Description du sujet de thèse

Title: Finite Element Modeling of the Physicochemical Mechanisms Underlying Asymmetric Cell Divisions in Spiralians
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Scientific Context:
In many marine invertebrates, embryonic development begins with spiral cleavage, an ancestral mode of cell division. In several evolutionary lineages, this process has independently given rise to asymmetric cell divisions through the formation of a unique cortical structure known as the polar lobe (PL)—a transient cytoplasmic protrusion. This structure plays a crucial role in the segregation of cell fate determinants, exerting a profound influence on early embryonic development.
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Scientific Objectives:
The goal of this PhD project is to develop an advanced numerical platform based on finite element modeling to simulate the mechano-chemical mechanisms involved in the formation of polar lobes. The project will focus on two main aspects:
1. WP5 – Mechano-chemical Modeling of the Cell Cortex:
Develop a three-dimensional model coupling the biochemical dynamics of GTPases (Rho, Rac) with the active mechanics of the cell cortex. The model must integrate mass fluxes, contractility, and spatial bifurcation phenomena leading to low-tension cortical domains that drive the extrusion of the polar lobe.
2. WP6 – Modeling Cytoplasmic Flows and Fate Determinant Segregation:
Extend the previous model by dynamically coupling the cortical surface with the surrounding cytoplasmic fluid. Using unfitted finite element methods (FEM), the goal is to predict how cytoplasmic flows affect the spatial distribution of solid particles representing cell fate determinants.
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Methodology:
• Development of 3D models based on nonlinear partial differential equations (PDEs) coupling advection, diffusion, chemical reactions, and membrane mechanics
• Numerical implementation using surface FEM on implicit geometries (e.g., trace-FEM and aggregated FEM)
• Calibration of the models using experimental data from WP3–4 (e.g., cortical tension measurements, light-sheet microscopy, tracking of molecular markers)
• Systematic comparison of simulation results with experimental observations in spiralian species (e.g., Ilyanassa, Chaetopterus)
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Candidate Profile:
The ideal candidate should have a strong background in physics or applied mathematics, with a keen interest in cell biology. Skills in the following areas will be highly valued:
• Physical modeling (e.g., continuum mechanics, fluid dynamics)
• Finite element methods or related numerical techniques
• Scientific programming (e.g., Python, C++, Julia, FEniCS, FreeFem, GridAp, or equivalent)
An openness to interdisciplinary work and collaboration with biologists is essential.

Contexte de travail

This PhD project is part of an international HFSP fellowship in collaboration with the teams of Vanessa Barone (Stanford University, USA) and Chema Martin-Duran (Queen Mary University London, UK), combining evolutionary biology, cell mechanics, and computational modeling to decipher the physicochemical mechanisms responsible for the formation and function of polar lobes.

Contraintes et risques

Full-time position.
No specific risks identified.