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.

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.

Accurate interatomic force fields via machine learning with covariant kernels

NASA Astrophysics Data System (ADS)

Glielmo, Aldo; Sollich, Peter; De Vita, Alessandro

2017-06-01

We present a novel scheme to accurately predict atomic forces as vector quantities, rather than sets of scalar components, by Gaussian process (GP) regression. This is based on matrix-valued kernel functions, on which we impose the requirements that the predicted force rotates with the target configuration and is independent of any rotations applied to the configuration database entries. We show that such covariant GP kernels can be obtained by integration over the elements of the rotation group SO (d ) for the relevant dimensionality d . Remarkably, in specific cases the integration can be carried out analytically and yields a conservative force field that can be recast into a pair interaction form. Finally, we show that restricting the integration to a summation over the elements of a finite point group relevant to the target system is sufficient to recover an accurate GP. The accuracy of our kernels in predicting quantum-mechanical forces in real materials is investigated by tests on pure and defective Ni, Fe, and Si crystalline systems.

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.

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

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

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.

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.

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Enabling Computational Nanotechnology through JavaGenes in a Cycle Scavenging Environment

NASA Technical Reports Server (NTRS)

Globus, Al; Menon, Madhu; Srivastava, Deepak; Biegel, Bryan A. (Technical Monitor)

2002-01-01

A genetic algorithm procedure is developed and implemented for fitting parameters for many-body inter-atomic force field functions for simulating nanotechnology atomistic applications using portable Java on cycle-scavenged heterogeneous workstations. Given a physics based analytic functional form for the force field, correlated parameters in a multi-dimensional environment are typically chosen to fit properties given either by experiments and/or by higher accuracy quantum mechanical simulations. The implementation automates this tedious procedure using an evolutionary computing algorithm operating on hundreds of cycle-scavenged computers. As a proof of concept, we demonstrate the procedure for evaluating the Stillinger-Weber (S-W) potential by (a) reproducing the published parameters for Si using S-W energies in the fitness function, and (b) evolving a "new" set of parameters using semi-empirical tightbinding energies in the fitness function. The "new" parameters are significantly better suited for Si cluster energies and forces as compared to even the published S-W potential.

Molecular dynamics simulations of the surface tension and structure of salt solutions and clusters.

PubMed

Sun, Lu; Li, Xin; Hede, Thomas; Tu, Yaoquan; Leck, Caroline; Ågren, Hans

2012-03-15

Sodium halides, which are abundant in sea salt aerosols, affect the optical properties of aerosols and are active in heterogeneous reactions that cause ozone depletion and acid rain problems. Interfacial properties, including surface tension and halide anion distributions, are crucial issues in the study of the aerosols. We present results from molecular dynamics simulations of water solutions and clusters containing sodium halides with the interatomic interactions described by a conventional force field. The simulations reproduce experimental observations that sodium halides increase the surface tension with respect to pure water and that iodide anions reach the outermost layer of water clusters or solutions. It is found that the van der Waals interactions have an impact on the distribution of the halide anions and that a conventional force field with optimized parameters can model the surface tension of the salt solutions with reasonable accuracy. © 2012 American Chemical Society

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

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.

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.

Efficient nonparametric n -body force fields from machine learning

NASA Astrophysics Data System (ADS)

Glielmo, Aldo; Zeni, Claudio; De Vita, Alessandro

2018-05-01

We provide a definition and explicit expressions for n -body Gaussian process (GP) kernels, which can learn any interatomic interaction occurring in a physical system, up to n -body contributions, for any value of n . The series is complete, as it can be shown that the "universal approximator" squared exponential kernel can be written as a sum of n -body kernels. These recipes enable the choice of optimally efficient force models for each target system, as confirmed by extensive testing on various materials. We furthermore describe how the n -body kernels can be "mapped" on equivalent representations that provide database-size-independent predictions and are thus crucially more efficient. We explicitly carry out this mapping procedure for the first nontrivial (three-body) kernel of the series, and we show that this reproduces the GP-predicted forces with meV /Å accuracy while being orders of magnitude faster. These results pave the way to using novel force models (here named "M-FFs") that are computationally as fast as their corresponding standard parametrized n -body force fields, while retaining the nonparametric character, the ease of training and validation, and the accuracy of the best recently proposed machine-learning potentials.

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.

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.

Learning a force field for the martensitic phase transformation in Zr

NASA Astrophysics Data System (ADS)

Zong, Hongxiang; Pilania, Ghanshyam; Ramprasad, Rampi; Lookman, Turab

Atomic simulations provide an effective means to understand the underlying physics of martensitic transformations under extreme conditions. However, this is still a challenge for certain phase transforming metals due to the lack of an accurate classical force field. Quantum molecular dynamics (QMD) simulations are accurate but expensive. During the course of QMD simulations, similar configurations are constantly visited and revisited. Machine Learning can effectively learn from past visits and, therefore, eliminate such redundancies. In this talk, we will discuss the development of a hybrid ML-QMD method in which on-demand, on-the-fly quantum mechanical (QM) calculations are performed to accelerate calculations of interatomic forces at much lower computational costs. Using Zirconium as a model system for which accurate atomisctic potentials are currently unvailable we will demonstrate the feasibility and effectiveness of our approach. Specifically, the computed structural phase transformation behavior within the ML-QMD approach will be compared with available experimental results. Furthermore, results on phonons, stacking fault energies, and activation barriers for the homogeneous martensitic transformation in Zr will be presented.

Building machine learning force fields for nanoclusters

NASA Astrophysics Data System (ADS)

Zeni, Claudio; Rossi, Kevin; Glielmo, Aldo; Fekete, Ádám; Gaston, Nicola; Baletto, Francesca; De Vita, Alessandro

2018-06-01

We assess Gaussian process (GP) regression as a technique to model interatomic forces in metal nanoclusters by analyzing the performance of 2-body, 3-body, and many-body kernel functions on a set of 19-atom Ni cluster structures. We find that 2-body GP kernels fail to provide faithful force estimates, despite succeeding in bulk Ni systems. However, both 3- and many-body kernels predict forces within an ˜0.1 eV/Å average error even for small training datasets and achieve high accuracy even on out-of-sample, high temperature structures. While training and testing on the same structure always provide satisfactory accuracy, cross-testing on dissimilar structures leads to higher prediction errors, posing an extrapolation problem. This can be cured using heterogeneous training on databases that contain more than one structure, which results in a good trade-off between versatility and overall accuracy. Starting from a 3-body kernel trained this way, we build an efficient non-parametric 3-body force field that allows accurate prediction of structural properties at finite temperatures, following a newly developed scheme [A. Glielmo et al., Phys. Rev. B 95, 214302 (2017)]. We use this to assess the thermal stability of Ni19 nanoclusters at a fractional cost of full ab initio calculations.

The dynamics of copper intercalated molybdenum ditelluride

NASA Astrophysics Data System (ADS)

Onofrio, Nicolas; Guzman, David; Strachan, Alejandro

2016-11-01

Layered transition metal dichalcogenides are emerging as key materials in nanoelectronics and energy applications. Predictive models to understand their growth, thermomechanical properties, and interaction with metals are needed in order to accelerate their incorporation into commercial products. Interatomic potentials enable large-scale atomistic simulations connecting first principle methods and devices. We present a ReaxFF reactive force field to describe molybdenum ditelluride and its interactions with copper. We optimized the force field parameters to describe the energetics, atomic charges, and mechanical properties of (i) layered MoTe2, Mo, and Cu in various phases, (ii) the intercalation of Cu atoms and small clusters within the van der Waals gap of MoTe2, and (iii) bond dissociation curves. The training set consists of an extensive set of first principles calculations computed using density functional theory (DFT). We validate the force field via the prediction of the adhesion of a single layer MoTe2 on a Cu(111) surface and find good agreement with DFT results not used in the training set. We characterized the mobility of the Cu ions intercalated into MoTe2 under the presence of an external electric field via finite temperature molecular dynamics simulations. The results show a significant increase in drift velocity for electric fields of approximately 0.4 V/Å and that mobility increases with Cu ion concentration.

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.

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.

Induced dipole-dipole coupling between two atoms at a migration resonance

NASA Astrophysics Data System (ADS)

Kaur, Maninder; Mian, Mahmood

2018-05-01

Results of numerical simulations for the resonant energy exchange phenomenon called Migration reaction between two cold Rydberg atoms are presented. The effect of spatial interatomic distance on the onset of peculiar coherent mechanism is investigated. Observation of Rabi-like population inversion oscillation at the resonance provides a clear signature of dipole induced exchange of electronic excitations between the atoms. Further we present the results for the dependence of expectation value of the interaction hamiltonian on the interatomic distance, which is responsible for energy exchange process. The results of this observation endorse the range of inter atomic distance within which the excitation exchange process occurs completely or partially. Migration process enhance the Rydberg-Rydberg interaction in the absence of an external field, under the condition of the zero permanent dipole moments. Our next observation sheds light on the fundamental mechanism of induced electric fields initiated by the oscillating dipoles in such energy exchange processes. We explore the dependence of induced electric field on the interatomic distance and angle between the dipoles highlighting the inverse power law dependence and anisotropic property of the field. We put forward an idea to utilise the coherent energy exchange process to build efficient and fast energy transfer channels by incorporating more atoms organised at successive distances with decreasing distance gradient.

Loosely-Bound Diatomic Molecules.

ERIC Educational Resources Information Center

Balfour, W. J.

1979-01-01

Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

NASA Astrophysics Data System (ADS)

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/˜knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

PubMed Central

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/∼knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery. PMID:28140407

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.

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.

Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering.

PubMed

Slepoy, A; Peters, M D; Thompson, A P

2007-11-30

Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. Copyright (c) 2007 Wiley Periodicals, Inc.

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.

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.

DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics

NASA Astrophysics Data System (ADS)

Wang, Han; Zhang, Linfeng; Han, Jiequn; E, Weinan

2018-07-01

Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in Python/C++ that has been designed to minimize the effort required to build deep learning based representation of potential energy and force field and to perform molecular dynamics. Potential applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems. DeePMD-kit is interfaced with TensorFlow, one of the most popular deep learning frameworks, making the training process highly automatic and efficient. On the other end, DeePMD-kit is interfaced with high-performance classical molecular dynamics and quantum (path-integral) molecular dynamics packages, i.e., LAMMPS and the i-PI, respectively. Thus, upon training, the potential energy and force field models can be used to perform efficient molecular simulations for different purposes. As an example of the many potential applications of the package, we use DeePMD-kit to learn the interatomic potential energy and forces of a water model using data obtained from density functional theory. We demonstrate that the resulted molecular dynamics model reproduces accurately the structural information contained in the original model.

Thermal nanostructure: An order parameter multiscale ensemble approach

NASA Astrophysics Data System (ADS)

Cheluvaraja, S.; Ortoleva, P.

2010-02-01

Deductive all-atom multiscale techniques imply that many nanosystems can be understood in terms of the slow dynamics of order parameters that coevolve with the quasiequilibrium probability density for rapidly fluctuating atomic configurations. The result of this multiscale analysis is a set of stochastic equations for the order parameters whose dynamics is driven by thermal-average forces. We present an efficient algorithm for sampling atomistic configurations in viruses and other supramillion atom nanosystems. This algorithm allows for sampling of a wide range of configurations without creating an excess of high-energy, improbable ones. It is implemented and used to calculate thermal-average forces. These forces are then used to search the free-energy landscape of a nanosystem for deep minima. The methodology is applied to thermal structures of Cowpea chlorotic mottle virus capsid. The method has wide applicability to other nanosystems whose properties are described by the CHARMM or other interatomic force field. Our implementation, denoted SIMNANOWORLD™, achieves calibration-free nanosystem modeling. Essential atomic-scale detail is preserved via a quasiequilibrium probability density while overall character is provided via predicted values of order parameters. Applications from virology to the computer-aided design of nanocapsules for delivery of therapeutic agents and of vaccines for nonenveloped viruses are envisioned.

Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

DOE PAGES

Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

2015-06-04

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

PubMed Central

2015-01-01

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

Self-enhanced catalytic activities of functionalized graphene sheets in the combustion of nitromethane: molecular dynamic simulations by molecular reactive force field.

PubMed

Zhang, Chaoyang; Wen, Yushi; Xue, Xianggui

2014-08-13

Functionalized graphene sheet (FGS) is a promising additive that enhances fuel/propellant combustion, and the determination of its mechanism has attracted much interest. In the present study, a series of molecular dynamic simulations based on a reactive force field (ReaxFF) are performed to explore the catalytic activity (CA) of FGS in the thermal decay of nitromethane (NM, CH3NO2). FGSs and pristine graphene sheets (GSs) are oxidized in hot NM liquid to increase their functionalities and subsequently show self-enhanced CAs during the decay. The CAs result from the interatomic exchanges between the functional groups on the sheets and the NM liquid, i.e., mainly between H and O atoms. CA is dependent on the density of NM, functionalities of sheets, and temperature. The GSs and FGSs that originally exhibit different functionalities tend to possess similar functionalities and consequently similar CAs as temperature increases. Other carbon materials and their oxides can accelerate combustion of other fuels/propellants similar to NM, provided that they can be dispersed and their key reaction steps in combustion are similar to NM.

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

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).

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

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.

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.

Polarizable atomic multipole X-ray refinement: application to peptide crystals

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

Schnieders, Michael J.; Fenn, Timothy D.; Howard Hughes Medical Institute

2009-09-01

A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussianmore » multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.« less

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.

GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2

NASA Astrophysics Data System (ADS)

Lin, Zhixiong; Bachmann, Stephan J.; van Gunsteren, Wilfred F.

2015-03-01

Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 models may be used in biomolecular simulations of protein denaturation.

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.

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.

New Distributed Multipole Methods for Accurate Electrostatics for Large-Scale Biomolecular Simultations

NASA Astrophysics Data System (ADS)

Sagui, Celeste

2006-03-01

An accurate and numerically efficient treatment of electrostatics is essential for biomolecular simulations, as this stabilizes much of the delicate 3-d structure associated with biomolecules. Currently, force fields such as AMBER and CHARMM assign ``partial charges'' to every atom in a simulation in order to model the interatomic electrostatic forces, so that the calculation of the electrostatics rapidly becomes the computational bottleneck in large-scale simulations. There are two main issues associated with the current treatment of classical electrostatics: (i) how does one eliminate the artifacts associated with the point-charges (e.g., the underdetermined nature of the current RESP fitting procedure for large, flexible molecules) used in the force fields in a physically meaningful way? (ii) how does one efficiently simulate the very costly long-range electrostatic interactions? Recently, we have dealt with both of these challenges as follows. In order to improve the description of the molecular electrostatic potentials (MEPs), a new distributed multipole analysis based on localized functions -- Wannier, Boys, and Edminston-Ruedenberg -- was introduced, which allows for a first principles calculation of the partial charges and multipoles. Through a suitable generalization of the particle mesh Ewald (PME) and multigrid method, one can treat electrostatic multipoles all the way to hexadecapoles all without prohibitive extra costs. The importance of these methods for large-scale simulations will be discussed, and examplified by simulations from polarizable DNA models.

Dipole-dipole interaction in cavity QED: The weak-coupling, nondegenerate regime

NASA Astrophysics Data System (ADS)

Donaire, M.; Muñoz-Castañeda, J. M.; Nieto, L. M.

2017-10-01

We compute the energies of the interaction between two atoms placed in the middle of a perfectly reflecting planar cavity, in the weak-coupling nondegenerate regime. Both inhibition and enhancement of the interactions can be obtained by varying the size of the cavity. We derive exact expressions for the dyadic Green's function of the cavity field which mediates the interactions and apply time-dependent quantum perturbation theory in the adiabatic approximation. We provide explicit expressions for the van der Waals potentials of two polarizable atomic dipoles and the electrostatic potential of two induced dipoles. We compute the van der Waals potentials in three different scenarios: two atoms in their ground states, two atoms excited, and two dissimilar atoms with one of them excited. In addition, we calculate the phase-shift rate of the two-atom wave function in each case. The effect of the two-dimensional confinement of the electromagnetic field on the dipole-dipole interactions is analyzed. This effect depends on the atomic polarization. For dipole moments oriented parallel to the cavity plates, both the electrostatic and the van der Waals interactions are exponentially suppressed for values of the cavity width much less than the interatomic distance, whereas for values of the width close to the interatomic distance, the strength of both interactions is higher than their values in the absence of cavity. For dipole moments perpendicular to the plates, the strength of the van der Waals interaction decreases for values of the cavity width close to the interatomic distance, while it increases for values of the width much less than the interatomic distance with respect to its strength in the absence of cavity. We illustrate these effects by computing the dipole-dipole interactions between two alkali atoms in circular Rydberg states.

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.

The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.

PubMed

Yao, Kun; Herr, John E; Toth, David W; Mckintyre, Ryker; Parkhill, John

2018-02-28

Traditional force fields cannot model chemical reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab initio accuracy at low cost. However a data-driven approach is naturally inefficient for long-range interatomic forces that have simple physical formulas. In this manuscript we construct a hybrid model chemistry consisting of a nearsighted neural network potential with screened long-range electrostatic and van der Waals physics. This trained potential, simply dubbed "TensorMol-0.1", is offered in an open-source Python package capable of many of the simulation types commonly used to study chemistry: geometry optimizations, harmonic spectra, open or periodic molecular dynamics, Monte Carlo, and nudged elastic band calculations. We describe the robustness and speed of the package, demonstrating its millihartree accuracy and scalability to tens-of-thousands of atoms on ordinary laptops. We demonstrate the performance of the model by reproducing vibrational spectra, and simulating the molecular dynamics of a protein. Our comparisons with electronic structure theory and experimental data demonstrate that neural network molecular dynamics is poised to become an important tool for molecular simulation, lowering the resource barrier to simulating chemistry.

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.

GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2

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

Lin, Zhixiong; Bachmann, Stephan J.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch

2015-03-07

Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 modelsmore » may be used in biomolecular simulations of protein denaturation.« less

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.

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

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.

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.

Theoretical analysis of uranium-doped thorium dioxide: Introduction of a thoria force field with explicit polarization

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

Shields, A. E.; Ruiz Hernandez, S. E.; Leeuw, N. H. de, E-mail: DeLeeuwN@Cardiff.ac.uk

2015-08-15

Thorium dioxide is used industrially in high temperature applications, but more insight is needed into the behavior of the material as part of a mixed-oxide (MOX) nuclear fuel, incorporating uranium. We have developed a new interatomic potential model including polarizability via a shell model, and commensurate with a prominent existing UO{sub 2} potential, to conduct configurational analyses and to investigate the thermophysical properties of uranium-doped ThO{sub 2}. Using the GULP and Site Occupancy Disorder (SOD) computational codes, we have analyzed the distribution of low concentrations of uranium in the bulk material, where we have not observed the formation of uraniummore » clusters or the dominance of a single preferred configuration. We have calculated thermophysical properties of pure thorium dioxide and Th{sub (1−x)}U{sub x}O{sub 2} which generated values in very good agreement with experimental data.« less

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.

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.

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.

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.

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.

Enhanced Thermal Diffusion of Li in Graphite by Alternating Vertical Electric Field: A Hybrid Quantum-Classical Simulation Study

NASA Astrophysics Data System (ADS)

Ohba, Nobuko; Ogata, Shuji; Tamura, Tomoyuki; Kobayashi, Ryo; Yamakawa, Shunsuke; Asahi, Ryoji

2012-02-01

Enhancing the diffusivity of the Li ion in a Li-graphite intercalation compound that has been used as a negative electrode in the Li-ion rechargeable battery, is important in improving both the recharging speed and power of the battery. In the compound, the Li ion creates a long-range stress field around itself by expanding the interlayer spacing of graphite. We advance the hybrid quantum-classical simulation code to include the external electric field in addition to the long-range stress field by first-principles simulation. In the hybrid code, the quantum region selected adaptively around the Li ion is treated using the real-space density-functional theory for electrons. The rest of the system is described with an empirical interatomic potential that includes the term relating to the dispersion force between the C atoms in different layers. Hybrid simulation runs for Li dynamics in graphite are performed at 423 K under various settings of the amplitude and frequency of alternating electric fields perpendicular to C-layers. We find that the in-plane diffusivity of the Li ion is enhanced significantly by the electric field if the amplitude is larger than 0.2 V/Å within its order and the frequency is as high as 1.7 THz. The microscopic mechanisms of the enhancement are explained.

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.

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.

Finite difference computation of Casimir forces

NASA Astrophysics Data System (ADS)

Pinto, Fabrizio

2016-09-01

In this Invited paper, we begin by a historical introduction to provide a motivation for the classical problems of interatomic force computation and associated challenges. This analysis will lead us from early theoretical and experimental accomplishments to the integration of these fascinating interactions into the operation of realistic, next-generation micro- and nanodevices both for the advanced metrology of fundamental physical processes and in breakthrough industrial applications. Among several powerful strategies enabling vastly enhanced performance and entirely novel technological capabilities, we shall specifically consider Casimir force time-modulation and the adoption of non-trivial geometries. As to the former, the ability to alter the magnitude and sign of the Casimir force will be recognized as a crucial principle to implement thermodynamical nano-engines. As to the latter, we shall first briefly review various reported computational approaches. We shall then discuss the game-changing discovery, in the last decade, that standard methods of numerical classical electromagnetism can be retooled to formulate the problem of Casimir force computation in arbitrary geometries. This remarkable development will be practically illustrated by showing that such an apparently elementary method as standard finite-differencing can be successfully employed to numerically recover results known from the Lifshitz theory of dispersion forces in the case of interacting parallel-plane slabs. Other geometries will be also be explored and consideration given to the potential of non-standard finite-difference methods. Finally, we shall introduce problems at the computational frontier, such as those including membranes deformed by Casimir forces and the effects of anisotropic materials. Conclusions will highlight the dramatic transition from the enduring perception of this field as an exotic application of quantum electrodynamics to the recent demonstration of a human climbing vertically on smooth glass.

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/.

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.

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.

Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity

NASA Astrophysics Data System (ADS)

Huang, Bing; von Lilienfeld, O. Anatole

2016-10-01

The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Inspired by the postulates of quantum mechanics, we introduce a hierarchy of representations which meet uniqueness and target similarity criteria. To systematically control target similarity, we simply rely on interatomic many body expansions, as implemented in universal force-fields, including Bonding, Angular (BA), and higher order terms. Addition of higher order contributions systematically increases similarity to the true potential energy and predictive accuracy of the resulting ML models. We report numerical evidence for the performance of BAML models trained on molecular properties pre-calculated at electron-correlated and density functional theory level of theory for thousands of small organic molecules. Properties studied include enthalpies and free energies of atomization, heat capacity, zero-point vibrational energies, dipole-moment, polarizability, HOMO/LUMO energies and gap, ionization potential, electron affinity, and electronic excitations. After training, BAML predicts energies or electronic properties of out-of-sample molecules with unprecedented accuracy and speed.

Error estimates for (semi-)empirical dispersion terms and large biomacromolecules.

PubMed

Korth, Martin

2013-10-14

The first-principles modeling of biomaterials has made tremendous advances over the last few years with the ongoing growth of computing power and impressive developments in the application of density functional theory (DFT) codes to large systems. One important step forward was the development of dispersion corrections for DFT methods, which account for the otherwise neglected dispersive van der Waals (vdW) interactions. Approaches at different levels of theory exist, with the most often used (semi-)empirical ones based on pair-wise interatomic C6R(-6) terms. Similar terms are now also used in connection with semiempirical QM (SQM) methods and density functional tight binding methods (SCC-DFTB). Their basic structure equals the attractive term in Lennard-Jones potentials, common to most force field approaches, but they usually use some type of cutoff function to make the mixing of the (long-range) dispersion term with the already existing (short-range) dispersion and exchange-repulsion effects from the electronic structure theory methods possible. All these dispersion approximations were found to perform accurately for smaller systems, but error estimates for larger systems are very rare and completely missing for really large biomolecules. We derive such estimates for the dispersion terms of DFT, SQM and MM methods using error statistics for smaller systems and dispersion contribution estimates for the PDBbind database of protein-ligand interactions. We find that dispersion terms will usually not be a limiting factor for reaching chemical accuracy, though some force fields and large ligand sizes are problematic.

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.

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.

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.

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.

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

On computing stress in polymer systems involving multi-body potentials from molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Fu, Yao; Song, Jeong-Hoon

2014-08-01

Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.

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

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

Understanding the EF-hand closing pathway using non-biased interatomic potentials.

PubMed

Dupuis, L; Mousseau, Normand

2012-01-21

The EF-hand superfamily of proteins is characterized by the presence of calcium binding helix-loop-helix structures. Many of these proteins undergo considerable motion responsible for a wide range of properties upon binding but the exact mechanism at the root of this motion is not fully understood. Here, we use an unbiased accelerated multiscale simulation scheme, coupled with two force fields - CHARMM-EEF1 and the extended OPEP - to explore in details the closing pathway, from the unbound holo state to the closed apo state, of two EF-hand proteins, the Calmodulin and Troponin C N-terminal nodules. Based on a number of closing simulations for these two sequences, we show that the EF-hand β-scaffold, identified as crucial by Grabarek for the EF-hand opening driven by calcium binding, is also important in closing the EF-hand. We also show the crucial importance of the phenylalanine situated at the end of first EF-hand helix, and identify an intermediate state modulating its behavior, providing a detailed picture of the closing mechanism for these two representatives of EF-hand proteins. © 2012 American Institute of Physics

Accurate atomistic potentials and training sets for boron-nitride nanostructures

NASA Astrophysics Data System (ADS)

Tamblyn, Isaac

Boron nitride nanotubes exhibit exceptional structural, mechanical, and thermal properties. They are optically transparent and have high thermal stability, suggesting a wide range of opportunities for structural reinforcement of materials. Modeling can play an important role in determining the optimal approach to integrating nanotubes into a supporting matrix. Developing accurate, atomistic scale models of such nanoscale interfaces embedded within composites is challenging, however, due to the mismatch of length scales involved. Typical nanotube diameters range from 5-50 nm, with a length as large as a micron (i.e. a relevant length-scale for structural reinforcement). Unlike their carbon-based counterparts, well tested and transferable interatomic force fields are not common for BNNT. In light of this, we have developed an extensive training database of BN rich materials, under conditions relevant for BNNT synthesis and composites based on extensive first principles molecular dynamics simulations. Using this data, we have produced an artificial neural network potential capable of reproducing the accuracy of first principles data at significantly reduced computational cost, allowing for accurate simulation at the much larger length scales needed for composite design.

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.

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

Mechanical behavior enhancement of defective graphene sheet employing boron nitride coating via atomistic study

NASA Astrophysics Data System (ADS)

Setoodeh, A. R.; Badjian, H.

2017-12-01

The most stable form of boron nitride polymorph naming hexagonal boron nitride sheet has recently been widely concerned like graphite due to its interesting features such as electrical insulation and high thermal conductivity. In this study, the molecular dynamic simulations are implemented to investigate the mechanical properties of single-layer graphene sheets under tensile and compressive loadings in the absence and presence of boron-nitride coating layers. In this introduced hybrid nanostructure, the benefit of combining both individual interesting features of graphene and boron-nitride sheets such as exceptional mechanical and electrical properties can be simultaneously achieved for future potential application in nano devices. The influences of chiral indices, boundary conditions and presence of mono-atomic vacancy defects as well as coating dimension on the mechanical behavior of the resulted hybrid structure are reported. The interatomic forces between the atoms are modeled by employing the AIREBO and Tersoff-Brenner potentials for carbon-carbon and boron-nitrogen atoms in each layer, respectively. Furthermore, the van der Waal interlayer forces of carbon-boron and carbon-nitrogen are estimated by the Lennard-Jones potential field. Besides the potential improvement in electrical and physical properties of the nanostructure, it is demonstrated that the buckling load capacity of the fully coated graphene sheet with 3% concentration of mono-atomic vacancy defects noticeably enhances by amounts of 24.1%.

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

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.

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.

Cooperatively coupled motion with superradiant and subradiant atoms

NASA Astrophysics Data System (ADS)

Lin, Guin-Dar; Lin, Kuan-Ting; Tang, Er-Siang

2017-04-01

We investigate the coupled motion of cooperative atoms subjected to the Doppler dissipative force. The dipole-dipole interaction introduces mutual decay channel and splits the super-radiant and sub-radiant states. The Doppler force is thus modified due to the collective emission and coupled recoil. Such a cooperative effect is more evident when the inter-atom separation is less than or comparable to a wavelength. In an optical molasses, we find that, along the axis of two atoms, there presents an effective potential with mechanically stable and unstable regions alternatively as their separation increases. Taking the cooperative Lamb shift into account, we map out the stability diagram and investigate the blockade effect. We thank the support from MOST of Taiwan under Grant No. 105-2112-M-002-015-MY3 and National Taiwan University under Grant No. NTU-ERP-105R891401.

Nuclear-relaxed elastic and piezoelectric constants of materials: Computational aspects of two quantum-mechanical approaches.

PubMed

Erba, Alessandro; Caglioti, Dominique; Zicovich-Wilson, Claudio Marcelo; Dovesi, Roberto

2017-02-15

Two alternative approaches for the quantum-mechanical calculation of the nuclear-relaxation term of elastic and piezoelectric tensors of crystalline materials are illustrated and their computational aspects discussed: (i) a numerical approach based on the geometry optimization of atomic positions at strained lattice configurations and (ii) a quasi-analytical approach based on the evaluation of the force- and displacement-response internal-strain tensors as combined with the interatomic force-constant matrix. The two schemes are compared both as regards their computational accuracy and performance. The latter approach, not being affected by the many numerical parameters and procedures of a typical quasi-Newton geometry optimizer, constitutes a more reliable and robust mean to the evaluation of such properties, at a reduced computational cost for most crystalline systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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.

On computing stress in polymer systems involving multi-body potentials from molecular dynamics simulation

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

Fu, Yao, E-mail: fu5@mailbox.sc.edu, E-mail: jhsong@cec.sc.edu; Song, Jeong-Hoon, E-mail: fu5@mailbox.sc.edu, E-mail: jhsong@cec.sc.edu

2014-08-07

Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifiesmore » the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.« less

A smoothed particle hydrodynamics framework for modelling multiphase interactions at meso-scale

NASA Astrophysics Data System (ADS)

Li, Ling; Shen, Luming; Nguyen, Giang D.; El-Zein, Abbas; Maggi, Federico

2018-01-01

A smoothed particle hydrodynamics (SPH) framework is developed for modelling multiphase interactions at meso-scale, including the liquid-solid interaction induced deformation of the solid phase. With an inter-particle force formulation that mimics the inter-atomic force in molecular dynamics, the proposed framework includes the long-range attractions between particles, and more importantly, the short-range repulsive forces to avoid particle clustering and instability problems. Three-dimensional numerical studies have been conducted to demonstrate the capabilities of the proposed framework to quantitatively replicate the surface tension of water, to model the interactions between immiscible liquids and solid, and more importantly, to simultaneously model the deformation of solid and liquid induced by the multiphase interaction. By varying inter-particle potential magnitude, the proposed SPH framework has successfully simulated various wetting properties ranging from hydrophobic to hydrophilic surfaces. The simulation results demonstrate the potential of the proposed framework to genuinely study complex multiphase interactions in wet granular media.

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).

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

Adhesive behavior of micro/nano-textured surfaces

NASA Astrophysics Data System (ADS)

Zhang, Yuyan; Wang, Xiaoli; Li, Hanqing; Wang, Ben

2015-02-01

A numerical model of the adhesive contact between a rigid smooth sphere and an elastic textured surface based on the Lennard-Jones interatomic potential law and the Hamaker summation method is established. Textures are considered by introducing the texture height distribution into the gap equation. Simulation results show that the pull-off force on textured surfaces decreases compared to that on smooth surfaces. Furthermore, effects of sphere-shaped textures on reducing adhesion are more obvious than cylinder-shaped or cube-shaped textures when the coverage area ratio, maximum height and interval of textures are fixed. For surfaces with sphere-shaped textures, variation trends of the mean pull-off force with texture density are not monotonous, and there exists a certain range of texture densities in which the mean pull-off force is small and its variation is insignificant. In addition, the pull-off force depends also on the maximum height and radius of textures. On one hand, if the texture radius is fixed, larger maximum height results in smaller pull-off force, and if the maximum height is fixed, the pull-off force tends to increase almost linearly with increases in texture radius. On the other hand, if the height-diameter ratio of textures is fixed, the pull-off force reaches a minimum at an optimum texture radius or maximum height.

Stopping power beyond the adiabatic approximation

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

Caro, M.; Correa, A. A.; Artacho, E.

2017-06-01

Energetic ions traveling in solids deposit energy in a variety of ways, being nuclear and electronic stopping the two avenues in which dissipation is usually treated. This separation between electrons and ions relies on the adiabatic approximation in which ions interact via forces derived from the instantaneous electronic ground state. In a more detailed view, in which non-adiabatic effects are explicitly considered, electronic excitations alter the atomic bonding, which translates into changes in the interatomic forces. In this work, we use time dependent density functional theory and forces derived from the equations of Ehrenfest dynamics that depend instantaneously on themore » time-dependent electronic density. With them we analyze how the inter-ionic forces are affected by electronic excitations in a model of a Ni projectile interacting with a Ni target, a metallic system with strong electronic stopping and shallow core level states. We find that the electronic excitations induce substantial modifications to the inter-ionic forces, which translate into nuclear stopping power well above the adiabatic prediction. Particularly, we observe that most of the alteration of the adiabatic potential in early times comes from the ionization of the core levels of the target ions, not readily screened by the valence electrons.« less

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

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.

Two- and three-body interatomic dispersion energy contributions to binding in molecules and solids

NASA Astrophysics Data System (ADS)

Anatole von Lilienfeld, O.; Tkatchenko, Alexandre

2010-06-01

We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C6 and C9, are computed "on the fly" from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang-Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiricially determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C60 dimer, a peptide (Ala10), an intercalated drug-DNA model [ellipticine-d(CG)2], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.

Two and three-body interatomic dispersion energy contributions to binding in molecules and solids.

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

von Lilienfeld-Toal, Otto Anatole; Tkatchenko, Alexandre

We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C{sub 6} and C{sub 9}, are computed 'on the fly' from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang-Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiriciallymore » determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C{sub 60} dimer, a peptide (Ala{sub 10}), an intercalated drug-DNA model [ellipticine-d(CG){sub 2}], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems.« less

A new parameter-free soft-core potential for silica and its application to simulation of silica anomalies

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

Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M.

2015-12-28

A core-softening of the effective interaction between oxygen atoms in water and silica systems and its role in developing anomalous thermodynamic, transport, and structural properties have been extensively debated. For silica, the progress with addressing these issues has been hampered by a lack of effective interaction models with explicit core-softening. In this work, we present an extension of a two-body soft-core interatomic force field for silica recently reported by us [S. Izvekov and B. M. Rice, J. Chem. Phys. 136(13), 134508 (2012)] to include three-body forces. Similar to two-body interaction terms, the three-body terms are derived using parameter-free force-matching ofmore » the interactions from ab initio MD simulations of liquid silica. The derived shape of the O–Si–O three-body potential term affirms the existence of repulsion softening between oxygen atoms at short separations. The new model shows a good performance in simulating liquid, amorphous, and crystalline silica. By comparing the soft-core model and a similar model with the soft-core suppressed, we demonstrate that the topology reorganization within the local tetrahedral network and the O–O core-softening are two competitive mechanisms responsible for anomalous thermodynamic and kinetic behaviors observed in liquid and amorphous silica. The studied anomalies include the temperature of density maximum locus and anomalous diffusivity in liquid silica, and irreversible densification of amorphous silica. We show that the O–O core-softened interaction enhances the observed anomalies primarily through two mechanisms: facilitating the defect driven structural rearrangements of the silica tetrahedral network and modifying the tetrahedral ordering induced interactions toward multiple characteristic scales, the feature which underlies the thermodynamic anomalies.« 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

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.

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

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.

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.

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.

Atomistically determined phase-field modeling of dislocation dissociation, stacking fault formation, dislocation slip, and reactions in fcc systems

NASA Astrophysics Data System (ADS)

Rezaei Mianroodi, Jaber; Svendsen, Bob

2015-04-01

The purpose of the current work is the development of a phase field model for dislocation dissociation, slip and stacking fault formation in single crystals amenable to determination via atomistic or ab initio methods in the spirit of computational material design. The current approach is based in particular on periodic microelasticity (Wang and Jin, 2001; Bulatov and Cai, 2006; Wang and Li, 2010) to model the strongly non-local elastic interaction of dislocation lines via their (residual) strain fields. These strain fields depend in turn on phase fields which are used to parameterize the energy stored in dislocation lines and stacking faults. This energy storage is modeled here with the help of the "interface" energy concept and model of Cahn and Hilliard (1958) (see also Allen and Cahn, 1979; Wang and Li, 2010). In particular, the "homogeneous" part of this energy is related to the "rigid" (i.e., purely translational) part of the displacement of atoms across the slip plane, while the "gradient" part accounts for energy storage in those regions near the slip plane where atomic displacements deviate from being rigid, e.g., in the dislocation core. Via the attendant global energy scaling, the interface energy model facilitates an atomistic determination of the entire phase field energy as an optimal approximation of the (exact) atomistic energy; no adjustable parameters remain. For simplicity, an interatomic potential and molecular statics are employed for this purpose here; alternatively, ab initio (i.e., DFT-based) methods can be used. To illustrate the current approach, it is applied to determine the phase field free energy for fcc aluminum and copper. The identified models are then applied to modeling of dislocation dissociation, stacking fault formation, glide and dislocation reactions in these materials. As well, the tensile loading of a dislocation loop is considered. In the process, the current thermodynamic picture is compared with the classical mechanical one as based on the Peach-Köhler force.

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

An equivalent dipole analysis of PZT ceramics and lead-free piezoelectric single crystals

NASA Astrophysics Data System (ADS)

Bell, Andrew J.

2016-04-01

The recently proposed Equivalent Dipole Model for describing the electromechanical properties of ionic solids in terms of 3 ions and 2 bonds has been applied to PZT ceramics and lead-free single crystal piezoelectric materials, providing analysis in terms of an effective ionic charge and the asymmetry of the interatomic force constants. For PZT it is shown that, as a function of composition across the morphotropic phase boundary, the dominant bond compliance peaks at 52% ZrO2. The stiffer of the two bonds shows little composition dependence with no anomaly at the phase boundary. The effective charge has a maximum value at 50% ZrO2, decreasing across the phase boundary region, but becoming constant in the rhombohedral phase. The single crystals confirm that both the asymmetry in the force constants and the magnitude of effective charge are equally important in determining the values of the piezoelectric charge coefficient and the electromechanical coupling coefficient. Both are apparently temperature dependent, increasing markedly on approaching the Curie temperature.

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.

Quantum Monte Carlo Simulation of condensed van der Waals Systems

NASA Astrophysics Data System (ADS)

Benali, Anouar; Shulenburger, Luke; Romero, Nichols A.; Kim, Jeongnim; Anatole von Lilienfeld, O.

2012-02-01

Van der Waals forces are as ubiquitous as infamous. While post-Hartree-Fock methods enable accurate estimates of these forces in molecules and clusters, they remain elusive for dealing with many-electron condensed phase systems. We present Quantum Monte Carlo [1,2] results for condensed van der Waals systems. Interatomic many-body contributions to cohesive energies and bulk modulus will be discussed. Numerical evidence is presented for crystals of rare gas atoms, and compared to experiments and methods [3]. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DoE's National Nuclear Security Administration under Contract No. DE-AC04-94AL85000.[4pt] [1] J. Kim, K. Esler, J. McMinis and D. Ceperley, SciDAC 2010, J. of Physics: Conference series, Chattanooga, Tennessee, July 11 2011 [0pt] [2] QMCPACK simulation suite, http://qmcpack.cmscc.org (unpublished)[0pt] [3] O. A. von Lillienfeld and A. Tkatchenko, J. Chem. Phys. 132 234109 (2010)

1,3,5-trinitro-1,3,5-triazine decomposition and chemisorption on Al(111) surface: first-principles molecular dynamics study.

PubMed

Umezawa, Naoto; Kalia, Rajiv K; Nakano, Aiichiro; Vashista, Priya; Shimojo, Fuyuki

2007-06-21

We have investigated the decomposition and chemisorption of a 1,3,5-trinitro-1,3,5-triazine (RDX) molecule on Al(111) surface using molecular dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). The real-space DFT calculations are based on higher-order finite difference and norm-conserving pseudopotential methods. Strong attractive forces between oxygen and aluminum atoms break N-O and N-N bonds in the RDX and, subsequently, the dissociated oxygen atoms and NO molecules oxidize the Al surface. In addition to these Al surface-assisted decompositions, ring cleavage of the RDX molecule is also observed. These reactions occur spontaneously without potential barriers and result in the attachment of the rest of the RDX molecule to the surface. This opens up the possibility of coating Al nanoparticles with RDX molecules to avoid the detrimental effect of oxidation in high energy density material applications.

Twisted ultrathin silicon nanowires: A possible torsion electromechanical nanodevice

NASA Astrophysics Data System (ADS)

Garcia, J. C.; Justo, J. F.

2014-11-01

Nanowires have been considered for a number of applications in nanometrology. In such a context, we have explored the possibility of using ultrathin twisted nanowires as torsion nanobalances to probe forces and torques at molecular level with high precision, a nanoscale system analogous to the Coulomb's torsion balance electrometer. In order to achieve this goal, we performed a first-principles investigation on the structural and electronic properties of twisted silicon nanowires, in their pristine and hydrogenated forms. The results indicated that wires with pentagonal and hexagonal cross-sections are the thinnest stable silicon nanostructures. Additionally, all wires followed a Hooke's law behavior for small twisting deformations. Hydrogenation leads to spontaneous twisting, but with angular spring constants considerably smaller than the ones for the respective pristine forms. We observed considerable changes on the nanowire electronic properties upon twisting, which allows to envision the possibility of correlating the torsional angular deformation with the nanowire electronic transport. This could ultimately allow a direct access to measurements on interatomic forces at molecular level.

REVIEWS OF TOPICAL PROBLEMS: Properties of matter in ultrahigh magnetic fields and the structure of the surface of neutron stars

NASA Astrophysics Data System (ADS)

Liberman, Mikhail A.; Johansson, B.

1995-02-01

The physical properties of atoms, molecules, and solids in ultrahigh magnetic fields B gg 109 G that are believed to exist on the surface of neutron stars are discussed. In these fields, atoms are strongly deformed and elongated along the magnetic field lines; the binding energy and ionizing energy of the atoms are substantially increased and the interatomic interaction is dramatically changed. This strongly modifies the properties of matter at the surface of magnetic neutron stars which are crucial for modelling the pulsar magnetosphere. A scenario for magnetosphere evolution is proposed which suggests free emission for a young pulsar and strong binding of the matter to the surface at a later stage. This later stage is due to strongly bound chains of alternate heavy atoms and light atoms accreted on the surface of the star.

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.

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

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.

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

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

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.

Built-in Electric Field Induced Mechanical Property Change at the Lanthanum Nickelate/Nb-doped Strontium Titanate Interfaces

DOE PAGES

Chien, TeYu; Liu, Jian; Yost, Andrew J.; ...

2016-01-08

The interactions between electric field and the mechanical properties of materials are important for the applications of microelectromechanical and nanoelectromechanical systems, but relatively unexplored for nanoscale materials. Here, we observe an apparent correlation between the change of the fractured topography of Nb-doped SrTiO 3 (Nb:STO) within the presence of a built-in electric field resulting from the Schottky contact at the interface of a metallic LaNiO 3 thin film utilizing cross-sectional scanning tunneling microscopy and spectroscopy. The change of the inter-atomic bond length mechanism is argued to be the most plausible origin. This picture is supported by the strong-electric-field-dependent permittivity inmore » STO and the existence of the dielectric dead layer at the interfaces of STO with metallic films. Finally, these results provided direct evidence and a possible mechanism for the interplay between the electric field and the mechanical properties on the nanoscale for perovskite materials.« 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°.

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.

Conducting a thermal conductivity survey

NASA Technical Reports Server (NTRS)

Allen, P. B.

1985-01-01

A physically transparent approximate theory of phonon decay rates is presented starting from a pair potential model of the interatomic forces in an insulator or semiconductor. The theory applies in the classical regime and relates the 3-phonon decay rate to the third derivative of the pair potential. Phonon dispersion relations do not need to be calculated, as sum rules relate all the needed quantities directly to the pair potential. The Brillouin zone averaged phonon lifetime turns out to involve a dimensionless measure of the anharmonicity multiplied by an effective density of states for 3-phonon decay. Results are given for rare gas and alkali halide crystals. For rare gases, the results are in good agreement with more elaborate perturbation calculations. Comparison to experimental data on phonon linewidths and thermal conductivity are made.

Non-collinear magnetism with analytic Bond-Order Potentials

NASA Astrophysics Data System (ADS)

Ford, Michael E.; Pettifor, D. G.; Drautz, Ralf

2015-03-01

The theory of analytic Bond-Order Potentials as applied to non-collinear magnetic structures of transition metals is extended to take into account explicit rotations of Hamiltonian and local moment matrix elements between locally and globally defined spin-coordinate systems. Expressions for the gradients of the energy with respect to the Hamiltonian matrix elements, the interatomic forces and the magnetic torques are derived. The method is applied to simulations of the rotation of magnetic moments in α iron, as well as α and β manganese, based on d-valent orthogonal tight-binding parametrizations of the electronic structure. A new weighted-average terminator is introduced to improve the convergence of the Bond-Order Potential energies and torques with respect to tight-binding reference values, although the general behavior is qualitatively correct for low-moment expansions.

A study on carbon nanotube bridge as a electromechanical memory device

NASA Astrophysics Data System (ADS)

Kang, Jeong Won; Ha Lee, Jun; Joo Lee, Hoong; Hwang, Ho Jung

2005-04-01

A nanoelectromechanical (NEM) nanotube random access memory (NRAM) device based on carbon nanotube (CNT) was investigated using atomistic simulations. For the CNT-based NEM memory, the mechanical properties of the CNT-bridge and van der Waals interactions between the CNT-bridge and substrate were very important. The critical amplitude of the CNT-bridge was 16% of the length of the CNT-bridge. As molecular dynamics time increased, the CNT-bridge went to the steady state under the electrostatic force with the damping of the potential and the kinetic energies of the CNT-bridge. The interatomic interaction between the CNT-bridge and substrate, value of the CNT-bridge slack, and damping rate of the CNT-bridge were very important for the operation of the NEM memory device as a nonvolatile memory.

Covalence of atoms in the heavier transition metals*

PubMed Central

Pauling, Linus

1977-01-01

The observed magnetic properties of the heavier transition metals permit them to have larger metallic valences than their iron-group congeners. With 0.72 metallic orbital, as found for the iron-group metals, the maximum metallic valence and minimum interatomic distance would occur for 8.28 transargononic electrons. The curves of observed interatomic distances for the close-packed metals of the second and third long periods have minima at this point, supporting the assignment of high valences to these metals. Values of the single-bond radii corresponding to these valences are calculated. PMID:16592407

Vibrational properties and bonding nature of Sb2Se3 and their implications for chalcogenide materials† †Electronic supplementary information (ESI) available: Additional computational data and discussion. See DOI: 10.1039/c5sc00825e Click here for additional data file.

PubMed Central

Deringer, Volker L.; Stoffel, Ralf P.; Wuttig, Matthias

2015-01-01

Antimony selenide (antimonselite, Sb2Se3) is a versatile functional material with emerging applications in solar cells. It also provides an intriguing prototype to study different modes of bonding in solid chalcogenides, all within one crystal structure. In this study, we unravel the complex bonding nature of crystalline Sb2Se3 by using an orbital-based descriptor (the crystal orbital Hamilton population, COHP) and by analysing phonon properties and interatomic force constants. We find particularly interesting behaviour for the medium-range Sb···Se contacts, which still contribute significant stabilisation but are much softer than the “traditional” covalent bonds. These results have implications for the assembly of Sb2Se3 nanostructures, and bond-projected force constants appear as a useful microscopic descriptor for investigating a larger number of chalcogenide functional materials in the future. PMID:29449929

An efficient and accurate framework for calculating lattice thermal conductivity of solids: AFLOW—AAPL Automatic Anharmonic Phonon Library

NASA Astrophysics Data System (ADS)

Plata, Jose J.; Nath, Pinku; Usanmaz, Demet; Carrete, Jesús; Toher, Cormac; de Jong, Maarten; Asta, Mark; Fornari, Marco; Nardelli, Marco Buongiorno; Curtarolo, Stefano

2017-10-01

One of the most accurate approaches for calculating lattice thermal conductivity, , is solving the Boltzmann transport equation starting from third-order anharmonic force constants. In addition to the underlying approximations of ab-initio parameterization, two main challenges are associated with this path: high computational costs and lack of automation in the frameworks using this methodology, which affect the discovery rate of novel materials with ad-hoc properties. Here, the Automatic Anharmonic Phonon Library (AAPL) is presented. It efficiently computes interatomic force constants by making effective use of crystal symmetry analysis, it solves the Boltzmann transport equation to obtain , and allows a fully integrated operation with minimum user intervention, a rational addition to the current high-throughput accelerated materials development framework AFLOW. An "experiment vs. theory" study of the approach is shown, comparing accuracy and speed with respect to other available packages, and for materials characterized by strong electron localization and correlation. Combining AAPL with the pseudo-hybrid functional ACBN0 is possible to improve accuracy without increasing computational requirements.

Revisiting PbTe to identify how thermal conductivity is really limited

NASA Astrophysics Data System (ADS)

Ju, Shenghong; Shiga, Takuma; Feng, Lei; Shiomi, Junichiro

2018-05-01

Due to the long range interaction in lead telluride (PbTe), the transverse optical (TO) phonon becomes soft around the Brillouin zone center. Previous studies have postulated that this zone-center softening causes the low thermal conductivity of PbTe through either enlarged phonon scattering phase space and/or strengthened lattice anharmonicity. In this paper, we reported an extensive sensitivity analysis of the PbTe thermal conductivity to various factors: range and magnitude of harmonic and anharmonic interatomic force constants and phonon wave vectors in the three-phonon scattering processes. The analysis reveals that the softening by long range harmonic interaction itself does not reduce thermal conductivity, and it is the large magnitude of the anharmonic (cubic) force constants that realizes low thermal conductivity, however, not through the TO phonons around the zone center but dominantly through the ones with larger wave vectors in the middle of Brillion zone. The paper clarifies that local band softening cannot be a direct finger print for low thermal conductivity and that the entire Brillion zone needs to be characterized on exploring low thermal conductivity materials.

Hierarchical Multiscale Modeling of Macromolecules and their Assemblies

PubMed Central

Ortoleva, P.; Singharoy, A.; Pankavich, S.

2013-01-01

Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character of such systems often makes traditional molecular dynamics simulation impractical, a multiscale approach has been presented that allows for long-time simulation with atomic detail based on the co-evolution of slowly-varying order parameters (OPs) with the quasi-equilibrium probability density of atomic configurations. However, this approach breaks down when the structural change is extreme, or when nearest-neighbor connectivity of atoms is not maintained. In the current study, a self-consistent approach is presented wherein OPs and a reference structure co-evolve slowly to yield long-time simulation for dynamical soft-matter phenomena such as structural transitions and self-assembly. The development begins with the Liouville equation for N classical atoms and an ansatz on the form of the associated N-atom probability density. Multiscale techniques are used to derive Langevin equations for the coupled OP-configurational dynamics. The net result is a set of equations for the coupled stochastic dynamics of the OPs and centers of mass of the subsystems that constitute a soft material body. The theory is based on an all-atom methodology and an interatomic force field, and therefore enables calibration-free simulations of soft matter, such as macromolecular assemblies. PMID:23671457

Empirical force field-based kinetic Monte Carlo simulation of precipitate evolution and growth in Al-Cu alloys

NASA Astrophysics Data System (ADS)

Joshi, Kaushik; Chaudhuri, Santanu

2016-10-01

Ability to accelerate the morphological evolution of nanoscale precipitates is a fundamental challenge for atomistic simulations. Kinetic Monte Carlo (KMC) methodology is an effective approach for accelerating the evolution of nanoscale systems that are dominated by so-called rare events. The quality and accuracy of energy landscape used in KMC calculations can be significantly improved using DFT-informed interatomic potentials. Using newly developed computational framework that uses molecular simulator LAMMPS as a library function inside KMC solver SPPARKS, we investigated formation and growth of Guiner-Preston (GP) zones in dilute Al-Cu alloys at different temperature and copper concentrations. The KMC simulations with angular dependent potential (ADP) predict formation of coherent disc-shaped monolayers of copper atoms (GPI zones) in early stage. Such monolayers are then gradually transformed into energetically favored GPII phase that has two aluminum layers sandwiched between copper layers. We analyzed the growth kinetics of KMC trajectory using Johnson-Mehl-Avrami (JMA) theory and obtained a phase transformation index close to 1.0. In the presence of grain boundaries, the KMC calculations predict the segregation of copper atoms near the grain boundaries instead of formation of GP zones. The computational framework presented in this work is based on open source potentials and MD simulator and can predict morphological changes during the evolution of the alloys in the bulk and around grain boundaries.

Molecular Dynamics Simulation of Carbon Nanotube Based Gears

NASA Technical Reports Server (NTRS)

Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)

1996-01-01

We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

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.

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.

Lattice dynamics and thermal conductivity of lithium fluoride via first-principles calculations

NASA Astrophysics Data System (ADS)

Liang, Ting; Chen, Wen-Qi; Hu, Cui-E.; Chen, Xiang-Rong; Chen, Qi-Feng

2018-04-01

The lattice thermal conductivity of lithium fluoride (LiF) is accurately computed from a first-principles approach based on an iterative solution of the Boltzmann transport equation. Real-space finite-difference supercell approach is employed to generate the second- and third-order interatomic force constants. The related physical quantities of LiF are calculated by the second- and third- order potential interactions at 30 K-1000 K. The calculated lattice thermal conductivity 13.89 W/(m K) for LiF at room temperature agrees well with the experimental value, demonstrating that the parameter-free approach can furnish precise descriptions of the lattice thermal conductivity for this material. Besides, the Born effective charges, dielectric constants and phonon spectrum of LiF accord well with the existing data. The lattice thermal conductivities for the iterative solution of BTE are also presented.

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.

A comprehensive study of Interatomic Coulombic Decay in argon dimers: Extracting R-dependent absolute decay rates from the experiment

DOE PAGES

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

2016-09-15

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.

ReaxFF Grand Canonical Monte Carlo simulation of adsorption and dissociation of oxygen on platinum (111)

NASA Astrophysics Data System (ADS)

Valentini, Paolo; Schwartzentruber, Thomas E.; Cozmuta, Ioana

2011-12-01

Atomic-level Grand Canonical Monte Carlo (GCMC) simulations equipped with a reactive force field (ReaxFF) are used to study atomic oxygen adsorption on a Pt(111) surface. The off-lattice GCMC calculations presented here rely solely on the interatomic potential and do not necessitate the pre-computation of surface adlayer structures and their interpolation. As such, they provide a predictive description of adsorbate phases. In this study, validation is obtained with experimental evidence (steric heats of adsorption and isotherms) as well as DFT-based state diagrams available in the literature. The ReaxFF computed steric heats of adsorption agree well with experimental data, and this study clearly shows that indirect dissociative adsorption of O2 on Pt(111) is an activated process at non-zero coverages, with an activation energy that monotonically increases with coverage. At a coverage of 0.25 ML, a highly ordered p(2 × 2) adlayer is found, in agreement with several low-energy electron diffraction observations. Isotherms obtained from the GCMC simulations compare qualitatively and quantitatively well with previous DFT-based state diagrams, but are in disagreement with the experimental data sets available. ReaxFF GCMC simulations at very high coverages show that O atoms prefer to bind in fcc hollow sites, at least up to 0.8 ML considered in the present work. At moderate coverages, little to no disorder appears in the Pt lattice. At high coverages, some Pt atoms markedly protrude out of the surface plane. This observation is in qualitative agreement with recent STM images of an oxygen covered Pt surface. The use of the GCMC technique based on a transferable potential is particularly valuable to produce more realistic systems (adsorbent and adsorbate) to be used in subsequent dynamical simulations (Molecular Dynamics) to address recombination reactions (via either Eley-Rideal or Langmuir-Hinshelwood mechanisms) on variously covered surfaces. By using GCMC and Molecular Dynamics simulations, the ReaxFF force field can be a valuable tool for understanding heterogeneous catalysis on a solid surface. Finally, the use of a reactive potential is a necessary requirement to investigate problems where dissociative adsorption occurs, as typical of many important catalytic processes.

Solar wind ion impacts into ice surfaces: A molecular-dynamics study using the REAX force field

NASA Astrophysics Data System (ADS)

Anders, Christian; Urbassek, Herbert M.

2017-01-01

Molecular dynamics simulation is used to study the effects of solar-wind ion irradiation on an ice target, focusing on the effects of nuclear energy deposition. A reactive force field (REAX) interatomic interaction potential is employed that allows us to model the breaking and formation of molecular bonds and hence to follow the chemistry occurring in the target. As ions we study H and He ions as typical constituents of the solar wind, and Ne as an example of a heavier ion; they impact at the speed of maximum flux in the solar wind, 400 km/s. The ice consists of a mixture of H2O, CO2, CH3OH and NH3. We find that molecular dissociations occur within 0.2 ps after ion impact and new products are formed up to a time of 1 ps; only water has a slower dynamics, due to highly mobile H atoms allowing for late recombinations. The number of dissociations, and hence also of product molecules increases from H over He to Ne ion projectiles and can be quantified by the amount of energy deposited in the target by these ions. The most abundant products formed include CO, OH and NH2. Reaction products are most complex for Ne impact, and include H3O, formaldehyde (H2CO), HO2, and NO. Formaldehyde is important as it is formed relatively frequently and is known as a precursor in the formation of sugars. In addition, molecules containing all CHON elements are formed, among which are CH2NO, CONH, methanolamine (CH5NO), and ethyne (C2H2). Repeated impacts generate novel, and more complex product species; we found CN, CH4, CH3NO, methylamine (CH3NH2), and acetamide (CH3CONH2), among others; the complex species are formed less frequently than the simple fragments. Sputtering occurs for all projectiles, even H. The ejecta are either original molecules - in particular CO2 - or simple fragments; only few product molecules are emitted.

Examination of the Atomic Pair Distribution Function (PDF) of SiC Nanocrystals by In-situ High Pressure Diffraction

NASA Technical Reports Server (NTRS)

Grzanka, E.; Stelmakh, S.; Gierlotka, S.; Zhao, Y.; Palosz, B.; Palosz, W.

2003-01-01

Key properties of nanocrystals are determined by their real atomic structure, therefore a reasonable understanding and meaningful interpretation of their properties requires a realistic model of the structure. In this paper we present an evidence of a complex response of the lattice distances to external pressure indicating a presence of a complex structure of Sic nanopowders. The experiments were performed on nanocrystalline Sic subjected to hydrostatic or isostatic pressure using synchrotron and neutron powder diffraction. Elastic properties of the samples were examined based on X-ray diffraction data using a Diamond Anvil Cell (DAC) in HASYLAB at DESY. The dependence'of the lattice parameters and of the Bragg reflections width with pressure exhibits a ha1 nature of the properties (compressibilities) of the powders and indicates a complex structure of the grains. We interpreted tws behaviour as originating from different elastic properties of the grain interior and surface. Analysis of the dependence of individual interatomic distances on pressure was based on in-situ neutron diffraction measurements done with HbD diffractometer at LANSCE in Los Alamos National Laboratory with the Paris-Edinburgh cell under pressures up to 8 GPa (Qmax = 26/A). Interatomic distances were obtained by PDF analysis using the PDFgetN program. We have found that the interatomic distances undergo a complex, non-monotonic changes. Even under substantial pressures a considerable relaxation of the lattice may take place: some interatomic distances increase with an increase in pressure. We relate this phenomenon to: (1), changes of the microstructure of the densified material, in particular breaking of its fractal chain structure and, (2), its complex structure resembling that of a material composed of two phases, each with its distinct elastic properties.

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.

Calculations on Isotope Separation by Laser Induced Photodissociation of Polyatomic Molecules. Final Report

DOE R&D Accomplishments Database

Lamb, W. E. Jr.

1978-11-01

This report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. Newton`s equations of motion were integrated for the atoms of the SF{sub 6} molecule including the laser field interaction. The first year`s work has been largely dedicated to obtaining a suitable interatomic potential valid for arbitrary configurations of the seven particles. This potential gives the correct symmetry of the molecule, the equilibrium configuration, the frequencies of the six distinct normal modes of oscillation and the correct (or assumed) value of the total potential energy of the molecule. Other conditions can easily be imposed in order to obtain a more refined potential energy function, for example, by making allowance for anharmonicity data. A suitable expression was also obtained for the interaction energy between a laser field and the polyatomic molecule. The electromagnetic field is treated classically, and it would be easily possible to treat the cases of time dependent pulses, frequency modulation and noise.

Thermal and elastic properties of solid neon

NASA Astrophysics Data System (ADS)

Acocella, Dominic; Horton, George K.; Cowley, E. Roger

2000-04-01

We apply the improved effective potential Monte Carlo (IEP) and the improved self-consistent (ISC) theories to study the thermal and elastic properties of natural solid Ne. As a first orientation, we use the (12-6) Lennard-Jones (LJ) potential for first-neighbor forces only. The two parameters in the potential are determined from the 0 K lattice spacing and the sublimation energy of the crystal. We also create a realistic interatomic potential for the Ne dimer based on our study of the existing literature. When supplemented by many-body contributions, this potential is also used with ISC and IEP. The results are then compared with the experimental data in the literature. We conclude that our realistic potential which we regard as the best currently available is not significantly superior in accounting for the experimental data to the LJ potential, though both give a decent account of the experimental data.

Gaussian approximation potential modeling of lithium intercalation in carbon nanostructures

NASA Astrophysics Data System (ADS)

Fujikake, So; Deringer, Volker L.; Lee, Tae Hoon; Krynski, Marcin; Elliott, Stephen R.; Csányi, Gábor

2018-06-01

We demonstrate how machine-learning based interatomic potentials can be used to model guest atoms in host structures. Specifically, we generate Gaussian approximation potential (GAP) models for the interaction of lithium atoms with graphene, graphite, and disordered carbon nanostructures, based on reference density functional theory data. Rather than treating the full Li-C system, we demonstrate how the energy and force differences arising from Li intercalation can be modeled and then added to a (prexisting and unmodified) GAP model of pure elemental carbon. Furthermore, we show the benefit of using an explicit pair potential fit to capture "effective" Li-Li interactions and to improve the performance of the GAP model. This provides proof-of-concept for modeling guest atoms in host frameworks with machine-learning based potentials and in the longer run is promising for carrying out detailed atomistic studies of battery materials.

Electronic processes in fast thermite chemical reactions: a first-principles molecular dynamics study.

PubMed

Shimojo, Fuyuki; Nakano, Aiichiro; Kalia, Rajiv K; Vashishta, Priya

2008-06-01

Rapid reaction of a molten metal with an oxide is the key to understanding recently discovered fast reactions in nanothermite composites. We have investigated the thermite reaction of Fe2O3 with aluminum by molecular dynamics simulations with interatomic forces calculated quantum mechanically in the framework of the density functional theory. A redox reaction to form iron metal and Al2O3 initiates with the rapid formation of Al-O bonds at the interface within 1 ps, followed by the propagation of the combustion front with a velocity of 70 m/s for at least 5 ps at 2000 K. The reaction time for an oxygen atom to change character from Fe2O3 type to Al2O3 type at the interface is estimated to be 1.7+/-0.9 ps , and bond-overlap population analysis has been used to calculate reaction rates.

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.

Breaking the icosahedra in boron carbide

PubMed Central

Xie, Kelvin Y.; An, Qi; Sato, Takanori; Breen, Andrew J.; Ringer, Simon P.; Goddard, William A.; Cairney, Julie M.; Hemker, Kevin J.

2016-01-01

Findings of laser-assisted atom probe tomography experiments on boron carbide elucidate an approach for characterizing the atomic structure and interatomic bonding of molecules associated with extraordinary structural stability. The discovery of crystallographic planes in these boron carbide datasets substantiates that crystallinity is maintained to the point of field evaporation, and characterization of individual ionization events gives unexpected evidence of the destruction of individual icosahedra. Statistical analyses of the ions created during the field evaporation process have been used to deduce relative atomic bond strengths and show that the icosahedra in boron carbide are not as stable as anticipated. Combined with quantum mechanics simulations, this result provides insight into the structural instability and amorphization of boron carbide. The temporal, spatial, and compositional information provided by atom probe tomography makes it a unique platform for elucidating the relative stability and interactions of primary building blocks in hierarchically crystalline materials. PMID:27790982

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.

POTENTIOLOGY (noun): study focusing on the development of new interatomic pair potential forms; sometimes pursued in an obsessive compulsive manner [The New Yorel Dictionary (2002, unpublished)].} IN SPECTROSCOPY: IT MATTERS

NASA Astrophysics Data System (ADS)

Le Roy, Robert J.

2009-06-01

Spectroscopists have long attempted to summarize what they know about small molecules in terms of a knowledge of potential energy curves or surfaces. For most of the past century, this involved deducing polynomial-expansion force-field coefficients from energy level expressions fitted to experimental data, or for diatomic molecules, by generating tables of many-digit RKR turning points from such expressions. In recent years, however, it has become increasingly common either to use high-level ab initio calculations to compute the desired potentials, or to determine parametrized global analytic potential functions from direct fits to spectroscopic data. In the former case, this invoked a need for robust, flexible, compact, and `portable' analytic potentials for summarizing the information contained in the (sometimes very large numbers of) ab initio points, and making them `user friendly'. In the latter case, the same properties are required for potentials used in the least-squares fitting procedure. In both cases, there is also a cardinal need for potential function forms that extrapolate sensibly, beyond the range of the experimental data or ab initio points. This talk will describe some recent developments in this area, and make a case for what is arguably the `best' general-purpose analytic potential function form now available. Applications to both diatomic molecules and simple polyatomic molecules will be discussed. footnote

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.

Native flexibility of structurally homologous proteins: insights from anisotropic network model.

PubMed

Sarkar, Ranja

2017-01-01

Single-molecule microscopic experiments can measure the mechanical response of proteins to pulling forces applied externally along different directions (inducing different residue pairs in the proteins by uniaxial tension). This response to external forces away from equilibrium should in principle, correlate with the flexibility or stiffness of proteins in their folded states. Here, a simple topology-based atomistic anisotropic network model (ANM) is shown which captures the protein flexibility as a fundamental property that determines the collective dynamics and hence, the protein conformations in native state. An all-atom ANM is used to define two measures of protein flexibility in the native state. One measure quantifies overall stiffness of the protein and the other one quantifies protein stiffness along a particular direction which is effectively the mechanical resistance of the protein towards external pulling force exerted along that direction. These measures are sensitive to the protein sequence and yields reliable values through computations of normal modes of the protein. ANM at an atomistic level (heavy atoms) explains the experimental (atomic force microscopy) observations viz., different mechanical stability of structurally similar but sequentially distinct proteins which, otherwise were implied to possess similar mechanical properties from analytical/theoretical coarse-grained (backbone only) models. The results are exclusively demonstrated for human fibronectin (FN) protein domains. The topology of interatomic contacts in the folded states of proteins essentially determines the native flexibility. The mechanical differences of topologically similar proteins are captured from a high-resolution (atomic level) ANM at a low computational cost. The relative trend in flexibility of such proteins is reflected in their stability differences that they exhibit while unfolding in atomic force microscopic (AFM) experiments.

Rapid insights from remote sensing in the geosciences

NASA Astrophysics Data System (ADS)

Plaza, Antonio

2015-03-01

The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP 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 on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the communication cost remains modest. We discuss a variety of strategies for implementing SNAP in the LAMMPS molecular dynamics package. We present scaling results obtained running SNAP on three different classes of machine: a conventional Intel Xeon CPU cluster; the Titan GPU-based system; and the combined Sequoia and Vulcan BlueGene/Q. The growing availability of capacity computing for atomistic materials modeling has encouraged the use of high-accuracy computationally intensive interatomic potentials, such as SNAP. These potentials also happen to scale well on petascale computing platforms. SNAP 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 on to a basis of hyperspherical harmonics in four dimensions. The computational cost per atom is much greater than that of simpler potentials such as Lennard-Jones or EAM, while the communication cost remains modest. We discuss a variety of strategies for implementing SNAP in the LAMMPS molecular dynamics package. We present scaling results obtained running SNAP on three different classes of machine: a conventional Intel Xeon CPU cluster; the Titan GPU-based system; and the combined Sequoia and Vulcan BlueGene/Q. 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 Energy's National Nuclear Security Admin. under Contract DE-AC04-94AL85000.

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.

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>.

The MOLDY short-range molecular dynamics package

NASA Astrophysics Data System (ADS)

Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

2011-12-01

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces. Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello-Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals. Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order- N scaling will fail. Different interatomic potential forms require recompilation of the code. Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects. Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop.

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.

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.

Surface passivation for tight-binding calculations of covalent solids.

PubMed

Bernstein, N

2007-07-04

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp(3) hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Surface passivation for tight-binding calculations of covalent solids

NASA Astrophysics Data System (ADS)

Bernstein, N.

2007-07-01

Simulation of a cluster representing a finite portion of a larger covalently bonded system requires the passivation of the cluster surface. We compute the effects of an explicit hybrid orbital passivation (EHOP) on the atomic structure in a model bulk, three-dimensional, narrow gap semiconductor, which is very different from the wide gap, quasi-one-dimensional organic molecules where most passivation schemes have been studied in detail. The EHOP approach is directly applicable to minimal atomic orbital basis methods such as tight-binding. Each broken bond is passivated by a hybrid created from an explicitly expressed linear combination of basis orbitals, chosen to represent the contribution of the missing neighbour, e.g. a sp3 hybrid for a single bond. The method is tested by computing the forces on atoms near a point defect as a function of cluster geometry. We show that, compared to alternatives such as pseudo-hydrogen passivation, the force on an atom converges to the correct bulk limit more quickly as a function of cluster radius, and that the force is more stable with respect to perturbations in the position of the cluster centre. The EHOP method also obviates the need for parameterizing the interactions between the system atoms and the passivating atoms. The method is useful for cluster calculations of non-periodic defects in large systems and for hybrid schemes that simulate large systems by treating finite regions with a quantum-mechanical model, coupled to an interatomic potential description of the rest of the system.

Modified dipole-dipole interaction and dissipation in an atomic ensemble near surfaces

NASA Astrophysics Data System (ADS)

Jones, Ryan; Needham, Jemma A.; Lesanovsky, Igor; Intravaia, Francesco; Olmos, Beatriz

2018-05-01

We study how the radiative properties of a dense ensemble of atoms can be modified when they are placed near or between metallic or dielectric surfaces. If the average separation between the atoms is comparable or smaller than the wavelength of the scattered photons, the coupling to the radiation field induces long-range coherent interactions based on the interatomic exchange of virtual photons. Moreover, the incoherent scattering of photons back to the electromagnetic field is known to be a many-body process, characterized by the appearance of superradiant and subradiant emission modes. By changing the radiation field properties, in this case by considering a layered medium where the atoms are near metallic or dielectric surfaces, these scattering properties can be dramatically modified. We perform a detailed study of these effects, with focus on experimentally relevant parameter regimes. We finish with a specific application in the context of quantum information storage, where the presence of a nearby surface is shown to increase the storage time of an atomic excitation that is transported across a one-dimensional chain.

Anomalous random correlations of force constants on the lattice dynamical properties of disordered Au-Fe alloys

NASA Astrophysics Data System (ADS)

Kangsabanik, Jiban; Chouhan, Rajiv K.; Johnson, D. D.; Alam, Aftab

2017-09-01

Gold iron (Au-Fe) alloys are of immense interest due to their biocompatibility, anomalous Hall conductivity, and applications in various medical treatments. However, irrespective of the method of preparation, they often exhibit a high level of disorder with properties sensitive to the thermal or magnetic annealing temperatures. We calculate the lattice dynamical properties of Au1 -xFex alloys using density functional theory methods where, being multisite properties, reliable interatomic force constant (IFC) calculations in disordered alloys remain a challenge. We follow a twofold approach: (1) an accurate IFC calculation in an environment with nominally zero chemical pair correlations to mimic the homogeneously disordered alloy and (2) a configurational averaging for the desired phonon properties (e.g., dispersion, density of states, and entropy). We find an anomalous change in the IFC's and phonon dispersion (split bands) near x =0.19 , which is attributed to the local stiffening of the Au-Au bonds when Au is in the vicinity of Fe. Other results based on mechanical and thermophysical properties reflect a similar anomaly: Phonon entropy, e.g., becomes negative below x =0.19 , suggesting a tendency for chemical unmixing, reflecting the onset of a miscibility gap in the phase diagram. Our results match fairly well with reported data wherever available.

Analysis of Carbon Nanotubes and Graphene Nanoribbons with Folded Racket Shapes

NASA Astrophysics Data System (ADS)

Borum, Andy; Plaut, Raymond; Dillard, David

2011-10-01

When carbon nanotubes and graphene nanoribbons become long, they may self-fold and form tennis racket-like shapes. This phenomenon is analyzed in two ways by treating a nanotube or nanoribbon as an elastica. First, an approach from adhesion science is used, in which the two sides of the racket handle are assumed to be straight and bonded together with constant or no separation. New analytical results are obtained involving the shape, bending energy, and adhesion energy of the self-folded structures. These relations show that the dimensions of the racket loop are proportional to the square root of the flexural rigidity. The second analysis uses the Lennard-Jones potential to model the van der Waals forces between the two sides of the racket. A nanoribbon is considered, and the interatomic forces are integrated along the length and across the width of the nanoribbon. The resulting integro-differential equations are solved using the finite difference method. The racket handle is found to be in compression and the separation between the two sides of the racket handle decreases in the direction of the racket loop. The results for the Lennard-Jones model approximately satisfy the relationship between the dimensions and the flexural rigidity found using the adhesion model.

Anomalous random correlations of force constants on the lattice dynamical properties of disordered Au-Fe alloys

DOE PAGES

Kangsabanik, Jiban; Chouhan, Rajiv K.; Johnson, D. D.; ...

2017-09-20

Here, gold iron (Au-Fe) alloys are of immense interest due to their biocompatibility, anomalous Hall conductivity, and applications in various medical treatments. However, irrespective of the method of preparation, they often exhibit a high level of disorder with properties sensitive to the thermal or magnetic annealing temperatures. We calculate the lattice dynamical properties of Au 1–xFe x alloys using density functional theory methods where, being multisite properties, reliable interatomic force constant (IFC) calculations in disordered alloys remain a challenge. We follow a twofold approach: an accurate IFC calculation in an environment with nominally zero chemical pair correlations to mimic themore » homogeneously disordered alloy and a configurational averaging for the desired phonon properties (e.g., dispersion, density of states, and entropy). We find an anomalous change in the IFC's and phonon dispersion (split bands) near x=0.19, which is attributed to the local stiffening of the Au-Au bonds when Au is in the vicinity of Fe. Other results based on mechanical and thermophysical properties reflect a similar anomaly: Phonon entropy, e.g., becomes negative below x=0.19, suggesting a tendency for chemical unmixing, reflecting the onset of a miscibility gap in the phase diagram. Our results match fairly well with reported data wherever available.« less

Anomalous random correlations of force constants on the lattice dynamical properties of disordered Au-Fe alloys

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

Kangsabanik, Jiban; Chouhan, Rajiv K.; Johnson, D. D.

Here, gold iron (Au-Fe) alloys are of immense interest due to their biocompatibility, anomalous Hall conductivity, and applications in various medical treatments. However, irrespective of the method of preparation, they often exhibit a high level of disorder with properties sensitive to the thermal or magnetic annealing temperatures. We calculate the lattice dynamical properties of Au 1–xFe x alloys using density functional theory methods where, being multisite properties, reliable interatomic force constant (IFC) calculations in disordered alloys remain a challenge. We follow a twofold approach: an accurate IFC calculation in an environment with nominally zero chemical pair correlations to mimic themore » homogeneously disordered alloy and a configurational averaging for the desired phonon properties (e.g., dispersion, density of states, and entropy). We find an anomalous change in the IFC's and phonon dispersion (split bands) near x=0.19, which is attributed to the local stiffening of the Au-Au bonds when Au is in the vicinity of Fe. Other results based on mechanical and thermophysical properties reflect a similar anomaly: Phonon entropy, e.g., becomes negative below x=0.19, suggesting a tendency for chemical unmixing, reflecting the onset of a miscibility gap in the phase diagram. Our results match fairly well with reported data wherever available.« less

Probing periodic potential of crystals via strong-field re-scattering

NASA Astrophysics Data System (ADS)

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

2018-06-01

Strong-field ionization and re-scattering phenomena have been used to image angstrom-scale structures of isolated molecules in the gas phase. These methods typically make use of the anisotropic response of the participating molecular orbital. Recently, an anisotropic strong-field response has also been observed in high-order harmonic generation (HHG) from bulk crystals (2016 Nat. Phys. 13 345). In a (100) cut magnesium oxide crystal, extreme ultraviolet high-harmonics are found to depend strongly on the crystal structure and inter-atomic bonding. Here, we extend these measurements to other two important crystal orientations: (111) and (110). We find that HHG from these orientations is also strongly anisotropic. The underlying dynamics is understood using a real-space picture, where high-harmonics are produced via coherent collision of strong-field driven electrons from the atomic sites, including from the nearest neighbor atoms. We find that harmonic efficiency is enhanced when semi-classical electron trajectories connect to the concentrated valence charge distribution regions around the atomic cores. Similarly, the efficiency is suppressed when the trajectories miss the atomic cores. These results further support the real-space picture of HHG with implications for retrieving the periodic potential of the crystal, if not the wavefunctions in three-dimensions.

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.

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.

Importance of interatomic spacing in catalytic reduction of oxygen in phosphoric acid

NASA Technical Reports Server (NTRS)

Jalan, V.; Taylor, E. J.

1983-01-01

A correlation between the nearest-neighbor distance and the oxygen reduction activity of various platinum alloys is reported. It is proposed that the distance between nearest-neighbor Pt atoms on the surface of a supported catalyst is not ideal for dual site absorption of O2 or 'HO2' and that the introduction of foreign atoms which reduce the Pt nearest-neighbor spacing would result in higher oxygen reduction activity. This may allow the critical 0-0 bond interatomic distance and hence the optimum Pt-Pt separation for bond rupture to be determined from quantum chemical calculations. A composite analysis shows that the data on supported Pt alloys are consistent with Appleby's (1970) data on bulk metals with respect to specific activity, activation energy, preexponential factor, and percent d-band character.

Observation of correlated electronic decay in expanding clusters triggered by near-infrared fields

PubMed Central

Schütte, B.; Arbeiter, M.; Fennel, T.; Jabbari, G.; Kuleff, A.I.; Vrakking, M.J.J.; Rouzée, A.

2015-01-01

When an excited atom is embedded into an environment, novel relaxation pathways can emerge that are absent for isolated atoms. A well-known example is interatomic Coulombic decay, where an excited atom relaxes by transferring its excess energy to another atom in the environment, leading to its ionization. Such processes have been observed in clusters ionized by extreme-ultraviolet and X-ray lasers. Here, we report on a correlated electronic decay process that occurs following nanoplasma formation and Rydberg atom generation in the ionization of clusters by intense, non-resonant infrared laser fields. Relaxation of the Rydberg states and transfer of the available electronic energy to adjacent electrons in Rydberg states or quasifree electrons in the expanding nanoplasma leaves a distinct signature in the electron kinetic energy spectrum. These so far unobserved electron-correlation-driven energy transfer processes may play a significant role in the response of any nano-scale system to intense laser light. PMID:26469997

Frontiers of Theoretical Research on Shape Memory Alloys: A General Overview

NASA Astrophysics Data System (ADS)

Chowdhury, Piyas

2018-03-01

In this concise review, general aspects of modeling shape memory alloys (SMAs) are recounted. Different approaches are discussed under four general categories, namely, (a) macro-phenomenological, (b) micromechanical, (c) molecular dynamics, and (d) first principles models. Macro-phenomenological theories, stemming from empirical formulations depicting continuum elastic, plastic, and phase transformation, are primarily of engineering interest, whereby the performance of SMA-made components is investigated. Micromechanical endeavors are generally geared towards understanding microstructural phenomena within continuum mechanics such as the accommodation of straining due to phase change as well as role of precipitates. By contrast, molecular dynamics, being a more recently emerging computational technique, concerns attributes of discrete lattice structures, and thus captures SMA deformation mechanism by means of empirically reconstructing interatomic bonding forces. Finally, ab initio theories utilize quantum mechanical framework to peek into atomistic foundation of deformation, and can pave the way for studying the role of solid-sate effects. With specific examples, this paper provides concise descriptions of each category along with their relative merits and emphases.

First principles Peierls-Boltzmann phonon thermal transport: A topical review

DOE PAGES

Lindsay, Lucas

2016-08-05

The advent of coupled thermal transport calculations with interatomic forces derived from density functional theory has ushered in a new era of fundamental microscopic insight into lattice thermal conductivity. Subsequently, significant new understanding of phonon transport behavior has been developed with these methods, and because they are parameter free and successfully benchmarked against a variety of systems, they also provide reliable predictions of thermal transport in systems for which little is known. This topical review will describe the foundation from which first principles Peierls-Boltzmann transport equation methods have been developed, and briefly describe important necessary ingredients for accurate calculations. Samplemore » highlights of reported work will be presented to illustrate the capabilities and challenges of these techniques, and to demonstrate the suite of tools available, with an emphasis on thermal transport in micro- and nano-scale systems. In conclusion, future challenges and opportunities will be discussed, drawing attention to prospects for methods development and applications.« less

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

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.

The self-consistent calculation of pseudo-molecule energy levels, construction of energy level correlation diagrams and an automated computation system for SCF-X(Alpha)-SW calculations

NASA Technical Reports Server (NTRS)

Schlosser, H.

1981-01-01

The self consistent calculation of the electronic energy levels of noble gas pseudomolecules formed when a metal surface is bombarded by noble gas ions is discussed along with the construction of energy level correlation diagrams as a function of interatomic spacing. The self consistent field x alpha scattered wave (SCF-Xalpha-SW) method is utilized. Preliminary results on the Ne-Mg system are given. An interactive x alpha programming system, implemented on the LeRC IBM 370 computer, is described in detail. This automated system makes use of special PROCDEFS (procedure definitions) to minimize the data to be entered manually at a remote terminal. Listings of the special PROCDEFS and of typical input data are given.

Effect of a core-softened O-O interatomic interaction on the shock compression of fused silica

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Weingarten, N. Scott; Byrd, Edward F. C.

2018-03-01

Isotropic soft-core potentials have attracted considerable attention due to their ability to reproduce thermodynamic, dynamic, and structural anomalies observed in tetrahedral network-forming compounds such as water and silica. The aim of the present work is to assess the relevance of effective core-softening pertinent to the oxygen-oxygen interaction in silica to the thermodynamics and phase change mechanisms that occur in shock compressed fused silica. We utilize the MD simulation method with a recently published numerical interatomic potential derived from an ab initio MD simulation of liquid silica via force-matching. The resulting potential indicates an effective shoulder-like core-softening of the oxygen-oxygen repulsion. To better understand the role of the core-softening we analyze two derivative force-matching potentials in which the soft-core is replaced with a repulsive core either in the three-body potential term or in all the potential terms. Our analysis is further augmented by a comparison with several popular empirical models for silica that lack an explicit core-softening. The first outstanding feature of shock compressed glass reproduced with the soft-core models but not with the other models is that the shock compression values at pressures above 20 GPa are larger than those observed under hydrostatic compression (an anomalous shock Hugoniot densification). Our calculations indicate the occurrence of a phase transformation along the shock Hugoniot that we link to the O-O repulsion core-softening. The phase transformation is associated with a Hugoniot temperature reversal similar to that observed experimentally. With the soft-core models, the phase change is an isostructural transformation between amorphous polymorphs with no associated melting event. We further examine the nature of the structural transformation by comparing it to the Hugoniot calculations for stishovite. For stishovite, the Hugoniot exhibits temperature reversal and associated phase transformation, which is a transition to a disordered phase (liquid or dense amorphous), regardless of whether or not the model accounts for core-softening. The onset pressures of the transformation predicted by different models show a wide scatter within 60-110 GPa; for potentials without core-softening, the onset pressure is much higher than 110 GPa. Our results show that the core-softening of the interaction in the oxygen subsystem of silica is the key mechanism for the structural transformation and thermodynamics in shock compressed silica. These results may provide an important contribution to a unified picture of anomalous response to shock compression observed in other network-forming oxides and single-component systems with core-softening of effective interactions.

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

A Relationship Between the 2-body Energy of Kaxiras Pandey and Pearson Takai Halicioglu Tiller Potential Functions

NASA Astrophysics Data System (ADS)

Lim, Teik-Cheng

2004-01-01

A parametric relationship between the Pearson Takai Halicioglu Tiller (PTHT) and the Kaxiras Pandey (KP) empirical potential energy functions is developed for the case of 2-body interaction. The need for such relationship arises when preferred parametric data and adopted software correspond to different potential functions. The analytical relationship was obtained by equating the potential functions' derivatives at zeroth, first and second order with respect to the interatomic distance at the equilibrium bond length, followed by comparison of coefficients in the repulsive and attractive terms. Plots of non-dimensional 2-body energy versus the nondimensional interatomic distance verified the analytical relationships developed herein. The discrepancy revealed in theoretical plots suggests that the 2-body PTHT and KP potentials are more suitable for curve-fitting "softer" and "harder" bonds respectively.

The effect of low temperature thermal annealing on the magnetic properties of Heusler Ni-Mn-Sn melt-spun ribbons

NASA Astrophysics Data System (ADS)

Llamazares, J. L. Sánchez; Quintana-Nedelcos, A.; Ríos-Jara, D.; Sánchez-Valdes, C. F.; García-Fernández, T.; García, C.

2016-03-01

We report the effect of low temperature vacuum annealing (823 K; 550 °C) on the elemental chemical composition, structural phase transition temperatures, phase structure, and magnetic properties of Ni50.6Mn36.3Sn13.1 as-solidified ribbons. Their elemental chemical composition, highly oriented columnar-like microstructure and single-phase character (L21-type crystal structure for austenite) remain unchanged after this low temperature annealing. Annealed ribbons show a reduction of interatomic distances which lead to a small change in the characteristic phase transition temperatures ( 3-6 K) but to a significant rise of 73 and 63% in the saturation magnetization of the martensite and austenite phases, respectively, that can be strictly ascribed to the strengthening of ferromagnetic interactions due to the change in interatomic distances.

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.

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.

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.

A classical mechanics model for the interpretation of piezoelectric property data

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

Bell, Andrew J., E-mail: a.j.bell@leeds.ac.uk

2015-12-14

In order to provide a means of understanding, the relationship between the primary electromechanical coefficients and simple crystal chemistry parameters for piezoelectric materials, a static analysis of a 3 atom, dipolar molecule has been undertaken to derive relationships for elastic compliance s{sup E}, dielectric permittivity ε{sup X}, and piezoelectric charge coefficient d in terms of an effective ionic charge and two inter-atomic force constants. The relationships demonstrate the mutual interdependence of the three coefficients, in keeping with experimental evidence from a large dataset of commercial piezoelectric materials. It is shown that the electromechanical coupling coefficient k is purely an expressionmore » of the asymmetry in the two force constants or bond compliances. The treatment is extended to show that the quadratic electrostriction relation between strain and polarization, in both centrosymmetric and non-centrosymmetric systems, is due to the presence of a non-zero 2nd order term in the bond compliance. Comparison with experimental data explains the counter-intuitive, positive correlation of k with s{sup E} and ε{sup X} and supports the proposition that high piezoelectric activity in single crystals is dominated by large compliance coupled with asymmetry in the sub-cell force constants. However, the analysis also shows that in polycrystalline materials, the dielectric anisotropy of the constituent crystals can be more important for attaining large charge coefficients. The model provides a completely new methodology for the interpretation of piezoelectric and electrostrictive property data and suggests methods for rapid screening for high activity in candidate piezoelectric materials, both experimentally and by novel interrogation of ab initio calculations.« less

Modeling of crack growth under mixed-mode loading by a molecular dynamics method and a linear fracture mechanics approach

NASA Astrophysics Data System (ADS)

Stepanova, L. V.

2017-12-01

Atomistic simulations of the central crack growth process in an infinite plane medium under mixed-mode loading using Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), a classical molecular dynamics code, are performed. The inter-atomic potential used in this investigation is the Embedded Atom Method (EAM) potential. Plane specimens with an initial central crack are subjected to mixed-mode loadings. The simulation cell contains 400,000 atoms. The crack propagation direction angles under different values of the mixity parameter in a wide range of values from pure tensile loading to pure shear loading in a wide range of temperatures (from 0.1 K to 800 K) are obtained and analyzed. It is shown that the crack propagation direction angles obtained by molecular dynamics coincide with the crack propagation direction angles given by the multi-parameter fracture criteria based on the strain energy density and the multi-parameter description of the crack-tip fields. The multi-parameter fracture criteria are based on the multi-parameter stress field description taking into account the higher order terms of the Williams series expansion of the crack tip fields.

Quantum molecular dynamics simulations of dense matter

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

Collins, L.; Kress, J.; Troullier, N.

1997-12-31

The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB,more » which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.« less

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.

Local structures around the substituted elements in mixed layered oxides

PubMed Central

Akama, Shota; Kobayashi, Wataru; Amaha, Kaoru; Niwa, Hideharu; Nitani, Hiroaki; Moritomo, Yutaka

2017-01-01

The chemical substitution of a transition metal (M) is an effective method to improve the functionality of a material, such as its electrochemical, magnetic, and dielectric properties. The substitution, however, causes local lattice distortion because the difference in the ionic radius (r) modifies the local interatomic distances. Here, we systematically investigated the local structures in the pure (x = 0.0) and mixed (x = 0.05 or 0.1) layered oxides, Na(M1−xM′x)O2 (M and M′ are the majority and minority transition metals, respectively), by means of extended X-ray absorption fine structure (EXAFS) analysis. We found that the local interatomic distance (dM-O) around the minority element approaches that around the majority element to reduces the local lattice distortion. We further found that the valence of the minority Mn changes so that its ionic radius approaches that of the majority M. PMID:28252008

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.

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

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

Feedback control of an interacting Bose-Einstein condensate using phase-contrast imaging

NASA Astrophysics Data System (ADS)

Szigeti, S. S.; Hush, M. R.; Carvalho, A. R. R.; Hope, J. J.

2010-10-01

The linewidth of an atom laser is limited by density fluctuations in the Bose-Einstein condensate (BEC) from which the atom laser beam is outcoupled. In this paper we show that a stable spatial mode for an interacting BEC can be generated using a realistic control scheme that includes the effects of the measurement backaction. This model extends the feedback theory, based on a phase-contrast imaging setup, presented by Szigeti, Hush, Carvalho, and Hope [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.80.013614 80, 013614 (2009)]. In particular, it is applicable to a BEC with large interatomic interactions and solves the problem of inadequacy of the mean-field (coherent state) approximation by utilizing a fixed number state approximation. Our numerical analysis shows the control to be more effective for a condensate with a large nonlinearity.

Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

PubMed

Croll, Tristan Ian; Andersen, Gregers Rom

2016-09-01

While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of <1.7, and strategies for working with such challenging data sets are suggested. Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement.

Current Status of Protein Force Fields for Molecular Dynamics

PubMed Central

Lopes, Pedro E.M.; Guvench, Olgun

2015-01-01

Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958

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'.

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.

Levitation forces of a bulk YBCO superconductor in gradient varying magnetic fields

NASA Astrophysics Data System (ADS)

Jiang, J.; Gong, Y. M.; Wang, G.; Zhou, D. J.; Zhao, L. F.; Zhang, Y.; Zhao, Y.

2015-09-01

The levitation forces of a bulk YBCO superconductor in gradient varying high and low magnetic fields generated from a superconducting magnet were investigated. The magnetic field intensity of the superconducting magnet was measured when the exciting current was 90 A. The magnetic field gradient and magnetic force field were both calculated. The YBCO bulk was cooled by liquid nitrogen in field-cooling (FC) and zero-field-cooling (ZFC) condition. The results showed that the levitation forces increased with increasing the magnetic field intensity. Moreover, the levitation forces were more dependent on magnetic field gradient and magnetic force field than magnetic field intensity.

A Gaussian Approximation Potential for Silicon

NASA Astrophysics Data System (ADS)

Bernstein, Noam; Bartók, Albert; Kermode, James; Csányi, Gábor

We present an interatomic potential for silicon using the Gaussian Approximation Potential (GAP) approach, which uses the Gaussian process regression method to approximate the reference potential energy surface as a sum of atomic energies. Each atomic energy is approximated as a function of the local environment around the atom, which is described with the smooth overlap of atomic environments (SOAP) descriptor. The potential is fit to a database of energies, forces, and stresses calculated using density functional theory (DFT) on a wide range of configurations from zero and finite temperature simulations. These include crystalline phases, liquid, amorphous, and low coordination structures, and diamond-structure point defects, dislocations, surfaces, and cracks. We compare the results of the potential to DFT calculations, as well as to previously published models including Stillinger-Weber, Tersoff, modified embedded atom method (MEAM), and ReaxFF. We show that it is very accurate as compared to the DFT reference results for a wide range of properties, including low energy bulk phases, liquid structure, as well as point, line, and plane defects in the diamond structure.

Stillinger-Weber potential for elastic and fracture properties in graphene and carbon nanotubes

NASA Astrophysics Data System (ADS)

Hossain, M. Z.; Hao, T.; Silverman, B.

2018-02-01

This paper presents a new framework for determining the Stillinger-Weber (SW) potential parameters for modeling fracture in graphene and carbon nanotubes. In addition to fitting the equilibrium material properties, the approach allows fitting the potential to the forcing behavior as well as the mechanical strength of the solid, without requiring ad hoc modification of the nearest-neighbor interactions for avoiding artificial stiffening of the lattice at larger deformation. Consistent with the first-principles results, the potential shows the Young’s modulus of graphene to be isotropic under symmetry-preserving and symmetry-breaking deformation conditions. It also shows the Young’s modulus of carbon nanotubes to be diameter-dependent under symmetry-breaking loading conditions. The potential addresses the key deficiency of existing empirical potentials in reproducing experimentally observed glass-like brittle fracture in graphene and carbon nanotubes. In simulating the entire deformation process leading to fracture, the SW-potential costs several factors less computational time compared to the state-of-the-art interatomic potentials that enables exploration of the fracture processes in large atomistic systems which are inaccessible otherwise.

Temperature-dependent infrared optical properties of 3C-, 4H- and 6H-SiC

NASA Astrophysics Data System (ADS)

Tong, Zhen; Liu, Linhua; Li, Liangsheng; Bao, Hua

2018-05-01

The temperature-dependent optical properties of cubic (3C) and hexagonal (4H and 6H) silicon carbide are investigated in the infrared range of 2-16 μm both by experimental measurements and numerical simulations. The temperature in experimental measurement is up to 593 K, while the numerical method can predict the optical properties at elevated temperatures. To investigate the temperature effect, the temperature-dependent damping parameter in the Lorentz model is calculated based on anharmonic lattice dynamics method, in which the harmonic and anharmonic interatomic force constants are determined from first-principles calculations. The infrared phonon modes of silicon carbide are determined from first-principles calculations. Based on first-principles calculations, the Lorentz model is parameterized without any experimental fitting data and the temperature effect is considered. In our investigations, we find that the increasing temperature induces a small reduction of the reflectivity in the range of 10-13 μm. More importantly, it also shows that our first-principles calculations can predict the infrared optical properties at high-temperature effectively which is not easy to be obtained through experimental measurements.

Achieving DFT accuracy with a machine-learning interatomic potential: Thermomechanics and defects in bcc ferromagnetic iron

NASA Astrophysics Data System (ADS)

Dragoni, Daniele; Daff, Thomas D.; Csányi, Gábor; Marzari, Nicola

2018-01-01

We show that the Gaussian Approximation Potential (GAP) machine-learning framework can describe complex magnetic potential energy surfaces, taking ferromagnetic iron as a paradigmatic challenging case. The training database includes total energies, forces, and stresses obtained from density-functional theory in the generalized-gradient approximation, and comprises approximately 150,000 local atomic environments, ranging from pristine and defected bulk configurations to surfaces and generalized stacking faults with different crystallographic orientations. We find the structural, vibrational, and thermodynamic properties of the GAP model to be in excellent agreement with those obtained directly from first-principles electronic-structure calculations. There is good transferability to quantities, such as Peierls energy barriers, which are determined to a large extent by atomic configurations that were not part of the training set. We observe the benefit and the need of using highly converged electronic-structure calculations to sample a target potential energy surface. The end result is a systematically improvable potential that can achieve the same accuracy of density-functional theory calculations, but at a fraction of the computational cost.

369 TFlop/s molecular dynamics simulations on the Roadrunner general-purpose heterogeneous supercomputer

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

Swaminarayan, Sriram; Germann, Timothy C; Kadau, Kai

2008-01-01

The authors present timing and performance numbers for a short-range parallel molecular dynamics (MD) code, SPaSM, that has been rewritten for the heterogeneous Roadrunner supercomputer. Each Roadrunner compute node consists of two AMD Opteron dual-core microprocessors and four PowerXCell 8i enhanced Cell microprocessors, so that there are four MPI ranks per node, each with one Opteron and one Cell. The interatomic forces are computed on the Cells (each with one PPU and eight SPU cores), while the Opterons are used to direct inter-rank communication and perform I/O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementationmore » of a standard Lennard-Jones pair potential benchmark reached a peak of 369 Tflop/s double-precision floating-point performance on the full Roadrunner system (27.7% of peak), corresponding to 124 MFlop/Watt/s at a price of approximately 3.69 MFlops/dollar. They demonstrate an initial target application, the jetting and ejection of material from a shocked surface.« less

Helium segregation on surfaces of plasma-exposed tungsten

DOE PAGES

Maroudas, Dimitrios; Blondel, Sophie; Hu, Lin; ...

2016-01-21

Here we report a hierarchical multi-scale modeling study of implanted helium segregation on surfaces of tungsten, considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations based on a reliable interatomic interaction potential, including molecular-statics simulations to understand the origin of helium surface segregation, targeted molecular-dynamics (MD) simulations of near-surface cluster reactions, and large-scale MD simulations of implanted helium evolution in plasma-exposed tungsten. We find that small, mobile He-n (1 <= n <= 7) clusters in the near-surface region are attracted to the surface due to an elastic interaction force that provides themore » thermodynamic driving force for surface segregation. Elastic interaction force induces drift fluxes of these mobile Hen clusters, which increase substantially as the migrating clusters approach the surface, facilitating helium segregation on the surface. Moreover, the clusters' drift toward the surface enables cluster reactions, most importantly trap mutation, in the near-surface region at rates much higher than in the bulk material. Moreover, these near-surface cluster dynamics have significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure. We integrate the findings of such atomic-scale simulations into a properly parameterized and validated spatially dependent, continuum-scale reaction-diffusion cluster dynamics model, capable of predicting implanted helium evolution, surface segregation, and its near-surface effects in tungsten. This cluster-dynamics model sets the stage for development of fully atomistically informed coarse-grained models for computationally efficient simulation predictions of helium surface segregation, as well as helium retention and surface morphological evolution, toward optimal design of plasma facing components.« less

Many-body interactions and high-pressure equations of state in rare-gas solids

NASA Astrophysics Data System (ADS)

Freiman, Yu. A.; Tretyak, S. M.

2007-06-01

The T =0K equations of state (EOS) of rare-gas solids (RGS) (He, Ne, Ar, Kr, and Xe) are calculated in the experimentally studied ranges of pressures with the two- and three-body interatomic forces taken into account. Solid-state corrections to the pure two-body Aziz et al. potentials included the long-range Axilrod-Teller three-body interaction and short-range three-body exchange interaction. The energy-scale and length-scale parameters of the latter were taken as adjustable parameters of theory. The calculated T =0K EOS for all RGS are in excellent agreement with experiment in the whole range of pressures. The calculated EOS for Ar, Kr, and Xe exhibit inflection points where the isothermal bulk moduli have non-physical maxima, indicating that account of only three-body forces becomes insufficient. These points lie at pressures 250, 200, and 175GPa (volume compressions of approximately 4.8, 4.1, and 3.6) for Ar, Kr, and Xe, respectively. No such points were found in the calculated EOS of He and Ne. The relative magnitude of the three-body contribution to the ground-state energy with respect to the two-body one as a function of the volume compression was found to be nonmonotonic in the sequence Ne-Ar-Kr-Xe. In a large range of compressions, Kr has the highest value of this ratio. This anomalously high three-body exchange force contributes to the EOS a negative pressure so large that the EOS for Kr and Ar as a function of compression nearly coincide. At compressions higher than approximately 3.5 the curves intersect, and further on, the EOS of Kr lies lower than that of Ar.

Helium segregation on surfaces of plasma-exposed tungsten

NASA Astrophysics Data System (ADS)

Maroudas, Dimitrios; Blondel, Sophie; Hu, Lin; Hammond, Karl D.; Wirth, Brian D.

2016-02-01

We report a hierarchical multi-scale modeling study of implanted helium segregation on surfaces of tungsten, considered as a plasma facing component in nuclear fusion reactors. We employ a hierarchy of atomic-scale simulations based on a reliable interatomic interaction potential, including molecular-statics simulations to understand the origin of helium surface segregation, targeted molecular-dynamics (MD) simulations of near-surface cluster reactions, and large-scale MD simulations of implanted helium evolution in plasma-exposed tungsten. We find that small, mobile He n (1  ⩽  n  ⩽  7) clusters in the near-surface region are attracted to the surface due to an elastic interaction force that provides the thermodynamic driving force for surface segregation. This elastic interaction force induces drift fluxes of these mobile He n clusters, which increase substantially as the migrating clusters approach the surface, facilitating helium segregation on the surface. Moreover, the clusters’ drift toward the surface enables cluster reactions, most importantly trap mutation, in the near-surface region at rates much higher than in the bulk material. These near-surface cluster dynamics have significant effects on the surface morphology, near-surface defect structures, and the amount of helium retained in the material upon plasma exposure. We integrate the findings of such atomic-scale simulations into a properly parameterized and validated spatially dependent, continuum-scale reaction-diffusion cluster dynamics model, capable of predicting implanted helium evolution, surface segregation, and its near-surface effects in tungsten. This cluster-dynamics model sets the stage for development of fully atomistically informed coarse-grained models for computationally efficient simulation predictions of helium surface segregation, as well as helium retention and surface morphological evolution, toward optimal design of plasma facing components.

ON ESTIMATING FORCE-FREENESS BASED ON OBSERVED MAGNETOGRAMS

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

Zhang, X. M.; Zhang, M.; Su, J. T., E-mail: xmzhang@nao.cas.cn

It is a common practice in the solar physics community to test whether or not measured photospheric or chromospheric vector magnetograms are force-free, using the Maxwell stress as a measure. Some previous studies have suggested that magnetic fields of active regions in the solar chromosphere are close to being force-free whereas there is no consistency among previous studies on whether magnetic fields of active regions in the solar photosphere are force-free or not. Here we use three kinds of representative magnetic fields (analytical force-free solutions, modeled solar-like force-free fields, and observed non-force-free fields) to discuss how measurement issues such asmore » limited field of view (FOV), instrument sensitivity, and measurement error could affect the estimation of force-freeness based on observed magnetograms. Unlike previous studies that focus on discussing the effect of limited FOV or instrument sensitivity, our calculation shows that just measurement error alone can significantly influence the results of estimates of force-freeness, due to the fact that measurement errors in horizontal magnetic fields are usually ten times larger than those in vertical fields. This property of measurement errors, interacting with the particular form of a formula for estimating force-freeness, would result in wrong judgments of the force-freeness: a truly force-free field may be mistakenly estimated as being non-force-free and a truly non-force-free field may be estimated as being force-free. Our analysis calls for caution when interpreting estimates of force-freeness based on measured magnetograms, and also suggests that the true photospheric magnetic field may be further away from being force-free than it currently appears to be.« less

On the modified Tabor parameter for the JKR-DMT transition in the presence of a liquid meniscus.

PubMed

Xu, Dewei; Liechti, Kenneth M; Ravi-Chandar, K

2007-11-15

The JKR, DMT, Maugis models and Tabor parameter for contact under normal loading have been developed based mainly on solid-solid (van der Waals) interactions. In this case, the characteristic length scale for the adhesive forces in the Tabor parameter is the equilibrium interatomic spacing. However, for contact in humid environments, where a liquid meniscus may be present, capillary forces with a longer force range related to the Kelvin radius dominate. Fogden and White [J. Colloid Interface Sci. 138 (1990) 414] introduced a parameter that includes the Kelvin radius for the JKR-DMT transition. This topic was also addressed by Maugis and Gauthier-Manuel [J. Adhes. Sci. Technol. 8 (1994) 1311] who included capillary effects within the frame work that Maugis had previously established. The parameters introduced by Fogden and White and Maugis and Gauthier-Manuel can be viewed as a modified Tabor parameter for the JKR-DMT transition. In the present work, the Kelvin equation linking the Kelvin radius and the relative humidity was explicitly included in the modified Tabor parameter. This provided a quantitative description of the JKR-DMT transition in terms of the relative humidity. This parameter was examined via load and contact radius measurements, where the latter were obtained from Bowden and Tabor's assumption that the friction force f=tauA. The friction experiments were conducted at two different humidity levels using a newly-developed mesoscale friction tester (MFT), which provides a very wide range of contact radii. The modified Tabor parameter was used to reexamine data from pull-off experiments in water and cyclohexane vapor environments [L.R. Fisher, J.N. Israelachvili, Colloids Surf. 3 (1981) 303 and H.K. Christenson, J. Colloid Interface Sci. 121 (1988) 170]. Finally, guidelines are presented for the appropriate choice of contact mechanics models to be used in interpreting data from SFA and AFM experiments in humid environments.

Interfacial electronic structure and full spectral Hamaker constants of Si{sub 3}N{sub 4} intergranular films from VUV and SR-VEEL spectroscopy

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

French, R.H.; Scheu, C.; Duscher, G.

1995-09-01

The interfacial electronic structure, presented as the interband transition strength J{sub cv}({omega}) of the interatomic bonds, can be determined by Kramers Kronig (KK) analysis of vacuum ultraviolet (VUV) reflectance or spatially resolved valence electron energy loss (SR-VEEL) spectra. For the wetted interfaces in Si{sub 3}N{sub 4}, equilibrium thin glass films are formed whose thickness is determined by a force balance between attractive and repulsive force terms KK analysis of J{sub cv}({omega}) to yield {var_epsilon}{sub 2}({xi}) for the phases present, permits the direct calculation of the configuration-dependent Hamaker constants for the attractive vdW forces from the interfacial electronic structure. Interband transitionmore » strengths and full spectral Hamaker constants for Si{sub 3}N{sub 4}samples containing a SiYAlON glass have been determined using SR-VEELS from grains and grain boundaries and compared with results from bulk VUV spectroscopy on separate samples of glass and nitride. The A{sub 121}Hamaker constant for Si{sub 3}N{sub 4} with glass of the bulk composition is 8 zJ (zJ = 10{sup {minus}21}J) from the more established optical method. The EELS method permits the determination of vdW forces based upon actual local compositions and structure, which may differ noticeably from bulk standards. Current results show that full spectral Hamaker constants determined from VUV and SR-VEEL measurements of uniform bulk samples agree, but care must be take in the single scattering and zero loss subtraction corrections, and more work is ongoing in this area. Still the results show that for the grain boundary films present in these polycrystalline Si{sub 3}N{sub 4} samples the glass composition is of lower index of refraction. This can arise from increased oxygen content in determined in situ from the SR-VEELS of a particular grain boundary film. 45 refs.« less

Electrophilicity: the "dark-side" of indole chemistry.

PubMed

Bandini, Marco

2013-08-28

Indole is by far one of the most popular heterocyclic scaffolds in nature. The intriguing and challenging molecular architectures of polycyclic, naturally occurring indolyl compounds constitute a continuous stimulus for development in organic synthesis. The field had a formidable boom across the new millennium when catalysis started revolutionizing the chemistry of indole, providing always more convincing and sustainable solutions to the selective "decoration" of this pharmacophore. A common guideline of these approaches relies on the intrinsic overexpression of electron density of the indole core. Despite less diffusion, the "dark-side" of indole reactivity, electrophilicity, has been also elegantly documented with direct applications towards the realization of specific interatomic connections that would be difficult to obtain by means of conventional indole reactivity. The present Perspective article summarizes the major findings that brought the research area from the pioneering findings of the 60s to the state of the art.

Superfluid state of atomic 6Li in a magnetic trap

NASA Astrophysics Data System (ADS)

Houbiers, M.; Ferwerda, R.; Stoof, H. T. C.; McAlexander, W. I.; Sackett, C. A.; Hulet, R. G.

1997-12-01

We report on a study of the superfluid state of spin-polarized atomic 6Li confined in a magnetic trap. Density profiles of this degenerate Fermi gas and the spatial distribution of the BCS order parameter are calculated in the local-density approximation. The critical temperature is determined as a function of the number of particles in the trap. Furthermore, we consider the mechanical stability of an interacting two-component Fermi gas, in the case of both attractive and repulsive interatomic interactions. For spin-polarized 6Li we also calculate the decay rate of the gas and show that within the mechanically stable regime of phase space, the lifetime is long enough to perform experiments on the gas below and above the critical temperature if a bias magnetic field of about 5 T is applied. Moreover, we propose that a measurement of the decay rate of the system might signal the presence of the superfluid state.

Spectroscopy of the three-photon laser excitation of cold Rubidium Rydberg atoms in a magneto-optical trap

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

Entin, V. M.; Yakshina, E. A.; Tretyakov, D. B.

2013-05-15

The spectra of the three-photon laser excitation 5S{sub 1/2} {yields} 5P{sub 3/2} {yields} 6S{sub 1/2}nP of cold Rb Rydberg atoms in an operating magneto-optical trap based on continuous single-frequency lasers at each stage are studied. These spectra contain two partly overlapping peaks of different amplitudes, which correspond to coherent three-photon excitation and incoherent three-step excitation due to the presence of two different ways of excitation through the dressed states of intermediate levels. A four-level theoretical model based on optical Bloch equations is developed to analyze these spectra. Good agreement between the experimental and calculated data is achieved by introducing additionalmore » decay of optical coherence induced by a finite laser line width and other broadening sources (stray electromagnetic fields, residual Doppler broadening, interatomic interactions) into the model.« less

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.

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

PubMed Central

Vanommeslaeghe, K.

2014-01-01

Background Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. Scope of Review As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular bimolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields’ parametrization philosophy and methodology. Major Conclusions Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1 microsecond on proteins, DNA, lipids and carbohydrates. General Significance Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers a model that is an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. PMID:25149274

Vacuum fluctuations and radiation reaction contributions to the resonance dipole-dipole interaction between two atoms near a reflecting boundary

NASA Astrophysics Data System (ADS)

Zhou, Wenting; Rizzuto, Lucia; Passante, Roberto

2018-04-01

We investigate the resonance dipole-dipole interaction energy between two identical atoms, one in the ground state and the other in the excited state, interacting with the electromagnetic field in the presence of a perfectly reflecting plane boundary. The atoms are prepared in a correlated (symmetric or antisymmetric) Bell-type state. Following a procedure due to Dalibard et al. [J. Dalibard et al., J. Phys. (Paris) 43, 1617 (1982);, 10.1051/jphys:0198200430110161700 J. Phys. (Paris) 45, 637 (1984), 10.1051/jphys:01984004504063700], we separate the contributions of vacuum fluctuations and radiation reaction (source) field to the resonance interaction energy between the two atoms and show that only the source field contributes to the interatomic interaction, while vacuum field fluctuations do not. By considering specific geometric configurations of the two-atom system with respect to the mirror and specific choices of dipole orientations, we show that the presence of the mirror significantly affects the resonance interaction energy and that different features appear with respect to the case of atoms in free space, for example, a change in the spatial dependence of the interaction. Our findings also suggest that the presence of a boundary can be exploited to tailor and control the resonance interaction between two atoms, as well as the related energy transfer process. The possibility of observing these phenomena is also discussed.

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

PubMed

Vanommeslaeghe, K; MacKerell, A D

2015-05-01

Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular biomolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields' parametrization philosophy and methodology. Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1μs on proteins, DNA, lipids and carbohydrates. Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. This article is part of a Special Issue entitled "Recent developments of molecular dynamics". Copyright © 2014 Elsevier B.V. All rights reserved.

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

Interatomic Coulombic Decay Mediated by Ultrafast Superexchange Energy Transfer.

PubMed

Miteva, Tsveta; Kazandjian, Sévan; Kolorenč, Přemysl; Votavová, Petra; Sisourat, Nicolas

2017-08-25

Inner-valence ionized states of atoms and molecules live shorter if these species are embedded in an environment due to the possibility for ultrafast deexcitation known as interatomic Coulombic decay (ICD). In this Letter we show that the lifetime of these ICD active states decreases further when a bridge atom is in proximity to the two interacting monomers. This novel mechanism, termed superexchange ICD, is an electronic correlation effect driven by the efficient energy transfer via virtual states of the bridge atom. The superexchange ICD is discussed in detail on the example of the NeHeNe trimer. We demonstrate that the decay width of the Ne^{+}(2s^{-1})  ^{2}Σ_{g}^{+} resonance increases 6 times in the presence of the He atom at a distance of 4 Å between the two Ne atoms. Using a simple model, we provide a qualitative explanation of the superexchange ICD and we derive analytical expressions for the dependence of the decay width on the distance between the neon atoms.

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

Single Platinum Atoms Electrocatalysts: Oxygen Reduction and Hydrogen Oxidation Reactions

DOE PAGES

Vukmirovic, Miomir B.; Teeluck, Krishani M.; Liu, Ping; ...

2017-08-08

We prepared atomically dispersed catalyst consisting of Pt atoms arranged in a c(2 × 2) array on RuO2(110) substrate. A large interatomic distance of Pt atoms in a c(2 × 2) phase precludes the reactants to interact with more than one Pt atoms. A strong bond of Pt atoms with RuO2 prevents agglomeration of Pt atoms to form 2D-islands or 3D-clusters. The activities of single Pt atom catalyst for the oxygen reduction and hydrogen oxidation reactions were determined and compared with those of bulk Pt. It has lower catalytic activity for the oxygen reduction reaction and similar activity for hydrogenmore » oxidation reaction compared to Pt(111). This was explained by a large calculated up-shift of the dband center of Pt atoms and larger Pt-Pt interatomic distance than that of Pt(111). Our information is of considerable interest for further development of electrocatalysis.« 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

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.

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.

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.

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.

Recent Developments and Applications of the CHARMM force fields

PubMed Central

Zhu, Xiao; Lopes, Pedro E.M.; MacKerell, Alexander D.

2011-01-01

Empirical force fields commonly used to describe the condensed phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical (QM) methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds and new theoretical developments (eg. polarizable methods) make force-field development a dynamic domain of research. Accordingly, a number of improvements and extensions of the CHARMM force fields have occurred over the years. The objective of the present review is to provide an up-to-date overview of the CHARMM force fields. A limited presentation on the historical aspects of force fields will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable force fields, including examples of recent applications of those force fields. PMID:23066428

The effect of force feedback delay on stiffness perception and grip force modulation during tool-mediated interaction with elastic force fields

PubMed Central

Karniel, Amir; Nisky, Ilana

2015-01-01

During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. PMID:25717155

The effect of force feedback delay on stiffness perception and grip force modulation during tool-mediated interaction with elastic force fields.

PubMed

Leib, Raz; Karniel, Amir; Nisky, Ilana

2015-05-01

During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. Copyright © 2015 the American Physiological Society.

Iron Isotopic Fractionation in Igneous Systems: Looking for Anharmonicity

NASA Astrophysics Data System (ADS)

Dauphas, N.; Roskosz, M.; Hu, M. Y.; Neuville, D. R.; Alp, E. E.; Hu, J.; Heard, A.; Zhao, J.

2017-12-01

Igneous rocks display variations in their Fe isotopic compositions that can be used to trace partial melting, magma differentiation, the origin of mineral zoning, and metasomatic processes. While tremendous progress has been made in our understanding of how iron isotopes can be fractionated at equilibrium or during diffusion, significant work remains to be done to establish equilibrium fractionation factors between phases relevant to igneous petrology. A virtue of iron isotope systematics is that iron possesses a Mössbauer isotope, 57Fe, and one can use the method of NRIXS to measure the force constant of iron bonds, from which beta-factors can be calculated. These measurements are done at a few synchrotron beamlines around the world, such as sector 3ID of the APS (Argonne). Tremendous insights have already been gained by applying this technique to Earth science materials. It was shown for instance that significant equilibrium fractionation exists between Fe2+ and Fe3+ at magmatic temperature, that the iron isotopic fractionation resulting from core formation must be small, and that iron isotopic fractionation is influenced by the polymerization of the melt. Combining NRIXS and ab initio studies, there are approximately 130 geologically-relevant solids and aqueous species for which beta-factors have been reported. A potential limitation of applying published NRIXS data to igneous petrology is that all the force constants have been measured at room temperature and the beta-factors are extrapolated to magmatic temperatures assuming that the systems are harmonic, which has never been demonstrated. One way to test this critical assumption is to measure the apparent force constant of iron bonds at various temperatures, so that the interatomic potential of iron bonds can be probed. A further virtue of NRIXS is that the data also allows us to derive the mean square displacement. If significant anharmonicity is present, it should be manifested as a decrease in the apparent force constant with increasing temperature and increasing mean square displacement. We have measured the Fe force constant of basalt glass and olivine using a wire furnace. At the conference, we will report on these experiments and will discuss some implications for igneous petrology.

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