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1

Adsorption behavior of poly(ethylene oxide) on kaolinite: Experimental and molecular simulation study

Wang Tingting, Wang Jing, Zhang Mingqing, Liu Bingfeng, Zhang Haijun, Li Jihui

Physicochemical Problems of Mineral Processing

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2024

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Vol. 60, iss. 2

art. no. 185900

EN

Poly(ethylene oxide) (PEO) adsorption behavior on kaolinite surfaces in an aqueous solution was investigated through experiments, the density functional theory (DFT), and molecular dynamics (MD) simulations. The experimental results showed that as the PEO concentration increased, the adsorption capacity first increased then slightly decreased and the turbidity change was opposite. The adsorption isotherm on the kaolinite surface was more suitable for the Langmuir model and valid for single-layer adsorption. The results of simulations showed that the PEO chains extended along the two basal surfaces of kaolinite or were partly adsorbed, forming loops and tails that caused most of the particles to flocculate, contributing to the turbidity lowering. When the number of PEO chains was excessive, their self- and inter-aggregation occurred with some PEO far from the surface, and the turbidity increased. On the kaolinite (001) surface, the hydrogen bonds between the PEO ether O and the hydroxyl groups constituted the main interaction mechanism. However, the hydrophobic force of the (CH2–CH2)–moiety of PEO might have dominated its adsorption on the (001̅) surface. The hydrogen bonds were stronger than the hydrophobic interactions.

2

Nitrosubstituted analogs of isoxazolines and isoxazolidines: a surprising estimation of their biological activity via molecular docking

Zawadzińska Karolina, Gostyński Bartłomiej

Scientiae Radices

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2023

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Vol. 2, Iss. 1

25--46

EN

The biological activities in the field of antimicrobial application of trihalomethylated isoxazolines and isoxazolidines were investigated by means of molecular docking. In our work, we compared these two groups of heterocyclic compounds due to their strength of non-covalent binding affinity with several exemplary proteins that are known to partake in various biological processes. The obtained results show that the investigated compounds possess higher binding affinities to selected proteins than many hitherto known and applied compounds.

3

Role of crystallographic orientation in material behaviour under nanoindentation: Molecular Dynamics study

Kurgan Aneta, Madej Lukasz

Materials Science Poland

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2023

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Vol. 41, No. 3

18--26

EN

The mechanical properties of materials can be analysed under deformation conditions by various laboratory tests. However, such experimental investigations become extremely complicated and often even impossible at the lower length scales where the arrangement of the atomic planes is considered. In this case, computational materials science is a robust alternative to extend the capabilities of laboratory tests. Therefore, the molecular dynamics technique was selected in the current work to evaluate the role of the local grain crystallographic orientation during nanoindentation testing. A pure aluminium sample was selected as a case study. For the sake of clarity, two distinctively different crystallographic orientations cube {100}<001> and hard {110}<011> were investigated in a set of arrangements: monocrystalline, bicrystalline, and polycrystalline. The influence of the substrate and the neighbouring grains on the material response to local deformation was evaluated. The research used two types of indenters: spherical and sharp-tipped. Results obtained were analysed with respect to the arrangement of atoms and load-displacement curves. This research proved that the role of crystallographic orientation in material behaviour under nanoindentation should not be neglected during the interpretation of data from this test.

4

Comparison of Wear Resistance in Polycrystalline and Monocrystalline Iron

Liu Zhiming, Zhang Qiang, Liu Fangying, Zhang Hezhe

Archives of Metallurgy and Materials

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2023

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Vol. 68, iss. 1

15--20

EN

In the present research, we used molecular dynamics simulation to determine the effect of cutting parameters on micro-grain boundary structures and Burgers vector distribution in single crystal iron and polycrystalline iron materials. The result showed that the destruction of the lattice in polycrystalline iron caused by the cutting tool was restricted to the contact surface area. In addition, in the precision machining process, a higher refining grain was observed on the iron surface. During the cutting process of single crystal iron, large-scale slip occurred along the <111> crystal direction on the {110} crystal plane. And the slip presented an annular shape.

5

Effect of Na+, Ca2+ on the hydration properties of quartz surface: a molecular dynamics simulation study

Liu Chunfu, Min Fan-fei, Chen Jun, Liu Ling-yun, Ren Bao, Lv Kai

Physicochemical Problems of Mineral Processing

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2022

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Vol. 58, iss. 3

art. no. 147452

EN

Effects of metal ions on the surface hydration of fine quartz are investigated by the theoretical methodologies. The hydration layer on the quartz surface is made up of three layers of water molecules, about 8-10 Å. The interaction energy of ions changes from -1.071 eV in water to -1.821 eV (Na+) and -1.896 eV (Ca2+) when ions are present. Metal ions improve the interaction of water molecules with the quartz surface, allowing more water molecules to enter the second and third hydration layers. In the presence of Na+, the diffusivity of water molecules is greater than in Ca2+ solutions. Increased interaction between water molecules and surfaces in the order Ca2+ > Na+ is consistent with metal ions’ propensity to hydrate.

6

Quantum-inspired evolutionary optimization of SLMoS2 two-phase structures

Kuś Wacław, Mrozek Adam

Computer Methods in Materials Science

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2022

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Vol. 22, No. 2

67--78

EN

The paper focuses on applying a Quantum Inspired Evolutionary Algorithm to achieve the optimization of 2D material containing two phases, 2H and 1T, of Molybdenum Disulphide (MoS2 ). The goal of the optimization is to obtain a nanostructure with tailored mechanical properties. The design variables describe the shape of inclusion made from phase 1T in the 2H unit cell. The modification of the size of the inclusions leads to changes in the mechanical properties. The problem is solved with the use of computed mechanical properties on the basis of the Molecular Statics approach with ReaxFF potentials.

7

What is Liquid? [in two dimensions]

Travis K. P., Hoover Wm. G., Hoover C. G., Hass A. B.

Computational Methods in Science and Technology

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2021

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Vol. 27, No. 1

5--23

EN

We consider the practicalities of defining, simulating, and characterizing “Liquids” from a pedagogical standpoint based on atomistic computer simulations. For simplicity and clarity we study two-dimensional systems throughout. In addition to the infinite-ranged Lennard-Jones 12/6 potential we consider two shorter-ranged families of pair potentials. At zero pressure one of them includes just nearest neighbors. The other longer-ranged family includes twelve additional neighbors. We find that these further neighbors can help stabilize the liquid phase. What about liquids? To implement Wikipedia’s definition of liquids as conforming to their container we begin by formulating and imposing smooth-container boundary conditions. To encourage conformation further we add a vertical gravitational field. Gravity helps stabilize the relatively vague liquid-gas interface. Gravity reduces the messiness associated with the curiously-named “spinodal” (tensile) portion of the phase diagram. Our simulations are mainly isothermal. We control the kinetic temperature with Nosé-Hoover thermostating, extracting or injecting heat so as to impose a mean kinetic temperature over time. Our simulations stabilizing density gradients and the temperature provide critical-point estimates fully consistent with previous efforts from free energy and Gibbs ensemble simulations. This agreement validates our approach.

8

Ion Distributions in Water/Graphene Interface: A Molecular Dynamics Study

Dweik J., Koabaz M., Younis J., Ghaddar A.

Computational Methods in Science and Technology

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2021

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Vol. 27, No. 1

29--35

EN

Classical Molecular Dynamics (MD) with a non-polarizable force field is used to quantify the ion size effect on structure and dynamics of the confined electrolyte solution by considering the series of sodium halides (NaX with X = = F, Cl, Br, and I). Ions and water transport were simulated through a rigid and neutral atomistic carbon wall (graphene). The results showed that the solid surface has a major effect on the ion distribution in nano-aqueous solutions near interfaces. Cl, Br, and I tend to be repelled from the regions where the density of water is high, while F was found to be significantly solvated by water. Due to confinement, the dynamical properties of the electrolyte solution were also observed on the anions and cations pairing through determining the self-diffusion coefficient.

9

$1000 SNOOK PRIZES FOR 2021 : The Information Dimensions of a Two-Dimensional Baker Map

Hoover Wm. G., Hoover C. G.

Computational Methods in Science and Technology

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2021

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Vol. 27, No. 2

93--94

EN

The fractal information dimension can be computed in three ways: (1) mapping points, (2) mapping regions (two-dimensional areas here), and (3) applying the Kaplan-Yorke conjecture. For the simplest nonequilibrium Baker N2 Map these three approaches can give different results. A pedagogical exploration and explanation of this situation is the 2021 Ian Snook Prize Problem.

10

Computational studies of the mitochondrial carrier family SLC25. Present status and future perspectives

Pasquadibisceglie Andrea, Polticelli Fabio

Bio-Algorithms and Med-Systems

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2021

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Vol. 17, no. 2

65--78

EN

The members of the mitochondrial carrier family, also known as solute carrier family 25 (SLC25), are transmembrane proteins involved in the translocation of a plethora of small molecules between the mitochondrial intermembrane space and the matrix. These transporters are characterized by three homologous domains structure and a transport mechanism that involves the transition between different conformations. Mutations in regions critical for these transporters’ function often cause several diseases, given the crucial role of these proteins in the mitochondrial homeostasis. Experimental studies can be problematic in the case of membrane proteins, in particular concerning the characterization of the structure–function relationships. For this reason, computational methods are often applied in order to develop new hypotheses or to support/explain experimental evidence. Here the computational analyses carried out on the SLC25 members are reviewed, describing the main techniques used and the outcome in terms of improved knowledge of the transport mechanism. Potential future applications on this protein family of more recent and advanced in silico methods are also suggested.

11

Molecular Dynamics Simulations of Thermal Conductivity of Penta-Graphene

Muna Isyna, Winczewski Szymon

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2020

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Vol. 24, No 3

191--220

EN

The thermal conductivity of penta-graphene (PG), a new two dimensional carbon allotrope and its dependence on temperature, strain, and direction are studied in this paper. The thermal conductivity of PG is investigated using a non-equilibrium molecular dynamics simulation (NEMD) with the Two Region Method by applying the optimized Tersoff interatomic potential. Our study shows that the thermal conductivity of PG (determined for the [100] direction) at the room temperature of 300 K is about 18.7 W/(m K), which is much lower than the thermal conductivity of graphene. As the temperature increases, the thermal conductivity of PG is decreasing because, unlike graphene, PG has lower phonon group velocities and few collective phonon excitations. The obtained dependence of the thermal conductivity on the temperature can be described as κ ∼ T −0.32. For the [110] direction the thermal conductivity at the room temperature of 300 K is very similar: about 17.8 W/(m K). In this case, the temperature dependence follows the κ ∼ T −0.3 relation. Our investigations reveal that the thermal conductivity of PG is isotropic, meaning that heat transport behavior is independent of the heat flow direction. Our results indicate that the thermal conductivity of PG depends in an interesting way on the applied strain: nonmonotonic up-and-down behavior is observed. The thermal conductivity increases between strains from 0% up to 12.5%, and it decreases above a strain of 12.5%. Our investigation highlights the fascinating thermal transport properties of penta-graphene. The ultra-low thermal conductivity, the decreasing thermal conductivity with the increasing temperature, and the ultra-high mechanical strength of PG show that PG possesses a great potential in thermoelectric and nanomechanics applications. We hope that these findings, made by means of simulations, will become a bridge to inspire and encourage the experimental works, especially in the synthesis of PG.

12

Application of the neural networks for developing new parametrization of the Tersoff potential for carbon

Nwachukwu Anthony Chukwuemeka, Winczewski Szymon

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2020

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Vol. 24, No 4

299--333

EN

Penta-graphene (PG) is a 2D carbon allotrope composed of a layer of pentagons having sp2- and sp3- bonded carbon atoms. A study carried out in 2018 has shown that the parameterization of the Tersoff potential proposed in 2005 by Ehrhart and Able (T05 potential) performs better than other potentials available for carbon, being able to reproduce structural and mechanical properties of the PG. In this work, we tried to improve the T05 potential by searching for its parameters giving a better reproduction of the structural and mechanical properties of the PG known from the ab initio calculations. We did this using Molecular Statics (MS) simulations and Neural Network (NN). Our test set consisted of the following structural properties: the lattice parameter a; the interlayer spacing h; two lengths of C-C bonds, d1 and d2 respectively; two valence angles, O1 and )2, respectively. We also examined the mechanical properties by calculating three elastic constants, C11, C12 and C66, and two elastic moduli, the Young’s modulus E and the Poisson’s ratio v. We used MS technique to compute the structural and mechanical properties of PG at T =0 K. The Neural Network used is composed of 2 hidden layers, with 20 and 10 nodes for the first and second layer, respectively. We used an Adams optimizer for the NN optimization and the Mean Squared Error as the loss function. We obtained inputs (about 80 000 different sets of potential parameters) for the Molecular Statics simulation by using randomly generated numbers. The outputs from these simulations became the inputs to our Neural Network. The Molecular Statics simulations were done with LAMMPS while the Neural Network and other computations were done with Python, Pytorch, Numpy, Pandas, GNUPLOT and Bash scripts. We obtained a parameterization which has a slightly better accuracy (lower relative errors of the calculated structural and mechanical properties) than the original parameterization.

13

Study of alkanethiol-based self-assembled monolayers coated with poly(methyl methacrylate) of various tacticity

Kozik Tomasz, Śniechowski Maciej, Łużny Wojciech

Polimery

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2020

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T. 65, nr 9

598--604

EN

Self-assembled monolayers (SAMs) have a large variety of applications. One particular ap-plication of alkanethiol-based SAMs is tuning the work function of metallic surfaces. In a recent study, it was determined that depositing a poly(methyl methacrylate) layer on selected SAMs further shifts the work function. The effect is sensitive to tacticity and neither the reason behind this nor the exact mechanism of the interaction was determined. The aim of this work is to study the problem by use of molecular dynamics simulations.

PL

Jednym zlicznych zastosowań samoorganizujących się monowarstw (SAMs) jest mody-fikacja pracy wyjścia powierzchni metalicznych. Wliteraturze można znaleźć opracowania dotyczące depozycji cienkich warstw poli(metakrylanu metylu) na wybranych samoorganizujących się monowar-stwach na bazie alkanotioli, prowadzącej do dalszych zmian wartości pracy wyjścia całej struktury. Uzyskany efekt wydaje się być zależny od taktyczności polimeru, jednakże wbadaniach eksperymen-talnych nie udało się określić przyczyn tego zjawiska. Wniniejszej pracy wspomniany efekt zbadano za pomocą symulacji komputerowych metodą dynamiki molekularnej.

14

Surface diffusion and cluster formation of gold on the silicon (111)

Plechystyy V., Shtablavyi I., Rybacki K., Winczewski S., Mudry S., Rybicki J.

Journal of Achievements in Materials and Manufacturing Engineering

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2020

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Vol. 101, nr 2

49--59

EN

Purpose: Investigation of the gold atoms behaviour on the surface of silicon by molecular dynamics simulation method. The studies were performed for the case of one, two and four atoms, as well as incomplete and complete filling of gold atoms on the silicon surface. Design/methodology/approach: Investigations were performed by the method of molecular dynamics simulation using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). MEAM potential of interatomic interaction was used for modelling. Molecular dynamic simulations were carried out in isothermal-isobaric ensemble (NpT) with a timestep 1.0 fs. Findings: As a result of studies, the preferred interaction between gold atoms and the formation of clusters at temperatures up to 800 K was revealed. Analysis of the temperature dependences of the number of large jumps of atoms made it possible to calculate the activation energy of a single jump. It was found that activation energy of single atomic displacement decreases with increasing number of gold atoms. Research limitations/implications: Only a limited number of sets of atoms were used in the study. It is possible that for another combination of atoms and a larger substrate surface, the formation of gold nanoislands on the silicon surface can be observed, which requires further research. Practical implications: The research results can be used to select the modes of gold sputtering to create gold nanoislands or nanopillars on the silicon surface. Originality/value: Computer modelling of the behaviour of gold atoms on the surface of silicon with the possibility of their self-organization and cluster formation was performed for the first time.

15

Time-symmetry breaking in Hamiltonian mechanics. Part 2, A memoir for Berni Julian Alder [1925–2020],

Hoover Wm. G., Hoover C. G.

Computational Methods in Science and Technology

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2020

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Vol. 26, No. 4

101--110

EN

This memoir honors the late Berni Julian Alder, who inspired both of us with his pioneering development of molecular dynamics. Berni’s work with Tom Wainwright, described in the 1959 Scientific American [1], brought Bill to interview at Livermore in 1962. Hired by Berni, Bill enjoyed over 40 years’ research at the Laboratory. Berni, along with Edward Teller, founded UC’s Department of Applied Science in 1963. Their motivation was to attract bright students to use the laboratory’s unparalleled research facilities. In 1972 Carol was offered a joint LLNL employee-DAS student appointment at Livermore. Bill, thanks to Berni’s efforts, was already a Professor there. Berni’s influence was directly responsible for our physics collaboration and our marriage in 1989. The present work is devoted to two early interests of Berni’s, irreversibility and shockwaves. Berni and Tom studied the irreversibility of Boltzmann’s “H function” in the early 1950s [2]. Berni called shockwaves the “most irreversible” of hydrodynamic processes [3]. Just this past summer, in simulating shockwaves with time-reversible classical mechanics, we found that reversed Runge-Kutta shockwave simulations yielded nonsteady rarefaction waves, not shocks. Intrigued by this unexpected result we studied the exponential Lyapunov instabilities in both wave types. Besides the Runge-Kutta and Leapfrog algorithms, we developed a precisely-reversible manybody algorithm based on trajectory storing, just changing the velocities’ signs to generate the reversed trajectories. Both shocks and rarefactions were precisely reversed. Separate simulations, forward and reversed, provide interesting examples of the Lyapunov-unstable symmetry-breaking models supporting the Second Law of Thermodynamics. We describe promising research directions suggested by this work.

16

Structure and dynamics of water adsorbed on the lignite surface: Molecular dynamics simulation

You Xiaofang, He Meng, Cao Xiaoqiang, Lyu Xianjun, Li Lin

Physicochemical Problems of Mineral Processing

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2019

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Vol. 55, iss. 1

10--20

EN

The effects of oxygen-containing functional groups on the structure and dynamic properties of water molecules near a lignite surface were investigated through molecular dynamics (MD) simulations. Because of its complex composition and structure, a graphite surface containing hydroxyl, carboxyl, and carbonyl groups was used to represent the lignite surface model. According to X-ray photoelectron spectroscopic (XPS) results, the composing proportion of hydroxyl, carbonyl and carboxyl is 21:13:6. The density profiles of oxygen and hydrogen atoms indicate that the brown coal surface characteristics influence the structural and dynamic properties of water molecules. The interfacial water is much more ordered than bulk water. The results of the radial distribution functions, mean square displacements, and local self-diffusion coefficients for the water molecules in the vicinity of three oxygen-containing functional groups confirmed that carboxyl groups are the preferential adsorption sites.

17

The molecular dynamics of nematic liquid crystal confined in porous membranes treated by different surfactants

Różański Stanisław Andrzej

Opto-Electronics Review

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2019

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Vol. 27, No. 4

339--344

EN

The molecular dynamics of the well-known nematic liquid crystal 4-n-pentyl-4′-cyanobiphenyl geometrically restricted in Anopore and Synpor porous membranes with various pore structure and treated by different surfactants (namely decanoic acid and lecithin) is compared. In the Anopore membrane the chosen surfactants induce the homeotropic orientation of the molecules on the walls of the cylindrical pores and observed corresponding relaxation processes (librational modes) are practically the same. The dielectric measurements of lecithin treated Synpor membranes reveals the reorientation of the molecules from planar to homeotropic on the complex multilayer structure present in their volume. The dielectric strengths of the observed two molecular processes (δ-process and librational mode) are inversed in the ratio compared to the untreated membranes. The observed differences in molecular dynamics results from the orientation of the liquid crystal molecules in untreated and treated membranes and the structure of the membranes themselves.

18

Improvements to the two-phase sandwich method for calculating the melting points of pure metals

Rybacki K., Winczewski S., Pleechystyy V., Rybicki J.

Computational Methods in Science and Technology

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2019

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Vol. 25, No. 2

105--116

EN

The thermophysical properties of metal alloys are often investigated via molecular dynamics (MD) simulations. An exact and reliable estimation of the thermophysical parameters from the MD data requires a properly and carefully elaborated methodology. In this paper, an improved two-phase sandwich method for the determination of the metal melting temperature is proposed, based on the solid-liquid equilibrium theory. The new method was successfully implemented using the LAMMPS software and the C++11 Standard Libraries and then applied to aluminum and copper systems. The results show that the proposed procedure allows more precise calculations of the melting temperature than the widely used onephase boundary methods.

19

Estimation of phonon relaxation time for silicon by means of using the velocity autocorrelation function of atoms in molecular dynamics

Andriyevsky Bohdan, Maliński M., Buryło Ł., Stadnyk V. Y., Romanuk M. O., Piekarski J., Andriyevska L.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2019

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Vol. 67, nr 3

651--656

EN

Results of the ab initio molecular dynamics calculations of silicon crystals are presented by means of analysis of the velocity autocorrelation function and determination of mean phonon relaxation time. The mean phonon relaxation time is crucial for prediction of the phonon-associated coefficient of thermal conductivity of materials. A clear correlation between the velocity autocorrelation function relaxation time and the coefficient of thermal diffusivity has been found. The analysis of the results obtained has indicated a decrease of the velocity autocorrelation function relaxation time t with increase of temperature. The method proposed may be used to estimate the coefficient of ther-mal diffusivity and thermal conductivity of the materials based on silicon and of other wide-bandgap semiconductors. The correlation between kinetic energy fluctuations and relaxation time of the velocity autocorrelation function has been calculated with the relatively high coefficient of determination R2 = 0.9396. The correlation obtained and the corresponding approach substantiate the use of kinetic energy fluctuations for the calculation of values related to heat conductivity in silicon-based semiconductors (coefficients of thermal conductivity and diffusivity).

20

Fluctuations of kinetic energy at molecular dynamics and the atomic interactions in crystals

Andriyevsky B., Piekarski J., Andriyevska L.

Zeszyty Naukowe Wydziału Elektroniki i Informatyki Politechniki Koszalińskiej

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2018

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Nr 12

19--24

EN

The calculation method of the molecular dynamics has been applied to study the correlation of the kinetic energy fluctuations and the relaxation time of the velocity autocorrelation function and the phonon relaxation time in a crystal. On the basis of the molecular dynamics data for silicon crystal obtained at different temperatures in the range 200 K – 1000 K the correlation between the kinetic energy fluctuations and the relaxation time of the velocity autocorrelation function has been calculated with the relatively high coefficient of determination R2 = 0.9396. The correlation obtained and the corresponding approach substantiate a use of the kinetic energy fluctuations for the calculation of values related to the heat conductivity in the silicon based semiconductors (coefficients of thermal conductivity and diffusivity).

PL

Obliczeniowa metoda dynamiki molekularnej została zastosowana do badania korelacji fluktuacji energii kinetycznej i czasu relaksacji autokorelacyjnej funkcji prędkości i czasu relaksacji fononów w krysztale. Na bazie danych dynamiki molekularnej kryształu krzemu otrzymanych w różnych temperaturach w zakresie 200 K – 1000 K została obliczona korelacja fluktuacji energii kinetycznej i czasu relaksacji autokorelacyjnej funkcji prędkości, która cechuje się stosunkowo wysokim współczynnikiem determinacji R2 = 0.9396. Otrzymana korelacja uzasadnia zastosowanie fluktuacji energii kinetycznej do badań obliczeniowych wielkości powiązanych z przewodnością cieplną półprzewodników na bazie krzemu (współczynniki przewodności i dyfuzyjności cieplnej).