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DNA Computing

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

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  1. DNA Computing Herman G. Meyer III Sept. 28, 2004

  2. Overview • DNA • DNA/CPU Comparison • Leonard M. Adleman • Proof of Concept Experiment

  3. 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

  4. DNA/CPU Comparison • CPU • Sequential Operations • addition, bit-shifting, logical operations (AND, OR, NOT, NOR) • DNA • Parallel Operations • Cut, Copy, Paste, Repair

  5. Leonard M. Adleman • Background in Mathematics & Computer Science • HIV Research • DNA/Turing Machine similar • Proof of Concept

  6. 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

  7. Programming the DNA • Cities • Flights

  8. 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

  9. Ligases • Bind molecules together • Concatenates DNA strands

  10. Polymerase • Copies DNA • Primers (Start, Complement of End) • PCR

  11. Gel Electrophoresis • Sort molecules by length • Molecules have a charge • Magnets used

  12. Checking Cities • Attach city complement to iron ball • Suspend ball in solution • Watson-Crick pairing attraction • Wrong answers poured out • Repeat for each city

  13. Did it work? • DNA remaining in test tube encoded the valid Hamiltonian Path

  14. 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

  15. 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

  16. Summary • DNA can be used for simple calculations • DNA is a compact form of data storage • DNA is exponentially parallel • DNA is redundant

  17. 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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