Members

1. Members • Andy Koswara • Albert Hartono • Budi Suryawijaya • Evin Hill • Hariyono Lie • Michael Ngantung

2. DNA COMPUTING • Structure of DNA (Albert) • Operations of DNA Molecules (Albert) • DNA to Electrical Device (Budi) • Traveling Salesman Problem (Michael) • Hamilton Path (Michael) • Hamilton Path Solution Using DNA (Hariyono) • DNA Architecture and Misc. (Evin) • Conclusion and The future of DNA Computing (Andy)

3. The Structure of DNA • DNA (Deoxyribo Nucleic Acid) consists three components: a sugar, a phosphate group, and a nitrogenous / base group . • Sugar has 5 carbon atoms. • Phosphate group is attached to the fifth carbon. • Base group is attached to the first carbon. • There is a hydroxyl group (OH) attached to the third carbon.

4. Chemical structure of a nucleotide with thymine base.

5. Four kinds of base groups: 1. Adenine (A) 2. Thymine (T) 3. Guanine (G) 4. Cytosine (C) Nucleotides can link together in two ways: 1. Phosphodiester bond 2. Hydrogen bond Phosphodiester bond is much stronger than hydrogen bond.

6. Operations on DNA Separating and fusing 1. Denaturation: heating until 85° C up to 95° C. 2. Renaturation: slowly cooling down.

7. Lengthening By using polymerases enzymes, we are able to add nucleotides to an existing DNA molecule.

8. A DNA primer sequence is bonded by a single stranded template.

9. Polymerases enzymes in action

10. Shortening and Cutting Nucleases enzymes is an enzyme that degrades DNA. Two kinds of nucleases enzymes: 1. Exonucleases (for shortening) 2. Endonucleases (for cutting)

11. Exonucleases III in action

12. Exonucleases Bal31 in action

13. Endonuclease in action

14. Endonuclease Eco RI in action

15. Endonuclease XmaI in actio

16. Linking Ligases enzymes is used for DNA linking. The process of DNA linking is called ligation.

17. Hydrogen bonding

18. Ligation

19. Blunt ligation

20. Modifying • Modifying enzymes is enzymes that modify DNA molecule by adding and deleting certain chemical components for various control of operations on DNA. • Example: • 1. Alkaline phosphatase • 2. Polynucleotide kinase

21. Alkaline phosphatase and Polynucleotide kinase

22. Multiplying Multiplying / amplifying DNA molecule uses PCR (Polymerase Chain Reaction) technique. Consists three basic steps: 1. Denaturation / separating 2. Priming 3. Extension

23. A double-stranded DNA

24. Denaturation

25. Priming

26. Extension

27. Reference: Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa: DNA Computing. New Computing Paradigms. Springer, New York : c1998.

28. DNA molecule to electrical device. A basic approach to build a DNA processor.

29. Assumptions. • Chemical bonds(in DNA) can act as tunnel junctions in the coulomb blockade regime, could emit electricity, given a proper coating. • Has the ability to coat a DNA strand with metal in nanometer scale.

30. Example: From DNA to SET transistor. • SET -> Single Electron Tunneling transistor. • In the nanometer scale, and would be able to operate at room temperature. • Function: used as an electrometer to measure the size and predicted the edge strips of 2DES(2 dimensional electron system) • Inspired by a paper from E.Ben Jacob, Z.Hermon and S.Caspi from Tel Aviv University.

31. The operation begins(1) • What a normal SET transistor would look like

32. The Operation(II) • Schematic image with 2 grains in DNA connected by P-bond. Dark circle->carbon atoms, white circles->oxygen atoms.

33. The operation(II cont) The Battle plan • P-bond -> tunneling junction. • H-bonds -> capacitor. • The grain itself -> inductive properties.

34. The operation(II) The justification(I) • P bond: Has 2  bonds, 1  bond. • The  electron can be shared with 2 oxygen, resembles an electron in well, put it on the lowest level. • When electron enters, it meet the barrier set by energy gap. • But the gap is narrow and small so the electron can walk trough.

35. The Battle plan(II)The justification(II) • H-bonds: Can be the capacitor. • The proton in the h-bond can screen a net charge density on either side, by movement. • Thus the net charge could be in the side of the h-bond. • The grains: Can be the inductive properties. • Due to the hopping of additional electrons. • But can be ignored (L & Lo is small, consistent to the usual SET)

36. The Battle Plan(III)The finishing touch. • Consist of 2 strands (1 main, 1 gate) • Connect the end base of the gate strand with a complimentary strand. • Both strands should be metal-coated, except (a) the grain in the main strand, which connect to the gate strand, the 2 adjacent P-bonds, (b) the connective h-bond. • Connect the main strand with voltage source (V)

37. The finishing touch (cont) • The end of the gate strand with another voltage source (Vg) that acts as gate source.

38. Some tricky stuff • Before coating, the DNA molecule should be in a solution contain enzyme that can only stick with the uncoated part. • After coating, the enzyme is released, and the coating will stick. • The coated end should be able to be connected with a voltage source.

39. Reviewing the assumption • Is it possible that DNA /other organic molecule could carry electricity ?

40. Reviewing the assumption(II) • Does present technology have the means to coat a strand of DNA? • Currently, the center for nano technology and Mitsubishi electric receive $ 4.2 million to develop lithography tools below 35 nano meters.

41. Traveling Salesman Problem

42. Problems • There is a certain traveling salesman that wants to minimize the time and money spent traveling around. • In order to do that he must minimize the distance he travels between the cities. • This is an easy for a computer to solve if there are only about 10 cities involved but when there are 20 cities it becomes completely impossible.

43. Calculation • The following calculations shows that it is impossible to calculate the traveling salesman problem for as many as 20 cities. • In this calculation, we will assume that the computer makes 10 calculations per route and that the computer performs 100 million calculations per second.

44. Calculation (Continued) • 10 cities = 10! Paths = 3628800 paths • (10 calculations / paths)(3628800 paths) / (100 million calculations / second) = .362 seconds to perform the calculation • 20 cities = 20! Paths = 2.43 x 10 ^ 18 paths • (10 calculations/paths)(2.43 x 10 ^ 18 paths) / (100 million calculations / second) = 2.433 x 10 ^ 11 seconds to perform the calculation.

45. Calculation (Continued) • As we can see from the calculation, it takes about 7,614 years for the computer to calculate the answer. • Since this Traveling Salesman issue is problematic, then we approximate the problem with Hamiltonian Path.

46. Hamilton Path • Hamilton Approximation • Hamiltonian Path Problem • Hamilton Algorithm • Combinatorial Explosion

47. Hamiltonian Approximation • Hamilton made some important observations back in the 19th century that can help us today with viewing the traveling salesman problem a little more practically • Instead of optimizing or making the shortest trip between all of the cities, our salesman only wants to visit all of the cities once • Each of these cities is considered a vertex on a graph. Now the problem is to pass through all of the vertices once without breaking the path and without passing through anyone twice

48. Hamiltonian Path Problem • Given a network of nodes and directed connections between them, is there a path through the network that begins with the start node and concludes with the end node visiting each node only once (“Hamiltonian path")? • “Does a Hamiltonian path exist, or not?”

49. Hamiltonian Path Problem (Cont.) End city Hamiltonian path does exist! Detroit Chicago Boston Start city Atlanta

50. Hamiltonian Path Problem (Cont.) Start city Hamiltonian path does not exist! Detroit Chicago Boston End city Atlanta