1 / 59

Kobi Benenson supervisor: Ehud Shapiro, Dept of Computer Science & Applied Math Acknowledgements:

A nanoscale programmable computing machine with input, output, software and hardware made of biomolecules Nature 414 , 430-434 (2001). Kobi Benenson supervisor: Ehud Shapiro, Dept of Computer Science & Applied Math Acknowledgements: Ehud Keinan (Technion), Zvi Livneh (WIS),

gunda
Download Presentation

Kobi Benenson supervisor: Ehud Shapiro, Dept of Computer Science & Applied Math Acknowledgements:

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. A nanoscale programmable computing machine with input, output, software and hardware made of biomolecules • Nature 414, 430-434 (2001) Kobi Benenson supervisor: Ehud Shapiro, Dept of Computer Science & Applied Math Acknowledgements: Ehud Keinan (Technion), Zvi Livneh (WIS), Tami Paz-Elizur (WIS), Rivka Adar (WIS), Aviv Regev (WIS), Irith Sagi (WIS), Ada Yonath (WIS)

  2. “Medicine in 2050: Doctor in a Cell” Molecular Output Molecular Input Programmable Computer

  3. Research goal: Design a simplest non-trivial molecular computing machine (two-state two-symbol finite automaton) that works on engineered inputs

  4. Finite automaton: an example An even number of b’s b S0, a S0 S0, b  S1 S1, a  S1 S1, b  S0 a a S0 S1 b Two-states, two-symbols automaton

  5. Automaton 1 An even number of b’s S0, a S0 S0, b  S1 S1, a  S1 S1, b  S0 b a b S0

  6. Automaton 1 An even number of b’s S0, b  S1 S0, a S0 S0, b  S1 S1, a  S1 S1, b  S0 b a b S0

  7. Automaton 1 An even number of b’s S0, a S0 S0, b  S1 S1, a  S1 S1, b  S0 a b S1

  8. Automaton 1 An even number of b’s S1, a  S1 S0, a S0 S0, b  S1 S1, a  S1 S1, b  S0 a b S1

  9. Automaton 1 An even number of b’s S0, a S0 S0, b  S1 S1, a  S1 S1, b  S0 b S1

  10. Automaton 1 An even number of b’s S1, b  S0 S0, a S0 S0, b  S1 S1, a  S1 S1, b  S0 b S1

  11. Automaton 1 An even number of b’s S0, a S0 S0, b  S1 S1, a  S1 S1, b  S0 S0 The output

  12. Rationale for the molecular design

  13. Rationale for the molecular design CTGGCT GACCGA CGCAGC GCGTCG a b

  14. Rationale for the molecular design CTGGCT GACCGA CGCAGC GCGTCG a b S0, a S0, b GGCT CAGC

  15. Rationale for the molecular design CTGGCT GACCGA CGCAGC GCGTCG a b S0, a S0, b GGCT CAGC S1, a S1, b CTGGCT GA CGCAGC CG

  16. Rationale for the molecular design Transitions S0, b CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG a b t

  17. Rationale for the molecular design Transitions S0, b CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG a b t S0, b  S1

  18. Rationale for the molecular design Transitions S1, a CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG b t S0, b  S1

  19. Rationale for the molecular design Transitions S1, a CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG b t S1, a  S1

  20. Rationale for the molecular design Transitions S1, b CGCAGCTGTCGC CGACAGCG t S1, a  S1

  21. Rationale for the molecular design Transitions S1, b CGCAGCTGTCGC CGACAGCG t S1, b  S0

  22. Rationale for the molecular design Transitions S0, t TCGC S1, b  S0

  23. Rationale for the molecular design Transitions S0, t TCGC Output: S0

  24. Rationale for the molecular design Transition procedure: a concept S0, b CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG a b t

  25. 4 nt GTCG 8 nt Rationale for the molecular design Transition procedure: a concept S0, b CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG a b t S0, b -> S1

  26. 4 nt GTCG 8 nt Rationale for the molecular design Transition procedure: a concept CAGCCTGGCTCGCAGCTGTCGC GACCGAGCGTCGACAGCG b t S0, b -> S1

  27. Rationale for the molecular design Transition procedure: a concept S1, a CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG b t S0, b -> S1

  28. Rationale for the molecular design Transition procedure: a concept S1, a CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG b t S1, a -> S1

  29. 6 nt GACC 10 nt Rationale for the molecular design Transition procedure: a concept S1, a CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG b t S1, a -> S1

  30. 6 nt GACC 10 nt Rationale for the molecular design Transition procedure: a concept CTGGCTCGCAGCTGTCGC GAGCGTCGACAGCG t S1, a -> S1

  31. Rationale for the molecular design Transition procedure: a concept S1, b CGCAGCTGTCGC CGACAGCG t S1, a -> S1

  32. 8 nt GCGT 12 nt Rationale for the molecular design Transition procedure: a concept S1, b CGCAGCTGTCGC CGACAGCG t S1, b -> S0

  33. 8 nt GCGT 12 nt Rationale for the molecular design Transition procedure: a concept CGCAGCTGTCGC CGACAGCG S1, b -> S0

  34. Rationale for the molecular design Transition procedure: a concept S0, t TCGC Output: S0

  35. Rationale for the molecular design In situ detection S0, t Detection molecule for S0 output TCGC AGCG Output: S0

  36. AGCG Rationale for the molecular design In situ detection Reporter molecule for S0 output TCGC Output: S0

  37. 4 nt GTCG 8 nt Inside the transition molecule S0,b -> S1

  38. Inside the transition molecule FokI 4 nt GGATGACGAC CCTACTGCTG GTCG 8 nt S0,b -> S1

  39. Inside the transition molecule FokI 9 nt 4 nt GGATGACGAC CCTACTGCTG GTCG 8 nt 13 nt S0,b -> S1

  40. 9 nt GGATGACGAC CCTACTGCTG GTCG 13 nt Inside the transition molecule FokI S0,b -> S1

  41. 6 nt GACC 10 nt Inside the transition molecule S1,a -> S1

  42. Inside the transition molecule FokI 9 nt 6 nt GGATGACG CCTACTGC GACC 10 nt 13 nt S1,a -> S1

  43. 9 nt GGATGACG CCTACTGC GACC 13 nt Inside the transition molecule FokI S1,a -> S1

  44. Inside the transition molecule 8 nt GCGT 12 nt S1,b -> S0

  45. Inside the transition molecule FokI 9 nt 8 nt GGATGG CCTACC GCGT 12 nt 13 nt S1,b -> S0

  46. 9 nt GGATGG CCTACC GCGT 13 nt Inside the transition molecule FokI S1,b -> S0

  47. Inside the transition molecule GGATGACGAC CCTACTGCTG S0 -> S1 GTCG S0 -> S0 GGATGACG CCTACTGC GACC S1 -> S1 GGATGG CCTACC S1 -> S0 GCGT

  48. Transition rules: complete list

  49. Automata programs used to test the molecular implementation

More Related