Objectives:
The project focuses on the use of IA to study reactions linked to the origin of life. The project will be carried out in the SITh team in collaboration with Prof. Damien Laage (ENS, Paris) and Dr. Rolf David on the AI aspects and with Prof. Yannick Vallée and Dr. Véronique Blandin on the prebiotic chemistry aspects. We would therefore like to study a reaction in aqueous medium on the SAH molecule, derived from SAM (S-adenosylmethionine), which would be a key step in the setting up of the protein factory. This study falls within the framework of the TRP (Thiol Rich Peptide) world hypothesis, which is linked to the RNA (ARN) world hypothesis [1].In view of the reagents used and the reaction paths proposed, simulations that explicitly include solvent effects are necessary. We will therefore propose to use the software under construction ArcaNN coupled with deepMD [2] to determine the mechanisms involved. The candidate will interact regularly with the experimental team in Grenoble but also with our theoretical collaborator in Paris.
Applicant profile:
The successful candidate will have expertise in computational chemistry. Knowledge of neural networks potential like deepMD2 or software for dynamics (cp2k or/and lammps for example) will be appreciated. An open mind and broader chemical culture will also be a key asset for interacting with the experimental team.Further information and application:
Contact Prof. Anne Milet by email (Anne.Milet@univ-grenoble-alpes.fr) ASAP. Please attach a
letter of motivation, CV, list of publications and recommendation letter(s) (pdf format).Bibliography:
[1] Vallee, Y.; Shalayel, I.; Ly, K.-D.; Rao, K. V. R.; De Paëpe, G.; Märker, K.; Milet, A. At the Very Beginning of Life on Earth: The Thiol-Rich Peptide (TRP) World Hypothesis. Int J Dev Biol 2017, 61 (8–9), 471–478. https://doi.org/10.1387/ijdb.170028yv.)
[2] Wang, H.; Zhang, L.; Han, J.; E, W. DeePMD-Kit: A Deep Learning Package for Many-Body Potential Energy Representation and Molecular Dynamics. Computer Physics Communications 2018, 228, 178–184. https://doi.org/10.1016/j.cpc.2018.03.016.
