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  • 1.
    B. Brant Carvalho, Paulo H.
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Ivanov, Mikhail
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Andersson, Ove
    Loerting, Thomas
    Bauer, Marion
    Tulk, Chris A.
    Haberl, Bianca
    Daemen, Luke L.
    Molaison, Jamie J.
    Amann-Winkel, Katrin
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Bull, Craig L.
    Funnell, Nicholas P.
    Häussermann, Ulrich
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Neutron scattering study of polyamorphic THF·17(H2O) – toward a generalized picture of amorphous states and structures derived from clathrate hydrates2023In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, no 21Article in journal (Refereed)
    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.

  • 2.
    Barros Brant Carvalho, Paulo Henrique
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Ivanov, Mikhail
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Andersson, Ove
    Department of Physics, Umeå University.
    Loerting, Thomas
    Institute of Physical Chemistry, University of Innsbruck.
    Bauer, Marion
    Institute of Physical Chemistry, University of Innsbruck.
    Tulk, Chris A.
    Neutron Scattering Division, Oak Ridge National Laboratory.
    Haberl, Bianca
    Neutron Scattering Division, Oak Ridge National Laboratory.
    Daemen, Luke L.
    Neutron Scattering Division, Oak Ridge National Laboratory.
    Molaison, Jamie J.
    Neutron Scattering Division, Oak Ridge National Laboratory.
    Amann-Winkel, Katrin
    Stockholm University, Faculty of Science, Department of Physics.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry. Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Bull, Craig L.
    ISIS Neutron and Muon Source, Rutherford Appleton Laboratory.
    Funnell, Nicholas P.
    ISIS Neutron and Muon Source, Rutherford Appleton Laboratory.
    Häussermann, Ulrich
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Inorganic and Structural Chemistry.
    Neutron scattering study of polyamorphic THF ∙ (H2O)17 – toward a generalized picture of amorphous states and structures derived from clathrate hydratesManuscript (preprint) (Other academic)
    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, very-HDA (VHDA), upon heat-cycling at 1.8 GPa to 180 K. Decompression of VHDA to atmospheric pressure below 130 K produces the third, recovered amorphous (RA) form. Results from a compilation of 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). The calculated density of (only in situ observable) HDA and VHDA at 2 GPa and 130 K is 1.287 and 1.328 g/cm3, respectively, whereas that of RA (at 1 atm) is 1.081 g/cm3. 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 ~23 H2O. The local water structure in HDA is reminiscent of pure HDA-ice, featuring 5-coordinated H2O. In VHDA, this structure is maintained but the local water structure is densified to resemble pure VHDA-ice with 6-coordinated H2O. The hydration structure of THF in RA constitutes ~18 H2O and the water structure corresponds to a strictly 4-coordinated network, as in the liquid. Both VHDA and RA can be considered as homogeneous, solid solutions of THF and water. The local water structure of water-rich (1:17) amorphous CHs resembles most that of the corresponding amorphous water ices when compared to guest-rich CHs, e.g., Ar ∙ ~6H2O. The proposed significance of different contributions of water local environments presents a simple view to justify neutron structure factor features.

  • 3.
    Ivanov, Mikhail
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Development of large-scale molecular and nanomaterial models2024Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Molecular simulations can access unique atomic-scale information about new materials, pharmaceuticals, and biological environments, making cost-effective predictions and aiding experimental studies. They are particularly useful for describing the mechanisms of nanoscale phenomena and the biological/inorganic interfaces. However, the computational cost of molecular simulations increases with the size of the system as well as with the model complexity, which is related to the accuracy of the simulation. This thesis aims to develop efficient large-scale molecular models that capture important structural details of the atomistic simulations. In particular, we focus on the TiO2-lipid interface, which forms in the living cells, exposed to TiO2 nanomaterials, but is also relevant in the context of biomedical applications. We have studied the interface using atomistic molecular dynamics simulations and found that the characteristics of the lipid adsorption depend on the type of the TiO2 surface, lipid headgroup composition, and the presence of cholesterol. We then derive a coarse-grained molecular model of the TiO2-lipid interface to enable the large-scale simulations of TiO2 nanoparticles interacting with model cell membranes. We show that the strength of the lipid adsorption increases with the size of the nanoparticle and that a small TiO2 nanoparticle can become partially wrapped by a lipid membrane. To improve the transferability of the coarse-grained model, we design and test an artificial neural network that learns the interactions in coarse-grained water-methanol solutions from the structural data obtained in multiple reference simulations at atomistic resolution. We show that in the studied system, the neural network learns the many-body interactions and accurately reproduces the structural properties of the solution at different concentrations. 

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  • 4.
    Ivanov, Mikhail
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Atomistic Molecular Dynamics Simulations of Lipids Near TiO2 Nanosurfaces2021In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 125, no 29, p. 8048-8059Article in journal (Refereed)
    Abstract [en]

    Understanding of interactions between inorganic nanomaterials and biomolecules, and particularly lipid bilayers, is crucial in many biotechnological and biomedical applications, as well as for the evaluation of possible toxic effects caused by nanoparticles. Here, we present a molecular dynamics study of adsorption of two important constituents of the cell membranes, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), lipids to a number of titanium dioxide planar surfaces, and a spherical nanoparticle under physiological conditions. By constructing the number density profiles of the lipid headgroup atoms, we have identified several possible binding modes and calculated their relative prevalence in the simulated systems. Our estimates of the adsorption strength, based on the total fraction of adsorbed lipids, show that POPE binds to the selected titanium dioxide surfaces stronger than DMPC, due to the ethanolamine group forming hydrogen bonds with the surface. Moreover, while POPE shows a clear preference toward anatase surfaces over rutile, DMPC has a particularly high affinity to rutile(101) and a lower affinity to other surfaces. Finally, we study how lipid concentration, addition of cholesterol, as well as titanium dioxide surface curvature may affect overall adsorption.

  • 5.
    Ivanov, Mikhail
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Development of a bottom-up coarse-grained model for interactions of lipids with TiO2 nanoparticles2024In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 45, no 16, p. 1364-1379Article in journal (Refereed)
    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.

  • 6.
    Ivanov, Mikhail
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Posysoev, Maksim
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab).
    Coarse-Grained Modeling Using Neural Networks Trained on Structural Data2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 19, p. 6704-6717Article in journal (Refereed)
    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.

  • 7.
    Ivanov, Mikhail
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Sizov, V
    Kudrev, A.
    Thermal unwinding of Polyadenylic center dot Polyuridylic acid complex with TMPyP4 porphyrin in aqueous solutions2020In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1202, article id 127365Article in journal (Refereed)
    Abstract [en]

    The molecular mechanism of Poly(A)center dot Poly(U) (Polyadenylic center dot Polyuridylic acid) polyribonucleotide denaturation was studied through a combination of molecular dynamics (MD) simulations and UV-Vis-melting experiments. UV-Vis absorption spectra of Poly(A)center dot Poly(U) were measured at different temperatures (20-70 degrees C) both in the absence and presence of porphyrin-ligand TMPyP4 in equilibrated aqueous solutions (pH 7.0). Thermal behavior of double-stranded structure of Poly(A)center dot Poly(U) altered by formation of the ternary [Poly(A)center dot Poly(U)]*(TMPyP4)(n) complexes was studied with the help of a new semi-soft chemometrics procedure, based on the analyses of fractions of species in solution versus temperature. The melting temperature in the presence of porphyrin is 1.2 degrees C higher than that for pure polyribonucleotide, which indicates that porphyrin binding contributes to the suppression of transition between the native ordered structure of Poly(A)center dot Poly(U) and disordered state. MD simulations were performed for the binding of TMPyP4 to (rA)(12)center dot(rU)(12) oligonucleotide to provide molecular-level insight into the mechanism of duplex dsRNA melting in the presence of TMPyP4. The results of MD simulations suggest a molecular mechanism of thermal stabilization of the native structure through the accommodation of TMPyP4 in double-stranded structure of (rA)(12)center dot(rU)(12) oligonucleotide groove close to the end of the ordered region of stacked nucleobase pairs.

  • 8. Kokot, Hana
    et al.
    Kokot, Boštjan
    Sebastijanović, Aleksandar
    Voss, Carola
    Podlipec, Rok
    Zawilska, Patrycja
    Berthing, Trine
    Ballester‐López, Carolina
    Høgh Danielsen, Pernille
    Contini, Claudia
    Ivanov, Mikhail
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Krišelj, Ana
    Čotar, Petra
    Zhou, Qiaoxia
    Ponti, Jessica
    Zhernovkov, Vadim
    Schneemilch, Matthew
    Doumandji, Zahra
    Pušnik, Mojca
    Umek, Polona
    Pajk, Stane
    Joubert, Olivier
    Schmid, Otmar
    Urbančič, Iztok
    Irmler, Martin
    Beckers, Johannes
    Lobaskin, Vladimir
    Halappanavar, Sabina
    Quirke, Nick
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Vogel, Ulla
    Koklič, Tilen
    Stoeger, Tobias
    Štrancar, Janez
    Prediction of Chronic Inflammation for Inhaled Particles: the Impact of Material Cycling and Quarantining in the Lung Epithelium2020In: Advanced Materials, ISSN 0935-9648, E-ISSN 1521-4095, Vol. 32, no 47, article id 2003913Article in journal (Refereed)
    Abstract [en]

    On a daily basis, people are exposed to a multitude of health-hazardous airborne particulate matter with notable deposition in the fragile alveolar region of the lungs. Hence, there is a great need for identification and prediction of material-associated diseases, currently hindered due to the lack of in-depth understanding of causal relationships, in particular between acute exposures and chronic symptoms. By applying advanced microscopies and omics to in vitro and in vivo systems, together with in silico molecular modeling, it is determined herein that the long-lasting response to a single exposure can originate from the interplay between the newly discovered nanomaterial quarantining and nanomaterial cycling between different lung cell types. This new insight finally allows prediction of the spectrum of lung inflammation associated with materials of interest using only in vitro measurements and in silico modeling, potentially relating outcomes to material properties for a large number of materials, and thus boosting safe-by-design-based material development. Because of its profound implications for animal-free predictive toxicology, this work paves the way to a more efficient and hazard-free introduction of numerous new advanced materials into our lives. 

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