strict self-assembly of discrete sierpinski triangles

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Strict Self-Assembly of Discrete Sierpinski Triangles Scott M. Summers Iowa State University

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Strict Self-Assembly of Discrete Sierpinski Triangles. Scott M. Summers Iowa State University. DNA tile, oversimplified:. Four single DNA strands bound by Watson-Crick pairing (A-T, C-G). DNA Tile Self-Assembly: Ned Seeman, starting in 1980s. DNA Tile Self-Assembly: - PowerPoint PPT Presentation

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Page 1: Strict Self-Assembly of Discrete Sierpinski Triangles

Strict Self-Assembly of Discrete Sierpinski Triangles

Scott M. Summers

Iowa State University

Page 2: Strict Self-Assembly of Discrete Sierpinski Triangles

DNA Tile Self-Assembly:Ned Seeman, starting in 1980s

Four single DNA strandsbound by Watson-Crickpairing (A-T, C-G).

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

DNA tile, oversimplified:

Page 3: Strict Self-Assembly of Discrete Sierpinski Triangles

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

DNA Tile Self-Assembly:Ned Seeman, starting in 1980s

DNA tile, oversimplified:

Page 4: Strict Self-Assembly of Discrete Sierpinski Triangles

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

T

A T

G

CG

C G

DNA Tile Self-Assembly:Ned Seeman, starting in 1980s

“Sticky ends” bind with their Watson-Crick complements,so that a regular array self-assembles.

DNA tile, oversimplified:

Page 5: Strict Self-Assembly of Discrete Sierpinski Triangles

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

“Sticky ends” bind with their Watson-Crick complements,so that a regular array self-assembles.

DNA Tile Self-Assembly:Ned Seeman, starting in 1980s

DNA tile, oversimplified:

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

Page 6: Strict Self-Assembly of Discrete Sierpinski Triangles

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

DNA Tile Self-Assembly:Ned Seeman, starting in 1980s

Choice of sticky endsallows one to programthe pattern of the array.

“Sticky ends” bind with their Watson-Crick complements,so that a regular array self-assembles.

DNA tile, oversimplified:

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

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A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

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T

T T

T

T

AT

AT

AT

AT

A

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A

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A

T

A

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A T

A T

A T

A T

A

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A

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A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

A

A

AA

A

A

T

T

T T

T

T

AT

AT

AT

AT

A

T

A

T

A

T

A

T

A T

A T

A T

A T

A

T

A

T

A

T

A

T

C

C

G

G

CG

CG

CG

C

G

C

G

C

G C

G

C G

C G

C G

C

G

C

G

Page 7: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

Page 8: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

Tile = unit square

Page 9: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

Y

ZX

Tile = unit square

Each side has a glue label and strength (0, 1, or 2 notches)

Page 10: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

Y

ZX

Tile = unit square

Each side has a glue label and strength (0, 1, or 2 notches)

If tiles abut with matching glue label and strength, then they bind with this glue’s strength

Page 11: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

RY

ZX

Tile = unit square

Each side has a glue label and strength (0, 1, or 2 notches)

If tiles abut with matching glue label and strength, then they bind with this glue’s strength

Tiles may have labels

Page 12: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

RY

ZX

Tile = unit square

Each side has a glue label and strength (0, 1, or 2 notches)

If tiles abut with matching glue label and strength, then they bind with this glue’s strength

Tiles may have labels

Tiles cannot be rotated

Page 13: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

RY

ZX

Tile = unit square

Each side has a glue label and strength (0, 1, or 2 notches)

If tiles abut with matching glue label and strength, then they bind with this glue’s strength

Tiles may have labels

Tiles cannot be rotated

Finitely many tile types

Page 14: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

RY

ZX

Tile = unit square

Each side has a glue label and strength (0, 1, or 2 notches)

If tiles abut with matching glue label and strength, then they bind with this glue’s strength

Tiles may have labels

Tiles cannot be rotated

Finitely many tile types

Infinitely many of each type available

Page 15: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

RY

ZX

Tile = unit square

Each side has a glue label and strength (0, 1, or 2 notches)

If tiles abut with matching glue label and strength, then they bind with this glue’s strength

Tiles may have labels

Tiles cannot be rotated

Finitely many tile types

Infinitely many of each type available

Assembly starts from a seed tile

Page 16: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

RY

ZX

Tile = unit square

Each side has a glue label and strength (0, 1, or 2 notches)

If tiles abut with matching glue label and strength, then they bind with this glue’s strength

Tiles may have labels

Tiles cannot be rotated

Finitely many tile types

Infinitely many of each type available

Assembly starts from a seed tile

Self-assembly proceeds in a random fashion with tiles attaching one at a time

Page 17: Strict Self-Assembly of Discrete Sierpinski Triangles

Theoretical Tile Self-Assembly: Erik Winfree, 1998

Tile = unit square

Each side has a glue label and strength (0, 1, or 2 notches)

If tiles abut with matching glue label and strength, then they bind with this glue’s strength

Tiles may have labels

Tiles cannot be rotated

Finitely many tile types

Infinitely many of each type available

Assembly starts from a seed tile

Self-assembly proceeds in a random fashion with tiles attaching one at a time

A tile can attach to the existing assembly if it binds with total strength at least the “temperature”

RY

ZX

Page 18: Strict Self-Assembly of Discrete Sierpinski Triangles

Tile Assembly Example

00

cc

1

X0

LL SLR

YcR

R

11

cn

0

11

nn

100

nn

0

Page 19: Strict Self-Assembly of Discrete Sierpinski Triangles

SX0

11c

0n0

0c

1c

11n

1n0

0n

0n

11c

0n

Temperature = 2

Tile Assembly Example

LLLR

YcR

R

YcR

R

YcR

R

SR

LX0LLX

0LL

YcR

R

Page 20: Strict Self-Assembly of Discrete Sierpinski Triangles

11c

0n

Cooperation is the key to computing with the Tile

Assembly Model.

Tile Assembly Example

SX0

11c

0n0

0c

1c

11n

1n0

0n

0n

Temperature = 2

LLLR

YcR

R

YcR

R

YcR

R

SR

LX0LLX

0LL

YcR

RX0

LL

YcR

R

11

cn

0

Page 21: Strict Self-Assembly of Discrete Sierpinski Triangles

S

Yc

Yc

Yc

Yc

X0

X0

11c

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n

00c

1c1

1c

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n

11c

0n1

1n

1n0

0n

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n

00c

1c0

0c

1c1

1c

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n

11c

0n0

0n

0n1

1n

1n0

0n

0n0

0n

0n0

0n

0n

00c

1c1

1c

0n1

1n

1n0

0n

0n0

0n

0n0

0n

0n

11c

0n1

1n

1n1

1n

1n0

0n

0n0

0n

0n

00n

0n

00n

0n

00n

0n

00c

1c0

0c

1c0

0c

1c1

1c

0n0

0n

0n

Tile Assembly Example

SX0

11c

0n0

0c

1c

11n

1n0

0n

0n

Temperature = 2

LLLR

YcR

R

R

R

R

R

R

R

R

R

R

YcR

R

YcR

R

YcR

R

YcR

R

X0

L L X0

L L X0

L L X0

L L X0

L L X0

L L L L L L L

Page 22: Strict Self-Assembly of Discrete Sierpinski Triangles

S

Yc

Yc

Yc

Yc

Yc

Yc

Yc

X0

X0

X0

X0

X0

X0

X0

11c

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n

00c

1c1

1c

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n

11c

0n1

1n

1n0

0n

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n

00c

1c0

0c

1c1

1c

0n0

0n

0n0

0n

0n0

0n

0n0

0n

0n

11c

0n0

0n

0n1

1n

1n0

0n

0n0

0n

0n0

0n

0n

00c

1c1

1c

0n1

1n

1n0

0n

0n0

0n

0n0

0n

0n

11c

0n1

1n

1n1

1n

1n0

0n

0n0

0n

0n

X0

00n

0n

00n

0n

00n

0n

Yc00c

1c0

0c

1c0

0c

1c1

1c

0n0

0n

0n

Tile Assembly Example

SX0

11c

0n0

0c

1c

11n

1n0

0n

0n

Temperature = 2

LLLR

YcR

R

R

R

R

R

R

R

R

R

R

R

R

R

R

R

R

R

R

L L L L L L L L L L L L L L L L L

Page 23: Strict Self-Assembly of Discrete Sierpinski Triangles

Another Tile Assembly Example

00

01

1

1 1

1

1 1

1

1

11

11

11

10

1

11

11

000

00

0

Page 24: Strict Self-Assembly of Discrete Sierpinski Triangles

Another Tile Assembly Example

1

1 1

11

000

11 1

11

10

111

01 0

00

00

000

11

111

01

111

10 0

00

11 1

11

10

111

01

000

00

000

00

111

10

111

10

000

11 0

00

00

000

11

000

11

000

11

111

10 0

00

11 0

00

00

000

00

111

01 1

11

01

000

00

111

01 0

00

11

000

11 1

11

10 0

00

11 0

00

00 0

00

00

000

00

000

00

000

00

000

00 0

00

00

111

01 0

00

11 0

00

00 0

00

00 0

00

00 0

00

00

000

11 0

00

00 0

00

00 0

00

00 0

00

00

000

00

000

00

The “discrete Sierpinski triangle”

Temperature = 2

000

11

1

1

11 1 1

1 11

1

1 11

1

1 11

1

1 11

1

1 11

1

1 11

1

1 11

1

1 11

1

111 1

11 1 1

11 1 1

11 1 1

11 1 1

11 1 1

11 1 1

11 1 1

11 1

Page 25: Strict Self-Assembly of Discrete Sierpinski Triangles

From: Algorithmic Self-Assembly of DNA Sierpinski Triangles Rothemund PWK, Papadakis N, Winfree E PLoS Biology Vol. 2, No. 12, e424 doi:10.1371/journal.pbio.0020424

Experimental Self-Assembly: Rothemund, Papadakis and Winfree, 2004

Page 26: Strict Self-Assembly of Discrete Sierpinski Triangles

Objective

Study the self-assembly of discrete fractal structures in the

Tile Assembly Model.

Typical test bed for new research on fractals: Sierpinski triangles

Page 27: Strict Self-Assembly of Discrete Sierpinski Triangles

Self-Assembly of Sierpinski Triangles

Page 28: Strict Self-Assembly of Discrete Sierpinski Triangles

Self-Assembly of Sierpinski Triangles

We have already seen theoretical and molecular self-assemblies of Sierpinski triangles.

But these are really just self-assemblies of entire two-dimensional surfaces onto which a picture of the Sierpinski triangle is “painted.”

But I want to study the more difficult problem of the self-assembly of shapes and nothing else, i.e., strict self-assembly.

Page 29: Strict Self-Assembly of Discrete Sierpinski Triangles

Some Formal Definitions

Page 30: Strict Self-Assembly of Discrete Sierpinski Triangles

Some Formal Definitions

Let X be a set of grid points.

The set X weakly self-assembles if there exists a finite set of tile types T that places “black” tiles on—and only on—every point that belongs to X.

The set X strictly self-assembles if there exists a finite set of tile types T that places tiles on—and only on—every point that belongs to X.

Page 31: Strict Self-Assembly of Discrete Sierpinski Triangles

Today’s Objective

Study the strict self-assembly of discrete Sierpinski triangles in

the Tile Assembly Model.

Page 32: Strict Self-Assembly of Discrete Sierpinski Triangles

Impossibility of the Strict Self-Assembly of the Discrete Sierpinski Triangle

THEOREM (Summers, Lathrop and Lutz, 2007). The discrete Sierpinski triangle does NOT strictly self-assemble in the Tile Assembly Model.

Why?

Page 33: Strict Self-Assembly of Discrete Sierpinski Triangles

Impossibility of the Strict Self-Assembly of the Discrete Sierpinski Triangle

Page 34: Strict Self-Assembly of Discrete Sierpinski Triangles

Impossibility of the Strict Self-Assembly of the Discrete Sierpinski Triangle

Assume (for the sake of contradiction) that S strictly self-assembles in the tile

set denoted as TDenote the discrete

Sierpinski triangle as SNow look at the points rk = (2k + 1,2k) for

all natural numbers k = 0, 1, 2, …

Page 35: Strict Self-Assembly of Discrete Sierpinski Triangles

Impossibility of the Strict Self-Assembly of the Discrete Sierpinski Triangle

Assume (for the sake of contradiction) that S strictly self-assembles in the tile

set denoted as T

Now look at the points rk = (2k + 1,2k) for all natural numbers k = 0, 1, 2, …

Since T is finite and S is infinite, there must be two numbers i and j such that T places the same tile type at ri and rj

Page 36: Strict Self-Assembly of Discrete Sierpinski Triangles

Impossibility of the Strict Self-Assembly of the Discrete Sierpinski Triangle

Assume (for the sake of contradiction) that S strictly self-assembles in the tile

set denoted as T

Now look at the points rk = (2k + 1,2k) for all natural numbers k = 0, 1, 2, …

Since T is finite and S is infinite, there must be two numbers i and j such that T places the same tile type at ri and rj

But then some structure other than S could just as easily strictly self-assemble in T—a contradiction!

Page 37: Strict Self-Assembly of Discrete Sierpinski Triangles

Impossibility of the Strict Self-Assembly of the Discrete Sierpinski Triangle

Assume (for the sake of contradiction) that S strictly self-assembles in the tile

set denoted as T

Now look at the points rk = (2k + 1,2k) for all natural numbers k = 0, 1, 2, …

Since T is finite and S is infinite, there must be two numbers i and j such that T places the same tile type at ri and rj

But then some structure other than S could just as easily strictly self-assemble in T—a contradiction!

Page 38: Strict Self-Assembly of Discrete Sierpinski Triangles

Now What?

Perhaps we could “approximately”

strictly self-assemble the discrete Sierpinski triangle

Page 39: Strict Self-Assembly of Discrete Sierpinski Triangles

The Fibered Sierpinski Triangle

Page 40: Strict Self-Assembly of Discrete Sierpinski Triangles

The Fibered Sierpinski Triangle

The First Stage

Page 41: Strict Self-Assembly of Discrete Sierpinski Triangles

The Fibered Sierpinski Triangle

Page 42: Strict Self-Assembly of Discrete Sierpinski Triangles

The Fibered Sierpinski Triangle

The Second Stage

Page 43: Strict Self-Assembly of Discrete Sierpinski Triangles

The Fibered Sierpinski Triangle

Page 44: Strict Self-Assembly of Discrete Sierpinski Triangles

The Fibered Sierpinski Triangle

The Third Stage

Page 45: Strict Self-Assembly of Discrete Sierpinski Triangles

The Fibered Sierpinski Triangle

Page 46: Strict Self-Assembly of Discrete Sierpinski Triangles

The Fibered Sierpinski Triangle

The Fourth Stage

Page 47: Strict Self-Assembly of Discrete Sierpinski Triangles

Similarity Between Fibered and Standard Sierpinski Triangle

Both fractals even share the same discrete fractal dimension

(i.e., log23 ≈ 1.585)

Page 48: Strict Self-Assembly of Discrete Sierpinski Triangles

THEOREM (Summers, Lathrop and Lutz, 2007). The fibered Sierpinski triangle strictly self-assembles in the Tile Assembly Model.

Strict Self-Assembly of the Fibered Sierpinski Triangle

In fact, our tile set contains only 51 unique tile types.

Page 49: Strict Self-Assembly of Discrete Sierpinski Triangles

The Key Observation

The fibered Sierpinski triangle is made up of a bunch of squares and

rectangles.

Page 50: Strict Self-Assembly of Discrete Sierpinski Triangles

Strict Self-Assembly of the Fibered Sierpinski Triangle (sketch)

0

01

11

0

0

1 0

11 0

011

111

10 0

110

1 0

0

0

1 0

11 0

11 0

111

Standard fixed-width counter

Modified fixed-width counter

100 100

Page 51: Strict Self-Assembly of Discrete Sierpinski Triangles

Strict Self-Assembly of the Fibered Sierpinski Triangle (sketch)

S

1

1

1

1

1

#

1 #

Page 52: Strict Self-Assembly of Discrete Sierpinski Triangles

1

Strict Self-Assembly of the Fibered Sierpinski Triangle (sketch)

#

10

1 0

11

1

1

0 1

0 1

1

1

#

Page 53: Strict Self-Assembly of Discrete Sierpinski Triangles

Strict Self-Assembly of the Fibered Sierpinski Triangle (sketch)

#

1

#

0 0

1 00

110

1 0 0

01 0

101

1 01

111

1

1

11

0

0

1 0

1

0

1

1

0 1

0

0

0

1

1

0

1

1

1

1

1

1

1

0 0

110

1 0 1

1

0 1

0 1

1

1

#

11

Page 54: Strict Self-Assembly of Discrete Sierpinski Triangles

Further Reading

Scott M Summers (with James I. Lathrop and Jack H. Lutz). Strict Self-

Assembly of Discrete Sierpinski Triangles. Theoretical Computer Science,

410:384—405, 2009.

Page 55: Strict Self-Assembly of Discrete Sierpinski Triangles

Summary

Page 56: Strict Self-Assembly of Discrete Sierpinski Triangles

Summary

The discrete Sierpinski triangle weakly self-assembles

The discrete Sierpinski triangle does not strictly self-assemble OPEN QUESTION: Does any (non-trivial) discrete self-

similar fractal strictly self-assemble?

The fibered Sierpinski triangle strictly self-assembles

Page 57: Strict Self-Assembly of Discrete Sierpinski Triangles

Any Questions?

Thank you!