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123 results on '"Yesylevskyy, Semen O."'

1. Flexoelectric and piezoelectric coupling in a bended MoS$_2$ monolayer

Author

Shevliakova, Hanna V., Yesylevskyy, Semen O., Kupchak, Ihor, Dovbeshko, Galina I., Kim, Yunseok, and Morozovska, Anna N.

Subjects
Condensed Matter - Materials Science, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Low-dimensional (LD) transition metal dichalcogenides (TMDs) in the form of nanoflakes, which consist of one or several layers, are the subject of intensive fundamental and applied research. Due to the size-induced transition from a bulk to nanoscale, they can be both nonpolar, piezoelectric or even ferroelectric. Also, in terms of electronic properties, they can be direct-band semiconductors, semi-metals or even metals. The tuning of the electronic properties in the LD-TMDs are commonly related with applied strains and strain gradients, which can affect strongly their polar properties via the piezoelectric and flexoelectric couplings. Using the density functional theory (DFT) and phenomenological Landau approach, we studied the bended 2H-MoS$_2$ monolayer and analyzed its flexoelectric and piezoelectric properties. The dependences of the dipole moment, strain and strain gradient on the coordinate along the layer were calculated. From these dependences the components of the flexoelectric and piezoelectric tensors have been determined and analyzed. Obtained results are useful for applications of LD-TMDs in strain engineering and flexible electronics., Comment: 19 pages, 7 figures, 1 appendix

Published
2021

5. Boosting performance of generative diffusion model for molecular docking by training on artificial binding pockets

Author

Voitsitskyi, Taras, primary, Bdzhola, Volodymyr, additional, Stratiichuk, Roman, additional, Koleiev, Ihor, additional, Ostrovsky, Zakhar, additional, Vozniak, Volodymyr, additional, Khropachov, Ivan, additional, Henitsoi, Pavlo, additional, Popryho, Leonid, additional, Zhytar, Roman, additional, Yesylevskyy, Semen O, additional, Nafiev, Alan, additional, and Starosyla, Serhii, additional

Published
2023
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16. Shape-independent model (SHIM) approach for studying aggregation by NMR diffusometry.

Author

Hernandez Santiago, Adrian A., Buchelnikov, Anatoly S., Rubinson, Maria A., Yesylevskyy, Semen O., Parkinson, John A., and Evstigneev, Maxim P.

Subjects
NUCLEAR magnetic resonance spectroscopy, DIFFUSION, COMPLEXATION reactions, MOLECULAR self-assembly, ENTHALPY, ENTROPY
Abstract

NMR diffusometry has been gaining wide popularity in various areas of applied chemistry for investigating diffusion and complexation processes in solid and aqueous phases. To date, the application of this method to study aggregation phenomena proceeding beyond the dimer stage of assembly has been restricted by the need for a priori knowledge of the aggregates' shape, commonly difficult to know in practice. We describe here a comprehensive analysis of aggregation parameter-dependency on the type and shape selected for modeling assembly processes, and report for the first time a shape-independent model (designated the SHIM approach), which may be used as an alternative in cases when information on aggregates' shapes is unavailable. The model can be used for determining equilibrium aggregation parameters from self-diffusion NMR data including equilibrium self-association constant and changes in enthalpy, ΔH, and entropy, ΔS. [ABSTRACT FROM AUTHOR]

Published
2015
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20. The influence of curvature on the properties of the plasma membrane. Insights from atomistic molecular dynamics simulations

Author

Yesylevskyy, Semen O., Rivel, Timothée, Ramseyer, Christophe, Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Université de Franche-Comté ( UFC ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)

Subjects
Physics::Biological Physics, [ SDV.BBM.BP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Cell Membrane, Lipid Bilayers, lcsh:R, lcsh:Medicine, Molecular Dynamics Simulation, Article, Quantitative Biology::Cell Behavior, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Condensed Matter::Soft Condensed Matter, Quantitative Biology::Subcellular Processes, Cholesterol, [ SDV.SP ] Life Sciences [q-bio]/Pharmaceutical sciences, [ PHYS.PHYS.PHYS-BIO-PH ] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [ PHYS.PHYS.PHYS-COMP-PH ] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], [ CHIM.THEO ] Chemical Sciences/Theoretical and/or physical chemistry, lipids (amino acids, peptides, and proteins), lcsh:Q, lcsh:Science, Phospholipids, ComputingMilieux_MISCELLANEOUS
Abstract

In this work we conduct a systematic analysis of the influence of curvature on various properties of a realistic model of mammalian plasma membrane with asymmetric lipid content of monolayers and a realistic concentration of cholesterol. In order to do this we developed new technique for simulating membranes with the global membrane curvature restricted to any desirable value while keeping free lateral diffusion of the lipids and without introducing artifacts or perturbing the membrane structure. We show that the thickness of the hydrophobic core of the concave monolayer decreases by approximately 1.3 Å in comparison to that of the flat membrane, while the thickness of the convex monolayer does not change. The order parameter of the lipid tails decreases significantly in the certain layers of the curved membrane. The area per lipid increases in the convex monolayer and decreases in the concave monolayer. The cholesterol inclination angle decreases when the curvature of a particular monolayer changes from concave to convex. The amount of cholesterol in the minor fraction located between the membrane leaflets is zero in the membrane with positive curvature and increases to 1.7% in the flat membrane and to 2.5% in the membrane with negative curvature.

Published
2017

21. Structures of single, double and triple layers of lipids adsorbed on graphene: Insights from all-atom molecular dynamics simulations

Author

Yesylevskyy , Semen, Rivel , Timothée, Ramseyer , Christophe, Yesylevskyy , Semen O., Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)

Subjects
[ SDV.BBM.BP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Materials science, Graphene, Nanotechnology, 02 engineering and technology, General Chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Micelle, 0104 chemical sciences, law.invention, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Hydrophobic mismatch, Molecular dynamics, law, Chemical physics, Monolayer, Atom, Water environment, Surface modification, lipids (amino acids, peptides, and proteins), General Materials Science, 0210 nano-technology, ComputingMilieux_MISCELLANEOUS
Abstract

Non-covalent functionalization of graphene with phospholipids is a promising technique for biosensing applications and intracellular delivery of analytical probes and drugs. However, molecular details of the self-assembly of lipids on graphene surface is still poorly understood and hard to control. There is a clear lack of understanding of why various kinds of lipid aggregates can form on graphene. In the current work, we address this question by investigating equilibrium and dynamical properties of lipid layers adsorbed on graphene in water environment and in vacuum using all-atom Molecular Dynamics simulations. It is shown that a variety of lipid aggregates can form on top of graphene depending on initial orientation, number of adsorbed lipid layers and the presence of water. The lipid layers self-organize and reorient in order to minimize hydrophobic mismatch on graphene-lipid, lipid-lipid and water-lipid interfaces. Obtained structures range from homogeneous layers to the networks of inverted micelle-like structures and weakly bound cylindrical micelles on top of monolayers. Our results are in excellent agreement with recent experimental findings. Another pronounced effect of graphene is the strong ordering of the lipid atoms which are in direct contact with it. In all studied systems at least two well-structured atomic shells are formed above the graphene surface at the distances of 0.35 and 0.85 nm.

Published
2017

22. Conjugation of squalene to gemcitabine as unique approach exploiting endogenous lipoproteins for drug delivery

Author

Sobot, Dunja, Mura, Simona, Yesylevskyy, Semen O., Dalbin, Laura, Cayre, Fanny, Bort, Guillaume, Mougin, Julie, Desmaële, Didier, Lepetre-Mouelhi, Sinda, Pieters, Grégory, Andreiuk, Bohdan, Klymchenko, Andrey S., Paul, Jean-Louis, Ramseyer, Christophe, Couvreur, Patrick, Institut Galien Paris-Sud (IGPS), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Innovation pour les Technologies des Energies Nouvelles et les nanomatériaux (LITEN), Institut National de L'Energie Solaire (INES), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Molécules bioactives, conception, isolement et synthèse (MBCIS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Service de Chimie Bio-Organique et de Marquage (SCBM), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biophotonique et Pharmacologie - UMR 7213 (LBP), Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), EA 4529, UFR de Pharmacie, Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Physico-chimie, pharmacotechnie, biopharmacie (PCPB), CONCEPTION ET EVALUATION DE NOUVEAUX AGENTS DE CONTRASTE VECTORISES POUR L'IRM, Conservatoire National des Arts et Métiers [CNAM] ( CNAM ) -ESPCI ParisTech-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Innovation pour les Technologies des Energies Nouvelles et les nanomatériaux ( LITEN ), Institut National de L'Energie Solaire ( INES ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre Scientifique et Technique du Bâtiment ( CSTB ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre Scientifique et Technique du Bâtiment ( CSTB ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Molécules bioactives, conception, isolement et synthèse ( MBCIS ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Service de Chimie Bio-Organique et de Marquage ( SCBM ), Département Médicaments et Technologies pour la Santé ( DMTS ), Direction de Recherche Fondamentale (CEA) ( DRF (CEA) ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) ( DRF (CEA) ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Laboratoire de Biophotonique et Pharmacologie - UMR 7213 ( LBP ), Centre National de la Recherche Scientifique ( CNRS ) -Réseau nanophotonique et optique, Université de Strasbourg ( UNISTRA ) -Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Strasbourg ( UNISTRA ) -Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Physico-chimie, pharmacotechnie, biopharmacie ( PCPB ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS), Lipides : systèmes analytiques et biologiques (Lip(Sys)²), Université Paris-Saclay, Laboratoire Chrono-environnement (UMR 6249) (LCE), ANR-10-LABX-0035,Nano-Saclay,Paris-Saclay multidisciplinary Nano-Lab(2010), European Project: 249835,EC:FP7:ERC,ERC-2009-AdG,TERNANOMED(2010), and Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)

Subjects
Squalene, [ SDV.BBM.BP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Science, Lipoproteins, Calorimetry, Ligands, Deoxycytidine, Article, Cell Line, Drug Delivery Systems, Cell Line, Tumor, Neoplasms, Fluorescence Resonance Energy Transfer, Animals, Humans, ComputingMilieux_MISCELLANEOUS, fungi, food and beverages, Gemcitabine, Rats, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Cholesterol, Receptors, LDL, A549 Cells, Liposomes, MCF-7 Cells, Nanoparticles, lipids (amino acids, peptides, and proteins)
Abstract

Once introduced in the organism, the interaction of nanoparticles with various biomolecules strongly impacts their fate. Here we show that nanoparticles made of the squalene derivative of gemcitabine (SQGem) interact with lipoproteins (LPs), indirectly enabling the targeting of cancer cells with high LP receptors expression. In vitro and in vivo experiments reveal preeminent affinity of the squalene-gemcitabine bioconjugates towards LP particles with the highest cholesterol content and in silico simulations further display their incorporation into the hydrophobic core of LPs. To the best of our knowledge, the use of squalene to induce drug insertion into LPs for indirect cancer cell targeting is a novel concept in drug delivery. Interestingly, not only SQGem but also other squalene derivatives interact similarly with lipoproteins while such interaction is not observed with liposomes. The conjugation to squalene represents a versatile platform that would enable efficient drug delivery by simply exploiting endogenous lipoproteins., The interaction of nanoparticles with a range of biomolecules once they have been injected within the body can affect their performance. Here, the authors demonstrate that squalene nanomaterials conjugated with anticancer drugs can interact with lipoproteins and can be used to target cancer cells.

Published
2017

27. Fluorescence Probes Exhibit Photoinduced Structural Planarization: Sensing In Vitroand In VivoMicroscopic Dynamics of Viscosity Free from Polarity Interference

Author

Wu, Cheng-Ham, Chen, Yi, Pyrshev, Kyrylo A., Chen, Yi-Ting, Zhang, Zhiyun, Chang, Kai-Hsin, Yesylevskyy, Semen O., Demchenko, Alexander P., and Chou, Pi-Tai

Abstract

We demonstrate the construction of wavelength λ-ratiometric images that allow visualizing the distribution of microscopic dynamics within living cells and tissues by using the newly developed principle of fluorescence response. The bent-to-planar motion in the excited state of incorporated fluorescence probes leads to elongation of the π-delocalization, resulting in microviscosity-dependent but polarity-insensitive interplay between well-separated blue and red bands in emission spectra. This allows constructing the exceptionally contrasted images of cellular dynamics. Moreover, the application of probes with increased affinity toward biological membranes allowed detecting the differences in dynamics between the plasma membrane and intracellular membrane structures. Such λ-ratiometric microviscosity imaging was extended for mapping the living tissues and observing their inflammation-dependent changes.

Published
2020
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35. Interaction of C60 fullerenes with asymmetric and curved lipid membranes: a molecular dynamics study.

Author

Cherniavskyi, Yevhen K., Ramseyer, Christophe, and Yesylevskyy, Semen O.

Abstract

Interaction of fullerenes with asymmetric and curved DOPC/DOPS bicelles is studied by means of coarse-grained molecular dynamics simulations. The effects caused by asymmetric lipid composition of the membrane leaflets and the curvature of the membrane are analyzed. It is shown that the aggregates of fullerenes prefer to penetrate into the membrane in the regions of the moderately positive mean curvature. Upon penetration into the hydrophobic core of the membrane fullerenes avoid the regions of the extreme positive or the negative curvature. Fullerenes increase the ordering of lipid tails, which are in direct contact with them, but do not influence other lipids significantly. Our data suggest that the effects of the membrane curvature should be taken into account in the studies concerning permeability of the membranes to fullerenes and fullerene-based drug delivery systems. [ABSTRACT FROM AUTHOR]

Published
2016
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48. Efficiency of the monofunctionalized C60 fullerenes as membrane targeting agents studied by all-atom molecular dynamics simulations.

Author

Yesylevskyy, Semen O., Kraszewski, Sebastian, Picaud, Fabien, and Ramseyer, Christophe

Subjects
*FULLERENES, *CELLULAR signal transduction, *MOLECULAR dynamics, *MEMBRANE proteins, *CHEMICAL affinity, *BILAYER lipid membranes, *HYDROPHOBIC interactions
Abstract

Transmembrane translocation of C60 fullerenes functionalized by the single amino-derivative in neutral and charged forms was studies by extensive all-atom molecular dynamics simulations. It is shown that these complexes exhibit very strong affinity to the membrane core, but their spontaneous translocation through the membrane is not possible at practical time scale. In contrast, free amino derivatives translocate through the membrane much easier than their complexes with fullerenes, but do not have pronounced affinity to the membrane interior. Our results suggest that monofunctionalized C60 could be extremely efficient membrane targeting agents, which facilitate accumulation of the water-soluble compounds in the hydrophobic core of lipid bilayer. [ABSTRACT FROM AUTHOR]

Published
2013
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49. The blind search for the closed states of hinge-bending proteins.

Author

Yesylevskyy, Semen O., Kharkyanen, Valery N., and Demchenko, Alexander P.

Abstract

The hinge-bending proteins provide the most pronounced example of the large-amplitude slow motions in a number of proteins, which are critical for their functioning. They are often used as the test ground for developing novel approaches to the simulation of slow protein dynamics. In the present study, we present the algorithm, which allows physically-consistent simulations of slow protein dynamics in globular proteins. Our algorithm is based on the hierarchical clustering of the correlation patterns (HCCP) technique of domain identification, which allows subdividing the protein into the hierarchy of the rigid-body-like clusters. The clusters are allowed to rotate relative to one another on the automatically identified hinges. The clusters are found in the course of automated, objective and well-tested procedure. In the present communication, our technique is applied to 10 hinge-bending proteins. For each of the proteins, we performed the blind search for the closed conformation, staring from the open one. Resulting closed conformations are compared with the closed states observed in crystallographic structures. It is shown that our technique produces realistic closed conformations for 8 out of 10 studied proteins. This demonstrates that HCCP technique can be used for finding alternative protein conformations and for sampling the slow motions in proteins. Proteins 2008. © 2007 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Published
2008
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50. Flexoelectric and Piezoelectric Coupling in a Bended MoS 2 Monolayer.

Author

Shevliakova, Hanna V., Yesylevskyy, Semen O., Kupchak, Ihor, Dovbeshko, Galina I., Kim, Yunseok, and Morozovska, Anna N.

Subjects
*STRAINS & stresses (Mechanics), *PIEZOELECTRICITY, *MONOMOLECULAR films, *DENSITY functional theory, *LANDAU theory, *ELECTRONICS engineers
Abstract

Low-dimensional (LD) transition metal dichalcogenides (TMDs) in the form of nanoflakes, which consist of one or several layers, are the subject of intensive fundamental and applied research. The tuning of the electronic properties of the LD-TMDs are commonly related with applied strains and strain gradients, which can strongly affect their polar properties via piezoelectric and flexoelectric couplings. Using the density functional theory and phenomenological Landau approach, we studied the bended 2H-MoS2 monolayer and analyzed its flexoelectric and piezoelectric properties. The dependences of the dipole moment, strain, and strain gradient on the coordinate along the layer were calculated. From these dependences, the components of the flexoelectric and piezoelectric tensors have been determined and analyzed. Our results revealed that the contribution of the flexoelectric effect dominates over the piezoelectric effect in both in-plane and out-of-plane directions of the monolayer. In accordance with our calculations, a realistic strain gradient of about 1 nm−1 can induce an order of magnitude higher than the flexoelectric response in comparison with the piezoelectric reaction. The value of the dilatational flexoelectric coefficient is almost two times smaller than the shear component. It appeared that the components of effective flexoelectric and piezoelectric couplings can be described by parabolic dependences of the corrugation. Obtained results are useful for applications of LD-TMDs in strain engineering and flexible electronics. [ABSTRACT FROM AUTHOR]

Published
2021
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