How to achieve these behaviours Non trivial 3D self assembly IL 33 Radiolara Self replication Ecoli division and replication In inorganic materials mechanical assemblies For programming complex assemblies at mm um nm 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 Addition of state to self assembly Air bearing table magnetically attractive parts Stateless parts 4 states per tile 2x2 assemblies 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 states enough for arbitrary bit string replication Pos a b c d Eo Fo 1 0 0 0 0 N N 2 0 1 0 0 Y Y 3 1 1 1 0 Y Y 4 1 0 0 1 N N 5 1 0 0 0 N N 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 Extensible to space filling 3D structures Right tetrahedron octahedron can produce arbitrary structure in 3d EXTRA SLIDES just in case not included 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 Jacobson toy train replicator Lohn NASA Programming static parts Mesoscale 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 Air table environs Energy basics Infinite orientational possibilities Catalysis and Allostery Molecular and cellular biology Wolfe S Wadsworth 1993 Computational Algorithmic self assembly of DNA Erik Winfree PhD Thesis California Institute of Technology 1998 Using lateral capillary forces to compute by selfassembly Paul W K Rothemund PNAS Feb 1 2000 Vol 97 no 3 984 989 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 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 Cooperative binding Genes Signals Ptashne Gann CSHL Press 2002 Weiss Homsy Knight DIMACS Irreversible vs reversible binding G M Whitesides PNAS Apr 16 2002 Vol 99 no 8 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 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 Proof methodology Space filling Starting at one face can you fold to 3 orthogonal faces Geometric primitive that allows return path Stitch by primitive A self replicating system Can a simple self replicating system be designed that is simply manufacturable in interestingly large numbers 6 state linear replicator Systems with state 2 states allostery 3 states catalysis 4 states dimer replication 5 states self replication of arbitrary bit strings SA UTM
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