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DNA Computing and Robotics:

DNA Computing and Robotics:. Milan N. Stojanovic NSF Center for Molecular Cybernetics Department of Medicine Columbia University. Engineering (Science?), Fun, and Applications. Suppose we have a set of primitives:. Sensor primitives:. Computing primitives:. Moving primitives:.

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DNA Computing and Robotics:

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  1. DNA Computing and Robotics: Milan N. Stojanovic NSF Center for Molecular Cybernetics Department of Medicine Columbia University Engineering (Science?), Fun, and Applications

  2. Suppose we have a set of primitives: Sensor primitives: Computing primitives: Moving primitives:

  3. Recipe for Computing Primitives: 1. Take Recognition Regions, Beacons (Tyagi and Kramer) S2 3. And combine (for computing elements, at least) them in: S1 E E S Phosphodiesterase (Joyce) Ligase (Szostak) Cf. modular design (e.g. Breaker…) 2. Take Nucleic acid catalysts,

  4. 250000 200000 150000 FU 100000 50000 0 0 100 200 300 400 t (min) Logic Gates: YES (Detector or Sensor Gate) Stojanovic et al., ChemBioChem 2001 Stojanovic et al., J. Am. Chem. Soc. 2002 Joyce 1995, Breaker 1999, Tyagi, Kramer 1996

  5. Three-input Gates Switching Primitives (Logic Gates): NOT AND

  6. B. Maya-II (Macdonald et al. Nano Lett. 2006) D. AND Hub with Beads (Rudchenko) (Yashin et al. JACS ~2007) C. DNA Calculator (Macdonald) 01 × 10 = 11 × 01 = 11 × 10 = 11 × 11 = 01 × 01 = (1×1=1) (1×2=2) (3×1=3) (3×2=6) (3×3=9) Some demonstrations of molecular computing: A. Full adder (Lederman et. al, Biochem. 2006)

  7. Implementation of Naughts-and-Crosses Playing Algorithm with Deoxiribozymes: Molecular Array of YES and ANDANDNOT Gates (MAYA) Stojanovic, Stefanovic, Nat. Biotech. 2003

  8. MAYA vs. Milan: Losing Game

  9. The Simplest Moving Primitive:

  10. But, what about multivalent design? Pei et. al JACS, 2006

  11. AFM Images of Spider at Starting Point Kyle Lund, Hao Yan, video now: with Nadine Dabby, Erik Winfree

  12. AFM images of Spider on Lanes of Substrates Kyle Lund, Hao Yan Video with: Nadine Dabby, Erik Winfree

  13. Center for Molecular Cybernetics Phase II?

  14. Erik Winfree (CS) Hao Yan (CHE) Niles Pierce (ApM) Paul Krapivsky (Phys) Sergei Rudchenko (BPh) Nils Walter (CHE) Milan Mrksich (CHE) Darko Stefanovic (CS/EE) Milan Stojanovic (MEDSci) Nadrian Seeman (CHE) Henry Hess (CHE/MATS) William Shih (CHE) Srboljub Mijailovich (ME) Natasha Yonoska (MATH) Satoshi Murata (CS/ME) Friedrich Simmel (P-CHE) Vojislav Stojkovic (CS) Qiao Lin (ME) Paul Rothemund (CHE/CS) Center Members & Friends Chemical Bonding Center NSF (CHE-0533096)

  15. Acknowledgments: • Postdocs: Steven Taylor, Renjun Pei, Dmitry Kolpashchikov, Joanne Macdonald • Tech’s: Stanka Semova, Erik Green, Payal Pallavi, Ma Li • High Shool Program: Harvey Lederman, Yang Lee, Marko Sutovic, Kiran Pendri, Wengho Lu, Kirill Lebedov, Srikanth Damera, George Lederman, Kaitlin Kyi. • Tiffany Elizabeth Mitchell • Collaborators: • Sergei Rudchenko (HSS), Ruslan Yashin • Darko Stefanovic (UNM), Mark Olah • Nils Walter (UM, Ann Arbor), Tony Manzo, Chamaree De Silva • Vincent Butler (Columbia) • Milan Mrksich (Chicago), Haim Tsubery • Erik Winfree (Caltech), Georg Seelig, Nadine Dabby • Hao Yan (ASU), Kyle Lund Current funding NSF (ITR, 3xEMT, and CBC), JDRF, NIH (NCI-R21) Lymphoma and Leukemia Society Scholarship Previously: NASA, NSF QuBIC, NSF Biophotonics, NIH (NIBIB), Searle

  16. Potential practical applications: 1. Cell-death by Boolean Calculations: 2. Glucose-triggered movement of catalytic nanoassemblies:

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