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Organisation -Oriented Chemical Programming

Organisation -Oriented Chemical Programming. Peter Dittrich Bio Systems Analysis Group Dept . of Mathematics and Computer Science Friedrich Schiller University Jena. Friedrich-Schiller-Universität Jena. Jena Centre for Bioinformatics. Motivation. Overview.

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Organisation -Oriented Chemical Programming

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  1. Organisation-Oriented Chemical Programming Peter Dittrich Bio Systems Analysis Group Dept. ofMathematicsand Computer Science Friedrich Schiller University Jena Friedrich-Schiller-Universität Jena Jena Centre for Bioinformatics

  2. Motivation Peter Dittrich - FSU & JCB Jena

  3. Overview Why using chemical-like systems? How to find the right chemical program? Example: Maximal independent set problem. Chemical Organization Theory Organization-oriented chemical programming Evolved vs. manual design Messy Chemistries Outlook: Three Open Problems Peter Dittrich - FSU & JCB Jena

  4. Real chemical computing Chemistry Helps Computing Artificial chemical computing [J. S. Astor, C. Adami:., Artificial Life6(3), 189-218, 2000] Peter Dittrich - FSU & JCB Jena

  5. Real chemical computing Chemistry Helps Computing Artificial chemical computing [J. S. Astor, C. Adami:., Artificial Life6(3), 189-218, 2000] Peter Dittrich - FSU & JCB Jena

  6. COG (MIT, Brooks et al.) Peter Dittrich - FSU & JCB Jena

  7. PSI (D. Dörner) Peter Dittrich - FSU & JCB Jena

  8. PSI (D. Dörner) Peter Dittrich - FSU & JCB Jena

  9. Growing Artificial NNs [Astor/Adami] [J. S. Astor, Christophs Adami: A Developmental Model for the Evolution of Artificial Neural Networks., Artificial Life6(3), 189-218, 2000 http://norgev.alife.org/] Peter Dittrich - FSU & JCB Jena

  10. Morpho-Genetic Systems genetic network (local rules) Arabidopsis wild type and ap3 mutant flower [Source: Espinosa-Soto, C., P. Padilla-Longoria, E. R. Alvarez-Buylla; The Plant Cell, 16:2923-2939 (2004)] Peter Dittrich - FSU & JCB Jena

  11. Amorphous Computing Peter Dittrich - FSU & JCB Jena

  12. Formation of Artificial Organs cf:. UweBrinkschulte et al. Peter Dittrich - FSU & JCB Jena

  13. Formation of Artificial Organs cf:. UweBrinkschulte et al. Peter Dittrich - FSU & JCB Jena

  14. Organic Middleware OCmu See T. Ungerer, Univ. Augsburg Peter Dittrich - FSU & JCB Jena

  15. Characteristics of Applications Low-level control in a distributed, dynamic, unpredictable, and unreliable IT system. Peter Dittrich - FSU & JCB Jena

  16. Why chemistry? Compare with conventional and connectionistic computing.

  17. “Invisible Networks” Peter Dittrich - FSU & JCB Jena

  18. Structure-Function-DualismSelf-Modification / Strange Loop • Dualism of • structure and function • data and program • Tape and machine • Self-modification(s. higher-order & generative programming) • Strange loop Examples: Pi-calculus FRAGLETS (Tschudin et al.) Peter Dittrich - FSU & JCB Jena

  19. Overview Why using chemical-like systems? How to find the right chemical program? Example: Maximal independent set problem. Chemical Organization Theory Organization-oriented chemical programming Evolved vs. manual design Messy Chemistries Outlook: Three Open Problems Peter Dittrich - FSU & JCB Jena

  20. Programming Chemical Systems MACRO (desired behavior) Instantiation Abstraction MICRO (reaction rules)

  21. Approaches • Optimization (e.g. EA) • Engineering (Design) • Compiling (e.g., DNA sticker model) • Copying (e.g., bionics) • Analytic/Proof Peter Dittrich - FSU & JCB Jena

  22. Approaches • Optimization(e.g. EA or „Trial and Error“) Evolving self-organizing systems is difficult. E.g.: (J. Ziegler / W. Banzhaf) Approx. 10 functional nodes evolvable Peter Dittrich - FSU & JCB Jena

  23. Approaches • Optimization (e.g. EA) • Engineering (Design) • Compiling (e.g., DNA sticker model) • Copying (e.g., bionics) • Analytic/Proof Peter Dittrich - FSU & JCB Jena

  24. Programming by human design requires predictability MACRO (desired behavior) Understand Causality Instantiation Abstraction MICRO (reaction rules) Peter Dittrich - FSU & JCB Jena

  25. Programming by human design requires predictability MACRO (desired behavior) can only partially explain the micro- macro-link (cf. halting problem) “A Theory of Emergence” Instantiation Abstraction MICRO (reaction rules) Peter Dittrich - FSU & JCB Jena

  26. Programming by human design requires predictability MACRO (desired behavior) many “partial” theories Instantiation Abstraction MICRO (reaction rules) Peter Dittrich - FSU & JCB Jena

  27. Overview Why using chemical-like systems? How to find the right chemical program? Example: Maximal independent set problem. Chemical Organization Theory Organization-oriented chemical programming Evolved vs. manual design Messy Chemistries Outlook: Three Open Problems Peter Dittrich - FSU & JCB Jena

  28. Sketch of an Example Application 1. Inject molecules 2. Molecules distribute 3. Cells differentiate (self-organize) 4. A cell is removed 5. Reorganize Peter Dittrich - FSU & JCB Jena

  29. Example: Chemical Program Reactions within a membrane Transport between membranes i and j [1] N. Matsumaru, T. Hinze, and P. Dittrich. Organization-oriented chemical programming for Distributed ArtifactsInternational Journal of Nanotechnology and Molecular Computation (submitted) Peter Dittrich - FSU & JCB Jena

  30. Example: MIS chemistry [1] N. Matsumaru, T. Hinze, and P. Dittrich. Organization-oriented chemical programming for Distributed ArtifactsInternational Journal of Nanotechnology and Molecular Computation (submitted) Peter Dittrich - FSU & JCB Jena

  31. Overview Why using chemical-like systems? How to find the right chemical program? Example: Maximal independent set problem. Chemical Organization Theory Organization-oriented chemical programming Evolved vs. manual design Messy Chemistries Outlook: Three Open Problems Peter Dittrich - FSU & JCB Jena

  32. „Chemical Organization“ Reaction inside the organization produce only species of that organization. Organization := a set of molecular species that is(algebraically) closed andself-maintaining Within a self-maintaining set, all species consumed by a reaction can be produced by a reaction within the self-maintzaining set while no species concentration in the set decreases. [Speroni di Fenizio/Dittrich (2005/7, Bull. Math. Biol. 2007) inspired by Fontana, Buss, Rössler, Eigen, Kauffman, Maturana, Varela, Uribe] Peter Dittrich - FSU & JCB Jena

  33. 4 4 1 1 2 2 3 3 Practical View Organization Chemical Organization Theory Organizations Reaction network [P. Dittrich, P. Speroni di Fenizi, Chemical Organization Theory, Bull. Math. Biol., 2007] Peter Dittrich - FSU & JCB Jena

  34. 4 {1,2,3,4} {2, 3} 1 {1} 2 3 { } Practical View Hasse diagram of organizations Chemical Organization Theory Organizations Reaction network [P. Dittrich, P. Speroni di Fenizi, Chemical Organization Theory, Bull. Math. Biol., 2007] Peter Dittrich - FSU & JCB Jena

  35. 4 {1,2,3,4} {2, 3} 1 {1} 2 3 { } Practical View Hasse diagram of organizations Chemical Organization Theory Thoerie chemischerOrganization [2] Organizations Reaction network [3] [4] [1] Dynamics [P. Dittrich, P. Speroni di Fenizi, Chemical Organization Theory, Bull. Math. Biol., 2007] Peter Dittrich - FSU & JCB Jena

  36. 1. Example: MIS chemistry [1] N. Matsumaru, T. Hinze, and P. Dittrich. Organization-oriented chemical programming for Distributed ArtifactsInternational Journal of Nanotechnology and Molecular Computation (submitted) Peter Dittrich - FSU & JCB Jena

  37. „Chemical Organization“ Reaction inside the organization produce only species of that organization. Organization := a set of molecular species that is(algebraically) closed andself-maintaining Within a self-maintaining set, all species consumed by a reaction can be produced by a reaction within the self-maintzaining set while no species concentration in the set decreases. [Speroni di Fenizio/Dittrich (2005/7, Bull. Math. Biol. 2007) inspired by Fontana, Buss, Rössler, Eigen, Kauffman, Maturana, Varela, Uribe] Peter Dittrich - FSU & JCB Jena

  38. 1. Example: MIS chemistry [1] N. Matsumaru, T. Hinze, and P. Dittrich. Organization-oriented chemical programming for Distributed ArtifactsInternational Journal of Nanotechnology and Molecular Computation (submitted) Peter Dittrich - FSU & JCB Jena

  39. 1. Example: MIS chemistry [1] N. Matsumaru, T. Hinze, and P. Dittrich. Organization-oriented chemical programming for Distributed ArtifactsInternational Journal of Nanotechnology and Molecular Computation (submitted) Peter Dittrich - FSU & JCB Jena

  40. 1. Example: MIS chemistry [1] N. Matsumaru, T. Hinze, and P. Dittrich. Organization-oriented chemical programming for Distributed ArtifactsInternational Journal of Nanotechnology and Molecular Computation (submitted) Peter Dittrich - FSU & JCB Jena

  41. 1. Example: MIS chemistry The empty organization [1] N. Matsumaru, T. Hinze, and P. Dittrich. Organization-oriented chemical programming for Distributed ArtifactsInternational Journal of Nanotechnology and Molecular Computation (submitted) Peter Dittrich - FSU & JCB Jena

  42. a + b -> 2 b a + c -> 2 c b 2 b -> d c -> d a d e b + c -> e -> a 2 c a ->b ->c ->d ->e -> Example 1 Peter Dittrich - FSU & JCB Jena

  43. 2 2 Example 1 Organization {a, b, d} b a d e c Peter Dittrich - FSU & JCB Jena

  44. Checking for Closure Organization {a, b, d} b 2 a d e 2 c Peter Dittrich - FSU & JCB Jena

  45. Checking for Self-Maintenance Organization {a, b, d} b 2 a d e 2 c Peter Dittrich - FSU & JCB Jena

  46. outside of org. = 0 0 0 0 0 0 Checking for Self-Maintenance Organization {a, b, d} b 2 1. Find flux vector a d e 2 c Peter Dittrich - FSU & JCB Jena

  47. 1. Find flux vector outside of org. = 0 inside of org. > 0 Checking for Self-Maintenance Organization {a, b, d} 1 b 2 9 8 10 a d e 1 0 1 0 0 0 2 c 0 Peter Dittrich - FSU & JCB Jena

  48. 0 outside of org. = 0 (closure) 0 Checking for Self-Maintenance Organization {a, b, d} 1 b 2 1. Find flux vector 9 8 outside of org. = 0 10 a d e 1 inside of org. > 0 0 1 0 0 0 2. Check production rates 2 c 0 Peter Dittrich - FSU & JCB Jena

  49. inside of org. 0 (self-maint.) Checking for Self-Maintenance Organization {a, b, d} 0 1 b 2 1. Find flux vector 9 8 outside of org. = 0 0 10 7 a d e 0 1 inside of org. > 0 0 1 0 0 0 2. Check production rates 2 c outside of org. = 0 (closure) 0 0 Peter Dittrich - FSU & JCB Jena

  50. 2 2 All Organizations All Organizations b a d e c Peter Dittrich - FSU & JCB Jena

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