Natalia V. Skorodumova

Adsorption of Cu, Ag, and Au atoms on graphene including van der Waals interactions

We performed a systematic density functional (DF) study of the adsorption of copper, silver, and gold adatoms on pristine graphene, especially accounting for van der Waals (vdW) interactions by the vdW-DF and PBE + D2 methods. In particular, we analyze the preferred adsorption site (among top, bridge, and hollow positions) together with the corresponding distortion of the graphene sheet and identify diffusion paths. Both vdW schemes show that the coinage metal atoms do bind to the graphene sheet and that in some cases the buckling of the graphene layer can be significant. Only the results for silver are qualitatively at variance with those obtained with the generalized gradient approximation, which gives no binding in this case. However in all three cases, we observe some quantitative differences between the vdW-DF and PBE + D2 methods. For instance the adsorption energies calculated with the PBE + D2 method are systematically higher than the ones obtained with vdW-DF. Moreover, the equilibrium distances computed with PBE + D2 are shorter than those calculated with the vdW-DF method.

Redox properties of CeO2-MO2 (M=Ti, Zr, Hf, or Th) solid solutions from first principles calculations

The authors have used density functional theory calculations to investigate how the redox thermodynamics and kinetics of CeO2 are influenced by forming solid solutions with TiO2, ZrO2, HfO2, and Th ...

Elastic Anisotropy of Earth's Inner Core

Earths solid-iron inner core is elastically anisotropic. Sound waves propagate faster along Earths spin axis than in the equatorial plane. This anisotropy has previously been explained by a preferred orientation of the iron alloy hexagonal crystals. However, hexagonal iron becomes increasingly isotropic on increasing temperature at pressures of the inner core and is therefore unlikely to cause the anisotropy. An alternative explanation, supported by diamond anvil cell experiments, is that iron adopts a body-centered cubic form in the inner core. We show, by molecular dynamics simulations, that the body-centered cubic iron phase is extremely anisotropic to sound waves despite its high symmetry. Direct simulations of seismic wave propagation reveal an anisotropy of 12%, a value adequate to explain the anisotropy of the inner core.

Origin of the low rigidity of the Earth's inner core

Earths solid-iron inner core has a low rigidity that manifests itself in the anomalously low velocities of shear waves as compared to shear wave velocities measured in iron alloys. Normally, when estimating the elastic properties of a polycrystal, one calculates an average over different orientations of a single crystal. This approach does not take into account the grain boundaries and defects that are likely to be abundant at high temperatures relevant for the inner core conditions. By using molecular dynamics simulations, we show that, if defects are considered, the calculated shear modulus and shear wave velocity decrease dramatically as compared to those estimates obtained from the averaged single-crystal values. Thus, the low shear wave velocity in the inner core is explained.

Small gold clusters on graphene, their mobility and clustering : a DFT study

Motivated by the experimentally observed high mobility of gold atoms on graphene and their tendency to form nanometer-sized clusters, we present a density functional theory study of the ground state structures of small gold clusters on graphene, their mobility and clustering. Our detailed analysis of the electronic structures identifies the opportunity to form strong gold-gold bonds and the graphene-mediated interaction of the pre-adsorbed fragments as the driving forces behind golds tendency to aggregate on graphene. While clusters containing up to three gold atoms have one unambiguous ground state structure, both gas phase isomers of a cluster with four gold atoms can be found on graphene. In the gas phase the diamond-shaped Au(4)(D) cluster is the ground state structure, whereas the Y-shaped Au(4)(Y) becomes the actual ground state when adsorbed on graphene. As we show, both clusters can be produced on graphene by two distinct clustering processes. We also studied in detail the stepwise formation of a gold dimer out of two pre-adsorbed adatoms, as well as the formation of Au(3). All reactions are exothermic and no further activation barriers, apart from the diffusion barriers, were found. The diffusion barriers of all studied clusters range from 4 to 36 meV only, and are substantially exceeded by the adsorption energies of - 0.1 to - 0.59 eV. This explains the high mobility of Au(1-4) on graphene along the C-C bonds.

Stability of the MgCO3 structures under lower mantle conditions

Abstract The presence of carbon in the Earth makes the search for high-pressure carbon-containing phases essential for our understanding of mineral compositions of the Earths mantle. In a recent study Isshiki et al. (2004) demonstrated that magnesite transforms into a new phase at lower mantle pressures. However, the structure of the emerging phase remained unknown. Here we show, by means of first principles calculations, that MgCO3 magnesite can transform into a pyroxene structure at 113 GPa, which further transforms into a CaTiO3-type structure at about 200 GPa.

Stability of gold nanowires at large Au-Au separations

The unusual structural stability of gold nanowires at large separations of gold atoms is explained from first-principles quantum mechanical calculations. We show that undetected light atoms, in particular hydrogen, stabilize the experimentally observed structures, which would be unstable in pure gold wires. The enhanced cohesion is due to the partial charge transfer from gold to the light atoms. This finding should resolve a long-standing controversy between theoretical predictions and experimental observations.

Dynamical stability of Fe-H in the Earth's mantle and core regions.

The core extends from the depth of 2,900 km to the center of the Earth and is composed mainly of an iron-rich alloy with nickel, with 10% of the mass comprised of lighter elements like hydrogen, but the exact composition is uncertain. We present a quantum mechanical first-principles study of the dynamical stability of FeH phases and their phonon densities of states at high pressure. Our free-energy calculations reveal a phonon-driven stabilization of dhcp FeH at low pressures, thus resolving the present contradiction between experimental observations and theoretical predictions. Calculations reveal a complex phase diagram for FeH under pressure with a dhcp → hcp → fcc sequence of structural transitions.

KMCLib: A general framework for lattice kinetic Monte Carlo (KMC) simulations

KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily extended and customized by the user to allow for the development of complex custom KMC models for specific systems without having to modify the core functionality of the program. Analysis modules and on-the-fly elementary step diffusion rate calculations can be implemented as plugins following a well-defined API. The plugin modules are loosely coupled to the core KMCLib program via the Python scripting language. KMCLib is written as a Python module with a backend C++ library. After initial compilation of the backend library KMCLib is used as a Python module; input to the program is given as a Python script executed using a standard Python interpreter. We give a detailed description of the features and implementation of the code and demonstrate its scaling behavior and parallel performance with a simple one-dimensional A-B-C lattice KMC model and a more complex three-dimensional lattice KMC model of oxygen-vacancy diffusion in a fluorite structured metal oxide. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis, and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. Program summary Program title: KMCLib Catalogue identifier: AESZ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AESZ_v1_0.html Program obtainable from: CPC Program Library, Queens University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 49 064 No. of bytes in distributed program, including test data, etc.: 1 575 172 Distribution format: tar.gz Programming language: Python and C++. Computer: Any computer that can run a C++ compiler and a Python interpreter. Operating system: Tested on Ubuntu 12.4 LTS, CentOS release 5.9, Mac OSX 10.5.8 and Mac OSX 10.8.2, but should run on any system that can have a C++ compiler, MPI and a Python interpreter. Has the code been vectorized or parallelized?: Yes. From one to hundreds of processors depending on the type of input and simulation. RAM: From a few megabytes to several gigabytes depending on input parameters and the size of the system to simulate. Classification: 4.13, 16.13. External routines: KMCLib uses an external Mersenne Twister pseudo random number generator that is included in the code. A Python 2.7 interpreter and a standard C++ runtime library are needed to run the serial version of the code. For running the parallel version an MPI implementation is needed, such as e.g. MPICH from http://www.mpich.org or Open-MPI from http://www.open-mpi.org. SWIG (obtainable from http://www.swig.org/) and CMake (obtainable from http://www.cmake.org/) are needed for building the backend module, Sphinx (obtainable from http://sphinx-doc.org) for building the documentation and CPPUNIT (obtainable from http://sourceforge.net/projects/cppunit/) for building the C++ unit tests. Nature of problem: Atomic scale simulation of slowly evolving dynamics is a great challenge in many areas of computational materials science and catalysis. When the rare-events dynamics of interest is orders of magnitude slower than the typical atomic vibrational frequencies a straight-forward propagation of the equations of motions for the particles in the simulation cannot reach time scales of relevance for modeling the slow dynamics. Solution method: KMCLib provides an implementation of the kinetic Monte Carlo (KMC) method that solves the slow dynamics problem by utilizing the separation of time scales between fast vibrational motion and the slowly evolving rare-events dynamics. Only the latter is treated explicitly and the system is simulated as jumping between fully equilibrated local energy minima on the slow-dynamics potential energy surface. Restrictions: KMCLib implements the lattice KMC method and is as such restricted to geometries that can be expressed on a grid in space. Unusual features: KMCLib has been designed to be easily customized, to allow for user-defined functionality and integration with other codes. The user can define her own on-the-fly rate calculator via a Python API, so that site-specific elementary process rates, or rates depending on long-range interactions or complex geometrical features can easily be included. KMCLib also allows for on-the-fly analysis with user-defined analysis modules. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis, and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. Additional comments: The full documentation of the program is distributed with the code and can also be found at http://www.github.com/leetmaa/KMCLib/manual Running time: From a few seconds to several days depending on the type of simulation and input parameters.

Random conductivity of δ-Bi2O3 films

The experimental investigation of the cubic δ-Bi2O3 phase grown on a (110) Au substrate at low temperature has disclosed a chaotic character of the conductivity at low voltage and temperature. Based on first-principles calculations, we show that the conductivity of this oxide strongly depends on the distribution of oxygen ions and that oxygen migration is able to cause a momentary switch of the conduction mechanism.