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Room temperature torsional deformation behaviour of bicrystal aluminium specimens (corresponding to Σ5 family) is studied by the application of constant twist rate using molecular dynamics simulations by employing the (embedded atom method) EAM potential. To simulate the torsional loading, periodic boundary condition is employed in x-direction, whereas shrink-wrapped boundary condition is applied in y- and z-directions. A constant twist rate of 1°/ps has been applied at either end of the samples in opposite directions. The variation of potential energy as a function of relative rotation between the ends of the specimen is recorded. The evolution of different types of dislocation and characteristics behaviour due to interactions among dislocations during deformation has been analysed. The populations of Shockley partial dislocations, dislocation loops, dislocation locks, and dislocation junctions increase as the torsional deformation progresses. The structural variations occurred in the specimen are explained with the aid of defect evolutions (such as vacancies population and amorphous atoms percentage as a function of torsion angle), and the grain boundary migration and grain rotation processes are described with atomic snapshots. Additionally, we have tried to correlate trends between grain boundary energy and various deformation mechanisms.

The pair contribution to the potential of sodium in the embedded atom model (EAM) is refined. Two potentials (EAM-2 and EAM-3) that differ in the shape of the embedding potentials are calculated from data on the shock compression and isothermal compression of sodium at 298 K. The main thermodynamic, structural, and diffusion properties of the models are calculated in two variants. The EAM-2 potential poorly describes the properties of sodium at 298 K, while the EAM-3 potential inaccurately characterizes the properties under conditions of shock compression. This means the fixed EAM potential fails to describe the temperature dependence of the properties of the metal. At 900 K, the pressure in the models with the EAM-3 potential is close to the data obtained ab initio. There is no prepeak of the pair correlation function of sodium, but the anomalous behavior of the pressure of the sodium bcc lattice at ∼19–25 GPa is confirmed. The melting lines in the sodium models are calculated in two variants with maxima at around 30 GPa. The problem of the predictive power of the embedded atom model is discussed.

Potassium, rubidium, aluminum, iron, nickel, and tin embedded atom models (EAMs) have been used as examples to ascertain how well the properties of a metal are described by EAM potentials calculated from the shape of shock adiabats and/or static compression data (from a function of cold pressure). Verification of the EAM potential implies an evaluation of its predictive power and an analysis of the agreement with experiment both at 0 or 298 K and under shock compression. To obtain consistent results, all contributions of collectivized electrons to energy and pressure need to be taken into consideration, especially in transition metals. Taking account of or ignoring electron contributions has little effect on the calculated melting lines of the models, self-diffusion coefficients, and viscosity. The shape of the melting line is sensitive to the behavior of the repulsive branch of the pair contribution to the EAM potential at small distances.

A set of embedded atom model (EAM) interatomic potentials was developed to represent highly idealized face-centered cubic (FCC) mixtures of Fe–Ni–Cr–Co–Al at near-equiatomic compositions. Potential functions for the transition metals and their crossed interactions are taken from our previous work for Fe–Ni–Cr–Co–Cu [D. Farkas and A. Caro: J. Mater. Res. 33 (19), 3218–3225, 2018], while cross-pair interactions involving Al were developed using a mix of the component pair functions fitted to known intermetallic properties. The resulting heats of mixing of all binary equiatomic random FCC mixtures not containing Al is low, but significant short-range ordering appears in those containing Al, driven by a large atomic size difference. The potentials are utilized to predict the relative stability of FCC quinary mixtures, as well as ordered L12 and B2 phases as a function of Al content. These predictions are in qualitative agreement with experiments. This interatomic potential set is developed to resemble but not model precisely the properties of this complex system, aiming at providing a tool to explore the consequences of the addition of a large size-misfit component into a high entropy mixture that develops multiphase microstructures.

The literature data on shock compression of compact and porous samples of a number of metals (copper, tin, lead, bismuth, iron, and nickel) and the use of these data in calculations of interparticle potentials in the embedded atom model (EAM) were considered. The Hugoniot shock adiabats of compact metals provide information for calculations of EAM potentials, but as the porosity of the initial samples increases, they become unsuitable for this purpose because of inconsistency with the data obtained on compact samples. Possible reasons for this inconsistency were considered.

In this paper, the uniaxial cold compaction process of metal nano-powders is numerically analyzed through the Molecular Dynamics (MD) method. The nano-powders consist of nickel and aluminum nano-particles in the pure and mixed forms with distinctive contributions. The numerical simulation is performed using the different number of nano-particles, mixing ratios of Ni and Al nano-particles, compaction velocities, and ambient temperatures in the canonical ensemble until the full-dense condition is achieved. In the MD analysis, the inter-atomic interaction between metal nano-particles is modeled by the many-body EAM potential, and the interaction between frictionless rigid die-walls and metal nano-particles is modeled by the pairwise Lennard-Jones inter-atomic potential. The mechanical behavior of metal nano-powders under the compaction process is numerically studied by plotting the relative density–pressure, mean stress-strain, and material characteristics–strain curves. Moreover, the nano-powder behavior is visualized by means of the centro-symmetry contour at various stages of the forming process. Finally, the evolution of top-punch velocity on the final stage of compaction process is studied by plotting the compaction pressure against the total energy at various compaction velocities.

In Ni-based single crystal superalloys, ruthenium is sometimes introduced as one of the creep resistances through retarding the thermally-activated deformation processes, such as dislocation glide and climb. In the present study, an embedded-atom-method potential of Ni–Al–Ru system was constructed. Using the present potential, the effect of Ru on the lattice misfit between γ (Ni) and γ ' (Ni3Al) phases was investigated. The results show that Ru doping decreases the lattice misfit, which is consistent with the calculations from first-principles. The interaction between Ru and misfit dislocation was also studied. The results of interaction energy between Ru and misfit dislocation, and the simulations of misfit dislocation motion in the Ru-doping system by molecular dynamics method both show that Ru possesses the pinning effect on the misfit dislocation. These results can provide useful help for further insights of the role of Ru in the alloys.

The effect of misfit dislocation networks (MDNs) on the stability and shear strength of Cr/TiN was investigated using a newly developed modified embedded atom model parameterized to pure Cr, CrTi, CrN, and Cr/TiN interfacial properties. The interfacial energy was lowest when the MDN was located in the Cr layer adjacent to the chemical interface, which also had the largest dislocation core widths. This was consistent with generalized stacking fault energies, which had lower energy barriers between the first and second Cr layers next to the chemical interface. As the MDN moved away from the interface, dislocation core widths consistently decreased along with the interfacial energy. For all positions of MDNs, shear failure occurred in the ceramic, between the first and second TiN layers next to the chemical interface. The lowest shear strength was found for the system with the MDN in the first Cr layer with respect to the chemical interface. Only for this particular configuration was there a significant plastic deformation present.

In recent years, nickel nanowires have been used as flexible electrode materials for their excellent mechanical properties. There are many studies on the mechanical properties of single crystal nickel nanowires, but it remains unclear for the polycrystalline nickel nanowires. In this study, using Molecular Dynamics (MD) simulation with EAM potential, the mechanical properties of polycrystalline nickel nanowires (PNWs) with different grain numbers (3, 6, 9 and 12) under uniaxial tension along the longitudinal were studied. Results shows that the fracture strength and modulus of elasticity of polycrystalline nickel nanowires decreases with the increase of the number of grains under the same size model. The fracture strength of polycrystalline nickel nanowires is 3.2∼5.7 GPa, which is much lower than that of single crystal nickel nanowires.

A scheme is proposed for the incorporation of a screened Coulomb interaction into an embedded-atom model, which allows one to describe two- and multicomponent solutions with strong component interaction by the molecular dynamics method. The effective particle charges satisfy the electroneutrality condition and are determined via minimization of the total energy. The potentials of the pure components and fitted cross pair potentials are used in the calculations, with allowance for the electronic contributions to energy and pressure. For pairs of 1–2 in Li–Pb solutions (1 is for Li, and 2 is for Pb), a pair potential of the form 8–4 is proposed. Calculations were performed for several Li–Pb melts at zero pressure and temperatures up to 1000 K, as well as for a Li17Pb83 solution under shock compression at temperatures up to 25 000 K and pressures up to 470 MPa. The thermodynamic properties of the Li17Pb83 solution are presented in tabular form. The diffusion and structural properties of this and other solutions, the Gruneisen coefficients, and the Hugoniot adiabat are also calculated.

We perform molecular dynamics simulations to understand the melting mechanism in Cu crystals (modeled using Embedded Atom Potential) with spherical voids of radii 0.5, 0.6 and 1.0 nm. Along with these systems defect-free Cu and a Cu crystal with layered void is also studied. We analyse crystallinity in these systems using Q6 bond-orientational order parameter, Lindemann index, radial distribution functions and coordination numbers. At 1 atm, all crystals melt between 1700 and 1800 K and melting temperature decreases with increase in void fraction. It is also found that at 900 K voids disintegrate and become a part of the crystal and between 900 and 1700 K crystals amorphize losing long-range order.

The potential of the embedded-atom model (EAM) for liquid antimony is calculated, and the molecular dynamics models are constructed for antimony at temperatures of up to 2023 K and under conditions of shock compression up to a pressure of 131 GPa. It is established that the EAM potential describes the behavior of the shoulder of pair correlation function (PCF). Good agreement with the experimental data is obtained for the structure and density of the liquid, the speed of sound at the binodal, and discrepancies are obtained with the experimental data for the energy. It is found that the self-diffusion coefficient is overstated near the melting point, but the discrepancy disappears upon heating; the calculated shock adiabat agrees with the experimental results; and the structure of liquid antimony models at pressures up to 8 GPa is not consistent with the diffraction data regarding the shape of the first PCF peak. It is concluded that the structural features of the anomalous metal (antimony) are determined by an existence of the interval to the right of the first PCF peak, at which the curvature of the interparticle potential is negative.

The effects of particle size (2–6 nm) and temperature (300–2700 K) on the stability and local structural evolutions of amorphous equiatomic FePt bulk/nanoalloys have been investigated by combining Embedded Atom Model (EAM) with classical molecular dynamics (MD) simulation method. The three dimensional (3D) atomic configuration of amorphous FePt NPs by means of Voronoi analysis reveals that, deformed bcc (d-bcc) and icosahedron (d-ico) type structures are most probable local atomic configurations for 2–6 nm sized Fe50Pt50 NPs both in liquid (1700 K) and glassy (300 K) states. It was shown that nano-scale phase separation takes place around 300 K for 2 nm sized FePt NPs that leads to formation of spherical core-shell segregated structure having Pt-Fe-rich core and Fe-rich surface. Compared to core region, more ordered and high dense configuration of atoms at the surface gives rise to decrease in surface entropy of NPs and hence bringing about surface energy anomaly with positive temperature coefficient above the glass transition temperatures. Below glass transition temperatures of the FePt nanoalloy particles, the thermodynamically stable amorphous phase (TSA) would appear. Glass transition temperature of amorphous Fe50Pt50 NPs increases with increasing particle size and eventually approaches to the glass temperature of bulk system for NPs diameters ≥ ∼16 nm. Results of current predictions are in good qualitative and semi-quantitative agreement with other theoretical and experimental findings reported in the literature.

Molecular dynamics simulations provide a large body of literature on pressure-induced phase transformations in iron. However, the role of interstitial carbon on phase transformations in iron under high pressure is still an open topic. We investigate the mechanical response of Fe-C single crystals and polycrystals using hydrostatic and uniaxial compression. We couple a recently developed Fe interatomic EAM potential, which faithfully describes the α → e transformation in iron, with several well-known Fe-C potentials. Our results show a three-wave profile demonstrating that the phase transformation is preceded by plasticity. Carbon strongly increases the transformation pressure but decreases the Hugoniot elastic limit in agreement with experimental results.

We propose an approach to materials prediction that uses a machine-learning interatomic potential to approximate quantum-mechanical energies and an active learning algorithm for the automatic selection of an optimal training dataset. Our approach significantly reduces the amount of density functional theory (DFT) calculations needed, resorting to DFT only to produce the training data, while structural optimization is performed using the interatomic potentials. Our approach is not limited to one (or a small number of) lattice types (as is the case for cluster expansion, for example) and can predict structures with lattice types not present in the training dataset. We demonstrate the effectiveness of our algorithm by predicting the convex hull for the following three systems: Cu-Pd, Co-Nb-V, and Al-Ni-Ti. Our method is three to four orders of magnitude faster than conventional high-throughput DFT calculations and explores a wider range of materials space. In all three systems, we found unreported stable structures compared to the AFLOW database. Because our method is much cheaper and explores much more of materials space than high-throughput methods or cluster expansion, and because our interatomic potentials have a systematically improvable accuracy compared to empirical potentials such as embedded atom model, it will have a significant impact in the discovery of new alloy phases, particularly those with three or more components.

The investigation is generalized to clusters with sizes up to 3000 atoms, covering this way the range of sizes experimentally available for low energy cluster beam deposition. The atomic scale modeling is carried on by both Molecular Dynamics and Metropolis Monte Carlo. This represents a huge series of simulations (175 cases) to which further calculations are added by spot when finer tuning of the parameters is necessary. Analyzing the results is a major task which is still in progress. This way, not only a realistic range of sizes is covered, but also the whole range of compositions and the temperature range relevant to the solid and the liquid states.

In this paper, a molecular dynamics model is proposed to describe the collision friction of a hinge mechanism in the space environment. The EAM potential is used to describe the interaction between atoms. Based on the model, the collision friction process and thermal properties between the indenter and smooth gold film surface at different indenter amplitudes, frequencies and crystal orientations are studied. The temperature distribution and collision friction mechanism of the gold film are analyzed. The simulation results show that increasing the vibration frequency of the indenter in a certain frequency range can reduce the friction force. The amplitude of the indenter and crystal orientations at different frequencies shows different effects on the average friction force and the surface temperature of the substrate. In addition, textures are also made on the gold film and the effects of texture width and texture depth on the friction and thermal properties are investigated. The results show that the textured surface can significantly reduce the friction force. The average friction force and the surface temperature of the substrate decrease with the increase of texture depth, and increase with the increase of texture width. The average friction force and the surface temperature of the substrate are more sensitive to the texture depth.

Hydrogen (H) trapping by helium-vacancy (He V) complexes in bulk and the near surface region of tungsten (W) have been investigated by molecular statics calculations that evaluate two different W H interatomic potentials, which use the same W He, He He and He H potentials. One of the W H potentials is a bond-order potential (BOP) developed by Juslin et al., while the other is an embedding atom method (EAM) potential developed by Wang et al.. Both potentials overestimate the H binding energies to He clusters in bulk W, as compared to DFT calculations, but properly predict the functional form of the H binding energies to He clusters with increasing number of He and H. The BOP simulations reveal that H binding energies to HexV complexes generally increase with increasing number of He. However, the EAM results indicate that the H binding energy as a function of number of He depends on the number of H, and the H binding energies change slightly at high He content. Compared with available DFT data, both BOP and EAM underestimate the H binding energies to HexV2Hm complexes. The BOP reproduces the He formation energy below a W surface, while the EAM potential better reproduces the H formation energy and the interactions between H and He V complexes. Based on these comparisons, we determine that the EAM potential is more accurate than BOP for large-scale molecular dynamics simulations of W He H interactions. The EAM potential predicts that the difference in the average binding energies of H to stable He V complexes near the W surface is less than 0.2 eV and the difference decreases with increasing He content. Thus, the EAM potential indicates that the effect of surfaces on H binding energies to large He V complexes below the W surfaces can be ignored.

The molecular dynamics method with many-body potential of interatomic interaction constructed in the embedded atom model is used to study the thermal characteristics of aluminum and metastable fcc titanium nanofilms with (0 0 1) and (1 1 0) surface orientation. It is shown that in Al films the linear coefficients of thermal expansion are positive in all the directions, except for the area close to the melting temperature. For fcc titanium the linear coefficients of thermal expansion in the film plane are negative in a wide temperature range. With increasing temperature, in Ti films the local vibrational densities of states of the surface atomic layers, polarized along the x , y , z axes, shift to the low-energy part of the spectrum only in those directions where a decrease in the lattice parameters is observed. The changes in the interface areas of Al films occurring with increase in temperature, lead to the growth of anharmonicity and a “softening” of the local vibration spectra near the critical temperature. It is shown that the negative coefficient of linear expansion is an indicator of the simulated system being in metastable state.

This thesis presents a powerful numerical fitting procedure for generating Embedded Atom Method (EAM) inter-atomic potentials for pure Face Centred Cubic (FCC) and Body Centred Cubic (BCC) metals. The numerical fitting procedure involves assuming a reasonable parameterized form for a portion of the EAM potential, and then fitting the remaining portion to select thermal and elastic properties of the metal. Molecular Dynamics (MD) simulation is used to effect the fitting procedure. The procedure is used to generate an EAM potential for copper, an FCC metal. This resulting EAM potential is used to conduct MD simulations of perfect copper crystals containing voids of different geometries. Following this, a bridged Finite Element-Molecular Dynamics (FE-MD) method is presented, which can be used to simulate large atomic systems much more efficiently than MD simulation alone. The method implements a novel element discretization scheme proposed by the author that is so general that it can be applied to any system of objects interacting with each other via any potential (simple or complex, EAM or otherwise). This bridged FE-MD method is used to reanalyze the voids in the copper crystal lattice. The resulting virial stress increment patterns are found to agree remarkably with the earlier MD simulation results. Furthermore, the bridged FE-MD method is much quicker than the pure MD simulation. These two facts prove the power and usefulness of the bridged FE-MD method, and validate the proposed element discretization scheme

The modified embedded atom method (MEAM) potentials improved by Jin et al. (Appl. Phys. A120 (2015), p. 189) were applied to calculate the mono- and bi-vacancy properties as well as the phonon dispersions for hexagonal close-packed (HCP) metals Be, Co, Hf, Mg, and Re. We expressed the formulas for calculating the mono- and bi-vacancy properties by the molecular static (MS) method based on the MEAM potentials for HCP metals. The lattice dynamics (LD) method and the MEAM potentials were adopted to calculate the phonon dispersion properties. The calculation results show better agreement with the experimental data than the previous calculations by using the unimproved embedded atom model.

The diffusion mechanism of carbon in iron plays a vital role in carburization processes, steel fabrication, and metal dusting corrosion. In this paper, using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo algorithm with on-the-fly catalog building that allows to obtain diffusion properties over large time scales taking full account of chemical and elastic effects coupled with an EAM potential, we investigate the effect of pressure on the diffusion properties of carbon in $85.{91}^{\ensuremath{\circ}}\phantom{\rule{4pt}{0ex}}\ensuremath{\langle}100\ensuremath{\rangle}$ symmetric tilt grain boundaries (GB) of $\ensuremath{\alpha}$-iron up to a pressure of 12 kbar at a single temperature of 600 K. We find that, while the effect of pressure can strongly modify the C stability and diffusivity in the GB in ways that depend closely on the local environment and the nature of the deformation, isotropic and uniaxial pressure can lead to opposite and nonmonotonous effects regarding segregation energy and activation barriers. These observations are relevant to understanding of the evolution of heterogeneous materials, where variations of local pressure can alter the carbon diffusion across the material.

Nanofluids formed by adding a small volume fraction of solid nanoparticles to the conventional fluid can greatly enhance the thermal transport performance of the conventional fluid. This study reveals the mechanism of thermal conductivity by studying the microscopic effect of nanoparticles in a Cu–Ar nanofluid on the base fluid. Due to the presence of a trapped, adsorbed Ar layer on the surface of the nanoparticle, under certain volume fractions, the influence of the nanoparticles with different sizes on the thermal conductivity is analyzed. The equilibrium molecular dynamics and nonequilibrium molecular dynamics methods are used to calculate and verify the thermal conductivity of the nanofluid, and the abilities of the Lennard–Jones (LJ) and embedded atom method (EAM) potential functions to accurately describe interactions between Cu atoms are compared. By calculating the contribution of different components to the thermal conductivity of the nanofluid, it is found that the composition of the base liquid plays a leading role, while the nanoparticle composition and the solid–liquid cross-section contribute very little. Through decomposition of the Green–Kubo formula (contains potential energy term (V), the kinetic energy term (K), the collision term (V)), it is found that the PV, KV, and VV terms are related to collisions (V) when the LJ potential function is used, which play a major role in the nanofluid’s thermal conductivity. Partial enthalpy terms h, PP, and KK contribute little to the thermal conductivity, and they hinder any decrease of the thermal conductivity as the size of the nanoparticles increases; meanwhile, the KP term remains basically constant. In systems described by the EAM potential function, the contributions of KP and PP are relatively high. Therefore, this paper analyzes the mechanism of increasing the thermal conductivity of Ar-based nanofluid from the perspective of molecular dynamics simulation and obtains the results.

Surface-enhanced Raman scattering (SERS) nanoprobes have shown tremendous potential in in vivo imaging. The development of single oligomer resolution in the SERS promotes experiments on DNA and protein identification using SERS as a nanobiosensor. As Raman scanners rely on a multiple spectrum acquisition, faster imaging in real-time is required. SERS weak signal requires averaging of the acquired spectra that erases information on conformation and interaction. To build spectral libraries, the simulation of measurement conditions and conformational variations for the nucleotides relative to enhancer nanostructures would be desirable. In the molecular dynamic (MD) model of a sensing system, we simulate vibrational spectra of the cytosine nucleotide in FF2/FF3 potential in the dynamic interaction with the Au20 nanoparticles (NP) (EAM potential). Fourier transfer of the density of states (DOS) was performed to obtain the spectra of bonds in reaction coordinates for nucleotides at a resolution of 20 to 40 cm−1. The Au20 was optimized by ab initio density functional theory with generalized gradient approximation (DFT GGA) and relaxed by MD. The optimal localization of nucleotide vs. NP was defined and the spectral modes of both components vs. interaction studied. Bond-dependent spectral maps of nucleotide and NP have shown response to interaction. The marker frequencies of the Au20—nucleotide interaction have been evaluated.

The paper discusses problems related to the description of metals and alloys internal structure. By classical molecular dynamics simulation, we developed and numerically implemented mathematical model to describe a microcracks and edge dislocations trapping of impurity atoms. The embedded atom model is used to construct the interatomic interaction potential. Based on the analysis of local strain and stress fields, estimates are made for the capture radius of impurity atoms by an microcracks and edge dislocations in Fe-C. Besides, the trapping forms regions near the microcracks and edge dislocations were clarified.

The growth of a thin film of a high-entropy AlCoCuFeNi alloy on a substrate of silicon (100) was studied using molecular dynamics modeling. The simulation was carried out using the embedded atom model to describe the interaction among Al–Co–Cu–Ni–Fe. Interaction between the atoms of Al, Co, Cu, Fe, Ni, and the Si substrate was modeled using the Lennard–Jones potential, and the interaction between the silicon atoms was described using the Stillinger–Weber potential. Total simulation time has reached 50 ns. It was found that at the first stage of deposition small clusters were formed and the process of crystallization started after ~5 ns of simulation, at the characteristic sizes of clusters of about 2 nm. At the end of the simulation, after the 50 ns of modeling, the simulated film contains a face-centered cubic phase, a body-centered cubic phase, a hexagonal close-packed phase, and an amorphous phase. An analysis of the radial distribution of atoms made it possible to determine the distances between the nearest neighbors and estimate the lattice parameters of these phases.

A method for the calculation of elastic constants in the NVT ensamble, using molecular dynamics (MD) simulation with a realistic many-body embedded-atom-model (EAM) potential, is studied in detail. It is shown that in such NVT MD simulations, the evaluation of elastic constants is robust and accurate, as it gives the elastic tensor in a single simulation which converges using a small number of time steps and particles. These results highlight the applicability of this method in: (i) the calculation of local elastic constants of non-homogeneous crystalline materials and (ii) in the calibration of interatomic potentials, as a fast and accurate alternative to the common method of explicit deformation, which requires a set of consistent simulations at different conditions. The method is demonstrated for the calculation of the elastic constants of copper in the temperature range of 0-1000K, and results agree with the target values used for the potential calibration. The various contributions to the values of the elastic constants, namely, the Born, stress fluctuation and ideal gas terms, are studied as a function of temperature., Comment: Accepted for publication in Physical Review E

This chapter begins by identifying four possible states or situations: continuous systems (state 1) modeled in discrete form (state 2), and naturally discrete systems (state 3) modeled in continuous form (state 4). We refer to state 2 as a discretized state whereas state 4 is referred to as a homogenized state. The analyses to follow are divided along these lines but the chapter begins with the discrete state because that is the new aspect of waves considered here.

The LL-37 peptide is an antimicrobial agent derived from human cathelicidin. In addition to their antimicrobial properties, these peptides can activate the immune system through various mechanisms and contribute to autoimmune diseases. In the current study, we describe the atomic behavior of this protein in an aqueous environment inside of metallic nanochannel (Fe nanochannel). For this purpose, Molecular Dynamics (MD) approach was implemented in equilibrium conditions. A Large Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used in this computational study. Computationally, the various atoms interaction described by Universal Force Field (UFF), TIP4P, and Embedded Atom Model (EAM). Furthermore, physical factors like potential energy, temperature, Radial Distribution Function (RDF), density/velocity/temperature profiles, and protein volume were calculated for atomic behavior description of the LL-37 protein-water system. MD outputs indicated the atomic stability of protein structure in an aqueous environment inside metallic nanochannels. Numerically, the LL-37 protein volume changes from 3906.81 A3 to 3900.11 A3 value after t = 10 ns. Also, the maximum density and velocity/temperature profiles reach 0.0225 atoms/A3 and 0.0124 A/fs/435.22 K (respectively), values detected in the initial/final and middle bins MD box.

Interaction potentials are critical to molecular dynamics simulations on fundamental mechanisms at atomic scales. Combination of well-developed single-element empirical potentials via cross interaction (CI) is an important and effective way to develop alloy embedded-atom method (EAM) potentials. In this work, based on neural-network (NN) models, firstly we proposed a framework to construct CI potential functions via utilizing single-element potentials. The framework contained four steps: (1) extracting characteristic points from single-element potential functions, (2) constructing CI functions by cubic spline interpolation, (3) evaluating the accuracy of CI functions by referring to first-principle (FP) data, and (4) searching for reasonable CI functions via NN models. Then with this framework, we developed a Zr–Nb alloy CI potential utilizing the MA-III (pure Zr potential developed by Mendelev and Ackland in 2007) and the Fellinger, Park and Wilkins (FPW) (pure Nb potential developed by FPW in 2010) potentials as single-element parts. The calculated results with this Zr–Nb alloy potential showed that: (1) the newly developed CI potential functions could simultaneously present the potential-function features of Zr and Nb; (2) the normalized energy–volume curves of L12 Zr3Nb, B2 ZrNb and L12 ZrNb3 calculated by this CI potential reasonably agreed with FP results; (3) the referred MA-III Zr and FPW Nb potentials can satisfactorily reproduce the priority of prismatic slip in Zr and the tension–compression asymmetry of 〈111〉{112} slip in Nb, while other ab initio developed Zr–Nb alloy potentials cannot. Our study indicates that, this NN based framework can take full advantage of single-element potentials, and is very convenient to develop EAM potentials of alloys; moreover, the new-developed Zr–Nb alloy EAM potential can reasonably describe the complicated deformation behaviors in Zr–Nb systems.

Recently, surface-enhanced Raman scattering (SERS) nanoprobes have shown tremendous potential in oncological imaging owing to the high sensitivity and specificity of their fingerprint-like spectra. As current Raman scanners rely on a slow, point-by-point spectrum acquisition, there is an unmet need for faster imaging in real-time. The development of single-molecule resolution in the tip-enhanced and surface-enhanced Raman spectroscopy (TERS & SERS) promotes experimental work on DNA and protein identification by the above methods and approaches a single oligomer resolution that leads to its use as a nanobiosensor. However, a weak signal requires multiple acquisitions of the averaged spectra to enhance the signal, and information on the molecular conformation and interaction is erased. The enhancer Au clusters of known geometry, size, and position relative to the measured molecule will help to build spectral libraries for single spectral signal prediction. As the simulation molecular dynamic (MD) model of a sensing system, we study vibrational spectra of the cytosine nucleotide in the dynamic interaction with the Au20 nanoparticles (NP) that can be later attached to graphene nanopore. We define nucleotide and NP localization and study the influence of interaction on the spectral modes of both the nucleotide and NP, as we had seen in the case of the nucleotide-graphene nanopore. The spectral maps of the nucleotides were built in FF2/FF3 potential. Fourier transfer of the density of states (DOS) was performed to obtain the spectra of various bonds in reaction coordinates for DNA nucleotides at a numerical resolution 20 to 40 cm-1. The pyramid-shaped Au20 NP was optimized by ab initio DFT GGA and relaxed by the MD calculation with the EAM potential with Δt=0.1fs. Spectral maps of the Au NP were acquired for each atom. The frequencies that can serve as markers of the corresponding Au – nucleotide interaction have been evaluated.

Functionally graded materials (FGM) eliminate the stress singularity in the interface between two different materials and therefore have a wide range of applications in high temperature environments such as engines, nuclear reactors, spacecrafts etc. Therefore, it is essential to study the mechanical properties of different FGM materials. This paper aims at establishing a method for modelling FGMs in molecular dynamics (MD) to get a better insight of their mechanical properties. In this study, the mechanical characteristics of Cu-Ni FGM nanowires (NW) under uniaxial loading have been investigated using the proposed method through MD simulations. In order to describe the inter-atomic forces and hence predict the properties properly, EAM (Embedded atom model) potential has been used. The nanowire is composed of an alloying constituent in the core and the other constituent graded functionally along the outward radial direction. Simple Linear and Exponential functions have been considered as the functions which defines the grading pattern. The alloying percentage on the surface has been varied from 0% to 50% for both Cu-cored and Ni-cored nanowires. All the simulations have been carried out at 300 K. The L/D ratios are 10.56 and 10.67 for Cu-cored and Ni-cored NWs, respectively. This study suggests that Ultimate Tensile Stress and Young's modulus increase with increasing surface Ni percentage in Cu-cored NWs. However, in Ni-cored NWs these values decrease with the increase of surface Cu percentage. Also, for the same surface percentage of Ni in Cu-cored NW, the values are higher in linearly graded FGMs than that in exponentially graded FGMs. While in Ni-cored NWs, exponentially graded FGM shows higher values of UTS and E than those in linearly graded FGM. Thus, grading functions and surface percentages can be used as parameters for modulating the mechanical properties of FGM nanowires., 8 pages, 3 Figures

Quantum-mechanical (QM) simulations, thanks to their predictive power, can provide significant insights into the nature and dynamics of defects such as vacancies, dislocations and grain boundaries. These considerations are essential in the context of the development of reliable, inexpensive and environmentally friendly alloys. However, despite significant progress in computer performance, QM simulations of defects are still extremely time-consuming with ab-initio/non-parametric methods. The two-centre Slater–Koster (SK) tight-binding (TB) models can achieve significant computational efficiency and provide an interpretable picture of the electronic structure. In some cases, this makes TB a compelling alternative to models based on abstraction of the electronic structure, such as the embedded atom model. The biggest challenge in the implementation of the SK method is the estimation of the optimal and transferable parameters that are used to construct the Hamiltonian matrix. In this paper, we will present results of the development of a data-driven framework, following the classical approach of adjusting parameters in order to recreate properties that can be measured or estimated using ab-initio or non-parametric methods. Distinct features include incorporation of data from QSGW (quasi-particle self-consistent GW approximation) calculations, as well as consideration of higher-order elastic constants. Furthermore, we provide a description of the optimisation procedure, omitted in many publications, including the design stage. We also apply modern optimisation techniques that allow us to minimise constraints on the parameter space. In summary, this paper introduces some methodological improvements to the semi-empirical approach while addressing associated challenges and advantages.

In this study, molecular dynamics method is used to estimate the atomic manner that effect on H2O/Cu Nanofluid behavior. The Copper Nanochannel with sphere barriers is simulated to study of H2O/Cu Nanofluid flow and the atomic interactions of these structures are described by Embedded Atom Model and Lennard-Jones force fields. For study of atomic behavior of these structures, physical parameters such as temperature, density and velocity profiles of Nanofluid reported. Molecular dynamics simulation results show that these parameters of H2O/Cu Nanofluid inside non-ideal Nanochannel affected by atomic barriers’ number and size changes. Numerically, we calculated the density and velocity profiles in Nanochannel with spherical barriers which show these numerical reports can be important for the heat transferring procedure in the industrial applications.

The development of transferable interatomic potentials for the diffusion of hydrogen on palladium surfaces can be of significant value for performing molecular simulations. These molecular simulations can, in turn, lead to a better understanding of palladium-hydrogen interactions at the atomic scale. Here, we have built upon previous work to develop an analytical palladium-hydrogen-embedded atom method (EAM) potential to better describe the potential energy surface for hydrogen on palladium surfaces. This EAM potential reproduces minima and transition states calculated with density functional theory for hydrogen on Pd(111) and Pd(110) surfaces. Additionally, this potential was tested by simulating the long timescale dynamics of hydrogen adsorbed on Pd(111). Our simulations show a barrier of ca. 0.49 eV for hydrogen diffusion into the bulk of Pd(111), which is consistent with experimental results.

In order to study the performance of interatomic potentials and their reliability at higher pressures, the phase diagrams of two different embedded-atom-type potential models (EAMs) and a modified embedded-atom model (MEAM) of lithium are compared. The calculations were performed by using the nested sampling technique in the pressure range 0.01–20 GPa, in order to determine the liquid–vapor critical point, the melting curve, and the different stable solid phases of the compared models. The low-pressure stable structure below the melting line is found to be the body-centered-cubic (bcc) structure in all cases, but the higher pressure phases and the ground-state structures show a great variation, being face-centered cubic (fcc), hexagonal close-packed (hcp), a range of different close-packed stacking variants, and highly symmetric open structures are observed as well. A notable behavior of the EAM of Nichol and Ackland (Phys. Rev. B: Condens. Matter Mater. Phys.2016, 93, 184101) is observed, that the model displays a maximum temperature in the melting line, similarly to experimental results.

Clusters of atoms in dense gold vapor are studied via atomistic simulation with the classical molecular dynamics method. For this purpose, we develop a new embedded atom model potential applicable to the lightest gold clusters and to the bulk gold. Simulation provides the equilibrium vapor phases at several subcritical temperatures, in which the clusters comprising up to 26 atoms are detected and analyzed. The cluster size distributions are found to match both the two-parameter model and the classical nucleation theory with the Tolman correction. For the gold liquid–vapor interface, the ratio of the Tolman length to the radius of a molecular cell in the liquid amounts to ∼0.16, almost exactly the value at which both models are identical. It is demonstrated that the lightest clusters have the chain-like structure, which is close to the freely jointed chain. Thus, the smallest clusters can be treated as the quasi-fractals with the fractal dimensionality close to two. Our analysis indicates that the cluster structural transition from the solid-like to chain-like geometry occurs in a wide temperature range around 2500 K.

Atomic-scale comprehension of structure and thermodynamic stability of metallic core–shell nanoparticles is important for viewpoints of both their synthesis and applications. Thermodynamic and structural properties of Al@Ni and Ni@Al core–shell nanoparticles are investigated at various temperatures by using molecular dynamics (MD) simulations within the interactions defined by the many-body embedded atom model (EAM). The sizes of Al@Ni core–shell nanoparticles and their pure counterparts are chosen as two different values of about 5 nm and 10 nm in this study. MD method is used to calculate the total energy, one-body particle density, radial distribution function, and heat capacity to estimate the melting temperatures of the core–shell systems considered in the present study. Our estimated melting temperatures of core–shell nanoparticles are also verified by doing common neighbor analysis (CNA). MD study shows that a distinct two-stage melting takes place during the heating of the Al@Ni core–shell nanoparticles, although their melting mechanism has started from surface into interior. It is reported that the width of the melting temperature of the core–shell nanoparticles is dependent not only on the bulk melting points of their pure metals but also on the ratio of the shell thickness and the core size of the nanoparticles. [Figure not available: see fulltext.]. © 2020, Springer Nature B.V.

We develop a long-time moving window framework using Molecular Dynamics (MD) to model shock wave propagation through a one-dimensional chain of atoms. The moving window formulation “follows” a propagating shock wave allowing us to model shock wave propagation much longer than conventional non-equilibrium MD (NEMD) simulations. This formulation also significantly decreases the required domain size and thus reduces the overall computational cost. The domain is divided into a purely atomistic “window” region containing the shock wave flanked by boundary or “continuum” regions on either end which incorporate continuum shock conditions. Spurious wave reflections are removed by employing a damping band method using the Langevin thermostat applied locally to the atoms in each continuum region. The moving window effect is achieved by adding/removing atoms to/from the window and boundary regions, and thus the shock wave front is focused at the center of the window region indefinitely. We simulate the shock through a one-dimensional chain of copper atoms using either the Lennard-Jones, modified Morse, or Embedded Atom Model (EAM) interatomic potential. We first perform verification studies to ensure proper implementation of the thermostat, potential functions, and damping band method, respectively. Next, we track the propagating shock and compare the actual shock velocity and average particle velocity to their corresponding analytical input values. From these comparisons, we optimize the linear shock Hugoniot relation for the given “lattice” orientation and compare these results to those in literature. When incorporated into the linear shock equation, these new Hugoniot parameters are shown to produce a stationary shock wave front. Finally, we perform one-dimensional moving window simulations of an unsteady, structured shock up to a few nanoseconds and characterize the increase in the shock front’s width.

We report large-scale molecular dynamics simulations of the glass formation from the liquid phase and homogeneous nucleation phenomena of pure zirconium. For this purpose, we have built a modified embedded atom model potential in order to reproduce relevant structural, dynamic, and thermodynamic properties from ab initio and experimental data near the melting point. By means of liquid-solid interface simulations, we show that this potential provides a thermodynamic melting temperature and densities of the solid and liquid state in good agreement with experiments. Using melt-quenching simulations with one million atoms, we determine the glass transition from the temperature evolution of the inherent structure energy as well as the nose of the time-temperature-transformation curve located in the deep undercooling regime. We identify the local structural origin of the glass-forming ability as a competition between bcc and fivefold polytetrahedral structures that may represent an impediment of rapid homogeneous nucleation at such high undercoolings. This suggests the ability of single elemental zirconium to form a glass from the melt with cooling rates of at least ${10}^{12}\phantom{\rule{4pt}{0ex}}\mathrm{K}/\mathrm{s}$, compatible with modern experiments.

The paper addressed issues related to the description of the internal structure of metals and alloys in terms of microvoids nucleation and evolution, which are one of the varieties of damages. By classical molecular dynamics simulation we develop and numerically implement a mathematical model for the description of the interaction of edge dislocations and microvoids taking into account temperature and strain external fields changes. The studied material is binary system Fe–C with 0.8 % volumetric carbon content, which corresponds to high-carbon steel. The construction of the interatomic potential is carried out by the Embedded Atom Model. The methods of introducing edge dislocations and micropores into the molecular dynamics system are considered. A scenario is considered in which microvoids act as a sink of vacancy, and qualitative and quantitative estimations of the interaction of edge dislocations and microvoids are obtained.

Microchannels are promising structures for the different processes such as mass and heat transfer processes. Previous researches indicated the atomic behavior of nanofluids in these structures improved appreciably. In the current numerical study, the atomic behavior of H2O-CuO nanofluid inside Pt microchannel is described using Molecular Dynamics simulation. The results are reported by calculating physical properties such as temperature, total energy, density, velocity, temperature profile, and aggregation time. In our simulations, H2O-CuO nanofluid inside Pt microchannel is represented by Universal Force Field, TIP4P, and Embedded Atom Model. The simulation results show that the total energy of atomic structures converged to -509910 eV value after 10 ns. This calculation estimated the atomic stability of structures. Also, simulations predicted microchannel thickness is an important parameter for nanofluid flow. By increasing microchannel thickness, the absorption force between Pt atoms and nanofluid particles increases. Numerically, by increasing microchannel thickness to 15, the maximum density, velocity, and temperature profiles reach 1.23 g/cm3, 0.0065 A/ps, and 264 K, respectively. Furthermore, by microchannel thickness increasing from 5 to 15, CuO nanoparticles’ aggregation time and potential energy increase from 1.32ns and -659328 eV to 2.11 ns and -721583 eV. Physically, because of the amplitude of the atomic displacement, this atomic process occurs and decreases with the enlargement of the atomic layers. The movement atomic of various particles of H2O/CuO nanofluid increases by microchannel walls thickening and nanoparticles aggregation phenomenon occur in higher time