Laboratory for Molecular Modeling
The laboratory pursues a variety of research topics in life and material sciences by fusing molecular modeling with artificial intelligence and machine learning. 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, nanofluidics, and biomedical applications of ultrasound.
Co-workers
Head of Laboratory
Representative Publications
1. Čoko Urban, Potisk Tilen, Praprotnik Matej. Virtual ultrasound machine operating in a GHz to MHz frequency range for particle-based biomedical simulations. Proceedings of the National Academy of Sciences of the United States of America. 2026, 123, e2610567123. Full text
2. Slejko Ema, Coste Amaury, Potisk Tilen, Zavadlav Julija, Praprotnik Matej. Achieving all-atom molecular dynamics accuracy from the Poisson-Boltzmann method through machine learning. The Journal of Chemical Physics. 2026, 164, 054107. Full text
3. Ntarakas Nikolaos, Lah Maša, Svenšek Daniel, Potisk Tilen, Praprotnik Matej. Dissipative particle dynamics models of encapsulated microbubbles and nanoscale gas vesicles for biomedical ultrasound simulations. ACS Applied Nano Materials. 2025, 8, 16053-16070. Full text
4. Jug Matevž, Potisk Tilen, Svenšek Daniel, Praprotnik Matej. Learning macroscopic equations of motion from dissipative particle dynamics simulations of fluids. Computer Methods in Applied Mechanics and Engineering. 2024, 432, 117379. Full text
5. Papež Petra, Merzel Franci, Praprotnik Matej. Sub-THz acoustic excitation of protein motion. The Journal of Chemical Physics. 2023, 159, 135101. Full text