Talks » Class » MontagnaMEW09

A Computational Framework for Multilevel Morphologies

Sara Montagna, Mirko Viroli
Complex systems in general exhibit a hierarchical organisation that has a crucial role in the static and dynamic characteristics of the systems themselves. These properties are highly dependent by the principles of downward and upward causation, where the behavior of the parts (down) is determined by the behavior of the whole (up), and the emergent behaviour of the whole is determined by the behaviour of the part. An example is given by biological systems: they are organised in different levels proteins, cells, tissues and so on and the constant interplay among these levels gives rise to their observed behaviour and structure. In this contest, an emblematic process is morphogenesis, which takes place at the beginning of the animal life and is responsible for the formation of the animal structure. Morphogenesis phenomena includes both cell-to-cell communication and intracellular dynamics: they work together, and influence each other in the formation of complex and elaborate patterns that are peculiar to the individual phenotype. We took inspiration from these biological phenomena to realise a computational frame- work to investigate both biological and artificial organisms capable to autonomously self- organise in complex structures. The computational framework allows the reproduction of multi-level and multi-compartments dynamics using the biochemical metaphor. It is based on (i) a high-level language to specify system structure, inner chemical behaviours, and stochastic actions to change system structure, and (ii) a simulation engine implementing an optimised version of Gillespie's SSA (stochastic simulation algorithm), which allows to exactly foresee the chemical evolution/diffusion of substances in the system. On the one hand, the framework aims at being a tool to investigate the realisation of self-organising morphogenetic systems, i.e. artificial systems which self-organise themselves exploiting bio-inspired morphogenetic processes. On the other hand this framework can be useful for modelling and simulation purposes of biological organisms during morphogenesis. One key mechanism in this contest is the spatial pattern formation of gene expressions. In particular we have investigated some phenomena that are responsible for the generation of Drosophila embryo segments, modelling the interaction among pathways inside the cell, that is responsible for its stabilisation into a specific genetic expression, and the the cell-to cell interactions mediated by cues, that enhance or inhibit the original cell?s activity and cause the formation of regions of cells with similar activity.

Presented by Sara Montagna
Morphogenetic Engineering Workshop
19/06/2009