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

PloS one, 2013-02, Vol.8 (2), p.e54228-e54228

2013

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

Nucleic acids research, 2019-06, Vol.47 (11), p.5550

2019

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Development of a bottom‐up coarse‐grained model for interactions of lipids with TiO 2 nanoparticles

Journal of computational chemistry, 2024-06, Vol.45 (16), p.1364-1379

2024

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Bottom-Up Coarse-Grained Modeling of DNA

Frontiers in molecular biosciences, 2021-03, Vol.8, p.645527-645527

2021

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Effect of Local Anesthetic Lidocaine on Electrostatic Properties of a Lipid Bilayer

Biophysical journal, 2008-01, Vol.94 (2), p.525-531

2008

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Electrostatic Origin of Salt-Induced Nucleosome Array Compaction

Biophysical journal, 2010-09, Vol.99 (6), p.1896-1905

2010

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

Biopolymers, 2014-10, Vol.101 (10), p.1051-1064

2014

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Force Field Development for Lipid Membrane Simulations

Biochimica et biophysica acta, 2016-10, Vol.1858 (10), p.2483-2497

2016

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

European biophysics journal, 2019-12, Vol.48 (8), p.813-824

2019

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Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles

Biophysical journal, 2024-06, Vol.123 (11), p.1414-1434

2024

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A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure

Scientific reports, 2018-01, Vol.8 (1), p.1543-14, Article 1543

2018

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Computationally based analysis of the energy efficiency of a CO2 capture process

Chemical engineering science, 2017, Vol.174, p.174-188

2017

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On the Competition between Water, Sodium Ions, and Spermine in Binding to DNA: A Molecular Dynamics Computer Simulation Study

Biophysical journal, 2002-06, Vol.82 (6), p.2860-2875

2002

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All-Atom MD Simulation of DNA Condensation Using Ab Initio Derived Force Field Parameters of Cobalt(III)-Hexammine

The journal of physical chemistry. B, 2017-08, Vol.121 (33), p.7761-7770

2017

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Transferable force-field for modelling of CO2, N2, O2 and Ar in all silica and Na+ exchanged zeolites

Modelling and simulation in materials science and engineering, 2016-03, Vol.24 (4)

2016

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Multiscale modeling of lipids and lipid bilayers

European biophysics journal, 2005-12, Vol.35 (1), p.53-61

Lyubartsev, Alexander P

2005

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NMR investigations of interactions between anesthetics and lipid bilayers

Biochimica et biophysica acta, 2008-11, Vol.1778 (11), p.2604-2611

2008

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

Computer physics communications, 2000-01, Vol.128 (3), p.565-589

2000

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Neutron scattering study of polyamorphic THF·17(HO) - toward a generalized picture of amorphous states and structures derived from clathrate hydrates

Physical chemistry chemical physics : PCCP, 2023-05, Vol.25 (21), p.14981-14991

2023

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Modelling chromatin structure and dynamics: status and prospects

Current opinion in structural biology, 2012-04, Vol.22 (2), p.151-159

2012

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

Biophysical journal, 1999-11, Vol.77 (5), p.2736-2749

1999

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

Journal of molecular biology, 2001-05, Vol.308 (5), p.907-917

2001

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

European biophysics journal, 2018-03, Vol.47 (2), p.109-130

2018

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Computer Modeling Demonstrates that Electrostatic Attraction of Nucleosomal DNA is Mediated by Histone Tails

Biophysical journal, 2006-06, Vol.90 (12), p.4305-4316

2006

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

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

Development of a bottom‐up coarse‐grained model for interactions of lipids with TiO 2 nanoparticles

Bottom-Up Coarse-Grained Modeling of DNA

Effect of Local Anesthetic Lidocaine on Electrostatic Properties of a Lipid Bilayer

Electrostatic Origin of Salt-Induced Nucleosome Array Compaction

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

Force Field Development for Lipid Membrane Simulations

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

Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles

A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure

Computationally based analysis of the energy efficiency of a CO2 capture process

On the Competition between Water, Sodium Ions, and Spermine in Binding to DNA: A Molecular Dynamics Computer Simulation Study

All-Atom MD Simulation of DNA Condensation Using Ab Initio Derived Force Field Parameters of Cobalt(III)-Hexammine

Transferable force-field for modelling of CO2, N2, O2 and Ar in all silica and Na+ exchanged zeolites

Multiscale modeling of lipids and lipid bilayers

NMR investigations of interactions between anesthetics and lipid bilayers

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

Neutron scattering study of polyamorphic THF·17(HO) - toward a generalized picture of amorphous states and structures derived from clathrate hydrates

Modelling chromatin structure and dynamics: status and prospects

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

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

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

Disease Prediction: Prediction of Chronic Inflammation for Inhaled Particles: the Impact of Material Cycling and Quarantining in the Lung Epithelium (Adv. Mater. 47/2020)

Computer Modeling Demonstrates that Electrostatic Attraction of Nucleosomal DNA is Mediated by Histone Tails

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