Applied Mathematics

Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was < 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation. S tatic and dynamic properties of both bulk and solvation water have garnered a lot of attention including several conflicting hypotheses. For example, the picture that water rotation can be desribed by simple Debye rotational diffusion was shown to be too simplistic by Laage and Hynes who demonstrated, using computer simulations, that instead of smooth rotation, water molecules undergo large-angle jumps 1 . This has since been confirmed by experiments 2 and independent simulations 3 . In a recent contribution, ab initio simulations of Kühne and Khaliullin 4 resolved the controversy regarding the interpretation of a series of x-ray experiments 5,6 that suggested water having anisotropic structure. Their simulations showed that the structure of water is tetrahedral but the energetics of the hydrogen bonds (HBs) are asymmetric.

The capabilities of time-resolved laser-induced incandescence (TiRe-LII), a combustion diagnostic used almost exclusively to measure soot primary particles, could potentially be extended to size aerosolized metal nanoparticles. In order to do this, however, it is necessary to characterize the thermal accommodation coefficient, a, which specifies the heat conduction rate between the laserenergized nanoparticles and the surrounding gas. This paper extends a molecular dynamics (MD) methodology to calculate a for Fe/He, Fe/Ar, Mo/He, and Mo/Ar systems. A comparative analysis of the results shows that a is most strongly influenced by the potential well between the gas molecule and nanoparticle surface. Finally, the MDderived value for a is used to recover the nanoparticle size distribution for TiRe-LII measurements made on molybdenum nanoparticles in argon.

The physical mechanisms behind hydrophobic hydration have been debated for over 65 years. Spectroscopic techniques have the ability to probe the dynamics of water in increasing detail, but many fundamental issues remain controversial. We have performed systematic first-principles ab initio Car−Parrinello molecular dynamics simulations over a broad temperature range and provide a detailed microscopic view on the dynamics of hydration water around a hydrophobic molecule, tetramethylurea. Our simulations provide a unifying view and resolve some of the controversies concerning femtosecond-infrared, THz−GHz dielectric relaxation, and nuclear magnetic resonance experiments and classical molecular dynamics simulations. Our computational results are in good quantitative agreement with experiments, and we provide a physical picture of the long-debated "iceberg" model; we show that the slow, long-time component is present within the hydration shell and that molecular jumps and over-coordination play important roles. We show that the structure and dynamics of hydration water around an organic molecule are non-uniform.

The ground state energies of Ag and Au in the face-centered cubic (FCC), body-centered cubic (BCC), simple cubic (SC) and the hypothetical diamond-like phase, and dimer were calculated as a function of bond length using density functional theory (DFT). These energies were then used to parameterize the many-body Gupta potential for Ag and Au. We propose a new parameterization scheme that adopts coordination dependence of the parameters using the well-known Tersoff potential as its starting point. This parameterization, over several phases of Ag and Au, was performed to guarantee transferability of the potentials and to make them appropriate for studies of related nanostructures. Depending on the structure, the energetics of the surface atoms play a crucial role in determining the details of the nanostructure. The accuracy of the parameters was tested by performing a 2 ns MD simulation of a cluster of 55 Ag atomsa well studied cluster of Ag, the most stable structure being the icosahedral one. Within this time scale, the initial FCC lattice was found to transform to the icosahedral structure at room temperature. The new set of parameters for Ag was then used in a temperature dependent atom-by-atom deposition of Ag nanoclusters of up to 1000 atoms. We find a deposition temperature of 500 ± 50 K where low energy clusters are generated, suggesting an optimal annealing temperature of 500 K for Ag cluster synthesis. Surface energies were also calculated via a 3 ns MD simulation.

This paper describes the application of timeresolved laser-induced incandescence (TiRe-LII), a combustion diagnostic used mainly for measuring soot primary particles, to size silicon nanoparticles formed within a plasma reactor. Inferring nanoparticle sizes from TiRe-LII data requires knowledge of the heat transfer through which the laser-heated nanoparticles equilibrate with their surroundings. Models of the free molecular conduction and evaporation are derived, including a thermal accommodation coefficient found through molecular dynamics. The model is used to analyze TiRe-LII measurements made on silicon nanoparticles synthesized in a low-pressure plasma reactor containing argon and hydrogen. Nanoparticle sizes inferred from the TiRe-LII data agree with the results of a Brunauer-Emmett-Teller analysis.

We have performed X-ray photoelectron spectroscopy (XPS) and high energy electron energy-loss spectroscopy (HEELS) calculations from first principles on a series of Monte Carlo generated amorphous carbon materials and have used a technique which separates the p* and r* components of the energy-loss near-edge structure spectra of carbon materials on the basis of the ab initio electronic structure calculations of graphite to determine the sp 3 fraction of the carbon systems. While the XPS technique is found to probe the local coordination geometry, the sp 3 fractions resulting from the HEELS technique are found to be in very good agreement with those based on the p-orbital axis vector analysis which accounts for the effects of non-planarity in 3-coordinated systems.

We describe a technique to determine the sp 3 / sp 2 ratio of carbon materials which is based on the electronenergy-loss spectroscopy and which uses the theoretical spectrum of graphite obtained from ab initio electronic structure calculations. The method relies on the separation of the * and * components of the carbon K edge of graphite. The resulting * spectrum is adopted and assumed to be transferable to other carbon systems given an appropriate parametrization of the broadening. The method is applied on a series of Monte Carlo generated amorphous carbon structures and is shown to be stable over a wide range of the energy windows for which spectral integration is performed. The sp 3 fractions obtained using this method are found to be in good agreement with those obtained from a microscopic scheme which uses the -orbital axis vector analysis (POAV1). From the electron energy loss calculations on the generated amorphous carbon structures, we conclude that the interchangeable use of coordination number and hybridization state can lead to an underestimation of the sp 3 fraction of generated amorphous carbon structures for low and moderate densities. For high densities the coordination method and the POAV1 approach gave the same results. The technique was also applied on a series of spectra of plasma deposited amorphous carbon and was found to be in good agreement with the results obtained from a functional fitting approach.

We perform density functional theory calculations on a series of armchair and zigzag nanotubes of diameters less than 1 nm using the all-electron full-potential͑-linearized͒-augmented-plane-wave method. Emphasis is laid on the effects of curvature, the electron-beam orientation, and the inclusion of the core hole on the carbon electron-energy-loss K edge. The electron-energy-loss near-edge spectra of all the studied tubes show strong curvature effects compared to that of flat graphene. The curvature-inducedhybridization is shown to have a more drastic effect on the electronic properties of zigzag tubes than on those of armchair tubes. We show that the core-hole effect must be accounted for in order to correctly reproduce electron-energy-loss measurements. We also find that the energy-loss near-edge spectra of these carbon systems are dominantly dipole selected and that they can be expressed simply as a proportionality with the local momentum projected density of states, thus portraying the weak energy dependence of the transition matrix elements. Compared to graphite, we report a reduction in the anisotropy as seen on the energy-loss near-edge spectra of carbon nanotubes.

The energy-loss near-edge structure (ELNES) spectra of several carbon allotropes (non-hydrogenated and hydrogenated face-centered cubic (FCC) carbon, rhombohedral carbon, glitter, hexagonite and lonsdaleite) are calculated within the supercell-core-excited density functional theory approach. In particular an experimental ELNES spectrum of 'new diamond' ('n-diamond') [Konyashin et al., Diamond Relat. Mater. 10, (2001) 99-102] is compared with the ELNES spectra of FCC carbon, rhombohedral carbon and the so-called glitter structure. Our calculations show that the ELNES spectrum considered in that publication cannot be that of FCC carbon.

Thermal diffuse scattered electrons significantly contribute to high-resolution transmission electron microscopy images. Their intensity adds to the background and is peaked at positions of atomic columns. In this paper we suggest an approximation to simulate intensity of thermal diffuse scattered electrons in plane-wave illumination transmission electron microscopy using an emission-potential multislice algorithm which is computationally less intensive than the frozen lattice approximation or the mutual intensity approach. Intensity patterns are computed for Au and InSb for different crystal orientations. These results are compared with intensities from the frozen lattice approximation based on uncorrelated vibration of atoms as well as with the frozen phonon approximation for Au. The frozen phonon method uses a detailed phonon model based on force constants we computed by a density functional theory approach. The comparison shows that our suggested emission-potential method is in close agreement with both the frozen lattice and the frozen phonon approximations.

We present a new method to measure structure factors from electron spot diffraction patterns recorded under almost parallel illumination in transmission electron microscopes. Bloch wave refinement routines have been developed to refine the crystal thickness, its orientation and structure factors by comparison of experimentally recorded and calculated intensities. Our method requires a modicum of computational effort, making it suitable for contemporary personal computers. Frozen lattice and Bloch wave simulations of GaAs diffraction patterns are used to derive optimised experimental conditions. Systematic errors are estimated from the application of the method to simulated diffraction patterns and rules for the recognition of physically reasonable initial refinement conditions are derived. The method is applied to the measurement of the 200 structure factor for GaAs. We found that the influence of inelastically scattered electrons is negligible. Additionally, we measured the 200 structure factor from zero loss filtered two-dimensional convergent beam electron diffraction patterns. The precision of both methods is found to be comparable and the results agree well with each other. A deviation of more than 20% from isolated atom scattering data is observed, whereas close agreement is found with structure factors obtained from density functional theory [A. Rosenauer, M. Schowalter, F. Glas, D. Lamoen, Phys. Rev. B 72 (2005), 085326-1], which account for the redistribution of electrons due to chemical bonding via modified atomic scattering amplitudes.

We use systematic 8 ns ab initio molecular dynamics (AIMD) to study the structure and dynamics of water in bulk, and close to both hydrophobic and hydrophilic (carbonyl) groups of tetramethylurea (TMU). We observe crossovers in the dynamical behavior around the hydrophobic group at TX = 256±4 K and another one at 265±5 K related to the relative strength of water-water and water-carbonyl hydrogen bonds (HBs). For bulk water, the temperature of the apparent divergence in relaxation times is located at Tc = 210 ± 10 K. To better identify the effects arising from the hydrophilic carbonyl group, systems of water with a methane molecule were used as references. These findings are related to the structural and thermodynamic transitions reported for proteins in solution and may also play a role in the mechanism of cold denaturation of proteins.

We present a technique to determine the sp 3 /sp 2 ratio of carbon materials which is based on the electron energy-loss spectroscopy and which uses the theoretical spectrum of graphite obtained from ab initio electronic structure calculations. The method relies on the separation of the π * and σ * components of the carbon K-edge of graphite. This π * spectrum is adopted and assumed to be transferable to other carbon systems given an appropriate parametrisation of the broadening. The method is applied on a series of Monte-Carlo generated amorphous carbon structures and is shown to be stable over a wide range of the energy windows for which spectral integration is performed. The results are found to be in good agreement with the sp 3 fraction obtained from a microscopic scheme which uses the π−orbital axis vector (POAV1) analysis. The technique was also applied on a series of experimental spectra of amorphous carbon and was found to be in good agreement with the results obtained from a functional fitting approach.

The approach used to fit the temperature dependence is described and resulting fit parameters are tabulated for each material. The Debye-Waller factors are deduced from generalized phonon densities of states which were derived from first principles using the WIEN2k and the ABINIT codes.

InN, ZnO and CdO with the wurtzite-type structure. The Debye-Waller factors were derived from phonon densities of states obtained from Hellmann-Feynman forces computed within the density-functional-theory formalism. The temperature dependences of the Debye-Waller factors were fitted and fit parameters are given.

We perform density functional theory calculations on a series of armchair and zigzag nanotubes of diameters less than 1nm using the all-electron Full-Potential(-Linearised)-Augmented-Plane-Wave (FPLAPW) method. Emphasis is laid on the effects of curvature, the electron beam orientation and the inclusion of the core-hole on the carbon electron energy loss K-edge. The electron energy loss near-edge spectra of all the studied tubes show strong curvature effects compared to that of flat graphene. The curvature induced π − σ hybridisation is shown to have a more drastic effect on the electronic properties of zigzag tubes than on those of armchair tubes. We show that the core-hole effect must be accounted for in order to correctly reproduce electron energy loss measurements. We also find that, the energy loss near edge spectra of these carbon systems are dominantly dipole selected and that they can be expressed simply as a proportionality with the local momentum projected density of states, thus portraying the weak energy dependence of the transition matrix elements. Compared to graphite, the ELNES of carbon nanotubes show a reduced anisotropy. I. INTRODUCTION Since the discovery of carbon nanotubes by Iijima [1] in 1991, much effort has been devoted experimentally [2, 3, 4, 5] and theoretically [6, 7, 8] to study this new material. The one dimensional character of single wall nanotubes (SWNT's) enables them to exhibit very interesting physical properties due to the quantum confinement of electrons in a one dimensional lattice. Remarkable optical, thermoelectric, mechanical and electronic properties can be expected. Doping or intercalation [9, 10, 11, 12, 13, 14, 15, 16, 17], structural defects [18, 19] and pressure effects [20] are known to enrich these properties. Resonant Raman spectroscopy and optical absorption spectroscopy [21, 22, 23, 24] have been widely used to describe the electronic structure of isolated and ropes of nanotubes. Scanning tunneling microscopy [19, 25] has also been used to detect the Van Hove spikes of SWNT's. Most of the theoretical studies are based on the application of the Born-von Karman boundary conditions to the two dimensional graphene sheet [7, 26] in a zonefolding technique and the all-valence tight-binding method [6, 26, 27]. This graphene zone-folding approach is known to be inaccurate to describe the unoccupied density of states (DOS) [28] a few eV's beyond the Fermi level. Density functional theory (DFT) calculations [28, 29] have also been carried out but very few calculations [29] probing core-loss spectra are available. Electron energy loss spectrum (EELS) and X-ray absorption spectroscopy (XAS) measurements are available but their theoretical interpretation is often limited to the site and angular momentum projected local density of states (LDOS). This interpretation does not account for transition matrix elements which are known to be important and sensitive to the momentum transfer direction for anisotropic