Atomic Potential Energy Research Articles

Theory of one-dimensional trapping of atoms by counterpropagating short pulse trains

We have developed a theory of the one-dimensional atomic trap formed by the resonant counterpropagating trains of the short small-area laser pulses. Atoms are trapped in the region where the counterpropagating pulses ‘collide’. We have derived the effective Hamiltonian which allows us to consider an atom in the polychromatic field of the pulse trains as the atom with the spatially modulated transition frequency in a standing monochromatic wave. We have obtained the expressions for the coordinate-dependent force exerted on the atom and the atom potential energy. The value of the potential barrier for typical femtosecond laser parameters for an atom with mass ∼100 amu is approximately 15 mK.

Multiscale Molecular Dynamics of Protein Aggregation

The 60's gave birth to the practical implementation of classical mechanics to unravel the dynamics and energetics of biomolecules. In the 70's the use of generalized force fields and more advanced integrative solutions to the microscopic understanding of nature (like hybrid QM/MM) were introduced. During the 80's, algorithms to obtain free energy values were further developed and in the 90's practical integration schemes of molecular mechanics force fields with other levels of detail (QM on one extreme and advances in implicit solvation on the other) were implemented in widely spread software. In the first decade of the XXIst century a considerable effort has been put in two seemingly discordant models for the simulation of biomolecules. On the one hand, extraordinary advances in computing technologies (both in terms of processor power and of new efficient parallel and distributed computing schemas) have allowed researchers to deal with bigger systems and longer simulations, reaching molecular processes including millions of particles or lying in the microsecond scale. On the other hand, the realization that the relevant answers to many biomolecular problems are not homogeneously distributed through the molecular structure, something already envisioned by the QM/MM pioneers more than three decades ago, has led researchers to find smart ways of putting different emphases on different ranges of the spatial or system time scale. In this context, e.g., molecular aggregation represents a paradigm for multiscalability, as molecular recognition can be understood with simple (semi-)macroscopic terms when the two fragments are far apart, while the atomic interactions need to be considered in full detail upon close distances. In this manuscript the current status of the techniques that use multiple scale representations of biomolecules are reviewed, and the findings are synthesized in a modular schema that can be extensively used when studying aggregation processes. It is shown that a smart alternative to brute force and massive computation of uninteresting regions in the all atom potential energy surface is the consideration of a simplified reference potential, explored thoroughly in the relevant regions, combined with a free energy perturbation approach that transforms this simple representation to a full atom representation.

Extending ligand field molecular mechanics to modelling organometallic π-bonded systems: applications to ruthenium–arenes

The ligand field molecular mechanics method has been extended to treat η(6)-arene ligands coordinated to a ruthenium(II) centre by employing a dummy atom located at the centroid of the arene ring and distributing the forces on the dummy to the arene carbon atoms. Angular overlap model parameters based on orbital energies derived from Kohn-Sham density functional theory (KS-DFT) calculations show that, relative to the Ru-dummy vector, the arene behaves as a very strong π donor and weak σ donor. Based on KS-DFT geometries, partial atomic charges and potential energy scans for a series of homoleptic and half sandwich complexes spanning arene, am(m)ine, imine, pyridyl, hydride and chloride ligands, a new LFMM force field has been developed which accurately reproduces the KS-DFT data. This FF was validated against 47 half-sandwich complexes obtained from the Cambridge Structural Database which, after minor corrections to account for the systematic errors between our chosen functional (BP86) and the experimental structures, yields a 'structurally tuned' FF where 93% of the Ru-L contacts are reproduced to 0.05 Å or better and all bar two bond lengths are within 0.1 Å of experiment. Over half the systems have non-hydrogen-atom rmsds of less than 0.5 Å. Larger differences are usually due to rotation of the arene moiety which is shown by ligand field molecular dynamics (LFMD) simulations to be an inherently low-energy process. Comparisons between LFMD and Car-Parrinello MD for [Ru(p-cymene)(ethylenediamine)Cl](+)show that LFMD is equally accurate but much faster enabling modelling of dynamic properties which occur on a timescale beyond the scope of CPMD.

New description of structural disorder in silica glass. II. Application of atomistic energy distribution analysis to pressure effects

Molecular dynamics (MD) simulations have been made to study changes in density, oxygen coordination number and bond exchange during compression and decompression of quartz, cristobalite and silica glass. The interaction energies calculated by MD are analyzed in terms of ‘atomistic energy distribution (AED) with which pair-interaction energies are divided into equal halves allocated to each atom. Therefore, each atom has the summed-up value (‘atomistic potential energy’) of half the pair-interaction energies. The calculated results show different patterns and profiles in first and second moments of AED in the three silica systems, which are used to interpret pressure-induced amorphization of quartz, crystal-crystal transition in cristobalite and densification in silica glass. Making use of a previous AED analysis of thermal effects in silica glass [J. Non-Cryst. Solids. 355 (2009) 694], we finally compare and ascertain structural transformations that are due to either thermal or mechanical effects.

The Improvement of Generalized Particle Method for Nano-Materials Molecular Dynamics Simulation

A generalized particle molecular dynamics simulation (GP) method has been proposed by J. Fan to solve the multi-scale problems in nano-materials. Although the method has attractive features, its acceleration equivalency hypothesis doesn’t meet the actual situation. In this paper an improved GP method is proposed. It assumes that the potential energy of generalized particles is equal to the potential energy of corresponding atomic groups in nano-materials. The parameters of improved GP method rest with the atomic structural details and corresponding atomic potential energy function. And by using open-source molecular simulation software DL-POLY, an example to compare the MD and the improved GP methods has been proposed, in which the Improved GP method presents sufficient accuracy

Slow-light enhancement of stimulated emission of atomic systems in photonic crystals

We demonstrate both theoretically and numerically that slow light can enhance the stimulated emission of four-level atomic systems in photonic crystals. By applying the Bloch-Floquet formalism and the semiclassical physical model of harmonic oscillators coupled to electromagnetic fields, we develop a formalism that relates the group velocity of slow light to the conversion rate between the electric field and atomic potential energy. From our numerical study of the stimulated emission in fiber Bragg gratings (FBGs) and nongrating fiber, a ninefold enhancement of stimulated emission is observed in a FBG over the nongrating fiber when pumping at the band edge, while a 20-fold enhancement of is observed when the frequency of the stimulated emission approaches the band edge.

The Possibilities of Nonlinear Ultrasonic Spectroscopy for the NDT in Civil Engineering

Current methods of non-destructive ultrasonic material testing are based on the analysis of elastic wave reflection, absorption and interference. These methods are difficult to apply to inhomogeneous building materials showing tiny cracks and defects distributed throughout the specimen bulk, or in the cases where the defect size is comparable with the wavelength. Analysis of these phenomena occurring in intricate shapes is also difficult. To cope with such problems, application of wave propagation related nonlinear effects and higher harmonic signal generation in the defect vicinity is advisable. Due to the presence of defects, the atomic potential energy ceases to be exactly harmonic. Second and third harmonic frequencies arise. In this domain, methods employing the nonlinear acoustic spectroscopy apply. These novel defectoscopic methods are based on the nonlinear behaviour of current defects and inhomogeneities regarding the elastic wave propagation processes. Unlike the electromagnetic and acoustic emission methods, which only allow the localization of currently emerging cracks and defects, the non-linear ultrasonic defectoscopy is all-defect-sensitive, thus constituting a method applicable to characterizing the quality and reliability of materials.

Study on the Phase Transition Behavior of Ni Nano-Clusters Using Molecular Dynamics Simulation

Structural phase transition of Ni nanocluster from cuboctahedron to icosahedron at 1100 K is investigated by means of molecular dynamics simulation. Radial distribution function and potential energy of each atom are calculated to study the transition phenomena in detail. At 1100 K, potential energy of interior atoms in the cluster is increased before the transition, while the periodicity of a0 in the radial distribution function is broken. Thus the interior atoms partially lose its crystallinity in advance of the transition. Rather potential energy of the surface starts to decrease relatively so much by changing the surface structure to icosahedron at/after the transition. Consequently, the system energy is decreased. Minimizing surface energy enables Ni nano cluster to drive the transition. In addition, the interior energy is increased to as much as that of icosahedron prior to the transition.

Elastic He + on He collision cross-sections and Monte Carlo calculation of the transport coefficients of He + ions in gaseous helium

Integral and differential cross-sections for elastic collisions of He + ions in the ground state ( 2S) with neutral He atoms are calculated, for centre-of-mass energies between 0.001 and 10 eV, using the partial waves method. The scattering phase shifts are calculated using the JWKB semi-classical approximation, with modified Tang–Toennies ion–atom (TTIA) potential energy curves, that describe spectroscopic data, dissociation energies and equilibrium internuclear distances, and the long-range interaction potentials. These cross-sections are used in a detailed three-dimensional Monte Carlo simulation model to calculate the main transport coefficients describing the ion drift through the neutral gas, as a function of the gas temperature and the reduced uniform electric field. Calculated drift velocities, ion mobilities, as well as longitudinal and transverse diffusion coefficients for He + atomic ions in gaseous He, at temperature T=293 K and reduced electric fields, E/N, in the 1 to 300 Td (1 Td=10 −17 V cm 2) range, are reported and compared with the limited experimental data available in the scientific literature. The calculated drift velocities range from 28.31 m s −1 at 1 Td to 3685.0 m s −1 at 300 Td.

Dislocation Stimulus Dependence of Atomic Collective Vibration in an Icosahedral Cluster

The dynamics of the monopole collective vibration of a Leonard-Jones 147-atom cluster has been examined using molecular dynamics simulation. It is found that the process of energy release of the vibrating cluster depends on the extent of the initial atomic dislocation stimulus. A relatively larger-scale perturbation will cause a faster decay of the vibration magnitude despite the higher potential and kinetic energy compared to the vibration stimulated by a small-scale dislocation stimulus. Due to the compression by the outermost shells, the potential energy of atoms in the inner shells increases while that of the outer shells decreases during the process of energy release until equilibrium state. Findings provide hitherto insight into the dynamics of energy releases of an atomic cluster induced by a sudden dislocation stimulus.

Spin-Flip Reaction of Re + CH4—A Relativistic Density Functional Theory Investigation

To explore the reaction mechanisms of methane dehydrogenation by gas-phase Re atom, the sextet, quartet, and doublet potential energy surfaces have been performed using density functional theory (DFT) and zero-order regular approximation relativistic corrections at the PW91/TZ2P level. The minimum energy reaction path is found to proceed through the following steps: (6)Re + CH(4) --> ReCH(4) ((6)1) --> H(3)CReH ((4)2) --> (4)TS2/3 --> H(2)CReH(2) ((4)3) --> (2)TS3/4 --> HCReH(3) ((2)4). Also, the reaction path involves the spin inversion twice in the different reaction steps. To better understand the spin inversion processes, the low energy crossing point is determined with the help of the density functional fractional occupation number approach. The first spin inversion, from the sextet state to the quartet state, makes the activation of the C-H bond energetically spontaneous. The second transition from the quartet state to the doublet state facilitates the cleavage of the second C-H bond, lowering the barrier from 186.1 to 24.2 kJ/mol. The overall reaction is calculated to be exothermic by 149.8 kJ/mol, and the final products in three spin states are investigated by NBO analysis, to compare the Re-C bonds and the C-H bonds.

Dynamics of cold atoms crossing a one-way barrier

We implemented an optical one-way potential barrier that allows ultracold $^{87}\text{R}\text{b}$ atoms to transmit through when incident on one side of the barrier but reflect from the other. This asymmetric barrier is a realization of Maxwell's demon, which can be employed to produce phase-space compression and has implications for cooling atoms and molecules not amenable to standard laser-cooling techniques. The barrier comprises two focused Gaussian laser beams that intersect the focus of a far-off-resonant single-beam optical dipole trap that holds the atoms. The main barrier beam presents a state-dependent potential to incident atoms, while the repumping barrier beam optically pumps atoms to a trapped state. We investigated the robustness of the barrier asymmetry to changes in the barrier-beam separation, the initial atomic potential energy, the intensity of the second beam, and the detuning of the first beam. We performed simulations of the atomic dynamics in the presence of the barrier, showing that the initial three-dimensional momentum distribution plays a significant role, and that light-assisted collisions are likely the dominant loss mechanism. We also carefully examined the relationship to Maxwell's demon and explicitly accounted for the apparent decrease in entropy for our particular system.

New model core potentials for gold

Four model core potentials (MCPs) for gold were developed using results from the third-order Douglas-Kroll-Hess relativistic all-electron calculations. The MCPs were developed with four different valence spaces, ranging from the 5p, 5d, and 6s orbitals to 5s, 4f, 5p, 5d, and 6s orbitals. The new MCPs were applied in the calculations of atomic properties and potential energy curves of AuH and Au(2). Results indicate that the 4f orbital may be excluded but the 5s orbital must be included in the valence space because of the importance of 5s-6s electron correlation. The model core potential that has the valence space comprising the 5s, 5p, 5d, and 6s orbitals is considered to be the most accurate and efficient of these new potentials.

New description of structural disorder in silica glass

Abstract Structural changes in cristobalite and silica glass and melt are investigated at high temperatures by molecular dynamics simulations. The calculated interaction energies are analyzed employing a new method called ‘atomistic energy distribution analysis’. Each pair-interaction energy is divided into equal halves which are allocated to each atom. Therefore, each atom has the summed-up value (‘atomistic potential energy’) of half the pair-interaction energies. First, an analysis of atomistic energy distribution functions show a correspondence with structural changes such as α–β phase transition, cristobalite melting and glass transition of SiO2, in harmony with the results obtained in our preceding study. Moreover, this study demonstrates the different roles of oxygen and silicon in terms of structural changes. Finally, newly defined order parameters offer the possibility of distinguishing structures resulting from different thermal histories through introduction of higher moments.

Phonon spectra prediction in carbon nanotubes using a manifold-based continuum finite element approach

This work develops a tensor-based, reduced-order shell (two-manifold) finite element formulation for predicting phonon spectra in finite-length cylindrical and toroidal carbon nanotubes (CNTs). The formulation does not require an assumed tube thickness. Displacements referencing two covariant basis vectors lying in the tangent space, and one basis vector orthogonal to the tangent space, capture the systems’ kinematics. These basis vectors compose a curvilinear coordinate system useful for capturing cylindrical, toroidal, and generically-curved nanotube configurations. The finite element procedure originates from a variational statement (Hamilton’s Principle) governing virtual work from internal, external (not considered), and inertial forces. Internal virtual work is related to changes in atomistic potential energy accounted for by an interatomic potential computed at reference area elements. Small virtual changes in the displacements allow a global mass and stiffness matrix to be computed, and these matrices then allow phonon spectra and energies to be predicted via a general eigenvalue problem. Results are generated for example cylindrical and toroidal CNTs documenting accurate prediction of phonon spectra, to include the expected longitudinal, torsional, bending, and breathing-like phonons.

Atomic bond fluctuations and crossover to potential-energy-landscape-influenced regime in supercooled liquid

The ideas related to potential-energy landscape and cooperativity of atomic rearrangements are widely discussed in the research field of glass transition. The crossover transition from high-temperature regime to potential-energy-landscape-influenced regime was extensively studied using the concept of inherent structure. However, the interpretation of this crossover behavior in terms of microscopic changes in real structures is still lacking. In this paper we present several observations on the crossover behavior on real structures. We compare fluctuations in the global properties (total number of bonds, total potential energy, pressure) versus fluctuations in the local properties (coordination number, atomic potential energy, local atomic pressure) by means of molecular dynamics simulations. We then show that the total and local fluctuations in the number of atomic bonds in the system depend on temperature differently above and below the temperature of crossover to the landscape-influenced regime. Similarly, the ratio between the global and local fluctuations in the potential energy and pressure changes in the vicinity of the crossover temperature, whereas the change is less distinct than in the case of the bond fluctuations. Our results indicate that local fluctuations become more correlated below the crossover temperature, most likely via the interaction through the dynamic shear elastic field.

Ground-state energy shift of He close to a surface and its relation with the scattering potential: A confinement model

The relation between scattering potential and ground-state energy shift of a helium atom (ion) close to a surface is investigated through use of a model of spatial limitation whereby the surface is represented by an infinitely rigid planar boundary. The model of an atom confined in a semi-infinite space with a plane boundary allows the variational evaluation of the ground-state energies and wave functions for He and ${\mathrm{He}}^{+}$ at different positions from the surface. The respective Born-Oppenheimer energy curves serve to model the ground-state energy shift for the elastic scattering channel in atom (ion) surface interactions. Independent calculations for the He-graphite and He-Al (111), (110), and (100) continuous planar potentials are carried out using high-quality ab initio calculations reported in the literature for the lowest He-C and He-Al binary interaction potentials. It is shown in this case that the He ground-state energy shift obtained within this model corresponds to an upper limit to the usual continuous planar potential. A discussion on the physical origin of this agreement is presented in terms of the static nature for the surface considered in both the hard-wall model and the atomic binary interactions used to construct the planar potentials, i.e., no account of the dynamic surface response is allowed as the projectile approaches. This is done by taking a reference pilot calculations based on electron nuclear dynamics for $100\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ He $({\mathrm{He}}^{+})$-benzene $({\mathrm{C}}_{6}{\mathrm{H}}_{6})$ interactions by considering the benzene molecule as a rough approximation to a local graphitic surface sector. It is found that the static planar potential provides a reasonable average representation of the interaction for neutral He, and supporting evidence for the use of the static O'Connor-Biersack potential is given. Finally, the effective scattering potential for $\mathrm{He}∕{\mathrm{He}}^{+}\text{\ensuremath{-}}\mathrm{Al}$ (111) is constructed through the use of the static planar potential for He-Al (111) considering the energy shift due to the classical image interaction for ${\mathrm{He}}^{+}$ approaching a perfectly Al (111) conducting plane before charge neutralization takes place. It is concluded that this scattering potential is directly related with the ground-state energy shift of the emerging already neutralized He atoms in $\mathrm{He}∕{\mathrm{He}}^{+}\text{\ensuremath{-}}\mathrm{Al}(111)$ grazing scattering experiments.

The elastic properties and energy characteristics of Au nanowires: an atomistic simulation study

This paper have performed molecular static calculations with the quantum corrected Sutten–Chen type many body potential to study size effects on the elastic modulus of Au nanowires with [100], [110] and [111] crystallographic directions, and to explore the preferential growth orientation of Au nanowires. The main focus of this work is the size effects on their surface characteristics. Using the common neighbour analysis, this paper deduces that surface region approximately consists of two layer atoms. Further, it extracts the elastic modulus of surface, and calculate surface energy of nanowire. The results show that for all three directions the Young's modulus of nanowire increases as the diameter increases. Similar trend has been observed for the Young's modulus of surface. However, the atomic average potential energy of nanowire shows an opposite change. Both the potential and surface energy of [110] nanowire are the lowest among all three orientational nanowires, which helps to explain why Au nanowires possess a [110] preferred orientation during the experimental growth proceeds.

Effect of solution speciation of impurities on α-glycine crystal habit: A molecular modeling study

In a recent work, we reported that solution speciation of certain “tailor-made” impurities (viz. aspartic and glutamic acids) controlled their stereoselective interactions at the α-glycine crystal interfaces [S.K. Poornachary, P.S. Chow, R.B.H. Tan, R.J. Davey, Cryst. Growth Des. 7(2) (2007) 254]. In this contribution, we rationalize this mechanism using molecular modeling and atom–atom potential energy calculations. The simulation results show preferential interaction of the impurity zwitterions on a flat (0 1 0) surface, and of the impurity anions either at the kink site on the (0 1 0) step, or on the (0 1 1) surface. We corroborate these results with the growth inhibition observed along b- and c-axes of α-glycine crystals in the presence of these impurities.

POTENTIAL ENERGY AS A PLUCKING CRITERION FOR LIQUID CLUSTER SIMULATIONS

We have investigated the liquid state of atomic clusters interacting through a classical pair-wise Lennard–Jones 6–12 potential, using constant energy molecular dynamics simulations. For larger clusters (N ≳ 500–600 atoms) desorption events are frequent and a cluster in the liquid state eventually always converts to a solid state. To study the cluster as it cools, one must isolate the central cluster from the desorbed atoms. In this paper, we investigate using the atomic potential energy as a very simple criterion for removing desorbed atoms from the simulation, and examine the spatial profile of atomic potential energy in various size liquid and solid clusters.