1. Montek Singh COMP790-084 Nov 17, 2011

2.  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.  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.  3 distinct DNA-functionalized objects assemble into a triad if sequences are carefully chosen

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

6.  Three rods, anchored to a solid ◦ assembly in several steps

7.  Extend the triangle into this structure

8.  Transistors ◦ “ring-gated field- effect transistor” ◦ RG-FET

9.  Nanowires (gold)

10.  2-input NAND

11.  Embed in a DNA cube of insulating unit cells ◦ gray-shaded ones are gates/wires

12.  Simple method:  More economical method: ◦ build one face at a time: only 15 unique sequences!

13.  Challenge: ◦ orientation is unpredictable  Idea: ◦ use self-discovery

14.  Idea: ◦ use self-discovery ◦ take cue from rectifier circuits

15.  Idea: use self-discovery

16.  Use hierarchical assembly

19.  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.  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.  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