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.

Problems implementing DNA computers stem from the physical nature of molecules and their reactions. The present theory of computation requires assumptions that, at best, are extremely crude approximations of the physical chemistry. Here I consider the hypothesis that discarding those assumptions in favor of more physically realistic descriptions would produce a more comprehensive theory of computing, yielding both theoretical insights and help in designing better molecular computers. I describe the discordances between the theories of physical biochemistry and computation, indicate some elements of a more comprehensive theory, and discuss some of the challenges the construction of a unified theory faces. keywords: molecular computing DNA computing physical biochemistry theory of computing 1 Hypothesis Molecular computing is justifiably exciting, not least for the alluring prospect of biologically-inspired machines nicely handling NP-complete problems. However, current molecular ...

Problems in implementing DNA and other types of molecular computers stem from the inherent physical nature of molecules and their reactions. The current theory of computation makes assumptions that at best are very crude approximations of the physical chemistry. A theory which took into account the physical chemistry would likely be very different from what we have now and should help in designing more optimal molecular computing systems. In this paper I describe briefly the discordance between these assumptions and the physical chemistry; indicate some of the properties a more physically realistic model might have; and sketch some of the possibilities for a computing system which exploited the physical chemistry. We are developing a model for networks of biochemical reactions and molecules incorporating treatments of both continuous and discrete aspects of biochemical systems. The formal system of the model provides an example of what a CPC might be if the problems of encodi...

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