Molecular Programming - Luca Cardelli

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Two-Domain Architecture • Signals: 1 toehold + 1 recognition region t x • Gates: “top-nicked double strands” with open toeholds t x t y t Garbage collection “built into” the gate operation In S. B. Cooper, E. Kashefi, P. Panangaden (Eds.): Developments in Computational Models (DCM 2010). EPTCS 25, 2010, pp. 33-47. May 2010.
Plasmidic Gate Technology Synthetic DNA is length-limited Finite error probability at each nucleotide addition, hence ~ 200nt max Bacteria can replicate plasmids for us Loops of DNA 1000’s nt, with extremely high fidelity Practically no structural limitations on gate fan-in/fan-out Only possible with two-domain architecture
Page 1 and 2: Molecular Programming Luca Cardelli
Page 3 and 4: The Hardware Argument Smaller and s
Page 5 and 6: Building the Smallest Things How d
Page 7 and 8: Programmed Self-Assembly Proteins D
Page 9 and 10: We can program... Computers. Comp
Page 11 and 12: We can program... Matter Complete
Page 13 and 14: Organizing Any Matter Use one kind
Page 15 and 16: Building Nano-Control Devices All
Page 17 and 18: The Biological Argument Biological
Page 19 and 20: Biological Languages Gene Networks
Page 21 and 22: Molecular Languages ... that we can
Page 23 and 24: Our Assembly Language: Chemistry A
Page 25 and 26: How do we “run” Chemistry? Che
Page 27 and 28: The role of DNA Computing Non-goal
Page 29 and 30: Short Domains t t t DNA double stra
Page 31 and 32: Strand Displacement t t x x “Toeh
Page 33 and 34: Strand Displacement t x Branch Migr
Page 35 and 36: Strand Displacement x t x Irreversi
Page 37 and 38: Bad Match t x x z y
Page 39: Bad Match t x z y Cannot proceed He
Page 43 and 44: Transducer x→y t Input x t a y t
Page 45 and 46: Transducer x→y t a y t t x t a t
Page 47 and 48: Transducer x→y x t y t t x t a t
Page 49 and 50: Transducer x→y x t y t t x t a t
Page 51 and 52: Transducer x→y x t t a t x t a t
Page 53 and 54: Transducer x→y x t Output t a t y
Page 55 and 56: Transducer x→y x Output t a t y t
Page 57 and 58: Transducer x→y a x t Output y t x
Page 59 and 60: Transducer x→y
Page 61 and 62: Tools and Techniques A software pip
Page 63 and 64: Molecular Compilation Programs “H
Page 65 and 66: A Language for DNA Structures Desc
Page 67 and 68: Reaction Graph and Export
Page 69 and 70: State Space Analysis
Page 71 and 72: Verification Quantitative theories
Page 73 and 74: Execution A software/wetware pipeli
Page 75 and 76: From Structures to Sequences www.nu
Page 77 and 78: From Sequences to Molecules Copy&P
Page 79 and 80: Add Water
Page 81 and 82: Output
Page 83 and 84: Delivery!
Page 85 and 86: Approximate Majority Algorithm Giv
Page 87 and 88: DNA Implementation, at U.W. Progra
Page 89 and 90: A Brief History of DNA Turing Machi
Page 91 and 92:
Questions?
Page 93:
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Molecular Programming - Luca Cardelli

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