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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. COSTE, Amaury, SLEJKO, Ema, ZAVADLAV, Julija, PRAPROTNIK, Matej. Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media. J. Chem. Theory Comput., 2024, 20, 411-420.
  2. PAPEŽ, Petra, MERZEL, Franci, PRAPROTNIK, Matej. Sub-THz acoustic excitation of protein motion. J. Chem. Phys., 2023, 159, 135101.
  3. PAPEŽ, Petra, MERZEL, Franci, PRAPROTNIK, Matej. Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism. J. Phys. Chem. B, 2023, 127, 7231-7243.
  4. POTISK, Tilen, SABLIĆ, Jurij, SVENŠEK, Daniel, SANZ-DE DIEGO, Elena, TERAN, Francisco J., PRAPROTNIK, Matej. Analyte-Driven Clustering of Bio-Conjugated Magnetic Nanoparticles. Adv. Theory Simul., 2023, 6, 2200796.
  5. DELLE SITE, Luigi, PRAPROTNIK, Matej. Molecular systems with open boundaries: Theory and simulation. Phys. Rep., 2017, 693, 1-56.
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