Molecular Computing

Speakers:

Overview of New Structures for DNA-Based Nanofabrication and Computation

Thom LaBean and Hao Yan, Duke University

This paper and two talks (by LaBean and Yan) present an overview of recent experimental progress by the Duke DNA NanoTech Group in our efforts to utilize novel DNA nanostructures for computational self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA tile type known as the 4x4 (a cross composed of four four-arm junctions) upon which we have deposited metal to form highly conductive nanowires and also are adapting multi-tile 4x4 sets for a variety of computational applications. We have recently described a DNA barcode lattice composed of DX tiles assembled on a long scaffold strand; the system translates information encoded in the scaffold strand into a specific and reprogrammable barcode pattern which is visible by atomic force microscopy. We have succeeded in demonstrating the first highly parallel computation via DNA tile self-assembly by using a single-layer superstructure made of DX tiles which computes the entire lookup table of pairwise XOR calculations up to a modest size input string length. We have prototyped a 2-state DNA lattice assembly containing actuator or motor components and demonstrated its ability to be controllably switched between the two states. We are currently working on a molecular robotics experiment aimed at demonstrating unidirectional motion of a small DNA fragment along a track constructed from DNA. Details of these and other ongoing projects will be presented here and in the talks.

A New Approach to Autonomous Kinase Computing

Jian-Qin Liu and Katsunori Shimohara, ATR, Japan

In this paper, we propose a new approach to kinase computing that will provide a strong possibility of autonomy in cell-based computing using signaling pathways. Based on the signaling mechanism of phosphorylation and dephosphorylation for basic computing processes, the complexity derived from 3-SAT computation by kinase computing is discussed. The experimental result obtained from a corresponding simulation shows that the related design scheme of kinase computing is controllable for the nonlinear phenomena of the curves of concentration vs. time in simulation. This work is necessary to achieve pathway designs for kinase computation with related biological faithfulness.

Combinatory Logic for Autonomous Molecular Computation

Bruce MacLennan, University of Tennessee, Knoxville

A small set of simple network-substitution operations, derived from combinatory logic, are sufficient to implement any computation that can be performed on a digital computer. These operations, which may be performed in any order or in parallel, provide an ideal model for autonomous molecular computation. After explaining the basic principles of molecular combinatory programming we give several examples of its use to create useful nanostructures (membranes, nanotubes, channels). We also present a possible implementation based on enzyme-mediated reorganization of large networks of molecular building blocks linked by hydrogen bonds.

Last modified: June 18, 2003 by Dan Ventura.