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1. General Introduction
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From Pattern Formation to Morphogenesis
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From Pattern Formation to Morphogenesis
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
Next:
1. General Introduction
Up:
From Pattern Formation to Morphogenesis
Previous:
From Pattern Formation to Morphogenesis