How to achieve these behaviours:

1. How to achieve these behaviours: Non-trivial 3D self assembly Self replication IL 33. Radiolara Ecoli – division and replication In inorganic materials, mechanical assemblies. For programming complex assemblies at mm, um, nm?

2. Meso (mm) micro nano Pre-programmed parts : crystallisation, (with errors) in 2d / 3d. Model: diffusion limited aggregation with annealing (reversible bonds) Apps: Photonic crystals, composite materials (nacre-esque), molecular scaffolding. Self-Assembly of 10-micron-Sized Objects into Ordered Three Dimensional Arrays. Clark, T.D., Tien, J., Duffy, D.C., Paul, K.E., Whitesides, G.M., J.Am.Chem.Soc. 2001, 123, 7677-7682 Algorithmic self-assembly of DNA, Erik Winfree, PhD Thesis, California Institute of Technology, 1998.

3. Addition of state to self assembly: Air bearing table, magnetically attractive parts. Stateless parts. 4 states per tile. 2x2 assemblies.

4. Adding state: “logic limited assembly” Self clocking assembly (serial tile addition along controlled growth front/s) Higher function – recognition, logic, reproduction. “2” states: Flexure based allostery Coupled mechanism limits # of states. Difficulty of designing entire system for unique energy minima whilst comparing all possible interactions Limitations on flexure size – build. Captured liquid bearing Decouples states, potentially simpler design task.

5. 5 states enough for arbitrary bit-string replication

6. Adding program to give structure.. Memory limit in state machine / simple machine model for specifying structure. Limited to “possible” structures Place program within structure, linearise program – facilitates replication…. 1 bit of state at each junction can completely specify arbitrary 2D structure. - Provided folding proceeds sequentially from one end. PDMS parts patterned hydrophobic / hydrophillic.

7. Extensible to space filling 3D structures. Right tetrahedron & octahedron can produce arbitrary structure in 3d.

9. EXTRA SLIDES: just in case… not included

10. Penrose Mechanical state machines for mimicking biological functions. Plywood models. Highly constrained assembly environments. Pre – CA, pre – Program size complexity: No analysis of number of states. Self replication video 1 Dimer replication, mutation Self replication video 2 Arbitrary bit string replication – “polymerase-less”

11. Jacobson toy train replicator..

12. Lohn, NASA

15. Programming static partsMesoscale Self-Assembly of Hexagonal Plates Using Lateral Capillary Forces: Synthesis Using the “Capillary Bond”. Bowden, N., Choi, I.S., Grzybowski, B.A., Whitesides, G.M., J.Am.Chem.Soc., 1999, 121, 5373-5391

16. Air table environs.

17. Energy basics Infinite orientational possibilities

18. Catalysis and Allostery Molecular and cellular biology., Wolfe.S., Wadsworth 1993.

19. Computational Algorithmic self-assembly of DNA, Erik Winfree, PhD Thesis, California Institute of Technology, 1998. Using lateral capillary forces to compute by self-assembly., Paul W.K. Rothemund., PNAS, Feb.1, 2000, Vol.97., no.3, 984-989.

20. 2D Surface – meniscus driven Hydrophobic / hydrophillic surfaces determine meniscii at edges of parts constrained at a fluid/fluid or fluid/gas interface. Curvature of surfaces determines attractive / repulsive forces Systems are driven to minimise surface energy Linearized Laplace equation: Order and Disorder: Mesoscale Self-Assembly and Waves. Bowden, Ned, B., PhD. Thesis, Dept. Chemistry and Chemical Biology, Harvard University, September 1999.

21. Scaling of meniscii forces Dominant and tuneable at mm scale Attraction and repulsion Unperturbed surfaces at micron scale Self-Assembly of Microscale Objects at a Liquid/Liquid Interface through Lateral Capillary Forces. Bowden, N., Arias, F., Deng, T., Whitesides, G.M., Langmuir 2001, 17, 1757-1765

22. Cooperative binding Genes & Signals, Ptashne, Gann, CSHL Press 2002 Weiss,Homsy,Knight, DIMACS

23. Irreversible vs. reversible binding.G.M.Whitesides, PNAS, Apr.16, 2002. Vol.99, no.8

24. Folding – linear Design of Three Dimensional, Millimeter-Scale Models for Molecular Folding. Clark, T.D., Boncheva, M., German, J.M., Weck, M., Whitesides, G.M., J.Am.Chem.Soc., Vol.124, No.1., 2002.,18-19. Biomimetic self-assembly of a functional asymmetrical electronic device.  Borcheva,M., Gracias, D.H., Jacobs, H.O., Whitesides, G.M., PNAS, Apr.16, 2002, Vol.99, no.8., pp4937-4940

25. Functional Forming Electrical Networks in Three Dimensions by Self-Assembly, Gracias, D.H., Tien, J., Breen, T.L., Hsu, C., Whitesides, G.M. Science, 18 August 2000, Vol. 289, 1170-1172

26. Proof: methodology Geometric primitive that allows return path Space filling Starting at one face can you fold to 3 orthogonal faces? Stitch by primitive

27. A self replicating system Can a simple self replicating system be designed that is simply manufacturable in interestingly large numbers?

28. 6 state linear replicator

29. Systems with state 2 states: allostery 3 states: catalysis 4 states: dimer replication 5 states: self replication of arbitrary bit strings

30. SA UTM