Публикации

Dusty plasma structures in glow discharge in helium in the temperature range of 5–300 K are investigated experimentally. We have described the experimental setup that makes it possible to continuously vary the temperature regime. The method for experimental data processing has been described. We have measured interparticle distances in the temperature range of 9–295 K and compared them with the Debye radius. We indicate the ranges of variations in experimental parameters in which plasma–dust structures are formed and various types of their behavior are manifested (rotation, vibrations of structures, formation of vertical linear chains, etc.). The applicability of the Yukawa potential to the description of the structural properties of a dusty plasma in the experimental conditions is discussed.

The Callovo-Oxfordian clay formation (COx) is the potential host rock for long term nuclear waste repository in France. The clayey component of COx consists mostly of illite, smectite and interstratified illite/smectite (I/S) clay minerals. We performed a series of molecular dynamics (MD) computer simulations in order to quantify the molecular scale mechanisms responsible for the adsorption and transport of ions at the hydrated surfaces of illite, smectite, and I/S clays. New structural models of illite, smectite, and I/S allowed us to identify several structurally different adsorption sites at the basal surfaces of all three clay substrates. Adsorption free energy profiles above each individual adsorption site on each clay surface for a wide range of metal cations were then calculated and the metal sorption properties for the three clay surfaces are compared in terms of the preferable sorption sites and their surface distributions, most stable adsorption distances, and free energies of adsorption. The resulting equilibrium constants for surface adsorption and ion exchange were calculated and found in general agreement with available literature data. The observed discrepancies between the exchange energies obtained in the current MD simulations and the values obtained through the interpretation of recent X-ray reflectivity measurements can be attributed to the differences in the description of the exchange reaction equilibria between the experimental conditions and the simplified conditions of our simulations.

Adsorption and mobility of radioactive Cs+ isotopes in soil are among the most important factors affecting the long-term environmental footprint of nuclear accidents such as Chernobyl (1986) and Fukushima Daiichi (2011). In particular, Cs+ ions can be retained through their exchange with K+ naturally present in muscovite mica, one of the common soil mineral components. The ClayFF force field allowed us to realistically represent local inhomogeneities of the structure, composition, and charge on the muscovite (001) surface and to identify three structurally different types of adsorption sites. We performed molecular dynamics simulations of Cs+ and K+ adsorption at the hydrated muscovite surface and used quasi-one-dimensional site-specific potential of mean force calculations to quantify the energetics of ion exchange in this system for each individual site and for the entire muscovite surface on average. Irrespective of the type of adsorption site, both K+ and Cs+ cations are preferably adsorbed on the basal (001) muscovite surface at the centers of ditrigonal cavities as inner sphere surface complexes. The free energy difference between the most favorable and the least favorable surface sites for Cs+/K+ ion exchange amounts to 11.7 kJ/mol, with the most favorable sites occupying half of the surface and the least favorable type  - 1/6 of the surface and the rest exhibiting an intermediate adsorption and ion exchange capacity. The simulation results are compared with available thermodynamic estimates based on recent X-ray reflectivity measurements.

Molecular scale understanding of the structure and properties of aqueous interfaces with clays, metal (oxy-) hydroxides, layered double hydroxides, and other inorganic phases is strongly affected by significant degrees of structural and compositional disorder of the interfaces. ClayFF was originally developed as a robust and flexible force field for classical molecular simulations of such systems (Cygan, R. T.; Liang, J.-J.; Kalinichev, A. G. J. Phys. Chem. B 2004, 108, 1255-1266). However, despite its success, multiple limitations have also become evident with its use. One of the most important limitations is the difficulty to accurately model the edges of finite size nanoparticles or pores rather than infinitely layered periodic structures. Here we propose a systematic approach to solve this problem by developing specific metal-O-H (M-O-H) bending terms for ClayFF, Ebend = k (theta - theta0)**2 to better describe the structure and dynamics of singly protonated hydroxyl groups at mineral surfaces, particularly edge surfaces. On the basis of a series of DFT calculations, the optimal values of the Al-O-H and Mg-O-H parameters for Al and Mg in octahedral coordination are determined to be theta0(AlOH) = theta0(MgOH) = 110°, k(AlOH) = 15 kcal mol(-1) rad(-2) and k(MgOH) = 6 kcal mol(-1) rad(-2). Molecular dynamics simulations were performed for fully hydrated models of the basal and edge surfaces of gibbsite, Al(OH)3, and brucite, Mg(OH)2, at the DFT level of theory and at the classical level, using ClayFF with and without the M-O-H term. The addition of the new bending term leads to a much more accurate representation of the orientation of O-H groups at the basal and edge surfaces. The previously observed unrealistic desorption of OH2 groups from the particle edges within the original ClayFF model is also strongly constrained by the new modification.

The epidermal growth factor receptor (EGFR) family is an important class of receptor tyrosine kinases, mediating a variety of cellular responses in normal biological processes and in pathological states of multicellular organisms. Different modes of dimerization of the human EGFR transmembrane domain (TMD) in different membrane mimetics recently prompted us to propose a novel signal transduction mechanism based on protein-lipid interaction. However, the experimental evidence for it was originally obtained with slightly different TMD fragments used in the two different mimetics, compromising the validity of the comparison. To eliminate ambiguity, we determined the nuclear magnetic resonance (NMR) structure of the bicelle-incorporated dimer of the EGFR TMD fragment identical to the one previously used in micelles. The NMR results augmented by molecular dynamics simulations confirm the mutual influence of the TMD and lipid environment, as is required for the proposed lipid-mediated activation mechanism. They also reveal the possible functional relevance of a subtle interplay between the concurrent processes in the lipid and protein during signal transduction. 

Monte Carlo and molecular dynamics computer simulations using the rigid TIP4P and the flexible BJH intermolecular H2O potentials were carried out for 50 states of supercritical water characterizing a very wide range of thermodynamic conditions, 573 ≤ T ≤ 1273 K; 0.02 ≤ rho ≤ 1.67 g/cm3; 10 ≤ P ≤ 10,000 MPa. Good agreement with available experimental data of the simulated thermodynamic and structural properties give confidence to the quantitative statistical analysis of intermolecular hydrogen bonding under the conditions studied. Energetic, geometric, and angular characteristics of supercritical H-bonds and their distributions at a given temperature remain almost invariant over the entire density range studied from dilute gas-like (~ 0.03 g·cm(-3)) to highly compressed liquid-like (~ 1.5 g·cm(-3)) states. The increase of temperature from ambient to supercritical affects the characteristics of H-bonding in water much more dramatically than the changes in density along any supercritical isotherm. Compared to H-bonds in liquid water under ambient conditions, the H-bonds at 773 K are, on average, 10% weaker, 5% longer, and less linear. Both above and below the H-bonding percolation threshold the fractions of H2O molecules involved in a certain number of H-bonds in liquid and supercritical water closely follow the universal binomial distribution as a function of the average number of H-bonds per one water molecule in the system, as predicted by the independent bond theory. This universal distribution remains intact even when dynamic criteria of H-bonding lifetimes are additionally applied.