Highly optimized embedded-atom-method potentials for fourteen fcc metals

International audience

Functional molecular liquids (FMLs) based on alkylated π-conjugated molecules have attracted attention as solvent-free and nonvolatile liquid materials with prominent optoelectronic features. Recently, novel FML compounds containing pyrene as the functional core were synthesized, and their rheological and photochemical properties were investigated. Although the molecules differ only in the number of alkyl chain substituents and their substitution positions, their viscosity coefficients are largely different beyond the Stokes-Einstein relation on the assumption of identical microscopic friction, indicating that local microscopic molecular interactions are crucial for the macroscopic rheological properties. Here, we report a theoretical study on the rheological properties of the alkyl-pyrene liquids by means of atomistic molecular dynamics (MD) simulations. We performed long-time MD simulations for tens of microseconds to obtain ample statistical samples of the alkyl-pyrene liquids and analyzed their liquid structures and diffusion dynamics based on spatiotemporal correlation functions. We found the formation of characteristic local liquid structures of π-π stacking of the pyrene moieties and locally anisotropic and anomalous diffusion dynamics, which remarkably vary depending on the alkyl substituent patterns. The present results provide an atomistic insight into the macroscopic rheological properties of alkyl-π FMLs and molecular design strategy for them.

Nowadays, the nano-machining process is used to produce high quality finished surfaces with precise form accuracy. To understand and analyze the chip formation mechanism of nano-machining process on an atomistic scale, since the experimentation is not an easy task, numerical simulation such as molecular dynamic (MD) simulation is a very useful method. In this paper, MD simulation of the nano-metric cutting of single-crystal copper was performed with a single crystal diamond tool. The model was solved with both pair wise Morse potential function and embedded atom method (EAM) potential to simulate the inter-atomic force between the work-piece and a rigid tool. The chip formation mechanism, dislocation generation, tool forces and generated temperature were investigated. Results show that the Morse potential cannot perform an appropriate defect formation and plastic deformation in nano-metric cutting of metals. Also, tool forces in Morse potential are more than the forces in EAM potential. Furthermore, the fluctuations of resultant forces in Morse potential are greater than that of EAM. In addition, using many-body interaction potentials like EAM can lead to substantial changes in surface energies, elastic-plastic properties and atomic displacement, compared with the pair-wise potentials like Morse. Finally, the atomic displacement investigation shows that in EAM potential study, only the atoms in a local region near the cutting process are displaced, but in Morse potential a large portion of atoms has affected during cutting process. Subsequently, the chip temperature in EAM potential is more than that of Morse potential.

Ce is a rare earth element in the periodic table. In the range of low temperature and low pressure, there are two face-centered-cubic (FCC) phases (<i>α</i>-Ce and <i>γ</i>-Ce) and a double-hexagonal-close-packed phase (<i>β</i>-Ce) for metallic Ce. At ambient temperature and about 0.7 GPa pressure, Ce undergoes <i>γ</i>→<i>α</i> phase transition with a volume shrink of 14%–17% discontinuously. In this paper, an embedded-atom method (EAM) potential compatible for <i>α</i>-Ce and <i>γ</i>-Ce was developed. This EAM potential has been employed to study several basic properties of cerium in these two FCC phases, such as equilibrium lattice constants, cohesive energies, and elastic constants. These results showed good accordance with experiments and first principle calculations. The lattice defects have been studied with the formation energy calculations of vacancies, interstitials, surfaces, stacking faults, and twinning defects in <i>α</i>-Ce and <i>γ</i>-Ce lattice. The lattice dynamics of <i>α</i>-Ce and <i>γ</i>-Ce have been analyzed using our EAM potential. The lattice vibrational entropy was calculated and plotted as functions of temperature for each phases. The vibrational entropy change across the <i>α</i>-<i>γ</i> phase transition showed to be ~0.67 <i>k</i><sub><i>B</i></sub> per atom at ambient temperature. Using molecular dynamics simulation with our EAM potential, several isotherms and radial distribution functions were calculated. These isotherms and radial distribution functions demonstrate a first order phase transition between two FCC structures, corresponding to <i>α</i>-Ce and <i>γ</i>-Ce, with a critical point sets at <i>T</i><sub>c</sub>≈550 K and <i>P</i><sub>c</sub>≈1.21 GPa. Thus the newly developed EAM potential could provide a reasonable description of FCC Ce and its <i>α</i>-<i>γ</i> phase transition within the scale of classical molecular dynamics simulation.

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

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 atomic level study of NiTi alloy at high temperature is very important to understand the mechanism of NiTi fabrication, in partial the process during the hot working. In the atomic investigation using molecular dynamics simulation, the use of the interatomic potential greatly affects the results. Therefore, the suitability of the interatomic potential applied in some specific condition has to be examined. In our previous work, we have tested the performance of EAM and MEAM potential to reproduce the lattice constant of NiTi alloy. Our previous results have shown that the MEAM potential work better than the EAM potential. In this research, we further investigate the performance of EAM and MEAM type potential to describe the melting behavior of nickel, titanium, and NiTi alloy. We find from the current result that the accuracy of the MEAM potential is better than EAM potential in high temperature MD simulations.

Potential energy surface (PES) of pure Au and AuAu′ (Au′ represents atoms which radius is 10% larger than normal size Au, the number ratio of Au:Au′= 3:1) during glass transition have been studied by a series of molecular dynamics (MD) simulations with embedded atom method (EAM) potentials. We investigate the effect of atomic size mismatch on PES noting that the PES of Au changes obviously while atomic size mismatch increases. Firstly, we find the inherent structure energy difference between high and low temperature become larger. Secondly, the distribution of inherent energy becomes broaden and the PES becomes crude at each temperature. Thirdly, the number of negative Hessian eigenvalue reduced implying weak atom re-arrangement ability. At last, the activation energy increases more quickly with the decreased temperatures at supercooled liquid region. All changes of PES by atomic size mismatch make for the better glass forming ability.

Molecular dynamics (MD) simulations with full-dimensional potential energy surfaces (PESs) obtained from high-level ab initio calculations are frequently used to model reaction dynamics of small molecules (i.e., molecules with up to 10 atoms). Construction of full-dimensional PESs for larger molecules is, however, not feasible since the number of ab initio calculations required grows rapidly with the increase of dimension. Only a small number of coordinates are often essential for describing the reactivity of even very large systems, and reduced-dimensional PESs with these coordinates can be built for reaction dynamics studies. While analytical methods based on transition-state theory framework are well established for analyzing the reduced-dimensional PESs, MD simulation algorithms capable of generating trajectories on such surfaces are more rare. In this work, we present a new MD implementation that utilizes the relaxed reduced-dimensional PES for standard microcanonical (NVE) and canonical (NVT) MD simulations. The method is applied to the pyramidal inversion of a NH3 molecule. The results from the MD simulations on a reduced, three-dimensional PES are validated against the ab initio MD simulations, as well as MD simulations on full-dimensional PES and experimental data.

Recent experimental and first-principles simulation studies have shown that in liquid phase of ethylene glycol (EG), an equilibrium between both more prevalent gauche conformers and less probable trans conformers of EG molecule exists. Gleaning into the complexities faced during classical molecular dynamics (MD) simulations of condensed phase EG due to its conformational richness and considering the aforesaid observations, here we propose a refined force-field for EG molecule for atomistic MD studies. By employing the refined parameters, we have thoroughly investigated the structure and dynamics of pure EG liquid and its aqueous mixtures and compared the results with the available experimental data. The proposed force-field justifies the important role played by intra- and intermolecular hydrogen bonding rendered by EG molecules. The simulated X-ray scattering structure function for pure EG liquid at 298 K is found to be in excellent agreement with experimental X-ray scattering structure function which precisely confirms the ability of the proposed force-field to mimic the structure of liquid phase EG. Additionally, the accuracy of the refined force-field for the microscopic dynamics and self-diffusion coefficient of pure as well as aqueous EG were also assessed here. Temperature dependence of hydrogen bonding interactions and their dynamics reveals that with increasing temperature the intermolecular hydrogen bonds in pure ethylene glycol becomes weaker and consequently render faster dynamics. In aqueous mixture, intermolecular hydrogen bonding interaction between EG molecules tends to decrease with decrease in ethylene glycol mole fraction due to invasion of water.

Growth of single-walled gold nanotubes confined in carbon nanotubes, studied by molecular dynamics simulations

Protein dynamics is a manifestation of the complex trajectories of these biomolecules on a multidimensional rugged potential energy surface (PES) driven by thermal energy. At present, computational methods such as atomistic molecular dynamics (MD) simulations can describe thermal protein conformational changes in fully solvated environments over millisecond timescales. Despite these advances, a quantitative assessment of protein dynamics remains a complicated topic, intricately linked to issues such as sampling convergence and the identification of appropriate reaction coordinates/structural features to describe protein conformational states and motions. Here, we present the cumulative variance of atomic coordinate fluctuations (CVCF) along trajectories as an intuitive PES sensitive metric to assess both the extent of sampling and protein dynamics captured in MD simulations. We first examine the sampling problem in model one- (1D) and two-dimensional (2D) PES to demonstrate that the CVCF when traced as a function of the sampling variable (time in MD simulations) can identify local and global equilibria. Further, even far from global equilibrium, a situation representative of standard MD trajectories of proteins, the CVCF can distinguish different PES and therefore resolve the resultant protein dynamics. We demonstrate the utility of our CVCF analysis by applying it to distinguish the dynamics of structurally homologous proteins from the ubiquitin family (ubiquitin, SUMO1, SUMO2) and ubiquitin protein-protein interactions. Our CVCF analysis reveals that differential side-chain dynamics from the structured part of the protein (the conserved β-grasp fold) present distinct protein PES to distinguish ubiquitin from SUMO isoforms. Upon binding to two functionally distinct protein partners (UBCH5A and UEV), intrinsic ubiquitin dynamics changes to reflect the binding context even though the two proteins have similar binding modes, which lead to negligible (sub-angstrom scale) structural changes.

The embedded atom method (EAM), where a highly accurate empirical inter-atomic potential calculation is possible in comparison with the two-body pair potential, is used for the molecular dynamics (MD) simulation. Parameters are fitted for Al and Cu so as to reproduce the metal properties such as elastic constants (C11, C12, and C44) and single vacancy formation energy. Micro-void motion in an Al crystal is simulated using the MD simulator for the EAM and the Morse potentials. The velocity of the micro-void under the EAM potential is less than that under the Morse potential. This discrepancy results from the difference in the surface adsorption energies of these potentials. To compare the accuracy of the Morse and the EAM potentials, surface adsorption energies are calculated. The calculated surface adsorption energy for EAM potential was 90% of the ab initio calculation and the one for the Morse potential was 16%, which implies accuracy of the EAM’s energy evaluation is higher than that of the Morse potential. The grain boundary diffusion for Al has been characterized by using the MD simulation with the EAM potential. Diffusivity and activation energy for several grain boundaries are calculated for several conditions. These simulation results are effective to find a way to improve the electromigration failure.

The combination of optical-Kerr-effect (OKE) spectroscopy and molecular dynamics simulations has provided us with a newfound ability to delve into the librational dynamics of liquids, revealing, in the process, some surprising commonalities among aromatic liquids. Benzene and biphenyl, for example, have remarkably similar OKE spectra despite marked differences in their shapes, sizes, and moments of inertia--and even more chemically distinct aromatics tend to have noticeable similarities in their spectra. We explore this universality by using a molecular dynamics simulation to investigate the librational dynamics of molten biphenyl and to predict its OKE spectrum, comparing the results with our previous calculations for liquid benzene. We suggest that the impressive level of quantitative agreement between these two liquids is largely a reflection of the fact that librations in these and other aromatic liquids act as torsional oscillations with oscillator frequencies selected from the liquid's librational bands. Since these bands are centered about the librational Einstein frequencies, the quantitative similarities between the liquids are essentially reflections of the near identities of their Einstein frequencies. Why then are the Einstein frequencies themselves so insensitive to molecular details? We show that, for nearly planar molecules, mean-square torques and moments of inertia tend to scale with molecular dimensions in much the same way. We demonstrate that this near cancellation provides both a quantitative explanation of the close relationship between benzene and biphenyl and a more general perspective on the similarities seen in the ultrafast dynamics of aromatic liquids.

Molecular structure and dynamics of liquids: aqueous urea solutions