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PLEX. M I T. CO. Y. Avogadro Scale Engineering & Fabricational Complexity. NSF-CBA Program Review MIT Cambridge, MA October 12, 2006. Molecular Machine (Jacobson) Group [email protected] 10 -10. 10 -9. 10 -8. 10 -7. 10 -6. 10 -5. 10 -4. 10 -3. 10 -2. red blood cell

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Presentation Transcript
slide1

PLEX

MIT

CO

Y

Avogadro Scale Engineering &

Fabricational Complexity

NSF-CBA Program Review

MIT Cambridge, MA October 12, 2006

Molecular Machine (Jacobson) Group [email protected]

complexity vs size

10-10

10-9

10-8

10-7

10-6

10-5

10-4

10-3

10-2

red blood cell

~5 m (SEM)

diatom

30 m

Complexity vs. Size

DNA

proteins

nm

Simple molecules

<1nm

bacteria

1 m

m

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

slide3

DNA Synthesis

Chemical Synthesis(Solid Phase Synthesis)

Biological Synthesis(Error Correcting Polymerase)

Error Rate:

1: 102

Error Rate:

1: 106

100 Steps per second

300 Seconds

Per step

3\'-5\' proofreading exonuclease

  • Beese et al. (1993), Science, 260, 352-355.

http://www.med.upenn.edu/naf/services/catalog99.pdf

http://www.biochem.ucl.ac.uk/bsm/xtal/teach/repl/klenow.html

slide4

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

slide5

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

n = 300

P = 0.9

P = 0.85

n

n

p

slide6

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)]

slide7

Synthetic Self Replication

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

Chris Emig

Jae Bum Joo

Jason Park

BioFAB

-Building a Fab for Biology-

Griffith, S. et. al.

“Robotics: Self-replication from random parts.”

Nature (2005), 437(7059), 636

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

  • 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

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