Contents

• Contents
  • 1. General Introduction
    • 1.1 From Pattern Formation to Morphogenesis
    • 1.2 Excitable Media and Oscillatory Systems
    • 1.3 A Two-Scale CA with Differential Adhesion
    • 1.4 The Cellular Slime Mould
      • 1.4.1 The life cycle
      • 1.4.2 Key elements of morphogenesis
      • 1.4.3 Model history
    • 1.5 This Thesis
• I. Pattern Formation in Homogeneous Excitable Media
  • 2. Spiral Breakup in Excitable Tissue due to Lateral Instability
    • 2.1 Introduction
    • 2.2 The Model
    • 2.3 Results
    • 2.4 Discussion
• II. Morphogenesis of Dictyostelium discoideum
  • 3. Migration and Thermotaxis of Dictyostelium discoideum Slugs, a Model Study
    • 3.1 Introduction
    • 3.2 The Model
      • 3.2.1 Description of the amoebae
      • 3.2.2 cAMP dynamics
      • 3.2.3 Chemotaxis
    • 3.3 Slug Migration
      • 3.3.1 Stability of the slug shape
      • 3.3.2 Motion velocity
      • 3.3.3 Cell sorting
    • 3.4 Thermotaxis
      • 3.4.1 Mechanism of thermosensitivity
      • 3.4.2 Thermosensitivity and the influence of stochastic noise
      • 3.4.3 A partially thermosensitive slug
    • 3.5 Discussion
      • 3.5.1 Slug motion and cell sorting
      • 3.5.2 Thermotaxis
  • 4. Phototaxis during the Slug Stage of Dictyostelium discoideum: a Model Study
    • 4.1 Introduction
    • 4.2 The Model
    • 4.3 Phototaxis
    • 4.4 Discussion
    • 4.5 Conclusions and Predictions
  • Colour Plates
  • 5. How Slime Moulds Self-Organise into a Fruiting Body: the ``Reverse Fountain'' Explained
    • 5.1 Introduction
    • 5.2 The Model
    • 5.3 Results
    • 5.4 Discussion
    • Appendix
    • 5.5 Methods
  • 6. Modelling Dictyostelium discoideum Morphogenesis: the Culmination
    • 6.1 Introduction
      • 6.1.1 Stalk formation
      • 6.1.2 Cell differentiation
      • 6.1.3 Cell movements
    • 6.2 The Model
      • 6.2.1 Adhesion
      • 6.2.2 Cell differentiation
      • 6.2.3 cAMP signalling
      • 6.2.4 Initial condition
    • 6.3 The Culmination of Dictyostelium discoideum
      • 6.3.1 Tube formation
      • 6.3.2 Stalk elongation
      • 6.3.3 The role of cAMP and pathfinder cells in stalk elongation
      • 6.3.4 Correction of orientation
      • 6.3.5 Anchoring
      • 6.3.6 Final configuration
      • 6.3.7 Cell adhesion
    • 6.4 Discussion
      • 6.4.1 Stalk formation
      • 6.4.2 cAMP signalling
      • 6.4.3 Model considerations
      • 6.4.4 Side-effects
      • 6.4.5 Conclusions
  • 7. Summarising Discussion
    • 7.1 A Short Review
    • 7.2 From Local Interactions towards Global Coordination
    • 7.3 Model Complexity
      • 7.3.1 From simple to simpler, to a little more complex
      • 7.3.2 Interaction of generic modules
        and interesting new observables
      • 7.3.3 Gene regulation and morphogenesis
      • 7.3.4 Evolving complexity
    • 7.4 Future Directions
    • 7.5 Conclusion
• Bibliography
• Samenvatting
• Curriculum Vitæ
• List of Publications
• Dankwoord