Results 1 
4 of
4
Design of an autonomous DNA nanomechanical device capable of universal computation and universal translational motion
, 2004
"... Abstract. 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 ..."
Abstract

Cited by 9 (4 self)
 Add to MetaCart
Abstract. 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 an autonomous DNA mechanical device capable of universal computation, by mimicking the operation of a universal Turing machine. Building on our prior theoretical design and prototype experimental construction of an autonomous unidirectional DNA walking device moving along a linear track, we present here the design of a nanomechanical DNA device that autonomously mimics the operation of a 2state 5color universal Turing machine. Our autonomous nanomechanical device, called an Autonomous DNA Turing Machine (ADTM), is thus capable of universal computation and hence complex translational motion, which we define as universal translational motion. 1
Molecular Tiling and DNA Selfassembly
"... Abstract. We examine hypotheses coming from the physical world and address new mathematical issues on tiling. We hope to bring to the attention of mathematicians the way that chemists use tiling in nanotechnology, where the aim is to propose building blocks and experimental protocols suitable for th ..."
Abstract
 Add to MetaCart
Abstract. We examine hypotheses coming from the physical world and address new mathematical issues on tiling. We hope to bring to the attention of mathematicians the way that chemists use tiling in nanotechnology, where the aim is to propose building blocks and experimental protocols suitable for the construction of 1D, 2D and 3D macromolecular assembly. We shall especially concentrate on DNA nanotechnology, which has been demonstrated in recent years to be the most effective programmable selfassembly system. Here, the controlled construction of supramolecular assemblies containing components of fixed sizes and shapes is the principal objective. We shall spell out the algorithmic properties and combinatorial constraints of “physical protocols”, to bring the working hypotheses of chemists closer to a mathematical formulation. 1 Introduction to Molecular Selfassembly Molecular selfassembly is the spontaneous organisation of molecules under thermodynamic equilibrium conditions into a structurally welldefined and rather
DNA BASED SELFASSEMBLY AND NANODEVICE: THEORY AND PRACTICE
, 2005
"... 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 addressed by the “bottomup ” nanoconstruction methodology based on selfassembly, a process in which substructures au ..."
Abstract
 Add to MetaCart
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 addressed by the “bottomup ” nanoconstruction methodology based on selfassembly, a process 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 WatsonCrick complementarity, has recently emerged as an excellent material for constructing selfassembled nanostructures. In this dissertation, we study four closely related aspects of DNA based selfassembly and nanodevices: complexity of selfassembly, faulttolerant selfassembly, DNA robotics devices, and DNA computing devices. Complexity of selfassembly. We establish a framework that models assemblies resulting from the cooperative effects of repulsion and attraction forces in a general setting of
Random Phenomena in Algorithmic Self Assembly: Computing Times at Nanoscale
"... Speed of computation and power consumption are two principal parameters of conventional computing devices implemented in microelectronic circuits. As performance of such devices approaches physical limits, new computing paradigms are emerging. This paper focuses on computing by molecular self assemb ..."
Abstract
 Add to MetaCart
Speed of computation and power consumption are two principal parameters of conventional computing devices implemented in microelectronic circuits. As performance of such devices approaches physical limits, new computing paradigms are emerging. This paper focuses on computing by molecular self assembly processes, where computing elements are fashioned from DNA. For purposes of analysis, DNAbased self assembly can be abstracted to growth models in two dimensions where computational elements modeled as tiles are selfassembled one by one, subject to some simple hierarchical rules, to fill a given template encoding a Boolean formula. While molecular computational devices are known to be extremely energy efficient, little is known concerning the fundamental question of computation times. In particular, given a function, we study the time required to determine its value for a given input. Error tolerance is a necessary concomitant issue of any DNAbased computing paradigm. We propose an effective pulsing technique for error recovery and extend our estimates of computing times to this more general model. Our overall analytical approach establishes a reference theory for stochastic modeling of molecular computing. The mathematics comes down to customized techniques drawn from a surprisingly large number of disparate areas, including probability theory, dynamical systems, optimal control theory, theory of networks, and simulations. 1