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Laboratory for Molecular Modeling

The laboratory pursues a variety of research topics in life and material sciences using molecular modeling approaches. Our research interests, which are at the interface of computational physics, chemistry, and applied mathematics, include: multiscale modeling and simulation of soft and biological matter, open boundary molecular simulations, nanofluidics, and study of structure and function of proteins and protein interactions.


Head of Laboratory

Representative Publications

  1. DELLE SITE, Luigi, PRAPROTNIK, Matej. Molecular systems with open boundaries: Theory and simulation. Physics Reports, 2017, 693, 1-56.
  2. ZAVADLAV, Julija, SABLIĆ, Jurij, PODGORNIK, Rudolf, PRAPROTNIK, Matej. Open-Boundary Molecular Dynamics of a DNA molecule in a hybrid explicit/implicit salt solution. Biophys. J., 2018, 114, 2352.
  3. ZAVADLAV, Julija, MARRINK, Siewert J., PRAPROTNIK, Matej. Multiscale simulation of protein hydratiom using SWINGER dynamical clustering algorithmJ. Chem. Theory Comput., 2018, 14, 1754.
  4. SABLIĆ, Jurij, DELGADO-BUSCALIONI, Rafael, PRAPROTNIK, Matej. Application of the Eckart frame to soft matter: rotation of star polymers under shear flow. Soft Matter, 2017, 13, 6988.
  5. POPADIĆ, Aleksandar, SVENŠEK, Daniel, PODGORNIK, Rudolf, PRAPROTNIK, Matej. Density-nematic coupling in isotropic linear polymers: acoustic and osmotix birefringence. Adv. Theory Simul., 2019, 2, 1900019.
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