Impacts of Sigma Coordinates on the Euler and Navier-Stokes Equations using Continuous Galerkin Methods

DTIC Science & Technology

2009-03-01

the 1- D local basis functions. The 1-D Lagrange polynomial local basis function, using Legendre -Gauss-Lobatto interpolation points, was defined by...cases were run using 10th order polynomials , with contours from -0.05 to 0.525 K with an interval of 0.025 K...after 700 s for reso- lutions: (a) 20, (b) 10, and (c) 5 m. All cases were run using 10th order polynomials , with contours from -0.05 to 0.525 K

Beta-function B-spline smoothing on triangulations

NASA Astrophysics Data System (ADS)

Dechevsky, Lubomir T.; Zanaty, Peter

2013-03-01

In this work we investigate a novel family of Ck-smooth rational basis functions on triangulations for fitting, smoothing, and denoising geometric data. The introduced basis function is closely related to a recently introduced general method introduced in utilizing generalized expo-rational B-splines, which provides Ck-smooth convex resolutions of unity on very general disjoint partitions and overlapping covers of multidimensional domains with complex geometry. One of the major advantages of this new triangular construction is its locality with respect to the star-1 neighborhood of the vertex on which the said base is providing Hermite interpolation. This locality of the basis functions can be in turn utilized in adaptive methods, where, for instance a local refinement of the underlying triangular mesh affects only the refined domain, whereas, in other method one needs to investigate what changes are occurring outside of the refined domain. Both the triangular and the general smooth constructions have the potential to become a new versatile tool of Computer Aided Geometric Design (CAGD), Finite and Boundary Element Analysis (FEA/BEA) and Iso-geometric Analysis (IGA).

Numerical study of the shape parameter dependence of the local radial point interpolation method in linear elasticity.

PubMed

Moussaoui, Ahmed; Bouziane, Touria

2016-01-01

The method LRPIM is a Meshless method with properties of simple implementation of the essential boundary conditions and less costly than the moving least squares (MLS) methods. This method is proposed to overcome the singularity associated to polynomial basis by using radial basis functions. In this paper, we will present a study of a 2D problem of an elastic homogenous rectangular plate by using the method LRPIM. Our numerical investigations will concern the influence of different shape parameters on the domain of convergence,accuracy and using the radial basis function of the thin plate spline. It also will presents a comparison between numerical results for different materials and the convergence domain by precising maximum and minimum values as a function of distribution nodes number. The analytical solution of the deflection confirms the numerical results. The essential points in the method are: •The LRPIM is derived from the local weak form of the equilibrium equations for solving a thin elastic plate.•The convergence of the LRPIM method depends on number of parameters derived from local weak form and sub-domains.•The effect of distributions nodes number by varying nature of material and the radial basis function (TPS).

Simple Test Functions in Meshless Local Petrov-Galerkin Methods

NASA Technical Reports Server (NTRS)

Raju, Ivatury S.

2016-01-01

Two meshless local Petrov-Galerkin (MLPG) methods based on two different trial functions but that use a simple linear test function were developed for beam and column problems. These methods used generalized moving least squares (GMLS) and radial basis (RB) interpolation functions as trial functions. These two methods were tested on various patch test problems. Both methods passed the patch tests successfully. Then the methods were applied to various beam vibration problems and problems involving Euler and Beck's columns. Both methods yielded accurate solutions for all problems studied. The simple linear test function offers considerable savings in computing efforts as the domain integrals involved in the weak form are avoided. The two methods based on this simple linear test function method produced accurate results for frequencies and buckling loads. Of the two methods studied, the method with radial basis trial functions is very attractive as the method is simple, accurate, and robust.

Atomic Cholesky decompositions: a route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency.

PubMed

Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

2009-04-21

Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

Atomic Cholesky decompositions: A route to unbiased auxiliary basis sets for density fitting approximation with tunable accuracy and efficiency

NASA Astrophysics Data System (ADS)

Aquilante, Francesco; Gagliardi, Laura; Pedersen, Thomas Bondo; Lindh, Roland

2009-04-01

Cholesky decomposition of the atomic two-electron integral matrix has recently been proposed as a procedure for automated generation of auxiliary basis sets for the density fitting approximation [F. Aquilante et al., J. Chem. Phys. 127, 114107 (2007)]. In order to increase computational performance while maintaining accuracy, we propose here to reduce the number of primitive Gaussian functions of the contracted auxiliary basis functions by means of a second Cholesky decomposition. Test calculations show that this procedure is most beneficial in conjunction with highly contracted atomic orbital basis sets such as atomic natural orbitals, and that the error resulting from the second decomposition is negligible. We also demonstrate theoretically as well as computationally that the locality of the fitting coefficients can be controlled by means of the decomposition threshold even with the long-ranged Coulomb metric. Cholesky decomposition-based auxiliary basis sets are thus ideally suited for local density fitting approximations.

Scanning tunneling microscopy current from localized basis orbital density functional theory

NASA Astrophysics Data System (ADS)

Gustafsson, Alexander; Paulsson, Magnus

2016-03-01

We present a method capable of calculating elastic scanning tunneling microscopy (STM) currents from localized atomic orbital density functional theory (DFT). To overcome the poor accuracy of the localized orbital description of the wave functions far away from the atoms, we propagate the wave functions, using the total DFT potential. From the propagated wave functions, the Bardeen's perturbative approach provides the tunneling current. To illustrate the method we investigate carbon monoxide adsorbed on a Cu(111) surface and recover the depression/protrusion observed experimentally with normal/CO-functionalized STM tips. The theory furthermore allows us to discuss the significance of s - and p -wave tips.

Assessing the utility of phase-space-localized basis functions: Exploiting direct product structure and a new basis function selection procedure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, James, E-mail: 9jhb3@queensu.ca; Carrington, Tucker, E-mail: Tucker.Carrington@queensu.ca

In this paper we show that it is possible to use an iterative eigensolver in conjunction with Halverson and Poirier’s symmetrized Gaussian (SG) basis [T. Halverson and B. Poirier, J. Chem. Phys. 137, 224101 (2012)] to compute accurate vibrational energy levels of molecules with as many as five atoms. This is done, without storing and manipulating large matrices, by solving a regular eigenvalue problem that makes it possible to exploit direct-product structure. These ideas are combined with a new procedure for selecting which basis functions to use. The SG basis we work with is orders of magnitude smaller than themore » basis made by using a classical energy criterion. We find significant convergence errors in previous calculations with SG bases. For sum-of-product Hamiltonians, SG bases large enough to compute accurate levels are orders of magnitude larger than even simple pruned bases composed of products of harmonic oscillator functions.« less

Analysis of STM images with pure and CO-functionalized tips: A first-principles and experimental study

NASA Astrophysics Data System (ADS)

Gustafsson, Alexander; Okabayashi, Norio; Peronio, Angelo; Giessibl, Franz J.; Paulsson, Magnus

2017-08-01

We describe a first-principles method to calculate scanning tunneling microscopy (STM) images, and compare the results to well-characterized experiments combining STM with atomic force microscopy (AFM). The theory is based on density functional theory with a localized basis set, where the wave functions in the vacuum gap are computed by propagating the localized-basis wave functions into the gap using a real-space grid. Constant-height STM images are computed using Bardeen's approximation method, including averaging over the reciprocal space. We consider copper adatoms and single CO molecules adsorbed on Cu(111), scanned with a single-atom copper tip with and without CO functionalization. The calculated images agree with state-of-the-art experiments, where the atomic structure of the tip apex is determined by AFM. The comparison further allows for detailed interpretation of the STM images.

Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction

NASA Astrophysics Data System (ADS)

Song, Chenchen; Martínez, Todd J.

2017-01-01

In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N2.5) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction.

PubMed

Song, Chenchen; Martínez, Todd J

2017-01-21

In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N 2.5 ) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

Basis set limit and systematic errors in local-orbital based all-electron DFT

NASA Astrophysics Data System (ADS)

Blum, Volker; Behler, Jörg; Gehrke, Ralf; Reuter, Karsten; Scheffler, Matthias

2006-03-01

With the advent of efficient integration schemes,^1,2 numeric atom-centered orbitals (NAO's) are an attractive basis choice in practical density functional theory (DFT) calculations of nanostructured systems (surfaces, clusters, molecules). Though all-electron, the efficiency of practical implementations promises to be on par with the best plane-wave pseudopotential codes, while having a noticeably higher accuracy if required: Minimal-sized effective tight-binding like calculations and chemically accurate all-electron calculations are both possible within the same framework; non-periodic and periodic systems can be treated on equal footing; and the localized nature of the basis allows in principle for O(N)-like scaling. However, converging an observable with respect to the basis set is less straightforward than with competing systematic basis choices (e.g., plane waves). We here investigate the basis set limit of optimized NAO basis sets in all-electron calculations, using as examples small molecules and clusters (N2, Cu2, Cu4, Cu10). meV-level total energy convergence is possible using <=50 basis functions per atom in all cases. We also find a clear correlation between the errors which arise from underconverged basis sets, and the system geometry (interatomic distance). ^1 B. Delley, J. Chem. Phys. 92, 508 (1990), ^2 J.M. Soler et al., J. Phys.: Condens. Matter 14, 2745 (2002).

A high-order multiscale finite-element method for time-domain acoustic-wave modeling

NASA Astrophysics Data System (ADS)

Gao, Kai; Fu, Shubin; Chung, Eric T.

2018-05-01

Accurate and efficient wave equation modeling is vital for many applications in such as acoustics, electromagnetics, and seismology. However, solving the wave equation in large-scale and highly heterogeneous models is usually computationally expensive because the computational cost is directly proportional to the number of grids in the model. We develop a novel high-order multiscale finite-element method to reduce the computational cost of time-domain acoustic-wave equation numerical modeling by solving the wave equation on a coarse mesh based on the multiscale finite-element theory. In contrast to existing multiscale finite-element methods that use only first-order multiscale basis functions, our new method constructs high-order multiscale basis functions from local elliptic problems which are closely related to the Gauss-Lobatto-Legendre quadrature points in a coarse element. Essentially, these basis functions are not only determined by the order of Legendre polynomials, but also by local medium properties, and therefore can effectively convey the fine-scale information to the coarse-scale solution with high-order accuracy. Numerical tests show that our method can significantly reduce the computation time while maintain high accuracy for wave equation modeling in highly heterogeneous media by solving the corresponding discrete system only on the coarse mesh with the new high-order multiscale basis functions.

A high-order multiscale finite-element method for time-domain acoustic-wave modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Kai; Fu, Shubin; Chung, Eric T.

Accurate and efficient wave equation modeling is vital for many applications in such as acoustics, electromagnetics, and seismology. However, solving the wave equation in large-scale and highly heterogeneous models is usually computationally expensive because the computational cost is directly proportional to the number of grids in the model. We develop a novel high-order multiscale finite-element method to reduce the computational cost of time-domain acoustic-wave equation numerical modeling by solving the wave equation on a coarse mesh based on the multiscale finite-element theory. In contrast to existing multiscale finite-element methods that use only first-order multiscale basis functions, our new method constructsmore » high-order multiscale basis functions from local elliptic problems which are closely related to the Gauss–Lobatto–Legendre quadrature points in a coarse element. Essentially, these basis functions are not only determined by the order of Legendre polynomials, but also by local medium properties, and therefore can effectively convey the fine-scale information to the coarse-scale solution with high-order accuracy. Numerical tests show that our method can significantly reduce the computation time while maintain high accuracy for wave equation modeling in highly heterogeneous media by solving the corresponding discrete system only on the coarse mesh with the new high-order multiscale basis functions.« less

A high-order multiscale finite-element method for time-domain acoustic-wave modeling

DOE PAGES

Gao, Kai; Fu, Shubin; Chung, Eric T.

2018-02-04

Accurate and efficient wave equation modeling is vital for many applications in such as acoustics, electromagnetics, and seismology. However, solving the wave equation in large-scale and highly heterogeneous models is usually computationally expensive because the computational cost is directly proportional to the number of grids in the model. We develop a novel high-order multiscale finite-element method to reduce the computational cost of time-domain acoustic-wave equation numerical modeling by solving the wave equation on a coarse mesh based on the multiscale finite-element theory. In contrast to existing multiscale finite-element methods that use only first-order multiscale basis functions, our new method constructsmore » high-order multiscale basis functions from local elliptic problems which are closely related to the Gauss–Lobatto–Legendre quadrature points in a coarse element. Essentially, these basis functions are not only determined by the order of Legendre polynomials, but also by local medium properties, and therefore can effectively convey the fine-scale information to the coarse-scale solution with high-order accuracy. Numerical tests show that our method can significantly reduce the computation time while maintain high accuracy for wave equation modeling in highly heterogeneous media by solving the corresponding discrete system only on the coarse mesh with the new high-order multiscale basis functions.« less

Employing general fit-bases for construction of potential energy surfaces with an adaptive density-guided approach

NASA Astrophysics Data System (ADS)

Klinting, Emil Lund; Thomsen, Bo; Godtliebsen, Ian Heide; Christiansen, Ove

2018-02-01

We present an approach to treat sets of general fit-basis functions in a single uniform framework, where the functional form is supplied on input, i.e., the use of different functions does not require new code to be written. The fit-basis functions can be used to carry out linear fits to the grid of single points, which are generated with an adaptive density-guided approach (ADGA). A non-linear conjugate gradient method is used to optimize non-linear parameters if such are present in the fit-basis functions. This means that a set of fit-basis functions with the same inherent shape as the potential cuts can be requested and no other choices with regards to the fit-basis functions need to be taken. The general fit-basis framework is explored in relation to anharmonic potentials for model systems, diatomic molecules, water, and imidazole. The behaviour and performance of Morse and double-well fit-basis functions are compared to that of polynomial fit-basis functions for unsymmetrical single-minimum and symmetrical double-well potentials. Furthermore, calculations for water and imidazole were carried out using both normal coordinates and hybrid optimized and localized coordinates (HOLCs). Our results suggest that choosing a suitable set of fit-basis functions can improve the stability of the fitting routine and the overall efficiency of potential construction by lowering the number of single point calculations required for the ADGA. It is possible to reduce the number of terms in the potential by choosing the Morse and double-well fit-basis functions. These effects are substantial for normal coordinates but become even more pronounced if HOLCs are used.

The local work function: Concept and implications

NASA Astrophysics Data System (ADS)

Wandelt, K.

1997-02-01

The term 'local work function' is now widely applied. The present work discusses the common physical basis of 'photoemission of adsorbed xenon (PAX)' and 'two-photon photonemissionspectroscopy of image potential states' as local work function probes. New examples with bimetallic and defective surfaces are presented which demonstrate the capability of PAX measurements for the characterization of heterogeneous surfaces on an atomic scale. Finally, implications of the existence of short-range variations of the surface potential at surface steps are addressed. In particular, dynamical work function change measurements are a sensitive probe for the step-density at surfaces and, as such, a powerful in-situ method to monitor film growth.

A Meshless Method Using Radial Basis Functions for Beam Bending Problems

NASA Technical Reports Server (NTRS)

Raju, I. S.; Phillips, D. R.; Krishnamurthy, T.

2004-01-01

A meshless local Petrov-Galerkin (MLPG) method that uses radial basis functions (RBFs) as trial functions in the study of Euler-Bernoulli beam problems is presented. RBFs, rather than generalized moving least squares (GMLS) interpolations, are used to develop the trial functions. This choice yields a computationally simpler method as fewer matrix inversions and multiplications are required than when GMLS interpolations are used. Test functions are chosen as simple weight functions as they are in the conventional MLPG method. Compactly and noncompactly supported RBFs are considered. Noncompactly supported cubic RBFs are found to be preferable. Patch tests, mixed boundary value problems, and problems with complex loading conditions are considered. Results obtained from the radial basis MLPG method are either of comparable or better accuracy than those obtained when using the conventional MLPG method.

On the importance of local orbitals using second energy derivatives for d and f electrons

NASA Astrophysics Data System (ADS)

Karsai, Ferenc; Tran, Fabien; Blaha, Peter

2017-11-01

The all-electron linearized augmented plane wave (LAPW) methods are among the most accurate to solve the Kohn-Sham equations of density functional theory for periodic solids. In the LAPW methods, the unit cell is partitioned into spheres surrounding the atoms, inside which the wave functions are expanded into spherical harmonics, and the interstitial region, where the wave functions are expanded in Fourier series. Recently, Michalicek et al. (2013) reported an analysis of the so-called linearization error, which is inherent to the basis functions inside the spheres, and advocated the use of local orbital basis functions involving the second energy derivative of the radial part (HDLO). In the present work, we report the implementation of such basis functions into the WIEN2k code, and discuss in detail the improvement in terms of accuracy. From our tests, which involve atoms from the whole periodic table, it is concluded that for ground-state properties (e.g., equilibrium volume) the use of HDLO is necessary only for atoms with d or f electrons in the valence and large atomic spheres. For unoccupied states which are not too high above the Fermi energy, HDLO systematically improve the band structure, which may be of importance for the calculation of optical properties.

A multiscale restriction-smoothed basis method for high contrast porous media represented on unstructured grids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Møyner, Olav, E-mail: olav.moyner@sintef.no; Lie, Knut-Andreas, E-mail: knut-andreas.lie@sintef.no

2016-01-01

A wide variety of multiscale methods have been proposed in the literature to reduce runtime and provide better scaling for the solution of Poisson-type equations modeling flow in porous media. We present a new multiscale restricted-smoothed basis (MsRSB) method that is designed to be applicable to both rectilinear grids and unstructured grids. Like many other multiscale methods, MsRSB relies on a coarse partition of the underlying fine grid and a set of local prolongation operators (multiscale basis functions) that map unknowns associated with the fine grid cells to unknowns associated with blocks in the coarse partition. These mappings are constructedmore » by restricted smoothing: Starting from a constant, a localized iterative scheme is applied directly to the fine-scale discretization to compute prolongation operators that are consistent with the local properties of the differential operators. The resulting method has three main advantages: First of all, both the coarse and the fine grid can have general polyhedral geometry and unstructured topology. This means that partitions and good prolongation operators can easily be constructed for complex models involving high media contrasts and unstructured cell connections introduced by faults, pinch-outs, erosion, local grid refinement, etc. In particular, the coarse partition can be adapted to geological or flow-field properties represented on cells or faces to improve accuracy. Secondly, the method is accurate and robust when compared to existing multiscale methods and does not need expensive recomputation of local basis functions to account for transient behavior: Dynamic mobility changes are incorporated by continuing to iterate a few extra steps on existing basis functions. This way, the cost of updating the prolongation operators becomes proportional to the amount of change in fluid mobility and one reduces the need for expensive, tolerance-based updates. Finally, since the MsRSB method is formulated on top of a cell-centered, conservative, finite-volume method, it is applicable to any flow model in which one can isolate a pressure equation. Herein, we only discuss single and two-phase incompressible models. Compressible flow, e.g., as modeled by the black-oil equations, is discussed in a separate paper.« less

Solution of Thermoelectricity Problems Energy Method

NASA Astrophysics Data System (ADS)

Niyazbek, Muheyat; Nogaybaeva, M. O.; Talp, Kuenssaule; Kudaikulov, A. A.

2018-06-01

On the basis of the fundamental laws of conservation of energy in conjunction with local quadratic spline functions was developed a universal computing algorithm, a method and associated software, which allows to investigate the Thermophysical insulated rod, with limited length, influenced by local heat flow, heat transfer and temperature

Efficient O(N) integration for all-electron electronic structure calculation using numeric basis functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Havu, V.; Fritz Haber Institute of the Max Planck Society, Berlin; Blum, V.

2009-12-01

We consider the problem of developing O(N) scaling grid-based operations needed in many central operations when performing electronic structure calculations with numeric atom-centered orbitals as basis functions. We outline the overall formulation of localized algorithms, and specifically the creation of localized grid batches. The choice of the grid partitioning scheme plays an important role in the performance and memory consumption of the grid-based operations. Three different top-down partitioning methods are investigated, and compared with formally more rigorous yet much more expensive bottom-up algorithms. We show that a conceptually simple top-down grid partitioning scheme achieves essentially the same efficiency as themore » more rigorous bottom-up approaches.« less

Useful lower limits to polarization contributions to intermolecular interactions using a minimal basis of localized orthogonal orbitals: theory and analysis of the water dimer.

PubMed

Azar, R Julian; Horn, Paul Richard; Sundstrom, Eric Jon; Head-Gordon, Martin

2013-02-28

The problem of describing the energy-lowering associated with polarization of interacting molecules is considered in the overlapping regime for self-consistent field wavefunctions. The existing approach of solving for absolutely localized molecular orbital (ALMO) coefficients that are block-diagonal in the fragments is shown based on formal grounds and practical calculations to often overestimate the strength of polarization effects. A new approach using a minimal basis of polarized orthogonal local MOs (polMOs) is developed as an alternative. The polMO basis is minimal in the sense that one polarization function is provided for each unpolarized orbital that is occupied; such an approach is exact in second-order perturbation theory. Based on formal grounds and practical calculations, the polMO approach is shown to underestimate the strength of polarization effects. In contrast to the ALMO method, however, the polMO approach yields results that are very stable to improvements in the underlying AO basis expansion. Combining the ALMO and polMO approaches allows an estimate of the range of energy-lowering due to polarization. Extensive numerical calculations on the water dimer using a large range of basis sets with Hartree-Fock theory and a variety of different density functionals illustrate the key considerations. Results are also presented for the polarization-dominated Na(+)CH4 complex. Implications for energy decomposition analysis of intermolecular interactions are discussed.

Steerable Principal Components for Space-Frequency Localized Images*

PubMed Central

Landa, Boris; Shkolnisky, Yoel

2017-01-01

As modern scientific image datasets typically consist of a large number of images of high resolution, devising methods for their accurate and efficient processing is a central research task. In this paper, we consider the problem of obtaining the steerable principal components of a dataset, a procedure termed “steerable PCA” (steerable principal component analysis). The output of the procedure is the set of orthonormal basis functions which best approximate the images in the dataset and all of their planar rotations. To derive such basis functions, we first expand the images in an appropriate basis, for which the steerable PCA reduces to the eigen-decomposition of a block-diagonal matrix. If we assume that the images are well localized in space and frequency, then such an appropriate basis is the prolate spheroidal wave functions (PSWFs). We derive a fast method for computing the PSWFs expansion coefficients from the images' equally spaced samples, via a specialized quadrature integration scheme, and show that the number of required quadrature nodes is similar to the number of pixels in each image. We then establish that our PSWF-based steerable PCA is both faster and more accurate then existing methods, and more importantly, provides us with rigorous error bounds on the entire procedure. PMID:29081879

Linear-scaling explicitly correlated treatment of solids: periodic local MP2-F12 method.

PubMed

Usvyat, Denis

2013-11-21

Theory and implementation of the periodic local MP2-F12 method in the 3*A fixed-amplitude ansatz is presented. The method is formulated in the direct space, employing local representation for the occupied, virtual, and auxiliary orbitals in the form of Wannier functions (WFs), projected atomic orbitals (PAOs), and atom-centered Gaussian-type orbitals, respectively. Local approximations are introduced, restricting the list of the explicitly correlated pairs, as well as occupied, virtual, and auxiliary spaces in the strong orthogonality projector to the pair-specific domains on the basis of spatial proximity of respective orbitals. The 4-index two-electron integrals appearing in the formalism are approximated via the direct-space density fitting technique. In this procedure, the fitting orbital spaces are also restricted to local fit-domains surrounding the fitted densities. The formulation of the method and its implementation exploits the translational symmetry and the site-group symmetries of the WFs. Test calculations are performed on LiH crystal. The results show that the periodic LMP2-F12 method substantially accelerates basis set convergence of the total correlation energy, and even more so the correlation energy differences. The resulting energies are quite insensitive to the resolution-of-the-identity domain sizes and the quality of the auxiliary basis sets. The convergence with the orbital domain size is somewhat slower, but still acceptable. Moreover, inclusion of slightly more diffuse functions, than those usually used in the periodic calculations, improves the convergence of the LMP2-F12 correlation energy with respect to both the size of the PAO-domains and the quality of the orbital basis set. At the same time, the essentially diffuse atomic orbitals from standard molecular basis sets, commonly utilized in molecular MP2-F12 calculations, but problematic in the periodic context, are not necessary for LMP2-F12 treatment of crystals.

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package.

PubMed

Womack, James C; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-28

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package

NASA Astrophysics Data System (ADS)

Womack, James C.; Mardirossian, Narbe; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-11-01

Accurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, τ, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of τ-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for τ-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement τ-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the τ-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the τ-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms.

Characterizing Atomistic Geometries and Potential Functions Using Strain Functionals

NASA Astrophysics Data System (ADS)

Kober, Edward; Mathew, Nithin; Rudin, Sven

2017-06-01

We demonstrate the use of strain tensor functionals for characterizing arbitrarily ordered atomistic structures. This approach defines a Gaussian-weighted neighborhood around each atom and characterizes that local geometry in terms of n-th order strain tensors, which are equivalent to the n-th order moments/derivatives of the neighborhood. Fourth order expansions can distinguish the cubic structures (and deformations thereof), but sixth order expansions are required to fully characterize hexagonal structures. These functions are continuous and smooth and much less sensitive to thermal fluctuations than other descriptors based on discrete neighborhoods. Reducing these metrics to rotational invariant descriptors allows a large number of defect structures to be readily identified and forms the basis of a classification scheme that allows molecular dynamics simulations to be readily analyzed. Applications to the analysis of shock waves impinging on samples of Cu, Ta and Ti will be presented. The method has been extended to vector fields as well, enabling the local stress to be cast in terms of rotationally invariant functions as well. The stress-strain correlations can then be used as the basis for developing and analyzing potential functions.

Quantum phase space with a basis of Wannier functions

NASA Astrophysics Data System (ADS)

Fang, Yuan; Wu, Fan; Wu, Biao

2018-02-01

A quantum phase space with Wannier basis is constructed: (i) classical phase space is divided into Planck cells; (ii) a complete set of Wannier functions are constructed with the combination of Kohn’s method and Löwdin method such that each Wannier function is localized at a Planck cell. With these Wannier functions one can map a wave function unitarily onto phase space. Various examples are used to illustrate our method and compare it to Wigner function. The advantage of our method is that it can smooth out the oscillations in wave functions without losing any information and is potentially a better tool in studying quantum-classical correspondence. In addition, we point out that our method can be used for time-frequency analysis of signals.

Cortical localization of cognitive function by regression of performance on event-related potentials

NASA Technical Reports Server (NTRS)

Montgomery, R. W.; Montgomery, L. D.; Guisado, R.

1992-01-01

This paper demonstrates a new method of mapping cortical localization of cognitive function, using electroencephalographic data. Cross-subject regression analyses are used to identify cortical sites and post-stimulus latencies where there is a high correlation between subjects' performance and their cognitive event-related potential amplitude. The procedure was tested using a mental arithmetic task and was found to identify essentially the same cortical regions that have been associated with such tasks on the basis of research with patients suffering localized cortical lesions. Thus, it appears to offer an inexpensive, noninvasive tool for exploring the dynamics of localization in neurologically normal subjects.

From plane waves to local Gaussians for the simulation of correlated periodic systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Booth, George H., E-mail: george.booth@kcl.ac.uk; Tsatsoulis, Theodoros; Grüneis, Andreas, E-mail: a.grueneis@fkf.mpg.de

2016-08-28

We present a simple, robust, and black-box approach to the implementation and use of local, periodic, atom-centered Gaussian basis functions within a plane wave code, in a computationally efficient manner. The procedure outlined is based on the representation of the Gaussians within a finite bandwidth by their underlying plane wave coefficients. The core region is handled within the projected augment wave framework, by pseudizing the Gaussian functions within a cutoff radius around each nucleus, smoothing the functions so that they are faithfully represented by a plane wave basis with only moderate kinetic energy cutoff. To mitigate the effects of themore » basis set superposition error and incompleteness at the mean-field level introduced by the Gaussian basis, we also propose a hybrid approach, whereby the complete occupied space is first converged within a large plane wave basis, and the Gaussian basis used to construct a complementary virtual space for the application of correlated methods. We demonstrate that these pseudized Gaussians yield compact and systematically improvable spaces with an accuracy comparable to their non-pseudized Gaussian counterparts. A key advantage of the described method is its ability to efficiently capture and describe electronic correlation effects of weakly bound and low-dimensional systems, where plane waves are not sufficiently compact or able to be truncated without unphysical artifacts. We investigate the accuracy of the pseudized Gaussians for the water dimer interaction, neon solid, and water adsorption on a LiH surface, at the level of second-order Møller–Plesset perturbation theory.« less

18 CFR 358.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... utility posts the information, by electronic means, required under this part 358. (c) Marketing functions... local distribution company operating under section 7(f) of the Natural Gas Act. (d) Marketing function... of a transmission provider who actively and personally engages on a day-to-day basis in marketing...

Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C

NASA Astrophysics Data System (ADS)

Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

2017-06-01

With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which—when stripped of BSSE—is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals—such as B97M-V—to recover large-basis results at a fraction of the cost.

On the Usage of Locally Dense Basis Sets in the Calculation of NMR Indirect Nuclear Spin-Spin Coupling Constants

NASA Astrophysics Data System (ADS)

Sanchez, Marina; Provasi, Patricio F.; Aucar, Gustavo A.; Sauer, Stephan P. A.

Locally dense basis sets (

B97-3c: A revised low-cost variant of the B97-D density functional method

NASA Astrophysics Data System (ADS)

Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas; Grimme, Stefan

2018-02-01

A revised version of the well-established B97-D density functional approximation with general applicability for chemical properties of large systems is proposed. Like B97-D, it is based on Becke's power-series ansatz from 1997 and is explicitly parametrized by including the standard D3 semi-classical dispersion correction. The orbitals are expanded in a modified valence triple-zeta Gaussian basis set, which is available for all elements up to Rn. Remaining basis set errors are mostly absorbed in the modified B97 parametrization, while an established atom-pairwise short-range potential is applied to correct for the systematically too long bonds of main group elements which are typical for most semi-local density functionals. The new composite scheme (termed B97-3c) completes the hierarchy of "low-cost" electronic structure methods, which are all mainly free of basis set superposition error and account for most interactions in a physically sound and asymptotically correct manner. B97-3c yields excellent molecular and condensed phase geometries, similar to most hybrid functionals evaluated in a larger basis set expansion. Results on the comprehensive GMTKN55 energy database demonstrate its good performance for main group thermochemistry, kinetics, and non-covalent interactions, when compared to functionals of the same class. This also transfers to metal-organic reactions, which is a major area of applicability for semi-local functionals. B97-3c can be routinely applied to hundreds of atoms on a single processor and we suggest it as a robust computational tool, in particular, for more strongly correlated systems where our previously published "3c" schemes might be problematic.

The Dynamical Mean Field Study of Competition between Ferromagnetism and Disorder in Ferromagnetic Semiconductors

NASA Astrophysics Data System (ADS)

Aryanpour, Karan

2003-03-01

We employ the Dynamical Mean Field Approximation (DMFA) to study the Janko-Zarand model [1] for the combination of large spin-orbit coupling and spatial disorder effects in GaAs doped with Mn. In this model the electronic dispersion and the spin-orbit coupling are simultaneously diagonalized and therefore, the Hamiltonian for the pure system takes a surprisingly simple form. The price for this simplicity is that the quantization axis for the spin must be rotated along the direction of momentum. This chiral basis greatly complicates the form of the hole-impurity interaction at a single site i. In the DMFA, since all the crossing Feynman diagrams for the hole-impurity interaction vanish, the problem simplifies to the local diagrams for the holes scattering off of a single Mn impurity site only. The diagrammatics for the self-energy reduces to the local Green functions and potentials in the non-chiral basis in which they have very simple forms. We first calculate the initial green function G(k) in the chiral basis and then rotate G(k) back into the non chiral basis and coarse grain it over all the k momenta. The hole-impurity interaction is greatly simplified in the non-chiral basis and can be averaged over all the spin configurations and orientations of the Mn atoms on the lattice.The self energy may be extracted from the averaged Green function, and used to recalculate the initial cluster Green function, etc. completing the DMFA self-consistent loop. We intend to calculate the spin and charge transport coefficients, and spectra such as the AC susceptibility and the ARPES which may be directly compared with experiment. [1] Phys. Rev. Lett.89,047201/1-4 (2002)

An improved local radial point interpolation method for transient heat conduction analysis

NASA Astrophysics Data System (ADS)

Wang, Feng; Lin, Gao; Zheng, Bao-Jing; Hu, Zhi-Qiang

2013-06-01

The smoothing thin plate spline (STPS) interpolation using the penalty function method according to the optimization theory is presented to deal with transient heat conduction problems. The smooth conditions of the shape functions and derivatives can be satisfied so that the distortions hardly occur. Local weak forms are developed using the weighted residual method locally from the partial differential equations of the transient heat conduction. Here the Heaviside step function is used as the test function in each sub-domain to avoid the need for a domain integral. Essential boundary conditions can be implemented like the finite element method (FEM) as the shape functions possess the Kronecker delta property. The traditional two-point difference method is selected for the time discretization scheme. Three selected numerical examples are presented in this paper to demonstrate the availability and accuracy of the present approach comparing with the traditional thin plate spline (TPS) radial basis functions.

Infinite occupation number basis of bosons: Solving a numerical challenge

NASA Astrophysics Data System (ADS)

Geißler, Andreas; Hofstetter, Walter

2017-06-01

In any bosonic lattice system, which is not dominated by local interactions and thus "frozen" in a Mott-type state, numerical methods have to cope with the infinite size of the corresponding Hilbert space even for finite lattice sizes. While it is common practice to restrict the local occupation number basis to Nc lowest occupied states, the presence of a finite condensate fraction requires the complete number basis for an exact representation of the many-body ground state. In this work we present a truncation scheme to account for contributions from higher number states. By simply adding a single coherent-tail state to this common truncation, we demonstrate increased numerical accuracy and the possible increase in numerical efficiency of this method for the Gutzwiller variational wave function and within dynamical mean-field theory.

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ratcliff, Laura E.; Genovese, Luigi; Mohr, Stephan

2015-06-21

In a recent paper, we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions are optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix ofmore » the system can be projected. In this paper, we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e., without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.« less

Mapped grid methods for long-range molecules and cold collisions

NASA Astrophysics Data System (ADS)

Willner, K.; Dulieu, O.; Masnou-Seeuws, F.

2004-01-01

The paper discusses ways of improving the accuracy of numerical calculations for vibrational levels of diatomic molecules close to the dissociation limit or for ultracold collisions, in the framework of a grid representation. In order to avoid the implementation of very large grids, Kokoouline et al. [J. Chem. Phys. 110, 9865 (1999)] have proposed a mapping procedure through introduction of an adaptive coordinate x subjected to the variation of the local de Broglie wavelength as a function of the internuclear distance R. Some unphysical levels ("ghosts") then appear in the vibrational series computed via a mapped Fourier grid representation. In the present work the choice of the basis set is reexamined, and two alternative expansions are discussed: Sine functions and Hardy functions. It is shown that use of a basis set with fixed nodes at both grid ends is efficient to eliminate "ghost" solutions. It is further shown that the Hamiltonian matrix in the sine basis can be calculated very accurately by using an auxiliary basis of cosine functions, overcoming the problems arising from numerical calculation of the Jacobian J(x) of the R→x coordinate transformation.

Relativistic hydrodynamics from quantum field theory on the basis of the generalized Gibbs ensemble method

NASA Astrophysics Data System (ADS)

Hayata, Tomoya; Hidaka, Yoshimasa; Noumi, Toshifumi; Hongo, Masaru

2015-09-01

We derive relativistic hydrodynamics from quantum field theories by assuming that the density operator is given by a local Gibbs distribution at initial time. We decompose the energy-momentum tensor and particle current into nondissipative and dissipative parts, and analyze their time evolution in detail. Performing the path-integral formulation of the local Gibbs distribution, we microscopically derive the generating functional for the nondissipative hydrodynamics. We also construct a basis to study dissipative corrections. In particular, we derive the first-order dissipative hydrodynamic equations without a choice of frame such as the Landau-Lifshitz or Eckart frame.

Two-step superresolution approach for surveillance face image through radial basis function-partial least squares regression and locality-induced sparse representation

NASA Astrophysics Data System (ADS)

Jiang, Junjun; Hu, Ruimin; Han, Zhen; Wang, Zhongyuan; Chen, Jun

2013-10-01

Face superresolution (SR), or face hallucination, refers to the technique of generating a high-resolution (HR) face image from a low-resolution (LR) one with the help of a set of training examples. It aims at transcending the limitations of electronic imaging systems. Applications of face SR include video surveillance, in which the individual of interest is often far from cameras. A two-step method is proposed to infer a high-quality and HR face image from a low-quality and LR observation. First, we establish the nonlinear relationship between LR face images and HR ones, according to radial basis function and partial least squares (RBF-PLS) regression, to transform the LR face into the global face space. Then, a locality-induced sparse representation (LiSR) approach is presented to enhance the local facial details once all the global faces for each LR training face are constructed. A comparison of some state-of-the-art SR methods shows the superiority of the proposed two-step approach, RBF-PLS global face regression followed by LiSR-based local patch reconstruction. Experiments also demonstrate the effectiveness under both simulation conditions and some real conditions.

Push it to the limit: Characterizing the convergence of common sequences of basis sets for intermolecular interactions as described by density functional theory

NASA Astrophysics Data System (ADS)

Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin

2016-05-01

With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.

ON THE BASIS PROPERTY OF THE HAAR SYSTEM IN THE SPACE \\mathscr{L}^{p(t)}(\\lbrack0,\\,1\\rbrack) AND THE PRINCIPLE OF LOCALIZATION IN THE MEAN

NASA Astrophysics Data System (ADS)

Sharapudinov, I. I.

1987-02-01

Let p=p(t) be a measurable function defined on \\lbrack0,\\,1\\rbrack. If p(t) is essentially bounded on \\lbrack0,\\,1\\rbrack, denote by \\mathscr{L}^{p(t)}(\\lbrack0,\\,1\\rbrack) the set of measurable functions f defined on \\lbrack0,\\,1\\rbrack for which \\int_0^1\\vert f(t)\\vert^{p(t)}dt<\\infty. The space \\mathscr{L}^{p(t)}(\\lbrack0,\\,1\\rbrack) with p(t)\\geqslant 1 is a normed space with norm \\displaystyle \\vert\\vert f\\vert\\vert _p=\\inf\\bigg\\{\\alpha>0:\\,\\int_0^1\\bigg\\vert\\frac{f(t)}{\\alpha}\\bigg\\vert^{p(t)}dt\\leqslant1\\bigg\\}.This paper examines the question of whether the Haar system is a basis in \\mathscr{L}^{p(t)}(\\lbrack0,\\,1\\rbrack). Conditions that are in a certain sense definitive on the function p(t) in order that the Haar system be a basis of \\mathscr{L}^{p(t)}(\\lbrack0,\\,1\\rbrack) are obtained. The concept of a localization principle in the mean is introduced, and its connection with the space \\mathscr{L}^{p(t)}(\\lbrack0,\\,1\\rbrack) is exhibited.Bibliography: 2 titles.

Data approximation using a blending type spline construction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalmo, Rune; Bratlie, Jostein

2014-11-18

Generalized expo-rational B-splines (GERBS) is a blending type spline construction where local functions at each knot are blended together by C{sup k}-smooth basis functions. One way of approximating discrete regular data using GERBS is by partitioning the data set into subsets and fit a local function to each subset. Partitioning and fitting strategies can be devised such that important or interesting data points are interpolated in order to preserve certain features. We present a method for fitting discrete data using a tensor product GERBS construction. The method is based on detection of feature points using differential geometry. Derivatives, which aremore » necessary for feature point detection and used to construct local surface patches, are approximated from the discrete data using finite differences.« less

Relativistic distribution function for particles with spin at local thermodynamical equilibrium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Becattini, F., E-mail: becattini@fi.infn.it; INFN Sezione di Firenze, Florence; Universität Frankfurt, Frankfurt am Main

2013-11-15

We present an extension of relativistic single-particle distribution function for weakly interacting particles at local thermodynamical equilibrium including spin degrees of freedom, for massive spin 1/2 particles. We infer, on the basis of the global equilibrium case, that at local thermodynamical equilibrium particles acquire a net polarization proportional to the vorticity of the inverse temperature four-vector field. The obtained formula for polarization also implies that a steady gradient of temperature entails a polarization orthogonal to particle momentum. The single-particle distribution function in momentum space extends the so-called Cooper–Frye formula to particles with spin 1/2 and allows us to predict theirmore » polarization in relativistic heavy ion collisions at the freeze-out. -- Highlights: •Single-particle distribution function in local thermodynamical equilibrium with spin. •Polarization of spin 1/2 particles in a fluid at local thermodynamical equilibrium. •Prediction of a new effect: a steady gradient of temperature induces a polarization. •Application to the calculation of polarization in relativistic heavy ion collisions.« less

A hexagonal orthogonal-oriented pyramid as a model of image representation in visual cortex

NASA Technical Reports Server (NTRS)

Watson, Andrew B.; Ahumada, Albert J., Jr.

1989-01-01

Retinal ganglion cells represent the visual image with a spatial code, in which each cell conveys information about a small region in the image. In contrast, cells of the primary visual cortex use a hybrid space-frequency code in which each cell conveys information about a region that is local in space, spatial frequency, and orientation. A mathematical model for this transformation is described. The hexagonal orthogonal-oriented quadrature pyramid (HOP) transform, which operates on a hexagonal input lattice, uses basis functions that are orthogonal, self-similar, and localized in space, spatial frequency, orientation, and phase. The basis functions, which are generated from seven basic types through a recursive process, form an image code of the pyramid type. The seven basis functions, six bandpass and one low-pass, occupy a point and a hexagon of six nearest neighbors on a hexagonal lattice. The six bandpass basis functions consist of three with even symmetry, and three with odd symmetry. At the lowest level, the inputs are image samples. At each higher level, the input lattice is provided by the low-pass coefficients computed at the previous level. At each level, the output is subsampled in such a way as to yield a new hexagonal lattice with a spacing square root of 7 larger than the previous level, so that the number of coefficients is reduced by a factor of seven at each level. In the biological model, the input lattice is the retinal ganglion cell array. The resulting scheme provides a compact, efficient code of the image and generates receptive fields that resemble those of the primary visual cortex.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Yishuai; Chiu, Janet; Miao, Lin

Three-dimensional topological insulators are bulk insulators with Z 2 topological electronic order that gives rise to conducting light-like surface states. These surface electrons are exceptionally resistant to localization by non-magnetic disorder, and have been adopted as the basis for a wide range of proposals to achieve new quasiparticle species and device functionality. Recent studies have yielded a surprise by showing that in spite of resisting localization, topological insulator surface electrons can be reshaped by defects into distinctive resonance states. Here we use numerical simulations and scanning tunnelling microscopy data to show that these resonance states have significance well beyond themore » localized regime usually associated with impurity bands. Lastly, at native densities in the model Bi 2X 3 (X=Bi, Te) compounds, defect resonance states are predicted to generate a new quantum basis for an emergent electron gas that supports diffusive electrical transport.« less

Kohn-Sham potentials from electron densities using a matrix representation within finite atomic orbital basis sets

NASA Astrophysics Data System (ADS)

Zhang, Xing; Carter, Emily A.

2018-01-01

We revisit the static response function-based Kohn-Sham (KS) inversion procedure for determining the KS effective potential that corresponds to a given target electron density within finite atomic orbital basis sets. Instead of expanding the potential in an auxiliary basis set, we directly update the potential in its matrix representation. Through numerical examples, we show that the reconstructed density rapidly converges to the target density. Preliminary results are presented to illustrate the possibility of obtaining a local potential in real space from the optimized potential in its matrix representation. We have further applied this matrix-based KS inversion approach to density functional embedding theory. A proof-of-concept study of a solvated proton transfer reaction demonstrates the method's promise.

Quasiparticle properties of DNA bases from GW calculations in a Wannier basis

NASA Astrophysics Data System (ADS)

Qian, Xiaofeng; Marzari, Nicola; Umari, Paolo

2009-03-01

The quasiparticle GW-Wannier (GWW) approach [1] has been recently developed to overcome the size limitations of conventional planewave GW calculations. By taking advantage of the localization properties of the maximally-localized Wannier functions and choosing a small set of polarization basis we reduce the number of Bloch wavefunctions products required for the evaluation of dynamical polarizabilities, and in turn greatly reduce memory requirements and computational efficiency. We apply GWW to study quasiparticle properties of different DNA bases and base-pairs, and solvation effects on the energy gap, demonstrating in the process the key advantages of this approach. [1] P. Umari,G. Stenuit, and S. Baroni, cond-mat/0811.1453

A systematic way for the cost reduction of density fitting methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kállay, Mihály, E-mail: kallay@mail.bme.hu

2014-12-28

We present a simple approach for the reduction of the size of auxiliary basis sets used in methods exploiting the density fitting (resolution of identity) approximation for electron repulsion integrals. Starting out of the singular value decomposition of three-center two-electron integrals, new auxiliary functions are constructed as linear combinations of the original fitting functions. The new functions, which we term natural auxiliary functions (NAFs), are analogous to the natural orbitals widely used for the cost reduction of correlation methods. The use of the NAF basis enables the systematic truncation of the fitting basis, and thereby potentially the reduction of themore » computational expenses of the methods, though the scaling with the system size is not altered. The performance of the new approach has been tested for several quantum chemical methods. It is demonstrated that the most pronounced gain in computational efficiency can be expected for iterative models which scale quadratically with the size of the fitting basis set, such as the direct random phase approximation. The approach also has the promise of accelerating local correlation methods, for which the processing of three-center Coulomb integrals is a bottleneck.« less

A fast solver for the Helmholtz equation based on the generalized multiscale finite-element method

NASA Astrophysics Data System (ADS)

Fu, Shubin; Gao, Kai

2017-11-01

Conventional finite-element methods for solving the acoustic-wave Helmholtz equation in highly heterogeneous media usually require finely discretized mesh to represent the medium property variations with sufficient accuracy. Computational costs for solving the Helmholtz equation can therefore be considerably expensive for complicated and large geological models. Based on the generalized multiscale finite-element theory, we develop a novel continuous Galerkin method to solve the Helmholtz equation in acoustic media with spatially variable velocity and mass density. Instead of using conventional polynomial basis functions, we use multiscale basis functions to form the approximation space on the coarse mesh. The multiscale basis functions are obtained from multiplying the eigenfunctions of a carefully designed local spectral problem with an appropriate multiscale partition of unity. These multiscale basis functions can effectively incorporate the characteristics of heterogeneous media's fine-scale variations, thus enable us to obtain accurate solution to the Helmholtz equation without directly solving the large discrete system formed on the fine mesh. Numerical results show that our new solver can significantly reduce the dimension of the discrete Helmholtz equation system, and can also obviously reduce the computational time.

Training radial basis function networks for wind speed prediction using PSO enhanced differential search optimizer

PubMed Central

2018-01-01

This paper presents an integrated hybrid optimization algorithm for training the radial basis function neural network (RBF NN). Training of neural networks is still a challenging exercise in machine learning domain. Traditional training algorithms in general suffer and trap in local optima and lead to premature convergence, which makes them ineffective when applied for datasets with diverse features. Training algorithms based on evolutionary computations are becoming popular due to their robust nature in overcoming the drawbacks of the traditional algorithms. Accordingly, this paper proposes a hybrid training procedure with differential search (DS) algorithm functionally integrated with the particle swarm optimization (PSO). To surmount the local trapping of the search procedure, a new population initialization scheme is proposed using Logistic chaotic sequence, which enhances the population diversity and aid the search capability. To demonstrate the effectiveness of the proposed RBF hybrid training algorithm, experimental analysis on publicly available 7 benchmark datasets are performed. Subsequently, experiments were conducted on a practical application case for wind speed prediction to expound the superiority of the proposed RBF training algorithm in terms of prediction accuracy. PMID:29768463

Training radial basis function networks for wind speed prediction using PSO enhanced differential search optimizer.

PubMed

Rani R, Hannah Jessie; Victoire T, Aruldoss Albert

2018-01-01

This paper presents an integrated hybrid optimization algorithm for training the radial basis function neural network (RBF NN). Training of neural networks is still a challenging exercise in machine learning domain. Traditional training algorithms in general suffer and trap in local optima and lead to premature convergence, which makes them ineffective when applied for datasets with diverse features. Training algorithms based on evolutionary computations are becoming popular due to their robust nature in overcoming the drawbacks of the traditional algorithms. Accordingly, this paper proposes a hybrid training procedure with differential search (DS) algorithm functionally integrated with the particle swarm optimization (PSO). To surmount the local trapping of the search procedure, a new population initialization scheme is proposed using Logistic chaotic sequence, which enhances the population diversity and aid the search capability. To demonstrate the effectiveness of the proposed RBF hybrid training algorithm, experimental analysis on publicly available 7 benchmark datasets are performed. Subsequently, experiments were conducted on a practical application case for wind speed prediction to expound the superiority of the proposed RBF training algorithm in terms of prediction accuracy.

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

2009-11-01

We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

First-Principles Momentum-Dependent Local Ansatz Wavefunction and Momentum Distribution Function Bands of Iron

NASA Astrophysics Data System (ADS)

Kakehashi, Yoshiro; Chandra, Sumal

2016-04-01

We have developed a first-principles local ansatz wavefunction approach with momentum-dependent variational parameters on the basis of the tight-binding LDA+U Hamiltonian. The theory goes beyond the first-principles Gutzwiller approach and quantitatively describes correlated electron systems. Using the theory, we find that the momentum distribution function (MDF) bands of paramagnetic bcc Fe along high-symmetry lines show a large deviation from the Fermi-Dirac function for the d electrons with eg symmetry and yield the momentum-dependent mass enhancement factors. The calculated average mass enhancement m*/m = 1.65 is consistent with low-temperature specific heat data as well as recent angle-resolved photoemission spectroscopy (ARPES) data.

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinski, Peter; Riplinger, Christoph; Neese, Frank, E-mail: evaleev@vt.edu, E-mail: frank.neese@cec.mpg.de

2015-07-21

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implementsmore » sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.« less

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals.

PubMed

Pinski, Peter; Riplinger, Christoph; Valeev, Edward F; Neese, Frank

2015-07-21

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implements sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.

Density functional theory calculations of the lowest energy quintet and triplet states of model hemes: role of functional, basis set, and zero-point energy corrections.

PubMed

Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman

2008-04-24

We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results insignificantly for iron(II) porphyrin coordinated with imidazole. Poor performance of a "locally dense" basis set with a large number of basis functions on the Fe center was observed in calculation of quintet-triplet gaps. Our results lead to a series of suggestions for density functional theory calculations of quintet-triplet energy gaps in ferrohemes with a single axial imidazole; these suggestions are potentially applicable for other transition-metal complexes.

Disorder enabled band structure engineering of a topological insulator surface

DOE PAGES

Xu, Yishuai; Chiu, Janet; Miao, Lin; ...

2017-02-03

Three-dimensional topological insulators are bulk insulators with Z 2 topological electronic order that gives rise to conducting light-like surface states. These surface electrons are exceptionally resistant to localization by non-magnetic disorder, and have been adopted as the basis for a wide range of proposals to achieve new quasiparticle species and device functionality. Recent studies have yielded a surprise by showing that in spite of resisting localization, topological insulator surface electrons can be reshaped by defects into distinctive resonance states. Here we use numerical simulations and scanning tunnelling microscopy data to show that these resonance states have significance well beyond themore » localized regime usually associated with impurity bands. Lastly, at native densities in the model Bi 2X 3 (X=Bi, Te) compounds, defect resonance states are predicted to generate a new quantum basis for an emergent electron gas that supports diffusive electrical transport.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liakh, Dmitry I

While the formalism of multiresolution analysis (MRA), based on wavelets and adaptive integral representations of operators, is actively progressing in electronic structure theory (mostly on the independent-particle level and, recently, second-order perturbation theory), the concepts of multiresolution and adaptivity can also be utilized within the traditional formulation of correlated (many-particle) theory which is based on second quantization and the corresponding (generally nonorthogonal) tensor algebra. In this paper, we present a formalism called scale-adaptive tensor algebra (SATA) which exploits an adaptive representation of tensors of many-body operators via the local adjustment of the basis set quality. Given a series of locallymore » supported fragment bases of a progressively lower quality, we formulate the explicit rules for tensor algebra operations dealing with adaptively resolved tensor operands. The formalism suggested is expected to enhance the applicability and reliability of local correlated many-body methods of electronic structure theory, especially those directly based on atomic orbitals (or any other localized basis functions).« less

Fast online generalized multiscale finite element method using constraint energy minimization

NASA Astrophysics Data System (ADS)

Chung, Eric T.; Efendiev, Yalchin; Leung, Wing Tat

2018-02-01

Local multiscale methods often construct multiscale basis functions in the offline stage without taking into account input parameters, such as source terms, boundary conditions, and so on. These basis functions are then used in the online stage with a specific input parameter to solve the global problem at a reduced computational cost. Recently, online approaches have been introduced, where multiscale basis functions are adaptively constructed in some regions to reduce the error significantly. In multiscale methods, it is desired to have only 1-2 iterations to reduce the error to a desired threshold. Using Generalized Multiscale Finite Element Framework [10], it was shown that by choosing sufficient number of offline basis functions, the error reduction can be made independent of physical parameters, such as scales and contrast. In this paper, our goal is to improve this. Using our recently proposed approach [4] and special online basis construction in oversampled regions, we show that the error reduction can be made sufficiently large by appropriately selecting oversampling regions. Our numerical results show that one can achieve a three order of magnitude error reduction, which is better than our previous methods. We also develop an adaptive algorithm and enrich in selected regions with large residuals. In our adaptive method, we show that the convergence rate can be determined by a user-defined parameter and we confirm this by numerical simulations. The analysis of the method is presented.

Ab initio calculations of optical properties of silver clusters: cross-over from molecular to nanoscale behavior

NASA Astrophysics Data System (ADS)

Titantah, John T.; Karttunen, Mikko

2016-05-01

Electronic and optical properties of silver clusters were calculated using two different ab initio approaches: (1) based on all-electron full-potential linearized-augmented plane-wave method and (2) local basis function pseudopotential approach. Agreement is found between the two methods for small and intermediate sized clusters for which the former method is limited due to its all-electron formulation. The latter, due to non-periodic boundary conditions, is the more natural approach to simulate small clusters. The effect of cluster size is then explored using the local basis function approach. We find that as the cluster size increases, the electronic structure undergoes a transition from molecular behavior to nanoparticle behavior at a cluster size of 140 atoms (diameter ~1.7 nm). Above this cluster size the step-like electronic structure, evident as several features in the imaginary part of the polarizability of all clusters smaller than Ag147, gives way to a dominant plasmon peak localized at wavelengths 350 nm ≤ λ ≤ 600 nm. It is, thus, at this length-scale that the conduction electrons' collective oscillations that are responsible for plasmonic resonances begin to dominate the opto-electronic properties of silver nanoclusters.

Cerebral localization in the nineteenth century--the birth of a science and its modern consequences.

PubMed

Steinberg, David A

2009-07-01

Although many individuals contributed to the development of the science of cerebral localization, its conceptual framework is the work of a single man--John Hughlings Jackson (1835-1911), a Victorian physician practicing in London. Hughlings Jackson's formulation of a neurological science consisted of an axiomatic basis, an experimental methodology, and a clinical neurophysiology. His axiom--that the brain is an exclusively sensorimotor machine--separated neurology from psychiatry and established a rigorous and sophisticated structure for the brain and mind. Hughlings Jackson's experimental method utilized the focal lesion as a probe of brain function and created an evolutionary structure of somatotopic representation to explain clinical neurophysiology. His scientific theory of cerebral localization can be described as a weighted ordinal representation. Hughlings Jackson's theory of weighted ordinal representation forms the scientific basis for modern neurology. Though this science is utilized daily by every neurologist and forms the basis of neuroscience, the consequences of Hughlings Jackson's ideas are still not generally appreciated. For example, they imply the intrinsic inconsistency of some modern fields of neuroscience and neurology. Thus, "cognitive imaging" and the "neurology of art"--two topics of modern interest--are fundamentally oxymoronic according to the science of cerebral localization. Neuroscientists, therefore, still have much to learn from John Hughlings Jackson.

Genetic effects on gene expression across human tissues

PubMed Central

2017-01-01

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease. PMID:29022597

Distributed wavefront reconstruction with SABRE for real-time large scale adaptive optics control

NASA Astrophysics Data System (ADS)

Brunner, Elisabeth; de Visser, Cornelis C.; Verhaegen, Michel

2014-08-01

We present advances on Spline based ABerration REconstruction (SABRE) from (Shack-)Hartmann (SH) wavefront measurements for large-scale adaptive optics systems. SABRE locally models the wavefront with simplex B-spline basis functions on triangular partitions which are defined on the SH subaperture array. This approach allows high accuracy through the possible use of nonlinear basis functions and great adaptability to any wavefront sensor and pupil geometry. The main contribution of this paper is a distributed wavefront reconstruction method, D-SABRE, which is a 2 stage procedure based on decomposing the sensor domain into sub-domains each supporting a local SABRE model. D-SABRE greatly decreases the computational complexity of the method and removes the need for centralized reconstruction while obtaining a reconstruction accuracy for simulated E-ELT turbulences within 1% of the global method's accuracy. Further, a generalization of the methodology is proposed making direct use of SH intensity measurements which leads to an improved accuracy of the reconstruction compared to centroid algorithms using spatial gradients.

Structural disorder within sendai virus nucleoprotein and phosphoprotein: insight into the structural basis of molecular recognition.

PubMed

Jensen, Malene Ringkjøbing; Bernadó, Pau; Houben, Klaartje; Blanchard, Laurence; Marion, Dominque; Ruigrok, Rob W H; Blackledge, Martin

2010-08-01

Intrinsically disordered regions of significant length are present throughout eukaryotic genomes, and are particularly prevalent in viral proteins. Due to their inherent flexibility, these proteins inhabit a conformational landscape that is too complex to be described by classical structural biology. The elucidation of the role that conformational flexibility plays in molecular function will redefine our understanding of the molecular basis of biological function, and the development of appropriate technology to achieve this aim remains one of the major challenges for the future of structural biology. NMR is the technique of choice for studying intrinsically disordered proteins, providing information about structure, flexibility and interactions at atomic resolution even in completely disordered proteins. In particular residual dipolar couplings (RDCs) are sensitive and powerful tools for determining local and long-range structural behaviour in flexible proteins. Here we describe recent applications of the use of RDCs to quantitatively describe the level of local structure in intrinsically disordered proteins involved in replication and transcription in Sendai virus.

Genetic effects on gene expression across human tissues.

PubMed

Battle, Alexis; Brown, Christopher D; Engelhardt, Barbara E; Montgomery, Stephen B

2017-10-11

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.

Communication: Practical and rigorous reduction of the many-electron quantum mechanical Coulomb problem to O(N{sup 2/3}) storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pederson, Mark R., E-mail: mark.pederson@science.doe.gov

2015-04-14

It is tacitly accepted that, for practical basis sets consisting of N functions, solution of the two-electron Coulomb problem in quantum mechanics requires storage of O(N{sup 4}) integrals in the small N limit. For localized functions, in the large N limit, or for planewaves, due to closure, the storage can be reduced to O(N{sup 2}) integrals. Here, it is shown that the storage can be further reduced to O(N{sup 2/3}) for separable basis functions. A practical algorithm, that uses standard one-dimensional Gaussian-quadrature sums, is demonstrated. The resulting algorithm allows for the simultaneous storage, or fast reconstruction, of any two-electron Coulombmore » integral required for a many-electron calculation on processors with limited memory and disk space. For example, for calculations involving a basis of 9171 planewaves, the memory required to effectively store all Coulomb integrals decreases from 2.8 Gbytes to less than 2.4 Mbytes.« less

High-resolution time-frequency representation of EEG data using multi-scale wavelets

NASA Astrophysics Data System (ADS)

Li, Yang; Cui, Wei-Gang; Luo, Mei-Lin; Li, Ke; Wang, Lina

2017-09-01

An efficient time-varying autoregressive (TVAR) modelling scheme that expands the time-varying parameters onto the multi-scale wavelet basis functions is presented for modelling nonstationary signals and with applications to time-frequency analysis (TFA) of electroencephalogram (EEG) signals. In the new parametric modelling framework, the time-dependent parameters of the TVAR model are locally represented by using a novel multi-scale wavelet decomposition scheme, which can allow the capability to capture the smooth trends as well as track the abrupt changes of time-varying parameters simultaneously. A forward orthogonal least square (FOLS) algorithm aided by mutual information criteria are then applied for sparse model term selection and parameter estimation. Two simulation examples illustrate that the performance of the proposed multi-scale wavelet basis functions outperforms the only single-scale wavelet basis functions or Kalman filter algorithm for many nonstationary processes. Furthermore, an application of the proposed method to a real EEG signal demonstrates the new approach can provide highly time-dependent spectral resolution capability.

Communication: practical and rigorous reduction of the many-electron quantum mechanical Coulomb problem to O(N(2/3)) storage.

PubMed

Pederson, Mark R

2015-04-14

It is tacitly accepted that, for practical basis sets consisting of N functions, solution of the two-electron Coulomb problem in quantum mechanics requires storage of O(N(4)) integrals in the small N limit. For localized functions, in the large N limit, or for planewaves, due to closure, the storage can be reduced to O(N(2)) integrals. Here, it is shown that the storage can be further reduced to O(N(2/3)) for separable basis functions. A practical algorithm, that uses standard one-dimensional Gaussian-quadrature sums, is demonstrated. The resulting algorithm allows for the simultaneous storage, or fast reconstruction, of any two-electron Coulomb integral required for a many-electron calculation on processors with limited memory and disk space. For example, for calculations involving a basis of 9171 planewaves, the memory required to effectively store all Coulomb integrals decreases from 2.8 Gbytes to less than 2.4 Mbytes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witte, Jonathon; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Neaton, Jeffrey B.

With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methodsmore » and systems examined, the most complete basis is Jensen’s pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.« less

The Physiological Basis for Thermal Comfort in Different Climates; a Preliminary Study (De fysiologische basis voor thermisch comfort onder diverse klimatologische omstandigheden; een voorstudie),

DTIC Science & Technology

1996-08-07

Thermal comfort is very important for optimal functioning of humans. It gives information about the thermal state of the body, by which the human...receptors and sending efferent information to the effectors by which the body controls its temperature. Thermal comfort is determined by the temperature...global thermal comfort are core temperature, temperature of the extremities and temperature of the environment. In local thermal comfort and pain

Functional imaging with low-resolution brain electromagnetic tomography (LORETA): a review.

PubMed

Pascual-Marqui, R D; Esslen, M; Kochi, K; Lehmann, D

2002-01-01

This paper reviews several recent publications that have successfully used the functional brain imaging method known as LORETA. Emphasis is placed on the electrophysiological and neuroanatomical basis of the method, on the localization properties of the method, and on the validation of the method in real experimental human data. Papers that criticize LORETA are briefly discussed. LORETA publications in the 1994-1997 period based localization inference on images of raw electric neuronal activity. In 1998, a series of papers appeared that based localization inference on the statistical parametric mapping methodology applied to high-time resolution LORETA images. Starting in 1999, quantitative neuroanatomy was added to the methodology, based on the digitized Talairach atlas provided by the Brain Imaging Centre, Montreal Neurological Institute. The combination of these methodological developments has placed LORETA at a level that compares favorably to the more classical functional imaging methods, such as PET and fMRI.

Earth Structure, Ice Mass Changes, and the Local Dynamic Geoid

NASA Astrophysics Data System (ADS)

Harig, C.; Simons, F. J.

2014-12-01

Spherical Slepian localization functions are a useful method for studying regional mass changes observed by satellite gravimetry. By projecting data onto a sparse basis set, the local field can be estimated more easily than with the full spherical harmonic basis. We have used this method previously to estimate the ice mass change in Greenland from GRACE data, and it can also be applied to other planetary problems such as global magnetic fields. Earth's static geoid, in contrast to the time-variable field, is in large part related to the internal density and rheological structure of the Earth. Past studies have used dynamic geoid kernels to relate this density structure and the internal deformation it induces to the surface geopotential at large scales. These now classical studies of the eighties and nineties were able to estimate the mantle's radial rheological profile, placing constraints on the ratio between upper and lower mantle viscosity. By combining these two methods, spherical Slepian localization and dynamic geoid kernels, we have created local dynamic geoid kernels which are sensitive only to density variations within an area of interest. With these kernels we can estimate the approximate local radial rheological structure that best explains the locally observed geoid on a regional basis. First-order differences of the regional mantle viscosity structure are accessible to this technique. In this contribution we present our latest, as yet unpublished results on the geographical and temporal pattern of ice mass changes in Antarctica over the past decade, and we introduce a new approach to extract regional information about the internal structure of the Earth from the static global gravity field. Both sets of results are linked in terms of the relevant physics, but also in being developed from the marriage of Slepian functions and geoid kernels. We make predictions on the utility of our approach to derive fully three-dimensional rheological Earth models, to be used for corrections for glacio-isostatic adjustment, as necessary for the interpretation of time-variable gravity observations in terms of ice sheet mass-balance studies.

Multivariate functional response regression, with application to fluorescence spectroscopy in a cervical pre-cancer study.

PubMed

Zhu, Hongxiao; Morris, Jeffrey S; Wei, Fengrong; Cox, Dennis D

2017-07-01

Many scientific studies measure different types of high-dimensional signals or images from the same subject, producing multivariate functional data. These functional measurements carry different types of information about the scientific process, and a joint analysis that integrates information across them may provide new insights into the underlying mechanism for the phenomenon under study. Motivated by fluorescence spectroscopy data in a cervical pre-cancer study, a multivariate functional response regression model is proposed, which treats multivariate functional observations as responses and a common set of covariates as predictors. This novel modeling framework simultaneously accounts for correlations between functional variables and potential multi-level structures in data that are induced by experimental design. The model is fitted by performing a two-stage linear transformation-a basis expansion to each functional variable followed by principal component analysis for the concatenated basis coefficients. This transformation effectively reduces the intra-and inter-function correlations and facilitates fast and convenient calculation. A fully Bayesian approach is adopted to sample the model parameters in the transformed space, and posterior inference is performed after inverse-transforming the regression coefficients back to the original data domain. The proposed approach produces functional tests that flag local regions on the functional effects, while controlling the overall experiment-wise error rate or false discovery rate. It also enables functional discriminant analysis through posterior predictive calculation. Analysis of the fluorescence spectroscopy data reveals local regions with differential expressions across the pre-cancer and normal samples. These regions may serve as biomarkers for prognosis and disease assessment.

Improved algorithms for the retrieval of the h2 Love number of Mercury from laser altimetry data

NASA Astrophysics Data System (ADS)

Thor, Robin; Kallenbach, Reinald; Christensen, Ulrich; Oberst, Jürgen; Stark, Alexander; Steinbrügge, Gregor

2017-04-01

We simulate measurements to be performed by the BepiColombo laser altimeter (BELA) aboard the Mercury Planetary Orbiter (MPO) of the BepiColombo mission and investigate whether coverage and accuracy will be sufficient to retrieve the h2 Love number of Mercury. The h2 Love number describes the tidal response of Mercury's surface and is a function of the materials in its interior and their properties and distribution. Therefore, it can serve as an important constraint for models of the internal structure. The tide-generating potential from the Sun causes periodic radial displacements of up to ˜2 m on Mercury which can be detected by laser altimetry. In this study, we simultaneously extract the static global shape, parametrized by local basis functions, and its variability in time. The usage of cubic splines as local basis functions in both longitudinal and latitudinal direction provides an improvement over the methodology of Koch et al. (2010, Planetary and Space Science, 58(14), 2022-2030) who used cubic splines in longitudinal direction, but only step functions in latitudinal direction. We achieve a relative 1σ accuracy of the h2 Love number of 1.7% assuming nominal data acquisition for BELA during a one-year mission, but considering only stochastic noise.

The physics of functional magnetic resonance imaging (fMRI)

NASA Astrophysics Data System (ADS)

Buxton, Richard B.

2013-09-01

Functional magnetic resonance imaging (fMRI) is a methodology for detecting dynamic patterns of activity in the working human brain. Although the initial discoveries that led to fMRI are only about 20 years old, this new field has revolutionized the study of brain function. The ability to detect changes in brain activity has a biophysical basis in the magnetic properties of deoxyhemoglobin, and a physiological basis in the way blood flow increases more than oxygen metabolism when local neural activity increases. These effects translate to a subtle increase in the local magnetic resonance signal, the blood oxygenation level dependent (BOLD) effect, when neural activity increases. With current techniques, this pattern of activation can be measured with resolution approaching 1 mm3 spatially and 1 s temporally. This review focuses on the physical basis of the BOLD effect, the imaging methods used to measure it, the possible origins of the physiological effects that produce a mismatch of blood flow and oxygen metabolism during neural activation, and the mathematical models that have been developed to understand the measured signals. An overarching theme is the growing field of quantitative fMRI, in which other MRI methods are combined with BOLD methods and analyzed within a theoretical modeling framework to derive quantitative estimates of oxygen metabolism and other physiological variables. That goal is the current challenge for fMRI: to move fMRI from a mapping tool to a quantitative probe of brain physiology.

The physics of functional magnetic resonance imaging (fMRI)

PubMed Central

Buxton, Richard B

2015-01-01

Functional magnetic resonance imaging (fMRI) is a methodology for detecting dynamic patterns of activity in the working human brain. Although the initial discoveries that led to fMRI are only about 20 years old, this new field has revolutionized the study of brain function. The ability to detect changes in brain activity has a biophysical basis in the magnetic properties of deoxyhemoglobin, and a physiological basis in the way blood flow increases more than oxygen metabolism when local neural activity increases. These effects translate to a subtle increase in the local magnetic resonance signal, the blood oxygenation level dependent (BOLD) effect, when neural activity increases. With current techniques, this pattern of activation can be measured with resolution approaching 1 mm3 spatially and 1 s temporally. This review focuses on the physical basis of the BOLD effect, the imaging methods used to measure it, the possible origins of the physiological effects that produce a mismatch of blood flow and oxygen metabolism during neural activation, and the mathematical models that have been developed to understand the measured signals. An overarching theme is the growing field of quantitative fMRI, in which other MRI methods are combined with BOLD methods and analyzed within a theoretical modeling framework to derive quantitative estimates of oxygen metabolism and other physiological variables. That goal is the current challenge for fMRI: to move fMRI from a mapping tool to a quantitative probe of brain physiology. PMID:24006360

The physics of functional magnetic resonance imaging (fMRI).

PubMed

Buxton, Richard B

2013-09-01

Functional magnetic resonance imaging (fMRI) is a methodology for detecting dynamic patterns of activity in the working human brain. Although the initial discoveries that led to fMRI are only about 20 years old, this new field has revolutionized the study of brain function. The ability to detect changes in brain activity has a biophysical basis in the magnetic properties of deoxyhemoglobin, and a physiological basis in the way blood flow increases more than oxygen metabolism when local neural activity increases. These effects translate to a subtle increase in the local magnetic resonance signal, the blood oxygenation level dependent (BOLD) effect, when neural activity increases. With current techniques, this pattern of activation can be measured with resolution approaching 1 mm(3) spatially and 1 s temporally. This review focuses on the physical basis of the BOLD effect, the imaging methods used to measure it, the possible origins of the physiological effects that produce a mismatch of blood flow and oxygen metabolism during neural activation, and the mathematical models that have been developed to understand the measured signals. An overarching theme is the growing field of quantitative fMRI, in which other MRI methods are combined with BOLD methods and analyzed within a theoretical modeling framework to derive quantitative estimates of oxygen metabolism and other physiological variables. That goal is the current challenge for fMRI: to move fMRI from a mapping tool to a quantitative probe of brain physiology.

Model's sparse representation based on reduced mixed GMsFE basis methods

NASA Astrophysics Data System (ADS)

Jiang, Lijian; Li, Qiuqi

2017-06-01

In this paper, we propose a model's sparse representation based on reduced mixed generalized multiscale finite element (GMsFE) basis methods for elliptic PDEs with random inputs. A typical application for the elliptic PDEs is the flow in heterogeneous random porous media. Mixed generalized multiscale finite element method (GMsFEM) is one of the accurate and efficient approaches to solve the flow problem in a coarse grid and obtain the velocity with local mass conservation. When the inputs of the PDEs are parameterized by the random variables, the GMsFE basis functions usually depend on the random parameters. This leads to a large number degree of freedoms for the mixed GMsFEM and substantially impacts on the computation efficiency. In order to overcome the difficulty, we develop reduced mixed GMsFE basis methods such that the multiscale basis functions are independent of the random parameters and span a low-dimensional space. To this end, a greedy algorithm is used to find a set of optimal samples from a training set scattered in the parameter space. Reduced mixed GMsFE basis functions are constructed based on the optimal samples using two optimal sampling strategies: basis-oriented cross-validation and proper orthogonal decomposition. Although the dimension of the space spanned by the reduced mixed GMsFE basis functions is much smaller than the dimension of the original full order model, the online computation still depends on the number of coarse degree of freedoms. To significantly improve the online computation, we integrate the reduced mixed GMsFE basis methods with sparse tensor approximation and obtain a sparse representation for the model's outputs. The sparse representation is very efficient for evaluating the model's outputs for many instances of parameters. To illustrate the efficacy of the proposed methods, we present a few numerical examples for elliptic PDEs with multiscale and random inputs. In particular, a two-phase flow model in random porous media is simulated by the proposed sparse representation method.

Model's sparse representation based on reduced mixed GMsFE basis methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Lijian, E-mail: ljjiang@hnu.edu.cn; Li, Qiuqi, E-mail: qiuqili@hnu.edu.cn

2017-06-01

In this paper, we propose a model's sparse representation based on reduced mixed generalized multiscale finite element (GMsFE) basis methods for elliptic PDEs with random inputs. A typical application for the elliptic PDEs is the flow in heterogeneous random porous media. Mixed generalized multiscale finite element method (GMsFEM) is one of the accurate and efficient approaches to solve the flow problem in a coarse grid and obtain the velocity with local mass conservation. When the inputs of the PDEs are parameterized by the random variables, the GMsFE basis functions usually depend on the random parameters. This leads to a largemore » number degree of freedoms for the mixed GMsFEM and substantially impacts on the computation efficiency. In order to overcome the difficulty, we develop reduced mixed GMsFE basis methods such that the multiscale basis functions are independent of the random parameters and span a low-dimensional space. To this end, a greedy algorithm is used to find a set of optimal samples from a training set scattered in the parameter space. Reduced mixed GMsFE basis functions are constructed based on the optimal samples using two optimal sampling strategies: basis-oriented cross-validation and proper orthogonal decomposition. Although the dimension of the space spanned by the reduced mixed GMsFE basis functions is much smaller than the dimension of the original full order model, the online computation still depends on the number of coarse degree of freedoms. To significantly improve the online computation, we integrate the reduced mixed GMsFE basis methods with sparse tensor approximation and obtain a sparse representation for the model's outputs. The sparse representation is very efficient for evaluating the model's outputs for many instances of parameters. To illustrate the efficacy of the proposed methods, we present a few numerical examples for elliptic PDEs with multiscale and random inputs. In particular, a two-phase flow model in random porous media is simulated by the proposed sparse representation method.« less

The Brainomics/Localizer database.

PubMed

Papadopoulos Orfanos, Dimitri; Michel, Vincent; Schwartz, Yannick; Pinel, Philippe; Moreno, Antonio; Le Bihan, Denis; Frouin, Vincent

2017-01-01

The Brainomics/Localizer database exposes part of the data collected by the in-house Localizer project, which planned to acquire four types of data from volunteer research subjects: anatomical MRI scans, functional MRI data, behavioral and demographic data, and DNA sampling. Over the years, this local project has been collecting such data from hundreds of subjects. We had selected 94 of these subjects for their complete datasets, including all four types of data, as the basis for a prior publication; the Brainomics/Localizer database publishes the data associated with these 94 subjects. Since regulatory rules prevent us from making genetic data available for download, the database serves only anatomical MRI scans, functional MRI data, behavioral and demographic data. To publish this set of heterogeneous data, we use dedicated software based on the open-source CubicWeb semantic web framework. Through genericity in the data model and flexibility in the display of data (web pages, CSV, JSON, XML), CubicWeb helps us expose these complex datasets in original and efficient ways. Copyright © 2015 Elsevier Inc. All rights reserved.

Wavelets in electronic structure calculations

NASA Astrophysics Data System (ADS)

Modisette, Jason Perry

1997-09-01

Ab initio calculations of the electronic structure of bulk materials and large clusters are not possible on today's computers using current techniques. The storage and diagonalization of the Hamiltonian matrix are the limiting factors in both memory and execution time. The scaling of both quantities with problem size can be reduced by using approximate diagonalization or direct minimization of the total energy with respect to the density matrix in conjunction with a localized basis. Wavelet basis members are much more localized than conventional bases such as Gaussians or numerical atomic orbitals. This localization leads to sparse matrices of the operators that arise in SCF multi-electron calculations. We have investigated the construction of the one-electron Hamiltonian, and also the effective one- electron Hamiltonians that appear in density-functional and Hartree-Fock theories. We develop efficient methods for the generation of the kinetic energy and potential matrices, the Hartree and exchange potentials, and the local exchange-correlation potential of the LDA. Test calculations are performed on one-electron problems with a variety of potentials in one and three dimensions.

Spherical space Bessel-Legendre-Fourier localized modes solver for electromagnetic waves.

PubMed

Alzahrani, Mohammed A; Gauthier, Robert C

2015-10-05

Maxwell's vector wave equations are solved for dielectric configurations that match the symmetry of a spherical computational domain. The electric or magnetic field components and the inverse of the dielectric profile are series expansion defined using basis functions composed of the lowest order spherical Bessel function, polar angle single index dependant Legendre polynomials and azimuthal complex exponential (BLF). The series expressions and non-traditional form of the basis functions result in an eigenvalue matrix formulation of Maxwell's equations that are relatively compact and accurately solvable on a desktop PC. The BLF matrix returns the frequencies and field profiles for steady states modes. The key steps leading to the matrix populating expressions are provided. The validity of the numerical technique is confirmed by comparing the results of computations to those published using complementary techniques.

Chebyshev polynomial filtered subspace iteration in the discontinuous Galerkin method for large-scale electronic structure calculations

DOE PAGES

Banerjee, Amartya S.; Lin, Lin; Hu, Wei; ...

2016-10-21

The Discontinuous Galerkin (DG) electronic structure method employs an adaptive local basis (ALB) set to solve the Kohn-Sham equations of density functional theory in a discontinuous Galerkin framework. The adaptive local basis is generated on-the-fly to capture the local material physics and can systematically attain chemical accuracy with only a few tens of degrees of freedom per atom. A central issue for large-scale calculations, however, is the computation of the electron density (and subsequently, ground state properties) from the discretized Hamiltonian in an efficient and scalable manner. We show in this work how Chebyshev polynomial filtered subspace iteration (CheFSI) canmore » be used to address this issue and push the envelope in large-scale materials simulations in a discontinuous Galerkin framework. We describe how the subspace filtering steps can be performed in an efficient and scalable manner using a two-dimensional parallelization scheme, thanks to the orthogonality of the DG basis set and block-sparse structure of the DG Hamiltonian matrix. The on-the-fly nature of the ALB functions requires additional care in carrying out the subspace iterations. We demonstrate the parallel scalability of the DG-CheFSI approach in calculations of large-scale twodimensional graphene sheets and bulk three-dimensional lithium-ion electrolyte systems. In conclusion, employing 55 296 computational cores, the time per self-consistent field iteration for a sample of the bulk 3D electrolyte containing 8586 atoms is 90 s, and the time for a graphene sheet containing 11 520 atoms is 75 s.« less

Analysis of Multi-Scale Phenomena in Heterogeneous Materials

DTIC Science & Technology

2011-02-22

requires the use of properties of the Catalan numbers to show that the series coefficients are exponentially bounded in the H1 Sobolev norm. This is joint...the use of a small number of optimal local basis functions. The local bases are supported on sub domains of fixed diameter within the computa- tional...not display a currently valid OMB control number . 1. REPORT DATE 22 FEB 2011 2. REPORT TYPE FINAL REPORT 3. DATES COVERED 03-01-2008 to 03-03

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindgren, Ingvar; Salomonson, Sten

The locality theorem in density-functional theory (DFT) states that the functional derivative of the Hohenberg-Kohn universal functional can be expressed as a local multiplicative potential function, and this is the basis of DFT and of the successful Kohn-Sham model. Nesbet has in several papers [Phys. Rev. A 58, R12 (1998); ibid.65, 010502 (2001); Adv. Quant. Chem, 43, 1 (2003)] claimed that this theorem is in conflict with fundamental quantum physics, and as a consequence that the Hohenberg-Kohn theory cannot be generally valid. We have commented upon these works [Comment, Phys. Rev. A 67, 056501 (2003)] and recently extended the argumentsmore » [Adv. Quantum Chem. 43, 95 (2003)]. We have shown that there is no such conflict and that the locality theorem is inherently exact. In the present work we have furthermore verified this numerically by constructing a local Kohn-Sham potential for the 1s2s{sup 3}S state of helium that generates the many-body electron density and shown that the corresponding 2s Kohn-Sham orbital eigenvalue agrees with the ionization energy to nine digits. Similar result is obtained with the Hartree-Fock density. Therefore, in addition to verifying the locality theorem, this result also confirms the so-called ionization-potential theorem.« less

Many-body calculations with deuteron based single-particle bases and their associated natural orbits

NASA Astrophysics Data System (ADS)

Puddu, G.

2018-06-01

We use the recently introduced single-particle states obtained from localized deuteron wave-functions as a basis for nuclear many-body calculations. We show that energies can be substantially lowered if the natural orbits (NOs) obtained from this basis are used. We use this modified basis for {}10{{B}}, {}16{{O}} and {}24{{Mg}} employing the bare NNLOopt nucleon–nucleon interaction. The lowering of the energies increases with the mass. Although in principle NOs require a full scale preliminary many-body calculation, we found that an approximate preliminary many-body calculation, with a marginal increase in the computational cost, is sufficient. The use of natural orbits based on an harmonic oscillator basis leads to a much smaller lowering of the energies for a comparable computational cost.

A weak Galerkin generalized multiscale finite element method

DOE PAGES

Mu, Lin; Wang, Junping; Ye, Xiu

2016-03-31

In this study, we propose a general framework for weak Galerkin generalized multiscale (WG-GMS) finite element method for the elliptic problems with rapidly oscillating or high contrast coefficients. This general WG-GMS method features in high order accuracy on general meshes and can work with multiscale basis derived by different numerical schemes. A special case is studied under this WG-GMS framework in which the multiscale basis functions are obtained by solving local problem with the weak Galerkin finite element method. Convergence analysis and numerical experiments are obtained for the special case.

A weak Galerkin generalized multiscale finite element method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mu, Lin; Wang, Junping; Ye, Xiu

In this study, we propose a general framework for weak Galerkin generalized multiscale (WG-GMS) finite element method for the elliptic problems with rapidly oscillating or high contrast coefficients. This general WG-GMS method features in high order accuracy on general meshes and can work with multiscale basis derived by different numerical schemes. A special case is studied under this WG-GMS framework in which the multiscale basis functions are obtained by solving local problem with the weak Galerkin finite element method. Convergence analysis and numerical experiments are obtained for the special case.

Orbital dependent functionals: An atom projector augmented wave method implementation

NASA Astrophysics Data System (ADS)

Xu, Xiao

This thesis explores the formulation and numerical implementation of orbital dependent exchange-correlation functionals within electronic structure calculations. These orbital-dependent exchange-correlation functionals have recently received renewed attention as a means to improve the physical representation of electron interactions within electronic structure calculations. In particular, electron self-interaction terms can be avoided. In this thesis, an orbital-dependent functional is considered in the context of Hartree-Fock (HF) theory as well as the Optimized Effective Potential (OEP) method and the approximate OEP method developed by Krieger, Li, and Iafrate, known as the KLI approximation. In this thesis, the Fock exchange term is used as a simple well-defined example of an orbital-dependent functional. The Projected Augmented Wave (PAW) method developed by P. E. Blochl has proven to be accurate and efficient for electronic structure calculations for local and semi-local functions because of its accurate evaluation of interaction integrals by controlling multiple moments. We have extended the PAW method to treat orbital-dependent functionals in Hartree-Fock theory and the Optimized Effective Potential method, particularly in the KLI approximation. In the course of study we develop a frozen-core orbital approximation that accurately treats the core electron contributions for above three methods. The main part of the thesis focuses on the treatment of spherical atoms. We have investigated the behavior of PAW-Hartree Fock and PAW-KLI basis, projector, and pseudopotential functions for several elements throughout the periodic table. We have also extended the formalism to the treatment of solids in a plane wave basis and implemented PWPAW-KLI code, which will appear in future publications.

Fast and accurate 3D tensor calculation of the Fock operator in a general basis

NASA Astrophysics Data System (ADS)

Khoromskaia, V.; Andrae, D.; Khoromskij, B. N.

2012-11-01

The present paper contributes to the construction of a “black-box” 3D solver for the Hartree-Fock equation by the grid-based tensor-structured methods. It focuses on the calculation of the Galerkin matrices for the Laplace and the nuclear potential operators by tensor operations using the generic set of basis functions with low separation rank, discretized on a fine N×N×N Cartesian grid. We prove the Ch2 error estimate in terms of mesh parameter, h=O(1/N), that allows to gain a guaranteed accuracy of the core Hamiltonian part in the Fock operator as h→0. However, the commonly used problem adapted basis functions have low regularity yielding a considerable increase of the constant C, hence, demanding a rather large grid-size N of about several tens of thousands to ensure the high resolution. Modern tensor-formatted arithmetics of complexity O(N), or even O(logN), practically relaxes the limitations on the grid-size. Our tensor-based approach allows to improve significantly the standard basis sets in quantum chemistry by including simple combinations of Slater-type, local finite element and other basis functions. Numerical experiments for moderate size organic molecules show efficiency and accuracy of grid-based calculations to the core Hamiltonian in the range of grid parameter N3˜1015.

Fast evaluation of solid harmonic Gaussian integrals for local resolution-of-the-identity methods and range-separated hybrid functionals.

PubMed

Golze, Dorothea; Benedikter, Niels; Iannuzzi, Marcella; Wilhelm, Jan; Hutter, Jürg

2017-01-21

An integral scheme for the efficient evaluation of two-center integrals over contracted solid harmonic Gaussian functions is presented. Integral expressions are derived for local operators that depend on the position vector of one of the two Gaussian centers. These expressions are then used to derive the formula for three-index overlap integrals where two of the three Gaussians are located at the same center. The efficient evaluation of the latter is essential for local resolution-of-the-identity techniques that employ an overlap metric. We compare the performance of our integral scheme to the widely used Cartesian Gaussian-based method of Obara and Saika (OS). Non-local interaction potentials such as standard Coulomb, modified Coulomb, and Gaussian-type operators, which occur in range-separated hybrid functionals, are also included in the performance tests. The speed-up with respect to the OS scheme is up to three orders of magnitude for both integrals and their derivatives. In particular, our method is increasingly efficient for large angular momenta and highly contracted basis sets.

Fast evaluation of solid harmonic Gaussian integrals for local resolution-of-the-identity methods and range-separated hybrid functionals

NASA Astrophysics Data System (ADS)

Golze, Dorothea; Benedikter, Niels; Iannuzzi, Marcella; Wilhelm, Jan; Hutter, Jürg

2017-01-01

An integral scheme for the efficient evaluation of two-center integrals over contracted solid harmonic Gaussian functions is presented. Integral expressions are derived for local operators that depend on the position vector of one of the two Gaussian centers. These expressions are then used to derive the formula for three-index overlap integrals where two of the three Gaussians are located at the same center. The efficient evaluation of the latter is essential for local resolution-of-the-identity techniques that employ an overlap metric. We compare the performance of our integral scheme to the widely used Cartesian Gaussian-based method of Obara and Saika (OS). Non-local interaction potentials such as standard Coulomb, modified Coulomb, and Gaussian-type operators, which occur in range-separated hybrid functionals, are also included in the performance tests. The speed-up with respect to the OS scheme is up to three orders of magnitude for both integrals and their derivatives. In particular, our method is increasingly efficient for large angular momenta and highly contracted basis sets.

An orthogonal oriented quadrature hexagonal image pyramid

NASA Technical Reports Server (NTRS)

Watson, Andrew B.; Ahumada, Albert J., Jr.

1987-01-01

An image pyramid has been developed with basis functions that are orthogonal, self-similar, and localized in space, spatial frequency, orientation, and phase. The pyramid operates on a hexagonal sample lattice. The set of seven basis functions consist of three even high-pass kernels, three odd high-pass kernels, and one low-pass kernel. The three even kernels are identified when rotated by 60 or 120 deg, and likewise for the odd. The seven basis functions occupy a point and a hexagon of six nearest neighbors on a hexagonal sample lattice. At the lowest level of the pyramid, the input lattice is the image sample lattice. At each higher level, the input lattice is provided by the low-pass coefficients computed at the previous level. At each level, the output is subsampled in such a way as to yield a new hexagonal lattice with a spacing sq rt 7 larger than the previous level, so that the number of coefficients is reduced by a factor of 7 at each level. The relationship between this image code and the processing architecture of the primate visual cortex is discussed.

Feature extraction across individual time series observations with spikes using wavelet principal component analysis.

PubMed

Røislien, Jo; Winje, Brita

2013-09-20

Clinical studies frequently include repeated measurements of individuals, often for long periods. We present a methodology for extracting common temporal features across a set of individual time series observations. In particular, the methodology explores extreme observations within the time series, such as spikes, as a possible common temporal phenomenon. Wavelet basis functions are attractive in this sense, as they are localized in both time and frequency domains simultaneously, allowing for localized feature extraction from a time-varying signal. We apply wavelet basis function decomposition of individual time series, with corresponding wavelet shrinkage to remove noise. We then extract common temporal features using linear principal component analysis on the wavelet coefficients, before inverse transformation back to the time domain for clinical interpretation. We demonstrate the methodology on a subset of a large fetal activity study aiming to identify temporal patterns in fetal movement (FM) count data in order to explore formal FM counting as a screening tool for identifying fetal compromise and thus preventing adverse birth outcomes. Copyright © 2013 John Wiley & Sons, Ltd.

Exploring biorthonormal transformations of pair-correlation functions in atomic structure variational calculations

NASA Astrophysics Data System (ADS)

Verdebout, S.; Jönsson, P.; Gaigalas, G.; Godefroid, M.; Froese Fischer, C.

2010-04-01

Multiconfiguration expansions frequently target valence correlation and correlation between valence electrons and the outermost core electrons. Correlation within the core is often neglected. A large orbital basis is needed to saturate both the valence and core-valence correlation effects. This in turn leads to huge numbers of configuration state functions (CSFs), many of which are unimportant. To avoid the problems inherent to the use of a single common orthonormal orbital basis for all correlation effects in the multiconfiguration Hartree-Fock (MCHF) method, we propose to optimize independent MCHF pair-correlation functions (PCFs), bringing their own orthonormal one-electron basis. Each PCF is generated by allowing single- and double-excitations from a multireference (MR) function. This computational scheme has the advantage of using targeted and optimally localized orbital sets for each PCF. These pair-correlation functions are coupled together and with each component of the MR space through a low dimension generalized eigenvalue problem. Nonorthogonal orbital sets being involved, the interaction and overlap matrices are built using biorthonormal transformation of the coupled basis sets followed by a counter-transformation of the PCF expansions. Applied to the ground state of beryllium, the new method gives total energies that are lower than the ones from traditional complete active space (CAS)-MCHF calculations using large orbital active sets. It is fair to say that we now have the possibility to account for, in a balanced way, correlation deep down in the atomic core in variational calculations.

The advantage of flexible neuronal tunings in neural network models for motor learning

PubMed Central

Marongelli, Ellisha N.; Thoroughman, Kurt A.

2013-01-01

Human motor adaptation to novel environments is often modeled by a basis function network that transforms desired movement properties into estimated forces. This network employs a layer of nodes that have fixed broad tunings that generalize across the input domain. Learning is achieved by updating the weights of these nodes in response to training experience. This conventional model is unable to account for rapid flexibility observed in human spatial generalization during motor adaptation. However, added plasticity in the widths of the basis function tunings can achieve this flexibility, and several neurophysiological experiments have revealed flexibility in tunings of sensorimotor neurons. We found a model, Locally Weighted Projection Regression (LWPR), which uniquely possesses the structure of a basis function network in which both the weights and tuning widths of the nodes are updated incrementally during adaptation. We presented this LWPR model with training functions of different spatial complexities and monitored incremental updates to receptive field widths. An inverse pattern of dependence of receptive field adaptation on experienced error became evident, underlying both a relationship between generalization and complexity, and a unique behavior in which generalization always narrows after a sudden switch in environmental complexity. These results implicate a model that is flexible in both basis function widths and weights, like LWPR, as a viable alternative model for human motor adaptation that can account for previously observed plasticity in spatial generalization. This theory can be tested by using the behaviors observed in our experiments as novel hypotheses in human studies. PMID:23888141

Mixed kernel function support vector regression for global sensitivity analysis

NASA Astrophysics Data System (ADS)

Cheng, Kai; Lu, Zhenzhou; Wei, Yuhao; Shi, Yan; Zhou, Yicheng

2017-11-01

Global sensitivity analysis (GSA) plays an important role in exploring the respective effects of input variables on an assigned output response. Amongst the wide sensitivity analyses in literature, the Sobol indices have attracted much attention since they can provide accurate information for most models. In this paper, a mixed kernel function (MKF) based support vector regression (SVR) model is employed to evaluate the Sobol indices at low computational cost. By the proposed derivation, the estimation of the Sobol indices can be obtained by post-processing the coefficients of the SVR meta-model. The MKF is constituted by the orthogonal polynomials kernel function and Gaussian radial basis kernel function, thus the MKF possesses both the global characteristic advantage of the polynomials kernel function and the local characteristic advantage of the Gaussian radial basis kernel function. The proposed approach is suitable for high-dimensional and non-linear problems. Performance of the proposed approach is validated by various analytical functions and compared with the popular polynomial chaos expansion (PCE). Results demonstrate that the proposed approach is an efficient method for global sensitivity analysis.

[Cardiac myxoma -- the influence of preoperative clinical presentation and surgical technique on late outcome].

PubMed

Mikić, Aleksandar; Obrenović-Krcanski, Bilijana; Kocica, Mladen; Vranes, Mile; Lacković, Vesna; Velinović, Milos; Miarković, Miroslav; Kovacević, Natasa; Djukić, Petar

2007-01-01

Cardiac myxomas are the most frequent primary tumours of the heart in adults, and they can be found in each of four cardiac chambers. Although biologically benign, due to their unfavourable localization, myxomas are considered "functionally malignant" tumours. Diagnosis of cardiac myxoma necessitates surgical treatment. To analyse: 1) the influence of localization, size and consistency of cardiac myxomas on preoperative symptomatology; 2) the influence of different surgical techniques (left, right, biatrial approach, tumour basis solving) on early, and late outcomes. From 1982 to 2000, at the Institute for Cardiovascular Diseases, Clinical Centre of Serbia, there were 46 patients with cardiac myxomas operated on, 67.4% of them women, mean age 47.1 +/- 16.3 years. The diagnosis was made according to clinical presentation, electrocardiographic and echocardiographic examinations and cardiac catheterization. Follow-up period was 4-18 (mean 7.8) years. In 41 (89.1%) patients, myxoma was localized in the left, while in 5 (10.9%), it was found in the right atrium. Average size was 5.8 x 3.8 cm (range: 1 x l cm to 9 x 8 cm) and 6 x 4 cm (range: 3 x 2 cm to 9 x 5 cm) for the left and right atrial myxomas, respectively. A racemous form predominated in the left (82.6%) and globous in the right (80%) atrium. Fatigue was the most common general (84.8%) and dyspnoea the most common cardiologic symptom (73.9%). Preoperative embolic events were present in 8 patients (4 pulmonary, 4 systemic). In our series: 1) different localization, size and consistency had no influence on the preoperative symptomatology; 2) surgical treatment applied, regardless of different approaches and basis solving, resulted in excellent functional improvements (63.1% patients in NYHA III and IV class preoperatively vs. 6.7% patients postoperatively) and had no influence on new postoperative rhythm disturbances (8.7% patients preoperatively vs. 24.4% patients postoperatively); 3) early (97.8%), and late survival rates (91.3%) were excellent; 4) there were no relapses during the follow-up period. Localization, size and consistency had no influence on the preoperative symptomatology. Excellent survival rate with significant functional improvement, rare postoperative complications and no recurrences, justify the applied strategies of surgical approach and tumour basis solving in our series.

Estimation and Application of Ecological Memory Functions in Time and Space

NASA Astrophysics Data System (ADS)

Itter, M.; Finley, A. O.; Dawson, A.

2017-12-01

A common goal in quantitative ecology is the estimation or prediction of ecological processes as a function of explanatory variables (or covariates). Frequently, the ecological process of interest and associated covariates vary in time, space, or both. Theory indicates many ecological processes exhibit memory to local, past conditions. Despite such theoretical understanding, few methods exist to integrate observations from the recent past or within a local neighborhood as drivers of these processes. We build upon recent methodological advances in ecology and spatial statistics to develop a Bayesian hierarchical framework to estimate so-called ecological memory functions; that is, weight-generating functions that specify the relative importance of local, past covariate observations to ecological processes. Memory functions are estimated using a set of basis functions in time and/or space, allowing for flexible ecological memory based on a reduced set of parameters. Ecological memory functions are entirely data driven under the Bayesian hierarchical framework—no a priori assumptions are made regarding functional forms. Memory function uncertainty follows directly from posterior distributions for model parameters allowing for tractable propagation of error to predictions of ecological processes. We apply the model framework to simulated spatio-temporal datasets generated using memory functions of varying complexity. The framework is also applied to estimate the ecological memory of annual boreal forest growth to local, past water availability. Consistent with ecological understanding of boreal forest growth dynamics, memory to past water availability peaks in the year previous to growth and slowly decays to zero in five to eight years. The Bayesian hierarchical framework has applicability to a broad range of ecosystems and processes allowing for increased understanding of ecosystem responses to local and past conditions and improved prediction of ecological processes.

Neuron hemilineages provide the functional ground plan for the Drosophila ventral nervous system

PubMed Central

Harris, Robin M; Pfeiffer, Barret D; Rubin, Gerald M; Truman, James W

2015-01-01

Drosophila central neurons arise from neuroblasts that generate neurons in a pair-wise fashion, with the two daughters providing the basis for distinct A and B hemilineage groups. 33 postembryonically-born hemilineages contribute over 90% of the neurons in each thoracic hemisegment. We devised genetic approaches to define the anatomy of most of these hemilineages and to assessed their functional roles using the heat-sensitive channel dTRPA1. The simplest hemilineages contained local interneurons and their activation caused tonic or phasic leg movements lacking interlimb coordination. The next level was hemilineages of similar projection cells that drove intersegmentally coordinated behaviors such as walking. The highest level involved hemilineages whose activation elicited complex behaviors such as takeoff. These activation phenotypes indicate that the hemilineages vary in their behavioral roles with some contributing to local networks for sensorimotor processing and others having higher order functions of coordinating these local networks into complex behavior. DOI: http://dx.doi.org/10.7554/eLife.04493.001 PMID:26193122

Imaging of the outer valence orbitals of CO by electron momentum spectroscopy — Comparison with high level MRSD-CI and DFT calculations

NASA Astrophysics Data System (ADS)

Fan, X. W.; Chen, X. J.; Zhou, S. J.; Zheng, Y.; Brion, C. E.; Frey, R.; Davidson, E. R.

1997-09-01

A newly constructed energy dispersive multichannel electron momentum spectrometer has been used to image the electron density of the outer valence orbitals of CO with high precision. Binding energy spectra are obtained at a coincidence energy resolution of 1.2 eV fwhm. The measured electron density profiles in momentum space for the outer valence orbitals of CO are compared with cross sections calculated using SCF wavefunctions with basis sets of varying complexity up to near-Hartree-Fock limit in quality. The effects of correlation and electronic relaxation on the calculated momentum profiles are investigated using large MRSD-CI calculations of the full ion-neutral overlap distributions, as well as large basis set DFT calculations with local and non-local (gradient corrected) functionals.

Hybrid preconditioning for iterative diagonalization of ill-conditioned generalized eigenvalue problems in electronic structure calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Yunfeng, E-mail: yfcai@math.pku.edu.cn; Department of Computer Science, University of California, Davis 95616; Bai, Zhaojun, E-mail: bai@cs.ucdavis.edu

2013-12-15

The iterative diagonalization of a sequence of large ill-conditioned generalized eigenvalue problems is a computational bottleneck in quantum mechanical methods employing a nonorthogonal basis for ab initio electronic structure calculations. We propose a hybrid preconditioning scheme to effectively combine global and locally accelerated preconditioners for rapid iterative diagonalization of such eigenvalue problems. In partition-of-unity finite-element (PUFE) pseudopotential density-functional calculations, employing a nonorthogonal basis, we show that the hybrid preconditioned block steepest descent method is a cost-effective eigensolver, outperforming current state-of-the-art global preconditioning schemes, and comparably efficient for the ill-conditioned generalized eigenvalue problems produced by PUFE as the locally optimal blockmore » preconditioned conjugate-gradient method for the well-conditioned standard eigenvalue problems produced by planewave methods.« less

Block-localized wavefunction (BLW) method at the density functional theory (DFT) level.

PubMed

Mo, Yirong; Song, Lingchun; Lin, Yuchun

2007-08-30

The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method incorporating the efficiency of molecular orbital (MO) theory. It can generate the wavefunction for a resonance structure or diabatic state self-consistently by partitioning the overall electrons and primitive orbitals into several subgroups and expanding each block-localized molecular orbital in only one subspace. Although block-localized molecular orbitals in the same subspace are constrained to be orthogonal (a feature of MO theory), orbitals between different subspaces are generally nonorthogonal (a feature of VB theory). The BLW method is particularly useful in the quantification of the electron delocalization (resonance) effect within a molecule and the charge-transfer effect between molecules. In this paper, we extend the BLW method to the density functional theory (DFT) level and implement the BLW-DFT method to the quantum mechanical software GAMESS. Test applications to the pi conjugation in the planar allyl radical and ions with the basis sets of 6-31G(d), 6-31+G(d), 6-311+G(d,p), and cc-pVTZ show that the basis set dependency is insignificant. In addition, the BLW-DFT method can also be used to elucidate the nature of intermolecular interactions. Examples of pi-cation interactions and solute-solvent interactions will be presented and discussed. By expressing each diabatic state with one BLW, the BLW method can be further used to study chemical reactions and electron-transfer processes whose potential energy surfaces are typically described by two or more diabatic states.

Inhibition of quantum transport due to 'scars' of unstable periodic orbits

NASA Technical Reports Server (NTRS)

Jensen, R. V.; Sanders, M. M.; Saraceno, M.; Sundaram, B.

1989-01-01

A new quantum mechanism for the suppression of chaotic ionization of highly excited hydrogen atoms explains the appearance of anomalously stable states in the microwave ionization experiments of Koch et al. A novel phase-space representation of the perturbed wave functions reveals that the inhibition of quantum transport is due to the selective excitation of wave functions that are highly localized near unstable periodic orbits in the chaotic classical phase space. The 'scarred' wave functions provide a new basis for the quantum description of a variety of classically chaotic systems.

The PKD domain distinguishes the trafficking and amyloidogenic properties of the pigment cell protein PMEL and its homologue GPNMB

PubMed Central

Theos, Alexander C.; Watt, Brenda; Harper, Dawn C.; Janczura, Karolina J.; Theos, Sarah C.; Herman, Kathryn E.; Marks, Michael S.

2013-01-01

SUMMARY Proteolytic fragments of the pigment cell-specific glycoprotein, PMEL, form the amyloid fibrillar matrix underlying melanins in melanosomes. The fibrils form within multivesicular endosomes to which PMEL is selectively sorted and that serve as melanosome precursors. GPNMB is a tissue-restricted glycoprotein with substantial sequence homology to PMEL but no known function, and was proposed to localize to non-fibrillar domains of distinct melanosome subcompartments in melanocytes. Here we confirm that GPNMB localizes to compartments distinct from the PMEL-containing multivesicular premelanosomes or late endosomes in melanocytes and HeLa cells, respectively, and is largely absent from fibrils. Using domain swapping, the unique PMEL localization is ascribed to its PKD domain, whereas the homologous PKD domain of GPNMB lacks apparent sorting function. The difference likely reflects extensive modification of the GPNMB PKD domain by N-glycosylation, nullifying its sorting function. These results reveal the molecular basis for the distinct trafficking and morphogenetic properties of PMEL and GPNMB, and support a deterministic function of the PMEL PKD domain in both protein sorting and amyloidogenesis. PMID:23452376

Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method

NASA Astrophysics Data System (ADS)

Neese, Frank; Wennmohs, Frank; Hansen, Andreas

2009-03-01

Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Møller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol-1. Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500 times faster. The method performs best in conjunction with large and flexible basis sets. These results open the way for large-scale chemical applications.

Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method.

PubMed

Neese, Frank; Wennmohs, Frank; Hansen, Andreas

2009-03-21

Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Moller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol(-1). Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500 times faster. The method performs best in conjunction with large and flexible basis sets. These results open the way for large-scale chemical applications.

Gammadelta T cells: functional plasticity and heterogeneity.

PubMed

Carding, Simon R; Egan, Paul J

2002-05-01

Gammadelta T cells remain an enigma. They are capable of generating more unique antigen receptors than alphabeta T cells and B cells combined, yet their repertoire of antigen receptors is dominated by specific subsets that recognize a limited number of antigens. A variety of sometimes conflicting effector functions have been ascribed to them, yet their biological function(s) remains unclear. On the basis of studies of gammadelta T cells in infectious and autoimmune diseases, we argue that gammadelta T cells perform different functions according to their tissue distribution, antigen-receptor structure and local microenvironment; we also discuss how and at what stage of the immune response they become activated.

A map of local adaptation in Arabidopsis thaliana.

PubMed

Fournier-Level, A; Korte, A; Cooper, M D; Nordborg, M; Schmitt, J; Wilczek, A M

2011-10-07

Local adaptation is critical for species persistence in the face of rapid environmental change, but its genetic basis is not well understood. Growing the model plant Arabidopsis thaliana in field experiments in four sites across the species' native range, we identified candidate loci for local adaptation from a genome-wide association study of lifetime fitness in geographically diverse accessions. Fitness-associated loci exhibited both geographic and climatic signatures of local adaptation. Relative to genomic controls, high-fitness alleles were generally distributed closer to the site where they increased fitness, occupying specific and distinct climate spaces. Independent loci with different molecular functions contributed most strongly to fitness variation in each site. Independent local adaptation by distinct genetic mechanisms may facilitate a flexible evolutionary response to changing environment across a species range.

Matrix-product-state method with local basis optimization for nonequilibrium electron-phonon systems

NASA Astrophysics Data System (ADS)

Heidrich-Meisner, Fabian; Brockt, Christoph; Dorfner, Florian; Vidmar, Lev; Jeckelmann, Eric

We present a method for simulating the time evolution of quasi-one-dimensional correlated systems with strongly fluctuating bosonic degrees of freedom (e.g., phonons) using matrix product states. For this purpose we combine the time-evolving block decimation (TEBD) algorithm with a local basis optimization (LBO) approach. We discuss the performance of our approach in comparison to TEBD with a bare boson basis, exact diagonalization, and diagonalization in a limited functional space. TEBD with LBO can reduce the computational cost by orders of magnitude when boson fluctuations are large and thus it allows one to investigate problems that are out of reach of other approaches. First, we test our method on the non-equilibrium dynamics of a Holstein polaron and show that it allows us to study the regime of strong electron-phonon coupling. Second, the method is applied to the scattering of an electronic wave packet off a region with electron-phonon coupling. Our study reveals a rich physics including transient self-trapping and dissipation. Supported by Deutsche Forschungsgemeinschaft (DFG) via FOR 1807.

Marine and Maritime Sector Skills Shortages in the South West of England: Developing Regional Training Provision

ERIC Educational Resources Information Center

Beer, Julian; Meethan, Kevin

2007-01-01

Clustering theory assumes that companies gravitate towards each other on the basis of locally and regionally specific resources and supply chain characteristics, which lead in turn to innovation and high-value economic development. In line with such thinking, UK government policy has devolved certain functions to regional development agencies such…

Estimation of reflectance from camera responses by the regularized local linear model.

PubMed

Zhang, Wei-Feng; Tang, Gongguo; Dai, Dao-Qing; Nehorai, Arye

2011-10-01

Because of the limited approximation capability of using fixed basis functions, the performance of reflectance estimation obtained by traditional linear models will not be optimal. We propose an approach based on the regularized local linear model. Our approach performs efficiently and knowledge of the spectral power distribution of the illuminant and the spectral sensitivities of the camera is not needed. Experimental results show that the proposed method performs better than some well-known methods in terms of both reflectance error and colorimetric error. © 2011 Optical Society of America

Polymorphism in and localization of the gene LCP2 (SLP-76) to chromosome 5q33.1-qter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sunden, S.L.F.; Carr, L.L.; Clements, J.L.

This report describes the localization of the human LCP2 gene to human chromosome 5q33.1-qter using single-stranded conformation polymorphisms analysis. This gene encodes an SH2 domain containing leukocyte protein of 76 kDa (SLP-76), which plays a functional role in T-cell activation. It remains to be determined whether mutations in this gene or translocations at this chromosome location are the genetic basis for various diseases, including lymphoblastic leukemia. 12 refs., 1 fig.

Frenkel versus charge-transfer exciton dispersion in molecular crystals

NASA Astrophysics Data System (ADS)

Cudazzo, Pierluigi; Gatti, Matteo; Rubio, Angel; Sottile, Francesco

2013-11-01

By solving the many-body Bethe-Salpeter equation at finite momentum transfer, we characterize the exciton dispersion in two prototypical molecular crystals, picene and pentacene, in which localized Frenkel excitons compete with delocalized charge-transfer excitons. We explain the exciton dispersion on the basis of the interplay between electron and hole hopping and electron-hole exchange interaction, unraveling a simple microscopic description to distinguish Frenkel and charge-transfer excitons. This analysis is general and can be applied to other systems in which the electron wave functions are strongly localized, as in strongly correlated insulators.

Local gravity field modeling using spherical radial basis functions and a genetic algorithm

NASA Astrophysics Data System (ADS)

Mahbuby, Hany; Safari, Abdolreza; Foroughi, Ismael

2017-05-01

Spherical Radial Basis Functions (SRBFs) can express the local gravity field model of the Earth if they are parameterized optimally on or below the Bjerhammar sphere. This parameterization is generally defined as the shape of the base functions, their number, center locations, bandwidths, and scale coefficients. The number/location and bandwidths of the base functions are the most important parameters for accurately representing the gravity field; once they are determined, the scale coefficients can then be computed accordingly. In this study, the point-mass kernel, as the simplest shape of SRBFs, is chosen to evaluate the synthesized free-air gravity anomalies over the rough area in Auvergne and GNSS/Leveling points (synthetic height anomalies) are used to validate the results. A two-step automatic approach is proposed to determine the optimum distribution of the base functions. First, the location of the base functions and their bandwidths are found using the genetic algorithm; second, the conjugate gradient least squares method is employed to estimate the scale coefficients. The proposed methodology shows promising results. On the one hand, when using the genetic algorithm, the base functions do not need to be set to a regular grid and they can move according to the roughness of topography. In this way, the models meet the desired accuracy with a low number of base functions. On the other hand, the conjugate gradient method removes the bias between derived quasigeoid heights from the model and from the GNSS/leveling points; this means there is no need for a corrector surface. The numerical test on the area of interest revealed an RMS of 0.48 mGal for the differences between predicted and observed gravity anomalies, and a corresponding 9 cm for the differences in GNSS/leveling points.

The effective local potential method: Implementation for molecules and relation to approximate optimized effective potential techniques

NASA Astrophysics Data System (ADS)

Izmaylov, Artur F.; Staroverov, Viktor N.; Scuseria, Gustavo E.; Davidson, Ernest R.; Stoltz, Gabriel; Cancès, Eric

2007-02-01

We have recently formulated a new approach, named the effective local potential (ELP) method, for calculating local exchange-correlation potentials for orbital-dependent functionals based on minimizing the variance of the difference between a given nonlocal potential and its desired local counterpart [V. N. Staroverov et al., J. Chem. Phys. 125, 081104 (2006)]. Here we show that under a mildly simplifying assumption of frozen molecular orbitals, the equation defining the ELP has a unique analytic solution which is identical with the expression arising in the localized Hartree-Fock (LHF) and common energy denominator approximations (CEDA) to the optimized effective potential. The ELP procedure differs from the CEDA and LHF in that it yields the target potential as an expansion in auxiliary basis functions. We report extensive calculations of atomic and molecular properties using the frozen-orbital ELP method and its iterative generalization to prove that ELP results agree with the corresponding LHF and CEDA values, as they should. Finally, we make the case for extending the iterative frozen-orbital ELP method to full orbital relaxation.

Coupled-cluster, Möller Plesset (MP2), Density Fitted Local MP2, and Density Functional Theory Examination of the Energetic and Structural Features of Hydrophobic Solvation: Water and Pentane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghadar, Yasaman; Clark, Aurora E.

2012-02-02

The interaction potentials between immiscible polar and non-polar solvents are a major driving force behind the formation of liquid:liquid interfaces. In this work, the interaction energy of water–pentane dimer has been determined using coupled-cluster theory with single double (triple) excitations [CCSD(T)], 2nd order Möller Plesset perturbation theory (MP2), density fitted local MP2 (DF-LMP2), as well as density functional theory using a wide variety of density functionals and several different basis sets. The M05-2X exchange correlation functionals exhibit excellent agreement with CCSD(T) and DF-LMP2 after taking into account basis set superposition error. The gas phase water–pentane interaction energy is found tomore » be quite sensitive to the specific pentane isomer (2,2- dimethylpropane vs. n-pentane) and relative orientation of the monomeric constituents. Subsequent solution phase cluster calculations of 2,2-dimethylpropane and n-pentane solvated by water indicate a positive free energy of solvation that is in good agreement with available experimental data. Structural parameters are quite sensitive to the density functional employed and reflect differences in the two-body interaction energy calculated by each method. In contrast, cluster calculations of pentane solvation of H2O solute are found to be inadequate for describing the organic solvent, likely due to limitations associated with the functionals employed (B3LYP, BHandH, and M05-2X).« less

Study on the “3F-in-1” Sustainable Reconstruction of Rural Architecture from Placeality Perspective--A Case Study of Caiyuan Village in Jingmen City, Hubei Province

NASA Astrophysics Data System (ADS)

Fangyu, Fu; Yu, Cao

2017-05-01

This paper takes Caiyuan Village in Jingmen City of Hubei Province as the research object, analyzes the production, life and ecological functions of rural buildings and the “3F-in-1” inherent mechanism from the local perspective. Based on the concept analysis of placeality and “3F-in-1”, this paper clarifies the relationship among the value of life function, production function, ecological function so as to analyze the “3F-in-1” mode of rural architecture with placeality. On this basis, this thesis puts forward the strategy of sustainable spatial transformation (1) preserve the traditional overall spatial structure of villages, (2) improve the adaptability and function of rural architecture, (3) extend the rural social culture, (4) pay attention to local perception, with a view to explore an organic system design method for the exhibition of placeality and sustainable development of beautiful countryside.

Competitive interactions between forest trees are driven by species' trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly.

PubMed

Kunstler, Georges; Lavergne, Sébastien; Courbaud, Benoît; Thuiller, Wilfried; Vieilledent, Ghislain; Zimmermann, Niklaus E; Kattge, Jens; Coomes, David A

2012-08-01

The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that interaction strengths are mainly driven by trait hierarchy and not by functional or phylogenetic similarity. On the basis of this result, we thus propose that functional and phylogenetic convergence in local tree community might be due to competition-sorting species with different competitive abilities and not only environmental filtering as commonly assumed. We then show a functional and phylogenetic convergence of forest structure with increasing plot age, which supports this view. © 2012 Blackwell Publishing Ltd/CNRS.

Kullback-Leibler Divergence-Based Differential Evolution Markov Chain Filter for Global Localization of Mobile Robots.

PubMed

Martín, Fernando; Moreno, Luis; Garrido, Santiago; Blanco, Dolores

2015-09-16

One of the most important skills desired for a mobile robot is the ability to obtain its own location even in challenging environments. The information provided by the sensing system is used here to solve the global localization problem. In our previous work, we designed different algorithms founded on evolutionary strategies in order to solve the aforementioned task. The latest developments are presented in this paper. The engine of the localization module is a combination of the Markov chain Monte Carlo sampling technique and the Differential Evolution method, which results in a particle filter based on the minimization of a fitness function. The robot's pose is estimated from a set of possible locations weighted by a cost value. The measurements of the perceptive sensors are used together with the predicted ones in a known map to define a cost function to optimize. Although most localization methods rely on quadratic fitness functions, the sensed information is processed asymmetrically in this filter. The Kullback-Leibler divergence is the basis of a cost function that makes it possible to deal with different types of occlusions. The algorithm performance has been checked in a real map. The results are excellent in environments with dynamic and unmodeled obstacles, a fact that causes occlusions in the sensing area.

Kullback-Leibler Divergence-Based Differential Evolution Markov Chain Filter for Global Localization of Mobile Robots

PubMed Central

Martín, Fernando; Moreno, Luis; Garrido, Santiago; Blanco, Dolores

2015-01-01

One of the most important skills desired for a mobile robot is the ability to obtain its own location even in challenging environments. The information provided by the sensing system is used here to solve the global localization problem. In our previous work, we designed different algorithms founded on evolutionary strategies in order to solve the aforementioned task. The latest developments are presented in this paper. The engine of the localization module is a combination of the Markov chain Monte Carlo sampling technique and the Differential Evolution method, which results in a particle filter based on the minimization of a fitness function. The robot’s pose is estimated from a set of possible locations weighted by a cost value. The measurements of the perceptive sensors are used together with the predicted ones in a known map to define a cost function to optimize. Although most localization methods rely on quadratic fitness functions, the sensed information is processed asymmetrically in this filter. The Kullback-Leibler divergence is the basis of a cost function that makes it possible to deal with different types of occlusions. The algorithm performance has been checked in a real map. The results are excellent in environments with dynamic and unmodeled obstacles, a fact that causes occlusions in the sensing area. PMID:26389914

Attractive electron-electron interactions within robust local fitting approximations.

PubMed

Merlot, Patrick; Kjærgaard, Thomas; Helgaker, Trygve; Lindh, Roland; Aquilante, Francesco; Reine, Simen; Pedersen, Thomas Bondo

2013-06-30

An analysis of Dunlap's robust fitting approach reveals that the resulting two-electron integral matrix is not manifestly positive semidefinite when local fitting domains or non-Coulomb fitting metrics are used. We present a highly local approximate method for evaluating four-center two-electron integrals based on the resolution-of-the-identity (RI) approximation and apply it to the construction of the Coulomb and exchange contributions to the Fock matrix. In this pair-atomic resolution-of-the-identity (PARI) approach, atomic-orbital (AO) products are expanded in auxiliary functions centered on the two atoms associated with each product. Numerical tests indicate that in 1% or less of all Hartree-Fock and Kohn-Sham calculations, the indefinite integral matrix causes nonconvergence in the self-consistent-field iterations. In these cases, the two-electron contribution to the total energy becomes negative, meaning that the electronic interaction is effectively attractive, and the total energy is dramatically lower than that obtained with exact integrals. In the vast majority of our test cases, however, the indefiniteness does not interfere with convergence. The total energy accuracy is comparable to that of the standard Coulomb-metric RI method. The speed-up compared with conventional algorithms is similar to the RI method for Coulomb contributions; exchange contributions are accelerated by a factor of up to eight with a triple-zeta quality basis set. A positive semidefinite integral matrix is recovered within PARI by introducing local auxiliary basis functions spanning the full AO product space, as may be achieved by using Cholesky-decomposition techniques. Local completion, however, slows down the algorithm to a level comparable with or below conventional calculations. Copyright © 2013 Wiley Periodicals, Inc.

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: application to SSSH.

PubMed

Kolmann, Stephen J; Jordan, Meredith J T

2010-02-07

One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol(-1) at the CCSD(T)/6-31G* level of theory, has a 4 kJ mol(-1) dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol(-1) lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol(-1) lower in energy at the CCSD(T)/6-31G* level of theory. Ideally, for sub-kJ mol(-1) thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: Application to SSSH

NASA Astrophysics Data System (ADS)

Kolmann, Stephen J.; Jordan, Meredith J. T.

2010-02-01

One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol-1 at the CCSD(T)/6-31G∗ level of theory, has a 4 kJ mol-1 dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol-1 lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol-1 lower in energy at the CCSD(T)/6-31G∗ level of theory. Ideally, for sub-kJ mol-1 thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

A two-stage approach to removing noise from recorded music

NASA Astrophysics Data System (ADS)

Berger, Jonathan; Goldberg, Maxim J.; Coifman, Ronald C.; Goldberg, Maxim J.; Coifman, Ronald C.

2004-05-01

A two-stage algorithm for removing noise from recorded music signals (first proposed in Berger et al., ICMC, 1995) is described and updated. The first stage selects the ``best'' local trigonometric basis for the signal and models noise as the part having high entropy [see Berger et al., J. Audio Eng. Soc. 42(10), 808-818 (1994)]. In the second stage, the original source and the model of the noise obtained from the first stage are expanded into dyadic trees of smooth local sine bases. The best basis for the source signal is extracted using a relative entropy function (the Kullback-Leibler distance) to compare the sum of the costs of the children nodes to the cost of their parent node; energies of the noise in corresponding nodes of the model noise tree are used as weights. The talk will include audio examples of various stages of the method and proposals for further research.

The problem of hole localization in inner-shell states of N2 and CO2 revisited with complete active space self-consistent field approach.

PubMed

Rocha, Alexandre B; de Moura, Carlos E V

2011-12-14

Potential energy curves for inner-shell states of nitrogen and carbon dioxide molecules are calculated by inner-shell complete active space self-consistent field (CASSCF) method, which is a protocol, recently proposed, to obtain specifically converged inner-shell states at multiconfigurational level. This is possible since the collapse of the wave function to a low-lying state is avoided by a sequence of constrained optimization in the orbital mixing step. The problem of localization of K-shell states is revisited by calculating their energies at CASSCF level based on both localized and delocalized orbitals. The localized basis presents the best results at this level of calculation. Transition energies are also calculated by perturbation theory, by taking the above mentioned MCSCF function as zeroth order wave function. Values for transition energy are in fairly good agreement with experimental ones. Bond dissociation energies for N(2) are considerably high, which means that these states are strongly bound. Potential curves along ground state normal modes of CO(2) indicate the occurrence of Renner-Teller effect in inner-shell states. © 2011 American Institute of Physics

DFT benchmark study for the oxidative addition of CH 4 to Pd. Performance of various density functionals

NASA Astrophysics Data System (ADS)

de Jong, G. Theodoor; Geerke, Daan P.; Diefenbach, Axel; Matthias Bickelhaupt, F.

2005-06-01

We have evaluated the performance of 24 popular density functionals for describing the potential energy surface (PES) of the archetypal oxidative addition reaction of the methane C-H bond to the palladium atom by comparing the results with our recent ab initio [CCSD(T)] benchmark study of this reaction. The density functionals examined cover the local density approximation (LDA), the generalized gradient approximation (GGA), meta-GGAs as well as hybrid density functional theory. Relativistic effects are accounted for through the zeroth-order regular approximation (ZORA). The basis-set dependence of the density-functional-theory (DFT) results is assessed for the Becke-Lee-Yang-Parr (BLYP) functional using a hierarchical series of Slater-type orbital (STO) basis sets ranging from unpolarized double-ζ (DZ) to quadruply polarized quadruple-ζ quality (QZ4P). Stationary points on the reaction surface have been optimized using various GGA functionals, all of which yield geometries that differ only marginally. Counterpoise-corrected relative energies of stationary points are converged to within a few tenths of a kcal/mol if one uses the doubly polarized triple-ζ (TZ2P) basis set and the basis-set superposition error (BSSE) drops to 0.0 kcal/mol for our largest basis set (QZ4P). Best overall agreement with the ab initio benchmark PES is achieved by functionals of the GGA, meta-GGA, and hybrid-DFT type, with mean absolute errors of 1.3-1.4 kcal/mol and errors in activation energies ranging from +0.8 to -1.4 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with an only slightly larger mean absolute error of 2.5 kcal/mol and an underestimation by -1.9 kcal/mol of the overall barrier (i.e., the difference in energy between the TS and the separate reactants). For comparison, with B3LYP we arrive at a mean absolute error of 3.8 kcal/mol and an overestimation of the overall barrier by 4.5 kcal/mol.

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

DOE PAGES

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; ...

2016-09-09

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing

In this paper, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesizedmore » by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated p-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. Finally, these four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.« less

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level.

PubMed

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing; Gajdos, Fruzsina; Heck, Alexander; de la Lande, Aurélien; Blumberger, Jochen; Elstner, Marcus

2016-10-11

In this article, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated π-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. These four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

Basis adaptation and domain decomposition for steady partial differential equations with random coefficients

DOE PAGES

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

2017-09-04

In this paper, we present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support ourmore » construction with numerical experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Lastly, our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

Basis adaptation and domain decomposition for steady-state partial differential equations with random coefficients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

We present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support our construction with numericalmore » experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

An efficient basis set representation for calculating electrons in molecules

DOE PAGES

Jones, Jeremiah R.; Rouet, Francois -Henry; Lawler, Keith V.; ...

2016-04-27

The method of McCurdy, Baertschy, and Rescigno, is generalised to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules. It uses a basis set of product sinc functions arrayed on a Cartesian grid, and yields 1 kcal/mol precision for valence transition energies with a grid resolution of approximately 0.1 bohr. The Coulomb matrix elements are replaced with matrix elements obtained from the kinetic energy operator. A resolution-of-the-identity approximation renders the primitive one- and two-electron matrix elements diagonal; in other words, the Coulomb operator is local with respect to the grid indices. Themore » calculation of contracted two-electron matrix elements among orbitals requires only O( Nlog (N)) multiplication operations, not O( N 4), where N is the number of basis functions; N = n 3 on cubic grids. The representation not only is numerically expedient, but also produces energies and properties superior to those calculated variationally. Absolute energies, absorption cross sections, transition energies, and ionisation potentials are reported for 1- (He +, H + 2), 2- (H 2, He), 10- (CH 4), and 56-electron (C 8H 8) systems.« less

Umbral Calculus and Holonomic Modules in Positive Characteristic

NASA Astrophysics Data System (ADS)

Kochubei, Anatoly N.

2006-03-01

In the framework of analysis over local fields of positive characteristic, we develop algebraic tools for introducing and investigating various polynomial systems. In this survey paper we describe a function field version of umbral calculus developed on the basis of a relation of binomial type satisfied by the Carlitz polynomials. We consider modules over the Weyl-Carlitz ring, a function field counterpart of the Weyl algebra. It is shown that some basic objects of function field arithmetic, like the Carlitz module, Thakur's hypergeometric polynomials, and analogs of binomial coefficients arising in the positive characteristic version of umbral calculus, generate holonomic modules.

Iterative refinement of implicit boundary models for improved geological feature reproduction

NASA Astrophysics Data System (ADS)

Martin, Ryan; Boisvert, Jeff B.

2017-12-01

Geological domains contain non-stationary features that cannot be described by a single direction of continuity. Non-stationary estimation frameworks generate more realistic curvilinear interpretations of subsurface geometries. A radial basis function (RBF) based implicit modeling framework using domain decomposition is developed that permits introduction of locally varying orientations and magnitudes of anisotropy for boundary models to better account for the local variability of complex geological deposits. The interpolation framework is paired with a method to automatically infer the locally predominant orientations, which results in a rapid and robust iterative non-stationary boundary modeling technique that can refine locally anisotropic geological shapes automatically from the sample data. The method also permits quantification of the volumetric uncertainty associated with the boundary modeling. The methodology is demonstrated on a porphyry dataset and shows improved local geological features.

Comment on “Rethinking first-principles electron transport theories with projection operators: The problems caused by partitioning the basis set” [J. Chem. Phys. 139, 114104 (2013)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandbyge, Mads, E-mail: mads.brandbyge@nanotech.dtu.dk

2014-05-07

In a recent paper Reuter and Harrison [J. Chem. Phys. 139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an “implicit decoupling assumption,” leading to wrong results for the current, different from what would be obtained by using an orthogonal basis, and dividing surfaces defined in real-space. We argue that this assumption is not required to be fulfilled to get exact results. We show how the current/transmission calculated by the standard Greens function method is independent of whether or not the chosen basis set is nonorthogonal, andmore » that the current for a given basis set is consistent with divisions in real space. The ambiguity known from charge population analysis for nonorthogonal bases does not carry over to calculations of charge flux.« less

[Biological security confronting bioterrorism].

PubMed

Suárez Fernández, Guillermo

2002-01-01

A review is made on Biosecurity at both local and global level in relationship with Bioterrorism as a real threat and its control and prevention. The function of the network of High Security Laboratories around the world able to make immediate diagnosis, research on vaccines, fundamental and urgent epidemiological studies, conform a steady basis to control natural infections and also the possible bioterrorism attacks.

Constrained and Unconstrained Localization for Automated Inspection of Marine Propellers

DTIC Science & Technology

1991-05-01

associated control polyhedron and hq, (0 < i < m - 1, 0 < j n - 1) are positive weights. B1 v(u) and Bj,’v) are the B-spline basis functions over open...Inspection by Database Matching. Technical Report CMU-RI-TR-85-4, The Robotics Institute, Carnegie Mellon University, March, 1985. Tuohy, S. T., Patrikalakis

Co-Localization of Stroop and Syntactic Ambiguity Resolution in Broca's Area: Implications for the Neural Basis of Sentence Processing

ERIC Educational Resources Information Center

January, David; Trueswell, John C.; Thompson-Schill, Sharon L.

2009-01-01

For over a century, a link between left prefrontal cortex and language processing has been accepted, yet the precise characterization of this link remains elusive. Recent advances in both the study of sentence processing and the neuroscientific study of frontal lobe function suggest an intriguing possibility: The demands to resolve competition…

Comparing success levels of different neural network structures in extracting discriminative information from the response patterns of a temperature-modulated resistive gas sensor

NASA Astrophysics Data System (ADS)

Hosseini-Golgoo, S. M.; Bozorgi, H.; Saberkari, A.

2015-06-01

Performances of three neural networks, consisting of a multi-layer perceptron, a radial basis function, and a neuro-fuzzy network with local linear model tree training algorithm, in modeling and extracting discriminative features from the response patterns of a temperature-modulated resistive gas sensor are quantitatively compared. For response pattern recording, a voltage staircase containing five steps each with a 20 s plateau is applied to the micro-heater of the sensor, when 12 different target gases, each at 11 concentration levels, are present. In each test, the hidden layer neuron weights are taken as the discriminatory feature vector of the target gas. These vectors are then mapped to a 3D feature space using linear discriminant analysis. The discriminative information content of the feature vectors are determined by the calculation of the Fisher’s discriminant ratio, affording quantitative comparison among the success rates achieved by the different neural network structures. The results demonstrate a superior discrimination ratio for features extracted from local linear neuro-fuzzy and radial-basis-function networks with recognition rates of 96.27% and 90.74%, respectively.

Multiscale Simulation Framework for Coupled Fluid Flow and Mechanical Deformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Thomas; Efendiev, Yalchin; Tchelepi, Hamdi

2016-05-24

Our work in this project is aimed at making fundamental advances in multiscale methods for flow and transport in highly heterogeneous porous media. The main thrust of this research is to develop a systematic multiscale analysis and efficient coarse-scale models that can capture global effects and extend existing multiscale approaches to problems with additional physics and uncertainties. A key emphasis is on problems without an apparent scale separation. Multiscale solution methods are currently under active investigation for the simulation of subsurface flow in heterogeneous formations. These procedures capture the effects of fine-scale permeability variations through the calculation of specialized coarse-scalemore » basis functions. Most of the multiscale techniques presented to date employ localization approximations in the calculation of these basis functions. For some highly correlated (e.g., channelized) formations, however, global effects are important and these may need to be incorporated into the multiscale basis functions. Other challenging issues facing multiscale simulations are the extension of existing multiscale techniques to problems with additional physics, such as compressibility, capillary effects, etc. In our project, we explore the improvement of multiscale methods through the incorporation of additional (single-phase flow) information and the development of a general multiscale framework for flows in the presence of uncertainties, compressible flow and heterogeneous transport, and geomechanics. We have considered (1) adaptive local-global multiscale methods, (2) multiscale methods for the transport equation, (3) operator-based multiscale methods and solvers, (4) multiscale methods in the presence of uncertainties and applications, (5) multiscale finite element methods for high contrast porous media and their generalizations, and (6) multiscale methods for geomechanics.« less

Multiscale analysis and computation for flows in heterogeneous media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Efendiev, Yalchin; Hou, T. Y.; Durlofsky, L. J.

Our work in this project is aimed at making fundamental advances in multiscale methods for flow and transport in highly heterogeneous porous media. The main thrust of this research is to develop a systematic multiscale analysis and efficient coarse-scale models that can capture global effects and extend existing multiscale approaches to problems with additional physics and uncertainties. A key emphasis is on problems without an apparent scale separation. Multiscale solution methods are currently under active investigation for the simulation of subsurface flow in heterogeneous formations. These procedures capture the effects of fine-scale permeability variations through the calculation of specialized coarse-scalemore » basis functions. Most of the multiscale techniques presented to date employ localization approximations in the calculation of these basis functions. For some highly correlated (e.g., channelized) formations, however, global effects are important and these may need to be incorporated into the multiscale basis functions. Other challenging issues facing multiscale simulations are the extension of existing multiscale techniques to problems with additional physics, such as compressibility, capillary effects, etc. In our project, we explore the improvement of multiscale methods through the incorporation of additional (single-phase flow) information and the development of a general multiscale framework for flows in the presence of uncertainties, compressible flow and heterogeneous transport, and geomechanics. We have considered (1) adaptive local-global multiscale methods, (2) multiscale methods for the transport equation, (3) operator-based multiscale methods and solvers, (4) multiscale methods in the presence of uncertainties and applications, (5) multiscale finite element methods for high contrast porous media and their generalizations, and (6) multiscale methods for geomechanics. Below, we present a brief overview of each of these contributions.« less

NMR, MRI, and spectroscopic MRI in inhomogeneous fields

DOEpatents

Demas, Vasiliki; Pines, Alexander; Martin, Rachel W; Franck, John; Reimer, Jeffrey A

2013-12-24

A method for locally creating effectively homogeneous or "clean" magnetic field gradients (of high uniformity) for imaging (with NMR, MRI, or spectroscopic MRI) both in in-situ and ex-situ systems with high degrees of inhomogeneous field strength. THe method of imaging comprises: a) providing a functional approximation of an inhomogeneous static magnetic field strength B.sub.0({right arrow over (r)}) at a spatial position {right arrow over (r)}; b) providing a temporal functional approximation of {right arrow over (G)}.sub.shim(t) with i basis functions and j variables for each basis function, resulting in v.sub.ij variables; c) providing a measured value .OMEGA., which is an temporally accumulated dephasing due to the inhomogeneities of B.sub.0({right arrow over(r)}); and d) minimizing a difference in the local dephasing angle .phi.({right arrow over (r)},t)=.gamma..intg..sub.0.sup.t{square root over (|{right arrow over (B)}.sub.1({right arrow over (r)},t')|.sup.2+({right arrow over (r)}{right arrow over (G)}.sub.shimG.sub.shim(t')+.parallel.{right arrow over (B)}.sub.0({right arrow over (r)}).parallel..DELTA..omega.({right arrow over (r)},t'/.gamma/).sup.2)}dt'-.OMEGA. by varying the v.sub.ij variables to form a set of minimized v.sub.ij variables. The method requires calibration of the static fields prior to minimization, but may thereafter be implemented without such calibration, may be used in open or closed systems, and potentially portable systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

In this paper, we present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support ourmore » construction with numerical experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Lastly, our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

Mesh-free based variational level set evolution for breast region segmentation and abnormality detection using mammograms.

PubMed

Kashyap, Kanchan L; Bajpai, Manish K; Khanna, Pritee; Giakos, George

2018-01-01

Automatic segmentation of abnormal region is a crucial task in computer-aided detection system using mammograms. In this work, an automatic abnormality detection algorithm using mammographic images is proposed. In the preprocessing step, partial differential equation-based variational level set method is used for breast region extraction. The evolution of the level set method is done by applying mesh-free-based radial basis function (RBF). The limitation of mesh-based approach is removed by using mesh-free-based RBF method. The evolution of variational level set function is also done by mesh-based finite difference method for comparison purpose. Unsharp masking and median filtering is used for mammogram enhancement. Suspicious abnormal regions are segmented by applying fuzzy c-means clustering. Texture features are extracted from the segmented suspicious regions by computing local binary pattern and dominated rotated local binary pattern (DRLBP). Finally, suspicious regions are classified as normal or abnormal regions by means of support vector machine with linear, multilayer perceptron, radial basis, and polynomial kernel function. The algorithm is validated on 322 sample mammograms of mammographic image analysis society (MIAS) and 500 mammograms from digital database for screening mammography (DDSM) datasets. Proficiency of the algorithm is quantified by using sensitivity, specificity, and accuracy. The highest sensitivity, specificity, and accuracy of 93.96%, 95.01%, and 94.48%, respectively, are obtained on MIAS dataset using DRLBP feature with RBF kernel function. Whereas, the highest 92.31% sensitivity, 98.45% specificity, and 96.21% accuracy are achieved on DDSM dataset using DRLBP feature with RBF kernel function. Copyright © 2017 John Wiley & Sons, Ltd.

Locally smeared operator product expansions in scalar field theory

DOE PAGES

Monahan, Christopher; Orginos, Kostas

2015-04-01

We propose a new locally smeared operator product expansion to decompose non-local operators in terms of a basis of smeared operators. The smeared operator product expansion formally connects nonperturbative matrix elements determined numerically using lattice field theory to matrix elements of non-local operators in the continuum. These nonperturbative matrix elements do not suffer from power-divergent mixing on the lattice, which significantly complicates calculations of quantities such as the moments of parton distribution functions, provided the smearing scale is kept fixed in the continuum limit. The presence of this smearing scale complicates the connection to the Wilson coefficients of the standardmore » operator product expansion and requires the construction of a suitable formalism. We demonstrate the feasibility of our approach with examples in real scalar field theory.« less

Efficient visibility encoding for dynamic illumination in direct volume rendering.

PubMed

Kronander, Joel; Jönsson, Daniel; Löw, Joakim; Ljung, Patric; Ynnerman, Anders; Unger, Jonas

2012-03-01

We present an algorithm that enables real-time dynamic shading in direct volume rendering using general lighting, including directional lights, point lights, and environment maps. Real-time performance is achieved by encoding local and global volumetric visibility using spherical harmonic (SH) basis functions stored in an efficient multiresolution grid over the extent of the volume. Our method enables high-frequency shadows in the spatial domain, but is limited to a low-frequency approximation of visibility and illumination in the angular domain. In a first pass, level of detail (LOD) selection in the grid is based on the current transfer function setting. This enables rapid online computation and SH projection of the local spherical distribution of visibility information. Using a piecewise integration of the SH coefficients over the local regions, the global visibility within the volume is then computed. By representing the light sources using their SH projections, the integral over lighting, visibility, and isotropic phase functions can be efficiently computed during rendering. The utility of our method is demonstrated in several examples showing the generality and interactive performance of the approach.

Narrative discourse deficits in amyotrophic lateral sclerosis.

PubMed

Ash, Sharon; Menaged, Anna; Olm, Christopher; McMillan, Corey T; Boller, Ashley; Irwin, David J; McCluskey, Leo; Elman, Lauren; Grossman, Murray

2014-08-05

We examined narrative discourse in amyotrophic lateral sclerosis (ALS) to assess the role of executive functioning in support of language and the neuroanatomical basis for such support. We analyzed a semistructured speech sample in 26 patients with ALS and 19 healthy seniors for narrative discourse features of coherence. Regression analyses related a measure of discourse coherence ("local connectedness") to gray matter atrophy and reduced white matter fractional anisotropy. Patients with ALS were impaired relative to controls on measures of discourse adequacy, including local connectedness and maintenance of the theme. These discourse measures were related to measures of executive functioning but not to motor functioning. Regressions related local connectedness to gray matter atrophy in ventral and dorsal prefrontal regions and to reduced fractional anisotropy in white matter tracts mediating projections between prefrontal regions. Patients with ALS exhibit deficits in their ability to organize narrative discourse. These deficits appear to be related in part to executive limitations. Consistent with the hypothesis that ALS is a multisystem disorder, this deficit is related to disease in prefrontal regions. © 2014 American Academy of Neurology.

Hyperfine coupling constants of the nitrogen and phosphorus atoms: A challenge for exact-exchange density-functional and post-Hartree-Fock methods

NASA Astrophysics Data System (ADS)

Kaupp, Martin; Arbuznikov, Alexei V.; Heßelmann, Andreas; Görling, Andreas

2010-05-01

The isotropic hyperfine coupling constants of the free N(S4) and P(S4) atoms have been evaluated with high-level post-Hartree-Fock and density-functional methods. The phosphorus hyperfine coupling presents a significant challenge to both types of methods. With large basis sets, MP2 and coupled-cluster singles and doubles calculations give much too small values for the phosphorus atom. Triple excitations are needed in coupled-cluster calculations to achieve reasonable agreement with experiment. None of the standard density functionals reproduce even the correct sign of this hyperfine coupling. Similarly, the computed hyperfine couplings depend crucially on the self-consistent treatment in exact-exchange density-functional theory within the optimized effective potential (OEP) method. Well-balanced auxiliary and orbital basis sets are needed for basis-expansion exact-exchange-only OEP approaches to come close to Hartree-Fock or numerical OEP data. Results from the localized Hartree-Fock and Krieger-Li-Iafrate approximations deviate notably from exact OEP data in spite of very similar total energies. Of the functionals tested, only full exact-exchange methods augmented by a correlation functional gave at least the correct sign of the P(S4) hyperfine coupling but with too low absolute values. The subtle interplay between the spin-polarization contributions of the different core shells has been analyzed, and the influence of even very small changes in the exchange-correlation potential could be identified.

Orthogonal polynomial projectors for the Projector Augmented Wave (PAW) formalism.

NASA Astrophysics Data System (ADS)

Holzwarth, N. A. W.; Matthews, G. E.; Tackett, A. R.; Dunning, R. B.

1998-03-01

The PAW method for density functional electronic structure calculations developed by Blöchl(Phys. Rev. B 50), 17953 (1994) and also used by our group(Phys. Rev. B 55), 2005 (1997) has numerical advantages of a pseudopotential technique while retaining the physics of an all-electron formalism. We describe a new method for generating the necessary set of atom-centered projector and basis functions, based on choosing the projector functions from a set of orthogonal polynomials multiplied by a localizing weight factor. Numerical benefits of the new scheme result from having direct control of the shape of the projector functions and from the use of a simple repulsive local potential term to eliminate ``ghost state" problems, which can haunt calculations of this kind. We demonstrate the method by calculating the cohesive energies of CaF2 and Mo and the density of states of CaMoO4 which shows detailed agreement with LAPW results over a 66 eV range of energy including upper core, valence, and conduction band states.

On the truncation of the number of excited states in density functional theory sum-over-states calculations of indirect spin spin coupling constants

NASA Astrophysics Data System (ADS)

Zarycz, M. Natalia C.; Provasi, Patricio F.; Sauer, Stephan P. A.

2015-12-01

It is investigated, whether the number of excited (pseudo)states can be truncated in the sum-over-states expression for indirect spin-spin coupling constants (SSCCs), which is used in the Contributions from Localized Orbitals within the Polarization Propagator Approach and Inner Projections of the Polarization Propagator (IPPP-CLOPPA) approach to analyzing SSCCs in terms of localized orbitals. As a test set we have studied the nine simple compounds, CH4, NH3, H2O, SiH4, PH3, SH2, C2H2, C2H4, and C2H6. The excited (pseudo)states were obtained from time-dependent density functional theory (TD-DFT) calculations with the B3LYP exchange-correlation functional and the specialized core-property basis set, aug-cc-pVTZ-J. We investigated both how the calculated coupling constants depend on the number of (pseudo)states included in the summation and whether the summation can be truncated in a systematic way at a smaller number of states and extrapolated to the total number of (pseudo)states for the given one-electron basis set. We find that this is possible and that for some of the couplings it is sufficient to include only about 30% of the excited (pseudo)states.

Separation of the global and local components in functional near-infrared spectroscopy signals using principal component spatial filtering

PubMed Central

Zhang, Xian; Noah, Jack Adam; Hirsch, Joy

2016-01-01

Abstract. Global systemic effects not specific to a task can be prominent in functional near-infrared spectroscopy (fNIRS) signals and the separation of task-specific fNIRS signals and global nonspecific effects is challenging due to waveform correlations. We describe a principal component spatial filter algorithm for separation of the global and local effects. The effectiveness of the approach is demonstrated using fNIRS signals acquired during a right finger-thumb tapping task where the response patterns are well established. Both the temporal waveforms and the spatial pattern consistencies between oxyhemoglobin and deoxyhemoglobin signals are significantly improved, consistent with the basic physiological basis of fNIRS signals and the expected pattern of activity associated with the task. PMID:26866047

Assigning the Cerium Oxidation State for CH2CeF2 and OCeF2 Based on Multireference Wave Function Analysis.

PubMed

Mooßen, Oliver; Dolg, Michael

2016-06-09

The geometric and electronic structure of the recently experimentally studied molecules ZCeF2 (Z = CH2, O) was investigated by density functional theory (DFT) and wave function-based ab initio methods. Special attention was paid to the Ce-Z metal-ligand bonding, especially to the nature of the interaction between the Ce 4f and the Z 2p orbitals and the possible multiconfigurational character arising from it, as well as to the assignment of an oxidation state of Ce reflecting the electronic structure. Complete active space self-consistent field (CASSCF) calculations were performed, followed by orbital rotations in the active orbital space. The methylene compound CH2CeF2 has an open-shell singlet ground state, which is characterized by a two-configurational wave function in the basis of the strongly mixed natural CASSCF orbitals. The system can also be described in a very compact way by the dominant Ce 4f(1) C 2p(1) configuration, if nearly pure Ce 4f and C 2p orbitals are used. In the basis of these localized orbitals, the molecule is almost monoconfigurational and should be best described as a Ce(III) system. The singlet ground state of the oxygen OCeF2 complex is of closed-shell character when a monoconfigurational wave function with very strongly mixed Ce 4f and O 2p CASSCF natural orbitals is used for the description. The transformation to orbitals localized on the cerium and oxygen atoms leads to a multiconfigurational wave function and reveals characteristics of a mixed valent Ce(IV)/Ce(III) compound. Additionally, the interactions of the localized active orbitals were analyzed by evaluating the expectation values of the charge fluctuation operator and the local spin operator. The Ce 4f and C 2p orbital interaction of the CH2CeF2 compound is weakly covalent and resembles the interaction of the H 1s orbitals in a stretched hydrogen dimer. In contrast, the interaction of the localized active orbitals for OCeF2 shows ionic character. Calculated vibrational Ce-C and Ce-O stretching frequencies at the DFT, CASSCF, second-order Rayleigh-Schrödinger perturbation theory (RS2C), multireference configuration interaction (MRCI), as well as single, doubles, and perturbative triples coupled cluster (CCSD(T)) level are reported and compared to experimental infrared absorption data in a Ne and Ar matrix.

Validity of virial theorem in all-electron mixed basis density functional, Hartree–Fock, and GW calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuwahara, Riichi; Accelrys K. K., Kasumigaseki Tokyu Building 17F, 3-7-1 Kasumigaseki, Chiyoda-ku, Tokyo 100-0013; Tadokoro, Yoichi

In this paper, we calculate kinetic and potential energy contributions to the electronic ground-state total energy of several isolated atoms (He, Be, Ne, Mg, Ar, and Ca) by using the local density approximation (LDA) in density functional theory, the Hartree–Fock approximation (HFA), and the self-consistent GW approximation (GWA). To this end, we have implemented self-consistent HFA and GWA routines in our all-electron mixed basis code, TOMBO. We confirm that virial theorem is fairly well satisfied in all of these approximations, although the resulting eigenvalue of the highest occupied molecular orbital level, i.e., the negative of the ionization potential, is inmore » excellent agreement only in the case of the GWA. We find that the wave function of the lowest unoccupied molecular orbital level of noble gas atoms is a resonating virtual bound state, and that of the GWA spreads wider than that of the LDA and thinner than that of the HFA.« less

Review of functional markers for improving cooking, eating, and the nutritional qualities of rice

PubMed Central

Lau, Wendy C. P.; Rafii, Mohd Y.; Ismail, Mohd R.; Puteh, Adam; Latif, Mohammad A.; Ramli, Asfaliza

2015-01-01

After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers’ preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated. PMID:26528304

NMR shieldings from density functional perturbation theory: GIPAW versus all-electron calculations

NASA Astrophysics Data System (ADS)

de Wijs, G. A.; Laskowski, R.; Blaha, P.; Havenith, R. W. A.; Kresse, G.; Marsman, M.

2017-02-01

We present a benchmark of the density functional linear response calculation of NMR shieldings within the gauge-including projector-augmented-wave method against all-electron augmented-plane-wave+local-orbital and uncontracted Gaussian basis set results for NMR shieldings in molecular and solid state systems. In general, excellent agreement between the aforementioned methods is obtained. Scalar relativistic effects are shown to be quite large for nuclei in molecules in the deshielded limit. The small component makes up a substantial part of the relativistic corrections.

NMR shieldings from density functional perturbation theory: GIPAW versus all-electron calculations.

PubMed

de Wijs, G A; Laskowski, R; Blaha, P; Havenith, R W A; Kresse, G; Marsman, M

2017-02-14

We present a benchmark of the density functional linear response calculation of NMR shieldings within the gauge-including projector-augmented-wave method against all-electron augmented-plane-wave+local-orbital and uncontracted Gaussian basis set results for NMR shieldings in molecular and solid state systems. In general, excellent agreement between the aforementioned methods is obtained. Scalar relativistic effects are shown to be quite large for nuclei in molecules in the deshielded limit. The small component makes up a substantial part of the relativistic corrections.

Estimation of Δ R/ R values by benchmark study of the Mössbauer Isomer shifts for Ru, Os complexes using relativistic DFT calculations

NASA Astrophysics Data System (ADS)

Kaneko, Masashi; Yasuhara, Hiroki; Miyashita, Sunao; Nakashima, Satoru

2017-11-01

The present study applies all-electron relativistic DFT calculation with Douglas-Kroll-Hess (DKH) Hamiltonian to each ten sets of Ru and Os compounds. We perform the benchmark investigation of three density functionals (BP86, B3LYP and B2PLYP) using segmented all-electron relativistically contracted (SARC) basis set with the experimental Mössbauer isomer shifts for 99Ru and 189Os nuclides. Geometry optimizations at BP86 theory of level locate the structure in a local minimum. We calculate the contact density to the wavefunction obtained by a single point calculation. All functionals show the good linear correlation with experimental isomer shifts for both 99Ru and 189Os. Especially, B3LYP functional gives a stronger correlation compared to BP86 and B2PLYP functionals. The comparison of contact density between SARC and well-tempered basis set (WTBS) indicated that the numerical convergence of contact density cannot be obtained, but the reproducibility is less sensitive to the choice of basis set. We also estimate the values of Δ R/ R, which is an important nuclear constant, for 99Ru and 189Os nuclides by using the benchmark results. The sign of the calculated Δ R/ R values is consistent with the predicted data for 99Ru and 189Os. We obtain computationally the Δ R/ R values of 99Ru and 189Os (36.2 keV) as 2.35×10-4 and -0.20×10-4, respectively, at B3LYP level for SARC basis set.

AdS/CFT and local renormalization group with gauge fields

NASA Astrophysics Data System (ADS)

Kikuchi, Ken; Sakai, Tadakatsu

2016-03-01

We revisit a study of local renormalization group (RG) with background gauge fields incorporated using the AdS/CFT correspondence. Starting with a (d+1)-dimensional bulk gravity coupled to scalars and gauge fields, we derive a local RG equation from a flow equation by working in the Hamilton-Jacobi formulation of the bulk theory. The Gauss's law constraint associated with gauge symmetry plays an important role. RG flows of the background gauge fields are governed by vector β-functions, and some of their interesting properties are known to follow. We give a systematic rederivation of them on the basis of the flow equation. Fixing an ambiguity of local counterterms in such a manner that is natural from the viewpoint of the flow equation, we determine all the coefficients uniquely appearing in the trace of the stress tensor for d=4. A relation between a choice of schemes and a virial current is discussed. As a consistency check, these are found to satisfy the integrability conditions of local RG transformations. From these results, we are led to a proof of a holographic c-theorem by determining a full family of schemes where a trace anomaly coefficient is related with a holographic c-function.

Sparseness- and continuity-constrained seismic imaging

NASA Astrophysics Data System (ADS)

Herrmann, Felix J.

2005-04-01

Non-linear solution strategies to the least-squares seismic inverse-scattering problem with sparseness and continuity constraints are proposed. Our approach is designed to (i) deal with substantial amounts of additive noise (SNR < 0 dB); (ii) use the sparseness and locality (both in position and angle) of directional basis functions (such as curvelets and contourlets) on the model: the reflectivity; and (iii) exploit the near invariance of these basis functions under the normal operator, i.e., the scattering-followed-by-imaging operator. Signal-to-noise ratio and the continuity along the imaged reflectors are significantly enhanced by formulating the solution of the seismic inverse problem in terms of an optimization problem. During the optimization, sparseness on the basis and continuity along the reflectors are imposed by jointly minimizing the l1- and anisotropic diffusion/total-variation norms on the coefficients and reflectivity, respectively. [Joint work with Peyman P. Moghaddam was carried out as part of the SINBAD project, with financial support secured through ITF (the Industry Technology Facilitator) from the following organizations: BG Group, BP, ExxonMobil, and SHELL. Additional funding came from the NSERC Discovery Grants 22R81254.

Assessment of existing local houses condition as analysis tools for shore housing improvement program in Weriagar district, Bintuni Bay

NASA Astrophysics Data System (ADS)

Firmansyah, F.; Fernando, A.; Allo, I. P. R.

2018-01-01

The housing assessment is a part of the pre-feasibility study inThe Shore Housing Improvement Program in Weriagar District, West Papua. The housing assessment was conducted to identify the physical condition of existing houses. The parameters of assessment formulated from local references, practices and also national building regulation that covers each building system components, such as building structure/frame, building floor, building cover, and building roof. This study aims to explains lessons from local practices and references, used as the formula to generate assessment parameter, elaborate with Indonesia building regulation. The result of housing assessment were used as a basis to develop the house improvement strategy, the design alternative for housing improvement and further planning recommendations. The local knowledges involved in housing improvement program expected that the local-based approach could respect to the local build culture, respect the local environment, and the most important can offer best suitable solutions for functional utility and livability.

The Strange (Hi)story of Particles and Waves

NASA Astrophysics Data System (ADS)

Zeh, H. Dieter

2016-03-01

This is an attempt of a non-technical but conceptually consistent presentation of quantum theory in a historical context. While the first part is written for a general readership, Section 5 may appear a bit provocative to some quantum physicists. I argue that the single-particle wave functions of quantum mechanics have to be correctly interpreted as field modes that are "occupied once" (i.e. first excited states of the corresponding quantum oscillators in the case of boson fields). Multiple excitations lead to apparent many-particle wave functions, while the quantum states proper are defined by wave function(al)s on the "configuration" space of fundamental fields, or on another, as yet elusive, fundamental local basis.

Equilibrium structure of δ-Bi(2)O(3) from first principles.

PubMed

Music, Denis; Konstantinidis, Stephanos; Schneider, Jochen M

2009-04-29

Using ab initio calculations, we have systematically studied the structure of δ-Bi(2)O(3) (fluorite prototype, 25% oxygen vacancies) probing [Formula: see text] and combined [Formula: see text] and [Formula: see text] oxygen vacancy ordering, random distribution of oxygen vacancies with two different statistical descriptions as well as local relaxations. We observe that the combined [Formula: see text] and [Formula: see text] oxygen vacancy ordering is the most stable configuration. Radial distribution functions for these configurations can be classified as discrete (ordered configurations) and continuous (random configurations). This classification can be understood on the basis of local structural relaxations. Up to 28.6% local relaxation of the oxygen sublattice is present in the random configurations, giving rise to continuous distribution functions. The phase stability obtained may be explained with the bonding analysis. Electron lone-pair charges in the predominantly ionic Bi-O matrix may stabilize the combined [Formula: see text] and [Formula: see text] oxygen vacancy ordering.

Interaction-induced effects on Bose-Hubbard parameters

NASA Astrophysics Data System (ADS)

Kremer, Mark; Sachdeva, Rashi; Benseny, Albert; Busch, Thomas

2017-12-01

We study the effects of repulsive on-site interactions on the broadening of the localized Wannier functions used for calculating the parameters to describe ultracold atoms in optical lattices. For this, we replace the common single-particle Wannier functions, which do not contain any information about the interactions, by two-particle Wannier functions obtained from an exact solution which takes the interactions into account. We then use these interaction-dependent basis functions to calculate the Bose-Hubbard model parameters, showing that they are substantially different both at low and high lattice depths from the ones calculated using single-particle Wannier functions. Our results suggest that density effects are not negligible for many parameter ranges and need to be taken into account in metrology experiments.

Comparative analysis of local spin definitions.

PubMed

Herrmann, Carmen; Reiher, Markus; Hess, Bernd A

2005-01-15

This work provides a survey of the definition of electron spin as a local property and its dependence on several parameters in actual calculations. We analyze one-determinant wave functions constructed from Hartree-Fock and, in particular, from Kohn-Sham orbitals within the collinear approach to electron spin. The scalar total spin operators S2 and Sz are partitioned by projection operators, as introduced by Clark and Davidson, in order to obtain local spin operators SASB and SzA, respectively. To complement the work of Davidson and co-workers, we analyze some features of local spins which have not yet been discussed in sufficient depth. The dependence of local spin on the choice of basis set, density functional, and projector is studied. We also discuss the results of Sz partitioning and show that SzA values depend less on these parameters than SASB values. Furthermore, we demonstrate that for small organic test molecules, a partitioning of Sz with preorthogonalized Lowdin projectors yields nearly the same results as one obtains using atoms-in-molecules projectors. In addition, the physical significance of nonzero SASB values for closed-shell molecules is investigated. It is shown that due to this problem, SASB values are useful for calculations of relative spin values, but not for absolute local spins, where SzA values appear to be better suited.

A partitioned correlation function interaction approach for describing electron correlation in atoms

NASA Astrophysics Data System (ADS)

Verdebout, S.; Rynkun, P.; Jönsson, P.; Gaigalas, G.; Froese Fischer, C.; Godefroid, M.

2013-04-01

The traditional multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis. For atoms with many closed core shells, or complicated shell structures, a large orbital basis is needed to saturate the different electron correlation effects such as valence, core-valence and correlation within the core shells. The large orbital basis leads to massive configuration state function (CSF) expansions that are difficult to handle, even on large computer systems. We show that it is possible to relax the orthonormality restriction on the orbital basis and break down the originally very large calculations into a series of smaller calculations that can be run in parallel. Each calculation determines a partitioned correlation function (PCF) that accounts for a specific correlation effect. The PCFs are built on optimally localized orbital sets and are added to a zero-order multireference (MR) function to form a total wave function. The expansion coefficients of the PCFs are determined from a low dimensional generalized eigenvalue problem. The interaction and overlap matrices are computed using a biorthonormal transformation technique (Verdebout et al 2010 J. Phys. B: At. Mol. Phys. 43 074017). The new method, called partitioned correlation function interaction (PCFI), converges rapidly with respect to the orbital basis and gives total energies that are lower than the ones from ordinary MCHF and CI calculations. The PCFI method is also very flexible when it comes to targeting different electron correlation effects. Focusing our attention on neutral lithium, we show that by dedicating a PCF to the single excitations from the core, spin- and orbital-polarization effects can be captured very efficiently, leading to highly improved convergence patterns for hyperfine parameters compared with MCHF calculations based on a single orthogonal radial orbital basis. By collecting separately optimized PCFs to correct the MR function, the variational degrees of freedom in the relative mixing coefficients of the CSFs building the PCFs are inhibited. The constraints on the mixing coefficients lead to small off-sets in computed properties such as hyperfine structure, isotope shift and transition rates, with respect to the correct values. By (partially) deconstraining the mixing coefficients one converges to the correct limits and keeps the tremendous advantage of improved convergence rates that comes from the use of several orbital sets. Reducing ultimately each PCF to a single CSF with its own orbital basis leads to a non-orthogonal CI approach. Various perspectives of the new method are given.

Nonlinear spline wavefront reconstruction through moment-based Shack-Hartmann sensor measurements.

PubMed

Viegers, M; Brunner, E; Soloviev, O; de Visser, C C; Verhaegen, M

2017-05-15

We propose a spline-based aberration reconstruction method through moment measurements (SABRE-M). The method uses first and second moment information from the focal spots of the SH sensor to reconstruct the wavefront with bivariate simplex B-spline basis functions. The proposed method, since it provides higher order local wavefront estimates with quadratic and cubic basis functions can provide the same accuracy for SH arrays with a reduced number of subapertures and, correspondingly, larger lenses which can be beneficial for application in low light conditions. In numerical experiments the performance of SABRE-M is compared to that of the first moment method SABRE for aberrations of different spatial orders and for different sizes of the SH array. The results show that SABRE-M is superior to SABRE, in particular for the higher order aberrations and that SABRE-M can give equal performance as SABRE on a SH grid of halved sampling.

Wavelet-based spectral finite element dynamic analysis for an axially moving Timoshenko beam

NASA Astrophysics Data System (ADS)

Mokhtari, Ali; Mirdamadi, Hamid Reza; Ghayour, Mostafa

2017-08-01

In this article, wavelet-based spectral finite element (WSFE) model is formulated for time domain and wave domain dynamic analysis of an axially moving Timoshenko beam subjected to axial pretension. The formulation is similar to conventional FFT-based spectral finite element (SFE) model except that Daubechies wavelet basis functions are used for temporal discretization of the governing partial differential equations into a set of ordinary differential equations. The localized nature of Daubechies wavelet basis functions helps to rule out problems of SFE model due to periodicity assumption, especially during inverse Fourier transformation and back to time domain. The high accuracy of WSFE model is then evaluated by comparing its results with those of conventional finite element and SFE results. The effects of moving beam speed and axial tensile force on vibration and wave characteristics, and static and dynamic stabilities of moving beam are investigated.

Electronic structure of stoichiometric and reduced ZnO from periodic relativistic all electron hybrid density functional calculations using numeric atom-centered orbitals.

PubMed

Viñes, Francesc; Illas, Francesc

2017-03-30

The atomic and electronic structure of stoichiometric and reduced ZnO wurtzite has been studied using a periodic relativistic all electron hybrid density functional (PBE0) approach and numeric atom-centered orbital basis set with quality equivalent to aug-cc-pVDZ. To assess the importance of relativistic effects, calculations were carried out without and with explicit inclusion of relativistic effects through the zero order regular approximation. The calculated band gap is ∼0.2 eV smaller than experiment, close to previous PBE0 results including relativistic calculation through the pseudopotential and ∼0.25 eV smaller than equivalent nonrelativistic all electron PBE0 calculations indicating possible sources of error in nonrelativistic all electron density functional calculations for systems containing elements with relatively high atomic number. The oxygen vacancy formation energy converges rather fast with the supercell size, the predicted value agrees with previously hybrid density functional calculations and analysis of the electronic structure evidences the presence of localized electrons at the vacancy site with a concomitant well localized peak in the density of states ∼0.5 eV above the top of the valence band and a significant relaxation of the Zn atoms near to the oxygen vacancy. Finally, present work shows that accurate results can be obtained in systems involving large supercells containing up to ∼450 atoms using a numeric atomic-centered orbital basis set within a full all electron description including scalar relativistic effects at an affordable cost. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A Hypothesis for Examining Skeletal Muscle Biopsy-Derived Sarcolemmal nNOSμ as Surrogate for Enteric nNOSα Function

PubMed Central

Chaudhury, Arun

2015-01-01

The pathophysiology of gastrointestinal motility disorders is controversial and largely unresolved. This provokes empiric approaches to patient management of these so-called functional gastrointestinal disorders. Preliminary evidence demonstrates that defects in neuronal nitric oxide synthase (nNOS) expression and function, the enzyme that synthesizes nitric oxide (NO), the key inhibitory neurotransmitter mediating mechano-electrical smooth muscle relaxation, is the major pathophysiological basis for sluggishness of oro-aboral transit of luminal contents. This opinion is an ansatz of the potential of skeletal muscle biopsy and examining sarcolemmal nNOSμ to provide complementary insights regarding nNOSα expression, localization, and function within enteric nerve terminals, the site of stimulated de novo NO synthesis. The main basis of this thesis is twofold: (a) the molecular similarity of the structures of nNOS α and μ, similar mechanisms of localizations to “active zones” of nitrergic synthesis, and same mechanisms of electron transfers during NO synthesis and (b) pragmatic difficulty to routinely obtain full-thickness biopsies of gastrointestinal tract, even in patients presenting with the most recalcitrant manifestations of stasis and delayed transit of luminal contents. This opinion attempts to provoke dialog whether this approach is feasible as a surrogate to predict catalytic potential of nNOSα and defects in nitrergic neurotransmission. This discussion makes an assumption that similar molecular mechanisms of nNOS defects shall be operant in both the enteric nerve terminals and the skeletal muscles. These overlaps of skeletal and gastrointestinal dysfunction are largely unknown, thus meriting that the thesis be validated in future by proof-of-principle experiments. PMID:26284245

Calculations of the excitation energies of all-trans and 11,12s-dicis retinals using localized molecular orbitals obtained by the elongation method

NASA Astrophysics Data System (ADS)

Kurihara, Youji; Aoki, Yuriko; Imamura, Akira

1997-09-01

In the present article, the excitation energies of the all-trans and the 11,12s-dicis retinals were calculated by using the elongation method. The geometries of these molecules were optimized with the 4-31G basis set by using the GAUSSIAN 92 program. The wave functions for the calculation of the excitation energies were obtained with CNDO/S approximation by the elongation method, which enables us to analyze electronic structures of aperiodic polymers in terms of the exciton-type local excitation and the charge transfer-type excitation. The excitation energies were calculated by using the single excitation configuration interaction (SECI) on the basis of localized molecular orbitals (LMOs). The LMOs were obtained in the process of the elongation method. The configuration interaction (CI) matrices were diagonalized by Davidson's method. The calculated results were in good agreement with the experimental data for absorption spectra. In order to consider the isomerization path from 11,12s-dicis to all-trans retinals, the barriers to the rotations about C11-C12 double and C12-C13 single bonds were evaluated.

Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1.

PubMed

Kronholm, Ilkka; Picó, F Xavier; Alonso-Blanco, Carlos; Goudet, Jérôme; de Meaux, Juliette

2012-07-01

Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation. © 2012 The Author(s).

Space-Pseudo-Time Method: Application to the One-Dimensional Coulomb Potential and Density Funtional Theory

NASA Astrophysics Data System (ADS)

Weatherford, Charles; Gebremedhin, Daniel

2016-03-01

A new and efficient way of evolving a solution to an ordinary differential equation is presented. A finite element method is used where we expand in a convenient local basis set of functions that enforce both function and first derivative continuity across the boundaries of each element. We also implement an adaptive step size choice for each element that is based on a Taylor series expansion. The method is applied to solve for the eigenpairs of the one-dimensional soft-coulomb potential and the hard-coulomb limit is studied. The method is then used to calculate a numerical solution of the Kohn-Sham differential equation within the local density approximation is presented and is applied to the helium atom. Supported by the National Nuclear Security Agency, the Nuclear Regulatory Commission, and the Defense Threat Reduction Agency.

A complete active space valence bond method with nonorthogonal orbitals

NASA Astrophysics Data System (ADS)

Hirao, Kimihiko; Nakano, Haruyuki; Nakayama, Kenichi

1997-12-01

A complete active space self-consistent field (SCF) wave function is transformed into a valence bond type representation built from nonorthogonal orbitals, each strongly localized on a single atom. Nonorthogonal complete active space SCF orbitals are constructed by Ruedenberg's projected localization procedure so that they have maximal overlaps with the corresponding minimum basis set of atomic orbitals of the free-atoms. The valence bond structures which are composed of such nonorthogonal quasiatomic orbitals constitute the wave function closest to the concept of the oldest and most simple valence bond method. The method is applied to benzene, butadiene, hydrogen, and methane molecules and compared to the previously proposed complete active space valence bond approach with orthogonal orbitals. The results demonstrate the validity of the method as a powerful tool for describing the electronic structure of various molecules.

A projection-free method for representing plane-wave DFT results in an atom-centered basis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunnington, Benjamin D.; Schmidt, J. R., E-mail: schmidt@chem.wisc.edu

2015-09-14

Plane wave density functional theory (DFT) is a powerful tool for gaining accurate, atomic level insight into bulk and surface structures. Yet, the delocalized nature of the plane wave basis set hinders the application of many powerful post-computation analysis approaches, many of which rely on localized atom-centered basis sets. Traditionally, this gap has been bridged via projection-based techniques from a plane wave to atom-centered basis. We instead propose an alternative projection-free approach utilizing direct calculation of matrix elements of the converged plane wave DFT Hamiltonian in an atom-centered basis. This projection-free approach yields a number of compelling advantages, including strictmore » orthonormality of the resulting bands without artificial band mixing and access to the Hamiltonian matrix elements, while faithfully preserving the underlying DFT band structure. The resulting atomic orbital representation of the Kohn-Sham wavefunction and Hamiltonian provides a gateway to a wide variety of analysis approaches. We demonstrate the utility of the approach for a diverse set of chemical systems and example analysis approaches.« less

SIEST-A-RT: a study of vacancy diffusion in crystalline silicon using a local-basis first-principle (SIESTA) activation technique (ART).

NASA Astrophysics Data System (ADS)

El Mellouhi, Fedwa; Mousseau, Normand; Ordejón, Pablo

2003-03-01

We report on a first-principle study of vacancy-induced self-diffusion in crystalline silicon. Our simulations are performed on supercells containing 63 and 215 atoms. We generate the diffusion paths using the activation-relaxation technique (ART) [1], which can sample efficiently the energy landscape of complex systems. The forces and energy are evaluated using SIESTA [2], a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible numerical linear combination of atomic orbitals basis set. Combining these two methods allows us to identify diffusion paths that would not be reachable with this degree of accuracy, using other methods. After a full relaxation of the neutral vacancy, we proceed to search for local diffusion paths. We identify various mechanisms like the formation of the four fold coordinated defect, and the recombination of dangling bonds by WWW process. The diffusion of the vacancy proceeds by hops to first nearest neighbor with an energy barrier of 0.69 eV. This work is funded in part by NSERC and NATEQ. NM is a Cottrell Scholar of the Research Corporation. [1] G. T. Barkema and N. Mousseau, Event-based relaxation of continuous disordered systems, Phys. Rev. Lett. 77, 4358 (1996); N. Mousseau and G. T. Barkema, Traveling through potential energy landscapes of disordered materials: ART, Phys. Rev. E 57, 2419 (1998). [2] Density functional method for very large systems with LCAO basis sets D. Sánchez-Portal, P. Ordejón, E. Artacho and J. M. Soler, Int. J. Quant. Chem. 65, 453 (1997).

Local activity determines functional connectivity in the resting human brain: a simultaneous FDG-PET/fMRI study.

PubMed

Riedl, Valentin; Bienkowska, Katarzyna; Strobel, Carola; Tahmasian, Masoud; Grimmer, Timo; Förster, Stefan; Friston, Karl J; Sorg, Christian; Drzezga, Alexander

2014-04-30

Over the last decade, synchronized resting-state fluctuations of blood oxygenation level-dependent (BOLD) signals between remote brain areas [so-called BOLD resting-state functional connectivity (rs-FC)] have gained enormous relevance in systems and clinical neuroscience. However, the neural underpinnings of rs-FC are still incompletely understood. Using simultaneous positron emission tomography/magnetic resonance imaging we here directly investigated the relationship between rs-FC and local neuronal activity in humans. Computational models suggest a mechanistic link between the dynamics of local neuronal activity and the functional coupling among distributed brain regions. Therefore, we hypothesized that the local activity (LA) of a region at rest determines its rs-FC. To test this hypothesis, we simultaneously measured both LA (glucose metabolism) and rs-FC (via synchronized BOLD fluctuations) during conditions of eyes closed or eyes open. During eyes open, LA increased in the visual system, and the salience network (i.e., cingulate and insular cortices) and the pattern of elevated LA coincided almost exactly with the spatial pattern of increased rs-FC. Specifically, the voxelwise regional profile of LA in these areas strongly correlated with the regional pattern of rs-FC among the same regions (e.g., LA in primary visual cortex accounts for ∼ 50%, and LA in anterior cingulate accounts for ∼ 20% of rs-FC with the visual system). These data provide the first direct evidence in humans that local neuronal activity determines BOLD FC at rest. Beyond its relevance for the neuronal basis of coherent BOLD signal fluctuations, our procedure may translate into clinical research particularly to investigate potentially aberrant links between local dynamics and remote functional coupling in patients with neuropsychiatric disorders.

First-principles investigation on Rydberg and resonance excitations: A case study of the firefly luciferin anion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noguchi, Yoshifumi, E-mail: y.noguchi@issp.u-tokyo.ac.jp; Hiyama, Miyabi; Akiyama, Hidefumi

2014-07-28

The optical properties of an isolated firefly luciferin anion are investigated by using first-principles calculations, employing the many-body perturbation theory to take into account the excitonic effect. The calculated photoabsorption spectra are compared with the results obtained using the time-dependent density functional theory (TDDFT) employing the localized atomic orbital (AO) basis sets and a recent experiment in vacuum. The present method well reproduces the line shape at the photon energy corresponding to the Rydberg and resonance excitations but overestimates the peak positions by about 0.5 eV. However, the TDDFT-calculated positions of some peaks are closer to those of the experiment.more » We also investigate the basis set dependency in describing the free electron states above vacuum level and the excitons involving the transitions to the free electron states and conclude that AO-only basis sets are inaccurate for free electron states and the use of a plane wave basis set is required.« less

Potential energy surface fitting by a statistically localized, permutationally invariant, local interpolating moving least squares method for the many-body potential: Method and application to N{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bender, Jason D.; Doraiswamy, Sriram; Candler, Graham V., E-mail: truhlar@umn.edu, E-mail: candler@aem.umn.edu

2014-02-07

Fitting potential energy surfaces to analytic forms is an important first step for efficient molecular dynamics simulations. Here, we present an improved version of the local interpolating moving least squares method (L-IMLS) for such fitting. Our method has three key improvements. First, pairwise interactions are modeled separately from many-body interactions. Second, permutational invariance is incorporated in the basis functions, using permutationally invariant polynomials in Morse variables, and in the weight functions. Third, computational cost is reduced by statistical localization, in which we statistically correlate the cutoff radius with data point density. We motivate our discussion in this paper with amore » review of global and local least-squares-based fitting methods in one dimension. Then, we develop our method in six dimensions, and we note that it allows the analytic evaluation of gradients, a feature that is important for molecular dynamics. The approach, which we call statistically localized, permutationally invariant, local interpolating moving least squares fitting of the many-body potential (SL-PI-L-IMLS-MP, or, more simply, L-IMLS-G2), is used to fit a potential energy surface to an electronic structure dataset for N{sub 4}. We discuss its performance on the dataset and give directions for further research, including applications to trajectory calculations.« less

CCHCR1 interacts with EDC4, suggesting its localization in P-bodies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ling, Y.H.; Wong, C.C.; Li, K.W.

2014-09-10

Coiled‐coil alpha‐helical rod protein 1 (CCHCR1) is suggested as a candidate biomarker for psoriasis for more than a decade but its function remains poorly understood because of the inconsistent findings in the literature. CCHCR1 protein is suggested to be localized in the cytoplasm, nucleus, mitochondria, or centrosome and to regulate various cellular functions, including steroidogenesis, proliferation, differentiation, and cytoskeleton organization. In this study, we attempted to find a consensus between these findings by identifying the interaction partners of CCHCR1 using co-immunoprecipiation with a stable cell line expressing EGFP-tagged CCHCR1. Out of more than 100 co-immunoprecipitants identified by liquid chromatography-tandem massmore » spectrometry (LC-MS/MS), the enhancer of mRNA-decapping protein 4 (EDC4), which is a processing body (P-body) component, was particularly found to be the major interacting partner of CCHCR1. Confocal imaging confirmed the localization of CCHCR1 in P-bodies and its N-terminus is required for this subcellular localization, suggesting that CCHCR1 is a novel P-body component. As P-bodies are the site for mRNA metabolism, our findings provide a molecular basis for the function of CCHCR1, any disruption of which may affect the transcriptome of the cell, and causing abnormal cell functions. - Highlights: • We identified CCHCR1 as a novel P-body component. • We identified EDC4 as the major interacting partner of CCHCR1. • N-terminus of CCHCR1 protein is required for its P-bodies localization.« less

Distinct regions of the Phytophthora essential effector Avh238 determine its function in cell death activation and plant immunity suppression.

PubMed

Yang, Bo; Wang, Qunqing; Jing, Maofeng; Guo, Baodian; Wu, Jiawei; Wang, Haonan; Wang, Yang; Lin, Long; Wang, Yan; Ye, Wenwu; Dong, Suomeng; Wang, Yuanchao

2017-04-01

Phytophthora pathogens secrete effectors to manipulate host innate immunity, thus facilitating infection. Among the RXLR effectors highly induced during Phytophthora sojae infection, Avh238 not only contributes to pathogen virulence but also triggers plant cell death. However, the detailed molecular basis of Avh238 functions remains largely unknown. We mapped the regions responsible for Avh238 functions in pathogen virulence and plant cell death induction using a strategy that combines investigation of natural variation and large-scale mutagenesis assays. The correlation between cellular localization and Avh238 functions was also evaluated. We found that the 79 th residue (histidine or leucine) of Avh238 determined its cell death-inducing activity, and that the 53 amino acids in its C-terminal region are responsible for promoting Phytophthora infection. Transient expression of Avh238 in Nicotiana benthamiana revealed that nuclear localization is essential for triggering cell death, while Avh238-mediated suppression of INF1-triggered cell death requires cytoplasmic localization. Our results demonstrate that a representative example of an essential Phytophthora RXLR effector can evolve to escape recognition by the host by mutating one nucleotide site, and can also retain plant immunosuppressive activity to enhance pathogen virulence in planta. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Propagation and stability of wavelike solutions of finite difference equations with variable coefficients

NASA Technical Reports Server (NTRS)

Giles, M. B.; Thompkins, W. T., Jr.

1985-01-01

The propagation and dissipation of wavelike solutions to finite difference equations is analyzed on the basis of an asymptotic approach in which a wave solution is expressed as a product of a complex amplitude and an oscillatory phase function whose frequency and wavenumber may also be complex. An asymptotic expansion leads to a local dispersion relation for wavenumber and frequency; the first-order terms produce an equation for the amplitude in which the local group velocity appears as the convection velocity of the amplitude. Equations for the motion of wavepackets and their interaction at boundaries are derived, and a global stability analysis is carried out.

Measurement of the local muscular metabolism by time-domain near infrared spectroscopy during knee flex-extension induced by functional electrical stimulation

NASA Astrophysics Data System (ADS)

Contini, D.; Spinelli, L.; Torricelli, A.; Ferrante, S.; Pedrocchi, A.; Molteni, F.; Ferrigno, G.; Cubeddu, R.

2009-02-01

We present a preliminary study that combines functional electrical stimulation and time-domain near infrared spectroscopy for a quantitative measurement of the local muscular metabolism during rehabilitation of post-acute stroke patients. Seven healthy subjects and nine post-acute stroke patients underwent a protocol of knee flex-extension of the quadriceps induced by functional electrical stimulation. During the protocol time-domain near infrared spectroscopy measurement were performed on both left and right muscle. Hemodynamic parameters (concentration of oxy- and deoxy-genated hemoglobin) during baseline did not show any significant differences between healthy subject and patients, while functional performances (knee angle amplitude) were distinctly different. Nevertheless, even if their clinical histories were noticeably different, there was no differentiation among functional performances of patients. On the basis of the hemodynamic parameters measured during the recovery phase, instead, it was possible to identify two classes of patients showing a metabolic trend similar or very different to the one obtained by healthy subjects. The presented results suggest that the combination of functional and metabolic information can give an additional tool to the clinicians in the evaluation of the rehabilitation in post-acute stroke patients.

Global/local methods for probabilistic structural analysis

NASA Technical Reports Server (NTRS)

Millwater, H. R.; Wu, Y.-T.

1993-01-01

A probabilistic global/local method is proposed to reduce the computational requirements of probabilistic structural analysis. A coarser global model is used for most of the computations with a local more refined model used only at key probabilistic conditions. The global model is used to establish the cumulative distribution function (cdf) and the Most Probable Point (MPP). The local model then uses the predicted MPP to adjust the cdf value. The global/local method is used within the advanced mean value probabilistic algorithm. The local model can be more refined with respect to the g1obal model in terms of finer mesh, smaller time step, tighter tolerances, etc. and can be used with linear or nonlinear models. The basis for this approach is described in terms of the correlation between the global and local models which can be estimated from the global and local MPPs. A numerical example is presented using the NESSUS probabilistic structural analysis program with the finite element method used for the structural modeling. The results clearly indicate a significant computer savings with minimal loss in accuracy.

Global/local methods for probabilistic structural analysis

NASA Astrophysics Data System (ADS)

Millwater, H. R.; Wu, Y.-T.

1993-04-01

A probabilistic global/local method is proposed to reduce the computational requirements of probabilistic structural analysis. A coarser global model is used for most of the computations with a local more refined model used only at key probabilistic conditions. The global model is used to establish the cumulative distribution function (cdf) and the Most Probable Point (MPP). The local model then uses the predicted MPP to adjust the cdf value. The global/local method is used within the advanced mean value probabilistic algorithm. The local model can be more refined with respect to the g1obal model in terms of finer mesh, smaller time step, tighter tolerances, etc. and can be used with linear or nonlinear models. The basis for this approach is described in terms of the correlation between the global and local models which can be estimated from the global and local MPPs. A numerical example is presented using the NESSUS probabilistic structural analysis program with the finite element method used for the structural modeling. The results clearly indicate a significant computer savings with minimal loss in accuracy.

Direct Density Functional Energy Minimization using an Tetrahedral Finite Element Grid

NASA Astrophysics Data System (ADS)

Vaught, A.; Schmidt, K. E.; Chizmeshya, A. V. G.

1998-03-01

We describe an O(N) (N proportional to volume) technique for solving electronic structure problems using the finite element method (FEM). A real--space tetrahedral grid is used as a basis to represent the electronic density, of a free or periodic system and Poisson's equation is solved as a boundary value problem. Nuclear cusps are treated using a local grid consisting of radial elements. These features facilitate the implementation of complicated energy functionals and permit a direct (constrained) energy minimization with respect to the density. We demonstrate the usefulness of the scheme by calculating the binding trends and polarizabilities of a number of atoms and molecules using a number of recently proposed non--local, orbital--free kinetic energy functionals^1,2. Scaling behavior, computational efficiency and the generalization to band--structure will also be discussed. indent 0 pt øbeylines øbeyspaces skip 0 pt ^1 P. Garcia-Gonzalez, J.E. Alvarellos and E. Chacon, Phys. Rev. B 54, 1897 (1996). ^2 A. J. Thakkar, Phys.Rev.B 46, 6920 (1992).

Locally indistinguishable orthogonal product bases in arbitrary bipartite quantum system

PubMed Central

Xu, Guang-Bao; Yang, Ying-Hui; Wen, Qiao-Yan; Qin, Su-Juan; Gao, Fei

2016-01-01

As we know, unextendible product basis (UPB) is an incomplete basis whose members cannot be perfectly distinguished by local operations and classical communication. However, very little is known about those incomplete and locally indistinguishable product bases that are not UPBs. In this paper, we first construct a series of orthogonal product bases that are completable but not locally distinguishable in a general m ⊗ n (m ≥ 3 and n ≥ 3) quantum system. In particular, we give so far the smallest number of locally indistinguishable states of a completable orthogonal product basis in arbitrary quantum systems. Furthermore, we construct a series of small and locally indistinguishable orthogonal product bases in m ⊗ n (m ≥ 3 and n ≥ 3). All the results lead to a better understanding of the structures of locally indistinguishable product bases in arbitrary bipartite quantum system. PMID:27503634

Lump solutions to nonlinear partial differential equations via Hirota bilinear forms

NASA Astrophysics Data System (ADS)

Ma, Wen-Xiu; Zhou, Yuan

2018-02-01

Lump solutions are analytical rational function solutions localized in all directions in space. We analyze a class of lump solutions, generated from quadratic functions, to nonlinear partial differential equations. The basis of success is the Hirota bilinear formulation and the primary object is the class of positive multivariate quadratic functions. A complete determination of quadratic functions positive in space and time is given, and positive quadratic functions are characterized as sums of squares of linear functions. Necessary and sufficient conditions for positive quadratic functions to solve Hirota bilinear equations are presented, and such polynomial solutions yield lump solutions to nonlinear partial differential equations under the dependent variable transformations u = 2(ln ⁡ f) x and u = 2(ln ⁡ f) xx, where x is one spatial variable. Applications are made for a few generalized KP and BKP equations.

Functional genomics of physiological plasticity and local adaptation in killifish.

PubMed

Whitehead, Andrew; Galvez, Fernando; Zhang, Shujun; Williams, Larissa M; Oleksiak, Marjorie F

2011-01-01

Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted phenotypes within different selective contexts, providing a comparative system in which to explore the genomic underpinnings of physiological plasticity and adaptive variation. Importantly, extensive variation exists among populations and species for tolerance to a variety of stressors, and we exploit this variation in comparative studies to yield insights into the genomic basis of evolved phenotypic variation. Notably, species of Fundulus occupy the continuum of osmotic habitats from freshwater to marine and populations within Fundulus heteroclitus span far greater variation in pollution tolerance than across all species of fish. Here, we explore how transcriptome regulation underpins extreme physiological plasticity on osmotic shock and how genomic and transcriptomic variation is associated with locally evolved pollution tolerance. We show that F. heteroclitus quickly acclimate to extreme osmotic shock by mounting a dramatic rapid transcriptomic response including an early crisis control phase followed by a tissue remodeling phase involving many regulatory pathways. We also show that convergent evolution of locally adapted pollution tolerance involves complex patterns of gene expression and genome sequence variation, which is confounded with body-weight dependence for some genes. Similarly, exploiting the natural phenotypic variation associated with other established and emerging model organisms is likely to greatly accelerate the pace of discovery of the genomic basis of phenotypic variation.

Functional Genomics of Physiological Plasticity and Local Adaptation in Killifish

PubMed Central

Galvez, Fernando; Zhang, Shujun; Williams, Larissa M.; Oleksiak, Marjorie F.

2011-01-01

Evolutionary solutions to the physiological challenges of life in highly variable habitats can span the continuum from evolution of a cosmopolitan plastic phenotype to the evolution of locally adapted phenotypes. Killifish (Fundulus sp.) have evolved both highly plastic and locally adapted phenotypes within different selective contexts, providing a comparative system in which to explore the genomic underpinnings of physiological plasticity and adaptive variation. Importantly, extensive variation exists among populations and species for tolerance to a variety of stressors, and we exploit this variation in comparative studies to yield insights into the genomic basis of evolved phenotypic variation. Notably, species of Fundulus occupy the continuum of osmotic habitats from freshwater to marine and populations within Fundulus heteroclitus span far greater variation in pollution tolerance than across all species of fish. Here, we explore how transcriptome regulation underpins extreme physiological plasticity on osmotic shock and how genomic and transcriptomic variation is associated with locally evolved pollution tolerance. We show that F. heteroclitus quickly acclimate to extreme osmotic shock by mounting a dramatic rapid transcriptomic response including an early crisis control phase followed by a tissue remodeling phase involving many regulatory pathways. We also show that convergent evolution of locally adapted pollution tolerance involves complex patterns of gene expression and genome sequence variation, which is confounded with body-weight dependence for some genes. Similarly, exploiting the natural phenotypic variation associated with other established and emerging model organisms is likely to greatly accelerate the pace of discovery of the genomic basis of phenotypic variation. PMID:20581107

Energy-switching potential energy surface for the water molecule revisited: A highly accurate singled-sheeted form.

PubMed

Galvão, B R L; Rodrigues, S P J; Varandas, A J C

2008-07-28

A global ab initio potential energy surface is proposed for the water molecule by energy-switching/merging a highly accurate isotope-dependent local potential function reported by Polyansky et al. [Science 299, 539 (2003)] with a global form of the many-body expansion type suitably adapted to account explicitly for the dynamical correlation and parametrized from extensive accurate multireference configuration interaction energies extrapolated to the complete basis set limit. The new function mimics also the complicated Sigma/Pi crossing that arises at linear geometries of the water molecule.

Incorporating surrogate species and seascape connectivity to improve marine conservation outcomes.

PubMed

Olds, Andrew D; Connolly, Rod M; Pitt, Kylie A; Maxwell, Paul S; Aswani, Shankar; Albert, Simon

2014-08-01

Conservation focuses on maintaining biodiversity and ecosystem functioning, but gaps in our knowledge of species biology and ecological processes often impede progress. For this reason, focal species and habitats are used as surrogates for multispecies conservation, but species-based approaches are not widely adopted in marine ecosystems. Reserves in the Solomon Islands were designed on the basis of local ecological knowledge to conserve bumphead parrotfish (Bolbometopon muricatum) and to protect food security and ecosystem functioning. Bumphead parrotfish are an iconic threatened species and may be a useful surrogate for multispecies conservation. They move across tropical seascapes throughout their life history, in a pattern of habitat use that is shared with many other species. We examined their value as a conservation surrogate and assessed the importance of seascape connectivity (i.e., the physical connectedness of patches in the seascape) among reefs, mangroves, and seagrass to marine reserve performance. Reserves were designed for bumphead parrotfish, but also enhanced the abundance of other species. Integration of local ecological knowledge and seascape connectivity enhanced the abundance of 17 other harvested fish species in local reserves. This result has important implications for ecosystem functioning and local villagers because many of these species perform important ecological processes and provide the foundation for extensive subsistence fisheries. Our findings suggest greater success in maintaining and restoring marine ecosystems may be achieved when they are managed to conserve surrogate species and preserve functional seascape connections. © 2014 Society for Conservation Biology.

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.

PubMed

Hoban, Sean; Kelley, Joanna L; Lotterhos, Katie E; Antolin, Michael F; Bradburd, Gideon; Lowry, David B; Poss, Mary L; Reed, Laura K; Storfer, Andrew; Whitlock, Michael C

2016-10-01

Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

High-order local maximum principle preserving (MPP) discontinuous Galerkin finite element method for the transport equation

NASA Astrophysics Data System (ADS)

Anderson, R.; Dobrev, V.; Kolev, Tz.; Kuzmin, D.; Quezada de Luna, M.; Rieben, R.; Tomov, V.

2017-04-01

In this work we present a FCT-like Maximum-Principle Preserving (MPP) method to solve the transport equation. We use high-order polynomial spaces; in particular, we consider up to 5th order spaces in two and three dimensions and 23rd order spaces in one dimension. The method combines the concepts of positive basis functions for discontinuous Galerkin finite element spatial discretization, locally defined solution bounds, element-based flux correction, and non-linear local mass redistribution. We consider a simple 1D problem with non-smooth initial data to explain and understand the behavior of different parts of the method. Convergence tests in space indicate that high-order accuracy is achieved. Numerical results from several benchmarks in two and three dimensions are also reported.

Solution of free-boundary problems using finite-element/Newton methods and locally refined grids - Application to analysis of solidification microstructure

NASA Technical Reports Server (NTRS)

Tsiveriotis, K.; Brown, R. A.

1993-01-01

A new method is presented for the solution of free-boundary problems using Lagrangian finite element approximations defined on locally refined grids. The formulation allows for direct transition from coarse to fine grids without introducing non-conforming basis functions. The calculation of elemental stiffness matrices and residual vectors are unaffected by changes in the refinement level, which are accounted for in the loading of elemental data to the global stiffness matrix and residual vector. This technique for local mesh refinement is combined with recently developed mapping methods and Newton's method to form an efficient algorithm for the solution of free-boundary problems, as demonstrated here by sample calculations of cellular interfacial microstructure during directional solidification of a binary alloy.

Relaxation of Actinide Surfaces: An All Electron Study

NASA Astrophysics Data System (ADS)

Atta-Fynn, Raymond; Dholabhai, Pratik; Ray, Asok

2006-10-01

Fully relativistic full potential density functional calculations with a linearized augmented plane wave plus local orbitals basis (LAPW + lo) have been performed to investigate the relaxations of heavy actinide surfaces, namely the (111) surface of fcc δ-Pu and the (0001) surface of dhcp Am using WIEN2k. This code uses the LAPW + lo method with the unit cell divided into non-overlapping atom-centered spheres and an interstitial region. The APW+lo basis is used to describe all s, p, d, and f states and LAPW basis to describe all higher angular momentum states. Each surface was modeled by a three-layer periodic slab separated by 60 Bohr vacuum with four atoms per surface unit cell. In general, we have found a contraction of the interlayer separations for both Pu and Am. We will report, in detail, the electronic and geometric structures of the relaxed surfaces and comparisons with the respective non-relaxed surfaces.

Optimization of the linear-scaling local natural orbital CCSD(T) method: Redundancy-free triples correction using Laplace transform.

PubMed

Nagy, Péter R; Kállay, Mihály

2017-06-07

An improved algorithm is presented for the evaluation of the (T) correction as a part of our local natural orbital (LNO) coupled-cluster singles and doubles with perturbative triples [LNO-CCSD(T)] scheme [Z. Rolik et al., J. Chem. Phys. 139, 094105 (2013)]. The new algorithm is an order of magnitude faster than our previous one and removes the bottleneck related to the calculation of the (T) contribution. First, a numerical Laplace transformed expression for the (T) fragment energy is introduced, which requires on average 3 to 4 times fewer floating point operations with negligible compromise in accuracy eliminating the redundancy among the evaluated triples amplitudes. Second, an additional speedup factor of 3 is achieved by the optimization of our canonical (T) algorithm, which is also executed in the local case. These developments can also be integrated into canonical as well as alternative fragmentation-based local CCSD(T) approaches with minor modifications. As it is demonstrated by our benchmark calculations, the evaluation of the new Laplace transformed (T) correction can always be performed if the preceding CCSD iterations are feasible, and the new scheme enables the computation of LNO-CCSD(T) correlation energies with at least triple-zeta quality basis sets for realistic three-dimensional molecules with more than 600 atoms and 12 000 basis functions in a matter of days on a single processor.

Molecular basis for repression of liver X receptor-mediated gene transcription by receptor-interacting protein 140

PubMed Central

Jakobsson, Tomas; Osman, Waffa; Gustafsson, Jan-Åke; Zilliacus, Johanna; Wärnmark, Anette

2007-01-01

Similarities in physiological roles of LXR (liver X receptors) and co-repressor RIP140 (receptor-interacting protein 140) in regulating energy homoeostasis and lipid and glucose metabolism suggest that the effects of LXR could at least partly be mediated by recruitment of the co-repressor RIP140. In the present study, we have elucidated the molecular basis for regulation of LXR transcriptional activity by RIP140. LXR is evenly localized in the nucleus and neither the N-terminal domain nor the LBD (ligand-binding domain) is necessary for nuclear localization. Both LXR subtypes, LXRα and LXRβ, interact with RIP140 and co-localize in diffuse large nuclear domains. Interaction and co-localization are dependent on the LBD of the receptor. The C-terminal domain of RIP140 is sufficient for full repressive effect. None of the C-terminal NR (nuclear receptor)-boxes is required for the co-repressor activity, whereas the NR-box-like motif as well as additional elements in the C-terminal region are required for full repressive function. The C-terminal NR-box-like motif is necessary for interaction with LXRβ, whereas additional elements are needed for strong interaction with LXRα. In conclusion, our results suggest that co-repression of LXR activity by RIP140 involves an atypical binding mode of RIP140 and a repression element in the RIP140 C-terminus. PMID:17391100

Optimization of the linear-scaling local natural orbital CCSD(T) method: Redundancy-free triples correction using Laplace transform

PubMed Central

2017-01-01

An improved algorithm is presented for the evaluation of the (T) correction as a part of our local natural orbital (LNO) coupled-cluster singles and doubles with perturbative triples [LNO-CCSD(T)] scheme [Z. Rolik et al., J. Chem. Phys. 139, 094105 (2013)]. The new algorithm is an order of magnitude faster than our previous one and removes the bottleneck related to the calculation of the (T) contribution. First, a numerical Laplace transformed expression for the (T) fragment energy is introduced, which requires on average 3 to 4 times fewer floating point operations with negligible compromise in accuracy eliminating the redundancy among the evaluated triples amplitudes. Second, an additional speedup factor of 3 is achieved by the optimization of our canonical (T) algorithm, which is also executed in the local case. These developments can also be integrated into canonical as well as alternative fragmentation-based local CCSD(T) approaches with minor modifications. As it is demonstrated by our benchmark calculations, the evaluation of the new Laplace transformed (T) correction can always be performed if the preceding CCSD iterations are feasible, and the new scheme enables the computation of LNO-CCSD(T) correlation energies with at least triple-zeta quality basis sets for realistic three-dimensional molecules with more than 600 atoms and 12 000 basis functions in a matter of days on a single processor. PMID:28576082

Quantum mechanics of a photon

NASA Astrophysics Data System (ADS)

Babaei, Hassan; Mostafazadeh, Ali

2017-08-01

A first-quantized free photon is a complex massless vector field A =(Aμ ) whose field strength satisfies Maxwell's equations in vacuum. We construct the Hilbert space H of the photon by endowing the vector space of the fields A in the temporal-Coulomb gauge with a positive-definite and relativistically invariant inner product. We give an explicit expression for this inner product, identify the Hamiltonian for the photon with the generator of time translations in H , determine the operators representing the momentum and the helicity of the photon, and introduce a chirality operator whose eigenfunctions correspond to fields having a definite sign of energy. We also construct a position operator for the photon whose components commute with each other and with the chirality and helicity operators. This allows for the construction of the localized states of the photon with a definite sign of energy and helicity. We derive an explicit formula for the latter and compute the corresponding electric and magnetic fields. These turn out to diverge not just at the point where the photon is localized but on a plane containing this point. We identify the axis normal to this plane with an associated symmetry axis and show that each choice of this axis specifies a particular position operator, a corresponding position basis, and a position representation of the quantum mechanics of a photon. In particular, we examine the position wave functions determined by such a position basis, elucidate their relationship with the Riemann-Silberstein and Landau-Peierls wave functions, and give an explicit formula for the probability density of the spatial localization of the photon.

Bacterial chemoreceptors: high-performance signaling in networked arrays.

PubMed

Hazelbauer, Gerald L; Falke, Joseph J; Parkinson, John S

2008-01-01

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on-off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device.

The calculations of small molecular conformation energy differences by density functional method

NASA Astrophysics Data System (ADS)

Topol, I. A.; Burt, S. K.

1993-03-01

The differences in the conformational energies for the gauche (G) and trans(T) conformers of 1,2-difluoroethane and for myo-and scyllo-conformer of inositol have been calculated by local density functional method (LDF approximation) with geometry optimization using different sets of calculation parameters. It is shown that in the contrast to Hartree—Fock methods, density functional calculations reproduce the correct sign and value of the gauche effect for 1,2-difluoroethane and energy difference for both conformers of inositol. The results of normal vibrational analysis for1,2-difluoroethane showed that harmonic frequencies calculated in LDF approximation agree with experimental data with the accuracy typical for scaled large basis set Hartree—Fock calculations.

Bacterial chemoreceptors: high-performance signaling in networked arrays

PubMed Central

Hazelbauer, Gerald L.; Falke, Joseph J.; Parkinson, John S.

2010-01-01

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on–off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device. PMID:18165013

Anomalous current from the covariant Wigner function

NASA Astrophysics Data System (ADS)

Prokhorov, George; Teryaev, Oleg

2018-04-01

We consider accelerated and rotating media of weakly interacting fermions in local thermodynamic equilibrium on the basis of kinetic approach. Kinetic properties of such media can be described by covariant Wigner function incorporating the relativistic distribution functions of particles with spin. We obtain the formulae for axial current by summation of the terms of all orders of thermal vorticity tensor, chemical potential, both for massive and massless particles. In the massless limit all the terms of fourth and higher orders of vorticity and third order of chemical potential and temperature equal zero. It is shown, that axial current gets a topological component along the 4-acceleration vector. The similarity between different approaches to baryon polarization is established.

Macrodactyly, syndactyly, and localized gigantism of the forefoot. A case report.

PubMed

Scapinelli, R; Baggio, M E

2005-01-01

On the basis of the observation of a rare case of lipomatous macrodactyly of the foot associated with syndactyly in a young child, the authors analyze the anatomopathologic and therapeutic aspects of the pathology and report the data found in the literature. This disease initially requires careful surveillance of its progression, and use of correct footwear. Surgery is indicated when deformity achieves unacceptable values, both functional and cosmetic, in early childhood.

Pseudopotential plane-wave calculation of the structural properties of yttrium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Y.; Chou, M.Y.

1991-11-01

The structural properties of hexagonal-close-packed yttrium are studied by using the plane-wave basis within the pseudopotential method and local-density-functional approximation. By employing a soft'' pseudopotential proposed by Troullier and Martins, satisfactory convergence is achieved with a plane-wave energy cutoff of 30--40 Ry for this early-transition-metal element. The overall results for the structural properties are in good agreement with experiment. It is found that the charge overlap between core and valence electrons has a substantial effect on the accuracy of the calculated structural properties. Two different calculations are performed with and without the outer-core 4{ital p} orbital included as a valencemore » state. In addition, as found in some other local-density calculations, the uncertainty in the results due to different exchange-correlation energy functionals may not be negligible in transition metals.« less

Neuropsychiatry. An old discipline in a new gestalt bridging biological psychiatry, neuropsychology, and cognitive neurology.

PubMed

Northoff, Georg

2008-06-01

The recent developments of psychiatry getting better insight into the biological basis of psychiatric disorders questions the old division between psychiatry and neurology. The present paper focus on the concept of neuropsychiatry, its historical antecedents and closely associated disciplines like biological psychiatry, behavioral neurology and neuropsychology. A special emphasis is put on the question of function and localization; the suggestions are made that the concept of neuronal integration may bridge the often discussed gap between localization and holism in the relation between function and brain regions. Examples of different mechanisms of neuronal integration are discussed and applied to specific neuropsychiatric disorders. It is concluded that the concept of neuronal integration may offer an appropriate conceptual tool to establish the concept of neuropsychiatry in a new and meaningful gestalt at the interface between biological psychiatry, neuropsychology and cognitive neurology.

Meshfree truncated hierarchical refinement for isogeometric analysis

NASA Astrophysics Data System (ADS)

Atri, H. R.; Shojaee, S.

2018-05-01

In this paper truncated hierarchical B-spline (THB-spline) is coupled with reproducing kernel particle method (RKPM) to blend advantages of the isogeometric analysis and meshfree methods. Since under certain conditions, the isogeometric B-spline and NURBS basis functions are exactly represented by reproducing kernel meshfree shape functions, recursive process of producing isogeometric bases can be omitted. More importantly, a seamless link between meshfree methods and isogeometric analysis can be easily defined which provide an authentic meshfree approach to refine the model locally in isogeometric analysis. This procedure can be accomplished using truncated hierarchical B-splines to construct new bases and adaptively refine them. It is also shown that the THB-RKPM method can provide efficient approximation schemes for numerical simulations and represent a promising performance in adaptive refinement of partial differential equations via isogeometric analysis. The proposed approach for adaptive locally refinement is presented in detail and its effectiveness is investigated through well-known benchmark examples.

Driving Human Motor Cortical Oscillations Leads to Behaviorally Relevant Changes in Local GABAA Inhibition: A tACS-TMS Study

PubMed Central

van Ede, Freek

2017-01-01

Beta and gamma oscillations are the dominant oscillatory activity in the human motor cortex (M1). However, their physiological basis and precise functional significance remain poorly understood. Here, we used transcranial magnetic stimulation (TMS) to examine the physiological basis and behavioral relevance of driving beta and gamma oscillatory activity in the human M1 using transcranial alternating current stimulation (tACS). tACS was applied using a sham-controlled crossover design at individualized intensity for 20 min and TMS was performed at rest (before, during, and after tACS) and during movement preparation (before and after tACS). We demonstrated that driving gamma frequency oscillations using tACS led to a significant, duration-dependent decrease in local resting-state GABAA inhibition, as quantified by short interval intracortical inhibition. The magnitude of this effect was positively correlated with the magnitude of GABAA decrease during movement preparation, when gamma activity in motor circuitry is known to increase. In addition, gamma tACS-induced change in GABAA inhibition was closely related to performance in a motor learning task such that subjects who demonstrated a greater increase in GABAA inhibition also showed faster short-term learning. The findings presented here contribute to our understanding of the neurophysiological basis of motor rhythms and suggest that tACS may have similar physiological effects to endogenously driven local oscillatory activity. Moreover, the ability to modulate local interneuronal circuits by tACS in a behaviorally relevant manner provides a basis for tACS as a putative therapeutic intervention. SIGNIFICANCE STATEMENT Gamma oscillations have a vital role in motor control. Using a combined tACS-TMS approach, we demonstrate that driving gamma frequency oscillations modulates GABAA inhibition in the human motor cortex. Moreover, there is a clear relationship between the change in magnitude of GABAA inhibition induced by tACS and the magnitude of GABAA inhibition observed during task-related synchronization of oscillations in inhibitory interneuronal circuits, supporting the hypothesis that tACS engages endogenous oscillatory circuits. We also show that an individual's physiological response to tACS is closely related to their ability to learn a motor task. These findings contribute to our understanding of the neurophysiological basis of motor rhythms and their behavioral relevance and offer the possibility of developing tACS as a therapeutic tool. PMID:28348136

An Efficient Multiscale Finite-Element Method for Frequency-Domain Seismic Wave Propagation

DOE PAGES

Gao, Kai; Fu, Shubin; Chung, Eric T.

2018-02-13

The frequency-domain seismic-wave equation, that is, the Helmholtz equation, has many important applications in seismological studies, yet is very challenging to solve, particularly for large geological models. Iterative solvers, domain decomposition, or parallel strategies can partially alleviate the computational burden, but these approaches may still encounter nontrivial difficulties in complex geological models where a sufficiently fine mesh is required to represent the fine-scale heterogeneities. We develop a novel numerical method to solve the frequency-domain acoustic wave equation on the basis of the multiscale finite-element theory. We discretize a heterogeneous model with a coarse mesh and employ carefully constructed high-order multiscalemore » basis functions to form the basis space for the coarse mesh. Solved from medium- and frequency-dependent local problems, these multiscale basis functions can effectively capture themedium’s fine-scale heterogeneity and the source’s frequency information, leading to a discrete system matrix with a much smaller dimension compared with those from conventional methods.We then obtain an accurate solution to the acoustic Helmholtz equation by solving only a small linear system instead of a large linear system constructed on the fine mesh in conventional methods.We verify our new method using several models of complicated heterogeneities, and the results show that our new multiscale method can solve the Helmholtz equation in complex models with high accuracy and extremely low computational costs.« less

An Efficient Multiscale Finite-Element Method for Frequency-Domain Seismic Wave Propagation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Kai; Fu, Shubin; Chung, Eric T.

The frequency-domain seismic-wave equation, that is, the Helmholtz equation, has many important applications in seismological studies, yet is very challenging to solve, particularly for large geological models. Iterative solvers, domain decomposition, or parallel strategies can partially alleviate the computational burden, but these approaches may still encounter nontrivial difficulties in complex geological models where a sufficiently fine mesh is required to represent the fine-scale heterogeneities. We develop a novel numerical method to solve the frequency-domain acoustic wave equation on the basis of the multiscale finite-element theory. We discretize a heterogeneous model with a coarse mesh and employ carefully constructed high-order multiscalemore » basis functions to form the basis space for the coarse mesh. Solved from medium- and frequency-dependent local problems, these multiscale basis functions can effectively capture themedium’s fine-scale heterogeneity and the source’s frequency information, leading to a discrete system matrix with a much smaller dimension compared with those from conventional methods.We then obtain an accurate solution to the acoustic Helmholtz equation by solving only a small linear system instead of a large linear system constructed on the fine mesh in conventional methods.We verify our new method using several models of complicated heterogeneities, and the results show that our new multiscale method can solve the Helmholtz equation in complex models with high accuracy and extremely low computational costs.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Xiaojun; Lei, Guangtsai; Pan, Guangwen

In this paper, the continuous operator is discretized into matrix forms by Galerkin`s procedure, using periodic Battle-Lemarie wavelets as basis/testing functions. The polynomial decomposition of wavelets is applied to the evaluation of matrix elements, which makes the computational effort of the matrix elements no more expensive than that of method of moments (MoM) with conventional piecewise basis/testing functions. A new algorithm is developed employing the fast wavelet transform (FWT). Owing to localization, cancellation, and orthogonal properties of wavelets, very sparse matrices have been obtained, which are then solved by the LSQR iterative method. This algorithm is also adaptive in thatmore » one can add at will finer wavelet bases in the regions where fields vary rapidly, without any damage to the system orthogonality of the wavelet basis functions. To demonstrate the effectiveness of the new algorithm, we applied it to the evaluation of frequency-dependent resistance and inductance matrices of multiple lossy transmission lines. Numerical results agree with previously published data and laboratory measurements. The valid frequency range of the boundary integral equation results has been extended two to three decades in comparison with the traditional MoM approach. The new algorithm has been integrated into the computer aided design tool, MagiCAD, which is used for the design and simulation of high-speed digital systems and multichip modules Pan et al. 29 refs., 7 figs., 6 tabs.« less

The C-terminal region of Ge-1 presents conserved structural features required for P-body localization.

PubMed

Jinek, Martin; Eulalio, Ana; Lingel, Andreas; Helms, Sigrun; Conti, Elena; Izaurralde, Elisa

2008-10-01

The removal of the 5' cap structure by the DCP1-DCP2 decapping complex irreversibly commits eukaryotic mRNAs to degradation. In human cells, the interaction between DCP1 and DCP2 is bridged by the Ge-1 protein. Ge-1 contains an N-terminal WD40-repeat domain connected by a low-complexity region to a conserved C-terminal domain. It was reported that the C-terminal domain interacts with DCP2 and mediates Ge-1 oligomerization and P-body localization. To understand the molecular basis for these functions, we determined the three-dimensional crystal structure of the most conserved region of the Drosophila melanogaster Ge-1 C-terminal domain. The region adopts an all alpha-helical fold related to ARM- and HEAT-repeat proteins. Using structure-based mutants we identified an invariant surface residue affecting P-body localization. The conservation of critical surface and structural residues suggests that the C-terminal region adopts a similar fold with conserved functions in all members of the Ge-1 protein family.

The quantum dynamics of electronically nonadiabatic chemical reactions

NASA Technical Reports Server (NTRS)

Truhlar, Donald G.

1993-01-01

Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally adiabatic functions in various quantum scattering algorithms.

Using Radial Basis Functions in Airborne Gravimetry for Local Geoid Improvement

NASA Astrophysics Data System (ADS)

Li, Xiaopeng

2017-04-01

Radial basis functions (RBF, Schmidt et al 2007, Klees and Wittwer 2007, Klees et al 2008) have been extensively used in satellite geodetic applications (Eicker 2008, Wittwer 2009, Naeimi 2013, among others). However, to date, to the author's knowledge, their roles in processing and modeling airborne gravity data have not been fully advocated or extensively investigated in detail, though compared with satellite missions, the airborne data is more suitable for this kind of localized basis functions especially considering the following facts: (1) Unlike the satellite missions that can provide global or near global data coverage, airborne gravity data is usually geographically limited. (2) It is also band limited in the frequency domain, considering that various filter banks and/or de-noising techniques (Li 2007) have to be applied to overcome the low signal-to-noise ratio problem that is present in airborne gravimetric systems. This is mainly due to the mechanical and mathematical limitations in computing the accelerations (both the kinematic and dynamic accelerations, Jekeli 2000). (3) It is much easier to formulate the RBF observation equations from an airborne gravimetric system (either a scalar one (Forsberg and Olesen 2010) or a vector one (Kwon and Jekeli 2001)) than from any satellite mission, especially compared with Gravity Recovery and Climate Experiment satellites (GRACE, Tapley et al. 2004) where many accurate background environmental models have to be used in order to separate out the gravity related functionals. As a result, in this study, a set of band-limited RBF is developed to model and downward continue the airborne gravity data for local geoid improvement. First, the algorithm is tested with synthesized data from global coefficient models such as EIGEN6c4 (Försteet al. 2014), during which the RBF not only successfully recovers a harmonic field but also presents filtering properties due to its particular design in the frequency domain. Then, the software is tested for the GSVS14 (Geoid Slope Validation Survey 2014) area as well as for the area around Puerto Rico and the U.S. Virgin Islands by using the real airborne gravity data from the Gravity for the Redefinition of the American Vertical Datum (GRAV-D, Smith 2007) project. The newly acquired cm-level accurate GPS/Leveling bench marks prove the RBF airborne enhanced geoid models are not inferior to other models computed by conventional approaches. By fully utilizing the three dimensional correlation information among the flight tracks, the RBF can also be used as a data editing tool for airborne data adjustment and cleaning.

Stable orthogonal local discriminant embedding for linear dimensionality reduction.

PubMed

Gao, Quanxue; Ma, Jingjie; Zhang, Hailin; Gao, Xinbo; Liu, Yamin

2013-07-01

Manifold learning is widely used in machine learning and pattern recognition. However, manifold learning only considers the similarity of samples belonging to the same class and ignores the within-class variation of data, which will impair the generalization and stableness of the algorithms. For this purpose, we construct an adjacency graph to model the intraclass variation that characterizes the most important properties, such as diversity of patterns, and then incorporate the diversity into the discriminant objective function for linear dimensionality reduction. Finally, we introduce the orthogonal constraint for the basis vectors and propose an orthogonal algorithm called stable orthogonal local discriminate embedding. Experimental results on several standard image databases demonstrate the effectiveness of the proposed dimensionality reduction approach.

[The conceptual bases for an entrepreneurial management of local health systems].

PubMed

Yepes, F J; Durán-Arenas, L

1994-01-01

Health management has become a fashion and it is now common to talk about strategic or service management, or of total quality management applied to health systems. However, all these elements of business management are being translated to health systems without a previous analysis on the implicit health model and the rationality of the prevalent production functions, which can lead to a higher level of efficiency but with an inadequate use of resources. This paper suggests the importance of integrating the advances in management and health sciences and proposes what are considered to be the conceptual basis for the design of a management tool geared to conduct local health systems with effectiveness, efficiency, quality and equity.

A hybrid linear/nonlinear training algorithm for feedforward neural networks.

PubMed

McLoone, S; Brown, M D; Irwin, G; Lightbody, A

1998-01-01

This paper presents a new hybrid optimization strategy for training feedforward neural networks. The algorithm combines gradient-based optimization of nonlinear weights with singular value decomposition (SVD) computation of linear weights in one integrated routine. It is described for the multilayer perceptron (MLP) and radial basis function (RBF) networks and then extended to the local model network (LMN), a new feedforward structure in which a global nonlinear model is constructed from a set of locally valid submodels. Simulation results are presented demonstrating the superiority of the new hybrid training scheme compared to second-order gradient methods. It is particularly effective for the LMN architecture where the linear to nonlinear parameter ratio is large.

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neilson, James R.; McQueen, Tyrel M.

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Representational analysis of extended disorder in atomistic ensembles derived from total scattering data

DOE PAGES

Neilson, James R.; McQueen, Tyrel M.

2015-09-20

With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atomsmore » in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. Lastly, this method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.« less

Concepts of soil mapping as a basis for the assessment of soil functions

NASA Astrophysics Data System (ADS)

Baumgarten, Andreas

2014-05-01

Soil mapping systems in Europe have been designed mainly as a tool for the description of soil characteristics from a morphogenetic viewpoint. Contrasting to the American or FAO system, the soil development has been in the main focus of European systems. Nevertheless , recent developments in soil science stress the importance of the functions of soils with respect to the ecosystems. As soil mapping systems usually offer a sound and extensive database, the deduction of soil functions from "classic" mapping parameters can be used for local and regional assessments. According to the used pedo-transfer functions and mapping systems, tailored approaches can be chosen for different applications. In Austria, a system mainly for spatial planning purposes has been developed that will be presented and illustrated by means of best practice examples.

Superconductivity in compensated and uncompensated semiconductors.

PubMed

Yanase, Youichi; Yorozu, Naoyuki

2008-12-01

We investigate the localization and superconductivity in heavily doped semiconductors. The crossover from the superconductivity in the host band to that in the impurity band is described on the basis of the disordered three-dimensional attractive Hubbard model for binary alloys. The microscopic inhomogeneity and the thermal superconducting fluctuation are taken into account using the self-consistent 1-loop order theory. The superconductor-insulator transition accompanies the crossover from the host band to the impurity band. We point out an enhancement of the critical temperature T c around the crossover. Further localization of electron wave functions leads to the localization of Cooper pairs and induces the pseudogap. We find that both the doping compensation by additional donors and the carrier increase by additional acceptors suppress the superconductivity. A theoretical interpretation is proposed for the superconductivity in the boron-doped diamond, SiC, and Si.

Superconductivity in compensated and uncompensated semiconductors

PubMed Central

Yanase, Youichi; Yorozu, Naoyuki

2008-01-01

We investigate the localization and superconductivity in heavily doped semiconductors. The crossover from the superconductivity in the host band to that in the impurity band is described on the basis of the disordered three-dimensional attractive Hubbard model for binary alloys. The microscopic inhomogeneity and the thermal superconducting fluctuation are taken into account using the self-consistent 1-loop order theory. The superconductor-insulator transition accompanies the crossover from the host band to the impurity band. We point out an enhancement of the critical temperature Tc around the crossover. Further localization of electron wave functions leads to the localization of Cooper pairs and induces the pseudogap. We find that both the doping compensation by additional donors and the carrier increase by additional acceptors suppress the superconductivity. A theoretical interpretation is proposed for the superconductivity in the boron-doped diamond, SiC, and Si. PMID:27878018

A space-based climatology of diurnal MLT tidal winds, temperatures and densities from UARS wind measurements

NASA Astrophysics Data System (ADS)

Svoboda, Aaron A.; Forbes, Jeffrey M.; Miyahara, Saburo

2005-11-01

A self-consistent global tidal climatology, useful for comparing and interpreting radar observations from different locations around the globe, is created from space-based Upper Atmosphere Research Satellite (UARS) horizontal wind measurements. The climatology created includes tidal structures for horizontal winds, temperature and relative density, and is constructed by fitting local (in latitude and height) UARS wind data at 95 km to a set of basis functions called Hough mode extensions (HMEs). These basis functions are numerically computed modifications to Hough modes and are globally self-consistent in wind, temperature, and density. We first demonstrate this self-consistency with a proxy data set from the Kyushu University General Circulation Model, and then use a linear weighted superposition of the HMEs obtained from monthly fits to the UARS data to extrapolate the global, multi-variable tidal structure. A brief explanation of the HMEs’ origin is provided as well as information about a public website that has been set up to make the full extrapolated data sets available.

Calculation of 125Te NMR Chemical Shifts at the Full Four-Component Relativistic Level with Taking into Account Solvent and Vibrational Corrections: A Gateway to Better Agreement with Experiment.

PubMed

Rusakova, Irina L; Rusakov, Yuriy Yu; Krivdin, Leonid B

2017-06-29

Four-component relativistic calculations of 125 Te NMR chemical shifts were performed in the series of 13 organotellurium compounds, potential precursors of the biologically active species, at the density functional theory level under the nonrelativistic and four-component fully relativistic conditions using locally dense basis set scheme derived from relativistic Dyall's basis sets. The relativistic effects in tellurium chemical shifts were found to be of as much as 20-25% of the total calculated values. The vibrational and solvent corrections to 125 Te NMR chemical shifts are about, accordingly, 6 and 8% of their total values. The PBE0 exchange-correlation functional turned out to give the best agreement of calculated tellurium shifts with their experimental values giving the mean absolute percentage error of 4% in the range of ∼1000 ppm, provided all corrections are taken into account.

Two-component hybrid time-dependent density functional theory within the Tamm-Dancoff approximation.

PubMed

Kühn, Michael; Weigend, Florian

2015-01-21

We report the implementation of a two-component variant of time-dependent density functional theory (TDDFT) for hybrid functionals that accounts for spin-orbit effects within the Tamm-Dancoff approximation (TDA) for closed-shell systems. The influence of the admixture of Hartree-Fock exchange on excitation energies is investigated for several atoms and diatomic molecules by comparison to numbers for pure density functionals obtained previously [M. Kühn and F. Weigend, J. Chem. Theory Comput. 9, 5341 (2013)]. It is further related to changes upon switching to the local density approximation or using the full TDDFT formalism instead of TDA. Efficiency is demonstrated for a comparably large system, Ir(ppy)3 (61 atoms, 1501 basis functions, lowest 10 excited states), which is a prototype molecule for organic light-emitting diodes, due to its "spin-forbidden" triplet-singlet transition.

Effective scheme for partitioning covalent bonds in density-functional embedding theory: From molecules to extended covalent systems.

PubMed

Huang, Chen; Muñoz-García, Ana Belén; Pavone, Michele

2016-12-28

Density-functional embedding theory provides a general way to perform multi-physics quantum mechanics simulations of large-scale materials by dividing the total system's electron density into a cluster's density and its environment's density. It is then possible to compute the accurate local electronic structures and energetics of the embedded cluster with high-level methods, meanwhile retaining a low-level description of the environment. The prerequisite step in the density-functional embedding theory is the cluster definition. In covalent systems, cutting across the covalent bonds that connect the cluster and its environment leads to dangling bonds (unpaired electrons). These represent a major obstacle for the application of density-functional embedding theory to study extended covalent systems. In this work, we developed a simple scheme to define the cluster in covalent systems. Instead of cutting covalent bonds, we directly split the boundary atoms for maintaining the valency of the cluster. With this new covalent embedding scheme, we compute the dehydrogenation energies of several different molecules, as well as the binding energy of a cobalt atom on graphene. Well localized cluster densities are observed, which can facilitate the use of localized basis sets in high-level calculations. The results are found to converge faster with the embedding method than the other multi-physics approach ONIOM. This work paves the way to perform the density-functional embedding simulations of heterogeneous systems in which different types of chemical bonds are present.

Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation.

PubMed

Ferenczy, György G

2013-04-05

Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods. Copyright © 2012 Wiley Periodicals, Inc.

Matrix basis for plane and modal waves in a Timoshenko beam.

PubMed

Claeyssen, Julio Cesar Ruiz; Tolfo, Daniela de Rosso; Tonetto, Leticia

2016-11-01

Plane waves and modal waves of the Timoshenko beam model are characterized in closed form by introducing robust matrix basis that behave according to the nature of frequency and wave or modal numbers. These new characterizations are given in terms of a finite number of coupling matrices and closed form generating scalar functions. Through Liouville's technique, these latter are well behaved at critical or static situations. Eigenanalysis is formulated for exponential and modal waves. Modal waves are superposition of four plane waves, but there are plane waves that cannot be modal waves. Reflected and transmitted waves at an interface point are formulated in matrix terms, regardless of having a conservative or a dissipative situation. The matrix representation of modal waves is used in a crack problem for determining the reflected and transmitted matrices. Their euclidean norms are seen to be dominated by certain components at low and high frequencies. The matrix basis technique is also used with a non-local Timoshenko model and with the wave interaction with a boundary. The matrix basis allows to characterize reflected and transmitted waves in spectral and non-spectral form.

Unconstrained handwritten numeral recognition based on radial basis competitive and cooperative networks with spatio-temporal feature representation.

PubMed

Lee, S; Pan, J J

1996-01-01

This paper presents a new approach to representation and recognition of handwritten numerals. The approach first transforms a two-dimensional (2-D) spatial representation of a numeral into a three-dimensional (3-D) spatio-temporal representation by identifying the tracing sequence based on a set of heuristic rules acting as transformation operators. A multiresolution critical-point segmentation method is then proposed to extract local feature points, at varying degrees of scale and coarseness. A new neural network architecture, referred to as radial-basis competitive and cooperative network (RCCN), is presented especially for handwritten numeral recognition. RCCN is a globally competitive and locally cooperative network with the capability of self-organizing hidden units to progressively achieve desired network performance, and functions as a universal approximator of arbitrary input-output mappings. Three types of RCCNs are explored: input-space RCCN (IRCCN), output-space RCCN (ORCCN), and bidirectional RCCN (BRCCN). Experiments against handwritten zip code numerals acquired by the U.S. Postal Service indicated that the proposed method is robust in terms of variations, deformations, transformations, and corruption, achieving about 97% recognition rate.

Grid-free density functional calculations on periodic systems.

PubMed

Varga, Stefan

2007-09-21

Density fitting scheme is applied to the exchange part of the Kohn-Sham potential matrix in a grid-free local density approximation for infinite systems with translational periodicity. It is shown that within this approach the computational demands for the exchange part scale in the same way as for the Coulomb part. The efficiency of the scheme is demonstrated on a model infinite polymer chain. For simplicity, the implementation with Dirac-Slater Xalpha exchange functional is presented only. Several choices of auxiliary basis set expansion coefficients were tested with both Coulomb and overlap metric. Their effectiveness is discussed also in terms of robustness and norm preservation.

Grid-free density functional calculations on periodic systems

NASA Astrophysics Data System (ADS)

Varga, Štefan

2007-09-01

Density fitting scheme is applied to the exchange part of the Kohn-Sham potential matrix in a grid-free local density approximation for infinite systems with translational periodicity. It is shown that within this approach the computational demands for the exchange part scale in the same way as for the Coulomb part. The efficiency of the scheme is demonstrated on a model infinite polymer chain. For simplicity, the implementation with Dirac-Slater Xα exchange functional is presented only. Several choices of auxiliary basis set expansion coefficients were tested with both Coulomb and overlap metric. Their effectiveness is discussed also in terms of robustness and norm preservation.

Memantine elicits spinal blockades of motor function, proprioception, and nociception in rats.

PubMed

Chen, Yu-Wen; Chiu, Chong-Chi; Liu, Kuo-Sheng; Hung, Ching-Hsia; Wang, Jhi-Joung

2015-12-01

Although memantine blocks sodium currents and produces local skin anesthesia, spinal anesthesia with memantine is unknown. The purpose of the study was to evaluate the local anesthetic effect of memantine in spinal anesthesia and its comparison with a widely used local anesthetic lidocaine. After intrathecally injecting the rats with five doses of each drug, the dose-response curves of memantine and lidocaine were constructed. The potencies of the drugs and durations of spinal anesthetic effects on motor function, proprioception, and nociception were compared with those of lidocaine. We showed that memantine produced dose-dependent spinal blockades in motor function, proprioception, and nociception. On a 50% effective dose (ED50 ) basis, the rank of potency was lidocaine greater than memantine (P < 0.05 for the differences). At the equipotent doses (ED25 , ED50 , ED75 ), the block duration produced by memantine was longer than that produced by lidocaine (P < 0.05 for the differences). Memantine, but not lidocaine, displayed more sensory/nociceptive block than motor block. The preclinical data demonstrated that memantine is less potent than lidocaine, whereas memantine produces longer duration of spinal anesthesia than lidocaine. Memantine shows a more sensory-selective action over motor blockade. © 2015 Société Française de Pharmacologie et de Thérapeutique.

41 CFR 101-8.304 - Effect of State or local law or other requirements and effect of employment opportunities.

Code of Federal Regulations, 2010 CFR

2010-07-01

... REGULATIONS GENERAL 8-NONDISCRIMINATION IN PROGRAMS RECEIVING FEDERAL FINANCIAL ASSISTANCE 8.3-Discrimination Prohibited on the Basis of Handicap § 101-8.304 Effect of State or local law or other requirements and effect... alleviated by the existence of any State or local law or other requirement that, on the basis of handicap...

41 CFR 101-8.304 - Effect of State or local law or other requirements and effect of employment opportunities.

Code of Federal Regulations, 2014 CFR

2014-07-01

... REGULATIONS GENERAL 8-NONDISCRIMINATION IN PROGRAMS RECEIVING FEDERAL FINANCIAL ASSISTANCE 8.3-Discrimination Prohibited on the Basis of Handicap § 101-8.304 Effect of State or local law or other requirements and effect... alleviated by the existence of any State or local law or other requirement that, on the basis of handicap...

41 CFR 101-8.304 - Effect of State or local law or other requirements and effect of employment opportunities.

Code of Federal Regulations, 2013 CFR

2013-07-01

... REGULATIONS GENERAL 8-NONDISCRIMINATION IN PROGRAMS RECEIVING FEDERAL FINANCIAL ASSISTANCE 8.3-Discrimination Prohibited on the Basis of Handicap § 101-8.304 Effect of State or local law or other requirements and effect... alleviated by the existence of any State or local law or other requirement that, on the basis of handicap...

41 CFR 101-8.304 - Effect of State or local law or other requirements and effect of employment opportunities.

Code of Federal Regulations, 2011 CFR

2011-07-01

... REGULATIONS GENERAL 8-NONDISCRIMINATION IN PROGRAMS RECEIVING FEDERAL FINANCIAL ASSISTANCE 8.3-Discrimination Prohibited on the Basis of Handicap § 101-8.304 Effect of State or local law or other requirements and effect... alleviated by the existence of any State or local law or other requirement that, on the basis of handicap...

41 CFR 101-8.304 - Effect of State or local law or other requirements and effect of employment opportunities.

Code of Federal Regulations, 2012 CFR

2012-07-01

... REGULATIONS GENERAL 8-NONDISCRIMINATION IN PROGRAMS RECEIVING FEDERAL FINANCIAL ASSISTANCE 8.3-Discrimination Prohibited on the Basis of Handicap § 101-8.304 Effect of State or local law or other requirements and effect... alleviated by the existence of any State or local law or other requirement that, on the basis of handicap...

A Functional Neuroimaging Study of Sound Localization: Visual Cortex Activity Predicts Performance in Early-Blind Individuals

PubMed Central

Gougoux, Frédéric; Zatorre, Robert J; Lassonde, Maryse; Voss, Patrice

2005-01-01

Blind individuals often demonstrate enhanced nonvisual perceptual abilities. However, the neural substrate that underlies this improved performance remains to be fully understood. An earlier behavioral study demonstrated that some early-blind people localize sounds more accurately than sighted controls using monaural cues. In order to investigate the neural basis of these behavioral differences in humans, we carried out functional imaging studies using positron emission tomography and a speaker array that permitted pseudo-free-field presentations within the scanner. During binaural sound localization, a sighted control group showed decreased cerebral blood flow in the occipital lobe, which was not seen in early-blind individuals. During monaural sound localization (one ear plugged), the subgroup of early-blind subjects who were behaviorally superior at sound localization displayed two activation foci in the occipital cortex. This effect was not seen in blind persons who did not have superior monaural sound localization abilities, nor in sighted individuals. The degree of activation of one of these foci was strongly correlated with sound localization accuracy across the entire group of blind subjects. The results show that those blind persons who perform better than sighted persons recruit occipital areas to carry out auditory localization under monaural conditions. We therefore conclude that computations carried out in the occipital cortex specifically underlie the enhanced capacity to use monaural cues. Our findings shed light not only on intermodal compensatory mechanisms, but also on individual differences in these mechanisms and on inhibitory patterns that differ between sighted individuals and those deprived of vision early in life. PMID:15678166

Super-resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.

PubMed

Miklosi, Andras G; Del Favero, Giorgia; Bulat, Tanja; Höger, Harald; Shigemoto, Ryuichi; Marko, Doris; Lubec, Gert

2018-06-01

Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins.

Critical Analysis of Cluster Models and Exchange-Correlation Functionals for Calculating Magnetic Shielding in Molecular Solids.

PubMed

Holmes, Sean T; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

2015-11-10

Calculations of the principal components of magnetic-shielding tensors in crystalline solids require the inclusion of the effects of lattice structure on the local electronic environment to obtain significant agreement with experimental NMR measurements. We assess periodic (GIPAW) and GIAO/symmetry-adapted cluster (SAC) models for computing magnetic-shielding tensors by calculations on a test set containing 72 insulating molecular solids, with a total of 393 principal components of chemical-shift tensors from 13C, 15N, 19F, and 31P sites. When clusters are carefully designed to represent the local solid-state environment and when periodic calculations include sufficient variability, both methods predict magnetic-shielding tensors that agree well with experimental chemical-shift values, demonstrating the correspondence of the two computational techniques. At the basis-set limit, we find that the small differences in the computed values have no statistical significance for three of the four nuclides considered. Subsequently, we explore the effects of additional DFT methods available only with the GIAO/cluster approach, particularly the use of hybrid-GGA functionals, meta-GGA functionals, and hybrid meta-GGA functionals that demonstrate improved agreement in calculations on symmetry-adapted clusters. We demonstrate that meta-GGA functionals improve computed NMR parameters over those obtained by GGA functionals in all cases, and that hybrid functionals improve computed results over the respective pure DFT functional for all nuclides except 15N.

45 CFR 1174.37 - Subgrants.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Regulations Relating to Public Welfare (Continued) NATIONAL FOUNDATION ON THE ARTS AND THE HUMANITIES NATIONAL... (whether on a cost reimbursement or fixed amount basis) of financial assistance to local and Indian tribal... fixed amount basis) of financial assistance to local and Indian tribal governments. Grantees shall: (1...

Type-curve estimation of statistical heterogeneity

NASA Astrophysics Data System (ADS)

Neuman, Shlomo P.; Guadagnini, Alberto; Riva, Monica

2004-04-01

The analysis of pumping tests has traditionally relied on analytical solutions of groundwater flow equations in relatively simple domains, consisting of one or at most a few units having uniform hydraulic properties. Recently, attention has been shifting toward methods and solutions that would allow one to characterize subsurface heterogeneities in greater detail. On one hand, geostatistical inverse methods are being used to assess the spatial variability of parameters, such as permeability and porosity, on the basis of multiple cross-hole pressure interference tests. On the other hand, analytical solutions are being developed to describe the mean and variance (first and second statistical moments) of flow to a well in a randomly heterogeneous medium. We explore numerically the feasibility of using a simple graphical approach (without numerical inversion) to estimate the geometric mean, integral scale, and variance of local log transmissivity on the basis of quasi steady state head data when a randomly heterogeneous confined aquifer is pumped at a constant rate. By local log transmissivity we mean a function varying randomly over horizontal distances that are small in comparison with a characteristic spacing between pumping and observation wells during a test. Experimental evidence and hydrogeologic scaling theory suggest that such a function would tend to exhibit an integral scale well below the maximum well spacing. This is in contrast to equivalent transmissivities derived from pumping tests by treating the aquifer as being locally uniform (on the scale of each test), which tend to exhibit regional-scale spatial correlations. We show that whereas the mean and integral scale of local log transmissivity can be estimated reasonably well based on theoretical ensemble mean variations of head and drawdown with radial distance from a pumping well, estimating the log transmissivity variance is more difficult. We obtain reasonable estimates of the latter based on theoretical variation of the standard deviation of circumferentially averaged drawdown about its mean.

Conceptual DFT: the chemical relevance of higher response functions.

PubMed

Geerlings, P; De Proft, F

2008-06-07

In recent years conceptual density functional theory offered a perspective for the interpretation/prediction of experimental/theoretical reactivity data on the basis of a series of response functions to perturbations in the number of electrons and/or external potential. This approach has enabled the sharp definition and computation, from first principles, of a series of well-known but sometimes vaguely defined chemical concepts such as electronegativity and hardness. In this contribution, a short overview of the shortcomings of the simplest, first order response functions is illustrated leading to a description of chemical bonding in a covalent interaction in terms of interacting atoms or groups, governed by electrostatics with the tendency to polarize bonds on the basis of electronegativity differences. The second order approach, well known until now, introduces the hardness/softness and Fukui function concepts related to polarizability and frontier MO theory, respectively. The introduction of polarizability/softness is also considered in a historical perspective in which polarizability was, with some exceptions, mainly put forward in non covalent interactions. A particular series of response functions, arising when the changes in the external potential are solely provoked by changes in nuclear configurations (the "R-analogues") are also systematically considered. The main part of the contribution is devoted to third order response functions which, at first sight, may be expected not to yield chemically significant information, as turns out to be for the hyperhardness. A counterexample is the dual descriptor and its R analogue, the initial hardness response, which turns out to yield a firm basis to regain the Woodward-Hoffmann rules for pericyclic reactions based on a density-only basis, i.e. without involving the phase, sign, symmetry of the wavefunction. Even the second order nonlinear response functions are shown possibly to bear interesting information, e.g. on the local and global polarizability. Its derivatives may govern the influence of charge on the polarizability, the R-analogues being the nuclear Fukui function and the quadratic and cubic force constants. Although some of the higher order derivatives may be difficult to evaluate a comparison with the energy expansion used in spectroscopy in terms of nuclear displacements, nuclear magnetic moments, electric and magnetic fields leads to the conjecture that, certainly cross terms may contain new, intricate information for understanding chemical reactivity.

First-Principles Momentum Dependent Local Ansatz Approach to the Momentum Distribution Function in Iron-Group Transition Metals

NASA Astrophysics Data System (ADS)

Kakehashi, Yoshiro; Chandra, Sumal

2017-03-01

The momentum distribution function (MDF) bands of iron-group transition metals from Sc to Cu have been investigated on the basis of the first-principles momentum dependent local ansatz wavefunction method. It is found that the MDF for d electrons show a strong momentum dependence and a large deviation from the Fermi-Dirac distribution function along high-symmetry lines of the first Brillouin zone, while the sp electrons behave as independent electrons. In particular, the deviation in bcc Fe (fcc Ni) is shown to be enhanced by the narrow eg (t2g) bands with flat dispersion in the vicinity of the Fermi level. Mass enhancement factors (MEF) calculated from the jump on the Fermi surface are also shown to be momentum dependent. Large mass enhancements of Mn and Fe are found to be caused by spin fluctuations due to d electrons, while that for Ni is mainly caused by charge fluctuations. Calculated MEF are consistent with electronic specific heat data as well as recent angle resolved photoemission spectroscopy data.

An Ab Initio Full Potential Fully Relativistic Study of the (0001) Surface of Double Hexagonal Close Packed Americium*

NASA Astrophysics Data System (ADS)

Gao, Da; Ray, Asok

2007-03-01

The electronic and geometric properties of bulk dhcp Am as well as quantum size effects in the surface energies and the work functions of the dhcp Am (0001) ultra thin films up to seven layers have been examined at nonmagnetic, ferromagnetic, and anti-ferromagnetic configurations via full-potential all-electron density-functional calculations with a mixed APW+lo/LAPW basis. The anti-ferromagnetic state including spin-orbit coupling is found to be the ground state of both bulk and the (0001) surface of dhcp Am with the 5f electrons primarily localized. Our results show that magnetic configurations and spin-orbit coupling play important roles in determining the equilibrium lattice constant, the bulk modulus as well as the localized feature of 5f electrons for dhcp Am. Quantum size effects are found to be more pronounced in work functions than in surface energies. *This work is supported by the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U. S. Department of Energy and the Welch Foundation, Houston, Texas.

Local Approximation and Hierarchical Methods for Stochastic Optimization

NASA Astrophysics Data System (ADS)

Cheng, Bolong

In this thesis, we present local and hierarchical approximation methods for two classes of stochastic optimization problems: optimal learning and Markov decision processes. For the optimal learning problem class, we introduce a locally linear model with radial basis function for estimating the posterior mean of the unknown objective function. The method uses a compact representation of the function which avoids storing the entire history, as is typically required by nonparametric methods. We derive a knowledge gradient policy with the locally parametric model, which maximizes the expected value of information. We show the policy is asymptotically optimal in theory, and experimental works suggests that the method can reliably find the optimal solution on a range of test functions. For the Markov decision processes problem class, we are motivated by an application where we want to co-optimize a battery for multiple revenue, in particular energy arbitrage and frequency regulation. The nature of this problem requires the battery to make charging and discharging decisions at different time scales while accounting for the stochastic information such as load demand, electricity prices, and regulation signals. Computing the exact optimal policy becomes intractable due to the large state space and the number of time steps. We propose two methods to circumvent the computation bottleneck. First, we propose a nested MDP model that structure the co-optimization problem into smaller sub-problems with reduced state space. This new model allows us to understand how the battery behaves down to the two-second dynamics (that of the frequency regulation market). Second, we introduce a low-rank value function approximation for backward dynamic programming. This new method only requires computing the exact value function for a small subset of the state space and approximate the entire value function via low-rank matrix completion. We test these methods on historical price data from the PJM Interconnect and show that it outperforms the baseline approach used in the industry.

Enhanced vibronic interaction caused by local lattice symmetry lowering in the (Fe, Mg)As2 ternary system

NASA Astrophysics Data System (ADS)

Pishtshev, A.; Rubin, P.

2018-04-01

By means of periodic density functional theory (DFT) electronic structure calculations, we investigate iron-site doping effects in a structural model of bulk FeAs2. Simulations performed within the projector augmented-wave method-Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) functional scheme reveal that the impacts of the two stoichiometric substitutions Fe → Mg and Fe → Ni are radically different with respect to the structural and electronic behavior of the dopants. In particular, unlike the Ni dopant, the Mg dopant incorporated in FeAs2 occupies a noncentral equilibrium position characterized by an off-center displacement from the reference higher-symmetry position. Analysis of the respective electron and vibrational factors allows us to explain this result in terms of the local pseudo Jahn-Teller effect (pJTE). On the basis of DFT calculations, we deduce which electron orbitals and lattice vibrational modes are appropriate for promoting the local instability at the origin of the pJTE. Quantitative evaluations of the pJTE parameters performed within the polyatomic formalism of an effective tight-binding model show that it is just the enhanced vibronic interaction in the Mg-[FeAs6] cluster that is responsible for the local lattice symmetry breaking.

Numerical and experimental study of curved and planar frequency selective surfaces with arbitrary illumination. M.S. Thesis - Maryland Univ., 1989

NASA Technical Reports Server (NTRS)

Caroglanian, Armen

1991-01-01

A frequency selective surface (FSS) composed of apertures in a metallic sheet is known as the inductive FSS. The infinite inductive FSS theory is derived and the aperture fields are solved by a spectral domain formulation with method of moments solution. Both full domain and subsectional basis functions are studied. A locally planar technique (LPT) is used to determine the forward scattered field from a generally shaped inductive FSS with arbitrary illumination.

Distribution and determination of cholinesterases in mammals

PubMed Central

Holmstedt, Bo

1971-01-01

This paper reviews the distribution of cholinesterases in the central nervous system, the ganglia, the striated muscle, and the blood of mammals, and discusses the correlation between the histochemical localization and the function of neuronal cholinesterase. Different methods for the determination of cholinesterase levels are reviewed, with particular reference to their practical value for field work. The Warburg method and the Tintometer and Acholest colorimetric methods are compared on the basis of cholinesterase levels determined in normal persons and in those suffering from parathion intoxication. PMID:4999484

Disrupted functional and structural networks in cognitively normal elderly subjects with the APOE ɛ4 allele.

PubMed

Chen, Yaojing; Chen, Kewei; Zhang, Junying; Li, Xin; Shu, Ni; Wang, Jun; Zhang, Zhanjun; Reiman, Eric M

2015-03-13

As the Apolipoprotein E (APOE) ɛ4 allele is a major genetic risk factor for sporadic Alzheimer's disease (AD), which has been suggested as a disconnection syndrome manifested by the disruption of white matter (WM) integrity and functional connectivity (FC), elucidating the subtle brain structural and functional network changes in cognitively normal ɛ4 carriers is essential for identifying sensitive neuroimaging based biomarkers and understanding the preclinical AD-related abnormality development. We first constructed functional network on the basis of resting-state functional magnetic resonance imaging and a structural network on the basis of diffusion tensor image. Using global, local and nodal efficiencies of these two networks, we then examined (i) the differences of functional and WM structural network between cognitively normal ɛ4 carriers and non-carriers simultaneously, (ii) the sensitivity of these indices as biomarkers, and (iii) their relationship to behavior measurements, as well as to cholesterol level. For ɛ4 carriers, we found reduced global efficiency significantly in WM and marginally in FC, regional FC dysfunctions mainly in medial temporal areas, and more widespread for WM network. Importantly, the right parahippocampal gyrus (PHG.R) was the only region with simultaneous functional and structural damage, and the nodal efficiency of PHG.R in WM network mediates the APOE ɛ4 effect on memory function. Finally, the cholesterol level correlated with WM network differently than with the functional network in ɛ4 carriers. Our results demonstrated ɛ4-specific abnormal structural and functional patterns, which may potentially serve as biomarkers for early detection before the onset of the disease.

Hybrid active contour model for inhomogeneous image segmentation with background estimation

NASA Astrophysics Data System (ADS)

Sun, Kaiqiong; Li, Yaqin; Zeng, Shan; Wang, Jun

2018-03-01

This paper proposes a hybrid active contour model for inhomogeneous image segmentation. The data term of the energy function in the active contour consists of a global region fitting term in a difference image and a local region fitting term in the original image. The difference image is obtained by subtracting the background from the original image. The background image is dynamically estimated from a linear filtered result of the original image on the basis of the varying curve locations during the active contour evolution process. As in existing local models, fitting the image to local region information makes the proposed model robust against an inhomogeneous background and maintains the accuracy of the segmentation result. Furthermore, fitting the difference image to the global region information makes the proposed model robust against the initial contour location, unlike existing local models. Experimental results show that the proposed model can obtain improved segmentation results compared with related methods in terms of both segmentation accuracy and initial contour sensitivity.

Subcellular Localization of Pseudomonas syringae pv. tomato Effector Proteins in Plants.

PubMed

Aung, Kyaw; Xin, Xiufang; Mecey, Christy; He, Sheng Yang

2017-01-01

Animal and plant pathogenic bacteria use type III secretion systems to translocate proteinaceous effectors to subvert innate immunity of their host organisms. Type III secretion/effector systems are a crucial pathogenicity factor in many bacterial pathogens of plants and animals. Pseudomonas syringae pv. tomato (Pst) DC3000 injects a total of 36 protein effectors that target a variety of host proteins. Studies of a subset of Pst DC3000 effectors demonstrated that bacterial effectors, once inside the host cell, are localized to different subcellular compartments, including plasma membrane, cytoplasm, mitochondria, chloroplast, and Trans-Golgi network, to carry out their virulence functions. Identifying the subcellular localization of bacterial effector proteins in host cells could provide substantial clues to understanding the molecular and cellular basis of the virulence activities of effector proteins. In this chapter, we present methods for transient or stable expression of bacterial effector proteins in tobacco and/or Arabidopsis thaliana for live cell imaging as well as confirming the subcellular localization in plants using fluorescent organelle markers or chemical treatment.

Quantum Dynamics with Short-Time Trajectories and Minimal Adaptive Basis Sets.

PubMed

Saller, Maximilian A C; Habershon, Scott

2017-07-11

Methods for solving the time-dependent Schrödinger equation via basis set expansion of the wave function can generally be categorized as having either static (time-independent) or dynamic (time-dependent) basis functions. We have recently introduced an alternative simulation approach which represents a middle road between these two extremes, employing dynamic (classical-like) trajectories to create a static basis set of Gaussian wavepackets in regions of phase-space relevant to future propagation of the wave function [J. Chem. Theory Comput., 11, 8 (2015)]. Here, we propose and test a modification of our methodology which aims to reduce the size of basis sets generated in our original scheme. In particular, we employ short-time classical trajectories to continuously generate new basis functions for short-time quantum propagation of the wave function; to avoid the continued growth of the basis set describing the time-dependent wave function, we employ Matching Pursuit to periodically minimize the number of basis functions required to accurately describe the wave function. Overall, this approach generates a basis set which is adapted to evolution of the wave function while also being as small as possible. In applications to challenging benchmark problems, namely a 4-dimensional model of photoexcited pyrazine and three different double-well tunnelling problems, we find that our new scheme enables accurate wave function propagation with basis sets which are around an order-of-magnitude smaller than our original trajectory-guided basis set methodology, highlighting the benefits of adaptive strategies for wave function propagation.

Axially deformed solution of the Skyrme–Hartree–Fock–Bogolyubov equations using the transformed harmonic oscillator basis (III) hfbtho (v3.00): A new version of the program

DOE PAGES

Perez, R. Navarro; Schunck, N.; Lasseri, R. -D.; ...

2017-07-05

Here, we describe the new version 3.00 of the code hfbtho that solves the nuclear Hartree–Fock (HF) or Hartree–Fock–Bogolyubov (HFB) problem by using the cylindrical transformed deformed harmonic oscillator basis. In the new version, we have implemented the following features: (i) the full Gogny force in both particle–hole and particle–particle channels, (ii) the calculation of the nuclear collective inertia at the perturbative cranking approximation, (iii) the calculation of fission fragment charge, mass and deformations based on the determination of the neck, (iv) the regularization of zero-range pairing forces, (v) the calculation of localization functions, (vi) a MPI interface for large-scalemore » mass table calculations.« less

Spectroscopic studies (FT-IR, FT-Raman, UV-Visible), normal co-ordinate analysis, first-order hyperpolarizability and HOMO, LUMO studies of 3,4-dichlorobenzophenone by using Density Functional Methods.

PubMed

Venkata Prasad, K; Samatha, K; Jagadeeswara Rao, D; Santhamma, C; Muthu, S; Mark Heron, B

2015-01-01

The vibrational frequencies of 3,4-dichlorobenzophenone (DCLBP) were obtained from the FT-IR and Raman spectral data, and evaluated based on the Density Functional Theory using the standard method B3LYP with 6-311+G(d,p) as the basis set. On the basis of potential energy distribution together with the normal-co-ordinate analysis and following the scaled quantum mechanical force methodology, the assignments for the various frequencies were described. The values of the electric dipole moment (μ) and the first-order hyperpolarizability (β) of the molecule were computed. The UV-absorption spectrum was also recorded to study the electronic transitions. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The NBO analysis, to study the intramolecular hyperconjugative interactions, was carried out. Mulliken's net charges were evaluated. The MEP and thermodynamic properties were also calculated. The electron density-based local reactivity descriptor, such as Fukui functions, was calculated to explain the chemical selectivity or reactivity site in 3,4-dichlorobenzophenone. Copyright © 2015 Elsevier B.V. All rights reserved.

Density Functional O(N) Calculations

NASA Astrophysics Data System (ADS)

Ordejón, Pablo

1998-03-01

We have developed a scheme for performing Density Functional Theory calculations with O(N) scaling.(P. Ordejón, E. Artacho and J. M. Soler, Phys. Rev. B, 53), 10441 (1996) The method uses arbitrarily flexible and complete Atomic Orbitals (AO) basis sets. This gives a wide range of choice, from extremely fast calculations with minimal basis sets, to greatly accurate calculations with complete sets. The size-efficiency of AO bases, together with the O(N) scaling of the algorithm, allow the application of the method to systems with many hundreds of atoms, in single processor workstations. I will present the SIESTA code,(D. Sanchez-Portal, P. Ordejón, E. Artacho and J. M. Soler, Int. J. Quantum Chem., 65), 453 (1997) in which the method is implemented, with several LDA, LSD and GGA functionals available, and using norm-conserving, non-local pseudopotentials (in the Kleinman-Bylander form) to eliminate the core electrons. The calculation of static properties such as energies, forces, pressure, stress and magnetic moments, as well as molecular dynamics (MD) simulations capabilities (including variable cell shape, constant temperature and constant pressure MD) are fully implemented. I will also show examples of the accuracy of the method, and applications to large-scale materials and biomolecular systems.

Chromatin Condensing Functions of the Linker Histone C-terminal Domain are mediated by Specific Amino Acid Composition and Intrinsic Protein Disorder†

PubMed Central

Lu, Xu; Hamkalo, Barbara; Parseghian, Missag H.; Hansen, Jeffrey C.

2009-01-01

Linker histones bind to the nucleosomes and linker DNA of chromatin fibers, causing changes in linker DNA structure and stabilization of higher order folded and oligomeric chromatin structures. Linker histones affect chromatin structure acting primarily through their ~100 residue C-terminal domain (CTD). We have previously shown that the ability of the linker histone H1° to alter chromatin structure was localized to two discontinuous 24-/25-residue CTD regions (Lu, X., and Hansen, J. C. (2004) J Biol Chem 279, 8701–8707). To determine the biochemical basis for these results, we have characterized chromatin model systems assembled with endogenous mouse somatic H1 isoforms, or recombinant H1° CTD mutants in which the primary sequence has been scrambled, the amino acid composition mutated, or the location of various CTD regions swapped. Our results indicate that specific amino acid composition plays a fundamental role in molecular recognition and function by the H1 CTD. Additionally, these experiments support a new molecular model for CTD function, and provide a biochemical basis for the redundancy observed in H1 isoform knockout experiments in vivo. PMID:19072710

47 CFR 69.111 - Tandem-switched transport and tandem charge.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., geographically averaged on a study-area-wide basis, that the incumbent local exchange carrier experiences based... exchange carrier experiences based on the prior year's annual use. Tandem-switched transport transmission..., geographically averaged on a study-area-wide basis, that the incumbent local exchange carrier experiences based...

Applying Molecular Bonding Concepts to the Solid State

NASA Astrophysics Data System (ADS)

Dunnington, Benjamin D.

In this thesis, we describe the extension and application of Natural Bond Orbital (NBO) analysis to periodic systems. This enables the translation of rigorous, quantum mechanical calculation results of solid systems into the localized lone pairs and two-center bonds of Lewis structures. Such localized bonding descriptions form the basic language of chemistry, and application of these ideas to solids allows for the understanding of complex phenomena in bulk systems using readily accessible concepts from molecular science. In addition to the algorithmic adjustments needed for to account for periodic boundary conditions in the NBO process, we also discuss methodology to interface the ubiquitous plane wave basis sets of the solid state with the atom-centered basis functions needed as input for NBO analysis. We will describe one method using projection of the plane wave eigenstates, and a second projection-free method that involves the direct calculation of matrix elements of the plane wave Hamiltonian in an atom-centered basis. The reliance of many localized, post-computational analysis techniques on an atom-centered description of the orbitals, means these interfaces will have applicability beyond our NBO development. An ideal area for application of such molecular descriptions of periodic systems is heterogeneous catalysis, where reactants from a gas/liquid phase react on a solid catalyst surface. Previous studies of these systems have originated from the delocalized perspective of the bulk catalyst. NBO provides an explicit description of the perturbative effect of the catalyst on the covalent bonds of the reactant, which is correlated with the catalytic activity of the material. Such a shift to an adsorbate focused description of surface reactivity will enable understanding of catalysis across a variety of materials.

Nonlinear Modeling by Assembling Piecewise Linear Models

NASA Technical Reports Server (NTRS)

Yao, Weigang; Liou, Meng-Sing

2013-01-01

To preserve nonlinearity of a full order system over a parameters range of interest, we propose a simple modeling approach by assembling a set of piecewise local solutions, including the first-order Taylor series terms expanded about some sampling states. The work by Rewienski and White inspired our use of piecewise linear local solutions. The assembly of these local approximations is accomplished by assigning nonlinear weights, through radial basis functions in this study. The efficacy of the proposed procedure is validated for a two-dimensional airfoil moving at different Mach numbers and pitching motions, under which the flow exhibits prominent nonlinear behaviors. All results confirm that our nonlinear model is accurate and stable for predicting not only aerodynamic forces but also detailed flowfields. Moreover, the model is robustness-accurate for inputs considerably different from the base trajectory in form and magnitude. This modeling preserves nonlinearity of the problems considered in a rather simple and accurate manner.

Nighttime image dehazing using local atmospheric selection rule and weighted entropy for visible-light systems

NASA Astrophysics Data System (ADS)

Park, Dubok; Han, David K.; Ko, Hanseok

2017-05-01

Optical imaging systems are often degraded by scattering due to atmospheric particles, such as haze, fog, and mist. Imaging under nighttime haze conditions may suffer especially from the glows near active light sources as well as scattering. We present a methodology for nighttime image dehazing based on an optical imaging model which accounts for varying light sources and their glow. First, glow effects are decomposed using relative smoothness. Atmospheric light is then estimated by assessing global and local atmospheric light using a local atmospheric selection rule. The transmission of light is then estimated by maximizing an objective function designed on the basis of weighted entropy. Finally, haze is removed using two estimated parameters, namely, atmospheric light and transmission. The visual and quantitative comparison of the experimental results with the results of existing state-of-the-art methods demonstrates the significance of the proposed approach.

Diagnostic Classification of Schizophrenia Patients on the Basis of Regional Reward-Related fMRI Signal Patterns

PubMed Central

Koch, Stefan P.; Hägele, Claudia; Haynes, John-Dylan; Heinz, Andreas; Schlagenhauf, Florian; Sterzer, Philipp

2015-01-01

Functional neuroimaging has provided evidence for altered function of mesolimbic circuits implicated in reward processing, first and foremost the ventral striatum, in patients with schizophrenia. While such findings based on significant group differences in brain activations can provide important insights into the pathomechanisms of mental disorders, the use of neuroimaging results from standard univariate statistical analysis for individual diagnosis has proven difficult. In this proof of concept study, we tested whether the predictive accuracy for the diagnostic classification of schizophrenia patients vs. healthy controls could be improved using multivariate pattern analysis (MVPA) of regional functional magnetic resonance imaging (fMRI) activation patterns for the anticipation of monetary reward. With a searchlight MVPA approach using support vector machine classification, we found that the diagnostic category could be predicted from local activation patterns in frontal, temporal, occipital and midbrain regions, with a maximal cluster peak classification accuracy of 93% for the right pallidum. Region-of-interest based MVPA for the ventral striatum achieved a maximal cluster peak accuracy of 88%, whereas the classification accuracy on the basis of standard univariate analysis reached only 75%. Moreover, using support vector regression we could additionally predict the severity of negative symptoms from ventral striatal activation patterns. These results show that MVPA can be used to substantially increase the accuracy of diagnostic classification on the basis of task-related fMRI signal patterns in a regionally specific way. PMID:25799236

Preface: Introductory Remarks: Linear Scaling Methods

NASA Astrophysics Data System (ADS)

Bowler, D. R.; Fattebert, J.-L.; Gillan, M. J.; Haynes, P. D.; Skylaris, C.-K.

2008-07-01

It has been just over twenty years since the publication of the seminal paper on molecular dynamics with ab initio methods by Car and Parrinello [1], and the contribution of density functional theory (DFT) and the related techniques to physics, chemistry, materials science, earth science and biochemistry has been huge. Nevertheless, significant improvements are still being made to the performance of these standard techniques; recent work suggests that speed improvements of one or even two orders of magnitude are possible [2]. One of the areas where major progress has long been expected is in O(N), or linear scaling, DFT, in which the computer effort is proportional to the number of atoms. Linear scaling DFT methods have been in development for over ten years [3] but we are now in an exciting period where more and more research groups are working on these methods. Naturally there is a strong and continuing effort to improve the efficiency of the methods and to make them more robust. But there is also a growing ambition to apply them to challenging real-life problems. This special issue contains papers submitted following the CECAM Workshop 'Linear-scaling ab initio calculations: applications and future directions', held in Lyon from 3-6 September 2007. A noteworthy feature of the workshop is that it included a significant number of presentations involving real applications of O(N) methods, as well as work to extend O(N) methods into areas of greater accuracy (correlated wavefunction methods, quantum Monte Carlo, TDDFT) and large scale computer architectures. As well as explicitly linear scaling methods, the conference included presentations on techniques designed to accelerate and improve the efficiency of standard (that is non-linear-scaling) methods; this highlights the important question of crossover—that is, at what size of system does it become more efficient to use a linear-scaling method? As well as fundamental algorithmic questions, this brings up implementation questions relating to parallelization (particularly with multi-core processors starting to dominate the market) and inherent scaling and basis sets (in both normal and linear scaling codes). For now, the answer seems to lie between 100-1,000 atoms, though this depends on the type of simulation used among other factors. Basis sets are still a problematic question in the area of electronic structure calculations. The linear scaling community has largely split into two camps: those using relatively small basis sets based on local atomic-like functions (where systematic convergence to the full basis set limit is hard to achieve); and those that use necessarily larger basis sets which allow convergence systematically and therefore are the localised equivalent of plane waves. Related to basis sets is the study of Wannier functions, on which some linear scaling methods are based and which give a good point of contact with traditional techniques; they are particularly interesting for modelling unoccupied states with linear scaling methods. There are, of course, as many approaches to linear scaling solution for the density matrix as there are groups in the area, though there are various broad areas: McWeeny-based methods, fragment-based methods, recursion methods, and combinations of these. While many ideas have been in development for several years, there are still improvements emerging, as shown by the rich variety of the talks below. Applications using O(N) DFT methods are now starting to emerge, though they are still clearly not trivial. Once systems to be simulated cross the 10,000 atom barrier, only linear scaling methods can be applied, even with the most efficient standard techniques. One of the most challenging problems remaining, now that ab initio methods can be applied to large systems, is the long timescale problem. Although much of the work presented was concerned with improving the performance of the codes, and applying them to scientificallyimportant problems, there was another important theme: extending functionality. The search for greater accuracy has given an implementation of density functional designed to model van der Waals interactions accurately as well as local correlation, TDDFT and QMC and GW methods which, while not explicitly O(N), take advantage of localisation. All speakers at the workshop were invited to contribute to this issue, but not all were able to do this. Hence it is useful to give a complete list of the talks presented, with the names of the sessions; however, many talks fell within more than one area. This is an exciting time for linear scaling methods, which are already starting to contribute significantly to important scientific problems. Applications to nanostructures and biomolecules A DFT study on the structural stability of Ge 3D nanostructures on Si(001) using CONQUEST Tsuyoshi Miyazaki, D R Bowler, M J Gillan, T Otsuka and T Ohno Large scale electronic structure calculation theory and several applications Takeo Fujiwara and Takeo Hoshi ONETEP:Linear-scaling DFT with plane waves Chris-Kriton Skylaris, Peter D Haynes, Arash A Mostofi, Mike C Payne Maximally-localised Wannier functions as building blocks for large-scale electronic structure calculations Arash A Mostofi and Nicola Marzari A linear scaling three dimensional fragment method for ab initio calculations Lin-Wang Wang, Zhengji Zhao, Juan Meza Peta-scalable reactive Molecular dynamics simulation of mechanochemical processes Aiichiro Nakano, Rajiv K. Kalia, Ken-ichi Nomura, Fuyuki Shimojo and Priya Vashishta Recent developments and applications of the real-space multigrid (RMG) method Jerzy Bernholc, M Hodak, W Lu, and F Ribeiro Energy minimisation functionals and algorithms CONQUEST: A linear scaling DFT Code David R Bowler, Tsuyoshi Miyazaki, Antonio Torralba, Veronika Brazdova, Milica Todorovic, Takao Otsuka and Mike Gillan Kernel optimisation and the physical significance of optimised local orbitals in the ONETEP code Peter Haynes, Chris-Kriton Skylaris, Arash Mostofi and Mike Payne A miscellaneous overview of SIESTA algorithms Jose M Soler Wavelets as a basis set for electronic structure calculations and electrostatic problems Stefan Goedecker Wavelets as a basis set for linear scaling electronic structure calculationsMark Rayson O(N) Krylov subspace method for large-scale ab initio electronic structure calculations Taisuke Ozaki Linear scaling calculations with the divide-and-conquer approach and with non-orthogonal localized orbitals Weitao Yang Toward efficient wavefunction based linear scaling energy minimization Valery Weber Accurate O(N) first-principles DFT calculations using finite differences and confined orbitals Jean-Luc Fattebert Linear-scaling methods in dynamics simulations or beyond DFT and ground state properties An O(N) time-domain algorithm for TDDFT Guan Hua Chen Local correlation theory and electronic delocalization Joseph Subotnik Ab initio molecular dynamics with linear scaling: foundations and applications Eiji Tsuchida Towards a linear scaling Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics Thomas Kühne, Michele Ceriotti, Matthias Krack and Michele Parrinello Partial linear scaling for quantum Monte Carlo calculations on condensed matter Mike Gillan Exact embedding of local defects in crystals using maximally localized Wannier functions Eric Cancès Faster GW calculations in larger model structures using ultralocalized nonorthogonal Wannier functions Paolo Umari Other approaches for linear-scaling, including methods formetals Partition-of-unity finite element method for large, accurate electronic-structure calculations of metals John E Pask and Natarajan Sukumar Semiclassical approach to density functional theory Kieron Burke Ab initio transport calculations in defected carbon nanotubes using O(N) techniques Blanca Biel, F J Garcia-Vidal, A Rubio and F Flores Large-scale calculations with the tight-binding (screened) KKR method Rudolf Zeller Acknowledgments We gratefully acknowledge funding for the workshop from the UK CCP9 network, CECAM and the ESF through the PsiK network. DRB, PDH and CKS are funded by the Royal Society. References [1] Car R and Parrinello M 1985 Phys. Rev. Lett. 55 2471 [2] Kühne T D, Krack M, Mohamed F R and Parrinello M 2007 Phys. Rev. Lett. 98 066401 [3] Goedecker S 1999 Rev. Mod. Phys. 71 1085

Assessment of the amide-I local modes in gamma- and beta-turns of peptides.

PubMed

Wang, Jianping

2009-07-14

The amide-I local modes, mainly the C[double bond, length as m-dash]O stretching vibrations, form the structural basis of femtosecond 2D IR spectroscopy in characterizing backbone structures and dynamics of peptides and proteins. In this work, a density functional theory (DFT) level of computational assessment of the amide-I local modes in oligomers mostly in the turn conformations was carried out. It is shown that local mode properties, including transition frequencies and transition dipole magnitudes and orientations, are slightly conformational dependent. However, the distributions of these properties in the peptide oligomers are narrow and have mean values almost identical to those from an isolated peptide monomer, justifying the prevalent use of a uniform local mode in modeling the 1D and 2D IR spectra. In addition, it is shown that the transition dipole magnitude and orientation of the peptide monomer predicted by the DFT calculations can be well approximated by electrostatic potential-based transition charge schemes, e.g. Merz-Singh-Kollman, CHELP, as well as CHELPG.

Driving Human Motor Cortical Oscillations Leads to Behaviorally Relevant Changes in Local GABAA Inhibition: A tACS-TMS Study.

PubMed

Nowak, Magdalena; Hinson, Emily; van Ede, Freek; Pogosyan, Alek; Guerra, Andrea; Quinn, Andrew; Brown, Peter; Stagg, Charlotte J

2017-04-26

Beta and gamma oscillations are the dominant oscillatory activity in the human motor cortex (M1). However, their physiological basis and precise functional significance remain poorly understood. Here, we used transcranial magnetic stimulation (TMS) to examine the physiological basis and behavioral relevance of driving beta and gamma oscillatory activity in the human M1 using transcranial alternating current stimulation (tACS). tACS was applied using a sham-controlled crossover design at individualized intensity for 20 min and TMS was performed at rest (before, during, and after tACS) and during movement preparation (before and after tACS). We demonstrated that driving gamma frequency oscillations using tACS led to a significant, duration-dependent decrease in local resting-state GABA A inhibition, as quantified by short interval intracortical inhibition. The magnitude of this effect was positively correlated with the magnitude of GABA A decrease during movement preparation, when gamma activity in motor circuitry is known to increase. In addition, gamma tACS-induced change in GABA A inhibition was closely related to performance in a motor learning task such that subjects who demonstrated a greater increase in GABA A inhibition also showed faster short-term learning. The findings presented here contribute to our understanding of the neurophysiological basis of motor rhythms and suggest that tACS may have similar physiological effects to endogenously driven local oscillatory activity. Moreover, the ability to modulate local interneuronal circuits by tACS in a behaviorally relevant manner provides a basis for tACS as a putative therapeutic intervention. SIGNIFICANCE STATEMENT Gamma oscillations have a vital role in motor control. Using a combined tACS-TMS approach, we demonstrate that driving gamma frequency oscillations modulates GABA A inhibition in the human motor cortex. Moreover, there is a clear relationship between the change in magnitude of GABA A inhibition induced by tACS and the magnitude of GABA A inhibition observed during task-related synchronization of oscillations in inhibitory interneuronal circuits, supporting the hypothesis that tACS engages endogenous oscillatory circuits. We also show that an individual's physiological response to tACS is closely related to their ability to learn a motor task. These findings contribute to our understanding of the neurophysiological basis of motor rhythms and their behavioral relevance and offer the possibility of developing tACS as a therapeutic tool. Copyright © 2017 Nowak et al.

Determination of many-electron basis functions for a quantum Hall ground state using Schur polynomials

NASA Astrophysics Data System (ADS)

Mandal, Sudhansu S.; Mukherjee, Sutirtha; Ray, Koushik

2018-03-01

A method for determining the ground state of a planar interacting many-electron system in a magnetic field perpendicular to the plane is described. The ground state wave-function is expressed as a linear combination of a set of basis functions. Given only the flux and the number of electrons describing an incompressible state, we use the combinatorics of partitioning the flux among the electrons to derive the basis wave-functions as linear combinations of Schur polynomials. The procedure ensures that the basis wave-functions form representations of the angular momentum algebra. We exemplify the method by deriving the basis functions for the 5/2 quantum Hall state with a few particles. We find that one of the basis functions is precisely the Moore-Read Pfaffian wave function.

Regulation of the Drosophila Hypoxia-Inducible Factor α Sima by CRM1-Dependent Nuclear Export ▿

PubMed Central

Romero, Nuria M.; Irisarri, Maximiliano; Roth, Peggy; Cauerhff, Ana; Samakovlis, Christos; Wappner, Pablo

2008-01-01

Hypoxia-inducible factor α (HIF-α) proteins are regulated by oxygen levels through several different mechanisms that include protein stability, transcriptional coactivator recruitment, and subcellular localization. It was previously reported that these transcription factors are mainly nuclear in hypoxia and cytoplasmic in normoxia, but so far the molecular basis of this regulation is unclear. We show here that the Drosophila melanogaster HIF-α protein Sima shuttles continuously between the nucleus and the cytoplasm. We identified the relevant nuclear localization signal and two functional nuclear export signals (NESs). These NESs are in the Sima basic helix-loop-helix (bHLH) domain and promote CRM1-dependent nuclear export. Site-directed mutagenesis of either NES provoked Sima nuclear retention and increased transcriptional activity, suggesting that nuclear export contributes to Sima regulation. The identified NESs are conserved and probably functional in the bHLH domains of several bHLH-PAS proteins. We propose that rapid nuclear export of Sima regulates the duration of cellular responses to hypoxia. PMID:18332128

Crustal deformation along the San Andreas, California

NASA Technical Reports Server (NTRS)

Li, Victor C.

1992-01-01

The goal is to achieve a better understanding of the regional and local deformation and crustal straining processes in western North America, particularly the effects of the San Andreas and nearby faults on the spatial and temporal crustal deformation behavior. Construction of theoretical models based on the mechanics of coupled elastic plate, viscoelastic foundation and large scale crack mechanics provide a rational basis for the interpretation of seismic and aseismic anomalies and expedite efforts in forecasting the stability of plate boundary deformation. Special focus is placed on the three dimensional time dependent surface deformation due to localized slippage in a elastic layer coupled to a visco-elastic substrate. The numerical analysis is based on a 3-D boundary element technique. Extension to visco-elastic coupling demands the derivation of 3-D time dependent Green's function. This method was applied to analyze the viscoelastic surface displacements due to a dislocated embedded patch. Surface uplift as a function of time and position are obtained. Comparisons between surface uplift for long and short dislocated patches are made.

Multi-variate joint PDF for non-Gaussianities: exact formulation and generic approximations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verde, Licia; Jimenez, Raul; Alvarez-Gaume, Luis

2013-06-01

We provide an exact expression for the multi-variate joint probability distribution function of non-Gaussian fields primordially arising from local transformations of a Gaussian field. This kind of non-Gaussianity is generated in many models of inflation. We apply our expression to the non-Gaussianity estimation from Cosmic Microwave Background maps and the halo mass function where we obtain analytical expressions. We also provide analytic approximations and their range of validity. For the Cosmic Microwave Background we give a fast way to compute the PDF which is valid up to more than 7σ for f{sub NL} values (both true and sampled) not ruledmore » out by current observations, which consists of expressing the PDF as a combination of bispectrum and trispectrum of the temperature maps. The resulting expression is valid for any kind of non-Gaussianity and is not limited to the local type. The above results may serve as the basis for a fully Bayesian analysis of the non-Gaussianity parameter.« less

Application of the dual-kinetic-balance sets in the relativistic many-body problem of atomic structure

NASA Astrophysics Data System (ADS)

Beloy, Kyle; Derevianko, Andrei

2008-09-01

The dual-kinetic-balance (DKB) finite basis set method for solving the Dirac equation for hydrogen-like ions [V.M. Shabaev et al., Phys. Rev. Lett. 93 (2004) 130405] is extended to problems with a non-local spherically-symmetric Dirac-Hartree-Fock potential. We implement the DKB method using B-spline basis sets and compare its performance with the widely-employed approach of Notre Dame (ND) group [W.R. Johnson, S.A. Blundell, J. Sapirstein, Phys. Rev. A 37 (1988) 307-315]. We compare the performance of the ND and DKB methods by computing various properties of Cs atom: energies, hyperfine integrals, the parity-non-conserving amplitude of the 6s-7s transition, and the second-order many-body correction to the removal energy of the valence electrons. We find that for a comparable size of the basis set the accuracy of both methods is similar for matrix elements accumulated far from the nuclear region. However, for atomic properties determined by small distances, the DKB method outperforms the ND approach. In addition, we present a strategy for optimizing the size of the basis sets by choosing progressively smaller number of basis functions for increasingly higher partial waves. This strategy exploits suppression of contributions of high partial waves to typical many-body correlation corrections.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anand, Nikhil; Genest, Vincent X.; Katz, Emanuel

We study 1+1 dimensional Φ 4 theory using the recently proposed method of conformal truncation. Starting in the UV CFT of free field theory, we construct a complete basis of states with definite conformal Casimir, C. We use these states to express the Hamiltonian of the full interacting theory in lightcone quantization. After truncating to states with C≤C max, we numerically diagonalize the Hamiltonian at strong coupling and study the resulting IR dynamics. We compute non-perturbative spectral densities of several local operators, which are equivalent to real-time, infinite-volume correlation functions. These spectral densities, which include the Zamolodchikov C-function along themore » full RG flow, are calculable at any value of the coupling. Near criticality, our numerical results reproduce correlation functions in the 2D Ising model.« less

Definitive Radiotherapy for Ewing Tumors of Extremities and Pelvis: Long-Term Disease Control, Limb Function, and Treatment Toxicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Indelicato, Daniel J.; Keole, Sameer R.; Shahlaee, Amir H.

2008-11-01

Purpose: More than 70% of Ewing tumors occur in the extremities and pelvis. This study identified factors influencing local control and functional outcomes after management with definitive radiotherapy (RT). Patients and Methods: A total of 75 patients with a localized Ewing tumor of the extremity or pelvis were treated with definitive RT at the University of Florida between 1970 and 2006 (lower extremity tumors in 30, pelvic tumors in 26, and upper extremity tumors in 19). RT was performed on a once-daily (40%) or twice-daily (60%) basis. The median dose was 55.2 Gy in 1.8-Gy daily fractions or 55.0 Gymore » in 1.2-Gy twice-daily fractions. The median observed follow-up was 4.7 years. Functional outcome was assessed using the Toronto Extremity Salvage Score. Results: The 10-year actuarial overall survival, cause-specific survival, freedom from relapse, and local control rate was 48%, 48%, 42%, and 71%, respectively. Of the 72 patients, 3 required salvage amputation. Inferior cause-specific survival was associated with larger tumors (81% for tumors <8 cm vs. 39% for tumors {>=}8 cm, p <0.05). No patient characteristics or treatment variables were predictive of local failure. No fractures occurred in patients treated with hyperfractionation or with tumors of the distal extremities. Severe late complications were more frequently associated with use of <8-MV photons and fields encompassing the entire bone or hemipelvis. A significantly better Toronto Extremity Salvage Score was associated with a late-effect biologically effective dose of <91.7 Gy{sub 3}. Conclusions: Limb preservation was effectively achieved through definitive RT. Treating limited field sizes with hyperfractionated high-energy RT could minimize long-term complications and provides superior functional outcomes.« less

14 CFR § 1251.109 - Effect of State or local law or other requirements and effect of employment opportunities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... NATIONAL AERONAUTICS AND SPACE ADMINISTRATION NONDISCRIMINATION ON BASIS OF HANDICAP General Provisions... local law or other requirement that, on the basis of handicap, imposes prohibitions or limits upon the eligibility of qualified handicapped persons to receive services or to practice any occupation or profession...

Cutaneous respirometry by dynamic measurement of mitochondrial oxygen tension for monitoring mitochondrial function in vivo.

PubMed

Harms, Floor A; Voorbeijtel, Wilhelmina J; Bodmer, Sander I A; Raat, Nicolaas J H; Mik, Egbert G

2013-09-01

Progress in diagnosis and treatment of mitochondrial dysfunction in chronic and acute disease could greatly benefit from techniques for monitoring of mitochondrial function in vivo. In this study we demonstrate the feasibility of in vivo respirometry in skin. Mitochondrial oxygen measurements by means of oxygen-dependent delayed fluorescence of protoporphyrin IX are shown to provide a robust basis for measurement of local oxygen disappearance rate (ODR). The fundamental principles behind the technology are described, together with an analysis method for retrievel of respirometry data. The feasibility and reproducibility of this clinically useful approach are demonstrated in a series of rats. Copyright © 2012 Elsevier B.V. All rights reserved.

Micrometeoroid/space debris effects on materials

NASA Technical Reports Server (NTRS)

Zwiener, James M.; Finckenor, Miria M.

1993-01-01

The Long Duration Exposure Facility (LDEF) micrometeoroid/space debris impact data has been reduced in terms that are convenient for evaluating the overall quantitative effect on material properties. Impact crater flux has been evaluated as a function of angle from velocity vector and as a function of crater size. This data is combined with spall data from flight and ground testing to calculate effective solar absorption and emittance values versus time. Results indicate that the surface damage from micrometeoroid/space debris does not significantly affect the overall surface optical thermal physical properties. Of course the local damage around impact craters radically alter optical properties. Damage to composites and solar cells on an overall basis was minimal.

Multi-temperature model derived from state-to-state kinetics for hypersonic entry in Jupiter atmosphere

NASA Astrophysics Data System (ADS)

Colonna, G.; D'Ambrosio, D.; D'Ammando, G.; Pietanza, L. D.; Capitelli, M.

2014-12-01

A state-to-state model of H2/He plasmas coupling the master equations for internal distributions of heavy species with the transport equation for the free electrons has been used as a basis for implementing a multi-temperature kinetic model. In the multi-temperature model internal distributions of heavy particles are Boltzmann, the electron energy distribution function is Maxwell, and the rate coefficients of the elementary processes become a function of local temperatures associated to the relevant equilibrium distributions. The state-to-state and multi-temperature models have been compared in the case of a homogenous recombining plasma, reproducing the conditions met during supersonic expansion though converging-diverging nozzles.

Toward an Integrative Computational Model of the Guinea Pig Cardiac Myocyte

PubMed Central

Gauthier, Laura Doyle; Greenstein, Joseph L.; Winslow, Raimond L.

2012-01-01

The local control theory of excitation-contraction (EC) coupling asserts that regulation of calcium (Ca2+) release occurs at the nanodomain level, where openings of single L-type Ca2+ channels (LCCs) trigger openings of small clusters of ryanodine receptors (RyRs) co-localized within the dyad. A consequence of local control is that the whole-cell Ca2+ transient is a smooth continuous function of influx of Ca2+ through LCCs. While this so-called graded release property has been known for some time, its functional importance to the integrated behavior of the cardiac ventricular myocyte has not been fully appreciated. We previously formulated a biophysically based model, in which LCCs and RyRs interact via a coarse-grained representation of the dyadic space. The model captures key features of local control using a low-dimensional system of ordinary differential equations. Voltage-dependent gain and graded Ca2+ release are emergent properties of this model by virtue of the fact that model formulation is closely based on the sub-cellular basis of local control. In this current work, we have incorporated this graded release model into a prior model of guinea pig ventricular myocyte electrophysiology, metabolism, and isometric force production. The resulting integrative model predicts the experimentally observed causal relationship between action potential (AP) shape and timing of Ca2+ and force transients, a relationship that is not explained by models lacking the graded release property. Model results suggest that even relatively subtle changes in AP morphology that may result, for example, from remodeling of membrane transporter expression in disease or spatial variation in cell properties, may have major impact on the temporal waveform of Ca2+ transients, thus influencing tissue level electromechanical function. PMID:22783206

Toward an integrative computational model of the Guinea pig cardiac myocyte.

PubMed

Gauthier, Laura Doyle; Greenstein, Joseph L; Winslow, Raimond L

2012-01-01

The local control theory of excitation-contraction (EC) coupling asserts that regulation of calcium (Ca(2+)) release occurs at the nanodomain level, where openings of single L-type Ca(2+) channels (LCCs) trigger openings of small clusters of ryanodine receptors (RyRs) co-localized within the dyad. A consequence of local control is that the whole-cell Ca(2+) transient is a smooth continuous function of influx of Ca(2+) through LCCs. While this so-called graded release property has been known for some time, its functional importance to the integrated behavior of the cardiac ventricular myocyte has not been fully appreciated. We previously formulated a biophysically based model, in which LCCs and RyRs interact via a coarse-grained representation of the dyadic space. The model captures key features of local control using a low-dimensional system of ordinary differential equations. Voltage-dependent gain and graded Ca(2+) release are emergent properties of this model by virtue of the fact that model formulation is closely based on the sub-cellular basis of local control. In this current work, we have incorporated this graded release model into a prior model of guinea pig ventricular myocyte electrophysiology, metabolism, and isometric force production. The resulting integrative model predicts the experimentally observed causal relationship between action potential (AP) shape and timing of Ca(2+) and force transients, a relationship that is not explained by models lacking the graded release property. Model results suggest that even relatively subtle changes in AP morphology that may result, for example, from remodeling of membrane transporter expression in disease or spatial variation in cell properties, may have major impact on the temporal waveform of Ca(2+) transients, thus influencing tissue level electromechanical function.

Mechanisms and use of neural transplants for brain repair.

PubMed

Dunnett, Stephen B; Björklund, Anders

2017-01-01

Under appropriate conditions, neural tissues transplanted into the adult mammalian brain can survive, integrate, and function so as to influence the behavior of the host, opening the prospect of repairing neuronal damage, and alleviating symptoms associated with neuronal injury or neurodegenerative disease. Alternative mechanisms of action have been postulated: nonspecific effects of surgery; neurotrophic and neuroprotective influences on disease progression and host plasticity; diffuse or locally regulated pharmacological delivery of deficient neurochemicals, neurotransmitters, or neurohormones; restitution of the neuronal and glial environment necessary for proper host neuronal support and processing; promoting local and long-distance host and graft axon growth; formation of reciprocal connections and reconstruction of local circuits within the host brain; and up to full integration and reconstruction of fully functional host neuronal networks. Analysis of neural transplants in a broad range of anatomical systems and disease models, on simple and complex classes of behavioral function and information processing, have indicated that all of these alternative mechanisms are likely to contribute in different circumstances. Thus, there is not a single or typical mode of graft function; rather grafts can and do function in multiple ways, specific to each particular context. Consequently, to develop an effective cell-based therapy, multiple dimensions must be considered: the target disease pathogenesis; the neurodegenerative basis of each type of physiological dysfunction or behavioral symptom; the nature of the repair required to alleviate or remediate the functional impairments of particular clinical relevance; and identification of a suitable cell source or delivery system, along with the site and method of implantation, that can achieve the sought for repair and recovery. © 2017 Elsevier B.V. All rights reserved.

Expression, sorting, and segregation of Golgi proteins during germ cell differentiation in the testis

PubMed Central

Au, Catherine E.; Hermo, Louis; Byrne, Elliot; Smirle, Jeffrey; Fazel, Ali; Simon, Paul H. G.; Kearney, Robert E.; Cameron, Pamela H.; Smith, Charles E.; Vali, Hojatollah; Fernandez-Rodriguez, Julia; Ma, Kewei; Nilsson, Tommy; Bergeron, John J. M.

2015-01-01

The molecular basis of changes in structure, cellular location, and function of the Golgi apparatus during male germ cell differentiation is unknown. To deduce cognate Golgi proteins, we isolated germ cell Golgi fractions, and 1318 proteins were characterized, with 20 localized in situ. The most abundant protein, GL54D of unknown function, is characterized as a germ cell–specific Golgi-localized type II integral membrane glycoprotein. TM9SF3, also of unknown function, was revealed to be a universal Golgi marker for both somatic and germ cells. During acrosome formation, several Golgi proteins (GBF1, GPP34, GRASP55) localize to both the acrosome and Golgi, while GL54D, TM9SF3, and the Golgi trafficking protein TMED7/p27 are segregated from the acrosome. After acrosome formation, GL54D, TM9SF3, TMED4/p25, and TMED7/p27 continue to mark Golgi identity as it migrates away from the acrosome, while the others (GBF1, GPP34, GRASP55) remain in the acrosome and are progressively lost in later steps of differentiation. Cytoplasmic HSP70.2 and the endoplasmic reticulum luminal protein-folding enzyme PDILT are also Golgi recruited but only during acrosome formation. This resource identifies abundant Golgi proteins that are expressed differentially during mitosis, meiosis, and postacrosome Golgi migration, including the last step of differentiation. PMID:25808494

Matrix basis for plane and modal waves in a Timoshenko beam

PubMed Central

Tolfo, Daniela de Rosso; Tonetto, Leticia

2016-01-01

Plane waves and modal waves of the Timoshenko beam model are characterized in closed form by introducing robust matrix basis that behave according to the nature of frequency and wave or modal numbers. These new characterizations are given in terms of a finite number of coupling matrices and closed form generating scalar functions. Through Liouville’s technique, these latter are well behaved at critical or static situations. Eigenanalysis is formulated for exponential and modal waves. Modal waves are superposition of four plane waves, but there are plane waves that cannot be modal waves. Reflected and transmitted waves at an interface point are formulated in matrix terms, regardless of having a conservative or a dissipative situation. The matrix representation of modal waves is used in a crack problem for determining the reflected and transmitted matrices. Their euclidean norms are seen to be dominated by certain components at low and high frequencies. The matrix basis technique is also used with a non-local Timoshenko model and with the wave interaction with a boundary. The matrix basis allows to characterize reflected and transmitted waves in spectral and non-spectral form. PMID:28018668

Application of ab initio many-body perturbation theory with Gaussian basis sets to the singlet and triplet excitations of organic molecules

NASA Astrophysics Data System (ADS)

Hamed, Samia; Rangel, Tonatiuh; Bruneval, Fabien; Neaton, Jeffrey B.

Quantitative understanding of charged and neutral excitations of organic molecules is critical in diverse areas of study that include astrophysics and the development of energy technologies that are clean and efficient. The recent use of local basis sets with ab initio many-body perturbation theory in the GW approximation and the Bethe-Saltpeter equation approach (BSE), methods traditionally applied to periodic condensed phases with a plane-wave basis, has opened the door to detailed study of such excitations for molecules, as well as accurate numerical benchmarks. Here, through a series of systematic benchmarks with a Gaussian basis, we report on the extent to which the predictive power and utility of this approach depend critically on interdependent underlying approximations and choices for molecules, including the mean-field starting point (eg optimally-tuned range separated hybrids, pure DFT functionals, and untuned hybrids), the GW scheme, and the Tamm Dancoff approximation. We demonstrate the effects of these choices in the context of Thiels' set while drawing analogies to linear-response time-dependent DFT and making comparisons to best theoretical estimates from higher-order wavefunction-based theories.

Antarctic Mass Loss from GRACE from Space- and Time-Resolved Modeling with Slepian Functions

NASA Astrophysics Data System (ADS)

Simons, F. J.; Harig, C.

2013-12-01

The melting of polar ice sheets is a major contributor to global sea-level rise. Antarctica is of particular interest since most of the mass loss has occurred in West Antarctica, however updated glacial isostatic adjustment (GIA) models and recent mass gains in East Antarctica have reduced the continent-wide integrated decadal trend of mass loss. Here we present a spatially and temporally resolved estimation of the Antarctic ice mass change using Slepian localization functions. With a Slepian basis specifically for Antarctica, the basis functions maximize their energy on the continent and we can project the geopotential fields into a sparse set of orthogonal coefficients. By fitting polynomial functions to the limited basis coefficients we maximize signal-to-noise levels and need not perform smoothing or destriping filters common to other approaches. In addition we determine an empirical noise covariance matrix from the GRACE data to estimate the uncertainty of mass estimation. When applied to large ice sheets, as in our own recent Greenland work, this technique is able to resolve both the overall continental integrated mass trend, as well as the spatial distribution of the mass changes over time. Using CSR-RL05 GRACE data between Jan. 2003 and Jan 2013, we estimate the regional accelerations in mass change for several sub-regions and examine how the spatial pattern of mass has changed. The Amundsen Sea coast of West Antarctica has experienced a large acceleration in mass loss (-26 Gt/yr^2). While mass loss is concentrated near Pine Island and Thwaites glaciers, it has also increased along the coast further towards the Ross ice shelf.

Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

NASA Astrophysics Data System (ADS)

Oberhofer, Harald; Blumberger, Jochen

2010-12-01

We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q-) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, ( {< {| {H_ab } |^2 } > } )^{1/2} = 6.7 {mH}, is significantly higher than the value obtained for the minimum energy structure, | {H_ab } | = 3.8 {mH}. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q- in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.

Singular value decomposition: a diagnostic tool for ill-posed inverse problems in optical computed tomography

NASA Astrophysics Data System (ADS)

Lanen, Theo A.; Watt, David W.

1995-10-01

Singular value decomposition has served as a diagnostic tool in optical computed tomography by using its capability to provide insight into the condition of ill-posed inverse problems. Various tomographic geometries are compared to one another through the singular value spectrum of their weight matrices. The number of significant singular values in the singular value spectrum of a weight matrix is a quantitative measure of the condition of the system of linear equations defined by a tomographic geometery. The analysis involves variation of the following five parameters, characterizing a tomographic geometry: 1) the spatial resolution of the reconstruction domain, 2) the number of views, 3) the number of projection rays per view, 4) the total observation angle spanned by the views, and 5) the selected basis function. Five local basis functions are considered: the square pulse, the triangle, the cubic B-spline, the Hanning window, and the Gaussian distribution. Also items like the presence of noise in the views, the coding accuracy of the weight matrix, as well as the accuracy of the accuracy of the singular value decomposition procedure itself are assessed.

Electron affinities of polycyclic aromatic hydrocarbons by means of B3LYP/6-31+G* calculations.

PubMed

Modelli, Alberto; Mussoni, Laura; Fabbri, Daniele

2006-05-25

The gas-phase experimental adiabatic electron affinities (AEAs) of the polycyclic aromatic hydrocarbons (PAHs) anthracene, tetracene, pentacene, chrysene, pyrene, benzo[a]pyrene, benzo[e]pyrene, and fluoranthene are well reproduced using the hybrid density functional method B3LYP with the 6-31+G* basis set, indicating that the smallest addition of diffuse functions to the basis set is suitable for a correct description of the stable PAH anion states. The calculated AEAs also give a very good linear correlation with available reduction potentials measured in solution. The AEAs (not experimentally available) of the isomeric benzo[ghi]fluoranthene and cyclopenta[cd]pyrene, commonly found in the environment, are predicted to be 0.817 and 1.108 eV, respectively, confirming the enhancement of the electron-acceptor properties associated with fusion of a peripheral cyclopenta ring. The calculated localization properties of the lowest unoccupied MO of cyclopenta[cd]pyrene, together with its relatively high electron affinity, account for a high reactivity at the ethene double bond of this PAH in reductive processes.

Health sector decentralization and local decision-making: Decision space, institutional capacities and accountability in Pakistan.

PubMed

Bossert, Thomas John; Mitchell, Andrew David

2011-01-01

Health sector decentralization has been widely adopted to improve delivery of health services. While many argue that institutional capacities and mechanisms of accountability required to transform decentralized decision-making into improvements in local health systems are lacking, few empirical studies exist which measure or relate together these concepts. Based on research instruments administered to a sample of 91 health sector decision-makers in 17 districts of Pakistan, this study analyzes relationships between three dimensions of decentralization: decentralized authority (referred to as "decision space"), institutional capacities, and accountability to local officials. Composite quantitative indicators of these three dimensions were constructed within four broad health functions (strategic and operational planning, budgeting, human resources management, and service organization/delivery) and on an overall/cross-function basis. Three main findings emerged. First, district-level respondents report varying degrees of each dimension despite being under a single decentralization regime and facing similar rules across provinces. Second, within dimensions of decentralization-particularly decision space and capacities-synergies exist between levels reported by respondents in one function and those reported in other functions (statistically significant coefficients of correlation ranging from ρ=0.22 to ρ=0.43). Third, synergies exist across dimensions of decentralization, particularly in terms of an overall indicator of institutional capacities (significantly correlated with both overall decision space (ρ=0.39) and accountability (ρ=0.23)). This study demonstrates that decentralization is a varied experience-with some district-level officials making greater use of decision space than others and that those who do so also tend to have more capacity to make decisions and are held more accountable to elected local officials for such choices. These findings suggest that Pakistan's decentralization policy should focus on synergies among dimensions of decentralization to encouraging more use of de jure decision space, work toward more uniform institutional capacity, and encourage greater accountability to local elected officials. Copyright © 2010 Elsevier Ltd. All rights reserved.

Comparative sensitivities of functional MRI sequences in detection of local recurrence of prostate carcinoma after radical prostatectomy or external-beam radiotherapy.

PubMed

Roy, Catherine; Foudi, Fatah; Charton, Jeanne; Jung, Michel; Lang, Hervé; Saussine, Christian; Jacqmin, Didier

2013-04-01

The aim of this retrospective study was to determine the respective accuracies of three types of functional MRI sequences-diffusion-weighted imaging (DWI), dynamic contrast-enhanced (DCE) MRI, and 3D (1)H-MR spectroscopy (MRS)-in the depiction of local prostate cancer recurrence after two different initial therapy options. From a cohort of 83 patients with suspicion of local recurrence based on prostate-specific antigen (PSA) kinetics who were imaged on a 3-T MRI unit using an identical protocol including the three functional sequences with an endorectal coil, we selected 60 patients (group A, 28 patients who underwent radical prostatectomy; group B, 32 patients who underwent external-beam radiation) who had local recurrence ascertained on the basis of a transrectal ultrasound-guided biopsy results and a reduction in PSA level after salvage therapy. All patients presented with a local relapse. Sensitivity with T2-weighted MRI and 3D (1)H-MRS sequences was 57% and 53%, respectively, for group A and 71% and 78%, respectively, for group B. DCE-MRI alone showed a sensitivity of 100% and 96%, respectively, for groups A and B. DWI alone had a higher sensitivity for group B (96%) than for group A (71%). The combination of T2-weighted imaging plus DWI plus DCE-MRI provided a sensitivity as high as 100% in group B. The performance of functional imaging sequences for detecting recurrence is different after radical prostatectomy and external-beam radiotherapy. DCE-MRI is a valid and efficient tool to detect prostate cancer recurrence in radical prostatectomy as well as in external-beam radiotherapy. The combination of DCE-MRI and DWI is highly efficient after radiation therapy. Three-dimensional (1)H-MRS needs to be improved. Even though it is not accurate enough, T2-weighted imaging remains essential for the morphologic analysis of the area.

Neurocardiology: Structure-Based Function.

PubMed

Ardell, Jeffrey L; Armour, John Andrew

2016-09-15

Cardiac control is mediated via a series of reflex control networks involving somata in the (i) intrinsic cardiac ganglia (heart), (ii) intrathoracic extracardiac ganglia (stellate, middle cervical), (iii) superior cervical ganglia, (iv) spinal cord, (v) brainstem, and (vi) higher centers. Each of these processing centers contains afferent, efferent, and local circuit neurons, which interact locally and in an interdependent fashion with the other levels to coordinate regional cardiac electrical and mechanical indices on a beat-to-beat basis. This control system is optimized to respond to normal physiological stressors (standing, exercise, and temperature); however, it can be catastrophically disrupted by pathological events such as myocardial ischemia. In fact, it is now recognized that autonomic dysregulation is central to the evolution of heart failure and arrhythmias. Autonomic regulation therapy is an emerging modality in the management of acute and chronic cardiac pathologies. Neuromodulation-based approaches that target select nexus points of this hierarchy for cardiac control offer unique opportunities to positively affect therapeutic outcomes via improved efficacy of cardiovascular reflex control. As such, understanding the anatomical and physiological basis for such control is necessary to implement effectively novel neuromodulation therapies. © 2016 American Physiological Society. Compr Physiol 6:1635-1653, 2016. Copyright © 2016 John Wiley & Sons, Inc.

Implementation of Two-Component Time-Dependent Density Functional Theory in TURBOMOLE.

PubMed

Kühn, Michael; Weigend, Florian

2013-12-10

We report the efficient implementation of a two-component time-dependent density functional theory proposed by Wang et al. (Wang, F.; Ziegler, T.; van Lenthe, E.; van Gisbergen, S.; Baerends, E. J. J. Chem. Phys. 2005, 122, 204103) that accounts for spin-orbit effects on excitations of closed-shell systems by employing a noncollinear exchange-correlation kernel. In contrast to the aforementioned implementation, our method is based on two-component effective core potentials as well as Gaussian-type basis functions. It is implemented in the TURBOMOLE program suite for functionals of the local density approximation and the generalized gradient approximation. Accuracy is assessed by comparison of two-component vertical excitation energies of heavy atoms and ions (Cd, Hg, Au(+)) and small molecules (I2, TlH) to other two- and four-component approaches. Efficiency is demonstrated by calculating the electronic spectrum of Au20.

How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements?

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2016-08-18

The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. By and large, the main strength of the hybrid Minnesota density functionals is that the best ones provide verymore » good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). Finally, as an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses.« less

Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

NASA Astrophysics Data System (ADS)

Goldfeld, Dahlia A.; Bochevarov, Arteum D.; Friesner, Richard A.

2008-12-01

This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G∗, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe

2016-07-28

Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set producesmore » <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.« less

Quantum formalism for classical statistics

NASA Astrophysics Data System (ADS)

Wetterich, C.

2018-06-01

In static classical statistical systems the problem of information transport from a boundary to the bulk finds a simple description in terms of wave functions or density matrices. While the transfer matrix formalism is a type of Heisenberg picture for this problem, we develop here the associated Schrödinger picture that keeps track of the local probabilistic information. The transport of the probabilistic information between neighboring hypersurfaces obeys a linear evolution equation, and therefore the superposition principle for the possible solutions. Operators are associated to local observables, with rules for the computation of expectation values similar to quantum mechanics. We discuss how non-commutativity naturally arises in this setting. Also other features characteristic of quantum mechanics, such as complex structure, change of basis or symmetry transformations, can be found in classical statistics once formulated in terms of wave functions or density matrices. We construct for every quantum system an equivalent classical statistical system, such that time in quantum mechanics corresponds to the location of hypersurfaces in the classical probabilistic ensemble. For suitable choices of local observables in the classical statistical system one can, in principle, compute all expectation values and correlations of observables in the quantum system from the local probabilistic information of the associated classical statistical system. Realizing a static memory material as a quantum simulator for a given quantum system is not a matter of principle, but rather of practical simplicity.

Multiscale image contrast amplification (MUSICA)

NASA Astrophysics Data System (ADS)

Vuylsteke, Pieter; Schoeters, Emile P.

1994-05-01

This article presents a novel approach to the problem of detail contrast enhancement, based on multiresolution representation of the original image. The image is decomposed into a weighted sum of smooth, localized, 2D basis functions at multiple scales. Each transform coefficient represents the amount of local detail at some specific scale and at a specific position in the image. Detail contrast is enhanced by non-linear amplification of the transform coefficients. An inverse transform is then applied to the modified coefficients. This yields a uniformly contrast- enhanced image without artefacts. The MUSICA-algorithm is being applied routinely to computed radiography images of chest, skull, spine, shoulder, pelvis, extremities, and abdomen examinations, with excellent acceptance. It is useful for a wide range of applications in the medical, graphical, and industrial area.

Agroecology in the tropics: Achieving a balance between land use and preservation

NASA Astrophysics Data System (ADS)

Gliessman, Stephen R.

1992-11-01

Agroecology is the application of ecological concepts and principles to the design and management of sustainable agricultural systems. An agroecological approach to agriculture has special importance in the humid tropics where agricultural development and the preservation of tropical forests are most often in direct conflict. It is proposed that a more sustainable approach to development is needed, where agroecosystems depend on low external inputs, function more on the use of locally available and renewable resources, have benign impacts on the environment, and are based on the knowledge and culture of the local inhabitants. Examples of traditional agroecosystem management in Mesoamerica that can provide this basis are presented. The preservation of both biological and cultural diversity are integral to the long-term sustainable management of natural resources in the tropics.

Vernetztes Engagement von Unternehmen - Von gut gemeint zu gut gemacht

NASA Astrophysics Data System (ADS)

Osterhoff, Frank

2016-03-01

A region's living conditions, especially the chances of economic and social participation, are shaped not only by overarching trends, legislation and local administrations, but also by local stakeholders. Corporate responsibility can be observed where corporate and societal goals are congruent. Conceptually, the involvement of firms can be divided into phases, which correspond to a development. A special form is the cooperation with others. But networking, as well as increasing demands on the outcome of responsibility strategies, creates special requirements for the organization of cooperation. For this purpose, professionalization is necessary, which can be achieved on the basis of certain guidelines. Because of its voluntary nature, corporate responsibility cannot take over a basic role in providing services for the public. It is limited by the original functions of the state.

Sound field reconstruction within an entire cavity by plane wave expansions using a spherical microphone array.

PubMed

Wang, Yan; Chen, Kean

2017-10-01

A spherical microphone array has proved effective in reconstructing an enclosed sound field by a superposition of spherical wave functions in Fourier domain. It allows successful reconstructions surrounding the array, but the accuracy will be degraded at a distance. In order to extend the effective reconstruction to the entire cavity, a plane-wave basis in space domain is used owing to its non-decaying propagating characteristic and compared with the conventional spherical wave function method in a low frequency sound field within a cylindrical cavity. The sensitivity to measurement noise, the effects of the numbers of plane waves, and measurement positions are discussed. Simulations show that under the same measurement conditions, the plane wave function method is superior in terms of reconstruction accuracy and data processing efficiency, that is, the entire sound field imaging can be achieved by only one time calculation instead of translations of local sets of coefficients with respect to every measurement position into a global one. An experiment was conducted inside an aircraft cabin mock-up for validation. Additionally, this method provides an alternative possibility to recover the coefficients of high order spherical wave functions in a global coordinate system without coordinate translations with respect to local origins.

Zn Coordination Chemistry:  Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory.

PubMed

Amin, Elizabeth A; Truhlar, Donald G

2008-01-01

We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn-ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree-Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree-Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree-Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 Å for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 Å) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 Å for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 Å in bond lengths, ∼0.2 D in dipole moments, and ∼4 kcal/mol in Zn-ligand bond energies) that cannot be neglected for accurate modeling, but the same density functionals that do well in all-electron nonrelativistic calculations do well with relativistic effective core potentials. Although most tests are carried out with augmented polarized triple-ζ basis sets, we also carried out some tests with an augmented polarized double-ζ basis set, and we found, on average, that with the smaller basis set DFT has no loss in accuracy for dipole moments and only ∼10% less accurate bond lengths.

Rapid Neocortical Dynamics: Cellular and Network Mechanisms

PubMed Central

Haider, Bilal; McCormick, David A.

2011-01-01

The highly interconnected local and large-scale networks of the neocortical sheet rapidly and dynamically modulate their functional connectivity according to behavioral demands. This basic operating principle of the neocortex is mediated by the continuously changing flow of excitatory and inhibitory synaptic barrages that not only control participation of neurons in networks but also define the networks themselves. The rapid control of neuronal responsiveness via synaptic bombardment is a fundamental property of cortical dynamics that may provide the basis of diverse behaviors, including sensory perception, motor integration, working memory, and attention. PMID:19409263

Self-organized synthesis of silver dendritic nanostructures via an electroless metal deposition method

NASA Astrophysics Data System (ADS)

Qiu, T.; Wu, X. L.; Mei, Y. F.; Chu, P. K.; Siu, G. G.

2005-09-01

Unique silver dendritic nanostructures, with stems, branches, and leaves, were synthesized with self-organization via a simple electroless metal deposition method in a conventional autoclave containing aqueous HF and AgNO3 solution. Their growth mechanisms are discussed in detail on the basis of a self-assembled localized microscopic electrochemical cell model. A process of diffusion-limited aggregation is suggested for the formation of the silver dendritic nanostructures. This nanostructured material is of great potential to be building blocks for assembling mini-functional devices of the next generation.

Characterization and storage of malaria antigens: Localization and chemical characterization of Plasmodium knowlesi schizont antigens

PubMed Central

Deans, J. A.; Cohen, S.

1979-01-01

The identification of malarial antigens that induce protective immunity could provide a rational basis for developing an effective antimalarial vaccine as well as specific serodiagnostic tests indicative of clinical immune status. Since protective immunity is probably induced by stage-dependent rather than stage-independent antigens, the antigenic composition of different stages of Plasmodium knowlesi has been compared, and a limited chemical characterization undertaken. This information should provide some insight into the types of preparative procedure appropriate for the purification of functionally important malarial antigens. PMID:120777

DGDFT: A massively parallel method for large scale density functional theory calculations.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-09-28

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10(-4) Hartree/atom in terms of the error of energy and 6.2 × 10(-4) Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-12-21

With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn-Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve a conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number of degrees of freedom required to represent the Kohn-Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, results in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as their dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080-10,800 atoms is only 10-25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5000-50,000 processors. We use DGDFT based ab initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 × 1 edge reconstruction appears in ACPNRs at room temperature.

DFT analysis on the molecular structure, vibrational and electronic spectra of 2-(cyclohexylamino)ethanesulfonic acid

NASA Astrophysics Data System (ADS)

Renuga Devi, T. S.; Sharmi kumar, J.; Ramkumaar, G. R.

2015-02-01

The FTIR and FT-Raman spectra of 2-(cyclohexylamino)ethanesulfonic acid were recorded in the regions 4000-400 cm-1 and 4000-50 cm-1 respectively. The structural and spectroscopic data of the molecule in the ground state were calculated using Hartee-Fock and Density functional method (B3LYP) with the correlation consistent-polarized valence double zeta (cc-pVDZ) basis set and 6-311++G(d,p) basis set. The most stable conformer was optimized and the structural and vibrational parameters were determined based on this. The complete assignments were performed based on the Potential Energy Distribution (PED) of the vibrational modes, calculated using Vibrational Energy Distribution Analysis (VEDA) 4 program. With the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties and Atomic charges were calculated using both Hartee-Fock and density functional method using the cc-pVDZ basis set and compared. The calculated HOMO-LUMO energy gap revealed that charge transfer occurs within the molecule. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge Including Atomic Orbital (GIAO) method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using Natural Bond Orbital (NBO) analysis. The first order hyperpolarizability (β) and Molecular Electrostatic Potential (MEP) of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemical reactivity site in the molecule.

New Basis Functions for the Electromagnetic Solution of Arbitrarily-shaped, Three Dimensional Conducting Bodies Using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2007-01-01

In this work, we present a new set of basis functions, de ned over a pair of planar triangular patches, for the solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped surfaces using the method of moments solution procedure. The basis functions are constant over the function subdomain and resemble pulse functions for one and two dimensional problems. Further, another set of basis functions, point-wise orthogonal to the first set, is also de ned over the same function space. The primary objective of developing these basis functions is to utilize them for the electromagnetic solution involving conducting, dielectric, and composite bodies. However, in the present work, only the conducting body solution is presented and compared with other data.

New Basis Functions for the Electromagnetic Solution of Arbitrarily-shaped, Three Dimensional Conducting Bodies using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2008-01-01

In this work, we present a new set of basis functions, defined over a pair of planar triangular patches, for the solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped surfaces using the method of moments solution procedure. The basis functions are constant over the function subdomain and resemble pulse functions for one and two dimensional problems. Further, another set of basis functions, point-wise orthogonal to the first set, is also defined over the same function space. The primary objective of developing these basis functions is to utilize them for the electromagnetic solution involving conducting, dielectric, and composite bodies. However, in the present work, only the conducting body solution is presented and compared with other data.

A Cubic Radial Basis Function in the MLPG Method for Beam Problems

NASA Technical Reports Server (NTRS)

Raju, I. S.; Phillips, D. R.

2002-01-01

A non-compactly supported cubic radial basis function implementation of the MLPG method for beam problems is presented. The evaluation of the derivatives of the shape functions obtained from the radial basis function interpolation is much simpler than the evaluation of the moving least squares shape function derivatives. The radial basis MLPG yields results as accurate or better than those obtained by the conventional MLPG method for problems with discontinuous and other complex loading conditions.

RG flow from Φ 4 theory to the 2D Ising model

DOE PAGES

Anand, Nikhil; Genest, Vincent X.; Katz, Emanuel; ...

2017-08-16

We study 1+1 dimensional Φ 4 theory using the recently proposed method of conformal truncation. Starting in the UV CFT of free field theory, we construct a complete basis of states with definite conformal Casimir, C. We use these states to express the Hamiltonian of the full interacting theory in lightcone quantization. After truncating to states with C≤C max, we numerically diagonalize the Hamiltonian at strong coupling and study the resulting IR dynamics. We compute non-perturbative spectral densities of several local operators, which are equivalent to real-time, infinite-volume correlation functions. These spectral densities, which include the Zamolodchikov C-function along themore » full RG flow, are calculable at any value of the coupling. Near criticality, our numerical results reproduce correlation functions in the 2D Ising model.« less

Large-area multiplexed sensing using MEMS and fiber optics

NASA Astrophysics Data System (ADS)

Miller, Michael B.; Clark, Richard L., Jr.; Bell, Clifton R.; Russler, Patrick M.

2000-06-01

Micro-electro-mechanical (MEMS) technology offers the ability to implement local and independent sensing and actuation functions through the coordinated response of discrete micro-electro-mechanical 'basis function' elements. The small size of micromechanical components coupled with the ability to reduce costs using volume manufacturing techniques opens up significant potential not only in military applications such as flight and engine monitoring and control, but in autonomous vehicle control, smart munitions, airborne reconnaissance, LADAR, missile guidance, and even in intelligent transportation systems and automotive guidance applications. In this program, Luna Innovations is developing a flexible, programmable interface which can be integrated direction with different types of MEMS sensors, and then used to multiplex many sensors ona single optical fiber to provide a unique combination of functions that will allow larger quantities of sensory input with better resolution than ever before possible.

A Window into the Brain: Advances in Psychiatric fMRI

PubMed Central

Zhan, Xiaoyan

2015-01-01

Functional magnetic resonance imaging (fMRI) plays a key role in modern psychiatric research. It provides a means to assay differences in brain systems that underlie psychiatric illness, treatment response, and properties of brain structure and function that convey risk factor for mental diseases. Here we review recent advances in fMRI methods in general use and progress made in understanding the neural basis of mental illness. Drawing on concepts and findings from psychiatric fMRI, we propose that mental illness may not be associated with abnormalities in specific local regions but rather corresponds to variation in the overall organization of functional communication throughout the brain network. Future research may need to integrate neuroimaging information drawn from different analysis methods and delineate spatial and temporal patterns of brain responses that are specific to certain types of psychiatric disorders. PMID:26413531

Formulation of improved basis sets for the study of polymer dynamics through diffusion theory methods.

PubMed

Gaspari, Roberto; Rapallo, Arnaldo

2008-06-28

In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum trajectory, with great savings in computational time required. This offers a theoretical bridge between the experimental static and dynamical properties of polymers.

Uniform electron gases. III. Low-density gases on three-dimensional spheres.

PubMed

Agboola, Davids; Knol, Anneke L; Gill, Peter M W; Loos, Pierre-François

2015-08-28

By combining variational Monte Carlo (VMC) and complete-basis-set limit Hartree-Fock (HF) calculations, we have obtained near-exact correlation energies for low-density same-spin electrons on a three-dimensional sphere (3-sphere), i.e., the surface of a four-dimensional ball. In the VMC calculations, we compare the efficacies of two types of one-electron basis functions for these strongly correlated systems and analyze the energy convergence with respect to the quality of the Jastrow factor. The HF calculations employ spherical Gaussian functions (SGFs) which are the curved-space analogs of Cartesian Gaussian functions. At low densities, the electrons become relatively localized into Wigner crystals, and the natural SGF centers are found by solving the Thomson problem (i.e., the minimum-energy arrangement of n point charges) on the 3-sphere for various values of n. We have found 11 special values of n whose Thomson sites are equivalent. Three of these are the vertices of four-dimensional Platonic solids - the hyper-tetrahedron (n = 5), the hyper-octahedron (n = 8), and the 24-cell (n = 24) - and a fourth is a highly symmetric structure (n = 13) which has not previously been reported. By calculating the harmonic frequencies of the electrons around their equilibrium positions, we also find the first-order vibrational corrections to the Thomson energy.

Investigating changes in brain network properties in HIV-associated neurocognitive disease (HAND) using mutual connectivity analysis (MCA)

NASA Astrophysics Data System (ADS)

Abidin, Anas Zainul; D'Souza, Adora M.; Nagarajan, Mahesh B.; Wismüller, Axel

2016-03-01

About 50% of subjects infected with HIV present deficits in cognitive domains, which are known collectively as HIV associated neurocognitive disorder (HAND). The underlying synaptodendritic damage can be captured using resting state functional MRI, as has been demonstrated by a few earlier studies. Such damage may induce topological changes of brain connectivity networks. We test this hypothesis by capturing the functional interdependence of 90 brain network nodes using a Mutual Connectivity Analysis (MCA) framework with non-linear time series modeling based on Generalized Radial Basis function (GRBF) neural networks. The network nodes are selected based on the regions defined in the Automated Anatomic Labeling (AAL) atlas. Each node is represented by the average time series of the voxels of that region. The resulting networks are then characterized using graph-theoretic measures that quantify various network topology properties at a global as well as at a local level. We tested for differences in these properties in network graphs obtained for 10 subjects (6 male and 4 female, 5 HIV+ and 5 HIV-). Global network properties captured some differences between these subject cohorts, though significant differences were seen only with the clustering coefficient measure. Local network properties, such as local efficiency and the degree of connections, captured significant differences in regions of the frontal lobe, precentral and cingulate cortex amongst a few others. These results suggest that our method can be used to effectively capture differences occurring in brain network connectivity properties revealed by resting-state functional MRI in neurological disease states, such as HAND.

Dexmedetomidine Disrupts the Local and Global Efficiencies of Large-scale Brain Networks.

PubMed

Hashmi, Javeria A; Loggia, Marco L; Khan, Sheraz; Gao, Lei; Kim, Jieun; Napadow, Vitaly; Brown, Emery N; Akeju, Oluwaseun

2017-03-01

A clear understanding of the neural basis of consciousness is fundamental to research in clinical and basic neuroscience disciplines and anesthesia. Recently, decreased efficiency of information integration was suggested as a core network feature of propofol-induced unconsciousness. However, it is unclear whether this finding can be generalized to dexmedetomidine, which has a different molecular target. Dexmedetomidine was administered as a 1-μg/kg bolus over 10 min, followed by a 0.7-μg · kg · h infusion to healthy human volunteers (age range, 18 to 36 yr; n = 15). Resting-state functional magnetic resonance imaging data were acquired during baseline, dexmedetomidine-induced altered arousal, and recovery states. Zero-lag correlations between resting-state functional magnetic resonance imaging signals extracted from 131 brain parcellations were used to construct weighted brain networks. Network efficiency, degree distribution, and node strength were computed using graph analysis. Parcellated brain regions were also mapped to known resting-state networks to study functional connectivity changes. Dexmedetomidine significantly reduced the local and global efficiencies of graph theory-derived networks. Dexmedetomidine also reduced the average brain connectivity strength without impairing the degree distribution. Functional connectivity within and between all resting-state networks was modulated by dexmedetomidine. Dexmedetomidine is associated with a significant drop in the capacity for efficient information transmission at both the local and global levels. These changes result from reductions in the strength of connectivity and also manifest as reduced within and between resting-state network connectivity. These findings strengthen the hypothesis that conscious processing relies on an efficient system of information transfer in the brain.

A new basis set for molecular bending degrees of freedom.

PubMed

Jutier, Laurent

2010-07-21

We present a new basis set as an alternative to Legendre polynomials for the variational treatment of bending vibrational degrees of freedom in order to highly reduce the number of basis functions. This basis set is inspired from the harmonic oscillator eigenfunctions but is defined for a bending angle in the range theta in [0:pi]. The aim is to bring the basis functions closer to the final (ro)vibronic wave functions nature. Our methodology is extended to complicated potential energy surfaces, such as quasilinearity or multiequilibrium geometries, by using several free parameters in the basis functions. These parameters allow several density maxima, linear or not, around which the basis functions will be mainly located. Divergences at linearity in integral computations are resolved as generalized Legendre polynomials. All integral computations required for the evaluation of molecular Hamiltonian matrix elements are given for both discrete variable representation and finite basis representation. Convergence tests for the low energy vibronic states of HCCH(++), HCCH(+), and HCCS are presented.

Photometry of resolved galaxies. V - NGC 6822

NASA Technical Reports Server (NTRS)

Hoessel, J. G.; Anderson, N.

1986-01-01

Three-color CCD frames of the local group irregular galaxy NGC 6822 have been reduced to GRI photometry for 3475 stars using RICHFLD point-spread function fitting techniques. The data are compared with earlier work on this galaxy, particularly with Kayser (1966) on a star-by-star basis. Color-magnitude diagrams are constructed from the data and compared with both theoretical stellar model tracks and the expected foreground star contamination. A luminosity function for the blue stars is derived; comparison of this luminosity function with those of 10 other irregular galaxies indicates that NGC 6822 has a typical young star population. The stellar birthrate and initial mass function are estimated for this galaxy. The slope at the bright end of the mass function looks similar to recent results for the Galaxy, the Magellanic Clouds, and the irregular galaxy Sextans A. NGC 6822 appears to be presently forming stars at a slower rate for its mass than Sextans A or the Magellanic Clouds.

Physical Model of the Genotype-to-Phenotype Map of Proteins

NASA Astrophysics Data System (ADS)

Tlusty, Tsvi; Libchaber, Albert; Eckmann, Jean-Pierre

2017-04-01

How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to function. We therefore treat protein as learning amorphous matter that evolves towards such a mechanical function: Genes are binary sequences that encode the connectivity of the amino acid network that makes a protein. The gene is evolved until the network forms a shear band across the protein, which allows for long-range, soft modes required for protein function. The evolution reduces the high-dimensional sequence space to a low-dimensional space of mechanical modes, in accord with the observed dimensional reduction between genotype and phenotype of proteins. Spectral analysis of the space of 1 06 solutions shows a strong correspondence between localization around the shear band of both mechanical modes and the sequence structure. Specifically, our model shows how mutations are correlated among amino acids whose interactions determine the functional mode.

Structural Basis and Function of XRN2-Binding by XTB Domains

PubMed Central

Richter, Hannes; Katic, Iskra; Gut, Heinz; Großhans, Helge

2016-01-01

The ribonuclease XRN2 is an essential player in RNA metabolism. In Caenorhabditis elegans, XRN2 functions with PAXT-1, which shares a putative XRN2-binding domain (XTBD) with otherwise unrelated mammalian proteins. Here, we characterize structure and function of an XTBD – XRN2 complex. Although XTBD stably interconnects two XRN2 domains through numerous interacting residues, mutation of a single critical residue suffices to disrupt XTBD – XRN2 complexes in vitro, and recapitulates paxt-1 null mutant phenotypes in vivo. Demonstrating conservation of function, vertebrate XTBD-containing proteins bind XRN2 in vitro, and human CDKN2AIPNL (C2AIL) can substitute for PAXT-1 in vivo. In vertebrates, where three distinct XTBD-containing proteins exist, XRN2 may partition to distinct stable heterodimeric complexes, likely differing in subcellular localization or function. In C. elegans, complex formation with the unique PAXT-1 serves to preserve the stability of XRN2 in the absence of substrate. PMID:26779609

75 FR 66054 - Nondiscrimination on the Basis of Disability in State and Local Government Services, Public...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-27

... Captioning and Video Description; and Nondiscrimination on the Basis of Disability by State and Local... San Francisco, CA, on a date to be announced in the near future on the ADA Home Page at http://www.ada... a location to be announced in the near future on the ADA Home Page at http://www.ada.gov . FOR...

Real-Time Multi-Target Localization from Unmanned Aerial Vehicles

PubMed Central

Wang, Xuan; Liu, Jinghong; Zhou, Qianfei

2016-01-01

In order to improve the reconnaissance efficiency of unmanned aerial vehicle (UAV) electro-optical stabilized imaging systems, a real-time multi-target localization scheme based on an UAV electro-optical stabilized imaging system is proposed. First, a target location model is studied. Then, the geodetic coordinates of multi-targets are calculated using the homogeneous coordinate transformation. On the basis of this, two methods which can improve the accuracy of the multi-target localization are proposed: (1) the real-time zoom lens distortion correction method; (2) a recursive least squares (RLS) filtering method based on UAV dead reckoning. The multi-target localization error model is established using Monte Carlo theory. In an actual flight, the UAV flight altitude is 1140 m. The multi-target localization results are within the range of allowable error. After we use a lens distortion correction method in a single image, the circular error probability (CEP) of the multi-target localization is reduced by 7%, and 50 targets can be located at the same time. The RLS algorithm can adaptively estimate the location data based on multiple images. Compared with multi-target localization based on a single image, CEP of the multi-target localization using RLS is reduced by 25%. The proposed method can be implemented on a small circuit board to operate in real time. This research is expected to significantly benefit small UAVs which need multi-target geo-location functions. PMID:28029145

Real-Time Multi-Target Localization from Unmanned Aerial Vehicles.

PubMed

Wang, Xuan; Liu, Jinghong; Zhou, Qianfei

2016-12-25

In order to improve the reconnaissance efficiency of unmanned aerial vehicle (UAV) electro-optical stabilized imaging systems, a real-time multi-target localization scheme based on an UAV electro-optical stabilized imaging system is proposed. First, a target location model is studied. Then, the geodetic coordinates of multi-targets are calculated using the homogeneous coordinate transformation. On the basis of this, two methods which can improve the accuracy of the multi-target localization are proposed: (1) the real-time zoom lens distortion correction method; (2) a recursive least squares (RLS) filtering method based on UAV dead reckoning. The multi-target localization error model is established using Monte Carlo theory. In an actual flight, the UAV flight altitude is 1140 m. The multi-target localization results are within the range of allowable error. After we use a lens distortion correction method in a single image, the circular error probability (CEP) of the multi-target localization is reduced by 7%, and 50 targets can be located at the same time. The RLS algorithm can adaptively estimate the location data based on multiple images. Compared with multi-target localization based on a single image, CEP of the multi-target localization using RLS is reduced by 25%. The proposed method can be implemented on a small circuit board to operate in real time. This research is expected to significantly benefit small UAVs which need multi-target geo-location functions.

LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis.

PubMed

Hong, Ye; Sonneville, Remi; Wang, Bin; Scheidt, Viktor; Meier, Bettina; Woglar, Alexander; Demetriou, Sarah; Labib, Karim; Jantsch, Verena; Gartner, Anton

2018-02-20

Faithful chromosome segregation and genome maintenance requires the removal of all DNA bridges that physically link chromosomes before cells divide. Using C. elegans embryos we show that the LEM-3/Ankle1 nuclease defines a previously undescribed genome integrity mechanism by processing DNA bridges right before cells divide. LEM-3 acts at the midbody, the structure where abscission occurs at the end of cytokinesis. LEM-3 localization depends on factors needed for midbody assembly, and LEM-3 accumulation is increased and prolonged when chromatin bridges are trapped at the cleavage plane. LEM-3 locally processes chromatin bridges that arise from incomplete DNA replication, unresolved recombination intermediates, or the perturbance of chromosome structure. Proper LEM-3 midbody localization and function is regulated by AIR-2/Aurora B kinase. Strikingly, LEM-3 acts cooperatively with the BRC-1/BRCA1 homologous recombination factor to promote genome integrity. These findings provide a molecular basis for the suspected role of the LEM-3 orthologue Ankle1 in human breast cancer.

Perturbation expansion theory corrected from basis set superposition error. I. Locally projected excited orbitals and single excitations.

PubMed

Nagata, Takeshi; Iwata, Suehiro

2004-02-22

The locally projected self-consistent field molecular orbital method for molecular interaction (LP SCF MI) is reformulated for multifragment systems. For the perturbation expansion, two types of the local excited orbitals are defined; one is fully local in the basis set on a fragment, and the other has to be partially delocalized to the basis sets on the other fragments. The perturbation expansion calculations only within single excitations (LP SE MP2) are tested for water dimer, hydrogen fluoride dimer, and colinear symmetric ArM+ Ar (M = Na and K). The calculated binding energies of LP SE MP2 are all close to the corresponding counterpoise corrected SCF binding energy. By adding the single excitations, the deficiency in LP SCF MI is thus removed. The results suggest that the exclusion of the charge-transfer effects in LP SCF MI might indeed be the cause of the underestimation for the binding energy. (c) 2004 American Institute of Physics.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Papajak, Ewa; Truhlar, Donald G.

We present sets of convergent, partially augmented basis set levels corresponding to subsets of the augmented “aug-cc-pV(n+d)Z” basis sets of Dunning and co-workers. We show that for many molecular properties a basis set fully augmented with diffuse functions is computationally expensive and almost always unnecessary. On the other hand, unaugmented cc-pV(n+d)Z basis sets are insufficient for many properties that require diffuse functions. Therefore, we propose using intermediate basis sets. We developed an efficient strategy for partial augmentation, and in this article, we test it and validate it. Sequentially deleting diffuse basis functions from the “aug” basis sets yields the “jul”,more » “jun”, “may”, “apr”, etc. basis sets. Tests of these basis sets for Møller-Plesset second-order perturbation theory (MP2) show the advantages of using these partially augmented basis sets and allow us to recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large systems. Similar truncations in the diffuse space can be performed for the aug-cc-pVxZ, aug-cc-pCVxZ, etc. basis sets.« less

Complex Genetic Effects on Early Vegetative Development Shape Resource Allocation Differences Between Arabidopsis lyrata Populations

PubMed Central

Remington, David L.; Leinonen, Päivi H.; Leppälä, Johanna; Savolainen, Outi

2013-01-01

Costs of reproduction due to resource allocation trade-offs have long been recognized as key forces in life history evolution, but little is known about their functional or genetic basis. Arabidopsis lyrata, a perennial relative of the annual model plant A. thaliana with a wide climatic distribution, has populations that are strongly diverged in resource allocation. In this study, we evaluated the genetic and functional basis for variation in resource allocation in a reciprocal transplant experiment, using four A. lyrata populations and F2 progeny from a cross between North Carolina (NC) and Norway parents, which had the most divergent resource allocation patterns. Local alleles at quantitative trait loci (QTL) at a North Carolina field site increased reproductive output while reducing vegetative growth. These QTL had little overlap with flowering date QTL. Structural equation models incorporating QTL genotypes and traits indicated that resource allocation differences result primarily from QTL effects on early vegetative growth patterns, with cascading effects on later vegetative and reproductive development. At a Norway field site, North Carolina alleles at some of the same QTL regions reduced survival and reproductive output components, but these effects were not associated with resource allocation trade-offs in the Norway environment. Our results indicate that resource allocation in perennial plants may involve important adaptive mechanisms largely independent of flowering time. Moreover, the contributions of resource allocation QTL to local adaptation appear to result from their effects on developmental timing and its interaction with environmental constraints, and not from simple models of reproductive costs. PMID:23979581

Underwater sonar image detection: A combination of non-local spatial information and quantum-inspired shuffled frog leaping algorithm.

PubMed

Wang, Xingmei; Liu, Shu; Liu, Zhipeng

2017-01-01

This paper proposes a combination of non-local spatial information and quantum-inspired shuffled frog leaping algorithm to detect underwater objects in sonar images. Specifically, for the first time, the problem of inappropriate filtering degree parameter which commonly occurs in non-local spatial information and seriously affects the denoising performance in sonar images, was solved with the method utilizing a novel filtering degree parameter. Then, a quantum-inspired shuffled frog leaping algorithm based on new search mechanism (QSFLA-NSM) is proposed to precisely and quickly detect sonar images. Each frog individual is directly encoded by real numbers, which can greatly simplify the evolution process of the quantum-inspired shuffled frog leaping algorithm (QSFLA). Meanwhile, a fitness function combining intra-class difference with inter-class difference is adopted to evaluate frog positions more accurately. On this basis, recurring to an analysis of the quantum-behaved particle swarm optimization (QPSO) and the shuffled frog leaping algorithm (SFLA), a new search mechanism is developed to improve the searching ability and detection accuracy. At the same time, the time complexity is further reduced. Finally, the results of comparative experiments using the original sonar images, the UCI data sets and the benchmark functions demonstrate the effectiveness and adaptability of the proposed method.

Underwater sonar image detection: A combination of non-local spatial information and quantum-inspired shuffled frog leaping algorithm

PubMed Central

Liu, Zhipeng

2017-01-01

This paper proposes a combination of non-local spatial information and quantum-inspired shuffled frog leaping algorithm to detect underwater objects in sonar images. Specifically, for the first time, the problem of inappropriate filtering degree parameter which commonly occurs in non-local spatial information and seriously affects the denoising performance in sonar images, was solved with the method utilizing a novel filtering degree parameter. Then, a quantum-inspired shuffled frog leaping algorithm based on new search mechanism (QSFLA-NSM) is proposed to precisely and quickly detect sonar images. Each frog individual is directly encoded by real numbers, which can greatly simplify the evolution process of the quantum-inspired shuffled frog leaping algorithm (QSFLA). Meanwhile, a fitness function combining intra-class difference with inter-class difference is adopted to evaluate frog positions more accurately. On this basis, recurring to an analysis of the quantum-behaved particle swarm optimization (QPSO) and the shuffled frog leaping algorithm (SFLA), a new search mechanism is developed to improve the searching ability and detection accuracy. At the same time, the time complexity is further reduced. Finally, the results of comparative experiments using the original sonar images, the UCI data sets and the benchmark functions demonstrate the effectiveness and adaptability of the proposed method. PMID:28542266

Increases in both cerebral glucose utilization and blood flow during execution of a somatosensory task.

PubMed

Ginsberg, M D; Chang, J Y; Kelley, R E; Yoshii, F; Barker, W W; Ingenito, G; Boothe, T E

1988-02-01

To investigate local metabolic and hemodynamic interrelationships during functional activation of the brain, paired studies of local cerebral glucose utilization (lCMRGlc) and blood flow (lCBF) were carried out in 10 normal subjects (9 right-handed, 1 ambidextrous) at rest and during a unilateral discriminative somatosensory/motor task--palpation and sorting of mah-jongg tiles by engraved design. The extent of activation was assessed on the basis of percentage difference images following normalization to compensate for global shifts. The somatosensory stimulus elevated lCMRGlc by 16.9 +/- 3.5% (mean +/- standard deviation) and lCBF by 26.5 +/- 5.1% in the contralateral sensorimotor cortical focus; smaller increments were noted in the homologous ipsilateral site. The increments of lCMRGlc and lCBF correlated poorly with one another in individual subjects. Stimulation of the right hand resulted in significantly higher contralateral lCMRGlc activation (19.6%) than did stimulation of the left hand (14.1%) (p less than 0.005), whereas the lCBF response was independent of the hand stimulated. Our results indicate that both glycolytic metabolism and blood flow increase locally with the execution of an active sensorimotor task and suggest that both measures may serve as reliable markers of functional activation of the normal brain.

CC2 oscillator strengths within the local framework for calculating excitation energies (LoFEx).

PubMed

Baudin, Pablo; Kjærgaard, Thomas; Kristensen, Kasper

2017-04-14

In a recent work [P. Baudin and K. Kristensen, J. Chem. Phys. 144, 224106 (2016)], we introduced a local framework for calculating excitation energies (LoFEx), based on second-order approximated coupled cluster (CC2) linear-response theory. LoFEx is a black-box method in which a reduced excitation orbital space (XOS) is optimized to provide coupled cluster (CC) excitation energies at a reduced computational cost. In this article, we present an extension of the LoFEx algorithm to the calculation of CC2 oscillator strengths. Two different strategies are suggested, in which the size of the XOS is determined based on the excitation energy or the oscillator strength of the targeted transitions. The two strategies are applied to a set of medium-sized organic molecules in order to assess both the accuracy and the computational cost of the methods. The results show that CC2 excitation energies and oscillator strengths can be calculated at a reduced computational cost, provided that the targeted transitions are local compared to the size of the molecule. To illustrate the potential of LoFEx for large molecules, both strategies have been successfully applied to the lowest transition of the bivalirudin molecule (4255 basis functions) and compared with time-dependent density functional theory.

Nuclear localization of the DNA repair scaffold XRCC1: Uncovering the functional role of a bipartite NLS

DOE PAGES

Kirby, Thomas W.; Gassman, Natalie R.; Smith, Cassandra E.; ...

2015-08-25

We have characterized the nuclear localization signal (NLS) of XRCC1 structurally using X-ray crystallography and functionally using fluorescence imaging. Crystallography and binding studies confirm the bipartite nature of the XRCC1 NLS interaction with Importin α (Impα) in which the major and minor binding motifs are separated by >20 residues, and resolve previous inconsistent determinations. Binding studies of peptides corresponding to the bipartite NLS, as well as its major and minor binding motifs, to both wild-type and mutated forms of Impα reveal pronounced cooperative binding behavior that is generated by the proximity effect of the tethered major and minor motifs ofmore » the NLS. The cooperativity stems from the increased local concentration of the second motif near its cognate binding site that is a consequence of the stepwise binding behavior of the bipartite NLS. We predict that the stepwise dissociation of the NLS from Impα facilitates unloading by providing a partially complexed intermediate that is available for competitive binding by Nup50 or the Importin β binding domain. This behavior gives a basis for meeting the intrinsically conflicting high affinity and high flux requirements of an efficient nuclear transport system.« less

Variational nonadiabatic dynamics in the moving crude adiabatic representation: Further merging of nuclear dynamics and electronic structure

NASA Astrophysics Data System (ADS)

Joubert-Doriol, Loïc; Izmaylov, Artur F.

2018-03-01

A new methodology of simulating nonadiabatic dynamics using frozen-width Gaussian wavepackets within the moving crude adiabatic representation with the on-the-fly evaluation of electronic structure is presented. The main feature of the new approach is the elimination of any global or local model representation of electronic potential energy surfaces; instead, the electron-nuclear interaction is treated explicitly using the Gaussian integration. As a result, the new scheme does not introduce any uncontrolled approximations. The employed variational principle ensures the energy conservation and leaves the number of electronic and nuclear basis functions as the only parameter determining the accuracy. To assess performance of the approach, a model with two electronic and two nuclear spacial degrees of freedom containing conical intersections between potential energy surfaces has been considered. Dynamical features associated with nonadiabatic transitions and nontrivial geometric (or Berry) phases were successfully reproduced within a limited basis expansion.

Linear scaling computation of the Fock matrix. II. Rigorous bounds on exchange integrals and incremental Fock build

NASA Astrophysics Data System (ADS)

Schwegler, Eric; Challacombe, Matt; Head-Gordon, Martin

1997-06-01

A new linear scaling method for computation of the Cartesian Gaussian-based Hartree-Fock exchange matrix is described, which employs a method numerically equivalent to standard direct SCF, and which does not enforce locality of the density matrix. With a previously described method for computing the Coulomb matrix [J. Chem. Phys. 106, 5526 (1997)], linear scaling incremental Fock builds are demonstrated for the first time. Microhartree accuracy and linear scaling are achieved for restricted Hartree-Fock calculations on sequences of water clusters and polyglycine α-helices with the 3-21G and 6-31G basis sets. Eightfold speedups are found relative to our previous method. For systems with a small ionization potential, such as graphitic sheets, the method naturally reverts to the expected quadratic behavior. Also, benchmark 3-21G calculations attaining microhartree accuracy are reported for the P53 tetramerization monomer involving 698 atoms and 3836 basis functions.

Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

PubMed

Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

2015-02-01

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages. Copyright © 2014 Elsevier Inc. All rights reserved.

Parental Socioeconomic Status and the Neural Basis of Arithmetic: Differential Relations to Verbal and Visuo-spatial Representations

PubMed Central

Demir, Özlem Ece; Prado, Jérôme; Booth, James R.

2015-01-01

We examined the relation of parental socioeconomic status (SES) to the neural bases of subtraction in school-age children (9- to 12-year-olds). We independently localized brain regions subserving verbal versus visuo-spatial representations to determine whether the parental SES-related differences in children’s reliance on these neural representations vary as a function of math skill. At higher SES levels, higher skill was associated with greater recruitment of the left temporal cortex, identified by the verbal localizer. At lower SES levels, higher skill was associated with greater recruitment of right parietal cortex, identified by the visuo-spatial localizer. This suggests that depending on parental SES, children engage different neural systems to solve subtraction problems. Furthermore, SES was related to the activation in the left temporal and frontal cortex during the independent verbal localizer task, but it was not related to activation during the independent visuo-spatial localizer task. Differences in activation during the verbal localizer task in turn were related to differences in activation during the subtraction task in right parietal cortex. The relation was stronger at lower SES levels. This result suggests that SES-related differences in the visuo-spatial regions during subtraction might be based in SES-related verbal differences. PMID:25664675

[Identification and analysis of the proteins interacted with Prestin in cochlear outer hair cells of guinea pig].

PubMed

Luo, X; Wang, J Y; Zhang, F L; Xia, Y

2018-01-07

Objective: To explore the regulation and mechanism of Prestin protein by identifying the proteins interacted with Prestin in cochlear outer hair cell(OHC) and analyzing their biological function. Methods: Co-immunoprecipitation combined mass spectrometry technology was used to isolate and identify the proteins interacted with Prestin protein of OHC, bioinformatics was used to construct Prestin protein interaction network. The proteins interacted with Prestin in OHC of guinea pig were determined by matching primary interaction mass spectrometry with protein interaction network, and annotated their functions. Results: The results of co-immunoprecipitation combined with mass spectrometry showed that 116 kinds of credible proteins could interact with Prestin. By constructing Prestin protein interaction network, matching the results of mass spectrometry and analyzing of sub-cellular localization, eight kinds of proteins were confirmed that they interacted with Prestin directly, namely EEF2, HSP90AB1, FN1, FLNA, EEF1A1, HSP90B1, ATP5A1, and ERH, respectively, which were mainly involved in the synthesis and transportation, transmembrane folding and localization, structural stability and signal transduction of Prestin protein. Conclusion: EEF2, HSP90AB1, FN1, FLNA, EEF1A1, HSP90B1, ATP5A1 and ERH provide molecular basis for sensory amplification function of OHCs by participating in biotransformation, transmembrane folding and localization, signal transduction and other biological processes of Prestin protein.

Human multidrug resistance protein 8 (MRP8/ABCC11), an apical efflux pump for steroid sulfates, is an axonal protein of the CNS and peripheral nervous system.

PubMed

Bortfeld, M; Rius, M; König, J; Herold-Mende, C; Nies, A T; Keppler, D

2006-01-01

Dehydroepiandrosterone 3-sulfate and other neurosteroids are synthesized in the CNS and peripheral nervous system where they may modulate neuronal excitability by interacting with ligand-gated ion channels. For this modulatory activity, neurosteroids have to be locally released from either neurons or glial cells. We here identify the integral membrane protein ABCC11 (multidrug resistance protein 8) as an ATP-dependent efflux pump for steroid sulfates, including dehydroepiandrosterone 3-sulfate, and localize it to axons of the human CNS and peripheral nervous system. ABCC11 mRNA was detected in human brain by real-time polymerase chain reaction. Antibodies raised against ABCC11 served to detect the protein in brain by immunoblotting and immunofluorescence microscopy. ABCC11 was preferentially found in the white matter of the brain and co-localized with neurofilaments indicating that it is an axonal protein. Additionally, ABCC11 was localized to axons of the peripheral nervous system. For functional studies, ABCC11 was expressed in polarized Madin-Darby canine kidney cells where it was sorted to the apical membrane. This apical sorting is in accordance with the localization of ABCC11 to the axonal membrane of neurons. Inside-out plasma membrane vesicles containing recombinant ABCC11 mediated ATP-dependent transport of dehydroepiandrosterone 3-sulfate with a Km value of 21 microM. This transport function together with the localization of the ABCC11 protein in vicinity to GABAA receptors is consistent with a role of ABCC11 in dehydroepiandrosterone 3-sulfate release from neurons to sites of dehydroepiandrosterone 3-sulfate-mediated receptor modulation. Our findings may provide a basis for the characterization of mutations in the human ABCC11 gene and their linkage with neurological disorders.

The basis function approach for modeling autocorrelation in ecological data

USGS Publications Warehouse

Hefley, Trevor J.; Broms, Kristin M.; Brost, Brian M.; Buderman, Frances E.; Kay, Shannon L.; Scharf, Henry; Tipton, John; Williams, Perry J.; Hooten, Mevin B.

2017-01-01

Analyzing ecological data often requires modeling the autocorrelation created by spatial and temporal processes. Many seemingly disparate statistical methods used to account for autocorrelation can be expressed as regression models that include basis functions. Basis functions also enable ecologists to modify a wide range of existing ecological models in order to account for autocorrelation, which can improve inference and predictive accuracy. Furthermore, understanding the properties of basis functions is essential for evaluating the fit of spatial or time-series models, detecting a hidden form of collinearity, and analyzing large data sets. We present important concepts and properties related to basis functions and illustrate several tools and techniques ecologists can use when modeling autocorrelation in ecological data.

Calculating vibrational spectra with sum of product basis functions without storing full-dimensional vectors or matrices.

PubMed

Leclerc, Arnaud; Carrington, Tucker

2014-05-07

We propose an iterative method for computing vibrational spectra that significantly reduces the memory cost of calculations. It uses a direct product primitive basis, but does not require storing vectors with as many components as there are product basis functions. Wavefunctions are represented in a basis each of whose functions is a sum of products (SOP) and the factorizable structure of the Hamiltonian is exploited. If the factors of the SOP basis functions are properly chosen, wavefunctions are linear combinations of a small number of SOP basis functions. The SOP basis functions are generated using a shifted block power method. The factors are refined with a rank reduction algorithm to cap the number of terms in a SOP basis function. The ideas are tested on a 20-D model Hamiltonian and a realistic CH3CN (12 dimensional) potential. For the 20-D problem, to use a standard direct product iterative approach one would need to store vectors with about 10(20) components and would hence require about 8 × 10(11) GB. With the approach of this paper only 1 GB of memory is necessary. Results for CH3CN agree well with those of a previous calculation on the same potential.

Complex Patterns of Local Adaptation in Teosinte

PubMed Central

Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

2013-01-01

Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

Tight-binding analysis of Si and GaAs ultrathin bodies with subatomic wave-function resolution

NASA Astrophysics Data System (ADS)

Tan, Yaohua P.; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy B.; Klimeck, Gerhard

2015-08-01

Empirical tight-binding (ETB) methods are widely used in atomistic device simulations. Traditional ways of generating the ETB parameters rely on direct fitting to bulk experiments or theoretical electronic bands. However, ETB calculations based on existing parameters lead to unphysical results in ultrasmall structures like the As-terminated GaAs ultrathin bodies (UTBs). In this work, it is shown that more transferable ETB parameters with a short interaction range can be obtained by a process of mapping ab initio bands and wave functions to ETB models. This process enables the calibration of not only the ETB energy bands but also the ETB wave functions with corresponding ab initio calculations. Based on the mapping process, ETB models of Si and GaAs are parameterized with respect to hybrid functional calculations. Highly localized ETB basis functions are obtained. Both the ETB energy bands and wave functions with subatomic resolution of UTBs show good agreement with the corresponding hybrid functional calculations. The ETB methods can then be used to explain realistically extended devices in nonequilibrium that cannot be tackled with ab initio methods.

STM contrast of a CO dimer on a Cu(1 1 1) surface: a wave-function analysis.

PubMed

Gustafsson, Alexander; Paulsson, Magnus

2017-12-20

We present a method used to intuitively interpret the scanning tunneling microscopy (STM) contrast by investigating individual wave functions originating from the substrate and tip side. We use localized basis orbital density functional theory, and propagate the wave functions into the vacuum region at a real-space grid, including averaging over the lateral reciprocal space. Optimization by means of the method of Lagrange multipliers is implemented to perform a unitary transformation of the wave functions in the middle of the vacuum region. The method enables (i) reduction of the number of contributing tip-substrate wave function combinations used in the corresponding transmission matrix, and (ii) to bundle up wave functions with similar symmetry in the lateral plane, so that (iii) an intuitive understanding of the STM contrast can be achieved. The theory is applied to a CO dimer adsorbed on a Cu(1 1 1) surface scanned by a single-atom Cu tip, whose STM image is discussed in detail by the outlined method.

STM contrast of a CO dimer on a Cu(1 1 1) surface: a wave-function analysis

NASA Astrophysics Data System (ADS)

Gustafsson, Alexander; Paulsson, Magnus

2017-12-01

We present a method used to intuitively interpret the scanning tunneling microscopy (STM) contrast by investigating individual wave functions originating from the substrate and tip side. We use localized basis orbital density functional theory, and propagate the wave functions into the vacuum region at a real-space grid, including averaging over the lateral reciprocal space. Optimization by means of the method of Lagrange multipliers is implemented to perform a unitary transformation of the wave functions in the middle of the vacuum region. The method enables (i) reduction of the number of contributing tip-substrate wave function combinations used in the corresponding transmission matrix, and (ii) to bundle up wave functions with similar symmetry in the lateral plane, so that (iii) an intuitive understanding of the STM contrast can be achieved. The theory is applied to a CO dimer adsorbed on a Cu(1 1 1) surface scanned by a single-atom Cu tip, whose STM image is discussed in detail by the outlined method.

Substituent effects on the redox states of locally functionalized single-walled carbon nanotubes revealed by in situ photoluminescence spectroelectrochemistry.

PubMed

Shiraishi, Tomonari; Shiraki, Tomohiro; Nakashima, Naotoshi

2017-11-09

Single-walled carbon nanotubes (SWNTs) with local chemical modification have been recognized as a novel near infrared (NIR) photoluminescent nanomaterial due to the emergence of a new red-shifted photoluminescence (PL) with enhanced quantum yields. As a characteristic feature of the locally functionalized SWNTs (lf-SWNTs), PL wavelength changes occur with the structural dependence of the substituent structures in the modified aryl groups, showing up to a 60 nm peak shift according to an electronic property difference of the aryl groups. Up to now, however, the structural effect on the electronic states of the lf-SWNTs has been discussed only on the basis of theoretical calculations due to the very limited amount of modifications. Herein, we describe the successfully-determined electronic states of the aryl-modified lf-SWNTs with different substituents (Ar-X SWNTs) using an in situ PL spectroelectrochemical method based on electrochemical quenching of the PL intensities analyzed by the Nernst equation. In particular, we reveal that the local functionalization of (6,5)SWNTs induced potential changes in the energy levels of the HOMO and the LUMO by -23 to -38 meV and +20 to +22 meV, respectively, compared to those of the pristine SWNTs, which generates exciton trapping sites with narrower band gaps. Moreover, the HOMO levels of the Ar-X SWNTs specifically shift in a negative potential direction by 15 meV according to an enhancement of the electron-accepting property of the substituents in the aryl groups that corresponds to an increase in the Hammet substituent constants, suggesting the importance of the dipole effect from the aryl groups on the lf-SWNTs to the level shift of the frontier orbitals. Our method is a promising way to characterize the electronic features of the lf-SWNTs.

Agroecology in the tropics: Achieving a balance between land use and preservation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gliessman, S.R.

Agroecology is the application of ecological concepts and principles to the design and management of sustainable agricultural systems. An agroecological approach to agriculture has special importance in the humid tropics where agricultural development and the preservation of tropical forests are most often in direct conflict. It is proposed that a more sustainable approach to development is needed, where agroecosystems depend on low external inputs, function more on the use of locally available and renewable resources, have benign impacts on the environment, and are based on the knowledge and culture of the local inhabitants. Examples of traditional agroecosystem management in Mesoamericamore » that can provide this basis are presented. The preservation of both biological and cultural diversity are integral to the long-term sustainable management of natural resources in the tropics.« less

The theory precision analyse of RFM localization of satellite remote sensing imagery

NASA Astrophysics Data System (ADS)

Zhang, Jianqing; Xv, Biao

2009-11-01

The tradition method of detecting precision of Rational Function Model(RFM) is to make use of a great deal check points, and it calculates mean square error through comparing calculational coordinate with known coordinate. This method is from theory of probability, through a large number of samples to statistic estimate value of mean square error, we can think its estimate value approaches in its true when samples are well enough. This paper is from angle of survey adjustment, take law of propagation of error as the theory basis, and it calculates theory precision of RFM localization. Then take the SPOT5 three array imagery as experiment data, and the result of traditional method and narrated method in the paper are compared, while has confirmed tradition method feasible, and answered its theory precision question from the angle of survey adjustment.

A Novel Consensus-Based Particle Swarm Optimization-Assisted Trust-Tech Methodology for Large-Scale Global Optimization.

PubMed

Zhang, Yong-Feng; Chiang, Hsiao-Dong

2017-09-01

A novel three-stage methodology, termed the "consensus-based particle swarm optimization (PSO)-assisted Trust-Tech methodology," to find global optimal solutions for nonlinear optimization problems is presented. It is composed of Trust-Tech methods, consensus-based PSO, and local optimization methods that are integrated to compute a set of high-quality local optimal solutions that can contain the global optimal solution. The proposed methodology compares very favorably with several recently developed PSO algorithms based on a set of small-dimension benchmark optimization problems and 20 large-dimension test functions from the CEC 2010 competition. The analytical basis for the proposed methodology is also provided. Experimental results demonstrate that the proposed methodology can rapidly obtain high-quality optimal solutions that can contain the global optimal solution. The scalability of the proposed methodology is promising.

Geometric constrained variational calculus. III: The second variation (Part II)

NASA Astrophysics Data System (ADS)

Massa, Enrico; Luria, Gianvittorio; Pagani, Enrico

2016-03-01

The problem of minimality for constrained variational calculus is analyzed within the class of piecewise differentiable extremaloids. A fully covariant representation of the second variation of the action functional based on a family of local gauge transformations of the original Lagrangian is proposed. The necessity of pursuing a local adaptation process, rather than the global one described in [1] is seen to depend on the value of certain scalar attributes of the extremaloid, here called the corners’ strengths. On this basis, both the necessary and the sufficient conditions for minimality are worked out. In the discussion, a crucial role is played by an analysis of the prolongability of the Jacobi fields across the corners. Eventually, in the appendix, an alternative approach to the concept of strength of a corner, more closely related to Pontryagin’s maximum principle, is presented.

Multi-sensor image fusion algorithm based on multi-objective particle swarm optimization algorithm

NASA Astrophysics Data System (ADS)

Xie, Xia-zhu; Xu, Ya-wei

2017-11-01

On the basis of DT-CWT (Dual-Tree Complex Wavelet Transform - DT-CWT) theory, an approach based on MOPSO (Multi-objective Particle Swarm Optimization Algorithm) was proposed to objectively choose the fused weights of low frequency sub-bands. High and low frequency sub-bands were produced by DT-CWT. Absolute value of coefficients was adopted as fusion rule to fuse high frequency sub-bands. Fusion weights in low frequency sub-bands were used as particles in MOPSO. Spatial Frequency and Average Gradient were adopted as two kinds of fitness functions in MOPSO. The experimental result shows that the proposed approach performances better than Average Fusion and fusion methods based on local variance and local energy respectively in brightness, clarity and quantitative evaluation which includes Entropy, Spatial Frequency, Average Gradient and QAB/F.

Characterizing and Understanding the Remarkably Slow Basis Set Convergence of Several Minnesota Density Functionals for Intermolecular Interaction Energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mardirossian, Narbe; Head-Gordon, Martin

2013-08-22

For a set of eight equilibrium intermolecular complexes, it is discovered in this paper that the basis set limit (BSL) cannot be reached by aug-cc-pV5Z for three of the Minnesota density functionals: M06-L, M06-HF, and M11-L. In addition, the M06 and M11 functionals exhibit substantial, but less severe, difficulties in reaching the BSL. By using successively finer grids, it is demonstrated that this issue is not related to the numerical integration of the exchange-correlation functional. In addition, it is shown that the difficulty in reaching the BSL is not a direct consequence of the structure of the augmented functions inmore » Dunning’s basis sets, since modified augmentation yields similar results. By using a very large custom basis set, the BSL appears to be reached for the HF dimer for all of the functionals. As a result, it is concluded that the difficulties faced by several of the Minnesota density functionals are related to an interplay between the form of these functionals and the structure of standard basis sets. It is speculated that the difficulty in reaching the basis set limit is related to the magnitude of the inhomogeneity correction factor (ICF) of the exchange functional. A simple modification of the M06-L exchange functional that systematically reduces the basis set superposition error (BSSE) for the HF dimer in the aug-cc-pVQZ basis set is presented, further supporting the speculation that the difficulty in reaching the BSL is caused by the magnitude of the exchange functional ICF. In conclusion, the BSSE is plotted with respect to the internuclear distance of the neon dimer for two of the examined functionals.« less

Planetary Transmission Diagnostics

NASA Technical Reports Server (NTRS)

Lewicki, David G. (Technical Monitor); Samuel, Paul D.; Conroy, Joseph K.; Pines, Darryll J.

2004-01-01

This report presents a methodology for detecting and diagnosing gear faults in the planetary stage of a helicopter transmission. This diagnostic technique is based on the constrained adaptive lifting algorithm. The lifting scheme, developed by Wim Sweldens of Bell Labs, is a time domain, prediction-error realization of the wavelet transform that allows for greater flexibility in the construction of wavelet bases. Classic lifting analyzes a given signal using wavelets derived from a single fundamental basis function. A number of researchers have proposed techniques for adding adaptivity to the lifting scheme, allowing the transform to choose from a set of fundamental bases the basis that best fits the signal. This characteristic is desirable for gear diagnostics as it allows the technique to tailor itself to a specific transmission by selecting a set of wavelets that best represent vibration signals obtained while the gearbox is operating under healthy-state conditions. However, constraints on certain basis characteristics are necessary to enhance the detection of local wave-form changes caused by certain types of gear damage. The proposed methodology analyzes individual tooth-mesh waveforms from a healthy-state gearbox vibration signal that was generated using the vibration separation (synchronous signal-averaging) algorithm. Each waveform is separated into analysis domains using zeros of its slope and curvature. The bases selected in each analysis domain are chosen to minimize the prediction error, and constrained to have the same-sign local slope and curvature as the original signal. The resulting set of bases is used to analyze future-state vibration signals and the lifting prediction error is inspected. The constraints allow the transform to effectively adapt to global amplitude changes, yielding small prediction errors. However, local wave-form changes associated with certain types of gear damage are poorly adapted, causing a significant change in the prediction error. The constrained adaptive lifting diagnostic algorithm is validated using data collected from the University of Maryland Transmission Test Rig and the results are discussed.

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures.

PubMed

Papior, Nick R; Calogero, Gaetano; Brandbyge, Mads

2018-06-27

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C 60 ). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

Reinforcement Learning with Orthonormal Basis Adaptation Based on Activity-Oriented Index Allocation

NASA Astrophysics Data System (ADS)

Satoh, Hideki

An orthonormal basis adaptation method for function approximation was developed and applied to reinforcement learning with multi-dimensional continuous state space. First, a basis used for linear function approximation of a control function is set to an orthonormal basis. Next, basis elements with small activities are replaced with other candidate elements as learning progresses. As this replacement is repeated, the number of basis elements with large activities increases. Example chaos control problems for multiple logistic maps were solved, demonstrating that the method for adapting an orthonormal basis can modify a basis while holding the orthonormality in accordance with changes in the environment to improve the performance of reinforcement learning and to eliminate the adverse effects of redundant noisy states.

Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures

NASA Astrophysics Data System (ADS)

Papior, Nick R.; Calogero, Gaetano; Brandbyge, Mads

2018-06-01

We present a simple way to describe the lowest unoccupied diffuse states in carbon nanostructures in density functional theory calculations using a minimal LCAO (linear combination of atomic orbitals) basis set. By comparing plane wave basis calculations, we show how these states can be captured by adding long-range orbitals to the standard LCAO basis sets for the extreme cases of planar sp 2 (graphene) and curved carbon (C60). In particular, using Bessel functions with a long range as additional basis functions retain a minimal basis size. This provides a smaller and simpler atom-centered basis set compared to the standard pseudo-atomic orbitals (PAOs) with multiple polarization orbitals or by adding non-atom-centered states to the basis.

A Bayesian spatial model for neuroimaging data based on biologically informed basis functions.

PubMed

Huertas, Ismael; Oldehinkel, Marianne; van Oort, Erik S B; Garcia-Solis, David; Mir, Pablo; Beckmann, Christian F; Marquand, Andre F

2017-11-01

The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach. This spatial model constitutes an elegant alternative to voxel-based approaches in neuroimaging studies; not only are their atoms biologically informed, they are also adaptive to high resolutions, represent high dimensions efficiently, and capture long-range spatial dependencies, which are important and challenging objectives for neuroimaging data. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Dark matter in 3D

DOE PAGES

Alves, Daniele S. M.; El Hedri, Sonia; Wacker, Jay G.

2016-03-21

We discuss the relevance of directional detection experiments in the post-discovery era and propose a method to extract the local dark matter phase space distribution from directional data. The first feature of this method is a parameterization of the dark matter distribution function in terms of integrals of motion, which can be analytically extended to infer properties of the global distribution if certain equilibrium conditions hold. The second feature of our method is a decomposition of the distribution function in moments of a model independent basis, with minimal reliance on the ansatz for its functional form. We illustrate our methodmore » using the Via Lactea II N-body simulation as well as an analytical model for the dark matter halo. Furthermore, we conclude that O(1000) events are necessary to measure deviations from the Standard Halo Model and constrain or measure the presence of anisotropies.« less

Electric-field-stimulated protein mechanics

PubMed Central

Hekstra, Doeke R.; White, K. Ian; Socolich, Michael A.; Henning, Robert W.; Šrajer, Vukica; Ranganathan, Rama

2017-01-01

The internal mechanics of proteins—the coordinated motions of amino acids and the pattern of forces constraining these motions—connects protein structure to function. Here we describe a new method combining the application of strong electric field pulses to protein crystals with time-resolved X-ray crystallography to observe conformational changes in spatial and temporal detail. Using a human PDZ domain (LNX2PDZ2) as a model system, we show that protein crystals tolerate electric field pulses strong enough to drive concerted motions on the sub-microsecond timescale. The induced motions are subtle, involve diverse physical mechanisms, and occur throughout the protein structure. The global pattern of electric-field-induced motions is consistent with both local and allosteric conformational changes naturally induced by ligand binding, including at conserved functional sites in the PDZ domain family. This work lays the foundation for comprehensive experimental study of the mechanical basis of protein function. PMID:27926732

Physiologic Basis for Improved Pulmonary Function after Lung Volume Reduction

PubMed Central

Fessler, Henry E.; Scharf, Steven M.; Ingenito, Edward P.; McKenna, Robert J.; Sharafkhaneh, Amir

2008-01-01

It is not readily apparent how pulmonary function could be improved by resecting portions of the lung in patients with emphysema. In emphysema, elevation in residual volume relative to total lung capacity reduces forced expiratory volumes, increases inspiratory effort, and impairs inspiratory muscle mechanics. Lung volume reduction surgery (LVRS) better matches the size of the lungs to the size of the thorax containing them. This restores forced expiratory volumes and the mechanical advantage of the inspiratory muscles. In patients with heterogeneous emphysema, LVRS may also allow space occupied by cysts to be reclaimed by more normal lung. Newer, bronchoscopic methods for lung volume reduction seek to achieve similar ends by causing localized atelectasis, but may be hindered by the low collateral resistance of emphysematous lung. Understanding of the mechanisms of improved function after LVRS can help select patients more likely to benefit from this approach. PMID:18453348

A spectral mimetic least-squares method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bochev, Pavel; Gerritsma, Marc

We present a spectral mimetic least-squares method for a model diffusion–reaction problem, which preserves key conservation properties of the continuum problem. Casting the model problem into a first-order system for two scalar and two vector variables shifts material properties from the differential equations to a pair of constitutive relations. We also use this system to motivate a new least-squares functional involving all four fields and show that its minimizer satisfies the differential equations exactly. Discretization of the four-field least-squares functional by spectral spaces compatible with the differential operators leads to a least-squares method in which the differential equations are alsomore » satisfied exactly. Additionally, the latter are reduced to purely topological relationships for the degrees of freedom that can be satisfied without reference to basis functions. Furthermore, numerical experiments confirm the spectral accuracy of the method and its local conservation.« less

A spectral mimetic least-squares method

DOE PAGES

Bochev, Pavel; Gerritsma, Marc

2014-09-01

We present a spectral mimetic least-squares method for a model diffusion–reaction problem, which preserves key conservation properties of the continuum problem. Casting the model problem into a first-order system for two scalar and two vector variables shifts material properties from the differential equations to a pair of constitutive relations. We also use this system to motivate a new least-squares functional involving all four fields and show that its minimizer satisfies the differential equations exactly. Discretization of the four-field least-squares functional by spectral spaces compatible with the differential operators leads to a least-squares method in which the differential equations are alsomore » satisfied exactly. Additionally, the latter are reduced to purely topological relationships for the degrees of freedom that can be satisfied without reference to basis functions. Furthermore, numerical experiments confirm the spectral accuracy of the method and its local conservation.« less

Two-time quantum transport and quantum diffusion.

PubMed

Kleinert, P

2009-05-01

Based on the nonequilibrium Green's function technique, a unified theory is developed that covers quantum transport and quantum diffusion in bulk semiconductors on the same footing. This approach, which is applicable to transport via extended and localized states, extends previous semiphenomenological studies and puts them on a firm microscopic basis. The approach is sufficiently general and applies not only to well-studied quantum-transport problems, but also to models, in which the Hamiltonian does not commute with the dipole operator. It is shown that even for the unified treatment of quantum transport and quantum diffusion in homogeneous systems, all quasimomenta of the carrier distribution function are present and fulfill their specific function. Particular emphasis is put on the double-time nature of quantum kinetics. To demonstrate the existence of robust macroscopic transport effects that have a true double-time character, a phononless steady-state current is identified that appears only beyond the generalized Kadanoff-Baym ansatz.

Formulation of strongly non-local, non-isothermal dynamics for heterogeneous solids based on the GENERIC with application to phase-field modeling

NASA Astrophysics Data System (ADS)

Hütter, Markus; Svendsen, Bob

2017-12-01

The purpose of the current work is the formulation of models for conservative and non-conservative dynamics in solid systems with the help of the General Equation for the Non-Equilibrium Reversible-Irreversible Coupling (GENERIC: e.g., Grmela and Öttinger, Phys. Rev. E 56(6), 6620 (1997); Öttinger and Grmela, Phys. Rev. E 56(6), 6633 (1997)). In this context, the resulting models are inherently spatially strongly non-local (i.e., functional) and non-isothermal in character. They are applicable in particular to the modeling of phase transitions as well as mass and heat transport in multiphase, multicomponent solids. In the last part of the work, the strongly non-local model formulation is reduced to weakly non-local form with the help of generalized gradient approximation of the energy and entropy functionals. On this basis, the current model formulation is shown to be consistent with and reduce to a recent non-isothermal generalization (Gladkov et al., J. Non-Equilib. Thermodyn. 41(2), 131 (2016)) of the well-known phase-field models of Cahn and Hilliard (J. Chem. Phys. 28(2), 258 (1958)) for conservative dynamics and of Allen and Cahn (Acta Metall. 27(6), 1085 (1979)) for non-conservative dynamics. Finally, the current approach is applied to derive a non-isothermal generalization of a phase-field crystal model for binary alloys (see, e.g., Elder et al., Phys. Rev. B 75(6), 064107 (2007)).

Forecasting hourly PM(10) concentration in Cyprus through artificial neural networks and multiple regression models: implications to local environmental management.

PubMed

Paschalidou, Anastasia K; Karakitsios, Spyridon; Kleanthous, Savvas; Kassomenos, Pavlos A

2011-02-01

In the present work, two types of artificial neural network (NN) models using the multilayer perceptron (MLP) and the radial basis function (RBF) techniques, as well as a model based on principal component regression analysis (PCRA), are employed to forecast hourly PM(10) concentrations in four urban areas (Larnaca, Limassol, Nicosia and Paphos) in Cyprus. The model development is based on a variety of meteorological and pollutant parameters corresponding to the 2-year period between July 2006 and June 2008, and the model evaluation is achieved through the use of a series of well-established evaluation instruments and methodologies. The evaluation reveals that the MLP NN models display the best forecasting performance with R (2) values ranging between 0.65 and 0.76, whereas the RBF NNs and the PCRA models reveal a rather weak performance with R (2) values between 0.37-0.43 and 0.33-0.38, respectively. The derived MLP models are also used to forecast Saharan dust episodes with remarkable success (probability of detection ranging between 0.68 and 0.71). On the whole, the analysis shows that the models introduced here could provide local authorities with reliable and precise predictions and alarms about air quality if used on an operational basis.

An Alternate Set of Basis Functions for the Electromagnetic Solution of Arbitrarily-Shaped, Three-Dimensional, Closed, Conducting Bodies Using Method of Moments

NASA Technical Reports Server (NTRS)

Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.

2008-01-01

In this work, we present an alternate set of basis functions, each defined over a pair of planar triangular patches, for the method of moments solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped, closed, conducting surfaces. The present basis functions are point-wise orthogonal to the pulse basis functions previously defined. The prime motivation to develop the present set of basis functions is to utilize them for the electromagnetic solution of dielectric bodies using a surface integral equation formulation which involves both electric and magnetic cur- rents. However, in the present work, only the conducting body solution is presented and compared with other data.

The basis function approach for modeling autocorrelation in ecological data.

PubMed

Hefley, Trevor J; Broms, Kristin M; Brost, Brian M; Buderman, Frances E; Kay, Shannon L; Scharf, Henry R; Tipton, John R; Williams, Perry J; Hooten, Mevin B

2017-03-01

Analyzing ecological data often requires modeling the autocorrelation created by spatial and temporal processes. Many seemingly disparate statistical methods used to account for autocorrelation can be expressed as regression models that include basis functions. Basis functions also enable ecologists to modify a wide range of existing ecological models in order to account for autocorrelation, which can improve inference and predictive accuracy. Furthermore, understanding the properties of basis functions is essential for evaluating the fit of spatial or time-series models, detecting a hidden form of collinearity, and analyzing large data sets. We present important concepts and properties related to basis functions and illustrate several tools and techniques ecologists can use when modeling autocorrelation in ecological data. © 2016 by the Ecological Society of America.

10 CFR 1042.420 - Access to schools operated by LEAs.

Code of Federal Regulations, 2011 CFR

2011-01-01

....420 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) NONDISCRIMINATION ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex... recipient that is a local educational agency shall not, on the basis of sex, exclude any person from...

28 CFR 54.420 - Access to schools operated by LEAs.

Code of Federal Regulations, 2013 CFR

2013-07-01

... BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 54.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex, exclude...

43 CFR 41.420 - Access to schools operated by LEAs.

Code of Federal Regulations, 2014 CFR

2014-10-01

... BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 41.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex, exclude...

Atomic and electronic basis for the serrations of refractory high-entropy alloys

NASA Astrophysics Data System (ADS)

Wang, William Yi; Shang, Shun Li; Wang, Yi; Han, Fengbo; Darling, Kristopher A.; Wu, Yidong; Xie, Xie; Senkov, Oleg N.; Li, Jinshan; Hui, Xi Dong; Dahmen, Karin A.; Liaw, Peter K.; Kecskes, Laszlo J.; Liu, Zi-Kui

2017-06-01

Refractory high-entropy alloys present attractive mechanical properties, i.e., high yield strength and fracture toughness, making them potential candidates for structural applications. Understandings of atomic and electronic interactions are important to reveal the origins for the formation of high-entropy alloys and their structure-dominated mechanical properties, thus enabling the development of a predictive approach for rapidly designing advanced materials. Here, we report the atomic and electronic basis for the valence-electron-concentration-categorized principles and the observed serration behavior in high-entropy alloys and high-entropy metallic glass, including MoNbTaW, MoNbVW, MoTaVW, HfNbTiZr, and Vitreloy-1 MG (Zr41Ti14Cu12.5Ni10Be22.5). We find that the yield strengths of high-entropy alloys and high-entropy metallic glass are a power-law function of the electron-work function, which is dominated by local atomic arrangements. Further, a reliance on the bonding-charge density provides a groundbreaking insight into the nature of loosely bonded spots in materials. The presence of strongly bonded clusters and weakly bonded glue atoms imply a serrated deformation of high-entropy alloys, resulting in intermittent avalanches of defects movement.

Detecting similarities among distant homologous proteins by comparison of domain flexibilities.

PubMed

Pandini, Alessandro; Mauri, Giancarlo; Bordogna, Annalisa; Bonati, Laura

2007-06-01

Aim of this work is to assess the informativeness of protein dynamics in the detection of similarities among distant homologous proteins. To this end, an approach to perform large-scale comparisons of protein domain flexibilities is proposed. CONCOORD is confirmed as a reliable method for fast conformational sampling. The root mean square fluctuation of alpha carbon positions in the essential dynamics subspace is employed as a measure of local flexibility and a synthetic index of similarity is presented. The dynamics of a large collection of protein domains from ASTRAL/SCOP40 is analyzed and the possibility to identify relationships, at both the family and the superfamily levels, on the basis of the dynamical features is discussed. The obtained picture is in agreement with the SCOP classification, and furthermore suggests the presence of a distinguishable familiar trend in the flexibility profiles. The results support the complementarity of the dynamical and the structural information, suggesting that information from dynamics analysis can arise from functional similarities, often partially hidden by a static comparison. On the basis of this first test, flexibility annotation can be expected to help in automatically detecting functional similarities otherwise unrecoverable.

Experimental and theoretical studies of (FT-IR, FT-Raman, UV-Visible and DFT) 4-(6-methoxynaphthalen-2-yl) butan-2-one.

PubMed

Govindasamy, P; Gunasekaran, S

2015-01-01

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 4000-50 cm(-1) and 4000-450 cm(-1) respectively for 4-(6-methoxynaphthalen-2-yl) butan-2-one (abbreviated as 4MNBO) molecule. Theoretical calculations were performed by density functional theory (DFT/B3LYP) method using 6-311G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and calculated wavenumber value of most of the fundamentals were very small. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The UV-Vis spectrum was recorded in the methanol solution. The energy, wavelength and oscillator's strength were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Thermodynamic properties of 4MNBO at different temperature have been calculated. The molecular electrostatic potential surface (MESP) and Frontier molecular orbital's (FMO's) analysis were investigated using theoretical calculations. Copyright © 2015 Elsevier B.V. All rights reserved.

Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohr, Stephan; Masella, Michel; Ratcliff, Laura E.

We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then introduce a simple and efficient formalism (which can be written as generalization of other well-known population analyses) to extract, from first principles, electrostatic multipoles for these fragments. The corresponding fragment multipoles can in this way be seen as reliable (pseudo-) observables. By applying our formalism within the code BigDFT, we show that the usage of a minimal set of in-situ optimized basis functions is of utmost importance for having at the same timemore » a proper fragment definition and an accurate description of the electronic structure. With this approach it becomes possible to simplify the modeling of environmental fragments by a set of multipoles, without notable loss of precision in the description of the active quantum mechanical region. Furthermore, this leads to a considerable reduction of the degrees of freedom by an effective coarsegraining approach, eventually also paving the way towards efficient QM/QM and QM/MM methods coupling together different levels of accuracy.« less

Genetic Basis of Melanin Pigmentation in Butterfly Wings

PubMed Central

Zhang, Linlin; Martin, Arnaud; Perry, Michael W.; van der Burg, Karin R. L.; Matsuoka, Yuji; Monteiro, Antónia; Reed, Robert D.

2017-01-01

Despite the variety, prominence, and adaptive significance of butterfly wing patterns, surprisingly little is known about the genetic basis of wing color diversity. Even though there is intense interest in wing pattern evolution and development, the technical challenge of genetically manipulating butterflies has slowed efforts to functionally characterize color pattern development genes. To identify candidate wing pigmentation genes, we used RNA sequencing to characterize transcription across multiple stages of butterfly wing development, and between different color pattern elements, in the painted lady butterfly Vanessa cardui. This allowed us to pinpoint genes specifically associated with red and black pigment patterns. To test the functions of a subset of genes associated with presumptive melanin pigmentation, we used clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing in four different butterfly genera. pale, Ddc, and yellow knockouts displayed reduction of melanin pigmentation, consistent with previous findings in other insects. Interestingly, however, yellow-d, ebony, and black knockouts revealed that these genes have localized effects on tuning the color of red, brown, and ochre pattern elements. These results point to previously undescribed mechanisms for modulating the color of specific wing pattern elements in butterflies, and provide an expanded portrait of the insect melanin pathway. PMID:28193726

Design of hybrid radial basis function neural networks (HRBFNNs) realized with the aid of hybridization of fuzzy clustering method (FCM) and polynomial neural networks (PNNs).

PubMed

Huang, Wei; Oh, Sung-Kwun; Pedrycz, Witold

2014-12-01

In this study, we propose Hybrid Radial Basis Function Neural Networks (HRBFNNs) realized with the aid of fuzzy clustering method (Fuzzy C-Means, FCM) and polynomial neural networks. Fuzzy clustering used to form information granulation is employed to overcome a possible curse of dimensionality, while the polynomial neural network is utilized to build local models. Furthermore, genetic algorithm (GA) is exploited here to optimize the essential design parameters of the model (including fuzzification coefficient, the number of input polynomial fuzzy neurons (PFNs), and a collection of the specific subset of input PFNs) of the network. To reduce dimensionality of the input space, principal component analysis (PCA) is considered as a sound preprocessing vehicle. The performance of the HRBFNNs is quantified through a series of experiments, in which we use several modeling benchmarks of different levels of complexity (different number of input variables and the number of available data). A comparative analysis reveals that the proposed HRBFNNs exhibit higher accuracy in comparison to the accuracy produced by some models reported previously in the literature. Copyright © 2014 Elsevier Ltd. All rights reserved.

Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis

DOE PAGES

Mohr, Stephan; Masella, Michel; Ratcliff, Laura E.; ...

2017-07-21

We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then introduce a simple and efficient formalism (which can be written as generalization of other well-known population analyses) to extract, from first principles, electrostatic multipoles for these fragments. The corresponding fragment multipoles can in this way be seen as reliable (pseudo-) observables. By applying our formalism within the code BigDFT, we show that the usage of a minimal set of in-situ optimized basis functions is of utmost importance for having at the same timemore » a proper fragment definition and an accurate description of the electronic structure. With this approach it becomes possible to simplify the modeling of environmental fragments by a set of multipoles, without notable loss of precision in the description of the active quantum mechanical region. Furthermore, this leads to a considerable reduction of the degrees of freedom by an effective coarsegraining approach, eventually also paving the way towards efficient QM/QM and QM/MM methods coupling together different levels of accuracy.« less

DFT analysis on the molecular structure, vibrational and electronic spectra of 2-(cyclohexylamino)ethanesulfonic acid.

PubMed

Renuga Devi, T S; Sharmi kumar, J; Ramkumaar, G R

2015-02-25

The FTIR and FT-Raman spectra of 2-(cyclohexylamino)ethanesulfonic acid were recorded in the regions 4000-400 cm(-1) and 4000-50 cm(-1) respectively. The structural and spectroscopic data of the molecule in the ground state were calculated using Hartee-Fock and Density functional method (B3LYP) with the correlation consistent-polarized valence double zeta (cc-pVDZ) basis set and 6-311++G(d,p) basis set. The most stable conformer was optimized and the structural and vibrational parameters were determined based on this. The complete assignments were performed based on the Potential Energy Distribution (PED) of the vibrational modes, calculated using Vibrational Energy Distribution Analysis (VEDA) 4 program. With the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties and Atomic charges were calculated using both Hartee-Fock and density functional method using the cc-pVDZ basis set and compared. The calculated HOMO-LUMO energy gap revealed that charge transfer occurs within the molecule. (1)H and (13)C NMR chemical shifts of the molecule were calculated using Gauge Including Atomic Orbital (GIAO) method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using Natural Bond Orbital (NBO) analysis. The first order hyperpolarizability (β) and Molecular Electrostatic Potential (MEP) of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemical reactivity site in the molecule. Copyright © 2014 Elsevier B.V. All rights reserved.

Nonlocal screening in metal surfaces

NASA Technical Reports Server (NTRS)

Krotscheck, E.; Kohn, W.

1986-01-01

Due to the effect of the nonuniform environment on the static screening of the Coulomb potential, the local-density approximation for the particle-hole interaction is found to be inadequate to determine the surface energy of simple metals. Use of the same set of single-particle states, and thus the same one-body density and the same work function, has eliminated the single-electron states in favor of the structure of the short-ranged correlations as the basis of this effect. A posteriori simplifications of the Fermi hypernetted-chain theory may be found to allow the same calculational accuracy with simpler computational tools.

Neurosemantics, neurons and system theory.

PubMed

Breidbach, Olaf

2007-08-01

Following the concept of internal representations, signal processing in a neuronal system has to be evaluated exclusively based on internal system characteristics. Thus, this approach omits the external observer as a control function for sensory integration. Instead, the configuration of the system and its computational performance are the effects of endogenous factors. Such self-referential operation is due to a strictly local computation in a network and, thereby, computations follow a set of rules that constitute the emergent behaviour of the system. These rules can be shown to correspond to a "logic" that is intrinsic to the system, an idea which provides the basis for neurosemantics.

Ab-initio calculation for cation vacancy formation energy in anti-fluorite structure

NASA Astrophysics Data System (ADS)

Saleel, V. P. Saleel Ahammad; Chitra, D.; Veluraja, K.; Eithiraj, R. D.

2018-04-01

Lithium oxide (Li2O) has been suggested as a suitable breeder blanket material for fusion reactors. Li+ vacancies are created by neutron irradiation, forming bulk defect complex whose extra character is experimentally unclear. We present a theoretical study of Li2O using density functional theory (DFT) with a plane-wave basis set. The generalized gradient approximation (GGA) and local-density approximation (LDA) were used for exchange and correlation. Here we address the total energy for defect free, cation defect, cation vacancy and vacancy formation energy in Li2O crystal in anti-fluorite structure.

Model of Cortical Organization Embodying a Basis for a Theory of Information Processing and Memory Recall

NASA Astrophysics Data System (ADS)

Shaw, Gordon L.; Silverman, Dennis J.; Pearson, John C.

1985-04-01

Motivated by V. B. Mountcastle's organizational principle for neocortical function, and by M. E. Fisher's model of physical spin systems, we introduce a cooperative model of the cortical column incorporating an idealized substructure, the trion, which represents a localized group of neurons. Computer studies reveal that typical networks composed of a small number of trions (with symmetric interactions) exhibit striking behavior--e.g., hundreds to thousands of quasi-stable, periodic firing patterns, any of which can be selected out and enhanced with only small changes in interaction strengths by using a Hebb-type algorithm.

Impaired coupling of local and global functional feedbacks underlies abnormal synchronization and negative symptoms of schizophrenia.

PubMed

Noh, Kyungchul; Shin, Kyung Soon; Shin, Dongkwan; Hwang, Jae Yeon; Kim, June Sic; Jang, Joon Hwan; Chung, Chun Kee; Kwon, Jun Soo; Cho, Kwang-Hyun

2013-04-10

Abnormal synchronization of brain oscillations is found to be associated with various core symptoms of schizophrenia. However, the underlying mechanism of this association remains yet to be elucidated. In this study, we found that coupled local and global feedback (CLGF) circuits in the cortical functional network are related to the abnormal synchronization and also correlated to the negative symptom of schizophrenia. Analysis of the magnetoencephalography data obtained from patients with chronic schizophrenia during rest revealed an increase in beta band synchronization and a reduction in gamma band power compared to healthy controls. Using a feedback identification method based on non-causal impulse responses, we constructed functional feedback networks and found that CLGF circuits were significantly reduced in schizophrenia. From computational analysis on the basis of the Wilson-Cowan model, we unraveled that the CLGF circuits are critically involved in the abnormal synchronization and the dynamical switching between beta and gamma bands power in schizophrenia. Moreover, we found that the abundance of CLGF circuits was negatively correlated with the development of negative symptoms of schizophrenia, suggesting that the negative symptom is closely related to the impairment of this circuit. Our study implicates that patients with schizophrenia might have the impaired coupling of inter- and intra-regional functional feedbacks and that the CLGF circuit might serve as a critical bridge between abnormal synchronization and the negative symptoms of schizophrenia.

Wannier-function-based constrained DFT with nonorthogonality-correcting Pulay forces in application to the reorganization effects in graphene-adsorbed pentacene

NASA Astrophysics Data System (ADS)

Roychoudhury, Subhayan; O'Regan, David D.; Sanvito, Stefano

2018-05-01

Pulay terms arise in the Hellmann-Feynman forces in electronic-structure calculations when one employs a basis set made of localized orbitals that move with their host atoms. If the total energy of the system depends on a subspace population defined in terms of the localized orbitals across multiple atoms, then unconventional Pulay terms will emerge due to the variation of the orbital nonorthogonality with ionic translation. Here, we derive the required exact expressions for such terms, which cannot be eliminated by orbital orthonormalization. We have implemented these corrected ionic forces within the linear-scaling density functional theory (DFT) package onetep, and we have used constrained DFT to calculate the reorganization energy of a pentacene molecule adsorbed on a graphene flake. The calculations are performed by including ensemble DFT, corrections for periodic boundary conditions, and empirical Van der Waals interactions. For this system we find that tensorially invariant population analysis yields an adsorbate subspace population that is very close to integer-valued when based upon nonorthogonal Wannier functions, and also but less precisely so when using pseudoatomic functions. Thus, orbitals can provide a very effective population analysis for constrained DFT. Our calculations show that the reorganization energy of the adsorbed pentacene is typically lower than that of pentacene in the gas phase. We attribute this effect to steric hindrance.

Quantum size effects on the (0001) surface of double hexagonal close packed americium

NASA Astrophysics Data System (ADS)

Gao, D.; Ray, A. K.

2007-01-01

Electronic structures of double hexagonal close-packed americium and the (0001) surface have been studied via full-potential all-electron density-functional calculations with a mixed APW+lo/LAPW basis. The electronic and geometric properties of bulk dhcp Am as well as quantum size effects in the surface energies and the work functions of the dhcp Am (0001) ultra thin films up to seven layers have been examined at nonmagnetic, ferromagnetic, and antiferromagnetic configurations with and without spin orbit coupling. The anti-ferromagnetic state including spin-orbit coupling is found to be the ground state of dhcp Am with the 5f electrons primarily localized. Our results show that both magnetic configurations and spin-orbit coupling play important roles in determining the equilibrium lattice constant, the bulk modulus as well as the localized feature of 5f electrons for dhcp Am. Our calculated equilibrium lattice constant and bulk modulus at the ground state are in good agreement with the experimental values respectively. The work function of dhcp Am (0001) 7-layer surface at the ground state is predicted to be 2.90 eV. The surface energy for dhcp Am (0001) semi-infinite surface energy at the ground state is predicted to be 0.84 J/m2. Quantum size effects are found to be more pronounced in work functions than in surface energies.

Blind compressive sensing dynamic MRI

PubMed Central

Lingala, Sajan Goud; Jacob, Mathews

2013-01-01

We propose a novel blind compressive sensing (BCS) frame work to recover dynamic magnetic resonance images from undersampled measurements. This scheme models the dynamic signal as a sparse linear combination of temporal basis functions, chosen from a large dictionary. In contrast to classical compressed sensing, the BCS scheme simultaneously estimates the dictionary and the sparse coefficients from the undersampled measurements. Apart from the sparsity of the coefficients, the key difference of the BCS scheme with current low rank methods is the non-orthogonal nature of the dictionary basis functions. Since the number of degrees of freedom of the BCS model is smaller than that of the low-rank methods, it provides improved reconstructions at high acceleration rates. We formulate the reconstruction as a constrained optimization problem; the objective function is the linear combination of a data consistency term and sparsity promoting ℓ1 prior of the coefficients. The Frobenius norm dictionary constraint is used to avoid scale ambiguity. We introduce a simple and efficient majorize-minimize algorithm, which decouples the original criterion into three simpler sub problems. An alternating minimization strategy is used, where we cycle through the minimization of three simpler problems. This algorithm is seen to be considerably faster than approaches that alternates between sparse coding and dictionary estimation, as well as the extension of K-SVD dictionary learning scheme. The use of the ℓ1 penalty and Frobenius norm dictionary constraint enables the attenuation of insignificant basis functions compared to the ℓ0 norm and column norm constraint assumed in most dictionary learning algorithms; this is especially important since the number of basis functions that can be reliably estimated is restricted by the available measurements. We also observe that the proposed scheme is more robust to local minima compared to K-SVD method, which relies on greedy sparse coding. Our phase transition experiments demonstrate that the BCS scheme provides much better recovery rates than classical Fourier-based CS schemes, while being only marginally worse than the dictionary aware setting. Since the overhead in additionally estimating the dictionary is low, this method can be very useful in dynamic MRI applications, where the signal is not sparse in known dictionaries. We demonstrate the utility of the BCS scheme in accelerating contrast enhanced dynamic data. We observe superior reconstruction performance with the BCS scheme in comparison to existing low rank and compressed sensing schemes. PMID:23542951

Modelling passive diastolic mechanics with quantitative MRI of cardiac structure and function.

PubMed

Wang, Vicky Y; Lam, H I; Ennis, Daniel B; Cowan, Brett R; Young, Alistair A; Nash, Martyn P

2009-10-01

The majority of patients with clinically diagnosed heart failure have normal systolic pump function and are commonly categorized as suffering from diastolic heart failure. The left ventricle (LV) remodels its structure and function to adapt to pathophysiological changes in geometry and loading conditions, which in turn can alter the passive ventricular mechanics. In order to better understand passive ventricular mechanics, a LV finite element (FE) model was customized to geometric data segmented from in vivo tagged magnetic resonance images (MRI) data and myofibre orientation derived from ex vivo diffusion tensor MRI (DTMRI) of a canine heart using nonlinear finite element fitting techniques. MRI tissue tagging enables quantitative evaluation of cardiac mechanical function with high spatial and temporal resolution, whilst the direction of maximum water diffusion in each voxel of a DTMRI directly corresponds to the local myocardial fibre orientation. Due to differences in myocardial geometry between in vivo and ex vivo imaging, myofibre orientations were mapped into the geometric FE model using host mesh fitting (a free form deformation technique). Pressure recordings, temporally synchronized to the tagging data, were used as the loading constraints to simulate the LV deformation during diastole. Simulation of diastolic LV mechanics allowed us to estimate the stiffness of the passive LV myocardium based on kinematic data obtained from tagged MRI. Integrated physiological modelling of this kind will allow more insight into mechanics of the LV on an individualized basis, thereby improving our understanding of the underlying structural basis of mechanical dysfunction under pathological conditions.

wannier90: A tool for obtaining maximally-localised Wannier functions

NASA Astrophysics Data System (ADS)

Mostofi, Arash A.; Yates, Jonathan R.; Lee, Young-Su; Souza, Ivo; Vanderbilt, David; Marzari, Nicola

2008-05-01

We present wannier90, a program for calculating maximally-localised Wannier functions (MLWF) from a set of Bloch energy bands that may or may not be attached to or mixed with other bands. The formalism works by minimising the total spread of the MLWF in real space. This is done in the space of unitary matrices that describe rotations of the Bloch bands at each k-point. As a result, wannier90 is independent of the basis set used in the underlying calculation to obtain the Bloch states. Therefore, it may be interfaced straightforwardly to any electronic structure code. The locality of MLWF can be exploited to compute band-structure, density of states and Fermi surfaces at modest computational cost. Furthermore, wannier90 is able to output MLWF for visualisation and other post-processing purposes. Wannier functions are already used in a wide variety of applications. These include analysis of chemical bonding in real space; calculation of dielectric properties via the modern theory of polarisation; and as an accurate and minimal basis set in the construction of model Hamiltonians for large-scale systems, in linear-scaling quantum Monte Carlo calculations, and for efficient computation of material properties, such as the anomalous Hall coefficient. wannier90 is freely available under the GNU General Public License from http://www.wannier.org/. Program summaryProgram title: wannier90 Catalogue identifier: AEAK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAK_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 556 495 No. of bytes in distributed program, including test data, etc.: 5 709 419 Distribution format: tar.gz Programming language: Fortran 90, perl Computer: any architecture with a Fortran 90 compiler Operating system: Linux, Windows, Solaris, AIX, Tru64 Unix, OSX RAM: 10 MB Word size: 32 or 64 Classification: 7.3 External routines:BLAS ( http://www/netlib.org/blas). LAPACK ( http://www.netlib.org/lapack). Both available under open-source licenses. Nature of problem: Obtaining maximally-localised Wannier functions from a set of Bloch energy bands that may or may not be entangled. Solution method: In the case of entangled bands, the optimally-connected subspace of interest is determined by minimising a functional which measures the subspace dispersion across the Brillouin zone. The maximally-localised Wannier functions within this subspace are obtained by subsequent minimisation of a functional that represents the total spread of the Wannier functions in real space. For the case of isolated energy bands only the second step of the procedure is required. Unusual features: Simple and user-friendly input system. Wannier functions and interpolated band structure output in a variety of file formats for visualisation. Running time: Test cases take 1 minute. References:N. Marzari, D. Vanderbilt, Maximally localized generalized Wannier functions for composite energy bands, Phys. Rev. B 56 (1997) 12847. I. Souza, N. Marzari, D. Vanderbilt, Maximally localized Wannier functions for entangled energy bands, Phys. Rev. B 65 (2001) 035109.

Effects of covert and overt paradigms in clinical language fMRI.

PubMed

Partovi, Sasan; Konrad, Florian; Karimi, Sasan; Rengier, Fabian; Lyo, John K; Zipp, Lisa; Nennig, Ernst; Stippich, Christoph

2012-05-01

The aim of this study was to assess the intrasubject and intersubject reproducibility of functional magnetic resonance imaging (fMRI) language paradigms on language localization and lateralization. Fourteen healthy volunteers were enrolled prospectively and underwent language fMRI using visually triggered covert and overt sentence generation (SG) and word generation (WG) paradigms. Semiautomated analysis of all functional data was performed using Brain Voyager on an individual basis. Regions of interest for Broca's area, Wernicke's area, and their contralateral homologues were drawn. The Euclidean coordinates of the center of gravidity (x, y, and z) of the respective blood oxygenation level-dependent (BOLD) activation cluster, and the correlation of the measured hemodynamic response to the applied reference function (r), relative BOLD signal change as BOLD signal characteristics were measured in each region of interest. Regional lateralization indexes were calculated for Broca's area, Wernicke's area, and their contralateral homologues separately. Wilcoxon's signed-rank test was applied for statistical comparisons (P values < .05 were considered significant). Ten of the 14 volunteers had three repeated measurements to test intrasession reproducibility and intersession reproducibility. Overall activation rates for the four paradigms were 89% for covert SG, 82% for overt SG, 89% for covert WG, and 100% for overt WG. When comparing covert and overt paradigms, language localization was significantly different in 17% (Euclidean coordinates) and 19% (BOLD signal characteristics), respectively. Language lateralization was significantly different in 75%. Intrasubject and intersubject reproducibility was excellent, with 3.3% significant differences among all five parameters for language localization and 0% significant differences for language lateralization using covert paradigms. Covert language paradigms (SG and WG) provided highly robust and reproducible localization and lateralization of essential language centers for scans performed on the same and different days. Their overt counterparts achieved confirmatory localization but lower lateralization capabilities. Reference data for presurgical application are provided. Copyright © 2012 AUR. Published by Elsevier Inc. All rights reserved.

The Globe. Neighbourhood Agenda 21: Going Local in Reading.

ERIC Educational Resources Information Center

Welsh, Richard

1994-01-01

Reports on the philosophy underlying a project to promote local community involvement in neighborhood plans as a basis for a citywide Local Agenda 21 and the first stages of Go Local on a Better Environment (GLOBE) introduced to give the project a popular identify and communicate the environmental message. (LZ)

Fall-to-Fall Testing versus Spring-to-Spring Testing: What Is the Impact on a Local Community's Chapter 1 Evaluation?

ERIC Educational Resources Information Center

Bushner, Diane E.

The impact of a decision by a local program under Chapter 1, the federally funded program of financial assistance to special educational needs of children, to test students fall-to-fall or spring-to-spring was studied. Students enrolled in a Chapter 1 reading program in 1988-89 were tested on a fall-to-spring basis, a spring-to-spring basis, and a…

Novel and recurrent FERMT1 gene mutations in Kindler syndrome.

PubMed

Techanukul, Tanasit; Sethuraman, Gomathy; Zlotogorski, Abraham; Horev, Liran; Macarov, Michal; Trainer, Alison; Fong, Kenneth; Lens, Marko; Medenica, Ljiljana; Ramesh, Venkatesh; McGrath, John A; Lai-Cheong, Joey E

2011-05-01

Kindler syndrome (OMIM 173650) is an autosomal recessive condition characterized by skin blistering, skin atrophy, photosensitivity, colonic inflammation and mucosal stenosis. Fewer than 100 cases have been described in the literature. First reported in 1954, the molecular basis of Kindler syndrome was elucidated in 2003 with the discovery of FERMT1 (KIND1) loss-of-function mutations in affected individuals. The FERMT1 gene encodes kindlin-1 (also known as fermitin family homologue 1), a 77 kDa protein that localizes at focal adhesions, where it plays an important role in integrin signalling. In the current study, we describe five novel and three recurrent loss-of-function FERMT1 mutations in eight individuals with Kindler syndrome, and provide an overview of genotype-phenotype correlation in this disorder.

Neural-endocrine-immune complex in the central modulation of tumorigenesis: facts, assumptions, and hypotheses.

PubMed

Mravec, Boris; Gidron, Yori; Kukanova, Barbara; Bizik, Jozef; Kiss, Alexander; Hulin, Ivan

2006-11-01

For the precise coordination of systemic functions, the nervous system uses a variety of peripherally and centrally localized receptors, which transmit information from internal and external environments to the central nervous system. Tight interconnections between the immune, nervous, and endocrine systems provide a base for monitoring and consequent modulation of immune system functions by the brain and vice versa. The immune system plays an important role in tumorigenesis. On the basis of rich interconnections between the immune, nervous and endocrine systems, the possibility that the brain may be informed about tumorigenesis is discussed in this review article. Moreover, the eventual modulation of tumorigenesis by central nervous system is also considered. Prospective consequences of the interactions between tumor and brain for diagnosis and therapy of cancer are emphasized.

Sculpting bespoke mountains: Determining free energies with basis expansions

NASA Astrophysics Data System (ADS)

Whitmer, Jonathan K.; Fluitt, Aaron M.; Antony, Lucas; Qin, Jian; McGovern, Michael; de Pablo, Juan J.

2015-07-01

The intriguing behavior of a wide variety of physical systems, ranging from amorphous solids or glasses to proteins, is a direct manifestation of underlying free energy landscapes riddled with local minima separated by large barriers. Exploring such landscapes has arguably become one of statistical physics's great challenges. A new method is proposed here for uniform sampling of rugged free energy surfaces. The method, which relies on special Green's functions to approximate the Dirac delta function, improves significantly on existing simulation techniques by providing a boundary-agnostic approach that is capable of mapping complex features in multidimensional free energy surfaces. The usefulness of the proposed approach is established in the context of a simple model glass former and model proteins, demonstrating improved convergence and accuracy over existing methods.

Neural basis of exertional fatigue in the heat: A review of magnetic resonance imaging methods.

PubMed

Tan, X R; Low, I C C; Stephenson, M C; Soong, T W; Lee, J K W

2018-03-01

The central nervous system, specifically the brain, is implicated in the development of exertional fatigue under a hot environment. Diverse neuroimaging techniques have been used to visualize the brain activity during or after exercise. Notably, the use of magnetic resonance imaging (MRI) has become prevalent due to its excellent spatial resolution and versatility. This review evaluates the significance and limitations of various brain MRI techniques in exercise studies-brain volumetric analysis, functional MRI, functional connectivity MRI, and arterial spin labeling. The review aims to provide a summary on the neural basis of exertional fatigue and proposes future directions for brain MRI studies. A systematic literature search was performed where a total of thirty-seven brain MRI studies associated with exercise, fatigue, or related physiological factors were reviewed. The findings suggest that with moderate dehydration, there is a decrease in total brain volume accompanied with expansion of ventricular volume. With exercise fatigue, there is increased activation of sensorimotor and cognitive brain areas, increased thalamo-insular activation and decreased interhemispheric connectivity in motor cortex. Under passive hyperthermia, there are regional changes in cerebral perfusion, a reduction in local connectivity in functional brain networks and an impairment to executive function. Current literature suggests that the brain structure and function are influenced by exercise, fatigue, and related physiological perturbations. However, there is still a dearth of knowledge and it is hoped that through understanding of MRI advantages and limitations, future studies will shed light on the central origin of exertional fatigue in the heat. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Mass-storage management for distributed image/video archives

NASA Astrophysics Data System (ADS)

Franchi, Santina; Guarda, Roberto; Prampolini, Franco

1993-04-01

The realization of image/video database requires a specific design for both database structures and mass storage management. This issue has addressed the project of the digital image/video database system that has been designed at IBM SEMEA Scientific & Technical Solution Center. Proper database structures have been defined to catalog image/video coding technique with the related parameters, and the description of image/video contents. User workstations and servers are distributed along a local area network. Image/video files are not managed directly by the DBMS server. Because of their wide size, they are stored outside the database on network devices. The database contains the pointers to the image/video files and the description of the storage devices. The system can use different kinds of storage media, organized in a hierarchical structure. Three levels of functions are available to manage the storage resources. The functions of the lower level provide media management. They allow it to catalog devices and to modify device status and device network location. The medium level manages image/video files on a physical basis. It manages file migration between high capacity media and low access time media. The functions of the upper level work on image/video file on a logical basis, as they archive, move and copy image/video data selected by user defined queries. These functions are used to support the implementation of a storage management strategy. The database information about characteristics of both storage devices and coding techniques are used by the third level functions to fit delivery/visualization requirements and to reduce archiving costs.

microRNA function in left-right neuronal asymmetry: perspectives from C. elegans.

PubMed

Alqadah, Amel; Hsieh, Yi-Wen; Chuang, Chiou-Fen

2013-09-23

Left-right asymmetry in anatomical structures and functions of the nervous system is present throughout the animal kingdom. For example, language centers are localized in the left side of the human brain, while spatial recognition functions are found in the right hemisphere in the majority of the population. Disruption of asymmetry in the nervous system is correlated with neurological disorders. Although anatomical and functional asymmetries are observed in mammalian nervous systems, it has been a challenge to identify the molecular basis of these asymmetries. C. elegans has emerged as a prime model organism to investigate molecular asymmetries in the nervous system, as it has been shown to display functional asymmetries clearly correlated to asymmetric distribution and regulation of biologically relevant molecules. Small non-coding RNAs have been recently implicated in various aspects of neural development. Here, we review cases in which microRNAs are crucial for establishing left-right asymmetries in the C. elegans nervous system. These studies may provide insight into how molecular and functional asymmetries are established in the human brain.

Structural white matter asymmetries in relation to functional asymmetries during speech perception and production.

PubMed

Ocklenburg, Sebastian; Hugdahl, Kenneth; Westerhausen, René

2013-12-01

Functional hemispheric asymmetries of speech production and perception are a key feature of the human language system, but their neurophysiological basis is still poorly understood. Using a combined fMRI and tract-based spatial statistics approach, we investigated the relation of microstructural asymmetries in language-relevant white matter pathways and functional activation asymmetries during silent verb generation and passive listening to spoken words. Tract-based spatial statistics revealed several leftward asymmetric clusters in the arcuate fasciculus and uncinate fasciculus that were differentially related to activation asymmetries in the two functional tasks. Frontal and temporal activation asymmetries during silent verb generation were positively related to the strength of specific microstructural white matter asymmetries in the arcuate fasciculus. In contrast, microstructural uncinate fasciculus asymmetries were related to temporal activation asymmetries during passive listening. These findings suggest that white matter asymmetries may indeed be one of the factors underlying functional hemispheric asymmetries. Moreover, they also show that specific localized white matter asymmetries might be of greater relevance for functional activation asymmetries than microstructural features of whole pathways. © 2013.

Local discretization method for overdamped Brownian motion on a potential with multiple deep wells.

PubMed

Nguyen, P T T; Challis, K J; Jack, M W

2016-11-01

We present a general method for transforming the continuous diffusion equation describing overdamped Brownian motion on a time-independent potential with multiple deep wells to a discrete master equation. The method is based on an expansion in localized basis states of local metastable potentials that match the full potential in the region of each potential well. Unlike previous basis methods for discretizing Brownian motion on a potential, this approach is valid for periodic potentials with varying multiple deep wells per period and can also be applied to nonperiodic systems. We apply the method to a range of potentials and find that potential wells that are deep compared to five times the thermal energy can be associated with a discrete localized state while shallower wells are better incorporated into the local metastable potentials of neighboring deep potential wells.

Local discretization method for overdamped Brownian motion on a potential with multiple deep wells

NASA Astrophysics Data System (ADS)

Nguyen, P. T. T.; Challis, K. J.; Jack, M. W.

2016-11-01

We present a general method for transforming the continuous diffusion equation describing overdamped Brownian motion on a time-independent potential with multiple deep wells to a discrete master equation. The method is based on an expansion in localized basis states of local metastable potentials that match the full potential in the region of each potential well. Unlike previous basis methods for discretizing Brownian motion on a potential, this approach is valid for periodic potentials with varying multiple deep wells per period and can also be applied to nonperiodic systems. We apply the method to a range of potentials and find that potential wells that are deep compared to five times the thermal energy can be associated with a discrete localized state while shallower wells are better incorporated into the local metastable potentials of neighboring deep potential wells.

A role for the membrane protein M6 in the Drosophila visual system.

PubMed

Zappia, María Paula; Bernabo, Guillermo; Billi, Silvia C; Frasch, Alberto C; Ceriani, María Fernanda; Brocco, Marcela Adriana

2012-07-04

Members of the proteolipid protein family, including the four-transmembrane glycoprotein M6a, are involved in neuronal plasticity in mammals. Results from our group previously demonstrated that M6, the only proteolipid protein expressed in Drosophila, localizes to the cell membrane in follicle cells. M6 loss triggers female sterility, which suggests a role for M6 in follicular cell remodeling. These results were the basis of the present study, which focused on the function and requirements of M6 in the fly nervous system. The present study identified two novel, tissue-regulated M6 isoforms with variable N- and C- termini, and showed that M6 is the functional fly ortholog of Gpm6a. In the adult brain, the protein was localized to several neuropils, such as the optic lobe, the central complex, and the mushroom bodies. Interestingly, although reduced M6 levels triggered a mild rough-eye phenotype, hypomorphic M6 mutants exhibited a defective response to light. Based on its ability to induce filopodium formation we propose that M6 is key in cell remodeling processes underlying visual system function. These results bring further insight into the role of M6/M6a in biological processes involving neuronal plasticity and behavior in flies and mammals.

A role for the membrane protein M6 in the Drosophila visual system

PubMed Central

2012-01-01

Background Members of the proteolipid protein family, including the four-transmembrane glycoprotein M6a, are involved in neuronal plasticity in mammals. Results from our group previously demonstrated that M6, the only proteolipid protein expressed in Drosophila, localizes to the cell membrane in follicle cells. M6 loss triggers female sterility, which suggests a role for M6 in follicular cell remodeling. These results were the basis of the present study, which focused on the function and requirements of M6 in the fly nervous system. Results The present study identified two novel, tissue-regulated M6 isoforms with variable N- and C- termini, and showed that M6 is the functional fly ortholog of Gpm6a. In the adult brain, the protein was localized to several neuropils, such as the optic lobe, the central complex, and the mushroom bodies. Interestingly, although reduced M6 levels triggered a mild rough-eye phenotype, hypomorphic M6 mutants exhibited a defective response to light. Conclusions Based on its ability to induce filopodium formation we propose that M6 is key in cell remodeling processes underlying visual system function. These results bring further insight into the role of M6/M6a in biological processes involving neuronal plasticity and behavior in flies and mammals. PMID:22762289

Empirical Orthogonal Function (EOF) Analysis of Storm-Time GPS Total Electron Content Variations

NASA Astrophysics Data System (ADS)

Thomas, E. G.; Coster, A. J.; Zhang, S.; McGranaghan, R. M.; Shepherd, S. G.; Baker, J. B.; Ruohoniemi, J. M.

2016-12-01

Large perturbations in ionospheric density are known to occur during geomagnetic storms triggered by dynamic structures in the solar wind. These ionospheric storm effects have long attracted interest due to their impact on the propagation characteristics of radio wave communications. Over the last two decades, maps of vertically-integrated total electron content (TEC) based on data collected by worldwide networks of Global Positioning System (GPS) receivers have dramatically improved our ability to monitor the spatiotemporal dynamics of prominent storm-time features such as polar cap patches and storm enhanced density (SED) plumes. In this study, we use an empirical orthogonal function (EOF) decomposition technique to identify the primary modes of spatial and temporal variability in the storm-time GPS TEC response at midlatitudes over North America during more than 100 moderate geomagnetic storms from 2001-2013. We next examine the resulting time-varying principal components and their correlation with various geophysical indices and parameters in order to derive an analytical representation. Finally, we use a truncated reconstruction of the EOF basis functions and parameterization of the principal components to produce an empirical representation of the geomagnetic storm-time response of GPS TEC for all magnetic local times local times and seasons at midlatitudes in the North American sector.

Combining Density Functional Theory and Green's Function Theory: Range-Separated, Nonlocal, Dynamic, and Orbital-Dependent Hybrid Functional.

PubMed

Kananenka, Alexei A; Zgid, Dominika

2017-11-14

We present a rigorous framework which combines single-particle Green's function theory with density functional theory based on a separation of electron-electron interactions into short- and long-range components. Short-range contribution to the total energy and exchange-correlation potential is provided by a density functional approximation, while the long-range contribution is calculated using an explicit many-body Green's function method. Such a hybrid results in a nonlocal, dynamic, and orbital-dependent exchange-correlation functional of a single-particle Green's function. In particular, we present a range-separated hybrid functional called srSVWN5-lrGF2 which combines the local-density approximation and the second-order Green's function theory. We illustrate that similarly to density functional approximations, the new functional is weakly basis-set dependent. Furthermore, it offers an improved description of the short-range dynamic correlation. The many-body contribution to the functional mitigates the many-electron self-interaction error present in many density functional approximations and provides a better description of molecular properties. Additionally, we illustrate that the new functional can be used to scale down the self-energy and, therefore, introduce an additional sparsity to the self-energy matrix that in the future can be exploited in calculations for large molecules or periodic systems.

The BioPlex Network: A Systematic Exploration of the Human Interactome.

PubMed

Huttlin, Edward L; Ting, Lily; Bruckner, Raphael J; Gebreab, Fana; Gygi, Melanie P; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Colby, Greg; Baltier, Kurt; Dong, Rui; Guarani, Virginia; Vaites, Laura Pontano; Ordureau, Alban; Rad, Ramin; Erickson, Brian K; Wühr, Martin; Chick, Joel; Zhai, Bo; Kolippakkam, Deepak; Mintseris, Julian; Obar, Robert A; Harris, Tim; Artavanis-Tsakonas, Spyros; Sowa, Mathew E; De Camilli, Pietro; Paulo, Joao A; Harper, J Wade; Gygi, Steven P

2015-07-16

Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80%-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. Network structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally related proteins. Finally, BioPlex, in combination with other approaches, can be used to reveal interactions of biological or clinical significance. For example, mutations in the membrane protein VAPB implicated in familial amyotrophic lateral sclerosis perturb a defined community of interactors. Copyright © 2015 Elsevier Inc. All rights reserved.

The BioPlex Network: A Systematic Exploration of the Human Interactome

PubMed Central

Huttlin, Edward L.; Ting, Lily; Bruckner, Raphael J.; Gebreab, Fana; Gygi, Melanie P.; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Colby, Greg; Baltier, Kurt; Dong, Rui; Guarani, Virginia; Vaites, Laura Pontano; Ordureau, Alban; Rad, Ramin; Erickson, Brian K.; Wühr, Martin; Chick, Joel; Zhai, Bo; Kolippakkam, Deepak; Mintseris, Julian; Obar, Robert A.; Harris, Tim; Artavanis-Tsakonas, Spyros; Sowa, Mathew E.; DeCamilli, Pietro; Paulo, Joao A.; Harper, J. Wade; Gygi, Steven P.

2015-01-01

SUMMARY Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. Network structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally-related proteins. Finally, BioPlex, in combination with other approaches can be used to reveal interactions of biological or clinical significance. For example, mutations in the membrane protein VAPB implicated in familial Amyotrophic Lateral Sclerosis perturb a defined community of interactors. PMID:26186194

Regional TEC dynamic modeling based on Slepian functions

NASA Astrophysics Data System (ADS)

Sharifi, Mohammad Ali; Farzaneh, Saeed

2015-09-01

In this work, the three-dimensional state of the ionosphere has been estimated by integrating the spherical Slepian harmonic function and Kalman filter. The spherical Slepian harmonic functions have been used to establish the observation equations because of their properties in local modeling. Spherical harmonics are poor choices to represent or analyze geophysical processes without perfect global coverage but the Slepian functions afford spatial and spectral selectivity. The Kalman filter has been utilized to perform the parameter estimation due to its suitable properties in processing the GPS measurements in the real-time mode. The proposed model has been applied to the real data obtained from the ground-based GPS observations across some portion of the IGS network in Europe. Results have been compared with the estimated TECs by the CODE, ESA, IGS centers and IRI-2012 model. The results indicated that the proposed model which takes advantage of the Slepian basis and Kalman filter is efficient and allows for the generation of the near-real-time regional TEC map.

Robust Joint Graph Sparse Coding for Unsupervised Spectral Feature Selection.

PubMed

Zhu, Xiaofeng; Li, Xuelong; Zhang, Shichao; Ju, Chunhua; Wu, Xindong

2017-06-01

In this paper, we propose a new unsupervised spectral feature selection model by embedding a graph regularizer into the framework of joint sparse regression for preserving the local structures of data. To do this, we first extract the bases of training data by previous dictionary learning methods and, then, map original data into the basis space to generate their new representations, by proposing a novel joint graph sparse coding (JGSC) model. In JGSC, we first formulate its objective function by simultaneously taking subspace learning and joint sparse regression into account, then, design a new optimization solution to solve the resulting objective function, and further prove the convergence of the proposed solution. Furthermore, we extend JGSC to a robust JGSC (RJGSC) via replacing the least square loss function with a robust loss function, for achieving the same goals and also avoiding the impact of outliers. Finally, experimental results on real data sets showed that both JGSC and RJGSC outperformed the state-of-the-art algorithms in terms of k -nearest neighbor classification performance.

First-principles calculations on the four phases of BaTiO3.

PubMed

Evarestov, Robert A; Bandura, Andrei V

2012-04-30

The calculations based on linear combination of atomic orbitals basis functions as implemented in CRYSTAL09 computer code have been performed for cubic, tetragonal, orthorhombic, and rhombohedral modifications of BaTiO(3) crystal. Structural and electronic properties as well as phonon frequencies were obtained using local density approximation, generalized gradient approximation, and hybrid exchange-correlation density functional theory (DFT) functionals for four stable phases of BaTiO(3). A comparison was made between the results of different DFT techniques. It is concluded that the hybrid PBE0 [J. P. Perdew, K. Burke, M. Ernzerhof, J. Chem. Phys. 1996, 105, 9982.] functional is able to predict correctly the structural stability and phonon properties both for cubic and ferroelectric phases of BaTiO(3). The comparative phonon symmetry analysis in BaTiO(3) four phases has been made basing on the site symmetry and irreducible representation indexes for the first time. Copyright © 2012 Wiley Periodicals, Inc.

Caenorhabditis elegans MES-3 is a target of GLD-1 and functions epigenetically in germline development.

PubMed Central

Xu, L; Paulsen, J; Yoo, Y; Goodwin, E B; Strome, S

2001-01-01

The maternal-effect sterile (MES) proteins are maternally supplied regulators of germline development in Caenorhabditis elegans. In the hermaphrodite progeny from mes mutant mothers, the germline dies during larval development. On the basis of the similarities of MES-2 and MES-6 to known transcriptional regulators and on the basis of the effects of mes mutations on transgene expression in the germline, the MES proteins are predicted to be transcriptional repressors. One of the MES proteins, MES-3, is a novel protein with no recognizable motifs. In this article we show that MES-3 is localized in the nuclei of embryos and germ cells, consistent with its predicted role in transcriptional regulation. Its distribution in the germline and in early embryos does not depend on the wild-type functions of the other MES proteins. However, its nuclear localization in midstage embryos and its persistence in the primordial germ cells depend on wild-type MES-2 and MES-6. These results are consistent with biochemical data showing that MES-2, MES-3, and MES-6 associate in a complex in embryos. The distribution of MES-3 in the adult germline is regulated by the translational repressor GLD-1: MES-3 is absent from the region of the germline where GLD-1 is known to be present, MES-3 is overexpressed in the germline of gld-1 mutants, and GLD-1 specifically binds the mes-3 3' untranslated region (3' UTR). Analysis of temperature-shifted mes-3(bn21ts) worms and embryos indicates that MES-3 function is required in the mother's germline and during embryogenesis to ensure subsequent normal germline development. We propose that MES-3 acts epigenetically to induce a germline state that is inherited through both meiosis and mitosis and that is essential for survival of the germline. PMID:11729149

Uniform electron gases. III. Low-density gases on three-dimensional spheres

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agboola, Davids; Knol, Anneke L.; Gill, Peter M. W., E-mail: peter.gill@anu.edu.au

2015-08-28

By combining variational Monte Carlo (VMC) and complete-basis-set limit Hartree-Fock (HF) calculations, we have obtained near-exact correlation energies for low-density same-spin electrons on a three-dimensional sphere (3-sphere), i.e., the surface of a four-dimensional ball. In the VMC calculations, we compare the efficacies of two types of one-electron basis functions for these strongly correlated systems and analyze the energy convergence with respect to the quality of the Jastrow factor. The HF calculations employ spherical Gaussian functions (SGFs) which are the curved-space analogs of Cartesian Gaussian functions. At low densities, the electrons become relatively localized into Wigner crystals, and the natural SGFmore » centers are found by solving the Thomson problem (i.e., the minimum-energy arrangement of n point charges) on the 3-sphere for various values of n. We have found 11 special values of n whose Thomson sites are equivalent. Three of these are the vertices of four-dimensional Platonic solids — the hyper-tetrahedron (n = 5), the hyper-octahedron (n = 8), and the 24-cell (n = 24) — and a fourth is a highly symmetric structure (n = 13) which has not previously been reported. By calculating the harmonic frequencies of the electrons around their equilibrium positions, we also find the first-order vibrational corrections to the Thomson energy.« less

49 CFR 25.420 - Access to schools operated by LEAs.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 25.420 Transportation Office of the Secretary of Transportation NONDISCRIMINATION ON THE BASIS OF SEX... Basis of Sex in Education Programs or Activities Prohibited § 25.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex, exclude any person...

40 CFR 5.420 - Access to schools operated by LEAs.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 5.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex, exclude...

40 CFR 5.420 - Access to schools operated by LEAs.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 5.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex, exclude...

29 CFR 99.205 - Basis for determining Federal awards expended.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 29 Labor 1 2010-07-01 2010-07-01 true Basis for determining Federal awards expended. 99.205 Section 99.205 Labor Office of the Secretary of Labor AUDITS OF STATES, LOCAL GOVERNMENTS, AND NON-PROFIT ORGANIZATIONS Audits § 99.205 Basis for determining Federal awards expended. (a) Determining Federal awards...

Configurational forces in electronic structure calculations using Kohn-Sham density functional theory

NASA Astrophysics Data System (ADS)

Motamarri, Phani; Gavini, Vikram

2018-04-01

We derive the expressions for configurational forces in Kohn-Sham density functional theory, which correspond to the generalized variational force computed as the derivative of the Kohn-Sham energy functional with respect to the position of a material point x . These configurational forces that result from the inner variations of the Kohn-Sham energy functional provide a unified framework to compute atomic forces as well as stress tensor for geometry optimization. Importantly, owing to the variational nature of the formulation, these configurational forces inherently account for the Pulay corrections. The formulation presented in this work treats both pseudopotential and all-electron calculations in a single framework, and employs a local variational real-space formulation of Kohn-Sham density functional theory (DFT) expressed in terms of the nonorthogonal wave functions that is amenable to reduced-order scaling techniques. We demonstrate the accuracy and performance of the proposed configurational force approach on benchmark all-electron and pseudopotential calculations conducted using higher-order finite-element discretization. To this end, we examine the rates of convergence of the finite-element discretization in the computed forces and stresses for various materials systems, and, further, verify the accuracy from finite differencing the energy. Wherever applicable, we also compare the forces and stresses with those obtained from Kohn-Sham DFT calculations employing plane-wave basis (pseudopotential calculations) and Gaussian basis (all-electron calculations). Finally, we verify the accuracy of the forces on large materials systems involving a metallic aluminum nanocluster containing 666 atoms and an alkane chain containing 902 atoms, where the Kohn-Sham electronic ground state is computed using a reduced-order scaling subspace projection technique [P. Motamarri and V. Gavini, Phys. Rev. B 90, 115127 (2014), 10.1103/PhysRevB.90.115127].

Experimental evaluation and basis function optimization of the spatially variant image-space PSF on the Ingenuity PET/MR scanner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kotasidis, Fotis A., E-mail: Fotis.Kotasidis@unige.ch; Zaidi, Habib; Geneva Neuroscience Centre, Geneva University, CH-1205 Geneva

2014-06-15

Purpose: The Ingenuity time-of-flight (TF) PET/MR is a recently developed hybrid scanner combining the molecular imaging capabilities of PET with the excellent soft tissue contrast of MRI. It is becoming common practice to characterize the system's point spread function (PSF) and understand its variation under spatial transformations to guide clinical studies and potentially use it within resolution recovery image reconstruction algorithms. Furthermore, due to the system's utilization of overlapping and spherical symmetric Kaiser-Bessel basis functions during image reconstruction, its image space PSF and reconstructed spatial resolution could be affected by the selection of the basis function parameters. Hence, a detailedmore » investigation into the multidimensional basis function parameter space is needed to evaluate the impact of these parameters on spatial resolution. Methods: Using an array of 12 × 7 printed point sources, along with a custom made phantom, and with the MR magnet on, the system's spatially variant image-based PSF was characterized in detail. Moreover, basis function parameters were systematically varied during reconstruction (list-mode TF OSEM) to evaluate their impact on the reconstructed resolution and the image space PSF. Following the spatial resolution optimization, phantom, and clinical studies were subsequently reconstructed using representative basis function parameters. Results: Based on the analysis and under standard basis function parameters, the axial and tangential components of the PSF were found to be almost invariant under spatial transformations (∼4 mm) while the radial component varied modestly from 4 to 6.7 mm. Using a systematic investigation into the basis function parameter space, the spatial resolution was found to degrade for basis functions with a large radius and small shape parameter. However, it was found that optimizing the spatial resolution in the reconstructed PET images, while having a good basis function superposition and keeping the image representation error to a minimum, is feasible, with the parameter combination range depending upon the scanner's intrinsic resolution characteristics. Conclusions: Using the printed point source array as a MR compatible methodology for experimentally measuring the scanner's PSF, the system's spatially variant resolution properties were successfully evaluated in image space. Overall the PET subsystem exhibits excellent resolution characteristics mainly due to the fact that the raw data are not under-sampled/rebinned, enabling the spatial resolution to be dictated by the scanner's intrinsic resolution and the image reconstruction parameters. Due to the impact of these parameters on the resolution properties of the reconstructed images, the image space PSF varies both under spatial transformations and due to basis function parameter selection. Nonetheless, for a range of basis function parameters, the image space PSF remains unaffected, with the range depending on the scanner's intrinsic resolution properties.« less

Non-parametric identification of multivariable systems: A local rational modeling approach with application to a vibration isolation benchmark

NASA Astrophysics Data System (ADS)

Voorhoeve, Robbert; van der Maas, Annemiek; Oomen, Tom

2018-05-01

Frequency response function (FRF) identification is often used as a basis for control systems design and as a starting point for subsequent parametric system identification. The aim of this paper is to develop a multiple-input multiple-output (MIMO) local parametric modeling approach for FRF identification of lightly damped mechanical systems with improved speed and accuracy. The proposed method is based on local rational models, which can efficiently handle the lightly-damped resonant dynamics. A key aspect herein is the freedom in the multivariable rational model parametrizations. Several choices for such multivariable rational model parametrizations are proposed and investigated. For systems with many inputs and outputs the required number of model parameters can rapidly increase, adversely affecting the performance of the local modeling approach. Therefore, low-order model structures are investigated. The structure of these low-order parametrizations leads to an undesired directionality in the identification problem. To address this, an iterative local rational modeling algorithm is proposed. As a special case recently developed SISO algorithms are recovered. The proposed approach is successfully demonstrated on simulations and on an active vibration isolation system benchmark, confirming good performance of the method using significantly less parameters compared with alternative approaches.

Flux-corrected transport algorithms for continuous Galerkin methods based on high order Bernstein finite elements

NASA Astrophysics Data System (ADS)

Lohmann, Christoph; Kuzmin, Dmitri; Shadid, John N.; Mabuza, Sibusiso

2017-09-01

This work extends the flux-corrected transport (FCT) methodology to arbitrary order continuous finite element discretizations of scalar conservation laws on simplex meshes. Using Bernstein polynomials as local basis functions, we constrain the total variation of the numerical solution by imposing local discrete maximum principles on the Bézier net. The design of accuracy-preserving FCT schemes for high order Bernstein-Bézier finite elements requires the development of new algorithms and/or generalization of limiting techniques tailored for linear and multilinear Lagrange elements. In this paper, we propose (i) a new discrete upwinding strategy leading to local extremum bounded low order approximations with compact stencils, (ii) high order variational stabilization based on the difference between two gradient approximations, and (iii) new localized limiting techniques for antidiffusive element contributions. The optional use of a smoothness indicator, based on a second derivative test, makes it possible to potentially avoid unnecessary limiting at smooth extrema and achieve optimal convergence rates for problems with smooth solutions. The accuracy of the proposed schemes is assessed in numerical studies for the linear transport equation in 1D and 2D.

Energy Decomposition Analysis Based on Absolutely Localized Molecular Orbitals for Large-Scale Density Functional Theory Calculations in Drug Design.

PubMed

Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

2016-07-12

We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design.

Individual differences in brain structure and resting brain function underlie cognitive styles: evidence from the Embedded Figures Test.

PubMed

Hao, Xin; Wang, Kangcheng; Li, Wenfu; Yang, Wenjing; Wei, Dongtao; Qiu, Jiang; Zhang, Qinglin

2013-01-01

Cognitive styles can be characterized as individual differences in the way people perceive, think, solve problems, learn, and relate to others. Field dependence/independence (FDI) is an important and widely studied dimension of cognitive styles. Although functional imaging studies have investigated the brain activation of FDI cognitive styles, the combined structural and functional correlates with individual differences in a large sample have never been investigated. In the present study, we investigated the neural correlates of individual differences in FDI cognitive styles by analyzing the correlations between Embedded Figures Test (EFT) score and structural neuroimaging data [regional gray matter volume (rGMV) was assessed using voxel-based morphometry (VBM)]/functional neuroimaging data [resting-brain functions were measured by amplitude of low-frequency fluctuation (ALFF)] throughout the whole brain. Results showed that the increased rGMV in the left inferior parietal lobule (IPL) was associated with the EFT score, which might be the structural basis of effective local processing. Additionally, a significant positive correlation between ALFF and EFT score was found in the fronto-parietal network, including the left inferior parietal lobule (IPL) and the medial prefrontal cortex (mPFC). We speculated that the left IPL might be associated with superior feature identification, and mPFC might be related to cognitive inhibition of global processing bias. These results suggested that the underlying neuroanatomical and functional bases were linked to the individual differences in FDI cognitive styles and emphasized the important contribution of superior local processing ability and cognitive inhibition to field-independent style.

Individual Differences in Brain Structure and Resting Brain Function Underlie Cognitive Styles: Evidence from the Embedded Figures Test

PubMed Central

Hao, Xin; Wang, Kangcheng; Li, Wenfu; Yang, Wenjing; Wei, Dongtao; Qiu, Jiang; Zhang, Qinglin

2013-01-01

Cognitive styles can be characterized as individual differences in the way people perceive, think, solve problems, learn, and relate to others. Field dependence/independence (FDI) is an important and widely studied dimension of cognitive styles. Although functional imaging studies have investigated the brain activation of FDI cognitive styles, the combined structural and functional correlates with individual differences in a large sample have never been investigated. In the present study, we investigated the neural correlates of individual differences in FDI cognitive styles by analyzing the correlations between Embedded Figures Test (EFT) score and structural neuroimaging data [regional gray matter volume (rGMV) was assessed using voxel-based morphometry (VBM)] / functional neuroimaging data [resting-brain functions were measured by amplitude of low-frequency fluctuation (ALFF)] throughout the whole brain. Results showed that the increased rGMV in the left inferior parietal lobule (IPL) was associated with the EFT score, which might be the structural basis of effective local processing. Additionally, a significant positive correlation between ALFF and EFT score was found in the fronto-parietal network, including the left inferior parietal lobule (IPL) and the medial prefrontal cortex (mPFC). We speculated that the left IPL might be associated with superior feature identification, and mPFC might be related to cognitive inhibition of global processing bias. These results suggested that the underlying neuroanatomical and functional bases were linked to the individual differences in FDI cognitive styles and emphasized the important contribution of superior local processing ability and cognitive inhibition to field-independent style. PMID:24348991

Segmental expression of Pax3/7 and engrailed homologs in tardigrade development.

PubMed

Gabriel, Willow N; Goldstein, Bob

2007-06-01

How morphological diversity arises through evolution of gene sequence is a major question in biology. In Drosophila, the genetic basis for body patterning and morphological segmentation has been studied intensively. It is clear that some of the genes in the Drosophila segmentation program are functioning similarly in certain other taxa, although many questions remain about when these gene functions arose and which taxa use these genes similarly to establish diverse body plans. Tardigrades are an outgroup to arthropods in the Ecdysozoa and, as such, can provide insight into how gene functions have evolved among the arthropods and their close relatives. We developed immunostaining methods for tardigrade embryos, and we used cross-reactive antibodies to investigate the expression of homologs of the pair-rule gene paired (Pax3/7) and the segment polarity gene engrailed in the tardigrade Hypsibius dujardini. We find that in H. dujardini embryos, Pax3/7 protein localizes not in a pair-rule pattern but in a segmentally iterated pattern, after the segments are established, in regions of the embryo where neurons later arise. Engrailed protein localizes in the posterior ectoderm of each segment before ectodermal segmentation is apparent. Together with previous results from others, our data support the conclusions that the pair-rule function of Pax3/7 is specific to the arthropods, that some of the ancient functions of Pax3/7 and Engrailed in ancestral bilaterians may have been in neurogenesis, and that Engrailed may have a function in establishing morphological boundaries between segments that is conserved at least among the Panarthropoda.

Functions of IQD proteins as hubs in cellular calcium and auxin signaling: A toolbox for shape formation and tissue-specification in plants?

PubMed

Bürstenbinder, Katharina; Mitra, Dipannita; Quegwer, Jakob

2017-06-03

Calcium (Ca 2+ ) ions play pivotal roles as second messengers in intracellular signal transduction, and coordinate many biological processes. Changes in intracellular Ca 2+ levels are perceived by Ca 2+ sensors such as calmodulin (CaM) and CaM-like (CML) proteins, which transduce Ca 2+ signals into cellular responses by regulation of diverse target proteins. Insights into molecular functions of CaM targets are thus essential to understand the molecular and cellular basis of Ca 2+ signaling. During the last decade, IQ67-domain (IQD) proteins emerged as the largest class of CaM targets in plants with mostly unknown functions. In the March issue of Plant Physiology, we presented the first comprehensive characterization of the 33-membered IQD family in Arabidopsis thaliana. We showed, by analysis of the subcellular localization of translational green fluorescent protein (GFP) fusion proteins, that most IQD members label microtubules (MTs), and additionally often localize to the cell nucleus or to membranes, where they recruit CaM Ca 2+ sensors. Important functions at MTs are supported by altered MT organization and plant growth in IQD gain-of-function lines. Because IQD proteins share structural hallmarks of scaffold proteins, we propose roles of IQDs in the assembly of macromolecular complexes to orchestrate Ca 2+ CaM signaling from membranes to the nucleus. Interestingly, expression of several IQDs is regulated by auxin, which suggests functions of IQDs as hubs in cellular auxin and calcium signaling to regulate plant growth and development.

Many-Body Theory of Pyrochlore Iridates and Related Materials

NASA Astrophysics Data System (ADS)

Wang, Runzhi

In this thesis we focus on two problems. First we propose a numerical method for generating optimized Wannier functions with desired properties. Second we perform the state of the art density functional plus dynamical mean-field calculations in pyrochlore iridates, to investigate the physics induced by the cooperation of spin-orbit coupling and electron correlation. We begin with the introduction for maximally localized Wannier functions and other related extensions. Then we describe the current research in the field of spin-orbit coupling and its interplay with correlation effects, followed by a brief introduction of the `hot' materials of iridates. Before the end of the introduction, we discuss the numerical methods employed in our work, including the density functional theory; dynamical mean-field theory and its combination with the exact diagonalization impurity solver. Then we propose our approach for constructing an optimized set of Wannier functions, which is a generalization of the functionality of the classic maximal localization method put forward by Marzari and Vanderbilt. Our work is motivated by the requirement of the effective description of the local subspace of the Hamiltonian by the beyond density functional theory methods. In extensions of density functional theory such as dynamical mean-field theory, one may want highly accurate description of particular local orbitals, including correct centers and symmetries; while the basis for the remaining degrees of freedom is unimportant. Therefore, we develop the selectively localized Wannier function approach which allows for a greater localization in the selected subset of Wannier functions and at the same time allows us to fix the centers and ensure the point symmetries. Applications in real materials are presented to demonstrate the power of our approach. Next we move to the investigation of pyrochlore iridates, focussing on the metal-insulator transition and material dependence in these compounds. We perform combined density functional plus dynamical mean-field calculations in Lu2Ir2O7, Y2Ir2O 7, Eu2Ir2O7, with spin-orbit coupling included and both single-site and cluster approximations appiled. A broad range of Weyl metal is predicted as the intervening phase in the metal-insulator transition. By comparing to experiments, we find that the single-site approximation fails to predict the gap values and substantial difference between the Y and Eu-compound, demonstrating the inadequacy of this approximation and indicating the key role played by the intersite effects. Finally, we provide a more accurate description of the vicinity of the metal-insulator and topological transitions implied by density functional plus cluster dynamical mean-field calculations of pyrochlore iridates. We find definitive evidence of the Weyl semimetal phase, the electronic structure of which can be approximately described as ``Weyl rings" with an extremely flat dispersion of one of the Weyl bands. This Weyl semimetal phase is further investigated by the k • p analysis fitting to the numerical results. We find that this unusual structure leads to interesting behavior in the optical conductivity including a Hall effect in the interband component, and to an enhanced susceptibility.

Blind restoration of retinal images degraded by space-variant blur with adaptive blur estimation

NASA Astrophysics Data System (ADS)

Marrugo, Andrés. G.; Millán, María. S.; Å orel, Michal; Å roubek, Filip

2013-11-01

Retinal images are often degraded with a blur that varies across the field view. Because traditional deblurring algorithms assume the blur to be space-invariant they typically fail in the presence of space-variant blur. In this work we consider the blur to be both unknown and space-variant. To carry out the restoration, we assume that in small regions the space-variant blur can be approximated by a space-invariant point-spread function (PSF). However, instead of deblurring the image on a per-patch basis, we extend individual PSFs by linear interpolation and perform a global restoration. Because the blind estimation of local PSFs may fail we propose a strategy for the identification of valid local PSFs and perform interpolation to obtain the space-variant PSF. The method was tested on artificial and real degraded retinal images. Results show significant improvement in the visibility of subtle details like small blood vessels.

Toward a transnational history of the social sciences.

PubMed

Heilbron, Johan; Guilhot, Nicolas; Jeanpierre, Laurent

2008-01-01

Historical accounts of the social sciences have too often accepted local or national institutions as a self-evident framework of analysis, instead of considering them as being embedded in transnational relations of various kinds. Evolving patterns of transnational mobility and exchange cut through the neat distinction between the local, the national, and the inter-national, and thus represent an essential component in the dynamics of the social sciences, as well as a fruitful perspective for rethinking their historical development. In this programmatic outline, it is argued that a transnational history of the social sciences may be fruitfully understood on the basis of three general mechanisms, which have structured the transnational flows of people and ideas in decisive ways: (a) the functioning of international scholarly institutions, (b) the transnational mobility of scholars, and (c) the politics of trans-national exchange of nonacademic institutions. The article subsequently examines and illustrates each of these mechanisms.

Temperature and composition dependence of short-range order and entropy, and statistics of bond length: the semiconductor alloy (GaN)(1-x)(ZnO)(x).

PubMed

Liu, Jian; Pedroza, Luana S; Misch, Carissa; Fernández-Serra, Maria V; Allen, Philip B

2014-07-09

We present total energy and force calculations for the (GaN)1-x(ZnO)x alloy. Site-occupancy configurations are generated from Monte Carlo (MC) simulations, on the basis of a cluster expansion model proposed in a previous study. Local atomic coordinate relaxations of surprisingly large magnitude are found via density-functional calculations using a 432-atom periodic supercell, for three representative configurations at x = 0.5. These are used to generate bond-length distributions. The configurationally averaged composition- and temperature-dependent short-range order (SRO) parameters of the alloys are discussed. The entropy is approximated in terms of pair distribution statistics and thus related to SRO parameters. This approximate entropy is compared with accurate numerical values from MC simulations. An empirical model for the dependence of the bond length on the local chemical environments is proposed.

Optimal charge control strategies for stationary photovoltaic battery systems

NASA Astrophysics Data System (ADS)

Li, Jiahao; Danzer, Michael A.

2014-07-01

Battery systems coupled to photovoltaic (PV) modules for example fulfill one major function: they locally decouple PV generation and consumption of electrical power leading to two major effects. First, they reduce the grid load, especially at peak times and therewith reduce the necessity of a network expansion. And second, they increase the self-consumption in households and therewith help to reduce energy expenses. For the management of PV batteries charge control strategies need to be developed to reach the goals of both the distribution system operators and the local power producer. In this work optimal control strategies regarding various optimization goals are developed on the basis of the predicted household loads and PV generation profiles using the method of dynamic programming. The resulting charge curves are compared and essential differences discussed. Finally, a multi-objective optimization shows that charge control strategies can be derived that take all optimization goals into account.

Incorporating evolutionary processes into population viability models.

PubMed

Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

2015-06-01

We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence. © 2014 Society for Conservation Biology.

The lowest-order weak Galerkin finite element method for the Darcy equation on quadrilateral and hybrid meshes

NASA Astrophysics Data System (ADS)

Liu, Jiangguo; Tavener, Simon; Wang, Zhuoran

2018-04-01

This paper investigates the lowest-order weak Galerkin finite element method for solving the Darcy equation on quadrilateral and hybrid meshes consisting of quadrilaterals and triangles. In this approach, the pressure is approximated by constants in element interiors and on edges. The discrete weak gradients of these constant basis functions are specified in local Raviart-Thomas spaces, specifically RT0 for triangles and unmapped RT[0] for quadrilaterals. These discrete weak gradients are used to approximate the classical gradient when solving the Darcy equation. The method produces continuous normal fluxes and is locally mass-conservative, regardless of mesh quality, and has optimal order convergence in pressure, velocity, and normal flux, when the quadrilaterals are asymptotically parallelograms. Implementation is straightforward and results in symmetric positive-definite discrete linear systems. We present numerical experiments and comparisons with other existing methods.

Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

NASA Astrophysics Data System (ADS)

Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

2015-03-01

Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

Evaluating excited state atomic polarizabilities of chromophores† †Electronic supplementary information (ESI) available: Basis set dependence, definition of bond charges, Romberg differentiation, python script to calculate atomic polarizabilities, influence of the cavity radius, atomic polarizabilities of coumarin 153, all tables in atomic units. See DOI: 10.1039/c7cp08549d

PubMed Central

Heid, Esther

2018-01-01

Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomic charge transfer and polarizability terms, and variation in the presence of an electric field has been used to evaluate atomic polarizabilities. On excitation, MQ undergoes very site-specific changes in polarizability while C153 shows significantly less variation. We also conclude that MQ cannot be adequately described by standard atomic polarizabilities based on atomic number and hybridization state. Changes in the molecular polarizability of MQ (on excitation) are not representative of the local site-specific changes in atomic polarizability, thus the overall molecular polarizability ratio does not provide a good approximation for local atom-specific polarizability changes on excitation. Accurate excited state force fields are needed for computer simulation of solvation dynamics. The chromophores considered in this study are often used as molecular probes. The methods and data reported here can be used for the construction of polarizable ground and excited state force fields. Atomic and molecular polarizabilities (ground and excited states) have been evaluated over a range of functionals and basis sets. Different mechanisms for including solvation effects have been examined; using a polarizable continuum model, explicit solvation and via sampling of clusters extracted from a MD simulation. A range of different solvents have also been considered. PMID:29542743

DIY EOS: Experimentally Validated Equations of State for Planetary Fluids to GPa Pressures, Tools for Understanding Planetary Processes and Habitability

NASA Astrophysics Data System (ADS)

Vance, Steven; Brown, J. Michael; Bollengier, Olivier

2016-10-01

Sound speeds are fundamental to seismology, and provide a path allowing the accurate determination of thermodynamic potentials. Prior equations of state (EOS) for pure ammonia (Harr and Gallagher 1978, Tillner-Roth et al. 1993) are based primarily on measured densities and heat capacities. Sound speeds, not included in the fitting, are poorly predicted.We couple recent high pressure sound speed data with prior densities and heat capacities to generate a new equation of state. Our representation fits both the earlier lower pressure work as well as measured sound speeds to 4 GPa and 700 K and the Hugoniot to 70 GPa and 6000 K.In contrast to the damped polynomial representation previously used, our equation of state is based on local basis functions in the form of tensor b-splines. Regularization allows the thermodynamic surface to be continued into regimes poorly sampled by experiments. We discuss application of this framework for aqueous equations of state validated by experimental measurements. Preliminary equations of state have been prepared applying the local basis function methodology to aqueous NH3, Mg2SO4, NaCl, and Na2SO4. We describe its use for developing new equations of state, and provide some applications of the new thermodynamic data to the interior structures of gas giant planets and ocean worlds.References:L. Haar and J. S. Gallagher. Thermodynamic properties of ammonia. American Chemical Society and the American Institute of Physics for the National Bureau of Standards, 1978.R. Tillner-Roth, F. Harms-Watzenberg, and H. Baehr. Eine neue fundamentalgleichung fuer ammoniak. DKV TAGUNGSBERICHT, 20:67-67, 1993.

Identification of Contractile Vacuole Proteins in Trypanosoma cruzi

PubMed Central

Park, Miyoung; Martins, Vicente P.; Atwood, James; Moles, Kristen; Collins, Dalis; Rohloff, Peter; Tarleton, Rick; Moreno, Silvia N. J.; Orlando, Ron; Docampo, Roberto

2011-01-01

Contractile vacuole complexes are critical components of cell volume regulation and have been shown to have other functional roles in several free-living protists. However, very little is known about the functions of the contractile vacuole complex of the parasite Trypanosoma cruzi, the etiologic agent of Chagas disease, other than a role in osmoregulation. Identification of the protein composition of these organelles is important for understanding their physiological roles. We applied a combined proteomic and bioinfomatic approach to identify proteins localized to the contractile vacuole. Proteomic analysis of a T. cruzi fraction enriched for contractile vacuoles and analyzed by one-dimensional gel electrophoresis and LC-MS/MS resulted in the addition of 109 newly detected proteins to the group of expressed proteins of epimastigotes. We also identified different peptides that map to at least 39 members of the dispersed gene family 1 (DGF-1) providing evidence that many members of this family are simultaneously expressed in epimastigotes. Of the proteins present in the fraction we selected several homologues with known localizations in contractile vacuoles of other organisms and others that we expected to be present in these vacuoles on the basis of their potential roles. We determined the localization of each by expression as GFP-fusion proteins or with specific antibodies. Six of these putative proteins (Rab11, Rab32, AP180, ATPase subunit B, VAMP1, and phosphate transporter) predominantly localized to the vacuole bladder. TcSNARE2.1, TcSNARE2.2, and calmodulin localized to the spongiome. Calmodulin was also cytosolic. Our results demonstrate the utility of combining subcellular fractionation, proteomic analysis, and bioinformatic approaches for localization of organellar proteins that are difficult to detect with whole cell methodologies. The CV localization of the proteins investigated revealed potential novel roles of these organelles in phosphate metabolism and provided information on the potential participation of adaptor protein complexes in their biogenesis. PMID:21437209

Rational Density Functional Selection Using Game Theory.

PubMed

McAnanama-Brereton, Suzanne; Waller, Mark P

2018-01-22

Theoretical chemistry has a paradox of choice due to the availability of a myriad of density functionals and basis sets. Traditionally, a particular density functional is chosen on the basis of the level of user expertise (i.e., subjective experiences). Herein we circumvent the user-centric selection procedure by describing a novel approach for objectively selecting a particular functional for a given application. We achieve this by employing game theory to identify optimal functional/basis set combinations. A three-player (accuracy, complexity, and similarity) game is devised, through which Nash equilibrium solutions can be obtained. This approach has the advantage that results can be systematically improved by enlarging the underlying knowledge base, and the deterministic selection procedure mathematically justifies the density functional and basis set selections.

Traditional foods and food systems: a revision of concepts emerging from qualitative surveys on-site in the Black Sea area and Italy.

PubMed

D'Antuono, L Filippo

2013-11-01

The European FP7 BaSeFood project included a traditional food study contextually analysing their function in local food systems to stimulate consumers' awareness and indicate co-existence options for different scale exploitation. Background concepts were (1) the available traditional foods definitions; (2) the theoretical background of food quality perceptions; and (3) the different levels of food functions. Field investigations were carried out by face-to-face in-depth qualitative interviews with local stakeholders, in the Black Sea region and Italy, on all aspects of traditional food production chains: raw materials, products, processes and perceptions. Critical and intercultural comparisons represented the basis of data analysis. Eight hundred and thirty-nine foods were documented. The direct experience perception of traditional food value observed in local contexts is somewhat contrasting with the present European tendency to communicate traditional food nature through registration or proprietary standards. Traditional foods are generally a combination of energetic staples with other available ingredients; their intrinsic variability makes the definition of 'standard' recipes little more than an artefact of convenience; cross-country variations are determined by available ingredients, social conditions and nutritional needs. Commercial production requires some degree of raw material and process standardisation. New technologies and rules may stimulate traditional food evolution, but may also represent a barrier for local stakeholders. A trend to work within supply chains by local stakeholders was detected. Specific health promoting values were rarely perceived as a fundamental character. The stable inclusion of traditional food systems in present food supply chains requires a recovery of consumers' awareness of traditional food quality appreciation. © 2013 Society of Chemical Industry.

Basis sets for the calculation of core-electron binding energies

NASA Astrophysics Data System (ADS)

Hanson-Heine, Magnus W. D.; George, Michael W.; Besley, Nicholas A.

2018-05-01

Core-electron binding energies (CEBEs) computed within a Δ self-consistent field approach require large basis sets to achieve convergence with respect to the basis set limit. It is shown that supplementing a basis set with basis functions from the corresponding basis set for the element with the next highest nuclear charge (Z + 1) provides basis sets that give CEBEs close to the basis set limit. This simple procedure provides relatively small basis sets that are well suited for calculations where the description of a core-ionised state is important, such as time-dependent density functional theory calculations of X-ray emission spectroscopy.

X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

PubMed

Genoni, Alessandro

2013-07-09

Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

SubCellProt: predicting protein subcellular localization using machine learning approaches.

PubMed

Garg, Prabha; Sharma, Virag; Chaudhari, Pradeep; Roy, Nilanjan

2009-01-01

High-throughput genome sequencing projects continue to churn out enormous amounts of raw sequence data. However, most of this raw sequence data is unannotated and, hence, not very useful. Among the various approaches to decipher the function of a protein, one is to determine its localization. Experimental approaches for proteome annotation including determination of a protein's subcellular localizations are very costly and labor intensive. Besides the available experimental methods, in silico methods present alternative approaches to accomplish this task. Here, we present two machine learning approaches for prediction of the subcellular localization of a protein from the primary sequence information. Two machine learning algorithms, k Nearest Neighbor (k-NN) and Probabilistic Neural Network (PNN) were used to classify an unknown protein into one of the 11 subcellular localizations. The final prediction is made on the basis of a consensus of the predictions made by two algorithms and a probability is assigned to it. The results indicate that the primary sequence derived features like amino acid composition, sequence order and physicochemical properties can be used to assign subcellular localization with a fair degree of accuracy. Moreover, with the enhanced accuracy of our approach and the definition of a prediction domain, this method can be used for proteome annotation in a high throughput manner. SubCellProt is available at www.databases.niper.ac.in/SubCellProt.

First cloning and characterization of two functional aquaporin genes from an arbuscular mycorrhizal fungus Glomus intraradices.

PubMed

Li, Tao; Hu, Ya-Jun; Hao, Zhi-Peng; Li, Hong; Wang, You-Shan; Chen, Bao-Dong

2013-01-01

Arbuscular mycorrhizal (AM) symbiosis is known to stimulate plant drought tolerance. However, the molecular basis for the direct involvement of AM fungi (AMF) in plant water relations has not been established. Two full-length aquaporin genes, namely GintAQPF1 and GintAQPF2, were cloned by rapid amplification of cDNA 5'- and 3'-ends from an AMF, Glomus intraradices. Aquaporin localization, activities and water permeability were examined by heterologous expression in yeast. Gene expression during symbiosis was also analyzed by quantitative real-time polymerase chain reaction. GintAQPF1 was localized to the plasma membrane of yeast, whereas GintAQPF2 was localized to both plasma and intracellular membranes. Transformed yeast cells exhibited a significant decrease in cell volume on hyperosmotic shock and faster protoplast bursting on hypo-osmotic shock. Polyethylene glycol (PEG) stimulated, but glycerol inhibited, the aquaporin activities. Furthermore, the expression of the two genes in arbuscule-enriched cortical cells and extraradical mycelia of maize roots was also enhanced significantly under drought stress. GintAQPF1 and GintAQPF2 are the first two functional aquaporin genes from AMF reported to date. Our data strongly support potential water transport via AMF to host plants, which leads to a better understanding of the important role of AMF in plant drought tolerance. © 2012 Research Centre for Eco-Environmental Sciences, CAS New Phytologist © 2012 New Phytologist Trust.

Assessment of conformational, spectral, antimicrobial activity, chemical reactivity and NLO application of Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone).

PubMed

Rawat, Poonam; Singh, R N

2015-04-05

An orange colored pyrrole dihydrazone: Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone) (PDBO) has been synthesized by reaction of oxalic acid dihydrazide with 2,5 diformyl-1H-pyrrole and has been characterized by spectroscopic analysis (1H, 13C NMR, UV-visible, FT-IR and DART Mass). The properties of the compound has been evaluated using B3LYP functional and 6-31G(d,p)/6-311+G(d,p) basis set. The symmetric (3319, 3320 cm(-1)) and asymmetric (3389, 3382 cm(-1)) stretching wave number confirm free NH2 groups in PDBO. NBO analysis shows, inter/intra molecular interactions within the molecule. Topological parameters have been analyzed by QTAIM theory and provide the existence of intramolecular hydrogen bonding (N-H⋯O). The local reactivity descriptors analyses determine the reactive sites within molecule. The calculated first hyperpolarizability value (β0=23.83×10(-30) esu) of pyrrole dihydrazone shows its suitability for non-linear optical (NLO) response. The preliminary bioassay suggested that the PDBO exhibits relatively good antibacterial and fungicidal activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Candida albicans, Aspergillus niger. The local reactivity descriptors--Fukui functions (fk+, fk-), local softnesses (sk+, sk-) and electrophilicity indices (ωk+, ωk-) analyses have been used to determine the reactive sites within molecule. Copyright © 2014 Elsevier B.V. All rights reserved.

Assessment of conformational, spectral, antimicrobial activity, chemical reactivity and NLO application of Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone)

NASA Astrophysics Data System (ADS)

Rawat, Poonam; Singh, R. N.

2015-04-01

An orange colored pyrrole dihydrazone: Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone) (PDBO) has been synthesized by reaction of oxalic acid dihydrazide with 2,5 diformyl-1H-pyrrole and has been characterized by spectroscopic analysis (1H, 13C NMR, UV-visible, FT-IR and DART Mass). The properties of the compound has been evaluated using B3LYP functional and 6-31G(d,p)/6-311+G(d,p) basis set. The symmetric (3319, 3320 cm-1) and asymmetric (3389, 3382 cm-1) stretching wave number confirm free NH2 groups in PDBO. NBO analysis shows, inter/intra molecular interactions within the molecule. Topological parameters have been analyzed by QTAIM theory and provide the existence of intramolecular hydrogen bonding (N-H⋯O). The local reactivity descriptors analyses determine the reactive sites within molecule. The calculated first hyperpolarizability value (β0 = 23.83 × 10-30 esu) of pyrrole dihydrazone shows its suitability for non-linear optical (NLO) response. The preliminary bioassay suggested that the PDBO exhibits relatively good antibacterial and fungicidal activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Candida albicans, Aspergillus niger. The local reactivity descriptors - Fukui functions (fk+, fk-), local softnesses (sk+, sk-) and electrophilicity indices (ωk+, ωk-) analyses have been used to determine the reactive sites within molecule.

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shimojo, Fuyuki; Hattori, Shinnosuke; Department of Physics, Kumamoto University, Kumamoto 860-8555

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at themore » peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.« less

Axially deformed solution of the Skyrme-Hartree-Fock-Bogolyubov equations using the transformed harmonic oscillator basis (III) HFBTHO (v3.00): A new version of the program

NASA Astrophysics Data System (ADS)

Perez, R. Navarro; Schunck, N.; Lasseri, R.-D.; Zhang, C.; Sarich, J.

2017-11-01

We describe the new version 3.00 of the code HFBTHO that solves the nuclear Hartree-Fock (HF) or Hartree-Fock-Bogolyubov (HFB) problem by using the cylindrical transformed deformed harmonic oscillator basis. In the new version, we have implemented the following features: (i) the full Gogny force in both particle-hole and particle-particle channels, (ii) the calculation of the nuclear collective inertia at the perturbative cranking approximation, (iii) the calculation of fission fragment charge, mass and deformations based on the determination of the neck, (iv) the regularization of zero-range pairing forces, (v) the calculation of localization functions, (vi) a MPI interface for large-scale mass table calculations. Program Files doi:http://dx.doi.org/10.17632/c5g2f92by3.1 Licensing provisions: GPL v3 Programming language: FORTRAN-95 Journal reference of previous version: M.V. Stoitsov, N. Schunck, M. Kortelainen, N. Michel, H. Nam, E. Olsen, J. Sarich, and S. Wild, Comput. Phys. Commun. 184 (2013). Does the new version supersede the previous one: Yes Summary of revisions: 1. the Gogny force in both particle-hole and particle-particle channels was implemented; 2. the nuclear collective inertia at the perturbative cranking approximation was implemented; 3. fission fragment charge, mass and deformations were implemented based on the determination of the position of the neck between nascent fragments; 4. the regularization method of zero-range pairing forces was implemented; 5. the localization functions of the HFB solution were implemented; 6. a MPI interface for large-scale mass table calculations was implemented. Nature of problem:HFBTHO is a physics computer code that is used to model the structure of the nucleus. It is an implementation of the energy density functional (EDF) approach to atomic nuclei, where the energy of the nucleus is obtained by integration over space of some phenomenological energy density, which is itself a functional of the neutron and proton intrinsic densities. In the present version of HFBTHO, the energy density derives either from the zero-range Skyrme or the finite-range Gogny effective two-body interaction between nucleons. Nuclear super-fluidity is treated at the Hartree-Fock-Bogolyubov (HFB) approximation. Constraints on the nuclear shape allows probing the potential energy surface of the nucleus as needed e.g., for the description of shape isomers or fission. The implementation of a local scale transformation of the single-particle basis in which the HFB solutions are expanded provide a tool to properly compute the structure of weakly-bound nuclei. Solution method: The program uses the axial Transformed Harmonic Oscillator (THO) single-particle basis to expand quasiparticle wave functions. It iteratively diagonalizes the Hartree-Fock-Bogolyubov Hamiltonian based on generalized Skyrme-like energy densities and zero-range pairing interactions or the finite-range Gogny force until a self-consistent solution is found. A previous version of the program was presented in M.V. Stoitsov, N. Schunck, M. Kortelainen, N. Michel, H. Nam, E. Olsen, J. Sarich, and S. Wild, Comput. Phys. Commun. 184 (2013) 1592-1604 with much of the formalism presented in the original paper M.V. Stoitsov, J. Dobaczewski, W. Nazarewicz, P. Ring, Comput. Phys. Commun. 167 (2005) 43-63. Additional comments: The user must have access to (i) the LAPACK subroutines DSYEEVR, DSYEVD, DSYTRF and DSYTRI, and their dependencies, which compute eigenvalues and eigenfunctions of real symmetric matrices, (ii) the LAPACK subroutines DGETRI and DGETRF, which invert arbitrary real matrices, and (iii) the BLAS routines DCOPY, DSCAL, DGEMM and DGEMV for double-precision linear algebra (or provide another set of subroutines that can perform such tasks). The BLAS and LAPACK subroutines can be obtained from the Netlib Repository at the University of Tennessee, Knoxville: http://netlib2.cs.utk.edu/.

On the representation of cells in bone marrow pathology by a scalar field: propagation through serial sections, co-localization and spatial interaction analysis.

PubMed

Weis, Cleo-Aron; Grießmann, Benedict Walter; Scharff, Christoph; Detzner, Caecilia; Pfister, Eva; Marx, Alexander; Zoellner, Frank Gerrit

2015-09-02

Immunohistochemical analysis of cellular interactions in the bone marrow in situ is demanding, due to its heterogeneous cellular composition, the poor delineation and overlap of functional compartments and highly complex immunophenotypes of several cell populations (e.g. regulatory T-cells) that require immunohistochemical marker sets for unambiguous characterization. To overcome these difficulties, we herein present an approach to describe objects (e.g. cells, bone trabeculae) by a scalar field that can be propagated through registered images of serial histological sections. The transformation of objects within images (e.g. cells) to a scalar field was performed by convolution of the object's centroids with differently formed radial basis function (e.g. for direct or indirect spatial interaction). On the basis of such a scalar field, a summation field described distributed objects within an image. After image registration i) colocalization analysis could be performed on basis scalar field, which is propagated through registered images, and - due to the shape of the field - were barely prone to matching errors and morphological changes by different cutting levels; ii) furthermore, depending on the field shape the colocalization measurements could also quantify spatial interaction (e.g. direct or paracrine cellular contact); ii) the field-overlap, which represents the spatial distance, of different objects (e.g. two cells) could be calculated by the histogram intersection. The description of objects (e.g. cells, cell clusters, bone trabeculae etc.) as a field offers several possibilities: First, co-localization of different markers (e.g. by immunohistochemical staining) in serial sections can be performed in an automatic, objective and quantifiable way. In contrast to multicolour staining (e.g. 10-colour immunofluorescence) the financial and technical requirements are fairly minor. Second, the approach allows searching for different types of spatial interactions (e.g. direct and indirect cellular interaction) between objects by taking field shape into account (e.g. thin vs. broad). Third, by describing spatially distributed groups of objects as summation field, it gives cluster definition that relies rather on the bare object distance than on the modelled spatial cellular interaction.

Polarization functions for the modified m6-31G basis sets for atoms Ga through Kr.

PubMed

Mitin, Alexander V

2013-09-05

The 2df polarization functions for the modified m6-31G basis sets of the third-row atoms Ga through Kr (Int J Quantum Chem, 2007, 107, 3028; Int J. Quantum Chem, 2009, 109, 1158) are proposed. The performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets were examined in molecular calculations carried out by the density functional theory (DFT) method with B3LYP hybrid functional, Møller-Plesset perturbation theory of the second order (MP2), quadratic configuration interaction method with single and double substitutions and were compared with those for the known 6-31G basis sets as well as with the other similar 641 and 6-311G basis sets with and without polarization functions. Obtained results have shown that the performances of the m6-31G, m6-31G(d,p), and m6-31G(2df,p) basis sets are better in comparison with the performances of the known 6-31G, 6-31G(d,p) and 6-31G(2df,p) basis sets. These improvements are mainly reached due to better approximations of different electrons belonging to the different atomic shells in the modified basis sets. Applicability of the modified basis sets in thermochemical calculations is also discussed. © 2013 Wiley Periodicals, Inc.

45 CFR 86.35 - Access to schools operated by L.E.A.s.

Code of Federal Regulations, 2012 CFR

2012-10-01

... NONDISCRIMINATION ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 86.35 Access to schools operated by L.E.A.s. A recipient which is a local educational agency shall not, on the basis of sex...

45 CFR 86.35 - Access to schools operated by L.E.A.s.

Code of Federal Regulations, 2010 CFR

2010-10-01

... NONDISCRIMINATION ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 86.35 Access to schools operated by L.E.A.s. A recipient which is a local educational agency shall not, on the basis of sex...

Excited State Charge Transfer reaction with dual emission from 5-(4-dimethylamino-phenyl)-penta-2,4-dienenitrile: Spectral measurement and theoretical density functional theory calculation

NASA Astrophysics Data System (ADS)

Jana, Sankar; Dalapati, Sasanka; Ghosh, Shalini; Kar, Samiran; Guchhait, Nikhil

2011-07-01

The excited state intramolecular charge transfer process in donor-chromophore-acceptor system 5-(4-dimethylamino-phenyl)-penta-2,4-dienenitrile (DMAPPDN) has been investigated by steady state absorption and emission spectroscopy in combination with Density Functional Theory (DFT) calculations. This flexible donor acceptor molecule DMAPPDN shows dual fluorescence corresponding to emission from locally excited and charge transfer state in polar solvent. Large solvatochromic emission shift, effect of variation of pH and HOMO-LUMO molecular orbital pictures support excited state intramolecular charge transfer process. The experimental findings have been correlated with the calculated structure and potential energy surfaces based on the Twisted Intramolecular Charge Transfer (TICT) model obtained at DFT level using B3LYP functional and 6-31+G( d, p) basis set. The theoretical potential energy surfaces for the excited states have been generated in vacuo and acetonitrile solvent using Time Dependent Density Functional Theory (TDDFT) and Time Dependent Density Functional Theory Polarized Continuum Model (TDDFT-PCM) method, respectively. All the theoretical results show well agreement with the experimental observations.

Basis Selection for Wavelet Regression

NASA Technical Reports Server (NTRS)

Wheeler, Kevin R.; Lau, Sonie (Technical Monitor)

1998-01-01

A wavelet basis selection procedure is presented for wavelet regression. Both the basis and the threshold are selected using cross-validation. The method includes the capability of incorporating prior knowledge on the smoothness (or shape of the basis functions) into the basis selection procedure. The results of the method are demonstrated on sampled functions widely used in the wavelet regression literature. The results of the method are contrasted with other published methods.

Fast localized orthonormal virtual orbitals which depend smoothly on nuclear coordinates.

PubMed

Subotnik, Joseph E; Dutoi, Anthony D; Head-Gordon, Martin

2005-09-15

We present here an algorithm for computing stable, well-defined localized orthonormal virtual orbitals which depend smoothly on nuclear coordinates. The algorithm is very fast, limited only by diagonalization of two matrices with dimension the size of the number of virtual orbitals. Furthermore, we require no more than quadratic (in the number of electrons) storage. The basic premise behind our algorithm is that one can decompose any given atomic-orbital (AO) vector space as a minimal basis space (which includes the occupied and valence virtual spaces) and a hard-virtual (HV) space (which includes everything else). The valence virtual space localizes easily with standard methods, while the hard-virtual space is constructed to be atom centered and automatically local. The orbitals presented here may be computed almost as quickly as projecting the AO basis onto the virtual space and are almost as local (according to orbital variance), while our orbitals are orthonormal (rather than redundant and nonorthogonal). We expect this algorithm to find use in local-correlation methods.

Theoretical Investigation Leading to Energy Storage in Atomic and Molecular Systems

DTIC Science & Technology

1990-12-01

can be calculated in a single run. 21 j) Non-gradient optimization of basis function exponents is possible. The source code can be modified to carry...basis. The 10s3p/5s3p basis consists of the 9s/4s contraction of Siegbahn and Liu (Reference 91) augmented by a diffuse s-type function ( exponent ...vibrational modes. Introduction of diffuse basis functions and optimization of the d-orbital exponents have a small but important effect on the

On the possibility of control restoration in some inverse problems of heat and mass transfer

NASA Astrophysics Data System (ADS)

Bilchenko, G. G.; Bilchenko, N. G.

2016-11-01

The hypersonic aircraft permeable surfaces effective heat protection problems are considered. The physic-chemical processes (the dissociation and the ionization) in laminar boundary layer of compressible gas are appreciated in mathematical model. The statements of direct problems of heat and mass transfer are given: according to preset given controls it is necessary to compute the boundary layer mathematical model parameters and determinate the local and total heat flows and friction forces and the power of blowing system. The A.A.Dorodnicyn's generalized integral relations method has been used as calculation basis. The optimal control - the blowing into boundary layer (for continuous functions) was constructed as the solution of direct problem in extreme statement with the use of this approach. The statement of inverse problems are given: the control laws ensuring the preset given local heat flow and local tangent friction are restored. The differences between the interpolation and the approximation statements are discussed. The possibility of unique control restoration is established and proved (in the stagnation point). The computational experiments results are presented.

FACTORS AFFECTING INFECTION OR REINFECTION WITH SCHISTOSOMA HAEMATOBIUM IN COASTAL KENYA: SURVIVAL ANALYSIS DURING A NINE-YEAR, SCHOOL-BASED TREATMENT PROGRAM

PubMed Central

SATAYATHUM, SUDTIDA A.; MUCHIRI, ERIC M.; OUMA, JOHN H.; WHALEN, CHRISTOPHER C.; KING, CHARLES H.

2010-01-01

Urinary schistosomiasis remains a significant burden for Africa and the Middle East. Success of regional control strategies will depend, in part, on what influence local environmental and behavioral factors have on individual risk for primary infection and/or reinfection. Based on experience in a multi-year (1984–1992), school-based Schistosoma haematobium control program in Coast Province, Kenya, we examined risk for infection outcomes as a function of age, sex, pretreatment morbidity, treatment regimen, water contact, and residence location, with the use of life tables and Cox proportional-hazards analysis. After adjustment, location of residence, age less than 12 years, pretreatment hematuria, and incomplete treatment were the significant independent predictors of infection, whereas sex and frequency of water contact were not. We conclude that local physical features and age-related factors play a predominant role in S. haematobium transmission in this setting. In large population-based control programs, treatment allocation strategies may need to be tailored to local conditions on a village-by-village basis. PMID:16837713

Pure state consciousness and its local reduction to neuronal space

NASA Astrophysics Data System (ADS)

Duggins, A. J.

2013-01-01

The single neuronal state can be represented as a vector in a complex space, spanned by an orthonormal basis of integer spike counts. In this model a scalar element of experience is associated with the instantaneous firing rate of a single sensory neuron over repeated stimulus presentations. Here the model is extended to composite neural systems that are tensor products of single neuronal vector spaces. Depiction of the mental state as a vector on this tensor product space is intended to capture the unity of consciousness. The density operator is introduced as its local reduction to the single neuron level, from which the firing rate can again be derived as the objective correlate of a subjective element. However, the relational structure of perceptual experience only emerges when the non-local mental state is considered. A metric of phenomenal proximity between neuronal elements of experience is proposed, based on the cross-correlation function of neurophysiology, but constrained by the association of theoretical extremes of correlation/anticorrelation in inseparable 2-neuron states with identical and opponent elements respectively.

A multi-agent quantum Monte Carlo model for charge transport: Application to organic field-effect transistors

NASA Astrophysics Data System (ADS)

Bauer, Thilo; Jäger, Christof M.; Jordan, Meredith J. T.; Clark, Timothy

2015-07-01

We have developed a multi-agent quantum Monte Carlo model to describe the spatial dynamics of multiple majority charge carriers during conduction of electric current in the channel of organic field-effect transistors. The charge carriers are treated by a neglect of diatomic differential overlap Hamiltonian using a lattice of hydrogen-like basis functions. The local ionization energy and local electron affinity defined previously map the bulk structure of the transistor channel to external potentials for the simulations of electron- and hole-conduction, respectively. The model is designed without a specific charge-transport mechanism like hopping- or band-transport in mind and does not arbitrarily localize charge. An electrode model allows dynamic injection and depletion of charge carriers according to source-drain voltage. The field-effect is modeled by using the source-gate voltage in a Metropolis-like acceptance criterion. Although the current cannot be calculated because the simulations have no time axis, using the number of Monte Carlo moves as pseudo-time gives results that resemble experimental I/V curves.

Reactivity of hemodynamic responses and functional connectivity to different states of alpha synchrony: a concurrent EEG-fMRI study.

PubMed

Wu, Lei; Eichele, Tom; Calhoun, Vince D

2010-10-01

Concurrent EEG-fMRI studies have provided increasing details of the dynamics of intrinsic brain activity during the resting state. Here, we investigate a prominent effect in EEG during relaxed resting, i.e. the increase of the alpha power when the eyes are closed compared to when the eyes are open. This phenomenon is related to changes in thalamo-cortical and cortico-cortical synchronization. In order to investigate possible changes to EEG-fMRI coupling and fMRI functional connectivity during the two states we adopted a data-driven approach that fuses the multimodal data on the basis of parallel ICA decompositions of the fMRI data in the spatial domain and of the EEG data in the spectral domain. The power variation of a posterior alpha component was used as a reference function to deconvolve the hemodynamic responses from occipital, frontal, temporal, and subcortical fMRI components. Additionally, we computed the functional connectivity between these components. The results showed widespread alpha hemodynamic responses and high functional connectivity during eyes-closed (EC) rest, while eyes open (EO) resting abolished many of the hemodynamic responses and markedly decreased functional connectivity. These data suggest that generation of local hemodynamic responses is highly sensitive to state changes that do not involve changes of mental effort or awareness. They also indicate the localized power differences in posterior alpha between EO and EC in resting state data are accompanied by spatially widespread amplitude changes in hemodynamic responses and inter-regional functional connectivity, i.e. low frequency hemodynamic signals display an equivalent of alpha reactivity. Copyright 2010 Elsevier Inc. All rights reserved.

Quasi Sturmian basis for the two-electon continuum

NASA Astrophysics Data System (ADS)

Zaytsev, A. S.; Ancarani, L. U.; Zaytsev, S. A.

2016-02-01

A new type of basis functions is proposed to describe a two-electron continuum which arises as a final state in electron-impact ionization and double photoionization of atomic systems. We name these functions, which are calculated in terms of the recently introduced quasi Sturmian functions, Convoluted Quasi Sturmian functions (CQS); by construction, they look asymptotically like a six-dimensional spherical wave. The driven equation describing an ( e, 3 e) process on helium in the framework of the Temkin-Poet model is solved numerically in the entire space (rather than in a finite region of space) using expansions on CQS basis functions. We show that quite rapid convergence of the solution expansion can be achieved by multiplying the basis functions by the logarithmic phase factor corresponding to the Coulomb electron-electron interaction.

Structured penalties for functional linear models-partially empirical eigenvectors for regression.

PubMed

Randolph, Timothy W; Harezlak, Jaroslaw; Feng, Ziding

2012-01-01

One of the challenges with functional data is incorporating geometric structure, or local correlation, into the analysis. This structure is inherent in the output from an increasing number of biomedical technologies, and a functional linear model is often used to estimate the relationship between the predictor functions and scalar responses. Common approaches to the problem of estimating a coefficient function typically involve two stages: regularization and estimation. Regularization is usually done via dimension reduction, projecting onto a predefined span of basis functions or a reduced set of eigenvectors (principal components). In contrast, we present a unified approach that directly incorporates geometric structure into the estimation process by exploiting the joint eigenproperties of the predictors and a linear penalty operator. In this sense, the components in the regression are 'partially empirical' and the framework is provided by the generalized singular value decomposition (GSVD). The form of the penalized estimation is not new, but the GSVD clarifies the process and informs the choice of penalty by making explicit the joint influence of the penalty and predictors on the bias, variance and performance of the estimated coefficient function. Laboratory spectroscopy data and simulations are used to illustrate the concepts.

Multiple-copy state discrimination: Thinking globally, acting locally

NASA Astrophysics Data System (ADS)

Higgins, B. L.; Doherty, A. C.; Bartlett, S. D.; Pryde, G. J.; Wiseman, H. M.

2011-05-01

We theoretically investigate schemes to discriminate between two nonorthogonal quantum states given multiple copies. We consider a number of state discrimination schemes as applied to nonorthogonal, mixed states of a qubit. In particular, we examine the difference that local and global optimization of local measurements makes to the probability of obtaining an erroneous result, in the regime of finite numbers of copies N, and in the asymptotic limit as N→∞. Five schemes are considered: optimal collective measurements over all copies, locally optimal local measurements in a fixed single-qubit measurement basis, globally optimal fixed local measurements, locally optimal adaptive local measurements, and globally optimal adaptive local measurements. Here an adaptive measurement is one in which the measurement basis can depend on prior measurement results. For each of these measurement schemes we determine the probability of error (for finite N) and the scaling of this error in the asymptotic limit. In the asymptotic limit, it is known analytically (and we verify numerically) that adaptive schemes have no advantage over the optimal fixed local scheme. Here we show moreover that, in this limit, the most naive scheme (locally optimal fixed local measurements) is as good as any noncollective scheme except for states with less than 2% mixture. For finite N, however, the most sophisticated local scheme (globally optimal adaptive local measurements) is better than any other noncollective scheme for any degree of mixture.

Multiple-copy state discrimination: Thinking globally, acting locally

DOE Office of Scientific and Technical Information (OSTI.GOV)

Higgins, B. L.; Pryde, G. J.; Wiseman, H. M.

2011-05-15

We theoretically investigate schemes to discriminate between two nonorthogonal quantum states given multiple copies. We consider a number of state discrimination schemes as applied to nonorthogonal, mixed states of a qubit. In particular, we examine the difference that local and global optimization of local measurements makes to the probability of obtaining an erroneous result, in the regime of finite numbers of copies N, and in the asymptotic limit as N{yields}{infinity}. Five schemes are considered: optimal collective measurements over all copies, locally optimal local measurements in a fixed single-qubit measurement basis, globally optimal fixed local measurements, locally optimal adaptive local measurements,more » and globally optimal adaptive local measurements. Here an adaptive measurement is one in which the measurement basis can depend on prior measurement results. For each of these measurement schemes we determine the probability of error (for finite N) and the scaling of this error in the asymptotic limit. In the asymptotic limit, it is known analytically (and we verify numerically) that adaptive schemes have no advantage over the optimal fixed local scheme. Here we show moreover that, in this limit, the most naive scheme (locally optimal fixed local measurements) is as good as any noncollective scheme except for states with less than 2% mixture. For finite N, however, the most sophisticated local scheme (globally optimal adaptive local measurements) is better than any other noncollective scheme for any degree of mixture.« less

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2011-01-01

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results of this study have shown that the energy landscape effect of oncogenic mutations may be allosteric eliciting global changes in the spatial distribution of highly frustrated residues. We have found that mutation-induced allosteric signaling may involve a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. The presented study has demonstrated that activation cancer mutations may affect the thermodynamic equilibrium between kinase states by allosterically altering the distribution of locally frustrated sites and increasing the local frustration in the inactive form, while eliminating locally frustrated sites and restoring structural rigidity of the active form. The energy landsape analysis of protein kinases and the proposed role of locally frustrated sites in activation mechanisms may have useful implications for bioinformatics-based screening and detection of functional sites critical for allosteric regulation in complex biomolecular systems. PMID:21998754

Dynamic characteristics of the thorax connected with the heart action.

PubMed

Juznic, G; Emri, I; Peterec, D; Prepadnik, M

1979-01-01

We determined the indices of local vibrations (resonance frequency, damping coefficient, stiffness constant, extinction time) and transfer function H(s) . 10(-6) for three somatotypes and three respiratory positions on 88 points of the thorax. The examinees were males (age 21 years). We found the resonance frequencies of 36.86--54.75 cps, damping coefficient (delta) 0.121--0.217. This means the damping is less than critical (delta = 1). We applied shocks (a force of 2 N) with a reflex hammer on 88 points of the thorax. The force diminished from the exciting place (say ictus) to the recording place (accelerometer on the sternum) from 2 to 0.2 N. The athletic type has the highest resonance frequency and stiffness constant; the leptosomic type has the highest damping; the longest extinction time belongs to the pyknic type. The pyknic type has also the highest value of the transfer function. The respiratory position (quiet respiration, Valsalva and Müller experiment) influences the values of the indices of local vibrations and of the transfer function. The influence is evident especially on the intercostal points: the transfer of the oscillations is alleviated at a higher stiffness of the thorax (Valsalva; the value of H(S) . 10(-6) rises from 7.00 to 9.39 sec2), it deteriorates at a small stiffness of the thorax (in Müller's experiment falls to 2.78 sec2). With the fall in the intrathoracic pressure the damping in the intercostal points decreases. On the basis of experiments the conclusion was made that a short testing of the thorax of an examinee will give the dynamic characteristics of the thorax (indices of local vibrations and transfer functions) of the individual. This procedure will alleviate the quantitative use of noninvasive mechanical methods in the assessment of the cardiovascular function.

Analysis of technical university information system

NASA Astrophysics Data System (ADS)

Savelyev, N. A.; Boyarkin, M. A.

2018-05-01

The paper covers a set and interaction of the existing higher education institution automated control systems in φ state budgetary educational institution of higher professional education "Industrial University of Tyumen ". A structural interaction of the existing systems and their functions has been analyzed which has become a basis for identification of a number of system-related and local (related to separate modules) drawbacks of the university activities automation. The authors suggested a new structure of the automated control system, consisting of three major subsystems: management support; training and methodology support; distance and supplementary education support. Functionality for each subsystem has been defined in accordance with the educational institution automation requirements. The suggested structure of the ACS will solve the challenges facing the university during reorganization and optimization of the processes of management of the institution activities as a whole.

Application of the exact exchange potential method for half metallic intermediate band alloy semiconductor.

PubMed

Fernández, J J; Tablero, C; Wahnón, P

2004-06-08

In this paper we present an analysis of the convergence of the band structure properties, particularly the influence on the modification of the bandgap and bandwidth values in half metallic compounds by the use of the exact exchange formalism. This formalism for general solids has been implemented using a localized basis set of numerical functions to represent the exchange density. The implementation has been carried out using a code which uses a linear combination of confined numerical pseudoatomic functions to represent the Kohn-Sham orbitals. The application of this exact exchange scheme to a half-metallic semiconductor compound, in particular to Ga(4)P(3)Ti, a promising material in the field of high efficiency solar cells, confirms the existence of the isolated intermediate band in this compound. (c) 2004 American Institute of Physics.

Physiological effects of indomethacin and celecobix: an S-transform laser Doppler flowmetry signal analysis

NASA Astrophysics Data System (ADS)

Assous, S.; Humeau, A.; Tartas, M.; Abraham, P.; L'Huillier, J. P.

2005-05-01

Conventional signal processing typically involves frequency selective techniques which are highly inadequate for nonstationary signals. In this paper, we present an approach to perform time-frequency selective processing of laser Doppler flowmetry (LDF) signals using the S-transform. The approach is motivated by the excellent localization, in both time and frequency, afforded by the wavelet basis functions. Suitably chosen Gaussian wavelet functions are used to characterize the subspace of signals that have a given localized time-frequency support, thus enabling a time-frequency partitioning of signals. In this paper, the goal is to study the influence of various pharmacological substances taken by the oral way (celecobix (Celebrex®), indomethacin (Indocid®) and placebo) on the physiological activity behaviour. The results show that no statistical differences are observed in the energy computed from the time-frequency representation of LDF signals, for the myogenic, neurogenic and endothelial related metabolic activities between Celebrex and placebo, and Indocid and placebo. The work therefore proves that these drugs do not affect these physiological activities. For future physiological studies, there will therefore be no need to exclude patients having taken cyclo-oxygenase 1 inhibitions.

A complete computational and spectroscopic study of 2-bromo-1, 4-dichlorobenzene - A frequently used benzene derivative

NASA Astrophysics Data System (ADS)

Vennila, P.; Govindaraju, M.; Venkatesh, G.; Kamal, C.; Mary, Y. Sheena; Panicker, C. Yohannan; Kaya, S.; Armaković, Stevan; Armaković, Sanja J.

2018-01-01

The coupled experimental and theoretical vibrational investigation of 2-bromo-1, 4-dichlorobenzene (BDB) molecule has been carried out and they have been duly compared with standard values in order to produce the reliability of the results. Results of DFT analysis carried out using B3LYP functional with 6-31 + G/6-311++G (d,p) basis set revealed that BDB has higher electronic density. The molecular geometry, 13C &1H Nuclear Magnetic Resonance (NMR), Natural Bond Orbital (NBO) and Natural Atomic Charge analyses have been obtained by DFT calculations. Nonlinear optical (NLO) properties, quantum chemical descriptors and first order hyperpolarizability have been calculated. In addition, Local reactivity properties reflected through average local ionization energies (ALIE), Fukui functions and bond dissociation energies have also been investigated. Besides investigation of docking properties, molecular dynamics simulations were also taken in account with a view to identify atoms that have relatively important interactions with water molecules. The title compound forms a stable complex with isopentenylpyrophosphate transferase with a binding affinity value as -4.6 kCal./Mol. and shows inhibitory activity against isopentenylpyrophosphate transferase.

Immunisation Registries at regional level in Italy and the roadmap for a future Italian National Registry.

PubMed

D'Ancona, F; Gianfredi, V; Riccardo, F; Iannazzo, S

2018-01-01

Immunization Information Systems, or Immunisation registries (IRs), are essential to monitor and evaluate the accessibility, quality and outcomes of immunisation programmes both at local and national level. We conducted a cross-sectional survey in order to investigate and map the level of IRs implementation obtained by the 21 Italian Regional Health Authorities. On this basis we defined a roadmap towards implementing an Italian National IR. We designed an online questionnaire. Data were collected from July to September 2016 from all the 21 Regional Health Authorities in charge of infectious diseases control and immunization management. 18/21 Italian Regions have fully implemented an IR, out of them, 11 use the same software for all Local Health Units. Two Regions have partially implemented their IRs and one Region is not yet computerised. The decentralization of the Italian Health System is reflected also on the IRs characteristics and functionalities in terms of fragmented implementation of IRs and diversity in the software systems and data flows in place. Future efforts should not only aim not only to clarify the functionalities of Regional IRs, but should also aim to define how aggregation of data at national level can be optimised.

Computation of geometries and frequencies of singlet and triplet nitromethane with density functional theory byusing gaussian type orbitals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jursic, B.S.

1996-12-31

The results of the computational study of the structures, energies, dipole moments and IR spectra for a singlet and a triplet nitromethane are presented. Five different hybrids (BHandH, BHandHLYP, B3LYP, B3P86 and B3PW91), local (SVWN), and nonlocal (BLYP) DFT methods are used with various sizes of the gaussian type of basis set. The obtained results are compared to the HF, MP2, and MCSCF ab initio calculations, as well as, to the experimental results. Becke`s three functional based hybrid DFT methods outperform the following: the ab initio (HF, MP2 and MCSCF), the Becke`s half-and-half based DFT methods, and the local (SVWNmore » or LSDA) and nonlocal (BLYP) DFT methods. The computed nitromethane geometry, the dipole moment, the energy difference, and the IR frequency are in extraordinary agreement with the experimental results. Thus, we are recommending the B3LYP and the B3PW91 as the methods of choice when the computational study of small {open_quotes}difficult{close_quotes} molecules is considered.« less

Inelastic transport theory from first principles: Methodology and application to nanoscale devices

NASA Astrophysics Data System (ADS)

Frederiksen, Thomas; Paulsson, Magnus; Brandbyge, Mads; Jauho, Antti-Pekka

2007-05-01

We describe a first-principles method for calculating electronic structure, vibrational modes and frequencies, electron-phonon couplings, and inelastic electron transport properties of an atomic-scale device bridging two metallic contacts under nonequilibrium conditions. The method extends the density-functional codes SIESTA and TRANSIESTA that use atomic basis sets. The inelastic conductance characteristics are calculated using the nonequilibrium Green’s function formalism, and the electron-phonon interaction is addressed with perturbation theory up to the level of the self-consistent Born approximation. While these calculations often are computationally demanding, we show how they can be approximated by a simple and efficient lowest order expansion. Our method also addresses effects of energy dissipation and local heating of the junction via detailed calculations of the power flow. We demonstrate the developed procedures by considering inelastic transport through atomic gold wires of various lengths, thereby extending the results presented in Frederiksen [Phys. Rev. Lett. 93, 256601 (2004)]. To illustrate that the method applies more generally to molecular devices, we also calculate the inelastic current through different hydrocarbon molecules between gold electrodes. Both for the wires and the molecules our theory is in quantitative agreement with experiments, and characterizes the system-specific mode selectivity and local heating.

Pre-evaluation and interactive editing of B-spline and GERBS curves and surfaces

NASA Astrophysics Data System (ADS)

Laksâ, Arne

2017-12-01

Interactive computer based geometry editing is very useful for designers and artists. Our goal has been to develop useful tools for geometry editing in a way that increases the ability for creative design. When we interactively editing geometry, we want to see the change happening gradually and smoothly on the screen. Pre-evaluation is a tool for increasing the speed of the graphics when doing interactive affine operation on control points and control surfaces. It is then possible to add details on surfaces, and change shape in a smooth and continuous way. We use pre-evaluation on basis functions, on blending functions and on local surfaces. Pre-evaluation can be made hierarchi-cally and is thus useful for local refinements. Sampling and plotting of curves, surfaces and volumes can today be handled by the GPU and it is therefore important to have a structured organization and updating system to be able to make interactive editing as smooth and user friendly as possible. In the following, we will show a structure for pre-evaluation and an optimal organisation of the computation and we will show the effect of implementing both of these techniques.

Modulation of human extrastriate visual processing by selective attention to colours and words.

PubMed

Nobre, A C; Allison, T; McCarthy, G

1998-07-01

The present study investigated the effect of visual selective attention upon neural processing within functionally specialized regions of the human extrastriate visual cortex. Field potentials were recorded directly from the inferior surface of the temporal lobes in subjects with epilepsy. The experimental task required subjects to focus attention on words from one of two competing texts. Words were presented individually and foveally. Texts were interleaved randomly and were distinguishable on the basis of word colour. Focal field potentials were evoked by words in the posterior part of the fusiform gyrus. Selective attention strongly modulated long-latency potentials evoked by words. The attention effect co-localized with word-related potentials in the posterior fusiform gyrus, and was independent of stimulus colour. The results demonstrated that stimuli receive differential processing within specialized regions of the extrastriate cortex as a function of attention. The late onset of the attention effect and its co-localization with letter string-related potentials but not with colour-related potentials recorded from nearby regions of the fusiform gyrus suggest that the attention effect is due to top-down influences from downstream regions involved in word processing.

NBO, conformational, NLO, HOMO-LUMO, NMR and electronic spectral study on 1-phenyl-1-propanol by quantum computational methods

NASA Astrophysics Data System (ADS)

Xavier, S.; Periandy, S.; Ramalingam, S.

2015-02-01

In this study, FT-IR, FT-Raman, NMR and UV spectra of 1-phenyl-1-propanol, an intermediate of anti-depressant drug fluoxetine, has been investigated. The theoretical vibrational frequencies and optimized geometric parameters have been calculated by using HF and density functional theory with the hybrid methods B3LYP, B3PW91 and 6-311+G(d,p)/6-311++G(d,p) basis sets. The theoretical vibrational frequencies have been found in good agreement with the corresponding experimental data. 1H and 13C NMR spectra were recorded and chemical shifts of the molecule were compared to TMS by using the Gauge-Independent Atomic Orbital (GIAO) method. A study on the electronic and optical properties, absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies are performed using HF and DFT methods. The thermodynamic properties (heat capacity, entropy and enthalpy) at different temperatures are also calculated. NBO analysis is carried out to picture the charge transfer between the localized bonds and lone pairs. The local reactivity of the molecule has been studied using the Fukui function. NLO properties related to polarizability and hyperpolarizability are also discussed.

A stability theorem for energy-balance climate models

NASA Technical Reports Server (NTRS)

Cahalan, R. F.; North, G. R.

1979-01-01

The paper treats the stability of steady-state solutions of some simple, latitude-dependent, energy-balance climate models. For north-south symmetric solutions of models with an ice-cap-type albedo feedback, and for the sum of horizontal transport and infrared radiation given by a linear operator, it is possible to prove a 'slope stability' theorem, i.e., if the local slope of the steady-state iceline latitude versus solar constant curve is positive (negative) the steady-state solution is stable (unstable). Certain rather weak restrictions on the albedo function and on the heat transport are required for the proof, and their physical basis is discussed.

Implementation of glider guns in the light-sensitive Belousov-Zhabotinsky medium.

PubMed

de Lacy Costello, Ben; Toth, Rita; Stone, Christopher; Adamatzky, Andrew; Bull, Larry

2009-02-01

In cellular automata models a glider gun is an oscillating pattern of nonquiescent states that periodically emits traveling localizations (gliders). The glider streams can be combined to construct functionally complete systems of logical gates and thus realize universal computation. The glider gun is the only means of ensuring the negation operation without additional external input and therefore is an essential component of a collision-based computing circuit. We demonstrate the existence of glider-gun-like structures in both experimental and numerical studies of an excitable chemical system-the light-sensitive Belousov-Zhabotinsky reaction. These discoveries could provide the basis for future designs of collision-based reaction-diffusion computers.

[The treatment of benign prostatic hyperplasia using the Mumie-Vitas preparation].

PubMed

Andriukhova, N N

1997-01-01

Overall thirty-eight patients presenting with stage I-II benign prostate hyperplasia received treatment with a new local drug preparation Mumiyo-Vitas, 0.2 g on a once- or twice-daily basis over six months. Effects were studied of the drug on the urologic symptomatology and quality of life of patients presenting with ongoing micturitional disturbances, functional state of detrusor vesicae, prostate volume and urethral resistance. Efficiency of the treatment given was assessed by the International system, uroflowmetry, ultrasonic investigation. Mumiyo-Vitas appeared to be of therapeutic benefit in those patients with subjective and objective symptoms of the urinary bladder obstruction who had innocent prostate hyperplasia.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perez, R. Navarro; Schunck, N.; Lasseri, R. -D.

Here, we describe the new version 3.00 of the code hfbtho that solves the nuclear Hartree–Fock (HF) or Hartree–Fock–Bogolyubov (HFB) problem by using the cylindrical transformed deformed harmonic oscillator basis. In the new version, we have implemented the following features: (i) the full Gogny force in both particle–hole and particle–particle channels, (ii) the calculation of the nuclear collective inertia at the perturbative cranking approximation, (iii) the calculation of fission fragment charge, mass and deformations based on the determination of the neck, (iv) the regularization of zero-range pairing forces, (v) the calculation of localization functions, (vi) a MPI interface for large-scalemore » mass table calculations.« less