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 DNA 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 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

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? 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

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.
Scientific American - August pp 54-61
Science - Vol Nov. 11, pp