Soft Matter Simulations

We use particle-based simulation methods to investigate the structure and dynamics of soft matter, both biological and inorganic. We have currently four areas of interest: fluorinated proteins, polymer-protein interactions, water and ions, and force pathways in proteins. We use mainly classical molecular dynamics or Monte Carlo methods and a variety of levels of description of matter (fixed-charge or polarizable all-atom, coarse-grained), with emphasis on advanced simulation techniques to enhance sampling of phase space thus allowing the calculation of thermodynamic observables such as relative free energies.

Polymer-protein interactions
Fluorinated proteins
Force pathways in proteins
Water and ions
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