Band structure interpolation using optimized local orbitals from linear-scaling density functional theory

© 2018 American Physical Society. Several approaches to linear-scaling density functional theory (LS-DFT) that seek to achieve accuracy equivalent to plane-wave methods do so by optimizing in situ a set of local orbitals in terms of which the density matrix can be accurately expressed. These local orbitals, which can also accurately represent the canonical Kohn-Sham orbitals, qualitatively resemble the maximally localized Wannier functions employed in band structure interpolation. As LS-DFT methods are increasingly being used in real-world applications demanding accurate band structures, it is natural to question the extent to which these optimized local orbitals can provide sufficient accuracy. In this paper, we present and compare, in principle and in practice, two methods for obtaining band structures. We apply these to a (10, 0) carbon nanotube as an example. By comparing with the results from a traditional plane-wave pseudopotential calculation, the optimized local orbitals are found to provide an excellent description of the occupied bands and some low-lying unoccupied bands, with consistent agreement across the Brillouin zone. However free-electron-like states derived from weakly bound states independent of the σ and π orbitals can only be found if additional local orbitals are included

Smart Focal Plane Technologies for VLT Instruments

As we move towards the era of ELTs, it is timely to think about the future role of the 8-m class telescopes. Under the OPTICON programme, novel technologies have been developed that are intended for use in multi-object and integral-field spectrographs. To date, these have been targeted at instrument concepts for the European ELT, but there are also significant possibilities for their inclusion in new VLT instruments, ensuring the continued success and productivity of these unique telescopes.Comment: 5 pages, to appear in the proceedings of the ESO Workshop "Science with the VLT in the ELT era

Measurement accuracy in accommodative response by the Nott method

The measurement of accommodative response is usually performed by means of the Nott method. The accommodative response values were obtained as described in the bibliography and considering that the neutralizing lens shapes the target image. The values in accommodative response differ according to the calculation method utilized. The accommodation and convergence values when the target is placed 40 cm away from the glasses are not the same in emmetropic and ametropic subjects. At the position of the effective binocular object, the initial values are indeed the same for both types of subjects. Comparing with experimental measurements using the Monocular Estimate Method (Mem), it was obtained the same values given the effect of the neutralizing lens. Optimizing the Nott method would require placing the target at a position where the effective binocular object is 40 cm. Furthermore, the effect of the neutralizing lens should be considered in the calculation method

Simulation of electron energy loss spectra of nanomaterials with linear-scaling density functional theory.

Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree with those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. Finally, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable.This work was performed using the Darwin Supercomputer of the University of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/), provided by Dell Inc. using Strategic Research Infrastructure Funding from the Higher Education Funding Council for England and funding from the Science and Technology Facilities Council. E.W.T. was supported by the EPSRC Cambridge NanoDTC, EP/G037221/1. L.E.R. was supported, in part, by DOE Office of Science User Facility under Contract DE-AC02-06CH11357. N.D.M.H. Acknowledges the support of the Winton Programme for the Physics of Sustainability. We wish to acknowledge the use of the EPSRC's Chemical Database Service at Daresbury

A predictive model for secondary RNA structure using graph theory and a neural network

Background: Determining the secondary structure of RNA from the primary structure is a challenging computational problem. A number of algorithms have been developed to predict the secondary structure from the primary structure. It is agreed that there is still room for improvement in each of these approaches. In this work we build a predictive model for secondary RNA structure using a graph-theoretic tree representation of secondary RNA structure. We model the bonding of two RNA secondary structures to form a larger secondary structure with a graph operation we call merge. We consider all combinatorial possibilities using all possible tree inputs, both those that are RNA-like in structure and those that are not. The resulting data from each tree merge operation is represented by a vector. We use these vectors as input values for a neural network and train the network to recognize a tree as RNA-like or not, based on the merge data vector. The network estimates the probability of a tree being RNA-like.Results: The network correctly assigned a high probability of RNA-likeness to trees previously identified as RNA-like and a low probability of RNA-likeness to those classified as not RNA-like. We then used the neural network to predict the RNA-likeness of the unclassified trees.Conclusions: There are a number of secondary RNA structure prediction algorithms available online. These programs are based on finding the secondary structure with the lowest total free energy. In this work, we create a predictive tool for secondary RNA structures using graph-theoretic values as input for a neural network. The use of a graph operation to theoretically describe the bonding of secondary RNA is novel and is an entirely different approach to the prediction of secondary RNA structures. Our method correctly predicted trees to be RNA-like or not RNA-like for all known cases. In addition, our results convey a measure of likelihood that a tree is RNA-like or not RNA-like. Given that the majority of secondary RNA folding algorithms return more than one possible outcome, our method provides a means of determining the best or most likely structures among all of the possible outcomes

Geometrical tests of cosmological models. III. The cosmology-evolution diagram at z=1

The rotational velocity of distant galaxies, when interpreted as a size (luminosity) indicator, may be used as a tool to select high redshift standard rods (candles) and probe world models and galaxy evolution via the classical angular diameter-redshift or Hubble diagram tests. We implement the proposed testing strategy using a sample of 30 rotators spanning the redshift range 0.2<z<1 with high resolution spectra and images obtained by the VIMOS/VLT Deep Redshift Survey (VVDS) and the Great Observatories Origins Deep Survey (GOODs). We show that by applying at the same time the angular diameter-redshift and Hubble diagrams to the same sample of objects (i.e. velocity selected galactic discs) one can derive a characteristic chart, the cosmology-evolution diagram, mapping the relation between global cosmological parameters and local structural parameters of discs such as size and luminosity. This chart allows to put constraints on cosmological parameters when general prior information about discs evolution is available. In particular, by assuming that equally rotating large discs cannot be less luminous at z=1 than at present (M(z=1) < M(0)), we find that a flat matter dominated cosmology (Omega_m=1) is excluded at a confidence level of 2sigma and an open cosmology with low mass density (Omega_m = 0.3) and no dark energy contribution is excluded at a confidence level greater than 1 sigma. Inversely, by assuming prior knowledge about the cosmological model, the cosmology-evolution diagram can be used to gain useful insights about the redshift evolution of the structural parameters of baryonic discs hosted in dark matter halos of nearly equal masses.Comment: 14 pages and 11 figures. A&A in pres

Jets and Topography: Jet Transitions and the Impact on Transport in the Antarctic Circumpolar Current

The Southern Ocean’s Antarctic Circumpolar Current (ACC) naturally lends itself to interpretations using a zonally averaged framework. Yet, navigation around steep and complicated bathymetric obstacles suggests that local dynamics may be far removed from those described by zonally symmetric models. In this study, both observational and numerical results indicate that zonal asymmetries, in the form of topography, impact global flow structure and transport properties. The conclusions are based on a suite of more than 1.5 million virtual drifter trajectories advected using a satellite altimetry–derived surface velocity field spanning 17 years. The focus is on sites of “cross front” transport as defined by movement across selected sea surface height contours that correspond to jets along most of the ACC. Cross-front exchange is localized in the lee of bathymetric features with more than 75% of crossing events occurring in regions corresponding to only 20% of the ACC’s zonal extent. These observations motivate a series of numerical experiments using a two-layer quasigeostrophic model with simple, zonally asymmetric topography, which often produces transitions in the front structure along the channel. Significantly, regimes occur where the equilibrated number of coherent jets is a function of longitude and transport barriers are not periodic. Jet reorganization is carried out by eddy flux divergences acting to both accelerate and decelerate the mean flow of the jets. Eddy kinetic energy is amplified downstream of topography due to increased baroclinicity related to topographic steering. The combination of high eddy kinetic energy and recirculation features enhances particle exchange. These results stress the complications in developing consistent circumpolar definitions of the ACC fronts

Surface circulation in the eastern North Atlantic, from drifters and altimetry

A description of the near-surface circulation and its properties is the result of the analysis of a drifting buoy data set in the eastern North Atlantic between the Iberian Peninsula, the Azores, and the Canary Islands. World Ocean Circulation Experiment-Tropical Ocean-Global Atmosphere experiment drifters equipped with holey sock drogues centered at 15 m depth collected a total of 14.4 years of data. The drifters sampled a rather inhomogeneous velocity field with a weak mean flow regime and eddies of different scales. They meandered southward everywhere in the study region, except in the Iberian coastal transition zone north of 41degreesN where they headed northward. The near-surface mean velocity field obtained from the drifter data set shows all important mean currents, including the poleward Portugal Coastal Countercurrent during the fall, winter, and early spring off western and northern Iberia, the southward Portugal Coastal Current, the slow offshore southward flow of the Portugal Current during the whole year, the southwestward Canary Current, and the eastward Azores Current, which extends to the vicinity of the African coast near the Gulf of Cadiz. Maps of the eddy kinetic energy field were obtained from the drifters and from satellite altimetry. It provides the largest part of the total kinetic energy. The rate of dispersion is estimated from the Lagrangian statistics of the drifting buoys. The dispersion of the drifters in the study region is well modeled by a simple description of eddy diffusion assuming homogeneous turbulence. Ensemble mean diffusivities K and the Langrangian integral length scales and timescales (L and T) were obtained for the zonal and meridional directions. The sea surface temperature measured along the drifter trajectories is used to produce estimates of the eddy diffusivity, which is compared with the diffusivity estimates obtained from the theory of Taylor. The eddy diffusivity is found to be approximately proportional to the eddy kinetic energy. Discrete eddies and meanders were observed using drifters and altimetry in order to map and describe their geographical distribution and characteristics in the eastern North Atlantic