МОДЕЛИРОВАНИЕ ТРАНСПОРТНЫХ СВОЙСТВ ВОДНЫХ РАСТВОРОВ САХАРОЗЫ МЕТОДОМ МОЛЕКУЛЯРНОЙ ДИНАМИКИ
Russian Journal of Physical Chemistry A. 2022. Т. 96. № 3. С. 373-380.
Дещеня В. И., Kondratyuk N., Ланкин А. В., Norman G.
The temperature dependence of density is calculated for an aqueous solution of sucrose by the molecular dynamics method. The coefficients of viscosity and diffusion are also obtained in the 273–343 K range of temperatures. The hydrodynamic radius of a sucrose molecule in an aqueous solution is calculated. The obtained data are compared with the experimental results.
, , 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
Molecular dynamics study of sucrose aqueous solutions: From solution structure to transport coefficients
, , et al., Journal of Molecular Liquids 2022 Vol. 367 Article 120456
In this work, we study the applicability of the equilibrium molecular dynamics methods for the prediction of both static and dynamic properties of sucrose aqueous solution for various concentrations and temperatures. The OPLS-AA force field with 1.14*CM1A charge corrections is used to describe the interactions in the model. We analyze the prediction power of the model against ...
Added: August 9, 2022
Dynamic clustering of lipids in hydrated two-component membranes: results of computer modeling and putative biological impact.
, , et al., Journal of Biomolecular Structure and Dynamics 2013 Vol. 31 No. 1 P. 87-95
Delineation and analysis of lateral clustering of lipids in model bilayers is an important step toward understanding of the physical processes underlying formation of lipid domains and rafts in cell membranes. Computer modeling methods represent a powerful tool to address the problem since they can detect clusters of only few lipid molecules – this issue ...
Added: November 14, 2013
, , , Acta Naturae 2015 Т. 7 № 4 С. 135-140
An efficient computational approach is developed to quantify the free energy of a spontaneous association of the α-helices of proteins in the membrane environment. The approach is based on the numerical decomposition of the free energy profiles of the transmembrane (TM) helices into components corresponding to protein-protein, protein-lipid, and protein-water interactions. The method was tested ...
Added: February 20, 2016
, , et al., AIP Conference Proceedings 2020 Vol. 2272 No. 1 P. 070055-1-070055-5
We present a new quantum accurate Spectral Neighbor Analysis Potential (SNAP) machine-learning potential for simulating carbon under extreme conditions of dynamic compression (pressures up to 1 TPa and temperatures up to 10,000 K). The development of SNAP potential involves (1) the generation of the training database comprised of the consistent and meaningful set of first-principles ...
Added: January 21, 2021
, Physical Review B: Condensed Matter and Materials Physics 2019 Vol. 100 P. 034703-1-034703-13
We study theoretically the nonequilibrium exciton transport in monolayer transition metal dichalcogenides. We consider the situation where excitons interact with nonequilibrium phonons, e.g., under the conditions of localized excitation where a “hot spot” is formed. We develop the theory of the exciton drag by the phonons and analyze in detail the regimes of diffusive propagation ...
Added: January 13, 2021
Specific refolding pathway of viscumin A chain in membrane-like medium reveals a possible mechanism of toxin entry into cell.
, , et al., Scientific Reports 2019 Vol. 9 No. 413 P. 1-12
How is a water-soluble globular protein able to spontaneously cross a cellular membrane? It is commonly accepted that it undergoes significant structural rearrangements on the lipid-water interface, thus acquiring membrane binding and penetration ability. In this study molecular dynamics (MD) simulations have been used to explore large-scale conformational changes of the globular viscumin A chain ...
Added: February 6, 2019
, , Journal of Nuclear Materials 2023 Vol. 573 Article 154123
The influence of helium pressure on the mechanisms of diffusion of the He-filled nanobubbles in fcc Al is investigated by the classical molecular dynamics. It is shown that at pressures <20 kbar gas suppresses self-diffusion, while the concentration of adatoms, rather than their mobility, plays a key role. However, as the pressure increases to values at which ...
Added: February 1, 2023
, , Carbon (the Netherlands) 2015 Vol. 87 P. 358-364
The graphite melting temperature remains poorly determined despite the considerable effort accomplished since the work of Bundy (1963). The absence of a consensus on its melting temperature at normal conditions has been considered as a technical problem that motivated more and more sophisticated experiments. The experimental evidences of the maximum on the graphite melting curve ...
Added: March 15, 2017
, , , Diamond and Related Materials 2019 Vol. 94 P. 14-20
Formation of carbon nanoparticles is an important type of complex non-equilibrium processes that require precise atomistic theoretical understanding. In this work, we consider the process of ultrafast cooling of pure carbon gas that results in nucleation of an onion-like fullerene. The model is based on molecular dynamics simulation with the interaction between carbon atoms described ...
Added: February 22, 2019
Reflecting Boundary Conditions for Classical and Quantum Molecular Dynamics Simulations of Nonideal Plasmas
, , , Contributions to Plasma Physics 2016 Vol. 56 P. 448-458
The influence of boundary conditions for the classical and wave packet molecular dynamics (MD) simulations of nonideal electron-ion plasma is studied. We start with the classical MD and perform a comprehensive study of convergence of the per-particle potential energy and pressure with the number of particles using both the nearest image method (periodic boundaries) and ...
Added: June 28, 2016
, Physical Review Letters 2020 Vol. 124 P. 166802
We study theoretically weak localization of excitons in atomically thin transition metal dichalcogenides. The constructive interference of excitonic de Broglie waves on the trajectories forming closed loops results in a decrease of the exciton diffusion coefficient. We calculate the interference contribution to the diffusion coefficient for the experimentally relevant situation of exciton scattering by acoustic ...
Added: January 13, 2021
, , et al., American Mineralogist 2020 Vol. 105 No. 9 P. 1349-1354
Pressure-temperature-volume (P-T-V) data on liquid iron-sulfur (Fe-S) alloys at the Earth’s outer core conditions (~136 to 330 GPa, ~4000 to 7000 K) have been obtained by first-principles molecular dynamics simulations. We developed a thermal equation of state (EoS) composed of Murnaghan and Mie-Grüneisen-Debye expressions for liquid Fe-S alloys. The density and sound velocity are calculated ...
Added: January 21, 2021
, , et al., Journal of Membrane Science 2020 Vol. 596 Article 117691
It is established that the values of the coefficients of self-diffusion of water in proton-exchange membranes at a fixed temperature and the amount of moisture content depend on the method of membrane manufacture, the length of the side chain (diameter of channels), but within the experimental error do not depend on the thickness of the ...
Added: October 12, 2022
, , et al., Journal of Physics B: Atomic, Molecular and Optical Physics 2018 Vol. 51 No. 01-4001 P. 1-9
Nano-plasmas produced, for example, in clusters after short-pulse laser irradiation, can show collective excitations, as derived from the time evolution of fluctuations in thermodynamic equilibrium. Molecular dynamical simulations are performed for various cluster sizes. New data are obtained for the minimum value of the stationary cluster charge. The bi-local autocorrelation function gives the spatial structure ...
Added: December 4, 2017
, , Journal of Physics B: Atomic, Molecular and Optical Physics 2015 Vol. 48 No. 01-5401 P. 1-7
Irradiation of nanosized metallic clusters by femtosecond laser pulses of moderate intensities (10^12 – 10^14 W/cm^2) leads to creation of the so-called electron–ion nanoplasma with size-dependent properties. Electron oscillations in such plasma are of interest in view of resonance absorption or probing of cluster dynamics in experiments. We study the electronic oscillations via molecular dynamics ...
Added: December 25, 2014
, , et al., Теплофизика высоких температур 2014 Т. 52 № 4 С. 494-503
Pressure fluctuations in equilibrium nonideal plasma are investigated by the method of classical molecular dynamics. Examples of plasma parameters at which the pressure fluctuation distribution function is not normal but can be approximated by the sum of two normal distributions were found. The electron-ion interaction is described by the Coulomb potential cutoff at the depth ...
Added: December 25, 2014
АТОМИСТИЧЕСКОЕ КОМПЬЮТЕРНОЕ МОДЕЛИРОВАНИЕ ГИДРОКАЛЮМИТА КАК АДСОРБЕНТА РАДИОАКТИВНЫХ АНИОНОВ ИЗ ВОДНЫХ РАСТВОРОВ
, , , Russian Journal of Physical Chemistry A 2022 Т. 96 № 4 С. 535-537
Results are presented from atomistic computer modeling of hydrocalumite (cement AFm-phase) with Cl− and I− anions in the interlayer space as a potential adsorbent of radionuclides 36Cl, 129I, 137Cs. Properties of the crystals themselves and the interaction between aqueous solutions of CsCl and CsI and surfaces of crystalline phases are studied. It is shown the ...
Added: May 16, 2022
Diffusion of a particle in the Gaussian random-energy landscape: Einstein relation and analytical properties of average velocity and diffusivity as functions of driving force
, Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 2018 Vol. 98 No. 1 P. 012128-1- 012128-8
We demonstrate that the Einstein relation for the diffusion of a particle in the random-energy landscape with the Gaussian density of states is an exclusive one-dimensional property and does not hold in higher dimensions. We also consider the analytical properties of the particle velocity and diffusivity for the limit of weak driving force and establish a connection between ...
Added: July 23, 2018
, , et al., Computer Physics Communications 2011 Vol. 182 P. 1974-1978
We report on simulation technique and benchmarks for molecular dynamics simulations of the relaxation processes in solids and liquids using the graphics processing units (GPUs). The implementation of a manybody potential such as the embedded atom method (EAM) on GPU is discussed. The benchmarks obtained by LAMMPS and HOOMD packages for simple Lennard-Jones liquids and ...
Added: October 28, 2013
Diffusion-Thermal Phase Transformations in Titanium Hydride Containing a Multi-Barrier System of Hydrogen Traps
, , et al., Inorganic Materials: Applied Research 2021 Vol. 12 No. 5 P. 1206-1213
Diffusion-thermal phase transformations in modified titanium hydride containing a multi-barrier system of hydrogen traps are considered. Modification of titanium hydride was carried out by the method of layer-by-layer electrochemical precipitation of metallic titanium and copper from organic and inorganic solutions of their salts. The creation of a multilayer coating (Ti–Cu) on the surface of the titanium hydride by the ...
Added: October 6, 2021
, , 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
Specific binding of the α-component of the lantibiotic lichenicidin to the peptidoglycan precursor lipid II predetermines its antimicrobial activity
, , 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
, , , Журнал физической химии 2015 Т. 89 № 5 С. 796-800
С помощью метода молекулярной динамики исследовано стеклование переохлажденного расплава алюминия при изобарном и изохорном охлаждении. Для моделирования алюминия используется потенциал погруженного атома. Рассмотрены три критерия стеклования – расщепление второго пика парной корреляционной функции, увеличение числа искосаэдрических кластеров и измене ние энергии активации самодиффузии. Показано, что температуры стеклования, определенные по этим трем критериям, совпадают в пределах погрешностей. По результатам моделирования опреде лена ...
Added: January 28, 2022