Systematic Design, Analysis and Control of Manufacturable Nano Machines

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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.