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DNA Computing. Herman G. Meyer III Sept. 28, 2004. Overview. DNA DNA/CPU Comparison Leonard M. Adleman Proof of Concept Experiment. DNA. Adenine, Thymine, Guanine, & Cytosine (A,T,C,G) Polymerase Watson-Crick Pairing (A-T,C-G) Cheap Compact Data Storage 1 cm^3 DNA = 10^12 CDs

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Dna computing l.jpg

DNA Computing

Herman G. Meyer III

Sept. 28, 2004


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Overview

  • DNA

  • DNA/CPU Comparison

  • Leonard M. Adleman

  • Proof of Concept Experiment


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DNA

  • Adenine, Thymine, Guanine, & Cytosine (A,T,C,G)

  • Polymerase

  • Watson-Crick Pairing (A-T,C-G)

  • Cheap

  • Compact Data Storage

    • 1 cm^3 DNA = 10^12 CDs

  • Redundant


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DNA/CPU Comparison

  • CPU

    • Sequential Operations

    • addition, bit-shifting, logical operations (AND, OR, NOT, NOR)

  • DNA

    • Parallel Operations

    • Cut, Copy, Paste, Repair


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Leonard M. Adleman

  • Background in Mathematics & Computer Science

  • HIV Research

  • DNA/Turing Machine similar

  • Proof of Concept


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Proof of Concept Experiment

  • Directed Hamiltonian Path

  • Pseudo code

    • Generate random paths

    • For each path

      • Check Start/End points

      • Check Length

      • Check that all vertices exist

    • If any path passes all tests, HP exists


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Programming the DNA

  • Cities

  • Flights


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Recipe

  • In a test tube add

    • 10^14 molecules of each city

    • 10^14 molecules of each flight

    • Water, ligase, salt

  • Answer generated in about one second

  • 100 trillion molecules representing wrong answers also generated


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Ligases

  • Bind molecules together

  • Concatenates DNA strands


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Polymerase

  • Copies DNA

  • Primers (Start, Complement of End)

  • PCR


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Gel Electrophoresis

  • Sort molecules by length

  • Molecules have a charge

  • Magnets used


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Checking Cities

  • Attach city complement to iron ball

  • Suspend ball in solution

  • Watson-Crick pairing attraction

  • Wrong answers poured out

  • Repeat for each city


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Did it work?

  • DNA remaining in test tube encoded the valid Hamiltonian Path


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Drawbacks

  • The process required much human intervention

  • Automation would be required for a “real” computer

  • Same method on 200 cities would require more than DNA than the mass of Earth


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Thoughts

  • Could a DNA Computer get sick?

    • Virus

    • Cancer

  • Is it biodegradable?

  • Could a virus spread from computer to humans?

  • If so, could virus writers spread more deadly viruses?

  • New level of bioterrorism


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Summary

  • DNA can be used for simple calculations

  • DNA is a compact form of data storage

  • DNA is exponentially parallel

  • DNA is redundant


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References

  • Ars Technica. http://arstechnica.com/reviews/2q00/dna/dna-5.html

  • Scientific American - August 1998. pp 54-61

  • Science - Vol. 266. Nov. 11, 1994. pp 1021-1024


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