Turing's Reaction-Diffusion System and Agent-Based Models in Biology - Lecture 2

Turing's reaction-diffusion system - 2
2021.1.20 Thirsty of Theoretical Biology
Experience the Turing system!
Original reaction-diffusion model
The simulations beautifully regenerate the animal pattern
an alternative mechanism Positional information model
How can we prove the existence of the Turing system?
[Code Walkthrough]
Prediction by the Turing simulation
Napoleon fish
How the pattern change?
Time course of pattern change
Skin patterns of fish show specific dynamics of Turing pattern
Parameter analysis of RD mechanism
Additional evidence II
Experiments to identify the real mechanism following the idea of "Reductionism"
Short range inhibition
Exclusion melanophores by xanthophores
Interaction occurs by the direct touch
Finding long range interaction
Melanophores in the center of the black stripe extend the long projection toward xanthophores
Major interactions between the pigment cells
To "tune" the activity of cx418, series of deletions at the amino-terminal are generated.
Modulation of single gene activity can generate variety of patterns
Is the identified mechanism equal to the RD model?
Identified network is similar to the Turing model.
Summary
Problem!! No diffusion in the real system.
Agent-based model
Merits of the Agent-based model
Agent Based Model
Original reaction-diffusion model
Diffusion from cell body Diffusion from cell projection
Representing the interaction profile by kernel
KT Model Simulator
Random Pattern Clear Field
[Demo]
KT model can generate standard patterns of the RD model
Inverted kernel make the waves with different wave length
Small change of the kernel cause the massive change of wave length
The kernel shape does not affect to the resulting pattern.
Nested patterns in simulation and in fish
Merits of the KT model
Periodic patterns in organisms
Zebra vs Horse