Intelligent nanomechanical devices that operate in an autonomous fashion are of great theoretical and practical interest. Recent successes in building large scale DNA nanostructures, in constructing DNA mechanical devices, and in DNA computing provide a solid foundation for the next step forward: designing autonomous DNA mechanical devices capable of arbitrarily complex behavior. One prototype system towards this goal can be a DNA mechanical device that is capable of universal computation, by mimicking the operation of a universal Turing machine. Building on our prior theoretical designs and a prototype experimental construction of autonomous unidirectional DNA walking devices that move along linear tracks, we present in this paper the design of a nanomechanical DNA device that autonomously mimics the operation of a 2-state 5color universal Turing machine. Our autonomous nanomechanical device, which we call an Autonomous DNA Turing Machine, is thus capable of universal computation and hence complex translational motion which we define as universal translational motion.

Abstract. Recent experimental progress in DNA lattice construction, DNA robotics, and DNA computing provides the basis for designing DNA cellular computing devices, i.e. autonomous nano-mechanical DNA computing devices embedded in DNA lattices. Once assembled, DNA cellular computing devices can serve as reusable, compact computing devices that perform (universal) computation, and programmable robotics devices that demonstrate complex motion. As a prototype of such devices, we recently reported the design of an Autonomous DNA Turing Machine, which is capable of universal sequential computation, and universal translational motion, i.e. the motion of the head of a single tape universal mechanical Turing machine. In this paper, we describe the design of an Autonomous DNA Cellular Automaton (ADCA), which can perform parallel universal computation by mimicking a one-dimensional (1D) universal cellular automaton. In the computation process, this device, embedded in a 1D DNA lattice, also demonstrates well coordinated parallel motion. The key technical innovation here is a molecular mechanism that synchronizes pipelined “molecular reaction waves”

The construction of complex systems at the 1- 100 nanometer (1 nanometer = ¡£¢¥¤§ ¦ meter) scale is a key challenge in current nanoscience. This challenge can be most effectively ad-dressed by the “bottom-up ” nano-construction methodology based on self-assembly, a pro-cess in which substructures autonomously associate with each other to form superstructures driven by the selective affinity of the substructures. DNA, with its immense information encoding capacity and well defined Watson-Crick complementarity, has recently emerged as an excellent material for constructing self-assembled nano-structures. In this disserta-tion, we study four closely related aspects of DNA based self-assembly and nano-devices: complexity of self-assembly, fault-tolerant self-assembly, DNA robotics devices, and DNA computing devices. Complexity of self-assembly. We establish a framework that models assemblies result-ing from the cooperative effects of repulsion and attraction forces in a general setting of