Self-Repairing and Self-Replicating Hardware: The Embryonics Approach

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1 Self-Repairing and Self-Replicating Hardware: The Embryonics Approach D. Mange, M. Sipper, A. Stauffer,, and G. Tempesti 2nd NASA/DoD Workshop on Evolvable Hardware Palo Alto, July 13-15, 2000 É C O L E F É D É E R

2 Caenorhabditis Elegans We understand completely the chromosome and role of the genes in the organism of the Elegans! Model for studies in genetics 11 December 1998

3 Multicellular Organization 959 somatic cells

4 Embryonics: Why? Design of robust integrated circuits able to: self-repair (healing) self-replicate (cloning)

5 Embryonics: Why? Today: space exploration nuclear plants avionics Tomorrow: molecular electronics

6 Embryonics: How? Iterative electronic circuit based on 3 features: multicellular organization cellular division cellular differentiation

7 Cellular Division mother cell daughter cell daughter cell

8 Cellular Differentiation Pharynx Intestine

9 BioWatch

10 The Future of Embryonics

11 Two kinds of Programmable Arrays Based on logic functions in cells Based on switchboxes Mixed Inputs and functions FF s Lookup Table ff primary inputs FF s mux ff memory memory Based on logic functions Based on switchboxes

12 Based on switching mux mux mux ff ff ff memory memory memory mux mux mux ff ff ff memory memory memory

13

14 Multicellular Organization CELL gene Organism is composed of bio-cells 2 B D F O R G 1 Y A C E X bio-cell = phenotype from genotype bio-cell = logic circuit (virtual) Chromosome = memory contents

15 MUXTREE Molecule Bio-cell has several molecule cells like this 8 memory cells Block SB NOBUS NIBUS WIBUS WOBUS SB DQ NOUT 10 R FF 10 B MUX 10 MUXTREE P WIBUS INIT WOBUS CK EOBUS EIBUS W1:0 N1:0 NOUT NOBUS NOUT NOUT NIBUS NOUT S1: SB E1:0 EOBUS EIBUS SIBUS SOBUS WIN WOUT L2:0 0 1 R2:0 EOUT EIN MOLCODE = MC19:0 CREG connection block (CB) switch block (SB) memory and test 0 L2:0 0 R2:0 N1:0 S1:0 E1:0W1:0 0 P R B SIBUS SOBUS 9 memory cells SIN 9+8+3=20 memory cells 20 programming bits in memory of the molecule cell

16 Embryonics Landscape ORG ORG ORG ORG Population level (population = Σ organisms) A C E ORG OG: operative genome a B D F CELL RG: ribosomic genome PG: polymerase genome b MUX c d e COMP MUX f MOLECULE d MOLCODE Organismic level (organism = Σ cells) Cellular level (cell = Σ molecules) Molecular level (basic FPGA's element) Operative genome is the same as chromosome in previous lectures Bio-cell is one or more FPGA cells

17 StopWatch START STOP RESET MIN SEC Max = 5 Max = 9

18 StopWatch MIN SEC

19 StopWatch CELL gene The whole counter is an organism The component module 6 or module 10 counter is a bio-cell A bio-cell is of course many FPGA cells in this model 1 Y ORG Count mod 6 X Count mod10 Count mod 6 StopWatch Count mod10 4 The organizm is one-dimensional It has four bio-cells There are two types of bio-cells: Count mod 6 Count mod 10

20 StopWatch OG: operative genome gene X Operative genome => for organism 4 genes gene => for bio-cell of the organism genes responsible for two types of bio-cells in the phenotype

21 StopWatch OG: operative genome X = (WX+1) mod 4 case of X: X = 1: Countmod 6 (10 minutes) X = 2: Countmod 10 (minutes) X = 3: Countmod 6 (10 seconds) X = 4: Countmod 10 (seconds)

22 StopWatch Term from genetics X=(WX+1)mod4 case of X: X =... HOX genes switch genes functional genes operative genome (OG)

23 Cellular Differentiation t t t X =

24 Self-Replication t2 t t1 1 Y t1 t2 t MOTHER ORG X

25 Self-Replication Directions of self-replication 1 t2 t3 t4 t5 t6 t7 t t1 DAUGHTER ORG # 1 DAUGHTER ORG # t1 t2 t t t5 t6 t Y MOTHER ORG DAUGHTER ORG # 2 X

26 Self-Repair Direction of self-repair KILL= Y X NEW ORGORIGINAL ORG SCAR NEW ORG SPARE SPARE CELLS CELL

27 Embryonics Landscape ORG ORG ORG ORG Population level (population = Σ organisms) ORG = StopWatch 10 Organismic level (organism = Σ cells) Cellular level??? (cell = Σ molecules) CELL Molecular level??? (basic FPGA's element) MOLECULE

28 MUXTREE Molecule NOBUS NIBUS WIBUS WOBUS SB DQ NOUT 10 R FF 10 B MUX 10 MUXTREE P WIBUS INIT WOBUS CK EOBUS EIBUS W1:0 N1:0 NOUT NOBUS NOUT NOUT NIBUS NOUT S1: SB E1:0 EOBUS EIBUS SIBUS SOBUS WIN WOUT L2:0 0 1 R2:0 EOUT EIN MOLCODE = MC19:0 CREG connection block (CB) switch block (SB) memory and test 0 L2:0 0 R2:0 N1:0 S1:0 E1:0W1:0 0 P R B SIBUS SOBUS SIN

29 NOBUS NIBUS NOUT MUXTREE 10 R WIBUS WOBUS WIN WOUT SB DQ FF MUX L2:0 0 1 R2:0 B P INIT Cell has only one flip-flop W CK EOBUS EIBUS This is programmable hardware EOUT EIN Is programmed to virtual hardware Virtual hardware is a FSM SIBUS SOBUS SIN

30 NOBUS NIBUS NOUT MUXTREE NOBUS NIBUS north 10 R NOUT WIBUS WOBUS SB DQ FF MUX B P INIT W CK EOBUS EIBUS R P INIT EOBUS EIBUS east L2:0 0 1 R2:0 EOUT EIN WIN WOUT SIBUS SOBUS SIN EOUT EIN WIN WOUT WIBUS west WOBUS SIBUS south SOBUS

31 Space Divider PG X=1 Separation concerns only some signals

32 Space Divider PG X= SPARE CELL

33 Cellular Self-Replication X= SPARE RG+OG CELL

34 Cellular Self-Repair faulty molecule X= SPARE RG+OG CELL

35 Cellular Self-Repair KILL=1 X= SPARE 4 CELL RG+OG Stuck-at-one, stuck-at-zero fault models

36 Molecular Implementation

37

38

39 Embryonics Landscape ORG ORG ORG ORG Population level (population = Σ organisms) ORG = StopWatch 10 Organismic level (organism = Σ cells) SMEM SBDM Cellular level (cell = Σ molecules) RG+OG PG CELL MUX COMP MUX MOLCODE Molecular level (basic FPGA's element) MOLECULE

40 Artificial Genome space divider programming data molecular codes X=(WX+1)mod4 case of X: X =... HOX genes switch genes functional genes polymerase genome (PG) ribosomic genome (RG) operative genome (OG)

41

42 Problems to solve Draw a modulo 6 counter using only flip-flops and multiplexed constants Do the same for module 10 counter. Design a complete watch, as in this lecture from such elements. Explain a methodology of realizing arbitrary autonomous machines in the switch/constant cellular model Explain how to realize arbitrary state machine with single input in this model

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