Systematic Design, Analysis and Control of Manufacturable Nano Machines

大自然发明了一种方法，将22种氨基酸联合收割机组合起来，构建起负责执行生物基本上所有关键功能的分子机器。在每个活细胞内，核糖体将遗传数据作为“组装指令”来组装长链分子，这些长链分子折叠成三维结构，其动态特性是其生物功能的基础。然而，设计和建造具有规定功能的人工纳米机器，用于执行医疗，环境和工业领域的任务仍然是一个挑战，部分原因是大自然通过进化开发的设计原理尚未得到很好的理解，因此不适用于工程纳米机器。科学家们一致认为，与按照精确规格设计的可互换部件的概念如何推动制造业革命类似，定制设计，控制和制造具有规定功能的纳米机器的能力将导致工程，医学和生物技术的新革命。然而，我们今天根本不知道如何设计和控制人工纳米机器。该项目旨在开发一个理论和计算框架，以系统地设计和分析可制造的分子机器，这些分子机器具有从预定义的分子组件库中获得的规定的迁移率和功能。如果成功，这项研究将提供框架和计算工具，系统地探索合成和可控分子机器和设备的设计空间，可能导致新的分子马达功能，可用于开发智能纳米机器人和材料。一个关键的观察是，纳米机器的设计主要是一个组合问题，其中有限数量的构建块将自组装成功能结构，而宏观尺度的设计是一个连续体，其中系统可以设计和制造到规定的尺寸以及物理特性。因此，本研究将发展一个系统化的设计流程与计算架构，以：（1）将奈米机器的衍生功能以输出连结的运动规格形式形式化;（2）设计并分析具有指定运动规格的不可约简单奈米机器（一个自由度）通过将可用的纳米组件组合成具有受约束的并且因此可控的运动的系统;（3）探索控制机制，通过外部物理刺激来操纵这些机器的运动;（4）探索策略，通过单独利用它们的运动或作为整体的一部分，将这些系统功能化为功能性纳米机器。这项研究的初步努力已经导致了两种结构的发现，这两种结构在理论上是可以制造的最简单的单自由度纳米机器。

Nature developed a way to combine 22 amino acids and build the molecular machinery responsible for carrying out essentially all of the critical functions in living things. Inside every living cell, ribosomes take genetic data as "assembly instructions" to assemble long chain molecules that fold into 3-dimensional structures whose dynamic properties underlie their biological functions. However, designing and building artificial nanomachines with prescribed functions for performing tasks in medical, environmental and industrial arenas remains a challenge, partly because the design principles developed by nature through evolution are not well understood and hence not applicable to engineered nanomachines. What scientists agree on is that, similarly with how the concept of interchangeable parts designed to precise specifications fueled the manufacturing revolution, the ability to custom design, control, and fabricate nanomachines with prescribed functions will lead to a new revolution in engineering, medicine, and biotechnology. However, we simply do not know today how to design and control artificial nanomachines. This project aims to develop a theoretical and computational framework to systematically design, and analyze manufacturable molecular machines with prescribed mobility and function obtained from a predefined library of molecular components. If successful, this research will provide the framework and computational tools to systematically explore the design space of synthetic and controllable molecular machines and devices, potentially leading to novel molecular motor functions that can be used to develop smart nanorobots and materials. One key observation is that the design of nanomachines is primarily a combinatorial problem in which a finite number of building blocks are to be self-assembled into a functional structure, whereas the macro-scale design is a continuum one in which systems can be designed and fabricated to prescribed dimensions as well as physical properties. Therefore, this research will develop a systematic design process and computational framework to: (1) formalize the derived function of nanomachines in the form of motion specifications of output link(s); (2) design, and analyze irreducibly simple nanomachines with prescribed motion specification (one degree of freedom) by combining available nano-components into systems having constrained, and consequently controllable motions; (3) explore control mechanisms to manipulate the motions of these machines via external physical stimuli; (4) explore strategies to functionalize these systems into functional nanomachines by exploiting their motions individually or as part of an ensemble. The initial efforts of this research have already led to the discovery of two structures that are theoretically among the simplest one degree of freedom nanomachines that can be fabricated.