生和博士后），使他们能够跨越这项工作所涉及的跨学科学科。

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.