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Quantum nuclear effects in water using centroid molecular dynamics
Journal of Physics: Conference Series. 2018. Vol. 946. No. 012109. P. 1–7.
The quantum nuclear effects are studied in water using centroid molecular dynamics (CMD) method. The aim is the calibration of CMD implementation in LAMMPS. The calculated intramolecular energy, atoms gyration radii and radial distribution functions are shown in comparison with previous works. The work is assumed to be the step toward to solution of the discrepancy between the simulation results and the experimental data of liquid n-alkane properties in our previous works.
Tararushkin E., Ruban A., Bu H. et al., Journal of Molecular Liquids 2026 Vol. 448 Article 129359
This study investigates the molecular mechanisms governing ammonium interactions with glauconite, a potassium- and iron-rich phyllosilicate, focusing on the structure and dynamics of aqueous NH4NO3 solutions confined at mineral interfaces. Glauconite-ammonium nanocomposites (GANs) were prepared with varying ammonium concentrations and characterized by X-ray diffraction, Fourier transform infrared spectroscopy, transmission electron microscopy, scanning electron microscopy, Brunauer-Emmett-Teller method, ...
Added: February 9, 2026
Болдырев К. А., Glushak A., Pisarev V. et al., Радиоактивные отходы 2024 № 3 С. 83–95
This article overviews global and Russian atomistic modelling experience in exploring the properties of clay and cement-based materials for the long-term safety assessment of high-level waste (HLW) repositories. It explains the general concept of molecular dynamics simulation providing some case studies solved based on it. It discusses the accuracy of the calculated parameters and coefficients, ...
Added: September 30, 2024
Titov I., Стройлов В. С., Русина П. В. et al., Russian Chemical Reviews 2021 Vol. 90 No. 7 P. 831–867
The review aims to present a classification and applicability analysis of methods for preliminary molecular modelling for targeted organic, catalytic and biocatalytic synthesis. The following three main approaches are considered as a primary classification of the methods: modelling of the target – ligand coordination without structural information on both the target and the resulting complex; ...
Added: December 24, 2021
Tabakmakher V., Gigolaev A., Peigneur S. et al., Biophysical Journal 2021 Vol. 120 No. 12 P. 2471–2481
ɑ-Hairpinins are a family of plant defense peptides with a common fold presenting two short ɑ-helices stabilized by two invariant S–S-bridges. We have shown previously that substitution of just two amino acid residues in a wheat ɑ-hairpinin Tk-AMP-X2 leads to Tk-hefu-2 that features specific affinity to voltage-gated potassium channels KV1.3. Here, we utilize a combined ...
Added: May 18, 2021
Priezjev N., Metals 2021 Vol. 11 P. 67
The effect of tensile stress applied during cooling of binary glasses on the potential energy states and mechanical properties is investigated using molecular dynamics simulations. We study the three-dimensional binary mixture that was first annealed near the glass transition temperature and then rapidly cooled under tension into the glass phase. It is found that at ...
Added: December 30, 2020
Kondratyuk N., Pisarev V., Ewen J., Journal of Chemical Physics 2020 Vol. 153 No. 15 P. 154502
Computational predictions of the high-pressure viscosity of hydrocarbon mixtures could help to accelerate the development of fuels and lubricants with improved performance. In this study, we use molecular dynamics simulations to study the viscosity and density of methylcyclohexane, 1-methylnaphthalene, and their binary mixtures at 323 K and pressures of up to 500 MPa. The simulation ...
Added: October 26, 2020
Gurina D., Budkov Y., Kiselev M. G., Journal of Physical Chemistry B 2020 Vol. 124 No. 38 P. 8410–8417
Fully atomistic molecular dynamics simulations are employed to study impregnation of the poly(methyl methacrylate) (PMMA) matrix with carbamazepine (CBZ) in supercritical carbon dioxide. The simulation box consists of 108 macromolecules of the polymer sample with the polymerization degree of 100, 57 molecules of CBZ, and 242,522 CO2 molecules. The simulation is performed at 333 K and ...
Added: September 16, 2020
Priezjev N., Journal of Non-Crystalline Solids 2021 Vol. 556 Article 120562
The influence of static stress and alternating loading direction on
the potential energy and mechanical properties of amorphous alloys
is investigated using molecular dynamics simulations. The model
glass is represented via a binary mixture which is first slowly
annealed well below the glass transition temperature and then
subjected to elastostatic loading either along a single direction or
along two and three ...
Added: August 9, 2020
Priezjev N., Journal of Non-Crystalline Solids 2020 Vol. 548 P. 120324
Added: June 16, 2020
Пахомов А., Фролова А., Табакмахер В. et al., Journal of Photochemistry and Photobiology B: Biology 2020 Vol. 206 P. 111853
The precise positioning of catalytic amino acids against the substrate in an enzyme active site is a crucial factor in biocatalysis. Biosynthesis of the chromophores of fluorescent proteins (FPs) is an autocatalytic process that must conform to these requirements. Here, we show that, in addition to the internal amino acid residues in the proximity of ...
Added: June 10, 2020
Kalikin N., Kurskaya M. V., Ivlev D. V. et al., Journal of Molecular Liquids 2020 Vol. 311 Article 113104
In this paper we present our study of carbamazepine solubility in supercritical carbon dioxide. We have calculated the solubility values along two isochores corresponding to the CO2 densities ρ = 1.1ρcr(CO2) and ρ = 1.3ρcr(CO2), where ρcr(CO2) is the critical density of CO2, in the temperature range from 313 to 383 K, as well as ...
Added: April 9, 2020
Terekhovich V., Вестник Ленинградского государственного университета имени А.С. Пушкина. Серия: Философия 2012 Т. 2 № 3 С. 49–59
Рассмотрена проблема детерминистической и телеологической интерпретации принципа наименьшего действия. Показано, что квантовый метод «интегралов по траекториям» можно использовать как онтологическую гипотезу о природе движения классических объектов. Тогда действующую и целевую причинность в этом принципе можно заменить на причинность вероятностную. ...
Added: March 4, 2020
Loganathan N., Bowers G. M., Ngouana-Wakou B. F. et al., Physical Chemistry Chemical Physics 2019 Vol. 21 P. 6917–6924
The interactions among fluid species such as H2O, CO2, and CH4 confined in nano- and meso-pores in shales and other rocks is of central concern to understanding the chemical behavior and transport properties of these species in the earth’s subsurface and is of special concern to geological C-sequestration and enhanced production of oil and natural ...
Added: November 2, 2019
Gurina D., Budkov Y., Kiselev M. G., Materials 2019 Vol. 12 No. 20 P. 3315
The swelling of a poly (methyl methacrylate) in supercritical carbon dioxide was studied by means of full atomistic classical molecular dynamics simulation. In order to characterize the polymer swelling, we calculated various properties related to the density, structure, and dynamics of polymer chains as a function of the simulation time, temperature, and pressure. In addition, ...
Added: October 11, 2019
Priezjev N., Journal of Non-Crystalline Solids 2019 Vol. 525 P. 119683
The effect of alternating shear orientation during cyclic loading on the relaxation dynamics in disordered solids is examined using molecular dynamics simulations. The model glass was initially prepared by rapid cooling from the liquid state and then subjected to cyclic shear along a single plane or periodically alternated in two or three dimensions. We showed ...
Added: August 19, 2019
Norman G., Pisarev V., Флейта Д. Ю., Письма в Журнал экспериментальной и теоретической физики 2019 Т. 109 № 10 С. 689–693
Исследованы равновесное и метастабильное состояния жидкости в окрестности точки фазового перехода жидкость–кристалл в металлическом расплаве. В качестве инструмента исследования выбрана
зависящая от времени четырехточечная корреляционная функция. Эта функция была предложена ранее
для выявления коллективных движений атомов в равновесной жидкости. Обнаружено характерное изменение поведения жидкости при переходе в метастабильную область. Количественно это проявляется в
особенности модифицированного четырехточечного коррелятора в ...
Added: May 22, 2019
Priezjev N., Journal of Non-Crystalline Solids 2019 Vol. 518 P. 128–133
We investigate the effect of a single heat treatment cycle on the potential energy states and mechanical properties of metallic glasses using molecular dynamics simulations. We consider the three-dimensional binary mixture, which was initially cooled with a computationally slow rate from the liquid state to the solid phase at a temperature well below the glass ...
Added: January 28, 2019
Semyonov V., Timofeev A., IEEE Transactions on Plasma Science 2018 Vol. 46 No. 5 P. 1855–1858
Dust particles under certain conditions can acquire kinetic energy of the order of 10 eV and higher, far above the temperature of gas and temperatures of ions and electrons in the discharge. Furthermore, significant difference of mean horizontal and vertical energy is observed. Such difference can be explained by the energy transfer between degrees of ...
Added: October 30, 2018
Efremov R., Pyrkova D., Krylov N., Biophysical Journal 2018 Vol. 114 No. 3 P. 601А–601А
Structure, dynamics, and functioning of hydrated lipid bilayers - model cell
membranes - are governed by a thin balance of intermolecular interactions between
constituents of these systems. Besides the hydrophobic effect, which determines
the overall bilayer skeleton, important contribution is made by Hbonds
between lipids, water, and ions. This determines crucial phenomena in
cell membranes: dynamic clustering, hydration, fine tuning ...
Added: October 26, 2018
Priezjev N., Journal of Materials Research 2019 Vol. 34 No. 15 P. 2664–2671
The influence of repeated thermal cycling on mechanical properties, structural relaxation, and evolution of the potential energy in binary glasses is investigated using molecular dynamics simulations. We consider a binary mixture with strongly non-additive cross interactions, which is annealed across the glass transition with different cooling rates and then exposed to one thousand thermal cycles ...
Added: October 25, 2018
Kirova E. M., Norman G., Pisarev V., Журнал физической химии 2018 Т. 92 № 10 С. 1525–1530
The behavior of the autocorrelation functions of shearing stress and the kinematic viscosity coefficient during glass transition processes is studied by means of molecular dynamics using the example of liquid aluminum. A film of liquid metal cooled at a rate of 2·1012 K/s is simulated. The dependence of the kinematic viscosity coefficient on temperature is ...
Added: October 22, 2018