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Emerging Technologies of Computation

Emerging Technologies of Computation. Montek Singh COMP790-084 Nov 17, 2011. Today: Computing using DNA. Two different technologies Previous Class: DNA as biochemical computer DNA molecules encode data enzymes, probes etc. manipulate data

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Emerging Technologies of Computation

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  1. Emerging Technologies of Computation Montek Singh COMP790-084 Nov 17, 2011

  2. Today: Computing using DNA • Two different technologies • Previous Class:DNA as biochemical computer • DNA molecules encode data • enzymes, probes etc. manipulate data • TODAY:DNA used to assemble electronic computer • DNA molecules used as scaffolding • nanoscale electronic components piggyback • DNA assembles the computer

  3. Basics of DNA Self-Assembly • Pioneering work by Chris Dwyer et al. • PhD at UNC; now faculty at Duke • Key Idea: • Exploit constraints on DNA bonding to design DNA sequences that will only come together in predictable ways • Piggy back components of interest on top of DNA: transistors, wires, etc. • Terminology: • functionalization: attaching DNA strand to a component of interest

  4. Forming a triad • 3 distinct DNA-functionalized objects assemble into a triad if sequences are carefully chosen

  5. Forming a grid • Extend idea to 2D grid • Protein attached to form the pattern “CAD”

  6. Basic cuilding block: Triangular structure • Three rods, anchored to a solid • assembly in several steps

  7. Cubic unit cell • Extend the triangle into this structure

  8. Electronic components • Transistors • “ring-gated field-effect transistor” • RG-FET

  9. Electronic components • Nanowires (gold)

  10. Let’s make a gate! • 2-input NAND

  11. Give it some structural support • Embed in a DNA cube of insulating unit cells • gray-shaded ones are gates/wires

  12. How many distinct DNA strands? • Simple method: • More economical method: • build one face at a time: only 15 unique sequences!

  13. Power and I/O • Challenge: • orientation is unpredictable • Idea: • use self-discovery

  14. Power and I/O • Idea: • use self-discovery • take cue from rectifier circuits

  15. Power and I/O • Idea: use self-discovery

  16. What about larger structures? • Use hierarchical assembly

  17. What about larger structures? • Use hierarchical assembly

  18. What about larger structures? • Use hierarchical assembly

  19. Challenges in self-assembly • Design and verification remain challenges • structures only with a handful of transistors • yield only about 50-70% • but… materials are cheap though • $40 for the “CAD” experiment • addressability • unique and independent functionalization • architectures, interconnection • inherent element of randomness • I/O especially difficult • CAD tool support • timing unpredictable

  20. Potential benefits of self-assembly • Really tiny! • unobtainable in silicon • … except electron beam, extreme UV or X-ray lithography • Potentially much larger scale • can produce in seconds what a commercial foundry does in days or weeks

  21. Further Reading • Design Automation: • Pistol et al., DAC 2006 • Dwyer, ICCAD 2005 • Routing: • Liu et al., JETC 2010 • Patwardhan et al, JETC 2006 • Nanoscale sensors: • Pistol et al., ASPLOS 2009, Micro 2010 • Nanoscale optical computing: • Pistol et al., Micro 2008

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