Avogadro Scale Engineering & Fabricational Complexity MIT Avogadro Scale Engineering & Fabricational Complexity NSF-CBA Program Review MIT Cambridge, MA October 12, 2006 Molecular Machine (Jacobson) Group jacobson@media.mit.edu

Complexity vs. Size m 10-10 10-5 10-9 10-7 10-6 10-8 10-4 10-3 10-2 red blood cell ~5 m (SEM) diatom 30 m Simple molecules <1nm DNA proteins nm bacteria 1 m m 10-10 10-5 10-9 10-7 10-6 10-8 10-4 10-3 10-2 SOI transistor width 0.12m Semiconductor Nanocrystal ~1 nm Circuit design Copper wiring width 0.1m Nanotube Transistor (Dekker) IBM PowerPC 750TM Microprocessor 7.56mm×8.799mm 6.35×106 transistors

Chemical Synthesis (Solid Phase Synthesis) DNA Synthesis Chemical Synthesis (Solid Phase Synthesis) Biological Synthesis (Error Correcting Polymerase) Error Rate: 1: 102 300 Seconds Per step Error Rate: 1: 106 100 Steps per second 3'-5' proofreading exonuclease http://www.med.upenn.edu/naf/services/catalog99.pdf Beese et al. (1993), Science, 260, 352-355. http://www.biochem.ucl.ac.uk/bsm/xtal/teach/repl/klenow.html

Resources for Exponential Scaling Resources which increase the complexity of a system exponentially with a linear addition of resources 1] Quantum Phase Space 2] Error Correcting Fabrication 3] Fault Tolerant Hardware Architectures 4] Fault Tolerant Software or Codes

Complexity Per Unit Cost [I]Non Error Correcting: A G T C [II] Triply Error Correcting: A G T C A G T C A G T C P = 0.9 n = 300 P = 0.85 n n p

Deinococcus radiodurans (3.2 Mb, 4-10 Copies of Genome ) D. radiodurans 1.75 million rads, 0 h D. radiodurans 1.75 million rads, 24 h Uniformed Services University of the Health [Nature Biotechnology 18, 85-90 (January 2000)] D. radiodurans: 1.7 Million Rads (17kGy) – 200 DS breaks E. coli: 25 Thousand Rads – 2 or 3 DS breaks http://www.ornl.gov/hgmis/publicat/microbial/image3.html photos provided by David Schwartz (University of Wisconsin, Madison)]

Synthetic Self Replication -Building a Fab for Biology- BioFAB -Building a Fab for Biology- “Robotics: Self-replication from random parts.” Nature (2005), 437(7059), 636 Griffith, S. et. al. Carr, P. et.al. .. “ Protein-mediated error correction for de novo DNA synthesis.” Nucleic Acids Research (2004), 32(20), e162/1-e162/9. Molecular Machines Group-MIT Faculty Joseph Jacobson Graduate Students Brian Chow David Kong Chris Emig Jae Bum Joo Sam Hwang Kimin Jun Undergrad Bram Sterling,Lu Chen,Ekatarina Pak,Michael Oh Research Scientists and Post Docs Peter Carr Sangjun Moon Alumni Saul Griffith Jason Park Air inlets Crushers Ganglion Multiple Visual sensors Muscles Pincers Sensory receptors Stridulatory pegs Wings http://www.thetech.org/exhibits_events/traveling/robotzoo/about/images/grasshopper.gif