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Reference : UMR5502-YOHDAV-008
Workplace : TOULOUSE
Date of publication : Wednesday, February 17, 2021
Scientific Responsible name : Yohan Davit and Pascal Swider
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 September 2021
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly
Description of the thesis topic
When bacteria develop onto a solid surface, they produce a matrix of extracellular polymeric substances and form a biofilm. Biofilm growth in porous media can clog pores and induce an important increase in pressure drop. In this work, we ask whether we can control this bioclogging and the permeability of porous structures? Developing new strategies to manage bacterial growth and a control theory for biofilms in porous media would have numerous applications in engineering, including in soil bioremediation or for creating novel classes of self-repairing materials. From a fundamental viewpoint, this implies that we understand the fundamental mechanisms of growth and development of bacteria in porous media.
To tackle this problem, we have developed an approach base on X-ray tomography to image the 3D distribution of biofilms in porous structures. More importantly, we have also developed a micro-bioreactor technology using 3D printing that can be used to study both bacterial growth in porous media and the system response in permeability. We want to characterize the pressure drop and control it, by using modifications of hydrodynamic, nutrient and temperature conditions; by introducing bacterial predators; and by altering communications between bacteria.
The goal of this PhD work is to develop a demonstration micro-bioreactor for which we can control precisely and in a reversible manner the permeability. We will use our existing technology (collaboration with the LAAS-CNRS), that we will adapt to allow for control engineering. The successful candidate will primarily work in a safety level 2 biology laboratory, manipulate microorganisms such as Pseudomonas aeruginosa PAO1 or Staphylococcus aureus, and participate actively to discussions within the team and with biologists.
We are looking for an extremely motivated student who will be fully involved in a multidisciplinary project at the interface between physics, fluid mechanics and microbiology. The relevant background includes chemical engineering, process engineering, experimental fluid mechanics, microfluidics, biophysics, bioengineering, microbiology or microbial ecology. The exact focus of the work (biophysics, engineering) and the tools (microfluidics, micro-bioreactors, simulations) can be tailored to the interest and background of the candidate.
This position is part of a large project (BEBOP, 2019-2024) funded by the European Research Council. The goal of BEBOP is to figure out how we can use bacteria to control the properties of porous structures (e.g. porosity, permeability). We envision that this will unlock a new generation of biotechnologies, such as self-repairing construction materials or self-cleaning bioreactors. The main scientific obstacle to this technology is the lack of understanding of the biophysical mechanisms associated with the development of bacterial populations within complex porous structures. Therefore, the first scientific objective of BEBOP is to gain insight into how fluid flow, transport phenomena and bacterial communities (biofilms) interact within connected heterogeneous structures. To this end, we combine microfluidic and 3D printed micro-bioreactor experiments; fluorescence and X-ray imaging; high performance computing bringing together CFD, individual-based models and pore network approaches. The second scientific objective of BEBOP is to create the primary building blocks toward a control theory of bacteria in porous media and to construct a demonstrator bioreactor for permeability control.
The research lab in Toulouse is the institute of fluid mechanics (Allee Camille Soula, 31400 Toulouse, France.), which is associated with both the University of Toulouse and the CNRS. This is one of the largest labs in fluid mechanics in France, with about 65 academics, 35 technicians and engineers, 80 PhD students and 20 postdocs. Research covers a wide range of topics in fluid mechanics (biomechanics, turbulence, multiphase systems, heat transfer, multiscale reactive transfers). IMFT is considered one of the best laboratories in its area in France.
Constraints and risks
- Work in a level 2 biological safety lab with constraining protocols
- Manipulate pathogenic bacteria
- Work with light sources including lasers
For more info about research activities @ Toulouse, http://yohan-davit.com
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