PhD student in experimental and digital biophysics M/F
PhD @French National Centre for Scientific Research posted 5 hours agoJob Description
General information
Job title: PhD student in experimental and numerical biophysics M/F
Reference: UMR5306-JEARIE-002
Number of positions: 1
Work location: VILLEURBANNE
Publication date: Friday, June 6, 2025
Type of contract: Fixed-term contract PhD student
Contract duration: 36 months
Thesis start date: October 1, 2025
Workload: Full
Remuneration: The remuneration is a minimum of €2,200.00 per month
Section(s) CN: 05 – Condensed matter: organization and dynamics
Description of the thesis subject
This thesis will focus on the spontaneous phase separation of a cluster of amoeboid cells under hypoxia, i.e., under oxygen deficiency conditions. At high density, a dividing population of Dictyostelium discoideum (Dicty) cells spontaneously separates into multicellular aggregates of well-defined size and into a cluster of individual cells. We have previously demonstrated that this phenomenon results from the competition between cell-cell adhesion and aerotaxis, i.e., the tendency of Dicty cells to follow oxygen gradients.
The proposed interdisciplinary project will aim to explore other aspects of this “microphase”-like phase separation:
1. The mechanism responsible for the movement of the aggregates, which remains unknown;
2. The highly dynamic nature of these aggregates, in marked contrast to phase separation in inert systems;
3. The three-dimensional structure of the aggregates and the role of oxygen gradients in this organization.
To achieve this, the recruited PhD student will develop both experimental and numerical approaches.
On the experimental side, the objectives will be:
• To conduct new, better controlled experiments to accurately quantify the dynamics of the process via image analysis, aggregate tracking and data analysis;
• To study the mechanism of aggregate locomotion, in particular by asking whether it results from cellular exchanges between aggregates and the “gas” of individual cells. This will be achieved by using single cell tracking in both phases, by live fluorescence microscopy in 3D (xy + time) or in 4D (xyz + time);
• To use cell biology approaches combined with 3D microscopy (rotating disk, light sheet) to characterize the three-dimensional structure of aggregates.
On the numerical level, the doctoral student will implement cellular Potts-type models reproducing the main characteristics of Dicty cells: persistent movement, cell adhesion and aerotaxis.
• The first objective will be to reproduce in 2D the complex dynamics observed and quantified experimentally;
• The second will be to develop three-dimensional simulations to test the hypothesis that vertical oxygen gradients are at the origin of the 3D structure of the aggregates.
Work context
The Lumière Matière Institute (iLM) is a CNRS-Université Lyon 1 research unit located on the Lyon Tech La Doua campus (accessible by public transport from the city center). With more than 300 employees, including around a hundred doctoral and post-doctoral students, the iLM is a major player in physics and chemistry research in the Auvergne Rhône Alpes region, internationally recognized for the excellence of its research.
The continuum between fundamental research, responding to major societal challenges, and innovation is at the heart of this unit’s approach. All staff are committed to promoting excellence and ethical and responsible research.
The thesis will be carried out within the Biophysics team at the Lumière Matière Institute in Lyon. It is part of a project funded by the ANR, involving biologists, biophysicists, theoretical physicists, and mathematicians. The profile sought is that of a candidate with dual experimental and theoretical skills, demonstrating a strong interest in research at the interface between physics and biology, and possessing solid skills in scientific programming of active matter systems. Experience in cell biology, 3D microscopy and/or Potts cellular modeling would be a plus.
