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Internship M2 2016-2017: Morphogenesis of Diatoms

Diatoms are microscopic unicellular algae that have the unique ability to incorporate silicon and synthesize with it a shell (called frustule) to protect themselves. The beauty of these frustules is exhibited as much by their geometry and regularity than by their incredible variety.

The phenomenology of the biological morphogenesis is the following: inside the ``Silica Deposition Vesicle’’, diffusing silica aggregates forming pores to create a very geometric silica grid which becomes a new frustule. The best modeling initiative made so far is based on Diffusion Limited Aggregation theory (DLA). While this idea is interesting, it has failed to persuade biologists of its relevance and leaves unanswered the problem of achieving the correct topology of the loops observed. We propose in this internship to revisit this idea by focusing on two improvements.

  1. The problem with the DLA theory is that the emerging patterns are not as regular as the ones observed in diatoms. We want to show that taking into account the moving boundaries can regularize them.
  1. Biological evidences indicate that silica aggregation is induced by a protein. Since this process would involve an interaction between three bodies, a "two species" DLA model where we could track the diffusion of the two species would be needed. This can be achieved within the framework of phase field modeling.
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We propose to investigate computationaly these two ideas. Some code have already been written in FreeFem++ and in FIPY (Python package for Finite Volume Element). No prior knowledge of these languages are necessary but enthousiathm for discovering new tools, and ease with the computer are important.

contact : (Room 710A)

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Biophysics, Dynamics of Out-of-Equilibrium Systems, Morphogenesis, embryogenesis, development, collective motion, self-organization, DERR Julien, DOUADY Stéphane, Proposition de stage ou de thèse, Ancienne proposition

Contact : Published on / Publié le 20 October 2014