Publications by authors named "Matej Praprotnik"

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Dissipative Particle Dynamics Models of Encapsulated Microbubbles and Nanoscale Gas Vesicles for Biomedical Ultrasound Simulations.
Nikolaos Ntarakas, Maša Lah, Daniel Svenšek, Tilen Potisk, Matej Praprotnik

ACS Appl Nano Mater· August 2025

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The need to implement FAIR principles in biomolecular simulations.
Rommie E Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Matej Praprotnik

Nat Methods· April 2025

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Open-boundary molecular dynamics of ultrasound using supramolecular water models.
Maša Lah, Nikolaos Ntarakas, Tilen Potisk, Petra Papež, Matej Praprotnik

J Chem Phys· January 2025

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Density-Nematic Coupling in Isotropic Solution of DNA: Multiscale Model.
Daniel Svenšek, Jaka Sočan, Matej Praprotnik

Macromol Rapid Commun· December 2024

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Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.
Amaury Coste, Ema Slejko, Julija Zavadlav, Matej Praprotnik

J Chem Theory Comput· January 2024

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Sub-THz acoustic excitation of protein motion.
Petra Papež, Franci Merzel, Matej Praprotnik

J Chem Phys· October 2023

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Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism.
Petra Papež, Franci Merzel, Matej Praprotnik

J Phys Chem B· August 2023

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Dissipative Particle Dynamics Simulation of Ultrasound Propagation through Liquid Water.
Petra Papež, Matej Praprotnik

J Chem Theory Comput· February 2022

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Accelerated Simulations of Molecular Systems through Learning of Effective Dynamics.
Pantelis R Vlachas, Julija Zavadlav, Matej Praprotnik, Petros Koumoutsakos

J Chem Theory Comput· January 2022

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Tuning the Dielectric Response of Water in Nanoconfinement through Surface Wettability.
Ermioni Papadopoulou, Julija Zavadlav, Rudolf Podgornik, Matej Praprotnik, Petros Koumoutsakos

ACS Nano· December 2021

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Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic.
Núria López, Luigi Del Debbio, Marc Baaden, Matej Praprotnik, Laura Grigori

Proc Natl Acad Sci U S A· November 2021

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From adaptive resolution to molecular dynamics of open systems.
Robinson Cortes-Huerto, Matej Praprotnik, Kurt Kremer, Luigi Delle Site

Eur Phys J B· September 2021

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SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids.
Julija Zavadlav, Siewert J Marrink, Matej Praprotnik

Interface Focus· June 2019

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Splay-density coupling in semiflexible main-chain nematic polymers with hairpins.
Aleksandar Popadić, Daniel Svenšek, Rudolf Podgornik, Kostas Ch Daoulas, Matej Praprotnik

Soft Matter· July 2018

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Adaptive resolution molecular dynamics technique: Down to the essential.
Christian Krekeler, Animesh Agarwal, Christoph Junghans, Matej Praprotnik, Luigi Delle Site

J Chem Phys· July 2018

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Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution.
Julija Zavadlav, Jurij Sablić, Rudolf Podgornik, Matej Praprotnik

Biophys J· May 2018

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Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm.
Julija Zavadlav, Siewert J Marrink, Matej Praprotnik

J Chem Theory Comput· March 2018

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Adaptive resolution simulations of biomolecular systems.
Julija Zavadlav, Staš Bevc, Matej Praprotnik

Eur Biophys J· December 2017

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On phonons and water flow enhancement in carbon nanotubes.
Eduardo R Cruz-Chú, Ermioni Papadopoulou, Jens H Walther, Aleksandar Popadić, Gengyun Li, Matej Praprotnik

Nat Nanotechnol· December 2017

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Application of the Eckart frame to soft matter: rotation of star polymers under shear flow.
Jurij Sablić, Rafael Delgado-Buscalioni, Matej Praprotnik

Soft Matter· October 2017

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Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics.
Julija Zavadlav, Matej Praprotnik

J Chem Phys· September 2017

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Deciphering the dynamics of star molecules in shear flow.
Jurij Sablić, Matej Praprotnik, Rafael Delgado-Buscalioni

Soft Matter· July 2017

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Order and interactions in DNA arrays: Multiscale molecular dynamics simulation.
Julija Zavadlav, Rudolf Podgornik, Matej Praprotnik

Sci Rep· July 2017

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Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles.
Julija Zavadlav, Siewert J Marrink, Matej Praprotnik

J Chem Theory Comput· August 2016

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Open boundary molecular dynamics of sheared star-polymer melts.
Jurij Sablić, Matej Praprotnik, Rafael Delgado-Buscalioni

Soft Matter· February 2016

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