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Non-Arrhenius diffusion in bcc titanium: vacancy-interstitialcy model
Physical Review B: Condensed Matter and Materials Physics. 2020. Vol. 102. P. 184110-1-184110-8.
Anomalous diffusion in some bcc metals is the long-standing topic in material science. In this work, I obtain the temperature dependence of the self-diffusion coefficient in bcc titanium directly from molecular dynamics (MD) calculation. MD simulations indicate that both vacancies and self-interstitials contribute to diffusivity in bcc Ti. The resultant self-diffusion coefficient is non-Arrhenius, but shows less curvature than observed in most experiments.
Belonoshko Anatoly B., Fu J., Bryk T. et al., Nature Communications 2019 Vol. 10 No. 1 P. 1-7
The Earth’s solid inner core is a highly attenuating medium. It consists mainly of iron. The high attenuation of sound wave propagation in the inner core is at odds with the widely accepted paradigm of hexagonal close-packed phase stability under inner core conditions, because sound waves propagate through the hexagonal iron without energy dissipation. Here ...
Added: January 20, 2021
Tamm M., Nazarov L. I., Gavrilov A. A. et al., Physical Review Letters 2015 Vol. 114 No. 17
The fractal globule state is a popular model for describing chromatin packing in eukaryotic nuclei. Here we provide a scaling theory and dissipative particle dynamics computer simulation for the thermal motion of monomers in the fractal globule state. Simulations starting from different entanglement-free initial states show good convergence which provides evidence supporting the existence of ...
Added: September 3, 2015
Kondratyuk N., Norman G., Stegailov V., Journal of Physics: Conference Series 2016 Vol. 774 No. 012039 P. 1-9
Molecular dynamics is applied to calculate diffusion coefficients of n-triacontane C30H62 using Einstein-Smoluchowski and Green-Kubo relations. The displacement 〈Δr2〉(t) has a subdiffusive part 〈Δr2〉 ~ t α, caused by molecular crowding at low temperatures. Longtime asymptotes of 〈v(0)v(t)〉 are collated with the hydrodynamic tail t-3/2 demonstrated for atomic liquids. The influence of these asymptotes on the compliance of Einstein-Smoluchowski ...
Added: April 7, 2017
Kondratyuk N., Pisarev V., Fluid Phase Equilibria 2019 Vol. 498 P. 151-159
Shear viscosity is one of the key subjects of molecular modeling studies since this quality is used in the development of lubricants. In this paper, we use molecular dynamics methods to predict viscosity dependence on pressure up to 1000 MPa for 2,2,4-trimethylhexane. The COMPASS class II force field is used to determine atomic interactions in ...
Added: October 21, 2019
Goryacheva E., Efremov R., Krylov N. et al., International Journal of Molecular Sciences 2023 Vol. 24 No. 7 Article 6403
The rapid development of new microscopy techniques for cell biology has exposed the
need for genetically encoded fluorescent tags with special properties. Fluorescent biomarkers of the
same color and spectral range and different fluorescent lifetimes (FLs) became useful for fluorescent
lifetime image microscopy (FLIM). One such tag, the green fluorescent protein BrUSLEE (Bright
Ultimately Short Lifetime Enhanced Emitter), having ...
Added: May 19, 2023
Bakulin I., Kondratyuk N., Lankin A. et al., Journal of Chemical Physics 2021 No. 155 Article 154501
Polyethers are promising compounds for creation of electrochemical energy storage systems. Molecular dynamics method can facilitate the search of such compounds which have the most potential. However, application of this method requires verification of the force fields. We perform molecular dynamics calculations of the physical properties of the aqueous 1,4-dioxane solution (density, enthalpy of mixing, ...
Added: October 15, 2021
Gavryushkin P., Belonoshko Anatoly B., Sagatov N. et al., Crystal Growth & Design 2021 Vol. 21 No. 1 P. 65-74
Using molecular dynamics simulation and evolutionary metadynamic calculations, a series of structures were revealed that possessed enthalpies and Gibbs energies lower than those of aragonite but higher than those of calcite. The structures are polytypes of calcite, differing in the stacking sequence of close-packed (cp) Ca layers. The two- and six-layered polytypes have hexagonal symmetry P6322 ...
Added: January 21, 2021
Kondratyuk N., Pisarev V., Fluid Phase Equilibria 2021 Vol. 544-545 Article 113100
In this paper, we use the molecular dynamics methods to predict the pressure-viscosity dependencies of model lubricant 1,1-diphenylethane up to 800 MPa along three isotherms: 37.8 °C, 60 °C and 98.9 °C. The precise COMPASS class II force field is used to determine atomic interactions in the model. The Green-Kubo method is used to calculate the shear viscosities. The time ...
Added: September 5, 2021
Lohan S., Konshina A. G., Efremov R. et al., Journal of Medicinal Chemistry 2023 Vol. 66 No. 1 P. 855-874
A series of small (7- to 12-mer) amphipathic cationic peptides were designed and synthesized with the ultimate goal of creating a set of short helical peptides with broad-range bactericidal activity and good selectivity toward the bacterial cells. Activity analysis identified a lead 12-mer peptide 8b with broad spectrum activity against Gram-positive (MIC=3.1-6.2 µg/mL) and Gram-negative ...
Added: February 21, 2023
Krot A. D., Vlasova I. E., Tararushkin E. et al., Minerals 2024 Vol. 14 No. 1 Article 109
A quantitative understanding of the molecular-scale mechanisms of radionuclide sorption on different clay minerals is crucial for the development and safe implementation of geological nuclear waste disposal technologies. We apply classical molecular dynamics (MD) computer simulations to study the adsorption of uranyl on the external basal surfaces of two typical clay models. In the illite ...
Added: January 25, 2024
Vasily V. Pisarev, Kalinichev A. G., Journal of Molecular Liquids 2022 Vol. 366 Article 120290
Shear flow of n-pentane in slit nanopores between clay surfaces is investigated by molecular dynamics simulations. Pyrophyllite and hydrated Na-montmorillonite are considered as representative examples of hydrophobic and hydrophilic clay surfaces, respectively. The viscosity-density relations and slip lengths are calculated for both pentane-clay interfaces for different pore widths. The results show that the viscosity-density dependencies ...
Added: September 21, 2022
Kondratyuk N., Norman G., Stegailov V., Journal of Chemical Physics 2016 Vol. 145 No. 204504 P. 204504-1-204504-9
iffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function ...
Added: April 7, 2017
Kliavinek S. S., Kolotova L., Journal of Non-Crystalline Solids 2021 Vol. 571 P. 121052
The glass transition of supercooled Zr Nb melt was studied by molecular dynamics modeling. Glass transition temperature was determined using by different criteria such as change of the heat capacity, diffusion coefficient and viscosity, the obtained data are in good agreement with each other. It is shown, that elastic modulus rise with the decrease ...
Added: January 28, 2022
Norman G., Pisarev V., Fleita D., Письма в Журнал экспериментальной и теоретической физики 2019 Т. 109 № 10 С. 689-693
Equilibrium and metastable states of a liquid are studied near the liquid-crystal phase transition point in a metallic melt using a time-dependent four-point correlation function. This function was proposed earlier for revealing the collective atomic motion in equilibrium liquids. The characteristic changes in the behavior of liquid when it passes to the region of metastability ...
Added: February 13, 2020
Kalikin N., Budkov Y., Kolesnikov A. L. et al., Fluid Phase Equilibria 2021 Vol. 544-545 Article 113096
Despite the modern level of development of computational chemistry methods and technological progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two computational schemes that can potentially solve this problem. We consider systems of poorly soluble drug compounds in supercritical carbon dioxide. Considering that the biggest contribution ...
Added: June 1, 2021
Gurina D., Budkov Y., Kiselev M. G., Journal of Molecular Liquids 2022 Vol. 352 Article 118758
A full-atomic classical molecular dynamics simulation of polylactide nanoparticle impregnation with carbamazepine in supercritical carbon dioxide was performed. The effect of temperature (333 K, 373 K), pressure (20 MPa, 40 MPa) and ethanol addition (1.7 mol.%) on the impregnation process was studied. Based on the solvent accessible surface area values it was concluded that a pressure increase and cosolvent addition ...
Added: February 19, 2022
Garkul A., Stegailov V., Scientific Reports 2022 Vol. 12 No. 1 Article 13325
Unlike conventional first-order phase transitions, the kinetics of amorphous-amorphous transitions has been much less studied. The ultrasonic experiments on the transformations between low-density and high-density amorphous ice induced by pressure or heating provided the pressure and temperature dependencies of elastic moduli. In this article, we make an attempt to build a microscopic picture of these ...
Added: August 8, 2022
Anna S. Bodrova, Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 2024 Vol. 109 No. 2 Article 024903
We investigate diffusion in polydisperse granular media. We derive the mean-squared displacement of granular particles in a polydisperse granular gas in a homogeneous cooling state, containing an arbitrary amount of species of different sizes and masses. We investigate both models of constant and time-dependent restitution coefficients and obtain a universal law for the size dependence ...
Added: February 15, 2024
Efremov R., International Journal of Molecular Sciences 2021 Vol. 22 No. 12 P. 1-20
To date, it has been reliably shown that the lipid bilayer/water interface can be thoroughly characterized by a sophisticated so-called “dynamic molecular portrait”. The latter reflects a combination of time-dependent surface distributions of various physicochemical properties, inherent in both model lipid bilayers and natural multi-component cell membranes. One of the most important features of biomembranes ...
Added: August 24, 2021
Bodrova A., Sokolov I. M., Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 2020 Vol. 101 No. 5 P. 052130
We consider a random two-phase process which we call a reset-return one. The particle starts
its motion at the origin. The rst, displacement, phase corresponds to a stochastic motion of a
particle and is nished at a resetting event. The second, return, phase corresponds to the particle's
motion towards the origin from the position it attained at the ...
Added: September 10, 2020
Orekhov M., Russian Journal of Physical Chemistry A 2021 Vol. 95 P. 2059-2064
Molecular dynamic models are created for properties of bivalent ions in organic solvents. It is shown that molecules of the considered solvents bound to ions via oxygen atoms. A theoretical model is developed that describes the ion coordination number. The coordination number in this model is determined by the ratio between the sizes of the ...
Added: October 14, 2021
Kirova E. M., Norman G., Pisarev V., Computational Materials Science 2020 Vol. 172 Article 109367
We present the results of the study of changes in liquid properties during ultrafast cooling. The molecular dynamics (MD) method is used, with aluminum melt as an example. Based on the changes in shear stress autocorrelation functions (SACF) with temperature in an ensemble of MD trajectories, we develop three approaches to the study of melt ...
Added: June 29, 2020
Panina I., Balandin S., Tsarev A. et al., International Journal of Molecular Sciences 2023 Vol. 24 No. 2 P. 1
To date, a number of lantibiotics have been shown to use lipid II — a highly conserved peptidoglycan precursor in the cytoplasmic membrane of bacteria — as their molecular target. The α-component (Lchα) of the two-component lantibiotic lichenicidin (Lchα), previously isolated from the Bacillus licheniformis VK21 strain, seems to contain two putative lipid II binding ...
Added: February 21, 2023
Kalikin N., Budkov Y., Kolesnikov A. L. et al., Russian Journal of Physical Chemistry B 2021 Vol. 15 No. 7 P. 1166-1170
We present the results of calculation of the solvation free energy, based on the classical density functional theory, for a series of 1,2,4-thiadiazole derivatives in supercritical carbon dioxide at three temperatures (308.15, 318.15 and 128.15). Using the obtained data, the solubility values of the chosen compounds are determined. The correlation between the value of the ...
Added: January 28, 2022