Molecular Programming - Luca Cardelli

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Action Plan Building a full software/hardware pipeline for a new fundamental technology Mathematical Foundations Programming Languages Analytical Methods and Tools Device Architecture and Manufacturing [~ concurrency theory in the 80’s] [~ software engineering in the 70’s] [~ formal methods in the 90’s] [~ electronics in the 60’s] To realize the potential of Molecular Programming “With no alien technology” [David Soloveichik] This is largely a ‘software problem’ even when working on device design
Our Assembly Language: Chemistry A Lingua Franca between Biology, Dynamical Systems, and Concurrent Languages Chemical Reaction Networks A + B r C + D (the program) Ordinary Differential Equations d[A]/dt = -r[A][B] … (the behavior) Rich analytical techniques based on Calculus But prone to combinatorial explosion E.g., due to the peculiarities of protein interactions
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: Molecular Languages ... that we can
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 and 40: Bad Match t x z y Cannot proceed He
Page 41 and 42: Plasmidic Gate Technology Syntheti
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:
©2013 Microsoft Corporation. All r
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Molecular Programming - Luca Cardelli

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