Do you enjoy working in an interdisciplinary research setting where computational chemistry and AI oriented research are joining forces? The Van 't Hoff Institute for Molecular Sciences , in collaboration with Microsoft Research Amsterdam, is looking for an ambitious PhD student to develop and apply novel computational techniques to answer important chemical/biological/physical questions. Many systems and processes in biology, medicine and material science consist of many interacting molecules that give rise to emergent, complex behaviour. Such complex systems undergo transitions between states, such as the folding of a protein, the association of a ligand, or a phase transition to another state or regime. These transitions are crucial to understand the systems behaviour, but are often rare and difficult to study. Molecular dynamics simulation is a powerful method to study such systems and processes, but since the events are rare and complex, special simulation methodology in combination with Machine Learning is required, to tack this enormous challenge.
What are you going to do?
This project focusses on using trajectory sampling to collect path ensembles at an atomistic resolution, in order to compute kinetics and free energy profiles. In addition, using Machine Learning one can extract the most important features, which creates crucial mechanistic insight and allows a grip on the transition of interest, and eventually even allows control and optimization of relevant model parameters in the molecular system. You will develop and apply such special simulation techniques to both simple catalytic processes, as well as biomolecular processes such as protein conformational changes, and binding/association reactions.
Tasks and responsibilities:
- Perform research in the computational chemistry theme of the van t Hoff Institute for Molecular Sciences
- Be and active member of the computational chemistry theme
- Take part actively in the collaboration with Microsoft Research Amsterdam
- Contribute to the teaching of BSc/MSc students.
- Publish and present your work within the project and on international scientific platforms.
- Contribute to the teaching activities of the department.
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