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

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Presentation transcript:

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 Redundant

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

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

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

Programming the DNA Cities Flights

Recipe In a test tube add Answer generated in about one second 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

Ligases Bind molecules together Concatenates DNA strands

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

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

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

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

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

Thoughts Could a DNA Computer get sick? Is it biodegradable? 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

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

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