MISOWASP - Linking Molecular scale Interactions of Soil Organic matter with WAter retention in Soil-Plant systems
Contact: Dr. Stephan Schott-Verdugo
Soil organic matter (SOM) and extracellular polymeric substances (EPS) play a central role in soil structure, water retention, nutrient cycling, and plant-microbe interactions. Their molecular behavior has profound effects on soil hydraulic properties and biome stability. However, despite advances in continuum modeling of soil and plant-water systems, the molecular-scale mechanisms underlying these processes remain poorly represented. This project aims to fill that gap by using molecular simulations to quantify the interactions of SOM and EPS with water and minerals, and to connect these insights with larger-scale soil and plant models.
A candidate for this project has:
- Strong background in Structural Bioinformatics and Molecular Dynamics (MD) simulations
- Experience in setting up and running MD simulations. Previous usage of the AMBER suite is an asset
- Knowledge on force fields structures and analyzing molecular trajectories to extract structural and energetic insights
- Familiarity with assembling complex molecular systems and integrating heterogeneous data sources
- Solid knowledge of Linux environments, including experience with HPC systems
- Practical experience working with conda environments and Python scripting
- Motivation to contribute to the development of an open-source molecular modeling platform for soil components
- Hands-on experience in using differential calculus
- Strong interest in using process-based mathematical modeling of carbon cycling in soil-plant systems
This position offers an exciting opportunity to work at the frontier of computational biophysics, soil science, and plant systems modeling, contributing to a novel framework that connects atomic-scale dynamics to ecosystem-level functions.