Chris Dwyer

DNA-functionalized single-walled carbon nanotubes

We present here the use of amino-terminated DNA strands in functionalizing the open ends and defect sites of oxidatively prepared single-walled carbon nanotubes, an important first step in realizing a DNA-guided self-assembly process for carbon nanotubes.

Semi-empirical SPICE models for carbon nanotube FET logic

To evaluate the potential of carbon nanotube field effect transistors (CNFETs) to replace silicon CMOS technology, we develop a SPICE model of CNFET nanoelectronics. Our model is parameterizable, and it enables composition of models of various aspects of nanoelectronic behavior. Comparing CNFET nanoelectronics against current CMOS technology and future projections for CMOS, we demonstrate that CNFET nanoelectronics can achieve significantly greater performance at a fraction of the switching energy.

Nanoscale Optical Computing Using Resonance Energy Transfer Logic

Drawing on the nanometer-placement capabilities of self-assembly fabrication methods, the authors propose a new nanoscale device based on a single-molecule optical phenomenon called resonance energy transfer. This device enables a complete integrated technology, providing a potential path to molecular-scale computing. The authors present several important circuit elements, show how to compose these elements into computational nodes, and outline initial steps toward a prototype system.

NANA: A nano-scale active network architecture

This article explores the architectural challenges introduced by emerging bottom-up fabrication of nanoelectronic circuits. The specific nanotechnology we explore proposes patterned DNA nanostructures as a scaffold for the placement and interconnection of carbon nanotube or silicon nanorod FETs to create a limited size circuit (node). Three characteristics of this technology that significantly impact architecture are (1) limited node size, (2) random node interconnection, and (3) high defect rates. We present and evaluate an accumulator-based active network architecture that is compatible with any technology that presents these three challenges. This architecture represents an initial, unoptimized solution for understanding the implications of DNA-guide self-assembly.

The design of DNA self-assembled computing circuitry

We present a design methodology for a nanoscale self-assembling fabrication process that uses the specificity of DNA hybridization to guide the formation of electrical circuitry. Custom design software allows us to specify the function of a structure in a way similar to that used by VLSI circuit designers. In an analogous manner to generating masks for a photolithographic process, our software generates an assembly procedure including DNA sequence allocation. We have found that the number of unique DNA sequences needed to assemble a structure scales with its surface area. Using a simple face-serial assembly order we can specify an unambiguous assembly sequence for a structure of any size with only 15 unique DNA sequences.

Scalable, low-cost, hierarchical assembly of programmable DNA nanostructures

We demonstrate a method for the assembly of fully programmable, large molecular weight DNA complexes. The method leverages sticky-end re-use in a hierarchical fashion to reduce the cost of fabrication by building larger complexes from smaller precursors. We have explored the use of controlled non-specific and specific binding between sticky-ends and demonstrate their use in hierarchical assembly. We conclude that it is feasible to scale this method beyond our demonstration of a fully programmable 8960 kD molecular weight 8 × 8 DNA grid for potential application to complex nanoscale system fabrication.

A defect tolerant self-organizing nanoscale SIMD architecture

The continual decrease in transistor size (through either scaled CMOS or emerging nano-technologies) promises to usher in an era of tera to peta-scale integration. However, this decrease in size is also likely to increase defect densities, contributing to the exponentially increasing cost of top-down lithography. Bottom-up manufacturing techniques, like self assembly, may provide a viable lower-cost alternative to top-down lithography, but may also be prone to higher defects. Therefore, regardless of fabrication methodology, defect tolerant architectures are necessary to exploit the full potential of future increased device densities.This paper explores a defect tolerant SIMD architecture. A key feature of our design is the ability of a large number of limited capability nodes with high defect rates (up to 30%) to self-organize into a set of SIMD processing elements. Despite node simplicity and high defect rates, we show that by supporting the familiar data parallel programming model the architecture can execute a variety of programs. The architecture efficiently exploits a large number of nodes and higher device densities to keep device switching speeds and power density low. On a medium sized system (~1cm2 area), the performance of the proposed architecture on our data parallel programs matches or exceeds the performance of an aggressively scaled out-of-order processor (128-wide, 8k reorder buffer, perfect memory system). For larger systems (>1cm2), the proposed architecture can match the performance of a chip multiprocessor with 16 aggressively scaled out-of-order cores.

DNA-Enabled Integrated Molecular Systems for Computation and Sensing

CONSPECTUS: Nucleic acids have become powerful building blocks for creating supramolecular nanostructures with a variety of new and interesting behaviors. The predictable and guided folding of DNA, inspired by nature, allows designs to manipulate molecular-scale processes unlike any other material system. Thus, DNA can be co-opted for engineered and purposeful ends. This Account details a small portion of what can be engineered using DNA within the context of computer architectures and systems. Over a decade of work at the intersection of DNA nanotechnology and computer system design has shown several key elements and properties of how to harness the massive parallelism created by DNA self-assembly. This work is presented, naturally, from the bottom-up beginning with early work on strand sequence design for deterministic, finite DNA nanostructure synthesis. The key features of DNA nanostructures are explored, including how the use of small DNA motifs assembled in a hierarchical manner enables full-addressability of the final nanostructure, an important property for building dense and complicated systems. A full computer system also requires devices that are compatible with DNA self-assembly and cooperate at a higher level as circuits patterned over many, many replicated units. Described here is some work in this area investigating nanowire and nanoparticle devices, as well as chromophore-based circuits called resonance energy transfer (RET) logic. The former is an example of a new way to bring traditional silicon transistor technology to the nanoscale, which is increasingly problematic with current fabrication methods. RET logic, on the other hand, introduces a framework for optical computing at the molecular level. This Account also highlights several architectural system studies that demonstrate that even with low-level devices that are inferior to their silicon counterparts and a substrate that harbors abundant defects, self-assembled systems can still outperform conventional systems. Further, the domain, that is, the physical environment, in which such self-assembled computers can operate transcends the usual limitations of silicon machines and opens up new and exciting horizons for their application. This Account also includes a look at simulation tools developed to streamline the design process at the strand, device, circuit, and architectural levels. These tools are essential for understanding how to best manipulate the devices into systems that explore the fundamentally new computing domains enabled by DNA nanotechnology.

DNA self-assembled parallel computer architectures

New varieties of computer architectures, capable of solving highly demanding computational problems, are enabled by the large manufacturing scale expected from self-assembling circuit fabrication (1012–1019 devices). However, these fabrication processes are in their infancy and even at maturity are expected to incur heavy yield penalties compared to conventional silicon technologies. To retain the advantages of this manufacturing scale, new architectures must efficiently use large collections of very simple circuits. This paper describes two such architectures that are enabled by self-assembly and examines their performance.

Thousand-fold increase in optical storage density by polychromatic address multiplexing on self-assembled DNA nanostructures.

A super-resolution optical storage technique enabled by DNA nanotechnology and the design of resonance energy transfer (RET) networks are demonstrated. The enhancement in storage density stems from non-linear interactions between excitons on the nanostructured RET circuits, which permit large-scale multiplexing with a small set of addressing wavelengths and a single output channel.