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Junior research scientist on modelling microbial communities in environmental biotechnology processes

ABG-110638 Job Any
2023-02-01 Permanent > €35,000 and < €45,000 annual gross
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French National Research Institute for Agriculture, Food, and the Environment (INRAE)
ANTONY - Ile-de-France - France
  • Computer science
  • Mathematics
microbial dynamics modeling, spatialized modeling, individual-based models, agent-based models, coupled biophysical-chemical modeling, bioprocess modeling, biokinetic modeling, microbial thermodynamics
Research and Development


The French National Research Institute for Agriculture, Food, and the Environment (INRAE) is a public research establishment under the dual authority of the Ministry of Agriculture and the Ministry of Research.

INRAE is recruiting researchers by open competition and offering permanent position.

It is a major player in research and innovation created on 1st of January 2020. INRAE is a research institute resulting from the merger of INRA and IRSTEA. It is a community of 12,000 people with more than 200 research units and 42 experimental units located throughout France.

The institute is among the world leaders in agricultural and food sciences, in plant and animal sciences, and is 11th in the world in ecology and environment. INRAE’s main goal is to be a key player in the transitions necessary to address major global challenges. In the face of the increase in population, climate change, scarcity of resources and decline in biodiversity, the institute develops solutions for multiperformance agriculture, high quality food and sustainable management of resources and ecosystems.

Position and assignments

You will work at the PROSE (bioPROcesses for Services to the Environment) research unit located in Antony (92), in the greater Paris region. Affiliated to the TRANSFORM and MICA departments, PROSE is an INRAE research unit and part of the University Paris-Saclay. With a staff of approximately 30 people (21 permanent staff), the PROSE unit conducts research on environmental biotechnologies, including wastewater treatment and recovery plants, anaerobic digesters, and bioelectrochemical processes for environmental biorefineries. Our studies address scales ranging from microbial communities to processes and are linked to major societal challenges such as sustainable development, the circular economy, and the bioeconomy. Our activities fall within a transdisciplinary approach combining microbial ecology, biogeochemistry, bioelectrochemistry, chemical engineering, physical measurements, and modelling. The unit is organized into 3 divisions: project management, analytical support, and experimentation. You will join the project management division and will work under the direct responsibility of PROSE’s unit Manager.
PROSE has been developing research approaches in mechanistic modelling of bioprocesses for more than ten years. This work focuses in particular on the dynamics of functional microbial populations in relation to the thermodynamic balances of the various metabolic reactions, gas-liquid interfacial transfer phenomena via digital/numerical fluid mechanics approaches, or modelling bioprocess functioning as a whole using biokinetic models (approaches such as the "Activated Sludge Model" or "Anaerobic Digestion Model").
Your mission will be to develop mathematical agent-based models (or individual-based models) coupling microbial growth, metabolic activity, and physicochemical processes (mass or heat transfer, shear stress, etc.) to represent the dynamics and spatial structuration of functional microbial communities at small scales (micrometric to millimetric).

The objective is to study the emergence of spatial microbial organisation patterns such as layers or clusters of functional populations within biofilms, granules, or flocs. To do this, you will draw on your skills in mathematical modelling and numerical simulation, which you will be able to interface with the various fields of expertise already present in the unit (microbial ecology, biogeochemistry, chemical engineering, multiphysical measurement and modelling, bioelectrochemistry), to build interpretable models and to enable their comparison with experimental observations. In a wider perspective, the work developed will aim to improve understanding of how modifications of the biotope such as changes in bioprocess operating parameters and their consequences on the physicochemical conditions at a local scale, can modulate the assembly, spatial structuration, and properties of functional microbial communities. In addition to the environmental biotechnology sector, you will also be encouraged to contribute to cross-disciplinary networks within the MICA department and more broadly within INRAE (ECOSYST network, HOLOFLUX, and DIGITBIO metaprogrammes) to identify possible scientific opportunities concerning other microbial ecosystems (food microbial communities, digestive tracts, etc.).

Possible exposure to organic waste and wastewater in the context of laboratory activities or assignments on industrial sites.

Geographic mobility:



Part time


Candidates must have a PhD or equivalent.
After a master's or engineering degree, a PhD in mathematical modelling applied to biological systems, preferably in the field of (bio)processes, is highly recommended. You have research experience beyond the thesis (postdoc), preferably in an international context.
Training in numerical approaches and command of at least one numerical environment allowing the spatialized modelling of coupled bio/physical/chemical processes is recommended. Good knowledge of agent-based modelling would be a real asset (Individual Based Modelling approaches). An extensive list of scientific publications in international peer-reviewed journals demonstrating your ability to promote the results of your research is essential. You appreciate teamwork and interdisciplinarity.
Candidates should have a good command of English (both written and spoken), and long-term international experience would also be desirable. Successful candidates who have not yet acquired this experience abroad will be required to do so after their probationary period (1st year).

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