Circuit and System Architecture for DNA-Guided Self-Assembly of Nanoelectronics

This paper explores the architectural challenges introduced by emerging bottom-up fabrication of nanoelectronic circuits and develops an architecture that meets these challenges. While our implementation is based on one specific technology, we believe the architecture is compatible with other emerging technologies. The specific nanotechnology we explore uses patterned DNA nanostructures and carbon nanotube FETs to create a hierarchical design. Patterned DNA nanostructures provide a scaffold for the placement and interconnection of CNFETs to create a limited size circuit (node). These nodes are interconnected using DNA-guided self-assembly, but without the control available in the patterned nanostructures, thus producing a random interconnect. 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 an accumulator-based active network architecture that addresses these three challenges.

[1]  Fullerene pipes , 1998, Science.

[2]  Qiang Fu,et al.  Selective Coating of Single Wall Carbon Nanotubes with Thin SiO2 Layer , 2002 .

[3]  David A. Maltz,et al.  Dynamic Source Routing in Ad Hoc Wireless Networks , 1994, Mobidata.

[4]  M. Zheng,et al.  DNA-assisted dispersion and separation of carbon nanotubes , 2003, Nature materials.

[5]  Yoon,et al.  Crossed nanotube junctions , 2000, Science.

[6]  M. G. Ancona.  Systolic processor designs using single-electron digital circuits , 1996 .

[7]  Paul Beckett,et al.  Towards nanocomputer architecture , 2002 .

[8]  Deborah Estrin,et al.  Directed diffusion: a scalable and robust communication paradigm for sensor networks , 2000, MobiCom '00.

[9]  C. Dekker,et al.  Logic Circuits with Carbon Nanotube Transistors , 2001, Science.

[10]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[11]  T. J. Fountain,et al.  The use of nanoelectronic devices in highly parallel computing systems , 1998, IEEE Trans. Very Large Scale Integr. Syst..

[12]  David Wetherall,et al.  Towards an active network architecture , 1996, CCRV.

[13]  P. Jonker,et al.  A defect-?and fault-tolerant architecture for nanocomputers , 2003 .

[14]  Ho-Seop Kim,et al.  An instruction set and microarchitecture for instruction level distributed processing , 2002, Proceedings 29th Annual International Symposium on Computer Architecture.

[15]  Chris Dwyer,et al.  DNA-functionalized single-walled carbon nanotubes , 2002 .

[16]  William J. Dally.  Virtual-channel flow control , 1990, ISCA '90.

[17]  J. Reif,et al.  Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes , 2000 .

[18]  Chris Dwyer,et al.  The design of DNA self-assembled computing circuitry , 2004, IEEE Transactions on Very Large Scale Integration (VLSI) Systems.

[19]  Michael Burrows,et al.  Autonet: A High-Speed, Self-Configuring Local Area Network Using Point-to-Point Links , 1991, IEEE J. Sel. Areas Commun..

[20]  A. S. Sadek,et al.  Fault-tolerant techniques for nanocomputers , 2002 .

[21]  Russell M. Taylor,et al.  Self-assembled computer architecture: design and fabrication theory , 2003 .

[22]  R. Smalley,et al.  Electronic Structure Control of Single-Walled Carbon Nanotube Functionalization , 2003, Science.

[23]  Hao Yan,et al.  Directed Nucleation Assembly of Barcode Patterned DNA Lattices , 2003 .

[24]  S. Tans,et al.  Room-temperature transistor based on a single carbon nanotube , 1998, Nature.

[25]  Gregory S. Snider,et al.  A Defect-Tolerant Computer Architecture: Opportunities for Nanotechnology , 1998 .

[26]  N. Seeman.  DNA engineering and its application to nanotechnology. , 1999, Trends in biotechnology.

[27]  Kees van Berkel,et al.  Single-track handshake signaling with application to micropipelines and handshake circuits , 1996, Proceedings Second International Symposium on Advanced Research in Asynchronous Circuits and Systems.

[28]  M. Dresselhaus,et al.  Structure-Based Carbon Nanotube Sorting by Sequence-Dependent DNA Assembly , 2003, Science.

[29]  Roger H. French,et al.  Lithographically Cut Single-Walled Carbon Nanotubes: Controlling Length Distribution and Introducing End-Group Functionality , 2003 .

[30]  John H. Reif,et al.  DNA Nanotubes: Construction and Characterization of Filaments Composed of TX-tile Lattice , 2002, DNA.

[31]  John H. Reif,et al.  Challenges and Applications for Self-Assembled DNA Nanostructures , 2000, DNA Computing.

[32]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[33]  Michael Krueger,et al.  Sequence-Specific Molecular Lithography on Single DNA Molecules , 2002, Science.

[34]  Seth Copen Goldstein,et al.  NanoFabrics: spatial computing using molecular electronics , 2001, ISCA 2001.

[35]  Seth Copen Goldstein,et al.  NanoFabrics: spatial computing using molecular electronics , 2001, Proceedings 28th Annual International Symposium on Computer Architecture.

[36]  Richard Martel,et al.  Vertical scaling of carbon nanotube field-effect transistors using top gate electrodes , 2002 .

[37]  André DeHon,et al.  Array-Based Architecture for FET-Based, , 2003 .

[38]  E. Braun,et al.  DNA-templated assembly and electrode attachment of a conducting silver wire , 1998, Nature.

[39]  T. Cao,et al.  Logic Gates and Computation from Assembled Nanowire Building Blocks , 2001 .