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Julija Zavadlav
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Adaptive resolution simulation of an atomistic protein in MARTINI water
J Zavadlav, MN Melo, SJ Marrink, M Praprotnik
The Journal of chemical physics 140 (5), 2014
962014
Adaptive resolution simulation of MARTINI solvents
J Zavadlav, MN Melo, AV Cunha, AH De Vries, SJ Marrink, M Praprotnik
Journal of Chemical Theory and Computation 10 (6), 2591-2598, 2014
622014
Adaptive resolution simulation of a DNA molecule in salt solution
J Zavadlav, R Podgornik, M Praprotnik
Journal of chemical theory and computation 11 (10), 5035-5044, 2015
612015
Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
J Zavadlav, MN Melo, SJ Marrink, M Praprotnik
The Journal of chemical physics 142 (24), 244118, 2015
492015
Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting
S Thaler, J Zavadlav
Nature Communications 12, 6884, 2021
452021
Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution
J Zavadlav, R Podgornik, MN Melo, SJ Marrink, M Praprotnik
The European Physical Journal Special Topics 225 (8), 1595-1607, 2016
332016
Adaptive resolution simulation of supramolecular water: The concurrent making, breaking, and remaking of water bundles
J Zavadlav, SJ Marrink, M Praprotnik
Journal of chemical theory and computation 12 (8), 4138-4145, 2016
332016
Accelerated Simulations of Molecular Systems through Learning of Effective Dynamics
PR Vlachas, J Zavadlav, M Praprotnik, P Koumoutsakos
Journal of Chemical Theory and Computation 18 (1), 538-549, 2021
322021
Order and interactions in DNA arrays: Multiscale molecular dynamics simulation
J Zavadlav, R Podgornik, M Praprotnik
Scientific Reports 7 (1), 4775-4786, 2017
282017
Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics
J Zavadlav, M Praprotnik
The Journal of Chemical Physics 147 (11), 114110, 2017
262017
Multiscale simulation of protein hydration using the SWINGER dynamical clustering algorithm.
J Zavadlav, SJ Marrink, M Praprotnik
Journal of chemical theory and computation 14 (3), 1754-1761, 2018
252018
Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution
J Zavadlav, J Sablić, R Podgornik, M Praprotnik
Biophysical Journal 114 (10), 2352, 2018
252018
Adaptive resolution simulations of biomolecular systems
J Zavadlav, S Bevc, M Praprotnik
European Biophysics Journal 46 (8), 821-835, 2017
252017
Bayesian selection for coarse-grained models of liquid water
J Zavadlav, G Arampatzis, P Koumoutsakos
Scientific Reports 9 (99), 2019
232019
Tuning the Dielectric Response of Water in Nanoconfinement through Surface Wettability
E Papadopoulou, J Zavadlav, R Podgornik, M Praprotnik, ...
ACS Nano 15 (12), 20311-20318, 2021
132021
SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids
J Zavadlav, SJ Marrink, M Praprotnik
Interface Focus 9 (3), 20180075, 2019
132019
Molecular Dynamics Simulation of High Density DNA Arrays
R Podgornik, J Zavadlav, M Praprotnik
Computation 6 (1), 3, 2018
132018
Back-mapping augmented adaptive resolution simulation
S Thaler, M Praprotnik, J Zavadlav
The Journal of Chemical Physics 153 (16), 2020
102020
Deep coarse-grained potentials via relative entropy minimization
S Thaler, M Stupp, J Zavadlav
The Journal of Chemical Physics 157 (24), 2022
92022
Scalable Bayesian Uncertainty Quantification for Neural Network Potentials: Promise and Pitfalls
S Thaler, G Doehner, J Zavadlav
Journal of Chemical Theory and Computation, 2023
72023
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