Montek Singh COMP Nov 17, 2011
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
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
3 distinct DNA-functionalized objects assemble into a triad if sequences are carefully chosen
Extend idea to 2D grid Protein attached to form the pattern “CAD”
Three rods, anchored to a solid ◦ assembly in several steps
Extend the triangle into this structure
Transistors ◦ “ring-gated field- effect transistor” ◦ RG-FET
Nanowires (gold)
2-input NAND
Embed in a DNA cube of insulating unit cells ◦ gray-shaded ones are gates/wires
Simple method: More economical method: ◦ build one face at a time: only 15 unique sequences!
Challenge: ◦ orientation is unpredictable Idea: ◦ use self-discovery
Idea: ◦ use self-discovery ◦ take cue from rectifier circuits
Idea: use self-discovery
Use hierarchical 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
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
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