Publikationen

Preprints

Thaler, Stephan; Fuchs, Paul; Cukarska, Ana; Zavadlav, Julija: Jaxsgmc: Modular Stochastic Gradient MCMC in Jax. DOI: 10.2139/ssrn.4523404

2023

  • Coste, Amaury; Slejko, Ema; Zavadlav, Julija; Praprotnik, Matej: Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media. Journal of Chemical Theory and Computation, 2023 mehr… BibTeX Volltext ( DOI )
  • Thaler, Stephan; Doehner, Gregor; Zavadlav, Julija: Scalable Bayesian Uncertainty Quantification for Neural Network Potentials: Promise and Pitfalls. Journal of Chemical Theory and Computation 19 (14), 2023, 4520–4532 mehr… BibTeX Volltext ( DOI )

2022

  • Thaler, Stephan; Stupp, Maximilian; Zavadlav, Julija: Deep Coarse-grained Potentials via Relative Entropy Minimization. The Journal of Chemical Physics 157, 2022, 244103 mehr… BibTeX Volltext ( DOI )
  • Thaler, Stephan; Zavadlav, Julija: Uncertainty Quantification for Molecular Models via Stochastic Gradient MCMC. MATHMOD 2022 Discussion Contribution Volume, ARGESIM Publisher Vienna, 2022 mehr… BibTeX Volltext ( DOI )

2021

  • Papadopoulou, Ermioni; Zavadlav, Julija; Podgornik, Rudolf; Praprotnik, Matej; Koumoutsakos, Petros: Tuning the Dielectric Response of Water in Nanoconfinement through Surface Wettability. ACS Nano 15 (12), 2021, 20311-20318 mehr… BibTeX Volltext ( DOI )
  • Thaler, Stephan; Zavadlav, Julija: Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting. Nature Communications 12 (1), 2021 mehr… BibTeX Volltext ( DOI )
  • Vlachas, Pantelis R.; Zavadlav, Julija; Praprotnik, Matej; Koumoutsakos, Petros: Accelerated Simulations of Molecular Systems through Learning of Effective Dynamics. Journal of Chemical Theory and Computation 18 (1), 2021, 538-549 mehr… BibTeX Volltext ( DOI )

2020

  • Thaler, S.; Praprotnik, M.; Zavadlav, J.: Back-mapping augmented adaptive resolution simulation. The Journal of Chemical Physics 153 (16), 2020, 164118 mehr… BibTeX Volltext ( DOI )

2019

  • Zavadlav, Julija; Arampatzis, Georgios; Koumoutsakos, Petros: Bayesian selection for coarse-grained models of liquid water. Scientific Reports 9 (1), 2019 mehr… BibTeX Volltext ( DOI )
  • Zavadlav, Julija; Marrink, Siewert J.; Praprotnik, Matej: SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus 9 (3), 2019, 20180075 mehr… BibTeX Volltext ( DOI )

2018

  • Podgornik, Rudolf; Zavadlav, Julija; Praprotnik, Matej: Molecular Dynamics Simulation of High Density DNA Arrays. Computation 6 (1), 2018, 3 mehr… BibTeX Volltext ( DOI )
  • Zavadlav, Julija; Marrink, Siewert J.; Praprotnik, Matej: Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm. Journal of Chemical Theory and Computation 14 (3), 2018, 1754-1761 mehr… BibTeX Volltext ( DOI )
  • Zavadlav, Julija; Sablić, Jurij; Podgornik, Rudolf; Praprotnik, Matej: Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution. Biophysical Journal 114 (10), 2018, 2352-2362 mehr… BibTeX Volltext ( DOI )

2017

  • Zavadlav, Julija; Bevc, Staš; Praprotnik, Matej: Adaptive resolution simulations of biomolecular systems. European Biophysics Journal 46 (8), 2017, 821-835 mehr… BibTeX Volltext ( DOI )
  • Zavadlav, Julija; Podgornik, Rudolf; Praprotnik, Matej: Order and interactions in DNA arrays: Multiscale molecular dynamics simulation. Scientific Reports 7 (1), 2017 mehr… BibTeX Volltext ( DOI )
  • Zavadlav, Julija; Praprotnik, Matej: Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics. The Journal of Chemical Physics 147 (11), 2017, 114110 mehr… BibTeX Volltext ( DOI )

2016

  • Zavadlav, J.; Podgornik, R.; Melo, M.N.; Marrink, S.J.; Praprotnik, M.: Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution. The European Physical Journal Special Topics 225 (8-9), 2016, 1595-1607 mehr… BibTeX Volltext ( DOI )
  • Zavadlav, Julija; Marrink, Siewert J.; Praprotnik, Matej: Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles. Journal of Chemical Theory and Computation 12 (8), 2016, 4138-4145 mehr… BibTeX Volltext ( DOI )

2015

  • Zavadlav, Julija; Melo, Manuel N.; Marrink, Siewert J.; Praprotnik, Matej: Adaptive resolution simulation of polarizable supramolecular coarse-grained water models. The Journal of Chemical Physics 142 (24), 2015, 244118 mehr… BibTeX Volltext ( DOI )
  • Zavadlav, Julija; Podgornik, Rudolf; Praprotnik, Matej: Adaptive Resolution Simulation of a DNA Molecule in Salt Solution. Journal of Chemical Theory and Computation 11 (10), 2015, 5035-5044 mehr… BibTeX Volltext ( DOI )

2014

  • Zavadlav, Julija; Melo, Manuel N.; Cunha, Ana V.; de Vries, Alex H.; Marrink, Siewert J.; Praprotnik, Matej: Adaptive Resolution Simulation of MARTINI Solvents. Journal of Chemical Theory and Computation 10 (6), 2014, 2591-2598 mehr… BibTeX Volltext ( DOI )
  • Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej: Adaptive resolution simulation of an atomistic protein in MARTINI water. The Journal of Chemical Physics 140 (5), 2014, 054114 mehr… BibTeX Volltext ( DOI )