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
- 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.
- PAPEŽ, Petra, MERZEL, Franci, PRAPROTNIK, Matej. Sub-THz acoustic excitation of protein motion. J. Chem. Phys., 2023, 159, 135101.
- 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.
- 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.
- DELLE SITE, Luigi, PRAPROTNIK, Matej. Molecular systems with open boundaries: Theory and simulation. Phys. Rep., 2017, 693, 1-56.