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.
Co-workers
Head of Laboratory
Expert fellows
Young Researchers
Representative Publications
- DELLE SITE, Luigi, PRAPROTNIK, Matej. Molecular systems with open boundaries: Theory and simulation. Physics Reports, 2017, 693, 1-56.
- 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.
- ZAVADLAV, Julija, MARRINK, Siewert J., PRAPROTNIK, Matej. Multiscale simulation of protein hydratiom using SWINGER dynamical clustering algorithm. J. Chem. Theory Comput., 2018, 14, 1754.
- 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.
- 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.