Programmable Self Assembly

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Programmable Self Assembly

• Concepts and recent experiments

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Outline

• Problem
• Microfabrication cost and complexity
• Bio-compatibility
• Solution
• Nanoscale self-assembly
• Theory
• Theoretical limits of self-assembly
• Experiments
• DNA self assembly
• Microscale assembly
• DNA-nanoparticle assembly
• Conclusions

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Problem - Microfab complexity

• Small 3D structures
• Layer by layer
• Alignment problems
• Lithography is 2D in nature
• Example
• No truly 3D photonic crystals

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Problem - Microfab costs
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Problem - Bio-compatibility

• Biomolecules (DNA, proteins, antibodies e t c)
  are not compatible with the chemicals used in
  traditional microfabrication
• Biomolecules have to be applied after all
  micromachining is done

• Biomolecules cannot be fully integrated in a
  layered 3D technology

OmniGrid DNA-arrayer
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Solution Nanoscale Self-assembly

• Bottom-up approach
• Smaller dimensions possible
• Ideal for 3D structures
• Technology can be made bio-compatible

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Theory - classes

• Different classes of self-assembly
• Crystal-type self-assembly
• All pieces are the same
• Unique-addressing-type self-assembly
• Every piece is unique
• Every piece has its predetermined position
• Programmable self-assembly
• Many, but not all, pieces are the same
• Not entirely deterministic
• Some structures more probable than others

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Theory - classes

• Crystal-type self-assembly
• All pieces are the same

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Theory - classes

• Unique-addressing-type self-assembly
• Every piece is unique
• Every piece has its predetermined position

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Theory - classes

• Programmable self-assembly
• Many, but not all, pieces are the same
• Not entirely deterministic
• Some structures more probable than others

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Theory - classes
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Theory - The Three to tango-conjecture
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Theory - The Three to tango-conjecture
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Theory - The Three to tango-conjecture
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Theory - The Three to tango-conjecture
The three to tango - conjecture In order to be
able to control the assembly size and structure
in a programmable self-assembly system the
following must hold An incoming building block
must interact with at least two other, already
assembled, blocks.
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Theory - The Tile Assembly Model
Counter tiles
Cook, Rothemund and Winfree, Self-Assembled
Circuit Patterns to to appear in DNA Computers 9,
LNCS 2943 (2004) California Institute of
Technology
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Theory - The Tile Assembly Model
The program-size complexity for programmable
self-assembly
PSA
O(logN)
25 uniqe block types 770 blocks total
How to identify the complexity of more
complicated structures?
How many different kinds of structures can be
built using the same blocks?
Rothemund and Winfree, The Program-Size
Complexity of Self-Assembled Squares, Proc. 32nd
ann. Symp. Theor. of Comp. (2000) University of
Southern California and California Institute of
Technology
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Graph Grammars
Theory - Graph Grammars
Conformal switching
Boo, J., Sticky Graphs - A tool to model
Self-Assembly, MSU Dept. of Math. Reports
(2004) Mid Sweden University
Eric Klavins, Robert Ghrist and David Lipsky,
Graph Grammars for Self-Assembling Robotic
Systems, Proceedings of the International
Conference on Robotics and Automation
(2004) University of Washington
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Experiments - DNA self-assembly
Winfree, Liu, Wenzler, Seeman, Design and
self-assembly of two-dimensional DNA crystals,
Nature 394 (1998) California Institute of
Technology / New York University
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Experiments - DNA self-assembly
Shih, M. M., J. D. Quispe, et al., A 1.7-kilobase
single-stranded DNA that folds into a nanoscale
octahedron, Nature 427, (2004). Skaggs Inst. for
Chem. Biol., La Jolla, Carlifornia
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Experiments - Microscale assembly
Lienemann, Greiner, Korvink, Xiong, Hanenin,
Böhringer, Modeling, Simulation, and
Experimentation of a Promising New Packaging
Technology Parallel Fluidic Self-Assembly of
Microdevices, Sensors Update 13 (2003) Albert
Ludwig University, Freiburg / University of
Washington
Clark, T. D., J. Tien, Duffy, Paul, Whitesides,
Self-assembly of 10?m-sized objects into
ordered three-dimensional arrays Journal of the
American Chemical Society 123(31),
(2001). Harvard University
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Experiments -DNA-Nanoparticle Assembly
Mirkin, Letsinger, Mucic, Storhoff, A DNA-based
method for rationally assembling nanoparticles
into macroscopic materials, Nature 382
(1996) Northwestern University, Evanston
Mirkin-type nanoparticles have only one function.
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Experiments -DNA-Nanoparticle Assembly
A PSA building block needs to have at least 4
different faces with separate functions, in 3D,
preferably 8. (the building block-conjecture)
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Experiments -DNA-Nanoparticle Assembly
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Experiments -DNA-Nanoparticle Assembly
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Experiments -DNA-Nanoparticle Assembly
Potential A technology for the production of PSA
building blocks of gold- or SiO2-nanoparticles
down to 20nm in size. Patent applications filed.
A nanoparticle with 2 functional edges!
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Conclusions

• Microfabrication is increasingly expensive and
  small 3D structures are very hard to make.
• Programmable self-assembly provides a path to
  effective nanofabrication
• The theoiries of self-assembly are insufficient.
  Main assumptions have been presented.
• DNA coated nanoparticles from Mid Sweden
  University will revolutionize nanotechnology
  within the next years.

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DNA basics
Four nucleotid bases A C T G adenine cytosine
thymine guanine Single stranded DNA string
AATGC GTCGT GGCTA Watson-Crick complement
TTACG CAGCA CCGAT
C
G
T
A
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Origami
Cells that produces origami
Radhika Nagpal, ProgrammableSelf-Assembly
Constructing Global Shape using
Biologically-inspired Local Interactions and
Origami Mathematics, Ph.D Thesis
(2001) Massachusetts Institute of Technology
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Cells that produces origami
Radhika Nagpal, ProgrammableSelf-Assembly
Constructing Global Shape using
Biologically-inspired Local Interactions and
Origami Mathematics, Ph.D Thesis
(2001) Massachusetts Institute of Technology
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Cells that produces origami
Radhika Nagpal, ProgrammableSelf-Assembly
Constructing Global Shape using
Biologically-inspired Local Interactions and
Origami Mathematics, Ph.D Thesis
(2001) Massachusetts Institute of Technology