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    ABSTRACT: A current-carrying resonant nanoscale device, simulated by non-adiabatic molecular dynamics, exhibits sharp activation of non-conservative current-induced forces with bias. The result, above the critical bias, is generalized rotational atomic motion with a large gain in kinetic energy. The activation exploits sharp features in the electronic structure, and constitutes, in effect, an ignition key for atomic-scale motors. A controlling factor for the effect is the non-equilibrium dynamical response matrix for small-amplitude atomic motion under current. This matrix can be found from the steady-state electronic structure by a simpler static calculation, providing a way to detect the likely appearance, or otherwise, of non-conservative dynamics, in advance of real-time modelling.
    Journal of Physics Condensed Matter 09/2012; 24(40):402203.
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    ABSTRACT: A mixed quantum-classical approach is introduced which allows the dynamical response of molecules driven far from equilibrium to be modeled. This method is applied to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations are possible. The approach is applied to the study of high harmonic generation in N(2) and benzene using linearly polarized laser pulses and, to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N(2) an enhancement of the cut-off harmonics is observed whenever the laser polarization is aligned perpendicular to the molecular axis. This enhancement is attributed to the symmetry properties of the Kohn-Sham orbital that responds predominantly to the pulse. In benzene we predict that a suppression in the cut-off harmonics occurs whenever the laser polarization is aligned parallel to the molecular plane. We attribute this suppression to the symmetry-induced response of the highest-occupied molecular orbital.
    The Journal of Chemical Physics 05/2012; 136(19):194303.
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    ABSTRACT: When biological matter is subjected to ionizing radiation, a wealth of secondary low-energy (<20 eV) electrons are produced. These electrons propagate inelastically, losing energy to the medium until they reach energies low enough to localize in regions of high electron affinity. We have recently shown that in fully solvated DNA fragments, nucleobases are particularly attractive for such excess electrons. The next question is what is their longer-term effect on DNA. It has been advocated that they can lead to strand breaks by cleavage of the phosphodiester C(3')-O(3') bond. Here we present a first-principles study of free energy barriers for the cleavage of this bond in fully solvated nucleotides. We have found that except for dAMP, the barriers are on the order of 6 kcal/mol, suggesting that bond cleavage is a regular feature at 300 K. Such low barriers are possible only as a result of solvent and thermal fluctuations. These findings support the notion that low-energy electrons can indeed lead to strand breaks in DNA.
    Journal of the American Chemical Society 05/2012; 134(22):9122-5.
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    ABSTRACT: We investigate the structure of the [bmim][Tf(2)N]/silica interface by simulating the indentation of a thin (4 nm) [bmim][Tf(2)N] film by a hard nanometric tip. The ionic liquid/silica interface is represented in atomistic detail, while the tip is modelled by a spherical mesoscopic particle interacting via an effective short-range potential. Plots of the normal force (F(z)) on the tip as a function of its distance from the silica surface highlight the effect of weak layering in the ionic liquid structure, as well as the progressive loss of fluidity in approaching the silica surface. The simulation results for F(z) are in near-quantitative agreement with new AFM data measured on the same [bmim][Tf(2)N]/silica interface under comparable thermodynamic conditions.
    Physical Chemistry Chemical Physics 02/2012; 14(7):2475-82.
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    ABSTRACT: Selected aspects of the ab initio modelling of room temperature ionic liquids are discussed in our contribution, focusing on thermal decomposition reactions, and on the determination of the electrochemical stability window of these compounds. In both cases, we emphasise the role of ab initio simulation methods, able to deal simultaneously with the ionic and electronic side of the systems and phenomena under investigation.
    Faraday Discussions 01/2012; 154:373-89; discussion 439-64, 465-71.
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    ABSTRACT: The role of dispersion or van de Waals (VDW) interactions in imidazolium-based room-temperature ionic liquids is studied within the framework of density functional theory, using a recently developed non-empirical functional [M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004)], as efficiently implemented in the SIESTA code [G. Román-Pérez and J. M. Soler, Phys. Rev. Lett. 103, 096102 (2009)]. We present results for the equilibrium structure and lattice parameters of several crystalline phases, finding a general improvement with respect to both the local density (LDA) and the generalized gradient approximations (GGA). Similar to other systems characterized by VDW bonding, such as rare gas and benzene dimers as well as solid argon, equilibrium distances and volumes are consistently overestimated by ≈7%, compared to -11% within LDA and 11% within GGA. The intramolecular geometries are retained, while the intermolecular distances and orientations are significantly improved relative to LDA and GGA. The quality is superior to that achieved with tailor-made empirical VDW corrections ad hoc [M. G. Del Pópolo, C. Pinilla, and P. Ballone, J. Chem. Phys. 126, 144705 (2007)]. We also analyse the performance of an optimized version of this non-empirical functional, where the screening properties of the exchange have been tuned to reproduce high-level quantum chemical calculations [J. Klimes, D. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 074203 (2010)]. The results for solids are even better with volumes and geometries reproduced within 2% of experimental data. We provide some insight into the issue of polymorphism of [bmim][Cl] crystals, and we present results for the geometry and energetics of [bmim][Tf] and [mmim][Cl] neutral and charged clusters, which validate the use of empirical force fields.
    The Journal of Chemical Physics 10/2011; 135(15):154505.
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    ABSTRACT: We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.
    Physical Review Letters 06/2011; 106(23):238108.
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    ABSTRACT: We address the question of the observed pinning of 12〈11¯0] ordinary screw dislocations in γ-TiAl, which leads to the characteristic trailing of dipoles in the microstructure. While it has been proposed that these may be variously intrinsic or extrinsic in nature, we are able to rule out the former mechanism. We do this by means of very large scale, three-dimensional atomistic simulations using the quantum mechanical bond order potential. We find that the kink-pair formation energy is large – 6eV – while the single kink migration energy is conversely very small – 0.13eV. Using these, and other atomistically derived, data, we make kinetic Monte Carlo simulations at realistic time and length scales to simulate dislocation mobility as a function of stress and temperature. In the temperature range of the stress anomaly in γ-TiAl, we determine whether one or several of the pinning and unzipping processes associated with generation of jogs are observed during our simulations. We conclude that the pinning of ordinary dislocations and anomalous mechanical behaviour in γ-TiAl must be attributed to a combination of extrinsic obstacles and extensive cross-slip in a crystal containing impurities.
    Acta Materialia - ACTA MATER. 01/2011; 59(3):1281-1290.
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    ABSTRACT: We demonstrate for the first time a tight binding model for water incorporating polarizable oxygen atoms. A novel aspect is that we adopt a "ground up" approach in that properties of the monomer and dimer only are fitted. Subsequently we make predictions of the structure and properties of hexamer clusters, ice-XI and liquid water. A particular feature, missing in current tight binding and semiempirical hamiltonians, is that we reproduce the almost two-fold increase in molecular dipole moment as clusters are built up toward the limit of bulk liquid. We concentrate on properties of liquid water, particularly dielectric constant and self diffusion coefficient, which are very well rendered in comparison with experiment. Finally we comment on the question of the contrasting densities of water and ice which is central to an understanding of the subtleties of the hydrogen bond.
    The Journal of Chemical Physics 01/2011; 134(4):044130.
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    ABSTRACT: We give a physical interpretation of the recently demonstrated nonconservative nature of interatomic forces in current-carrying nanostructures. We start from the analytical expression for the curl of these forces, and evaluate it for a point defect in a current-carrying system. We obtain a general definition of the capacity of electrical current flow to exert a nonconservative force, and thus do net work around closed paths, by a formal noninvasive test procedure. Second, we show that the gain in atomic kinetic energy over time, generated by nonconservative current-induced forces, is equivalent to the uncompensated stimulated emission of directional phonons. This connection with electron-phonon interactions quantifies explicitly the intuitive notion that nonconservative forces work by angular momentum transfer.
    Beilstein Journal of Nanotechnology 01/2011; 2:727-33.
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