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1

Measuring the sea: Marsili’s oceanographic cruise (1679-1680) and the roots of oceanography

PINARDI, NADIA, ÖZSOY, EMIN, LATIF, MOHAMMED ABDUL, MORONI, FRANCA, GRANDI, ALESSANDRO, MANZELLA, GIUSEPPE, DE STROBEL, FEDERICO, LYUBARTSEV, VLADYSLAV

Journal:

Journal of Physical Oceanography

Year:

2018

Language:

english

File:

PDF, 24.95 MB

english, 2018

2

Molecular dynamics simulations of local anesthetic articaine in a lipid bilayer

Enamul H. Mojumdar, Alexander P. Lyubartsev

Journal:

Biophysical Chemistry

Year:

2010

Language:

english

File:

PDF, 1.40 MB

english, 2010

3

New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures

Alexei M. Nikitin, Alexander P. Lyubartsev

Journal:

Journal of Computational Chemistry

Year:

2007

Language:

english

File:

PDF, 373 KB

english, 2007

4

MagiC: Software Package for Multiscale Modeling

Mirzoev, Alexander, Lyubartsev, Alexander P.

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.71 MB

english, 2013

5

Free energy calculations for Lennard-Jones systems and water using the expanded ensemble method A Monte Carlo and molecular dynamics simulation study

Lyubartsev, Alexander P., Laaksonen, Aatto, Vorontsov-Velyaminov, Pavel N.

Journal:

Molecular Physics

Year:

1994

Language:

english

File:

PDF, 967 KB

english, 1994

6

New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles

Lyubartsev, A. P., Martsinovski, A. A., Shevkunov, S. V., Vorontsov-Velyaminov, P. N.

Journal:

The Journal of Chemical Physics

Year:

1992

Language:

english

File:

PDF, 920 KB

english, 1992

7

Molecular Dynamics Simulation Study of Glycerol–Water Liquid Mixtures

Egorov, Andrei V., Lyubartsev, Alexander P., Laaksonen, Aatto

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 2.46 MB

english, 2011

8

Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations

Saeedi, Marzieh, Lyubartsev, Alexander P., Jalili, Seifollah

Journal:

Biophysical Chemistry

Year:

2017

Language:

english

File:

PDF, 1.70 MB

english, 2017

9

Diffusion and reaction pathways of water near fully hydrated TiO 2 surfaces from ab initio molecular dynamics

Agosta, Lorenzo, Brandt, Erik G., Lyubartsev, Alexander P.

Journal:

The Journal of Chemical Physics

Year:

2017

Language:

english

File:

PDF, 13.08 MB

english, 2017

10

Cholesterol in phospholipid bilayers: positions and orientations inside membranes with different unsaturation degrees

Ermilova, Inna, Lyubartsev, Alexander P.

Journal:

Year:

2019

Language:

english

File:

PDF, 5.05 MB

english, 2019

11

A multiscale analysis of DNA phase separation: from atomistic to mesoscale level

Sun, Tiedong, Mirzoev, Alexander, Minhas, Vishal, Korolev, Nikolay, Lyubartsev, Alexander P, Nordenskiöld, Lars

Journal:

Nucleic Acids Research

Year:

2019

Language:

english

File:

PDF, 3.63 MB

english, 2019

12

Competitive substitution of hexammine cobalt(III) for Na+ and K+ ions in oriented DNA fibers

Nikolay Korolev, Alexander P. Lyubartsev, Allan Rupprecht, Lars Nordenskiöld

Journal:

Year:

2001

Language:

english

File:

PDF, 156 KB

english, 2001

13

Molecular dynamics simulation study of oriented polyamine- and Na-DNA: Sequence specific interactions and effects on DNA structure

Nikolay Korolev, Alexander P. Lyubartsev, Aatto Laaksonen, Lars Nordenskiöld

Journal:

Year:

2004

Language:

english

File:

PDF, 673 KB

english, 2004

14

Calculation of Canonical Properties and Excited States by Path Integral Numerical Methods

P. N. Vorontsov-Velyaminov, M. A. Voznesenskiy, E. A. Polyakov, A. P. Lyubartsev

Journal:

Contributions to Plasma Physics

Year:

2011

Language:

english

File:

PDF, 122 KB

english, 2011

15

Modification of the CHARMM force field for DMPC lipid bilayer

Carl-Johan Högberg, Alexei M. Nikitin, Alexander P. Lyubartsev

Journal:

Journal of Computational Chemistry

Year:

2008

Language:

english

File:

PDF, 897 KB

english, 2008

16

Entropic Sampling of Free and Ring Polymer Chains

Nikolai A. Volkov, Anton A. Yurchenko, Alexander P. Lyubartsev, Pavel N. Vorontsov-Velyaminov

Journal:

Macromolecular Theory and Simulations

Year:

2005

Language:

english

File:

PDF, 230 KB

english, 2005

17

Two-Dimensional Wang–Landau Algorithm for Osmotic Pressure Calculations in a Polyelectrolyte–Membrane System

Nikolay A. Volkov, Pavel N. Vorontsov-Velyaminov, Alexander P. Lyubartsev

Journal:

Macromolecular Theory and Simulations

Year:

2011

Language:

english

File:

PDF, 1.10 MB

english, 2011

18

Theoretical approximations to X-ray absorption spectroscopy of liquid water and ice

M. Leetmaa, M.P. Ljungberg, A. Lyubartsev, A. Nilsson, L.G.M. Pettersson

Journal:

Journal of Electron Spectroscopy and Related Phenomena

Year:

2010

Language:

english

File:

PDF, 1.34 MB

english, 2010

19

Dynamical and structural properties of charged and uncharged lidocaine in a lipid bilayer

Carl-Johan Högberg, Arnold Maliniak, Alexander P. Lyubartsev

Journal:

Biophysical Chemistry

Year:

2007

Language:

english

File:

PDF, 845 KB

english, 2007

20

Multiscale modeling of lipids and lipid assemblies

Alexander Lyubartsev

Journal:

Chemistry and Physics of Lipids

Year:

2007

Language:

english

File:

PDF, 53 KB

english, 2007

21

Cation-induced polyelectrolyte–polyelectrolyte attraction in solutions of DNA and nucleosome core particles

Nikolay Korolev, Alexander P. Lyubartsev, Lars Nordenskiöld

Journal:

Advances in Colloid and Interface Science

Year:

2010

Language:

english

File:

PDF, 2.13 MB

english, 2010

22

Reconstruction of pair interaction potentials from radial distribution functions

Alexander P. Lyubartsev, Aatto Laaksonen

Journal:

Computer Physics Communications

Year:

1999

Language:

english

File:

PDF, 36 KB

english, 1999

23

Spatial distribution functions as a tool in the analysis of ribonucleic acids hydration — molecular dynamics studies

K Kulińska, T Kuliński, A Lyubartsev, A Laaksonen, R.W Adamiak

Journal:

Computers & Chemistry

Year:

2000

Language:

english

File:

PDF, 486 KB

english, 2000

24

Application of the Poisson Boltzmann polyelectrolyte model for analysis of thermal denaturation of DNA in the presence of Na+ and polyamine cations

Nikolay Korolev, Alexander P. Lyubartsev, Lars Nordenskiöld

Journal:

Biophysical Chemistry

Year:

2003

Language:

english

File:

PDF, 194 KB

english, 2003

25

Solvating, manipulating, damaging, and repairing DNA in a computer

Juraj Bunta, Martin Dahlberg, Leif Eriksson, Nikolai Korolev, Aatto Laaksonen, Raimo Lohikoski, Alexander Lyubartsev, Miroslav Pinak, Patric Schyman

Journal:

International Journal of Quantum Chemistry

Year:

2007

Language:

english

File:

PDF, 579 KB

english, 2007

26

First and Second Hydration Shell of Ni2+Studied by Molecular Dynamics Simulations

Andrei V. Egorov, Andrei V. Komolkin, Alexander P. Lyubartsev, Aatto Laaksonen

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2006

Language:

english

File:

PDF, 372 KB

english, 2006

27

A molecular dynamics simulation study of polyamine– and sodium–DNA. Interplay between polyamine binding and DNA structure

Nikolay Korolev, Alexander P. Lyubartsev, Aatto Laaksonen, Lars Nordenskiöld

Journal:

European Biophysics Journal

Year:

2004

Language:

english

File:

PDF, 2.62 MB

english, 2004

28

Multiscale modeling of lipids and lipid bilayers

Alexander P. Lyubartsev

Journal:

European Biophysics Journal

Year:

2005

Language:

english

File:

PDF, 823 KB

english, 2005

29

Solute–Solvent Interactions in Aqueous Glycylglycine–CuCl2Solutions: Acoustical and Molecular Dynamics Perspective

Mysore Sridhar Santosh, Alexander Lyubartsev, Alexander Mirzoev, Denthaje Krishna Bhat

Journal:

Journal of Solution Chemistry

Year:

2011

Language:

english

File:

PDF, 575 KB

english, 2011

30

Visualization of the results of hydrothermodynamic modeling

V. G. Lyubartsev, S. P. Lyubartseva

Journal:

Physical Oceanography

Year:

2007

Language:

english

File:

PDF, 600 KB

english, 2007

31

Molecular dynamics investigations of local anesthetic lidocaine in DMPC lipid bilayer

Carl Johan Högberg, Arnold Maliniak, Alexander Lyubartsev

Journal:

Chemistry and Physics of Lipids

Year:

2007

Language:

english

File:

PDF, 50 KB

english, 2007

32

Determination of effective pair potentials from ab initio simulations: application to liquid water

A.P. Lyubartsev, A. Laaksonen

Journal:

Chemical Physics Letters

Year:

2000

Language:

english

File:

PDF, 350 KB

english, 2000

33

M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures

Alexander P. Lyubartsev, Aatto Laaksonen

Journal:

Computer Physics Communications

Year:

2000

Language:

english

File:

PDF, 227 KB

english, 2000

34

Simulation of polymers by the Monte Carlo method using the Wang-Landau algorithm

P. N. Vorontsov-Velyaminov, N. A. Volkov, A. A. Yurchenko, A. P. Lyubartsev

Journal:

Polymer Science Series A

Year:

2010

Language:

english

File:

PDF, 840 KB

english, 2010

35

Conformational characteristics of single flexible polyelectrolyte chain

C. G. Jesudason, A. P. Lyubartsev, A. Laaksonen

Journal:

The European Physical Journal E

Year:

2009

Language:

english

File:

PDF, 760 KB

english, 2009

36

Effective solvent mediated potentials of Na+ and Cl− ions in aqueous solution: temperature dependence

Mirzoev, Alexander, Lyubartsev, Alexander P.

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.90 MB

english, 2011

37

The polyelectrolyte properties of chromatin

Korolev, Nikolay, Allahverdi, Abdollah, Lyubartsev, Alexander P., Nordenskiöld, Lars

Journal:

Year:

2012

Language:

english

File:

PDF, 1.05 MB

english, 2012

38

Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach

Lyubartsev, Alexander, Laaksonen, Aatto

Journal:

Physical Review E

Year:

1995

Language:

english

File:

PDF, 319 KB

english, 1995

39

Osmotic and activity coefficients from effective potentials for hydrated ions

Lyubartsev, Alexander P., Laaksonen, Aatto

Journal:

Physical Review E

Year:

1997

Language:

english

File:

PDF, 205 KB

english, 1997

40

Recent development in computer simulations of lipid bilayers

Lyubartsev, Alexander P., Rabinovich, Alexander L.

Journal:

Year:

2010

Language:

english

File:

PDF, 324 KB

english, 2010

41

Reconstruction of the spectrum of the radiance coefficient from measurements at fixed wavelengths

V. G. Lyubartsev, S. P. Lyubartseva, A. V. Mishonov

Journal:

Physical Oceanography

Year:

1994

Language:

english

File:

PDF, 286 KB

english, 1994

42

Multidisciplinary marine environmental database for the Aral Sea

V.G Lyubartsev, V.L Vladymyrov, V.V Myroshnychenko

Journal:

Journal of Marine Systems

Year:

2004

Language:

english

File:

PDF, 489 KB

english, 2004

43

Modelling chromatin structure and dynamics: status and prospects

Nikolay Korolev, Yanping Fan, Alexander P Lyubartsev, Lars Nordenskiöld

Journal:

Current Opinion in Structural Biology

Year:

2012

Language:

english

File:

PDF, 1.32 MB

english, 2012

44

An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes

Jämbeck, Joakim P. M., Lyubartsev, Alexander P.

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 1.90 MB

english, 2012

45

Solubility of Organic Compounds in Water/Octanol Systems. A Expanded Ensemble Molecular Dynamics Simulation Study of log P Parameters

Lyubartsev, Alexander P., Jacobsson, Sven P., Sundholm, Göran, Laaksonen, Aatto

Journal:

Journal of Physical Chemistry B

Year:

2001

Language:

english

File:

PDF, 81 KB

english, 2001

46

Partial atomic charges and their impact on the free energy of solvation

Joakim P. M. Jämbeck, Francesca Mocci, Alexander P. Lyubartsev, Aatto Laaksonen

Journal:

Journal of Computational Chemistry

Year:

2012

Language:

english

File:

PDF, 677 KB

english, 2012

47

Determination of Free Energy from Chemical Potentials: Application of the Expanded Ensemble Method

Lyubartsev, A. P., Laaksonen, A., Vorontsov-velyaminov, P. N.

Journal:

Molecular Simulation

Year:

1996

Language:

english

File:

PDF, 763 KB

english, 1996

48

Spermine: an “invisible” component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study

Nikolay Korolev, Alexander P Lyubartsev, Lars Nordenskiöld, Aatto Laaksonen

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 462 KB

english, 2001

49

NMR investigations of interactions between anesthetics and lipid bilayers

Vasco Castro, Baltzar Stevensson, Sergey V. Dvinskikh, Carl-Johan Högberg, Alexander P. Lyubartsev, Herbert Zimmermann, Dick Sandström, Arnold Maliniak

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2008

Language:

english

File:

PDF, 372 KB

english, 2008

50

Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide−Water Mixture

Vishnyakov, Aleksey, Lyubartsev, Alexander P., Laaksonen, Aatto

Journal:

Journal of Physical Chemistry A

Year:

2001

Language:

english

File:

PDF, 722 KB

english, 2001

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