Missions

The research project aims to characterize at the molecular level the origin of specific ion effects in catalysis by a ribozyme (RNA-based enzyme). The project will build on methods and protocols developed in recent years in the team to dynamically explore (DFTB3/MM-MD) the reaction pathway in the presence of different ions. The free energy profile will then be refined using recent ML/MM-MD methodologies. The researcher will also be involved in the parametrization and evaluation of a new Amber-OL15-ECC force field for the description of ion-nucleic acid interactions.

Activities

- QM/MM-MD simulations
- training and evaluation of an ML/MM-MD methodology
- molecular dynamics simulations
- alchemical free energy calculations
- machine learning potentials
- detailed analysis of simulations (writing scripts)
- independent writing of scientific articles
- presentation of results in English

Skills

- PhD in theoretical or biophysical chemistry
- experience in molecular dynamics for complex (biological) systems
- desired experience in some of the following fields: advanced sampling /alchemical calculations, QM/MM, RNA modeling, Neural Network Potentials
- programming for simulation analysis
- mastery of English (C1). Knowledge of French not necessary.

Work Context

The Laboratory of Theoretical Biochemistry (11 permanent researchers, about thirty members in total) is located in the heart of Paris, in a very scientifically stimulating environment. We are specialized in modeling, at different scales, of biological systems. This project is supported by ANR funding.