Praprotnik, Matej: search on Z-Library

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1

Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation Study

Praprotnik, Matej, Janežič, Dušanka, Mavri, Janez

Journal:

Journal of Physical Chemistry A

Year:

2004

Language:

english

File:

PDF, 190 KB

english, 2004

2

On phonons and water flow enhancement in carbon nanotubes

Cruz-Chú, Eduardo R., Papadopoulou, Ermioni, Walther, Jens H., Popadić, Aleksandar, Li, Gengyun, Praprotnik, Matej, Koumoutsakos, Petros

Journal:

Nature Nanotechnology

Year:

2017

Language:

english

File:

PDF, 429 KB

english, 2017

3

Fractional dimensions of phase space variables: a tool for varying the degrees of freedom of a system in a multiscale treatment

Praprotnik, Matej, Kremer, Kurt, Site, Luigi Delle

Journal:

Journal of Physics A Mathematical and Theoretical

Year:

2007

Language:

english

File:

PDF, 167 KB

english, 2007

4

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

Zavadlav, Julija, Melo, Manuel N., Marrink, Siewert J., Praprotnik, Matej

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 1.86 MB

english, 2015

5

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

Zavadlav, Julija, Marrink, Siewert J., Praprotnik, Matej

Journal:

Interface Focus

Year:

2019

Language:

english

File:

PDF, 1.26 MB

english, 2019

6

Molecular Dynamics Simulation of High Density DNA Arrays

Podgornik, Rudolf, Zavadlav, Julija, Praprotnik, Matej

Journal:

Year:

2018

Language:

english

File:

PDF, 3.38 MB

english, 2018

7

Statistical Physics Problems in Adaptive Resolution Computer Simulations of Complex Fluids

Matej Praprotnik, Simon Poblete, Kurt Kremer

Journal:

Journal of Statistical Physics

Year:

2011

Language:

english

File:

PDF, 1.23 MB

english, 2011

8

Molecular dynamics integration and molecular vibrational theory. II. Simulation of nonlinear molecules

Praprotnik, Matej, Janežič, Dušanka

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 413 KB

english, 2005

9

Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles

Zavadlav, Julija, Marrink, Siewert J., Praprotnik, Matej

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 3.07 MB

english, 2016

10

Adaptive resolution simulation of an atomistic protein in MARTINI water

Zavadlav, Julija, Melo, Manuel Nuno, Marrink, Siewert J., Praprotnik, Matej

Journal:

The Journal of Chemical Physics

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

11

Concurrent triple-scale simulation of molecular liquids

Delgado-Buscalioni, Rafael, Kremer, Kurt, Praprotnik, Matej

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 1.31 MB

english, 2008

12

AIP Conference Proceedings [AIP INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2009: (ICCMSE 2009) - Rhodes, Greece (29 September–4 October 2009)] - Recent algorithmic development of parallel force decomposition and Hamiltonian splitting methods for macromolecular simulation

Janezic, Dusanka, Borstnik, Urban, Praprotnik, Matej, Penca, Matej, Janezic, Matej, Poljanec, Ksenija

Year:

2012

Language:

english

File:

PDF, 273 KB

english, 2012

13

Molecular systems with open boundaries: Theory and simulation

Delle Site, Luigi, Praprotnik, Matej

Journal:

Physics Reports

Year:

2017

Language:

english

File:

PDF, 2.36 MB

english, 2017

14

Adaptive resolution molecular dynamics technique: Down to the essential

Krekeler, Christian, Agarwal, Animesh, Junghans, Christoph, Praprotnik, Matej, Delle Site, Luigi

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 11.05 MB

english, 2018

15

Coupling atomistic and continuum hydrodynamics through a mesoscopic model: Application to liquid water

Delgado-Buscalioni, Rafael, Kremer, Kurt, Praprotnik, Matej

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 870 KB

english, 2009

16

Adaptive resolution simulation of a DNA molecule in salt solution

Zavadlav, Julija, Podgornik, Rudolf, Praprotnik, Matej

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 1.94 MB

english, 2015

17

Open boundary molecular dynamics of sheared star-polymer melts

Sablić, Jurij, Praprotnik, Matej, Delgado-Buscalioni, Rafael

Journal:

Year:

2016

Language:

english

File:

PDF, 12.27 MB

english, 2016

18

Isotropic Polymers: Density–Nematic Coupling in Isotropic Linear Polymers: Acoustic and Osmotic Birefringence (Adv. Theory Simul. 5/2019)

Popadić, Aleksandar, Svenšek, Daniel, Podgornik, Rudolf, Praprotnik, Matej

Journal:

Advanced Theory and Simulations

Year:

2019

File:

PDF, 19.17 MB

2019

19

Adaptive resolution simulation of liquid water

Praprotnik, Matej, Matysiak, Silvina, Site, Luigi Delle, Kremer, Kurt, Clementi, Cecilia

Journal:

Journal of Physics Condensed Matter

Year:

2007

Language:

english

File:

PDF, 591 KB

english, 2007

20

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Zavadlav, Julija, Podgornik, Rudolf, Praprotnik, Matej

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 2.14 MB

english, 2017

21

Multiscale simulation of water flow past a C540 fullerene

Jens H. Walther, Matej Praprotnik, Evangelos M. Kotsalis, Petros Koumoutsakos

Journal:

Journal of Computational Physics

Year:

2012

Language:

english

File:

PDF, 647 KB

english, 2012

22

A macromolecule in a solvent: Adaptive resolution molecular dynamics simulation

Praprotnik, Matej, Delle Site, Luigi, Kremer, Kurt

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 568 KB

english, 2007

23

Molecular dynamics integration and molecular vibrational theory. III. The infrared spectrum of water

Praprotnik, Matej, Janežič, Dušanka

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 908 KB

english, 2005

24

Deciphering the dynamics of star molecules in shear flow

Sablić, Jurij, Praprotnik, Matej, Delgado-Buscalioni, Rafael

Journal:

Year:

2017

Language:

english

File:

PDF, 1.61 MB

english, 2017

25

ENZO: A Web Tool for Derivation and Evaluation of Kinetic Models of Enzyme Catalyzed Reactions

Bevc, Staš, Konc, Janez, Stojan, Jure, Hodošček, Milan, Penca, Matej, Praprotnik, Matej, Janežič, Dušanka, Bogyo, Matthew

Journal:

Year:

2011

Language:

english

File:

PDF, 937 KB

english, 2011

26

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

Popadić, Aleksandar, Svenšek, Daniel, Podgornik, Rudolf, Daoulas, Kostas, Praprotnik, Matej

Journal:

Year:

2018

Language:

english

File:

PDF, 2.79 MB

english, 2018

27

Adaptive molecular resolution via a continuous change of the phase space dimensionality

Praprotnik, Matej, Kremer, Kurt, Delle Site, Luigi

Journal:

Physical Review E

Year:

2007

Language:

english

File:

PDF, 79 KB

english, 2007

28

Isotropic Polymers: Density–Nematic Coupling in Isotropic Linear Polymers: Acoustic and Osmotic Birefringence (Adv. Theory Simul. 5/2019)

Popadić, Aleksandar, Svenšek, Daniel, Podgornik, Rudolf, Praprotnik, Matej

Journal:

Advanced Theory and Simulations

Year:

2019

File:

PDF, 19.17 MB

2019

29

New all-atom force field for molecular dynamics simulation of an AlPO4-34 molecular sieve

Matej Praprotnik, Stanko Hočevar, Milan Hodošček, Matej Penca, Dušanka Janežič

Journal:

Journal of Computational Chemistry

Year:

2008

Language:

english

File:

PDF, 294 KB

english, 2008

30

Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators

Janežič, Dušanka, Praprotnik, Matej, Merzel, Franci

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 518 KB

english, 2005

31

Adaptive resolution simulation of salt solutions

Bevc, Staš, Junghans, Christoph, Kremer, Kurt, Praprotnik, Matej

Journal:

New Journal of Physics

Year:

2013

Language:

english

File:

PDF, 806 KB

english, 2013

32

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

Sablić, Jurij, Delgado-Buscalioni, Rafael, Praprotnik, Matej

Journal:

Year:

2017

Language:

english

File:

PDF, 2.03 MB

english, 2017

33

Adaptive resolution simulations of biomolecular systems

Zavadlav, Julija, Bevc, Staš, Praprotnik, Matej

Journal:

European Biophysics Journal

Year:

2017

Language:

english

File:

PDF, 2.19 MB

english, 2017

34

[AIP COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING: Theory and Computation: Old Problems and New Challenges. Lectures Presented at the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007): VOLUME 1 - ()] AIP Conference Proceedings - Molecular Modeling—A New Approach

Janežič, Dušanka, Konc, Janez, Praprotnik, Matej, Penca, Matej, Poljanec, Ksenija, Simos, Theodore E., Maroulis, George

Year:

2007

Language:

english

File:

PDF, 816 KB

english, 2007

35

Symplectic molecular dynamics integration using normal mode analysis

Dušanka Janežič, Matej Praprotnik

Journal:

International Journal of Quantum Chemistry

Year:

2001

Language:

english

File:

PDF, 203 KB

english, 2001

36

Adaptive resolution simulation of liquid water

Praprotnik, Matej, Matysiak, Silvina, Site, Luigi Delle, Kremer, Kurt, Clementi, Cecilia

Journal:

Journal of Physics Condensed Matter

Year:

2008

Language:

english

File:

PDF, 41 KB

english, 2008

37

Molecular Dynamics Integration Meets Standard Theory of Molecular Vibrations

Praprotnik, Matej, Janežič, Dušanka

Journal:

Journal of Chemical Information and Modeling

Year:

2005

Language:

english

File:

PDF, 103 KB

english, 2005

38

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

Zavadlav, Julija, Sablić, Jurij, Podgornik, Rudolf, Praprotnik, Matej

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 2.27 MB

english, 2018

39

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

Popadić, Aleksandar, Svenšek, Daniel, Podgornik, Rudolf, Praprotnik, Matej

Journal:

Advanced Theory and Simulations

Year:

2019

Language:

english

File:

PDF, 1.17 MB

english, 2019

40

Particle-Continuum Coupling and its Scaling Regimes: Theory and Applications

Delle Site, Luigi, Praprotnik, Matej, Bell, John B., Klein, Rupert

Journal:

Advanced Theory and Simulations

Year:

2020

Language:

english

File:

PDF, 896 KB

english, 2020

41

STOCK: Structure mapper and online coarse-graining kit for molecular simulations

Bevc, Staš, Junghans, Christoph, Praprotnik, Matej

Journal:

Journal of Computational Chemistry

Year:

2015

Language:

english

File:

PDF, 1.08 MB

english, 2015

42

Extending the Adress Multiscale Scheme for Protein and Bilayer Applications

Melo, Manuel N., Zavadlav, Julija, Praprotnik, Matej, Marrink, Siewert J.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 57 KB

english, 2016

43

Simulation approaches to soft matter: Generic statistical properties vs. chemical details

Matej Praprotnik, Christoph Junghans, Luigi Delle Site, Kurt Kremer

Journal:

Computer Physics Communications

Year:

2008

Language:

english

File:

PDF, 1.20 MB

english, 2008

44

Coupling different levels of resolution in molecular simulations

Poblete, Simón, Praprotnik, Matej, Kremer, Kurt, Delle Site, Luigi

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 673 KB

english, 2010

45

Modeling diffusive dynamics in adaptive resolution simulation of liquid water

Matysiak, Silvina, Clementi, Cecilia, Praprotnik, Matej, Kremer, Kurt, Delle Site, Luigi

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 936 KB

english, 2008

46

Multiscale simulation of protein hydration using the SWINGER dynamical clustering algorithm

Zavadlav, Julija, Marrink, Siewert J., Praprotnik, Matej

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 2.75 MB

english, 2018

47

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

Praprotnik, Matej, Site, Luigi Delle, Kremer, Kurt

Journal:

Annual Review of Physical Chemistry

Year:

2008

Language:

english

File:

PDF, 867 KB

english, 2008

48

Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids

Praprotnik, Matej, Delle Site, Luigi, Kremer, Kurt

Journal:

Physical Review E

Year:

2006

Language:

english

File:

PDF, 390 KB

english, 2006

49

Adaptive Resolution Simulation of MARTINI Solvents

Zavadlav, Julija, Melo, Manuel N., Cunha, Ana V., de Vries, Alex H., Marrink, Siewert J., Praprotnik, Matej

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 3.80 MB

english, 2014

50

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly

Praprotnik, Matej, Delle Site, Luigi, Kremer, Kurt

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 637 KB

english, 2005

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