On the Systematic Design and Analysis of Artificial Molecular Machines

Inside every cell, ribosomes, the natural molecular factories, use genetic data as “building instructions” to assemble 20 types of amino acids into long chain molecules that become functional when folded into specific 3-D structures. In many cases the functions of these molecules are tied to their controllable motion properties. These natural molecular machines have optimally evolved to conduct very specific biological tasks in living organisms, but the natural “design” process is far from being understood well enough to be reproducible. Furthermore, the 20 amino acids of the standard genetic code are only a tiny fraction of the number of α-amino acid chemical structures that could not only play a role in the natural processes supporting human life, but also in the engineering of the artificial nano-machines of the future. This thesis formulates a theoretical and computational framework to enable systematic explorations of the design space of self-assembled nano machines with prescribed mobility. One of the key differences between designing at the macro and nano scales is that, in the latter case, one does not have the freedom to fabricate “components” of desired shapes and sizes. Instead, the types of possible nano components that are either available or can be fabricated are finitely many. Therefore, we propose a systematic strategy and computational infrastructure to design manufacturable molecular machines with prescribed mobility and function obtained from a predefined library of molecular components. Furthermore, we investigate the design space of one-degree of freedom (DOF) nano-machines, which are known to be the simplest, most effective, robust, and widely used designs at the macro-scale because of their completely predictable and repeatable motion. The resulting synthesis procedure is the first of its kind and capable of synthesizing functional linkages with prescribed mobility constructed from a soup of primitive entities. The preliminary investigations have already led to the discovery of novel, never before seen one degree of freedom nano-machines, which have been proven both in simulations and experiments to self-assemble into one degree-of freedom nano-robots. Equally important, the proposed systematic approach can enumerate an ATLAS of candidate nano-mechanisms with prescribed mobility, and can be used by `nano-designers,’ e.g, synthetic chemists, biochemists, biologists, pharmacists, and engineers, to explore the vast design spaces of artificial molecular machines of the future, and develop, for example, novel drug delivery agents, nano-robots and sensors, as well as programmable matter