Mots-Clés

scientific computing, molecular modeling, molecular dynamics, multi-scale representations

Description

Title of the internship: Integration of backmapping methods from mesoscopic to atomistic scales

Subject of the internship:

MEDyC laboratory uses and develops various computer tools to model, at different scales, the extracellular matrix and the membrane on which it rests. These tools include molecular dynamics (Gromacs, Plumed, LAMMPS, ...) at atomistic and coarse grain scales as well as rigid body mesoscopic modeling (Unity3D) and the development of an online database dedicated to lipids and membrane objects. (https://limonada.univ-reims.fr/). Switching to a finer resolution scale is not trivial, especially between the mesoscopic and atomistic scales. The laboratory therefore wishes to add new functionalities to its tools allowing these changes of scale.

The internship will focus on the development and adaptation of reverse mapping methods that can be integrated into the tools used in the laboratory. This includes the porting and development of C ++ or Python code to Plumed programs mainly written in C ++ and / or the development of Python code which can be integrated into the LIMONADA code.

Educational project: This internship will allow the student to participate to the computer development of new methods in a scientific research environment.

Profile: The student, bioinformatician or computer scientist must have good knowledge of C++, bash and python programming under linux. It will integrate a team of biologists, bioinformaticians and biophysicists of around ten people

Duration - period: 4 to 6 months - January to June / July 2022

Team - location: Molecular Modeling and Multiscale Imaging (MIME) team Bat. 18, Campus Moulin de la Cover, 51100 Reims

Contact: jean-marc.crowet@univ-reims.fr (Molecular dynamics, Modeling) hua.wong@univ-reims.fr (Rigid bodies, Mesoscopic modeling)

Keywords: scientific computing, molecular modeling, molecular dynamics, multi-scale representations