Near-field excitation exchange between motionless point atoms located near the conductive surface

NASA Astrophysics Data System (ADS)

Kuraptsev, Aleksei S.; Sokolov, Igor M.

2018-04-01

On the basis of quantum microscopic approach we study the excitation dynamics of two motionless point atoms located near the perfectly conducting mirror. We have analyzed the spontaneous decay rate of individual atoms near the mirror as well as the strength of dipole-dipole interaction between different atoms. It is shown that the spontaneous decay rate of an excited atom significantly depends on the distance from this atom to the mirror. In the case when the interatomic separation is less or comparable with the wavelength of resonant radiation, the spontaneous decay dynamics of an excited atom is described by multi-exponential law. It depends both the interatomic separation and the spatial orientation of diatomic quasimolecule.

Non-patchy strategy for inter-atomic distances from Extended X-ray Absorption Fine Structure

PubMed Central

Xu, Gu; Li, Guifang; LI, Xianya; Liang, Yi; Feng, Zhechuan

2017-01-01

Extended X-ray Absorption Fine Structure (EXAFS) has been one of the few structural probes available for crystalline, non-crystalline and even highly disordered specimens. However, the data analysis involves a patchy and tinkering process, including back-and-forth fitting and filtering, leading to ambiguous answers sometimes. Here we try to resolve this long standing problem, to extract the inter-atomic distances from the experimental data by a single step minimization, in order to replace the tedious and tinkering process. The new strategy is built firmly by the mathematical logic, and made straightforward and undeniable. The finding demonstrates that it is possible to break off from the traditional patchy model fitting, and to remove the logical confusion of a priori prediction of the structure to be matched with experimental data, making it a much more powerful technique than the existing methods. The new method is expected to benefit EXAFS users covering all disciplines. Also, it is anticipated that the current work to be the motivation and inspiration to the further efforts. PMID:28181529

VoroMQA: Assessment of protein structure quality using interatomic contact areas.

PubMed

Olechnovič, Kliment; Venclovas, Česlovas

2017-06-01

In the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge-based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue-residue or atom-atom interactions collected from experimentally determined structures. Here, we present VoroMQA (Voronoi tessellation-based Model Quality Assessment), a new method for the estimation of protein structure quality. Our method combines the idea of statistical potentials with the use of interatomic contact areas instead of distances. Contact areas, derived using Voronoi tessellation of protein structure, are used to describe and seamlessly integrate both explicit interactions between protein atoms and implicit interactions of protein atoms with solvent. VoroMQA produces scores at atomic, residue, and global levels, all in the fixed range from 0 to 1. The method was tested on the CASP data and compared to several other single-model quality assessment methods. VoroMQA showed strong performance in the recognition of the native structure and in the structural model selection tests, thus demonstrating the efficacy of interatomic contact areas in estimating protein structure quality. The software implementation of VoroMQA is freely available as a standalone application and as a web server at http://bioinformatics.lt/software/voromqa. Proteins 2017; 85:1131-1145. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

An automated method for modeling proteins on known templates using distance geometry.

PubMed

Srinivasan, S; March, C J; Sudarsanam, S

1993-02-01

We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. Starting with the sequence alignment of a family of homologous proteins, tertiary structures are modeled using the known 3D structure of one member of the family as a template. Homologous interatomic distances from the template are used as constraints. For nonhomologous regions in the model protein, the lower and the upper bounds for the interatomic distances are imposed by steric constraints and the globular dimensions of the template, respectively. Distance geometry is used to embed an ensemble of structures consistent with these distance bounds. Structures are selected from this ensemble based on minimal distance error criteria, after a penalty function optimization step. These structures are then refined using energy optimization methods. The method is tested by simulating the alpha-chain of horse hemoglobin using the alpha-chain of human hemoglobin as the template and by comparing the generated models with the crystal structure of the alpha-chain of horse hemoglobin. We also test the packing efficiency of this method by reconstructing the atomic positions of the interior side chains beyond C beta atoms of a protein domain from a known 3D structure. In both test cases, models retain the template constraints and any additionally imposed constraints while the packing of the interior residues is optimized with no short contacts or bond deformations. To demonstrate the use of this method in simulating structures of proteins with nonhomologous disulfides, we construct a model of murine interleukin (IL)-4 using the NMR structure of human IL-4 as the template. The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry.

Kinetics of homogeneous nucleation on many-component systems

NASA Technical Reports Server (NTRS)

Hirschfelder, J. O.

1974-01-01

Reiss's (1950) classical treatment of the kinetics of homogeneous nucleation in a system containing two chemical components is extended to many-component systems. The formulation is analogous to the pseudostationary-state theory of chemical reaction rates, with the free energy as a function of the composition of the embryo taking the place of the potential energy as a function of interatomic distances.

Kinetics of homogeneous nucleation in many component systems

NASA Technical Reports Server (NTRS)

Hirschfelder, J. O.

1974-01-01

Reiss's classical treatment of the kinetics of homogeneous nucleation in a system containing two chemical components is extended to many-component systems. The formulation is analogous to the pseudo-stationary state theory of chemical reaction rates with the free energy as a function of the composition of the embryo taking the place of the potential energy as a function of interatomic distances.

Geometrical eigen-subspace framework based molecular conformation representation for efficient structure recognition and comparison

NASA Astrophysics Data System (ADS)

Li, Xiao-Tian; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-04-01

We have developed an extended distance matrix approach to study the molecular geometric configuration through spectral decomposition. It is shown that the positions of all atoms in the eigen-space can be specified precisely by their eigen-coordinates, while the refined atomic eigen-subspace projection array adopted in our approach is demonstrated to be a competent invariant in structure comparison. Furthermore, a visual eigen-subspace projection function (EPF) is derived to characterize the surrounding configuration of an atom naturally. A complete set of atomic EPFs constitute an intrinsic representation of molecular conformation, based on which the interatomic EPF distance and intermolecular EPF distance can be reasonably defined. Exemplified with a few cases, the intermolecular EPF distance shows exceptional rationality and efficiency in structure recognition and comparison.

The NRL Program on Electroactive Polymers.

DTIC Science & Technology

1980-09-15

cell of a point in an aggregate involves selecting the smallest cell formed by planes perpendicularly bisecting all the point to neighbor vectors . Such...plane perpendicular to the interatomic vector is located nearer the smaller atom by bisecting the distance between the sur- faces of spheres whose...density waves (and consequent novel excitations such as solitons (6)). The physical structure as well as the chemical bonding of such polymeric

Pair-correlation function of a metastable helium Bose-Einstein condensate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zin, Pawel; Trippenbach, Marek; Gajda, Mariusz

2004-02-01

The pair-correlation function is one of the basic quantities to characterize the coherence properties of a Bose-Einstein condensate. We calculate this function in the experimentally important case of a zero temperature Bose-Einstein condensate in a metastable triplet helium state using the variational method with a pair-excitation ansatz. We compare our result with a pair-correlation function obtained for the hard-sphere potential with the same scattering length. Both functions are practically indistinguishable for distances greater than the scattering length. At smaller distances, due to interatomic interactions, the helium condensate shows strong correlations.

Resonance dispersion interaction of alkali metal atoms in Rydberg states

NASA Astrophysics Data System (ADS)

Kamenski, A. A.; Mokhnenko, S. N.; Ovsyannikov, V. D.

2017-06-01

With the use of second-order perturbation theory in the long-range interatomic interaction for the degenerate states of two Rydberg atoms we have obtained a general formula for the dependence of atomic interaction energy on the interatomic distance R in the presence of the Förster resonance. Inside of the ‘Förster sphere’ (R < RF) this dependence transforms to the formula for electric dipole interaction energy ΔEd - d = C3/R3 and for R > RF it transforms to the formula for the van der Waals interaction energy ΔEVdW = -C6/R6. The van der Waals constant C6 is represented as an expansion in terms of irreducible components which define the dependence on the interatomic axis orientation relative to the quantisation axis of projections M of the total angular momentum J. The numerical values of the irreducible components of tensor C6 were calculated for rubidium atoms in the same Rydberg states |nlJM> with large quantum numbers n. We present the calculated resonance interaction energy of two rubidium atoms in the states |43D5/2M>, whose total energy exceeds by only 8 MHz the total energy of one of the atoms in the state |45P3/2M> and of the other in the state |41F7/2M>.

Magnetism and exchange interaction of small rare-earth clusters; Tb as a representative

PubMed Central

Peters, Lars; Ghosh, Saurabh; Sanyal, Biplab; van Dijk, Chris; Bowlan, John; de Heer, Walt; Delin, Anna; Di Marco, Igor; Eriksson, Olle; Katsnelson, Mikhail I.; Johansson, Börje; Kirilyuk, Andrei

2016-01-01

Here we follow, both experimentally and theoretically, the development of magnetism in Tb clusters from the atomic limit, adding one atom at a time. The exchange interaction is, surprisingly, observed to drastically increase compared to that of bulk, and to exhibit irregular oscillations as a function of the interatomic distance. From electronic structure theory we find that the theoretical magnetic moments oscillate with cluster size in exact agreement with experimental data. Unlike the bulk, the oscillation is not caused by the RKKY mechanism. Instead, the inter-atomic exchange is shown to be driven by a competition between wave-function overlap of the 5d shell and the on-site exchange interaction, which leads to a competition between ferromagnetic double-exchange and antiferromagnetic super-exchange. This understanding opens up new ways to tune the magnetic properties of rare-earth based magnets with nano-sized building blocks. PMID:26795239

Facet-Dependent Cr(VI) Adsorption of Hematite Nanocrystals.

PubMed

Huang, Xiaopeng; Hou, Xiaojing; Song, Fahui; Zhao, Jincai; Zhang, Lizhi

2016-02-16

In this study, the adsorption process of Cr(VI) on the hematite facets was systematically investigated with synchrotron-based Cr K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy, in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, density-functional theory calculation, and surface complexation models. Structural model fitting of EXAFS spectroscopy suggested that the interatomic distances of Cr-Fe were, respectively, 3.61 Å for the chromate coordinated hematite nanoplates with exposed {001} facets, 3.60 and 3.30 Å for the chromate coordinated hematite nanorods with exposed {001} and {110} facets, which were characteristic of inner-sphere complexation. In situ ATR-FTIR spectroscopy analysis confirmed the presence of two inner-sphere surface complexes with C3ν and C2ν symmetry, while the C3ν and C2ν species were assigned to monodentate and bidentate inner-sphere surface complexes with average Cr-Fe interatomic distances of 3.60 and 3.30 Å, respectively. On the basis of these experimental and theoretical results, we concluded that HCrO4(-) as dominated Cr(VI) species was adsorbed on {001} and {110} facets in inner-sphere monodentate mononuclear and bidentate binuclear configurations, respectively. Moreover, the Cr(VI) adsorption performance of hematite facets was strongly dependent on the chromate complexes formed on the hematite facets.

Energy of the Isolated Metastable Iron-Nickel FCC Nanocluster with a Carbon Atom in the Tetragonal Interstice.

PubMed

Bondarenko, Natalya V; Nedolya, Anatoliy V

2017-12-01

The energy of the isolated iron-nickel nanocluster was calculated by molecular mechanics method using Lennard-Jones potential. The cluster included a carbon atom that drifted from an inside octahedral interstice to a tetrahedral interstice in [Formula: see text] direction and after that in <222> direction to the surface. In addition, one of 14 iron atoms was replaced by a nickel atom, the position of which was changing during simulation.The energy of the nanocluster was estimated at the different interatomic distances. As a result of simulation, the optimal interatomic distances of Fe-Ni-C nanocluster was chosen for the simulation, in which height of the potential barrier was maximal and face-centered cubic (FCC) nanocluster was the most stable.It is shown that there were three main positions of a nickel atom that significantly affected nanocluster's energy.The calculation results indicated that position of the carbon atom in the octahedral interstice was more energetically favorable than tetrahedral interstice in the case of FCC nanocluster. On the other side, the potential barrier was smaller in the direction [Formula: see text] than in the direction <022>.This indicates that there are two ways for carbon atom to drift to the surface of the nanocluster.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Path-integral simulation of ice Ih: The effect of pressure

NASA Astrophysics Data System (ADS)

Herrero, Carlos P.; Ramírez, Rafael

2011-12-01

The effect of pressure on structural and thermodynamic properties of ice Ih has been studied by means of path-integral molecular dynamics simulations at temperatures between 50 and 300 K. Interatomic interactions were modeled by using the effective q-TIP4P/F potential for flexible water. Positive (compression) and negative (tension) pressures have been considered, which allowed us to approach the limits for the mechanical stability of this solid water phase. We have studied the pressure dependence of the crystal volume, bulk modulus, interatomic distances, atomic delocalization, and kinetic energy. The spinodal point at both negative and positive pressures is derived from the vanishing of the bulk modulus. For P<0, the spinodal pressure changes from -1.38 to - 0.73 GPa in the range from 50 to 300 K. At positive pressure the spinodal is associated with ice amorphization, and at low temperatures it is found to be between 1.1 and 1.3 GPa. Quantum nuclear effects cause a reduction of the metastability region of ice Ih.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rist, J.; Miteva, T.; Gaire, B.

In this paper we present a comprehensive and detailed study of Interatomic Coulombic Decay (ICD) occurring after irradiating argon dimers with XUV-synchrotron radiation. A manifold of different decay channels is observed and the corresponding initial and final states are assigned. Additionally, the effect of nuclear dynamics on the ICD electron spectrum is examined for one specific decay channel. The internuclear distance-dependent width Γ(R) of the decay is obtained from the measured kinetic energy release distribution of the ions employing a classical nuclear dynamics model.

Frenkel pair recombinations in UO2: Importance of explicit description of polarizability in core-shell molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Devynck, Fabien; Iannuzzi, Marcella; Krack, Matthias

2012-05-01

The oxygen and uranium Frenkel pair (FP) recombination mechanisms are studied in UO2 using an empirical interatomic potential accounting for the polarizability of the ions, namely a dynamical core-shell model. The results are compared to a more conventional rigid-ion model. Both model types have been implemented into the cp2k program package and thoroughly validated. The overall picture indicates that the FP recombination mechanism is a complex process involving several phenomena. The FP recombination can happen instantaneously when the distance between the interstitial and the vacancy is small or can be thermally activated at larger separation distances. However, other criteria can prevail over the interstitial-vacancy distance. The surrounding environment of the FP defect, the mechanical stiffness of the matrix, and the orientation of the migration path are shown to be major factors acting on the FP lifetime. The core-shell and rigid-ion models provide a similar qualitative description of the FP recombination mechanism. However, the FP stabilities determined by both models significantly differ in the lower temperature range considered. Indeed, the recombination time of the oxygen and uranium FPs can be up to an order of magnitude lower in the core-shell model at T=600 K and T=1800 K, respectively. These differences highlight the importance of the explicit description of polarizability on some crucial properties such as the resistance to amorphization. This refined description of the interatomic interactions would certainly affect the description of the recrystallization process following a displacement cascade. In turn, the self-healing phase would be better accounted for in the core-shell model and the misestimate inherent to the lack of polarizability in the rigid-ion model corrected.

Interatomic potentials in condensed matter via the maximum-entropy principle

NASA Astrophysics Data System (ADS)

Carlsson, A. E.

1987-09-01

A general method is described for the calculation of interatomic potentials in condensed-matter systems by use of a maximum-entropy Ansatz for the interatomic correlation functions. The interatomic potentials are given explicitly in terms of statistical correlation functions involving the potential energy and the structure factor of a ``reference medium.'' Illustrations are given for Al-Cu alloys and a model transition metal.

Sparsity of the normal matrix in the refinement of macromolecules at atomic and subatomic resolution.

PubMed

Jelsch, C

2001-09-01

The normal matrix in the least-squares refinement of macromolecules is very sparse when the resolution reaches atomic and subatomic levels. The elements of the normal matrix, related to coordinates, thermal motion and charge-density parameters, have a global tendency to decrease rapidly with the interatomic distance between the atoms concerned. For instance, in the case of the protein crambin at 0.54 A resolution, the elements are reduced by two orders of magnitude for distances above 1.5 A. The neglect a priori of most of the normal-matrix elements according to a distance criterion represents an approximation in the refinement of macromolecules, which is particularly valid at very high resolution. The analytical expressions of the normal-matrix elements, which have been derived for the coordinates and the thermal parameters, show that the degree of matrix sparsity increases with the diffraction resolution and the size of the asymmetric unit.

Application of Powder Diffraction Methods to the Analysis of Short- and Long-Range Atomic Order in Nanocrystalline Diamond and SiC: The Concept of the Apparent Lattice Parameter (alp)

NASA Technical Reports Server (NTRS)

Palosz, B.; Grzanka, E.; Gierlotka, S.; Stelmakh, S.; Pielaszek, R.; Bismayer, U.; Weber, H.-P.; Palosz, W.

2003-01-01

Two methods of the analysis of powder diffraction patterns of diamond and SiC nanocrystals are presented: (a) examination of changes of the lattice parameters with diffraction vector Q ('apparent lattice parameter', alp) which refers to Bragg scattering, and (b), examination of changes of inter-atomic distances based on the analysis of the atomic Pair Distribution Function, PDF. Application of these methods was studied based on the theoretical diffraction patterns computed for models of nanocrystals having (i) a perfect crystal lattice, and (ii), a core-shell structure, i.e. constituting a two-phase system. The models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the shell. X-ray and neutron experimental diffraction data of nanocrystalline SiC and diamond powders of the grain diameter from 4 nm up to micrometers were used. The effects of the internal pressure and strain at the grain surface on the structure are discussed based on the experimentally determined dependence of the alp values on the Q-vector, and changes of the interatomic distances with the grain size determined experimentally by the atomic Pair Distribution Function (PDF) analysis. The experimental results lend a strong support to the concept of a two-phase, core and the surface shell structure of nanocrystalline diamond and SiC.

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

PubMed Central

Schmidt, Michael W.; Ivanic, Joseph; Ruedenberg, Klaus

2014-01-01

An analysis based on the variation principle shows that in the molecules H2+, H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation. PMID:24880263

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion.

PubMed

Schmidt, Michael W; Ivanic, Joseph; Ruedenberg, Klaus

2014-05-28

An analysis based on the variation principle shows that in the molecules H2 (+), H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.

Structural Characterization of Poorly-Crystalline Scorodite, Iron (III)-arsenate Co-precipitates and Uranium Millneutralized Raffinate Solids using X-ray Absorption Fine Structure Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, N.; Jiang, D; Cutler, J

X-ray absorption fine structure (XAFS) is used to characterize the mineralogy of the iron(III)-arsenate(V) precipitates produced during the raffinate (aqueous effluent) neutralization process at the McClean Lake uranium mill in northern Saskatchewan, Canada. To facilitate the structural characterization of the precipitated solids derived from the neutralized raffinate, a set of reference compounds were synthesized and analyzed. The reference compounds include crystalline scorodite, poorly-crystalline scorodite, iron(III)-arsenate co-precipitates obtained under different pH conditions, and arsenate-adsorbed on goethite. The poorly-crystalline scorodite (prepared at pH 4 with Fe/As = 1) has similar As local structure as that of crystalline scorodite. Both As and Femore » K-edge XAFS of poorly-crystalline scorodite yield consistent results on As-Fe (or Fe-As) shell. From As K-edge analysis the As-Fe shell has an inter-atomic distance of 3.33 {+-} 0.02 A and coordination number of 3.2; while from Fe K-edge analysis the Fe-As distance and coordination number are 3.31 {+-} 0.02 A and 3.8, respectively. These are in contrast with the typical arsenate adsorption on bidentate binuclear sites on goethite surfaces, where the As-Fe distance is 3.26 {+-} 0.03 A and coordination number is close to 2. A similar local structure identified in the poorly-crystalline scorodite is also found in co-precipitation solids (Fe(III)/As(V) = 3) when precipitated at the same pH (pH = 4): As-Fe distance 3.30 {+-} 0.03 A and coordination number 3.9; while at pH = 8 the co-precipitate has As-Fe distance of 3.27 {+-} 0.03 A and coordination number about 2, resembling more closely the adsorption case. The As local structure in the two neutralized raffinate solid series (precipitated at pH values up to 7) closely resembles that in the poorly-crystalline scorodite. All of the raffinate solids have the same As-Fe inter-atomic distance as that in the poorly-crystalline scorodite, and a systematic decrease in the As-Fe coordination is observed when pH is progressively increased; the basic poorly-crystalline scorodite structural feature remains in the raffinate solid up to pH 7.« less

Structural characterization of poorly-crystalline scorodite, iron(III)-arsenate co-precipitates and uranium mill neutralized raffinate solids using X-ray absorption fine structure spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, N; Jiang, D T; Cutler, J

X-ray absorption fine structure (XAFS) is used to characterize the mineralogy of the iron(III)-arsenate(V) precipitates produced during the raffinate (aqueous effluent) neutralization process at the McClean Lake uranium mill in northern Saskatchewan, Canada. To facilitate the structural characterization of the precipitated solids derived from the neutralized raffinate, a set of reference compounds were synthesized and analyzed. The reference compounds include crystalline scorodite, poorly-crystalline scorodite, iron(III)-arsenate co-precipitates obtained under different pH conditions, and arsenate-adsorbed on goethite. The poorly-crystalline scorodite (prepared at pH 4 with Fe/As = 1) has similar As local structure as that of crystalline scorodite. Both As and Femore » K-edge XAFS of poorly-crystalline scorodite yield consistent results on As-Fe (or Fe-As) shell. From As K-edge analysis the As-Fe shell has an inter-atomic distance of 3.33 ± 0.02 Å and coordination number of 3.2; while from Fe K-edge analysis the Fe-As distance and coordination number are 3.31 ± 0.02 Å and 3.8, respectively. These are in contrast with the typical arsenate adsorption on bidentate binuclear sites on goethite surfaces, where the As-Fe distance is 3.26 ± 0.03 Å and coordination number is close to 2. A similar local structure identified in the poorly-crystalline scorodite is also found in co-precipitation solids (Fe(III)/As(V) = 3) when precipitated at the same pH (pH = 4): As-Fe distance 3.30 ± 0.03 Å and coordination number 3.9; while at pH = 8 the co-precipitate has As-Fe distance of 3.27 ± 0.03 Å and coordination number about 2, resembling more closely the adsorption case. The As local structure in the two neutralized raffinate solid series (precipitated at pH values up to 7) closely resembles that in the poorly-crystalline scorodite. All of the raffinate solids have the same As-Fe inter-atomic distance as that in the poorly-crystalline scorodite, and a systematic decrease in the As-Fe coordination is observed when pH is progressively increased; the basic poorly-crystalline scorodite structural feature remains in the raffinate solid up to pH 7.« less

Interatomic potential at small internuclear distances. A simple formula for the screening constant

NASA Astrophysics Data System (ADS)

Zinoviev, A. N.

2017-09-01

A simple formula for estimating the screening constant has been proposed. This formula fits well experimental data on the interaction potentials. Quantitative description of the experiment for the effect of electronic screening on the nuclear synthesis reaction cross-section for the D+-D system has been obtained. A conclusion has been made that the differences between the measured cross-sections and their theoretically predicted values, which take place in more complicated cases nuclear synthesis reactions, are not caused by uncertainties in the knowledge of potentials.

Nanopowder synthesis based on electric explosion technology

NASA Astrophysics Data System (ADS)

Kryzhevich, D. S.; Zolnikov, K. P.; Korchuganov, A. V.; Psakhie, S. G.

2017-10-01

A computer simulation of the bicomponent nanoparticle formation during the electric explosion of copper and nickel wires was carried out. The calculations were performed in the framework of the molecular dynamics method using many-body potentials of interatomic interaction. As a result of an electric explosion of dissimilar metal wires, bicomponent nanoparticles having different stoichiometry and a block structure can be formed. It is possible to control the process of destruction and the structure of the formed bicomponent nanoparticles by varying the distance between the wires and the loading parameters.

Relationship between covalence and displacive phase transition temperature in RAO{sub 4} and LiAO{sub 3} (R = rare-earth element and A = Nb and Ta)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsunekawa, S.; Fukuda, T.; Kimiyama, T.

Crystal structure analyses by TOF neutron powder diffraction are performed for R TaO{sub 4} (R = rare-earth element) and the Ta-O interatomic distances are determined. The relationship between the covalency of A-O bonds (A = Nb and Ta), which show the most shortening upon phase transition, and the transition temperature is discussed for RAO{sub 4} and LiAO{sub 3}, and the parameters of Ta-O covalence are determined.

Beyond packing of hard spheres: The effects of core softness, non-additivity, intermediate-range repulsion, and many-body interactions on the glass-forming ability of bulk metallic glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Kai; Fan, Meng; Liu, Yanhui

When a liquid is cooled well below its melting temperature at a rate that exceeds the critical cooling rate R{sub c}, the crystalline state is bypassed and a metastable, amorphous glassy state forms instead. R{sub c} (or the corresponding critical casting thickness d{sub c}) characterizes the glass-forming ability (GFA) of each material. While silica is an excellent glass-former with small R{sub c} < 10{sup −2} K/s, pure metals and most alloys are typically poor glass-formers with large R{sub c} > 10{sup 10} K/s. Only in the past thirty years have bulk metallic glasses (BMGs) been identified with R{sub c} approachingmore » that for silica. Recent simulations have shown that simple, hard-sphere models are able to identify the atomic size ratio and number fraction regime where BMGs exist with critical cooling rates more than 13 orders of magnitude smaller than those for pure metals. However, there are a number of other features of interatomic potentials beyond hard-core interactions. How do these other features affect the glass-forming ability of BMGs? In this manuscript, we perform molecular dynamics simulations to determine how variations in the softness and non-additivity of the repulsive core and form of the interatomic pair potential at intermediate distances affect the GFA of binary alloys. These variations in the interatomic pair potential allow us to introduce geometric frustration and change the crystal phases that compete with glass formation. We also investigate the effect of tuning the strength of the many-body interactions from zero to the full embedded atom model on the GFA for pure metals. We then employ the full embedded atom model for binary BMGs and show that hard-core interactions play the dominant role in setting the GFA of alloys, while other features of the interatomic potential only change the GFA by one to two orders of magnitude. Despite their perturbative effect, understanding the detailed form of the intermetallic potential is important for designing BMGs with cm or greater casting thickness.« less

An atomistic fingerprint algorithm for learning ab initio molecular force fields

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions.

PubMed

Calligari, Paolo; Gerolin, Marco; Abergel, Daniel; Polimeno, Antonino

2017-01-10

In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed.

Formation of 2D nanoparticles with block structure in simultaneous electric explosion of conductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kryzhevich, Dmitrij S., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Zolnikov, Konstantin P., E-mail: kryzhev@ispms.ru, E-mail: kost@ispms.ru; Abdrashitov, Andrei V.

2014-11-14

A molecular dynamics simulation of nanoparticle formation in simultaneous electric explosion of conductors is performed. Interatomic interaction is described using potentials calculated in the framework of the embedded atom method. High-rate heating results in failure of the conductors with the formation of nanoparticles. The influence of the heating rate, temperature distribution over the specimen cross-section and the distance between simultaneously exploded conductors on the structure of formed nanoparticles is studied. The calculation results show that the electric explosion of conductors allows the formation of nanoparticles with block structure.

Hydrides of intermetallic compounds with a H/M ratio greater than unity obtained at high hydrogen pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Semenenko, K.N.; Klyamkin, S.N.

1993-11-01

Novel hydride phases with H/M > 1 based on Zr{sub 2}Pd, Hf{sub 2}Pd, and Hf{sub 2}Cu (structures of the MoSi{sub 2} type) have been synthesized at high H{sub 2} pressures. The X-ray diffraction investigations of the resulting hydrides have been carried out. Some factors determining the maximum hydrogen content in the hydrides of intermetallic compounds are discussed. A model structure of the hydrides obtained is proposed, which assumes the possibility of direct H-H interactions when the interatomic distances are less than 1 {angstrom}.

Effect of biaxial strain on the magnetism of Fe16N2: Density-functional investigations

NASA Astrophysics Data System (ADS)

Zhou, Wei; Liu, Lijuan; Wu, Ping

2014-02-01

The effect of biaxial strain on the magnetism of α″-Fe16N2 was investigated by the first principles calculations. The GGA, GGA + U and HSE06 calculations give the same result that the magnetic moments increase with the biaxial strain in the ab plane. All non-equivalent Fe atoms contribute to the increase of magnetic moments, although the variations of inter-atomic distances between non-equivalent Fe and N are different. Additionally, the magnetic anisotropy of Fe16N2 could be controlled by the biaxial strain.

Density-functional formulation of the generalized pseudopotential theory. III. Transition-metal interatomic potentials

NASA Astrophysics Data System (ADS)

Moriarty, John A.

1988-08-01

The first-principles, density-functional version of the generalized pseudopotential theory (GPT) developed in papers I and II of this series [Phys. Rev. B 16, 2537 (1977); 26, 1754 (1982)] for empty- and filled-d-band metals is here extended to pure transition metals with partially filled d bands. The present focus is on a rigorous, real-space expansion of the bulk total energy in terms of widely transferable, structure-independent interatomic potentials, including both central-force pair interactions and angular-force triplet and quadruplet interactions. To accomplish this expansion, a specialized set of starting equations is derived from the basic local-density formalism for a pure metal, including refined expansions for the exchange-correlation terms and a simplified yet accurate representation of the cohesive energy. The parent pseudo-Green's-function formalism of the GPT is then used to develop these equations in a plane-wave, localized-d-state basis. In this basis, the cohesive energy divides quite naturally into a large volume component and a smaller structural component. The volume component,which includes all one-ion intra-atomic energy contributions, already gives a good description of the cohesion in lowest order. The structural component is expanded in terms of weak interatomic matrix elements and gives rise to a multi-ion series which establishes the interatomic potentials. Special attention is focused on the dominant d-electron contributions to this series and complete formal results for the two-ion, three-ion, and four-ion d-state potentials (vd2, vd3, and vd4) are derived. In addition, a simplified model is used to demonstrate that while vd3 can be of comparable importance to vd2, vd4 is inherently small and the series is rapidly convergent beyond three-ion interactions. Analytic model forms are also derived for vd2 and vd3 in the case of canonical d bands. In this limit, vd2 is purely attractive and varies with interatomic distance as r-10, while vd3 is weak and attractive for almost empty or filled d bands and maximum in strength and repulsive for half-filled d bands. Full first-principles expressions are then developed for the total two-ion and three-ion potentials and implemented for all 20 3d and 4d transition metals. The first-principles potentials qualitatively display all of the trends predicted by the model results, but they also reflect additional effects, including long-range hybridization tails which must be suitably screened in real-space calculations. Finally, illustrative application of the first-principles potentials is made to the calculation of the [100] phonon spectrum for V and Cr, where the importance of three-ion angular forces is explicitly demonstrated.

Stress-induced crystal transition of poly(butylene succinate) studied by terahertz and low-frequency Raman spectroscopy and quantum chemical calculation

NASA Astrophysics Data System (ADS)

Tatsuoka, Seika; Sato, Harumi

2018-05-01

We measured terahertz (THz) and low-frequency Raman spectra of Poly (butylene succinate) (PBS) which shows the crystal transition from α to β by stretching. For the assignment of the absorption peaks in the low-frequency region, we performed quantum chemical calculations with Cartesian-coordinate tensor transfer (CCT) method. Four major peaks appeared in the THz spectra of PBS at around 58, 76, 90, and 100 cm-1, and in the low-frequency Raman spectra a peak was observed at 88 cm-1. The THz peak at 100 cm-1 and the Raman peak at 88 cm-1 show a shift to a lower wavenumber region with increasing temperature. The quantum chemical calculation of β crystal form reveals the new peak appears above 100 cm-1. It was found that two kinds of peaks overlapped at around 100 cm-1 in the THz spectra of PBS. One of them can be assigned to a weak hydrogen bond between the C=O and CH2 groups in the intermolecular chains, which is perpendicular to the molecular chain of the α crystal form. Another one showed a parallel polarization which can be assigned to the intramolecular interaction between O (ether) and H-C groups in the β crystal form. The position of the peak at around 100 cm-1 in the perpendicular polarization changed to a lower wavenumber region with stretching, because of the weakening of the intermolecular hydrogen bonding by increasing the interatomic distances. On the other hand, that of the parallel polarization shifts to a higher wavenumber region because of the shortening of the interatomic distance from α to β crystal form (the strength of the intramolecular hydrogen bonding became stronger) by stretching.

Hydrogen bonds in concreto and in computro

NASA Astrophysics Data System (ADS)

Stouten, Pieter F. W.; Kroon, Jan

1988-07-01

Molecular dynamics simulations of liquid water and liquid methanol have been carried out. For both liquids an effective pair potential was used. The models were fitted to the heat of vaporization, pressure and various radial distribution functions resulting from diffraction experiments on liquids. In both simulations 216 molecules were put in a cubic periodical ☐. The system was loosely coupled to a temperature bath and to a pressure bath. Following an initial equilibration period relevant data were sampled during 15 ps. The distributions of oxygen—oxygen distances in hydrogen bonds obtained from the two simulations are essentially the same. The distribution obtained from crystal data is somewhat different: the maximum has about the same position, but the curve is much narrower, which can be expected merely from the fact that diffraction experiments only supply average atomic positions and hence average interatomic distances. When thermal motion is taken into account a closer likeness is observed.

Universal aspects of brittle fracture, adhesion, and atomic force microscopy

NASA Technical Reports Server (NTRS)

Banerjea, Amitava; Ferrante, John; Smith, John R.

1989-01-01

This universal relation between binding energy and interatomic separation was originally discovered for adhesion at bimetallic interfaces involving the simple metals Al, Zn, Mg, and Na. It is shown here that the same universal relation extends to adhesion at transition-metal interfaces. Adhesive energies have been computed for the low-index interfaces of Al, Ni, Cu, Ag, Fe, and W, using the equivalent-crystal theory (ECT) and keeping the atoms in each semiinfinite slab fixed rigidly in their equilibrium positions. These adhesive energy curves can be scaled onto each other and onto the universal adhesion curve. The effect of tip shape on the adhesive forces in the atomic-force microscope (AFM) is studied by computing energies and forces using the ECT. While the details of the energy-distance and force-distance curves are sensitive to tip shape, all of these curves can be scaled onto the universal adhesion curve.

Transition State Geometry Measurements from 13C Isotope Effects. The Experimental Transition State for the Epoxidation of Alkenes with Oxaziridines

PubMed Central

Hirschi, Jennifer S.; Takeya, Tetsuya; Hang, Chao; Singleton, Daniel A.

2009-01-01

We suggest here and evaluate a methodology for the measurement of specific interatomic distances from a combination of theoretical calculations and experimentally measured 13C kinetic isotope effects. This process takes advantage of a broad diversity of transition structures available for the epoxidation of 2-methyl-2-butene with oxaziridines. From the isotope effects calculated for these transition structures, a theory-independent relationship between the C-O bond distances of the newly forming bonds and the isotope effects is established. Within the precision of the measurement, this relationship in combination with the experimental isotope effects provides a highly accurate picture of the C-O bonds forming at the transition state. The diversity of transition structures also allows an evaluation of the Schramm process for defining transition state geometries based on calculations at non-stationary points, and the methodology is found to be reasonably accurate. PMID:19146405

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-06-01

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-06-28

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Lattice Stability and Interatomic Potential of Non-equilibrium Warm Dense Gold

NASA Astrophysics Data System (ADS)

Chen, Z.; Mo, M.; Soulard, L.; Recoules, V.; Hering, P.; Tsui, Y. Y.; Ng, A.; Glenzer, S. H.

2017-10-01

Interatomic potential is central to the calculation and understanding of the properties of matter. A manifestation of interatomic potential is lattice stability in the solid-liquid transition. Recently, we have used frequency domain interferometry (FDI) to study the disassembly of ultrafast laser heated warm dense gold nanofoils. The FDI measurement is implemented by a spatial chirped single-shot technique. The disassembly of the sample is characterized by the change in phase shift of the reflected probe resulted from hydrodynamic expansion. The experimental data is compared with the results of two-temperature molecular dynamic simulations based on a highly optimized embedded-atom-method (EAM) interatomic potential. Good agreement is found for absorbed energy densities of 0.9 to 4.3MJ/kg. This provides the first demonstration of the applicability of an EAM interatomic potential in the non-equilibrium warm dense matter regime. The MD simulations also reveal the critical role of pressure waves in solid-liquid transition in ultrafast laser heated nanofoils. This work is supported by DOE Office of Science, Fusion Energy Science under FWP 100182, and SLAC LDRD program.

Origin of Noncubic Scaling Law in Disordered Granular Packing.

PubMed

Xia, Chengjie; Li, Jindong; Kou, Binquan; Cao, Yixin; Li, Zhifeng; Xiao, Xianghui; Fu, Yanan; Xiao, Tiqiao; Hong, Liang; Zhang, Jie; Kob, Walter; Wang, Yujie

2017-06-09

Recent diffraction experiments on metallic glasses have unveiled an unexpected noncubic scaling law between density and average interatomic distance, which led to the speculation of the presence of fractal glass order. Using x-ray tomography we identify here a similar noncubic scaling law in disordered granular packing of spherical particles. We find that the scaling law is directly related to the contact neighbors within the first nearest neighbor shell, and, therefore, is closely connected to the phenomenon of jamming. The seemingly universal scaling exponent around 2.5 arises due to the isostatic condition with a contact number around 6, and we argue that the exponent should not be universal.

Consecutive magnetic phase diagram of UCoGe-URhGe-UIrGe system

NASA Astrophysics Data System (ADS)

Pospíšil, Jiří; Haga, Yoshinori; Miyake, Atsushi; Kambe, Shinsaku; Tateiwa, Naoyuki; Tokunaga, Yo; Honda, Fuminori; Nakamura, Ai; Homma, Yoshiya; Tokunaga, Masashi; Aoki, Dai; Yamamoto, Etsuji

2018-05-01

We prepared single crystals in UCo1-xRhxGe and UIr1-xRhxGe systems to establish a complex dU-U-T (dU-U is the shortest interatomic uranium distance and T is temperature) magnetic phase diagram. This recognized a characteristic maximum in magnetic susceptibility at temperature Tmax along the b axis as an important parameter. Three magnetically ordered regions can be distinguished within this scope; first a ferromagnetic region with Curie temperature

Ab Initio Potential Energy Surface for H-H2

NASA Technical Reports Server (NTRS)

Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

1993-01-01

Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

Local structure of NiPd solid solution alloys and its response to ion irradiation

DOE PAGES

Zhang, Fuxiang; Ullah, Mohammad Wali; Zhao, Shijun; ...

2018-04-27

The local structure of Ni$-$Pd solid solution alloys with compositions of Ni 80Pd 20 and Ni 50Pd 50 was investigated with anomalous X-ray diffraction, X-ray absorption and theoretical calculation/simulation. The fcc lattice is distorted for both alloys, and the Pd$-$Pd atomic pair distance is +4.4% and +1.4% larger than ideal values in Ni 80Pd 20 and Ni 50Pd 50 alloys, respectively. The corresponding atomic pair distance of Ni$-$Ni is -1.8% and -3.0% less than the ideal values. Different short-range orders in the alloys were quantitatively identified at the atomic level. In Ni 80Pd 20, Pd atoms are likely to formmore » Pd$-$Pd pairs, while Pd atoms are connected with Pd atoms in the second shell in the equiatomic solid solution alloy. Upon ion irradiation, little change of interatomic distance, but modification of chemical short-range order was observed. The number of Pd$-$Pd pairs decreases to the lowest value at 0.1 dpa, and further irradiation make it increase.« less

Local structure of NiPd solid solution alloys and its response to ion irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Fuxiang; Ullah, Mohammad Wali; Zhao, Shijun

The local structure of Ni$-$Pd solid solution alloys with compositions of Ni 80Pd 20 and Ni 50Pd 50 was investigated with anomalous X-ray diffraction, X-ray absorption and theoretical calculation/simulation. The fcc lattice is distorted for both alloys, and the Pd$-$Pd atomic pair distance is +4.4% and +1.4% larger than ideal values in Ni 80Pd 20 and Ni 50Pd 50 alloys, respectively. The corresponding atomic pair distance of Ni$-$Ni is -1.8% and -3.0% less than the ideal values. Different short-range orders in the alloys were quantitatively identified at the atomic level. In Ni 80Pd 20, Pd atoms are likely to formmore » Pd$-$Pd pairs, while Pd atoms are connected with Pd atoms in the second shell in the equiatomic solid solution alloy. Upon ion irradiation, little change of interatomic distance, but modification of chemical short-range order was observed. The number of Pd$-$Pd pairs decreases to the lowest value at 0.1 dpa, and further irradiation make it increase.« less

Size-dependent characterization of embedded Ge nanocrystals: Structural and thermal properties

NASA Astrophysics Data System (ADS)

Araujo, L. L.; Giulian, R.; Sprouster, D. J.; Schnohr, C. S.; Llewellyn, D. J.; Kluth, P.; Cookson, D. J.; Foran, G. J.; Ridgway, M. C.

2008-09-01

A combination of conventional and synchrotron-based techniques has been used to characterize the size-dependent structural and thermal properties of Ge nanocrystals (NCs) embedded in a silica (a-SiO2) matrix. Ge NC size distributions with four different diameters ranging from 4.0 to 9.0 nm were produced by ion implantation and thermal annealing as characterized with small-angle x-ray scattering and transmission electron microscopy. The NCs were well represented by the superposition of bulklike crystalline and amorphous environments, suggesting the formation of an amorphous layer separating the crystalline NC core and the a-SiO2 matrix. The amorphous fraction was quantified with x-ray-absorption near-edge spectroscopy and increased as the NC diameter decreased, consistent with the increase in surface-to-volume ratio. The structural parameters of the first three nearest-neighbor shells were determined with extended x-ray-absorption fine-structure (EXAFS) spectroscopy and evolved linearly with inverse NC diameter. Specifically, increases in total disorder, interatomic distance, and the asymmetry in the distribution of distances were observed as the NC size decreased, demonstrating that finite-size effects govern the structural properties of embedded Ge NCs. Temperature-dependent EXAFS measurements in the range of 15-300 K were employed to probe the mean vibrational frequency and the variation of the interatomic distance distribution (mean value, variance, and asymmetry) with temperature for all NC distributions. A clear trend of increased stiffness (higher vibrational frequency) and decreased thermal expansion with decreasing NC size was evident, confirming the close relationship between the variation of structural and thermal/vibrational properties with size for embedded Ge NCs. The increase in surface-to-volume ratio and the presence of an amorphous Ge layer separating the matrix and crystalline NC core are identified as the main factors responsible for the observed behavior, with the surrounding a-SiO2 matrix also contributing to a lesser extent. Such results are compared to previous reports and discussed in terms of the influence of the surface-to-volume ratio in objects of nanometer dimensions.

OpenKIM - Building a Knowledgebase of Interatomic Models

NASA Astrophysics Data System (ADS)

Bierbaum, Matthew; Tadmor, Ellad; Elliott, Ryan; Wennblom, Trevor; Alemi, Alexander; Chen, Yan-Jiun; Karls, Daniel; Ludvik, Adam; Sethna, James

2014-03-01

The Knowledgebase of Interatomic Models (KIM) is an effort by the computational materials community to provide a standard interface for the development, characterization, and use of interatomic potentials. The KIM project has developed an API between simulation codes and interatomic models written in several different languages including C, Fortran, and Python. This interface is already supported in popular simulation environments such as LAMMPS and ASE, giving quick access to over a hundred compatible potentials that have been contributed so far. To compare and characterize models, we have developed a computational processing pipeline which automatically runs a series of tests for each model in the system, such as phonon dispersion relations and elastic constant calculations. To view the data from these tests, we created a rich set of interactive visualization tools located online. Finally, we created a Web repository to store and share these potentials, tests, and visualizations which can be found at https://openkim.org along with futher information.

Origin of Noncubic Scaling Law in Disordered Granular Packing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Chengjie; Li, Jindong; Kou, Binquan

Recent diffraction experiments on metallic glasses have unveiled an unexpected non-cubic scaling law between density and average interatomic distance, which lead to the speculations on the presence of fractal glass order. Using X-ray tomography we identify here a similar non-cubic scaling law in disordered granular packing of spherical particles. We find that the scaling law is directly related to the contact neighbors within first nearest neighbor shell, and therefore is closely connected to the phenomenon of jamming. The seemingly universal scaling exponent around 2.5 arises due to the isostatic condition with contact number around 6, and we argue that themore » exponent should not be universal.« less

The structural properties of PbF2 by molecular dynamics

NASA Astrophysics Data System (ADS)

Chergui, Y.; Nehaoua, N.; Telghemti, B.; Guemid, S.; Deraddji, N. E.; Belkhir, H.; Mekki, D. E.

2010-08-01

This work presents the use of molecular dynamics (MD) and the code of Dl_Poly, in order to study the structure of fluoride glass after melting and quenching. We are realized the processing phase liquid-phase, simulating rapid quenching at different speeds to see the effect of quenching rate on the operation of the devitrification. This technique of simulation has become a powerful tool for investigating the microscopic behaviour of matter as well as for calculating macroscopic observable quantities. As basic results, we calculated the interatomic distance, angles and statistics, which help us to know the geometric form and the structure of PbF2. These results are in experimental agreement to those reported in literature.

Correlation Functions and Glass Structure

NASA Astrophysics Data System (ADS)

Chergui, Y.; Nehaoua, N.; Telghemti, B.; Guemid, S.; Deraddji, N. E.; Belkhir, H.; Mekki, D. E.

2011-04-01

This work presents the use of molecular dynamics (MD) and the code of Dl Poly, in order to study the structure of fluoride glass after melting and quenching. We are realized the processing phase liquid-phase, simulating rapid quenching at different speeds to see the effect of quenching rate on the operation of the devitrification. This technique of simulation has become a powerful tool for investigating the microscopic behaviour of matter as well as for calculating macroscopic observable quantities. As basic results, we calculated the interatomic distance, angles and statistics, which help us to know the geometric form and the structure of PbF2. These results are in experimental agreement to those reported in literature.

Diatomic interhalogens - Systematics and implications of spectroscopic interatomic potentials and curve crossings

NASA Technical Reports Server (NTRS)

Child, M. S.; Bernstein, R. B.

1973-01-01

Spectroscopically derived potential curves for the low-lying excited states of homonuclear and heteronuclear diatomic interhalogens are systematized by the spin-orbit state of their dissociation products. The implications of spectroscopic interatomic potentials and curve crossings are discussed.

MEAM interatomic force calculation subroutine for LAMMPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stukowski, A.

2010-10-25

Interatomic force and energy calculation subroutine tobe used with the molecular dynamics simulation code LAMMPS (Ref a.). The code evaluates the total energy and atomic forces (energy gradient) according to cubic spine-based variant (Ref b.) of the Modified Embedded Atom Method (MEAM).

Effect of oxygen impurities on properties of the ternary superconductor SnMo/sub 6/S/sub 8/: Extended x-ray-absorption fine-structure determination of bond distances and local-density cluster calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guenzburger, D.; Ellis, D.E.; Montano, P.A.

1985-10-01

Electronic structure calculations were performed for clusters representing the Chevrel-phase SnMo/sub 6/S/sub 8/, with and without oxygen doping. In order to obtain the local structure around the Sn atom, extended x-ray-absorption fine-structure (EXAFS) measurements were made with synchro- tron radiation. The interatomic distances obtained experimentally were used in the calculations. The effect of oxygen doping on the Moessbauer isomer shift and quadrupole splitting values of /sup 119/Sn was investigated theoretically and compared with reported experimental values. The effect of oxygen substitution on the density of states at the Fermi energy of the (Mo/sub 6/S/sub 8/)/sup 2 -/ cluster was alsomore » studied. The results suggest that oxygen doping does not alter significantly the electronic structure of SnMo/sub 6/S/sub 8/.« less

Conformational analysis of a quinolonic ribonucleoside with anti-HSV-1 activity

NASA Astrophysics Data System (ADS)

Yoneda, Julliane D.; Velloso, Marcia Helena R.; Leal, Kátia Z.; Azeredo, Rodrigo B. de V.; Sugiura, Makiko; Albuquerque, Magaly G.; Santos, Fernanda da C.; Souza, Maria Cecília B. V. de; Cunha, Anna Claudia; Seidl, Peter R.; Alencastro, Ricardo B. de; Ferreira, Vitor F.

2011-01-01

The infections caused by the Herpes Simplex Virus are one of the most common sources of diseases in adults and several natural nucleoside analogues are currently used in the treatment of these infections. In vitro tests of a series of quinolonic ribonucleosides derivatives synthesized by part of our group indicated that some of them have antiviral activity against HSV-1. The conformational analysis of bioactive compounds is extremely important in order to better understand their chemical structures and biological activity. In this work, we have carried out a nuclear relaxation NMR study of 6-Me ribonucleoside derivative in order to determine if the syn or anti conformation is preferential. The NMR analysis permits the determination of inter-atomic distances by using techniques which are based on nuclear relaxation and related phenomena. Those techniques are non-selective longitudinal or spin-lattice relaxation rates and NULL pulse sequence, which allow the determination of distances between pairs of hydrogen atoms. The results of NMR studies were compared with those obtained by molecular modeling.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eremin, N. N., E-mail: neremin@geol.msu.ru; Grechanovsky, A. E.; Marchenko, E. I.

Semi-empirical and ab initio theoretical investigation of crystal structure geometry, interatomic distances, phase densities and elastic properties for some CaAl{sub 2}O{sub 4} phases under pressures up to 200 GPa was performed. Two independent simulation methods predicted the appearance of a still unknown super-dense CaAl{sub 2}O{sub 4} modification. In this structure, the Al coordination polyhedron might be described as distorted one with seven vertices. Ca atoms were situated inside polyhedra with ten vertices and Ca–O distances from 1.96 to 2.49 Å. It became the densest modification under pressures of 170 GPa (density functional theory prediction) or 150 GPa (semi-empirical prediction). Bothmore » approaches indicated that this super-dense CaAl{sub 2}O{sub 4} modification with a “stuffed α-PbO{sub 2}” type structure could be a probable candidate for mutual accumulation of Ca and Al in the lower mantle. The existence of this phase can be verified experimentally using high pressure techniques.« less

Parallel algorithms for the molecular conformation problem

NASA Astrophysics Data System (ADS)

Rajan, Kumar

Given a set of objects, and some of the pairwise distances between them, the problem of identifying the positions of the objects in the Euclidean space is referred to as the molecular conformation problem. This problem is known to be computationally difficult. One of the most important applications of this problem is the determination of the structure of molecules. In the case of molecular structure determination, usually only the lower and upper bounds on some of the interatomic distances are available. The process of obtaining a tighter set of bounds between all pairs of atoms, using the available interatomic distance bounds is referred to as bound-smoothing . One method for bound-smoothing is to use the limits imposed by the triangle inequality. The distance bounds so obtained can often be tightened further by applying the tetrangle inequality---the limits imposed on the six pairwise distances among a set of four atoms (instead of three for the triangle inequalities). The tetrangle inequality is expressed by the Cayley-Menger determinants. The sequential tetrangle-inequality bound-smoothing algorithm considers a quadruple of atoms at a time, and tightens the bounds on each of its six distances. The sequential algorithm is computationally expensive, and its application is limited to molecules with up to a few hundred atoms. Here, we conduct an experimental study of tetrangle-inequality bound-smoothing and reduce the sequential time by identifying the most computationally expensive portions of the process. We also present a simple criterion to determine which of the quadruples of atoms are likely to be tightened the most by tetrangle-inequality bound-smoothing. This test could be used to enhance the applicability of this process to large molecules. We map the problem of parallelizing tetrangle-inequality bound-smoothing to that of generating disjoint packing designs of a certain kind. We map this, in turn, to a regular-graph coloring problem, and present a simple, parallel algorithm for tetrangle-inequality bound-smoothing. We implement the parallel algorithm on the Intel Paragon X/PS, and apply it to real-life molecules. Our results show that with this parallel algorithm, tetrangle inequality can be applied to large molecules in a reasonable amount of time. We extend the regular graph to represent more general packing designs, and present a coloring algorithm for this graph. This can be used to generate constant-weight binary codes in parallel. Once a tighter set of distance bounds is obtained, the molecular conformation problem is usually formulated as a non-linear optimization problem, and a global optimization algorithm is then used to solve the problem. Here we present a parallel, deterministic algorithm for the optimization problem based on Interval Analysis. We implement our algorithm, using dynamic load balancing, on a network of Sun Ultra-Sparc workstations. Our experience with this algorithm shows that its application is limited to small instances of the molecular conformation problem, where the number of measured, pairwise distances is close to the maximum value. However, since the interval method eliminates a substantial portion of the initial search space very quickly, it can be used to prune the search space before any of the more efficient, nondeterministic methods can be applied.

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

NASA Astrophysics Data System (ADS)

Ito, Tomonori; Akiyama, Toru; Nakamura, Kohji

2016-05-01

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.

Electronic interaction anisotropy between open-shell lanthanide atoms and helium from cold collision experiment

NASA Astrophysics Data System (ADS)

Krems, R. V.; Buchachenko, A. A.

2005-09-01

Based on measurements of the Zeeman relaxation in a cold gas of He3 [C. I. Hancox, S. C. Doret, M. I. Hummon, L. Luo, and J. M. Doyle, Nature (London) 431, 281 (2004)], we show that the electronic interaction anisotropy between rare-earth atoms with nonzero electronic orbital angular momenta and helium is extremely small. The interaction of the rare-earth atoms with He gives rise to several adiabatic potentials with different electronic symmetries. It is demonstrated that the energy splitting between these potentials does not exceed 0.09cm-1 at interatomic distances larger than the turning point for collisions at 0.8K, including the region of the van der Waals interaction minima.

Probing quantum effects in lithium

NASA Astrophysics Data System (ADS)

Deemyad, Shanti; Zhang, Rong

2018-05-01

In periodic table lithium is the first element immediately after helium and the lightest metal. While fascinating quantum nature of condensed helium is suppressed at high densities, lithium is expected to adapt more quantum solid behavior under compression. This is due to the presence of long range interactions in metallic systems for which an increase in the de-Boer parameter (λ/σ, where σ is the minimum interatomic distance and λ is the de-Broglie wavelength) is predicted at higher densities [1,2]. Physics of dense lithium offers a rich playground to look for new emergent quantum phenomena in condensed matter and has been subject of many theoretical and experimental investigations. In this article recent progress in studying the quantum nature of dense lithium will be discussed.

The structure of K3C60 and the mechanism of superconductivity.

PubMed Central

Pauling, L

1991-01-01

Analysis of the interatomic distances in the superconducting substance K3C60 indicates that each of the K atoms in tetrahedral interstices between C60 spheres accepts three electrons from C60, thus becoming quadricovalent; its four bonds resonate among the 24 adjacent carbon atoms to give a strong framework in which the negative charges are localized on these K atoms. The electric current is carried by the motion of positive charges (holes) through the network of C60 spheres and the K atoms in octahedral holes. Superconductivity is favored by the localization of the negative charges on the tetrahedral K atoms and their noninvolvement in valence-bond resonance, decreasing the rate of mutual extinction of electrons and holes. PMID:11607222

Crystal structure and chemical bonding in the mixed anion compound BaSF.

PubMed

Driss, D; Cadars, S; Deniard, P; Mevellec, J-Y; Corraze, B; Janod, E; Cario, L

2017-11-28

BaSF was synthesised by a solid state reaction at high temperature and its crystal structure was determined thanks to X-ray diffraction on a single crystal. This transparent yellow fluorochalcogenide has an intergrowth structure built from the stacking of fluorite type layers and sulfur layers. In BaSF sulfur atoms form dimers with interatomic distances as short as 2.1074(10) Å. DFT calculations confirm that this compound is a band insulator with the Fermi level lying in between the antibonding π* and σ* molecular orbitals of the sulfur dimers. Reflectance measurements show that the optical band gap of BaSF is about 2.7 eV in good agreement with the value found from DFT calculations.

Inelastic X-ray Scattering Studies of Plasmons in Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Upton, M. H.; Klie, R. F.; Hill, J. P.; Gog, T.; Casa, D.; Ku, W.; Zhu, Y.; Sfeir, M. Y.; Misewich, J.; Eres, G.; Lowndes, D.

2007-03-01

We investigate the physical parameters controlling the low energy screening in carbon nanotubes via electron energy loss spectroscopy and inelastic x-ray scattering. Two plasmon-like features are observed, one near 9 eV (the so- called π plasmon) and one near 20 eV (the so-called π+σ plasmon). At large nanotube diameters, the π+σ plasmon energies depend exclusively on the number of walls and not on the radius or chiral vector. This shift indicates a change of strength of screening and the effective interaction at inter-atomic distance, and thus suggests an alternative mechanism of tuning the properties of the nanotube in addition to the well-known control provided by chirality and tube diameter.

Saturation and negative temperature coefficient of electrical resistivity in liquid iron-sulfur alloys at high densities from first-principles calculations

NASA Astrophysics Data System (ADS)

Wagle, Fabian; Steinle-Neumann, Gerd; de Koker, Nico

2018-03-01

We report results on electronic transport properties of liquid Fe-S alloys at conditions of planetary cores, computed using first-principle techniques in the Kubo-Greenwood formalism. We describe a combined effect of resistivity saturation due to temperature, compression, and chemistry by comparing the electron mean free path from the Drude response of optical conductivity to the mean interatomic distance. At high compression and high sulfur concentration the Ioffe-Regel condition is satisfied, and the temperature coefficient of resistivity changes sign from positive to negative. We show that this happens due to a decrease in the d density of states at the Fermi level in response to thermal broadening.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grochola, A.; Kowalczyk, P.; Szczepkowski, J.

Comprehensive spectroscopic studies of hot and ultracold samples of NaCs molecules were combined to complete the investigation of the (3){Omega}=1 <- X {sup 1}{Sigma}{sup +} transition for the NaCs molecule. Polarization labeling, photoassociation, and pulsed laser depletion spectroscopy were used to collect data on rovibrational levels of the (3){Omega}=1 state [here described as the c {sup 3}{Sigma}{sup +} state in Hund's case (a) notation]. The highest observed level was v=72 located {approx}5 GHz below the atomic asymptote Na(3 {sup 2}S{sub 1/2}) + Cs(6 {sup 2}P{sub 3/2}). Approximately 1400 levels were used to construct the potential energy curve of the (3){Omega}=1more » state for the full range of interatomic distances.« less

Attainment of 40.5 pm spatial resolution using 300 kV scanning transmission electron microscope equipped with fifth-order aberration corrector.

PubMed

Morishita, Shigeyuki; Ishikawa, Ryo; Kohno, Yuji; Sawada, Hidetaka; Shibata, Naoya; Ikuhara, Yuichi

2018-02-01

The achievement of a fine electron probe for high-resolution imaging in scanning transmission electron microscopy requires technological developments, especially in electron optics. For this purpose, we developed a microscope with a fifth-order aberration corrector that operates at 300 kV. The contrast flat region in an experimental Ronchigram, which indicates the aberration-free angle, was expanded to 70 mrad. By using a probe with convergence angle of 40 mrad in the scanning transmission electron microscope at 300 kV, we attained the spatial resolution of 40.5 pm, which is the projected interatomic distance between Ga-Ga atomic columns of GaN observed along [212] direction.

MOLECULAR DYNAMICS OF CASCADES OVERLAP IN TUNGSTEN WITH 20-KEV PRIMARY KNOCK-ON ATOMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Nandipati, Giridhar; Roche, Kenneth J.

2015-04-16

Molecular dynamics simulations are performed to investigate the mutual influence of two subsequent cascades in tungsten. The influence is studied using 20-keV primary knock-on atoms, to induce one cascade after another separated by 15 ps, in a lattice temperature of 1025 K (i.e. 0.25 of the melting temperature of the interatomic potential). The center of mass of the vacancies at the peak damage during the cascade is taken as the location of the cascade. The distance between this location to that of the next cascade is taken as the overlap parameter. Empirical fits describing the number of surviving vacancies andmore » interstitial atoms as a function of overlap are presented.« less

Supramolecular assembly in the epiisopiloturine hydrochloride salt

NASA Astrophysics Data System (ADS)

Mafud, Ana Carolina; Reinheimer, Eric W.; Lima, Filipe Camargo Dalmatti Alves; Batista, Larissa Fernandes; de Paula, Karina; Véras, Leiz Maria Costa; de Souza de Almeida Leite, José Roberto; Venancio, Tiago; Mascarenhas, Yvonne Primerano

2017-05-01

Epiisopiloturine hydrochloride (Epi-HCl) salt was synthetized from epiisopiloturine, an in vivo anthelmintic compound against Schistosoma mansoni worms. Despite there being no acute toxicity in mammalian cells, the compound's water insolubility makes its administration difficult. In this communication, we report the characterization of Epi-HCl its features by spectroscopy, thermal analysis, and PXRD. The single crystals suitable to X-ray diffraction were grown by slow evaporation technique. To better understand the nature of Epi-HCl' solid state, SS-NMR was also used. The salt's intramolecular structure was maintained via cation-pi intramolecular interactions, which in conjunction with hydrogen bonding, gives rise to an extended supramolecular assembly. The interatomic distances within the cations and environment around the chloride anion vary as function of temperature, suggesting a packing relaxation.

Crystal structure of simple metals at high pressures

NASA Astrophysics Data System (ADS)

Degtyareva, Olga

2010-09-01

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structures found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.

Development of an inter-atomic potential for the Pd-H binary system.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zimmerman, Jonathan A.; Hoyt, Jeffrey John; Leonard, Francois Leonard

2007-09-01

Ongoing research at Sandia National Laboratories has been in the area of developing models and simulation methods that can be used to uncover and illuminate the material defects created during He bubble growth in aging bulk metal tritides. Previous efforts have used molecular dynamics calculations to examine the physical mechanisms by which growing He bubbles in a Pd metal lattice create material defects. However, these efforts focused only on the growth of He bubbles in pure Pd and not on bubble growth in the material of interest, palladium tritide (PdT), or its non-radioactive isotope palladium hydride (PdH). The reason formore » this is that existing inter-atomic potentials do not adequately describe the thermodynamics of the Pd-H system, which includes a miscibility gap that leads to phase separation of the dilute (alpha) and concentrated (beta) alloys of H in Pd at room temperature. This document will report the results of research to either find or develop inter-atomic potentials for the Pd-H and Pd-T systems, including our efforts to use experimental data and density functional theory calculations to create an inter-atomic potential for this unique metal alloy system.« less

Study of interatomic interactions and phonons in magnesium chalcogenides

NASA Astrophysics Data System (ADS)

Gupta, Yuhit; Sinha, M. M.

2018-05-01

Alkaline earth chalcogenides (AECs) are very important compounds because of these possess semiconducting properties besides having large band gap mostly of the order of 7-10 eV which is the characteristic properties of insulators. These compounds are having many important optoelectronic properties, which serves its role in the production of many electronic devices. These are found in many crystallographic phases such as rock salt (B1), zinc blende (B3), wurtzite (B5) and nickel arsenide (B8) phase. A de-Launay angular force (DAF) model has been used to study the interatomic interactions and phonons of MgX (X=S, Se, Te) in zinc blende structure. The interatomic interaction in the form of central and angular forces up to second nearest neighbors has been considered. The interatomic interaction Mg-X is found to be strongest and its value is highest for MgS compared to others. This is because of small bond length in MgS compared to others. Zone centre phonons have been calculated for MgX and are in agreement with other available results. The phonon dispersion curves in three high symmetric direction are calculated for MgX (X=S, Se, Te) and are interpreted in light of other existing results.

Crystal structure of simple metals at high pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Degtyareva, Olga

2010-10-22

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structuresmore » found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.« less

Atomicrex—a general purpose tool for the construction of atomic interaction models

NASA Astrophysics Data System (ADS)

Stukowski, Alexander; Fransson, Erik; Mock, Markus; Erhart, Paul

2017-07-01

We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands of atoms or more, because electronic structure methods become computationally too expensive at this scale. atomicrex covers a wide range of interatomic potential types and fulfills many needs in atomistic model development. As inputs, it supports experimental property values as well as ab initio energies and forces, to which models can be fitted using various optimization algorithms. The open architecture of atomicrex allows it to be used in custom model development scenarios beyond classical interatomic potentials while thanks to its Python interface it can be readily integrated e.g., with electronic structure calculations or machine learning algorithms.

Evaluation of copper, aluminum, and nickel interatomic potentials on predicting the elastic properties

NASA Astrophysics Data System (ADS)

Rassoulinejad-Mousavi, Seyed Moein; Mao, Yijin; Zhang, Yuwen

2016-06-01

Choice of appropriate force field is one of the main concerns of any atomistic simulation that needs to be seriously considered in order to yield reliable results. Since investigations on the mechanical behavior of materials at micro/nanoscale have been becoming much more widespread, it is necessary to determine an adequate potential which accurately models the interaction of the atoms for desired applications. In this framework, reliability of multiple embedded atom method based interatomic potentials for predicting the elastic properties was investigated. Assessments were carried out for different copper, aluminum, and nickel interatomic potentials at room temperature which is considered as the most applicable case. Examined force fields for the three species were taken from online repositories of National Institute of Standards and Technology, as well as the Sandia National Laboratories, the LAMMPS database. Using molecular dynamic simulations, the three independent elastic constants, C11, C12, and C44, were found for Cu, Al, and Ni cubic single crystals. Voigt-Reuss-Hill approximation was then implemented to convert elastic constants of the single crystals into isotropic polycrystalline elastic moduli including bulk modulus, shear modulus, and Young's modulus as well as Poisson's ratio. Simulation results from massive molecular dynamic were compared with available experimental data in the literature to justify the robustness of each potential for each species. Eventually, accurate interatomic potentials have been recommended for finding each of the elastic properties of the pure species. Exactitude of the elastic properties was found to be sensitive to the choice of the force fields. Those potentials that were fitted for a specific compound may not necessarily work accurately for all the existing pure species. Tabulated results in this paper might be used as a benchmark to increase assurance of using the interatomic potential that was designated for a problem.

On the continuum mechanics approach for the analysis of single walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Chaudhry, M. S.; Czekanski, A.

2016-04-01

Today carbon nanotubes have found various applications in structural, thermal and almost every field of engineering. Carbon nanotubes provide great strength, stiffness resilience properties. Evaluating the structural behavior of nanoscale materials is an important task. In order to understand the materialistic behavior of nanotubes, atomistic models provide a basis for continuum mechanics modelling. Although the properties of bulk materials are consistent with the size and depends mainly on the material but the properties when we are in Nano-range, continuously change with the size. Such models start from the modelling of interatomic interaction. Modelling and simulation has advantage of cost saving when compared with the experiments. So in this project our aim is to use a continuum mechanics model of carbon nanotubes from atomistic perspective and analyses some structural behaviors of nanotubes. It is generally recognized that mechanical properties of nanotubes are dependent upon their structural details. The properties of nanotubes vary with the varying with the interatomic distance, angular orientation, radius of the tube and many such parameters. Based on such models one can analyses the variation of young's modulus, strength, deformation behavior, vibration behavior and thermal behavior. In this study some of the structural behaviors of the nanotubes are analyzed with the help of continuum mechanics models. Using the properties derived from the molecular mechanics model a Finite Element Analysis of carbon nanotubes is performed and results are verified. This study provides the insight on continuum mechanics modelling of nanotubes and hence the scope to study the effect of various parameters on some structural behavior of nanotubes.

Resonance interatomic energy in a Schwarzschild spacetime

NASA Astrophysics Data System (ADS)

Zhou, Wenting; Yu, Hongwei

2017-08-01

We study, in the Schwarzschild spacetime, the resonance interatomic energy (RIE) of two static identical atoms with an interatomic separation L along the radial direction and correlated by a symmetric/antisymmetric entangled state. The atoms are assumed to be coupled to massless scalar fields in the Boulware, Unruh, and Hartle-Hawking vacua, and approximate analytical results are obtained both at infinity and near the horizon. Our results show that at infinity, the RIE approaches that in a flat spacetime, while, near the horizon, they can deviate dramatically from each other. Besides, different from other atomic radiative properties such as the Lamb shift of a single atom or the interatomic energy between two uncorrelated atoms, which can be obviously affected by the thermal character of quantum fields, the RIE of two atoms in a symmetric/antisymmetric entangled state in the Boulware, Unruh, and Hartle-Hawking vacua are exactly the same as a result of the fact that the RIE of two such atoms depends only on the atomic self-reaction, i.e., it does not feel the vacuum fluctuations. This suggests that the RIE of two static atoms in a symmetric/antisymmetric entangled state outside a black hole is oblivious to the Hawking radiation, in contrast to those uncorrelated atoms.

Influence of Fe/Co ratio on structural and magnetic properties of (Fe100-xCox)84.5Nb5B8.5P2 alloy

NASA Astrophysics Data System (ADS)

Gehlot, K.; Kane, S. N.; Sinha, A. K.; Ghodke, N.; Varga, L. K.

2018-05-01

Structural and magnetic properties of a series of (Fe100-xCox)84.5Nb5B8.5P2 (x = 20, 40, 60) have been investigated respectively by using synchrotron x-ray diffraction and magnetic measurements. Results show that Fe/Co ratio: i) affects stability of the alloy against crystallization, ii) shows evidence for ordering, which has considerable effect on magnetic properties, iii) influences the grain diameter and volume fraction of the formed nano-grains range between 4.8 - 9.5 nm and 1.5 - 9 %, affects magnetic properties considerably. An empirical relation is obtained, which shows linear relationship between interatomic distances for 1st, 2nd co-ordination shell, suggests strong correlation between structural, magnetic properties.

Adiabatic passage of radio-frequency-assisted Förster resonances in Rydberg atoms for two-qubit gates and the generation of Bell states

NASA Astrophysics Data System (ADS)

Beterov, I. I.; Hamzina, G. N.; Yakshina, E. A.; Tretyakov, D. B.; Entin, V. M.; Ryabtsev, I. I.

2018-03-01

High-fidelity entangled Bell states are of great interest in quantum physics. Entanglement of ultracold neutral atoms in two spatially separated optical dipole traps is promising for implementation of quantum computing and quantum simulation and for investigation of Bell states of material objects. We propose a method to entangle two atoms via long-range Rydberg-Rydberg interaction. Alternative to previous approaches, based on Rydberg blockade, we consider radio-frequency-assisted Stark-tuned Förster resonances in Rb Rydberg atoms. To reduce the sensitivity of the fidelity of Bell states to the fluctuations of interatomic distance, we propose to use the double adiabatic passage across the radio-frequency-assisted Stark-tuned Förster resonances, which results in a deterministic phase shift of the collective two-atom state.

A revised set of values of single-bond radii derived from the observed interatomic distances in metals by correction for bond number and resonance energy

PubMed Central

Pauling, Linus; Kamb, Barclay

1986-01-01

An earlier discussion [Pauling, L. (1947) J. Am. Chem. Soc. 69, 542] of observed bond lengths in elemental metals with correction for bond number and resonance energy led to a set of single-bond metallic radii with values usually somewhat less than the corresponding values obtained from molecules and complex ions. A theory of resonating covalent bonds has now been developed that permits calculation of the number of resonance structures per atom and of the effective resonance energy per bond. With this refined method of correcting the observed bond lengths for the effect of resonance energy, a new set of single-bond covalent radii, in better agreement with values from molecules and complex ions, has been constructed. PMID:16593698

Excited hydrogen bonds in the molecular mechanism of muscle contraction.

PubMed

Bespalova, S V; Tolpygo, K B

1991-11-21

The mechanism of muscle contraction is considered. The hydrolysis of an ATP molecule is assumed to produce the excitation of hydrogen bonds A--H...B between electronegative atoms A and B, which are contained in the myosin head and actin filament. This excitation energy epsilon f depends on the interatomic distance AB = R and generates the tractive force f = -delta epsilon f/delta R, that makes atoms AB approach each other. The swing of the myosin head results in macroscopic mutual displacement of actin and myosin polymers. The motion of the actin filament under the action of this force is studied. The conditions under which a considerable portion of the excitation energy converts into the potential tension energy of the actin filament are analysed, and the probability of higher muscle efficiency existence is discussed.

Potential energy curves of the Na2+ molecular ion from all-electron ab initio relativistic calculations

NASA Astrophysics Data System (ADS)

Bewicz, Anna; Musiał, Monika; Kucharski, Stanisław A.

2017-11-01

The equation-of-motion coupled-cluster method for electron affinity calculations has been used to study potential energy curves (PECs) for the Na+2 molecular ion. Although the studied molecule represents the open shell system the applied approach employs the closed shell Na+ 22 ion as the reference. In addition the Na+ 22 system dissociates into the closed shell fragments; hence, the restricted Hartree-Fock scheme can be used within the whole range of interatomic distances, from 2 to 45 Å. We used large basis set engaging 268 basis functions with all 21 electrons correlated. The relativistic effects are included via second-order Douglas-Kroll method. The computed PECs, spectroscopic molecular constants and vibrational energy levels agree well with experimental values if the latter are available or with other theoretical data.

Specific features of nonvalent interactions in orthorhombic perovskites

NASA Astrophysics Data System (ADS)

Serezhkin, V. N.; Pushkin, D. V.; Serezhkina, L. B.

2014-07-01

It is established that isostructural orthorhombic perovskites ABO3 (sp. gr. Pnma in different systems, no. 62, Z = 4), depending on the specificity of nonvalent interactions (which determine the combinatorial-topological type of the Voronoi-Dirichlet polyhedra (VDPs) of four basis atoms), are divided into ten different stereotypes. It is shown by the example of 259 perovskites belonging to the DyCrO3 stereotype that VDP characteristics can be used to quantitatively estimate the distortion of BO6 octahedra, including that caused by the Jahn-Teller effect. It is found that one of the causes of the distortion of the coordination polyhedra of atoms in the structure of orthorhombic perovskites is heteroatomic metal-metal interactions, for which the interatomic distances are much shorter than the sum of the Slater radii of A and B atoms.

Thermal motion in proteins: Large effects on the time-averaged interaction energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goethe, Martin, E-mail: martingoethe@ub.edu; Rubi, J. Miguel; Fita, Ignacio

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothingmore » effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.« less

Thermal motion in proteins: Large effects on the time-averaged interaction energies

NASA Astrophysics Data System (ADS)

Goethe, Martin; Fita, Ignacio; Rubi, J. Miguel

2016-03-01

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

Structure of aqueous cesium metaborate solutions by X-ray scattering and DFT calculation

NASA Astrophysics Data System (ADS)

Zhang, W. Q.; Fang, C. H.; Fang, Y.; Zhu, F. Y.; Zhou, Y. Q.; Liu, H. Y.; Li, W.

2018-05-01

In the present work, precise radial distribution function (RDF) of cesium metaborate solutions with salt-water molar ratio of 1:25, 1:30 and 1:35 in large scattering vector range (3.91-214.26 nm-1) were obtained by X-ray scattering. Polyborate species were given using Newton iteration method with measured pH and literature equilibrium constants. In model calculation, structural parameters such as the coordination number, interatomic distance and Debye-Waller factor were given through model calculation. The B-O(H2O) distance was determined to be ∼0.37 nm with the hydration number of ∼7.8 for B(OH)4-. The Cs-B distance of the contact ions CsB(OH)40 was measured to be ∼0.46 nm with interaction number of ∼0.77. The interaction distances and coordination number for the first shell and the second shell of Cs-O(W) are ∼0.325 nm, ∼0.517 nm and ∼8.0, ∼11, respectively. Five low-energy configurations of [Cs(H2O)8]+ were given with DFT calculation, including the first and the second hydration shell, and the most stable eight-coordinated one is close to the model calculation. Furthermore, the effect of concentration is discussed in the X-ray scattering analysis part, showing that hydration degree changes with the concentration. For the coordination number and distance of Cs-O(H2O) and H-bonding decrease with the increasing concentration. The coordination number of Cs-O(H2O) keep stable, and the coordination distance changes from 3.25 nm to 3.30 nm. For H-bonding, which the coordination number varies from 2.20 to 2.24, and the coordination distance varies from 2.76 nm to 2.78 nm with the decreasing concentration.

DEVELOPMENT OF INTERATOMIC POTENTIALS IN TUNGSTEN-RHENIUM SYSTEMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Nandipati, Giridhar; Kurtz, Richard J.

2016-09-01

Reference data are generated using the ab initio method to fit interatomic potentials for the W-Re system. The reference data include single phases of W and Re, strained structures, slabs, systems containing several concentrations of vacancies, systems containing various types of interstitial defects, melt structures, structures in the σ and χ phases, and structures containing several concentrations of solid solutions of Re in bcc W and W in hcp Re. Future work will start the fitting iterations.

SNAP: Automated Generation of High-Accuracy Interatomic Potentials using Quantum Data

NASA Astrophysics Data System (ADS)

Thompson, Aidan; Wood, Mitchell; Phillpot, Simon

Molecular dynamics simulation is a powerful computational method for bridging between macroscopic continuum models and quantum models treating a few hundred atoms, but it is limited by the accuracy of the interatomic potential. Sound physical and chemical understanding have led to good potentials for certain systems, but it is difficult to extend them to new materials and properties. The solution is obvious but challenging: develop more complex potentials that reproduce large quantum datasets. The growing availability of large data sets has made it possible to use automated machine-learning approaches for interatomic potential development. In the SNAP approach, the interatomic potential depends on a very general set of atomic neighborhood descriptors, based on the bispectrum components of the density projected onto the surface of the unit 3-sphere. Previously, this approach was demonstrated for tantalum, reproducing the screw dislocation Peierls barrier. In this talk, it will be shown that the SNAP method is capable of reproducing a wide range of energy landscapes relevant to diverse material science applications: i) point defects in indium phosphide, ii) stability of tungsten surfaces at high temperatures, and iii) formation of intrinsic defects in uranium. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corp., for the U.S. Dept. of Energys National Nuclear Security Admin. under contract DE-AC04-94AL85000.

Impact of Short-Range Forces on Defect Production from High-Energy Collisions

DOE PAGES

Stoller, R. E.; Tamm, A.; Béland, L. K.; ...

2016-04-25

Primary radiation damage formation in solid materials typically involves collisions between atoms that have up to a few hundred keV of kinetic energy. The distance between two colliding atoms can approach 0.05 nm during these collisions. At such small atomic separations, force fields fitted to equilibrium properties tend to significantly underestimate the potential energy of the colliding dimer. To enable molecular dynamics simulations of high-energy collisions, it is common practice to use a screened Coulomb force field to describe the interactions and to smoothly join this to the equilibrium force field at a suitable interatomic spacing. But, there is nomore » accepted standard method for choosing the parameters used in the joining process, and our results prove that defect production is sensitive to how the force fields are linked. A new procedure is presented that involves the use of ab initio calculations to determine the magnitude and spatial dependence of the pair interactions at intermediate distances, along with systematic criteria for choosing the joining parameters. Results are presented for the case of nickel, which demonstrate the use and validity of the procedure.« less

Structure of siderite FeCO[subscript 3] to 56 GPa and hysteresis of its spin-pairing transition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lavina, Barbara; Dera, Przemyslaw; Downs, Robert T.

2010-09-17

The structure of siderite, FeCO{sub 3}, was determined to 56 GPa, beyond the spin-pairing transition of its iron d electrons. Fe{sup 2+} in the siderite structure is in the high-spin state at low pressures and transforms to the low-spin (LS) state over a narrow pressure range, 44 to 45 GPa, that is concomitant with a shrinkage of the octahedral bond distance by 4%, and a volume collapse of 10%. The structural rearrangements associated with the electronic transition are nearly isotropic in contrast with other properties of siderite, which mostly are highly anisotropic. Robust refinements of the crystal structure from single-crystalmore » x-ray diffraction data were performed at small pressure intervals in order to accurately evaluate the variation in the interatomic distances and to define the geometry of the carbonate hosting LS-Fe{sup 2+}. Thermal vibrations are remarkably lowered in the LS-Sd as shown by atomic displacement parameters. The formation of like-spin domains at the transition shows a hysteresis of more than 3 GPa, compatible with a strong cooperative contribution of neighboring clusters to the transition.« less

Evaluation of copper, aluminum, and nickel interatomic potentials on predicting the elastic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rassoulinejad-Mousavi, Seyed Moein; Mao, Yijin; Zhang, Yuwen, E-mail: zhangyu@missouri.edu

Choice of appropriate force field is one of the main concerns of any atomistic simulation that needs to be seriously considered in order to yield reliable results. Since investigations on the mechanical behavior of materials at micro/nanoscale have been becoming much more widespread, it is necessary to determine an adequate potential which accurately models the interaction of the atoms for desired applications. In this framework, reliability of multiple embedded atom method based interatomic potentials for predicting the elastic properties was investigated. Assessments were carried out for different copper, aluminum, and nickel interatomic potentials at room temperature which is considered asmore » the most applicable case. Examined force fields for the three species were taken from online repositories of National Institute of Standards and Technology, as well as the Sandia National Laboratories, the LAMMPS database. Using molecular dynamic simulations, the three independent elastic constants, C{sub 11}, C{sub 12}, and C{sub 44}, were found for Cu, Al, and Ni cubic single crystals. Voigt-Reuss-Hill approximation was then implemented to convert elastic constants of the single crystals into isotropic polycrystalline elastic moduli including bulk modulus, shear modulus, and Young's modulus as well as Poisson's ratio. Simulation results from massive molecular dynamic were compared with available experimental data in the literature to justify the robustness of each potential for each species. Eventually, accurate interatomic potentials have been recommended for finding each of the elastic properties of the pure species. Exactitude of the elastic properties was found to be sensitive to the choice of the force fields. Those potentials that were fitted for a specific compound may not necessarily work accurately for all the existing pure species. Tabulated results in this paper might be used as a benchmark to increase assurance of using the interatomic potential that was designated for a problem.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morante, S., E-mail: morante@roma2.infn.it; Rossi, G.C., E-mail: rossig@roma2.infn.it; Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Compendio del Viminale, Piazza del Viminale 1, I-00184 Rome

We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg–Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann–Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.

Influence of Parameters of a Reactive Interatomic Potential on the Properties of Saturated Hydrocarbons

DTIC Science & Technology

2017-01-01

Methodology 3 2.1 Modified Embedded-Atom Method Theory 3 2.1.1 Embedding Energy Function 3 2.1.2 Screening Factor 8 2.1.3 Modified Embedded-Atom...Simulation Methodology 2.1 Modified Embedded-Atom Method Theory In the EAM and MEAM formalisms1,2,5 the total energy of a system of atoms (Etot) is...An interatomic potential for saturated hydrocarbons using the modified embedded-atom method (MEAM), a semiempirical many-body potential based on

Fast Model Generalized Pseudopotential Theory Interatomic Potential Routine

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-03-18

MGPT is an unclassified source code for the fast evaluation and application of quantum-based MGPT interatomic potentials for mrtals. The present version of MGPT has been developed entirely at LLNL, but is specifically designed for implementation in the open-source molecular0dynamics code LAMMPS maintained by Sandia National Laboratories. Using MGPT in LAMMPS, with separate input potential data, one can perform large-scale atomistic simulations of the structural, thermodynamic, defeat and mechanical properties of transition metals with quantum-mechanical realism.

The relation between the Gross Pitaevskii and Bogoliubov descriptions of a dilute Bose gas

NASA Astrophysics Data System (ADS)

Leggett, A. J.

2003-07-01

I formulate a 'pseudo-paradox' in the theory of a dilute Bose gas with repulsive interactions: the standard expression for the ground state energy within the Gross-Pitaevskii (GP) approximation is lower than that in the Bogoliubov approximation, and hence, by the standard variational argument, the former should prima facie be a better approximation than the latter to the true ground state—a conclusion which is of course opposite to the established wisdom concerning this problem. It is shown that the pseudo-paradox is (unsurprisingly) resolved by a correct transcription of the two-body scattering theory to the many-body case; however, contrary to what appears to be a widespread belief, the resolution has nothing to do with any spurious ultraviolet divergences which result from the replacement of the true interatomic potential by a delta-function pseudopotential. Rather, it relates to an infrared divergence which has the consequence that (a) the most obvious form of the GP 'approximation' actually does not correspond to any well-defined ansatz for the many-body wavefunction, and (b) that the 'best shot' at such a wavefunction always produces an energy which exceeds, or at best equals, that calculated in the Bogoliubov approximation. In fact, the necessity of the latter may be seen as a consequence of the need to reduce the Fock term in the energy, which is absent in the two-particle problem but dominant in the many-body case; it does this by increasing the density correlations, at distances less than or approximately equal to the correlation length \\xi , above the value extrapolated from the two-body case. As a by-product I devise an alternative formulation of the Bogoliubov approximation which does not require the explicit replacement of the true interatomic potential by a delta-function pseudopotential.

Time evolution, Lamb shift, and emission spectra of spontaneous emission of two identical atoms

NASA Astrophysics Data System (ADS)

Wang, Da-Wei; Li, Zheng-Hong; Zheng, Hang; Zhu, Shi-Yao

2010-04-01

A unitary transformation method is used to investigate the dynamic evolution of two multilevel atoms, in the basis of symmetric and antisymmetric states, with one atom being initially prepared in the first excited state and the other in the ground state. The unitary transformation guarantees that our calculations are based on the ground state of the atom-field system and the self-energy is subtracted at the beginning. The total Lamb shifts of the symmetric and antisymmetric states are divided into transformed shift and dynamic shift. The transformed shift is due to emitting and reabsorbing of virtual photons, by a single atom (nondynamic single atomic shift) and between the two atoms (quasi-static shift). The dynamic shift is due to the emitting and reabsorbing of real photons, by a single atom (dynamic single atomic shift) and between the two atoms (dynamic interatomic shift). The emitting and reabsorbing of virtual and real photons between the two atoms result in the interatomic shift, which does not exist for the one-atom case. The spectra at the long-time limit are calculated. If the distance between the two atoms is shorter than or comparable to the wavelength, the strong coupling between the two atoms splits the spectrum into two peaks, one from the symmetric state and the other from the antisymmetric state. The origin of the red or blue shifts for the symmetric and antisymmetric states mainly lies in the negative or positive interaction energy between the two atoms. In the investigation of the short time evolution, we find the modification of the effective density of states by the interaction between two atoms can modulate the quantum Zeno and quantum anti-Zeno effects in the decays of the symmetric and antisymmetric states.

Crucial role of nuclear dynamics for electron injection in a dye–semiconductor complex

DOE PAGES

Monti, Adriano; Negre, Christian F. A.; Batista, Victor S.; ...

2015-06-05

In this study, we investigate the electron injection from a terrylene-based chromophore to the TiO 2 semiconductor bridged by a recently proposed phenyl-amide-phenyl molecular rectifier. The mechanism of electron transfer is studied by means of quantum dynamics simulations using an extended Hückel Hamiltonian. It is found that the inclusion of the nuclear motion is necessary to observe the photoinduced electron transfer. In particular, the fluctuations of the dihedral angle between the terrylene and the phenyl ring modulate the localization and thus the electronic coupling between the donor and acceptor states involved in the injection process. The electron propagation shows characteristicmore » oscillatory features that correlate with interatomic distance fluctuations in the bridge, which are associated with the vibrational modes driving the process. The understanding of such effects is important for the design of functional dyes with optimal injection and rectification properties.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smedskjaer, Morten M., E-mail: mos@bio.aau.dk; Bauchy, Mathieu; Mauro, John C.

The properties of glass are determined not only by temperature, pressure, and composition, but also by their complete thermal and pressure histories. Here, we show that glasses of identical composition produced through thermal annealing and through quenching from elevated pressure can result in samples with identical density and mean interatomic distances, yet different bond angle distributions, medium-range structures, and, thus, macroscopic properties. We demonstrate that hardness is higher when the density increase is obtained through thermal annealing rather than through pressure-quenching. Molecular dynamics simulations reveal that this arises because pressure-quenching has a larger effect on medium-range order, while annealing hasmore » a larger effect on short-range structures (sharper bond angle distribution), which ultimately determine hardness according to bond constraint theory. Our work could open a new avenue towards industrially useful glasses that are identical in terms of composition and density, but with differences in thermodynamic, mechanical, and rheological properties due to unique structural characteristics.« less

Magnetic field-induced changes of lattice parameters and thermal expansion behavior of the CoMnSi compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kou, R. H.; Gao, J.; Wang, G.

2016-02-01

The crystal structure of the CoMnSi compound during zero-field cooling and field cooling from room temperature down to 200 K was studied using the synchrotron radiation X-ray diffraction technique. The results show that the lattice parameters and thermal expansion behavior of the sample are changed by the applied magnetic fields. The lattice contracts along the a axis, but expands along the b and c axes. Due to enlarged and anisotropic changes under a magnetic field of 6 T, the lattice shows an invar-like behavior along all three axes. Critical interatomic distances and bond angles also show large changes under themore » influence of such a high magnetic field. These magnetic field-induced changes of the lattice are discussed with respect to their contributions to the large magnetocaloric effect of the CoMnSi compound.« less

Structural, thermal and optical properties of KTi(0.92)La(0.08)OPO4 and KTi(0.94)Nd(0.06)OPO4.

PubMed

Sadhasivam, S; Perumal, Rajesh Narayana; Ramasamy, P

2015-10-05

KTi0.92La0.08OPO4 (KTP:La) and KTi0.94Nd0.06OPO4 (KTP:Nd) single crystals are grown using high temperature top seeded flux growth technique. The strain derived from doping is calculated from Williamson-Hall relation. The packing structure and lattice parameter of the grown crystals are analyzed using single crystal X-ray diffraction. The bonding, distortion and change in inter-atomic distances by strain effects of doping are assessed by Raman spectroscopy. Thermal stabilities of grown crystals are evaluated by specific heat capacity measurement. Pronounced high specific heat capacity is recorded as 1.16 J/gK at 498 K for KTP:Nd. Second harmonic generation intensities are measured for KTP:Nd and KTP:La single crystal. Copyright © 2015 Elsevier B.V. All rights reserved.

Correlation of molecular valence- and K-shell photoionization resonances with bond lengths

NASA Technical Reports Server (NTRS)

Sheehy, J. A.; Gil, T. J.; Winstead, C. L.; Farren, R. E.; Langhoff, P. W.

1989-01-01

The relationship between the interatomic distance and the positions of valence-shell and K-shell sigma(asterisk) photoionization resonances is investigated theoretically for the molecules C2, F2, N2, O2, CO, NO, C2H2, C2H4, C2H6, HCN, H2CO, N20, CO2, and C2N2. The results of molecular-orbital computations are presented in three-dimensional diagrams, which are shown to be similar to the wave functions of a particle in a cylindrical well, confirming the validity of free-electron molecular-orbital (FEMO) approximations for modeling the potential along the symmetry axis. FEMO orbital energies and resonance positions are found to be in good agreement with previous theoretical and experimental results. Also included is a Feshbach-Fano analysis of the relevance of virtual-valence orbitals to the appearance of single-channel resonances in molecular photoionization cross sections.

In-line three-dimensional holography of nanocrystalline objects at atomic resolution

PubMed Central

Chen, F.-R.; Van Dyck, D.; Kisielowski, C.

2016-01-01

Resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we report a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose rate electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. We apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1–2 Å, which is smaller than inter-atomic distances. PMID:26887849

Revised Space Groups for Three Molybdenum(V) Phosphate Compounds

NASA Astrophysics Data System (ADS)

Leclaire, A.; Borel, M. M.; Guesdon, A.; Marsh, Richard E.

2001-06-01

The space groups of three previously described Mo(V) phosphate structures are revised. (1) δ-KMo2P3O13, originally reported as triclinic, Poverline1, is revised to monoclinic, C2/c; it is identical to the compound previously identified as K4Mo8P12O52. (2) The compound formulated as [Mo12CdP8O50(OH)12]Cd [N(CH3)4]2(H3O)6·5H2O, originally described as monoclinic, Pn, is revised to P21/n (also monoclinic). (3) Rb3O2(MoO)4(PO4)4, originally reported as orthorhombic, C2221, is revised to tetragonal, P43212. The general descriptions of the structures are unchanged; however, for compound 2 the revision involves the addition of a center of symmetry and, as a result, there are significant changes in the interatomic distances and angles.

Computer simulation of metal wire explosion under high rate heating

NASA Astrophysics Data System (ADS)

Zolnikov, K. P.; Kryzhevich, D. S.; Korchuganov, A. V.

2017-05-01

Synchronous electric explosion of metal wires and synthesis of bicomponent nanoparticles were investigated on the base of molecular dynamics method. Copper and nickel nanosized crystallites of cylindrical shape were chosen as conductors for explosion. The embedded atom approximation was used for calculation of the interatomic interactions. The agglomeration process after explosion metal wires was the main mechanism for particle synthesis. The distribution of chemical elements was non-uniform over the cross section of the bicomponent particles. The copper concentration in the surface region was higher than in the bulk of the synthesized particle. By varying the loading parameters (heating temperature, the distance between the wires) one can control the size and internal structure of the synthesized bicomponent nanoparticles. The obtained results showed that the method of molecular dynamics can be effectively used to determine the optimal technological mode of nanoparticle synthesis on the base of electric explosion of metal wires.

High-density amorphous ice: A path-integral simulation

NASA Astrophysics Data System (ADS)

Herrero, Carlos P.; Ramírez, Rafael

2012-09-01

Structural and thermodynamic properties of high-density amorphous (HDA) ice have been studied by path-integral molecular dynamics simulations in the isothermal-isobaric ensemble. Interatomic interactions were modeled by using the effective q-TIP4P/F potential for flexible water. Quantum nuclear motion is found to affect several observable properties of the amorphous solid. At low temperature (T = 50 K) the molar volume of HDA ice is found to increase by 6%, and the intramolecular O-H distance rises by 1.4% due to quantum motion. Peaks in the radial distribution function of HDA ice are broadened with respect to their classical expectancy. The bulk modulus, B, is found to rise linearly with the pressure, with a slope ∂B/∂P = 7.1. Our results are compared with those derived earlier from classical and path-integral simulations of HDA ice. We discuss similarities and discrepancies with those earlier simulations.

Spiral chain structure of high pressure selenium-II{sup '} and sulfur-II from powder x-ray diffraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujihisa, Hiroshi; Yamawaki, Hiroshi; Sakashita, Mami

2004-10-01

The structure of high pressure phases, selenium-II{sup '} (Se-II{sup '}) and sulfur-II (S-II), for {alpha}-Se{sub 8} (monoclinic Se-I) and {alpha}-S{sub 8} (orthorhombic S-I) was studied by powder x-ray diffraction experiments. Se-II{sup '} and S-II were found to be isostructural and to belong to the tetragonal space group I4{sub 1}/acd, which is made up of 16 atoms in the unit cell. The structure consisted of unique spiral chains with both 4{sub 1} and 4{sub 3} screws. The results confirmed that the structure sequence of the pressure-induced phase transitions for the group VIb elements depended on the initial molecular form. The chemicalmore » bonds of the phases are also discussed from the interatomic distances that were obtained.« less

Observation of fast and slow interatomic Coulombic decay in argon dimers induced by electron-impact ionization

NASA Astrophysics Data System (ADS)

Ren, Xueguang; Miteva, Tsveta; Kolorenč, Přemysl; Gokhberg, Kirill; Kuleff, Alexander I.; Cederbaum, Lorenz S.; Dorn, Alexander

2017-09-01

We investigate the interatomic Coulombic decay (ICD) in argon dimers induced by electron-impact ionization (E0=90 eV ) using a multiparticle coincidence experiment in which the momentum vectors and, consequently, the kinetic energies for electrons and fragment ions are determined. The signature of the ICD process is obtained from a correlation map between ejected electron energy and kinetic energy release (KER) for Ar++Ar+ fragment ions where low-energy ICD electrons can be identified. Furthermore, two types of ICD processes, termed fast and slow interatomic decay, are separated by the ICD initial-state energies and projectile energy losses. The dependence of the energies of emitted low-energy ICD electrons on the initial-state energy is studied. ICD electron energy spectra and KER spectra are obtained separately for fast and slow decay processes where the KER spectra for the slow decay channel are strongly influenced by nuclear motion. The KER and ICD electron energy spectra are well reproduced by ab initio calculations.

Interatomic Coulombic decay cascades in multiply excited neon clusters

PubMed Central

Nagaya, K.; Iablonskyi, D.; Golubev, N. V.; Matsunami, K.; Fukuzawa, H.; Motomura, K.; Nishiyama, T.; Sakai, T.; Tachibana, T.; Mondal, S.; Wada, S.; Prince, K. C.; Callegari, C.; Miron, C.; Saito, N.; Yabashi, M.; Demekhin, Ph. V.; Cederbaum, L. S.; Kuleff, A. I.; Yao, M.; Ueda, K.

2016-01-01

In high-intensity laser light, matter can be ionized by direct multiphoton absorption even at photon energies below the ionization threshold. However on tuning the laser to the lowest resonant transition, the system becomes multiply excited, and more efficient, indirect ionization pathways become operative. These mechanisms are known as interatomic Coulombic decay (ICD), where one of the species de-excites to its ground state, transferring its energy to ionize another excited species. Here we show that on tuning to a higher resonant transition, a previously unknown type of interatomic Coulombic decay, intra-Rydberg ICD occurs. In it, de-excitation of an atom to a close-lying Rydberg state leads to electron emission from another neighbouring Rydberg atom. Moreover, systems multiply excited to higher Rydberg states will decay by a cascade of such processes, producing even more ions. The intra-Rydberg ICD and cascades are expected to be ubiquitous in weakly-bound systems exposed to high-intensity resonant radiation. PMID:27917867

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

DOE PAGES

Senftle, Thomas; Hong, Sungwook; Islam, Md Mahbubul; ...

2016-03-04

The 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 ReaxFFmore » 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. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.« less

Direct evidence of two interatomic relaxation mechanisms in argon dimers ionized by electron impact

PubMed Central

Ren, Xueguang; Jabbour Al Maalouf, Elias; Dorn, Alexander; Denifl, Stephan

2016-01-01

In weakly bound systems like liquids and clusters electronically excited states can relax in inter-particle reactions via the interplay of electronic and nuclear dynamics. Here we report on the identification of two prominent examples, interatomic Coulombic decay (ICD) and radiative charge transfer (RCT), which are induced in argon dimers by electron collisions. After initial ionization of one dimer constituent ICD and RCT lead to the ionization of its neighbour either by energy transfer to or by electron transfer from the neighbour, respectively. By full quintuple-coincidence measurements, we unambiguously identify ICD and RCT, and trace the relaxation dynamics as function of the collisional excited state energies. Such interatomic processes multiply the number of electrons and shift their energies down to the critical 1–10 eV range, which can efficiently cause chemical degradation of biomolecules. Therefore, the observed relaxation channels might contribute to cause efficient radiation damage in biological systems. PMID:27000407

INFLUENCE OF MASS ON DISPLACEMENT THRESHOLD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Selby, A.; Nandipati, Giridhar

2014-12-30

Molecular dynamics simulations are performed to investigate the effect of mass on displacement threshold energy in Cr, Mo, Fe and W. For each interatomic potential, the mass of the atoms is varied among those metals for a total of 16 combinations. The average threshold energy over all crystal directions is calculated within the irreducible crystal directions using appropriate weighting factors. The weighting factors account for the different number of equivalent directions among the grid points and the different solid angle coverage of each grid point. The grid points are constructed with a Miller index increment of 1/24 for a totalmore » of 325 points. For each direction, 10 simulations each with a different primary-knock-on atom are performed. The results show that for each interatomic potential, the average threshold energy is insensitive to the mass; i.e., the values are the same within the standard error. In the future, the effect of mass on high-energy cascades for a given interatomic potential will be investigated.« less

Thermodynamic scaling of glassy dynamics and dynamic heterogeneities in metallic glass-forming liquid

NASA Astrophysics Data System (ADS)

Hu, Yuan-Chao; Shang, Bao-Shuang; Guan, Peng-Fei; Yang, Yong; Bai, Hai-Yang; Wang, Wei-Hua

2016-09-01

A ternary metallic glass-forming liquid is found to be not strongly correlating thermodynamically, but its average dynamics, dynamic heterogeneities including the high order dynamic correlation length, and static structure are still well described by thermodynamic scaling with the same scaling exponent γ. This may indicate that the metallic liquid could be treated as a single-parameter liquid. As an intrinsic material constant stemming from the fundamental interatomic interactions, γ is theoretically predicted from the thermodynamic fluctuations of the potential energy and the virial. Although γ is conventionally understood merely from the repulsive part of the inter-particle potentials, the strong correlation between γ and the Grüneisen parameter up to the accuracy of the Dulong-Petit approximation demonstrates the important roles of anharmonicity and attractive force of the interatomic potential in governing glass transition of metallic glassformers. These findings may shed light on how to understand metallic glass formation from the fundamental interatomic interactions.

Symmetry and novelty in the electronic and geometric structure of nanoalloys:. the case of Ag27Cu7

NASA Astrophysics Data System (ADS)

Ortigoza, M. Alcántara; Rahman, T. S.

2008-04-01

Nanoparticles of bimetallic alloys have been shown to possess composition dependent characteristics which distinguish themselves from the corresponding bulk alloys. Taking the 34-atom nanoalloy of Ag and Cu (Ag27Cu7), we show using first principles electronic structure calculations that this core-shell alloy indeed has perfect D5h symmetry and consists of only 6 non-equivalent (2 Cu and 4 Ag) atoms. Analysis of the interatomic bond lengths and detailed electronic structure further reveal that the Cu atoms play a major role in controlling the characteristics of the nanoalloy. The higher cohesive energy, together with shorter bond length for Cu, compared to Ag, conspire to produce a hierarchy in the relative strengths of the Ag - Cu, Ag - Ag, and Cu - Cu bonds and corresponding interatomic bond lengths, point to the uniqueness in the characteristics of this nanoalloy. Charge density plots of Ag27Cu7 provide further insights into the relative strengths of the various interatomic bonds.

Peierls-Nabarro modeling of dislocations in UO2

NASA Astrophysics Data System (ADS)

Skelton, Richard; Walker, Andrew M.

2017-11-01

Under conditions of high stress or low temperature, glide of dislocations plays an important role in the deformation of UO2. In this paper, the Peierls-Nabarro model is used to calculate the core widths and Peierls stresses of ½<110> edge and screw dislocations gliding on {100}, {110}, and {111}. The energy of the inelastic displacement field in the dislocation core is parameterized using generalized stacking fault energies, which are calculated atomistically using interatomic potentials. We use seven different interatomic potential models, representing the variety of different models available for UO2. The different models broadly agree on the relative order of the strengths of the different slip systems, with the 1/2<110>{100} edge dislocation predicted to be the weakest slip system and 1/2<110>{110} the strongest. However, the calculated Peierls stresses depend strongly on the interatomic potential used, with values ranging between 2.7 and 12.9 GPa for glide of 1/2<110>{100} edge dislocations, 16.4-32.3 GPa for 1/2<110>{110} edge dislocations, and 6.8-13.6 GPa for 1/2<110>{111} edge dislocations. The glide of 1/2<110> screw dislocations in UO2 is also found to depend on the interatomic potential used, with some models predicting similar Peierls stresses for glide on {100} and {111}, while others predict a unique easy glide direction. Comparison with previous fully atomistic calculations show that the Peierls-Nabarro model can accurately predict dislocation properties in UO2.

Evaluating variability with atomistic simulations: the effect of potential and calculation methodology on the modeling of lattice and elastic constants

NASA Astrophysics Data System (ADS)

Hale, Lucas M.; Trautt, Zachary T.; Becker, Chandler A.

2018-07-01

Atomistic simulations using classical interatomic potentials are powerful investigative tools linking atomic structures to dynamic properties and behaviors. It is well known that different interatomic potentials produce different results, thus making it necessary to characterize potentials based on how they predict basic properties. Doing so makes it possible to compare existing interatomic models in order to select those best suited for specific use cases, and to identify any limitations of the models that may lead to unrealistic responses. While the methods for obtaining many of these properties are often thought of as simple calculations, there are many underlying aspects that can lead to variability in the reported property values. For instance, multiple methods may exist for computing the same property and values may be sensitive to certain simulation parameters. Here, we introduce a new high-throughput computational framework that encodes various simulation methodologies as Python calculation scripts. Three distinct methods for evaluating the lattice and elastic constants of bulk crystal structures are implemented and used to evaluate the properties across 120 interatomic potentials, 18 crystal prototypes, and all possible combinations of unique lattice site and elemental model pairings. Analysis of the results reveals which potentials and crystal prototypes are sensitive to the calculation methods and parameters, and it assists with the verification of potentials, methods, and molecular dynamics software. The results, calculation scripts, and computational infrastructure are self-contained and openly available to support researchers in performing meaningful simulations.

Facilitating the selection and creation of accurate interatomic potentials with robust tools and characterization

NASA Astrophysics Data System (ADS)

Trautt, Zachary T.; Tavazza, Francesca; Becker, Chandler A.

2015-10-01

The Materials Genome Initiative seeks to significantly decrease the cost and time of development and integration of new materials. Within the domain of atomistic simulations, several roadblocks stand in the way of reaching this goal. While the NIST Interatomic Potentials Repository hosts numerous interatomic potentials (force fields), researchers cannot immediately determine the best choice(s) for their use case. Researchers developing new potentials, specifically those in restricted environments, lack a comprehensive portfolio of efficient tools capable of calculating and archiving the properties of their potentials. This paper elucidates one solution to these problems, which uses Python-based scripts that are suitable for rapid property evaluation and human knowledge transfer. Calculation results are visible on the repository website, which reduces the time required to select an interatomic potential for a specific use case. Furthermore, property evaluation scripts are being integrated with modern platforms to improve discoverability and access of materials property data. To demonstrate these scripts and features, we will discuss the automation of stacking fault energy calculations and their application to additional elements. While the calculation methodology was developed previously, we are using it here as a case study in simulation automation and property calculations. We demonstrate how the use of Python scripts allows for rapid calculation in a more easily managed way where the calculations can be modified, and the results presented in user-friendly and concise ways. Additionally, the methods can be incorporated into other efforts, such as openKIM.

Investigating energy-based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1.

PubMed

Zhu, Guanhua; Liu, Wei; Bao, Chenglong; Tong, Dudu; Ji, Hui; Shen, Zuowei; Yang, Daiwen; Lu, Lanyuan

2018-05-01

The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates. © 2018 Wiley Periodicals, Inc.

N-tuple topological/geometric cutoffs for 3D N-linear algebraic molecular codifications: variability, linear independence and QSAR analysis.

PubMed

García-Jacas, C R; Marrero-Ponce, Y; Barigye, S J; Hernández-Ortega, T; Cabrera-Leyva, L; Fernández-Castillo, A

2016-12-01

Novel N-tuple topological/geometric cutoffs to consider specific inter-atomic relations in the QuBiLS-MIDAS framework are introduced in this manuscript. These molecular cutoffs permit the taking into account of relations between more than two atoms by using (dis-)similarity multi-metrics and the concepts related with topological and Euclidean-geometric distances. To this end, the kth two-, three- and four-tuple topological and geometric neighbourhood quotient (NQ) total (or local-fragment) spatial-(dis)similarity matrices are defined, to represent 3D information corresponding to the relations between two, three and four atoms of the molecular structures that satisfy certain cutoff criteria. First, an analysis of a diverse chemical space for the most common values of topological/Euclidean-geometric distances, bond/dihedral angles, triangle/quadrilateral perimeters, triangle area and volume was performed in order to determine the intervals to take into account in the cutoff procedures. A variability analysis based on Shannon's entropy reveals that better distribution patterns are attained with the descriptors based on the cutoffs proposed (QuBiLS-MIDAS NQ-MDs) with regard to the results obtained when all inter-atomic relations are considered (QuBiLS-MIDAS KA-MDs - 'Keep All'). A principal component analysis shows that the novel molecular cutoffs codify chemical information captured by the respective QuBiLS-MIDAS KA-MDs, as well as information not captured by the latter. Lastly, a QSAR study to obtain deeper knowledge of the contribution of the proposed methods was carried out, using four molecular datasets (steroids (STER), angiotensin converting enzyme (ACE), thermolysin inhibitors (THER) and thrombin inhibitors (THR)) widely used as benchmarks in the evaluation of several methodologies. One to four variable QSAR models based on multiple linear regression were developed for each compound dataset following the original division into training and test sets. The results obtained reveal that the novel cutoff procedures yield superior performances relative to those of the QuBiLS-MIDAS KA-MDs in the prediction of the biological activities considered. From the results achieved, it can be suggested that the proposed N-tuple topological/geometric cutoffs constitute a relevant criteria for generating MDs codifying particular atomic relations, ultimately useful in enhancing the modelling capacity of the QuBiLS-MIDAS 3D-MDs.

Polarization effects in silver delafossite systems

NASA Astrophysics Data System (ADS)

Panapitiya, Gihan; Lewis, James P.

Delafossites are a promising class of materials which has applications in catalysis and optoelectronic devices. Even though much work has been carried out on the cuprate family of delafossites, little is known about the structural and electronic properties of it's silver counterpart. In this work, we present a computational study for two delafossite oxides of the form AgB1 - x FexO2 (For B = Al,Ga). A large number of structures are studied by varying the Fe alloying percentage(x) from 0 to 5 and by choosing the impurity sites randomly. We find that the local structural changes occurring at the vicinity of Fe atoms in these two systems have opposite trends with regard to the O-O distance. The reason for this difference in the trends is identified as the polarization effects on the inter-atomic distances caused by the displacements in O atoms resulting from the incorporation of Fe in sites, previously occupied by either Al or Ga. We believe that these effects are mediated by the differences in the atomic radii of Fe, Al and Ga. Higher alloying levels coupled with nearest neighbor Fe atoms can intensify these distortions in the structure creating deformations in the O-Ag-O bonds, which are directly related to the formation of the conduction band edge in these systems.

Thermal conductivity and phonon transport properties of silicon using perturbation theory and the environment-dependent interatomic potential

NASA Astrophysics Data System (ADS)

Pascual-Gutiérrez, José A.; Murthy, Jayathi Y.; Viskanta, Raymond

2009-09-01

Silicon thermal conductivities are obtained from the solution of the linearized phonon Boltzmann transport equation without the use of any parameter-fitting. Perturbation theory is used to compute the strength of three-phonon and isotope scattering mechanisms. Matrix elements based on Fermi's golden rule are computed exactly without assuming either average or mode-dependent Grüeisen parameters, and with no underlying assumptions of crystal isotropy. The environment-dependent interatomic potential is employed to describe the interatomic force constants and the perturbing Hamiltonians. A detailed methodology to accurately find three-phonon processes satisfying energy- and momentum-conservation rules is also described. Bulk silicon thermal conductivity values are computed across a range of temperatures and shown to match experimental data very well. It is found that about two-thirds of the heat transport in bulk silicon may be attributed to transverse acoustic modes. Effective relaxation times and mean free paths are computed in order to provide a more complete picture of the detailed transport mechanisms and for use with carrier transport models based on the Boltzmann transport equation.

Ab initio interatomic potentials and the thermodynamic properties of fluids

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-07-01

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Ab initio interatomic potentials and the thermodynamic properties of fluids.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-07-14

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Sensitivity of Force Fields on Mechanical Properties of Metals Predicted by Atomistic Simulations

NASA Astrophysics Data System (ADS)

Rassoulinejad-Mousavi, Seyed Moein; Zhang, Yuwen

Increasing number of micro/nanoscale studies for scientific and engineering applications, leads to huge deployment of atomistic simulations such as molecular dynamics and Monte-Carlo simulation. Many complains from users in the simulation community arises for obtaining wrong results notwithstanding of correct simulation procedure and conditions. Improper choice of force field, known as interatomic potential is the likely causes. For the sake of users' assurance, convenience and time saving, several interatomic potentials are evaluated by molecular dynamics. Elastic properties of multiple FCC and BCC pure metallic species are obtained by LAMMPS, using different interatomic potentials designed for pure species and their alloys at different temperatures. The potentials created based on the Embedded Atom Method (EAM), Modified EAM (MEAM) and ReaX force fields, adopted from available open databases. Independent elastic stiffness constants of cubic single crystals for different metals are obtained. The results are compared with the experimental ones available in the literature and deviations for each force field are provided at each temperature. Using current work, users of these force fields can easily judge on the one they are going to designate for their problem.

FAST TRACK COMMUNICATION: A Be-W interatomic potential

NASA Astrophysics Data System (ADS)

Björkas, C.; Henriksson, K. O. E.; Probst, M.; Nordlund, K.

2010-09-01

In this work, an interatomic potential for the beryllium-tungsten system is derived. It is the final piece of a potential puzzle, now containing all possible interactions between the fusion reactor materials beryllium, tungsten and carbon as well as the plasma hydrogen isotopes. The potential is suitable for plasma-wall interaction simulations and can describe the intermetallic Be2W and Be12W phases. The interaction energy between a Be surface and a W atom, and vice versa, agrees qualitatively with ab initio calculations. The potential can also reasonably describe BexWy molecules with x, y = 1, 2, 3, 4.

Quantum effect on the nucleation of plastic deformation carriers and destruction in crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khon, Yury A., E-mail: khon@ispms.tsc.ru; Kaminskii, Petr P., E-mail: ppk@ispms.tsc.ru

2015-10-27

New concepts on the irreversible crystal deformation as a structure transformation caused by a change in interatomic interactions at fluctuations of the electron density under loading are described. The change in interatomic interactions lead to the excitation of dynamical displacements of atoms. A model and a theory of a deformable pristine crystal taking into account the excitation of thermally activated and dynamical displacements of atoms are suggested. New mechanisms of the nucleation of plastic deformation carriers and destruction in pristine crystals at the real value of the deforming stress are studied.

Statistical mechanical foundation of the peridynamic nonlocal continuum theory: energy and momentum conservation laws.

PubMed

Lehoucq, R B; Sears, Mark P

2011-09-01

The purpose of this paper is to derive the energy and momentum conservation laws of the peridynamic nonlocal continuum theory using the principles of classical statistical mechanics. The peridynamic laws allow the consideration of discontinuous motion, or deformation, by relying on integral operators. These operators sum forces and power expenditures separated by a finite distance and so represent nonlocal interaction. The integral operators replace the differential divergence operators conventionally used, thereby obviating special treatment at points of discontinuity. The derivation presented employs a general multibody interatomic potential, avoiding the standard assumption of a pairwise decomposition. The integral operators are also expressed in terms of a stress tensor and heat flux vector under the assumption that these fields are differentiable, demonstrating that the classical continuum energy and momentum conservation laws are consequences of the more general peridynamic laws. An important conclusion is that nonlocal interaction is intrinsic to continuum conservation laws when derived using the principles of statistical mechanics.

Non a Priori Automatic Discovery of 3D Chemical Patterns: Application to Mutagenicity.

PubMed

Rabatel, Julien; Fannes, Thomas; Lepailleur, Alban; Le Goff, Jérémie; Crémilleux, Bruno; Ramon, Jan; Bureau, Ronan; Cuissart, Bertrand

2017-10-01

This article introduces a new type of structural fragment called a geometrical pattern. Such geometrical patterns are defined as molecular graphs that include a labelling of atoms together with constraints on interatomic distances. The discovery of geometrical patterns in a chemical dataset relies on the induction of multiple decision trees combined in random forests. Each computational step corresponds to a refinement of a preceding set of constraints, extending a previous geometrical pattern. This paper focuses on the mutagenicity of chemicals via the definition of structural alerts in relation with these geometrical patterns. It follows an experimental assessment of the main geometrical patterns to show how they can efficiently originate the definition of a chemical feature related to a chemical function or a chemical property. Geometrical patterns have provided a valuable and innovative approach to bring new pieces of information for discovering and assessing structural characteristics in relation to a particular biological phenotype. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

In-situ XAFS study for calcination process of Cr catalyst supported on γ-Al2O3 and SiO2

NASA Astrophysics Data System (ADS)

Watanabe, T.; Ikeda, K.; Katayama, M.; Inada, Y.

2016-05-01

The catalytic performance is largely affected by the oxidation state of supported Cr species, and its control changes the activity of Cr catalysts and the selectivity of products. In this study, the calcination process of the supported Cr catalysts on γ-Al2O3 and SiO2 was investigated by in-situ XAFS spectroscopy. The hydrate species was first supported by the impregnation method and was converted to CrO3 via Cr2O3 during the calcination process on both supporting materials. It was found that the temperature to complete the oxidation from Cr2O3 to CrO3 on SiO2 was higher than that on γ-Al2O3. The similarity of the interatomic distance between the surface oxygen atoms of the intermediate Cr2O3 species to that of SiO2 contributes to the stabilization of Cr2O3 on SiO2 during the calcination process.

XAFS Study of the Ferro- and Antiferromagnetic Binuclear Copper(II) Complexes of Azomethine Based Tridentate Ligands

NASA Astrophysics Data System (ADS)

Vlasenko, Valery G.; Vasilchenko, Igor S.; Pirog, Irina V.; Shestakova, Tatiana E.; Uraev, Ali I.; Burlov, Anatolii S.; Garnovskii, Alexander D.

2007-02-01

Binuclear copper complexes are known to be models for metalloenzymes containing copper active sites, and some of them are of considerable interest due to their magnetic and charge transfer properties. The reactions of the complex formation of bibasic tridentate heterocyclic imines with copper acetate leads to two types of chelates with mono deprotonated ligands and with totally deprotonated ligands. Cu K-edge EXAFS has been applied to determine the local structure around the metal center in copper(II) azomethine complexes with five tridentate ligands: 1-(salycilideneimino)- or 1-(2-tosylaminobenzilideneimino)-2-amino(oxo, thio)benzimidazoles. It has been found that some of the chelates studied are bridged binuclear copper complexes, and others are mononuclear complexes. The copper-copper interatomic distances in the bridged binuclear copper complexes were found to be 2.85-3.01 Å. Variable temperature magnetic susceptibility data indicate the presence of both ferromagnetic and antiferromagnetic interactions within the dimer, the former is dominating at low temperatures and the latter at high temperatures.

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

PubMed Central

Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; van Driel, Tim B.; Adachi, Shin-ichi; Bordage, Amélie; Bressler, Christian; Chabera, Pavel; Christensen, Morten; Dohn, Asmus O.; Galler, Andreas; Gawelda, Wojciech; Gosztola, David; Haldrup, Kristoffer; Harlang, Tobias; Liu, Yizhu; Møller, Klaus B.; Németh, Zoltán; Nozawa, Shunsuke; Pápai, Mátyás; Sato, Tokushi; Sato, Takahiro; Suarez-Alcantara, Karina; Togashi, Tadashi; Tono, Kensuke; Uhlig, Jens; Vithanage, Dimali A.; Wärnmark, Kenneth; Yabashi, Makina; Zhang, Jianxin; Sundström, Villy; Nielsen, Martin M.

2015-01-01

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined. PMID:25727920

Electron core ionization in compressed alkali metal cesium

NASA Astrophysics Data System (ADS)

Degtyareva, V. F.

2018-01-01

Elements of groups I and II in the periodic table have valence electrons of s-type and are usually considered as simple metals. Crystal structures of these elements at ambient pressure are close-packed and high-symmetry of bcc and fcc-types, defined by electrostatic (Madelung) energy. Diverse structures were found under high pressure with decrease of the coordination number, packing fraction and symmetry. Formation of complex structures can be understood within the model of Fermi sphere-Brillouin zone interactions and supported by Hume-Rothery arguments. With the volume decrease there is a gain of band structure energy accompanied by a formation of many-faced Brillouin zone polyhedra. Under compression to less than a half of the initial volume the interatomic distances become close to or smaller than the ionic radius which should lead to the electron core ionization. At strong compression it is necessary to assume that for alkali metals the valence electron band overlaps with the upper core electrons, which increases the valence electron count under compression.

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

DOE PAGES

Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; ...

2015-03-02

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances.more » Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.« less

Few Ramachandran Angle Changes Provide Interaction Strength Increase in Aβ42 versus Aβ40 Amyloid Fibrils

NASA Astrophysics Data System (ADS)

Bastidas, Oscar H.; Green, Benjamin; Sprague, Mary; Peters, Michael H.

2016-11-01

The pathology of Alzheimer’s disease can ultimately be traced to the increased aggregation stability of Aβ42 peptides which possess two extra residues (Ile 41 & Ala 42) that the non-pathological strain (Aβ40) lacks. We have found Aβ42 fibrils to exhibit stronger energies in inter-chain interactions and we have also identified the cause for this increase to be the result of different Ramachandran angle values in certain residues of the Aβ42 strain compared to Aβ40. These unique angle configurations result in the peptide planes in the fibril structures to be more vertical along the fibril axis for Aβ42 which thus reduces the inter-atomic distance between interacting atoms on vicinal peptide chains thereby increasing the electrostatic interaction energies. We lastly postulate that these different Ramachandran angle values could possibly be traced to the unique conformational folding avenues sampled by the Aβ42 peptide owing to the presence of its two extra residues.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

Formation of graphene on BN substrate by vapor deposition method and size effects on its structure

NASA Astrophysics Data System (ADS)

Giang, Nguyen Hoang; Hanh, Tran Thi Thu; Ngoc, Le Nhu; Nga, Nguyen To; Van Hoang, Vo

2018-04-01

We report MD simulation of the growth of graphene by the vapor deposition on a two-dimensional hBN substrate. The systems (containing carbon vapor and hBN substrate) are relaxed at high temperature (1500 K), and then it is cooled down to room one (300 K). Carbon atoms interact with the substrate via the Lennard-Jones potential while the interaction between carbon atoms is computed via the Tersoff potential. Depending on the size of the model, different crystalline honeycomb structures have been found. Structural properties of the graphene obtained at 300 K are studied by analyzing radial distribution functions (RDFs), coordination numbers, ring statistics, interatomic distances, bond-angle distributions and 2D visualization of atomic configurations. We find that the models containing various numbers of atoms have a honeycomb structure. Besides, differences in structural properties of graphene formed by the vapor deposition on the substrate and free standing one are found. Moreover, the size effect on the structure is significant.

Fluorescence detection of white-beam X-ray absorption anisotropy: towards element-sensitive projections of local atomic structure

PubMed Central

Korecki, P.; Tolkiehn, M.; Dąbrowski, K. M.; Novikov, D. V.

2011-01-01

Projections of the atomic structure around Nb atoms in a LiNbO3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples. PMID:21997909

Observation of dynamic atom-atom correlation in liquid helium in real space

DOE PAGES

Dmowski, W.; Diallo, S. O.; Lokshin, K.; ...

2017-05-04

Liquid 4He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom–atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4He atoms in the Bose–Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDFmore » peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom–atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.« less

Observation of dynamic atom-atom correlation in liquid helium in real space

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dmowski, W.; Diallo, S. O.; Lokshin, K.

Liquid 4He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom–atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4He atoms in the Bose–Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDFmore » peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom–atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.« less

Observation of dynamic atom-atom correlation in liquid helium in real space.

PubMed

Dmowski, W; Diallo, S O; Lokshin, K; Ehlers, G; Ferré, G; Boronat, J; Egami, T

2017-05-04

Liquid 4 He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom-atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4 He atoms in the Bose-Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDF peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom-atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.

The behavior of small helium clusters near free surfaces in tungsten

NASA Astrophysics Data System (ADS)

Barashev, A. V.; Xu, H.; Stoller, R. E.

2014-11-01

The results of a computational study of helium-vacancy clusters in tungsten are reported. A recently developed atomistic kinetic Monte Carlo method employing empirical interatomic potentials was used to investigate the behavior of clusters composed of three interstitial-helium atoms near {1 1 1}, {1 1 0} and {1 0 0} free surfaces. Multiple configurations were examined and the local energy landscape was characterized to determine cluster mobility and the potential for interactions with the surface. The clusters were found to be highly mobile if far from the surface, but were attracted and bound to the surface when within a distance of a few lattice parameters. When near the surface, the clusters were transformed into an immobile configuration due to the creation of a Frenkel pair; the vacancy was incorporated into what became a He3-vacancy complex. The corresponding interstitial migrated to and became an adatom on the free surface. This process can contribute to He retention, and may be responsible for the observed deterioration of the plasma-exposed tungsten surfaces.

Varying electronegativity of OH/O- groups depending on the nature and strength of H-bonding in phenol/phenolate involved in H-bond complexation.

PubMed

Krygowski, Tadeusz M; Szatyłowicz, Halina

2006-06-08

Application of the Domenicano et al. method of estimating group electronegativity from angular geometry of the ring in monosubstituted benzene derivatives allowed us to find how the electronegativity of OH/O(-) groups in H-bonded complexes of phenol and phenolate depends on the nature and strength of H-bond. For complexes in which the OH group is only proton donating in the H-bond, a linear dependence of the estimated electronegativity on O...O(N) interatomic distance was found for experimental (CSD base retrieved) data. The following rule is observed: the weaker the H-bond is, the more electronegative the OH group is. If apart from this kind of interaction the oxygen is proton accepting, then an increase of electronegativity is observed. Modeling (B3LYP/6-311+G) the variation of the strength of the H-bond by the fluoride anion approaching the OH leads to qualitatively the same picture as the scatter plots for experimental data.

Toward pressure-induced multiferroicity in PrMn2O5

NASA Astrophysics Data System (ADS)

Peng, W.; Balédent, V.; Chattopadhyay, S.; Lepetit, M.-B.; Yahia, G.; Colin, C. V.; Gooch, M. J.; Pasquier, C. R.; Auban-Senzier, P.; Greenblatt, M.; Foury-Leylekian, P.

2017-08-01

The series of multiferroics R Mn2O5 is extensively studied for its quasicollinear spin arrangement, which results in an electrical polarization according to the exchange-striction model. Variations of the interatomic distances modified by the external pressure can strongly influence the multiferroic properties. Understanding this influence is of great importance, especially for the future realization of multiferroic devices. As PrMn2O5 is paraelectric at ambient pressure, it is the most suitable candidate to search for pressure induced multiferroicity. In this paper, we report the emergence of a new pressure induced magnetic phase in PrMn2O5 determined by powder neutron diffraction under pressure. This new magnetic phase presenting at relatively low pressure becomes completely exclusive at 8 GPa. The determination of its magnetic structure has thus been possible for the first time. More importantly, the magnetic structure stabilized under pressure should induce a strong spontaneous electric polarization due to the nearly perfect collinearity of the Mn3 + and Mn4 + spins.

In situ stress observation in oxide films and how tensile stress influences oxygen ion conduction

PubMed Central

Fluri, Aline; Pergolesi, Daniele; Roddatis, Vladimir; Wokaun, Alexander; Lippert, Thomas

2016-01-01

Many properties of materials can be changed by varying the interatomic distances in the crystal lattice by applying stress. Ideal model systems for investigations are heteroepitaxial thin films where lattice distortions can be induced by the crystallographic mismatch with the substrate. Here we describe an in situ simultaneous diagnostic of growth mode and stress during pulsed laser deposition of oxide thin films. The stress state and evolution up to the relaxation onset are monitored during the growth of oxygen ion conducting Ce0.85Sm0.15O2-δ thin films via optical wafer curvature measurements. Increasing tensile stress lowers the activation energy for charge transport and a thorough characterization of stress and morphology allows quantifying this effect using samples with the conductive properties of single crystals. The combined in situ application of optical deflectometry and electron diffraction provides an invaluable tool for strain engineering in Materials Science to fabricate novel devices with intriguing functionalities. PMID:26912416

In-line three-dimensional holography of nanocrystalline objects at atomic resolution

DOE PAGES

Chen, F. -R.; Van Dyck, D.; Kisielowski, C.

2016-02-18

We report that resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we show a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose ratemore » electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. Lastly, we apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1–2 Å, which is smaller than inter-atomic distances.« less

An initial analysis of short- and medium-range correlations potential non-Pt catalysts in CoNx

NASA Astrophysics Data System (ADS)

Peterson, Joe

2009-10-01

A potential show stopper for the development of fuel cells for the commercial automotive industry is the design of low-cost catalysts. The best catalysts are based on platinum, which is a rare and expensive noble metal. Our group has been involved in the characterization of potential materials for non-Pt catalysts. In this presentation, I will present some preliminary neutron scattering data from a nanocrystalline powder sample of CoNx. It is apparent that the diffraction data cannot be analyzed with standard Riedveld refinement, and we have to invoke pair distribution function (PDF) analysis. The PDF provides insight into short-range correlations, as it measures the probabilities of short- and mid-range interatomic distances in a material. The analysis reveals a strong incoherent scattering response, which is indicative of the presence of hydrogen in the sample. After correcting for the incoherent scattering, one obtains the normalized scattering function S(Q), whose Fourier transform yields the PDF.

An initial analysis of short- and medium-range correlations potential non-Pt catalysts in CoNx

NASA Astrophysics Data System (ADS)

Peterson, Joe

2010-03-01

A potential show stopper for the development of fuel cells for the commercial automotive industry is the design of low-cost catalysts. The best catalysts are based on platinum, which is a rare and expensive noble metal. Our group has been involved in the characterization of potential materials for non-Pt catalysts. In this presentation, I will present some preliminary neutron scattering data from a nanocrystalline powder sample of CoNx. It is apparent that the diffraction data cannot be analyzed with standard Riedveld refinement, and we have to invoke pair distribution function (PDF) analysis. The PDF provides insight into short-range correlations, as it measures the probabilities of short- and mid-range interatomic distances in a material. The analysis reveals a strong incoherent scattering response, which is indicative of the presence of hydrogen in the sample. After correcting for the incoherent scattering, one obtains the normalized scattering function S(Q), whose Fourier transform yields the PDF.

Pressure Induced Iron Spin Crossover in MgGeO3 Perovskite and Post-perovskite

NASA Astrophysics Data System (ADS)

Wentzcovitch, R. M.; Shukla, G.; Topsakal, M.

2014-12-01

MgGeO3-perovskite is known to be a low-pressure analog of MgSiO3-perovskite in many respects, but especially in regard to the post-perovskite transition. As such, investigation of spin state changes in Fe-bearing MgGeO3 might help to clarify some aspects of this type of state change in Fe-bearing MgSiO3. Using DFT+U calculations, we have investigated pressure induced state changes in Fe-bearing MgGeO3 perovskite and post-perovskite. Owing to the relatively larger atomic size of germanium compared to silicon, germanate phases have larger unit cell volume and interatomic distances than equivalent silicate phases at same pressures. As a result, all pressure induced state changes in iron occur at higher pressures in germanate phases than in the silicate ones, be it a spin state change or position change of (ferrous) iron in the perovskite cage. The effect of iron in the post-perovskite transition is also investigated.

Preparation and crystal structure of U3Fe2C5: An original uranium-iron carbide

NASA Astrophysics Data System (ADS)

Henriques, M. S.; Paixão, J. A.; Henriques, M. S. C.; Gonçalves, A. P.

2015-09-01

The U3Fe2C5 compound was prepared from the elements by arc-melting, followed by an heat-treatment in an induction furnace, at 1250 °C for 1 h and 1300 °C for 2 h. The crystal structure of this phase was determined by direct methods from single crystal X-ray diffraction data. U3Fe2C5 crystallizes in an original tetragonal crystal structure, with space group I4/mmm, a = 3.4980(3) Å and c = 19.8380(15) Å as lattice constants and two formula units per cell. This new type structure is characterized by the simultaneous presence of isolated and pairs of carbon atoms, the interatomic distances in the pairs being similar to a typical carbon-carbon double bond length found in a molecule. U3Fe2C5 is closely related to UC and UFeC2, and can be seen as build from two (distorted) UFeC2 unit cells and a UC layer.

Materials discovery at high pressures

NASA Astrophysics Data System (ADS)

Zhang, Lijun; Wang, Yanchao; Lv, Jian; Ma, Yanming

2017-02-01

Pressure is a fundamental thermodynamic variable that can be used to control the properties of materials, because it reduces interatomic distances and profoundly modifies electronic orbitals and bonding patterns. It is thus a versatile tool for the creation of exotic materials not accessible at ambient conditions. Recently developed static and dynamic high-pressure experimental techniques have led to the synthesis of many functional materials with excellent performance: for example, superconductors, superhard materials and high-energy-density materials. Some of these advances have been aided and accelerated by first-principles crystal-structure searching simulations. In this Review, we discuss recent progress in high-pressure materials discovery, placing particular emphasis on the record high-temperature superconductivity in hydrogen sulfide and on nanotwinned cubic boron nitride and diamond, the hardest known materials. Energy materials and exotic chemical materials obtained under high pressures are also discussed. The main drawback of high-pressure materials is their destabilization after pressure release; this problem and its possible solutions are surveyed in the conclusions, which also provide an outlook on the future developments in the field.

Exact solution of a one-dimensional model of strained epitaxy on a periodically modulated substrate

NASA Astrophysics Data System (ADS)

Tokar, V. I.; Dreyssé, H.

2005-03-01

We consider a one-dimensional lattice gas model of strained epitaxy with the elastic strain accounted for through a finite number of cluster interactions comprising contiguous atomic chains. Interactions of this type arise in the models of strained epitaxy based on the Frenkel-Kontorova model. Furthermore, the deposited atoms interact with the substrate via an arbitrary periodic potential of period L . This model is solved exactly with the use of an appropriately adopted technique developed recently in the theory of protein folding. The advantage of the proposed approach over the standard transfer-matrix method is that it reduces the problem to finding the largest eigenvalue of a matrix of size L instead of 2L-1 , which is vital in the case of nanostructures where L may measure in hundreds of interatomic distances. Our major conclusion is that the substrate modulation always facilitates the size calibration of self-assembled nanoparticles in one- and two-dimensional systems.

Physically founded phonon dispersions of few-layer materials and the case of borophene

DOE PAGES

Carrete, Jesús; Li, Wu; Lindsay, Lucas; ...

2016-04-21

By building physically sound interatomic force constants,we offer evidence of the universal presence of a quadratic phonon branch in all unstrained 2D materials, thus contradicting much of the existing literature. Through a reformulation of the interatomic force constants (IFCs) in terms of internal coordinates, we find that a delicate balance between the IFCs is responsible for this quadraticity. We use this approach to predict the thermal conductivity of Pmmn borophene, which is comparable to that of MoS 2, and displays a remarkable in-plane anisotropy. Ultimately, these qualities may enable the efficient heat management of borophene devices in potential nanoelectronic applications

Elasticity and dislocation anelasticity of crystals

NASA Astrophysics Data System (ADS)

Nikanorov, S. P.; Kardashev, B. K.

The book is concerned with the application of the results of physical acoustic studies of elasticity and dislocation anelasticity to the investigation of interatomic interactions and interactions between lattice defects. The analysis of the potential functions determining the energy of interatomic interactions is based on a study of the elastic properties of crystals over a wide temperature range; data on the dislocation structure and on the interaction between dislocations and point defects are based mainly on a study of inelastic effects. Particular attention is given to the relationship between microplastic effects and the initial stage of plastic deformation under conditions of elastic oscillations, when the multiplication of dislocations is negligible.

Elasticity and dislocation inelasticity of crystals

NASA Astrophysics Data System (ADS)

Nikanorov, S. P.; Kardashev, B. K.

The use of methods of physical acoustics for studying the elasticity and dislocation inelasticity of crystals is discussed, as is the application of the results of such studies to the analysis of interatomic and lattice defect interactions. The analysis of the potential functions determining the energy of interatomic interactions is based on an analysis of the elastic properties of crystals over a wide temperature range. The data on the dislocation structure and the interaction between dislocations and point defects are obtained from a study of inelastic effects. Particular attention is given to the relationship between microplastic effects under conditions of elastic oscillations and the initial stage of plastic deformation.

Investigation of matter-antimatter interaction for possible propulsion applications

NASA Technical Reports Server (NTRS)

Morgan, D. L., Jr.

1974-01-01

Matter-antimatter annihilation is discussed as a means of rocket propulsion. The feasibility of different means of antimatter storage is shown to depend on how annihilation rates are affected by various circumstances. The annihilation processes are described, with emphasis on important features of atom-antiatom interatomic potential energies. A model is developed that allows approximate calculation of upper and lower bounds to the interatomic potential energy for any atom-antiatom pair. Formulae for the upper and lower bounds for atom-antiatom annihilation cross-sections are obtained and applied to the annihilation rates for each means of antimatter storage under consideration. Recommendations for further studies are presented.

A Wsbnd Ne interatomic potential for simulation of neon implantation in tungsten

NASA Astrophysics Data System (ADS)

Backman, Marie; Juslin, Niklas; Huang, Guiyang; Wirth, Brian D.

2016-08-01

An interatomic pair potential for Wsbnd Ne is developed for atomistic molecular dynamics simulations of neon implantation in tungsten. The new potential predicts point defect energies and binding energies of small clusters that are in good agreement with electronic structure calculations. Molecular dynamics simulations of small neon clusters in tungsten show that trap mutation, in which an interstitial neon cluster displaces a tungsten atom from its lattice site, occurs for clusters of three or more neon atoms. However, near a free surface, trap mutation can occur at smaller sizes, including even a single neon interstitial in close proximity to a (100) or (110) surface.

Visualizing global properties of a molecular dynamics trajectory.

PubMed

Zhou, Hao; Li, Shangyang; Makowski, Lee

2016-01-01

Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one-dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule. © 2015 Wiley Periodicals, Inc.

Chiral magnetism of magnetic adatoms generated by Rashba electrons

NASA Astrophysics Data System (ADS)

Bouaziz, Juba; dos Santos Dias, Manuel; Ziane, Abdelhamid; Benakki, Mouloud; Blügel, Stefan; Lounis, Samir

2017-02-01

We investigate long-range chiral magnetic interactions among adatoms mediated by surface states spin-splitted by spin-orbit coupling. Using the Rashba model, the tensor of exchange interactions is extracted wherein a thepseudo-dipolar interaction is found, in addition to the usual isotropic exchange interaction and the Dzyaloshinskii-Moriya interaction. We find that, despite the latter interaction, collinear magnetic states can still be stabilized by the pseudo-dipolar interaction. The interadatom distance controls the strength of these terms, which we exploit to design chiral magnetism in Fe nanostructures deposited on a Au(111) surface. We demonstrate that these magnetic interactions are related to superpositions of the out-of-plane and in-plane components of the skyrmionic magnetic waves induced by the adatoms in the surrounding electron gas. We show that, even if the interatomic distance is large, the size and shape of the nanostructures dramatically impacts on the strength of the magnetic interactions, thereby affecting the magnetic ground state. We also derive an appealing connection between the isotropic exchange interaction and the Dzyaloshinskii-Moriya interaction, which relates the latter to the first-order change of the former with respect to spin-orbit coupling. This implies that the chirality defined by the direction of the Dzyaloshinskii-Moriya vector is driven by the variation of the isotropic exchange interaction due to the spin-orbit interaction.

Reconstruction of interatomic vectors by principle component analysis of nuclear magnetic resonance data in multiple alignments

NASA Astrophysics Data System (ADS)

Hus, Jean-Christophe; Bruschweiler, Rafael

2002-07-01

A general method is presented for the reconstruction of interatomic vector orientations from nuclear magnetic resonance (NMR) spectroscopic data of tensor interactions of rank 2, such as dipolar coupling and chemical shielding anisotropy interactions, in solids and partially aligned liquid-state systems. The method, called PRIMA, is based on a principal component analysis of the covariance matrix of the NMR parameters collected for multiple alignments. The five nonzero eigenvalues and their eigenvectors efficiently allow the approximate reconstruction of the vector orientations of the underlying interactions. The method is demonstrated for an isotropic distribution of sample orientations as well as for finite sets of orientations and internuclear vectors encountered in protein systems.

Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

PubMed

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

Molecular dynamics for near melting temperatures simulations of metals using modified embedded-atom method

NASA Astrophysics Data System (ADS)

Etesami, S. Alireza; Asadi, Ebrahim

2018-01-01

Availability of a reliable interatomic potential is one of the major challenges in utilizing molecular dynamics (MD) for simulations of metals at near the melting temperatures and melting point (MP). Here, we propose a novel approach to address this challenge in the concept of modified-embedded-atom (MEAM) interatomic potential; also, we apply the approach on iron, nickel, copper, and aluminum as case studies. We propose adding experimentally available high temperature elastic constants and MP of the element to the list of typical low temperature properties used for the development of MD interatomic potential parameters. We show that the proposed approach results in a reasonable agreement between the MD calculations of melting properties such as latent heat, expansion in melting, liquid structure factor, and solid-liquid interface stiffness and their experimental/computational counterparts. Then, we present the physical properties of mentioned elements near melting temperatures using the new MEAM parameters. We observe that the behavior of elastic constants, heat capacity and thermal linear expansion coefficient at room temperature compared to MP follows an empirical linear relation (α±β × MP) for transition metals. Furthermore, a linear relation between the tetragonal shear modulus and the enthalpy change from room temperature to MP is observed for face-centered cubic materials.

Local structure in solid solutions of stabilised zirconia with actinide dioxides (UO{sub 2}, NpO{sub 2})

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walter, Marcus, E-mail: marcus.walter@vkta.d; Somers, Joseph; Bouexiere, Daniel

2011-04-15

The local structure of (Zr,Lu,U)O{sub 2-x} and (Zr,Y,Np)O{sub 2-x} solid solutions has been investigated by extended X-ray absorption fine structure (EXAFS). Samples were prepared by mixing reactive (Zr,Lu)O{sub 2-x} and (Zr,Y)O{sub 2-x} precursor materials with the actinide oxide powders, respectively. Sintering at 1600 {sup o}C in Ar/H{sub 2} yields a fluorite structure with U(IV) and Np(IV). As typical for stabilised zirconia the metal-oxygen and metal-metal distances are characteristic for the different metal ions. The bond lengths increase with actinide concentration, whereas highest adaptation to the bulk stabilised zirconia structure was observed for U---O and Np---O bonds. The Zr---O bond showsmore » only a slight increase from 2.14 A at 6 mol% actinide to 2.18 A at infinite dilution in UO{sub 2} and NpO{sub 2}. The short interatomic distance between Zr and the surrounding oxygen and metal atoms indicate a low relaxation of Zr with respect to the bulk structure, i.e. a strong Pauling behaviour. -- Graphical abstract: Metal-oxygen bond distances in (Zr,Lu,U)O{sub 2-x} solid solutions with different oxygen vacancy concentrations (Lu/Zr=1 and Lu/Zr=0.5). Display Omitted Research Highlights: {yields} EXAFS indicates high U and Np adaption to the bulk structure of stabilised zirconia. {yields} Zr---O bond length is 2.18 A at infinite Zr dilution in UO{sub 2} and NpO{sub 2}. {yields} Low relaxation (strong Pauling behaviour) of Zr explains its low solubility in UO{sub 2}.« less

Sparkle model for AM1 calculation of lanthanide complexes: improved parameters for europium.

PubMed

Rocha, Gerd B; Freire, Ricardo O; Da Costa, Nivan B; De Sá, Gilberto F; Simas, Alfredo M

2004-04-05

In the present work, we sought to improve our sparkle model for the calculation of lanthanide complexes, SMLC,in various ways: (i) inclusion of the europium atomic mass, (ii) reparametrization of the model within AM1 from a new response function including all distances of the coordination polyhedron for tris(acetylacetonate)(1,10-phenanthroline) europium(III), (iii) implementation of the model in the software package MOPAC93r2, and (iv) inclusion of spherical Gaussian functions in the expression which computes the core-core repulsion energy. The parametrization results indicate that SMLC II is superior to the previous version of the model because Gaussian functions proved essential if one requires a better description of the geometries of the complexes. In order to validate our parametrization, we carried out calculations on 96 europium(III) complexes, selected from Cambridge Structural Database 2003, and compared our predicted ground state geometries with the experimental ones. Our results show that this new parametrization of the SMLC model, with the inclusion of spherical Gaussian functions in the core-core repulsion energy, is better capable of predicting the Eu-ligand distances than the previous version. The unsigned mean error for all interatomic distances Eu-L, in all 96 complexes, which, for the original SMLC is 0.3564 A, is lowered to 0.1993 A when the model was parametrized with the inclusion of two Gaussian functions. Our results also indicate that this model is more applicable to europium complexes with beta-diketone ligands. As such, we conclude that this improved model can be considered a powerful tool for the study of lanthanide complexes and their applications, such as the modeling of light conversion molecular devices.

Interatomic relaxation processes induced in neon dimers by electron-impact ionization

NASA Astrophysics Data System (ADS)

Yan, S.; Zhang, P.; Stumpf, V.; Gokhberg, K.; Zhang, X. C.; Xu, S.; Li, B.; Shen, L. L.; Zhu, X. L.; Feng, W. T.; Zhang, S. F.; Zhao, D. M.; Ma, X.

2018-01-01

We report an experimental observation of the interatomic Coulombic decay (ICD) and radiative charge-transfer (RCT) processes in a Ne dimer (e ,2 e ) following a 380-eV electron impact. By detecting the N e+-N e+ cation pair and one of the emitted electrons in coincidence, the fingerprint of the ICD process initiated by the inner-valence ionization of Ne is obtained. Furthermore, the experimental results and ab initio calculations together unambiguously confirm the occurrence of the RCT process, and we show that most of the low-energy electrons produced in ionization of the Ne dimers are due to the ICD, which strongly suggests the importance of the ICD in causing radiation damage in a biological medium.

Simple formalism for efficient derivatives and multi-determinant expansions in quantum Monte Carlo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Filippi, Claudia, E-mail: c.filippi@utwente.nl; Assaraf, Roland, E-mail: assaraf@lct.jussieu.fr; Moroni, Saverio, E-mail: moroni@democritos.it

2016-05-21

We present a simple and general formalism to compute efficiently the derivatives of a multi-determinant Jastrow-Slater wave function, the local energy, the interatomic forces, and similar quantities needed in quantum Monte Carlo. Through a straightforward manipulation of matrices evaluated on the occupied and virtual orbitals, we obtain an efficiency equivalent to algorithmic differentiation in the computation of the interatomic forces and the optimization of the orbital parameters. Furthermore, for a large multi-determinant expansion, the significant computational gain afforded by a recently introduced table method is here extended to the local value of any one-body operator and to its derivatives, inmore » both all-electron and pseudopotential calculations.« less

Analytic Interatomic Forces in the Random Phase Approximation

NASA Astrophysics Data System (ADS)

Ramberger, Benjamin; Schäfer, Tobias; Kresse, Georg

2017-03-01

We discuss that in the random phase approximation (RPA) the first derivative of the energy with respect to the Green's function is the self-energy in the G W approximation. This relationship allows us to derive compact equations for the RPA interatomic forces. We also show that position dependent overlap operators are elegantly incorporated in the present framework. The RPA force equations have been implemented in the projector augmented wave formalism, and we present illustrative applications, including ab initio molecular dynamics simulations, the calculation of phonon dispersion relations for diamond and graphite, as well as structural relaxations for water on boron nitride. The present derivation establishes a concise framework for forces within perturbative approaches and is also applicable to more involved approximations for the correlation energy.

Comparative investigation of the solution species [U(CO3)5]6- and the crystal structure of Na6[U(CO3)5].12H2O.

PubMed

Hennig, Christoph; Ikeda-Ohno, Atsushi; Emmerling, Fanziska; Kraus, Werner; Bernhard, Gert

2010-04-21

The limiting U(IV) carbonate species in aqueous solution was investigated by comparing its structure parameters with those of the complex preserved in a crystal structure. The solution species prevails in aqueous solution of 0.05 M U(IV) and 1 M NaHCO(3) at pH 8.3. Single crystals of Na(6)[U(CO(3))(5)].12H(2)O were obtained directly from this mother solution. The U(IV) carbonate complex in the crystal structure was identified as a monomeric [U(CO(3))(5)](6-) anionic complex. The interatomic distances around the U(IV) coordination polyhedron show average distances of U-O = 2.461(8) A, U-C = 2.912(4) A and U-O(dist) = 4.164(6) A. U L(3)-edge EXAFS spectra were collected from the solid Na(6)[U(CO(3))(5)].12H(2)O and the corresponding solution. The first shell of the Fourier transforms (FTs) revealed, in both samples, a coordination of ten oxygen atoms at an average U-O distance of 2.45 +/- 0.02 A, the second shell originates from five carbon atoms with a U-C distance of 2.91 +/- 0.02 A, and the third shell was fit with single and multiple scattering paths of the distal oxygen at 4.17 +/- 0.02 A. These data indicate the identity of the [U(CO(3))(5)](6-) complex in solid and solution state. The high negative charge of the [U(CO(3))(5)](6-) anion is compensated by Na(+) cations. In solid state the Na(+) cations form a bridging network between the [U(CO(3))(5)](6-) units, while in liquid state the Na(+) cations seem to be located close to the anionic complex. The average metal-oxygen distances of the coordination polyhedron show a linear correlation to the radius contraction of the neighbouring actinide(IV) ions and indicate the equivalence of the [An(CO(3))(5)](6-) coordination within the series of thorium, uranium, neptunium and plutonium.

First-principles interatomic potentials for transition-metal aluminides. III. Extension to ternary phase diagrams

NASA Astrophysics Data System (ADS)

Widom, Mike; Al-Lehyani, Ibrahim; Moriarty, John A.

2000-08-01

Modeling structural and mechanical properties of intermetallic compounds and alloys requires detailed knowledge of their interatomic interactions. The first two papers of this series [Phys. Rev. B 56, 7905 (1997); 58, 8967 (1998)] derived first-principles interatomic potentials for transition-metal (TM) aluminides using generalized pseudopotential theory (GPT). Those papers focused on binary alloys of aluminum with first-row transition metals and assessed the ability of GPT potentials to reproduce and elucidate the alloy phase diagrams of Al-Co and Al-Ni. This paper addresses the phase diagrams of the binary alloy Al-Cu and the ternary systems Al-Co-Cu and Al-Co-Ni, using GPT pair potentials calculated in the limit of vanishing transition-metal concentration. Despite this highly simplifying approximation, we find rough agreement with the known low-temperature phase diagrams, up to 50% total TM concentration provided the Co fraction is below 25%. Full composition-dependent potentials and many-body interactions would be required to correct deficiencies at higher Co concentration. Outside this troublesome region, the experimentally determined stable and metastable phases all lie on or near the convex hull of a scatter plot of energy versus composition. We verify, qualitatively, reported solubility ranges extending binary alloys into the ternary diagram in both Al-Co-Cu and Al-Co-Ni. Finally, we reproduce previously conjectured transition-metal positions in the decagonal quasicrystal phase.

Evaluation of interatomic potentials for rainbow scattering under axial channeling at KCl(0 0 1) surface by three-dimensional computer simulations based on binary collision approximation

NASA Astrophysics Data System (ADS)

Takeuchi, Wataru

2017-05-01

The rainbow angles corresponding to prominent peaks in the angular distributions of scattered projectiles with small angle, attributed to rainbow scattering (RS), under axial surface channeling conditions are strongly influenced by the interatomic potentials between projectiles and target atoms. The dependence of rainbow angles on normal energy of projectile energy to the target surface, being experimentally obtained by Specht et al. for RS of He, N, Ne and Ar atoms under <1 0 0> and <1 1 0> axial channeling conditions at a KCl(0 0 1) surface with projectile energies of 1-60 keV, was evaluated by the three-dimensional computer simulations using the ACOCT code based on the binary collision approximation with interatomic pair potentials. Good agreement between the ACOCT results using the ZBL pair potential and the individual pair potentials calculated from Hartree-Fock (HF) wave functions and the experimental ones was found for RS of He, N and Ne atoms from the atomic rows along <1 0 0> direction. For <1 1 0> direction, the ACOCT results employing the Moliere pair potential with adjustable screening length of O'Connor-Biersack (OB) formula, the ZBL pair potential and the individual HF pair potentials except for Ar → KCl using the OB pair potential are nearly in agreement with the experimental ones.

High-pressure structural study of MnF 2

DOE PAGES

Stavrou, Elissaios; Yao, Yansun; Goncharov, Alexander F.; ...

2015-02-01

In this study, manganese fluoride (MnF 2) with the tetragonal rutile-type structure has been studied using a synchrotron angle-dispersive powder x-ray diffraction and Raman spectroscopy in a diamond anvil cell up to 60 GPa at room temperature combined with first-principles density functional calculations. The experimental data reveal two pressure-induced structural phase transitions with the following sequence: rutile → SrI 2 type (3 GPa)→ α–PbCl 2 type (13 GPa). Complete structural information, including interatomic distances, has been determined in the case of MnF 2 including the exact structure of the debated first high-pressure phase. First-principles density functional calculations confirm this phasemore » transition sequence, and the two calculated transition pressures are in excellent agreement with the experiment. Lattice dynamics calculations also reproduce the experimental Raman spectra measured for the ambient and high-pressure phases. The results are discussed in line with the possible practical use of rutile-type fluorides in general and specifically MnF 2 as a model compound to reveal the HP structural behavior of rutile-type SiO 2 (Stishovite).« less

Construction of crystal structure prototype database: methods and applications.

PubMed

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-26

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Thermal stability of Ag, Al, Sn, Pb, and Hg films reinforced by 2D (C, Si) crystals and the formation of interfacial fluid states in them upon heating. MD experiment

NASA Astrophysics Data System (ADS)

Polukhin, V. A.; Kurbanova, E. D.

2016-02-01

Molecular dynamics simulation is used to study the thermal stability of the interfacial states of metallic Al, Ag, Sn, Pb, and Hg films (i.e., the structural elements of superconductor composites and conducting electrodes) reinforced by 2D graphene and silicene crystals upon heating up to disordering and to analyze the formation of nonautonomous fluid pseudophases in interfaces. The effect of perforation defects in reinforcing 2D-C and 2D-Si planes with passivated edge covalent bonds on the atomic dynamics is investigated. As compared to Al and Ag, the diffusion coefficients in Pd and Hg films increase monotonically with temperature during thermally activated disordering processes, the interatomic distances decrease, the sizes decrease, drops form, and their density profile grows along the normal. The coagulation of Pb and Hg drops is accompanied by a decrease in the contact angle, the reduction of the interface contact with graphene, and the enhancement of its corrugation (waviness).

Gold atoms and clusters on MgO(100) films; an EPR and IRAS study

NASA Astrophysics Data System (ADS)

Yulikov, M.; Sterrer, M.; Risse, T.; Freund, H.-J.

2009-06-01

Single gold atoms deposited on single crystalline MgO(1 0 0) films grown on Mo(1 0 0) are characterized by electron paramagnetic resonance spectroscopy as well as IR spectroscopy using CO as probe molecules. In this article we describe the first angular dependent measurements to determine the principal hyperfine components of a secondary hyperfine interaction, namely, with 17O of the MgO. The values determined here are in perfect agreement with theoretical expectations and corroborate the previously reported binding mechanism of Au atoms on the oxygen anions of the MgO terrace. The temperature dependent EPR data reveal an onset of Au atom mobility at about 80 K while the formation of Au particles occurs only above 125 K. By an analysis of the EPR line width in combination with STM measurements it is possible to deduce an increase of the interatomic distance above 80 K. The Au/CO complexes show a somewhat smaller temperature stability as compared to the Au atoms. The observed thermal stability is in perfect agreement with theoretical predictions for CO desorption.

Anomalous Thermal Expansion of HoCo0.5Cr0.5O3 Probed by X-ray Synchrotron Powder Diffraction.

PubMed

Hreb, Vasyl; Vasylechko, Leonid; Mykhalichko, Vitaliya; Prots, Yurii

2017-12-01

Mixed holmium cobaltite-chromite HoCo 0.5 Cr 0.5 O 3 with orthorhombic perovskite structure (structure type GdFeO 3 , space group Pbnm) was obtained by solid state reaction of corresponding oxides in air at 1373 K. Room- and high-temperature structural parameters were derived from high-resolution X-ray synchrotron powder diffraction data collected in situ in the temperature range of 300-1140 K. Analysis of the results obtained revealed anomalous thermal expansion of HoCo 0.5 Cr 0.5 O 3 , which is reflected in a sigmoidal temperature dependence of the unit cell parameters and in abnormal increase of the thermal expansion coefficients with a broad maxima near 900 K. Pronounced anomalies are also observed for interatomic distances and angles within Co/CrO 6 octahedra, tilt angles of octahedra and atomic displacement parameters. The observed anomalies are associated with the changes of spin state of Co 3+ ions and insulator-metal transition occurring in HoCo 0.5 Cr 0.5 O 3 .

Electrical resistivity of liquid iron with high concentration of light element impurities

NASA Astrophysics Data System (ADS)

Wagle, F.; Steinle-Neumann, G.

2017-12-01

The Earth's outer core mainly consists of liquid iron, enriched with several weight percent of lighter elements, such as silicon, oxygen, sulfur or carbon. Electrical resistivities of alloys of this type determine the stability of the geodynamo. Both computational and experimental results show that resistivites of Fe-based alloys deviate significantly from values of pure Fe. Using optical conductivity values computed with the Kubo-Greenwood formalism for DFT-based molecular dynamics results, we analyze the high-P and T behavior of resitivities for Fe-alloys containing various concentrations of sulfur, oxygen and silicon. As the electron mean free path length in amorphous and liquid material becomes comparable to interatomic distances at high P and T, electron scattering is expected to be dominated by the short-range order, rather than T-dependent vibrational contributions, and we describe such correlations in our results. In analogy to macroscopic porous media, we further show that resistivity of a liquid metal-nonmetal alloy is determined to first order by the resistivity of the metallic matrix and the volume fraction of non-metallic impurities.

Hydrogen bonding between hydrides of the upper-right part of the periodic table

NASA Astrophysics Data System (ADS)

Simončič, Matjaž; Urbic, Tomaz

2018-05-01

One of the most important electrostatic interactions between molecules is most definitely the hydrogen bond. Understanding the basis of this interaction may offer us the insight needed to understand its effect on the macroscopic scale. Hydrogen bonding is for example the reason for anomalous properties in compounds like water and naturally life as we know it. The strength of the bond depends on numerous factors, among them the electronegativity of participating atoms. In this work we calculated the strength of hydrogen bonds between hydrides of the upper-right part of the periodic table (C, N, O, F, P, S, Cl, As, Se, Br) using quantum-chemical methods. The aim was to determine what influences the strength of strong and weak hydrogen bonds in simple hydrides. Various relationships were checked. A relation between the strength of the bond and the electronegativity of the participating atoms was found. We also observed a correlation between the strength of hydrogen bonds and the inter-atomic distances, along with the dependence on the charge transfer on the atom of the donor. We also report characteristic geometries of different dimers.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siqueira, M. C.; Maia, R. N. A.; Araujo, R. M. T.

In this article, we investigated structural and thermal properties of an amorphous alloy of the Ga–Se system. The amorphous GaSe{sub 9} alloy was produced by mechanical alloying and it was studied using EXAFS spectroscopy and cumulant expansion method. We also made reverse Monte Carlo simulations using the total structure factor S(K) obtained from x-ray diffraction and the EXAFS χ(k) oscillations on Se and Ga K edges as input data. Several parameters, such as average coordination numbers and interatomic distances, structural and thermal disorders, asymmetry of the partial distribution functions g{sub ij}(r), and Einstein and Debye temperatures, were determined. The g{submore » ij}{sup E}(r) functions were reconstructed from the cumulants C{sub 1}, C{sub 2}, and C{sub 3} obtained from the Einstein model, and they were compared to the g{sub ij}{sup RMC}(r) functions obtained from the simulations. The simulations also furnished the partial bond angle distribution functions Θ{sub ijℓ}(cosθ), which describe the angular distribution of bonds between first neighbors, and give information about the kind of structural units present in the alloy.« less

Some Structural Properties of the Mixed Lead-Magnesium Hydroxyapatites

NASA Astrophysics Data System (ADS)

Kaaroud, K.; Ben Moussa, S.; Brigui, N.; Badraoui, B.

2018-02-01

Lead-magnesium hydroxyapatite solid solutions Pb(10- x)Mg x (PO4)6(OH)2 have been prepared via a hydrothermal process. They were characterized by X-ray powder diffraction, Transmission Electron Microscopy (TEM), chemical and IR spectroscopic analyses. The results of the structural refinement indicated that the limits of lead-magnesium solid solutions ( x ≤ 1.5), a regular decrease of the lattice constant a and a preferential magnesium distribution in site S(I). Through the progressive replacement of Pb2+ ( r = 0.133 nm) by the smaller cation Mg2+ ( r = 0.072 nm), all interatomic distances decrease in accordance with the decrease of the cell parameters. According to what could be expected from the coordinance of the metallic sites S(I) (hexacoordination) and S(II) (heptacoordination), the small magnesium cation preferentially occupies the four sites S(I). The results of the TEM analysis confirm the presence of magnesium in the starting solution and reveals the decrease in the average size of crystals. The IR spectra show the presence of the absorption bands characteristic for the apatite structure.

Anomalous Thermal Expansion of HoCo0.5Cr0.5O3 Probed by X-ray Synchrotron Powder Diffraction

NASA Astrophysics Data System (ADS)

Hreb, Vasyl; Vasylechko, Leonid; Mykhalichko, Vitaliya; Prots, Yurii

2017-07-01

Mixed holmium cobaltite-chromite HoCo0.5Cr0.5O3 with orthorhombic perovskite structure (structure type GdFeO3, space group Pbnm) was obtained by solid state reaction of corresponding oxides in air at 1373 K. Room- and high-temperature structural parameters were derived from high-resolution X-ray synchrotron powder diffraction data collected in situ in the temperature range of 300-1140 K. Analysis of the results obtained revealed anomalous thermal expansion of HoCo0.5Cr0.5O3, which is reflected in a sigmoidal temperature dependence of the unit cell parameters and in abnormal increase of the thermal expansion coefficients with a broad maxima near 900 K. Pronounced anomalies are also observed for interatomic distances and angles within Co/CrO6 octahedra, tilt angles of octahedra and atomic displacement parameters. The observed anomalies are associated with the changes of spin state of Co3+ ions and insulator-metal transition occurring in HoCo0.5Cr0.5O3.

Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

PubMed Central

Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

2015-01-01

Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants. PMID:26597773

Construction of crystal structure prototype database: methods and applications

NASA Astrophysics Data System (ADS)

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-01

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Monte Carlo analysis of neutron diffuse scattering data

NASA Astrophysics Data System (ADS)

Goossens, D. J.; Heerdegen, A. P.; Welberry, T. R.; Gutmann, M. J.

2006-11-01

This paper presents a discussion of a technique developed for the analysis of neutron diffuse scattering data. The technique involves processing the data into reciprocal space sections and modelling the diffuse scattering in these sections. A Monte Carlo modelling approach is used in which the crystal energy is a function of interatomic distances between molecules and torsional rotations within molecules. The parameters of the model are the spring constants governing the interactions, as they determine the correlations which evolve when the model crystal structure is relaxed at finite temperature. When the model crystal has reached equilibrium its diffraction pattern is calculated and a χ2 goodness-of-fit test between observed and calculated data slices is performed. This allows a least-squares refinement of the fit parameters and so automated refinement can proceed. The first application of this methodology to neutron, rather than X-ray, data is outlined. The sample studied was deuterated benzil, d-benzil, C14D10O2, for which data was collected using time-of-flight Laue diffraction on SXD at ISIS.

MDTRA: a molecular dynamics trajectory analyzer with a graphical user interface.

PubMed

Popov, Alexander V; Vorobjev, Yury N; Zharkov, Dmitry O

2013-02-05

Most of existing software for analysis of molecular dynamics (MD) simulation results is based on command-line, script-guided processes that require the researchers to have an idea about programming language constructions used, often applied to the one and only product. Here, we describe an open-source cross-platform program, MD Trajectory Reader and Analyzer (MDTRA), that performs a large number of MD analysis tasks assisted with a graphical user interface. The program has been developed to facilitate the process of search and visualization of results. MDTRA can handle trajectories as sets of protein data bank files and presents tools and guidelines to convert some other trajectory formats into such sets. The parameters analyzed by MDTRA include interatomic distances, angles, dihedral angles, angles between planes, one-dimensional and two-dimensional root-mean-square deviation, solvent-accessible area, and so on. As an example of using the program, we describe the application of MDTRA to analyze the MD of formamidopyrimidine-DNA glycosylase, a DNA repair enzyme from Escherichia coli. Copyright © 2012 Wiley Periodicals, Inc.

Measurements of relative chemical shift tensor orientations in solid-state NMR: new slow magic angle spinning dipolar recoupling experiments.

PubMed

Jurd, Andrew P S; Titman, Jeremy J

2009-08-28

Solid-state NMR experiments can be used to determine conformational parameters, such as interatomic distances and torsion angles. The latter can be obtained from measurements of the relative orientation of two chemical shift tensors, if the orientation of these with respect to the surrounding bonds is known. In this paper, a new rotor-synchronized magic angle spinning (MAS) dipolar correlation experiment is described which can be used in this way. Because the experiment requires slow MAS rates, a novel recoupling sequence, designed using symmetry principles, is incorporated into the mixing period. This recoupling sequence is based in turn on a new composite cyclic pulse referred to as COAST (for combined offset and anisotropy stabilization). The new COAST-C7(2)(1) sequence is shown to give good theoretical and experimental recoupling efficiency, even when the CSA far exceeds the MAS rate. In this regime, previous recoupling sequences, such as POST-C7(2)(1), exhibit poor recoupling performance. The effectiveness of the new method has been explored by a study of the dipeptide L-phenylalanyl-L-phenylalanine.

Empirical potential for molecular simulation of graphene nanoplatelets

NASA Astrophysics Data System (ADS)

Bourque, Alexander J.; Rutledge, Gregory C.

2018-04-01

A new empirical potential for layered graphitic materials is reported. Interatomic interactions within a single graphene sheet are modeled using a Stillinger-Weber potential. Interatomic interactions between atoms in different sheets of graphene in the nanoplatelet are modeled using a Lennard-Jones interaction potential. The potential is validated by comparing molecular dynamics simulations of tensile deformation with the reported elastic constants for graphite. The graphite is found to fracture into graphene nanoplatelets when subjected to ˜15% tensile strain normal to the basal surface of the graphene stack, with an ultimate stress of 2.0 GPa and toughness of 0.33 GPa. This force field is useful to model molecular interactions in an important class of composite systems comprising 2D materials like graphene and multi-layer graphene nanoplatelets.

Interatomic Coulombic Decay: The Mechanism for Rapid Deexcitation of Hollow Atoms.

PubMed

Wilhelm, Richard A; Gruber, Elisabeth; Schwestka, Janine; Kozubek, Roland; Madeira, Teresa I; Marques, José P; Kobus, Jacek; Krasheninnikov, Arkady V; Schleberger, Marika; Aumayr, Friedrich

2017-09-08

The impact of a highly charged ion onto a solid gives rise to charge exchange between the ion and target atoms, so that a slow ion gets neutralized in the vicinity of the surface. Using highly charged Ar and Xe ions and the surface-only material graphene as a target, we show that the neutralization and deexcitation of the ions proceeds on a sub-10 fs time scale. We further demonstrate that a multiple Interatomic Coulombic Decay (ICD) model can describe the observed ultrafast deexcitation. Other deexcitation mechanisms involving nonradiative decay and quasimolecular orbital formation during the impact are not important, as follows from the comparison of our experimental data with the results of first-principles calculations. Our method also enables the estimation of ICD rates directly.

Data-Driven Learning of Total and Local Energies in Elemental Boron

NASA Astrophysics Data System (ADS)

Deringer, Volker L.; Pickard, Chris J.; Csányi, Gábor

2018-04-01

The allotropes of boron continue to challenge structural elucidation and solid-state theory. Here we use machine learning combined with random structure searching (RSS) algorithms to systematically construct an interatomic potential for boron. Starting from ensembles of randomized atomic configurations, we use alternating single-point quantum-mechanical energy and force computations, Gaussian approximation potential (GAP) fitting, and GAP-driven RSS to iteratively generate a representation of the element's potential-energy surface. Beyond the total energies of the very different boron allotropes, our model readily provides atom-resolved, local energies and thus deepened insight into the frustrated β -rhombohedral boron structure. Our results open the door for the efficient and automated generation of GAPs, and other machine-learning-based interatomic potentials, and suggest their usefulness as a tool for materials discovery.

Data-Driven Learning of Total and Local Energies in Elemental Boron.

PubMed

Deringer, Volker L; Pickard, Chris J; Csányi, Gábor

2018-04-13

The allotropes of boron continue to challenge structural elucidation and solid-state theory. Here we use machine learning combined with random structure searching (RSS) algorithms to systematically construct an interatomic potential for boron. Starting from ensembles of randomized atomic configurations, we use alternating single-point quantum-mechanical energy and force computations, Gaussian approximation potential (GAP) fitting, and GAP-driven RSS to iteratively generate a representation of the element's potential-energy surface. Beyond the total energies of the very different boron allotropes, our model readily provides atom-resolved, local energies and thus deepened insight into the frustrated β-rhombohedral boron structure. Our results open the door for the efficient and automated generation of GAPs, and other machine-learning-based interatomic potentials, and suggest their usefulness as a tool for materials discovery.

Atomistic methodologies for material properties of 2D materials at the nanoscale

NASA Astrophysics Data System (ADS)

Zhang, Zhen

Research on two dimensional (2D) materials, such as graphene and MoS2, now involves thousands of researchers worldwide cutting across physics, chemistry, engineering and biology. Due to the extraordinary properties of 2D materials, research extends from fundamental science to novel applications of 2D materials. From an engineering point of view, understanding the material properties of 2D materials under various conditions is crucial for tailoring the electrical and mechanical properties of 2D-material-based devices at the nanoscale. Even at the nanoscale, molecular systems typically consist of a vast number of atoms. Molecular dynamics (MD) simulations enable us to understand the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. From a continuum approach, mechanical properties and thermal properties, such as strain, stress, and heat capacity, are well defined and experimentally measurable. In MD simulations, material systems are considered to be discrete, and only interatomic potential, interatomic forces, and atom positions are directly obtainable. Besides, most of the fracture mechanics concepts, such as stress intensity factors, are not applicable since there is no singularity in MD simulations. However, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at the nanoscale. Therefore, equivalent definition of a physical quantity both in atomic scale and macroscopic scale is necessary in order to understand molecular and continuum scale phenomena concurrently. This work introduces atomistic simulation methodologies, based on interatomic potential and interatomic forces, as a tool to unveil the mechanical properties, thermal properties and fracture mechanical properties of 2D materials at the nanoscale. Among many 2D materials, graphene and MoS2 have attracted intense interest. Therefore, we applied our methodologies to graphene and MoS2 as examples. Young's modulus, Poison's ratio, heat conductivity, heat capacity, and energy release rate at the nanoscale are studied. These findings lend compelling insights into the atomistic mechanisms of graphene and MoS2, and provide useful guidelines for the design of 2D-material-based nanodevices.

Xenon Defects in Uranium Dioxide From First Principles and Interatomic Potentials

NASA Astrophysics Data System (ADS)

Thompson, Alexander

In this thesis, we examine the defect energetics and migration energies of xenon atoms in uranium dioxide (UO2) from first principles and interatomic potentials. We also parameterize new, accurate interatomic potentials for xenon and uranium dioxide. To achieve accurate energetics and provide a foundation for subsequent calculations, we address difficulties in finding consistent energetics within Hubbard U corrected density functional theory (DFT+U). We propose a method of slowly ramping the U parameter in order to guide the calculation into low energy orbital occupations. We find that this method is successful for a variety of materials. We then examine the defect energetics of several noble gas atoms in UO2 for several different defect sites. We show that the energy to incorporate large noble gas atoms into interstitial sites is so large that it is energetically favorable for a Schottky defect cluster to be created to relieve the strain. We find that, thermodynamically, xenon will rarely ever be in the interstitial site of UO2. To study larger defects associated with the migration of xenon in UO 2, we turn to interatomic potentials. We benchmark several previously published potentials against DFT+U defect energetics and migration barriers. Using a combination of molecular dynamics and nudged elastic band calculations, we find a new, low energy migration pathway for xenon in UO2. We create a new potential for xenon that yields accurate defect energetics. We fit this new potential with a method we call Iterative Potential Refinement that parameterizes potentials to first principles data via a genetic algorithm. The potential finds accurate energetics for defects with relatively low amounts of strain (xenon in defect clusters). It is important to find accurate energetics for these sorts of low-strain defects because they essentially represent small xenon bubbles. Finally, we parameterize a new UO2 potential that simultaneously yields accurate vibrational properties and defect energetics, important properties for UO2 because of the high temperature and defective reactor environment.. Previously published potentials could only yield accurate defect energetics or accurate phonons, but never both.

Thermal transport in UO 2 with defects and fission products by molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Xiang-Yang; Cooper, Michael William Donald; Mcclellan, Kenneth James

2015-10-14

The importance of the thermal transport in nuclear fuel has motivated a wide range of experimental and modelling studies. In this report, the reduction of thermal transport in UO 2 due to defects and fission products has been investigated using non-equilibrium MD simulations, with two sets of empirical potentials for studying the degregation of UO 2 thermal conductivity including a Buckingham type interatomic potential and a recently developed EAM type interatomic potential. Additional parameters for U 5+ and Zr 4+ in UO 2 have been developed for the EAM potential. The thermal conductivity results from MD simulations are then correctedmore » for the spin-phonon scattering through Callaway model formulations. To validate the modelling results, comparison was made with experimental measurements on single crystal hyper-stoichiometric UO 2+x samples.« less

Literature review report on atomistic modeling tools for FeCrAl alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yongfeng; Schwen, Daniel; Martinez, Enrique

2015-12-01

This reports summarizes the literature review results on atomistic tools, particularly interatomic potentials used in molecular dynamics simulations, for FeCrAl ternary alloys. FeCrAl has recently been identified as a possible cladding concept for accident tolerant fuels for its superior corrosion resistance. Along with several other concepts, an initial evaluation and recommendation are desired for FeCrAl before it’s used in realistic fuels. For this purpose, sufficient understanding on the in-reactor behavior of FeCrAl needs to be grained in a relatively short timeframe, and multiscale modeling and simulations have been selected as an efficient measure to supplement experiments and in-reactor testing formore » better understanding on FeCrAl. For the limited knowledge on FeCrAl alloys, the multiscale modeling approach relies on atomistic simulations to obtain the missing material parameters and properties. As a first step, atomistic tools have to be identified and this is the purpose of the present report. It was noticed during the literature survey that no interatomic potentials currently available for FeCrAl. Here, we summarize the interatomic potentials available for FeCr alloys for possible molecular dynamics studies using FeCr as surrogate materials. Other atomistic methods such as lattice kinetic Monte Carlo are also included in this report. A couple of research topics at the atomic scale are suggested based on the literature survey.« less

Embedded-atom-method interatomic potentials from lattice inversion.

PubMed

Yuan, Xiao-Jian; Chen, Nan-Xian; Shen, Jiang; Hu, Wangyu

2010-09-22

The present work develops a physically reliable procedure for building the embedded-atom-method (EAM) interatomic potentials for the metals with fcc, bcc and hcp structures. This is mainly based on Chen-Möbius lattice inversion (Chen et al 1997 Phys. Rev. E 55 R5) and first-principles calculations. Following Baskes (Baskes et al 2007 Phys. Rev. B 75 094113), this new version of the EAM eliminates all of the prior arbitrary choices in the determination of the atomic electron density and pair potential functions. Parameterizing the universal form deduced from the calculations within the density-functional scheme for homogeneous electron gas as the embedding function, the new-type EAM potentials for Cu, Fe and Ti metals have successfully been constructed by considering interatomic interactions up to the fifth neighbor, the third neighbor and the seventh neighbor, respectively. The predictions of elastic constants, structural energy difference, vacancy formation energy and migration energy, activation energy of vacancy diffusion, latent heat of melting and relative volume change on melting all satisfactorily agree with the experimental results available or first-principles calculations. The predicted surface energies for low-index crystal faces and the melting point are in agreement with the experimental data to the same extent as those calculated by other EAM-type potentials such as the FBD-EAM, 2NN MEAM and MS-EAM. In addition, the order among the predicted low-index surface energies is also consistent with the experimental information.

An improved interatomic potential for xenon in UO2: a combined density functional theory/genetic algorithm approach.

PubMed

Thompson, Alexander E; Meredig, Bryce; Wolverton, C

2014-03-12

We have created an improved xenon interatomic potential for use with existing UO2 potentials. This potential was fit to density functional theory calculations with the Hubbard U correction (DFT + U) using a genetic algorithm approach called iterative potential refinement (IPR). We examine the defect energetics of the IPR-fitted xenon interatomic potential as well as other, previously published xenon potentials. We compare these potentials to DFT + U derived energetics for a series of xenon defects in a variety of incorporation sites (large, intermediate, and small vacant sites). We find the existing xenon potentials overestimate the energy needed to add a xenon atom to a wide set of defect sites representing a range of incorporation sites, including failing to correctly rank the energetics of the small incorporation site defects (xenon in an interstitial and xenon in a uranium site neighboring uranium in an interstitial). These failures are due to problematic descriptions of Xe-O and/or Xe-U interactions of the previous xenon potentials. These failures are corrected by our newly created xenon potential: our IPR-generated potential gives good agreement with DFT + U calculations to which it was not fitted, such as xenon in an interstitial (small incorporation site) and xenon in a double Schottky defect cluster (large incorporation site). Finally, we note that IPR is very flexible and can be applied to a wide variety of potential forms and materials systems, including metals and EAM potentials.

Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

PubMed

Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

1981-08-04

The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

Tris(phosphinoamide)-supported uranium-cobalt heterobimetallic complexes featuring Co → U dative interactions.

PubMed

Napoline, J Wesley; Kraft, Steven J; Matson, Ellen M; Fanwick, Phillip E; Bart, Suzanne C; Thomas, Christine M

2013-10-21

A series of tris- and tetrakis(phosphinoamide) U/Co complexes has been synthesized. The uranium precursors, (η(2)-Ph2PN(i)Pr)4U (1), (η(2)-(i)Pr2PNMes)4U (2), (η(2)-Ph2PN(i)Pr)3UCl (3), and (η(2)-(i)Pr2PNMes)3UI (4), were easily accessed via addition of the appropriate stoichiometric equivalents of [Ph2PN(i)Pr]K or [(i)Pr2PNMes]K to UCl4 or UI4(dioxane)2. Although the phosphinoamide ligands in 1 and 4 have been shown to coordinate to U in an η(2)-fashion in the solid state, the phosphines are sufficiently labile in solution to coordinate cobalt upon addition of CoI2, generating the heterobimetallic Co/U complexes ICo(Ph2PN(i)Pr)3U[η(2)-Ph2PN(i)Pr] (5), ICo((i)Pr2PNMes)3U[η(2)-((i)Pr2PNMes)] (6), ICo(Ph2PN(i)Pr)3UI (7), and ICo((i)Pr2PNMes)3UI (8). Structural characterization of complexes 5 and 7 reveals reasonably short Co-U interatomic distances, with 7 exhibiting the shortest transition metal-uranium distance ever reported (2.874(3) Å). Complexes 7 and 8 were studied by cyclic voltammetry to examine the influence of the metal-metal interaction on the redox properties compared with both monometallic Co and heterobimetallic Co/Zr complexes. Theoretical studies are used to further elucidate the nature of the transition metal-actinide interaction.

A second-order unconstrained optimization method for canonical-ensemble density-functional methods

NASA Astrophysics Data System (ADS)

Nygaard, Cecilie R.; Olsen, Jeppe

2013-03-01

A second order converging method of ensemble optimization (SOEO) in the framework of Kohn-Sham Density-Functional Theory is presented, where the energy is minimized with respect to an ensemble density matrix. It is general in the sense that the number of fractionally occupied orbitals is not predefined, but rather it is optimized by the algorithm. SOEO is a second order Newton-Raphson method of optimization, where both the form of the orbitals and the occupation numbers are optimized simultaneously. To keep the occupation numbers between zero and two, a set of occupation angles is defined, from which the occupation numbers are expressed as trigonometric functions. The total number of electrons is controlled by a built-in second order restriction of the Newton-Raphson equations, which can be deactivated in the case of a grand-canonical ensemble (where the total number of electrons is allowed to change). To test the optimization method, dissociation curves for diatomic carbon are produced using different functionals for the exchange-correlation energy. These curves show that SOEO favors symmetry broken pure-state solutions when using functionals with exact exchange such as Hartree-Fock and Becke three-parameter Lee-Yang-Parr. This is explained by an unphysical contribution to the exact exchange energy from interactions between fractional occupations. For functionals without exact exchange, such as local density approximation or Becke Lee-Yang-Parr, ensemble solutions are favored at interatomic distances larger than the equilibrium distance. Calculations on the chromium dimer are also discussed. They show that SOEO is able to converge to ensemble solutions for systems that are more complicated than diatomic carbon.

Strength of the repulsive part of the interatomic potential determines fragility in metallic liquids

NASA Astrophysics Data System (ADS)

Pueblo, Christopher E.; Sun, Minhua; Kelton, K. F.

2017-08-01

The dynamical behaviour of liquids is frequently characterized by the fragility, which can be defined from the temperature dependence of the shear viscosity, η (ref. ). For a strong liquid, the activation energy for η changes little with cooling towards the glass transition temperature, Tg. The change is much greater in fragile liquids, with the activation energy becoming very large near Tg. While fragility is widely recognized as an important concept--believed, for example, to play an important role in glass formation--the microscopic origin of fragility is poorly understood. Here, we present new experimental evidence showing that fragility reflects the strength of the repulsive part of the interatomic potential, which can be determined from the steepness of the pair distribution function near the hard-sphere cutoff. On the basis of an analysis of scattering data from ten different metallic alloy liquids, we show that stronger liquids have steeper repulsive potentials.

A general transformation to canonical form for potentials in pairwise interatomic interactions.

PubMed

Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

2015-06-14

A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

Strong field control of the interatomic Coulombic decay process in quantum dots

NASA Astrophysics Data System (ADS)

Haller, Anika; Chiang, Ying-Chih; Menger, Maximilian; Aziz, Emad F.; Bande, Annika

2017-01-01

In recent years the laser-induced interatomic Coulombic decay (ICD) process in paired quantum dots has been predicted (Bande, 2013). In this work we target the enhancement of ICD by scanning over a range of strong-field laser intensities. The GaAs quantum dots are modeled by a one-dimensional double-well potential in which simulations are done with the space-resolved multi-configuration time-dependent Hartree method including antisymmetrization to account for the fermions. As a novelty a complementary state-resolved ansatz is developed to consolidate the interpretation of transient state populations, widths obtained for the ICD and the competing direct ionization channel, and Fano peak profiles in the photoelectron spectra. The major results are that multi-photon processes are unimportant even for the strongest fields. Further, below- π to π pulses display the highest ICD efficiency while the direct ionization becomes less dominant.

Atomic bonding effects in annular dark field scanning transmission electron microscopy. I. Computational predictions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Odlyzko, Michael L.; Mkhoyan, K. Andre, E-mail: mkhoyan@umn.edu; Himmetoglu, Burak

2016-07-15

Annular dark field scanning transmission electron microscopy (ADF-STEM) image simulations were performed for zone-axis-oriented light-element single crystals, using a multislice method adapted to include charge redistribution due to chemical bonding. Examination of these image simulations alongside calculations of the propagation of the focused electron probe reveal that the evolution of the probe intensity with thickness exhibits significant sensitivity to interatomic charge transfer, accounting for observed thickness-dependent bonding sensitivity of contrast in all ADF-STEM imaging conditions. Because changes in image contrast relative to conventional neutral atom simulations scale directly with the net interatomic charge transfer, the strongest effects are seen inmore » crystals with highly polar bonding, while no effects are seen for nonpolar bonding. Although the bonding dependence of ADF-STEM image contrast varies with detector geometry, imaging parameters, and material temperature, these simulations predict the bonding effects to be experimentally measureable.« less

Extending the accuracy of the SNAP interatomic potential form

NASA Astrophysics Data System (ADS)

Wood, Mitchell A.; Thompson, Aidan P.

2018-06-01

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functions in EAM. The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similar to artificial neural network potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting. The quality of this new potential form is measured through a robust cross-validation analysis.

Influence of Al grain boundaries segregations and La-doping on embrittlement of intermetallic NiAl

NASA Astrophysics Data System (ADS)

Kovalev, Anatoly I.; Wainstein, Dmitry L.; Rashkovskiy, Alexander Yu.

2015-11-01

The microscopic nature of intergranular fracture of NiAl was experimentally investigated by the set of electron spectroscopy techniques. The paper demonstrates that embrittlement of NiAl intermetallic compound is caused by ordering of atomic structure that leads to formation of structural aluminum segregations at grain boundaries (GB). Such segregations contain high number of brittle covalent interatomic bonds. The alloying by La increases the ductility of material avoiding Al GB enrichment and disordering GB atomic structure. The influence of La alloying on NiAl mechanical properties was investigated. GB chemical composition, atomic and electronic structure transformations after La doping were investigated by AES, XPS and EELFS techniques. To qualify the interatomic bonds metallicity the Fermi level (EF) position and electrons density (neff) in conduction band were determined in both undoped and doped NiAl. Basing on experimental results the physical model of GB brittleness formation was proposed.

Analytical interatomic potential for modeling nonequilibrium processes in the W-C-H system

NASA Astrophysics Data System (ADS)

Juslin, N.; Erhart, P.; Träskelin, P.; Nord, J.; Henriksson, K. O. E.; Nordlund, K.; Salonen, E.; Albe, K.

2005-12-01

A reactive interatomic potential based on an analytical bond-order scheme is developed for the ternary system W-C-H. The model combines Brenner's hydrocarbon potential with parameter sets for W-W, W-C, and W-H interactions and is adjusted to materials properties of reference structures with different local atomic coordinations including tungsten carbide, W-H molecules, as well as H dissolved in bulk W. The potential has been tested in various scenarios, such as surface, defect, and melting properties, none of which were considered in the fitting. The intended area of application is simulations of hydrogen and hydrocarbon interactions with tungsten, which have a crucial role in fusion reactor plasma-wall interactions. Furthermore, this study shows that the angular-dependent bond-order scheme can be extended to second nearest-neighbor interactions, which are relevant in body-centered-cubic metals. Moreover, it provides a possibly general route for modeling metal carbides.

Thermal conductance of suspended nanoribbons: interplay between strain and interatomic potential nonlinearity

NASA Astrophysics Data System (ADS)

Barreto, Roberto; Florencia Carusela, M.; Monastra, Alejandro G.

2017-10-01

We investigate the role that nonlinearity in the interatomic potential has on the thermal conductance of a suspended nanoribbon when it is subjected to a longitudinal strain. To focus on the first cubic and quartic nonlinear terms of a general potential, we propose an atomic system based on an α-β Fermi-Pasta-Ulam nearest neighbor interaction. We perform classical molecular dynamics simulations to investigate the contribution of longitudinal, transversal and flexural modes to the thermal conductance as a function of the α-β parameters and the applied strain. We compare the cases where atoms are allowed to vibrate only in plane (2D) with the case of vibrations in and out of plane (3D). We find that the dependence of conductance on α and β relies on a crossover phenomenon between linear/nonlinear delocalized/localized flexural and transversal modes, driven by an on/off switch of the strain.

Interatomic interactions in M2(C8H4O4)2C6H12N2 (M = Zn, Cu, Co, Ni) metal-organic framework polymers: X-ray photoelectron spectroscopy, QTAIM and ELF study

NASA Astrophysics Data System (ADS)

Kozlova, S. G.; Ryzhikov, M. R.; Samsonenko, D. G.; Kalinkin, A. V.

2017-12-01

Interatomic interactions in M2(C8H4O4)2C6H12N2 (M = Co, Ni, Cu, Zn) metal-organic framework polymers have been studied with the methods of quantum chemistry and X-ray photoelectron spectroscopy. Interactions of C6H12N2 molecules and C8H4O42- anions with metal atoms are shown to be of closed-shell type. C6H12N2 molecules are positively charged, the value of the charge slightly depends on the type of the metal atoms. Msbnd M interactions are described as "intermediate interactions" with some covalence contribution which reaches maximum for the interactions between cobalt atoms. The obtained quantum-chemical data agree with those obtained from photoelectron spectroscopy measurements.

Safety and licensing of a small modular gas-cooled reactor system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, N.W.; Kelley, A.P. Jr.

A modular side-by-side high-temperature gas-cooled reactor (SBS-HTGR) is being developed by Interatom/Kraftwerk Union (KWU). The General Electric Company and Interatom/KWU entered into a proprietary working agreement to continue develop jointly of the SBS-HTGR. A study on adapting the SBS-HTGR for application in the US has been completed. The study investigated the safety characteristics and the use of this type of design in an innovative approach to licensing. The safety objective guiding the design of the modular SBS-HTGR is to control radionuclide release by the retention of fission products within the fuel particles with minimal reliance on active design features. Themore » philosophy on which this objective is predicated is that by providing a simple safety case, the safety criteria can be demonstrated as being met with high confidence through conduct of a full-scale module safety test.« less

Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Motta, Mario; Zhang, Shiwei

2018-05-01

We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

Internal electric fields and color shift in Cr3+-based gemstones

NASA Astrophysics Data System (ADS)

Aramburu, J. A.; Garcia-Fernandez, P.; García-Lastra, J. M.; Barriuso, M. T.; Moreno, M.

2012-06-01

Seeking to better understand the origin of the different colors of emerald and ruby, both ab initio periodic and cluster calculations have been carried out. The calculations reproduce the interatomic distances measured for pure Be3Si6Al2O18 and Al2O3 as well as the Cr3+-O2- distances in emerald and ruby. The mean Cr3+-O2- distance for Be3Si6Al2O18:Cr3+ and Al2O3:Cr3+ is found to be practically equal to 1.97 Å, in agreement with recent experimental values. The present calculations confirm that the variations of optical properties due to Cr3+ impurities along the series of ionic oxides can be understood merely through the CrO69- unit but subject to the electric field due to the rest of the lattice ions. As a salient feature it is proved that changes in electronic density and covalency due to the internal field are not the cause of the color shift. Therefore, the red color of ruby is not due to the polarization of the electronic cloud around chromium as a result of the C3 local symmetry. The present study also demonstrates that the variation of the ligand field splitting parameter, 10Dq, induced by the internal electric field comes mainly from the contributions of first shells of ions around the CrO69- unit. As a consequence, 10Dq in emerald is not influenced by the internal field, as the contribution from Be2+ first neighbors is practically compensated by that of Si4+ second neighbors. In contrast, in ruby the t2g levels are shifted by the internal field 0.24 eV more than the eg ones, so explaining the color shift in this gemstone in comparison with emerald. This result is shown to arise partially from the asymmetric form of the internal electrostatic potential along the C3 axis in Al2O3.

Computational identification of a phospholipidosis toxicophore using (13)C and (15)N NMR-distance based fingerprints.

PubMed

Slavov, Svetoslav H; Wilkes, Jon G; Buzatu, Dan A; Kruhlak, Naomi L; Willard, James M; Hanig, Joseph P; Beger, Richard D

2014-12-01

Modified 3D-SDAR fingerprints combining (13)C and (15)N NMR chemical shifts augmented with inter-atomic distances were used to model the potential of chemicals to induce phospholipidosis (PLD). A curated dataset of 328 compounds (some of which were cationic amphiphilic drugs) was used to generate 3D-QSDAR models based on tessellations of the 3D-SDAR space with grids of different density. Composite PLS models averaging the aggregated predictions from 100 fully randomized individual models were generated. On each of the 100 runs, the activities of an external blind test set comprised of 294 proprietary chemicals were predicted and averaged to provide composite estimates of their PLD-inducing potentials (PLD+ if PLD is observed, otherwise PLD-). The best performing 3D-QSDAR model utilized a grid with a density of 8ppm×8ppm in the C-C region, 8ppm×20ppm in the C-N region and 20ppm×20ppm in the N-N region. The classification predictive performance parameters of this model evaluated on the basis of the external test set were as follows: accuracy=0.70, sensitivity=0.73 and specificity=0.66. A projection of the most frequently occurring bins on the standard coordinate space suggested a toxicophore composed of an aromatic ring with a centroid 3.5-7.5Å distant from an amino-group. The presence of a second aromatic ring separated by a 4-5Å spacer from the first ring and at a distance of between 5.5Å and 7Å from the amino-group was also associated with a PLD+ effect. These models provide comparable predictive performance to previously reported models for PLD with the added benefit of being based entirely on non-confidential, publicly available training data and with good predictive performance when tested in a rigorous, external validation exercise. Published by Elsevier Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pani, M., E-mail: marcella@chimica.unige.it; Institute SPIN-CNR, Corso Perrone 24, 16152 Genova; Morozkin, A.V.

The title compounds have been synthesized and characterized both from the structural and magnetic point of view. Both crystallize in a new monoclinic structure strictly related to the tetragonal BaCd{sub 11} type. The structure was solved by means of X-ray single-crystal techniques for GdNi{sub 8}Si{sub 3} and confirmed for TbNi{sub 8}Si{sub 3} on powder data; the corresponding lattice parameters (obtained from Guinier powder patterns) are a=6.3259(2), b=13.7245(5), c=7.4949(3) Å, β=113.522(3)°, V{sub cell}=596.64(3) Å{sup 3} and a=6.3200(2), b=13.6987(4), c=7.4923(2) Å, β=113.494(2)°, V{sub cell}=594.88(2) Å{sup 3}. The symmetry relationship between the tI48-I4{sub 1}/amd BaCd{sub 11} aristotype and the new ordered mS48-C2/c GdNi{submore » 8}Si{sub 3} derivative is described via the Bärnighausen formalism within the group theory. The large Gd–Gd (Tb–Tb) distances, mediated via Ni–Si network, likely lead to weak magnetic interactions. Low-field magnetization vs temperature measurements indicate weak and field-sensitive antiferromagnetic ground state, with ordering temperatures of 3 K in GdNi{sub 8}Si{sub 3} and about 2–3 K in TbNi{sub 8}Si{sub 3}. On the other hand, the isothermal field-dependent magnetization data show the presence of competing interactions in both compounds, with a field-induced ferromagnetic behavior for GdNi{sub 8}Si{sub 3} and a ferrimagnetic-like behavior in TbNi{sub 8}Si{sub 3} at the ordering temperature T{sub C/N} of about (or slightly higher than) 3K. The magnetocaloric effect, quantified in terms of isothermal magnetic entropy change ΔS{sub m}, has the maximum values of –19.8 J(kg K){sup −1} (at 4 K for 140 kOe field change) and −12.1 J(kg K){sup −1} (at 12 K for 140 kOe field change) in GdNi{sub 8}Si{sub 3} and TbNi{sub 8}Si{sub 3}, respectively. - Graphical abstract: GdNi{sub 8}Si{sub 3} and TbNi{sub 8}Si{sub 3} compounds are isostructural, and crystallize in a new monoclinic type strictly related to the tetragonal BaCd{sub 11} structure. The large R–R interatomic distances mediated via Ni–Si network lead to a weak magnetism in both compounds. - Highlights: • Novel RNi{sub 8}Si{sub 3} (R=Gd, Tb) compounds have been synthesized and characterized. • GdNi{sub 8}Si{sub 3} and TbNi{sub 8}Si{sub 3} are isostructural compounds, belonging to a new monoclinic structure type. • The monoclinic GdNi{sub 8}Si{sub 3} type is an ordered derivative of the tetragonal BaCd{sub 11} type. • The large R–R interatomic distances mediated via Ni–Si network lead to a weak magnetism. • Both compounds GdNi{sub 8}Si{sub 3} and TbNi{sub 8}Si{sub 3} show antiferromagnetic-like order around 3 K.« less

Interactions of C+(2PJ) with rare gas atoms: incipient chemical interactions, potentials and transport coefficients

NASA Astrophysics Data System (ADS)

Tuttle, William D.; Thorington, Rebecca L.; Viehland, Larry A.; Breckenridge, W. H.; Wright, Timothy G.

2018-03-01

Accurate interatomic potentials were calculated for the interaction of a singly charged carbon cation, C+, with a single rare gas atom, RG (RG = Ne-Xe). The RCCSD(T) method and basis sets of quadruple-ζ and quintuple-ζ quality were employed; each interaction energy was counterpoise corrected and extrapolated to the basis set limit. The lowest C+(2P) electronic term of the carbon cation was considered, and the interatomic potentials calculated for the diatomic terms that arise from these: 2Π and 2Σ+. Additionally, the interatomic potentials for the respective spin-orbit levels were calculated, and the effect on the spectroscopic parameters was examined. In doing this, anomalously large spin-orbit splittings for RG = Ar-Xe were found, and this was investigated using multi-reference configuration interaction calculations. The latter indicated a small amount of RG → C+ electron transfer and this was used to rationalize the observations. This is taken as evidence of an incipient chemical interaction, which was also examined via contour plots, Birge-Sponer plots and various population analyses across the C+-RG series (RG = He-Xe), with the latter showing unexpected results. Trends in several spectroscopic parameters were examined as a function of the increasing atomic number of the RG atom. Finally, each set of RCCSD(T) potentials was employed, including spin-orbit coupling to calculate the transport coefficients for C+ in RG, and the results were compared with the limited available data. This article is part of the theme issue `Modern theoretical chemistry'.

Quantum-chemical study of the effect of ligands on the structure and properties of gold clusters

NASA Astrophysics Data System (ADS)

Golosnaya, M. N.; Pichugina, D. A.; Oleinichenko, A. V.; Kuz'menko, N. E.

2017-02-01

The structures of [Au4(dpmp)2X2]2+clusters, where X =-C≡CH,-CH3,-SCH3,-F,-Cl,-Br,-I, dpmp is bis((diphenylphosphino)methyl)(phenyl)phosphine, are calculated at the level of density functional theory with the PBE functional and a modified Dirac-Coulomb-Breit Hamiltonian in an all-electron basis set (Λ). Using the example of [Au4(dpmp)2(C≡CC6H5)2]2+, the interatomic distances and bond angles calculated by means of PBE0/LANL2DZ, TPSS/LANL2DZ, TPSSh/LANL2DZ, and PBE/Λ are compared to X-ray crystallography data. It is shown that PBE/Λ yields the most accurate calculation of the geometrical parameters of this cluster. The ligand effect on the electronic stability of a cluster and the stability in reactions of decomposition into different fragments is studied, along with the capability of ligand exchange. Stability is predicted for [Au4(dpmp)2F2]2+ and [Au4(dpmp)2(SCH3)2]2+, while [Au4(dpmp)2I2]2+ cluster is unstable and its decomposes into two identical fragments is supposed.

Structural Analysis of Cubane-Type Iron Clusters

PubMed Central

Tan, Lay Ling; Holm, R. H.; Lee, Sonny C.

2013-01-01

The generalized cluster type [M4(μ3-Q)4Ln]x contains the cubane-type [M4Q4]z core unit that can approach, but typically deviates from, perfect Td symmetry. The geometric properties of this structure have been analyzed with reference to Td symmetry by a new protocol. Using coordinates of M and Q atoms, expressions have been derived for interatomic separations, bond angles, and volumes of tetrahedral core units (M4, Q4) and the total [M4Q4] core (as a tetracapped M4 tetrahedron). Values for structural parameters have been calculated from observed average values for a given cluster type. Comparison of calculated and observed values measures the extent of deviation of a given parameter from that required in an exact tetrahedral structure. The procedure has been applied to the structures of over 130 clusters containing [Fe4Q4] (Q = S2−, Se2−, Te2−, [NPR3]−, [NR]2−) units, of which synthetic and biological sulfide-bridged clusters constitute the largest subset. General structural features and trends in structural parameters are identified and summarized. An extensive database of structural properties (distances, angles, volumes) has been compiled in Supporting Information. PMID:24072952

Structural Analysis of Cubane-Type Iron Clusters.

PubMed

Tan, Lay Ling; Holm, R H; Lee, Sonny C

2013-07-13

The generalized cluster type [M 4 (μ 3 -Q) 4 L n ] x contains the cubane-type [M 4 Q 4 ] z core unit that can approach, but typically deviates from, perfect T d symmetry. The geometric properties of this structure have been analyzed with reference to T d symmetry by a new protocol. Using coordinates of M and Q atoms, expressions have been derived for interatomic separations, bond angles, and volumes of tetrahedral core units (M 4 , Q 4 ) and the total [M 4 Q 4 ] core (as a tetracapped M 4 tetrahedron). Values for structural parameters have been calculated from observed average values for a given cluster type. Comparison of calculated and observed values measures the extent of deviation of a given parameter from that required in an exact tetrahedral structure. The procedure has been applied to the structures of over 130 clusters containing [Fe 4 Q 4 ] (Q = S 2- , Se 2- , Te 2- , [NPR 3 ] - , [NR] 2- ) units, of which synthetic and biological sulfide-bridged clusters constitute the largest subset. General structural features and trends in structural parameters are identified and summarized. An extensive database of structural properties (distances, angles, volumes) has been compiled in Supporting Information.

Evidence for a second-order phase transition around 350 K in Ce3Rh4Sn13

NASA Astrophysics Data System (ADS)

Kuo, C. N.; Chen, W. T.; Tseng, C. W.; Hsu, C. J.; Huang, R. Y.; Chou, F. C.; Kuo, Y. K.; Lue, C. S.

2018-03-01

We report an observation of a phase transition in Ce3Rh4Sn13 with the transition temperature T*≃350 K by means of synchrotron x-ray powder diffraction, specific heat, electrical resistivity, Seebeck coefficient, thermal conductivity, as well as 119Sn nuclear magnetic resonance (NMR) measurements. The phase transition has been characterized by marked features near T* in all measured physical quantities. The lack of thermal hysteresis in the specific heat indicates a second-order phase transition in nature. From the NMR analysis, the change in the transferred hyperfine coupling constant for two tin sites has been resolved. The obtained result has been associated with the reduction in the averaged interatomic distance between Ce and Sn atoms, particularly for the Sn2 atoms. It indicates that the movement of the Sn2 atoms, which deforms the high-temperature structure, shortens the Ce-Sn2 bond length at low temperatures. We therefore provide a concise picture that the observed second-order phase transition at T* of Ce3Rh4Sn13 should be characterized by a structural modulation essentially due to lattice distortions arising from phonon instability.

Total Scattering and Pair Distribution Function Analysis in Modelling Disorder in PZN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitfield, Ross E.; Goossens, Darren J; Welberry, T. R.

2016-01-01

The ability of the pair distribution function (PDF) analysis of total scattering (TS) from a powder to determine the local ordering in ferroelectric PZN (PbZn 1/3Nb 2/3O 3) has been explored by comparison with a model established using single-crystal diffuse scattering (SCDS). While X-ray PDF analysis is discussed, the focus is on neutron diffraction results because of the greater extent of the data and the sensitivity of the neutron to oxygen atoms, the behaviour of which is important in PZN. The PDF was shown to be sensitive to many effects not apparent in the average crystal structure, including variations inmore » the B-site—O separation distances and the fact that (110) Pb 2+ displacements are most likely. A qualitative comparison between SCDS and the PDF shows that some features apparent in SCDS were not apparent in the PDF. These tended to pertain to short-range correlations in the structure, rather than to interatomic separations. For example, in SCDS the short-range alternation of the B-site cations was quite apparent in diffuse scattering at (½ ½ ½), whereas it was not apparent in the PDF.« less

Phonon optimized interatomic potential for aluminum

NASA Astrophysics Data System (ADS)

Muraleedharan, Murali Gopal; Rohskopf, Andrew; Yang, Vigor; Henry, Asegun

2017-12-01

We address the problem of generating a phonon optimized interatomic potential (POP) for aluminum. The POP methodology, which has already been shown to work for semiconductors such as silicon and germanium, uses an evolutionary strategy based on a genetic algorithm (GA) to optimize the free parameters in an empirical interatomic potential (EIP). For aluminum, we used the Vashishta functional form. The training data set was generated ab initio, consisting of forces, energy vs. volume, stresses, and harmonic and cubic force constants obtained from density functional theory (DFT) calculations. Existing potentials for aluminum, such as the embedded atom method (EAM) and charge-optimized many-body (COMB3) potential, show larger errors when the EIP forces are compared with those predicted by DFT, and thus they are not particularly well suited for reproducing phonon properties. Using a comprehensive Vashishta functional form, which involves short and long-ranged interactions, as well as three-body terms, we were able to better capture interactions that reproduce phonon properties accurately. Furthermore, the Vashishta potential is flexible enough to be extended to Al2O3 and the interface between Al-Al2O3, which is technologically important for combustion of solid Al nano powders. The POP developed here is tested for accuracy by comparing phonon thermal conductivity accumulation plots, density of states, and dispersion relations with DFT results. It is shown to perform well in molecular dynamics (MD) simulations as well, where the phonon thermal conductivity is calculated via the Green-Kubo relation. The results are within 10% of the values obtained by solving the Boltzmann transport equation (BTE), employing Fermi's Golden Rule to predict the phonon-phonon relaxation times.

Anharmonic interatomic force constants and thermal conductivity from Grüneisen parameters: An application to graphene

NASA Astrophysics Data System (ADS)

Lee, Ching Hua; Gan, Chee Kwan

2017-07-01

Phonon-mediated thermal conductivity, which is of great technological relevance, arises due fundamentally to anharmonic scattering from interatomic potentials. Despite its prevalence, accurate first-principles calculations of thermal conductivity remain challenging, primarily due to the high computational cost of anharmonic interatomic force constant (IFC) calculations. Meanwhile, the related anharmonic phenomenon of thermal expansion is much more tractable, being computable from the Grüneisen parameters associated with phonon frequency shifts due to crystal deformations. In this work, we propose an approach for computing the largest cubic IFCs from the Grüneisen parameter data. This allows an approximate determination of the thermal conductivity via a much less expensive route. The key insight is that although the Grüneisen parameters cannot possibly contain all the information on the cubic IFCs, being derivable from spatially uniform deformations, they can still unambiguously and accurately determine the largest and most physically relevant ones. By fitting the anisotropic Grüneisen parameter data along judiciously designed deformations, we can deduce (i.e., reverse-engineer) the dominant cubic IFCs and estimate three-phonon scattering amplitudes. We illustrate our approach by explicitly computing the largest cubic IFCs and thermal conductivity of graphene, especially for its out-of-plane (flexural) modes that exhibit anomalously large anharmonic shifts and thermal conductivity contributions. Our calculations on graphene not only exhibit reasonable agreement with established density-functional theory results, but they also present a pedagogical opportunity for introducing an elegant analytic treatment of the Grüneisen parameters of generic two-band models. Our approach can be readily extended to more complicated crystalline materials with nontrivial anharmonic lattice effects.

Size-dependent disproportionation (in 2-20 nm regime) and hybrid Bond Valence derived interatomic potentials for BaTaO2N

NASA Astrophysics Data System (ADS)

Anbalagan, Kousika; Thomas, Tiju

2018-05-01

Interatomic potentials for complex materials (like ceramic systems) are important for realistic molecular dynamics (MD) simulations. Such simulations are relevant for understanding equilibrium, transport and dynamical properties of materials, especially in the nanoregime. Here we derive a hybrid interatomic potential (based on bond valence (BV) derived Morse and Coulomb terms), for modeling a complex ceramic, barium tantalum oxynitride (BaTaO2N). This material has been chosen due to its relevance for capacitive and photoactive applications. However, the material presents processing challenges such as the emergence of non-stoichiometric phases during processing, demonstrating complex processing-property correlations. This makes MD investigations of this material both scientifically and technologically relevant. The BV based hybrid potential presented here has been used for simulating sintering of BaTaO2N nanoparticles ( 2-20 nm) under different conditions (using the relevant canonical ensemble). Notably, we show that sintering of particles of diameter < 10 nm requires no external sintering aids such as the addition of barium sources (since stoichiometry is preserved during heat treatment in this size regime). Also, we observe that sintering of particles > 10 nm in size results in the formation of a cluster of tantalum and oxygen atoms at the interface of the BaTaO2N particles. This is in agreement with the experimental reports. The results presented here suggest that the potential proposed can be used to explore dynamical properties of BaTaO2N and related systems. This work will also open avenues for development of nanoscience-enabled aid-free sintering approaches to this and related materials.

Spin Polarization of Rb and Cs n p P2 3/2 (n =5 , 6) Atoms by Circularly Polarized Photoexcitation of a Transient Diatomic Molecule

NASA Astrophysics Data System (ADS)

Mironov, A. E.; Hewitt, J. D.; Eden, J. G.

2017-03-01

We report the selective population of Rb or Cs n p P2 3/2 (n =5 , 6; F =4 , 5) hyperfine states by the photodissociation of a transient, alkali-rare gas diatomic molecule. Circularly polarized (σ-), amplified spontaneous emission (ASE) on the D2 line of Rb or Cs (780.0 and 852.1 nm, respectively) is generated when Rb-Xe or Cs-Xe ground state collision pairs are photoexcited by a σ+-polarized optical field having a wavelength within the D2 blue satellite continuum, associated with the B Σ2 1/2 +←X Σ2 1/2 + (free←free ) transition of the diatomic molecule. The degree of spin polarization of Cs (6 p P3/2 2 ), specifically, is found to be dependent on the interatomic distance (R ) at which the excited complex is born, a result attributed to the structure of the B Σ2 1/2 + state. For Cs-Xe atomic pairs, tuning the wavelength of the optical field from 843 to 848 nm varies the degree of circular polarization of the ASE from 63% to almost unity because of the perturbation, in the 5 ≤R ≤6 Å interval, of the Σ2 1/2 + potential by a d σ molecular orbital associated with a higher Λ 2 electronic state. Monitoring only the Cs 6 p P3/2 2 spin polarization reveals a previously unobserved interaction of CsXe (B Σ2 1/2 + ) with the lowest vibrational levels of a Λ 2 state derived from Cs (5 d )+Xe . By inserting a molecular intermediate into the alkali atom excitation mechanism, these experiments realize electronic spin polarization through populating no more than two n p P2 3/2 hyperfine states, and demonstrate a sensitive spectroscopic probe of R -dependent state-state interactions and their impact on interatomic potentials.

Investigations of interatomic interaction in InAs-InAs1-xSbx heterostructures on a base of x-ray diffractometry

NASA Astrophysics Data System (ADS)

Babjuck, T. I.; Buntar, A. G.; Shevtchuk, L. S.

2001-06-01

Hetero-transitions on a base of InAs and AnSb compounds permitted to obtain cheap light diodes and detectors with the atmosphere maximal transparency region sensibility. There is assumed simultaneously, that the phon radiation in InAs-InAs1-xSbx is not large, which positively effects on receiver parameters. Changing the composition of InAs-InAs1- xSbx solution, one may obtain the structure with the width of forbidden zone of the want of 0.35 to 0,1 eV. There is developed the heterostructures crystalline lattice parameters determining method (for substrate and film) with the DRON-3M x-ray diffractometer. There was found the nonlinear dependence of the heterostructures lattice parameter on the composition. Investigations of interatomic interaction in dependence on composition and also on the forbidden zone width Eg(x) have show, that solid solutions InAs-InAs1- xSbx may be used for the obtaining of infra-red receiver.

Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link Between Experiments.

PubMed

Cheng, Bingqing; Behler, Jörg; Ceriotti, Michele

2016-06-16

One of the most prominent consequences of the quantum nature of light atomic nuclei is that their kinetic energy does not follow a Maxwell-Boltzmann distribution. Deep inelastic neutron scattering (DINS) experiments can measure this effect. Thus, the nuclear quantum kinetic energy can be probed directly in both ordered and disordered samples. However, the relation between the quantum kinetic energy and the atomic environment is a very indirect one, and cross-validation with theoretical modeling is therefore urgently needed. Here, we use state of the art path integral molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen nuclei in liquid, solid, and gas-phase water close to the triple point, comparing three different interatomic potentials and validating our results against equilibrium isotope fractionation measurements. We will then show how accurate simulations can draw a link between extremely precise fractionation experiments and DINS, therefore establishing a reliable benchmark for future measurements and providing key insights to increase further the accuracy of interatomic potentials for water.

Anisotropic high-harmonic generation in bulk crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

You, Yong Sing; Reis, David A.; Ghimire, Shambhu

2016-11-21

The microscopic valence electron density determines the optical, electronic, structural and thermal properties of materials. However, current techniques for measuring this electron charge density are limited: for example, scanning tunnelling microscopy is confined to investigations at the surface, and electron diffraction requires very thin samples to avoid multiple scattering. Therefore, an optical method is desirable for measuring the valence charge density of bulk materials. Since the discovery of high-harmonic generation (HHG) in solids, there has been growing interest in using HHG to probe the electronic structure of solids. Here, using single-crystal MgO, we demonstrate that high-harmonic generation in solids ismore » sensitive to interatomic bonding. We find that harmonic efficiency is enhanced (diminished) for semi-classical electron trajectories that connect (avoid) neighbouring atomic sites in the crystal. Finally, these results indicate the possibility of using materials’ own electrons for retrieving the interatomic potential and thus the valence electron density, and perhaps even wavefunctions, in an all-optical setting.« less

Extending the accuracy of the SNAP interatomic potential form

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, Mitchell A.; Thompson, Aidan P.

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functionsmore » in EAM. It is also argued that the quadratic SNAP form is a special case of an artificial neural network (ANN). The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similarly to ANN potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting, as measured by cross-validation analysis.« less

Extending the accuracy of the SNAP interatomic potential form

DOE PAGES

Wood, Mitchell A.; Thompson, Aidan P.

2018-03-28

The Spectral Neighbor Analysis Potential (SNAP) is a classical interatomic potential that expresses the energy of each atom as a linear function of selected bispectrum components of the neighbor atoms. An extension of the SNAP form is proposed that includes quadratic terms in the bispectrum components. The extension is shown to provide a large increase in accuracy relative to the linear form, while incurring only a modest increase in computational cost. The mathematical structure of the quadratic SNAP form is similar to the embedded atom method (EAM), with the SNAP bispectrum components serving as counterparts to the two-body density functionsmore » in EAM. It is also argued that the quadratic SNAP form is a special case of an artificial neural network (ANN). The effectiveness of the new form is demonstrated using an extensive set of training data for tantalum structures. Similarly to ANN potentials, the quadratic SNAP form requires substantially more training data in order to prevent overfitting, as measured by cross-validation analysis.« less

Coupled thermomechanical behavior of graphene using the spring-based finite element approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Georgantzinos, S. K., E-mail: sgeor@mech.upatras.gr; Anifantis, N. K., E-mail: nanif@mech.upatras.gr; Giannopoulos, G. I., E-mail: ggiannopoulos@teiwest.gr

The prediction of the thermomechanical behavior of graphene using a new coupled thermomechanical spring-based finite element approach is the aim of this work. Graphene sheets are modeled in nanoscale according to their atomistic structure. Based on molecular theory, the potential energy is defined as a function of temperature, describing the interatomic interactions in different temperature environments. The force field is approached by suitable straight spring finite elements. Springs simulate the interatomic interactions and interconnect nodes located at the atomic positions. Their stiffness matrix is expressed as a function of temperature. By using appropriate boundary conditions, various different graphene configurations aremore » analyzed and their thermo-mechanical response is approached using conventional finite element procedures. A complete parametric study with respect to the geometric characteristics of graphene is performed, and the temperature dependency of the elastic material properties is finally predicted. Comparisons with available published works found in the literature demonstrate the accuracy of the proposed method.« less

An atomic finite element model for biodegradable polymers. Part 1. Formulation of the finite elements.

PubMed

Gleadall, Andrew; Pan, Jingzhe; Ding, Lifeng; Kruft, Marc-Anton; Curcó, David

2015-11-01

Molecular dynamics (MD) simulations are widely used to analyse materials at the atomic scale. However, MD has high computational demands, which may inhibit its use for simulations of structures involving large numbers of atoms such as amorphous polymer structures. An atomic-scale finite element method (AFEM) is presented in this study with significantly lower computational demands than MD. Due to the reduced computational demands, AFEM is suitable for the analysis of Young's modulus of amorphous polymer structures. This is of particular interest when studying the degradation of bioresorbable polymers, which is the topic of an accompanying paper. AFEM is derived from the inter-atomic potential energy functions of an MD force field. The nonlinear MD functions were adapted to enable static linear analysis. Finite element formulations were derived to represent interatomic potential energy functions between two, three and four atoms. Validation of the AFEM was conducted through its application to atomic structures for crystalline and amorphous poly(lactide). Copyright © 2015 Elsevier Ltd. All rights reserved.

New interatomic potentials of W, Re and W-Re alloy for radiation defects

NASA Astrophysics Data System (ADS)

Chen, Yangchun; Li, Yu-Hao; Gao, Ning; Zhou, Hong-Bo; Hu, Wangyu; Lu, Guang-Hong; Gao, Fei; Deng, Huiqiu

2018-04-01

Tungsten (W) and W-based alloys have been considered as promising candidates for plasma-facing materials (PFMs) in future fusion reactors. The formation of rhenium (Re)-rich clusters and intermetallic phases due to high energy neutron irradiation and transmutations significantly induces the hardening and embrittlement of W. In order to better understand these phenomena, in the present work, new interatomic potentials of W-W, Re-Re and W-Re, suitable for description of radiation defects in such alloys, have been developed. The fitted potentials not only reproduce the results of the formation energy, binding energy and migration energy of various radiation defects and the physical properties from the extended database obtained from DFT calculations, but also predict well the relative stability of different interstitial dislocation loops in W, as reported in experiments. These potentials are applicable for describing the evolution of defects in W and W-Re alloys, thus providing a possibility for the detailed understanding of the precipitation mechanism of Re in W under irradiation.

Role of interatomic bonding in the mechanical anisotropy and interlayer cohesion of CSH crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dharmawardhana, C.C.; Misra, A.; Aryal, S.

2013-10-15

Atomic scale properties of calcium silicate hydrate (CSH), the main binding phase of hardened Portland cement, are not well understood. Over a century of intense research has identified almost 50 different crystalline CSH minerals which are mainly categorized by their Ca/Si ratio. The electronic structure and interatomic bonding in four major CSH crystalline phases with structures close to those found in hardened cement are investigated via ab initio methods. Our result reveals the critical role of hydrogen bonding and importance of specifying precise locations for water molecules. Quantitative analysis of contributions from different bond types to the overall cohesion showsmore » that while the Si-O covalent bonds dominate, the hydrogen bonding and Ca-O bonding are also very significant. Calculated results reveal the correlation between bond topology and interlayer cohesion. The overall bond order density (BOD) is found to be a more critical measure than the Ca/Si ratio in classifying different CSH crystals.« less

Critical assessment of Pt surface energy - An atomistic study

NASA Astrophysics Data System (ADS)

Kim, Jin-Soo; Seol, Donghyuk; Lee, Byeong-Joo

2018-04-01

Despite the fact that surface energy is a fundamental quantity in understanding surface structure of nanoparticle, the results of experimental measurements and theoretical calculations for the surface energy of pure Pt show a wide range of scattering. It is necessary to further ensure the surface energy of Pt to find the equilibrium shape and atomic configuration in Pt bimetallic nanoparticles accurately. In this article, we critically assess and optimize the Pt surface energy using a semi-empirical atomistic approach based on the second nearest-neighbor modified embedded-atom method interatomic potential. That is, the interatomic potential of pure Pt was adjusted in a way that the surface segregation tendency in a wide range of Pt binary alloys is reproduced in accordance with experimental information. The final optimized Pt surface energy (mJ/m2) is 2036 for (100) surface, 2106 for (110) surface, and 1502 for (111) surface. The potential can be utilized to find the equilibrium shape and atomic configuration of Pt bimetallic nanoparticles more accurately.

Crossing Over from Attractive to Repulsive Interactions in a Tunneling Bosonic Josephson Junction.

PubMed

Spagnolli, G; Semeghini, G; Masi, L; Ferioli, G; Trenkwalder, A; Coop, S; Landini, M; Pezzè, L; Modugno, G; Inguscio, M; Smerzi, A; Fattori, M

2017-06-09

We explore the interplay between tunneling and interatomic interactions in the dynamics of a bosonic Josephson junction. We tune the scattering length of an atomic ^{39}K Bose-Einstein condensate confined in a double-well trap to investigate regimes inaccessible to other superconducting or superfluid systems. In the limit of small-amplitude oscillations, we study the transition from Rabi to plasma oscillations by crossing over from attractive to repulsive interatomic interactions. We observe a critical slowing down in the oscillation frequency by increasing the strength of an attractive interaction up to the point of a quantum phase transition. With sufficiently large initial oscillation amplitude and repulsive interactions, the system enters the macroscopic quantum self-trapping regime, where we observe coherent undamped oscillations with a self-sustained average imbalance of the relative well population. The exquisite agreement between theory and experiments enables the observation of a broad range of many body coherent dynamical regimes driven by tunable tunneling energy, interactions and external forces, with applications spanning from atomtronics to quantum metrology.

Exchange repulsive potential adaptable for electronic structure changes during chemical reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yokogawa, D., E-mail: d.yokogawa@chem.nagoya-u.ac.jp

2015-04-28

Hybrid methods combining quantum mechanical (QM) and classical calculations are becoming important tools in chemistry. The popular approach to calculate the interaction between QM and classical calculations employs interatomic potentials. In most cases, the interatomic potential is constructed of an electrostatic (ES) potential and a non-ES potential. Because QM treatment is employed in the calculation of the ES potential, the electronic change can be considered in this ES potential. However, QM treatment of the non-ES potential is difficult because of high computational cost. To overcome this difficulty of evaluating the non-ES potential, we proposed an exchange repulsive potential as themore » main part of the non-ES potential on the basis of a QM approach. This potential is independent of empirical parameters and adaptable for electronic structure. We combined this potential with the reference interaction site model self-consistent field explicitly including spatial electron density distribution and successfully applied it to the chemical reactions in aqueous phase.« less

A quantum perturbative pair distribution for determining interatomic potentials from extended x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Piazza, F.

2002-11-01

In this paper we develop a technique for determining interatomic potentials in materials in the quantum regime from single-shell extended x-ray absorption spectroscopy (EXAFS) spectra. We introduce a pair distribution function, based on ordinary quantum time-independent perturbation theory. In the proposed scheme, the model potential parameters enter the distribution through a fourth-order Taylor expansion of the potential, and are directly refined in the fit of the model signal to the experimental spectrum. We discuss in general the validity of our theoretical framework, namely the quantum regime and perturbative treatment, and work out a simple tool for monitoring the sensitivity of our theory in determining lattice anharmonicities based on the statistical F-test. As an example, we apply our formalism to an EXAFS spectrum at the Ag K edge of AgI at T = 77 K. We determine the Ag-I potential parameters and find good agreement with previous studies.

An interatomic pair potential for cadmium selenide

NASA Astrophysics Data System (ADS)

Rabani, Eran

2002-01-01

We have developed a set of interatomic pair potentials for cadmium selenide based on a form similar to the Born-Mayer model. We show that this simple form of the pair potential, which has been used to describe the properties of alkali halides in the sixfold-coordinate structure, provides a realistic description of the properties of cadmium selenide in all three crystal structures: wurtzite, zinc blende, and rocksalt. Using the new pair potential we have studied the pressure-induced phase transition from the fourfold-coordinate wurtzite structure to the sixfold-coordinate rocksalt structure. The pressure transformation and the equation of state are in good agreement with experimental observations. Using the dispersion term in our pair potential we have also calculated the Hamaker constant for cadmium selenide within the framework of the original microscopic approach due to Hamaker. The results indicate that for ionic materials many-body terms that are included in the Lifshitz theory are well captured by the simple pair potential.

Interatomic potential to study plastic deformation in tungsten-rhenium alloys

NASA Astrophysics Data System (ADS)

Bonny, G.; Bakaev, A.; Terentyev, D.; Mastrikov, Yu. A.

2017-04-01

In this work, an interatomic potential for the W-Re system is fitted and benchmarked against experimental and density functional theory (DFT) data, of which part are generated in this work. Having in mind studies related to the plasticity of W-Re alloys under irradiation, emphasis is put on fitting point-defect properties, elastic constants, and dislocation properties. The developed potential can reproduce the mechanisms responsible for the experimentally observed softening, i.e., decreasing shear moduli, decreasing Peierls barrier, and asymmetric screw dislocation core structure with increasing Re content in W-Re solid solutions. In addition, the potential predicts elastic constants in reasonable agreement with DFT data for the phases forming non-coherent precipitates (σ- and χ-phases) in W-Re alloys. In addition, the mechanical stability of the different experimentally observed phases is verified in the temperature range of interest (700-1500 K). As a conclusion, the presented potential provides an excellent tool to study plasticity in W-Re alloys at the atomic level.

Potential energy function for CH3+CH3 ⇆ C2H6: Attributes of the minimum energy path

NASA Astrophysics Data System (ADS)

Robertson, S. H.; Wardlaw, D. M.; Hirst, D. M.

1993-11-01

The region of the potential energy surface for the title reaction in the vicinity of its minimum energy path has been predicted from the analysis of ab initio electronic energy calculations. The ab initio procedure employs a 6-31G** basis set and a configuration interaction calculation which uses the orbitals obtained in a generalized valence bond calculation. Calculated equilibrium properties of ethane and of isolated methyl radical are compared to existing theoretical and experimental results. The reaction coordinate is represented by the carbon-carbon interatomic distance. The following attributes are reported as a function of this distance and fit to functional forms which smoothly interpolate between reactant and product values of each attribute: the minimum energy path potential, the minimum energy path geometry, normal mode frequencies for vibrational motion orthogonal to the reaction coordinate, a torsional potential, and a fundamental anharmonic frequency for local mode, out-of-plane CH3 bending (umbrella motion). The best representation is provided by a three-parameter modified Morse function for the minimum energy path potential and a two-parameter hyperbolic tangent switching function for all other attributes. A poorer but simpler representation, which may be satisfactory for selected applications, is provided by a standard Morse function and a one-parameter exponential switching function. Previous applications of the exponential switching function to estimate the reaction coordinate dependence of the frequencies and geometry of this system have assumed the same value of the range parameter α for each property and have taken α to be less than or equal to the ``standard'' value of 1.0 Å-1. Based on the present analysis this is incorrect: The α values depend on the property and range from ˜1.2 to ˜1.8 Å-1.

Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haskins, William E.; Leavell, Michael D.; Lane, Pamela

2005-03-01

Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurementmore » using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.« less

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

NASA Astrophysics Data System (ADS)

Sieradzan, Adam K.; Makowski, Mariusz; Augustynowicz, Antoni; Liwo, Adam

2017-03-01

A general and systematic method for the derivation of the functional expressions for the effective energy terms in coarse-grained force fields of polymer chains is proposed. The method is based on the expansion of the potential of mean force of the system studied in the cluster-cumulant series and expanding the all-atom energy in the Taylor series in the squares of interatomic distances about the squares of the distances between coarse-grained centers, to obtain approximate analytical expressions for the cluster cumulants. The primary degrees of freedom to average about are the angles for collective rotation of the atoms contained in the coarse-grained interaction sites about the respective virtual-bond axes. The approach has been applied to the revision of the virtual-bond-angle, virtual-bond-torsional, and backbone-local-and-electrostatic correlation potentials for the UNited RESidue (UNRES) model of polypeptide chains, demonstrating the strong dependence of the torsional and correlation potentials on virtual-bond angles, not considered in the current UNRES. The theoretical considerations are illustrated with the potentials calculated from the ab initio potential-energy surface of terminally blocked alanine by numerical integration and with the statistical potentials derived from known protein structures. The revised torsional potentials correctly indicate that virtual-bond angles close to 90° result in the preference for the turn and helical structures, while large virtual-bond angles result in the preference for polyproline II and extended backbone geometry. The revised correlation potentials correctly reproduce the preference for the formation of β-sheet structures for large values of virtual-bond angles and for the formation of α-helical structures for virtual-bond angles close to 90°.

Long-range interactions of hydrogen atoms in excited states. III. n S -1 S interactions for n ≥3

NASA Astrophysics Data System (ADS)

Adhikari, C. M.; Debierre, V.; Jentschura, U. D.

2017-09-01

The long-range interaction of excited neutral atoms has a number of interesting and surprising properties such as the prevalence of long-range oscillatory tails and the emergence of numerically large van der Waals C6 coefficients. Furthermore, the energetically quasidegenerate n P states require special attention and lead to mathematical subtleties. Here we analyze the interaction of excited hydrogen atoms in n S states (3 ≤n ≤12 ) with ground-state hydrogen atoms and find that the C6 coefficients roughly grow with the fourth power of the principal quantum number and can reach values in excess of 240 000 (in atomic units) for states with n =12 . The nonretarded van der Waals result is relevant to the distance range R ≪a0/α , where a0 is the Bohr radius and α is the fine-structure constant. The Casimir-Polder range encompasses the interatomic distance range a0/α ≪R ≪ℏ c /L , where L is the Lamb shift energy. In this range, the contribution of quasidegenerate excited n P states remains nonretarded and competes with the 1 /R2 and 1 /R4 tails of the pole terms, which are generated by lower-lying m P states with 2 ≤m ≤n -1 , due to virtual resonant emission. The dominant pole terms are also analyzed in the Lamb shift range R ≫ℏ c /L . The familiar 1 /R7 asymptotics from the usual Casimir-Polder theory is found to be completely irrelevant for the analysis of excited-state interactions. The calculations are carried out to high precision using computer algebra in order to handle a large number of terms in intermediate steps of the calculation for highly excited states.

Collisional Dynamics of the Cesium D1 and D2 Transitions

DTIC Science & Technology

2010-09-01

37 14. Comparison of Phase Changing Probability and Polarizability ...Phase Changing Probability and Polarizability for D2 Transition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 25...theoretically determined the values for broadening and shift rates for cesium with Argon , Krypton, and Xenon from the interatomic potentials [27]. The rates

Computer modelling of solid alkali metal carboxylates

NASA Astrophysics Data System (ADS)

Barreto, L. S.; Mort, K. A.; Jackson, R. A.; Alves, O. L.

2000-11-01

A computational study of solid lithium acetate dihydrate and anhydrous sodium acetate is presented. Interatomic potentials are obtained by empirical fitting to experimental structural data for both materials and the resulting potentials were found to be transferable to different phases of the same materials, giving good agreement with the experimental structure.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chuvashova, Irina, E-mail: irina.chuvashova@gmail.com; Bayerisches Geoinstitut, University of Bayreuth, D-95440 Bayreuth; Bykova, Elena

In the present study single crystals of rhombohedral α-B were investigated under pressure to 60 GPa by means of single-crystal X-ray diffraction. The bulk modulus of α-B was found to be K=224(7) GPa (K′=3.0(3)). Measurements of interatomic distances as a function of pressure revealed that the intericosahedral two-center two-electron (2c–2e) bonds are almost as stiff as some of intraicosahedral ones. The three-center two-electron (3c–2e) intericosahedral bonds show much higher compliance compared to other bonds in α-B. The vibrational properties of α-B under pressure were investigated by Raman spectroscopy at pressures up to 160 GPa and IR spectroscopy at pressures upmore » to 53 GPa. - Graphical abstract: The rhombohedral α-B is highly incompressible and extremely stable: it maintains its crystal structure up to 160 GPa and its intericosahedral 2e2c bonds are almost as stiff as some of intraicosahedral ones. - Highlights: • Structural stability of α-B has been investigated up to 160 GPa on single crystals. • Single-crystal x-ray diffraction reveals that α-B is highly incompressible. • Compressibility of B{sub 12} icosahedra is considerably lower than that of the bulk material. • Intericosahedral 2e2c bonds are almost as stiff as some of intraicosahedral ones.« less

Comparative study of local atomic structures in Zr2CuxNi1-x (x = 0, 0.5, 1) metallic glasses

NASA Astrophysics Data System (ADS)

Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

2015-11-01

Extensive analysis has been performed to understand the key structural motifs accounting for the difference in glass forming ability in the Zr-Cu and Zr-Ni binary alloy systems. Here, the reliable atomic structure models of Zr2CuxNi1-x (x = 0, 0.5, 1) are constructed using the combination of X-ray diffraction experiments, ab initio molecular dynamics simulations and a constrained reverse Monte Carlo method. We observe a systematic variation of the interatomic distance of different atomic pairs with respect to the alloy composition. The ideal icosahedral content in all samples is limited, despite the high content of five-fold symmetry motifs. We also demonstrate that the population of Z-clusters in Zr2Cu glass is much higher than that in the Zr2Ni and Zr2Cu0.5Ni0.5 samples. And Z12 ⟨0, 0, 12, 0⟩ Voronoi polyhedra clusters prefer to form around Cu atoms, while Ni-centered clusters are more like Z11 ⟨0, 2, 8, 1⟩ clusters, which is less energetically stable compared to Z12 clusters. These two different structural properties may account for the higher glass forming ability of Zr2Cu alloy than that of Zr2Ni alloy.

Spectroscopic and structural investigation of interaction of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thione potassium salt with molecular iodine

NASA Astrophysics Data System (ADS)

Ivolgina, Victoria A.; Chernov'yants, Margarita S.

2018-06-01

The interest in the study of heteroaromatic thioamides which are known to exhibit antithyroid activity is stimulated by the variety and an unusual structure their complexes with molecular iodine. The directions of dithiones investigation are diversity enough, however a few works are devoted to the study them as the potential thyreostatics. The ability of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thion potassium salt to form the outer-sphere charge-transfer complex in dilute chloroform solution, coordinating 2 iodine molecules has been studied by UV-vis spectroscopy (lgβ = 7.91). The compound of the 5,5‧-disulfanediylbis(3-phenyl-1,3,4-thiadiazole-2(3H)-thione) - product of irreversible oxidation of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thione potassium salt has been isolated and characterized by X-ray diffraction. Intermolecular interactions between sulfur atoms are observed with very short interatomic distance, shorter than sum of van der Waals radii. The contact between heterocyclic sulfur and heterocyclic nitrogen is also slightly short - 3.169 Å (0.053 Å less than vdW radii sum). This investigation constitutes a starting point for study of novel antithyroid drugs in future.

The multiple roles of small-angle tilt grain boundaries in annihilating radiation damage in SiC

DOE PAGES

Jiang, Hao; Wang, Xing; Szlufarska, Izabela

2017-02-09

Lattice defects generated by radiation damage can diffuse to grain boundaries (GBs) and be annihilated at GBs. However, the precise role of GBs in annihilating the segregated defects remains unclear. Here, we employed multi-scale models to determine how interstitials are annihilated at small-angle tilt GBs (STGBs) in SiC. First of all, we found the pipe diffusion of interstitials in STGBs is slower than bulk diffusion. This is because the increased interatomic distance at dislocation cores raises the migration barrier of interstitial dumbbells. Furthermore, we found both the annihilation of interstitials at jogs and jog nucleation from clusters are diffusion-controlled andmore » can occur under off-stoichiometric interstitial fluxes. Finally, a dislocation line model is developed to predict the role of STGBs in annihilating radiation damage. This model includes defect flux to GBs, pipe diffusion in STGBs, and the interaction of defects with jogs. The model predicts the role of STGBs in annihilating defects depends on the rate of defects segregation to and diffusion along STGBs. STGBs mainly serve as diffusion channel for defects to reach other sinks when defect diffusivity is high at boundaries. As a result, when defect diffusivity is low, most of the defects segregated to STGBs are annihilated by dislocation climb.« less

EXAFS and XANES investigation of the ETS-10 microporous titanosilicate.

PubMed

Prestipino, C; Solari, P L; Lamberti, C

2005-07-14

In this work, we report state-of-the-art analysis of both Ti K-edge high-resolution XANES and EXAFS data collected on the ETS-10 molecular sieve at the GILDA BM8 beamline of the ESRF facility. The interatomic distances and the angles obtained in our EXAFS study are in fair agreement with the single-crystal XRD data of Wang and Jacobson (Chem. Commun. 1999, 973) and with the recent ab initio periodic study of Damin et al. (J. Phys. Chem. B 2004, 108, 1328) Differently from previous EXAFS work (J. Phys. Chem. 1996, 100, 449), our study supports a model of ETS-10 where the Ti atoms are bonded with two equivalent axial oxygen atoms. This model is also able to reproduce the edge and the post-edge region of the XANES spectrum. Conversely, the weak but well-defined pre-edge peak at 4971.3 eV can be explained only by assuming that a fraction of Ti atoms are in a local geometry similar to that of the pentacoordinated Ti sites in the ETS-4 structure. These Ti atoms in ETS-10 should be the terminal of the -Ti-O-Ti-O-Ti- chains, of which the actual number is strongly increased by the high crystal defectivity (Ti vacancies).

Ballistic Phonon Penetration Depth in Amorphous Silicon Dioxide.

PubMed

Yang, Lin; Zhang, Qian; Cui, Zhiguang; Gerboth, Matthew; Zhao, Yang; Xu, Terry T; Walker, D Greg; Li, Deyu

2017-12-13

Thermal transport in amorphous silicon dioxide (a-SiO 2 ) is traditionally treated as random walks of vibrations owing to its greatly disordered structure, which results in a mean free path (MFP) approximately the same as the interatomic distance. However, this picture has been debated constantly and in view of the ubiquitous existence of thin a-SiO 2 layers in nanoelectronic devices, it is imperative to better understand this issue for precise thermal management of electronic devices. Different from the commonly used cross-plane measurement approaches, here we report on a study that explores the in-plane thermal conductivity of double silicon nanoribbons with a layer of a-SiO 2 sandwiched in-between. Through comparing the thermal conductivity of the double ribbon samples with that of corresponding single ribbons, we show that thermal phonons can ballistically penetrate through a-SiO 2 of up to 5 nm thick even at room temperature. Comprehensive examination of double ribbon samples with various oxide layer thicknesses and van der Waals bonding strengths allows for extraction of the average ballistic phonon penetration depth in a-SiO 2 . With solid experimental data demonstrating ballistic phonon transport through a-SiO 2 , this work should provide important insight into thermal management of electronic devices.

X-ray absorption spectroscopy as a tool investigating arsenic(III) and arsenic(V) sorption by an aluminum-based drinking-water treatment residual.

PubMed

Makris, Konstantinos C; Sarkar, Dibyendu; Parsons, Jason G; Datta, Rupali; Gardea-Torresdey, Jorge L

2009-11-15

Historic applications of arsenical pesticides to agricultural land have resulted in accumulation of residual arsenic (As) in such soils. In situ immobilization represents a cost-effective and least ecological disrupting treatment technology for soil As. Earlier work in our laboratory showed that drinking-water treatment residuals (WTRs), a low-cost, waste by-product of the drinking-water treatment process exhibit a high affinity for As. Wet chemical experiments (sorption kinetics and desorption) were coupled with X-ray absorption spectroscopy measurements to elucidate the bonding strength and type of As(V) and As(III) sorption by an aluminum-based WTR. A fast (1h), followed by a slower sorption stage resulted in As(V) and As(III) sorption capacities of 96% and 77%, respectively. Arsenic desorption with a 5mM oxalate from the WTR was minimal, being always <4%. X-ray absorption spectroscopy data showed inner-sphere complexation between As and surface hydroxyls. Reaction time (up to 48h) had no effect on the initial As oxidation state for sorbed As(V) and As(III). A combination of inner-sphere bonding types occurred between As and Al on the WTR surface because mixed surface geometries and interatomic distances were observed.

Total scattering and pair distribution function analysis in modelling disorder in PZN (PbZn1/3Nb2/3O3)

PubMed Central

Whitfield, Ross E.; Goossens, Darren J.; Welberry, T. Richard

2016-01-01

The ability of the pair distribution function (PDF) analysis of total scattering (TS) from a powder to determine the local ordering in ferroelectric PZN (PbZn1/3Nb2/3O3) has been explored by comparison with a model established using single-crystal diffuse scattering (SCDS). While X-ray PDF analysis is discussed, the focus is on neutron diffraction results because of the greater extent of the data and the sensitivity of the neutron to oxygen atoms, the behaviour of which is important in PZN. The PDF was shown to be sensitive to many effects not apparent in the average crystal structure, including variations in the B-site—O separation distances and the fact that 〈110〉 Pb2+ displacements are most likely. A qualitative comparison between SCDS and the PDF shows that some features apparent in SCDS were not apparent in the PDF. These tended to pertain to short-range correlations in the structure, rather than to interatomic separations. For example, in SCDS the short-range alternation of the B-site cations was quite apparent in diffuse scattering at (½ ½ ½), whereas it was not apparent in the PDF. PMID:26870378

Spectroscopic and structural investigation of interaction of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thione potassium salt with molecular iodine.

PubMed

Ivolgina, Victoria A; Chernov'yants, Margarita S

2018-06-15

The interest in the study of heteroaromatic thioamides which are known to exhibit antithyroid activity is stimulated by the variety and an unusual structure their complexes with molecular iodine. The directions of dithiones investigation are diversity enough, however a few works are devoted to the study them as the potential thyreostatics. The ability of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thion potassium salt to form the outer-sphere charge-transfer complex in dilute chloroform solution, coordinating 2 iodine molecules has been studied by UV-vis spectroscopy (lgβ=7.91). The compound of the 5,5'-disulfanediylbis(3-phenyl-1,3,4-thiadiazole-2(3H)-thione) - product of irreversible oxidation of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thione potassium salt has been isolated and characterized by X-ray diffraction. Intermolecular interactions between sulfur atoms are observed with very short interatomic distance, shorter than sum of van der Waals radii. The contact between heterocyclic sulfur and heterocyclic nitrogen is also slightly short - 3.169Å (0.053Å less than vdW radii sum). This investigation constitutes a starting point for study of novel antithyroid drugs in future. Copyright © 2018 Elsevier B.V. All rights reserved.

The multiple roles of small-angle tilt grain boundaries in annihilating radiation damage in SiC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Hao; Wang, Xing; Szlufarska, Izabela

Lattice defects generated by radiation damage can diffuse to grain boundaries (GBs) and be annihilated at GBs. However, the precise role of GBs in annihilating the segregated defects remains unclear. Here, we employed multi-scale models to determine how interstitials are annihilated at small-angle tilt GBs (STGBs) in SiC. First of all, we found the pipe diffusion of interstitials in STGBs is slower than bulk diffusion. This is because the increased interatomic distance at dislocation cores raises the migration barrier of interstitial dumbbells. Furthermore, we found both the annihilation of interstitials at jogs and jog nucleation from clusters are diffusion-controlled andmore » can occur under off-stoichiometric interstitial fluxes. Finally, a dislocation line model is developed to predict the role of STGBs in annihilating radiation damage. This model includes defect flux to GBs, pipe diffusion in STGBs, and the interaction of defects with jogs. The model predicts the role of STGBs in annihilating defects depends on the rate of defects segregation to and diffusion along STGBs. STGBs mainly serve as diffusion channel for defects to reach other sinks when defect diffusivity is high at boundaries. As a result, when defect diffusivity is low, most of the defects segregated to STGBs are annihilated by dislocation climb.« less

Molecular Static Third-Order Polarizabilities of Carbon-Cage Fullerene and Their Correlation with Three Geometric Properties: Symmetry, Aromaticity, and Size

NASA Technical Reports Server (NTRS)

Moore, C. E.; Cardelino, B. H.; Frazier, D. O.; Niles, J.; Wang, X.-Q.

1998-01-01

The static third-order polarizabilities (gamma) of C60, C70, five isomers of C78 and two isomers of C84 were analyzed in terms of three properties, from a geometric point of view: symmetry, aromaticity and size. The polarizability values were based on the finite field approximation using a semiempirical Hamiltonian (AM1) and applied to molecular structures obtained from density functional theory calculations. Symmetry was characterized by the molecular group order. The selection of 6-member rings as aromatic was determined from an analysis of bond lengths. Maximum interatomic distance and surface area were the parameters considered with respect to size. Based on triple linear regression analysis, it was found that the static linear polarizability (alpha) and gamma in these molecules respond differently to geometrical properties: alpha depends almost exclusively on surface area while gamma is affected by a combination of number of aromatic rings, length and group order, in decreasing importance. In the case of alpha, valence electron contributions provide the same information as all-electron estimates. For gamma, the best correlation coefficients are obtained when all-electron estimates are used and when the dependent parameter is ln(gamma) instead of gamma.

Solid-state NMR detection of 14N-13C dipolar couplings between amino acid side groups provides constraints on amyloid fibril architecture.

PubMed

Middleton, David A

2011-02-01

Solid-state nuclear magnetic resonance (SSNMR) is a powerful technique for the structural analysis of amyloid fibrils. With suitable isotope labelling patterns, SSNMR can provide constraints on the secondary structure, alignment and registration of β-strands within amyloid fibrils and identify the tertiary and quaternary contacts defining the packing of the β-sheet layers. Detection of (14)N-(13)C dipolar couplings may provide potentially useful additional structural constraints on β-sheet packing within amyloid fibrils but has not until now been exploited for this purpose. Here a frequency-selective, transfer of population in double resonance SSNMR experiment is used to detect a weak (14)N-(13)C dipolar coupling in amyloid-like fibrils of the peptide H(2)N-SNNFGAILSS-COOH, which was uniformly (13)C and (15)N labelled across the four C-terminal amino acids. The (14)N-(13)C interatomic distance between leucine and asparagine side groups is constrained between 2.4 and 3.8 Å, which allows current structural models of the β-spine arrangement within the fibrils to be refined. This procedure could be useful for the general structural analysis of other proteins in condensed phases and environments, such as biological membranes. Copyright © 2011 John Wiley & Sons, Ltd.

A naturally-occurring new lead-based halocuprate(I)

NASA Astrophysics Data System (ADS)

Welch, Mark D.; Rumsey, Michael S.; Kleppe, Annette K.

2016-06-01

Pb2Cu(OH)2I3 is a new type of halocuprate(I) that is a framework of alternating [Pb4(OH)4]4+ and [Cu2I6]4- units. The structure has been determined in orthorhombic space group Fddd to R1=0.037, wR2=0.057, GoF=1.016. Unit cell parameters are a=16.7082(9) Å, b=20.8465(15) Å, c=21.0159(14) Å, V=7320.0(8) Å3 (Z=32). There is no synthetic counterpart. The structure is based upon a cubane-like Pb4(OH)4 nucleus that is coordinated to sixteen iodide ions. Cu+ ions are inserted into pairs of adjacent edge-sharing tetrahedral sites in the iodide motif to form [Cu2I6]4- groups. The Raman spectrum of Pb2Cu(OH)2I3 has two O-H stretching modes and as such is consistent with space group Fddd, with two non-equivalent OH groups, rather than the related space group I41/acd which has only one non-equivalent OH group. Consideration of the 18-electron rule implies that there is a Cu=Cu double bond, which may be consistent with the short Cu…Cu distance of 2.78 Å, although the dearth of published data on the interpretation of Cu…Cu distances in halocuprate(I) compounds does not allow a clear-cut interpretation of this interatomic distance. The orthorhombic structure is compared with that of the synthetic halocuprate(I) compound Pb2Cu(OH)2BrI2 with space group I41/acd and having chains of corner-linked CuI4 tetrahedra rather than isolated Cu2I6 pairs. The paired motif found in Pb2Cu(OH)2I3 cannot be achieved in space group I41/acd and, conversely, the chain motif cannot be achieved in space group Fddd. As such, the space group defines either a chain or an isolated-pair motif. The existence of Pb2Cu(OH)2I3 suggests a new class of inorganic halocuprate(I)s based upon the Pb4(OH)4 group.

Perspective: Machine learning potentials for atomistic simulations

NASA Astrophysics Data System (ADS)

Behler, Jörg

2016-11-01

Nowadays, computer simulations have become a standard tool in essentially all fields of chemistry, condensed matter physics, and materials science. In order to keep up with state-of-the-art experiments and the ever growing complexity of the investigated problems, there is a constantly increasing need for simulations of more realistic, i.e., larger, model systems with improved accuracy. In many cases, the availability of sufficiently efficient interatomic potentials providing reliable energies and forces has become a serious bottleneck for performing these simulations. To address this problem, currently a paradigm change is taking place in the development of interatomic potentials. Since the early days of computer simulations simplified potentials have been derived using physical approximations whenever the direct application of electronic structure methods has been too demanding. Recent advances in machine learning (ML) now offer an alternative approach for the representation of potential-energy surfaces by fitting large data sets from electronic structure calculations. In this perspective, the central ideas underlying these ML potentials, solved problems and remaining challenges are reviewed along with a discussion of their current applicability and limitations.

Interatomic Coulombic Decay Effects in Theoretical DNA Recombination Systems Involving Protein Interaction Sites

NASA Astrophysics Data System (ADS)

Vargas, E. L.; Rivas, D. A.; Duot, A. C.; Hovey, R. T.; Andrianarijaona, V. M.

2015-03-01

DNA replication is the basis for all biological reproduction. A strand of DNA will ``unzip'' and bind with a complimentary strand, creating two identical strands. In this study, we are considering how this process is affected by Interatomic Coulombic Decay (ICD), specifically how ICD affects the individual coding proteins' ability to hold together. ICD mainly deals with how the electron returns to its original state after excitation and how this affects its immediate atomic environment, sometimes affecting the connectivity between interaction sites on proteins involved in the DNA coding process. Biological heredity is fundamentally controlled by DNA and its replication therefore it affects every living thing. The small nature of the proteins (within the range of nanometers) makes it a good candidate for research of this scale. Understanding how ICD affects DNA molecules can give us invaluable insight into the human genetic code and the processes behind cell mutations that can lead to cancer. Authors wish to give special thanks to Pacific Union College Student Senate in Angwin, California, for their financial support.

Physical Realization of von Neumann Lattices in Rotating Bose Gases with Dipole Interatomic Interactions.

PubMed

Cheng, Szu-Cheng; Jheng, Shih-Da

2016-08-22

This paper reports a novel type of vortex lattice, referred to as a bubble crystal, which was discovered in rapidly rotating Bose gases with long-range interactions. Bubble crystals differ from vortex lattices which possess a single quantum flux per unit cell, while atoms in bubble crystals are clustered periodically and surrounded by vortices. No existing model is able to describe the vortex structure of bubble crystals; however, we identified a mathematical lattice, which is a subset of coherent states and exists periodically in the physical space. This lattice is called a von Neumann lattice, and when it possesses a single vortex per unit cell, it presents the same geometrical structure as an Abrikosov lattice. In this report, we extend the von Neumann lattice to one with an integral number of flux quanta per unit cell and demonstrate that von Neumann lattices well reproduce the translational properties of bubble crystals. Numerical simulations confirm that, as a generalized vortex, a von Neumann lattice can be physically realized using vortex lattices in rapidly rotating Bose gases with dipole interatomic interactions.

Effect of alloying on screw dislocation structure in Mo: atomistic modelling approach with ab-initio parametrization

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.

2005-03-01

The plastic deformation in bcc metals is realized by the motion of screw dislocations with a complex star-like non-planar core. In this case, the direct investigation of the solute effect by first principles electronic structure calculations is a challenging problem for which we follow a combined approach that includes atomistic dislocation modelling with ab-initio parametrization of interatomic interactions. The screw dislocation core structure in Mo alloys is described within the model of atomic row displacements along a dislocation line with the interatomic row potential estimated from total energy full-potential linear muffin-tin orbital (FLMTO) calculations with the generalized gradient approximation (GGA) for the exchange-correlation potential. We demonstrate (1) that the solute effect on the dislocation structure is different for ``hard'' and ``easy'' cores and (2) that the softener addition in a ``hard'' core gives rise to a structural transformation into a configuration with a lower energy through an intermediate state. The softener solute is shown to disturb locally the three-fold symmetry of the dislocation core and the dislocation structure tends to the split planar core.

Probing the interatomic potential of solids with strong-field nonlinear phononics

NASA Astrophysics Data System (ADS)

von Hoegen, A.; Mankowsky, R.; Fechner, M.; Först, M.; Cavalleri, A.

2018-03-01

Nonlinear optical techniques at visible frequencies have long been applied to condensed matter spectroscopy. However, because many important excitations of solids are found at low energies, much can be gained from the extension of nonlinear optics to mid-infrared and terahertz frequencies. For example, the nonlinear excitation of lattice vibrations has enabled the dynamic control of material functions. So far it has only been possible to exploit second-order phonon nonlinearities at terahertz field strengths near one million volts per centimetre. Here we achieve an order-of-magnitude increase in field strength and explore higher-order phonon nonlinearities. We excite up to five harmonics of the A1 (transverse optical) phonon mode in the ferroelectric material lithium niobate. By using ultrashort mid-infrared laser pulses to drive the atoms far from their equilibrium positions, and measuring the large-amplitude atomic trajectories, we can sample the interatomic potential of lithium niobate, providing a benchmark for ab initio calculations for the material. Tomography of the energy surface by high-order nonlinear phononics could benefit many aspects of materials research, including the study of classical and quantum phase transitions.

Density Scaling of Glassy Dynamics and Dynamic Heterogeneities in Glass-forming Liquids.

NASA Astrophysics Data System (ADS)

Hu, Yuan-Chao; Yang, Yong; Wang, Wei-Hua

The discovery of density scaling in strongly correlating systems is an important progress for understanding the dynamic behaviors of supercooled liquids. Here we found for a ternary metallic glass-forming liquid, it is not strongly correlating thermodynamically, but its average dynamics, dynamic heterogeneities and static structure are still well described by density scaling with the same scaling exponent γ. As an intrinsic material constant stemming from the fundamental interatomic interactions, γ is theoretically predicted from the thermodynamic fluctuations of potential energy and the virial. Although γ is conventionally understood merely from the repulsive part of the inter-particle potentials, the strong correlation between γ and the Grüneisen parameter up to the accuracy of the Dulong-Petit approximation demonstrates the important roles of anharmonicity and attractive force of the interatomic potential in governing glass transition of metallic glass-formers. The supercooled dynamics and density scaling behaviors will also be discussed in model glass-forming liquids with tunable attractive potentials to further quantify the nonperturbative roles of attractive interactions. We acknowledge the support from ''Peter Ho Conference Scholarships'' of City University of Hong Kong.

Dzyaloshinskii-Moriya interaction and magnetic anisotropies in Uranium compounds

NASA Astrophysics Data System (ADS)

Sandratskii, L. M.

2018-05-01

We report on the first-principles study of complex noncollinear magnetic structures in Uranium compounds. We contrast two cases. The first is the periodic magnetic structure of U2Pd2In with exactly orthogonal atomic moments, the second is an incommensurate plane spiral structure of UPtGe where the angle between atomic moments of nearest neighbors is also close to 90°. We demonstrate that the hierarchy of magnetic interactions leading to the formation of the magnetic structure is opposite in the two cases. In U2Pd2In, the magnetic anisotropy plays the leading role, followed by the Dzyaloshinskii-Moriya interaction (DMI) interaction specifying the chirality of the structure. Here, the interatomic exchange interaction does not play important role. In UPtGe the hierarchy of the interactions is opposite. The leading interaction is the interatomic exchange interaction responsible for the formation of the incommensurate spiral structure followed by the DMI responsible for the selected chirality of the helix. The magnetic anisotropy is very weak that is a prerequisite for keeping the distortion of the helical structure weak.

A tungsten-rhenium interatomic potential for point defect studies

DOE PAGES

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-28

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Jingchao, E-mail: zhang@unl.edu, E-mail: yyue@whu.edu.cn; Hong, Yang; Yue, Yanan, E-mail: zhang@unl.edu, E-mail: yyue@whu.edu.cn

As the dimensions of nanocircuits and nanoelectronics shrink, thermal energies are being generated in more confined spaces, making it extremely important and urgent to explore for efficient heat dissipation pathways. In this work, the phonon energy transport across graphene and hexagonal boron-nitride (h-BN) interface is studied using classic molecular dynamics simulations. Effects of temperature, interatomic bond strength, heat flux direction, and functionalization on interfacial thermal transport are investigated. It is found out that by hydrogenating graphene in the hybrid structure, the interfacial thermal resistance (R) between graphene and h-BN can be reduced by 76.3%, indicating an effective approach to manipulatemore » the interfacial thermal transport. Improved in-plane/out-of-plane phonon couplings and broadened phonon channels are observed in the hydrogenated graphene system by analyzing its phonon power spectra. The reported R results monotonically decrease with temperature and interatomic bond strengths. No thermal rectification phenomenon is observed in this interfacial thermal transport. Results reported in this work give the fundamental knowledge on graphene and h-BN thermal transport and provide rational guidelines for next generation thermal interface material designs.« less

On macromolecular refinement at subatomic resolution with interatomic scatterers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afonine, Pavel V., E-mail: pafonine@lbl.gov; Grosse-Kunstleve, Ralf W.; Adams, Paul D.

2007-11-01

Modelling deformation electron density using interatomic scatters is simpler than multipolar methods, produces comparable results at subatomic resolution and can easily be applied to macromolecules. A study of the accurate electron-density distribution in molecular crystals at subatomic resolution (better than ∼1.0 Å) requires more detailed models than those based on independent spherical atoms. A tool that is conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8–1.0 Å, the number of experimental data is insufficient for full multipolar model refinement. As an alternative, a simpler model composed of conventional independent spherical atoms augmented bymore » additional scatterers to model bonding effects has been proposed. Refinement of these mixed models for several benchmark data sets gave results that were comparable in quality with the results of multipolar refinement and superior to those for conventional models. Applications to several data sets of both small molecules and macromolecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package.« less

A tungsten-rhenium interatomic potential for point defect studies

NASA Astrophysics Data System (ADS)

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-01

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures in the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancies and self-interstitial defects sufficiently accurately and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).

Deformation of periodic nanovoid structures in Mg single crystals

NASA Astrophysics Data System (ADS)

Xu, Shuozhi; Su, Yanqing; Zare Chavoshi, Saeed

2018-01-01

Large scale molecular dynamics (MD) simulations in Mg single crystal containing periodic cylindrical voids subject to uniaxial tension along the z direction are carried out. Models with different initial void sizes and crystallographic orientations are explored using two interatomic potentials. It is found that (i) a larger initial void always leads to a lower yield stress, in agreement with an analytic prediction; (ii) in the model with x[\\bar{1}100]-y[0001]-z[11\\bar{2}0] orientations, the two potentials predict different types of tension twins and phase transformation; (iii) in the model with x[0001]-y[11\\bar{2}0]-z[\\bar{1}100] orientations, the two potentials identically predict the nucleation of edge dislocations on the prismatic plane, which then glide away from the void, resulting in extrusions at the void surface; in the case of the smallest initial void, these surface extrusions pinch the void into two voids. Besides bringing new physical understanding of the nanovoid structures, our work highlights the variability and uncertainty in MD simulations arising from the interatomic potential, an issue relatively lightly addressed in the literature to date.

A tungsten-rhenium interatomic potential for point defect studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

An existence criterion for low-dimensional materials

NASA Astrophysics Data System (ADS)

Chen, Jiapeng; Wang, Biao; Hu, Yangfan

2017-10-01

The discovery of graphene and other two-dimensional (2-D) materials has stimulated a general interest in low-dimensional (low-D) materials. Whereas long time ago, Peierls (1935) and Landau's (1937) theoretical work demonstrated that any one- and two-dimensional materials could not exist in any finite temperature environment. Then, two basic issues became a central concern for many researchers: How can stable low-D materials exist? What kind of low-D materials are stable? Here, we establish an energy stability criterion for low-D materials, which seeks to provide a clear answer to these questions. For a certain kind of element, the stability of its specific low-D structure is determined by several derivatives of its interatomic potential. This atomistic-based approach is then applied to study any straight/planar, low-D, equal-bond-length elemental materials. We found that 1-D monatomic chains, 2-D honeycomb lattices, square lattices, and triangular lattices are the only four permissible structures, and the stability of these structures can only be understood by assuming multi-body interatomic potentials. Using this approach, the stable existence of graphene, silicene and germanene can be explained.

Research Directed at Developing a Classical Theory to Describe Isotope Separation of Polyatomic Molecules Illuminated by Intense Infrared Radiation. Final Report for period May 7, 1979 to September 30, 1979; Extension December 31, 1997

DOE R&D Accomplishments Database

Lamb, W. E. Jr.

1981-12-01

This final report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. This process is investigated by treating the molecule, sulfur hexafluoride, as a system of seven classical particles that obey the Newtonian equations of motion. A minicomputer is used to integrate these differential equations. The particles are acted on by interatomic forces, and by the time-dependent electric field of the laser. We have a very satisfactory expression for the interaction of the laser and the molecule which is compatible with infrared absorption and spectroscopic data. The interatomic potential is capable of improvement, and progress on this problem is still being made. We have made several computer runs of the dynamical behavior of the molecule using a reasonably good model for the interatomic force law. For the laser parameters chosen, we find that typically the molecule passes quickly through the resonance region into the quasi-continuum and even well into the real continuum before dissociation actually occurs. When viewed on a display terminal, the motions are exceedingly complex. As an aid to the visualization of the process, we have made a number of 16 mm movies depicting a three-dimensional representation of the motion of the seven particles. These show even more clearly the enormous complexity of the motions, and make clear the desirability of finding ways of characterizing the motion in simple ways without giving all of the numerical detail. One of the ways to do this is to introduce statistical parameters such as a temperature associated with the distribution of kinetic energies of the single particle. We have made such an analysis of our data runs, and have found favorable indications that such methods will prove useful in keeping track of the dynamical histories.

Surface Electrochemistry of Metals

DTIC Science & Technology

1993-04-30

maxima along the 12 directions of open channels .vhich are also the interatomic directions). Elastic scattering angular distributions always contain... scatterer geometric relationships for such samples. Distributions from ordered atomic bilayers reveal that the Auger signal from the underlayer is attenuated...are developing a theoretical model and computational code which include both elastic scattering and inhomogeneous inelastic scattering . We seek

Topological properties of the electron density of solids and molecules. Recent developments in Oviedo.

PubMed

Luaña, Víctor; Costales, Aurora; Mori-Sánchez, Paula; Blanco, Miguel A; Martín Pendás, A

2004-09-01

Some of the latest advances in the analysis of electron density are reviewed, including: (a) topological indices that provide a useful characterization of the global properties of the density; (b) specific results on some prototypical metal and low heteropolarity systems; and (c) calculation of the local curvature of the interatomic surface.

Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well. The robustness of the algorithm with respect to the only free parameter it involves is ascertained. The method is then applied to perform tensile tests on gold nanopillars on strain rates as low as 100/s, bringing out the perils of high strain-rate molecular dynamics calculations. We also calculate temperature and stress dependence of activation free energy for surface nucleation of dislocations in pristine gold nanopillars under realistic loads. While maintaining fully atomistic resolution, we reach the fraction-of-a-second time scale regime. It is found that the activation free energy depends significantly and nonlinearly on the driving force (stress or strain) and temperature, leading to very high activation entropies for surface dislocation nucleation.

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble

NASA Astrophysics Data System (ADS)

Müller, Christian L.; Sbalzarini, Ivo F.; van Gunsteren, Wilfred F.; Žagrović, Bojan; Hünenberger, Philippe H.

2009-06-01

The concept of high-resolution shapes (also referred to as folds or states, depending on the context) of a polymer chain plays a central role in polymer science, structural biology, bioinformatics, and biopolymer dynamics. However, although the idea of shape is intuitively very useful, there is no unambiguous mathematical definition for this concept. In the present work, the distributions of high-resolution shapes within the ideal random-walk ensembles with N =3,…,6 beads (or up to N =10 for some properties) are investigated using a systematic (grid-based) approach based on a simple working definition of shapes relying on the root-mean-square atomic positional deviation as a metric (i.e., to define the distance between pairs of structures) and a single cutoff criterion for the shape assignment. Although the random-walk ensemble appears to represent the paramount of homogeneity and randomness, this analysis reveals that the distribution of shapes within this ensemble, i.e., in the total absence of interatomic interactions characteristic of a specific polymer (beyond the generic connectivity constraint), is significantly inhomogeneous. In particular, a specific (densest) shape occurs with a local probability that is 1.28, 1.79, 2.94, and 10.05 times (N =3,…,6) higher than the corresponding average over all possible shapes (these results can tentatively be extrapolated to a factor as large as about 1028 for N =100). The qualitative results of this analysis lead to a few rather counterintuitive suggestions, namely, that, e.g., (i) a fold classification analysis applied to the random-walk ensemble would lead to the identification of random-walk "folds;" (ii) a clustering analysis applied to the random-walk ensemble would also lead to the identification random-walk "states" and associated relative free energies; and (iii) a random-walk ensemble of polymer chains could lead to well-defined diffraction patterns in hypothetical fiber or crystal diffraction experiments. The inhomogeneous nature of the shape probability distribution identified here for random walks may represent a significant underlying baseline effect in the analysis of real polymer chain ensembles (i.e., in the presence of specific interatomic interactions). As a consequence, a part of what is called a polymer shape may actually reside just "in the eye of the beholder" rather than in the nature of the interactions between the constituting atoms, and the corresponding observation-related bias should be taken into account when drawing conclusions from shape analyses as applied to real structural ensembles.

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

PubMed

Müller, Christian L; Sbalzarini, Ivo F; van Gunsteren, Wilfred F; Zagrović, Bojan; Hünenberger, Philippe H

2009-06-07

The concept of high-resolution shapes (also referred to as folds or states, depending on the context) of a polymer chain plays a central role in polymer science, structural biology, bioinformatics, and biopolymer dynamics. However, although the idea of shape is intuitively very useful, there is no unambiguous mathematical definition for this concept. In the present work, the distributions of high-resolution shapes within the ideal random-walk ensembles with N=3,...,6 beads (or up to N=10 for some properties) are investigated using a systematic (grid-based) approach based on a simple working definition of shapes relying on the root-mean-square atomic positional deviation as a metric (i.e., to define the distance between pairs of structures) and a single cutoff criterion for the shape assignment. Although the random-walk ensemble appears to represent the paramount of homogeneity and randomness, this analysis reveals that the distribution of shapes within this ensemble, i.e., in the total absence of interatomic interactions characteristic of a specific polymer (beyond the generic connectivity constraint), is significantly inhomogeneous. In particular, a specific (densest) shape occurs with a local probability that is 1.28, 1.79, 2.94, and 10.05 times (N=3,...,6) higher than the corresponding average over all possible shapes (these results can tentatively be extrapolated to a factor as large as about 10(28) for N=100). The qualitative results of this analysis lead to a few rather counterintuitive suggestions, namely, that, e.g., (i) a fold classification analysis applied to the random-walk ensemble would lead to the identification of random-walk "folds;" (ii) a clustering analysis applied to the random-walk ensemble would also lead to the identification random-walk "states" and associated relative free energies; and (iii) a random-walk ensemble of polymer chains could lead to well-defined diffraction patterns in hypothetical fiber or crystal diffraction experiments. The inhomogeneous nature of the shape probability distribution identified here for random walks may represent a significant underlying baseline effect in the analysis of real polymer chain ensembles (i.e., in the presence of specific interatomic interactions). As a consequence, a part of what is called a polymer shape may actually reside just "in the eye of the beholder" rather than in the nature of the interactions between the constituting atoms, and the corresponding observation-related bias should be taken into account when drawing conclusions from shape analyses as applied to real structural ensembles.

Controllable deposition of platinum layers on oxide surfaces for the synthesis of fuel cell catalysts

DOE PAGES

Vukmirovic, Miomir B.; Kuttiyiel, Kurian A.; Meng, Hui; ...

2016-09-13

Reducing the amount of Pt, the most costly component of both anode and cathode fuel cell catalysts, has attracted considerable attention from the research community. An approach is reported herein to deposit sub-monolayer to multilayer amounts of Pt and other noble metals on metal oxides and oxidized carbon materials. The process is exemplified by Pt deposition on RuO 2(110). The Pt deposit consists of Pt atoms arranged in a c(2×2) array, that is, a 0.25 monolayer (ML). The deposit has lower catalytic activity for the oxygen reduction reaction (ORR) and similar activity for the hydrogen oxidation reaction compared to Pt(111).more » These activities are explained by a large calculated upshift of the d-band center of Pt atoms and larger Pt–Pt interatomic distances than those of Pt(111). A catalyst with Pt coverage larger than 0.25 ML on oxide surfaces and oxidized carbon materials is shown to be active for the ORR as well as for other electrocatalytic reactions. A PtRhSnO 2/C catalyst shows high activity for ethanol oxidation as a result of its ability to effectively cleave the C–C bond in ethanol. Furthermore, Pt deposited on reduced graphene oxide shows high Pt mass ORR activity and good stability.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiedemeier, Heribert, E-mail: wiedeh@rpi.edu

The observed linear (Na-, K-halides) and near-linear (Mg-, Sr-, Zn-, Cd-, and Hg-chalcogenides) dependences of Schottky constants on reciprocal interatomic distances yield the relation logK{sub S}=((s{sub s}1/T)+i{sub s})1/d{sub (A−B)}+(s{sub i}1/T)+i{sub i}, where K{sub S} is the product of metal and non-metal thermal equilibrium vacancy concentrations, and s{sub s}, i{sub s}, s{sub i} and i{sub i} are the group specific slope and intercept values obtained from an extended analysis of the above log K{sub S} versus 1/d{sub (A−B)} data. The previously reported linear dependences of log K{sub S} on the Born–Haber lattice energies [1] are the basis for combining the earliermore » results [1] with the Born–Mayer lattice energy equation to yield a new thermodynamic relationship, namely logK{sub S}=−(2.303nRT){sup −1}(c{sub (B−M)}/d{sub (A−B)}−I{sub e}), where c{sub (B−M)} is the product of the constants of the Born–Mayer equation and I{sub e} is the metal ionization energy of the above compounds. These results establish a correlation between point defect concentrations and basic thermodynamic, coulombic, and structural solid state properties for selected I–VII and II–VI semiconductor materials. - Graphical abstract: Display Omitted.« less

Long- and Short-Range Structure of Ferrimagnetic Iron-Chromium Maghemites.

PubMed

García-Guaderrama, Marco; Montero-Cabrera, María E; Morán, Emilio; Alario-Franco, Miguel A; Fuentes-Cobas, Luis E; Macías-Ríos, Edgar; Esparza-Ponce, Hilda E; Fuentes-Montero, María E

2015-12-07

Maghemite-like materials containing Fe(3+) and Cr(3+) in comparable amounts have been prepared by solution-combustion synthesis. The conditions of synthesis and the magnetic properties are described. These materials are ferrimagnetic and are much more stable than pure iron maghemite since their maghemite-hematite transformation takes place at about ∼ 700 °C instead of ∼ 300 °C, as usually reported. These materials were studied by synchrotron radiation X-ray diffraction (XRD) and by X-ray absorption fine structure (XAFS) of the K-absorption edge of two elements. High-resolution XRD patterns were processed by means of the Rietveld method. Thus, maghemites were studied by XAFS in both Fe and Cr K-edges to clarify the short-range structure of the investigated systems. Pre-edge decomposition and theoretical modeling of X-ray absorption near edge structure transitions were performed. The extended X-ray absorption fine structure (EXAFS) spectra were fitted considering the facts that the central atom of Fe is able to occupy octahedral and tetrahedral sites, each with a weight adjustment, while Cr occupies only octahedral sites. Interatomic distances were determined for x = 1, by fitting simultaneously both Fe and Cr K-edges average EXAFS spectra. The results showed that the cation vacancies tend to follow a regular pattern within the structure of the iron-chromium maghemite (FeCrO3).

Solid state solubility of copper oxides in hydroxyapatite

NASA Astrophysics Data System (ADS)

Zykin, Mikhail A.; Vasiliev, Alexander V.; Trusov, Lev A.; Dinnebier, Robert E.; Jansen, Martin; Kazin, Pavel E.

2018-06-01

Samples containing copper oxide doped hydroxyapatite with the composition Ca10(PO4)6(CuxOH1-x-δ)2, x = 0.054 - 0.582, in the mixture with CuO/Cu2O were prepared by a solid-state high-temperature treatment at varying annealing temperatures and at different partial water vapor and oxygen pressures. The crystal structures of the apatite compounds were refined using powder X-ray diffraction patterns and the content of copper ions x in the apatite was determined. Copper ions enter exclusively into the apatite trigonal channels formally substituting protons of OH-groups and the hexagonal cell parameters grow approximately linearly with x, the channel volume mostly expanding while the remaining volume of the crystal lattice changing only slightly. The equilibrium copper content in the apatite increases drastically, by almost a factor of 10 with the annealing temperature rising from 800° to 1200°C. The reduction of the water partial pressure leads to a further increase of x, while the dependence of x on the oxygen partial pressure exhibits a maximum. The observed relations are consistent with the proposed chemical reactions implying the copper introduction is followed by the release of a considerable quantity of gaseous products - water and oxygen. The analysis of interatomic distances suggests that the maximum content of copper ions in the channel cannot exceed 2/3.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Efthimiopoulos, I.; Tsurkan, V.; Loidl, A.

We have conducted high-pressure measurements on the CuCr2O4 and CuCr2Se4 spinels to unravel the structural systematics of these materials under compression. Our studies have revealed diverse structural behavior in these two compounds. In particular, CuCr2O4 retains its ambient-pressure I41/amd structure up to 50 GPa. Close inspection of the lattice and interatomic parameters reveals a compressibility change near 23 GPa, which is accompanied by an expansion of the apical Cr–O bond distances. We speculate that an outer Cr3+ 3d orbital reorientation might be at play in this system, manifesting as the change in compressibility at that pressure point. On the othermore » hand, CuCr2Se4 undergoes a structural transformation from the starting Fd3¯m phase toward a monoclinic structure initiated at ~8 GPa and completed at ~20 GPa. This high-pressure behavior resembles that of ZnCr2Se4, and it appears that, unlike similar chalcogenide Cr spinels, steric effects take a leading role in this pressure-induced Fd3¯m → monoclinic transition. Close comparison of our results with the reported literature yields significant insights behind the pressure-induced structural systematics of this important family of materials, thus both allowing for the careful manipulation of the structural/physical properties of these systems by strain and promoting our understanding of similar pressure-induced effects in relevant systems.« less

Relationship between structural and dynamic properties of Al-rich Al-Cu melts: Beyond the Stokes-Einstein relation

NASA Astrophysics Data System (ADS)

Jakse, N.; Pasturel, A.

2016-12-01

We perform ab initio molecular dynamics simulations to study structural and transport properties in liquid A l1 -xC ux alloys, with copper composition x ≤0.4 , in relation to the applicability of the Stokes-Einstein (SE) equation in these melts. To begin, we find that self-diffusion coefficients and viscosity are composition dependent, while their temperature dependence follows an Arrhenius-type behavior, except for x =0.4 at low temperature. Then, we find that the applicability of the SE equation is also composition dependent, and its breakdown in the liquid regime above the liquidus temperature can be related to different local ordering around each species. In this case, we emphasize the difficulty of extracting effective atomic radii from interatomic distances found in liquid phases, but we see a clear correlation between transport properties and local ordering described through the structural entropy approximated by the two-body contribution. We use these findings to reformulate the SE equation within the framework of Rosenfeld's scaling law in terms of partial structural entropies, and we demonstrate that the breakdown of the SE relation can be related to their temperature dependence. Finally, we also use this framework to derive a simple relation between the ratio of the self-diffusivities of the components and the ratio of their partial structural entropies.

Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism

PubMed Central

Xu, Rui-Gang; Jenkins, Huw T.; Chechik, Maria; Blagova, Elena V.; Lopatina, Anna; Klimuk, Evgeny; Minakhin, Leonid; Severinov, Konstantin

2017-01-01

Abstract Bacteriophages and large dsDNA viruses encode sophisticated machinery to translocate their DNA into a preformed empty capsid. An essential part of this machine, the large terminase protein, processes viral DNA into constituent units utilizing its nuclease activity. Crystal structures of the large terminase nuclease from the thermophilic bacteriophage G20c show that it is most similar to the RuvC family of the RNase H-like endonucleases. Like RuvC proteins, the nuclease requires either Mn2+, Mg2+ or Co2+ ions for activity, but is inactive with Zn2+ and Ca2+. High resolution crystal structures of complexes with different metals reveal that in the absence of DNA, only one catalytic metal ion is accommodated in the active site. Binding of the second metal ion may be facilitated by conformational variability, which enables the two catalytic aspartic acids to be brought closer to each other. Structural comparison indicates that in common with the RuvC family, the location of the two catalytic metals differs from other members of the RNase H family. In contrast to a recently proposed mechanism, the available data do not support binding of the two metals at an ultra-short interatomic distance. Thus we postulate that viral terminases cleave DNA by the canonical RuvC-like mechanism. PMID:28100693

Analysis of Self-Associating Proteins by Singular Value Decomposition of Solution Scattering Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williamson, Tim E.; Craig, Bruce A.; Kondrashkina, Elena

2008-07-08

We describe a method by which a single experiment can reveal both association model (pathway and constants) and low-resolution structures of a self-associating system. Small-angle scattering data are collected from solutions at a range of concentrations. These scattering data curves are mass-weighted linear combinations of the scattering from each oligomer. Singular value decomposition of the data yields a set of basis vectors from which the scattering curve for each oligomer is reconstructed using coefficients that depend on the association model. A search identifies the association pathway and constants that provide the best agreement between reconstructed and observed data. Using simulatedmore » data with realistic noise, our method finds the correct pathway and association constants. Depending on the simulation parameters, reconstructed curves for each oligomer differ from the ideal by 0.050.99% in median absolute relative deviation. The reconstructed scattering curves are fundamental to further analysis, including interatomic distance distribution calculation and low-resolution ab initio shape reconstruction of each oligomer in solution. This method can be applied to x-ray or neutron scattering data from small angles to moderate (or higher) resolution. Data can be taken under physiological conditions, or particular conditions (e.g., temperature) can be varied to extract fundamental association parameters ({Delta}H{sub ass}, S{sub ass}).« less

Enhancing Magnetic Functionality with Scandium: Breaking Stereotypes in the Design of Rare Earth Materials

DOE PAGES

Mudryk, Yaroslav; Paudyal, Durga; Liu, Jing; ...

2017-04-11

Replacement of strongly magnetic gadolinium with weakly magnetic scandium unexpectedly enhances ferromagnetic interactions in (Gd 1–xSc x) 5Ge 4. Based upon this counterintuitive experimental finding we demonstrate the unique role 3d 1 electrons of scandium atoms play in mediating magnetic interactions between the gadolinium atoms from the neighboring layers in the Sm 5Ge 4-type crystal lattice. Scandium substitutions at and below 20% rapidly increase the Curie temperature, TC, of the Gd 5Ge 4 parent, eliminate both the kinetic arrest and hysteresis, and drastically improve reversibility of the first-order magnetostructural transformation at T C. In agreement with first-principles predictions, higher thanmore » 20% Sc leads to the formation of a closely related Pu 5Rh 4-type structure where the first-order magnetostructural transformation is replaced by a conventional second-order ferromagnetic ordering that remains accompanied by a continuous rearrangement of the crystal lattice. In conclusion, comparison of two materials with similar structures and compositions shows that significantly stronger magnetocaloric effect occurs in the first-order material, which also shows very small hysteresis. Furthermore, we demonstrate that a behavior of a specific interatomic distance can predict anomalous physical properties in a series of alloys where compositional dependence of lattice parameters suggests a rather trivial solid solubility and uninteresting magnetism.« less

Effect of humic acid on nickel(II) sorption to Ca-montmorillonite by batch and EXAFS techniques study.

PubMed

Hu, Jun; Tan, Xiaoli; Ren, Xuemei; Wang, Xiangke

2012-09-21

The influence of humic acid (HA) on Ni(II) sorption to Ca-montmorillonite was examined by using a combination of batch sorption experiments and extended X-ray absorption fine structure (EXAFS) spectroscopy technique. The sorption of Ni(II) on HA-montmorillonite hybrids is strongly dependent on pH and temperature. At low pH, the sorption of Ni(II) is mainly dominated by Ni-HA-montmorillonite and outer-sphere surface complexation. The EXAFS results indicate that the first coordination shell of Ni(II) consists of ∼6 O atoms at the interatomic distances of ∼2.04 Å in an octahedral structure. At high pH, binary Ni-montmorillonite surface complexation is the dominant sorption mechanism. EXAFS analysis indicates the formation of mononuclear complexes located at the edges of Ca-montmorillonite platelets at pH 7.5, while a Ni-Al layered double hydroxide (LDH) phase at the Ca-montmorillonite surface formed with pH 8.5. At pH 10.0, the dissolved HA-Ni(II) complexation inhibits the precipitation of Ni hydroxide, and Ni-Al LDH phase forms. The rise of temperature increases the sorption capacity of Ni(II), and promotes Ni-Al LDH phase formation and the growth of crystallites. The results are important to evaluate the physicochemical behavior of Ni(II) in the natural environment.

ABC transporter Cdr1p harbors charged residues in the intracellular loop and nucleotide-binding domain critical for protein trafficking and drug resistance.

PubMed

Shah, Abdul Haseeb; Banerjee, Atanu; Rawal, Manpreet Kaur; Saxena, Ajay Kumar; Mondal, Alok Kumar; Prasad, Rajendra

2015-08-01

The ABC transporter Cdr1 protein of Candida albicans, which plays a major role in antifungal resistance, has two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The 12 transmembrane helices of TMDs that are interconnected by extracellular and intracellular loops (ICLs) mainly harbor substrate recognition sites where drugs bind while cytoplasmic NBDs hydrolyze ATP which powers drug efflux. The coupling of ATP hydrolysis to drug transport requires proper communication between NBDs and TMDs typically accomplished by ICLs. This study examines the role of cytoplasmic ICLs of Cdr1p by rationally predicting the critical residues on the basis of their interatomic distances. Among nine pairs that fall within a proximity of <4 Å, an ion pair between K577 of ICL1 and E315 of NBD1 was found to be critical. The substitution, swapping and changing of the length or charge of K577 or E315 by directed mutagenesis led to a misfolded, non-rescuable protein entrapped in intracellular structures. Furthermore, the equipositional ionic pair-forming residues from ICL3 and NBD2 (R1260 and E1014) did not impact protein trafficking. These results point to a new role for ICL/NBD interacting residues in PDR ABC transporters in protein folding and trafficking. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Basis set limit and systematic errors in local-orbital based all-electron DFT

NASA Astrophysics Data System (ADS)

Blum, Volker; Behler, Jörg; Gehrke, Ralf; Reuter, Karsten; Scheffler, Matthias

2006-03-01

With the advent of efficient integration schemes,^1,2 numeric atom-centered orbitals (NAO's) are an attractive basis choice in practical density functional theory (DFT) calculations of nanostructured systems (surfaces, clusters, molecules). Though all-electron, the efficiency of practical implementations promises to be on par with the best plane-wave pseudopotential codes, while having a noticeably higher accuracy if required: Minimal-sized effective tight-binding like calculations and chemically accurate all-electron calculations are both possible within the same framework; non-periodic and periodic systems can be treated on equal footing; and the localized nature of the basis allows in principle for O(N)-like scaling. However, converging an observable with respect to the basis set is less straightforward than with competing systematic basis choices (e.g., plane waves). We here investigate the basis set limit of optimized NAO basis sets in all-electron calculations, using as examples small molecules and clusters (N2, Cu2, Cu4, Cu10). meV-level total energy convergence is possible using <=50 basis functions per atom in all cases. We also find a clear correlation between the errors which arise from underconverged basis sets, and the system geometry (interatomic distance). ^1 B. Delley, J. Chem. Phys. 92, 508 (1990), ^2 J.M. Soler et al., J. Phys.: Condens. Matter 14, 2745 (2002).

Local Fine Structural Insight into Mechanism of Electrochemical Passivation of Titanium.

PubMed

Wang, Lu; Yu, Hongying; Wang, Ke; Xu, Haisong; Wang, Shaoyang; Sun, Dongbai

2016-07-20

Electrochemically formed passive film on titanium in 1.0 M H2SO4 solution and its thickness, composition, chemical state, and local fine structure are examined by Auger electron spectroscopy (AES), X-ray photoelectron spectroscopy (XPS), and X-ray absorption fine structure. AES analysis reveals that the thickness and composition of oxide film are proportional to the reciprocal of current density in potentiodynamic polarization. XPS depth profiles of the chemical states of titanium exhibit the coexistence of various valences cations in the surface. Quantitative X-ray absorption near edge structure analysis of the local electronic structure of the topmost surface (∼5.0 nm) shows that the ratio of [TiO2]/[Ti2O3] is consistent with that of passivation/dissolution of electrochemical activity. Theoretical calculation and analysis of extended X-ray absorption fine structure spectra at Ti K-edge indicate that both the structures of passivation and dissolution are distorted caused by the appearance of two different sites of Ti-O and Ti-Ti. And the bound water in the topmost surface plays a vital role in structural disorder confirmed by XPS. Overall, the increase of average Ti-O coordination causes the electrochemical passivation, and the dissolution is due to the decrease of average Ti-Ti coordination. The structural variations of passivation in coordination number and interatomic distance are in good agreement with the prediction of point defect model.

Surface Impact Simulations of Helium Nanodroplets

DTIC Science & Technology

2015-06-30

mechanical delocalization of the individual helium atoms in the droplet and the quan- tum statistical effects that accompany the interchange of identical...incorporates the effects of atomic delocaliza- tion by treating individual atoms as smeared-out probability distributions that move along classical...probability density distributions to give effec- tive interatomic potential energy curves that have zero-point averaging effects built into them [25

Interatomic potentials for HeAr, HeKr, and HeXe from multiproperty fits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danielson, L.J.; Keil, M.

1988-01-15

Crossed molecular beam measurements of differential cross sections (DCS) are reported for elastic scattering of He by Ar, Kr, and Xe at high resolution. Interatomic potentials are determined by simultaneously fitting the DCS's, as well as mixture viscosity and interaction second virial data. Bias due to systematic and potential model errors are examined and are used to estimate the accuracy of the potential energy curves obtained. Attractive well depths are 2.59, 2.67, and 2.64 meV +- 3% for HeAr, HeKr, and HeXe, respectively, agreeing with the best available HeAr potential and a previously proposed HeKr potential, but significantly deeper thanmore » previously reported potentials for HeXe. The HeXe attractive well is also considerably broader than previously reported. Attractive minimum positions are 3.48, 3.70, and 4.00 A ( +- 0.03 A) for HeAr, HeKr, and HeXe, respectively. Including the accurate diffusion data of Dunlop and co-workers (Physica A 95, 561 (1979)) and the absolute integral cross sections of Pirani and Vecchiocattivi (J. Chem. Phys. 66, 372 (1977) and revisions thereto) verify the error bounds for all three potentials.« less

Interatomic interaction effects on second-order momentum correlations and Hong-Ou-Mandel interference of double-well-trapped ultracold fermionic atoms

NASA Astrophysics Data System (ADS)

Brandt, Benedikt B.; Yannouleas, Constantine; Landman, Uzi

2018-05-01

Identification and understanding of the evolution of interference patterns in two-particle momentum correlations as a function of the strength of interatomic interactions are important in explorations of the nature of quantum states of trapped particles. Together with the analysis of two-particle spatial correlations, they offer the prospect of uncovering fundamental symmetries and structure of correlated many-body states, as well as opening vistas into potential control and utilization of correlated quantum states as quantum-information resources. With the use of the second-order density matrix constructed via exact diagonalization of the microscopic Hamiltonian, and an analytic Hubbard-type model, we explore here the systematic evolution of characteristic interference patterns in the two-body momentum and spatial correlation maps of two entangled ultracold fermionic atoms in a double well, for the entire attractive- and repulsive-interaction range. We uncover quantum-statistics-governed bunching and antibunching, as well as interaction-dependent interference patterns, in the ground and excited states, and interpret our results in light of the Hong-Ou-Mandel interference physics, widely exploited in photon indistinguishability testing and quantum-information science.

Size-dependent plastic deformation of twinned nanopillars in body-centered cubic tungsten

NASA Astrophysics Data System (ADS)

Xu, Shuozhi; Startt, Jacob K.; Payne, Thomas G.; Deo, Chaitanya S.; McDowell, David L.

2017-05-01

Compared with face-centered cubic metals, twinned nanopillars in body-centered cubic (BCC) systems are much less explored partly due to the more complicated plastic deformation behavior and a lack of reliable interatomic potentials for the latter. In this paper, the fault energies predicted by two semi-empirical interatomic potentials in BCC tungsten (W) are first benchmarked against density functional theory calculations. Then, the more accurate potential is employed in large scale molecular dynamics simulations of tensile and compressive loading of twinned nanopillars in BCC W with different cross sectional shapes and sizes. A single crystal, a twinned crystal, and single crystalline nanopillars are also studied as references. Analyses of the stress-strain response and defect nucleation reveal a strong tension-compression asymmetry and a weak pillar size dependence in the yield strength. Under both tensile and compressive loading, plastic deformation in the twinned nanopillars is dominated by dislocation slip on {110} planes that are nucleated from the intersections between the twin boundary and the pillar surface. It is also found that the cross sectional shape of nanopillars affects the strength and the initial site of defect nucleation but not the overall stress-strain response and plastic deformation behavior.

Thermal conductivity of silicon using reverse non-equilibrium molecular dynamics

NASA Astrophysics Data System (ADS)

El-Genk, Mohamed S.; Talaat, Khaled; Cowen, Benjamin J.

2018-05-01

Simulations are performed using the reverse non-equilibrium molecular dynamics (rNEMD) method and the Stillinger-Weber (SW) potential to determine the input parameters for achieving ±1% convergence of the calculated thermal conductivity of silicon. These parameters are then used to investigate the effects of the interatomic potentials of SW, Tersoff II, Environment Dependent Interatomic Potential (EDIP), Second Nearest Neighbor, Modified Embedded-Atom Method (MEAM), and Highly Optimized Empirical Potential MEAM on determining the bulk thermal conductivity as a function of temperature (400-1000 K). At temperatures > 400 K, data collection and swap periods of 15 ns and 150 fs, system size ≥6 × 6 UC2 and system lengths ≥192 UC are adequate for ±1% convergence with all potentials, regardless of the time step size (0.1-0.5 fs). This is also true at 400 K, except for the SW potential, which requires a data collection period ≥30 ns. The calculated bulk thermal conductivities using the rNEMD method and the EDIP potential are close to, but lower than experimental values. The 10% difference at 400 K increases gradually to 20% at 1000 K.

Atomistic properties of γ uranium.

PubMed

Beeler, Benjamin; Deo, Chaitanya; Baskes, Michael; Okuniewski, Maria

2012-02-22

The properties of the body-centered cubic γ phase of uranium (U) are calculated using atomistic simulations. First, a modified embedded-atom method interatomic potential is developed for the high temperature body-centered cubic (γ) phase of U. This phase is stable only at high temperatures and is thus relatively inaccessible to first principles calculations and room temperature experiments. Using this potential, equilibrium volume and elastic constants are calculated at 0 K and found to be in close agreement with previous first principles calculations. Further, the melting point, heat capacity, enthalpy of fusion, thermal expansion and volume change upon melting are calculated and found to be in reasonable agreement with experiment. The low temperature mechanical instability of γ U is correctly predicted and investigated as a function of pressure. The mechanical instability is suppressed at pressures greater than 17.2 GPa. The vacancy formation energy is analyzed as a function of pressure and shows a linear trend, allowing for the calculation of the extrapolated zero pressure vacancy formation energy. Finally, the self-defect formation energy is analyzed as a function of temperature. This is the first atomistic calculation of γ U properties above 0 K with interatomic potentials.

Atomistic properties of γ uranium

NASA Astrophysics Data System (ADS)

Beeler, Benjamin; Deo, Chaitanya; Baskes, Michael; Okuniewski, Maria

2012-02-01

The properties of the body-centered cubic γ phase of uranium (U) are calculated using atomistic simulations. First, a modified embedded-atom method interatomic potential is developed for the high temperature body-centered cubic (γ) phase of U. This phase is stable only at high temperatures and is thus relatively inaccessible to first principles calculations and room temperature experiments. Using this potential, equilibrium volume and elastic constants are calculated at 0 K and found to be in close agreement with previous first principles calculations. Further, the melting point, heat capacity, enthalpy of fusion, thermal expansion and volume change upon melting are calculated and found to be in reasonable agreement with experiment. The low temperature mechanical instability of γ U is correctly predicted and investigated as a function of pressure. The mechanical instability is suppressed at pressures greater than 17.2 GPa. The vacancy formation energy is analyzed as a function of pressure and shows a linear trend, allowing for the calculation of the extrapolated zero pressure vacancy formation energy. Finally, the self-defect formation energy is analyzed as a function of temperature. This is the first atomistic calculation of γ U properties above 0 K with interatomic potentials.

Development of a machine learning potential for graphene

NASA Astrophysics Data System (ADS)

Rowe, Patrick; Csányi, Gábor; Alfè, Dario; Michaelides, Angelos

2018-02-01

We present an accurate interatomic potential for graphene, constructed using the Gaussian approximation potential (GAP) machine learning methodology. This GAP model obtains a faithful representation of a density functional theory (DFT) potential energy surface, facilitating highly accurate (approaching the accuracy of ab initio methods) molecular dynamics simulations. This is achieved at a computational cost which is orders of magnitude lower than that of comparable calculations which directly invoke electronic structure methods. We evaluate the accuracy of our machine learning model alongside that of a number of popular empirical and bond-order potentials, using both experimental and ab initio data as references. We find that whilst significant discrepancies exist between the empirical interatomic potentials and the reference data—and amongst the empirical potentials themselves—the machine learning model introduced here provides exemplary performance in all of the tested areas. The calculated properties include: graphene phonon dispersion curves at 0 K (which we predict with sub-meV accuracy), phonon spectra at finite temperature, in-plane thermal expansion up to 2500 K as compared to NPT ab initio molecular dynamics simulations and a comparison of the thermally induced dispersion of graphene Raman bands to experimental observations. We have made our potential freely available online at [http://www.libatoms.org].

Evolution of sp{sup 2} networks with substrate temperature in amorphous carbon films: Experiment and theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gago, R.; Centro de Micro-Analisis de Materiales, Universidad Autonoma de Madrid, Campus de Cantoblanco, 28049 Madrid; Vinnichenko, M.

2005-07-01

The evolution of sp{sup 2} hybrids in amorphous carbon (a-C) films deposited at different substrate temperatures was studied experimentally and theoretically. The bonding structure of a-C films prepared by filtered cathodic vacuum arc was assessed by the combination of visible Raman spectroscopy, x-ray absorption, and spectroscopic ellipsometry, while a-C structures were generated by molecular-dynamics deposition simulations with the Brenner interatomic potential to determine theoretical sp{sup 2} site distributions. The experimental results show a transition from tetrahedral a-C (ta-C) to sp{sup 2}-rich structures at {approx}500 K. The sp{sup 2} hybrids are mainly arranged in chains or pairs whereas graphitic structures aremore » only promoted for sp{sup 2} fractions above 80%. The theoretical analysis confirms the preferred pairing of isolated sp{sup 2} sites in ta-C, the coalescence of sp{sup 2} clusters for medium sp{sup 2} fractions, and the pronounced formation of rings for sp{sup 2} fractions >80%. However, the dominance of sixfold rings is not reproduced theoretically, probably related to the functional form of the interatomic potential used.« less

Molecular dynamics simulations of intergranular fracture in UO2 with nine empirical interatomic potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yongfeng Zhang; Paul C Millett; Michael R Tonks

The intergranular fracture behavior of UO2 was studied using molecular dynamics simulations with a bicrystal model. The anisotropic fracture behavior due to the different grain boundary characters was investigated with the View the MathML source symmetrical tilt S5 and the View the MathML source symmetrical tilt S3 ({1 1 1} twin) grain boundaries. Nine interatomic potentials, seven rigid-ion plus two core–shell ones, were utilized to elucidate possible potential dependence. Initiating from a notch, crack propagation along grain boundaries was observed for most potentials. The S3 boundary was found to be more prone to fracture than the S5 one, indicated bymore » a lower energy release rate associated with the former. However, some potential dependence was identified on the existence of transient plastic deformation at crack tips, and the results were discussed regarding the relevant material properties including the excess energies of metastable phases and the critical energy release rate for intergranular fracture. In general, local plasticity at crack tips was observed in fracture simulations with potentials that predict low excess energies for metastable phases and high critical energy release rates for intergranular fracture.« less

A modified Stillinger-Weber potential for TlBr and its polymorphic extension

DOE PAGES

Zhou, Xiaowang; Foster, Michael E.; Jones, Reese E.; ...

2015-04-30

TlBr is promising for g- and x- radiation detection, but suffers from rapid performance degradation under the operating external electric fields. To enable molecular dynamics (MD) studies of this degradation, we have developed a Stillinger-Weber type of TlBr interatomic potential. During this process, we have also addressed two problems of wider interests. First, the conventional Stillinger-Weber potential format is only applicable for tetrahedral structures (e.g., diamond-cubic, zinc-blende, or wurtzite). Here we have modified the analytical functions of the Stillinger-Weber potential so that it can now be used for other crystal structures. Second, past modifications of interatomic potentials cannot always bemore » applied by a broad community because any new analytical functions of the potential would require corresponding changes in the molecular dynamics codes. Here we have developed a polymorphic potential model that simultaneously incorporates Stillinger-Weber, Tersoff, embedded-atom method, and any variations (i.e., modified functions) of these potentials. As a result, we have implemented this polymorphic model in MD code LAMMPS, and demonstrated that our TlBr potential enables stable MD simulations under external electric fields.« less

Speciation and characterization of arsenic in Ketza River mine tailings using X-ray absorption spectroscopy.

PubMed

Paktunc, Dogan; Foster, Andrea; Laflamme, Gilles

2003-05-15

Ketza River mine tailings deposited underwater and those exposed near the tailings impoundment contain approximately 4 wt % As. Column-leaching tests indicated the potential for high As releases from the tailings. The tailings are composed dominantly of iron oxyhydroxides, quartz, calcite, dolomite, muscovite, ferric arsenates, and calcium-iron arsenates. Arsenopyrite and pyrite are trace constituents. Chemical compositions of iron oxyhydroxide and arsenate minerals are highly variable. The XANES spectra indicate that arsenic occurs as As(V) in tailings, but air-drying prior to analysis may have oxidized lower-valent As. The EXAFS spectra indicate As-Fe distances of 3.35-3.36 A for the exposed tailings and 3.33-3.35 A for the saturated tailings with coordination numbers of 0.96-1.11 and 0.46-0.64, respectively. The As-Ca interatomic distances ranging from 4.15 to 4.18 A and the coordination numbers of 4.12-4.58 confirm the presence of calcium-iron arsenates in the tailings. These results suggest that ferric arsenates and inner-sphere corner sharing or bidentate-binuclear attachment of arsenate tetrahedra onto iron hydroxide octahedra are the dominant form of As in the tailings. EXAFS spectra indicate that the exposed tailings are richer in arsenate minerals whereas the saturated tailings are dominated by the iron oxyhydroxides, which could help explain the greater release of As from the exposed tailings during leaching tests. It is postulated that the dissolution of ferric arsenates during flow-through experiments caused the high As releases from both types of tailings. Arsenic tied to iron oxyhydroxides as adsorbed species are considered stable; however, iron oxyhydroxides having low Fe/As molar ratios may not be as stable. Continued As releases from the tailings are likely due to dissolution of both ferric and calcium-iron arsenates and desorption of As from high-As bearing iron oxyhydroxides during aging.

Speciation and characterization of arsenic in Ketza River mine tailings using x-ray absorption spectroscopy

USGS Publications Warehouse

Paktunc, D.; Foster, A.; Laflamme, G.

2003-01-01

Ketza River mine tailings deposited underwater and those exposed near the tailings impoundment contain approximately 4 wt % As. Column-leaching tests indicated the potential for high As releases from the tailings. The tailings are composed dominantly of iron oxyhydroxides, quartz, calcite, dolomite, muscovite, ferric arsenates, and calcium-iron arsenates. Arsenopyrite and pyrite are trace constituents. Chemical compositions of iron oxyhydroxide and arsenate minerals are highly variable. The XANES spectra indicate that arsenic occurs as As(V) in tailings, but air-drying prior to analysis may have oxidized lower-valent As. The EXAFS spectra indicate As-Fe distances of 3.35-3.36 A?? for the exposed tailings and 3.33-3.35 A?? for the saturated tailings with coordination numbers of 0.96-1.11 and 0.46-0.64, respectively. The As-Ca interatomic distances ranging from 4.15 to 4.18 A?? and the coordination numbers of 4.12-4.58 confirm the presence of calcium-iron arsenates in the tailings. These results suggest that ferric arsenates and inner-sphere corner sharing or bidentatebinuclear attachment of arsenate tetrahedra onto iron hydroxide octahedra are the dominant form of As in the tailings. EXAFS spectra indicate that the exposed tailings are richer in arsenate minerals whereas the saturated tailings are dominated by the iron oxyhydroxides, which could help explain the greater release of As from the exposed tailings during leaching tests. It is postulated that the dissolution of ferric arsenates during flow-through experiments caused the high As releases from both types of tailings. Arsenic tied to iron oxyhydroxides as adsorbed species are considered stable; however, iron oxyhydroxides having low Fe/As molar ratios may not be as stable. Continued As releases from the tailings are likely due to dissolution of both ferric and calcium-iron arsenates and desorption of As from high-As bearing iron oxyhydroxides during aging.

Synthesis and structural characterization of ferrous trioctahedral smectites: Implications for clay mineral genesis and detectability on Mars

NASA Astrophysics Data System (ADS)

Chemtob, Steven M.; Nickerson, Ryan D.; Morris, Richard V.; Agresti, David G.; Catalano, Jeffrey G.

2015-06-01

Widespread detections of phyllosilicates in Noachian terrains on Mars imply a history of near-surface fluid-rock interaction. Ferrous trioctahedral smectites are thermodynamically predicted products of basalt weathering on early Mars, but to date only Fe3+-bearing dioctahedral smectites have been identified from orbital observations. In general, the physicochemical properties of ferrous smectites are poorly studied because they are susceptible to air oxidation. In this study, eight Fe2+-bearing smectites were synthesized from Fe2+-Mg-Al silicate gels at 200°C under anoxic conditions. Samples were characterized by inductively coupled plasma optical emission spectrometry, powder X-ray diffraction, Fe K-edge X-ray absorption spectroscopy (XAS), Mössbauer spectroscopy, and visible/near-infrared (VNIR) reflectance spectroscopy. The range of redox states was Fe3+/ΣFe = 0 to 0.06 ± 0.01 as determined by both XAS and, for short integration times, Mössbauer. The smectites have 060 distances (d(060)) between 1.53 and 1.56 Å, indicating a trioctahedral structure. d(060) and XAS-derived interatomic Fe-(Fe,Mg,Al) distance scaled with Fe content. Smectite VNIR spectra feature OH/H2O absorption bands at 1.4 and 1.9 µm, (Fe2+,Mg,Al)3-OH stretching bands near 1.4 µm, and Fe2+Fe2+Fe2+-OH, MgMgMg-OH, AlAl(Mg,Fe2+)-OH, and AlAl-OH combination bands at 2.36 µm, 2.32 µm 2.25 µm, and 2.20 µm, respectively. The spectra for ferrous saponites are distinct from those for dioctahedral ferric smectites, permitting their differentiation from orbital observations. X-ray diffraction patterns for synthetic high-Mg ferrosaponite and high-Mg ferrian saponite are both consistent with the Sheepbed saponite detected by the chemistry and mineralogy (CheMin) instrument at Gale Crater, Mars, suggesting that anoxic basalt alteration was a viable pathway for clay mineral formation on early Mars.

The relation between ferroelasticity and superconductivity

NASA Technical Reports Server (NTRS)

Molak, A.; Manka, R.

1991-01-01

The high-temperature superconductivity is explained widely by the layered crystal structure. The one- and two-dimensional subsystems and their interaction are investigated here. It is assumed that the high-T(sub c) superconductivity takes place in the two-dimensional subsystem and the increase of the phase transition temperature from 60 K up to 90 K is the consequence of turning on the influence of one-dimensional chains. The interaction between the two subsystems is transferred along the c axis by the phonons of breathing mode, which causes the hybridization of the electronic bonds between these subsystems. The experimental works indicate that the existence of both the chains Cu(1)-O and their interaction with the superconducting plane of Cu(2)-O modify the temperature of the transition to the superconducting state. It is seen from the neutron scattering data that the rates of the interatomic distance dependencies on temperature are changed around 240 K and 90 K. The 'zig-zag' order in Cu(1)-O chains has been postulated but, on the other hand, the vibrations with a large amplitude only were reported. The bi-stabilized situation of the oxygen ions can be caused by the change of distance between these ions and the Ba ions. It leads to the appearance of a two-well potential. Its parameters depend on temperature and the dynamics of the oxygen ions' movement. They can induce the antipolar order, which can be, however, more or less chaotic. The investigation of the ferroelastic properties of Y-Ba-Cu-O samples lead to the conclusion that they are related to jumps of ions inside the given chain and not to a diffusion between different sites in the ab plane. Researchers deduce, thus, that the fluctuating oxygen ions from these chains create dipoles in the ab plane. They can be described with the pseudo-spin formalism (- Pauli matrices). The system can be described with the Ising model. The pseudo-spins interact with phonons and influence the superconductivity in the second subsystem.

The relation between ferroelasticity and superconductivity

NASA Technical Reports Server (NTRS)

Molak, A.; Manka, R.

1990-01-01

The high-temperature superconductivity is explained widely by the layered crystal structure. The one- and two-dimensional subsystems and their interaction are investigated here. It is assumed that the high-T(sub c) superconductivity takes place in the two-dimensional subsystem and the increase of the phase transition temperature from 60 K up to 90 K is the consequence of turning on the influence of one-dimensional chains. The interaction between the two subsystems is transferred along the c axis by the phonons of breathing mode, which causes the hybridization of the electronic bonds between these subsystems. The experimental works indicate that the existence of both the chains Cu(1)-O and their interaction with the superconducting plane of Cu(2)-O modify the temperature of the transition to the superconducting state. It is seen from the neutron scattering data that the rates of the interatomic distance dependencies on temperature are changed around 140 K and 90 K. The 'zig-zag' order in Cu(1)-O chains has been postulated but, on the other hand, the vibrations with a large amplitude only were reported. The bi-stabilized situation of the oxygen ions can be caused by the change of distance between these ions and the Ba ions. It leads to the appearance of a two-well potential. Its parameters depend on temperature and the dynamics of the oxygen ions' movement. They can induce the antipolar order, which can be, however, more or less chaotic. The investigation of the ferroelastic properties of Y-Ba-Cu-O samples lead to the conclusion that they are related to jumps of ions inside the given chain and not to a diffusion between different sites in the ab plane. Researchers deduce thus that the fluctuating oxygen ions from these chains create dipoles in the ab plane. They can be described with the pseudo-spin formalism/ - Pauli matrices/. The system can be described with the Ising model. The pseudo-spins interact with phonons and influence the superconductivity in the second subsystem.

Quantum chemical calculations of interatomic potentials for computer simulation of solids

NASA Technical Reports Server (NTRS)

1977-01-01

A comprehensive mathematical model by which the collective behavior of a very large number of atoms within a metal or alloy can accurately be simulated was developed. Work was done in order to predict and modify the strength of materials to suit our technological needs. The method developed is useful in studying atomic interactions related to dislocation motion and crack extension.

Mathematical Research in Materials Science: Opportunities and Perspectives. Part 2

DTIC Science & Technology

1993-01-01

spheres and Lennard - Jones potentials , but have not been extended to a general framework that will allow input from more complicated interatomic...focuses on directions for potentially promising collaboration between materials scientists and mathematical scientists, and encourages both communities...interface between the mathematical sciences and other fields. The purpose of this report is not only to focus on directions for potentially promising

Orbital Exponent Optimization in Elementary VB Calculations of the Chemical Bond in the Ground State of Simple Molecular Systems

ERIC Educational Resources Information Center

Magnasco, Valerio

2008-01-01

Orbital exponent optimization in the elementary ab-initio VB calculation of the ground states of H[subscript 2][superscript +], H[subscript 2], He[subscript 2][superscript +], He[subscript 2] gives a fair description of the exchange-overlap component of the interatomic interaction that is important in the bond region. Correct bond lengths and…

An Investigation of the Interatomic Bonding Characteristics of a Ti - 51at.% Al Alloy by X-Ray Diffraction

DTIC Science & Technology

1991-06-01

GROUP SUBGROUP X-ray Diffraction, XRD, TiAI, titanium , aluminum, bonding characteristics, titanium aluminides , Debye-Waller temperature factor...XRD Powder Particles (575X) .............. 47 viii I. INTRODUCTION Titanium aluminides are recognized for their high specific strength, particularly at...bonding characteristics of binary titanium aluminides . Upon the introduction of a third element to the system, a rearrangement of the valence

Development of an interatomic potential for the simulation of defects, plasticity, and phase transformations in titanium

DOE PAGES

Mendelev, M. I.; Underwood, T. L.; Ackland, G. J.

2016-10-17

New interatomic potentials describing defects, plasticity, and high temperature phase transitions for Ti are presented. Fitting the martensitic hcp-bcc phase transformation temperature requires an efficient and accurate method to determine it. We apply a molecular dynamics method based on determination of the melting temperature of competing solid phases, and Gibbs-Helmholtz integration, and a lattice-switch Monte Carlo method: these agree on the hcp-bcc transformation temperatures to within 2 K. We were able to develop embedded atom potentials which give a good fit to either low or high temperature data, but not both. The first developed potential (Ti1) reproduces the hcp-bcc transformationmore » and melting temperatures and is suitable for the simulation of phase transitions and bcc Ti. Two other potentials (Ti2 and Ti3) correctly describe defect properties and can be used to simulate plasticity or radiation damage in hcp Ti. The fact that a single embedded atom method potential cannot describe both low and high temperature phases may be attributed to neglect of electronic degrees of freedom, notably bcc has a much higher electronic entropy. As a result, a temperature-dependent potential obtained from the combination of potentials Ti1 and Ti2 may be used to simulate Ti properties at any temperature.« less

Analysis of fcc metals fracture behaviour: Fracture behaviour of fcc metals: brittle/ductile behaviour criteria : with ab-initio, embedded atom and pseudopotential parameterization for Au, Ir and Al. analysis for Au, Ir and Al.

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.; Katsnelson, M. I.; Mryasov, Oleg N.; Freeman, A. J.; Trefilov, M. V.

1998-03-01

Theoretical analysis of the fracture behaviour of fcc Au, Ir and Al have been performed within various brittle/ductile criteria (BDC) with ab-initio, embedded atom (EAM), and pseudopotential parameterizations. We systematically examined several important aspects of the fracture behaviour: (i) dislocation structure, (ii) energetics of the cleavage decohesion and (iii) character of the interatomic interactions. Unit dislocation structures were analyzed within a two dimensional generalization of the Peierls-Nabarro model with restoring forces determined from ab-initio total energy calculations and found to be split with well defined highly mobile partials for all considered metals. We find from ab-initio and pseudopotential that in contrast with most of fcc metals, cleavage decohesion curve for Al appreciably differs from UBER relation. Finally, using ab-initio, EAM and pseudopotential parameterizations, we demonstrate that (i) Au (as a typical example of a ductile metal) is well described within existing BDC's, (ii) anomalous cleavage-like crack propagation of Ir is driven predominantly by it's high elastic modulus and (iii) Al is not described within BDC due to it's long-range interatomic interactions (and hence requires adjustments of the brittle/ductile criteria).

Automated generation of quantum-accurate classical interatomic potentials for metals and semiconductors

NASA Astrophysics Data System (ADS)

Thompson, Aidan; Foiles, Stephen; Schultz, Peter; Swiler, Laura; Trott, Christian; Tucker, Garritt

2013-03-01

Molecular dynamics (MD) is a powerful condensed matter simulation tool for bridging between macroscopic continuum models and quantum models (QM) treating a few hundred atoms, but is limited by the accuracy of available interatomic potentials. Sound physical and chemical understanding of these interactions have resulted in a variety of concise potentials for certain systems, but it is difficult to extend them to new materials and properties. The growing availability of large QM data sets has made it possible to use more automated machine-learning approaches. Bartók et al. demonstrated that the bispectrum of the local neighbor density provides good regression surrogates for QM models. We adopt a similar bispectrum representation within a linear regression scheme. We have produced potentials for silicon and tantalum, and we are currently extending the method to III-V compounds. Results will be presented demonstrating the accuracy of these potentials relative to the training data, as well as their ability to accurately predict material properties not explicitly included in the training data. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Dept. of Energy Nat. Nuclear Security Admin. under Contract DE-AC04-94AL85000.

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samolyuk, German D.; Osetskiy, Yury N.; Stoller, Roger E.

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascademore » production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (~0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential.« less

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

DOE PAGES

Samolyuk, German D.; Osetskiy, Yury N.; Stoller, Roger E.

2015-06-03

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascademore » production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (~0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential.« less

Two Stages of Impact Fracture of Polycrystalline ZnS and ZnSe Compounds

NASA Astrophysics Data System (ADS)

Shcherbakov, I. P.; Dunaev, A. A.; Chmel', A. E.

2018-04-01

Mechanoluminescence (ML) in ductile solids is caused by the motion of charged dislocations in the deformable material. Interatomic bond ruptures followed by electronic structure reconfiguration are the main source of ML in brittle bodies. We studied ML in ceramics composed of mixed ionic/covalent ZnS and ZnSe compounds, which are generated during impact loading higher than the limit deformation. Depending on synthesis method and thermal treatment, the resulting ceramics had different size and geometry of grains and intergrain boundary structure, which presumably may have a significant effect on the dislocation glide. In both materials, the time sweeps of ML pulses have two well-resolved peaks. The position of the peaks along the time axis is substantially dependent on the size of ceramic-forming grains and, to a smaller extent, on the barrier properties of intergrain boundaries. The first peak is associated with plastic deformation preceding disintegration of the crystal structure. The second peak emerges upon crack nucleation as interatomic bonds are ruptured and the material is undergoing local deformation in tips of propagating cracks. The distributions of ML pulse amplitudes (the dependences between the number of pulses and their amplitude) calculated for both peaks individually follow the power law, which demonstrates that the electronic processes having different excitation mechanisms (dislocation motion vs bond rupture) are correlated.

Statistical theory of diffusion in concentrated bcc and fcc alloys and concentration dependencies of diffusion coefficients in bcc alloys FeCu, FeMn, FeNi, and FeCr

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaks, V. G.; Khromov, K. Yu., E-mail: khromov-ky@nrcki.ru; Pankratov, I. R.

2016-07-15

The statistical theory of diffusion in concentrated bcc and fcc alloys with arbitrary pairwise interatomic interactions based on the master equation approach is developed. Vacancy–atom correlations are described using both the second-shell-jump and the nearest-neighbor-jump approximations which are shown to be usually sufficiently accurate. General expressions for Onsager coefficients in terms of microscopic interatomic interactions and some statistical averages are given. Both the analytical kinetic mean-field and the Monte Carlo methods for finding these averages are described. The theory developed is used to describe sharp concentration dependencies of diffusion coefficients in several iron-based alloy systems. For the bcc alloys FeCu,more » FeMn, and FeNi, we predict the notable increase of the iron self-diffusion coefficient with solute concentration c, up to several times, even though values of c possible for these alloys do not exceed some percent. For the bcc alloys FeCr at high temperatures T ≳ 1400 K, we show that the very strong and peculiar concentration dependencies of both tracer and chemical diffusion coefficients observed in these alloys can be naturally explained by the theory, without invoking exotic models discussed earlier.« less

Classical and quantum simulations of warm dense carbon

NASA Astrophysics Data System (ADS)

Whitley, Heather; Sanchez, David; Hamel, Sebastien; Correa, Alfredo; Benedict, Lorin

We have applied classical and DFT-based molecular dynamics (MD) simulations to study the equation of state of carbon in the warm dense matter regime (ρ = 3.7 g/cc, 0.86 eV

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

PubMed

West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

2017-02-09

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the juxtaposed nonbonded quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions, and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. The theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.

Preparing isolated vibrational wave packets with light-induced molecular potentials by chirped laser pulses

NASA Astrophysics Data System (ADS)

Vatasescu, Mihaela

2012-05-01

We consider a specific wave packet preparation arising from the control of tunneling in the 0g-(6s,6p3/2) double well potential of a Cs2 cold molecule with chirped laser pulses. Such a possibility to manipulate the population dynamics in the 0g-(6s,6p3/2) potential appears in a pump-dump scheme designed to form cold molecules by photoassociation of two cold cesium atoms. The initial population in the 0g-(6s,6p3/2) double well is a wave packet prepared in the outer well at large interatomic distances (94 a0) by a photoassociation step with a first chirped pulse, being a superposition of several vibrational states whose energies surround the energy of a tunneling resonance. Our present work is focused on a second delayed chirped pulse, coupling the 0g-(6s,6p3/2) surface with the a3Σu+(6s,6s) one in the zone of the double well barrier (15 a0) and creating deeply bound cold molecules in the a3Σu+(6s,6s) state. We explore the parameters choice (intensity, duration, chirp rate and sign) for this second pulse, showing that picoseconds pulses with a negative chirp can lead to trapping of population in the inner well in strongly bound vibrational states, out of the resonant tunneling able to transfer it back to the outer well.

Research on structures, mechanical properties, and mechanical responses of TKX-50 and TKX-50 based PBX with molecular dynamics.

PubMed

Ma, Song; Li, Yajin; Li, Yang; Luo, Yunjun

2016-02-01

To improve the practicality and safety of a novel explosive dihydroxylamm onium 5,5'-bis (tetrazole)-1,1'-diolate (TKX-50), polyvinylidene difluoride (PVDF) and polychlorotrifluoroe-thylene (PCTFE) were respectively added to the TKX-50, forming the polymer-bonded explosives (PBX). Interfacial and mechanical properties of PBX were investigated through molecular dynamics (MD) method, desensitizing mechanisms of fluorine-polymers for TKX-50 were researched by compression and bulk shear simulations. Results show that the binding energies (E bind ) between polymers (PVDF or PCTFE) and TKX-50 surfaces all rank in order of (011) > (100) > (010), shorter interatomic distance and the resulted higher potentials lead to higher E bind on TKX-50/PVDF interfaces than that on PCTFE/TKX-50 interfaces. Compared with TKX-50, the ductility of PBX is improved due to the isotropic mechanical property and flexibility of fluorine-polymers especially the PCTFE. Desensitizing effect of fluorine-polymers for TKX-50 is found under loading condition, which is attributed to the enhanced compressibility and buffer capacity against external pressure in compression, as well as the improved lubricity to reduce the sliding potentials in bulk shear process. Graphical Abstract Comparisons of the internal stress and slide potentials of the novel explosive,TKX-50 and its based PBX. Desensitizing effects can be found by the adding of fluorine-polymers, it owes to their better flexibility and lubricity as well as the amorphous nature.

Computational identification of structural factors affecting the mutagenic potential of aromatic amines: study design and experimental validation.

PubMed

Slavov, Svetoslav H; Stoyanova-Slavova, Iva; Mattes, William; Beger, Richard D; Brüschweiler, Beat J

2018-07-01

A grid-based, alignment-independent 3D-SDAR (three-dimensional spectral data-activity relationship) approach based on simulated 13 C and 15 N NMR chemical shifts augmented with through-space interatomic distances was used to model the mutagenicity of 554 primary and 419 secondary aromatic amines. A robust modeling strategy supported by extensive validation including randomized training/hold-out test set pairs, validation sets, "blind" external test sets as well as experimental validation was applied to avoid over-parameterization and build Organization for Economic Cooperation and Development (OECD 2004) compliant models. Based on an experimental validation set of 23 chemicals tested in a two-strain Salmonella typhimurium Ames assay, 3D-SDAR was able to achieve performance comparable to 5-strain (Ames) predictions by Lhasa Limited's Derek and Sarah Nexus for the same set. Furthermore, mapping of the most frequently occurring bins on the primary and secondary aromatic amine structures allowed the identification of molecular features that were associated either positively or negatively with mutagenicity. Prominent structural features found to enhance the mutagenic potential included: nitrobenzene moieties, conjugated π-systems, nitrothiophene groups, and aromatic hydroxylamine moieties. 3D-SDAR was also able to capture "true" negative contributions that are particularly difficult to detect through alternative methods. These include sulphonamide, acetamide, and other functional groups, which not only lack contributions to the overall mutagenic potential, but are known to actively lower it, if present in the chemical structures of what otherwise would be potential mutagens.

Geometrically frustrated GdInO3: An exotic system to study negative thermal expansion and spin-lattice coupling

NASA Astrophysics Data System (ADS)

Paul, Barnita; Chatterjee, Swastika; Roy, Anushree; Midya, A.; Mandal, P.; Grover, Vinita; Tyagi, A. K.

2017-02-01

In this article, we report negative thermal expansion and spin frustration in hexagonal GdInO3. Rietveld refinements of the x-ray diffraction patterns reveal that the negative thermal expansion in the temperature range of 50-100 K stems from the triangular lattice of Gd3 + ions. The downward deviation of the low-temperature inverse susceptibility (χ-1) versus T plot from the Curie-Weiss law and the large value of the ratio, | θCW|/ TN>28 , where θCW and TN are respectively Curie-Weiss and Neel temperature, indicate a strong spin frustration, which inhibits long-range magnetic ordering down to 1.8 K. Magnetostriction measurements clearly demonstrate a spin-lattice coupling in the system. Low-temperature anomalous phonon softening, as obtained from temperature-dependent Raman measurements, also reveals the same. Our experimental observations are supported by first-principles density functional theory calculations of the electronic and phonon dispersion in GdInO3. The calculations suggest that the GdInO3 lattice is highly frustrated at low temperature. Further, the calculated normal mode frequencies of the Gd-related Γ point phonon modes reveal significant magnetoelastic coupling in this system. The competitive role of magnetic interaction energy and thermal stabilization energy in determining the change in interatomic distances is the possible origin for the negative thermal expansion in GdInO3 over a limited range of temperature.

Generative Topographic Mapping of Conformational Space.

PubMed

Horvath, Dragos; Baskin, Igor; Marcou, Gilles; Varnek, Alexandre

2017-10-01

Herein, Generative Topographic Mapping (GTM) was challenged to produce planar projections of the high-dimensional conformational space of complex molecules (the 1LE1 peptide). GTM is a probability-based mapping strategy, and its capacity to support property prediction models serves to objectively assess map quality (in terms of regression statistics). The properties to predict were total, non-bonded and contact energies, surface area and fingerprint darkness. Map building and selection was controlled by a previously introduced evolutionary strategy allowed to choose the best-suited conformational descriptors, options including classical terms and novel atom-centric autocorrellograms. The latter condensate interatomic distance patterns into descriptors of rather low dimensionality, yet precise enough to differentiate between close favorable contacts and atom clashes. A subset of 20 K conformers of the 1LE1 peptide, randomly selected from a pool of 2 M geometries (generated by the S4MPLE tool) was employed for map building and cross-validation of property regression models. The GTM build-up challenge reached robust three-fold cross-validated determination coefficients of Q 2 =0.7…0.8, for all modeled properties. Mapping of the full 2 M conformer set produced intuitive and information-rich property landscapes. Functional and folding subspaces appear as well-separated zones, even though RMSD with respect to the PDB structure was never used as a selection criterion of the maps. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

X-ray absorption spectroscopy: EXAFS (Extended X-ray Absorption Fine Structure) and XANES (X-ray Absorption Near Edge Structure)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alp, E.E.; Mini, S.M.; Ramanathan, M.

1990-04-01

The x-ray absorption spectroscopy (XAS) had been an essential tool to gather spectroscopic information about atomic energy level structure in the early decades of this century. It has also played an important role in the discovery and systematization of rare-earth elements. The discovery of synchrotron radiation in 1952, and later the availability of broadly tunable synchrotron based x-ray sources have revitalized this technique since the 1970's. The correct interpretation of the oscillatory structure in the x-ray absorption cross-section above the absorption edge by Sayers et. al. has transformed XAS from a spectroscopic tool to a structural technique. EXAFS (Extended X-raymore » Absorption Fine Structure) yields information about the interatomic distances, near neighbor coordination numbers, and lattice dynamics. An excellent description of the principles and data analysis techniques of EXAFS is given by Teo. XANES (X-ray Absorption Near Edge Structure), on the other hand, gives information about the valence state, energy bandwidth and bond angles. Today, there are about 50 experimental stations in various synchrotrons around the world dedicated to collecting x-ray absorption data from the bulk and surfaces of solids and liquids. In this chapter, we will give the basic principles of XAS, explain the information content of essentially two different aspects of the absorption process leading to EXAFS and XANES, and discuss the source and samples limitations.« less

A concise synthesis of a highly substituted 6-(1H-benzimidazol-1-yl)-5-nitrosopyrimidin-2-amine: synthetic sequence and the molecular and supramolecular structures of one product and two intermediates.

PubMed

Cobo, Justo; Vicentes, Daniel E; Rodríguez, Ricaurte; Marchal, Antonio; Glidewell, Christopher

2018-06-01

A concise and efficient synthesis of 6-benzimidazolyl-5-nitrosopyrimidines has been developed using Schiff base-type intermediates derived from N 4 -(2-aminophenyl)-6-methoxy-5-nitrosopyrimidine-2,4-diamine. 6-Methoxy-N 4 -{2-[(4-methylbenzylidene)amino]phenyl}-5-nitrosopyrimidine-2,4-diamine, (I), and N 4 -{2-[(ethoxymethylidene)amino]phenyl}-6-methoxy-5-nitrosopyrimidine-2,4-diamine, (III), both crystallize from dimethyl sulfoxide solution as the 1:1 solvates C 19 H 18 N 6 O 2 ·C 2 H 6 OS, (Ia), and C 14 H 16 N 6 O 3 ·C 2 H 6 OS, (IIIa), respectively. The interatomic distances in these intermediates indicate significant electronic polarization within the substituted pyrimidine system. In each of (Ia) and (IIIa), intermolecular N-H...O hydrogen bonds generate centrosymmetric four-molecule aggregates. Oxidative ring closure of intermediate (I), effected using ammonium hexanitratocerate(IV), produced 4-methoxy-6-[2-(4-methylphenyl-1H-benzimidazol-1-yl]-5-nitrosopyrimidin-2-amine, C 19 H 16 N 6 O 2 , (II) [Cobo et al. (2018). Private communication (CCDC 1830889). CCDC, Cambridge, England], where the extent of electronic polarization is much less than in (Ia) and (IIIa). A combination of N-H...N and C-H...O hydrogen bonds links the molecules of (II) into complex sheets.

Local elasticity map and plasticity in a model Lennard-Jones glass.

PubMed

Tsamados, Michel; Tanguy, Anne; Goldenberg, Chay; Barrat, Jean-Louis

2009-08-01

In this work we calculate the local elastic moduli in a weakly polydispersed two-dimensional Lennard-Jones glass undergoing a quasistatic shear deformation at zero temperature. The numerical method uses coarse-grained microscopic expressions for the strain, displacement, and stress fields. This method allows us to calculate the local elasticity tensor and to quantify the deviation from linear elasticity (local Hooke's law) at different coarse-graining scales. From the results a clear picture emerges of an amorphous material with strongly spatially heterogeneous elastic moduli that simultaneously satisfies Hooke's law at scales larger than a characteristic length scale of the order of five interatomic distances. At this scale, the glass appears as a composite material composed of a rigid scaffolding and of soft zones. Only recently calculated in nonhomogeneous materials, the local elastic structure plays a crucial role in the elastoplastic response of the amorphous material. For a small macroscopic shear strain, the structures associated with the nonaffine displacement field appear directly related to the spatial structure of the elastic moduli. Moreover, for a larger macroscopic shear strain we show that zones of low shear modulus concentrate most of the strain in the form of plastic rearrangements. The spatiotemporal evolution of this local elasticity map and its connection with long term dynamical heterogeneity as well as with the plasticity in the material is quantified. The possibility to use this local parameter as a predictor of subsequent local plastic activity is also discussed.

Electronic and geometrical properties of monoatomic and diatomic 2D honeycomb lattices. A DFT study

NASA Astrophysics Data System (ADS)

Rojas, Ángela; Rey, Rafael; Fonseca, Karen; Grupo de Óptica e Información Cuántica Team

Since the discovery of graphene by Geim and Novoselov at 2004, several analogous systems have been theoretically and experimentally studied, due to their technological interest. Both monoatomic lattices, such as silicine and germanene, and diatomic lattices (h-GaAs and h-GaN) have been studied. Using Density Functional Theory we obtain and confirm the chemical stability of these hexagonal 2D systems through the total energy curves as a function of interatomic distance. Unlike graphene, silicine and germanene, gapless materials, h-GaAs and h-GaN exhibit electronic gaps, different from that of the bulk, which could be interesting for the industry. On the other hand, the ab initio band structure calculations for graphene, silicene and germanene show a non-circular cross section around K points, at variance with the prediction of usual Tight-binding models. In fact, we have found that Dirac cones display a dihedral group symmetry. This implies that Fermi speed can change up to 30 % due to the orientation of the wave vector, for both electrons and holes. Traditional analytic studies use the Dirac equation for the electron dynamics at low energies. However, this equation assumes an isotropic, homogeneous and uniform space. Authors would like to thank the División de Investigación Sede Bogotá for their financial support at Universidad Nacional de Colombia. A. M. Rojas-Cuervo would also like to thank the Colciencias, Colombia.

Resonance oscillations of nonreciprocal long-range van der Waals forces between atoms in electromagnetic fields

NASA Astrophysics Data System (ADS)

Sherkunov, Yury

2018-03-01

We study theoretically the van der Waals interaction between two atoms out of equilibrium with an isotropic electromagnetic field. We demonstrate that at large interatomic separations, the van der Waals forces are resonant, spatially oscillating, and nonreciprocal due to resonance absorption and emission of virtual photons. We suggest that the van der Waals forces can be controlled and manipulated by tuning the spectrum of artificially created random light.

Hierarchical optimization for neutron scattering problems

DOE PAGES

Bao, Feng; Archibald, Rick; Bansal, Dipanshu; ...

2016-03-14

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Hierarchical optimization for neutron scattering problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, Feng; Archibald, Rick; Bansal, Dipanshu

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Lattice Thermal Conductivity of Ultra High Temperature Ceramics ZrB2 and HfB2 from Atomistic Simulations

NASA Technical Reports Server (NTRS)

Lawson, John W.; Murray, Daw S.; Bauschlicher, Charles W., Jr.

2011-01-01

Atomistic Green-Kubo simulations are performed to evaluate the lattice thermal conductivity for single crystals of the ultra high temperature ceramics ZrB2 and HfB2 for a range of temperatures. Recently developed interatomic potentials are used for these simulations. Heat current correlation functions show rapid oscillations which can be identified with mixed metal-Boron optical phonon modes. Agreement with available experimental data is good.

Density and glass forming ability in amorphous atomic alloys: The role of the particle softness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Douglass, Ian; Hudson, Toby; Harrowell, Peter

A key property of glass forming alloys, the anomalously small volume difference with respect to the crystal, is shown to arise as a direct consequence of the soft repulsive potentials between metals. This feature of the inter-atomic potential is demonstrated to be responsible for a significant component of the glass forming ability of alloys due to the decrease in the enthalpy of fusion and the associated depression of the freezing point.

Calculations of lattice vibrational mode lifetimes using Jazz: a Python wrapper for LAMMPS

NASA Astrophysics Data System (ADS)

Gao, Y.; Wang, H.; Daw, M. S.

2015-06-01

Jazz is a new python wrapper for LAMMPS [1], implemented to calculate the lifetimes of vibrational normal modes based on forces as calculated for any interatomic potential available in that package. The anharmonic character of the normal modes is analyzed via the Monte Carlo-based moments approximation as is described in Gao and Daw [2]. It is distributed as open-source software and can be downloaded from the website http://jazz.sourceforge.net/.

When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms.

PubMed

Petković, Milena; Nakarada, Đura; Etinski, Mihajlo

2018-05-25

Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra-atomic and inter-atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms. Identification of energy components with the greatest contribution to the variation of the overall energy (intra-atomic and inter-atomic terms that involve hydroquinone's oxygen and the carbon atom covalently bound to it, the transferring hydrogen and methoxy radical's oxygen), is performed using the Relative energy gradient method. Additionally, the Interacting Quantum Fragments approach shed light on the nature of dominant interactions among selected fragments: both Coulomb and exchange-correlation contributions are of comparable importance when considering interactions of the transferring hydrogen atom with all other atoms, whereas the exchange-correlation term dominates interaction between methoxy radical's methyl group and hydroquinone's aromatic ring. This study represents one of the first applications of Interacting Quantum Fragments approach on first order saddle points. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

West, Aaron C.; Schmidt, Michael W.; Gordon, Mark S.

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the non-bonded juxtaposed quasi-atoms andmore » a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. Lastly, the theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.« less

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions

DOE PAGES

West, Aaron C.; Schmidt, Michael W.; Gordon, Mark S.; ...

2017-01-30

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the non-bonded juxtaposed quasi-atoms andmore » a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. Lastly, the theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.« less

Anomalous properties of the acoustic excitations in glasses on the mesoscopic length scale.

PubMed

Monaco, Giulio; Mossa, Stefano

2009-10-06

The low-temperature thermal properties of dielectric crystals are governed by acoustic excitations with large wavelengths that are well described by plane waves. This is the Debye model, which rests on the assumption that the medium is an elastic continuum, holds true for acoustic wavelengths large on the microscopic scale fixed by the interatomic spacing, and gradually breaks down on approaching it. Glasses are characterized as well by universal low-temperature thermal properties that are, however, anomalous with respect to those of the corresponding crystalline phases. Related universal anomalies also appear in the low-frequency vibrational density of states and, despite a longstanding debate, remain poorly understood. By using molecular dynamics simulations of a model monatomic glass of extremely large size, we show that in glasses the structural disorder undermines the Debye model in a subtle way: The elastic continuum approximation for the acoustic excitations breaks down abruptly on the mesoscopic, medium-range-order length scale of approximately 10 interatomic spacings, where it still works well for the corresponding crystalline systems. On this scale, the sound velocity shows a marked reduction with respect to the macroscopic value. This reduction turns out to be closely related to the universal excess over the Debye model prediction found in glasses at frequencies of approximately 1 THz in the vibrational density of states or at temperatures of approximately 10 K in the specific heat.

Conformational analysis of bis(methylthio)methane and diethyl sulfide molecules in the liquid phase: reverse Monte Carlo studies using classical interatomic potential functions.

PubMed

Gereben, Orsolya; Pusztai, László

2013-11-13

Series of flexible molecule reverse Monte Carlo calculations, using bonding and non-bonding interatomic potential functions (FMP-RMC), were performed starting from previous molecular dynamics results that had applied the OPLS-AA and EncadS force fields. During RMC modeling, the experimental x-ray total scattering structure factor was approached. The discrepancy between experimental and calculated structure factors, in comparison with the molecular dynamics results, decreased substantially in each case. The room temperature liquid structure of bis(methylthio)methane is excellently described by the FMP-RMC simulation that applied the EncadS force field parameters. The main conformer was found to be AG with 55.2%, followed by 37.2% of G(+)G(+) (G(-)G(-)) and 7.6% of AA; the stability of the G(+)G(+) (G(-)G(-)) conformer is most probably caused by the anomer effect. The liquid structure of diethyl sulfide can be best described by applying the OPLS-AA force field parameters during FMP-RMC simulation, although in this case the force field parameters were found to be not fully compatible with experimental data. Here, the two main conformers are AG (50.6%) and the AA (40%). In addition to findings on the actual real systems, a fairly detailed comparison between traditional and FMP-RMC methodology is provided.

Resonant interatomic Coulombic decay in HeNe: Electron angular emission distributions

NASA Astrophysics Data System (ADS)

Mhamdi, A.; Trinter, F.; Rauch, C.; Weller, M.; Rist, J.; Waitz, M.; Siebert, J.; Metz, D.; Janke, C.; Kastirke, G.; Wiegandt, F.; Bauer, T.; Tia, M.; Cunha de Miranda, B.; Pitzer, M.; Sann, H.; Schiwietz, G.; Schöffler, M.; Simon, M.; Gokhberg, K.; Dörner, R.; Jahnke, T.; Demekhin, Ph. Â. V.

2018-05-01

We present a joint experimental and theoretical study of resonant interatomic Coulombic decay (RICD) in HeNe employing high resolution cold target recoil ion momentum spectroscopy and ab initio electronic structure and nuclear dynamics calculations. In particular, laboratory- and molecular-frame angular emission distributions of RICD electrons are examined in detail. The exciting-photon energy-dependent anisotropy parameter β (ω ) , measured for decay events that populate bound HeNe+ ions, is in agreement with the calculations performed for the ground ionic state X2Σ1/2 + . A contribution from the a2Π3 /2 final ionic state is found to be negligible. For the He +Ne+ fragmentation channel, the observed laboratory-frame angular distribution of RICD electrons is explained by a slow homogeneous dissociation of bound vibrational levels of the final ionic state A2Π1 /2 into vibrational continua of the lower lying states X2Σ1/2 + and a2Π3 /2 . Our calculations predict that the angular distributions of RICD electrons in the body-fixed dipole plane provide direct access to the electronic character (i.e., symmetry) of intermediate vibronic resonances. However, because of the very slow dissociation of the A2Π1 /2 state, the molecular-frame angular distributions of RICD electrons in the He +Ne+ fragmentation channel are inaccessible to our coincidence experiment.

Inverse scattering transform and soliton solutions for square matrix nonlinear Schrödinger equations with non-zero boundary conditions

NASA Astrophysics Data System (ADS)

Prinari, Barbara; Demontis, Francesco; Li, Sitai; Horikis, Theodoros P.

2018-04-01

The inverse scattering transform (IST) with non-zero boundary conditions at infinity is developed for an m × m matrix nonlinear Schrödinger-type equation which, in the case m = 2, has been proposed as a model to describe hyperfine spin F = 1 spinor Bose-Einstein condensates with either repulsive interatomic interactions and anti-ferromagnetic spin-exchange interactions (self-defocusing case), or attractive interatomic interactions and ferromagnetic spin-exchange interactions (self-focusing case). The IST for this system was first presented by Ieda et al. (2007) , using a different approach. In our formulation, both the direct and the inverse problems are posed in terms of a suitable uniformization variable which allows to develop the IST on the standard complex plane, instead of a two-sheeted Riemann surface or the cut plane with discontinuities along the cuts. Analyticity of the scattering eigenfunctions and scattering data, symmetries, properties of the discrete spectrum, and asymptotics are derived. The inverse problem is posed as a Riemann-Hilbert problem for the eigenfunctions, and the reconstruction formula of the potential in terms of eigenfunctions and scattering data is provided. In addition, the general behavior of the soliton solutions is analyzed in detail in the 2 × 2 self-focusing case, including some special solutions not previously discussed in the literature.

Formation of nanocolloidal metacinnabar in mercury-DOM-sulfide systems

USGS Publications Warehouse

Gerbig, Chase A.; Kim, Christopher S.; Stegemeier, John P.; Ryan, Joseph N.; Aiken, George R.

2011-01-01

Direct determination of mercury (Hg) speciation in sulfide-containing environments is confounded by low mercury concentrations and poor analytical sensitivity. Here we report the results of experiments designed to assess mercury speciation at environmentally relevant ratios of mercury to dissolved organic matter (DOM) (i.e., <4 nmol Hg (mg DOM)−1) by combining solid phase extraction using C18 resin with extended X-ray absorption fine structure (EXAFS) spectroscopy. Aqueous Hg(II) and a DOM isolate were equilibrated in the presence and absence of 100 μM total sulfide. In the absence of sulfide, mercury adsorption to the resin increased as the Hg:DOM ratio decreased and as the strength of Hg-DOM binding increased. EXAFS analysis indicated that in the absence of sulfide, mercury bonds with an average of 2.4 ± 0.2 sulfur atoms with a bond length typical of mercury-organic thiol ligands (2.35 Å). In the presence of sulfide, mercury showed greater affinity for the C18 resin, and its chromatographic behavior was independent of Hg:DOM ratio. EXAFS analysis showed mercury–sulfur bonds with a longer interatomic distance (2.51–2.53 Å) similar to the mercury–sulfur bond distance in metacinnabar (2.53 Å) regardless of the Hg:DOM ratio. For all samples containing sulfide, the sulfur coordination number was below the ideal four-coordinate structure of metacinnabar. At a low Hg:DOM ratio where strong binding DOM sites may control mercury speciation (1.9 nmol mg–1) mercury was coordinated by 2.3 ± 0.2 sulfur atoms, and the coordination number rose with increasing Hg:DOM ratio. The less-than-ideal coordination numbers indicate metacinnabar-like species on the nanometer scale, and the positive correlation between Hg:DOM ratio and sulfur coordination number suggests progressively increasing particle size or crystalline order with increasing abundance of mercury with respect to DOM. In DOM-containing sulfidic systems nanocolloidal metacinnabar-like species may form, and these species need to be considered when addressing mercury biogeochemistry.

Bond-length distributions for ions bonded to oxygen: alkali and alkaline-earth metals.

PubMed

Gagné, Olivier Charles; Hawthorne, Frank Christopher

2016-08-01

Bond-length distributions have been examined for 55 configurations of alkali-metal ions and 29 configurations of alkaline-earth-metal ions bonded to oxygen, for 4859 coordination polyhedra and 38 594 bond distances (alkali metals), and for 3038 coordination polyhedra and 24 487 bond distances (alkaline-earth metals). Bond lengths generally show a positively skewed Gaussian distribution that originates from the variation in Born repulsion and Coulomb attraction as a function of interatomic distance. The skewness and kurtosis of these distributions generally decrease with increasing coordination number of the central cation, a result of decreasing Born repulsion with increasing coordination number. We confirm the following minimum coordination numbers: ([3])Li(+), ([3])Na(+), ([4])K(+), ([4])Rb(+), ([6])Cs(+), ([3])Be(2+), ([4])Mg(2+), ([6])Ca(2+), ([6])Sr(2+) and ([6])Ba(2+), but note that some reported examples are the result of extensive dynamic and/or positional short-range disorder and are not ordered arrangements. Some distributions of bond lengths are distinctly multi-modal. This is commonly due to the occurrence of large numbers of structure refinements of a particular structure type in which a particular cation is always present, leading to an over-representation of a specific range of bond lengths. Outliers in the distributions of mean bond lengths are often associated with anomalous values of atomic displacement of the constituent cations and/or anions. For a sample of ([6])Na(+), the ratio Ueq(Na)/Ueq(bonded anions) is partially correlated with 〈([6])Na(+)-O(2-)〉 (R(2) = 0.57), suggesting that the mean bond length is correlated with vibrational/displacement characteristics of the constituent ions for a fixed coordination number. Mean bond lengths also show a weak correlation with bond-length distortion from the mean value in general, although some coordination numbers show the widest variation in mean bond length for zero distortion, e.g. Li(+) in [4]- and [6]-coordination, Na(+) in [4]- and [6]-coordination. For alkali-metal and alkaline-earth-metal ions, there is a positive correlation between cation coordination number and the grand mean incident bond-valence sum at the central cation, the values varying from 0.84 v.u. for ([5])K(+) to 1.06 v.u. for ([8])Li(+), and from 1.76 v.u. for ([7])Ba(2+) to 2.10 v.u. for ([12])Sr(2+). Bond-valence arguments suggest coordination numbers higher than [12] for K(+), Rb(+), Cs(+) and Ba(2+).

Inter-atomic force constants of BaF{sub 2} by diffuse neutron scattering measurement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakuma, Takashi, E-mail: sakuma@mx.ibaraki.ac.jp; Makhsun,; Sakai, Ryutaro

2015-04-16

Diffuse neutron scattering measurement on BaF{sub 2} crystals was performed at 10 K and 295 K. Oscillatory form in the diffuse scattering intensity of BaF{sub 2} was observed at 295 K. The correlation effects among thermal displacements of F-F atoms were obtained from the analysis of oscillatory diffuse scattering intensity. The force constants among neighboring atoms in BaF{sub 2} were determined and compared to those in ionic crystals and semiconductors.

First-principles study of point defects at a semicoherent interface

DOE PAGES

Metsanurk, E.; Tamm, A.; Caro, A.; ...

2014-12-19

Most of the atomistic modeling of semicoherent metal-metal interfaces has so far been based on the use of semiempirical interatomic potentials. Here, we show that key conclusions drawn from previous studies are in contradiction with more precise ab-initio calculations. In particular we find that single point defects do not delocalize, but remain compact near the interfacial plane in Cu-Nb multilayers. Lastly, we give a simple qualitative explanation for this difference on the basis of the well known limited transferability of empirical potentials.

Interatomic scattering in energy dependent photoelectron spectra of Ar clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patanen, M.; Benkoula, S.; Nicolas, C.

2015-09-28

Soft X-ray photoelectron spectra of Ar 2p levels of atomic argon and argon clusters are recorded over an extended range of photon energies. The Ar 2p intensity ratios between atomic argon and clusters’ surface and bulk components reveal oscillations similar to photoelectron extended X-ray absorption fine structure signal (PEXAFS). We demonstrate here that this technique allows us to analyze separately the PEXAFS signals from surface and bulk sites of free-standing, neutral clusters, revealing a bond contraction at the surface.

Foraging on the potential energy surface: a swarm intelligence-based optimizer for molecular geometry.

PubMed

Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D; Sebastiani, Daniel

2012-11-21

We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

Effect of Static Strains on Diffusion

NASA Technical Reports Server (NTRS)

Girifalco, L. A.; Grimes, H. H.

1961-01-01

A theory is developed that gives the diffusion coefficient in strained systems as an exponential function of the strain. This theory starts with the statistical theory of the atomic jump frequency as developed by Vineyard. The parameter determining the effect of strain on diffusion is related to the changes in the inter-atomic forces with strain. Comparison of the theory with published experimental results for the effect of pressure on diffusion shows that the experiments agree with the form of the theoretical equation in all cases within experimental error.

Molecular structure, interatomic interactions and vibrational analysis of 1,4-diazabicyclo[3.2.1]octane parent ring system

NASA Astrophysics Data System (ADS)

Britvin, Sergey N.; Rumyantsev, Andrey M.; Zobnina, Anastasia E.; Padkina, Marina V.

2017-02-01

Molecular structure of 1,4-diazabicyclo[3.2.1]octane, a parent ring of TAN1251 family of alkaloids, is herein characterized for the first time in comparison with the structure of nortropane (8-azabicyclo[3.2.1]octane), the parent framework of tropane ring system. The methods of study involve X-ray structural analysis, DFT geometry optimizations with infrared frequency calculations followed by natural bond orbital (NBO) analysis, and vibrational analysis of infrared spectrum.

Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry

NASA Astrophysics Data System (ADS)

Wehmeyer, Christoph; Falk von Rudorff, Guido; Wolf, Sebastian; Kabbe, Gabriel; Schärf, Daniel; Kühne, Thomas D.; Sebastiani, Daniel

2012-11-01

We present a stochastic, swarm intelligence-based optimization algorithm for the prediction of global minima on potential energy surfaces of molecular cluster structures. Our optimization approach is a modification of the artificial bee colony (ABC) algorithm which is inspired by the foraging behavior of honey bees. We apply our modified ABC algorithm to the problem of global geometry optimization of molecular cluster structures and show its performance for clusters with 2-57 particles and different interatomic interaction potentials.

Tunneling of Two Interacting Fermions

NASA Astrophysics Data System (ADS)

Ishmukhamedov, Ilyas; Ishmukhamedov, Altay

2018-04-01

We consider two interacting atoms subject to a one-dimensional anharmonic trap and magnetic field gradient. This system has been recently investigated by the Heidelberg group in the experiment on two 6Li atoms. In the present paper the tunneling of two cold 6Li atoms, initially prepared in the center-of-mass and relative motion excited state, is explored and full time-dependent simulation of the tunneling dynamics is performed. The dynamics is analyzed for the interatomic coupling strength ranging from strong attraction to strong repulsion.

Harmonic and anharmonic oscillations investigated by using a microcomputer-based Atwood's machine

NASA Astrophysics Data System (ADS)

Pecori, Barbara; Torzo, Giacomo; Sconza, Andrea

1999-03-01

We describe how the Atwood's machine, interfaced to a personal computer through a rotary encoder, is suited for investigating harmonic and anharmonic oscillations, exploiting the buoyancy force acting on a body immersed in water. We report experimental studies of oscillators produced by driving forces of the type F=-kxn with n=1,2,3, and F=-k sgn(x). Finally we suggest how this apparatus can be used for showing to the students a macroscopic model of interatomic forces.

Unveiling Surface Redox Charge Storage of Interacting Two-Dimensional Hetero-Nanosheets in Hierarchical Architectures

DOE PAGES

Mahmood, Qasim; Bak, Seong-Min; Kim, Min G.; ...

2015-03-03

Two-dimensional (2D) heteronanosheets are currently the focus of intense study due to the unique properties that emerge from the interplay between two low-dimensional nanomaterials with different properties. However, the properties and new phenomena based on the two 2D heteronanosheets interacting in a 3D hierarchical architecture have yet to be explored. Here, we unveil the surface redox charge storage mechanism of surface-exposed WS2 nanosheets assembled in a 3D hierarchical heterostructure using in situ synchrotron X-ray absorption and Raman spectroscopic methods. The surface dominating redox charge storage of WS2 is manifested in a highly reversible and ultrafast capacitive fashion due to themore » interaction of heteronanosheets and the 3D connectivity of the hierarchical structure. In contrast, compositionally identical 2D WS2 structures fail to provide a fast and high capacitance with different modes of lattice vibration. The distinctive surface capacitive behavior of 3D hierarchically structured heteronanosheets is associated with rapid proton accommodation into the in-plane W–S lattice (with the softening of the E2g bands), the reversible redox transition of the surface-exposed intralayers residing in the electrochemically active 1T phase of WS2 (with the reversible change in the interatomic distance and peak intensity of W–W bonds), and the change in the oxidation state during the proton insertion/deinsertion process. This proposed mechanism agrees with the dramatic improvement in the capacitive performance of the two heteronanosheets coupled in the hierarchical structure.« less

Effect of component substitution on the atomic dynamics in glass-forming binary metallic melts

NASA Astrophysics Data System (ADS)

Nowak, B.; Holland-Moritz, D.; Yang, F.; Voigtmann, Th.; Evenson, Z.; Hansen, T. C.; Meyer, A.

2017-08-01

We investigate the substitution of early transition metals (Zr, Hf, and Nb) in Ni-based binary glass-forming metallic melts and the impact on structural and dynamical properties by using a combination of neutron scattering, electrostatic levitation (ESL), and isotopic substitution. The self-diffusion coefficients measured by quasielastic neutron scattering (QENS) identify a sluggish diffusion as well as an increased activation energy by almost a factor of 2 for Hf35Ni65 compared to Zr36Ni64 . This finding can be explained by the locally higher packing density of Hf atoms in Hf35Ni65 compared to Zr atoms in Zr36Ni64 , which has been derived from interatomic distances by analyzing the measured partial structure factors. Furthermore, QENS measurements of liquid Hf35Ni65 prepared with 60Ni , which has a vanishing incoherent scattering cross section, have demonstrated that self-diffusion of Hf is slowed down compared to the concentration weighted self-diffusion of Hf and Ni. This implies a dynamical decoupling between larger Hf and smaller Ni atoms, which can be related to a saturation effect of unequal atomic nearest-neighbor pairs, that was observed recently for Ni-rich compositions in Zr-Ni metallic melts. In order to establish a structure-dynamics relation, measured partial structure factors have been used as an input for mode-coupling theory (MCT) of the glass transition to calculate self-diffusion coefficients for the different atomic components. Remarkably, MCT can reproduce the increased activation energy for Hf35Ni65 as well as the dynamical decoupling between Hf and Ni atoms.

Constant size descriptors for accurate machine learning models of molecular properties

NASA Astrophysics Data System (ADS)

Collins, Christopher R.; Gordon, Geoffrey J.; von Lilienfeld, O. Anatole; Yaron, David J.

2018-06-01

Two different classes of molecular representations for use in machine learning of thermodynamic and electronic properties are studied. The representations are evaluated by monitoring the performance of linear and kernel ridge regression models on well-studied data sets of small organic molecules. One class of representations studied here counts the occurrence of bonding patterns in the molecule. These require only the connectivity of atoms in the molecule as may be obtained from a line diagram or a SMILES string. The second class utilizes the three-dimensional structure of the molecule. These include the Coulomb matrix and Bag of Bonds, which list the inter-atomic distances present in the molecule, and Encoded Bonds, which encode such lists into a feature vector whose length is independent of molecular size. Encoded Bonds' features introduced here have the advantage of leading to models that may be trained on smaller molecules and then used successfully on larger molecules. A wide range of feature sets are constructed by selecting, at each rank, either a graph or geometry-based feature. Here, rank refers to the number of atoms involved in the feature, e.g., atom counts are rank 1, while Encoded Bonds are rank 2. For atomization energies in the QM7 data set, the best graph-based feature set gives a mean absolute error of 3.4 kcal/mol. Inclusion of 3D geometry substantially enhances the performance, with Encoded Bonds giving 2.4 kcal/mol, when used alone, and 1.19 kcal/mol, when combined with graph features.

Quaternary Chalcogenide-Based Misfit Nanotubes LnS(Se)-TaS(Se)2 (Ln = La, Ce, Nd, and Ho): Synthesis and Atomic Structural Studies.

PubMed

Lajaunie, Luc; Radovsky, Gal; Tenne, Reshef; Arenal, Raul

2018-01-16

We have synthesized quaternary chalcogenide-based misfit nanotubes LnS(Se)-TaS 2 (Se) (Ln = La, Ce, Nd, and Ho). None of the compounds described here were reported in the literature as a bulk compound. The characterization of these nanotubes, at the atomic level, has been developed via different transmission electron microscopy techniques, including high-resolution scanning transmission electron microscopy, electron diffraction, and electron energy-loss spectroscopy. In particular, quantification at sub-nanometer scale was achieved by acquiring high-quality electron energy-loss spectra at high energy (∼between 1000 and 2500 eV). Remarkably, the sulfur was found to reside primarily in the distorted rocksalt LnS lattice, while the Se is associated with the hexagonal TaSe 2 site. Consequently, these quaternary misfit layered compounds in the form of nanostructures possess a double superstructure of La/Ta and S/Se with the same periodicity. In addition, the interlayer spacing between the layers and the interatomic distances within the layer vary systematically in the nanotubes, showing clear reduction when going from the lightest (La atom) to the heaviest (Ho) atom. Amorphous layers, of different nature, were observed at the surface of the nanotubes. For La-based NTs, the thin external amorphous layer (inferior to 10 nm) can be ascribed to a Se deficiency. Contrarily, for Ho-based NTs, the thick amorphous layer (between 10 and 20 nm) is clearly ascribed to oxidation. All of these findings helped us to understand the atomic structure of these new compounds and nanotubes thereof.

High resolution x-ray fluorescence spectroscopy - a new technique for site- and spin-selectivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xin

1996-12-01

X-ray spectroscopy has long been used to elucidate electronic and structural information of molecules. One of the weaknesses of x-ray absorption is its sensitivity to all of the atoms of a particular element in a sample. Through out this thesis, a new technique for enhancing the site- and spin-selectivity of the x-ray absorption has been developed. By high resolution fluorescence detection, the chemical sensitivity of K emission spectra can be used to identify oxidation and spin states; it can also be used to facilitate site-selective X-ray Absorption Near Edge Structure (XANES) and site-selective Extended X-ray Absorption Fine Structure (EXAFS). Themore » spin polarization in K fluorescence could be used to generate spin selective XANES or spin-polarized EXAFS, which provides a new measure of the spin density, or the nature of magnetic neighboring atoms. Finally, dramatic line-sharpening effects by the combination of absorption and emission processes allow observation of structure that is normally unobservable. All these unique characters can enormously simplify a complex x-ray spectrum. Applications of this novel technique have generated information from various transition-metal model compounds to metalloproteins. The absorption and emission spectra by high resolution fluorescence detection are interdependent. The ligand field multiplet model has been used for the analysis of K{alpha} and K{beta} emission spectra. First demonstration on different chemical states of Fe compounds has shown the applicability of site selectivity and spin polarization. Different interatomic distances of the same element in different chemical forms have been detected using site-selective EXAFS.« less

Layer-by-layer evolution of structure, strain, and activity for the oxygen evolution reaction in graphene-templated Pt monolayers.

PubMed

Abdelhafiz, Ali; Vitale, Adam; Joiner, Corey; Vogel, Eric; Alamgir, Faisal M

2015-03-25

In this study, we explore the dimensional aspect of structure-driven surface properties of metal monolayers grown on a graphene/Au template. Here, surface limited redox replacement (SLRR) is used to provide precise layer-by-layer growth of Pt monolayers on graphene. We find that after a few iterations of SLRR, fully wetted 4-5 monolayer Pt films can be grown on graphene. Incorporating graphene at the Pt-Au interface modifies the growth mechanism, charge transfers, equilibrium interatomic distances, and associated strain of the synthesized Pt monolayers. We find that a single layer of sandwiched graphene is able to induce a 3.5% compressive strain on the Pt adlayer grown on it, and as a result, catalytic activity is increased due to a greater areal density of the Pt layers beyond face-centered-cubic close packing. At the same time, the sandwiched graphene does not obstruct vicinity effects of near-surface electron exchange between the substrate Au and adlayers Pt. X-ray photoelectron spectroscopy (XPS) and extended X-ray absorption fine structure (EXAFS) techniques are used to examine charge mediation across the Pt-graphene-Au junction and the local atomic arrangement as a function of the Pt adlayer dimension. Cyclic voltammetry (CV) and the oxygen reduction reaction (ORR) are used as probes to examine the electrochemically active area of Pt monolayers and catalyst activity, respectively. Results show that the inserted graphene monolayer results in increased activity for the Pt due to a graphene-induced compressive strain, as well as a higher resistance against loss of the catalytically active Pt surface.

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

PubMed Central

2017-01-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac–Coulomb and Dirac–Coulomb–Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved. PMID:28595411

New Insight into the Local Structure of Hydrous Ferric Arsenate Using Full-Potential Multiple Scattering Analysis, Density Functional Theory Calculations, and Vibrational Spectroscopy.

PubMed

Wang, Shaofeng; Ma, Xu; Zhang, Guoqing; Jia, Yongfeng; Hatada, Keisuke

2016-11-15

Hydrous ferric arsenate (HFA) is an important arsenic-bearing precipitate in the mining-impacted environment and hydrometallurgical tailings. However, there is no agreement on its local atomic structure. The local structure of HFA was reprobed by employing a full-potential multiple scattering (FPMS) analysis, density functional theory (DFT) calculations, and vibrational spectroscopy. The FPMS simulations indicated that the coordination number of the As-Fe, Fe-As, or both in HFA was approximately two. The DFT calculations constructed a structure of HFA with the formula of Fe(HAsO 4 ) x (H 2 AsO 4 ) 1-x (OH) y ·zH 2 O. The presence of protonated arsenate in HFA was also evidenced by vibrational spectroscopy. The As and Fe K-edge X-ray absorption near-edge structure spectra of HFA were accurately reproduced by FPMS simulations using the chain structure, which was also a reasonable model for extended X-Ray absorption fine structure fitting. The FPMS refinements indicated that the interatomic Fe-Fe distance was approximately 5.2 Å, consistent with that obtained by Mikutta et al. (Environ. Sci. Technol. 2013, 47 (7), 3122-3131) using wavelet analysis. All of the results suggested that HFA was more likely to occur as a chain with AsO 4 tetrahedra and FeO 6 octahedra connecting alternately in an isolated bidentate-type fashion. This finding is of significance for understanding the fate of arsenic and the formation of ferric arsenate minerals in an acidic environment.

In Situ Observation of Oxygen Vacancy Dynamics and Ordering in the Epitaxial LaCoO3 System.

PubMed

Jang, Jae Hyuck; Kim, Young-Min; He, Qian; Mishra, Rohan; Qiao, Liang; Biegalski, Michael D; Lupini, Andrew R; Pantelides, Sokrates T; Pennycook, Stephen J; Kalinin, Sergei V; Borisevich, Albina Y

2017-07-25

Vacancy dynamics and ordering underpin the electrochemical functionality of complex oxides and strongly couple to their physical properties. In the field of the epitaxial thin films, where connection between chemistry and film properties can be most clearly revealed, the effects related to oxygen vacancies are attracting increasing attention. In this article, we report a direct, real-time, atomic level observation of the formation of oxygen vacancies in the epitaxial LaCoO 3 thin films and heterostructures under the influence of the electron beam utilizing scanning transmission electron microscopy (STEM). In the case of LaCoO 3 /SrTiO 3 superlattice, the formation of the oxygen vacancies is shown to produce quantifiable changes in the interatomic distances, as well as qualitative changes in the symmetry of the Co sites manifested as off-center displacements. The onset of these changes was observed in both the [100] pc and [110] pc orientations in real time. Additionally, annular bright field images directly show the formation of oxygen vacancy channels along [110]pc direction. In the case of 15 u.c. LaCoO 3 thin film, we observe the sequence of events during beam-induced formation of oxygen vacancy ordered phases and find them consistent with similar processes in the bulk. Moreover, we record the dynamics of the nucleation, growth, and defect interaction at the atomic scale as these transformations happen. These results demonstrate that we can track dynamic oxygen vacancy behavior with STEM, generating atomic-level quantitative information on phase transformation and oxygen diffusion.

The Economics of van der Waals Force Engineering

NASA Astrophysics Data System (ADS)

Pinto, Fabrizio

2008-01-01

As micro-electro-mechanical system (MEMS) fabrication continues on an ever-decreasing scale, new technological challenges must be successfully negotiated if Moore's Law is to be an even approximately valid model of the future of device miniaturization. Among the most significant obstacles is the existence of strong surface forces related to quantum mechanical van der Waals interatomic interactions, which rapidly diverge as the distance between any two neutral boundaries decreases. The van der Waals force is a contributing factor in several device failures and limitations, including, for instance, stiction and oscillator non-linearities. In the last decade, however, it has been conclusively shown that van der Waals forces are not just a MEMS limitation but can be engineered in both magnitude and sign so as to enable classes of proprietary inventions which either deliver novel capabilities or improve upon existing ones. The evolution of van der Waals force research from an almost exclusively theoretical field in quantum-electro-dynamics to an enabling nanotechnology discipline represents a useful example of the ongoing paradigm shift from government-centered to private-capital funded R&D in cutting-edge physics leading to potentially profitable products. In this paper, we discuss the reasons van der Waals force engineering may lead to the creation of thriving markets both in the short and medium terms by highlighting technical challenges that can be competitively addressed by this novel approach. We also discuss some notable obstacles to the cultural transformation of the academic research community required for the emergence of a functional van der Waals force engineering industry worldwide.

Enhanced initial protein adsorption on engineered nanostructured cubic zirconia.

PubMed

Sabirianov, R F; Rubinstein, A; Namavar, F

2011-04-14

Motivated by experimentally-observed biocompatibility enhancement of nanoengineered cubic zirconia (ZrO(2)) coatings to mesenchymal stromal cells, we have carried out computational analysis of the initial immobilization of one known structural fragment of the adhesive protein (fibronectin) on the corresponding surface. We constructed an atomistic model of the ZrO(2) nano-hillock of 3-fold symmetry based on Atom Force Microscopy and Transmission Electron Microscopy images. First principle quantum mechanical calculations show a substantial variation of electrostatic potential at the hillock due to the presence of surface features such as edges and vertexes. Using an implemented Monte Carlo simulated annealing method, we found the orientation of the immobilized protein on the ZrO(2) surface and the contribution of the amino acid residues from the protein sequence to the adsorption energy. Accounting for the variation of the dielectric permittivity at the protein-implant interface, we used a model distance-dependent dielectric function to describe the inter-atom electrostatic interactions in the adsorption potential. We found that the initial immobilization of the rigid protein fragment on the nanostructured pyramidal ZrO(2) surface is achieved with a magnitude of adsorption energy larger than that of the protein on the smooth (atomically flat) surface. The strong attractive electrostatic interactions are a major contributing factor in the enhanced adsorption at the nanostructured surface. In the case of adsorption on the flat, uncharged surface this factor is negligible. We show that the best electrostatic and steric fit of the protein to the inorganic surface corresponds to a minimum of the adsorption energy determined by the non-covalent interactions.

Structure and ionic diffusion of alkaline-earth ions in mixed cation glasses A 2O–2MO–4SiO 2 with molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konstantinou, Konstantinos; Sushko, Petr; Duffy, Dorothy M.

2015-05-15

A series of mixed cation silicate glasses of the composition A2O – 2MO – 4SiO2, with A=Li,Na,K and M=Ca,Sr,Ba has been investigated by means of molecular dynamics simulations in order to understand the effect of the nature of the cations on the mobility of the alkaline-earth ions within the glass network. The size of the alkaline-earth cation was found to affect the inter-atomic distances, the coordination number distributions and the bond angle distributions , whereas the medium-range order was almost unaffected by the type of the cation. All the alkaline-earth cations contribute to lower vibrational frequencies but it is observedmore » that that there is a shift to smaller frequencies and the vibrational density of states distribution gets narrower as the size of the alkaline-earth increases. The results from our modeling for the ionic diffusion of the alkaline-earth cations are in a qualitative agreement with the experimental observations in that there is a distinct correlation between the activation energy for diffusion of alkaline earth-ions and the cation radii ratio. An asymmetrical linear behavior in the diffusion activation energy with increasing size difference is observed. The results can be described on the basis of a theoretical model that relates the diffusion activation energy to the electrostatic interactions of the cations with the oxygens and the elastic deformation of the silicate network.« less

Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

NASA Astrophysics Data System (ADS)

Jäger, Benjamin; Bich, Eckard

2017-06-01

A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac-Coulomb and Dirac-Coulomb-Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved.

Potential Energy Curves and Transport Properties for the Interaction of He with Other Ground-state Atoms

NASA Technical Reports Server (NTRS)

Partridge, Harry; Stallcop, James R.; Levin, Eugene; Arnold, Jim (Technical Monitor)

2001-01-01

The interactions of a He atom with a heavier atom are examined for 26 different elements, which are consecutive members selected from three rows (Li - Ne, Na - Ar, and K,Ca, Ga - Kr) and column 12 (Zn,Cd) of the periodic table. Interaction energies are determined wing high-quality ab initio calculations for the states of the molecule that would be formed from each pair of atoms in their ground states. Potential energies are tabulated for a broad range of Interatomic separation distances. The results show, for example, that the energy of an alkali interaction at small separations is nearly the same as that of a rare-gas interaction with the same electron configuration for the dosed shells. Furthermore, the repulsive-range parameter for this region is very short compared to its length for the repulsion dominated by the alkali-valence electron at large separations (beyond about 3-4 a(sub 0)). The potential energies in the region of the van der Waals minimum agree well with the most accurate results available. The ab initio energies are applied to calculate scattering cross sections and obtain the collision integrals that are needed to determine transport properties to second order. The theoretical values of Li-He total scattering cross sections and the rare-gas atom-He transport properties agree well (to within about 1%) with the corresponding measured data. Effective potential energies are constructed from the ab initio energies; the results have been shown to reproduce known transport data and can be readily applied to predict unknown transport properties for like-atom interactions.

Multi-Dimensional Simulation of LWR Fuel Behavior in the BISON Fuel Performance Code

NASA Astrophysics Data System (ADS)

Williamson, R. L.; Capps, N. A.; Liu, W.; Rashid, Y. R.; Wirth, B. D.

2016-11-01

Nuclear fuel operates in an extreme environment that induces complex multiphysics phenomena occurring over distances ranging from inter-atomic spacing to meters, and times scales ranging from microseconds to years. To simulate this behavior requires a wide variety of material models that are often complex and nonlinear. The recently developed BISON code represents a powerful fuel performance simulation tool based on its material and physical behavior capabilities, finite-element versatility of spatial representation, and use of parallel computing. The code can operate in full three dimensional (3D) mode, as well as in reduced two dimensional (2D) modes, e.g., axisymmetric radial-axial ( R- Z) or plane radial-circumferential ( R- θ), to suit the application and to allow treatment of global and local effects. A BISON case study was used to illustrate analysis of Pellet Clad Mechanical Interaction failures from manufacturing defects using combined 2D and 3D analyses. The analysis involved commercial fuel rods and demonstrated successful computation of metrics of interest to fuel failures, including cladding peak hoop stress and strain energy density. In comparison with a failure threshold derived from power ramp tests, results corroborate industry analyses of the root cause of the pellet-clad interaction failures and illustrate the importance of modeling 3D local effects around fuel pellet defects, which can produce complex effects including cold spots in the cladding, stress concentrations, and hot spots in the fuel that can lead to enhanced cladding degradation such as hydriding, oxidation, CRUD formation, and stress corrosion cracking.

Multi-Dimensional Simulation of LWR Fuel Behavior in the BISON Fuel Performance Code

DOE PAGES

Williamson, R. L.; Capps, N. A.; Liu, W.; ...

2016-09-27

Nuclear fuel operates in an extreme environment that induces complex multiphysics phenomena occurring over distances ranging from inter-atomic spacing to meters, and times scales ranging from microseconds to years. To simulate this behavior requires a wide variety of material models that are often complex and nonlinear. The recently developed BISON code represents a powerful fuel performance simulation tool based on its material and physical behavior capabilities, finite-element versatility of spatial representation, and use of parallel computing. The code can operate in full three dimensional (3D) mode, as well as in reduced two dimensional (2D) modes, e.g., axisymmetric radial-axial (R-Z) ormore » plane radial-circumferential (R-θ), to suit the application and to allow treatment of global and local effects. A BISON case study was used in this paper to illustrate analysis of Pellet Clad Mechanical Interaction failures from manufacturing defects using combined 2D and 3D analyses. The analysis involved commercial fuel rods and demonstrated successful computation of metrics of interest to fuel failures, including cladding peak hoop stress and strain energy density. Finally, in comparison with a failure threshold derived from power ramp tests, results corroborate industry analyses of the root cause of the pellet-clad interaction failures and illustrate the importance of modeling 3D local effects around fuel pellet defects, which can produce complex effects including cold spots in the cladding, stress concentrations, and hot spots in the fuel that can lead to enhanced cladding degradation such as hydriding, oxidation, CRUD formation, and stress corrosion cracking.« less

Role of the Heavy Metal's Crystal Phase in Oscillations of Perpendicular Magnetic Anisotropy and the Interfacial Dzyaloshinskii-Moriya Interaction in W /Co -Fe -B /MgO Films

NASA Astrophysics Data System (ADS)

Kim, Gyu Won; Samardak, Alexander S.; Kim, Yong Jin; Cha, In Ho; Ognev, Alexey V.; Sadovnikov, Alexandr V.; Nikitov, Sergey A.; Kim, Young Keun

2018-06-01

The interfacial Dzyaloshinskii-Moriya interaction (IDMI) generally arises in "heavy-metal-ferromagnet" (HM-FM) heterostructures due the strong spin-orbit coupling in HMs and plays a crucial role in the nucleation of Dzyaloshinskii domain walls and Skyrmions that can be efficiently moved by spin-orbit torques. We study the IDMI in W /Co -Fe -B /MgO /Ta films with perpendicular magnetic anisotropy for different crystal structures and thicknesses of W layers treated by postsputtering annealing at 300 °C and 400 °C . We employ Brillouin light scattering spectroscopy to precisely measure the energy density and sign of the IDMI. We reveal two peaks associated with the IDMI: one for the amorphouslike phase of W, and another for α -W . The samples with pure β -W underlayers show the smallest values of IDMI. The sign of the IDMI is positive for all samples with the observed maximum effective and surface values of Deff=0.88 erg /cm2 and Ds=0.51 ×10-7 erg /cm , respectively. We report on the oscillating behavior of the IDMI as a function of thickness, which correlates with the surface anisotropy energy demonstrating common spin-orbit coupling and a robust dependence on the structural properties of the materials used. We ascribe the oscillations of the surface anisotropy and the IDMI mainly to the near inversely proportional dependence on the squared interatomic distance between the HM and FM atoms promoted by the thickness-driven crystal phase formation of W.

Wide angle X-ray scattering (WAXS) study of "two-line" ferrihydrite structure: Effect of arsenate sorption and counterion variation and comparison with EXAFS results

USGS Publications Warehouse

Waychunas, G.A.; Fuller, C.C.; Rea, B.A.; Davis, J.A.

1996-01-01

Wide angle X-ray scattering (WAXS) measurements have been made on a suite of "two-line" ferrihydrite (FHY2) samples containing varying amounts of coprecipitated arsenate. Samples prepared at pH 8 with counter ions chloride, nitrate, and a mixture of both also were examined. The raw WAXS scattering functions show that "two-line" ferrihydrite actually has a large number of non-Bragg (i.e., diffuse scattering) maxima up to our observation limit of 16 A??-1. The type of counter ion used during synthesis produces no significant change in this function. In unarsenated samples, Radial Distribution Functions (RDFs) produced from the scattering functions show a well-defined Fe-O peak at 2.02 A?? in excellent agreement with the mean distance of 2.01 A?? from extended X-ray absorption fine structure (EXAFS) analysis. The area under the Fe-O peak is consistent with only octahedral oxygen coordination about iron, and an iron coordination about oxygen of 2.2, in agreement with the EXAFS results, the sample composition, and XANES measurements. The second peak observed in the RDFs is clearly divided into two populations of correlations, at 3.07 and 3.52 A??, respectively. These distances are close to the EXAFS-derived Fe-Fe subshell distances of 3.02-3.05 and 3.43-3.46 A??, respectively, though this is misleading as the RDF peaks also include contributions from O-Fe and O-O correlations. Simulated RDFs of the FeOOH polymorphs indicate how the observed RDF structure relates to the EXAFS pair-correlation function, and allow comparisons with an ordered ferrihydrite structure. The effect of increasing arsenate content is dramatic, as the RDF peaks are progressively smeared out, indicating a wider range of interatomic distances even at moderate surface coverages, and a loss of longer range correlations. At an As/Fe ratio of 0.68, the surface saturation level of arsenate, the RDF shows little order beyond what would be expected from small pieces of dioctahedral Fe oxyhydroxyl chains or small "sheet" units. Analysis of the first RDF peak yields components due to As-O and Fe-O correlations. As the As-O component at 1.67 A?? increases in size, the Fe-O component decreases, reflecting a decrease in Fe coordination about the average oxygen. This reduction is consistent with a decrease in mean crystallite size as suggested by EXAFS studies. Analysis of the second RDF peak components shows the progressive decrease in Fe-Fe correlations, and the enhancement of As-Fe correlations, as arsenate level increases. Comparison of the experimental RDF from coprecipitated arsenate-saturated FHY2 with simulated RDFs of model iron oxyhydroxyl structures further constrains possible sizes and geometry for the precipitates, and is consistent with sorbed complexes of the bidentate binuclear (apical oxygen sharing) type.

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

NASA Astrophysics Data System (ADS)

Samolyuk, G. D.; Osetsky, Y. N.; Stoller, R. E.

2015-10-01

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascade production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (∼0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential. The Gao-Weber potential appears to give a more realistic description of cascade dynamics in SiC, but still has some shortcomings when the defect migration barriers are compared to the ab initio results.

Probing the interface of doped isotopically mixed helium droplets by the directional anisotropy of interatomic Coulombic decay.

PubMed

Kryzhevoi, Nikolai V; Mateo, David; Pi, Martí; Barranco, Manuel; Cederbaum, Lorenz S

2013-11-07

Interatomic Coulombic decay (ICD) represents an efficient electronic relaxation mechanism of an ionized or an excited system embedded in an environment. The type of this environment and its size have a great impact on the ICD performance. It is stressed that ICD is sensitive to the arrangement of neighboring atoms when the initially created vacancy has a polarization direction. This is demonstrated in the present paper for the case of a 3p-ionized Ca surrounded by He atoms. Useful explicit expressions are derived for the ICD widths which show that the neighbors located along the polarization direction of the ionized orbital have the largest contribution to the ICD rate. By comparison with ab initio results for small clusters, we also show that in a helium environment, the pairwise approximation represents a reliable approach for computing ICD widths. Using this approximation and the density distribution of the helium atoms obtained within density functional theory, we explore ICD in large isotopically mixed helium droplets doped with Ca. A special emphasis is given to the difference between the ICD widths for the Ca3p orbitals directed perpendicular and parallel to the droplet surface. Depending on the size and isotopic composition of the droplet, Ca resides in the interfacial layer between the (4)He core and the (3)He outer shell. Hence, ICD studies in these droplets may provide valuable information on the properties of this interface.

On the role of structure-dynamic relationship in determining the excess entropy of mixing and chemical ordering in binary square-well liquid alloys

NASA Astrophysics Data System (ADS)

Lalneihpuii, R.; Shrivastava, Ruchi; Mishra, Raj Kumar

2018-05-01

Using statistical mechanical model with square-well (SW) interatomic potential within the frame work of mean spherical approximation, we determine the composition dependent microscopic correlation functions, interdiffusion coefficients, surface tension and chemical ordering in Ag-Cu melts. Further Dzugutov universal scaling law of normalized diffusion is verified with SW potential in binary mixtures. We find that the excess entropy scaling law is valid for SW binary melts. The partial and total structure factors in the attractive and repulsive regions of the interacting potential are evaluated and then Fourier transformed to get partial and total radial distribution functions. A good agreement between theoretical and experimental values for total structure factor and the reduced radial distribution function are observed, which consolidates our model calculations. The well-known Bhatia-Thornton correlation functions are also computed for Ag-Cu melts. The concentration-concentration correlations in the long wavelength limit in liquid Ag-Cu alloys have been analytically derived through the long wavelength limit of partial correlation functions and apply it to demonstrate the chemical ordering and interdiffusion coefficients in binary liquid alloys. We also investigate the concentration dependent viscosity coefficients and surface tension using the computed diffusion data in these alloys. Our computed results for structure, transport and surface properties of liquid Ag-Cu alloys obtained with square-well interatomic interaction are fully consistent with their corresponding experimental values.

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

NASA Astrophysics Data System (ADS)

Thompson, A. P.; Swiler, L. P.; Trott, C. R.; Foiles, S. M.; Tucker, G. J.

2015-03-01

We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

Heat conduction in diatomic chains with correlated disorder

NASA Astrophysics Data System (ADS)

Savin, Alexander V.; Zolotarevskiy, Vadim; Gendelman, Oleg V.

2017-01-01

The paper considers heat transport in diatomic one-dimensional lattices, containing equal amounts of particles with different masses. Ordering of the particles in the chain is governed by single correlation parameter - the probability for two neighboring particles to have the same mass. As this parameter grows from zero to unity, the structure of the chain varies from regular staggering chain to completely random configuration, and then - to very long clusters of particles with equal masses. Therefore, this correlation parameter allows a control of typical cluster size in the chain. In order to explore different regimes of the heat transport, two interatomic potentials are considered. The first one is an infinite potential wall, corresponding to instantaneous elastic collisions between the neighboring particles. In homogeneous chains such interaction leads to an anomalous heat transport. The other one is classical Lennard-Jones interatomic potential, which leads to a normal heat transport. The simulations demonstrate that the correlated disorder of the particle arrangement does not change the convergence properties of the heat conduction coefficient, but essentially modifies its value. For the collision potential, one observes essential growth of the coefficient for fixed chain length as the limit of large homogeneous clusters is approached. The thermal transport in these models remains superdiffusive. In the Lennard-Jones chain the effect of correlation appears to be not monotonous in the limit of low temperatures. This behavior stems from the competition between formation of long clusters mentioned above, and Anderson localization close to the staggering ordered state.

Infrared spectra of some sulfides and their analogs of binary composition in the long-wave region

NASA Technical Reports Server (NTRS)

Povarennykh, A. S.; Sidorenko, G. A.; Solntseva, L. S.; Solntsev, B. P.

1981-01-01

The far infrared spectra (500-60/cm) of some simple sulfides and their analogs were studied. In all, 22 minerals with different structure types were investigated, out of which 14 are sulfides (galena, alabandite, pyrrhotite, sphalerite, wurtzite, cinnabar, realgar, orpiment, getchelite antimonite, molybdenite, pyrite, marcasite and heazlewoodite) 6 arsenides (niccolite, domeykite, arsenopyrite, lollingite, rammelsbergite and skutterudite), one telluride (tetradymite) and native arsenic. The main bands of infrared absorption spectra of the minerals are compared with the relative strength of the interatomic bonds and their interpretation is given.

Dislocation core structures of tungsten with dilute solute hydrogen

NASA Astrophysics Data System (ADS)

Wang, Yinan; Li, Qiulin; Li, Chengliang; Shu, Guogang; Xu, Ben; Liu, Wei

2017-12-01

In this paper, a combination of quantum mechanical and interatomic potential-based atomistic calculations are used to predict the core structures of screw and edge dislocations in tungsten in the presence of a particular concentration of hydrogen atoms. These configurations of the core structures are the results of two competing energies: the interaction between the partial dislocations and the corresponding generalized stacking fault energy in between the two partial dislocations, which are presented in this work. With this, we can precisely predict the configurations of the hydrogen-doped dislocation core structures.

Multiscale Modeling of Non-crystalline Ceramics (Glass) (FY11)

DTIC Science & Technology

2012-01-01

interatomic potential model for oxides, silicates, and silica-based glasses. J. Phys. Chem. B 2006, 110 (24), 11780–11795. 9. van Beest , B. W. H.; Kramer, G. J...DIRECTOR US ARMY RESEARCH LAB IMNE ALC HRR 2800 POWDER MILL RD ADELPHI MD 20783-1197 1 DIRECTOR US ARMY RESEARCH LAB RDRL CIO LL 2800 POWDER MILL RD...ADELPHI MD 20783-1197 1 DIRECTOR US ARMY RESEARCH LAB RDRL CIO MT 2800 POWDER MILL RD ADELPHI MD 20783-1197 1 DIRECTOR US ARMY RESEARCH LAB RDRL D 2800

AB Initi Molecular Dynamics Simulation of the Amorphous Structure of Ca-Mg-Cu and Ca-Mg-Zn Alloys (Postprint)

DTIC Science & Technology

2012-09-26

characteristic coordination poly- hedra present in an amorphous structure.[23,42] A coor- dination polyhedron is defined as an i-centered cluster with...vertices at the first-shell atom positions and edges coinciding with the interatomic bonds in the first shell.[45] Each coordination polyhedron can be...assigned a Voronoi signature (n3, n4, n5, n6), where nm is the number of vertices common to m polyhedron faces (or edges).[46] m is also called the

Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.

PubMed

Olechnovic, Kliment; Margelevicius, Mindaugas; Venclovas, Ceslovas

2011-03-01

We present Voroprot, an interactive cross-platform software tool that provides a unique set of capabilities for exploring geometric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as the additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes, interatomic contact surfaces, solvent accessible surfaces, pockets and cavities inside protein structure. Voroprot is available for Windows, Linux and Mac OS X operating systems and can be downloaded from http://www.ibt.lt/bioinformatics/voroprot/.

Enhanced squeezing of a collective spin via control of its qudit subsystems.

PubMed

Norris, Leigh M; Trail, Collin M; Jessen, Poul S; Deutsch, Ivan H

2012-10-26

Unitary control of qudits can improve the collective spin squeezing of an atomic ensemble. Preparing the atoms in a state with large quantum fluctuations in magnetization strengthens the entangling Faraday interaction. The resulting increase in interatomic entanglement can be converted into metrologically useful spin squeezing. Further control can squeeze the internal atomic spin without compromising entanglement, providing an overall multiplicative factor in the collective squeezing. We model the effects of optical pumping and study the tradeoffs between enhanced entanglement and decoherence. For realistic parameters we see improvements of ~10 dB.

g_contacts: Fast contact search in bio-molecular ensemble data

NASA Astrophysics Data System (ADS)

Blau, Christian; Grubmuller, Helmut

2013-12-01

Short-range interatomic interactions govern many bio-molecular processes. Therefore, identifying close interaction partners in ensemble data is an essential task in structural biology and computational biophysics. A contact search can be cast as a typical range search problem for which efficient algorithms have been developed. However, none of those has yet been adapted to the context of macromolecular ensembles, particularly in a molecular dynamics (MD) framework. Here a set-decomposition algorithm is implemented which detects all contacting atoms or residues in maximum O(Nlog(N)) run-time, in contrast to the O(N2) complexity of a brute-force approach. Catalogue identifier: AEQA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQA_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 8945 No. of bytes in distributed program, including test data, etc.: 981604 Distribution format: tar.gz Programming language: C99. Computer: PC. Operating system: Linux. RAM: ≈Size of input frame Classification: 3, 4.14. External routines: Gromacs 4.6[1] Nature of problem: Finding atoms or residues that are closer to one another than a given cut-off. Solution method: Excluding distant atoms from distance calculations by decomposing the given set of atoms into disjoint subsets. Running time:≤O(Nlog(N)) References: [1] S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J.C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and Erik Lindahl, Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics 29 (7) (2013).

Local Structure Analysis and Interface Layer Effect of Phase-Change Recording Material Using Actual Media

NASA Astrophysics Data System (ADS)

Nakai, Tsukasa; Yoshiki, Masahiko; Satoh, Yasuhiro; Ashida, Sumio

2008-07-01

The influences of the interface layer on crystal structure, the local atomic arrangement, and the electronic and chemical structure of a GeBiTe (GBT) phase-change recording material have been investigated using X-ray diffraction (XRD), X-ray absorption fine structure (XAFS), and hard X-ray photoelectron spectroscopy (HX-PES) methods using actual rewritable high-speed HD DVD media without special sample processing. XRD results showed that the crystal structure of laser-crystallized GBT alloy in the actual HD DVD media is the same as that of GeSbTe (GST) alloy, which has a NaCl-type structure. No differences between samples with and without interface layers were found. The lattice constant of GBT is larger than that of GST. Bi increases the lattice constant of GST with respect to the Bi substitution ratio of Sb. According to HX-PES, the DOS of in the recording film amorphous state with an interface layer is closer to that of the crystalline state than the recording film without an interface layer. From XAFS results, clear differences between amorphous (Amo.) and crystalline states (Cry.) were observed. The interatomic distance of amorphous recording material is independent of the existence of an interface layer. On the other hand, the coordination number varied slightly due to the presence of the interface layer. Therefore, the electronic state of the recording layer changes because of the interface layer, although the local structure changes only slightly except for the coordination number. Combining these results, we conclude that the interface layer changes the electronic state of the recording layer and promotes crystallization, but only affects the local structure of the atomic arrangement slightly.

Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation

PubMed Central

Moritsugu, Kei; Koike, Ryotaro; Yamada, Kouki; Kato, Hiroaki; Kidera, Akinori

2015-01-01

Molecular dynamics (MD) simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a “Motion Tree”, to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC) transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory. PMID:26148295

X-Ray Absorption Near Edge Structure And Extended X-Ray Absorption Fine Structure Analysis of Standards And Biological Samples Containing Mixed Oxidation States of Chromium(III) And Chromium(VI)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parsons, J.G.; Dokken, K.; Peralta-Videa, J.R.

For the first time a method has been developed for the extended X-ray absorption fine structure (EXAFS) data analyses of biological samples containing multiple oxidation states of chromium. In this study, the first shell coordination and interatomic distances based on the data analysis of known standards of potassium chromate (Cr(VI)) and chromium nitrate hexahydrate (Cr(III)) were investigated. The standards examined were mixtures of the following molar ratios of Cr(VI):Cr(III), 0:1, 0.25:0.75, 0.5:0.5, 0.75:0.25, and 1:0. It was determined from the calibration data that the fitting error associated with linear combination X-ray absorption near edge structure (LC-XANES) fittings was approximately {+-}10%more » of the total fitting. The peak height of the Cr(VI) pre-edge feature after normalization of the X-ray absorption (XAS) spectra was used to prepare a calibration curve. The EXAFS fittings of the standards were also investigated and fittings to lechuguilla biomass samples laden with different ratios of Cr(III) and Cr(VI) were performed as well. An excellent agreement between the XANES data and the data presented in the EXAFS spectra was observed. The EXFAS data also presented mean coordination numbers directly related to the ratios of the different chromium oxidation states in the sample. The chromium oxygen interactions had two different bond lengths at approximately 1.68 and 1.98 {angstrom} for the Cr(VI) and Cr(III) in the sample, respectively.« less

Dynamic Structure of Bombolitin II Bound to Lipid Bilayers as Revealed by Solid-state NMR and Molecular-Dynamics Simulation

PubMed Central

Toraya, Shuichi; Javkhlantugs, Namsrai; Mishima, Daisuke; Nishimura, Katsuyuki; Ueda, Kazuyoshi; Naito, Akira

2010-01-01

Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membranes were determined by solid-state 31P and 13C NMR spectroscopy. 31P NMR spectra showed that BLT2-DPPC membranes were disrupted into small particles below the gel-to-liquid crystalline phase transition temperature (Tc) and fused to form a magnetically oriented vesicle system where the membrane surface is parallel to the magnetic fields above the Tc. 13C NMR spectra of site-specifically 13C-labeled BLT2 at the carbonyl carbons were observed and the chemical shift anisotropies were analyzed to determine the dynamic structure of BLT2 bound to the magnetically oriented vesicle system. It was revealed that the membrane-bound BLT2 adopted an α-helical structure, rotating around the membrane normal with the tilt angle of the helical axis at 33°. Interatomic distances obtained from rotational-echo double-resonance experiments further showed that BLT2 adopted a straight α-helical structure. Molecular dynamics simulation performed in the BLT2-DPPC membrane system showed that the BLT2 formed a straight α-helix and that the C-terminus was inserted into the membrane. The α-helical axis is tilted 30° to the membrane normal, which is almost the same as the value obtained from solid-state NMR. These results suggest that the membrane disruption induced by BLT2 is attributed to insertion of BLT2 into the lipid bilayers. PMID:21081076

Calculation of binary magnetic properties and potential energy curve in xenon dimer: second virial coefficient of (129)Xe nuclear shielding.

PubMed

Hanni, Matti; Lantto, Perttu; Runeberg, Nino; Jokisaari, Jukka; Vaara, Juha

2004-09-22

Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift delta, the anisotropy of the shielding tensor Delta sigma, the nuclear quadrupole coupling tensor component along the internuclear axis chi( parallel ), and the spin-rotation constant C( perpendicular ) are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction (CP) method. Electron correlation effects are systematically studied via the Hartree-Fock, complete active space self-consistent field, second-order Møller-Plesset many-body perturbation, and coupled-cluster singles and doubles (CCSD) theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD(CP) binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of delta, Delta sigma, chi (parallel), and C (perpendicular) in the nu=0, J=0 rovibrational ground state of the xenon dimer are also reported.

Hydrostatic pressure and temperature effect on the Raman spectra of the molecular crystal 2-amine-1,3,4-thiadiazole

NASA Astrophysics Data System (ADS)

de Toledo, T. A.; da Costa, R. C.; Bento, R. R. F.; Pizani, P. S.

2018-03-01

The structural, thermal and vibrational properties of the molecular crystal 2-amine-1,3,4-thiadiazole (ATD) were investigated combining X-ray diffraction, infrared spectroscopy, Raman scattering (in solid and in solution) and thermal analysis as experimental techniques and first principle calculations based on density functional theory using PZ, BLYP in condensed-phase and B3LYP/cc-pVTZ in isolated molecule methods. The structural stability and phonon anharmonicity were also studied using Raman spectroscopy at different temperatures and hydrostatic pressures. A reasonable agreement was obtained between calculated and experimental results. The main difference between experimental and computed structural and vibrational spectra occurred in the intermolecular bond distance Nsbnd H⋯N and stretching modes of NH2. The vibrational spectra were interpreted and assigned based on group theory and functional group analysis assisted by theoretical results, which led to a more comprehensive knowledge about external and internal modes at different thermodynamic conditions. As temperature increases, it was observed the line-width increases and red-shifts, indicating a phonon anharmonicity without a temperature-induced phase transition in the range 10-413 K. However, ATD crystal undergoes a phase transition in the temperature range 413-475 K, as indicated by thermal analysis curve and Raman spectra. Furthermore, increasing pressure from ambient to 3.1 GPa, it was observed the splitting of the external Raman bands centered at 122 cm-1 (at 0.2 GPa), 112 cm-1 (1.1 GPa), 93 cm-1 (2.4 GPa) in two components as well as the appearance of new band near 50 cm-1 at 1.1 GPa, indicating a possible phase-transition. The blue-shift of the Raman bands was associated to anharmonicity of the interatomic potential caused by unit cell contraction.

Sparkle/AM1 Parameters for the Modeling of Samarium(III) and Promethium(III) Complexes.

PubMed

Freire, Ricardo O; da Costa, Nivan B; Rocha, Gerd B; Simas, Alfredo M

2006-01-01

The Sparkle/AM1 model is extended to samarium(III) and promethium(III) complexes. A set of 15 structures of high crystallographic quality (R factor < 0.05 Å), with ligands chosen to be representative of all samarium complexes in the Cambridge Crystallographic Database 2004, CSD, with nitrogen or oxygen directly bonded to the samarium ion, was used as a training set. In the validation procedure, we used a set of 42 other complexes, also of high crystallographic quality. The results show that this parametrization for the Sm(III) ion is similar in accuracy to the previous parametrizations for Eu(III), Gd(III), and Tb(III). On the other hand, promethium is an artificial radioactive element with no stable isotope. So far, there are no promethium complex crystallographic structures in CSD. To circumvent this, we confirmed our previous result that RHF/STO-3G/ECP, with the MWB effective core potential (ECP), appears to be the most efficient ab initio model chemistry in terms of coordination polyhedron crystallographic geometry predictions from isolated lanthanide complex ion calculations. We thus generated a set of 15 RHF/STO-3G/ECP promethium complex structures with ligands chosen to be representative of complexes available in the CSD for all other trivalent lanthanide cations, with nitrogen or oxygen directly bonded to the lanthanide ion. For the 42 samarium(III) complexes and 15 promethium(III) complexes considered, the Sparkle/AM1 unsigned mean error, for all interatomic distances between the Ln(III) ion and the ligand atoms of the first sphere of coordination, is 0.07 and 0.06 Å, respectively, a level of accuracy comparable to present day ab initio/ECP geometries, while being hundreds of times faster.

Density, structure, and dynamics of water: The effect of van der Waals interactions

NASA Astrophysics Data System (ADS)

Wang, Jue; Román-Pérez, G.; Soler, Jose M.; Artacho, Emilio; Fernández-Serra, M.-V.

2011-01-01

It is known that ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions, based on the generalized gradient approximation (GGA) to density functional theory (DFT), with commonly used functionals fail to produce structural and diffusive properties in reasonable agreement with experiment. This is true for canonical, constant temperature simulations where the density of the liquid is fixed to the experimental density. The equilibrium density, at ambient conditions, of DFT water has recently been shown by Schmidt et al. [J. Phys. Chem. B, 113, 11959 (2009)] to be underestimated by different GGA functionals for exchange and correlation, and corrected by the addition of interatomic pair potentials to describe van der Waals (vdW) interactions. In this contribution we present a DFT-AIMD study of liquid water using several GGA functionals as well as the van der Waals density functional (vdW-DF) of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. As expected, we find that the density of water is grossly underestimated by GGA functionals. When a vdW-DF is used, the density improves drastically and the experimental diffusivity is reproduced without the need of thermal corrections. We analyze the origin of the density differences between all the functionals. We show that the vdW-DF increases the population of non-H-bonded interstitial sites, at distances between the first and second coordination shells. However, it excessively weakens the H-bond network, collapsing the second coordination shell. This structural problem is partially associated to the choice of GGA exchange in the vdW-DF. We show that a different choice for the exchange functional is enough to achieve an overall improvement both in structure and diffusivity.

Magnetic behavior of R2Fe14B hydrides (R = Gd, Tb, Dy, Ho and Er)

NASA Astrophysics Data System (ADS)

Zhang, L. Y.; Pourarian, F.; Wallace, W. E.

1988-01-01

R 2Fe 14B systems, with R = Gd, Tb, By, HoandEr were hydrogenated to the composition R 2Fe 14BH x where x ranges from 3.7 to 5.4. The pressure-composition isotherms (PCIs) of the hydrides showed only a solid solution behavior. No plateau pressure region was observed between room temperature and 300° C and at pressures down to 10 -2 atm. The absorbed hydrogen leads to an increase of 2.6 to 3.4% in unit cell volume, without a change in crystal structure. Magnetic characteristics of the present compounds were investigated over the temperature range 4.2 to 1100 K and at applied field up to 20 kOe. Saturation magnetization, Ms, and magnetic ordering temperature, Tc, were enhanced upon hydrogenation. Tc, is found to be dependent on the hydriding composition. Hydrogen induces a spin-reorientation effect (SR) in Gd- and Dy-containing compounds, while it has a marked influence in raising the spin-reorientation temperature, TSR, in the Er 2Fe 14B compound. The hydride involving Tb appears to remain uniaxial to the lowest temperature studied. In all cases the anisotropy fields, HA/' were significally reduced by hydrogen absorption. These varied magnetic behaviors can be ascribed to the effects: (1) variations in the interatomic distances, (2) strengthening the 3d-3d and weakening the 4f-3d exchange interactions and (3) the interstitial site occupations of hydrogen in the lattice. The spin-reorientation phenomena observed for Gd 2Fe 14BH x suggest that there is competition among the 6 Fe sublattices in regard to the sign and temperature coefficient of anisotropy.

A cross-polarization based rotating-frame separated-local-field NMR experiment under ultrafast MAS conditions

NASA Astrophysics Data System (ADS)

Zhang, Rongchun; Damron, Joshua; Vosegaard, Thomas; Ramamoorthy, Ayyalusamy

2015-01-01

Rotating-frame separated-local-field solid-state NMR experiments measure highly resolved heteronuclear dipolar couplings which, in turn, provide valuable interatomic distances for structural and dynamic studies of molecules in the solid-state. Though many different rotating-frame SLF sequences have been put forth, recent advances in ultrafast MAS technology have considerably simplified pulse sequence requirements due to the suppression of proton-proton dipolar interactions. In this study we revisit a simple two-dimensional 1H-13C dipolar coupling/chemical shift correlation experiment using 13C detected cross-polarization with a variable contact time (CPVC) and systematically study the conditions for its optimal performance at 60 kHz MAS. In addition, we demonstrate the feasibility of a proton-detected version of the CPVC experiment. The theoretical analysis of the CPVC pulse sequence under different Hartmann-Hahn matching conditions confirms that it performs optimally under the ZQ (w1H - w1C = ±wr) condition for polarization transfer. The limits of the cross polarization process are explored and precisely defined as a function of offset and Hartmann-Hahn mismatch via spin dynamics simulation and experiments on a powder sample of uniformly 13C-labeled L-isoleucine. Our results show that the performance of the CPVC sequence and subsequent determination of 1H-13C dipolar couplings are insensitive to 1H/13C frequency offset frequency when high RF fields are used on both RF channels. Conversely, the CPVC sequence is quite sensitive to the Hartmann-Hahn mismatch, particularly for systems with weak heteronuclear dipolar couplings. We demonstrate the use of the CPVC based SLF experiment as a tool to identify different carbon groups, and hope to motivate the exploration of more sophisticated 1H detected avenues for ultrafast MAS.

The calculated magnetic, electronic and thermodynamic properties of Ce{sub 3}Co{sub 29}Si{sub 4}B{sub 10} compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huo, Jin-Rong; Wang, Xiao-Xu; Cloud Computing Department, Beijing Computing Center, Beijing 100084

2016-05-15

The magnetic moment, lattice parameter and atom fraction coordinates for Ce{sub 3}Co{sub 29}Si{sub 4}B{sub 10} are calculated by the first-principles GGA+U method, and the results indicate that the calculated and experimental values are basically accordant when U=2.6 eV. We study the interaction effect and orbital hybridization between Co and Ce atoms. The projected density of states at U=2.6 eV which provided by Co-2c, Ce-2b and Ce-4d sites are contrasted with else U values. Meanwhile the electron density of states for different sites and the distance between various atoms are exhibited. In addition, the thermodynamic properties of Ce{sub 3}Co{sub 29}Si{sub 4}B{submore » 10} are evaluated by using a series of interatomic pair potentials. - Graphical abstract: Change of the total magnetic moment for Ce{sub 3}Co{sub 29}Si{sub 4}B{sub 10} along with the value of U. There is a sharply decline of the curve at U=2.6 eV and, at the moment, the total magnetic moment of the compound have a good agreement with the experimental data. - Highlights: • We research of quaternary rare earth and transition metal compounds. • We perform the calculation of magnetic moment and electronic structure by GGA+U method. • The orbital hybridization between Co and Ce atoms is displayed and analyzed. • Show the plot of projected density of states for different sites more clearly. • Calculate the thermodynamic property of rare-earth transition metal compound.« less

Application of x-ray absorption fine structure (XAFS) to local-order analysis in Fe-Cr maghemite-like materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montero-Cabrera, M. E., E-mail: elena.montero@cimav.edu.mx; Fuentes-Cobas, L. E.; Macías-Ríos, E.

2015-07-23

The maghemite-like oxide system γ-Fe{sub 2-x}Cr{sub x}O{sub 3} (x=0.75, 1 and 1.25) was studied by X-ray absorption fine structure (XAFS) and by synchrotron radiation X-ray diffraction (XRD). Measurements were performed at the Stanford Synchrotron Radiation Lightsource at room temperature, at beamlines 2-1, 2-3 and 4-3. High-resolution XRD patterns were processed by means of the Rietveld method. In cases of atoms being neighbors in the Periodic Table, the order/disorder degree of the considered solutions is indiscernible by “normal” (absence of “anomalous scattering”) diffraction experiments. Thus, maghemite-like materials were investigated by XAFS in both Fe and Cr K-edges to clarify, via short-rangemore » structure characterization, the local ordering of the investigated system. Athena and Artemis graphic user interfaces for IFEFFIT and FEFF8.4 codes were employed for XAFS spectra interpretation. Pre-edge decomposition and theoretical modeling of X-ray absorption near edge structure (XANES) transitions were performed. By analysis of the Cr K-edge XANES, it has been confirmed that Cr is located in an octahedral environment. Fitting of the extended X-ray absorption fine structure (EXAFS) spectra was performed under the consideration that the central atom of Fe is allowed to occupy octa- and tetrahedral positions, while Cr occupies only octahedral ones. Coordination number of neighboring atoms, interatomic distances and their quadratic deviation average were determined for x=1, by fitting simultaneously the EXAFS spectra of both Fe and Cr K-edges. The results of fitting the experimental spectra with theoretical standards showed that the cation vacancies tend to follow a regular pattern within the structure of the iron-chromium maghemite (FeCrO{sub 3})« less

Dipole-dipole resonance line shapes in a cold Rydberg gas

NASA Astrophysics Data System (ADS)

Richards, B. G.; Jones, R. R.

2016-04-01

We have explored the dipole-dipole mediated, resonant energy transfer reaction, 32 p3 /2+32 p3 /2→32 s +33 s , in an ensemble of cold 85Rb Rydberg atoms. Stark tuning is employed to measure the population transfer probability as a function of the total electronic energy difference between the initial and final atom-pair states over a range of Rydberg densities, 2 ×108≤ρ ≤3 ×109 cm-3. The observed line shapes provide information on the role of beyond nearest-neighbor interactions, the range of Rydberg atom separations, and the electric field inhomogeneity in the sample. The widths of the resonance line shapes increase approximately linearly with the Rydberg density and are only a factor of 2 larger than expected for two-body, nearest-neighbor interactions alone. These results are in agreement with the prediction [B. Sun and F. Robicheaux, Phys. Rev. A 78, 040701(R) (2008), 10.1103/PhysRevA.78.040701] that beyond nearest-neighbor exchange interactions should not influence the population transfer process to the degree once thought. At low densities, Gaussian rather than Lorentzian line shapes are observed due to electric field inhomogeneities, allowing us to set an upper limit for the field variation across the Rydberg sample. At higher densities, non-Lorentzian, cusplike line shapes characterized by sharp central peaks and broad wings reflect the random distribution of interatomic distances within the magneto-optical trap (MOT). These line shapes are well reproduced by an analytic expression derived from a nearest-neighbor interaction model and may serve as a useful fingerprint for characterizing the position correlation function for atoms within the MOT.

Organic electrolyte-based rechargeable zinc-ion batteries using potassium nickel hexacyanoferrate as a cathode material

NASA Astrophysics Data System (ADS)

Chae, Munseok S.; Heo, Jongwook W.; Kwak, Hunho H.; Lee, Hochun; Hong, Seung-Tae

2017-01-01

This study demonstrates an organic electrolyte-based rechargeable zinc-ion battery (ZIB) using Prussian blue (PB) analogue potassium nickel hexacyanoferrate K0.86Ni[Fe(CN)6]0.954(H2O)0.766 (KNF-086) as the cathode material. KNF-086 is prepared via electrochemical extraction of potassium ions from K1.51Ni[Fe(CN)6]0.954(H2O)0.766 (KNF-151). The cell is composed of a KNF-086 cathode, a zinc metal anode, and a 0.5 M Zn(ClO4)2 acetonitrile electrolyte. This cell shows a reversible discharge capacity of 55.6 mAh g-1 at 0.2 C rate with the discharge voltage at 1.19 V (vs. Zn2+/Zn). As evidenced by Fourier electron density analysis with powder XRD data, the zinc-inserted phase is confirmed as Zn0.32K0.86Ni[Fe(CN)6]0.954(H2O)0.766 (ZKNF-086), and the position of the zinc ion in ZKNF-086 is revealed as the center of the large interstitial cavities of the cubic PB. Compared to KNF-086, ZKNF-086 exhibits a decreased unit cell parameter (0.9%) and volume (2.8%) while the interatomic distance of d(Fe-C) increased (from 1.84 to 1.98 Å), and the oxidation state of iron decreases from 3 to 2.23. The organic electrolyte system provides higher zinc cycling efficiency (>99.9%) than the aqueous system (ca. 80%). This result demonstrates an organic electrolyte-based ZIB, and offers a crucial basis for understanding the electrochemical intercalation chemistry of zinc ions in organic electrolytes.

Ab initio based study of the ArO- photoelectron spectra: Selectivity of spin-orbit transitions

NASA Astrophysics Data System (ADS)

Buchachenko, A. A.; Jakowski, Jacek; Chałasiński, Grzegorz; Szczȩśniak, M. M.; Cybulski, S. M.

2000-04-01

A combined ab initio atoms-in-molecule approach was implemented to model the photoelectron spectra of the ArO- anion. The lowest adiabatic states of Σ and Π symmetry of ArO and ArO- were investigated using the fourth-order Møller-Plessett perturbation theory including bond functions. The total energies were dissected into electrostatic, exchange, induction, and dispersion components. The complex of Ar with atomic oxygen is only weakly bound, primarily by dispersion interaction. The Π state possesses a deeper minimum (Re=3.4Å,De=380μEh) than the Σ state (Re=3.8Å,De=220μEh). In contrast, the anion complex is fairly strongly bound, primarily by ion-induced dipole induction forces, and the Σ state possesses a deeper minimum at shorter interatomic distances (Re=3.02Å,De=3600μEh) than the Π state (Re=3.35Å,De=2400μEh). The Σ-Π splittings in both systems are mainly due to differences in the exchange repulsion terms. Atoms-in-molecule models were used to account for the spin-orbit interaction, and to generate adiabatic relativistic potentials and wave functions. Collisional properties, diffusion, and mobility coefficients of O and O- in Ar, and absolute total Ar+O scattering cross sections, were calculated and found to agree well with the available experimental data. The photoelectron spectra were simulated within vibronic model, and were found in excellent agreement with the experimental measurements. The bimodal electron kinetic energy distribution was shown to stem from the strong selectivity of spin-orbit transitions, which split into two dense groups, depending on the initial electronic state of the anion. The latter feature cannot be described without explicit consideration of electronic intensity factor.

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Aidan P.; Swiler, Laura P.; Trott, Christian R.

2015-03-15

Here, we present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1].more » The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.« less

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, A.P., E-mail: athomps@sandia.gov; Swiler, L.P., E-mail: lpswile@sandia.gov; Trott, C.R., E-mail: crtrott@sandia.gov

2015-03-15

We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. Themore » SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.« less

Nitroxoline Molecule: Planar or Not? A Story of Battle between π-π Conjugation and Interatomic Repulsion.

PubMed

Tikhonov, Denis S; Sharapa, Dmitry I; Otlyotov, Arseniy A; Solyankin, Peter M; Rykov, Anatolii N; Shkurinov, Alexander P; Grikina, Olga E; Khaikin, Leonid S

2018-02-15

The conformational properties of the nitro group in nitroxoline (8-hydroxy-5-nitroquinoline, NXN) were investigated in the gas phase by means of gas electron diffraction (GED) and quantum chemical calculations, and also with solid-state analysis performed using terahertz time-domain spectroscopy (THz-TDS). The results of the GED refinement show that in the equilibrium structure the NO 2 group is twisted by angle ϕ = 8 ± 3° with respect to the 8-hydroxyoquinoline plane. This is the result of interatomic repulsion of oxygen in the NO 2 group from the closest hydrogen, which overcomes the energy gain from the π-π conjugation of the nitro group and aromatic system of 8-hydroxyoquinoline. The computation of equilibrium geometry using MP2/cc-pVXZ (X = T, Q) shows a large overestimation of the ϕ value, while DFT with the cc-pVTZ basis set performs reasonably well. On the other hand, DFT computations with double-ζ basis sets yield a planar structure of NXN. The refined potential energy surface of the torsion vibration the of nitro group in the condensed phase derived from the THz-TDS data indicates the NXN molecule to be planar. This result stays in good agreement with the previous X-ray structure determination. The strength of the π-system conjugation for the NO 2 group and 8-hydroxyoquinoline is discussed using NBO analysis, being further supported by comparison of the refined semiexperimental gas-phase structure of NXN from GED with other nitrocompounds.

Nonmetallic electronegativity equalization and point-dipole interaction model including exchange interactions for molecular dipole moments and polarizabilities.

PubMed

Smalø, Hans S; Astrand, Per-Olof; Jensen, Lasse

2009-07-28

The electronegativity equalization model (EEM) has been combined with a point-dipole interaction model to obtain a molecular mechanics model consisting of atomic charges, atomic dipole moments, and two-atom relay tensors to describe molecular dipole moments and molecular dipole-dipole polarizabilities. The EEM has been phrased as an atom-atom charge-transfer model allowing for a modification of the charge-transfer terms to avoid that the polarizability approaches infinity for two particles at infinite distance and for long chains. In the present work, these shortcomings have been resolved by adding an energy term for transporting charges through individual atoms. A Gaussian distribution is adopted for the atomic charge distributions, resulting in a damping of the electrostatic interactions at short distances. Assuming that an interatomic exchange term may be described as the overlap between two electronic charge distributions, the EEM has also been extended by a short-range exchange term. The result is a molecular mechanics model where the difference of charge transfer in insulating and metallic systems is modeled regarding the difference in bond length between different types of system. For example, the model is capable of modeling charge transfer in both alkanes and alkenes with alternating double bonds with the same set of carbon parameters only relying on the difference in bond length between carbon sigma- and pi-bonds. Analytical results have been obtained for the polarizability of a long linear chain. These results show that the model is capable of describing the polarizability scaling both linearly and nonlinearly with the size of the system. Similarly, a linear chain with an end atom with a high electronegativity has been analyzed analytically. The dipole moment of this model system can either be independent of the length or increase linearly with the length of the chain. In addition, the model has been parametrized for alkane and alkene chains with data from density functional theory calculations, where the polarizability behaves differently with the chain length. For the molecular dipole moment, the same two systems have been studied with an aldehyde end group. Both the molecular polarizability and the dipole moment are well described as a function of the chain length for both alkane and alkene chains demonstrating the power of the presented model.

Theoretical study of electron correlation effects in transition metal dimers

NASA Technical Reports Server (NTRS)

Das, G. P.; Jaffe, R. L.

1984-01-01

Introduction of partially localized orbitals is shown to reduce the number of terms needed to describe the bonding in transition metal clusters. Using this formalism, it is possible to compute the various intra- and inter-atomic electron correlation contributions to the bond energy. Calculations demonstrate the relative importance of several kinds of electron correlation terms involving the 3p, 3d, and 4s electrons. Improved interaction potentials are obtained for the dimers V(2) and Cr(2) when additional correlation is added to the CAS SCF results of Walch, Bauschlicher, Roos, and Nelin (1983).

Synchronization of a self-sustained cold-atom oscillator

NASA Astrophysics Data System (ADS)

Heimonen, H.; Kwek, L. C.; Kaiser, R.; Labeyrie, G.

2018-04-01

Nonlinear oscillations and synchronization phenomena are ubiquitous in nature. We study the synchronization of self-oscillating magneto-optically trapped cold atoms to a weak external driving. The oscillations arise from a dynamical instability due the competition between the screened magneto-optical trapping force and the interatomic repulsion due to multiple scattering of light. A weak modulation of the trapping force allows the oscillations of the cloud to synchronize to the driving. The synchronization frequency range increases with the forcing amplitude. The corresponding Arnold tongue is experimentally measured and compared to theoretical predictions. Phase locking between the oscillator and drive is also observed.

Helium Purge Flow Prevention of Atmospheric Contamination of the Cryogenically Cooled Optics of Orbiting Infrared Telescopes: Calculation of He-O Differential Cross Section,

DTIC Science & Technology

1981-06-05

interactions. Aquilanti and coworkers were able to obtain two analytic forms for the interatomic potential --a Lennard - Jones (12, 6) and an exp(a, 6) function...Sec. UI.D 38 ences between the 3R and 3E- potential functions which described the interac- tions of ground-state oxygen and helium atoms. Instead, for...AO-AIOI 152 AEROSPACE CORP EL SEUMOO CA CHEMISTRY AND PHYSICS LAD r/6 17 HELIUM PLRE FLOW PREVENTION OF ATMOSPHERIC CONTAMINATION OF TAR fTCiO )JN81

Virial Coefficients for the Liquid Argon

NASA Astrophysics Data System (ADS)

Korth, Micheal; Kim, Saesun

2014-03-01

We begin with a geometric model of hard colliding spheres and calculate probability densities in an iterative sequence of calculations that lead to the pair correlation function. The model is based on a kinetic theory approach developed by Shinomoto, to which we added an interatomic potential for argon based on the model from Aziz. From values of the pair correlation function at various values of density, we were able to find viral coefficients of liquid argon. The low order coefficients are in good agreement with theoretical hard sphere coefficients, but appropriate data for argon to which these results might be compared is difficult to find.

Evaporation kinetics of Mg2SiO4 crystals and melts from molecular dynamics simulations

NASA Technical Reports Server (NTRS)

Kubicki, J. D.; Stolper, E. M.

1993-01-01

Computer simulations based on the molecular dynamics (MD) technique were used to study the mechanisms and kinetics of free evaporation from crystalline and molten forsterite (i.e., Mg2SiO4) on an atomic level. The interatomic potential employed for these simulations reproduces the energetics of bonding in forsterite and in gas-phase MgO and SiO2 reasonably accurately. Results of the simulation include predicted evaporation rates, diffusion rates, and reaction mechanisms for Mg2SiO4(s or l) yields 2Mg(g) + 20(g) + SiO2(g).

Dark-soliton dynamics in Bose-Einstein condensates at finite temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, B.; Proukakis, N. P.; Barenghi, C. F.

2007-05-15

The dynamics of a dark soliton in an elongated Bose-Einstein condensate is studied at finite temperatures. In addition to accurately reproducing all stages of the decay of the soliton observed in the experiment of Burger et al. [Phys. Rev. Lett. 83, 5198 (1999)], our numerical simulations reveal the existence of an experimentally accessible parameter regime for which phase-imprinted dark solitons can execute at least one full axial oscillation prior to their decay. The dependence of the decay time scale on temperature and initial soliton depth is analyzed and the role of interatomic collisions quantified.

Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

2017-02-01

The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

EON: software for long time simulations of atomic scale systems

NASA Astrophysics Data System (ADS)

Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

2014-07-01

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

Intra- and inter-atomic optical transitions of Fe, Co, and Ni ferrocyanides studied using first-principles many-electron calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watanabe, Shinta, E-mail: s-watanabe@nucl.nagoya-u.ac.jp, E-mail: j-onoe@nucl.nagoya-u.ac.jp; Sawada, Yuki; Nakaya, Masato

We have investigated the electronic structures and optical properties of Fe, Co, and Ni ferrocyanide nanoparticles using first-principles relativistic many-electron calculations. The overall features of the theoretical absorption spectra for Fe, Ni, and Co ferrocyanides calculated using a first-principles many-electron method well reproduced the experimental one. The origins of the experimental absorption spectra were clarified by performing a configuration analysis based on the many-electron wave functions. For Fe ferrocyanide, the experimental absorption peaks originated from not only the charge-transfer transitions from Fe{sup 2+} to Fe{sup 3+} but also the 3d-3d intra-transitions of Fe{sup 3+} ions. In addition, the spin crossovermore » transition of Fe{sup 3+} predicted by the many-electron calculations was about 0.24 eV. For Co ferrocyanide, the experimental absorption peaks were mainly attributed to the 3d-3d intra-transitions of Fe{sup 2+} ions. In contrast to the Fe and Co ferrocyanides, Ni ferrocyanide showed that the absorption peaks originated from the 3d-3d intra-transitions of Ni{sup 3+} ions in a low-energy region, while from both the 3d-3d intra-transitions of Fe{sup 2+} ions and the charge-transfer transitions from Fe{sup 2+} to Ni{sup 3+} in a high-energy region. These results were quite different from those of density-functional theory (DFT) calculations. The discrepancy between the results of DFT calculations and those of many-electron calculations suggested that the intra- and inter-atomic transitions of transition metal ions are significantly affected by the many-body effects of strongly correlated 3d electrons.« less

Analysis of oxygen binding-energy variations for BaO on W

NASA Astrophysics Data System (ADS)

Haas, G. A.; Shih, A.; Mueller, D.; Thomas, R. E.

Interatomic Auger analyses have been made of different forms of BaO layers on W substrates. Variations in Auger spectroscopy energies of the Ba4dBa5pO2p interatomic Auger transition were found to be largely governed by the O2p binding energy of the BaO adsorbate. This was illustrated by comparing results of the Auger data values with values derived from O2p binding energies using ultraviolet photoelectron spectroscopy. Very good agreement was observed not only for the W<100> substrate but also for the W<110> substrate which showed two oxygen-induced electronics state. Variations in binding energy were noted for different states of BaO lattice formation and for different amounts of oxidation, ranging from the transition of Ba to BaO and continuing to the BaO 2 stoichiometry and beyond. Effects were also reported for adsorbate alignment and thermal activation (i.e., reduction) of the oxidized state. An empirical relationship was found suggesting that the more tightly bound the O2p states of the BaO adsorbate were, the lower its work function would be. This link between binding energy and work function was observed to be valid not only for cases of poisoning by oxidation, but held as well during reactivation by the subsequent reduction of the oxide. In addition, this relationship also appeared to predict the low work function obtained through the introduction of substances such as Sc to the BaO-W system. Possible qualitative reasons which might contribute to this are discussed in terms of enhanced dipole effects and shifts in band structure.

Elucidation of the atomic-scale mechanism of the anisotropic oxidation rate of 4H-SiC between the (0001) Si-face and ( 000 1 ¯ ) C-face by using a new Si-O-C interatomic potential

NASA Astrophysics Data System (ADS)

Takamoto, So; Yamasaki, Takahiro; Ohno, Takahisa; Kaneta, Chioko; Hatano, Asuka; Izumi, Satoshi

2018-05-01

Silicon carbide (SiC) is an attractive semiconductor material for applications in power electronic devices. However, fabrication of a high-quality SiC/SiO2 interface has been a challenge. It is well-known that there is a great difference in the oxidation rate between the Si-face and the C-face and that the quality of oxide on the Si-face is greater than that on the C-face. However, the atomistic mechanism of the thermal oxidation of SiC remains to be solved. In this paper, a new Si-O-C interatomic potential was developed to reproduce the kinetics of the thermal oxidation of SiC. Using this newly developed potential, large-scale SiC oxidation simulations at various temperatures were performed. The results showed that the activation energy of the Si-face is much larger than that of the C-face. In the case of the Si-face, a flat and aligned interface structure including Si1+ was created. Based on the estimated activation energies of the intermediate oxide states, it is proposed that the stability of the flat interface structure is the origin of the high activation energy of the oxidation of the Si-face. In contrast, in the case of the C-face, it is found that the Si atom at the interface is easily pulled up by the O atoms. This process generates the disordered interface and decreases the activation energy of the oxidation. It is also proposed that many excess C atoms are created in the case of the C-face.

Abstract ID: 176 Geant4 implementation of inter-atomic interference effect in small-angle coherent X-ray scattering for materials of medical interest.

PubMed

Paternò, Gianfranco; Cardarelli, Paolo; Contillo, Adriano; Gambaccini, Mauro; Taibi, Angelo

2018-01-01

Advanced applications of digital mammography such as dual-energy and tomosynthesis require multiple exposures and thus deliver higher dose compared to standard mammograms. A straightforward manner to reduce patient dose without affecting image quality would be removal of the anti-scatter grid, provided that the involved reconstruction algorithms are able to take the scatter figure into account [1]. Monte Carlo simulations are very well suited for the calculation of X-ray scatter distribution and can be used to integrate such information within the reconstruction software. Geant4 is an open source C++ particle tracking code widely used in several physical fields, including medical physics [2,3]. However, the coherent scattering cross section used by the standard Geant4 code does not take into account the influence of molecular interference. According to the independent atomic scattering approximation (the so-called free-atom model), coherent radiation is indistinguishable from primary radiation because its angular distribution is peaked in the forward direction. Since interference effects occur between x-rays scattered by neighbouring atoms in matter, it was shown experimentally that the scatter distribution is affected by the molecular structure of the target, even in amorphous materials. The most important consequence is that the coherent scatter distribution is not peaked in the forward direction, and the position of the maximum is strongly material-dependent [4]. In this contribution, we present the implementation of a method to take into account inter-atomic interference in small-angle coherent scattering in Geant4, including a dedicated data set of suitable molecular form factor values for several materials of clinical interest. Furthermore, we present scatter images of simple geometric phantoms in which the Rayleigh contribution is rigorously evaluated. Copyright © 2017.

Assessment of Simple Models for Molecular Simulation of Ethylene Carbonate and Propylene Carbonate as Solvents for Electrolyte Solutions.

PubMed

Chaudhari, Mangesh I; Muralidharan, Ajay; Pratt, Lawrence R; Rempe, Susan B

2018-02-12

Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples. The basic results discussed suggest that an empirically parameterized, non-polarizable force field can reproduce experimental structural, thermodynamic, and dielectric properties of EC and PC liquids with acceptable accuracy. More sophisticated force fields might include molecular polarizability and Buckingham-model description of inter-atomic overlap repulsions as extensions to Lennard-Jones models of van der Waals interactions. Simple approaches should be similarly successful also for applications to organic molecular ions in EC/PC solutions, but the important case of Li[Formula: see text] deserves special attention because of the particularly strong interactions of that small ion with neighboring solvent molecules. To treat the Li[Formula: see text] ions in liquid EC/PC solutions, we identify interaction models defined by empirically scaled partial charges for ion-solvent interactions. The empirical adjustments use more basic inputs, electronic structure calculations and ab initio molecular dynamics simulations, and also experimental results on Li[Formula: see text] thermodynamics and transport in EC/PC solutions. Application of such models to the mechanism of Li[Formula: see text] transport in glassy SEI models emphasizes the advantage of long time-scale molecular dynamics studies of these non-equilibrium materials.

Optimal utilization of total elastic scattering cross section data for the determination of interatomic potentials

NASA Technical Reports Server (NTRS)

Bernstein, R. B.; Labudde, R. A.

1972-01-01

The problem of inversion is considered in relation to absolute total cross sections Q(v) for atom-atom collisions and their velocity dependence, and the glory undulations and the transition to high velocity behavior. There is a limit to the amount of information available from Q(v) even when observations of good accuracy (e.g., + or - 0.25%) are in hand over an extended energy range (from thermal energies upward by a factor of greater than 1000 in relative kinetic energy). Methods were developed for data utilization, which take full advantage of the accuracy of the experimental Q(v) measurements.

The Strength of the Metal. Aluminum Oxide Interface

NASA Technical Reports Server (NTRS)

Pepper, S. V.

1984-01-01

The strength of the interface between metals and aluminum oxide is an important factor in the successful operation of devices found throughout modern technology. One finds the interface in machine tools, jet engines, and microelectronic integrated circuits. The strength of the interface, however, should be strong or weak depending on the application. The diverse technological demands have led to some general ideas concerning the origin of the interfacial strength, and have stimulated fundamental research on the problem. Present status of our understanding of the source of the strength of the metal - aluminum oxide interface in terms of interatomic bonds are reviewed. Some future directions for research are suggested.

Atomistic modeling for interfacial properties of Ni-Al-V ternary system

NASA Astrophysics Data System (ADS)

Dong, Wei-ping; Lee, Byeong-Joo; Chen, Zheng

2014-05-01

Interatomic potentials for Ni-Al-V ternary systems have been developed based on the second-nearest-neighbor modified embedded-atom method potential formalism. The potentials can describe various fundamental physical properties of the relevant materials in good agreement with experimental information. The potential is utilized for an atomistic computation of interfacial properties of Ni-Al-V alloys. It is found that vanadium atoms segregate on the γ-fcc/L12 interface and this segregation affects the interfacial properties. The applicability of the atomistic approach to an elaborate alloy design of advanced Ni-based superalloys through the investigation of the effect of alloying elements on interfacial properties is discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Hua; College of Physics and Optoelectronics, Taiyuan University of Technology, Taiyuan 030024; Kioussis, Nicholas, E-mail: nick.kioussis@csun.edu

Using ab initio based calculations, we have calculated the intrinsic lattice thermal conductivity of chiral tellurium. We show that the interplay between the strong covalent intrachain and weak van der Waals interchain interactions gives rise to the phonon band gap between the lower and higher optical phonon branches. The underlying mechanism of the large anisotropy of the thermal conductivity is the anisotropy of the phonon group velocities and of the anharmonic interatomic force constants (IFCs), where large interchain anharmonic IFCs are associated with the lone electron pairs. We predict that tellurium has a large three-phonon scattering phase space that resultsmore » in low thermal conductivity. The thermal conductivity anisotropy decreases under applied hydrostatic pressure.« less

Electrostatic Hellmann-Feynman theorem applied to long-range interatomic forces - The hydrogen molecule.

NASA Technical Reports Server (NTRS)

Steiner, E.

1973-01-01

The use of the electrostatic Hellmann-Feynman theorem for the calculation of the leading term in the 1/R expansion of the force of interaction between two well-separated hydrogen atoms is discussed. Previous work has suggested that whereas this term is determined wholly by the first-order wavefunction when calculated by perturbation theory, the use of the Hellmann-Feynman theorem apparently requires the wavefunction through second order. It is shown how the two results may be reconciled and that the Hellmann-Feynman theorem may be reformulated in such a way that only the first-order wavefunction is required.

A method of solid-solid phase equilibrium calculation by molecular dynamics

NASA Astrophysics Data System (ADS)

Karavaev, A. V.; Dremov, V. V.

2016-12-01

A method for evaluation of solid-solid phase equilibrium curves in molecular dynamics simulation for a given model of interatomic interaction is proposed. The method allows to calculate entropies of crystal phases and provides an accuracy comparable with that of the thermodynamic integration method by Frenkel and Ladd while it is much simpler in realization and less intense computationally. The accuracy of the proposed method was demonstrated in MD calculations of entropies for EAM potential for iron and for MEAM potential for beryllium. The bcc-hcp equilibrium curves for iron calculated for the EAM potential by the thermodynamic integration method and by the proposed one agree quite well.

Final Report for DE-FG02-99ER45795

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, John Warren

The research supported by this grant focuses on atomistic studies of defects, phase transitions, electronic and magnetic properties, and mechanical behaviors of materials. We have been studying novel properties of various emerging nanoscale materials on multiple levels of length and time scales, and have made accurate predictions on many technologically important properties. A significant part of our research has been devoted to exploring properties of novel nano-scale materials by pushing the limit of quantum mechanical simulations, and development of a rigorous scheme to design accurate classical inter-atomic potentials for larger scale atomistic simulations for many technologically important metals and metalmore » alloys.« less

Coupled-resonator waveguide perfect transport single-photon by interatomic dipole-dipole interaction

NASA Astrophysics Data System (ADS)

Yan, Guo-an; Lu, Hua; Qiao, Hao-xue; Chen, Ai-xi; Wu, Wan-qing

2018-06-01

We theoretically investigate single-photon coherent transport in a one-dimensional coupled-resonator waveguide coupled to two quantum emitters with dipole-dipole interactions. The numerical simulations demonstrate that the transmission spectrum of the photon depends on the two atoms dipole-dipole interactions and the photon-atom couplings. The dipole-dipole interactions may change the dip positions in the spectra and the coupling strength may broaden the frequency band width in the transmission spectrum. We further demonstrate that the typical transmission spectra split into two dips due to the dipole-dipole interactions. This phenomenon may be used to manufacture new quantum waveguide devices.

Metal-atom Interactions and Clustering in Organic Semiconductor Systems

NASA Astrophysics Data System (ADS)

Tomita, Yoko; Park, Tea-uk; Nakayama, Takashi

2017-07-01

The interatomic interactions and clustering of metal atoms have been studied by first-principles calculations in graphene, pentacene, and polyacetylene as representative organic systems. It is shown that long-range repulsive Coulomb interaction appears between metal atoms with small electronegativity such as Al due to their ionization on host organic molecules, inducing their scattered distribution in organic systems. On the other hand, metal atoms with large electronegativity such as Au are weakly bonded to organic molecules, easily diffuse in molecular solids, and prefer to combine with each other owing to their short-range strong metallic-bonding interaction, promoting metal cluster generation in organic systems.

Observations of density fluctuations in an elongated Bose gas: ideal gas and quasicondensate regimes.

PubMed

Esteve, J; Trebbia, J-B; Schumm, T; Aspect, A; Westbrook, C I; Bouchoule, I

2006-04-07

We report in situ measurements of density fluctuations in a quasi-one-dimensional 87Rb Bose gas at thermal equilibrium in an elongated harmonic trap. We observe an excess of fluctuations compared to the shot-noise level expected for uncorrelated atoms. At low atomic density, the measured excess is in good agreement with the expected "bunching" for an ideal Bose gas. At high density, the measured fluctuations are strongly reduced compared to the ideal gas case. We attribute this reduction to repulsive interatomic interactions. The data are compared with a calculation for an interacting Bose gas in the quasicondensate regime.

Refined potentials for rare gas atom adsorption on rare gas and alkali-halide surfaces

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Heinbockel, J. H.; Outlaw, R. A.

1985-01-01

The utilization of models of interatomic potential for physical interaction to estimate the long range attractive potential for rare gases and ions is discussed. The long range attractive force is calculated in terms of the atomic dispersion properties. A data base of atomic dispersion parameters for rare gas atoms, alkali ion, and halogen ions is applied to the study of the repulsive core; the procedure for evaluating the repulsive core of ion interactions is described. The interaction of rare gas atoms on ideal rare gas solid and alkali-halide surfaces is analyzed; zero coverage absorption potentials are derived.

Thermo physical Properties of Multiferroic Rare Earth Manganite GdMnO3

NASA Astrophysics Data System (ADS)

Choithrani, Renu; Gaur, N. K.

2008-04-01

We have investigated the thermophysical properties of multiferroic rare earth manganite GdMnO3 in the temperature range 15 K⩽T⩽300 K. We have applied interatomic potential to study the Specific heat (C) as a function of temperature. The calculated Specific heat values are closer to the available experimental data. At room temperature, the orthorhombic GdMnO3 phase is indicative of a strong Jahn-Teller distortion. In addition, we have reported the cohesive energy (φ), molecular force constant (f), compressibility (β), Restrahalen frequency (ν0), Debye temperature (ΘD) and Groneisen parameter (γ) at temperature 15 K⩽T⩽300 K.

Dynamical Correlation In Some Liquid Alkaline Earth Metals Near Melting

NASA Astrophysics Data System (ADS)

Thakore, B. Y.; Suthar, P. H.; Khambholja, S. G.; Gajjar, P. N.; Jani, A. R.

2010-12-01

The study of dynamical variables: velocity autocorrelation function (VACF) and power spectrum of liquid alkaline earth metals (Ca, Sr, and Ba) have been presented based on the static harmonic well approximation. The effective interatomic potential for liquid metals is computed using our well recognized model potential with the exchange correlation functions due to Hartree, Taylor, Ichimaru and Utsumi, Farid et al. and Sarkar et al. It is observed that the VACF computed using Sarkar et al. gives the good agreement with available molecular dynamics simulation (MD) results [Phys Rev. B 62, 14818 (2000)]. The shoulder of the power spectrum depends upon the type of local field correlation function used.

A new look at the atomic level virial stress: on continuum-molecular system equivalence

NASA Astrophysics Data System (ADS)

Zhou, Min

2003-09-01

The virial stress is the most commonly used definition of stress in discrete particle systems. This quantity includes two parts. The first part depends on the mass and velocity (or, in some versions, the fluctuation part of the velocity) of atomic particles, reflecting an assertion that mass transfer causes mechanical stress to be applied on stationary spatial surfaces external to an atomic-particle system. The second part depends on interatomic forces and atomic positions, providing a continuum measure for the internal mechanical interactions between particles. Historic derivations of the virial stress include generalization from the virial theorem of Clausius (1870) for gas pressure and solution of the spatial equation of balance of momentum. The virial stress is stress-like a measure for momentum change in space. This paper shows that, contrary to the generally accepted view, the virial stress is not a measure for mechanical force between material points and cannot be regarded as a measure for mechanical stress in any sense. The lack of physical significance is both at the individual atom level in a time-resolved sense and at the system level in a statistical sense. It is demonstrated that the interatomic force term alone is a valid stress measure and can be identified with the Cauchy stress. The proof in this paper consists of two parts. First, for the simple conditions of rigid translation, uniform tension and tension with thermal oscillations, the virial stress yields clearly erroneous interpretations of stress. Second, the conceptual flaw in the generalization from the virial theorem for gas pressure to stress and the confusion over spatial and material equations of balance of momentum in theoretical derivations of the virial stress that led to its erroneous acceptance as the Cauchy stress are pointed out. Interpretation of the virial stress as a measure for mechanical force violates balance of momentum and is inconsistent with the basic definition of stress. The versions of the virial-stress formula that involve total particle velocity and the thermal fluctuation part of the velocity are demonstrated to be measures of spatial momentum flow relative to, respectively, a fixed reference frame and a moving frame with a velocity equal to the part of particle velocity not included in the virial formula. To further illustrate the irrelevance of mass transfer to the evaluation of stress, an equivalent continuum (EC) for dynamically deforming atomistic particle systems is defined. The equivalence of the continuum to discrete atomic systems includes (i) preservation of linear and angular momenta, (ii) conservation of internal, external and inertial work rates, and (iii) conservation of mass. This equivalence allows fields of work- and momentum-preserving Cauchy stress, surface traction, body force and deformation to be determined. The resulting stress field depends only on interatomic forces, providing an independent proof that as a measure for internal material interaction stress is independent of kinetic energy or mass transfer.

Nanoparticulate mackinawite formation; a stopped and continuous flow XANES and EXAFS investigation

NASA Astrophysics Data System (ADS)

Butler, I. B.; Bell, A. M.; Charnock, J. M.; Rickard, D.; Vaughan, D. J.; Oldroyd, A.

2009-12-01

The sequestration of sulfur and iron within sedimentary iron sulfides, and ultimately as pyrite, is a major sink in global biogeochemical cycles of those elements and has impacts on global carbon and oxygen cycles. The formation of the metastable black iron (II) monosulfide mackinawite is a key process because mackinawite forms in aqueous solutions where the Fe(II) and S(-II) IAP exceeds mackinawite’s Ksp. Mackinawite is the first formed iron sulfide phase, a consequence of Ostwald’s step rule and is a reactant phase during the formation of thermodynamically stable sedimentary iron sulfide minerals such as pyrite. The reaction of dissolved Fe(II) and sulfide is extremely fast and reactions in the environmentally significant near-neutral pH range tend to completion in <1 second. We have combined stopped and continuous flow techniques with X-ray absorption spectroscopy to evaluate the products of the fast precipitation kinetics of mackinawite over millisecond timescales. EXAFS spectra and data collected during flow experiments were compared with those from a well characterised freeze-dried nanoparticulate mackinawite standard and with published data. Published work has used Rietveld crystal structure refinement to determine bond distances of 2.2558 and 2.5976Å for Fe-S and Fe-Fe respectively. In our experiments Fe K edge XANES is consistent with tetrahedrally coordinated Fe in the precipitated sulfide phase. EXAFS data show that local Fe-S and Fe-Fe coordination and interatomic distances (Fe-S = 2.24Å; Fe-Fe = 2.57Å) are consistent with those determined for the standard mackinawite and published data. The coordination and spacing are developed in the precipitated phase after <10ms reaction at pH5, and considerably faster in experiments at near neutral to alkaline pH. No evidence for phases structurally intermediate between hexaqua Fe(II) and precipitated mackinawite was observed. Aqueous FeS° cluster complexes previously identified as intermediates during mackinawite formation and iron sulfide mineral transformations did not contribute significantly to the EXAFS spectra collected. For environmental, geological and biogeochemical applications, the precipitation of the mineral mackinawite can be considered to proceed rapidly from aqueous Fe(II) and S(-II) ions to the nanoparticulate crystalline mineral. The materials labelled “disordered mackinawite”, or “amorphous FeS” phase which have been widely quoted in the iron sulfide literature do not form at any stage of the precipitation of mackinawite from aqueous solutions. Physical and chemical properties previously ascribed to an amorphous or disordered structure are a consequence of the nanoparticulate form of the first precipitated solid.

Elastic response of binary hard-sphere fluids

NASA Astrophysics Data System (ADS)

Rickman, J. M.; Ou-Yang, H. Daniel

2011-07-01

We derive expressions for the high-frequency, wave-number-dependent elastic constants of a binary hard-sphere fluid and employ Monte Carlo computer simulation to evaluate these constants in order to highlight the impact of composition and relative sphere diameter on the elastic response of this system. It is found that the elastic constant c11(k) exhibits oscillatory behavior as a function of k whereas the high-frequency shear modulus, for example, does not. This behavior is shown to be dictated by the angular dependence (in k⃗ space) of derivatives of the interatomic force at contact. The results are related to recent measurements of the compressibility of colloidal fluids in laser trapping experiments.

Structural properties and glass transition in Aln clusters

NASA Astrophysics Data System (ADS)

Sun, D. Y.; Gong, X. G.

1998-02-01

We have studied the structural and dynamical properties of several Aln clusters by the molecular-dynamics method combined with simulated annealing. The well-fitted glue potential is used to describe the interatomic interaction. The obtained atomic structures for n=13, 55, and 147 are in agreement with results from ab initio calculations. Our results have demonstrated that the disordered cluster Al43 can be considered as a glass cluster. The obtained thermal properties of glass cluster Al43 are clearly different from the results for high-symmetry clusters, its melting behavior has properties similar to those of a glass solid. The present studies also show that the surface melting behavior does not exist in the studied Aln clusters.

Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

NASA Astrophysics Data System (ADS)

Zhang, Linfeng; Han, Jiequn; Wang, Han; Car, Roberto; E, Weinan

2018-04-01

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

Analytical W-He and H-He interatomic potentials for a W-H-He system

NASA Astrophysics Data System (ADS)

Li, Xiao-Chun; Shu, Xiaolin; Liu, Yi-Nan; Yu, Yi; Gao, F.; Lu, Guang-Hong

2012-07-01

We have constructed W-He and H-He analytical bond-order potentials for a W-H-He system. In combination with the previously self-developed W-H potential [X.-C. Li, X. Shu, Y.-N. Liu, F. Gao, G.-H. Lu, J. Nucl. Mater. 408 (2011) 12] and the Hartree-Fock-dispersion pair potential (Aziz-potential) for He-He interactions, we demonstrate that such potentials behave well for reproducing various properties of the W-H-He system such as defect formation energies, structural properties, and diffusion barriers. Such potentials can be employed to model both the He behaviours and the H-He synergetic effects in the W-H-He system.

The application of inverse Broyden's algorithm for modeling of crack growth in iron crystals.

PubMed

Telichev, Igor; Vinogradov, Oleg

2011-07-01

In the present paper we demonstrate the use of inverse Broyden's algorithm (IBA) in the simulation of fracture in single iron crystals. The iron crystal structure is treated as a truss system, while the forces between the atoms situated at the nodes are defined by modified Morse inter-atomic potentials. The evolution of lattice structure is interpreted as a sequence of equilibrium states corresponding to the history of applied load/deformation, where each equilibrium state is found using an iterative procedure based on IBA. The results presented demonstrate the success of applying the IBA technique for modeling the mechanisms of elastic, plastic and fracture behavior of single iron crystals.

Charge ordering in stoichiometric FeTe: Scanning tunneling microscopy and spectroscopy

DOE PAGES

Li, Wei; Yin, Wei -Guo; Wang, Lili; ...

2016-01-04

In this study, we use scanning tunneling microscopy and spectroscopy to reveal a unique stripy charge order in a parent phase of iron-based superconductors in stoichiometric FeTe epitaxy films. The charge order has unusually the same—usually half—period as the spin order. We also found highly anisotropic electron band dispersions being large and little along the ferromagnetic (crystallographic b) and antiferromagnetic (a) directions, respectively. Our data suggest that the microscopic mechanism is likely of the Stoner type driven by interatomic Coulomb repulsion V ij, and that V ij and charge fluctuations, so far much neglected, are important to the understanding ofmore » iron-based superconductors.« less

Thermodynamically accessible titanium clusters TiN, N = 2-32.

PubMed

Lazauskas, Tomas; Sokol, Alexey A; Buckeridge, John; Catlow, C Richard A; Escher, Susanne G E T; Farrow, Matthew R; Mora-Fonz, David; Blum, Volker W; Phaahla, Tshegofatso M; Chauke, Hasani R; Ngoepe, Phuti E; Woodley, Scott M

2018-05-10

We have performed a genetic algorithm search on the tight-binding interatomic potential energy surface (PES) for small TiN (N = 2-32) clusters. The low energy candidate clusters were further refined using density functional theory (DFT) calculations with the PBEsol exchange-correlation functional and evaluated with the PBEsol0 hybrid functional. The resulting clusters were analysed in terms of their structural features, growth mechanism and surface area. The results suggest a growth mechanism that is based on forming coordination centres by interpenetrating icosahedra, icositetrahedra and Frank-Kasper polyhedra. We identify centres of coordination, which act as centres of bulk nucleation in medium sized clusters and determine the morphological features of the cluster.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Tapan; Das, B. P.; Pai, Ramesh V.

We present a scenario where a supersolid is induced in one of the components of a mixture of two species bosonic atoms where there are no long-range interactions. We study a system of normal and hard-core boson mixture with only the former possessing long-range interactions. We consider three cases: the first where the total density is commensurate and the other two where it is incommensurate to the lattice. By suitable choices of the densities of normal and hard-core bosons and the interaction strengths between them, we predict that the charge density wave and the supersolid orders can be induced inmore » the hard-core species as a result of the competing interatomic interactions.« less

Computational model for noncontact atomic force microscopy: energy dissipation of cantilever.

PubMed

Senda, Yasuhiro; Blomqvist, Janne; Nieminen, Risto M

2016-09-21

We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments. We attribute this dissipation to the hysteresis and nonconservative properties of the interatomic force that acts between the atoms in the tip and sample surface. The dissipation rate strongly depends on the parameters used in the computational model.

Atomic bonding effects in annular dark field scanning transmission electron microscopy. II. Experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Odlyzko, Michael L.; Held, Jacob T.; Mkhoyan, K. Andre, E-mail: mkhoyan@umn.edu

2016-07-15

Quantitatively calibrated annular dark field scanning transmission electron microscopy (ADF-STEM) imaging experiments were compared to frozen phonon multislice simulations adapted to include chemical bonding effects. Having carefully matched simulation parameters to experimental conditions, a depth-dependent bonding effect was observed for high-angle ADF-STEM imaging of aluminum nitride. This result is explained by computational predictions, systematically examined in the preceding portion of this study, showing the propagation of the converged STEM beam to be highly sensitive to net interatomic charge transfer. Thus, although uncertainties in experimental conditions and simulation accuracy remain, the computationally predicted experimental bonding effect withstands the experimental testing reportedmore » here.« less

Strength of the interatomic potential derived from angular scans in LEIS

NASA Astrophysics Data System (ADS)

Primetzhofer, D.; Markin, S. N.; Draxler, M.; Beikler, R.; Taglauer, E.; Bauer, P.

2008-09-01

Angular scans were performed for a Cu(1 0 0) single crystal and He + ions. The results were compared to MARLOWE, KALYPSO and FAN simulations to obtain information on the interaction potential. The influence of the used evaluation procedure on the deduced scattering potential was investigated. The scattering potential is found to be weaker than what is predicted by an uncorrected TFM potential. It was found that the use of a single screening correction factor is applicable in a wide range of impact parameters. It is further shown that selection of single scattering trajectories and a limitation of information depth to the surface layers is possible for neutral and charge integrated spectra.

Monte Carlo simulation of elongating metallic nanowires in the presence of surfactants

NASA Astrophysics Data System (ADS)

Gimenez, M. Cecilia; Reinaudi, Luis; Leiva, Ezequiel P. M.

2015-12-01

Nanowires of different metals undergoing elongation were studied by means of canonical Monte Carlo simulations and the embedded atom method representing the interatomic potentials. The presence of a surfactant medium was emulated by the introduction of an additional stabilization energy, represented by a parameter Q. Several values of the parameter Q and temperatures were analyzed. In general, it was observed for all studied metals that, as Q increases, there is a greater elongation before the nanowire breaks. In the case of silver, linear monatomic chains several atoms long formed at intermediate values of Q and low temperatures. Similar observations were made for the case of silver-gold alloys when the medium interacted selectively with Ag.

Mechanism for transient migration of xenon in UO{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, X.-Y.; Uberuaga, B. P.; Andersson, D. A.

2011-04-11

In this letter, we report recent work on atomistic modeling of diffusion migration events of the fission gas product xenon in UO{sub 2} nuclear fuel. Under nonequilibrium conditions, Xe atoms can occupy the octahedral interstitial site, in contrast to the thermodynamically most stable uranium substitutional site. A transient migration mechanism involving Xe and two oxygen atoms is identified using basin constrained molecular dynamics employing a Buckingham type interatomic potential. This mechanism is then validated using density functional theory calculations using the nudged elastic band method. An overall reduction in the migration barrier of 1.6-2.7 eV is obtained compared to vacancy-mediatedmore » diffusion on the uranium sublattice.« less

Assessment of empirical potential for MOX nuclear fuels and thermomechanical properties

NASA Astrophysics Data System (ADS)

Balboa, Hector; Van Brutzel, Laurent; Chartier, Alain; Le Bouar, Yann

2017-11-01

We assess five empirical interatomic potentials in the approximation of rigid ions and pair interactions for the (U1-y,Puy)O solid solution. The assessment compares available experimental data and Fink's recommendation with simulations on: the structural, thermodynamics, and mechanical properties over the full range of plutonium composition, from pure UO2 to pure PuO2 and for temperatures ranging from 300 K to the melting point. The best results are obtained by potentials referred as Cooper and Potashnikov potentials. The first one reproduces more accurately recommendations for the thermodynamics and mechanical properties exhibiting ductile-like behaviour during crack propagation, while the second one gives brittle behaviour at low temperature.

Quantum Nonlinear Optics without real Photons

NASA Astrophysics Data System (ADS)

Macrí, Vincenzo; Frisk Kockum, Anton; Stassi, Roberto; di Stefano, Omar; Savasta, Salvatore; Nori, Franco

We propose a physical process analogous to spontaneous parametric down-conversion, where one excited atom directly transfers its excitation to a couple of spatially-separated atoms with probability approaching one. The interaction is mediated by the exchange of virtual, rather than real, photons. This nonlinear optical process is coherent and reversible, so that the two excited atoms can transfer back the excitation to the first one: the atomic analogue of sum-frequency generation. The parameters used here correspond to experimentally-demonstrated values in circuit QED. This approach can be extended to consider other nonlinear interatomic processes, e.g. four-qubit mixing, and is an attractive architecture for the realization of quantum devices on a chip. Univ. of Michigan, USA.

Quantum Nonlinear Optics without Photons

NASA Astrophysics Data System (ADS)

Macrı, Vincenzo

Here we propose a physical process analogous to spontaneous parametric down-conversion, where one excited atom directly transfers its excitation to a couple of spatially separated atoms with probability approaching one. The interaction is mediated by the exchange of virtual rather than real photons. This nonlinear optical process is coherent and reversible, so that the couple of excited atoms can transfer back the excitation to the first one: the analogous for atoms of sum-frequency generation. The parameters used here correspond to experimentally-demonstrated values in circuit QED. This approach can be expanded to consider other nonlinear inter-atomic processes as the four-qubit mixing and is an attractive architecture for the realization of quantum devices on a chip.

Molecular dynamics modeling of helium bubbles in austenitic steels

NASA Astrophysics Data System (ADS)

Jelea, A.

2018-06-01

The austenitic steel devices from pressurized water reactors are continuously subjected to neutron irradiation that produces crystalline point defects and helium atoms in the steel matrix. These species evolve into large defects such as dislocation loops and helium filled bubbles. This paper analyzes, through molecular dynamics simulations with recently developed interatomic potentials, the impact of the helium/steel interface on the helium behavior in nanosize bubbles trapped in an austenitic steel matrix. It is shown that the repulsive helium-steel interactions induce higher pressures in the bubble compared to bulk helium at the same temperature and average density. A new equation of state for helium is proposed in order to take into account these interface effects.

Simulation of uniaxial deformation of hexagonal crystals (Mg, Be)

NASA Astrophysics Data System (ADS)

Vlasova, A. M.; Kesarev, A. G.

2017-12-01

Molecular dynamics (MD) simulations were performed for the nanocompression loading of nanocrystalline magnesium and beryllium modeled by an interatomic potential of the embedded atom method (EAM). It is shown that the main deformation modes are prismatic slip and twinning for magnesium, and only prismatic slip for beryllium. The formation of stable configurations of dislocation grids in magnesium and beryllium was observed. Dislocation networks are formed in the habit plane of the twin in a magnesium nanocrystall. Some dislocation reactions are suggested to explain the appearance of such networks. Shockley partial dislocations in a beryllium nanocrystall form grids in the slip plane. A strong anisotropy between slip systems was observed, which is in agreement with experimental data.

Ultrasonic studies of aluminium-substituted Bi(Pb)-2223 superconductors

NASA Astrophysics Data System (ADS)

Solunke, M. B.; Sharma, P. U.; Pandya, M. P.; Lakhani, V. K.; Modi, K. B.; Venugopal Reddy, P.; Shah, S. S.

2005-09-01

The compositional dependence of elastic properties of Al^{3+}-substitu- ted Bi(Pb)-2223 superconducting system with the general formula Bi_{1.7-x}Al_xPb_{0.3}Sr_2Ca_2- Cu_3O_y (x = 0.0, 0.1, 0.2 and 0.3) have been studied by means of ultrasonic pulse transmission (UPT) technique at 1 MHz (300 K). The elastic moduli of the specimens are computed and corrected to zero porosity. The observed variation of elastic constants with aluminium substitution has been explained on the basis of the strength of interatomic bonding. The applicability of heterogeneous metal mixture rule for estimating elastic constants and transition temperature has been tested.

Superfluid Boson-Fermion Mixture: Structure Formation and Collective Periodic Motion

NASA Astrophysics Data System (ADS)

Mitra, A.

2018-01-01

Multiple periodic domain formation due to a modulation instability in a boson-fermion mixture superfluid in the unitary regime has been studied. The periodicity of the structure evolves with time. At the early stage of evolution, bosonic domains show the periodic nature, whereas the periodicity in the fermionic (Cooper pair) domains appears at the late stage of evolution. The nature of interatomic interspecies interactions affects the domain formation. In a harmonic trap, the mixture executes an undamped oscillation. The frequency of the oscillation depends on the relative coupling strength between boson-fermion and fermion-fermion. The repulsive boson-fermion interaction reduces the oscillation frequency, whereas the attractive interaction enhances the frequency significantly.

Navigating at Will on the Water Phase Diagram

NASA Astrophysics Data System (ADS)

Pipolo, S.; Salanne, M.; Ferlat, G.; Klotz, S.; Saitta, A. M.; Pietrucci, F.

2017-12-01

Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in the topology of the interatomic network, we are able to systematically track transitions among liquid, amorphous, and crystalline forms throughout the whole phase diagram of water, including the nucleation of crystals above and below the melting point. Our approach, based on molecular dynamics and enhanced sampling or free energy calculation techniques, is not specific to water and could be applied to very different structural phase transitions, paving the way towards the prediction of kinetic routes connecting polymorphic structures in a range of materials.

Affinity capillary electrophoresis and density functional theory study of noncovalent interactions of cyclic peptide [Gly6 ]-antamanide with small cations.

PubMed

Pangavhane, Sachin; Böhm, Stanislav; Makrlík, Emanuel; Ruzza, Paolo; Kašička, Václav

2017-08-01

ACE and density functional theory were employed to study the noncovalent interactions of cyclic decapeptide glycine-6-antamanide ([Gly 6 ]AA), synthetic derivative of native antamanide (AA) peptide from the deadly poisonous fungus Amanita phalloides, with small cations (Li + , Rb + , Cs + , NH 4 + , and Ca 2+ ) in methanol. The strength of these interactions was quantified by the apparent stability constants of the appropriate complexes determined by ACE. The stability constants were calculated using the nonlinear regression analysis of the dependence of the effective electrophoretic mobility of [Gly 6 ]AA on the concentration of the above ions in the BGE (methanolic solution of 20 mM chloroacetic acid, 10 mM Tris, pH MeOH 7.8, containing 0-70 mM concentrations of the above ions added in the form of chlorides). Prior to stability constant calculation, the effective mobilities measured at actual temperature inside the capillary and at variable ionic strength of the BGEs were corrected to the values corresponding to the reference temperature of 25°C and to the constant ionic strength of 10 mM. From the above ions, Rb + and Cs + cations interacted weakly with [Gly 6 ]AA but no interactions of [Gly 6 ]AA with univalent Li + and NH 4 + ions and divalent Ca 2+ ion were observed. The apparent stability constants of [Gly 6 ]AA-Rb + and [Gly 6 ]AA-Cs + complexes were found to be equal to 13 ± 4 and 22 ± 3 L/mol, respectively. The structural characteristics of these complexes, such as position of the Rb + and Cs + ions in the cavity of the [Gly 6 ]AA molecule and the interatomic distances within these complexes, were obtained by the density functional theory calculations. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Location of MTBE and toluene in the channel system of the zeolite mordenite: Adsorption and host-guest interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arletti, Rossella, E-mail: rossella.arletti@unito.it; Martucci, Annalisa; Alberti, Alberto

This paper reports a study of the location of Methyl Tertiary Butyl Ether (MTBE) and toluene molecules adsorbed in the pores of the organophylic zeolite mordenite from an aqueous solution. The presence of these organic molecules in the zeolite channels was revealed by structure refinement performed by the Rietveld method. About 3 molecules of MTBE and 3.6 molecules of toluene per unit cell were incorporated into the cavities of mordenite, representing 75% and 80% of the total absorption capacity of this zeolite. In both cases a water molecule was localized inside the side pocket of mordenite. The saturation capacity determinedmore » by the adsorption isotherms, obtained by batch experiments, and the weight loss given by thermogravimetric (TG) analyses were in very good agreement with these values. The interatomic distances obtained after the structural refinements suggest MTBE could be connected to the framework through a water molecule, while toluene could be bonded to framework oxygen atoms. The rapid and high adsorption of these hydrocarbons into the organophylic mordenite zeolite makes this cheap and environmental friendly material a suitable candidate for the removal of these pollutants from water. - graphical abstract: Location of MTBE (a) and toluene (b) in mordenite channels (projection along the [001] direction). Highlights: Black-Right-Pointing-Pointer We investigated the MTBE and toluene adsorption process into an organophilic zeolite mordenite. Black-Right-Pointing-Pointer The presence of MTBE and toluene in mordenite was determined by X-ray diffraction studies. Black-Right-Pointing-Pointer About 3 molecules of MTBE and 3.6 molecules of toluene per unit cell were incorporated into the zeolite cavities. Black-Right-Pointing-Pointer MTBE is connected to the framework through a water molecule. Black-Right-Pointing-Pointer Toluene is directly bonded to framework oxygen atoms.« less

Image charge models for accurate construction of the electrostatic self-energy of 3D layered nanostructure devices.

PubMed

Barker, John R; Martinez, Antonio

2018-04-04

Efficient analytical image charge models are derived for the full spatial variation of the electrostatic self-energy of electrons in semiconductor nanostructures that arises from dielectric mismatch using semi-classical analysis. The methodology provides a fast, compact and physically transparent computation for advanced device modeling. The underlying semi-classical model for the self-energy has been established and validated during recent years and depends on a slight modification of the macroscopic static dielectric constants for individual homogeneous dielectric regions. The model has been validated for point charges as close as one interatomic spacing to a sharp interface. A brief introduction to image charge methodology is followed by a discussion and demonstration of the traditional failure of the methodology to derive the electrostatic potential at arbitrary distances from a source charge. However, the self-energy involves the local limit of the difference between the electrostatic Green functions for the full dielectric heterostructure and the homogeneous equivalent. It is shown that high convergence may be achieved for the image charge method for this local limit. A simple re-normalisation technique is introduced to reduce the number of image terms to a minimum. A number of progressively complex 3D models are evaluated analytically and compared with high precision numerical computations. Accuracies of 1% are demonstrated. Introducing a simple technique for modeling the transition of the self-energy between disparate dielectric structures we generate an analytical model that describes the self-energy as a function of position within the source, drain and gated channel of a silicon wrap round gate field effect transistor on a scale of a few nanometers cross-section. At such scales the self-energies become large (typically up to ~100 meV) close to the interfaces as well as along the channel. The screening of a gated structure is shown to reduce the self-energy relative to un-gated nanowires.

Image charge models for accurate construction of the electrostatic self-energy of 3D layered nanostructure devices

NASA Astrophysics Data System (ADS)

Barker, John R.; Martinez, Antonio

2018-04-01

Efficient analytical image charge models are derived for the full spatial variation of the electrostatic self-energy of electrons in semiconductor nanostructures that arises from dielectric mismatch using semi-classical analysis. The methodology provides a fast, compact and physically transparent computation for advanced device modeling. The underlying semi-classical model for the self-energy has been established and validated during recent years and depends on a slight modification of the macroscopic static dielectric constants for individual homogeneous dielectric regions. The model has been validated for point charges as close as one interatomic spacing to a sharp interface. A brief introduction to image charge methodology is followed by a discussion and demonstration of the traditional failure of the methodology to derive the electrostatic potential at arbitrary distances from a source charge. However, the self-energy involves the local limit of the difference between the electrostatic Green functions for the full dielectric heterostructure and the homogeneous equivalent. It is shown that high convergence may be achieved for the image charge method for this local limit. A simple re-normalisation technique is introduced to reduce the number of image terms to a minimum. A number of progressively complex 3D models are evaluated analytically and compared with high precision numerical computations. Accuracies of 1% are demonstrated. Introducing a simple technique for modeling the transition of the self-energy between disparate dielectric structures we generate an analytical model that describes the self-energy as a function of position within the source, drain and gated channel of a silicon wrap round gate field effect transistor on a scale of a few nanometers cross-section. At such scales the self-energies become large (typically up to ~100 meV) close to the interfaces as well as along the channel. The screening of a gated structure is shown to reduce the self-energy relative to un-gated nanowires.

Low Resolution Refinement of Atomic Models Against Crystallographic Data.

PubMed

Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N

2017-01-01

This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, ProSMART and LORESTR, which are available as part of the CCP4 software suite.

Temperature effect on the structure and conformational fluctuations in two zinc knuckles from the mouse mammary tumor virus.

PubMed

Nedjoua, Drici; Krallafa, Abdelghani Mohamed

2018-06-01

Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation, and apoptosis. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins, and small molecules. In this study, we investigated the structural properties, in solution, of the proximal and distal zinc knuckles of the nucleocapsid (NC) protein from the mouse mammary tumor virus (MMTV) (MMTV NC). For this purpose, we performed a series of molecular dynamics simulations in aqueous solution at 300 K, 333 K, and 348 K. The temperature effect was evaluated in terms of root mean square deviation of the backbone atoms and root mean square fluctuation of the coordinating residue atoms. The stability of the zinc coordination sphere was analyzed based upon the time profile of the interatomic distances between the zinc ions and the chelator atoms. The results indicate that the hydrophobic character of the proximal zinc finger is dominant at 333 K. The low mobility of the coordinating residues suggests that the strong electrostatic effect exerted by the zinc ion on its coordinating residues is not influenced by the increase in temperature. The evolution of the structural parameters of the coordination sphere of the distal zinc finger at 300 K gives us a reasonable picture of the unfolding pathway, as proposed by Bombarda and coworkers (Bombarda et al., 2005), which can predict the binding order of the four conserved ligand-binding residues. Our results support the conclusion that the structural features can vary significantly between the two zinc knuckles of MMTV NC. Copyright © 2018 Elsevier Ltd. All rights reserved.

Full potential calculations on the electron bandstructures of Sphalerite, Pyrite and Chalcopyrite

NASA Astrophysics Data System (ADS)

Edelbro, R.; Sandström, Å.; Paul, J.

2003-02-01

The bulk electronic structures of Sphalerite, Pyrite and Chalcopyrite have been calculated within an ab initio, full potential, density functional approach. The exchange term was approximated with the Dirac exchange functional, the Vosko-Wilk-Nusair parameterization of the Cepler-Alder free electron gas was used for correlation and linear combinations of Gaussian type orbitals were used as basis functions. The Sphalerite (zinc blende) band gap was calculated to be direct with a width of 2.23 eV. The Sphalerite valence band was 5.2 eV wide and composed of a mixture of sulfur and zinc orbitals. The band below the valence band located around -6.2 eV was mainly composed of Zn 3d orbitals. The S 3s orbitals gave rise to a band located around -12.3 eV. Pyrite was calculated to be a semiconductor with an indirect band gap of 0.51 eV, and a direct gap of 0.55 eV. The valence band was 1.25 eV wide and mainly composed of non-bonding Fe 3d orbitals. The band below the valence band was 4.9 eV wide and composed of a mixture of sulfur and iron orbitals. Due to the short inter-atomic distance between the sulfur dumbbells, the S 3s orbitals in Pyrite were split into a bonding and an anti-bonding range. Chalcopyrite was predicted to be a conductor, with no band-crossings at the Fermi level. The bands at -13.2 eV originate from the sulfur 3s orbitals and were quite similar to the sulfur 3s bands in Sphalerite, though somewhat shifted to lower energy. The top of the valence band consisted of a mixture of orbitals from all the atoms. The lower part of the same band showed metal character. Computational modeling as a tool for illuminating the flotation and leaching processes of Pyrite and Chalcopyrite, in connection with surface science experiments, is discussed.

Final Report for Award DE-SC0005403. Improved Electrochemical Performance of Strained Lattice Electrolytes via Modulated Doping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hertz, Joshua L.; Prasad, Ajay K.

2015-09-06

The enclosed document provides a final report to document the research performed at the University of Delaware under Grant DE-SC0005403: Improved Electrochemical Performance of Strained Lattice Electrolytes via Modulated Doping. The ultimate goal of this project was to learn how to systematically strain the inter-atomic distance in thin ceramic films and how to use this newfound control to improve the ease by which oxygen ions can conduct through the films. Increasing the ionic conductivity of ceramics holds the promise of drastic improvements in the performance of solid oxide fuel cells, chemical sensors, gas permeation membranes, and related devices. Before thismore » work, the experimental evidence advocating for strain-based techniques was often controversial and poorly characterized. Enabling much of this work was a new method to quickly create a very wide range of ceramic nanostructures that was established during the first phase of the project. Following this initial phase, we created a variety of promising nanostructured epitaxial films and multilayers with systematic variations in lattice mismatch and dopant content. Over the course of the work, a positive effect of tensile atomic strain on the oxygen conductivity was conclusively found using a few different forms of samples and experimental techniques. The samples were built by sputtering, an industrially scalable technique, and thus the technological implementation of these results may be economically feasible. Still, two other results consistently achieved over multiple efforts in this work give pause. The first of these results was that very specific, pristine surfaces upon which to build the nanostructures were strictly required in order to achieve measurable results. The second of these results was that compressively strained films with concomitant reductions in oxygen conductivity are much easier to obtain relative to tensile-strained films with increased conductivity.« less

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

PubMed

Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

2018-02-15

Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align/. njyudj@njust.edu.cn or zhng@umich.edu. Supplementary data are available at Bioinformatics online.

The exact solution of a four-body Coulomb problem

NASA Astrophysics Data System (ADS)

Ray, Hasi

2018-03-01

The elastic collision between two H-like atoms utilizing an ab initio static-exchange model (SEM) in the center of mass (CM) frame considering the system as a four-body Coulomb problem where all the Coulomb interaction terms in the direct and exchange channels are treated exactly, is studied thoroughly. A coupled-channel methodology in momentum space is used to solve Lippman-Schwinger equation following the integral approach. The new SEM code [Ray, Pramana 83, 907 (2014)] in which the Born-Oppenheimer (BO) scattering amplitude acts as input to derive the SEM amplitude using partial wave analysis, is utilized to study the s-, p-, d-wave elastic phase shifts and the corresponding partial cross sections. An augmented-Born approximation is used to include the contribution of higher partial waves more accurately to determine the total/integrated elastic cross sections. The effective range theory is used to determine the scattering lengths and effective ranges in the s-wave elastic scattering. The systems studied are Ps-Ps, Ps-Mu, Ps-H, Ps-D, Ps-T, Mu-Mu, Mu-H, Mu-D, Mu-T, H-H, H-D, H-T, D-D, D-T, T-T. The SEM includes the non-adiabatic short-range effects due to exchange. The MSEM code [Ray, Pramana 83, 907 (2014)] is used to study the effect of the long-range van der Waals interaction due to induced dipole polarizabilities of the atoms in H(1s)-H(1s) elastic collision. The dependence of scattering length on the reduced mass of the system and the dependence of scattering length on the strength of long-range van der Waals interaction that varies with the minimum interatomic distance are observed. Contribution to the Topical Issue "Low Energy Positron and Electron Interactions", edited by James Sullivan, Ron White, Michael Bromley, Ilya Fabrikant, and David Cassidy.

XPS and Ag L3-edge XANES characterization of silver and silver-gold sulfoselenides

NASA Astrophysics Data System (ADS)

Mikhlin, Yuri L.; Pal'yanova, Galina A.; Tomashevich, Yevgeny V.; Vishnyakova, Elena A.; Vorobyev, Sergey A.; Kokh, Konstantin A.

2018-05-01

Gold and silver sulfoselenides are of interest as materials with high ionic conductivity and promising magnetoresistive, thermoelectric, optical, and other physico-chemical properties, which are strongly dependent on composition and structure. Here, we applied X-ray photoelectron spectroscopy and Ag L3 X-ray absorption near-edge structure (XANES) to study the electronic structures of low-temperature compounds and solid solutions Ag2SxSe1-x (0 < x < 1), AgAuS, and Ag3AuSxSe2-x (x = 0, 1, 2). Upon substitution of Se with S, a steady increase in the positive charge at Ag(I) sites and only minor changes in the local charge at chalcogen atoms were found from the photoelectron Ag 3d, S 2p, Se 3d, and Ag M4,5VV Auger spectra. The intensity of the Ag L3-edge peak, which is known to correlate with hole counts in the Ag 4d shell having a formal d10 configuration, was enhanced by 20-25% from Ag2Se to Ag2S and from Ag3AuSe2 to Ag3AuS2. The effect of gold is more pronounced, and the number of Ag d holes and the negative charge of S and Se notably decreased for Au-containing compounds; in particular, the Ag L3-edge peak is about 35% lower for AgAuS relative to Ag2S. At the same time, the Au 4f binding energy and, therefore, charge at Au(I) sites increase with increasing S content due to the transfer of electron density from Au to Ag atoms. It was concluded that the effects mainly originate from shortening of the metal-chalcogen and especially the Ausbnd Ag interatomic distances in substances having similar coordination geometry.

Characterization of Structure and Function of ZS-9, a K+ Selective Ion Trap

PubMed Central

Stavros, Fiona; Yang, Alex; Leon, Alejandro; Nuttall, Mark; Rasmussen, Henrik S.

2014-01-01

Hyperkalemia, a condition in which serum potassium ions (K+) exceed 5.0 mmol/L, is a common electrolyte disorder associated with substantial morbidity. Current methods of managing hyperkalemia, including organic polymer resins such as sodium polystyrene sulfonate (SPS), are poorly tolerated and/or not effective. Sodium zirconium cyclosilicate (ZS-9) is under clinical development as an orally administered, non-absorbed, novel, inorganic microporous zirconium silicate compound that selectively removes excess K+ in vivo. The development, structure and ion exchange properties of ZS-9 and its hypothesized mechanism of action are described. Based on calculation of the interatomic distances between the atoms forming the ZS-9 micropores, the size of the pore opening was determined to be ∼3 Å (∼diameter of unhydrated K+). Unlike nonspecific organic polymer resins like SPS, the ZS-9 K+ exchange capacity (KEC) was unaffected by the presence of calcium (Ca2+) or magnesium ions (Mg2+) and showed>25-fold selectivity for K+ over either Ca2+ or Mg2+. Conversely, the selectivity of SPS for K+ was only 0.2–0.3 times its selectivity for Ca2+ or Mg2+in mixed ionic media. It is hypothesized that the high K+ specificity of ZS-9 is attributable to the chemical composition and diameter of the micropores, which possibly act in an analogous manner to the selectivity filter utilized by physiologic K+ channels. This hypothesized mechanism of action is supported by the multi-ion exchange studies. The effect of pH on the KEC of ZS-9 was tested in different media buffered to mimic different portions of the human gastrointestinal tract. Rapid K+ uptake was observed within 5 minutes - mainly in the simulated small intestinal and large intestinal fluids, an effect that was sustained for up to 1 hour. If approved, ZS-9 will represent a novel, first-in-class therapy for hyperkalemia with improved capacity, selectivity, and speed for entrapping K+ when compared to currently available options. PMID:25531770

Bonding of xenon to oxygen in magmas at depth

NASA Astrophysics Data System (ADS)

Leroy, Clémence; Sanloup, Chrystèle; Bureau, Hélène; Schmidt, Burkhard C.; Konôpková, Zuzana; Raepsaet, Caroline

2018-02-01

The field of noble gases chemistry has witnessed amazing advances in the last decade with over 100 compounds reported including Xe oxides and Xe-Fe alloys stable at the pressure-temperature conditions of planetary interiors. The chemistry of Xe with planetary materials is nonetheless still mostly ignored, while Xe isotopes are used to trace a variety of key planetary processes from atmosphere formation to underground nuclear tests. It is indeed difficult to incorporate the possibility of Xe reactivity at depth in isotopic geochemical models without a precise knowledge of its chemical environment. The structure of Xe doped hydrous silica-rich melts is investigated by in situ high energy synchrotron X-ray diffraction using resistive heating diamond anvil cells. Obtained pair distribution functions reveal the oxidation of Xe between 0.2 GPa and 4 GPa at high T up to 1000 K. In addition to the usual interatomic distances, a contribution at 2.05 ± 0.05 Å is observed. This contribution is not observed in the undoped melt, and is interpreted as the Xe-O bond, with a coordination number of about 12 consistent with Xe insertion in rings of the melt structure. Xe solubility measurements by electron microprobe and particle induced X-rays emission analysis confirm that Xe and Ar have similar solubility values in wt% in silicate melts. These values are nonetheless an order of magnitude higher than those theoretically calculated for Xe. The formation of Xe-O bonds explains the enhanced solubility of Xe in deep continental crust magmas, revealing a mechanism that could store Xe and fractionate its isotopes. Xenon is indeed atypical among noble gases, the atmosphere being notably depleted in elemental Xe, and very strongly depleted in Xe light isotopes. These observations are known as the 'missing' Xe paradox, and could be solved by the present findings.

Archetypal structure of ultrathin alumina films: Grazing-incidence x-ray diffraction on Ni(111)

NASA Astrophysics Data System (ADS)

Prévot, G.; Le Moal, S.; Bernard, R.; Croset, B.; Lazzari, R.; Schmaus, D.

2012-05-01

We have studied by grazing-incidence x-ray diffraction the atomic structure of an ultrathin alumina film grown on Ni(111). We show that, since there is neither registry between the film and the substrate nor induced Ni relaxations, this system appears to be a prototypical freestanding oxide layer. We have been able to unambiguously determine the three-dimensional structure of the film, which consists of a substrate/Al16/O24/Al24/O28 stacking within a (18.23 × 10.53 Å) R0° unit cell. From the different Al coordinations (3/4/5) in the layer and from the precise determination of the Al-O interatomic distances, we conclude that the film structure presents some similarities with the η phase of bulk alumina, which also has a high surface/bulk ratio. The precise comparison between these two structures allows us to explain that the perfect 3 ratio between the two sides of the mesh of the film is governed by the stacking of the two central planes, combining oxygen close-packed atoms below Al atoms in tetrahedral or pyramidal positions. Moreover, Al atoms at the interface plane of the ultrathin film adopt a quasitrihedral configuration, which confirms that, in the alumina η phase, Al atoms with such a coordination are located near the surface of the nanocrystals. The atomic structure is also very close to the one first proposed by Kresse [G. Kresse, M. Schmid, E. Napetschnig, M. Shishkin, L. Köhler, and P. Varga, ScienceSCIEAS0036-807510.1126/science.1107783 308, 1440 (2005)] for alumina films on NiAl(110). This strongly suggests that this atomic model, within small variations, can be extended to ultrathin alumina film on numerous other metal substrates and may be quasi-intrinsic to a freestanding layer rather than governed by the interactions between the film and the substrate.

Characterization of structure and function of ZS-9, a K+ selective ion trap.

PubMed

Stavros, Fiona; Yang, Alex; Leon, Alejandro; Nuttall, Mark; Rasmussen, Henrik S

2014-01-01

Hyperkalemia, a condition in which serum potassium ions (K+) exceed 5.0 mmol/L, is a common electrolyte disorder associated with substantial morbidity. Current methods of managing hyperkalemia, including organic polymer resins such as sodium polystyrene sulfonate (SPS), are poorly tolerated and/or not effective. Sodium zirconium cyclosilicate (ZS-9) is under clinical development as an orally administered, non-absorbed, novel, inorganic microporous zirconium silicate compound that selectively removes excess K+ in vivo. The development, structure and ion exchange properties of ZS-9 and its hypothesized mechanism of action are described. Based on calculation of the interatomic distances between the atoms forming the ZS-9 micropores, the size of the pore opening was determined to be ∼ 3 Å (∼ diameter of unhydrated K+). Unlike nonspecific organic polymer resins like SPS, the ZS-9 K+ exchange capacity (KEC) was unaffected by the presence of calcium (Ca2+) or magnesium ions (Mg2+) and showed>25-fold selectivity for K+ over either Ca2+ or Mg2+. Conversely, the selectivity of SPS for K+ was only 0.2-0.3 times its selectivity for Ca2+ or Mg2+in mixed ionic media. It is hypothesized that the high K+ specificity of ZS-9 is attributable to the chemical composition and diameter of the micropores, which possibly act in an analogous manner to the selectivity filter utilized by physiologic K+ channels. This hypothesized mechanism of action is supported by the multi-ion exchange studies. The effect of pH on the KEC of ZS-9 was tested in different media buffered to mimic different portions of the human gastrointestinal tract. Rapid K+ uptake was observed within 5 minutes - mainly in the simulated small intestinal and large intestinal fluids, an effect that was sustained for up to 1 hour. If approved, ZS-9 will represent a novel, first-in-class therapy for hyperkalemia with improved capacity, selectivity, and speed for entrapping K+ when compared to currently available options.

Multiscale structural changes of atomic order in severely deformed industrial aluminum

NASA Astrophysics Data System (ADS)

Samoilenko, Z. A.; Ivakhnenko, N. N.; Pushenko, E. I.; Pashinskaya, E. G.; Varyukhin, V. N.

2016-02-01

The regularities of multiscale structural changes in the atomic order of the aluminum alloy AD-1 after a severe cold plastic deformation by conventional rolling in smooth rolls or in rolls with relief recesses favorable for shear deformation have been investigated. It has been found that there are four types of structural fractions that differ in scale and perfection of atomic order: crystallographic planes with a long-range order; nanoscale fragments of the planes ( D = 100-300 Å) with an incipient long-range order; smaller groups of atoms ( D = 20-30 Å) of amorphized structure; and the least ordered structural fraction of intercluster medium, keeping only a short-range atomic order (2-3 interatomic distances, 10 Å). The presence of diffuse halo bands in the region of intense Debye lines indicates phase transitions of the order → disorder type with the formation of one to three groups of amorphous clusters with the dominance, in the nanometer scale, of the atomic order characteristic of the family of planes (111), (220), and (311) of crystalline aluminum. We have found a dynamic phase transition with the changing crystallographic order of aluminum, with the matrix structure of a face-centered cubic (FCC) lattice, in the form of nanosized local groups of atoms, that is, the deformation clusters of aluminum with a simple cubic K6 lattice. In the case of conventional rolling, the development of large clusters 50-500 Å in size is observed; however, in the use of rolls with relief recesses, the difference in the sizes of the clusters is one half as much: 50-250 Å. Based on the analysis of the integrated intensity of incoherent X-ray scattering by the samples, we have elucidated the nature of the lowest measured density for the sample subjected to conventional rolling, which consists in the volume concentration of disorderly arranged atoms, the highest of the compared structures, which indicates the formation therein of the greatest amount of fluctuation "voids."

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jäger, Benjamin, E-mail: benjamin.jaeger@uni-rostock.de; Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only atmore » a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.« less

Transverse discrete breathers in unstrained graphene

NASA Astrophysics Data System (ADS)

Barani, Elham; Lobzenko, Ivan P.; Korznikova, Elena A.; Soboleva, Elvira G.; Dmitriev, Sergey V.; Zhou, Kun; Marjaneh, Aliakbar Moradi

2017-02-01

Discrete breathers (DB) are spatially localized vibrational modes of large amplitude in defect-free nonlinear lattices. The search for DBs in graphene is of high importance, taking into account that this one atom thick layer of carbon is promising for a number of applications. There exist several reports on successful excitation of DBs in graphene, based on molecular dynamics and ab initio simulations. In a recent work by Hizhnyakov with co-authors the possibility to excite a DB with atoms oscillating normal to the graphene sheet has been reported. In the present study we use a systematic approach for finding initial conditions to excite transverse DBs in graphene. The approach is based on the analysis of the frequency-amplitude dependence for a delocalized, short-wavelength vibrational mode. This mode is a symmetry-dictated exact solution to the dynamic equations of the atomic motion, regardless the mode amplitude and regardless the type of interatomic potentials used in the simulations. It is demonstrated that if the AIREBO potential is used, the mode frequency increases with the amplitude bifurcating from the upper edge of the phonon spectrum for out-of-plane phonons. Then a bell-shaped function is superimposed on this delocalized mode to obtain a spatially localized vibrational mode, i.e., a DB. Placing the center of the bell-shaped function at different positions with respect to the lattice sites, three different DBs are found. Typically, the degree of spatial localization of DBs increases with the DB amplitude, but the transverse DBs in graphene reported here demonstrate the opposite trend. The results are compared to those obtained with the use of the Savin interatomic potential and no transverse DBs are found in this case. The results of this study contribute to a better understanding of the nonlinear dynamics of graphene and they call for the ab initio simulations to verify which of the two potentials used in this study is more precise.

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas.

PubMed

Jäger, Benjamin; Hellmann, Robert; Bich, Eckard; Vogel, Eckhard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.

Development of a Modified Embedded Atom Force Field for Zirconium Nitride Using Multi-Objective Evolutionary Optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Narayanan, Badri; Sasikumar, Kiran; Mei, Zhi-Gang

2016-07-07

Zirconium nitride (ZrN) exhibits exceptional mechanical, chemical, and electrical properties, which make it attractive for a wide range of technological applications, including wear-resistant coatings, protection from corrosion, cutting/shaping tools, and nuclear breeder reactors. Despite its broad usability, an atomic scale understanding of the superior performance of ZrN, and its response to external stimuli, for example, temperature, applied strain, and so on, is not well understood. This is mainly due to the lack of interatomic potential models that accurately describe the interactions between Zr and N atoms. To address this challenge, we develop a modified embedded atom method (MEAM) interatomic potentialmore » for the Zr–N binary system by training against formation enthalpies, lattice parameters, elastic properties, and surface energies of ZrN (and, in some cases, also Zr3N4) obtained from density functional theory (DFT) calculations. The best set of MEAM parameters are determined by employing a multiobjective global optimization scheme driven by genetic algorithms. Our newly developed MEAM potential accurately reproduces structure, thermodynamics, energetic ordering of polymorphs, as well as elastic and surface properties of Zr–N compounds, in excellent agreement with DFT calculations and experiments. As a representative application, we employed molecular dynamics simulations based on this MEAM potential to investigate the atomic scale mechanisms underlying fracture of bulk and nanopillar ZrN under applied uniaxial strains, as well as the impact of strain rate on their mechanical behavior. These simulations indicate that bulk ZrN undergoes brittle fracture irrespective of the strain rate, while ZrN nanopillars show quasi-plasticity owing to amorphization at the crack front. The MEAM potential for Zr–N developed in this work is an invaluable tool to investigate atomic-scale mechanisms underlying the response of ZrN to external stimuli (e.g, temperature, pressure etc.), as well as other interesting phenomena such as precipitation.« less

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

NASA Astrophysics Data System (ADS)

Inatomi, Yuya; Kangawa, Yoshihiro; Ito, Tomonori; Suski, Tadeusz; Kumagai, Yoshinao; Kakimoto, Koichi; Koukitu, Akinori

2017-07-01

The composition pulling effect in metalorganic vapor-phase InGaN epitaxy was theoretically investigated by thermodynamic analysis. The excess energies of biaxial-strained In x Ga1- x N 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.

The spectrum of density fluctuations of noble gases probed by THz neutron and x-ray spectroscopy

DOE PAGES

Cunsolo, Alessandro

2016-02-26

Approximately 50 years of inelastic scattering studies of noble gases are reviewed to illustrate the main advances achieved in the understanding of the THz dynamics of simple systems. The gradual departure of the spectral shape from the hydrodynamic regime is discussed with an emphasis on the phenomenology of fast (sub- ps) relaxation processes. This review shows that relaxation phenomena in noble gases have an essentially collisional origin, which is also revealed by the parallelism between their characteristic timescale and the interatomic collision time. In addition, recent THz spectroscopy results on noble gases at extreme thermodynamic conditions are discussed to illustratemore » the need for a revision of our current understanding of the supercritical phase.« less

Size and habit evolution of PETN crystals - a lattice Monte Carlo study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zepeda-Ruiz, L A; Maiti, A; Gee, R

2006-02-28

Starting from an accurate inter-atomic potential we develop a simple scheme of generating an ''on-lattice'' molecular potential of short range, which is then incorporated into a lattice Monte Carlo code for simulating size and shape evolution of nanocrystallites. As a specific example, we test such a procedure on the morphological evolution of a molecular crystal of interest to us, e.g., Pentaerythritol Tetranitrate, or PETN, and obtain realistic facetted structures in excellent agreement with experimental morphologies. We investigate several interesting effects including, the evolution of the initial shape of a ''seed'' to an equilibrium configuration, and the variation of growth morphologymore » as a function of the rate of particle addition relative to diffusion.« less

Dislocation nucleation from symmetric tilt grain boundaries in body-centered cubic vanadium

NASA Astrophysics Data System (ADS)

Xu, Shuozhi; Su, Yanqing

2018-05-01

We perform molecular dynamics (MD) simulations with two interatomic potentials to study dislocation nucleation from six symmetric tilt grain boundaries (GB) using bicrystal models in body-centered cubic vanadium. The influences of the misorientation angle are explored in the context of activated slip systems, critical resolved shear stress (CRSS), and GB energy. It is found that for four GBs, the activated slip systems are not those with the highest Schmid factor, i.e., the Schmid law breaks down. For all misorientation angles, the bicrystal is associated with a lower CRSS than their single crystalline counterparts. Moreover, the GB energy decreases in compressive loading at the yield point with respect to the undeformed configuration, in contrast to tensile loading.

Analytical bond order potential for simulations of BeO 1D and 2D nanostructures and plasma-surface interactions

NASA Astrophysics Data System (ADS)

Byggmästar, J.; Hodille, E. A.; Ferro, Y.; Nordlund, K.

2018-04-01

An analytical interatomic bond order potential for the Be-O system is presented. The potential is fitted and compared to a large database of bulk BeO and point defect properties obtained using density functional theory. Its main applications include simulations of plasma-surface interactions involving oxygen or oxide layers on beryllium, as well as simulations of BeO nanotubes and nanosheets. We apply the potential in a study of oxygen irradiation of Be surfaces, and observe the early stages of an oxide layer forming on the Be surface. Predicted thermal and elastic properties of BeO nanotubes and nanosheets are simulated and compared with published ab initio data.

A molecular dynamics study of melting and dissociation of tungsten nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Min; Wang, Jun; Fu, Baoqin

2015-12-15

Molecular dynamics simulations were conducted to study the melting and dissociation of free tungsten nanoparticles. For the various interatomic potentials applied, the melting points of the tungsten nanoparticles increased with increasing nanoparticle diameter. Combining these results with the melting point of bulk tungsten in the experiment, the melting point of nanoparticles with diameters ranging from 4 to 12 nm could be determined. As the temperature increases, free nanoparticles are subject to dissociation phenomena. The dissociation rate was observed to follow Arrhenius behavior, and the Meyer–Neldel rule was obeyed. These results are useful in understanding the behavior of tungsten dust generatedmore » in nuclear fusion devices as well as for the preparation, formation, and application of tungsten powders.« less

Kinetics versus thermodynamics in materials modeling: The case of the di-vacancy in iron

NASA Astrophysics Data System (ADS)

Djurabekova, F.; Malerba, L.; Pasianot, R. C.; Olsson, P.; Nordlund, K.

2010-07-01

Monte Carlo models are widely used for the study of microstructural and microchemical evolution of materials under irradiation. However, they often link explicitly the relevant activation energies to the energy difference between local equilibrium states. We provide a simple example (di-vacancy migration in iron) in which a rigorous activation energy calculation, by means of both empirical interatomic potentials and density functional theory methods, clearly shows that such a link is not granted, revealing a migration mechanism that a thermodynamics-linked activation energy model cannot predict. Such a mechanism is, however, fully consistent with thermodynamics. This example emphasizes the importance of basing Monte Carlo methods on models where the activation energies are rigorously calculated, rather than deduced from widespread heuristic equations.

Homogenization Models for Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Muc, A.; Jamróz, M.

2004-03-01

Two homogenization models for evaluating Young's modulus of nanocomposites reinforced with single-walled and multi-walled carbon nanotubes are presented. The first model is based on a physical description taking into account the interatomic interaction and nanotube geometry. The elementary cell, here a nanotube with a surrounding resin layer, is treated as a homogeneous body — a material continuum. The second model, similar to a phenomenological engineering one, is obtained by combining the law of mixture with the Cox mechanical model. This model describes the stress distribution along stretched short fibers surrounded by a resin matrix. The similarities between composite materials reinforced with short fibers and nanotubes are elucidated. The results obtained are compared with those for classical microcomposites to demonstrate the advantages and disadvantages of both the composite materials.

Monte Carlo simulation of elongating metallic nanowires in the presence of surfactants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gimenez, M. Cecilia; Reinaudi, Luis, E-mail: luis.reinaudi@unc.edu.ar; Leiva, Ezequiel P. M.

2015-12-28

Nanowires of different metals undergoing elongation were studied by means of canonical Monte Carlo simulations and the embedded atom method representing the interatomic potentials. The presence of a surfactant medium was emulated by the introduction of an additional stabilization energy, represented by a parameter Q. Several values of the parameter Q and temperatures were analyzed. In general, it was observed for all studied metals that, as Q increases, there is a greater elongation before the nanowire breaks. In the case of silver, linear monatomic chains several atoms long formed at intermediate values of Q and low temperatures. Similar observations weremore » made for the case of silver-gold alloys when the medium interacted selectively with Ag.« less

Effect of the substituent and hydrogen bond on the geometry and electronic properties of OH and O(-) groups in para-substituted phenol and phenolate derivatives.

PubMed

Szatylowicz, Halina; Krygowski, Tadeusz M

2010-10-14

Interrelations between intra- and intermolecular interactions were analyzed by using computational modeling of the para-X-substituted derivatives of phenol and phenolate (where X = NO, NO(2), CHO, COMe, COOH, CONH(2), Cl, F, H, Me, OMe, and OH) and their equilibrium H-bonded complexes with HB and B(-) (where HB = HF and HCN and B(-) = F(-) and CN(-)). B3LYP/6-311++G** computation was applied. Both the substituent effect and H-bonding changed the electronic properties of the -O(-) and -OH groups and geometric parameters of phenol and phenolate derivatives and their H-bonded complexes. C-O bond lengths and aromaticity indices of the ring were found to depend linearly on σ(p)(-) of the substituents. In the first case the greatest sensitivity on the substituent effect was for 4-X-C(6)H(4)OH···CN(-) and 4-X-C(6)H(4)O(-)···HF complexes, whereas for 4-X-C(6)H(4)O(-)···HCN systems it was comparable with that for phenol derivatives and a little smaller than that for 4-X-C(6)H(4)O(-) derivatives. This means that the strength of H-bonding may considerably change the sensitivity of the C-O bond length to the substituent effect. The greatest sensitivity of the aromaticity indices, both HOMA and NICS(1)zz, to σ(p)(-) was found for phenolate and then for phenolate H-bonded complexes, followed by phenol complexes, and the lowest sensitivity was observed for phenol derivatives. The interatomic proton-acceptor distance, being a measure of the H-bond strength, was found to depend linearly on σ(p)(-) of the substituents with a positive slope for O···HB (HF or HCN) interactions and a negative slope for OH···B(-) interactions. NBO charges on the oxygen and hydrogen atoms also depend on σ(p)(-) of the substituents. In the latter case for strong H-bonded complexes (energy less than ∼-20 kcal/mol) the substituent effect works oppositely for 4-X-C(6)H(4)OH···B(-) in comparison with the 4-X-C(6)H(4)O(-)···HB systems. Moreover, following the Espinoza et al. [J. Chem. Phys. 2002, 117, 5529] and Grabowski et al. [J. Phys. Chem. B 2006, 110, 6444] classifications, the above and q(H) vs proton-acceptor distance relationships suggest a partially covalent character of the hydrogen bond for these complexes and the degree of its covalent nature depending on the substituent.

Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2016-05-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.

Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2015-05-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

Equivalent-Continuum Modeling of Nano-Structured Materials

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Gates, Thomas S.; Nicholson, Lee M.; Wise, Kristopher E.

2001-01-01

A method has been developed for modeling structure-property relationships of nano-structured materials. This method serves as a link between computational chemistry and solid mechanics by substituting discrete molecular structures with an equivalent-continuum model. It has been shown that this substitution may be accomplished by equating the vibrational potential energy of a nano-structured material with the strain energy of representative truss and continuum models. As an important example with direct application to the development and characterization of single-walled carbon nanotubes, the model has been applied to determine the effective continuum geometry of a graphene sheet. A representative volume element of the equivalent-continuum model has been developed with an effective thickness. This effective thickness has been shown to be similar to, but slightly smaller than, the interatomic spacing of graphite.