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Nanoscale Programmable Computing Machine with Biomolecules

This research paper discusses the design of a nanoscale programmable computing machine made of biomolecules, capable of input, output, and running software and hardware. The aim is to create a simple but functional molecular computing machine using engineered inputs.

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Nanoscale Programmable Computing Machine with Biomolecules

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  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

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