Personal information

Websites & social links

https://www.cmm.ki.si/~praprot

Other IDs

ResearcherID: G-8571-2019

Keywords

Multiscale Modeling & Simulation, Open Boundary Molecular Dynamics, Nanofluidics, Soft & Biological Matter

Countries

Slovenia

Activities

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Employment (1)

Kemijski institut: Ljubljana, SI

1998 to present | Head of Laboratory (Theory Department; Laboratory for Molecular Modeling)
Employment
Source: Self-asserted source
Matej Praprotnik

Education and qualifications (4)

University of Ljubljana: Ljubljana, SI

2018 to present | Full Professor (Faculty of Mathematics and Physics; Department of Physics)
Qualification
Source: Self-asserted source
Matej Praprotnik

University of Ljubljana: Ljubljana, SI

2003 to present | Ph.D. Physics
Education
Source: Self-asserted source
Matej Praprotnik

University of Ljubljana: Ljubljana, SI

1998 to present | B.S. Physics
Education
Source: Self-asserted source
Matej Praprotnik

Max-Planck-Institut für Polymerforschung: Mainz, Rheinland-Pfalz, DE

2004 to 2008 | Postdoctoral Researcher (Theory Group)
Education
Source: Self-asserted source
Matej Praprotnik

Professional activities (12)

Slovenian Biophysical Society: Ljubljana, SI

Member of Executive Board
Service
Source: Self-asserted source
Matej Praprotnik

Partnership for Advanced Computing In Europe: Bruxelles, Bruxelles, BE

2019 to present | Vice-Chair of PRACE Scientific Steering Committee
Service
Source: Self-asserted source
Matej Praprotnik

MDPI AG: Basel, BS, CH

2019 to present | Editorial Board Member (Polymers)
Service
Source: Self-asserted source
Matej Praprotnik

Nature Publishing Group: London, London, GB

2018 to present | Editorial Board Member (Scientific Reports)
Service
Source: Self-asserted source
Matej Praprotnik

Kemijski institut: Ljubljana, SI

2018 to present | Member of Scientific Council
Service
Source: Self-asserted source
Matej Praprotnik

CECAM (Centre Européen de Calcul Atomique et Moléculaire): Lausanne, CH

2017 to present | Council Member
Service
Source: Self-asserted source
Matej Praprotnik

Partnership for Advanced Computing In Europe: Bruxelles, Bruxelles, BE

2016 to present | Member of PRACE Scientific Steering Committee
Service
Source: Self-asserted source
Matej Praprotnik

Independent Research Fund Denmark: Copenhagen, DK

2017 to 2019 | International Review Panel Member
Service
Source: Self-asserted source
Matej Praprotnik

Slovenian Biophysical Society: Ljubljana, SI

2015 to 2019 | President
Service
Source: Self-asserted source
Matej Praprotnik

Slovenian Biophysical Society: Ljubljana, SI

2011 to 2019 | Member of Executive Board
Service
Source: Self-asserted source
Matej Praprotnik

ETH Zurich: Zurich, CH

2017 to 2018 | Academic Guest (Computational Science & Engineering Laboratory)
Invited position
Source: Self-asserted source
Matej Praprotnik

ETH Zurich: Zurich, CH

2009 to 2010 | Academic Guest (Computational Science & Engineering Laboratory)
Invited position
Source: Self-asserted source
Matej Praprotnik

Funding (1)

Multiscale modeling and simulation of soft and biological matter in and out of equilibrium

2020-01 to 2025-12 | Grant
Javna Agencija za Raziskovalno Dejavnost RS (Ljubljana, SI)
GRANT_NUMBER:

P1-0002
Source: Self-asserted source
Matej Praprotnik
grade
Preferred source (of 2)‎

Works (27)

Open-boundary molecular dynamics of ultrasound using supramolecular water models

The Journal of Chemical Physics
2025-01-14 | Journal article
DOI: 10.1063/5.0238348
Contributors: Maša Lah; Nikolaos Ntarakas; Tilen Potisk; Petra Papež; Matej Praprotnik
Source: check_circle
Crossref

Learning macroscopic equations of motion from dissipative particle dynamics simulations of fluids

Computer Methods in Applied Mechanics and Engineering
2024-12 | Journal article
DOI: 10.1016/j.cma.2024.117379
Contributors: Matevž Jug; Daniel Svenšek; Tilen Potisk; Matej Praprotnik
Source: check_circle
Crossref

Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media

Journal of Chemical Theory and Computation
2024-01-09 | Journal article
DOI: 10.1021/acs.jctc.3c00984
Contributors: Amaury Coste; Ema Slejko; Julija Zavadlav; Matej Praprotnik
Source: check_circle
Crossref

Sub-THz acoustic excitation of protein motion

The Journal of Chemical Physics
2023-10-07 | Journal article
DOI: 10.1063/5.0163801
Contributors: Petra Papež; Franci Merzel; Matej Praprotnik
Source: check_circle
Crossref

Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism

The Journal of Physical Chemistry B
2023-08-24 | Journal article
DOI: 10.1021/acs.jpcb.3c02324
Contributors: Petra Papež; Franci Merzel; Matej Praprotnik
Source: check_circle
Crossref

Analyte‐Driven Clustering of Bio‐Conjugated Magnetic Nanoparticles

Advanced Theory and Simulations
2023-05 | Journal article
DOI: 10.1002/adts.202200796
Contributors: Tilen Potisk; Jurij Sablić; Daniel Svenšek; Elena Sanz‐de Diego; Francisco J. Teran; Matej Praprotnik
Source: check_circle
Crossref

Suspension of discrete microscopic oscillators as a model of an ultrasonic metafluid

Physical Review B
2022-06-27 | Journal article
DOI: 10.1103/PhysRevB.105.224317
Contributors: Aljaž Draškovič-Bračun; Tilen Potisk; Matej Praprotnik; Daniel Svenšek
Source: check_circle
Crossref

Dissipative Particle Dynamics Simulation of Ultrasound Propagation through Liquid Water

Journal of Chemical Theory and Computation
2022-02-08 | Journal article
DOI: 10.1021/acs.jctc.1c01020
Contributors: Petra Papež; Matej Praprotnik
Source: check_circle
Crossref

Accelerated Simulations of Molecular Systems through Learning of Effective Dynamics

Journal of Chemical Theory and Computation
2022-01-11 | Journal article
DOI: 10.1021/acs.jctc.1c00809
Contributors: Pantelis R. Vlachas; Julija Zavadlav; Matej Praprotnik; Petros Koumoutsakos
Source: check_circle
Crossref

Tuning the Dielectric Response of Water in Nanoconfinement through Surface Wettability

ACS Nano
2021-12-28 | Journal article
DOI: 10.1021/acsnano.1c08512
Contributors: Ermioni Papadopoulou; Julija Zavadlav; Rudolf Podgornik; Matej Praprotnik; Petros Koumoutsakos
Source: check_circle
Crossref

Lessons learned from urgent computing in Europe: Tackling the COVID-19 pandemic

Proceedings of the National Academy of Sciences
2021-11-16 | Journal article
DOI: 10.1073/pnas.2024891118
Contributors: Núria López; Luigi Del Debbio; Marc Baaden; Matej Praprotnik; Laura Grigori; Catarina Simões; Serge Bogaerts; Florian Berberich; Thomas Lippert; Janne Ignatius et al.
Source: check_circle
Crossref

From adaptive resolution to molecular dynamics of open systems

The European Physical Journal B
2021-09 | Journal article
DOI: 10.1140/epjb/s10051-021-00193-w
Contributors: Robinson Cortes-Huerto; Matej Praprotnik; Kurt Kremer; Luigi Delle Site
Source: check_circle
Crossref

Back-mapping augmented adaptive resolution simulation

The Journal of Chemical Physics
2020-10-28 | Journal article
DOI: 10.1063/5.0025728
Contributors: S. Thaler; M. Praprotnik; J. Zavadlav
Source: check_circle
Crossref

SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids

Interface Focus
2019-06-06 | Journal article
DOI: 10.1098/rsfs.2018.0075
Contributors: Julija Zavadlav; Siewert J. Marrink; Matej Praprotnik
Source: check_circle
Crossref

Density–Nematic Coupling in Isotropic Linear Polymers: Acoustic and Osmotic Birefringence

Advanced Theory and Simulations
2019-05 | Journal article
DOI: 10.1002/adts.201900019
Contributors: Aleksandar Popadić; Daniel Svenšek; Rudolf Podgornik; Matej Praprotnik
Source: check_circle
Crossref

Splay–density coupling in semiflexible main-chain nematic polymers with hairpins

Soft Matter
2018 | Journal article
DOI: 10.1039/C8SM00835C
Contributors: Aleksandar Popadić; Daniel Svenšek; Rudolf Podgornik; Kostas Ch. Daoulas; Matej Praprotnik
Source: check_circle
Crossref

Adaptive resolution molecular dynamics technique: Down to the essential

The Journal of Chemical Physics
2018-07-14 | Journal article
DOI: 10.1063/1.5031206
Contributors: Christian Krekeler; Animesh Agarwal; Christoph Junghans; Matej Praprotnik; Luigi Delle Site
Source: check_circle
Crossref

Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm

Journal of Chemical Theory and Computation
2018-03-13 | Journal article
DOI: 10.1021/acs.jctc.7b01129
Contributors: Julija Zavadlav; Siewert J. Marrink; Matej Praprotnik
Source: check_circle
Crossref

Molecular Dynamics Simulation of High Density DNA Arrays

Computation
2018-01 | Journal article
DOI: 10.3390/computation6010003
Source: check_circle
Multidisciplinary Digital Publishing Institute
grade
Preferred source (of 2)‎

Application of the Eckart frame to soft matter: rotation of star polymers under shear flow

Soft Matter
2017 | Journal article
DOI: 10.1039/C7SM00616K
Contributors: Jurij Sablić; Rafael Delgado-Buscalioni; Matej Praprotnik
Source: check_circle
Crossref

Deciphering the dynamics of star molecules in shear flow

Soft Matter
2017 | Journal article
DOI: 10.1039/C7SM00364A
Contributors: Jurij Sablić; Matej Praprotnik; Rafael Delgado-Buscalioni
Source: check_circle
Crossref

Adaptive resolution simulations of biomolecular systems

European Biophysics Journal
2017-12 | Journal article
DOI: 10.1007/s00249-017-1248-0
Contributors: Julija Zavadlav; Staš Bevc; Matej Praprotnik
Source: check_circle
Crossref

On phonons and water flow enhancement in carbon nanotubes

Nature Nanotechnology
2017-12-06 | Journal article
DOI: 10.1038/nnano.2017.234
Contributors: Eduardo R. Cruz-Chú; Ermioni Papadopoulou; Jens H. Walther; Aleksandar Popadić; Gengyun Li; Matej Praprotnik; Petros Koumoutsakos
Source: check_circle
Crossref

Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics

The Journal of Chemical Physics
2017-09-21 | Journal article
DOI: 10.1063/1.4986916
Contributors: Julija Zavadlav; Matej Praprotnik
Source: check_circle
Crossref

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Scientific Reports
2017-07-06 | Journal article
DOI: 10.1038/s41598-017-05109-2
Contributors: Julija Zavadlav; Rudolf Podgornik; Matej Praprotnik
Source: check_circle
Crossref

Molecular systems with open boundaries: Theory and simulation

Physics Reports
2017-06 | Journal article
DOI: 10.1016/j.physrep.2017.05.007
Contributors: Luigi Delle Site; Matej Praprotnik
Source: check_circle
Crossref

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

The Journal of Chemical Physics
2015-06-28 | Journal article
DOI: 10.1063/1.4923008
Contributors: Julija Zavadlav; Manuel N. Melo; Siewert J. Marrink; Matej Praprotnik
Source: check_circle
Crossref

Peer review (11 reviews for 4 publications/grants)

Review activity for ACS omega. (2)
Review activity for Advanced theory and simulations. (1)
Review activity for Journal of chemical theory and computation : (7)
Review activity for Macromolecules. (1)
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