Predicting large area surface reconstructions using molecular dynamics methods.

In this paper we discuss a new simulation method that can be used to predict preferred surface reconstructions of model systems by Molecular Dynamics (MD). The method overcomes the limitations imposed by periodic boundary conditions for finite boundary MD simulations which can normally prevent reconstructions. By simulating only the reconstructed surface layer and by removing the periodic boundary effects and the free energy barriers to reconstruction, the method allows surfaces to reconstruct to a preferred structure. We test the method on three types of surfaces: (i) the Au(100) and Pt(100) hexagonally reconstructed surface, (ii) the Au(111) herringbone surfaces, and (iii) the triangularly reconstructed Ag surface layer on a Pt(111) substrate and find the method readily finds lower surface energy reconstructions as preferred by the potential.

Site-dependent stability and electronic structure of single vacancy point defects in hexagonal graphene nano-flakes.

Graphene nano-flakes and quantum dots have considerable potential as components for nanodevices, since the finite in-plane dimension and additional edge and corner states provide potential for band gap engineering. However, like semi-infinite graphene membranes, they may contain different configurations of vacancy point defects that may be difficult to predict or control. In this paper we use density functional tight binding simulations to explore the impact of different geometric configurations of vacancies in unterminated (radical), mono-hydride and di-hydride terminated nano-flakes with zigzag or armchair edges. The results reveal that the planar structure is more uniformly preserved (with less distortion) when vacancies are located near the edges and corners, due to the combined effect of vacancy-edge-corner reconstructions, and passivating the circumference reduces the scattering of the band gap, but not the scattering of the energy of the Fermi level. In general, and regardless of the possible application, the use of zigzag-edged nano-flakes with stable edge/corner passivation is desirable to ensure reliability, and reduce the impact of an unknown number and configurations of vacancies.

Linear and nonlinear density response functions for a simple atomic fluid.

We use molecular dynamics simulations to investigate the linear and nonlinear density response functions for simple fluids under the influence of spatially periodic external fields. Using a direct Fourier space decomposition of the instantaneous microscopic density for the perturbed fluid we can clearly identify the distinct order of response. Using a single component sinusoidal longitudinal force for a set of wavelengths and amplitudes we show that in the linear response regime the proportionality between the external field amplitude and the density perturbation can be used to determine the linear density response function, and hence the pair correlation function, static liquid structure factor, and lowest order direct correlation function. We show also that for large external field amplitudes a single component external field can be used to determine the form for lowest order and second lowest order nonlinear response functions for restricted regions of the total response function spaces.

Computation of thermodynamic and transport properties to predict thermophoretic effects in an argon-krypton mixture.

Thermophoresis is the movement of molecules caused by a temperature gradient. Here we report the results of a study of thermophoresis using non-equilibrium molecular dynamics simulations of a confined argon-krypton fluid subject to two different temperatures at thermostated walls. The resulting temperature profile between the walls is used along with the Soret coefficient to predict the concentration profile that develops across the channel. We obtain the Soret coefficient by calculating the mutual diffusion and thermal diffusion coefficients. We report an appropriate method for calculating the transport coefficients for binary systems, using the Green-Kubo integrals and radial distribution functions obtained from equilibrium molecular dynamics simulations of the bulk fluid. Our method has the unique advantage of separating the mutual diffusion and thermal diffusion coefficients, and calculating the sign and magnitude of their individual contributions to thermophoresis in binary mixtures.

Modelling the role of size, edge structure and terminations on the electronic properties of trigonal graphene nanoflakes.

Graphene nanoflakes provide a range of opportunities for engineering graphene for future applications, due to the large number of configurational degrees of freedom associated with the addition of different types of corners and edge states in the structure. Since these materials can, in principle, span the molecular to macroscale dimensions, the electronic properties may also be discrete or continuous, depending on the application in mind. However, since the widespread use of graphene nanoflakes will require them to be predictable, stable and robust against variations associated with some degree of structural polydispersivity, the development of a complete understanding of the relationship between structure, properties and property dispersion is essential. In this paper we used electronic structure computer simulations to model the thermodynamic, mechanical and electronic properties of trigonal graphene nanoflakes with acute (highly reactive) corners. We find that these acute corners introduce new features that are different to the obtuse corners characteristic of hexagonal graphene nanoflakes, as well as different electronic states in the vicinity of the Fermi level. The structure and properties are sensitive to size and functionalization, and may provide new insights into the engineering of graphene nanoflake components.

The electronic and structural properties of novel organomodified Si nanosheets.

We show that the properties of a new class of functional materials, silicon nanosheets modified with phenyl groups and H atoms, are highly promising for applications such as electronic devices. This novel material retains the sp(3) structure after functionalisation, resulting in a wide (direct) band gap of 1.92 eV.

Zero-variance zero-bias quantum Monte Carlo estimators for the electron density at a nucleus.

We derive new quantum Monte Carlo (QMC) estimators for the electronic density at the position of a point nucleus using the zero-variance and zero-bias principles. The resulting estimators are highly efficient, and are significantly simpler to implement and use than alternative methods, as they contain no adjustable parameters. In addition, they can be used in both variational and diffusion QMC calculations. Our best estimator is used to calculate the most accurate available estimates of the total electron density at the nucleus for the first-row atoms Li-Ne, the Ar atom, and the diatomic molecules B(2), N(2), and F(2).

The observation of formation and annihilation of solitons and standing strain wave superstructures in a two-dimensional colloidal crystal.

Confining a colloidal crystal within a long narrow channel produced by two parallel walls can be used to impose a mesoscale superstructure of a predominantly mechanical elastic character [Chui et al., EPL 83, 58004 (2008)]. When the crystal is compressed in the direction perpendicular to the walls, we obtain a structural transition when the number of rows of particles parallel to the walls decreases by one. All the particles of this vanishing row are distributed throughout the crystal. If the confining walls are structured (say with a corrugation along the length of the walls), then these extra particles are distributed neither uniformly nor randomly; rather, defect structures are created along the boundaries resembling "soliton staircases," inducing a nonuniform strain pattern within the crystal. Here, we study the conditions of stability, formation, and annihilation of these solitons using a coarse grained description of the dynamics. The processes are shown by comparing superimposed configurations as well as molecular animations obtained from our simulations. Also, the corresponding normal and shear stresses during the transformation are calculated. A study of these dynamical processes should be useful for controlling strain wave superstructures in the self-assembly of various nano- and mesoscaled particles.

Anisotropic intracule densities and electron correlation in H2: a quantum Monte Carlo study.

We derive efficient quantum Monte Carlo estimators for the anisotropic intracule and extracule densities. These estimators are used in conjunction with an accurate explicitly correlated wave function to investigate the bond-length dependence of electron correlation effects in the ground-state H(2) molecule. It is shown that the localized increase in the magnitude of the correlation energy as the bond is stretched is accompanied by highly anisotropic correlation effects. In addition, we find a small long-range part of the Coulomb hole, which is present even at the equilibrium bond length.

Modeling the crystallization of gold nanoclusters-the effect of the potential energy function.

The crystallization dynamics of 5083 atom gold nanoclusters, which were quenched from the melt, were studied by molecular dynamics (MD) using the EAM 'Glue' and 'Force-matched' potentials to compare and contrast how the crystallization dynamics is affected by these potential energy functions. MD simulations from each potential showed the formation of gold nanoclusters of icosahedral morphology during the quenching process, which is in good agreement with the experimental studies of gold nanoclusters formed under vacuum. The effect of the potential on the evolution of cluster (surface and interior) morphology during the crystallization process is discussed.

Influence of substrate morphology on the growth of gold nanoparticles.

We have simulated the vacuum deposition and subsequent growth of gold nanoparticles on various substrates in order to explore the effects that substrate morphology has on the resultant morphology of gold nanoparticles. The substrates and conditions explored included, the three low index faces, namely, (111), (100), and (110) for both fcc and bcc crystalline substrate structures, including various substrate lattice constants and temperatures. Firstly, we cataloged the major nanoparticle morphologies produced overall. While some substrates were found to produce a mixture of the main nanoparticle morphologies we were successful in identifying certain substrates and temperature conditions for which only I(h), D(h), or certain fcc crystalline nanoparticles can be grown almost exclusively. The substrate characteristics, temperature conditions, and governing growth dynamics are analyzed. We shed light on the balance between substrate influences and vacuum growth tendencies. From observations we can speculate that a substrate alters both the free energy stability of gold nanoparticles and/or the free energy barriers to transformation between certain morphologies. As such we find that substrates are an effective tool in templating the selective growth of desired nanoparticles or surface nanostructures.

Effect of S arrangement on Fe(110) properties at 1/3 monolayer coverage: a DFT study.

Using density functional theory calculations, we compare the relative stabilities and properties of different arrangements of S on Fe(110) at a 1/3 monolayer coverage, including two observed experimentally. For all studied arrangements, S is adsorbed in the three high-symmetry adsorption sites: 4-fold hollow, 3-fold hollow, bridge, and atop sites. The binding energy, work function change, adsorption geometry, charge density distribution, magnetic properties, and density of states are determined and compared. The most stable overlayer arrangement corresponds to the overlayer seen by experiment after dissociative adsorption of H2S and has S adsorbed in 4-fold hollow sites. In the other arrangements, the S atoms are located closer to each other on the surface reducing the stability of the overlayer. S causes a minor adsorbate-induced reconstruction of the Fe surface and quenches the magnetic moment of the Fe atoms it bonds to directly. It adsorbs as an electropositive species, causing a positive work function change and forms polar covalent bonds to the surface.

Density functional theory study of hydrogen bonding in ionic molecular materials.

Crystal structures are usually described in geometric terms. However, it is the energetics of intermolecular interactions that determine the chemical and physical properties of molecular materials.(1) In this paper, we use density functional theory (DFT) in combination with numerical basis sets to analyze the hydrogen bonding interactions in a family of novel ionic molecular materials. We find that the calculated binding energies are consistent with those of other ionic hydrogen bonded systems. We also examine electron density distributions for the systems of interest to gain insight into the nature of the hydrogen bonding interaction and investigate the effects of different aspects of the crystal field on the geometry of the hydrogen bond.

Viscosity of a binary mixture: approach to the hydrodynamic limit.

We have used equilibrium and nonequilibrium molecular dynamics simulations to study the solute self-diffusion coefficient and the shear rate dependence of the solution viscosity in solutions of model nanocolloidal particles that range in mass ratio from mu=1 up to mu=50 and size ratio from s=1 up to s=4.03 at various concentrations. The zero shear rate viscosities and the initial rates of shear thinning were determined from data in the shear rate region in which the suspension is strongly shear thinning while the solvent remains Newtonian or is weakly shear thinning. The rate of shear thinning increased dramatically with solute volume fraction, regardless of whether the increase was due to increasing solute size or increasing the solute concentration. In a series of simulations in which the mass ratio was varied while keeping the size ratio fixed at s=1, we found that the approach of the viscosities and self-diffusion coefficients to their limiting mass ratio independent values was well described by a rather simple exponential dependence on mass ratio. The concentration dependence of the limiting infinite mass ratio values of the self-diffusion coefficients and zero shear rate viscosities were determined, and used to compute the hydrodynamic radius RH of the solute particles by various methods. The values of RH that were obtained by the different methods were reasonably consistent with each other, and indicated that the radius at which the slip boundary condition holds is slightly smaller than the cross-interaction radius between the solute and solvent particles.

Dynamical signatures of freezing: stable fluids, metastable fluids, and crystals.

Mean squared displacements and velocity auto correlation functions are calculated using molecular dynamics for hard spheres under a range of conditions (i) for the equilibrium fluid below freezing; (ii) for the metastable fluid above freezing; and (iii) for the hard sphere crystal, both in the metastable region between freezing and melting, and in the stable region above melting. In addition, simulations are carried out for a metastable Lennard-Jones system. The results confirm recent studies that indicated the disappearance of the classical Alder long-time tail, and show that they apply to systems other than the metastable hard sphere fluid. The implications of these results for our understanding of crystallization and the glass transition are discussed.

Coverage-dependent adsorption of atomic sulfur on Fe(110): a DFT study.

Adsorption of atomic sulfur at different coverages on the Fe(110) surface is examined using density functional theory (DFT) in order to investigate the effect that adsorbate-adsorbate interactions may have on the surface properties. S is adsorbed in the high-symmetry adsorption sites: 4-fold hollow, bridge, and atop sites in the following surface arrangements: c(2 x 2) and p(1 x 1) which correspond to coverages of 1/2 and 1 monolayer, respectively. The binding energy, work function change, adsorption geometry, charge density distribution, magnetic properties, and density of states are examined and compared to our previous study of S adsorbed at 1/4 monolayer coverage and p(2 x 2) arrangement [Spencer et al. Surf. Sci. 2003, 540, 420]. It was found that S forms polar covalent bonds to the surface. The bonding goes from being S-Fe dominated at the low coverages to being S-S dominated at the higher coverages where the S atoms are located closer together on the surface and interact with each other.

Effect of sulfur coverage on Fe(110) adhesion: a DFT study.

The effect of adsorbed S at different coverages on the adhesion of Fe(110) surfaces in match and mismatch is examined using density functional theory (DFT). S is adsorbed in atop, bridge, and 4-fold hollow sites on one side of the interface in c(2 x 2) and p(1 x 1) arrangements, corresponding to coverages of 1/2 and 1 monolayer, respectively. The calculated adhesion energy values at different interfacial separations are fitted to the universal binding energy relation, and the effect of the S coverages on the adhesive strength is analyzed. The effect of relaxation of the interfaces at equilibrium is also investigated, and the resulting interfacial structures and related magnetic and charge density properties are compared.

Ripple induced changes in the wavefunction of graphene: an example of a fundamental symmetry breaking.

Ideally, graphene may be regarded as a strictly 2-D structure. However, as it exists in a 3-D world, perturbations often distort this ideal 2-D structure. Under a variety of conditions graphene has been shown to develop ripples, which may have undesirable consequences for a variety of properties of graphene, such as electron transport. In addition to this, it has been speculated that ripples may be an intrinsic property of graphene, and it has also been suggested that unlocking the secrets of these ripples could be useful in the search for (an understanding of) the elusive Higgs boson. However, ripples in graphene can only be avoided, or utilized, if they can be reproducibly detected. Here we explore the most fundamental aspect of these ripples, that is, the effect of a static ripple structure on various properties of large graphene nanoflakes. We find that the mechanical, thermodynamic and electronic properties are unaltered by this fundamental rippling, but this spontaneous symmetry breaking induces a significant change in the structure of the wavefunction. This profound effect occurs only at the most basic level, but it should be, in principle, experimentally observable.

Motion, relaxation dynamics, and diffusion processes in two-dimensional colloidal crystals confined between walls.

The dynamical behavior of single-component two-dimensional colloidal crystals confined in a slit geometry is studied by Langevin dynamics simulation of a simple model. The colloids are modeled as pointlike particles, interacting with the repulsive part of the Lennard-Jones potential, and the fluid molecules in the colloidal suspension are not explicitly considered. Considering a crystalline strip of triangular lattice structure with n=30 rows, the (one-dimensional) walls confining the strip are chosen as two rigidly fixed crystalline rows at each side, commensurate with the lattice structure and, thus, stabilizing long-range order. The case when the spacing between the walls is incommensurate with the ideal triangular lattice is also studied, where (due to a transition in the number of rows, n → n-1) the confined crystal is incommensurate with the confining boundaries, and a soliton staircase forms along the walls. It is shown that mean-square displacements (MSDs) of particles as a function of time show an overshoot and then saturate at a horizontal plateau in the commensurate case, the value of the plateau being largest in the center of the strip. Conversely, when solitons are present, MSDs are largest in the rows containing the solitons, and all MSDs do not settle down at well-defined plateaus in the direction parallel to the boundaries, due to the lack of positional long-range order in ideal two-dimensional crystals. The MSDs of the solitons (which can be treated like quasiparticles at very low temperature) have also been studied and their dynamics are found to be about an order of magnitude slower than that of the colloidal particles themselves. Finally, transport of individual colloidal particles by diffusion processes is studied: both standard vacancy-interstitial pair formation and cooperative ring rotation processes are identified. These processes require thermal activation, with activation energies of the order of 10T(m) (T(m) being the melting temperature of the crystal), while the motions due to long-wavelength phonons decrease only linearly in temperature.

Quantum mechanical properties of graphene nano-flakes and quantum dots.

In recent years considerable attention has been given to methods for modifying and controlling the electronic and quantum mechanical properties of graphene quantum dots. However, as these types of properties are indirect consequences of the wavefunction of the material, a more efficient way of determining properties may be to engineer the wavefunction directly. One way of doing this may be via deliberate structural modifications, such as producing graphene nanostructures with specific sizes and shapes. In this paper we use quantum mechanical simulations to determine whether the wavefunction, quantified via the distribution of the highest occupied molecular orbital, has a direct and reliable relationship to the physical structure, and whether structural modifications can be useful for wavefunction engineering. We find that the wavefunction of small molecular graphene structures can be different from those of larger nanoscale counterparts, and the distribution of the highest occupied molecular orbital is strongly affected by the geometric shape (but only weakly by edge and corner terminations). This indicates that both size and shape may be more useful parameters in determining quantum mechanical and electronic properties, which should then be reasonably robust against variations in the chemical passivation or functionalisation around the circumference.