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My research involves theoretical and molecular dynamics simulation studies
of diverse protein-protein interactions in biomolecules, and biomolecular complexes
and aggregates. Current state of the art experiments on single molecules enable
researchers to go beyound the endemble averaged picture and to analyze the
entire distributions of the molecular characteristics. In my research group, we
study the kinetics of formation/rupture of the hydrophobic interactions between
linear hydrocarbon chains, such as hexadecane molecules, and between bulky
hydrophobic solutes, such as fullerenes. We also study forced unfolding of proteins
and protein tandems, and the forced rupture of protein-protein complexes and
aggregates. Specific examples include the diubiquitin tandem, the tandem
of fibrinogen and fibronectin, the knob-hole interaction in fibrin, and the Abeta
amyloid fibril. To tackle these problems, we use all-atom molecular dynamics
simulations, Langevin dynamics simulations, as well as theoretical models and
advanced statistical data analyses.
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