Mots-Clés
molecular dynamics
artificial intelligence
knowledge graph
simulation
Description
We offer a PhD position that applies artificial intelligence and knowledge graphs to the exploration of molecular dynamics simulation data.
Context and research project:
Molecular dynamics is an essential simulation technique for studying molecular behavior across a variety of fields, ranging from materials science to biology. These simulations generate high-value data due to the specialized expertise required for their setup and analysis, as well as the significant computational resources involved in their production. In line with open science principles, many researchers share their molecular dynamics simulations in public data repositories. Unfortunately, these datasets are often inadequately identified and annotated, significantly limiting their reuse (see paper https://elifesciences.org/articles/90061).
The main objectives of this PhD project are to:
- Enrich metadata describing molecular dynamics simulation datasets;
- Extract relevant information from datasets as well as from scientific publications related to molecular dynamics;
- Build a knowledge graph linking datasets and publications;
- Develop interactive methods for exploring this knowledge graph.
This PhD thesis will be conducted at the Laboratory of Theoretical Biochemistry (LBT, http://www-lbt.ibpc.fr/) in Paris, France. LBT has extensive expertise in theoretical and computational biochemistry, at the intersection between biology, chemistry, physics, and computer science.
This research is part of the European LUMEN project, which aims to create an innovative platform for the discoverability and exploration of research outputs.
Candidate Profile:
We seek a motivated candidate holding a Master’s degree in computational chemistry, bioinformatics, or a closely related field. Applicants should demonstrate a keen interest in software development and methodological innovation, particularly involving artificial intelligence. Given the large volume of data involved, we are looking for someone meticulous with strong organizational skills.
Please submit your application, including a cover letter, a curriculum vitae, and contact details for two scientific references by email before May 12th.