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Relaxation and collective excitations of cluster nano-plasmas
Journal of Physics B: Atomic, Molecular and Optical Physics. 2018. Vol. 51. No. 01-4001. P. 1-9.
Reinholz H., Röpke G., Broda I., Morozov I., Bystryi R., Lavrinenko Y.
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 of the eigenmodes, for which energy eigenvalues are obtained. By varying the cluster size, starting from a few-particle cluster, the emergence of macroscopic properties such as collective excitations is shown.
Bystryi R.G., Morozov I.V., 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
Orekhov N. D., Stegailov V., 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
Pyrkova D. V., Tarasova N. K., Krylov N. 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
Быстрый Р.Г., Лавриненко Я. С., Ланкин А. В. 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
Остроумова Г. М., Орехов Н. Д., Stegailov V., 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
Lavrinenko Y. S., Morozov I.V., Valuev I. A., 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
Fleita D., Norman G., Pisarev V., Journal of Physics: Condensed Matter 2020 Vol. 32 No. 21 P. 214009
The previously discovered features of the temperature behaviour of four-point spatial correlators allow us to study transitions to metastable states. Similar integral characteristics simultaneously study microscopic effects (vortex formation and clustering) and the effect of these phenomena on the thermodynamics of the whole system. It is shown that spatial and temporal behaviour of correlators in ...
Added: February 18, 2020
Fleita D., Norman Genri E., Pisarev Vasily V., Journal of Physics: Conference Series 2018 Vol. 946 No. 1 P. 012102-1-012102-7
This paper discusses the results of the application method of spatial correlation functions on a glass-forming liquid of a pure metal melt by performing molecular dynamics simulations. We define a high-order correlation function that quantifies a spatial correlation of single-particle displacements in liquids and amorphous systems. Time dependencies of the different 4-point spatial functions for ...
Added: October 31, 2018
Kondratyuk N., Lankin A., Norman G. et al., Journal of Physics: Conference Series 2015 Vol. 653 No. 012107 P. 1-9
Molecular modelling is used to calculate transport properties and to study relaxation of liquid n-triacontane (C30H62). The problem is important in connection with the behavior of liquid isolators in a pre-breakdown state. Two all-atom models and a united-atom model are used. Shear viscosity is calculated using the Green–Kubo formula. The force fields are compared with each other using the ...
Added: April 7, 2017
Aseev L. V., Chugunov A. O., Efremov R. et al., Journal of Bacteriology 2013 Vol. 195 No. 1 P. 95-104
Ribosomal protein S2 is an essential component of translation machinery, and its viable mutated variants conferring distinct
phenotypes serve as a valuable tool in studying the role of S2 in translation regulation. One of a few available rpsB mutants,
rpsB1, shows thermosensitivity and ensures enhanced expression of leaderless mRNAs. In this study, we identified the nature of ...
Added: November 14, 2013
Bragin P. E., Kuznetsov A.S., Bocharova O. V. et al., Biochimica et Biophysica Acta - Biomembranes 2018 Vol. 1860 No. 12 P. 2486-2498
The interaction between the elements of the secondary structure is the key process, determining the spatial structure and activity of a membrane protein. The transmembrane (TM) helix-helix interaction is known to be especially important for the function of so-called type I or bitopic membrane proteins, which have small TM domains, consisting of a single ⍺-helix. ...
Added: September 25, 2018
Morozov I., Норман Г. Э., Журнал экспериментальной и теоретической физики 2005 Т. 127 № 2 С. 412-430
Плазменные волны и характер столкновений частиц в равновесной двухкомпонентной неидеальной плазме, состоящей из невырожденных электронов и однократно заряженных ионов, рассмотрены на основе моделирования методом молекулярной динамики (МД). Определены дисперсия частоты и декремента затухания ленгмюровских волн. Указан метод обобщения теории плазменных волн в идеальной плазме для расширения области применимости теории в сторону неидеальной плазмы. Определены проводимость ...
Added: March 14, 2014
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
Efremov R., Нольде Д. Е., Волынский П. Е. 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
Pisarev V., Starikov S., Journal of Physics: Condensed Matter 2014 Vol. 26 P. 475401
Added: April 5, 2017
Lankin A. V., Norman G., Orekhov M., Russian Journal of Physical Chemistry A 2016 Vol. 90 No. 5 P. 962-968
The solvated shells of an ion, its velocity autocorrelation functions, and diffusion coefficient D are found, and the interrelations between them are analyzed. ...
Added: April 5, 2017
Morozov I., Norman G. E., Insepov Z. et al., Physical Review Special Topics - Accelerators and Beams 2012 Vol. 15 P. 053501
This paper describes the surface environment of the dense plasma arcs that damage rf accelerators, tokamaks, and other high gradient structures. We simulate the dense, nonideal plasma sheath near a metallic surface using molecular dynamics (MD) to evaluate sheaths in the non-Debye region for high density, low temperature plasmas. We use direct two-component MD simulations ...
Added: October 28, 2013
Belonoshko Anatoly B., Willman J., Williams A. 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
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
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
Timofeev A., Morozov I., Stegailov V. et al., Программные системы: теория и приложения 2014 Т. 5 № 1 С. 191-244
Рассматривается подход, позволяющий выявить, для каких задач нужны суперкомпьютеры эксафлопсного класса. Возможности подхода рассмотрены на примерах актуальных задач материаловедения, физики конденсированного вещества и плотной плазмы, для решения которых необходимо атомистическое моделирование на современных и создаваемых в настоящее время суперкомпьютерах. Для каждой задачи проведено соответствие между набором изучаемых явлений и требуемым уровнем быстродействия (числа ядер) вычислительной ...
Added: August 11, 2014
Fleita D., Norman G., Pisarev V., Journal of Physics: Conference Series 2018 Vol. 946 P. 012102
This paper discusses the results of the application method of spatial correlation functions on a glass-forming liquid of a pure metal melt by performing molecular dynamics simulations. We define a high-order correlation function that quantifies a spatial correlation of single-particle displacements in liquids and amorphous systems. Time dependencies of the different 4-point spatial functions for ...
Added: February 18, 2020
Дещеня В. И., Kondratyuk N., Ланкин А. В. et al., Журнал физической химии 2022 Т. 96 № 3 С. 373-380
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 ...
Added: October 24, 2022
Morozov I.V., Kazennov A. M., Bystryi R.G. 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