PhD Position in Molecular Modeling

Type de poste
Niveau d'étude minimal
Dates
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce
Localisation
Adresse

Université de Reims Champagne Ardenne - UFR SEN - Campus Moulin de la Housse - Batiment 18
51687 Reims 2
France

Contacts
Pr. Manuel Dauchez
Dr. Nicolas Belloy
Email du/des contacts
manuel.dauchez@univ-reims.fr
nicolas.belloy@univ-reims.fr
Description

ESCRIME - Extension d’un Simulateur de Corps RIgides pour la Matrice Extracellulaire
Extracellular matrix (ECM) plays a key role in supporting tissues and organs. Many diseases are related to dysfunction of ECM components due to changes in their structures and/or the generation of fragments with deleterious effects. Due to technological limitations not allowing its observation at the mesoscopic scale, the precise organization of the ECM remains poorly known, with rare or fuzzy experimental data. Using physical engines such as Unity3D, as well as rigid-bodies dynamics, we have developed a demonstrator for modeling and simulating large biological macromolecules in the form of dynamic chains of interacting rigid bodies [1]. This specific development allowed us to obtain results showing how parameters such as flexibility or the nature and number of interactions between molecules can induce different 3D structures depending on the compartments of ECM considered. This project aims at extending/validating this approach to ECM components, for instance elastin and its monomer tropoelastin, to better understand the complexity of the ECM. In the long term, in an integrative approach, we want to parameterize the set of interactions referenced in some databases like MatrixDB [2], to carry out the related simulations and discuss the various models trying for several decades to explain the elasticity and the structural properties of the ECM. Depending on the progress of the project, we plan to study the assembly and polymerization of elastin, to study the behavior of ECM components in crowded environments, to make our virtual model of the ECM more complex.
This project is funded by Region GrandEst and Université de Reims Champagne-Ardenne. The candidate will work in Team MIME, UMR CNRS/URCA 7369 MEDyC (www.univ-reims.fr/medyc/) in Reims.
Candidates should have a strong background in computer science and/or biophysics and/or biochemistry. Preliminary experience in programming (C#, python, Unity …) and/or molecular simulations will be key advantages.
Applications are now open. Please send a CV, a motivation letter and at least one reference letter to Pr. M. Dauchez (manuel.dauchez@univ-reims.fr) and Dr. N. Belloy (nicolas.belloy@univ-reims.fr) before June 21, 2019.

[1] Wong, Hua, Jessica Prévoteau-Jonquet, Stéphanie Baud, Manuel Dauchez, and Nicolas Belloy. “Mesoscopic Rigid Body Modelling of the Extracellular Matrix Self-Assembly.” Journal of Integrative Bioinformatics 15, no. 2 (June 26, 2018). https://doi.org/10.1515/jib-2018-0009.
[2] Chautard, Emilie, Lionel Ballut, Nicolas Thierry-Mieg, and Sylvie Ricard-Blum. “MatrixDB, a Database Focused on Extracellular Protein-Protein and Protein-Carbohydrate Interactions.” Bioinformatics (Oxford, England) 25, no. 5 (March 1, 2009): 690–91. https://doi.org/10.1093/bioinformatics/btp025.

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