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Lyubartsev, Alexander P.ORCID iD iconorcid.org/0000-0002-9390-5719
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Publications (10 of 112) Show all publications
Saeedimasine, M., Rahmani, R. & Lyubartsev, A. P. (2024). Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning. Journal of Chemical Information and Modeling
Open this publication in new window or tab >>Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning
2024 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960XArticle in journal (Refereed) Epub ahead of print
Abstract [en]

Adsorption free energies of 32 small biomolecules (amino acids side chains, fragments of lipids, and sugar molecules) on 33 different nanomaterials, computed by the molecular dynamics - metadynamics methodology, have been analyzed using statistical machine learning approaches. Multiple unsupervised learning algorithms (principal component analysis, agglomerative clustering, and K-means) as well as supervised linear and nonlinear regression algorithms (linear regression, AdaBoost ensemble learning, artificial neural network) have been applied. As a result, a small set of biomolecules has been identified, knowledge of adsorption free energies of which to a specific nanomaterial can be used to predict, within the developed machine learning model, adsorption free energies of other biomolecules. Furthermore, the methodology of grouping of nanomaterials according to their interactions with biomolecules has been presented.

National Category
Biophysics Theoretical Chemistry Physical Chemistry
Identifiers
urn:nbn:se:su:diva-229076 (URN)10.1021/acs.jcim.3c01606 (DOI)001203614700001 ()38623916 (PubMedID)2-s2.0-85190749149 (Scopus ID)
Available from: 2024-05-07 Created: 2024-05-07 Last updated: 2024-05-07
Ivanov, M. & Lyubartsev, A. P. (2024). Development of a bottom-up coarse-grained model for interactions of lipids with TiO2 nanoparticles. Journal of Computational Chemistry, 45(16), 1364-1379
Open this publication in new window or tab >>Development of a bottom-up coarse-grained model for interactions of lipids with TiO2 nanoparticles
2024 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 45, no 16, p. 1364-1379Article in journal (Refereed) Published
Abstract [en]

Understanding interactions of inorganic nanoparticles with biomolecules is important in many biotechnology, nanomedicine, and toxicological research, however, the size of typical nanoparticles makes their direct modeling by atomistic simulations unfeasible. Here, we present a bottom-up coarse-graining approach for modeling titanium dioxide (TiO2) nanomaterials in contact with phospholipids that uses the inverse Monte Carlo method to optimize the effective interactions from the structural data obtained in small-scale all-atom simulations of TiO2 surfaces with lipids in aqueous solution. The resulting coarse-grained models are able to accurately reproduce the structural details of lipid adsorption on different titania surfaces without the use of an explicit solvent, enabling significant computational resource savings and favorable scaling. Our coarse-grained simulations show that small spherical TiO2 nanoparticles (𝑟=2 nm) can only be partially wrapped by a lipid bilayer with phosphoethanolamine headgroups, however, the lipid adsorption increases with the radius of the nanoparticle. The current approach can be used to study the effect of the size and shape of TiO2 nanoparticles on their interactions with cell membrane lipids, which can be a determining factor in membrane wrapping as well as the recently discovered phenomenon of nanoquarantining, which involves the formation of layered nanomaterial–lipid structures.

Keywords
coarse-graining, inverse Monte Carlo, lipid membrane, nanotoxicity, titanium dioxide
National Category
Theoretical Chemistry Physical Chemistry
Identifiers
urn:nbn:se:su:diva-227228 (URN)10.1002/jcc.27310 (DOI)001173652500001 ()38380763 (PubMedID)2-s2.0-85186417241 (Scopus ID)
Available from: 2024-03-06 Created: 2024-03-06 Last updated: 2024-05-08Bibliographically approved
Saeedimasine, M., Grote, F. & Lyubartsev, A. P. (2023). Ab Initio Derived Classical Force Field for Molecular Dynamics Simulations of ZnO Surfaces in Biological Environment. Journal of Physical Chemistry A, 127(25), 5446-5457
Open this publication in new window or tab >>Ab Initio Derived Classical Force Field for Molecular Dynamics Simulations of ZnO Surfaces in Biological Environment
2023 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 127, no 25, p. 5446-5457Article in journal (Refereed) Published
Abstract [en]

Zinc oxide nanostructures are used in an ever increasing line of applications in technology and biomedical fields. This requires a detailed understanding of the phenomena that occur at the surface particularly in aqueous environments and in contact with biomolecules. In this work, we used ab initio molecular dynamics (AIMD) simulations to determine structural details of ZnO surfaces in water and to develop a general and transferable classical force field for hydrated ZnO surfaces. AIMD simulations show that water molecules dissociate near unmodified ZnO surfaces, forming hydroxyl groups at about 65% of the surface Zn atoms and protonating 3-coordinated surface oxygen atoms, while the rest of the surface Zn atoms bind molecularly adsorbed waters. Several force field atom types for ZnO surface atoms were identified by analysis of the specific connectivities of atoms. The analysis of the electron density was then used to determine partial charges and Lennard-Jones parameters for the identified force field atom types. The obtained force field was validated by comparison with AIMD results and with available experimental data on adsorption and immersion enthalpies, as well as adsorption free energies of several amino acids in methanol. The developed force field can be used for modeling of ZnO in aqueous and other fluid environments and in interaction with biomolecules.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-229531 (URN)10.1021/acs.jpca.3c00424 (DOI)001009945900001 ()37314246 (PubMedID)2-s2.0-85163509873 (Scopus ID)
Available from: 2024-05-24 Created: 2024-05-24 Last updated: 2024-05-24Bibliographically approved
Rahmani, R. & Lyubartsev, A. P. (2023). Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating. Nanomaterials, 13(15), Article ID 2239.
Open this publication in new window or tab >>Biomolecular Adsorprion at ZnS Nanomaterials: A Molecular Dynamics Simulation Study of the Adsorption Preferences, Effects of the Surface Curvature and Coating
2023 (English)In: Nanomaterials, E-ISSN 2079-4991, Vol. 13, no 15, article id 2239Article in journal (Refereed) Published
Abstract [en]

The understanding of interactions between nanomaterials and biological molecules is of primary importance for biomedical applications of nanomaterials, as well as for the evaluation of their possible toxic effects. Here, we carried out extensive molecular dynamics simulations of the adsorption properties of about 30 small molecules representing biomolecular fragments at ZnS surfaces in aqueous media. We computed adsorption free energies and potentials of mean force of amino acid side chain analogs, lipids, and sugar fragments to ZnS (110) crystal surface and to a spherical ZnS nanoparticle. Furthermore, we investigated the effect of poly-methylmethacrylate (PMMA) coating on the adsorption preferences of biomolecules to ZnS. We found that only a few anionic molecules: aspartic and glutamic acids side chains, as well as the anionic form of cysteine show significant binding to pristine ZnS surface, while other molecules show weak or no binding. Spherical ZnS nanoparticles show stronger binding of these molecules due to binding at the edges between different surface facets. Coating of ZnS by PMMA changes binding preferences drastically: the molecules that adsorb to a pristine ZnS surface do not adsorb on PMMA-coated surfaces, while some others, particularly hydrophobic or aromatic amino-acids, show high binding affinity due to binding to the coating. We investigate further the hydration properties of the ZnS surface and relate them to the binding preferences of biomolecules.

Keywords
zinc sulfide, surface properties, biomolecular adsorption, molecular dynamics
National Category
Nano Technology Materials Engineering Physical Sciences Physical Chemistry
Identifiers
urn:nbn:se:su:diva-221114 (URN)10.3390/nano13152239 (DOI)001046278000001 ()37570556 (PubMedID)2-s2.0-85167657281 (Scopus ID)
Available from: 2023-09-19 Created: 2023-09-19 Last updated: 2023-09-19Bibliographically approved
Ivanov, M., Posysoev, M. & Lyubartsev, A. P. (2023). Coarse-Grained Modeling Using Neural Networks Trained on Structural Data. Journal of Chemical Theory and Computation, 19(19), 6704-6717
Open this publication in new window or tab >>Coarse-Grained Modeling Using Neural Networks Trained on Structural Data
2023 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 19, p. 6704-6717Article in journal (Refereed) Published
Abstract [en]

We propose a method of bottom-up coarse-graining, in which interactions within a coarse-grained model are determined by an artificial neural network trained on structural data obtained from multiple atomistic simulations. The method uses ideas of the inverse Monte Carlo approach, relating changes in the neural network weights with changes in average structural properties, such as radial distribution functions. As a proof of concept, we demonstrate the method on a system interacting by a Lennard-Jones potential modeled by a simple linear network and a single-site coarse-grained model of methanol-water solutions. In the latter case, we implement a nonlinear neural network with intermediate layers trained by atomistic simulations carried out at different methanol concentrations. We show that such a network acts as a transferable potential at the coarse-grained resolution for a wide range of methanol concentrations, including those not included in the training set.

National Category
Physical Sciences Materials Chemistry
Identifiers
urn:nbn:se:su:diva-223178 (URN)10.1021/acs.jctc.3c00516 (DOI)001069923500001 ()37712507 (PubMedID)
Available from: 2023-10-26 Created: 2023-10-26 Last updated: 2024-03-11Bibliographically approved
B. Brant Carvalho, P. H., Ivanov, M., Andersson, O., Loerting, T., Bauer, M., Tulk, C. A., . . . Häussermann, U. (2023). Neutron scattering study of polyamorphic THF·17(H2O) – toward a generalized picture of amorphous states and structures derived from clathrate hydrates. Physical Chemistry, Chemical Physics - PCCP (21)
Open this publication in new window or tab >>Neutron scattering study of polyamorphic THF·17(H2O) – toward a generalized picture of amorphous states and structures derived from clathrate hydrates
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2023 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, no 21Article in journal (Refereed) Published
Abstract [en]

From crystalline tetrahydrofuran clathrate hydrate, THF–CH (THF·17H2O, cubic structure II), three distinct polyamorphs can be derived. First, THF–CH undergoes pressure-induced amorphization when pressurized to 1.3 GPa in the temperature range 77–140 K to a form which, in analogy to pure ice, may be called high-density amorphous (HDA). Second, HDA can be converted to a densified form, VHDA, upon heat-cycling at 1.8 GPa to 180 K. Decompression of VHDA to atmospheric pressure below 130 K produces the third form, recovered amorphous (RA). Results from neutron scattering experiments and molecular dynamics simulations provide a generalized picture of the structure of amorphous THF hydrates with respect to crystalline THF–CH and liquid THF·17H2O solution (∼2.5 M). Although fully amorphous, HDA is heterogeneous with two length scales for water–water correlations (less dense local water structure) and guest–water correlations (denser THF hydration structure). The hydration structure of THF is influenced by guest–host hydrogen bonding. THF molecules maintain a quasiregular array, reminiscent of the crystalline state, and their hydration structure (out to 5 Å) constitutes ∼23H2O. The local water structure in HDA is reminiscent of pure HDA-ice featuring 5-coordinated H2O. In VHDA, the hydration structure of HDA is maintained but the local water structure is densified and resembles pure VHDA-ice with 6-coordinated H2O. The hydration structure of THF in RA constitutes ∼18 H2O molecules and the water structure corresponds to a strictly 4-coordinated network, as in the liquid. Both VHDA and RA can be considered as homogeneous.

National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:su:diva-218073 (URN)10.1039/d3cp00539a (DOI)000991791600001 ()37211856 (PubMedID)
Available from: 2023-06-13 Created: 2023-06-13 Last updated: 2023-10-12Bibliographically approved
Grote, F., Lyubartsev, A. P., Dvinskikh, S. V., Rinwa, V. & Holmbäck, J. (2023). Phase equilibrium, dynamics and rheology of phospholipid–ethanol mixtures: a combined molecular dynamics, NMR and viscometry study. Physical Chemistry, Chemical Physics - PCCP, 25(23), 15905-15915
Open this publication in new window or tab >>Phase equilibrium, dynamics and rheology of phospholipid–ethanol mixtures: a combined molecular dynamics, NMR and viscometry study
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2023 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 25, no 23, p. 15905-15915Article in journal (Refereed) Published
Abstract [en]

Binary mixtures of ethanol and phospholipids DOPC and DOPE have been investigated in a composition range relevant for topical drug delivery applications. This was done using a combined computer simulation and experimental approach where molecular dynamics simulations of ethanol–lipid mixtures with different compositions were performed. Several key properties including diffusion coefficients, longitudinal relaxation times, and shear viscosity were computed. In addition, diffusion coefficients, viscosities and NMR longitudinal relaxation times were measured experimentally for comparison and in order to validate the results from simulation. Diffusion coefficients and relaxation times obtained from simulations are in good agreement with results from NMR and computed viscosities are in reasonable agreement with viscometry experiments indicating that the simulations provide a realistic description of the ethanol–phospholipid mixtures. Structural changes in the simulated systems were investigated using an analysis based on radial distribution functions. This showed that the structure of ethanol–DOPC mixtures remains essentially unchanged in the investigated concentration range while ethanol–DOPE mixtures undergo structural rearrangements with the tendency for forming small aggregates on the 100 ns time scale consisting of less than 10 lipids. Although our simulations and experiments indicate that no larger aggregates form, they also show that DOPE has stronger aggregation tendency than DOPC. This highlights the importance of the character of the lipid headgroup for lipid aggregation in ethanol and gives new insights into phase equilibrium, dynamics and rheology that could be valuable for the development of advanced topical drug delivery formulations.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-220447 (URN)10.1039/d3cp00425b (DOI)000999450700001 ()37260055 (PubMedID)2-s2.0-85162089775 (Scopus ID)
Available from: 2023-08-30 Created: 2023-08-30 Last updated: 2023-08-30Bibliographically approved
Sun, T., Minhas, V., Mirzoev, A., Korolev, N., Lyubartsev, A. P. & Nordenskiöld, L. (2022). A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions. Journal of Chemical Theory and Computation, 18(6), 3948-3960
Open this publication in new window or tab >>A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions
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2022 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 18, no 6, p. 3948-3960Article in journal (Refereed) Published
Abstract [en]

The nucleosome core particle (NCP) is a large complex of 145–147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome–nucleosome attraction in the presence of multivalent cations (Mg(H2O)62+ or Co(NH3)63+) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP–NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers. 

National Category
Chemical Sciences Biological Sciences
Identifiers
urn:nbn:se:su:diva-206889 (URN)10.1021/acs.jctc.2c00083 (DOI)000811877500001 ()35580041 (PubMedID)2-s2.0-85131601450 (Scopus ID)
Available from: 2022-06-30 Created: 2022-06-30 Last updated: 2022-06-30Bibliographically approved
Zhou, X., Yan, F., Lyubartsev, A. P., Shen, B., Zhai, J., Conesa, J. C. & Hedin, N. (2022). Efficient Production of Solar Hydrogen Peroxide Using Piezoelectric Polarization and Photoinduced Charge Transfer of Nanopiezoelectrics Sensitized by Carbon Quantum Dots. Advanced Science, 9(18), Article ID 2105792.
Open this publication in new window or tab >>Efficient Production of Solar Hydrogen Peroxide Using Piezoelectric Polarization and Photoinduced Charge Transfer of Nanopiezoelectrics Sensitized by Carbon Quantum Dots
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2022 (English)In: Advanced Science, E-ISSN 2198-3844, Vol. 9, no 18, article id 2105792Article in journal (Refereed) Published
Abstract [en]

Piezoelectric semiconductors have emerged as redox catalysts, and challenges include effective conversion of mechanical energy to piezoelectric polarization and achieving high catalytic activity. The catalytic activity can be enhanced by simultaneous irradiation of ultrasound and light, but the existing piezoelectric semiconductors have trouble absorbing visible light. A piezoelectric catalyst is designed and tested for the generation of hydrogen peroxide (H2O2). It is based on Nb-doped tetragonal BaTiO3 (BaTiO3:Nb) and is sensitized by carbon quantum dots (CDs). The photosensitizer injects electrons into the conduction band of the semiconductor, while the piezoelectric polarization directed electrons to the semiconductor surface, allowing for a high-rate generation of H2O2. The piezoelectric polarization field restricts the recombination of photoinduced electron–hole pairs. A production rate of 1360 µmol gcatalyst−1 h−1 of H2O2 is achieved under visible light and ultrasound co-irradiation. Individual piezo- and photocatalysis yielded lower production rates. Furthermore, the CDs enhance the piezocatalytic activity of the BaTiO3:Nb. It is noted that moderating the piezoelectricity of BaTiO3:Nb via microstructure modulation influences the piezophotocatalytic activity. This work shows a new methodology for synthesizing H2O2 by using visible light and mechanical energy.

Keywords
carbon quantum dots, hydrogen peroxide, Nb-doped BaTiO3, piezocatalysis, piezoelectric polarization, piezophotocatalysis
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-204410 (URN)10.1002/advs.202105792 (DOI)000786488600001 ()35451215 (PubMedID)2-s2.0-85128574371 (Scopus ID)
Available from: 2022-05-04 Created: 2022-05-04 Last updated: 2022-08-05Bibliographically approved
B. Brant Carvalho, P. H., Mace, A., Nangoi, I. M., Leitão, A. A., Tulk, C. A., Molaison, J. J., . . . Häussermann, U. (2022). Exploring High-Pressure Transformations in Low-Z (H2, Ne) Hydrates at Low Temperatures. Crystals, 12(1), Article ID 9.
Open this publication in new window or tab >>Exploring High-Pressure Transformations in Low-Z (H2, Ne) Hydrates at Low Temperatures
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2022 (English)In: Crystals, ISSN 2073-4352, Vol. 12, no 1, article id 9Article in journal (Refereed) Published
Abstract [en]

The high pressure structural behavior of H2 and Ne clathrate hydrates with approximate composition H2/Ne·~4H2O and featuring cubic structure II (CS-II) was investigated by neutron powder diffraction using the deuterated analogues at ~95 K. CS-II hydrogen hydrate transforms gradually to isocompositional C1 phase (filled ice II) at around 1.1 GPa but may be metastably retained up to 2.2 GPa. Above 3 GPa a gradual decomposition into C2 phase (H2·H2O, filled ice Ic) and ice VIII’ takes place. Upon heating to 200 K the CS-II to C1 transition completes instantly whereas C1 decomposition appears sluggish also at 200 K. C1 was observed metastably up to 8 GPa. At 95 K C1 and C2 hydrogen hydrate can be retained below 1 GPa and yield ice II and ice Ic, respectively, upon complete release of pressure. In contrast, CS-II neon hydrate undergoes pressure-induced amorphization at 1.9 GPa, thus following the general trend for noble gas clathrate hydrates. Upon heating to 200 K amorphous Ne hydrate crystallizes as a mixture of previously unreported C2 hydrate and ice VIII’.

Keywords
hydrogen hydrate, neon hydrate, pressure effects, neutron diffraction, molecular dynamics, clathrate hydrates
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-201882 (URN)10.3390/cryst12010009 (DOI)000749277100001 ()
Available from: 2022-02-10 Created: 2022-02-10 Last updated: 2023-02-03Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-9390-5719

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