1. Notes for temperature 1 self- assembly Days 15, 16, 17 and 18 of Comp Sci 480

2. What is temperature 1 self-assembly? We have already seen examples of temperature 1 self-assembly –Sometimes called “non-cooperative self- assembly” Same aTAM rules apply –Never mind the temperature (it’s always 1) –If tiles abut with matching glue labels (and positive strength), then they bind

3. Why study temperature 1? Theoretically: not much is known about “the power” of temperature 1 self- assembly –What kind of things can be uniquely assembled at temperature 1? –What are the tile complexities? Temperature 1 is easily implemented in the lab (so I’ve been told…) –Can assemble things with low error rates

4. Self-assembly of NxN squares at temperature 1

5. Full squares (review) This is an NxN square… If |T| < N 2, then there must be two locations (A and B) that get the same tile type… Full-connectivity assumption gives us this connected path of tiles, i.e., we can get from A to B… Then we can “pump” the segment from A to B infinitely many times, which contradicts the “unique assembly” assumption 123 Assumptions: –Every tile binds with all of its neighbors (full-connectivity) –Tile set must uniquely produce an assembly In this situation, N 2 unique tile types are sufficient and necessary… –Proven by Rothemund and Winfree in 2000 –Proof idea (three easy steps)…

6. No glue mismatches Assume that your tile set cannot have glue mismatches in the growing (uniquely produced) assembly What is a glue mismatch? –Example… –Strengths OR labels do not match –Locally deterministic tile sets can have mismatches –Tile sets with glue mismatches may still uniquely produce an assembly In this situation, 2N – 1 unique tile types are necessary to build an NxN square –Proven by Manuch, et. al., in 2010 –Not as “easy” to prove as you might think –Possible project idea: review/present this proof in class S 1 A A B B C 1 2 C D X 2 D X

7. In general No assumptions about connectivity or glue mismatches –Just assume the final assembly is uniquely produced 2N – 1 tile types are sufficient –Proven by Rothemund and Winfree in 2000 –“Comb” construction… Conjecture : –2N – 1 tile types are necessary –No “real” progress on this problem since 2010 –Previous arguments about glue mismatches and full-connectivity do not apply –Very important open problem One example of difficulty of “lower bound” proofs in self- assembly 2134AB C AB C AB C AB C

8. Infinite assemblies…

9. Infinite assemblies at temperature 1 What kinds of infinite shapes can we build at temperature 1? Let’s see…

10. A line – boring! S11111S111111111111111

11. A slanted “comb” S Still not very interesting!

12. Other examples? Can you think of an example of a temperature 1 tile set that uniquely produces an “interesting” infinite assembly –I.e., one that doesn’t just repeat stuff over and over I can’t think of any…

13. An observation It *seems* like infinite assemblies that are uniquely produced at temperature 1 are “simple” –Can’t prove this –“Simple” ≈ infinitely repeating, periodic segments of tiles Why? Infinite assemblies contain long paths of tiles Long paths of tiles must contain repetitions (consequence of Pigeonhole Principle) –I.e., sub-paths of tiles that begin and end with the same tile type are (can be) “pumped” indefinitely Formalize this notion of “simplicity”…

14. Pumpability definition We say that a temperature 1 tile set T, that uniquely produces an infinite assembly A, is “pumpable” if… …there exists a constant c, such that, for every path π of connected tiles in A of length at least c, there is a sub-path of π that begins and ends with the same tile type that can be repeated indefinitely Note: The infinitely repeated sub-path is a sub- assembly of A Note: The constant c depends on the tile set! –That is, it can/should be different for each tile set

15. Pumpability example S A S A S Suppose c = 8 (for the sake of example) S Assume the tile set that produces this assembly is pumpable… The above is a finite portion of an infinite, uniquely produced assembly

16. Warm-up examples Prove/disprove: every pumpable tile set is locally deterministic Prove/disprove: every locally deterministic tile set is pumpable

17. A line S11111S111111111111111 Is this tile set pumpable? YES What is the pumpability constant c? c=3 c=2 ??? YES

18. A slanted “comb” S Is this tile set pumpable? YES What is the pumpability constant c? c=9 c=8 ??? NO

19. Repeated sub-paths Important: NOT every sub-path along a VERY long path that begins and ends with the same tile type can be pumped… Look at the sub-paths that start at the seed and end at a B tile –Examples of arbitrarily long paths, with sub-paths that begin/end with the same tile type, but those sub-paths cannot be pumped because they get blocked by earlier portions of the path SBBBB

20. Pumpability conjecture Conjecture: every temperature 1 tile system that uniquely produces an infinite assembly is pumpable –Formalized/conjectured by Doty, et. al., in 2009 Currently still open… –An offensive problem! –Most researchers believe it’s true –Has been called the “most important problem in theoretical tile self-assembly”

21. Consequences of pumpability Consider any temperature 1 tile set Suppose some tile types are “black” and others “non-black” The set of points that receive “black” tiles in T is (sort of) a regular language –I.e., only very simple, easy to analyze sets of points can be uniquely assembled at temperature 1 Consequence: arbitrary Turing machines cannot be simulated at temperature 1 in any tile set that uniquely produces an assembly –NO fractal patterns either!

22. What now? Temperature 1 probably can’t be used to uniquely produce “interesting” shapes and patterns –Or uniquely self-assemble finite shapes efficiently Should we just give up and go home?

23. No!

24. (Just barely) 3D self-assembly What about 3D temperature 1 self-assembly? For 3D temperature 1 self-assembly, we allow two 2D planes (z = 0 and z = 1) –This is all we need in order to do interesting stuff! Same aTAM rules apply, except instead of 2D unit squares, we have 3D (unit) cubes… –i.e., 1x1x1 cubes with labels and strengths on all 6 sides

25. 3D self-assembly example Glue labels are implicitly defined (otherwise, too many details) Very important: we construct our 3D tile set so that when a tile binds, it does so deterministically (no other tile can bind in that location on that side)

26. Squares It is possible to uniquely produce an NxN square at temperature 1 in 3D with tile complexity of O(log N) –Proven by Cook, et. al. in 2011 Full construction has too many details for us to cover in class Instead, we will study an “easier” problem, which is central to uniquely building NxN squares in 3D at temperature 1… …Self-assemble a binary counter at temperature 1, i.e., uniquely produce a Nxk rectangle using O(k) unique tile types

27. 3D counter Goal: uniquely produce a Nxk (k columns, N rows) rectangle using O(k) unique tile types –Some tiles (cubes) will be placed in the z=1 plane of the Nxk rectangle We will implement a kind of zig-zag counter Strategy: build a 3D tile temperature 1 tile set that “simulates” the behavior of the 2D temperature 2 zig-zag counter tile set Key properties: –3D simulation will have a scale factor “blow up” You’ll see what I mean… –Use non-determinism to guess bit values encoded using geometry, NOT glue labels (very clever technique in self- assembly)

28. The seed row S0101010100 ! 12121212 Bits are encoded in the geometry of the path “Bumps” in the z = 1 plane encode 1 “Bumps” in the z = 0 plane encode 0 Every bit knows its own position in the counter (underlined digit)… …very important!

29. Increment right to left S0101010100 ! 111 1 11N N 12121212001010101001010101 00 0 001010101N N 11 1 1 12121212 $ The green tiles “guess” what the next bit is (always guesses correctly thanks to geometry of previous portion of path) Increment rows encode bit values in bumps shifted one tile to the left… … very important! The next (copy) row will shift them back one tile to the right.

30. 1 Copy left to right S ! 111 1 11N N 12121212001010101001010101 00 0 001010101N N1 11 1 1 12121212 $ 1 1111 1 111 1212121201010101 00 0 0 0 01010101111 1 11 10101010 ! Current value of counter (101) encoded in bump pattern along top row of assembly… (the value of the previous encoded value – plus one!)

31. The macro blocks… (these will implicitly define the tile set)

32. The seed row (even start value) 0 0 0 b1b1 b11b11 10 b k-1 b k-1 k-1 k-1 For each i = 0, 1, …, k-1, if b i is 0, create the following macro block: S0i0i0i0i ! For each i = 0, 1, …, k-1, if b i is 1, create the following macro block: 1i1i1i1i Simulated tile types: The seed initiates the macro block for bit k-1 The macro block for i initiates the macro block for i-1 A special tile type binds to macro block for bit 0 to start the counter NOTE: For odd start values, change the north glue on the bit k-1 tile type to strength 2 and the north glue on the bit 0 tile type to strength 1.

33. 00 ! Increment bit 0 111 1 11N N 10101010 1 1010 n 0 00 ! 0 0 00C C 10101010 0 0 c 1010 00 00 00

34. Increment bit k-1, no carry 1 1k-1 n 11 1 1 $ 0 0k-1 n 00 0 0$ 0 0NN

35. C Increment bit k-1, yes carry 0 1k-1 c STOP 1k-1 stop 0 0k-1 c 1k-1 11 1 1$ 0k-1 1k-1 C

36. 11 Increment bits i=1,…,k-2, no carry 00 0 00i0i0i0iN 0N 0 0i0i n 0i0i n 1 1i1i n 1i1i n 0i0i0i0i 11 1 1N N 1i1i1i1i 1 1i1i1i1i NN

37. 11 Increment bits i=1,…,k-2, yes carry 11 1 1N N 1 0i0i c 1i1i n 0 1i1i c 0i0i c 00 0 0C C 1i1i1i1i 0 1i1i1i1i 00 0i0i0i0i CC 0i0i0i0i

38. Copy bit k-1 1 1k-1 0 0k-1 1 1k-1 $ 1 1111 1 111 $0000 0 000 0 0k-1

39. Copy bit 0 0 0 0 1 1010 1010 1 11 10101010 111 1 11 10101010 !0 0000 0 00 !0 00 00 00 0 00

40. Copy bits i=1,…,k-2 0 0i0i 0i0i 00101010100 0 0 0 0i0i0i0i 0i0i0i0i 1 1i1i 1i1i 011 1 1 1i1i1i1i 1 1i1i1i1i

41. Correctness The 3D temperature 1 counter self-assembles exactly like the 2D temperature 2 zig-zag counter –Technically: The 2D temperature 2 zig-zag counter has a unique assembly sequence –How many assembly sequences does the 3D temperature 1 binary counter have? Many! Since each macro block is something like 4x5 or 4x4 tiles, we actually assemble a rectangle with dimensions O(N) x O(k), where the hidden constant is ≤ 5 in each case –Scale factor blow-up (a.k.a., “resolution loss”) –Can still be used to build an NxN square exactly Just more details to consider!

42. Tile complexity Each macro block is a path of tiles of constant length (i.e., there exists a constant c such that no macro block path is greater than c) There are nine groups of macro blocks Each group has O(k) macro blocks (at most two macro blocks per bit position) Overall tile complexity of 3D counter: O(k)

43. Better tile complexity? Currently: O(log N) –Can we achieve O(log N / log log N)? Can we implement the optimal encoding scheme in 3D at temperature 1? Just have to make the optimal encoding scheme zig-zag –Seems feasible Not obvious how to implement optimal encoding scheme in 3D at temperature 1 Open problem

44. 3D Turing machine simulation Can simulate a Turing machine at temperature 1 in 3D (with just two planes)… Simulate a “zig-zag” 2D temperature 2 Turing machine simulation tile set More complicated than the previous construction for NxN squares

45. In general Can simulate any 2D temperature 2 “zig-zag” tile set at temperature 1 in 3D –Proven by Cook, et. al., in 2011 –Includes efficient self-assembly of NxN squares, Turing machine simulations, etc. 2D temperature 2  3D temperature 1 results in a O(1) scale factor blow-up –Tile complexity: O(|T|*log |G|), where T is the 2D temperature 2 tile set and G is the set of all strength 1 glue labels in T Special case for NxN squares: O(|T|) –3D temperature 1 can do anything that 2D “zig-zag” temperature 2 can do

46. Something completely different…

47. Temperature 1 self-assembly with a single negative glue What if every glue strength was restricted to be either be strength 0 or 1 and there could be a single glue of strength -1? –The temperature is 1 –“Restricted glue Tile Assembly Model” (rgTAM) –Slight generalization of temperature 1 self- assembly What is the “expressiveness” of this model?

48. Restricted glue self-assembly Same rules as temperature 1, but exactly one glue is allowed – but not required – to be negative –If no negative glue on any tiles, then pretty much the same as temperature 1 Not formally proven Key: A tile that has the negative glue on any side must bind on at least two sides –This is reminiscent of temperature 2 (cooperative-binding) self-assembly…

49. Restricted glue model example SSSS The red square is the unique negative glue allowed by the model… It is present on two of the tile types in this example

50. Some tile complexities How efficiently can we assemble NxN squares in the restricted glue model? Choose NOT to use the unique negative glue: “comb” construction: 2N-1 Choose to USE the negative glue: O(log N)

51. Efficient binary counter As with the 3D square construction, we will study an easier problem: Count in binary efficiently That is, assemble an Nxk rectangle using O(k) unique tile types

52. Simulate a zig-zag counter Just like the 3D temperature 1 binary counter, our restricted glue binary counter will simulate the 2D temperature 2 zig-zag binary counter with macro blocks Key differences: –Our simulation will be 2D –It will have a unique assembly sequence (unlike the 3D counter) Our restricted glue binary counter will have a scale factor blow-up –Final (uniquely produced) assembly will have dimensions O(N) x O(k)

53. The macro blocks Don’t define each macro block Just look at some examples of how the counter assembles

54. The seed row S 12120101 1212 0101 0 0 In general… 1i1i 1i1i The negative glue on a “bump” encodes a 1 0i0i 0i0i The negative glue on a “dent” encodes a 0

55. Increment right to left S 12120101 1212 0101 0 0!C01111010N0101NNN0101N1212NN121210100101N1212 010100101 102021212 These tiles essentially “guess” the correct bit value from the previous seed/copy row – depending on location of the negative glue (is it on the bump or the dent?)… 1010 Carry/no carry signal propagated east to west Bit values are determined using the geometry of the path and the placement of the negative glue

56. Copy left to right 1212121201011010!101012120202 101011010 0 Start the next increment row! $tart the copy row… 1N01011010N 1212 01011010 S 12120101 1212 0101 0 0C0N0101N1212!111010NNNN12120101$1212

57. Simulated tile set The seed row (k tile types  k macro blocks) Increment –Bit 0 (2 tile types  2 macro blocks) –Bit k-1 (2 tile types  2 macro blocks) –Bits 1,…,k-1 (4k tile types  4k macro blocks) Copy –Bit 0 (2 tile types  2 macro blocks) –Bit k-1 (2 tile types  2 macro blocks) –Bits 1,…,k-1 (2k tile types  2k macro blocks) Each macro block has O(1) unique tile types Tile complexity: O(k)

58. What else? Can we build a restricted glue binary counter that uniquely assembles an Nxk rectangle using O(k / log k) unique tile types? –Can the optimal encoding scheme be made to work in the restricted glue model? –Hmmm… It is possible to simulate an arbitrary Turing machine in the restricted glue model –Or simulate any 2D temperature 2 “zig-zag” system What is the tile complexity? Just like in 3D! Open question: Is the restricted glue model “equivalent” to the 3D temperature 1 model? –That is, can you do anything in the restricted glue model that you can do in 3D temperature 1… and can you do everything in the 3D temperature 1 model that you can do in the restricted glue model? –Hmmm…

59. Temperature 1 summary Tile complexities of uniquely producing 2D NxN squares at temperature 1: –Full-connectivity: N 2 –No glue mismatches: 2N – 1 –In general: ≤ 2N – 1 Proving ≥ 2N – 1 is still open 3D self-assembly of NxN squares: –All you need is two 2D planes (z=0 and z=1) –Tile complexity is O(log N) Is O(log N / log log N) possible? Drawback: not fully connected (not even close!) Can simulate Turing machines at temperature 1 in 3D –Use two 2D planes –Turing machine simulation must “zig-zag” Can efficiently assemble NxN squares and simulate Turing machines in the restricted glue model –Is 3D temperature 1 self-assembly equivalent to the restricted glue assembly model?