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Affinity Based Model of Multicellular Development

Affinity Based Model of Multicellular Development. Oisín Mac Aodha 4ECE. 02/04/2007. Introduction. This project investigates if it is possible to model the development of multicellular organisms. Presentation Structure: - Background - Brief introduction to genetic algorithms (GAs)

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Affinity Based Model of Multicellular Development

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

  2. Introduction 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 Affinity Based Model of Multicellular Development

  3. Background 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. Affinity Based Model of Multicellular Development

  4. Genetic Algorithms Affinity Based Model of Multicellular Development

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

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

  7. Why Use Development? 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. Affinity Based Model of Multicellular Development

  8. Modelling Development 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. Affinity Based Model of Multicellular Development

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

  10. Affinity Matrix 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 Based Model of Multicellular Development

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

  16. Cell Division 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. Affinity Based Model of Multicellular Development

  17. Cell Direction 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. Affinity Based Model of Multicellular Development

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

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

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

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

  22. Morphogens 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. Affinity Based Model of Multicellular Development

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

  24. French Flag Affinity Based Model of Multicellular Development

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

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

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