1. 1 Proceedings of the 24 th Annual ACM-SIAM Symposium on Discrete Algorithms January, 2013 Fuel Efficient Computation in Passive Self-Assembly Robert SchwellerUniversity of Texas Pan-American Michael ShermanUniversity of Texas Pan-American

2. 2 Tile Assembly Model (Rothemund, Winfree, Adleman) T = G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50% Tile Set: Glue Function: x ed cba

3. 3 T = d e x ed cba Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

4. 4 T = d e x ed cba Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

5. 5 T = d e x ed cba bc Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

6. 6 T = d e x ed cba bc Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

7. 7 T = d e x ed cba bc Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

8. 8 T = d e x ed cba bca Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

9. 9 T = d e x ed cba bca Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

10. 10 T = d e x ed cba bca Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

11. 11 T = d e x ed cba bca Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

12. 12 T = x ed cba abc d e Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

13. 13 T = x ed cba x abc d e Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

14. 14 T = abc d e x x ed cba Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

15. 15 T = x ed cba abc d e xx Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

16. 16 T = x ed cba abc d e xx x Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

17. 17 T = x ed cba abc d e xx xx Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50%

18. 18 T = x ed cba abc d e xx xx Tile Assembly Model (Rothemund, Winfree, Adleman) G(y) = 100% G(g) = 100% G(r) = 100% G(b) = 100% G(p) = 50% G(w) = 50% What is this model capable above? -efficient assembly of shapes/patterns -shape and pattern replication - computation

19. BEAKER 11010110_ State: q 3 State: q 2 State: q 3 Goal: Scalable, universal molecular computation -More than just a (really cool) computer -Algorithmic manipulation of matter at the nanoscale

20. Simulation of Cellular Automata Slide stolen from: Andrew Winslow [Rothemund, Papadakis, Winfree, 2004]

21. 110 Turing Machine simulation in the TAM 10110_ State: q 0 State: q 3 State: q 2 State: q 7 State: q 2 State: q 3 Slide stolen from: Matt Patitz 10110 00110-01110--01110--- [Rothemund, Winfree, 2000]

22. Limited Scalability Space in-efficient -Entire history of computation stored in assembly Fuel Guzzling - Each computation step burns many tiles Goal: Fuel efficient, space efficient universal computation 11010110_ State: q 3 State: q 2 State: q 3 10110 00110-01110--01110--- Turing Machine simulation in the TAM [Rothemund, Winfree, 2000]

23. Goal: Fuel efficient, space efficient universal computation Problem: Assemblies only grow larger Solution: Negative strength glues Negative Glues Our Result: Tile assembly is capable of space efficient, fuel efficient universal computaion with the use of negative and positive strength glues.

24. Negative Glues - Example 200 % 100 % Negative glues previously considered in: [Reif, Sahu, Yin 2005] [Doty, Kari, Masson 2010] [Patitz, Schweller, Summers, 2011]

25. Negative Glues - Example 200 % 100 % -50% 100% -50% 100% -Negative glues can prevent attachments. -Can they do anything deeper?

26. Negative Glues - Example 200 % 100 % -100% 200% -100% 200% Increase strength

27. Negative Glues - Example 200 % 100 % -100% 200% Key Idea: -Stable assemblies can combine to form unstable assemblies -Allows “diss-assembly”

28. High Level Sketch of Universal Computation 1 01 0 0

29. 1 01 0 0

30. 1 01 0

31. 1 01 0

32. 1 01 0 1

33. 1 01 0 1

34. Bit Flipping -30% 1 75% 25% 0 -30% 90 30 70

35. Bit Flipping -30% 1 25% 0 -30% 90 30 70 25 75

36. Bit Flipping 1 25% 0 -30% 90 30 70 25 -30% 40% 90% 75

37. Bit Flipping 1 25% 0 7090 30 -30% 2590 4075

38. Bit Flipping 10 90 4070 25 75

39. 30% Bit Flipping 1 15% 70%90% 75 90 40

40. Bit Flipping 1 70% 30% 75 90 4090 15

41. Bit Flipping 1 90 30 70 10% 90% -60% 75 90 40 15

42. Bit Flipping 1 90 30 70 90% -60% 90 10 90% 75 90 40 15

43. Bit Flipping 1 90 30 70 15 75 15 40 10 -60 90 10 90 -60 90 40 15 75

44. Oscillator 01 Expended fueld

45. Oscillator 0110 Expended fueld

46. Graph Walking 01 10 01 Simple Example of Graph Walking : More General Result: Theorem: For any directed graph G=(V,E), there exists a size O(V+E) tile set that walks graph G in a fuel- efficient manner.

47. Extension: Double Bit Flipping 1001

48. Turing Machine Simulation 0 1 01 0 Current bit: 0 State: GREEN  Flip bit to 1, move right, change to state PURPLE 10 Current bit: 0 State: PURPLE  Flip bit to 1, move left, change to state ORANGE 11 Current bit: 1 State: ORANGE  Flip bit to 0, move left, change to state GREEN 00 O(1) garbage produced per computation step

49. Tape Extension Gadget 1100 0 Also: need an infinite tape

50. Universal Tile Self-Assembly O(Tape*Steps)O(Tape) O(Tape)O(1) SpaceFuel Old Way Negative Glues 01010101100 [Rothemund, Winfree, 2000]

51. Why is Passive, Fuel Efficient Computation Important? Passive Self-Assembly – Most active models have no current implementation at the nanoscale – Informs when more active components are truly necessary – May lead to connection to active self-assembly: Implement an active model within a passive model Fuel Efficiency – Particle starvation a practical problem in experimentation – Necessary for a scalable molecular computer Negative Glues – Informs experimentalists that negative glues implementation should be fruitful – Sheds light on natural computation and phenomena Charged particles, magnets Protein folding ATP Synthases

52. Open Problems Compact Graph Walking – Many graphs can likely be fuel efficiently walked by sub linear sized tile systems. O(log |V|) tiles? Negative Glues: Necessary? – Amortized fuel-efficiency? Two-tape Turing machine simulation Simulation of active models – Signal tiles? Fuel Rods? – No depletion of monomers