Search Results - "Lyubartsev, Alexander P."

Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids by Jämbeck, Joakim P. M, Lyubartsev, Alexander P

“…An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio…”
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An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes by Jämbeck, Joakim P. M, Lyubartsev, Alexander P

“…Biological membranes are versatile in composition and host intriguing molecular processes. In order to be able to study these systems, an accurate model…”
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Another Piece of the Membrane Puzzle: Extending Slipids Further by Jämbeck, Joakim P. M, Lyubartsev, Alexander P

“…To be able to model complex biological membranes in a more realistic manner, the force field Slipids (Stockholm lipids) has been extended to include parameters…”
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Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels by Minhas, Vishal, Sun, Tiedong, Mirzoev, Alexander, Korolev, Nikolay, Lyubartsev, Alexander P, Nordenskiöld, Lars

“…Accurate parametrization of force fields (FFs) is of ultimate importance for computer simulations to be reliable and to possess a predictive power. In this…”
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A multiscale analysis of DNA phase separation: from atomistic to mesoscale level by Sun, Tiedong, Mirzoev, Alexander, Minhas, Vishal, Korolev, Nikolay, Lyubartsev, Alexander P, Nordenskiöld, Lars

“…DNA condensation and phase separation is of utmost importance for DNA packing in vivo with important applications in medicine, biotechnology and polymer…”
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An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions by Fan, Yanping, Korolev, Nikolay, Lyubartsev, Alexander P, Nordenskiöld, Lars

“…In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear…”
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Exploring Carbamazepine Polymorph Crystal Growth in Water by Enhanced Sampling Simulations by Herboth, Radost, Lyubartsev, Alexander P

“…In this work, the polymorphism of the active pharmaceutical ingredient carbamazepine (CBZ) was investigated by using molecular dynamics simulations with an…”
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Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers by Jämbeck, Joakim P. M, Lyubartsev, Alexander P

“…Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in…”
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Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating by Rahmani, Roja, Lyubartsev, Alexander P

“…The understanding of interactions between nanomaterials and biological molecules is of primary importance for biomedical applications of nanomaterials, as well…”
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Implicit solvent systematic coarse-graining of dioleoylphosphatidylethanolamine lipids: From the inverted hexagonal to the bilayer structure by Mortezazadeh, Saeed, Jamali, Yousef, Naderi-Manesh, Hossein, Lyubartsev, Alexander P

“…Lamellar and hexagonal lipid structures are of particular importance in the biological processes such as membrane fusion and budding. Atomistic simulations of…”
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Molecular Dynamics Simulation Study of Glycerol–Water Liquid Mixtures by Egorov, Andrei V, Lyubartsev, Alexander P, Laaksonen, Aatto

“…To study the effects of water on conformational dynamics of polyalcohols, Molecular Dynamics simulations of glycerol–water liquid mixtures have been carried…”
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New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures by Nikitin, Alexei M., Lyubartsev, Alexander P.

“…A new six site flexible acetonitrile molecular model is developed. The AMBER force field was used for description of intramolecular parameters, the atomic…”
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Bottom-Up Coarse-Grained Modeling of DNA by Sun, Tiedong, Minhas, Vishal, Korolev, Nikolay, Mirzoev, Alexander, Lyubartsev, Alexander P, Nordenskiöld, Lars

“…Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations…”
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Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations by Korolev, Nikolay, Yu, Hang, Lyubartsev, Alexander P., Nordenskiöld, Lars

“…ABSTRACT The positively charged N‐terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription,…”
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Effect of Local Anesthetic Lidocaine on Electrostatic Properties of a Lipid Bilayer by Högberg, Carl-Johan, Lyubartsev, Alexander P.

“…The influence of the local anesthetic lidocaine on electrostatic properties of a lipid membrane bilayer was studied by molecular dynamics simulations. The…”
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Electrostatic Origin of Salt-Induced Nucleosome Array Compaction by Korolev, Nikolay, Allahverdi, Abdollah, Yang, Ye, Fan, Yanping, Lyubartsev, Alexander P., Nordenskiöld, Lars

“…The physical mechanism of the folding and unfolding of chromatin is fundamentally related to transcription but is incompletely characterized and not fully…”
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Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids by Grote, Fredrik, Lyubartsev, Alexander P

“…The molecular mechanics force field Slipids developed in a series of works by Jämbeck and Lyubartsev (J. Phys. Chem. B 2012, 116, 3164–3179; J. Chem. Theory…”
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A Molecular Dynamics Investigation of the Influence of Hydration and Temperature on Structural and Dynamical Properties of a Dimyristoylphosphatidylcholine Bilayer by Högberg, Carl-Johan, Lyubartsev, Alexander P

“…A series of molecular dynamics simulations of dimyristoylphosphatidylcholine bilayers, with different levels of hydration and temperature, were performed to…”
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Cation-induced polyelectrolyte–polyelectrolyte attraction in solutions of DNA and nucleosome core particles by Korolev, Nikolay, Lyubartsev, Alexander P., Nordenskiöld, Lars

“…The paper reviews our current studies on the experimentally induced cation compaction and aggregation in solutions of DNA and nucleosome core particles and the…”
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A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo by Nikolay Korolev, Di Luo, Alexander P. Lyubartsev, Lars Nordenskiöld

“…Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution…”
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