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List of works by Alexander P Lyubartsev

2D to 3D crossover of the magnetic properties in ordered arrays of iron oxide nanocrystals

article

A Bottom-Up Coarse-Grained Model for Nucleosome–Nucleosome Interactions with Explicit Ions

scientific article published on 17 May 2022

A molecular dynamics investigation of the influence of hydration and temperature on structural and dynamical properties of a dimyristoylphosphatidylcholine bilayer

scientific article published on 01 July 2006

A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations.

scientific article

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

scientific article

A new AMBER-compatible force field parameter set for alkanes

scientific article published on 19 February 2014

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

scientific article

An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions

scientific article

Another Piece of the Membrane Puzzle: Extending Slipids Further

scientific article

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

scientific article published in May 2003

Assessing the electric-field approximation to IR and Raman spectra of dilute HOD in D2O

scientific article published on 01 July 2009

Atomistic Perspective on Biomolecular Adsorption on Functionalized Carbon Nanomaterials under Ambient Conditions

scientific article published on 29 December 2020

Bead-Fourier path integral molecular dynamics

scientific article published on 27 June 2003

Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations.

scientific article

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

scientific article published on 01 October 1995

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

scientific article published on 26 August 2009

Centroid molecular dynamics: comparison with exact results for model systems.

scientific article

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

scientific article published on 01 December 2018

Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations

scientific article published on 03 February 2017

Competitive binding of Mg2+, Ca2+, Na+, and K+ ions to DNA in oriented DNA fibers: experimental and Monte Carlo simulation results

scientific article

Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails

scientific article published on 24 March 2006

Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles

scientific article published on March 2009

Conformational characteristics of single flexible polyelectrolyte chain

scientific article published on 29 November 2009

Curvature sensing by cardiolipin in simulated buckled membranes

scientific article published on 15 January 2019

Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids

scientific article published in March 2012

Determination of solvation free energies by adaptive expanded ensemble molecular dynamics

scientific article

Diffusion and reaction pathways of water near fully hydrated TiO2 surfaces from ab initio molecular dynamics

scientific article published on July 2017

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

scientific article published on 25 October 2006

Effect of lipid saturation on amyloid-beta peptide partitioning and aggregation in neuronal membranes: molecular dynamics simulations

scientific article published on 26 October 2019

Effect of local anesthetic lidocaine on electrostatic properties of a lipid bilayer.

scientific article published on 24 August 2007

Effective macroion-macroion potentials in asymmetric electrolytes

scientific article published on 09 January 2001

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

scientific article published on 11 February 2011

Electrostatic Origin of Salt-Induced Nucleosome Array Compaction ⬇️

scientific article published on September 22, 2010

Entropic sampling of flexible polyelectrolytes within the Wang-Landau algorithm.

scientific article published on 11 January 2007

Evaluation of effective ion-ion potentials in aqueous electrolytes

scientific article published on 28 March 2002

Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers

scientific article published on 14 May 2013

Extension of the Slipids Force Field to Polyunsaturated Lipids.

scientific article published on 14 December 2016

Hierarchical Multiscale Modelling Scheme from First Principles to Mesoscale

scientific article published in May 2009

Implicit inclusion of atomic polarization in modeling of partitioning between water and lipid bilayers

scientific article published on 01 April 2013

Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure

scientific article published on 05 April 2019

MagiC: Software Package for Multiscale Modeling.

scientific article published on 25 February 2013

Magic v.3: An integrated software package for systematic structure-based coarse-graining

scientific article published in 2019

Modification of the CHARMM force field for DMPC lipid bilayer.

scientific article

Molecular Dynamics Investigation of Dipeptide - Transition Metal Salts in Aqueous Solutions ⬇️

scientific article published on November 18, 2010

Molecular Dynamics Investigation of23Na NMR Relaxation in Oligomeric DNA Aqueous Solution

article

Molecular Dynamics Simulations of Furfural and 5-Hydroxymethylfurfural at Ambient and Hydrothermal Conditions

scientific article published on 28 August 2018

Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model

scientific article published on 01 January 2014

Molecular conformations in a phospholipid bilayer extracted from dipolar couplings: a computer simulation study.

scientific article published on 13 November 2007

Molecular dynamics simulation study of glycerol-water liquid mixtures

scientific article published on 11 November 2011

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

scientific article

Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations

scientific article published in October 2014

Molecular dynamics simulations of local anesthetic articaine in a lipid bilayer

scientific article published on 12 October 2010

Multiscale coarse-grained simulations of ionic liquids: comparison of three approaches to derive effective potentials

scientific article published on 17 April 2013

Multiscale modeling of lipids and lipid bilayers

scientific article published on 31 August 2005

Multiscale modelling of nucleosome core particle aggregation.

scientific article published on 7 January 2015

NMR investigations of interactions between anesthetics and lipid bilayers.

scientific article published on 5 August 2008

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

scientific article

One dimensional model for water and aqueous solutions. Part V. Monte Carlo simulation of dilute solutions of hard rod in waterlike particles

scientific article published on 01 November 2009

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

scientific article published on 20 September 2012

Path-integral Monte Carlo method in quantum statistics for a system ofNidentical fermions

scientific article published on 01 December 1993

Path-integral-expanded-ensemble Monte Carlo method in treatment of the sign problem for fermions.

scientific article published on 3 December 2009

Phase transitions and thermodynamic properties of dense assemblies of truncated nanocubes and cuboctahedra

scientific article published on 2 July 2012

Quantum chemical and molecular dynamics modelling of hydroxylated polybrominated diphenyl ethers.

scientific article published on 13 October 2017

Simulations of one- and two-electron systems by Bead-Fourier path integral molecular dynamics

scientific article published on 01 July 2005

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

scientific article published in 2006

Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics

scientific article published in January 2005

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

scientific article published on 01 May 2000

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

scientific article

Systematic coarse-graining of molecular models by the Newton inversion method

scientific article published in January 2010

Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids

scientific article published on 29 April 2014

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

Topological and spatial aspects of the hydration of solutes of extreme solvation entropy.

scientific article published in October 1999

Unperturbed hydrocarbon chains and liquid phase bilayer lipid chains: a computer simulation study

scientific article published on 11 July 2017

Update to the general amber force field for small solutes with an emphasis on free energies of hydration

scientific article published on 31 March 2014

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