Empirical Interatomic Potentials Research Articles

Comparison of different interatomic potentials for MD simulations of AlN

As an important semiconductor material as well as promising protective coating material, AlN has attracted increasing attention. In the past decades, the physical and mechanical properties of AlN have been studied by several researchers with molecular dynamics (MD) simulation, using a number of empirical interatomic potentials, but the results differ markedly from each other. It is known that a realistic interatomic potential is significantly important in an accurate MD simulation. In this article, we compared the mechanical and physical properties of AlN obtained with MD simulations using different kinds of typical interatomic potentials, including Tersoff potential, Vashishta potential and Comb3 potential, for the purpose to explore their validity, availability and accuracy in MD simulations. Based on the analysis of the obtained results, we suggested a proper choice of interatomic potentials for AlN in MD simulations.

Assessment of halloysite nanotubes as vehicles of isoniazid

Equilibrium and thermodynamic aspects of the adsorption of isoniazid (INH) onto halloysite nanotubes (HLNTs) and characteristics of the resultant drug/nanocarrier systems are investigated. Equilibrium studies were performed in aqueous medium at different times, temperatures and drug concentrations. The overall adsorption process was explained as the result of two simple processes: adsorption on the activated sites of HLNTs and precipitation of INH on HLNTs surface. Formation of the INH-loaded HLNTs was spontaneous, endothermic and endoentropic, increasing the thermodynamic stability of the system (ΔH=70.40kJ/mol; ΔS=0.2519kJ/molK). Solid state characterization corroborated the effective interaction between the components that was also described by modeling at molecular level by quantum mechanics calculations along with empirical interatomic potentials. Transmission electron microphotographs confirmed the double allocation and homogeneous distribution of INH in the nanohybrids. FTIR spectra revealed the interaction via hydrogen bonds between the inner hydroxyl groups of HLNTs and N in INH molecules. Loading of INH in the nanohybrids was approximately 20% w/w. Effective loading of INH and activation energies of the interactions enable to propose the designed nanohybrids in the development of modified drug delivery systems.

Empirical interatomic potentials optimized for phonon properties

Molecular dynamics simulations have been extensively used to study phonons and gain insight, but direct comparisons to experimental data are often difficult, due to a lack of accurate empirical interatomic potentials for different systems. As a result, this issue has become a major barrier to realizing the promise associated with advanced atomistic-level modeling techniques. Here, we present a general method for specifically optimizing empirical interatomic potentials from ab initio inputs for the study of phonon transport properties, thereby resulting in phonon optimized potentials. The method uses a genetic algorithm to directly fit the empirical parameters of the potential to the key properties that determine whether or not the atomic level dynamics and most notably the phonon transport are described properly.

Theoretical study of the composition pulling effect in InGaN metalorganic vapor-phase epitaxy growth

The composition pulling effect in metalorganic vapor-phase InGaN epitaxy was theoretically investigated by thermodynamic analysis. The excess energies of biaxial-strained InxGa1−xN were numerically calculated using empirical interatomic potentials considering different situations: (i) coherent growth on GaN(0001), (ii) coherent growth on In0.2Ga0.8N(0001), and (iii) bulk growth. Using the excess energies, the excess chemical potentials of InN and GaN alloys were computed. Our results show that compressive strain suppresses In incorporation, whereas tensile strain promotes it. Moreover, assuming chemical equilibrium, the relationship between the solid composition and the growth conditions was predicted. The results successfully reproduced the typical composition pulling effect.

Electron and phonon transport in twisted graphene nanoribbons

We theoretically study the electronic, thermal and thermoelectric properties of graphene nanoribbons under torsional deformations. The modelling follows a nonequilibrium Green’s function approach in the ballistic transport regime, describing the electrical and phononic properties through ab initio density functional theory and empirical interatomic potentials, respectively. We consider two different types of deformations, a continuous twist of a given angle applied to the nanoribbon, and two consecutive twists applied in opposite angular directions. The numerical results are carefully analysed in terms of spatially-resolved electron eigenchannels, polarization-dependent phonon transmission and thermoelectric figure-of-merit.

Molecular modeling and infrared and Raman spectroscopy of the crystal structure of the chiral antiparasitic drug Praziquantel

Anthelmintic praziquantel (PZQ) and its molecular and crystal lattice structures were studied by means of atomistic calculations based on empirical interatomic potentials and quantum mechanical methods (DFT). This chiral drug presents several crystal polymorphs due to the enantiomers (either R or S) or the racemic crystal, and different molecular conformations. The relative configurations of the carbonyl groups in PZQ define these conformations that produce different polymorphs. The polarity of these conformers is quite different and their relative population can vary in media with different polarity. Crystal structures of PZQ were studied by infrared and Raman spectroscopy and their spectroscopical properties were calculated by quantum mechanical methods, assigning many of their bands, and finding a good agreement with experimental data.

Adsorption of Sulfonamides on Phyllosilicate Surfaces by Molecular Modeling Calculations

Sulfamides belong to a great group of antibiotics used for decades for human therapeutics and farm livestock. This intensive use has generated an important environmental risk due to the presence of these compounds in wastewaters and soils close to worldwide farm industries. The molecular structure and physicochemical properties of these molecules are interesting for evaluating the molecular interactions with surfaces of clay minerals. These interactions are important to know the mobility of these compounds through soils and to design new nanomaterials for drug delivery. The molecular structure and conformational analysis of the sulfonamides, sulfamethoxypyridazine and sulfamethoxydiazine, as models of sulfonamides, have been studied with quantum mechanical calculations and force fields based on empirical interatomic potentials calculations. The adsorption of these drugs on a phyllosilicate surface of (001) plane has been investigated, finding that it is an exothermic process for both sulfonamides.

Atomistic Model Analysis of Buckling Behavior of Compressed Carbon Nanotubes

We carried out the atomistic structural instability (ASI) analysis with an empirical interatomic potential for carbon nanotubes (CNTs) under axial compression with the aim to reveal the mechanism of buckling. We investigated how ‘latent’ instability modes develop until one of them is activated at the structural instability. For pristine single-walled carbon nanotubes (SWCNTs), Euler-type buckling was found in relatively thin nanotubes, while buckling modes corresponding to change in the cross-sectional shape (radial buckling) were found in thick nanotubes. The crossover between the Euler-type buckling and radial buckling modes was clearly seen in the ASI analysis. While the reduction of Hessian eigenvalues in the pristine nanotubes and nanotubes with a vacancy is nearly linear until instability, rapid decrease of eigenvalues just before instability was found in models with Stone-Wales defects. This is due to localization of instability mode vectors around the defects that tends to arise before structural instability.

Atomistic simulations of screw dislocations in bcc tungsten: From core structures and static properties to interaction with vacancies

Atomistic simulations have been used to investigate the core structures, static properties of isolated 1/2 <111> screw dislocations, and their interaction with vacancies in bcc tungsten (W) based on three empirical interatomic potentials. Differential displacement maps show that only one embedded atom method potential is able to reproduce the compact non-degenerate core as evidenced by ab initio calculations. The obtained strain energy and stress distribution from atomistic simulations are, in general, consistent with elasticity theory predictions. In particular, one component of the calculated shear stress, which is not present according to elasticity theory, is non-negligible in the core region of our dislocation model. The differences between the results calculated from three interatomic potentials are in details, such as the specific value and the symmetry, but the trend of spatial distributions of static properties in the long range are close to each other. By calculating the binding energies between the dislocations and vacancies, we demonstrate that the dislocations act as vacancy sinks, which may be important for the nucleation and growth of hydrogen bubbles in W under irradiation.

Development of an empirical interatomic potential for the Ag–Ti system

Two interatomic potential mixing rules for the Ti–Ag system were investigated based on the embedded-atom method (EAM) elemental potentials. First principles calculations were performed using SIESTA for various configurations of the Ti–Ag system to see which model best fitted the ab initio results. The results showed that the surface energies, especially that of Ti, were not well fitted by either model and the surface binding energies differed from the ab initio calculations. As a result, the modified embedded-atom method (MEAM) was investigated. In contrast to the other models, surface energies for pure Ti calculated by MEAM were in good agreement with the experimental data and the ab initio results. The MEAM mixing rule was used to investigate Ag ad-atoms on Ti and Ti ad-atoms on Ag. The results showed good agreement with SIESTA after parameter optimisation.

Theoretical study for misfit dislocation formation at InAs/GaAs(001) interface

The formation of misfit dislocations (MDs) at InAs/GaAs(001) interface is theoretically investigated using empirical interatomic potentials and ab initio calculations. The calculated cohesive energy using empirical interatomic potentials demonstrate that InAs/GaAs(001) system with 5/7 MD core structure is stabilized compared with coherently grown system when the thickness of InAs wetting layer is larger than 1 monolayer (ML). This result suggests that lattice strain is relaxed by incorporating MD to proceed the growth of InAs wetting layers. The estimated critical thickness of MD formation and dislocation formation energy for InAs/GaAs(001) are 0.5 ML and 1.51eV/Å, respectively, which are favorably compared with those of InAs/GaAs(110) interface. Using the calculated results of MDs by empirical interatomic potentials and surface energies by ab initio calculations, we furthermore evaluate growth modes of InAs on GaAs(001) substrate on the basis of macroscopic theories. The estimation of free energies reveals that two-dimensional growth with MDs and Stranski-Krastanov coherent growth simultaneously appear around 0.6 ML. These results suggest that the formation MDs at InAs/GaAs(001) interface is crucial for the wetting layer growth on GaAs(001) substrate.

Molecular structure of vapor-deposited amorphous selenium

The structure of amorphous selenium is clouded with much uncertainty and contradictory results regarding the dominance of polymeric chains versus monomer rings. The analysis of the diffraction radial distribution functions are inconclusive because of the similarities between the crystalline allotropes of selenium in terms of the coordination number, bond length, bond angle, and dihedral angle. Here, we took a much different approach and probed the molecular symmetry of the thermodynamically unstable amorphous state via analysis of structural phase transformations. We verified the structure of the converted metastable and stable crystalline structures using scanning transmission electron microscopy. In addition, given that no experimental technique can tell us the exact three-dimensional atomic arrangements in glassy semiconductors, we performed molecular-dynamic simulations using a well-established empirical three-body interatomic potential. We developed a true vapor-deposited process for the deposition of selenium molecules onto a substrate using empirical molecular vapor compositions and densities. We prepared both vapor-deposited and melt-quenched samples and showed that the simulated radial distribution functions match very well to experiment. The combination of our experimental and molecular-dynamic analyses shows that the structures of vapor- and melt-quenched glassy/amorphous selenium are quite different, based primarily on rings and chains, respectively, reflecting the predominant structure of the parent phase in its thermodynamic equilibrium.

Ab initioscaling laws for the formation energy of nanosized interstitial defect clusters in iron, tungsten, and vanadium

The size limitation of ab initio calculations impedes first-principles simulations of crystal defects at nanometer sizes. Considering clusters of self-interstitial atoms as a paradigm for such crystal defects, we have developed an ab initio--accuracy model to predict formation energies of defect clusters with various geometries and sizes. Our discrete-continuum model combines the discrete nature of energetics of interstitial clusters and continuum elasticity for a crystalline solid matrix. The model is then applied to interstitial dislocation loops with $\ensuremath{\langle}100\ensuremath{\rangle}$ and $1/2\ensuremath{\langle}111\ensuremath{\rangle}$ Burgers vectors, and to C15 clusters in body-centered-cubic crystals Fe, W, and V, to determine their relative stabilities as a function of size. We find that in Fe the C15 clusters were more stable than dislocation loops if the number of self-interstitial atoms involved was fewer than 51, which corresponds to a C15 cluster with a diameter of $1.5$ nm. In V and W, the $1/2\ensuremath{\langle}111\ensuremath{\rangle}$ loops represent the most stable configurations for all defect sizes, which is at odds with predictions derived from simulations performed using some empirical interatomic potentials. Further, the formation energies predicted by the discrete-continuum model are reparametrized by a simple analytical expression giving the formation energy of self-interstitial clusters as a function of their size. The analytical scaling laws are valid over a very broad range of defect sizes, and they can be used in multiscale techniques including kinetic Monte Carlo simulations and cluster dynamics or dislocation dynamics studies.

First principles study of the C/Si ratio effect on the ideal shear strength of β–SiC

The effect of the C/Si atomic ratio on the ideal shear strength of β-SiC is investigated with first principles calculations. SiC samples with different C/Si ratios are generated by Monte Carlo (MC) simulations with empirical inter-atomic SiC potential. Each SiC sample is sheared along the direction and the stress-strain curve is calculated from first principles. The results show that the ideal shear strength of SiC decreases with the increase of C/Si ratio. For a non-stoichiometric SiC sample, a C–C bond inside a large carbon cluster breaks first under shear strain condition due to the internal strain around the carbon clusters. Because the band gap is narrowed under shear strain conditions, a local maximum stress appears in the elastic region of the stress-strain curve for each SiC sample at certain strain condition. The yield strength may increase with the increase of C/Si ratio.

Theoretical investigations of compositional inhomogeneity around threading dislocations in III–nitride semiconductor alloys

The compositional inhomogeneity of group III elements around threading dislocations in III–nitride semiconductors are theoretically investigated using empirical interatomic potentials and Monte Carlo simulations. We find that the calculated atomic arrangements around threading dislocations in Al0.3Ga0.7N and In0.2Ga0.8N depend on the lattice strain around dislocation cores. Consequently, compositional inhomogeneity arises around edge dislocation cores to release the strain induced by dislocation cores. In contrast, the compositional inhomogeneity in screw dislocation is negligible owing to relatively small strain induced by dislocation cores compared with edge dislocation. These results indicate that the strain relief around dislocation cores is decisive in determining the atomic arrangements and resultant compositional inhomogeneity around threading dislocations in III–nitride semiconductor alloys.

Systematic approach to developing empirical interatomic potentials for III–N semiconductors

A systematic approach to the derivation of empirical interatomic potentials is developed for III–N semiconductors with the aid of ab initio calculations. The parameter values of empirical potential based on bond order potential are determined by reproducing the cohesive energy differences among 3-fold coordinated hexagonal, 4-fold coordinated zinc blende, wurtzite, and 6-fold coordinated rocksalt structures in BN, AlN, GaN, and InN. The bond order p is successfully introduced as a function of the coordination number Z in the form of p = a exp(−bZn) if Z ≤ 4 and p = (4/Z)α if Z ≥ 4 in empirical interatomic potential. Moreover, the energy difference between wurtzite and zinc blende structures can be successfully evaluated by considering interaction beyond the second-nearest neighbors as a function of ionicity. This approach is feasible for developing empirical interatomic potentials applicable to a system consisting of poorly coordinated atoms at surfaces and interfaces including nanostructures.

The ReaxFF reactive force-field: development, applications and future directions

AbstractThe reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. This article provides an overview of the development, application, and future directions of the ReaxFF method.

Tersoff potential with improved accuracy for simulating graphene in molecular dynamics environment

Graphene is an elementary unit for various carbon based nanostructures. The recent technological developments have made it possible to manufacture hybrid and sandwich structures with graphene. In order to model these nanostructures in atomistic scale, a compatible interatomic potential is required to successfully model these nanostructures. In this article, an interatomic potential with modified cut-off function for Tersoff potential was proposed to avoid overestimation and also to predict the realistic mechanical behavior of single sheet of graphene. In order to validate the modified form of cut-off function for Tersoff potential, simulations were performed with different set of temperatures and strain rates, and results were made to compare with available experimental data and molecular dynamics simulation results obtained with the help of other empirical interatomic potentials.

Potential Optimization Software for Materials (POSMat)

The Potential Optimization Software for Materials package (POSMat) is presented. POSMat is a powerful tool for the optimization of classical empirical interatomic potentials for use in atomic scale simulations, of which molecular dynamics is the most ubiquitous. Descriptions of the empirical formalisms and targetable properties available are given. POSMat includes multiple tools, including schemes and strategies to aid in the optimization process. Samples of the inputs and outputs are given as well as an example for fitting an MgO Buckingham potential, which illustrates how the targeted properties can influence the results of a developed potential. Approaches and tools for the expansion of POSMat to other interatomic descriptions and optimization algorithms are described. Program summaryProgram title: POSMatCatalogue identifier: AEZP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEZP_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU GPL v3No. of lines in distributed program, including test data, etc.: 515982No. of bytes in distributed program, including test data, etc.: 12342365Distribution format: tar.gzProgramming language: Fortran2013.Computer: Linux Cluster.Operating system: Linux.Has the code been vectorized or parallelized?: Yes, via the OMPRAM: 200 MBClassification: 6.5, 4.9, 7.7, 7.8.External routines: LAPACK, DISLINNature of problem:Develops interatomic potentials for materials systems for a few select formalisms.Solution method:Iterative optimization techniques are employed to decrease error between targeted materials properties and those calculated from the current parameter set.Running time:Problem dependent. The NCOH runs take seconds, the Al runs 1 and 2 take minutes and run 3 takes approximately 2.5 hours.

Diameter Dependence of Lattice Thermal Conductivity of Single-Walled Carbon Nanotubes: Study from Ab Initio.

The effects of temperature, tube length, defects, and surface functionalization on the thermal conductivity (κ) of single-walled carbon nanotubes (SWCNTs) were well documented in literature. However, diameter dependence of thermal conductivity of SWCNTs received less attentions. So far, diverse trends of the diameter dependence have been discussed by different methods and all the previous results were based on empirical interatomic potentials. In this paper, we emphasize to clarify accurate κ values of SWCNTs with different diameters and in-plane κ of graphene. All the studies were under the framework of anharmonic lattice dynamics and Boltzmann transport equation (BTE) based on first principle calculations. We try to infer the right trend of diameter dependent thermal conductivity of SWCNTs. We infer that graphene is the limitation as SWCNT with an infinite diameter. We analyzed the thermal conductivity contributions from each phonon mode in SWCNTs to explain the trend. Meanwhile, we also identify the extremely low thermal conductivity of ultra-thin SWCNTs.