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Organisation -Oriented Chemical Programming

Delve into organization-oriented chemical programming, using chemical-like systems to solve complex problems. Explore real chemical computing applications, advantages over conventional computing, and challenges in evolving artificial neural networks. Learn how to program chemical systems for desired behavior with a focus on optimization and design.

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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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