Teaching assistant at:

1. Chemical Modelling (KZ7002)

- Developing and supervising student research projects in the field of molecular modelling (Molecular dynamics, Coarse-grained simulations, DFT)

- Leading exercise sessions on the theory of chemical modelling (classical and quantum mechanics, statistical thermodynamics)

2. Computational Data Analysis in Chemistry (KZ4016)

- Teaching the basics of programming, data analysis and statistics with MATLAB

My PhD project, “Modeling interactions between phospholipids and inorganic surfaces”, aims to develop new computational models for large-scale simulations of inorganic materials with phospholipids - the core constituents of cell membranes. These models may be used to provide molecular insights into the nanotoxicity problem.

The latest development in the project has been the use of machine learning for parametrizing transferable low-resolution molecular models.

A selection from Stockholm University publication database

• Atomistic Molecular Dynamics Simulations of Lipids Near TiO2 Nanosurfaces

  2021. Mikhail Ivanov, Alexander P. Lyubartsev. Journal of Physical Chemistry B 125 (29), 8048-8059

  Article

  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.

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• Thermal unwinding of Polyadenylic center dot Polyuridylic acid complex with TMPyP4 porphyrin in aqueous solutions

  2020. Mikhail Ivanov, V Sizov, A. Kudrev. Journal of Molecular Structure 1202

  Article

  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.

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• Prediction of Chronic Inflammation for Inhaled Particles: the Impact of Material Cycling and Quarantining in the Lung Epithelium

  2020. Hana Kokot (et al.). Advanced Materials 32 (47), 2003913-2003913

  Article

  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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• Neutron scattering study of polyamorphic THF ∙ (H₂O)₁₇ – toward a generalized picture of amorphous states and structures derived from clathrate hydrates

  Paulo Henrique Barros Brant Carvalho (et al.).

  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.

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Show all publications by Mikhail Ivanov at Stockholm University