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Inria
2019-01276 - Post-Doctoral Research Visit F/M [BIOCORE] Mathematical models and control of microbial communities
Inria
Inria couvre l’ensemble du spectre des recherches au coeur de ces domaines d’activités, et intervient sur les questions, en lien avec le numérique, posées par les autres sciences et par les acteurs économiques et sociétaux.
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Publié: il y a 20 jours
Date limite d'inscription: févr. 25
Localisation: Valbonne, France
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2019-01276 - Post-Doctoral Research Visit F/M [BIOCORE] Mathematical models and control of microbial communities

Contract type: Public service fixed-term contract

Renewable contract: Oui

Level of qualifications required: PhD or equivalent

Function: Post-Doctoral Research Visit

About the research centre or Inria department

The Inria Sophia Antipolis - Méditerranée center counts 37 research teams and 9 support departments. The center's staff (about 600 people including 400 Inria employees) is composed of scientists of different nationalities (250 foreigners of 50 nationalities), engineers, technicians and administrators. 1/3 of the staff are civil servants, the others are contractual. The majority of the research teams at the center are located in Sophia Antipolis and Nice in the Alpes-Maritimes. Six teams are based in Montpellier and a team is hosted by the computer science department of the University of Bologna in Italy. The Center is a member of the University and Institution Community (ComUE) "Université Côte d'Azur (UCA)".

Context

The study of genetic regulatory networks has taken a qualitative leap through the use of modern genomic techniques that allow simultaneous measurement of the expression levels of all genes of an organism. In addition to high-throughput experimental methods, approaches in mathematics and computer science will be indispensable for analyzing the dynamics of genetic regulatory networks. BIOCORE team applies mathematical and computational methods from Control Theory and Dynamical Systems to the study of models of genetic networks and more general biological networks (metabolic networks, signaling networks...).

Assignment

Within the framework of the IPL COSY (real time COntrol of SYnthetic microbial communities), see https://project.inria.fr/iplcosy/, the general aim is to exploit complex microbial communities into a micro-bioreactor system to optimize a specific objective via real-time control.

A mathematical model, consisting of a system of nonlinear ordinary differential equations, has been written for the analysis and control of two synthetic communities of Escherichia coli bacteria (producer and cleaner) in a continuous bioreactor.

The first task is to study this dynamical model, the stability of equilibria, the possible bifurcations, and in particular the possibility of coexistence of the two populations.

The second task will be to control the system (several controls are possible), in particular the composition of the community, and to optimize an objective like the maximization of the production of a molecule of interest.

The above analysis will also be carried out for fed-batch cultures in a fermenter (bioreactor), the condition most relevant for industrial biotechnological processes.

The work is done in collaboration with IBIS Inria Team (Grenoble) within the IPL Cosy project

Some references:

Milias-Argeitis et al. (2016). Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth. Nat Commun, 7(12546).

Yegorov, I., Mairet, F., de Jong, H. et al. . Optimal control of bacterial growth for the maximization of metabolite production. J. Math. Biol. (2018) https://doi.org/10.1007/s00285-018-1299-6, in press

H.de Jong, S.Casagranda, N.Giordano, E.Cinquemani, D.Ropers, J.Geiselmann, J.-L.Gouzé, “Mathematical modelling of microbes: Metabolism, gene expression and growth”. Journal of the Royal Society Interface, 14:20170502, 2017

Main activities

  • Study the dynamical behaviors of  models
  • control the models

see

Web page of JL Gouze: http://www-sop.inria.fr/members/Jean-Luc.Gouze/JLGouze-eng.html 
Web page of M. Chaves: http://www-sop.inria.fr/members/Madalena.Chaves

see also IBIS web page: https://team.inria.fr/ibis/

and IPL CoSy webpage: https://project.inria.fr/iplcosy/

Benefits package

  • Subsidized meals
  • Partial reimbursement of public transport costs
  • Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
  • Possibility of teleworking (after 6 months of employment) and flexible organization of working hours
  • Professional equipment available (video conferencing, loan of computer equipment, etc.)
  • Social, cultural and sports events and activities
  • Access to vocational training
  • Social security coverage

Remuneration

Salary: 2650 € brut mensuel

General Information

  • Theme/Domain: Modeling and Control for Life Sciences
  • Town/city: Sophia Antipolis
  • Inria Center: CRI Sophia Antipolis - Méditerranée
  • Starting date: 2019-04-01
  • Duration of contract: 1 year, 7 months
  • Deadline to apply: 2019-02-25

Contacts

The keys to success

We are looking for an applied mathematician with a  background in the analysis of dynamical systems, and familiar with control theory. In addition, we expect a strong motivation to work on biological applications in genomics.

About Inria

Inria, the French national research institute for the digital sciences, promotes scientific excellence and technology transfer to maximise its impact. It employs 2,400 people. Its 200 agile project teams, generally with academic partners, involve more than 3,000 scientists in meeting the challenges of computer science and mathematics, often at the interface of other disciplines. Inria works with many companies and has assisted in the creation of over 160 startups. It strives to meet the challenges of the digital transformation of science, society and the economy.

Instruction to apply

Defence Security : 
This position is likely to be situated in a restricted area (ZRR), as defined in Decree No. 2011-1425 relating to the protection of national scientific and technical potential (PPST).Authorisation to enter an area is granted by the director of the unit, following a favourable Ministerial decision, as defined in the decree of 3 July 2012 relating to the PPST. An unfavourable Ministerial decision in respect of a position situated in a ZRR would result in the cancellation of the appointment.

Recruitment Policy : 
As part of its diversity policy, all Inria positions are accessible to people with disabilities.

Warning : you must enter your e-mail address in order to save your application to Inria. Applications must be submitted online on the Inria website. Processing of applications sent from other channels is not guaranteed.

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