On-Surface Synthesis and Characterization of a High-Spin Aza-[5]-Triangulene

Triangulenes are a class of open-shell triangular graphene flakes with total spin increasing with their size. In the last years, on-surface-synthesis strategies have permitted fabricating and engineering triangulenes of various sizes and structures with atomic precision. However, direct proof of the increasing total spin with their size remains elusive. In this work, we report the combined in-solution and on-surface synthesis of a large nitrogen-doped triangulene (aza-[5]-triangulene) on a Au(111) surface, and the detection of its high-spin ground state. Bond-resolved scanning tunneling microscopy images uncovered radical states distributed along the zigzag edges, which were detected as weak zero-bias resonances in scanning tunneling spectra. These spectral features reveal the partial Kondo screening of a high-spin state. Through a combination of several simulation tools, we find that the observed distribution of radical states is explained by a quintet ground state (S=2), instead of the quartet state (S=3/2) expected for the neutral species. This confirms that electron transfer to the metal substrate raises the spin of the ground state. We further provide a qualitative description of the change of (anti)aromaticity introduced by N-substitution, and its role in the charge stabilization on a surface, resulting in an S=2 aza-triangulene on Au(111).

Real-space observation of ultraconfined in-plane anisotropic acoustic terahertz plasmon polaritons

Thin layers of in-plane anisotropic materials can support ultraconfined polaritons, whose wavelengths depend on the propagation direction. Such polaritons hold potential for the exploration of fundamental material properties and the development of novel nanophotonic devices. However, the real-space observation of ultraconfined in-plane anisotropic plasmon polaritons (PPs)-which exist in much broader spectral ranges than phonon polaritons-has been elusive. Here we apply terahertz nanoscopy to image in-plane anisotropic low-energy PPs in monoclinic Ag₂Te platelets. The hybridization of the PPs with their mirror image-by placing the platelets above a Au layer-increases the direction-dependent relative polariton propagation length and the directional polariton confinement. This allows for verifying a linear dispersion and elliptical isofrequency contour in momentum space, revealing in-plane anisotropic acoustic terahertz PPs. Our work shows high-symmetry (elliptical) polaritons on low-symmetry (monoclinic) crystals and demonstrates the use of terahertz PPs for local measurements of anisotropic charge carrier masses and damping.

Modular implementation of the linear- and cubic-scaling orbital minimization methods in electronic structure codes using atomic orbitals

We present a code modularization approach to design efficient and massively parallel cubic- and linear-scaling solvers for electronic structure calculations using atomic orbitals. The modular implementation of the orbital minimization method, in which linear algebra and parallelization issues are handled via external libraries, is demonstrated in the SIESTA code. The distributed block compressed sparse row (DBCSR) and scalable linear algebra package (ScaLAPACK) libraries are used for algebraic operations with sparse and dense matrices, respectively. The MatrixSwitch and libOMM libraries, recently developed within the Electronic Structure Library, facilitate switching between different matrix formats and implement the energy minimization. We show results comparing the performance of several cubic-scaling algorithms, and also demonstrate the parallel performance of the linear-scaling solvers, and their supremacy over the cubic-scaling solvers for insulating systems with sizes of several hundreds of atoms.

Inelastic scattering of electrons in water from first principles: cross sections and inelastic mean free path for use in Monte Carlo track-structure simulations of biological damage

Modelling the inelastic scattering of electrons in water is fundamental, given their crucial role in biological damage. In Monte Carlo track-structure (MC-TS) codes used to assess biological damage, the energy loss function (ELF), from which cross sections are extracted, is derived from different semi-empirical optical models. Only recently have first ab initio results for the ELF and cross sections in water become available. For benchmarking purpose, in this work, we present ab initio linear-response time-dependent density functional theory calculations of the ELF of liquid water. We calculated the inelastic scattering cross sections, inelastic mean free paths, and electronic stopping power and compared our results with recent calculations and experimental data showing a good agreement. In addition, we provide an in-depth analysis of the contributions of different molecular orbitals, species and orbital angular momenta to the total ELF. Moreover, we present single-differential cross sections computed for each molecular orbital channel, which should prove useful for MC-TS simulations.

Inelastic scattering of electrons in water from first principles: cross sections and inelastic mean free path for use in Monte Carlo track-structure simulations of biological damage

Modelling the inelastic scattering of electrons in water is fundamental, given their crucial role in biological damage. In Monte Carlo track-structure (MC-TS) codes used to assess biological damage, the energy loss function (ELF), from which cross sections are extracted, is derived from different semi-empirical optical models. Only recently have first ab initio results for the ELF and cross sections in water become available. For benchmarking purpose, in this work, we present ab initio linear-response time-dependent density functional theory calculations of the ELF of liquid water. We calculated the inelastic scattering cross sections, inelastic mean free paths, and electronic stopping power and compared our results with recent calculations and experimental data showing a good agreement. In addition, we provide an in-depth analysis of the contributions of different molecular orbitals, species and orbital angular momenta to the total ELF. Moreover, we present single-differential cross sections computed for each molecular orbital channel, which should prove useful for MC-TS simulations.

Semi-empirical and Linear-Scaling DFT Methods to Characterize duplex DNA and G-quadruplexes in Presence of Interacting Small Molecules

The computational study of DNA and its interaction with ligands is a highly relevant area of research, with significant consequences for developing new therapeutic strategies. However, the computational description of...

Electrostatics and domains in ferroelectric superlattices

The electrostatics arising in ferroelectric/dielectric two-dimensional heterostructures and superlattices is revisited within a Kittel model in order to define and complete a clear paradigmatic reference for domain formation. The screening of the depolarizing field in isolated ferroelectric or polar thin films via the formation of 180° domains is well understood, where the width of the domains w grows as the square-root of the film thickness d, following Kittel's Law for thick enough films (w ≪ d). For thinner films, a minimum is reached for w before diverging to a monodomain. Although this behaviour is known to be qualitatively unaltered when the dielectric environment of the film is modified, we consider the quantitative changes in that behaviour induced on the ferroelectric film by different dielectric settings: as deposited on a dielectric substrate, sandwiched between dielectrics, and in a superlattice of alternating ferroelectric/dielectric films. The model assumes infinitely thin domain walls, and therefore is not expected to be reliable for film thickness in the nanometre scale. The polarization field P(r) does vary in space, deviating from ±P _S , following the depolarizing field in linear response, but the model does not include a polarization-gradient term as would appear in a Ginzburg-Landau free energy. The model is, however, worth characterizing, both as paradigmatic reference, and as applicable to not-so-thin films. The correct renormalization of parameters is obtained for the thick-film square-root behaviour in the mentioned settings, and the sub-Kittel regime is fully characterized. New results are presented alongside well-known ones for a comprehensive description. Among the former, a natural separation between strong and weak ferroelectric coupling in superlattices is found, which depends exclusively on the dielectric anisotropy of the ferroelectric layer.

Ab initio electronic stopping power for protons in Ga0.5In0.5P/GaAs/Ge triple-junction solar cells for space applications

Motivated by the radiation damage of solar panels in space, firstly, the results of Monte Carlo particle transport simulations are presented for proton impact on triple-junction Ga0.5In0.5P/GaAs/Ge solar cells, showing the proton projectile penetration in the cells as a function of energy. It is followed by a systematic ab initio investigation of the electronic stopping power (ESP) for protons in different layers of the cell at the relevant velocities via real-time time-dependent density functional theory calculations. The ESP is found to depend significantly on different channelling conditions, which should affect the low-velocity damage predictions, and which are understood in terms of impact parameter and electron density along the path. Additionally, we explore the effect of the interface between the layers of the multilayer structure on the energy loss of a proton, along with the effect of strain in the lattice-matched solar cell. Both effects are found to be small compared with the main bulk effect. The interface energy loss has been found to increase with decreasing proton velocity, and in one case, there is an effective interface energy gain.

Efficient ab initio calculation of electronic stopping in disordered systems via geometry pre-sampling: Application to liquid water

Knowledge of the electronic stopping curve for swift ions, S_e(v), particularly around the Bragg peak, is important for understanding radiation damage. Experimentally, however, the determination of such a feature for light ions is very challenging, especially in disordered systems such as liquid water and biological tissue. Recent developments in real-time time-dependent density functional theory (rt-TDDFT) have enabled the calculation of S_e(v) along nm-sized trajectories. However, it is still a challenge to obtain a meaningful statistically averaged S_e(v) that can be compared to observations. In this work, taking advantage of the correlation between the local electronic structure probed by the projectile and the distance from the projectile to the atoms in the target, we devise a trajectory pre-sampling scheme to select, geometrically, a small set of short trajectories to accelerate the convergence of the averaged S_e(v) computed via rt-TDDFT. For protons in liquid water, we first calculate the reference probability distribution function (PDF) for the distance from the proton to the closest oxygen atom, ϕ_R(r_p→O), for a trajectory of a length similar to those sampled experimentally. Then, short trajectories are sequentially selected so that the accumulated PDF reproduces ϕ_R(r_p→O) to increasingly high accuracy. Using these pre-sampled trajectories, we demonstrate that the averaged S_e(v_p) converges in the whole velocity range with less than eight trajectories, while other averaging methods using randomly and uniformly distributed trajectories require approximately ten times the computational effort. This allows us to compare the S_e(v_p) curve to experimental data and assess widely used empirical tables based on Bragg's rule.

The CECAM electronic structure library and the modular software development paradigm

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.

Gap variability upon packing in organic photovoltaics

The variation of the HOMO-LUMO band gap is explored for varying packing arrangements of the 4mod BT-4TIC donor-acceptor molecule pair, by means of a high-throughput ab-initio random structure search of packing possibilities. 350 arrangements of the dimer have been relaxed from initial random dispositions, using non-local density-functional theory. We find that the electronic band gap varies within 0.3 eV, and that this magnitude, the binding energy, and the geometry are not significantly correlated. A clearly favoured structure is found with a binding energy of 1.75±0.07 eV, with all but three other arrangements displaying values of less than one third of this highest binding one, which involves the aliphatic chain of 4TIC.

Entropic bonding of the type 1 pilus from experiment and simulation

The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing β -strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy experiments and steered molecular dynamics simulations (Alonso-Caballero et al. 2018 Nat. Commun. 9, 2758. (doi:10.1038/s41467-018-05107-6)). In this work, we perform a quantitative comparison between experiment and simulation, showing a good agreement in the underlying work values for the unfolding. The simulation results are then used to estimate the free energy difference for the detachment of FimG from the complementing strand of the neighbouring subunit in the chain, FimF. Finally, we show that the large free energy difference for the unravelling and detachment of the subunits which leads to the high stability of the chain is entirely entropic in nature.

Prediction of the near-IR spectra of ices by ab initio molecular dynamics

Use of ab initio molecular dynamics to predict the near-IR spectra of ices and application to astronomical models.

Core Electrons in the Electronic Stopping of Heavy Ions

Electronic stopping power in the keV/Å range is accurately calculated from first principles for high atomic-number projectiles and the effect of core states is carefully assessed. The energy loss to electrons in self-irradiated nickel is studied using real-time time-dependent density functional theory. Different core states are explicitly included in the simulations to understand their involvement in the dissipation mechanism. The core electrons of the projectile are found to open additional dissipation channels as the projectile velocity increases. Almost all of the energy loss is accounted for, even for high projectile velocities, when core electrons as deep as 2s^{2}2p^{6} are explicitly treated. In addition to their expected excitation at high velocities, a flapping dynamical response of the projectile core electrons is observed at intermediate velocities. The empirical reference data are well reproduced in the projectile velocity range of 1.0-12.0 a.u. (1.5-210 MeV).

Simulations of water nano-confined between corrugated planes

Water confined to nanoscale widths in two dimensions between ideal planar walls has been the subject of ample study, aiming at understanding the intrinsic response of water to confinement, avoiding the consideration of the chemistry of actual confining materials. In this work, we study the response of such nanoconfined water to the imposition of a periodicity in the confinement by means of computer simulations, both using empirical potentials and from first-principles. For that we propose a periodic confining potential emulating the atomistic oscillation of the confining walls, which allows varying the lattice parameter and amplitude of the oscillation. We do it for a triangular lattice, with several values of the lattice parameter: one which is ideal for commensuration with layers of Ih ice and other values that would correspond to more realistic substrates. For the former, the phase diagram shows an overall rise of the melting temperature. The liquid maintains a bi-layer triangular structure, however, despite the fact that it is not favoured by the external periodicity. The first-principles liquid is significantly affected by the modulation in its layering and stacking even at relatively small amplitudes of the confinement modulation. Beyond some critical modulation amplitude, the hexatic phase present in flat confinement is replaced by a trilayer crystalline phase unlike any of the phases encountered for flat confinement. For more realistic lattice parameters, the liquid does not display higher tendency to freeze, but it clearly shows inhomogeneous behaviour as the strength of the rugosity increases. In spite of this expected inhomogeneity, the structural and dynamical response of the liquid is surprisingly insensitive to the external modulation. Although the first-principles calculations give a more triangular liquid than the one observed with empirical potentials (TIP4P/2005), both agree remarkably well for the main conclusions of the study.

Stopping power beyond the adiabatic approximation

Energetic ions traveling in solids deposit energy in a variety of ways, being nuclear and electronic stopping the two avenues in which dissipation is usually treated. This separation between electrons and ions relies on the adiabatic approximation in which ions interact via forces derived from the instantaneous electronic ground state. In a more detailed view, in which non-adiabatic effects are explicitly considered, electronic excitations alter the atomic bonding, which translates into changes in the interatomic forces. In this work, we use time dependent density functional theory and forces derived from the equations of Ehrenfest dynamics that depend instantaneously on the time-dependent electronic density. With them we analyze how the inter-ionic forces are affected by electronic excitations in a model of a Ni projectile interacting with a Ni target, a metallic system with strong electronic stopping and shallow core level states. We find that the electronic excitations induce substantial modifications to the inter-ionic forces, which translate into nuclear stopping power well above the adiabatic prediction. In particular, we observe that most of the alteration of the adiabatic potential in early times comes from the ionization of the core levels of the target ions, not readily screened by the valence electrons.

Simulations and spectra of water in CO matrices

Models for the inclusion of water molecules in carbon monoxide matrices are developed using density functional theory applied to amorphous solid systems. The models cover a large range of systems for smaller or larger CO matrices with different water content, consisting of either individual H₂O molecules or small clusters linked by H-bonds. The vibrational spectra of the samples are predicted at the minimum of their potential energy surface. The spectra allow instances where the water molecules remain isolated or form aggregates to be discerned, and they also provide an indication of the strength of the H-bonding, when present. The calculations support recent experimental observations that linked IR bands at 3707 cm^-1 and 3617 cm^-1 to the presence of unbound water molecules in water-poor CO/H₂O mixed ices. Assignment of some observed bands to water dimers or trimers is suggested as well. The residual static pressure in fixed-volume simulation cells is also calculated.

Electronic and magnetic properties of superconducting LnO1-x F x BiS2 (Ln = La, Ce, Pr, and Nd) from first principles

A density functional theory study of the BiS2 superconductors containing rare-earths: LnO1-x F x BiS2 (Ln  =  La, Ce, Pr, and Nd) is presented. We find that CeO0.5F0.5BiS2 has competing ferromagnetic and weak antiferromagnetic tendencies, the first one corresponding to experimental results. We show that PrO0.5F0.5BiS2 has a strong tendency for magnetic order, which can be ferromagnetic or antiferromagnetic depending on subtle differences in 4f orbital occupations. We demonstrate that NdO0.5F0.5BiS2 has a stable magnetic ground state with weak tendency to order. Finally, we show that the change of rare earth does not affect the Fermi surface, and predict that CeOBiS2 should display a pressure induced phase transition to a metallic, if not superconducting, phase under pressure.

Continuous melting through a hexatic phase in confined bilayer water

Liquid water is not only of obvious importance but also extremely intriguing, displaying many anomalies that still challenge our understanding of such an a priori simple system. The same is true when looking at nanoconfined water: The liquid between constituents in a cell is confined to such dimensions, and there is already evidence that such water can behave very differently from its bulk counterpart. A striking finding has been reported from computer simulations for two-dimensionally confined water: The liquid displays continuous or discontinuous melting depending on its density. In order to understand this behavior, we have analyzed the melting exhibited by a bilayer of nanoconfined water by means of molecular dynamics simulations. At high density we observe the continuous melting to be related to the phase change of the oxygens only, with the hydrogens remaining liquidlike throughout. Moreover, we find an intermediate hexatic phase for the oxygens between the liquid and a triangular solid ice phase, following the Kosterlitz-Thouless-Halperin-Nelson-Young theory for two-dimensional melting. The liquid itself tends to maintain the local structure of the triangular ice, with its two layers being strongly correlated yet with very slow exchange of matter. The decoupling in the behavior of the oxygens and hydrogens gives rise to a regime in which the complexity of water seems to disappear, resulting in what resembles a simple monoatomic liquid. This intrinsic tendency of our simulated water may be useful for understanding novel behaviors in other confined and interfacial water systems.

Enhanced Configurational Entropy in High-Density Nanoconfined Bilayer Ice

A novel kind of crystal order in high-density nanoconfined bilayer ice is proposed from molecular dynamics and density-functional theory simulations. A first-order transition is observed between a low-temperature proton-ordered solid and a high-temperature proton-disordered solid. The latter is shown to possess crystalline order for the oxygen positions, arranged on a close-packed triangular lattice with AA stacking. Uniquely among the ice phases, the triangular bilayer is characterized by two levels of disorder (for the bonding network and for the protons) which results in a configurational entropy twice that of bulk ice.

Structural and configurational properties of nanoconfined monolayer ice from first principles

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations.

Effects of stoichiometric doping in superconducting Bi-O-S compounds

Newly discovered Bi-O-S compounds remain an enigma in attempts to understand their electronic properties. A recent study of Bi4O4S3 has shown it to be a mixture of two phases, Bi2OS2 and Bi3O2S3, the latter being superconducting (Phelan et al 2013 J. Am. Chem. Soc. 135 5372-4). Using density functional theory, we explore the electronic structure of both the phases and the effect of the introduction of extra BiS2 bilayers. Our results demonstrate that the S2 layers dope the bismuth-sulphur bands and this causes metallisation. The bands at the Fermi level are of clear two-dimensional character. One band manifold is confined to the two adjacent, square-lattice bismuth-sulphur planes, a second manifold is confined to the square lattice of sulphur dimers. We show that the introduction of extra BiS2 bilayers does not influence the electronic structure. Finally, we also show that spin-orbit coupling does not have any significant effect on the states close to the Fermi level at the energy scale considered.

Species fractionation in atomic chains from mechanically stretched alloys

Bettini et al (2006 Nat. Nanotechnol. 1 182-5) reported the first experimental realization of linear atomic chains (LACs) composed of different atoms (Au and Ag). The different contents of Au and Ag were observed in the chains from what was found in the bulk alloys, which raises the question of what the wire composition is, if it is in equilibrium with a bulk alloy. In this work we address the thermodynamic driving force for species fractionation in LACs under tension, and we present the density-functional theory results for Ag-Au chain alloys. A pronounced stabilization of the wires with an alternating Ag-Au sequence is observed, which could be behind the experimentally observed Au enrichment in LACs from alloys with high Ag content.

The origin of two-dimensional electron gases at oxide interfaces: insights from theory

The response of oxide thin films to polar discontinuities at interfaces and surfaces has generated enormous activity due to the variety of interesting effects that it gives rise to. A case in point is the discovery of the electron gas at the interface between LaAlO3 and SrTiO3, which has since been shown to be quasi-two-dimensional, switchable, magnetic and/or superconducting. Despite these findings, the origin of the two-dimensional electron gas is highly debated and several possible mechanisms remain. Here we review the main proposed mechanisms and attempt to model expected effects in a quantitative way with the ambition of better constraining what effects can/cannot explain the observed phenomenology. We do it in the framework of a phenomenological model constructed to provide an understanding of the electronic and/or redox screening of the chemical charge in oxide heterostructures. We also discuss the effect of intermixing, both conserving and not conserving the total stoichiometry.

Optimal finite-range atomic basis sets for liquid water and ice

Finite-range numerical atomic orbitals are the basis functions of choice for several first principles methods, due to their flexibility and scalability. Generating and testing such basis sets, however, remains a significant challenge for the end user. We discuss these issues and present a new scheme for generating improved polarization orbitals of finite range. We then develop a series of high-accuracy basis sets for the water molecule, and report on their performance in describing the monomer and dimer, two phases of ice, and liquid water at ambient and high density. The tests are performed by comparison with plane-wave calculations, and show the atomic orbital basis sets to exhibit an excellent level of transferability and consistency. The highest-order bases (quadruple-ζ) are shown to give accuracies comparable to a plane-wave kinetic energy cutoff of at least ~1000 eV for quantities such as energy differences and ionic forces, as well as achieving significantly greater accuracies for total energies and absolute pressures.

Electronic stopping power in gold: the role of d electrons and the H/He anomaly

The electronic stopping power of H and He moving through gold is obtained to high accuracy using time-evolving density-functional theory, thereby bringing usual first principles accuracies into this kind of strongly coupled, continuum nonadiabatic processes in condensed matter. The two key unexplained features of what observed experimentally have been reproduced and understood: (i) The nonlinear behavior of stopping power versus velocity is a gradual crossover as excitations tail into the d-electron spectrum; and (ii) the low-velocity H/He anomaly (the relative stopping powers are contrary to established theory) is explained by the substantial involvement of the d electrons in the screening of the projectile even at the lowest velocities where the energy loss is generated by s-like electron-hole pair formation only.

Nonadiabatic forces in ion-solid interactions: the initial stages of radiation damage

The Born-Oppenheimer approximation is the keystone for molecular dynamics simulations of radiation damage processes; however, actual materials response involves nonadiabatic energy exchange between nuclei and electrons. In this work, time dependent density functional theory is used to calculate the electronic excitations produced by energetic protons in Al. We study the influence of these electronic excitations on the interatomic forces and find that they differ substantially from the adiabatic case, revealing a nontrivial connection between electronic and nuclear stopping that is absent in the adiabatic case. These results unveil new effects in the early stages of radiation damage cascades.

Probing surface and bulk electrochemical processes on the LaAlO3-SrTiO3 interface

Local electrochemical phenomena on the surfaces of the LaAlO(3)-SrTiO(3) heterostructure are explored using unipolar and bipolar dynamic electrochemical strain microscopy (D-ESM). The D-ESM suggests the presence of at least two distinct electrochemical processes, including fast reversible low-voltage process and slow high-voltage process. The latter process is associated with static surface deformations in the sub-nanometer regime. These behaviors are compared with Kelvin probe force microscopy hysteresis data. The possible origins of observed phenomena are discussed, and these studies suggest that charge-writing behavior in LAO-STO includes a strong surface/bulk electrochemical component and is more complicated than simple screening by surface adsorbates.

Proposal of a one-dimensional electron gas in the steps at the LaAlO3-SrTiO3 interface

The two-dimensional electron gas at the interface between LaAlO(3) and SrTiO(3) has become one of the most fascinating and highly debated oxide systems of recent times. Here we propose that a one-dimensional electron gas can be engineered at the step edges of the LaAlO(3)/SrTiO(3) interface. These predictions are supported by first-principles calculations and electrostatic modeling which elucidate the origin of the one-dimensional electron gas as an electronic reconstruction to compensate a net surface charge in the step edge. The results suggest a novel route to increasing the functional density in these electronic interfaces.

Dispersion interactions in room-temperature ionic liquids: results from a non-empirical density functional

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.

Density, structure, and dynamics of water: the effect of van der Waals interactions

It is known that ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions, based on the generalized gradient approximation (GGA) to density functional theory (DFT), with commonly used functionals fail to produce structural and diffusive properties in reasonable agreement with experiment. This is true for canonical, constant temperature simulations where the density of the liquid is fixed to the experimental density. The equilibrium density, at ambient conditions, of DFT water has recently been shown by Schmidt et al. [J. Phys. Chem. B, 113, 11959 (2009)] to be underestimated by different GGA functionals for exchange and correlation, and corrected by the addition of interatomic pair potentials to describe van der Waals (vdW) interactions. In this contribution we present a DFT-AIMD study of liquid water using several GGA functionals as well as the van der Waals density functional (vdW-DF) of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. As expected, we find that the density of water is grossly underestimated by GGA functionals. When a vdW-DF is used, the density improves drastically and the experimental diffusivity is reproduced without the need of thermal corrections. We analyze the origin of the density differences between all the functionals. We show that the vdW-DF increases the population of non-H-bonded interstitial sites, at distances between the first and second coordination shells. However, it excessively weakens the H-bond network, collapsing the second coordination shell. This structural problem is partially associated to the choice of GGA exchange in the vdW-DF. We show that a different choice for the exchange functional is enough to achieve an overall improvement both in structure and diffusivity.

Linear Scaling DFT Calculations with Numerical Atomic Orbitals

We have recently developed a method to perform Density Functional Theory calculations in systems with a very large number of atoms, which is based on the use of numerical atomic orbitals as basis sets. The method incorporates Order-N techniques both in the calculation of the Kohn-Sham hamiltonian matrix elements and in the solution of the wave functions, which make the CPU time and memory to scale linearly with the number of atoms, allowing calculations in very large system. In this work, we present results on several test systems to show that the approach and the basis sets used with our method are able to provide an accuracy similar to that of other standard DFT techniques.

The net charge at interfaces between insulators

The issue of the net charge at insulating oxide interfaces is briefly reviewed with the ambition of dispelling myths of such charges being affected by covalency and related charge density effects. For electrostatic analysis purposes, the net charge at such interfaces is defined by the counting of discrete electrons and core ion charges, and by the definition of the reference polarization of the separate, unperturbed bulk materials. The arguments are illustrated for the case of a thin film of LaAlO(3) over SrTiO(3) in the absence of free carriers, for which the net charge is exactly 0.5e per interface formula unit, if the polarization response in both materials is referred to zero bulk values. Further consequences of the argument are extracted for structural and chemical alterations of such interfaces, in which internal rearrangements are distinguished from extrinsic alterations (changes of stoichiometry, redox processes), only the latter affecting the interfacial net charge. The arguments are reviewed alongside the proposal of Stengel and Vanderbilt (2009 Phys. Rev. B 80 241103) of using formal polarization values instead of net interfacial charges, based on the interface theorem of Vanderbilt and King-Smith (1993 Phys. Rev. B 48 4442-55). Implications for non-centrosymmetric materials are discussed, as well as for interfaces for which the charge mismatch is an integer number of polarization quanta.

Mixed Approach to Incorporate Self-Consistency into Order-N LCAO Methods

We present a method for selfconsistent Density Functional Theory calculations in which the effort required is proportional to the size of the system, thus allowing the aplication to problems with a very large size. The method is based on the LCAO approximation, and uses a mixed approach to obtain the Hamiltonian integrals between atomic orbitals with Order-N effort. We show the performance and the convergence properties of the method in several silicon and carbon systems, and in a DNA periodic chain.

The flexoelectricity of barium and strontium titanates from first principles

We present ab initio calculations of the longitudinal flexoelectricity for BaTiO(3) and SrTiO(3) using a direct approach. The calculated value for SrTiO(3) agrees with recently reported measurements. For BaTiO(3), however, the theoretical values are smaller than the measured ones; possible reasons for the discrepancy are discussed.

eScience for molecular-scale simulations and the eMinerals project

We review the work carried out within the eMinerals project to develop eScience solutions that facilitate a new generation of molecular-scale simulation work. Technological developments include integration of compute and data systems, developing of collaborative frameworks and new researcher-friendly tools for grid job submission, XML data representation, information delivery, metadata harvesting and metadata management. A number of diverse science applications will illustrate how these tools are being used for large parameter-sweep studies, an emerging type of study for which the integration of computing, data and collaboration is essential.

Ferrielectric twin walls in CaTiO3

Sizeable spontaneous polarization has been found in the (100) twin walls of CaTiO3, a definitely nonpolar material. Theoretical simulations of these walls show an extremely rich texture of the local polarization at and close to the walls, including a strong antiferroelectric component, and local nonzero contributions perpendicular to the wall plane, which do not contribute to the net dipole. Individual Ti displacements of 2 pm off the octahedron center give rise to a net polarization corresponding to a displacement of 0.6 pm in the direction of the bisector of the twin angle.

Nature of the structural transformations in B2O3 glass under high pressure

We study high-pressure polyamorphism of B2O3 glass using x-ray diffraction up to 10 GPa in the 300-700 K temperature range, in situ volumetric measurements up to 9 GPa, and first-principles simulations. Under pressure, glass undergoes two-stage transformations including a gradual increase of the first B-O (O-B) coordination numbers above 5 GPa. The fraction of boron atoms in the fourfold-coordinated state at P<10 GPa is smaller than was assumed from inelastic x-ray scattering spectroscopy data, but is considerably larger than was previously suggested by the classical molecular dynamics simulations. The observed transformations under both compression and decompression are broad in hydrostatic conditions. On the basis of ab initio results, we also predict one more transformation to a superdense phase, in which B atoms are sixfold coordinated.

The SIESTA method; developments and applicability

Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.

The SIESTA method; developments and applicability

Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.