Molecular Dynamics Integration Time Step Dependence of the Split Integration Symplectic Method on System Density. - Dusanka Janezic; Matej Praprotnik (J. Chem. Inf. Comput. Sci., 2003)

Molecular Dynamics Integration Meets Standard Theory of Molecular Vibrations. - Matej Praprotnik; Dusanka Janezic (J. Chem. Inf. Model., 2005)

Simulation approaches to soft matter: Generic statistical properties vs. chemical details. - Matej Praprotnik; Christoph Junghans; Luigi Delle Site; Kurt Kremer (Comput. Phys. Commun., 2008)

New all-atom force field for molecular dynamics simulation of an AlPO4-34 molecular sieve. - Matej Praprotnik; Stanko Hocevar; Milan Hodoscek; Matej Penca; Dusanka Janezic (J. Comput. Chem., 2008)

Multiscale simulation of water flow past a C540 fullerene. - Jens H. Walther; Matej Praprotnik; Evangelos M. Kotsalis; Petros Koumoutsakos (J. Comput. Phys., 2012)

STOCK: Structure mapper and online coarse-graining kit for molecular simulations. - Stas Bevc; Christoph Junghans; Matej Praprotnik (J. Comput. Chem., 2015)

Molecular Dynamics Simulation of High Density DNA Arrays. - Rudolf Podgornik; Julija Zavadlav; Matej Praprotnik (Comput., 2018)

Accelerated Simulations of Molecular Systems through Learning of their Effective Dynamics. - Pantelis-Rafail Vlachas; Julija Zavadlav; Matej Praprotnik; Petros Koumoutsakos (CoRR, 2021)

Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic. - Núria López; Luigi Del Debbio; Marc Baaden; Matej Praprotnik; Laura Grigori; Catarina Simões; Serge Bogaerts; Florian Berberich; Thomas Lippert; Janne Ignatius; Philippe Lavocat; Oriol Pineda; et al. (Proc. Natl. Acad. Sci. USA, 2021)

Exploring engagement dynamics between journalists and news consumers in Social XR. - Arno Verhofstadt; Iris Jennes; Wendy Van den Broeck; Natasja Van Buggenhout; Marie Hospital; Delphine Ramond; Alexandre Grosbois; Matej Praprotnik; Sabrina Povsic Stimec; Kaella Kolle (IMX Workshops, 2024)