1. Affinity Based Model of Multicellular Development Oisín Mac Aodha 4ECE 02/04/2007

2. This project investigates if it is possible to model the development of multicellular organisms. Presentation Structure: - Background - Brief introduction to genetic algorithms (GAs) - Introduction to development - Modelling development - Experimental results - Conclusions Introduction Affinity Based Model of Multicellular Development

3. As the drive towards nano-scale fabrication continues we may soon reach a point where physical manipulation of atomic scale components will become impossible. A possible alternative to the current top-down lithographic process would be a bottom up manufacturing process where the pre-existing components of a system can automatically self assemble to produce the desired behavior. Background Affinity Based Model of Multicellular Development

4. Genetic Algorithms Affinity Based Model of Multicellular Development

5. The goal is to evolve an a population whose individuals comprise of just 1s. Ones Max Problem Affinity Based Model of Multicellular Development

6. Development Affinity Based Model of Multicellular Development http://www.microscopy-uk.org.uk/ Development is the process by which organisms grow and develop.

7. As the problem becomes more complex so will the processing time required by a GA to find the best solution. Development allows a more complex genotype to phenotype mapping compared to the one to one mapping provided by a GA. May contribute to achieving the levels of complexity as seen in nature. Why Use Development? Affinity Based Model of Multicellular Development

8. Development was modelled using Java by creating a gene regulatory network. Corresponding classes were created for the objects found in nature including: Protein, Gene, Chromosome, Cell and Phenotype. GA was used to evolve the genome (configuration) used data for development. Modelling Development Affinity Based Model of Multicellular Development

9. In a GRN, a gene produces a protein. The protein produced subsequently affects other genes and ultimately cell behavior. Gene Regulatory Network Affinity Based Model of Multicellular Development

10. The affinity matrix contains the protein-gene interaction strengths. The gene transcribes a new protein when the evolved threshold for the gene is exceeded. Affinity Matrix Affinity Based Model of Multicellular Development

11. The following results were obtained using the configuration data below. Single Cell Results Affinity Based Model of Multicellular Development

12. Flat Concentration Affinity Based Model of Multicellular Development

13. Linear Concentration Affinity Based Model of Multicellular Development

14. Heterochrony Affinity Based Model of Multicellular Development

15. Next stage was to expand the current single cell model to allow for multicellular development. Cells have the ability to: - Divide - Die - Communicate (via signalling proteins) Multicellular Development Affinity Based Model of Multicellular Development

16. Cell division is the process by which a parent cell divides into two cells. The genome of the parent cell is transferred is copied and transferred to the new cell. Protein concentrations are distributed between the cells. Cell Division Affinity Based Model of Multicellular Development

17. The direction a cell divides in is based on the concentration of the direction protein. The direction around the unit circle corresponds to the eight possible neighbouring locations a cell has in a 2D grid. Cell Direction Affinity Based Model of Multicellular Development

18. The multicellular model has nine proteins with the following functions: Protein Functions Affinity Based Model of Multicellular Development

19. For the multicellular experiments the fitness was based on the position of the cells. Multicellular Results Affinity Based Model of Multicellular Development

20. Line Affinity Based Model of Multicellular Development Step 1 Step 10 Step 20 fitness = (1/cellsInside) + (cellsOutside/desiredLength)

21. Square Affinity Based Model of Multicellular Development Step 7 Step 15 Step 20 fitness = (size*size) – cellsInside + cellsOutside

22. A morphogen is a substance which governs the positions of the various specialized cell types within an organism. It spreads from a localised source and forms a concentration gradient across a developing organism. Based on Wolpert’s French flag model. Morphogens Affinity Based Model of Multicellular Development

23. morphogenConc = sourceConc x (1 / (sourceConc + distanceFromSource)) Morphogen Gradients Affinity Based Model of Multicellular Development

24. French Flag Affinity Based Model of Multicellular Development

25. Research: - Inter cell communication - More complex development model - 3D organisms - Environmental effects during development Possible Applications: - Self developing systems - Fault repairing circuits Future Research Affinity Based Model of Multicellular Development

26. Questions Affinity Based Model of Multicellular Development http://ohm.nuigalway.ie/0607/03macaodha