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At least 667 records · Page 37

Refining perovskite structures to pair distribution function data using collective Glazer modes as a basis

Structural modelling of octahedral tilts in perovskites is typically carried out using the symmetry constraints of the resulting space group. In most cases, this introduces more degrees of freedom than those strictly necessary to describe only the octahedral tilts. It can therefore be a challenge to disentangle the octahedral tilts from other structural distortions such as cation displacements and octahedral distortions. This paper reports the development of constraints for modelling pure octahedral tilts and implementation of the constraints in diffpy-CMI, a powerful package to analyse pair distribution function (PDF) data. The model in the program allows features in the PDF that come from rigid tilts to be separated from non-rigid relaxations, providing an intuitive picture of the tilting. The model has many fewer refinable variables than the unconstrained space group fits and provides robust and stable refinements of the tilt components. It further demonstrates the use of the model on the canonical tilted perovskite CaTiO 3 which has the known Glazer tilt system α + β – β – . The Glazer model fits comparably to the corresponding space-group model Pnma below r = 14 Å and becomes progressively worse than the space-group model at higher r due to non-rigid distortions in the real material.

36 MATERIALS SCIENCE↗

Symbolic Laplace transforms of special functions

A MACSYMA implementation of the Laplace transform for special functions is described. The generalized hypergeometric functions are used as a basis for the representation of approximately fifty special functions. Only a relatively small number of formulas that generally involve generalized hypergeometric functions are utilized for the integration stage. A sample of actual examples and their timing is provided.

Avgoustis, Y.↗

The Heats of Formation of GaCl3 and its Fragments

The heats of formation of GaC13 and its fragments are computed. The geometries and frequencies are obtained at the B3LYP level. The CCSD(T) approach is used to solve the correlation problem. The effect of Ga 3d correlation is studied, and found to affect the bond energies by up to 1 kcal/mol. Both basis set extrapolation and bond functions are considered as ways to approach the basis set limit. Spin-orbit and scalar relativistic effects are also considered.

Bauschlicher, Charles W., Jr.↗

Elimination of the linearization error in APW/LAPW basis set: Dirac-Kohn-Sham equations

Here, a detailed account of the implementation of equations of the relativistic density functional theory (RDFT) using basis sets of APW/LAPW type with flexible extensions provided by local orbitals is given. Earlier discoveries of the importance of the high derivative local orbital (HDLO) extension of the APW/LAPW basis set for enhancing the accuracy of DFT calculations are confirmed using a fully relativistic approach and α – U as an example. High energy local orbitals (HELO's), however indispensable for GW calculations, are considerably less efficient in enhancing the accuracy of DFT applications. It is shown that a simplified approach to the relativistic effects, namely considering them only inside the muffin-tin (MT) spheres, produces basically identical results (as compared to fully relativistic approach) for the electronic free energy of the five materials considered in this work. By comparing the effect of the simplified approach on the electronic free energy with its effect on the electronic kinetic energy we conclude that the insensitivity of the free energy to the way we describe the relativistic effects in the interstitial region is related to the variational property of this quantity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The Dissociation Energies of He2, HeH, and ArH; A Bond Function Study

The bond energies and bond lengths are determined for He2, HeH, and ArH at the CCSD(T) level using both atom-centered basis sets and those that include bond functions. The addition of bond functions dramatically improves the rate of convergence of the results with respect to the size of the atom-centered basis set; with bond functions, triple zeta atom-centered basis set, outperform quintuple zeta basis sets without bond functions. The addition of bond functions also reduces the number of diffuse functions that must be added to the atom-centered sets. Employing bond functions appear to offer a very cost effective method of computing the interaction between weakly bound systems, especially for He.

Bauschlicher, Charles W., Jr.↗

Systematic Evaluation of Counterpoise Correction in Density Functional Theory

A widespread belief persists that the Boys–Bernardi function counterpoise (CP) procedure “overcorrects” supramolecular interaction energies for the effects of basis-set superposition error. To the extent that this is true for correlated wave function methods, it is usually an artifact of low-quality basis sets. The question has not been considered systematically in the context of density functional theory, however, where basis-set convergence is generally less problematic. We present a systematic assessment of the CP procedure for a representative set of functionals and basis sets, considering both benchmark data sets of small dimers and larger supramolecular complexes. The latter include layered composite polymers with ~150 atoms and ligand–protein models with ~300 atoms. Provided that CP correction is used, we find that intermolecular interaction energies of nearly complete-basis quality can be obtained using only double-ζ basis sets. Furthermore, this is less expensive as compared to triple-ζ basis sets without CP correction. CP-corrected interaction energies are less sensitive to the presence of diffuse basis functions as compared to uncorrected energies, which is important because diffuse functions are expensive and often numerically problematic for large systems. Our results upend the conventional wisdom that CP “overcorrects” for basis-set incompleteness. In small basis sets, CP correction is mandatory in order to demonstrate that the results do not rest on error cancellation.

74 ATOMIC AND MOLECULAR PHYSICS↗

Transfer function concept for ultrasonic characterization of material microstructures

The approach given depends on treating material microstructures as elastomechanical filters that have analytically definable transfer functions. These transfer functions can be defined in terms of the frequency dependence of the ultrasonic attenuation coefficient. The transfer function concept provides a basis for synthesizing expressions that characterize polycrystalline materials relative to microstructural factors such as mean grain size, grain-size distribution functions, and grain boundary energy transmission. Although the approach is nonrigorous, it leads to a rational basis for combining the previously mentioned diverse and fragmented equations for ultrasonic attenuation coefficients.

Vary, A.↗

Improved techniques for outgoing wave variational principle calculations of converged state-to-state transition probabilities for chemical reactions

Improved techniques and well-optimized basis sets are presented for application of the outgoing wave variational principle to calculate converged quantum mechanical reaction probabilities. They are illustrated with calculations for the reactions D + H2 yields HD + H with total angular momentum J = 3 and F + H2 yields HF + H with J = 0 and 3. The optimization involves the choice of distortion potential, the grid for calculating half-integrated Green's functions, the placement, width, and number of primitive distributed Gaussians, and the computationally most efficient partition between dynamically adapted and primitive basis functions. Benchmark calculations with 224-1064 channels are presented.

Mielke, Steven L.↗

Feature Detection and Curve Fitting Using Fast Walsh Transforms for Shock Tracking: Applications

Walsh functions form an orthonormal basis set consisting of square waves. Square waves make the system well suited for detecting and representing functions with discontinuities. Given a uniform distribution of 2p cells on a one-dimensional element, it has been proven that the inner product of the Walsh Root function for group p with every polynomial of degree < or = (p - 1) across the element is identically zero. It has also been proven that the magnitude and location of a discontinuous jump, as represented by a Heaviside function, are explicitly identified by its Fast Walsh Transform (FWT) coefficients. These two proofs enable an algorithm that quickly provides a Weighted Least Squares fit to distributions across the element that include a discontinuity. The detection of a discontinuity enables analytic relations to locally describe its evolution and provide increased accuracy. Time accurate examples are provided for advection, Burgers equation, and Riemann problems (diaphragm burst) in closed tubes and de Laval nozzles. New algorithms to detect up to two C0 and/or C1 discontinuities within a single element are developed for application to the Riemann problem, in which a contact discontinuity and shock wave form after the diaphragm bursts.

Gnoffo, Peter A.↗

Galaxy bispectrum in the spherical Fourier-Bessel basis

The bispectrum, the three-point correlation in Fourier space, is a crucial statistic for studying many effects targeted by the next-generation galaxy surveys, such as primordial non-Gaussianity (PNG) and general relativistic (GR) effects on large scales. In this work we develop a formalism for the bispectrum in the spherical Fourier-Bessel (SFB) basis—a natural basis for computing correlation functions on the curved sky, as it diagonalizes the Laplacian operator in spherical coordinates. Working in the SFB basis allows for line-of-sight effects such as redshift space distortions and GR to be accounted for exactly, i.e., without having to resort to perturbative expansions to go beyond the plane-parallel approximation. Only analytic results for the SFB bispectrum exist in the literature given the intensive computations needed. We numerically calculate the SFB bispectrum for the first time, enabled by a few techniques: We implement a template decomposition of the redshift-space kernel Z 2 into Legendre polynomials, and separately treat the PNG and velocity-divergence terms. We derive an identity to integrate a product of three spherical harmonics connected by a Dirac delta function as a simple sum and use it to investigate the limit of a homogeneous and isotropic Universe. Furthermore, we present a formalism for convolving the signal with separable window functions and use a toy spherically symmetric window to demonstrate the computation and give insights into the properties of the observed bispectrum signal. While our implementation remains computationally challenging, it is a step toward a feasible full extraction of information on large scales via a SFB bispectrum analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

U-splines: Splines over unstructured meshes

U-splines are a novel approach to the construction of a spline basis for representing smooth objects in Computer-Aided Design (CAD) and Computer-Aided Engineering (CAE). A spline is a piecewise-defined function that satisfies continuity constraints between adjacent cells in a mesh. U-splines differ from existing spline constructions, such as Non-Uniform Rational B-splines (NURBS), subdivision surfaces, T-splines, and hierarchical B-splines, in that they can accommodate local variation in cell size, polynomial degree, and smoothness simultaneously over more varied mesh configurations. Mixed cell types (e.g., triangle and quadrilateral cells in the same mesh) and T-junctions are also supported, although the continuity of interfaces with triangle and tetrahedral cells is limited in the present work. The U-spline algorithm introduces a new technique for using local null space solutions to construct basis functions for the global spline null space problem. The U-spline construction is presented for curves, surfaces, and volumes with higher dimensional generalizations possible. Lastly, a set of requirements are given to ensure that the U-spline basis is positive, forms a partition of unity, is complete, and is locally linearly independent.

42 ENGINEERING↗

Black light - How sensors filter spectral variation of the illuminant

Visual sensor responses may be used to classify objects on the basis of their surface reflectance functions. In a color image, the image data are represented as a vector of sensor responses at each point in the image. This vector depends both on the surface reflectance functions and on the spectral power distribution of the ambient illumination. Algorithms designed to classify objects on the basis of their surface reflectance functions typically attempt to overcome the dependence of the sensor responses on the illuminant by integrating sensor data collected from multiple surfaces. In machine vision applications, it is shown that it is often possible to design the sensor spectral responsivities so that the vector direction of the sensor responses does not depend upon the illuminant. The conditions under which this is possible are given and an illustrative calculation is performed. In biological systems, where the sensor responsivities are fixed, it is shown that some changes in the illumination cause no change in the sensor responses. Such changes in illuminant are called black illuminants. It is possible to express any illuminant as the sum of two unique components. One component is a black illuminant. The second component is called the visible component. The visible component of an illuminant completely characterizes the effect of the illuminant on the vector of sensor responses.

Brainard, David H.↗

Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail

Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each RNP incorporates multiple copies of nucleoprotein (NP), a fragment of the viral genome (vRNA), and a viral RNA-dependent RNA polymerase (POL), and is responsible for packaging the viral genome and performing critical functions including replication and transcription. A complete model of an Influenza RNP in atomic detail can elucidate the structural basis for viral genome functions, and identify potential targets for viral therapeutics. In this work we construct a model of a complete Influenza A RNP complex in atomic detail using multiple sources of structural and sequence information and a series of homology-modeling techniques, including a motif-matching fragment assembly method. Our final model provides a rationale for experimentally-observed changes to viral polymerase activity in numerous mutational assays. Further, our model reveals specific interactions between the three primary structural components of the RNP, including potential targets for blocking POL-binding to the NP-vRNA complex. The methods developed in this work open the possibility of elucidating other functionally-relevant atomic-scale interactions in additional RNP structures and other biomolecular complexes.

59 BASIC BIOLOGICAL SCIENCES↗

Unsteady Solution of Non-Linear Differential Equations Using Walsh Function Series

Walsh functions form an orthonormal basis set consisting of square waves. The discontinuous nature of square waves make the system well suited for representing functions with discontinuities. The product of any two Walsh functions is another Walsh function - a feature that can radically change an algorithm for solving non-linear partial differential equations (PDEs). The solution algorithm of non-linear differential equations using Walsh function series is unique in that integrals and derivatives may be computed using simple matrix multiplication of series representations of functions. Solutions to PDEs are derived as functions of wave component amplitude. Three sample problems are presented to illustrate the Walsh function series approach to solving unsteady PDEs. These include an advection equation, a Burgers equation, and a Riemann problem. The sample problems demonstrate the use of the Walsh function solution algorithms, exploiting Fast Walsh Transforms in multi-dimensions (O(Nlog(N))). Details of a Fast Walsh Reciprocal, defined here for the first time, enable inversion of aWalsh Symmetric Matrix in O(Nlog(N)) operations. Walsh functions have been derived using a fractal recursion algorithm and these fractal patterns are observed in the progression of pairs of wave number amplitudes in the solutions. These patterns are most easily observed in a remapping defined as a fractal fingerprint (FFP). A prolongation of existing solutions to the next highest order exploits these patterns. The algorithms presented here are considered a work in progress that provide new alternatives and new insights into the solution of non-linear PDEs.

Gnoffo, Peter A.↗

Postbuckling of laminated anisotropic panels

A two-part study of the buckling and postbuckling of laminated anisotropic plates with bending-extensional coupling is presented. The first part involves the development and application of a modified Rayleigh-Ritz analysis technique. Modifications made to the classical technique can be grouped into three areas. First, known symmetries of anisotropic panels are exploited in the selection of approximation functions. Second, a reduced basis technique based on these same symmetries is applied in the linear range. Finally, geometric boundary conditions are enforced via an exterior penalty function approach, rather than relying on choice of approximation functions to satisfy these boundary conditions. Numerical results are presented for both the linear and nonlinear range, with additional studies made to determine the effect of variation in penalty parameter and number of basis vectors. In the second part, six panels possessing anisotropy and bending-extensional coupling are tested. Detailed comparisons are made between experiment and finite element results in order to gain insight into the postbuckling and failure characteristics of such panels. The panels are constructed using two different lamination sequences, and panels with three different aspect ratios were constructed for each lamination sequence.

Jeffrey, Glenda L.↗

Calculation of Coupled Vibroacoustics Response Estimates from a Library of Available Uncoupled Transfer Function Sets

The design and theoretical basis of a new database tool that quickly generates vibroacoustic response estimates using a library of transfer functions (TFs) is discussed. During the early stages of a launch vehicle development program, these response estimates can be used to provide vibration environment specification to hardware vendors. The tool accesses TFs from a database, combines the TFs, and multiplies these by input excitations to estimate vibration responses. The database is populated with two sets of uncoupled TFs; the first set representing vibration response of a bare panel, designated as H(sup s), and the second set representing the response of the free-free component equipment by itself, designated as H(sup c). For a particular configuration undergoing analysis, the appropriate H(sup s) and H(sup c) are selected and coupled to generate an integrated TF, designated as H(sup s +c). This integrated TF is then used with the appropriate input excitations to estimate vibration responses. This simple yet powerful tool enables a user to estimate vibration responses without directly using finite element models, so long as suitable H(sup s) and H(sup c) sets are defined in the database libraries. The paper discusses the preparation of the database tool and provides the assumptions and methodologies necessary to combine H(sup s) and H(sup c) sets into an integrated H(sup s + c). An experimental validation of the approach is also presented.

Smith, Andrew↗

The effect of hydrogen-bonding on flavin’s infrared absorption spectrum

Cluster and continuum solvation computational models are employed to model the effect of hydrogen bonding interactions on the vibrational modes of lumiflavin. Calculated spectra were compared to experimental Fourier-transform infrared (FTIR) spectra in the diagnostic 1450–1800 cm –1 range, where intense V C=C , V C=N , V C 2 =O , and V C 4 =O stretching modes of flavin’s isoalloxazine ring are found. Local mode analysis is used to describe the strength of hydrogen-bonding in cluster models. The computations indicate that V C=C and V C=N mode frequencies are relatively insensitive to intermolecular interactions while the V C 2 =O and V C 4 =O modes are sensitive to direct (and also indirect for V C 2 =O ) hydrogen-bonding interactions. Although flavin is neutral, basis sets without the diffuse functions provide incorrect relative frequencies and intensities. The 6-31+G* basis set is found to be adequate for this system, and there is limited benefit to considering larger basis sets. Calculated vibrational mode frequencies agree with experimentally determined frequencies in solution when cluster models with multiple water molecules are used. Accurate simulation of relative FTIR band intensities, on the other hand, requires a continuum (or possibly quantum mechanical/molecular mechanical) model that accounts for long-range electrostatic effects. Lastly, an experimental peak at ca. 1624 cm –1 that is typically assigned to the V C 2 =O vibrational stretching mode has a complicated shape that suggests multiple underlying contributions. Our calculations show that this band has contributions from both the C 6 –C 7 and C 2 = O stretching vibrations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗