2018-00488 - [PostDoc2018-BIOCORE]Control and optimal control of bacterial growth

Niveau de diplôme exigé : Thèse ou équivalent

Fonction : Post-Doctorant

A propos du centre ou de la direction fonctionnelle

Le centre Inria Sophia Antipolis - Méditerranée compte 37 équipes de recherche, ainsi que 9 services d’appui à la recherche. Le personnel du centre (600 personnes environ dont 400 salariés Inria) est composé de scientifiques de différentes nationalités (250 personnes étrangères sur 50 nationalités), d’Ingénieurs, de Techniciens et d’Administratifs. 1/3 du personnel est fonctionnaire, les autres sont contractuels. La  majorité des équipes de recherche du centre sont localisées à Sophia  Antipolis et Nice dans les Alpes-Maritimes. Six équipes sont  implantées à Montpellier et une équipe est  hébergée par le département d'informatique de l'université de Bologne en Italie. Le Centre est membre de la Communauté d’Université et d’Établissement (ComUE) « Université Côte d’Azur (UCA) ».

Contexte et atouts du poste

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...).

 

Mission confiée

The general goal of this work is to design control strategies for improving product yield and productivity in E coli bacteria.

 

The Gene Expression Machinery of this bacterium has been modified (by techniques of genetic engineering) to obtain a strain where a chemical inducer controls the expression of RNA polymerase (an enzyme needed for the expression of the genes).

A simplified dynamical model of this controlled GEM will be developed (with our partners) and studied.

We will notably characterize the transients towards steady states and their duration, as well as the dependence of these properties on the concentrations of nutrients and inducer in the medium. Moreover, the possibility to externally adjust transients by choosing appropriate nutrients and inducer concentrations provides control parameters for, in the first place, the satisfaction of some biological constraints on the variables and dynamical behavior , and secondly, the optimization of product yield. Using optimal control, computer simulation and optimization, we will design control laws, possibly including feedback. The above analysis will also be carried out for fed-batch cultures in a fermenter (bioreactor), the condition most relevant for industrial biotechnological processes.

 

Principales activités

Mathematical modelling

Study of models (dynamical systems)

Numerical simulations

Control and optimal control

 

Compétences

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

Dynamical systems

Modelling

Control

Optimal control

see also

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

 

Keywords: Gene networks, biological models, control, dynamical systems, computational biology, numerical simulation

 

Avantages sociaux

  • Restauration subventionnée
  • Transports publics remboursés partiellement
  • Sécurité sociale
  • Congés payés
  • Aménagement du temps de travail
  • Installations sportives

Rémunération

Salaire: 2650 € brut mensuel