Research interests
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. 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.