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Program continues to run for stationary config. input U waste input′ d′ U d′′ C′ C energy 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 42 Thermodynamics of a Configuration • Either, configuration is a stable state – damage may shift to undesirable equilibrium • Or, configuration is a stationary state of a non-equilibrium system – continuously reconfigures self – self-repair as return to original stationary state – adaptation & damage recovery as move to different stationary state 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 43 Useful Media for Computational Synthesis • For pure computation, move as little matter & energy as possible • For synthesis, need to control atoms & molecules as well as electrons • Need sufficiently wide variety of controllable atoms & molecules • Goal: structures on the order of optical wavelengths (100s of nm) 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 44 Models of Computation for Synthesis • Need massive parallelism to control detailed organization of state • Need tolerance to errors in state – synthesis program should be tolerant – configured computer should be tolerant 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 45 Locus of Control of Detailed Organization • Reorganizing atoms & molecules ⇒ vast amount of detailed control • Heterosynthesis – external configuration controller determines fine structure of medium (high bandwidth) • Autosynthesis – external configuration controller determines general boundary conditions (low BW) – fine structure results from self-organization 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 46 General Model of Radical Reconfiguration • Synthesis controller – low bandwidth to outside world – bandwidth to medium: • high for heterosynthesis • low for autosynthesis • Synthetic medium – molar parallelism of interactions • simple for heterosynthesis • complex for autosynthesis – what are suitable synthetic media?

Micro-organisms can be viewed a micro-robots with capabilities for: – – – – – – – – – locomotion sensing control simple (low-precision analog) computation assembly collective, coordinated behavior reproduction self-defense metabolism (matter/energy acquisition, growth, repair) • Can be genetically-engineered for our purposes 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 58 The Programmable Microorganism (“Promorg”) • Noncoding DNA can be used for “genetic circuits” – in eukaryotes, 10–70% – equivalent of about 3000 genes in yeast • Equipped with an assortment of generally useful sensors & receptors (especially for selforganization) • Special-purpose modifications for particular applications • Research: principles of design & self-organization 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 59 Tentative Capabilities • Neutral proteins for programmable control – gene regulatory & coding sequences – connections can be regulated by external signals • Membrane & cytoplasm receptors for: – chemical signals – light, etc.

Cazamine 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 48 Example: Activation-Inhibition System • Let σ be the logistic sigmoid function • Activator A and inhibitor I may diffuse at different rates in x and y directions • Cell is “on” if activator + bias exceeds inhibitor "A "2A "2A = dAx 2 + dAy 2 + k A# [ mA ( A + B $ I )] "t "x "y "I " 2I " 2I = dIx 2 + dIy 2 + k I# [ mI ( A + B $ I )] "t "x "y 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 49 Double Activation-Inhibition System • Two independently diffusing activation-inhibition pairs • May have different diffusion rates in X and Y directions – In this example, I1y >> I1x and I2x >> I2y • Colors in simulation: – – – – green = system 1 active red = system 2 active yellow = both active black = neither active 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 50 Formation of Pattern • Random initial state • System stabilizes to < 1% cell changes • Modest noise (annealing noise) improves regularity 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 51 Stationary State • System is being continually maintained in a stationary state • Continuing change < 1% 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 52 Recovery from Damage • Simulated damage • Damage destroys activators & inhibitors as well as structure • System repairs self by returning to stationary state • No explicit repair signal 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 53 Reconfiguration: Orthogonal Structure • Exchange inhibitor diffusion rates for systems 1 & 2 • Vertical stripes become horizontal • Horizontal stripes become vertical • No explicit reconfiguration signal 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 54 Summary of Radical Reconfiguration • Computation can be used to rearrange matter • External control of initial and boundary conditions • Detailed structure by self-organization with molar parallelism • Stationary states can be used for self-repair and adaptation 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 55 Programmable Microorganisms for Artificial Morphogenesis Artificial Morphogenesis • Based on models of embryological development • Cells migrate by local interaction & chemical signals • Possible implementation: “programmable” micro-organisms 6 March 2007 Self-Organization for NanoComputation & Nano-Assembly 57 Why Micro-Organisms?

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