My expertise is focused on characterizing and understanding conformational transitions in biomolecules, including proteins and DNA, using advanced molecular simulation techniques. Throughout my career I have been interested in the mechanisms underlying sensing and signal propagation in proteins. During my PhD I predicted the structure of the active, transient state of a light receptor. As a postdoc, I elucidated the mechanisms of signal transduction in a bacterial blue light receptor and chemotaxis receptors using rare event simulation methods, including path-sampling and metadynamics. As a VENI researcher I investigated conformational transitions of the Histone-like Nucleoid Structuring protein H-NS using different levels of detail. Including all atoms explicitly enabled me to discover ion-induced conformational changes causing H-NS to switch from stiffening DNA to bridging DNA. At a larger time and length scales, I developed a model for the compaction of DNA by H-NS. Recently, I have predicted the mechanisms and associated rate constants of the Watson-Crick to Hoogsteen transition in DNA, and for the interaction between H-NS and DNA. In 2023, I developed a simulation protocol, together with my PhD student Thor van Heesch, to predict dissociation free energies for protein DNA complexes, which can be generally applied to almost any protein-DNA complex.
Throughout my career I have recognized promising developments in simulation techniques and applied these to relevant biological problems, in close collaboration with various experimental groups.
During my career I have taught several courses in molecular simulation and structural elucidation of biomolecules. My expertise in these topics resulted in courses on biochemistry and thermodynamics. In 2028 I combined my knowledge of biochemistry with my experience in thermodynamics and started teaching the course How to design an alien: Life on other planets. In this course, students from different disciplines design lifeforms for exoplanets. In 2022 I became programme director of the chemistry bachelor in Amsterdam, a joint degree between the University of Amsterdam and the Free University of Amsterdam.