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Agent Based Model
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Classroom Contents
Turing's Reaction-Diffusion System and Agent-Based Models in Biology - Lecture 2
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- 1 Turing's reaction-diffusion system - 2
- 2 2021.1.20 Thirsty of Theoretical Biology
- 3 Experience the Turing system!
- 4 Original reaction-diffusion model
- 5 The simulations beautifully regenerate the animal pattern
- 6 an alternative mechanism Positional information model
- 7 How can we prove the existence of the Turing system?
- 8 [Code Walkthrough]
- 9 Prediction by the Turing simulation
- 10 Napoleon fish
- 11 How the pattern change?
- 12 Time course of pattern change
- 13 Skin patterns of fish show specific dynamics of Turing pattern
- 14 Parameter analysis of RD mechanism
- 15 Additional evidence II
- 16 Experiments to identify the real mechanism following the idea of "Reductionism"
- 17 Short range inhibition
- 18 Exclusion melanophores by xanthophores
- 19 Interaction occurs by the direct touch
- 20 Finding long range interaction
- 21 Melanophores in the center of the black stripe extend the long projection toward xanthophores
- 22 Major interactions between the pigment cells
- 23 To "tune" the activity of cx418, series of deletions at the amino-terminal are generated.
- 24 Modulation of single gene activity can generate variety of patterns
- 25 Is the identified mechanism equal to the RD model?
- 26 Identified network is similar to the Turing model.
- 27 Summary
- 28 Problem!! No diffusion in the real system.
- 29 Agent-based model
- 30 Merits of the Agent-based model
- 31 Agent Based Model
- 32 Original reaction-diffusion model
- 33 Diffusion from cell body Diffusion from cell projection
- 34 Representing the interaction profile by kernel
- 35 KT Model Simulator
- 36 Random Pattern Clear Field
- 37 [Demo]
- 38 KT model can generate standard patterns of the RD model
- 39 Inverted kernel make the waves with different wave length
- 40 Small change of the kernel cause the massive change of wave length
- 41 The kernel shape does not affect to the resulting pattern.
- 42 Nested patterns in simulation and in fish
- 43 Merits of the KT model
- 44 Periodic patterns in organisms
- 45 Zebra vs Horse
