Recent Publications

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  1. Title: Modelling non-adiabatic processes using correlated electron-ion dynamics

    Author(s): McEniry E.J., Wang Y., Dundas D., Todorov T.N., Stella L., Miranda R.P., Fisher A.J., Horsfield A.P., Race C.P., Mason D.R., Foulkes W.M.C., Sutton A.P.

    European Physical Journal B , 77, No. 3, pp. 305-329 (October 2010)

    doi: 10.1140/epjb/e2010-00280-5

    Here we survey the theory and applications of a family of methods (correlated electron-ion dynamics, or CEID) that can be applied to a diverse range of problems involving the non-adiabatic exchange of energy between electrons and nuclei. The simplest method, which is a paradigm for the others, is Ehrenfest Dynamics. This is applied to radiation damage in metals and the evolution of excited states in conjugated polymers. It is unable to reproduce the correct heating of nuclei by current carrying electrons, so we introduce a moment expansion that allows us to restore the spontaneous emission of phonons. Because of the widespread use of Non-Equilibrium Green's Functions for computing electric currents in nanoscale systems, we present a comparison of this formalism with that of CEID with open boundaries. When there is strong coupling between electrons and nuclei, the moment expansion does not converge. We thus conclude with a reworking of the CEID formalism that converges systematically and in a stable manner.

  2. Title: First-principles study of substitutional metal impurities in graphene: structural, electronic and magnetic properties

    Author(s): Santos E.J.G., Ayuela A., D Sánchez-Portal D.

    New Journal of Physics, 12, pp. 053012- (May 2010)

    doi: 10.1088/1367-2630/12/5/053012

    We present a theoretical study using density functional calculations of the structural, electronic and magnetic properties of 3d transition metal, noble metal and Zn atoms interacting with carbon monovacancies in graphene. We pay special attention to the electronic and magnetic properties of these substitutional impurities and find that they can be fully understood using a simple model based on the hybridization between the states of the metal atom, particularly the d shell, and the defect levels associated with an unreconstructed D3h carbon vacancy. We identify three different regimes associated with the occupation of different carbon–metal hybridized electronic levels: (i) bonding states are completely filled for Sc and Ti, and these impurities are non-magnetic; (ii) the non-bonding d shell is partially occupied for V, Cr and Mn and, correspondingly, these impurities present large and localized spin moments; (iii) antibonding states with increasing carbon character are progressively filled for Co, Ni, the noble metals and Zn. The spin moments of these impurities oscillate between 0 and 1μB and are increasingly delocalized. The substitutional Zn suffers a Jahn–Teller-like distortion from the C3v symmetry and, as a consequence, has a zero spin moment. Fe occupies a distinct position at the border between regimes (ii) and (iii) and shows a more complex behavior: while it is non-magnetic at the level of generalized gradient approximation (GGA) calculations, its spin moment can be switched on using GGA+U calculations with moderate values of the U parameter.

  3. Title: Structure and Dynamics of 1-Ethyl-3-methylimidazolium Acetate via Molecular Dynamics and Neutron Diffraction

    Author(s): Bowron D.T., D'Agostino C., Gladden L.F., Hardacre C., Holbrey J.D., Lagunas M.C., McGregor J., Mantle M.D., Mullan C.L., Youngs T.G.A.,

    Journal of Physical Chemistry B, 114, No. 23, pp. 7760-7768 (Jun 17 2010)


    The liquid state structure of the ionic liquid, 1-ethyl-3-methylimidazolium acetate ([C(2)mim][OAc]), an excellent nonderivitizing solvent for cellulosic biomass, has been investigated at 323 K by molecular dynamics (MD) simulation and by neutron diffraction using the SANDALS diffractometer at ISIS to provide experimental differential neutron scattering cross sections from HID isotopically substituted materials. Ion-ion radial distribution functions both calculated from MD and derived from the empirical potential structure refinement (EPSR) model to the experimental data show the alternating shell structure of anions around the cation, as anticipated. Spatial probability distributions reveal the main anion-to-cation features as in-plane interactions of anions with the three imidazolium ring hydrogens and cation-cation planar stacking above/below the imidazolium rings. Interestingly, the presence of the polarized hydrogen-bond acceptor (HBA) anion (acetate) leads to an increase in anion-anion tail-tail structuring within each anion shell, an indicator of the onset of hydrophobic regions within the anion regions of the liquid. MD simulations show the importance of scaling of the effective ionic charges in the basic simulation approach to accurately reproduce both the observed experimental neutron scattering cross sections and ion self-diffusion coefficients.

  4. Title: Multi-pulse scheme for enhancing electron localization through vibrational wavepacket manipulation

    Author(s): Calvert C.R., King R.B., Bryan W.A., Newell W.R., McCann J.F.

    Journal of Physics B: Atomic, Molecular and Optical Physics, 43, pp. 011001- (JAN 2010)

    doi: 10.1088/0953-4075/43/1/011001

    A novel scheme for enhancing electron localization in intense-field dissociation is outlined. Through manipulation of a bound vibrational wavepacket in the exemplar deuterium molecular ion, simulations demonstrate that the application of multiple phase-locked, few-cycle IR pulses can provide a powerful scheme for directing the molecular dissociation pathway. By tuning the time delay and carrier–envelope–phase for a sequence of pulse interactions, the probability of the electron being localized to a chosen nucleus can be enhanced to above 80%.

  5. Title: Small angle neutron scattering from 1-alkyl-3-methylimidazolium hexafluorophosphate ionic liquids ([C(n)mim][PF6], n=4, 6, and 8)

    Author(s): Hardacre C., Holbrey J.D., Mullan C.L., Youngs T.G.A., Bowron D.T.,

    Journal of Chemical Physics B, 133, No. 7, pp. 074510- (Aug 21 2010)


    The presence of local anisotropy in the bulk, isotropic, and ionic liquid phases-leading to local mesoscopic inhomogeneity-with nanoscale segregation and expanding nonpolar domains on increasing the length of the cation alkyl-substituents has been proposed on the basis of molecular dynamics (MD) simulations. However, there has been little conclusive experimental evidence for the existence of intermediate mesoscopic structure between the first/second shell correlations shown by neutron scattering on short chain length based materials and the mesophase structure of the long chain length ionic liquid crystals. Herein, small angle neutron scattering measurements have been performed on selectively H/D-isotopically substituted 1-alkyl-3-methylimidazolium hexafluorophosphate ionic liquids with butyl, hexyl, and octyl substituents. The data show the unambiguous existence of a diffraction peak in the low-Q region for all three liquids which moves to longer distances (lower Q), sharpens, and increases in intensity with increasing length of the alkyl substituent. It is notable, however, that this peak occurs at lower values of Q (longer length scale) than predicted in any of the previously published MD simulations of ionic liquids, and that the magnitude of the scattering from this peak is comparable with that from the remainder of the amorphous ionic liquid. This strongly suggests that the peak arises from the second coordination shells of the ions along the vector of alkyl-chain substituents as a consequence of increasing the anisotropy of the cation, and that there is little or no long-range correlated nanostructure in these ionic liquids.

  6. Title: Magnetism of substitutional Co impurities in graphene: Realization of single π vacancies

    Author(s): Santos E.J.G., Sánchez-Portal D., Ayuela A.

    Physical Review B, 81, No. 12, pp. 125433- (26 March 2010)

    doi: 10.1103/PhysRevB.81.125433

    We report ab initio calculations of the structural, electronic, and magnetic properties of a graphene monolayer substitutionally doped with Co (Cosub) atoms. These calculations are done within density-functional theory using the generalized gradient approximation. We focus in Co because among traditional ferromagnetic elements (Fe, Co, and Ni), only Cosub atoms induce spin polarization in graphene. Our results show the complex magnetism of Co substitutional impurities in graphene, which is mapped into simple models such as the π-vacancy and Heisenberg model. The links established in our work can be used to bring into contact the engineering of nanostructures with the results of π models in defective graphene. In principle, the structures considered here can be fabricated using electron irradiation to create defects and depositing Co at the same time.

  7. Title: Screening of pairs of ions dissolved in ionic liquids

    Author(s): Lynden-Bell R.M.

    Physical Chemistry Chemical Physics, 12, No. 8, pp. 1733-1740 (2010)

    doi: 10.1039/b916987c

    The properties of pairs of solute ions in the ionic liquid, dimethylimidazolium chloride or [dmim][Cl], are studied as a function of their separation. The potential of mean force curves show that there is only a small stabilisation of ion pairs with opposite charges followed by a barrier to separation. Ion pairs with the same charge are also stabilised by solvent screening due to induced polarisation of the solvent. In both cases screening is essentially complete outside the first shell, but is large even when there is no solvent between the ions. Charge distributions in the solvation shells around ion pairs are shown and the results interpreted with the aid of a simple model of two ions in an spheroidal cavity in a conducting medium. The actual or Madelung potential experienced by the second solute ion is found to decay rapidly with distance and does not show the oscillations found in the Poisson potential around a single solute ion. We conclude that ionic liquids provide very effective electrostatic screening between solute molecules.

  8. Title: Microscopic Origin of Channeled Flow in Lamellar Titanium Aluminide

    Author(s): Katzarov I.H., Paxton A.T.

    Physical Review Letters, 104, No. 22, Art. No. 225502 (2010)

    doi: 10.1103/PhysRevLett.104.225502

    Full Text

    We employ a quantum mechanical bond order potential in an atomistic simulation of channeled flow. We show that the original hypothesis that this is achieved by a cooperative deployment of slip and twinning is correct, first because a twin is able to “protect” a 60° ordinary dislocation from becoming sessile, and second because the two processes are found to be activated by Peierls stresses of similar magnitude. In addition we show an explicit demonstration of the lateral growth of a twin, again at a similar level of stress. Thus these simultaneous processes are shown to be capable of channeling deformation into the observed state of plane strain in so-called “A”-oriented mechanical testing of titanium aluminide superalloy.

  9. Title: Spin-Polarization Mechanisms of the Nitrogen-Vacancy Center in Diamond

    Author(s): Delaney P., Greer J.C., Larsson J.A.

    Nano Letters, 10, No. 2, pp. 610-614 (2010)

    doi: 10.1021/nl903646p

    The nitrogen-vacancy (NV) center in diamond has shown great promise for quantum information due to the ease of initializing the qubit and of reading out its state. Here we show the leading mechanism for these effects gives results opposite from experiment; instead both must rely on new physics. Furthermore, NV centers fabricated in nanometer-sized diamond clusters are stable, motivating a bottom-up qubit approach, with the possibility of quite different optical properties to bulk.

  10. Title: Nonconservative generalized current-induced forces

    Author(s): Todorov T.N., Dundas D., McEniry E.J.

    Physical Review B, 81, No. 7, Art. No. 075416 (2010)

    doi: 10.1103/PhysRevB.81.075416

    A recent result for the curl of forces on ions under steady-state current in atomic wires with noninteracting electrons is extended to generalized forces on classical degrees of freedom in the presence of mean-field electron-electron screening. Current is described within a generic multiterminal picture, forces within the Ehrenfest approximation, and screening within an adiabatic, but not necessarily spatially local, mean-field picture.

  11. Title: Aten-An Application for the Creation, Editing, and Visualization of Coordinates for Glasses, Liquids, Crystals, and Molecules

    Author(s): Youngs T.G.A.,

    Journal of Computational Chemistry, 31, No. 3, pp. 639-648 (2010)

    doi: 10.1002/jcc.21359

    Aten is a tool for Linux, Mac, and Windows platforms to ease the creation, editing, and visualization of coordinates for use in, for example, molecular dynamics simulations. The code handles gas-phase molecules in addition to crystals, surfaces, and liquids, providing standard tools to edit "by the atom" along with specific "by the box" methods suited to periodic systems, including full crystallographic spacegroup packing definitions. Visualization of systems encompasses the standard drawing styles and may be mixed with an arbitrary number of other basic objects, such as arrows and geometric objects allowing creation of scenes involving vector fields, coarse-grained particles, etc. Standard molecular mechanics forcefields can be read in, edited, applied to molecules using the built-in chemical typing language, and subsequently used to calculate energies and forces, minimize energies with respect to coordinates, decompose energies into contribution by molecule type, etc. Monte Carlo methods are available with which to generate random configurations of N-component systems, or solvate around molecules or in specific regions within existing configurations. Supported file formats are governed by user-defined "filters," which provide flexibility of input/output as well as the ability to define custom or extended formats of traditional files. Forcefield descriptions for loaded systems can be output and formatted for use as input to common codes. All features can be accessed by a comprehensive GUI and scripting language based on the C syntax. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 31: 639-648, 2010

  12. Title: Solid and liquid charge-transfer complex formation between 1-methylnaphthalene and 1-alkyl-cyanopyridinium bis{(trifluoromethyl)sulfonyl}imide ionic liquids

    Author(s): Hardacre C., Holbrey J.D., Mullan C.L., Nieuwenhuyzen M., Youngs T.G.A., Bowron D.T., Teat S.J.,

    Physical Chemistry Chemical Physics, 12, No. 8, pp. 1842-1853 (2010)

    doi: 10.1039/b921160h

    Liquid charge-transfer (CT) complexes were observed to form on contacting electron-rich aromatics with electron withdrawing group appended 1-alkyl-4-cyanopyridinium ionic liquids (ILs). Cooling below the melting point of the ionic liquid resulted in crystallisation of ionic liquid from the complex for 2-cyano and 3-cyano pyridinium isomers and in the formation of a 1 : 1 IL : aromatic crystalline CT-complex with the 4-cyanopyridinium isomer. The liquid structure of a 1 : 1 mixture of 1-methyl-4-cyanopyridinium bis{(trifluoromethyl)sulfonyl} imide with 1-methylnaphthalene has been probed by neutron diffraction experiments and molecular dynamics simulations. A high degree of correlation between the experimental data and the simulations was found with a significant displacement of the anions from around the cation by the aromatic species and the resulting structure having pi-pi stacks between the cations and the aromatic.

  13. Title: Ionic liquids through the looking glass: theory mirrors experiment and provides further insight into aromatic substitution processes

    Author(s): Jones S.G., Yau H.M., Davies E., Hook J.M., Youngs T.G.A., Harper J.B., Croft A.K.,

    Physical Chemistry Chemical Physics, 12, No. 8, pp. 1873-1878 (2010)

    doi: 10.1039/b919831h

    Aromatic substitution of 1-fluoro-2,4-dinitrobenzene has been shown to proceed more rapidly in an ionic liquid than in ethanol, primarily due to entropic, rather than enthalpic, effects. By using molecular dynamics simulations, an anion-pi interaction appears to contribute to strong ordering within the starting material complex that accounts for the relative differences in the SNAr k.

  14. Title: Atom probe tomography analysis of the distribution of rhenium in nickel alloys

    Author(s): Mottura A., Warnken N., Miller M.K., Finnis M.W., Reed R.C.,

    Acta Materialia, 58, No. 3, pp. 931-942 (2010)

    doi: 10.1016/j.actamat.2009.10.008

    Atom probe tomography (APT) is used to characterise the distributions of rhenium in a binary Ni-Re alloy and the nickel-based single-crystal CMSX-4 superalloy. A purpose-built algorithm is developed to quantify the size distribution of solute clusters, and applied to the APT datasets to critique the hypothesis that rhenium is prone to the formation of clusters in these systems. No evidence is found to indicate that rhenium forms solute clusters above the level expected from random fluctuations. In CMSX-4, enrichment of Re is detected in the matrix phase close to the matrix/precipitate (gamma/gamma') phase boundaries. Phase field modelling indicates that this is due to the migration of the gamma/gamma' interface during cooling from the temperature of operation. Thus, neither clustering of rhenium nor interface enrichments can be the cause of the enhancement in high temperature mechanical properties conferred by rhenium, alloying. (C) 2009 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  15. Title: Small cluster model of the NV centre in diamond

    Author(s): Delaney P., Larsson J.A.,

    Proceedings of The Tenth International Meeting On Hole Burning, Single Molecule And Related Spectroscopies, 3, No. 4, pp. 1533-1537 (2010)

    doi: 10.1016/j.phpro.2010.01.217

    The singlet E-1 and (1)A(1) energy levels of the Nitrogen-Vacancy centre's ground state configuration each need two Slater determinants in theoretical models, posing difficulties for Density-Functional Theory (DFT) and Hartree-Fock approaches. Configuration Interaction (CI) can handle such states, but not the C284H144N- and C163H100N- clusters of our recent DFT study as CI computer time and memory scale worse than DFT with system size. Using smaller clusters to model bulk diamond introduces size errors. We examine the smaller diamond cluster C42H42N- using DFT to quantify the size error: if not too large it opens the way to CI calculations of these states. (C) 2009 Elsevier B. V. All rights reserved

  16. Title: Solid-liquid interface free energy through metadynamics simulations

    Author(s): Angioletti-Uberti S., Ceriotti M., Lee P.D., Finnis M.W.,

    Physical Review B, 81, No. 12 (2010)

    doi: 10.1103/PhysRevB.81.125416

    The solid-liquid interface free energy gamma(sl) is a key parameter controlling nucleation and growth during solidification and other phenomena. There are intrinsic difficulties in obtaining accurate experimental values, and the previous approaches to compute gamma(sl) with atomistic simulations are computationally demanding. We present an approach which is to obtain gamma(sl) from a free-energy map of the phase transition reconstructed by metadynamics. We apply this to the benchmark case of a Lennard-Jones potential, and the results confirm the most reliable data obtained previously. We demonstrate several advantages of our approach: it is simple to implement, robust and free of hysteresis problems, it allows a rigorous and unbiased estimate of the statistical uncertainty, and it returns a good estimate of the thermodynamic limit with system sizes of a just a few hundred atoms. It is therefore attractive for applications which require more realistic and specific models of interatomic forces.

  17. Title: A genetic algorithm for predicting the structures of interfaces in multicomponent systems

    Author(s): Chua A.L.S., Benedek N.A., Chen L., Finnis M.W., Sutton A.P.,

    Nature Materials, 9, No. 5, pp. 418-422 (2010)

    doi: 10.1038/nmat2712

    Recent years have seen great advances in our ability to predict crystal structures from first principles. However, previous algorithms have focused on the prediction of bulk crystal structures, where the global minimum is the target. Here, we present a general atomistic approach to simulate in multicomponent systems the structures and free energies of grain boundaries and heterophase interfaces with fixed stoichiometric and non-stoichiometric compositions. The approach combines a new genetic algorithm using empirical interatomic potentials to explore the configurational phase space of boundaries, and thereafter refining structures and free energies with first-principles electronic structure methods. We introduce a structural order parameter to bias the genetic algorithm search away from the global minimum ( which would be bulk crystal), while not favouring any particular structure types, unless they lower the energy. We demonstrate the power and efficiency of the algorithm by considering non-stoichiometric grain boundaries in a ternary oxide, SrTiO3.

  18. Title: Density-potential mapping in time-dependent density-functional theory

    Author(s): Maitra N.T., Todorov T.N., Woodward C., Burke K.,

    Physical Review A, 81, No. 4 (2010)

    doi: 10.1103/PhysRevA.81.042525

    The key questions of uniqueness and existence in time-dependent density-functional theory are usually formulated only for potentials and densities that are analytic in time. Simple examples, standard in quantum mechanics, lead, however, to nonanalyticities. We reformulate these questions in terms of a nonlinear Schrodinger equation with a potential that depends nonlocally on the wave function.

  19. Title: Thermodynamic properties and atomistic structure of the dry amorphous silica surface from a reactive force field model

    Author(s): Cabriolu R., Ballone P.,

    Physical Review B, 81, No. 15 (2010)

    doi: 10.1103/PhysRevB.81.155432

    A force field model of the Keating type supplemented by rules to break, form, and interchange bonds is applied to investigate thermodynamic and structural properties of the amorphous SiO2 surface. A simulated quench from the liquid phase has been carried out for a silica sample made of 3888 silicon and 7776 oxygen atoms arranged on a slab similar to 40 angstrom thick, periodically repeated along two directions. The quench results into an amorphous sample, exposing two parallel square surfaces of similar to 42 nm(2) area each. Thermal averages computed during the quench allow us to determine the surface thermodynamic properties as a function of temperature. The surface tension turns out to be gamma=310 +/- 20 erg/cm(2) at room temperature and gamma=270 +/- 30 at T=2000 K, in fair agreement with available experimental estimates. The entropy contribution Ts-s to the surface tension is relatively low at all temperatures, representing at most similar to 20% of the surface energy. Almost without exceptions, Si atoms are fourfold coordinated and oxygen atoms are twofold coordinated. Twofold and threefold rings appear only at low concentration and are preferentially found in proximity of the surface. Above the glass temperature T-g=1660 +/- 50 K, the mobility of surface atoms is, as expected, slightly higher than that of bulk atoms. The computation of the height-height correlation function shows that the silica surface is rough in the equilibrium and undercooled liquid phase, becoming smooth below the glass temperature T-g.

  20. Title: Atomic-scale characterization of the SrTiO3 Sigma 3 (112) [(1)over-bar10] grain boundary

    Author(s): Dudeck K.J., Benedek N.A., Finnis M.W., Cockayne D.J.H.,

    Physical Review B, 81, No. 13 (2010)

    doi: 10.1103/PhysRevB.81.134109

    The strontium titanate Sigma 3 (112) [(1) over bar 10] grain boundary has been investigated using aberration-corrected high-resolution transmission electron microscopy and exit wave-function reconstruction. By quantitatively comparing the experimental exit wave phase with that expected from relaxed model structures obtained by density-functional theory, it has been possible to differentiate between two proposed structures not significantly different in their calculated energies, and to deduce information about three-dimensional atomic arrangements near the boundary using the reconstructed exit wave-function phase.

  21. Title: Electronic structure and total energy of interstitial hydrogen in iron: Tight binding models

    Author(s): Paxton A.T., Elsässer C.

    Physical Review B, 82, No. 23, Art. No. 23512 (2010)

    doi: 10.1103/PhysRevB.82.235125

    Full Text

    An application of the tight binding approximation is presented for the description of electronic structure and interatomic force in magnetic iron, both pure and containing hydrogen impurities. We assess the simple canonical d-band description in comparison to a non orthogonal model including s and d bands. The transferability of our models is tested against known properties including the segregation energies of hydrogen to vacancies and to surfaces of iron. In many cases agreement is remarkably good, opening up the way to quantum mechanical atomistic simulation of the effects of hydrogen on mechanical properties.

  22. Title: Phonons, Instabilities and Origin of Polarization in KDP

    Author(s): Colizzi G., Lasave J., Kohanoff J.J., Migoni R.

    Ferroelectrics, 401, pp. 200- (2010)


  23. Title: Shell Model Study of Local and Global Energy Barriers in KDP

    Author(s): Koval S., Lasave J., Kohanoff J.J, Migoni R.

    Ferroelectrics, 401, pp. 103 - (2010)


  24. Title: Quasiparticle calculations of the electronic properties of ZrO2 and HfO2 polymorphs and their interface with Si

    Author(s): Gruening M., Shaltaf R., Rignanese G-M.,

    Phys. Rev. B, 81, pp. 035330- (2010)


  25. Title: Electronic properties of interfaces and defects from many-body perturbation theory: Recent developments and applications

    Author(s): Giantomassi M., Stankovski M., Shaltaf R., Gruening M., Bruneval F., Rinke P., Rignanese G-M.,

    physica status solidi (2010)

    doi: 10.1002/pssb.201046094

  26. Title: A self-learning algorithm for biased molecular dynamics

    Author(s): Tribello G., Ceriotti M., Parrinello M.

    Proc. Natl. Acad Sci U.S.A. , 107, pp. 17509-17514 (2010)


  27. Title: Asprich peptides are occluded in calcite and permanently disorder biomineral crystals

    Author(s): Metzler R., Tribello G., Parrinello M., Gilbert P.

    J. Am. Chem. Soc. , 132, pp. 11585-11591 (2010)


  28. Title: Ab initio potentials of F + Li-2 accessible at ultracold temperatures

    Author(s): Wright K.W.A., Lane I.

    Physical Review A, 82, pp. 032715- (2010)

    doi: 10.1103/PhysRevA.82.032715

    Ab initio calculations for the strongly exoergic Li2+F harpoon reaction are presented using density-functional theory, complete active space self-consistent field, and multireference configuration interaction methods to argue that this reaction would be an ideal candidate for investigation with ultracold molecules. The lowest six states are calculated with the aug-correlation-consistent polarized valence triple-zeta basis set and at least two can be accessed by a ground rovibronic Li2 molecule with zero collision energy at all reaction geometries. The large reactive cross section (characteristic of harpoon reactions) and chemiluminescent products are additional attractive features of these reactions.