january 18, 2010

109
1 January 18, 2010 Shape Replication through Self- Assembly and Rnase Enzymes Zachary Abel Harvard University Nadia Benbernou Massachusetts Institute of Technology Mirela Damian Villanova University Erik D. Demaine Massachusetts Institute of Technology Martin Demaine Massachusetts Institute of Technology Robin Flatland Siena College Skott D. KominersHarvard University Robert Schweller University of Texas Pan American Read: Replicate:

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Shape Replication through Self-Assembly and Rnase Enzymes . January 18, 2010. Read:. Replicate:. Zachary Abel Harvard University Nadia Benbernou Massachusetts Institute of Technology Mirela Damian Villanova University Erik D. Demaine Massachusetts Institute of Technology - PowerPoint PPT Presentation

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Page 1: January 18, 2010

1

January 18, 2010

Shape Replication through Self-Assembly and Rnase Enzymes

Zachary Abel Harvard UniversityNadia Benbernou Massachusetts Institute of TechnologyMirela Damian Villanova UniversityErik D. Demaine Massachusetts Institute of TechnologyMartin Demaine Massachusetts Institute of TechnologyRobin Flatland Siena CollegeSkott D. Kominers Harvard UniversityRobert Schweller University of Texas Pan American

Read: Replicate:

Page 2: January 18, 2010

2

Outline

• Basic Model• RNA enzyme model• Shape replication

• Precise yield shape replication• Infinite yield shape replication

Page 3: January 18, 2010

3

Tile Assembly Model(Rothemund, Winfree, Adleman)

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2

Tile Set:

Glue Function:

Temperature:

x ed

cba

Page 4: January 18, 2010

4

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2

d

e

x ed

cba

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 5: January 18, 2010

5

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2d

e

x ed

cba

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 6: January 18, 2010

6

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2d

e

x ed

cba

b c

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 7: January 18, 2010

7

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2d

e

x ed

cba

b c

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 8: January 18, 2010

8

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2d

e

x ed

cba

b c

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 9: January 18, 2010

9

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2d

e

x ed

cba

b ca

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 10: January 18, 2010

10

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2d

e

x ed

cba

b ca

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 11: January 18, 2010

11

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2d

e

x ed

cba

b ca

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 12: January 18, 2010

12

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2d

e

x ed

cba

b ca

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 13: January 18, 2010

13

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2

x ed

cba

a b c

d

e

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 14: January 18, 2010

14

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2

x ed

cba

x

a b c

d

e

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 15: January 18, 2010

15

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2

a b c

d

e

x

x ed

cba

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 16: January 18, 2010

16

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2

x ed

cba

a b c

d

e

x x

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 17: January 18, 2010

17

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2

x ed

cba

a b c

d

e

x x

x

Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 18: January 18, 2010

18

T = G(y) = 2G(g) = 2G(r) = 2G(b) = 2G(p) = 1G(w) = 1

t = 2

x ed

cba

a b c

d

e

x x

x x

(Basic)Tile Assembly Model(Rothemund, Winfree, Adleman)

Page 19: January 18, 2010

19

Outline

• Basic Model• RNA enzyme model• Shape replication

• Precise yield shape replication• Infinite yield shape replication

Page 20: January 18, 2010

20

RNA enzyme Self-Assembly(suggested by Rothemund, Winfree 2000)

RNA tile types DNA tile types

RNA assembly model: • Assembly occurs over a number of stages.

• At each stage you may:1) Add a new collection of tile types

- Allow for further growth- All added types have infinite count

2) Add an Rnase enzyme- Dissolve all RNA tile types- May break apart assemblies

All tile types are of either DNA or RNA makeup:

Page 21: January 18, 2010

21

RNA enzyme Self-Assembly

Stage 1:

Page 22: January 18, 2010

22

RNA enzyme Self-Assembly

Stage 1:

Page 23: January 18, 2010

23

RNA enzyme Self-Assembly

Stage 1:

Stage 2:

Page 24: January 18, 2010

24

RNA enzyme Self-Assembly

Stage 1:

Stage 2:

Page 25: January 18, 2010

25

RNA enzyme Self-Assembly

Stage 1:

Stage 2:

Stage 3: Enzyme

Page 26: January 18, 2010

26

RNA enzyme Self-Assembly

Stage 1:

Stage 2:

Stage 3: Enzyme

Page 27: January 18, 2010

27

RNA enzyme Self-Assembly

Stage 1:

Stage 2:

Stage 3: Enzyme

Page 28: January 18, 2010

28

RNA enzyme Self-Assembly

Stage 1:

Stage 2:

Stage 3: Enzyme

Stage 4:

Page 29: January 18, 2010

29

RNA enzyme Self-Assembly

Stage 1:

Stage 2:

Stage 3: Enzyme

Stage 4:

Page 30: January 18, 2010

30

RNA enzyme Self-Assembly

Stage 1:

Stage 2:

Stage 3: Enzyme

Stage 4:

Page 31: January 18, 2010

31

RNA enzyme Self-Assembly

Stage 1:

Stage 2:

Stage 3: Enzyme

Stage 4:

Page 32: January 18, 2010

32

RNA enzyme Self-AssemblyMetrics for efficiency:

• Tile complexity: total number of distinct tile types used in the system.

• Stage complexity: total number of distinct stages used.

Stage 1:

Stage 2:

Stage 3: Enzyme

Stage 4:

Page 33: January 18, 2010

33

Outline

• Basic Model• RNA enzyme model• Shape replication

• Precise yield shape replication• Infinite yield shape replication

Page 34: January 18, 2010

Shape Replication Problem

Design an assembly system (algorithm) that will replicate a large number of copies given a single copy of a pre-assembled input shape.

Precise Yield: Replicate exactly n copies for a given n

Infinite Yield: Replicate infinite copies-in practice, the number of copies should only be limited by the volume of particles available.

Page 35: January 18, 2010

35

Outline

• Basic Model• RNA enzyme model• Shape replication

• Precise yield shape replication• Infinite yield shape replication

Page 36: January 18, 2010

Precise Yield: rectangles

Page 37: January 18, 2010

Precise Yield: rectangles

a a a aaaaaaa

a a a a

aaaaaa

Page 38: January 18, 2010

Precise Yield: rectangles

n n n neeeeee

wwwwww

s s ss

Page 39: January 18, 2010

Precise Yield: rectangles

n n n neeeeee

wwwwww

s s ss

n

w

x xyy

Page 40: January 18, 2010

Precise Yield: rectangles

n n n neeeeee

wwwwww

s s ss

nw

Page 41: January 18, 2010

Precise Yield: rectangles

n n n neeeeee

wwwwww

s s ss

nw n

e

sw s

e

Page 42: January 18, 2010

Precise Yield: rectangles

n n n neeeeee

wwwwww

s s ss

nw

ne

sw s

e

Page 43: January 18, 2010

Precise Yield: rectangles

n n n neeeeee

ww

w

w

ww

s s ss

a

wa

a

a

Page 44: January 18, 2010

Precise Yield: rectangles

n ne

e

w

wss

Step 1: Coat shape with layer of RNA

Page 45: January 18, 2010

Precise Yield: rectangles

n ne

e

w

wss

Step 2: Coat shape with layer of DNAStep 1: Coat shape with layer of RNA

Page 46: January 18, 2010

Precise Yield: rectanglesStep 2: Coat shape with layer of DNA.Step 3: Add enzyme.

Step 1: Coat shape with layer of RNA.

Page 47: January 18, 2010

Precise Yield: rectanglesStep 2: Coat shape with layer of DNA.Step 3: Add enzyme.

Step 1: Coat shape with layer of RNA.

Page 48: January 18, 2010

Precise Yield: rectanglesStep 2: Coat shape with layer of DNA.Step 3: Add enzyme.Step 4: Coat frame with layer of RNA.

Step 1: Coat shape with layer of RNA.

Page 49: January 18, 2010

Precise Yield: rectanglesStep 2: Coat shape with layer of DNA.Step 3: Add enzyme.Step 4: Coat frame with layer of RNA.

Step 1: Coat shape with layer of RNA.

Page 50: January 18, 2010

Precise Yield: rectanglesStep 2: Coat shape with layer of DNA.Step 3: Add enzyme.Step 4: Coat frame with layer of RNA.Step 5: Fill frame with DNA.

Step 1: Coat shape with layer of RNA.

Page 51: January 18, 2010

Precise Yield: rectanglesStep 2: Coat shape with layer of DNA.Step 3: Add enzyme.Step 4: Coat frame with layer of RNA.Step 5: Fill frame with DNA.

Step 1: Coat shape with layer of RNA.

Page 52: January 18, 2010

Precise Yield: rectanglesStep 2: Coat shape with layer of DNA.Step 3: Add enzyme.Step 4: Coat frame with layer of RNA.Step 5: Fill frame with DNA.Step 6: Add enzyme.

Step 1: Coat shape with layer of RNA.

Page 53: January 18, 2010

Precise Yield: rectanglesStep 2: Coat shape with layer of DNA.Step 3: Add enzyme.Step 4: Coat frame with layer of RNA.Step 5: Fill frame with DNA.Step 6: Add enzyme.

Step 1: Coat shape with layer of RNA.

Page 54: January 18, 2010

Precise Yield: General Shapes

Page 55: January 18, 2010

Precise Yield: General Shapes

Page 56: January 18, 2010

Precise Yield: General Shapes

Page 57: January 18, 2010

Precise Yield: rectangles

Page 58: January 18, 2010

Tile types O(1)

Stages O(log n)

Precise Yield:n copies

Precise Yield: rectangles

Tile types O(log n)

Stages O(1)

Precise Yield:n copies

Page 59: January 18, 2010

59

Outline

• Basic Model• RNA enzyme model• Shape replication

• Precise yield shape replication• Infinite yield shape replication

Page 60: January 18, 2010

Infinite Yield: Rectangles

n n n neeeeee

wwwwww

s s ss

Page 61: January 18, 2010

Infinite Yield: Rectangles

n n n neeeeee

wwwwww

s s ss

sw

a

Page 62: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

s sa

s

Stair step tiles:

xx

Page 63: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

s s

Stair step tiles:

xx

bx

Page 64: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

s s

Stair step tiles:

xx

a

b

Page 65: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

s

s

Stair step tiles:

xx

ab

Page 66: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

s

Stair step tiles:

xx

b

a

b

Page 67: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

s

Stair step tiles:

xx

b

a

b

Page 68: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

s

Stair step tiles:

xx

b

a

b

Page 69: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

Stair step tiles:

xx

b

bb

a

Page 70: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

Stair step tiles:

xx

Page 71: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

Stair step tiles:

xx

Page 72: January 18, 2010

Infinite Yield: Rectangles

as

bs

bs

a

b

Stair step tiles:

xx

Page 73: January 18, 2010

Infinite Yield: Rectangles

Tile types O(1)

Stages O(1)

Infinite Yield:Rectangles

Page 74: January 18, 2010

Infinite Yield: General Shapes

Page 75: January 18, 2010

Infinite Yield: General ShapesStep 1: Coat with RNA

Page 76: January 18, 2010

Infinite Yield: General ShapesStep 2: Create rectangular DNA encasing

Page 77: January 18, 2010

Infinite Yield: Binary counter tool

c c c cc c c c c c c c c c c c c c c cc c cc

Page 78: January 18, 2010

Infinite Yield: Binary counter tool

1 c c c cc c c c c c c c c c c c c c c cc c cm

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c01 mm

n

Page 79: January 18, 2010

1

Infinite Yield: Binary counter tool

1 c c c cc c c c c c c c c c c c c c cc c c0 0

m

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c01 mm

n

Page 80: January 18, 2010

1

Infinite Yield: Binary counter tool

1 c c c cc c c c c c c c c c c c c cc c c0

m

1 1n

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c01 mm

n

Page 81: January 18, 2010

1

Infinite Yield: Binary counter tool

1 c c c cc c c c c c c c c c c c c cc c c

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c

0

0

m

1 1

1 mmn

1

Page 82: January 18, 2010

1

Infinite Yield: Binary counter tool

1 c c c cc c c c c c c c c c c c cc c c

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c

0

0

1

1 mmn

10 0cm

Page 83: January 18, 2010

1

Infinite Yield: Binary counter tool

1 c c c cc c c c c c c c c c c c cc c c

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c

0

0

m

1

1 mmn

10 0

10 0

Page 84: January 18, 2010

1

Infinite Yield: Binary counter tool

1 c c c c c c c c c c c c c c c cc c c

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c

0

0

m

1

1 mmn

10

10 0

1 1n

Page 85: January 18, 2010

1

Infinite Yield: Binary counter tool

1 c c c c c c c c c c c c c c c cc c c

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c

0

0

m

1

1 mmn

10

10

1 1

n0 0

Page 86: January 18, 2010

1

Infinite Yield: Binary counter tool

1 c c c c c c c c c c c c c c c cc c c

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c

0

0

m

1

1 mmn

10

10

1 1

0 01

Page 87: January 18, 2010

1

Infinite Yield: Binary counter tool

1

0

0 10 0 1 1nn

nn

0 11 0 0 1cc

nc

1 m

m

xx

Binary counter tiles:

c

0

0

1

1 mmn

10

10

101

011

111

000

100

010

101

1 1 1 1

011

111

1 1

0001

0 100

010

101

011

111

0 0 0 01 1 1 1

01

11

000

100

010

101

011

11

11

11

11

Page 88: January 18, 2010

Infinite Yield: General Shapes

Page 89: January 18, 2010

Infinite Yield: General Shapes

1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

1 1 1 1 1

1 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 0

0 0 0 0

1 1 1 1

1 1 1 1 …

Page 90: January 18, 2010

Infinite Yield: General Shapes

1 1 1 1 0 0 0 0 0 01 1 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 11 1 1 1 11 1 1 1 1

0 0 0 0 0 1 1 1 1 11 1 1 1 1

1 1 1 1 11 1 1 1 1

11

1 1 1 1 1 1 1 1 1 1 1 0 0 0 01 1 1 1

0 0 0 00 0 0 0

Page 91: January 18, 2010

Infinite Yield: General Shapes

1 1 1 1 0 0 0 0 0 01 1 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 11 1 1 1 11 1 1 1 1

0 0 0 0 0 1 1 1 1 11 1 1 1 1

1 1 1 1 11 1 1 1 1

11

1 1 1 1 1 1 1 1 1 1 1 0 0 0 01 1 1 1

0 0 0 00 0 0 0

0 0 0 00 0 0 00 0 0 00 0 0 00 0 0 000 0 0 000 0 0 0

00

0 0 000 0 000 0 0 00 0 0 00 00 0 0 0 0 0 0 0 0 0

1 1 1 1 0 0 0 0 01 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 1

0 0 0 00 0 0 000 0 0 00 0 0 0

00

0 0 000 0 000 0 0 0 0 0 00 00 0 0 0 0 0

01

1

0

0 0 0 0 0 01 1 1 1 1 1

0 0 0 0 0 0

0 0 0 00 0

0 01 1

0 0

0 0

1 1 1 100 0 000 0 000 0 0

1000

Step 3: Label each face with unique binary code

Page 92: January 18, 2010

Infinite Yield: General Shapes

1 1 1 1 0 0 0 0 0 01 1 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 11 1 1 1 11 1 1 1 1

0 0 0 0 0 1 1 1 1 11 1 1 1 1

1 1 1 1 11 1 1 1 1

11

1 1 1 1 1 1 1 1 1 1 1 0 0 0 01 1 1 1

0 0 0 00 0 0 0

0 0 0 00 0 0 00 0 0 00 0 0 00 0 0 000 0 0 000 0 0 0

00

0 0 000 0 000 0 0 00 0 0 00 00 0 0 0 0 0 0 0 0 0

1 1 1 1 0 0 0 0 01 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 1

0 0 0 00 0 0 000 0 0 00 0 0 0

00

0 0 000 0 000 0 0 0 0 0 00 00 0 0 0 0 0

01

1

0

0 0 0 0 0 01 1 1 1 1 1

0 0 0 0 0 0

0 0 0 00 0

0 01 1

0 0

0 0

1 1 1 100 0 000 0 000 0 0

1000

Step 4: Enzyme.

Page 93: January 18, 2010

Infinite Yield: General Shapes

0 0 0 01 1 1 1

1 1 1 1

0 0 0 0

0 0 0 01 1 1 1

1 1 1 1

0 0 0 0

0 0 0 01 1 1 1

1 1 1 1

0 0 0 0

0 0 0 01 1 1 1

1 1 1 1

0 0 0 0

0 0 0 01 1 1 1

1 1 1 1

0 0 0 0

Step 5: Infinitely replicate all labeled rectangles

Page 94: January 18, 2010

Infinite Yield: General Shapes

1 1 1 1 0 0 0 0 0 01 1 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 11 1 1 1 11 1 1 1 1

0 0 0 0 0 1 1 1 1 11 1 1 1 1

1 1 1 1 11 1 1 1 1

11

1 1 1 1 1 1 1 1 1 1 1 0 0 0 01 1 1 1

0 0 0 00 0 0 0

0 0 0 00 0 0 00 0 0 00 0 0 00 0 0 000 0 0 000 0 0 0

00

0 0 000 0 000 0 0 00 0 0 00 00 0 0 0 0 0 0 0 0 0

1 1 1 1 0 0 0 0 01 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 1

0 0 0 00 0 0 000 0 0 00 0 0 0

00

0 0 000 0 000 0 0 0 0 0 00 00 0 0 0 0 0

01

1

0

0 0 0 0 0 01 1 1 1 1 1

0 0 0 0 0 0

0 0 0 00 0

0 01 1

0 0

0 0

1 1 1 100 0 000 0 000 0 0

1000

Page 95: January 18, 2010

Infinite Yield: General ShapesReassembly?

0 0 0 01 1 1 1

1 1 1 1

0 0 0 0

0 0 0 0 0 01 1 1 1 1 1

0 0 0 0 0 0

0 0 0 00 0

Page 96: January 18, 2010

Infinite Yield: General ShapesReassembly?

0 0 0 11 1 1 1

1 1 1 0

0 0 0 0

0 0 0 0 0 01 1 1 1 1 1

0 0 0 0 0 1

0 0 0 00 0

Page 97: January 18, 2010

Infinite Yield: General ShapesReassembly?

0 0 0 11 1 1 1

1 1 1 0

0 0 0 0

0 0 0 0 0 01 1 1 1 1 1

0 0 0 0 0 1

0 0 0 00 0

Page 98: January 18, 2010

Infinite Yield: General ShapesReassembly?

0 0 0 11 1 1 1

1 1 1 0

0 0 0 0

0 0 0 0 0 01 1 1 1 1 1

0 0 0 0 0 1

0 0 0 00 00101

0 11 00 01 1

10

1

1

Page 99: January 18, 2010

Infinite Yield: General Shapes

1 1 1 1 0 0 0 0 0 01 1 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 11 1 1 1 11 1 1 1 1

0 0 0 0 0 1 1 1 1 11 1 1 1 1

1 1 1 1 11 1 1 1 1

11

1 1 1 1 1 1 1 1 1 1 1 0 0 0 01 1 1 1

0 0 0 00 0 0 0

0 0 0 00 0 0 00 0 0 00 0 0 00 0 0 000 0 0 000 0 0 0

00

0 0 000 0 000 0 0 00 0 0 00 00 0 0 0 0 0 0 0 0 0

1 1 1 1 0 0 0 0 01 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 1

0 0 0 00 0 0 000 0 0 00 0 0 0

00

0 0 000 0 000 0 0 0 0 0 00 00 0 0 0 0 0

01

1

0

0 0 0 0 0 01 1 1 1 1 1

0 0 0 0 0 0

0 0 0 00 0

0 01 1

0 0

0 0

1 1 1 100 0 000 0 000 0 0

1000

Step 6: Reassemble, fill in frame, break out copies with enzyme.

Page 100: January 18, 2010

Infinite Yield: General Shapes

1 1 1 1 0 0 0 0 0 01 1 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 11 1 1 1 11 1 1 1 1

0 0 0 0 0 1 1 1 1 11 1 1 1 1

1 1 1 1 11 1 1 1 1

11

1 1 1 1 1 1 1 1 1 1 1 0 0 0 01 1 1 1

0 0 0 00 0 0 0

0 0 0 00 0 0 00 0 0 00 0 0 00 0 0 000 0 0 000 0 0 0

00

0 0 000 0 000 0 0 00 0 0 00 00 0 0 0 0 0 0 0 0 0

1 1 1 1 0 0 0 0 01 1 1 1 1

1 1 1 1 11 1 1 1 1 0 0 0 0 0 0

1 1 1 1 1 1

0 0 0 0 0 00 0 0 01 1 1 1

1 1 1 1

0 0 0 00 0 0 000 0 0 00 0 0 0

00

0 0 000 0 000 0 0 0 0 0 00 00 0 0 0 0 0

01

1

0

0 0 0 0 0 01 1 1 1 1 1

0 0 0 0 0 0

0 0 0 00 0

0 01 1

0 0

0 0

1 1 1 100 0 000 0 000 0 0

1000

Tile types O(1)

Stages O(1)

Infinite Yield:Vertically convex

Page 101: January 18, 2010

Infinite Yield: Non-vertically convex shapes

• Grow counter along surface of shape

Page 102: January 18, 2010

000100100011

0100

0101

0110

0111

1000

1001

1010

• Grow counter along surface of shape

Start end

Infinite Yield: Non-vertically convex shapes

Page 103: January 18, 2010

0001

0010

0011

0100

0101

0110

0111

1000

1001

1010

• Grow counter along surface of shape

• Break apart with enzyme

Infinite Yield: Non-vertically convex shapes

Page 104: January 18, 2010

0001

0010

0011

0100

0101

0110

0111

1000

1001

1010

• Grow counter along surface of shape

• Break apart

with enzyme

• Replicate

Infinite Yield: Non-vertically convex shapes

Page 105: January 18, 2010

0001

0010

0011

0100

0101

0110

0111

1000

1001

1010

• Grow counter along surface of shape

• Break apart

with enzyme

• Replicate

• Reassemble

Infinite Yield: Non-vertically convex shapes

Page 106: January 18, 2010

0001

00100011

0100

0101

0110

0111

1000

1001

1010

• Grow counter along surface of shape

• Break apart

with enzyme

• Replicate

• Reassemble

Infinite Yield: Non-vertically convex shapes

Page 107: January 18, 2010

107

Tile types O(1)

Stages O(1)

Infinite Yield:

Infinite Yield: General Shapes

Page 108: January 18, 2010

Future Work

• Replicate and improve-Hybrid algorithms for replication and modification

• Extension to 3D-Planarity/spacial constraint

• Replication of internal pattern

• Staged enzyme model for assembly from scratch- Seems to be very powerful for this

• Temperature changes to perform replication

Page 109: January 18, 2010

109

January 18, 2010

Thank you. Questions?

Zachary Abel Harvard UniversityNadia Benbernou Massachusetts Institute of TechnologyMirela Damian Villanova UniversityErik D. Demaine Massachusetts Institute of TechnologyMartin Demaine Massachusetts Institute of TechnologyRobin Flatland Siena CollegeSkott D. Kominers Harvard UniversityRobert Schweller University of Texas Pan American

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