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1

The orbital-dependent correlation energy functional resulting from second order Kohn-Sham perturbation theory leads to atomic correlation potentials with correct shell structure and asymptotic behavior. The absolute magnitude of the exact correlation potential, however, is greatly overestimated. In addition, this functional is variationally instable, which shows up for systems with nearly degenerate highest occupied and lowest unoccupied levels like Be. In

Hong Jiang; Eberhard Engel

2006-01-01

2

Using complex degrees of freedom in the Kohn-Sham self-interaction correction

NASA Astrophysics Data System (ADS)

The Perdew-Zunger self-interaction correction (SIC) to local and semilocal density functionals systematically underestimates molecular bond lengths, yet improves many other ground-state properties. An alternative definition of a SIC is reached by using the Perdew-Zunger energy with a global, multiplicative Kohn-Sham potential instead of the orbital-specific potentials of traditional SIC. Due to the unitary variance of the SIC energy, the most general construction of the SIC Kohn-Sham potential involves a unitary transformation of the Kohn-Sham orbitals. We systematically investigate the Kohn-Sham version of the SIC, in particular with respect to the bond-length question, and present a detailed analysis of the influence of different unitary transformations. Using a complex-valued energy-minimizing transformation appears to be the most favorable approach, and we explain this result by analyzing orbital densities. We discuss how to calculate the transformations efficiently.

Hofmann, D.; Klüpfel, S.; Klüpfel, P.; Kümmel, S.

2012-06-01

3

The orbital-dependent correlation energy functional resulting from second order Kohn-Sham perturbation theory leads to atomic correlation potentials with correct shell structure and asymptotic behavior. The absolute magnitude of the exact correlation potential, however, is greatly overestimated. In addition, this functional is variationally instable, which shows up for systems with nearly degenerate highest occupied and lowest unoccupied levels like Be. In this contribution we examine the simplest resummation of the Kohn-Sham perturbation series which has the potential to resolve both the inaccuracy and the instability problem of the second order expression. This resummation includes only the hole-hole terms of the Epstein-Nesbet series of diagrams, which has the advantage that the resulting functional is computationally as efficient as the pure second order expression. The hole-hole Epstein-Nesbet functional is tested for a number of atoms and ions. It is found to reproduce correlation and ground state energies with an accuracy comparable to that of state-of-the-art generalized gradient approximations. The correlation potential, on the other hand, is dramatically improved compared to that obtained from generalized gradient approximations. The same applies to all quantities directly related to the potential, as, for instance, Kohn-Sham eigenvalues and excitation energies. Most importantly, however, the hole-hole Epstein-Nesbet functional turned out to be variationally stable for all neutral as well as all singly and doubly ionized atoms considered so far, including the case of Be. PMID:17115739

Jiang, Hong; Engel, Eberhard

2006-11-14

4

A new approach to calculating quantum functional sensitivity maps of transition probabilities is described in this paper. This approach is based on the log-derivative version of the Kohn variational principle and is applied here to the collinear H+H[sub 2] hydrogen exchange reaction. The sensitivity maps provide detailed quantitative information about how variations in the potential energy surface affect the state-to-state transition probabilities. The key issues investigated are (i) the evolution of sensitivity structure in the 0.30--1.50 eV range of total energy; (ii) the comparison of sensitivity structure on the Porter--Karplus, the Liu--Siegbahn--Truhlar--Horowitz, and the double-many-body-expansion potential energy surfaces; and (iii) the range of linearity for first order sensitivity predictions.

Chang, J.; Brown, N.J. (Energy and Environment Division, Lawrence Berkeley Laboratory, Berkeley, California 94720 (United States)); D'Mello, M. (Thinking Machines Corp., 245 First Street, Cambridge, Massachusetts 02142-1214 (United States)); Wyatt, R.E. (Department of Chemistry and Institute for Theoretical Chemistry, University of Texas, Austin, Texas 78712 (United States)); Rabitz, H. (Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States))

1992-11-01

5

NASA Technical Reports Server (NTRS)

We report on the first part of a study of electron-hydrogen scattering, using a method which allows for the ab initio calculation of total and elastic cross sections at higher energies. In its general form the method uses complex 'radial' correlation functions, in a (Kohn) T-matrix formalism. The titled method, abbreviated Complex Correlation Kohn T (CCKT) method, is reviewed, in the context of electron-hydrogen scattering, including the derivation of the equation for the (complex) scattering function, and the extraction of the scattering information from the latter. The calculation reported here is restricted to S-waves in the elastic region, where the correlation functions can be taken, without loss of generality, to be real. Phase shifts are calculated using Hylleraas-type correlation functions with up to 95 terms. Results are rigorous lower bounds; they are in general agreement with those of Schwartz, but they are more accurate and outside his error bounds at a couple of energies,

Bhatia, A. K.; Temkin, A.; Fisher, Richard R. (Technical Monitor)

2001-01-01

6

ERIC Educational Resources Information Center

Alfie Kohn made the case for competition being destructive to education. The truth may be that there are two separate ways to contest: true competition, which is a healthy desire to excel, and decompetition, which is the unhealthy desire merely to beat the opponent. Decompetition leads to the ills that Kohn enumerated. Educators should teach their…

Shields, David Light; Bredemeier, Brenda Light

2010-01-01

7

NASA Astrophysics Data System (ADS)

Two open-shell formulations of the symmetry-adapted perturbation theory are presented. They are based on the spin-unrestricted Kohn-Sham (SAPT(UKS)) and unrestricted Hartree-Fock (SAPT(UHF)) descriptions of the monomers, respectively. The key reason behind development of SAPT(UKS) is that it is more compatible with density functional theory (DFT) compared to the previous formulation of open-shell SAPT based on spin-restricted Kohn-Sham method of ?uchowski et al. [J. Chem. Phys. 129, 084101 (2008)]. The performance of SAPT(UKS) and SAPT(UHF) is tested for the following open-shell van der Waals complexes: He...NH, H2O...HO2, He...OH, Ar...OH, Ar...NO. The results show an excellent agreement between SAPT(UKS) and SAPT(ROKS). Furthermore, for the first time SAPT based on DFT is shown to be suitable for the treatment of interactions involving ?-state radicals (He...OH, Ar...OH, Ar...NO). In the interactions of transition metal dimers (3?u+)Au2 and (13?g+)Cr2 we show that SAPT is incompatible with the use of effective core potentials. The interaction energies of both systems expressed instead as supermolecular UHF interaction plus dispersion from SAPT(UKS) result in reasonably accurate potential curves.

Hapka, Micha?; ?uchowski, Piotr S.; Szcze?niak, Ma?gorzata M.; Cha?asi?ski, Grzegorz

2012-10-01

8

NASA Astrophysics Data System (ADS)

We propose a general constraint on the occupations of single-particle orbitals within (hybrid) density-functional theory that allows a variational total energy formulation for extended systems containing arbitrary electronic excitations. This method is simple to implement and is ideal for studying structural relaxations and molecular-dynamics simulations in the presence of excitations since accurate forces can be calculated via the Hellman-Feynman theorem.

Sadigh, Babak

2012-02-01

9

A Rigorous Extension of the Kohn-Sham Equation for Strongly Correlated Electron Systems

By introducing a set of auxiliary equations representing a many-body system, we have derived an extension of the Kohn-Sham scheme for the density functional theory. These equations consist of a Kohn-Sham-type equation determining single-particle orbitals and an eigen-value equation for an effective many-body problem. A variational method similar to the Kohn-Sham technique was utilized to derive effective interactions as well

Koichi Kusakabe

2001-01-01

10

Variational Bayesian Stochastic Complexity of Mixture Models

The Variational Bayesian framework has been widely used to ap- proximate the Bayesian learning. In various applications, it has provided computational tractability and good generalization per- formance. In this paper, we discuss the Variational Bayesian learn- ing of the mixture of exponential families and provide some ad- ditional theoretical support by deriving the asymptotic form of the stochastic complexity. The

Kazuho Watanabe; Sumio Watanabe

2005-01-01

11

ERIC Educational Resources Information Center

An interview with educator-author Alfie Kohn discusses student motivation and the need to move away from giving rewards, praise as a form of control, the importance of genuine encouragement that fosters intrinsic motivation and lifelong learning, and the role of mentors in supporting teachers who seek to change or improve traditional teaching…

Swan, Deborah

1997-01-01

12

Kohn-Sham potential with discontinuity for band gap materials

NASA Astrophysics Data System (ADS)

We model a Kohn-Sham potential with the discontinuity at integer particle numbers starting from the approximation by (GLLB) Gritsenko [Phys. Rev. A 51, 1944 (1995)10.1103/PhysRevA.51.1944]. We evaluate the Kohn-Sham gap and the discontinuity to obtain the quasiparticle gap. This allows us to compare the Kohn-Sham gaps to those obtained by accurate many-body perturbation-theory-based optimized potential methods. In addition, the resulting quasiparticle band gap is compared to experimental gaps. In the GLLB model potential, the exchange-correlation hole is modeled using a generalized gradient approximation (GGA) energy density and the response of the hole-to-density variations is evaluated by using the common-denominator approximation and homogeneous electron-gas-based assumptions. In our modification, we have chosen the PBEsol potential as the GGA to model the exchange hole and add a consistent correlation potential. The method is implemented in the GPAW code, which allows efficient parallelization to study large systems. A fair agreement for Kohn-Sham and the quasiparticle band gaps with semiconductors and other band gap materials is obtained with a potential which is as fast as GGA to calculate.

Kuisma, M.; Ojanen, J.; Enkovaara, J.; Rantala, T. T.

2010-09-01

13

Stochastic complexities of general mixture models in variational Bayesian learning

In this paper, we focus on variational Bayesian learning of general mixture models. Variational Bayesian learning was proposed as an approximation of Bayesian learning. While it has provided computational tractability and good generalization in many applications, little has been done to investigate its theoretical properties.The asymptotic form was obtained for the stochastic complexity, or the free energy in the variational

Kazuho Watanabe; Sumio Watanabe

2007-01-01

14

Local-scaling transformations are used in the present work to obtain accurate Kohn--Sham 1[ital s] and 2[ital s] orbitals for the beryllium atom by means of a density-constrained variation of the single-determinant kinetic energy functional. An analytic representation of these Kohn--Sham orbitals is given and the quality of the different types of orbitals generated is discussed with particular reference to their

Eduardo V. Ludeña; Jorge Maldonado; Roberto López-Boada; Toshikatsu Koga; Eugene S. Kryachko

1995-01-01

15

Local-scaling transformations are used in the present work to obtain accurate Kohn–Sham 1s and 2s orbitals for the beryllium atom by means of a density-constrained variation of the single-determinant kinetic energy functional. An analytic representation of these Kohn–Sham orbitals is given and the quality of the different types of orbitals generated is discussed with particular reference to their kinetic energy

Jorge Maldonado; Roberto Lo´pez-Boada; Toshikatsu Koga; Eugene S. Kryachko

1995-01-01

16

The Jost-Kohn inversion procedure

NASA Technical Reports Server (NTRS)

Conditions are considered that must be imposed on a class of quantum mechanical problems to obtain reasonable results by the Jost-Kohn procedure. The discussion is restricted to problems in three space-dimensions without assuming any radial or other symmetry of the potential.

Prosser, R. T.

1972-01-01

17

Fermi Surface of Lead from Kohn Anomalies

The dispersion relations for phonons in lead determined by neutron spectrometry exhibit a large number of Kohn anomalies, which may all be related to the Fermi surface in a consistent manner by considering both electron transitions diametrically across the Fermi surface and nondiametral transitions between points with parallel tangent planes. Factors affecting the size and shape of anomalies are reviewed.

R. Stedman; L. Almqvist; G. Nilsson; G. Raunio

1967-01-01

18

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations are thus a possible source of heritable phenotypic variation in the absence of DNA sequence change. However, attempts to assess the prevalence of stable epigenetic variation in natural and experimental populations and to quantify its impact on complex traits have been

Frank Johannes; Emmanuelle Porcher; Felipe K. Teixeira; Vera Saliba-Colombani; Matthieu Simon; Nicolas Agier; Agnès Bulski; Juliette Albuisson; Fabiana Heredia; Pascal Audigier; David Bouchez; Christine Dillmann; Philippe Guerche; Vincent Colot

2009-01-01

19

The role of variation, error, and complexity in manufacturing defects

Variation in component properties and dimensions is a widely recognized factor in product defects which can be quantified and controlled by Statistical Process Control methodologies. Our studies have shown, however, that traditional statistical methods are ineffective in characterizing and controlling defects caused by error. The distinction between error and variation becomes increasingly important as the target defect rates approach extremely low values. Motorola data substantiates our thesis that defect rates in the range of several parts per million can only be achieved when traditional methods for controlling variation are combined with methods that specifically focus on eliminating defects due to error. Complexity in the product design, manufacturing processes, or assembly increases the likelihood of defects due to both variation and error. Thus complexity is also a root cause of defects. Until now, the absence of a sound correlation between defects and complexity has obscured the importance of this relationship. We have shown that assembly complexity can be quantified using Design for Assembly (DFA) analysis. High levels of correlation have been found between our complexity measures and defect data covering tens of millions of assembly operations in two widely different industries. The availability of an easily determined measure of complexity, combined with these correlations, permits rapid estimation of the relative defect rates for alternate design concepts. This should prove to be a powerful tool since it can guide design improvement at an early stage when concepts are most readily modified.

Hinckley, C.M. [Sandia National Labs., Livermore, CA (United States); Barkan, P. [Stanford Univ., CA (United States)

1994-03-01

20

Kohn-Sham potential with discontinuity for band gap materials

We model a Kohn-Sham potential with the discontinuity at integer particle numbers starting from the approximation by (GLLB) Gritsenko [Phys. Rev. A 51, 1944 (1995)10.1103\\/PhysRevA.51.1944]. We evaluate the Kohn-Sham gap and the discontinuity to obtain the quasiparticle gap. This allows us to compare the Kohn-Sham gaps to those obtained by accurate many-body perturbation-theory-based optimized potential methods. In addition, the resulting

M. Kuisma; J. Ojanen; J. Enkovaara; T. T. Rantala

2010-01-01

21

Exact Kohn-Sham scheme based on perturbation theory

An exact formal Kohn-Sham scheme is derived with the help of perturbation theory. Through the introduction of a basis set this Kohn-Sham scheme can be used to perform, in principle, exact Kohn-Sham calculations. As a demonstration, only zeroth- and first-order terms in the underlying perturbation theory are considered. As a result an exact basis set ``exchange-only'' method is obtained. The

Andreas Görling; Mel Levy

1994-01-01

22

Singleparticle states, Kohn anomaly, and pairing fluctuations in one dimension

We compute the single-particle spectral density, susceptibility near the Kohn anomaly, and pair propagator for a one-dimensional\\u000a interacting-electron gas. With an attractive interaction, the pair propagator is divergent in the zero-temperature limit and\\u000a the Kohn singularity is removed. For repulsive interactions, the Kohn singularity is stronger than the free-particle case\\u000a and the pair propagator is finite. The low-temperature behavior of

A. Luther; I. Peschel

1975-01-01

23

Complex variation of the superficial palmar arch — Case report

Summary This article describes a complex variation in the pattern of blood supply to the palm of the hand. In the present case; a) the superficial palmar branch of the radial a. coursed superficial to the thenar mm.; b) The princeps pollicis and radialis indicis aa. arose from the superficial palmar branch of the radial a.; c) The first and

S. Önderoglu; R. Basar; K. M. Erbil; M. Cumhur

1997-01-01

24

Complex variation of the superficial palmar arch - Case report

This article describes a complex variation in the pattern of blood supply to the palm of the hand. In the present case; a) the superficial palmar branch of the radial a. coursed superficial to the thenar mm.; b) The princeps pollicis and radialis indicis aa. arose from the superficial palmar branch of the radial a.; c) The first and second

S. Önderoglu; R. Basar; K. M. Erbil; M. Cumhur

1997-01-01

25

Are Kohn-Sham conductances accurate?

We use Fermi-liquid relations to address the accuracy of conductances calculated from the single-particle states of exact Kohn-Sham (KS) density functional theory. We demonstrate a systematic failure of this procedure for the calculation of the conductance, and show how it originates from the lack of renormalization in the KS spectral function. In certain limits this failure can lead to a large overestimation of the true conductance. We also show, however, that the KS conductances can be accurate for single-channel molecular junctions and systems where direct Coulomb interactions are strongly dominant. PMID:21231333

Mera, H; Niquet, Y M

2010-11-19

26

The equivalence of the log derivative Kohn principle with the R-matrix method

NASA Astrophysics Data System (ADS)

The log derivative version of Kohn's variational principle, as discussed by Manolopoulos and Wyatt in 1988, is shown to be equivalent to the R-matrix method. Both methods yield identical S matrices when the same basis set is adopted. The working equations of both methods appear to be quite different at first glance, but we show that even here the relationship is much closer than one might have expected.

Meyer, Hans-Dieter

1994-07-01

27

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations are thus a possible source of heritable phenotypic variation in the absence of DNA sequence change. However, attempts to assess the prevalence of stable epigenetic variation in natural and experimental populations and to quantify its impact on complex traits have been hampered by the confounding effects of DNA sequence polymorphisms. To overcome this problem as much as possible, two parents with little DNA sequence differences, but contrasting DNA methylation profiles, were used to derive a panel of epigenetic Recombinant Inbred Lines (epiRILs) in the reference plant Arabidopsis thaliana. The epiRILs showed variation and high heritability for flowering time and plant height (?30%), as well as stable inheritance of multiple parental DNA methylation variants (epialleles) over at least eight generations. These findings provide a first rationale to identify epiallelic variants that contribute to heritable variation in complex traits using linkage or association studies. More generally, the demonstration that numerous epialleles across the genome can be stable over many generations in the absence of selection or extensive DNA sequence variation highlights the need to integrate epigenetic information into population genetics studies.

Saliba-Colombani, Vera; Simon, Matthieu; Agier, Nicolas; Bulski, Agnes; Albuisson, Juliette; Heredia, Fabiana; Audigier, Pascal; Bouchez, David; Dillmann, Christine; Guerche, Philippe; Hospital, Frederic; Colot, Vincent

2009-01-01

28

Relationship of Kohn–Sham eigenvalues to excitation energies

In Kohn–Sham density functional theory, only the highest occupied eigenvalue has a rigorous physical meaning, viz., it is the negative of the lowest ionization energy. Here, we demonstrate that for finite systems, the unoccupied true Kohn–Sham eigenvalues (as opposed to the those obtained from the commonly used approximate density functionals) are also meaningful in that good approximations to excitation energies

A. Savin; C. J. Umrigar; Xavier Gonze

1998-01-01

29

Calculus structure on the Lie conformal algebra complex and the variational complex

We construct a calculus structure on the Lie conformal algebra cochain complex. By restricting to degree one chains, we recover the structure of a g-complex introduced in [A. De Sole and V. G. Kac, Commun. Math. Phys. 292, 667 (2009)]. A special case of this construction is the variational calculus, for which we provide explicit formulas.

De Sole, Alberto [Dipartimento di Matematica, Universita di Roma ''La Sapienza'', 00185 Roma (Italy); Hekmati, Pedram [School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005 (Australia); Kac, Victor G. [Department of Mathematics, MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States)

2011-05-15

30

Complex variation of the superficial palmar arch--case report.

This article describes a complex variation in the pattern of blood supply to the palm of the hand. In the present case; a) the superficial palmar branch of the radial a. coursed superficial to the thenar mm.; b) The princeps pollicis and radialis indicis aa. arose from the superficial palmar branch of the radial a.; c) The first and second common palmar digital aa. arose as a common trunk from the superficial palmar arch. PMID:9210247

Onderoglu, S; Basar, R; Erbil, K M; Cumhur, M

1997-01-01

31

Structure of the optimized effective Kohn-Sham exchange potential and its gradient approximations

An analysis of the structure of the optimized effective Kohn-Sham exchange potential v, and its gradient approximations is presented. The potential is decomposed into the Slater potential v{sub s} and the response of v{sub s} to density variations, v{sub resp}. The latter exhibits peaks that reflect the atomic shell structure. Kohn-Sham exchange potentials derived from current gradient approaches for the exchange energy are shown to be quite reasonable for the Slater potential, but they fail to approximate the response part, which leads to poor overall potentials. Improved potentials are constructed by a direct fit of v{sub x} with a gradient-dependent Pade approximant form. The potentials obtained possess proper asymptotic and scaling properties and reproduce the shell structure of the exact v{sub x}. 44 refs., 7 figs., 4 tabs.

Gritsenko, O.; Van Leeuwen, R.; Baerends, E.J. [Vrije Universiteit, Amsterdam (Netherlands)] [Vrije Universiteit, Amsterdam (Netherlands)

1996-01-05

32

Kohn-Sham potentials and wave functions from electron densities

A method is introduced that allows the determination of the Kohn-Sham effective potential and the corresponding Kohn-Sham orbitals belonging to an arbitrary electron density with boundary conditions of a bound and finite system. For atoms or molecules the exchange-correlation potential and the exchange-correlation energy can be obtained also. The procedure easily can be implemented using existing density-functional programs.

Andreas Görling

1992-01-01

33

Structural variation and genome complexity: is dispensable really dispensable?

Structural variants (SVs) such as copy number variants (CNVs) and presence/absence variants (PAVs) substantially contribute to genetic variation and have an important effect on phenotypic diversity. Since unbalanced SVs are by definition sequences present only in some individuals, they have therefore been referred to as dispensable genome and are not necessary for survival, even though they may provide an important contribution to phenotypic diversity within the species. However, some multi-copy sequences of the dispensable genomes (e.g., multigene families) may be needed in a given proportion by each individual, thus belonging to a conditionally dispensable portion of the pan-genome. Another interesting aspect reported by recent studies is that the rate at which SVs are formed might be influenced by the mating system and by common environmental stresses. In conclusion the dispensable genome plays an important role in genome evolution and in the complex interplay between the genome and the environment. PMID:24548794

Marroni, Fabio; Pinosio, Sara; Morgante, Michele

2014-04-01

34

Climatic variation and the distribution of an amphibian polyploid complex

1. The establishment of polyploid populations involves the persistence and growth of the polyploid in the presence of the progenitor species. Although there have been a number of animal polyploid species documented, relatively few inquiries have been made into the large-scale mechanisms of polyploid establishment in animal groups. Herein we investigate the influence of regional climatic conditions on the distributional patterns of a diploid-tetraploid species pair of gray treefrogs, Hyla chrysoscelis and H. versicolor (Anura: Hylidae) in the mid-Atlantic region of eastern North America. 2. Calling surveys at breeding sites were used to document the distribution of each species. Twelve climatic models and one elevation model were generated to predict climatic and elevation values for gray treefrog breeding sites. A canonical analysis of discriminants was used to describe relationships between climatic variables, elevation and the distribution of H. chrysoscelis and H. versicolor. 3. There was a strong correlation between several climatic variables, elevation and the distribution of the gray treefrog complex. Specifically, the tetraploid species almost exclusively occupied areas of higher elevation, where climatic conditions were relatively severe (colder, drier, greater annual variation). In contrast, the diploid species was restricted to lower elevations, where climatic conditions were warmer, wetter and exhibited less annual variation. 4. Clusters of syntopic sites were associated with areas of high variation in annual temperature and precipitation during the breeding season. 5. Our data suggest that large-scale climatic conditions have played a role in the establishment of the polyploid H. versicolor in at least some portions of its range. The occurrence of the polyploid and absence of the progenitor in colder, drier and more varied environments suggests the polyploid may posses a tolerance of severe environmental conditions that is not possessed by the diploid progenitor. 6. Our findings support the hypothesis that increased tolerance to severe environmental conditions is a plausible mechanism of polyploid establishment.

Otto, C.R.V.; Snodgrass, J.W.; Forester, D.C.; Mitchell, J.C.; Miller, R.W.

2007-01-01

35

Structural genomic variation in childhood epilepsies with complex phenotypes.

A genetic contribution to a broad range of epilepsies has been postulated, and particularly copy number variations (CNVs) have emerged as significant genetic risk factors. However, the role of CNVs in patients with epilepsies with complex phenotypes is not known. Therefore, we investigated the role of CNVs in patients with unclassified epilepsies and complex phenotypes. A total of 222 patients from three European countries, including patients with structural lesions on magnetic resonance imaging (MRI), dysmorphic features, and multiple congenital anomalies, were clinically evaluated and screened for CNVs. MRI findings including acquired or developmental lesions and patient characteristics were subdivided and analyzed in subgroups. MRI data were available for 88.3% of patients, of whom 41.6% had abnormal MRI findings. Eighty-eight rare CNVs were discovered in 71 out of 222 patients (31.9%). Segregation of all identified variants could be assessed in 42 patients, 11 of which were de novo. The frequency of all structural variants and de novo variants was not statistically different between patients with or without MRI abnormalities or MRI subcategories. Patients with dysmorphic features were more likely to carry a rare CNV. Genome-wide screening methods for rare CNVs may provide clues for the genetic etiology in patients with a broader range of epilepsies than previously anticipated, including in patients with various brain anomalies detectable by MRI. Performing genome-wide screens for rare CNVs can be a valuable contribution to the routine diagnostic workup in patients with a broad range of childhood epilepsies. PMID:24281369

Helbig, Ingo; Swinkels, Marielle E M; Aten, Emmelien; Caliebe, Almuth; van 't Slot, Ruben; Boor, Rainer; von Spiczak, Sarah; Muhle, Hiltrud; Jähn, Johanna A; van Binsbergen, Ellen; van Nieuwenhuizen, Onno; Jansen, Floor E; Braun, Kees P J; de Haan, Gerrit-Jan; Tommerup, Niels; Stephani, Ulrich; Hjalgrim, Helle; Poot, Martin; Lindhout, Dick; Brilstra, Eva H; Møller, Rikke S; Koeleman, Bobby Pc

2014-07-01

36

Breakdown of the Kohn theorem near a Feshbach resonance in a magnetic trap

NASA Astrophysics Data System (ADS)

We study the collective excitation frequencies of a harmonically trapped 85Rb Bose-Einstein condensate (BEC) in the vicinity of a Feshbach resonance. To this end, we solve the underlying Gross-Pitaevskii (GP) equation by using a Gaussian variational approach and obtain the coupled set of ordinary differential equations for the widths and the center of mass of the condensate. A linearization shows that the dipole-mode frequency decreases when the bias magnetic field approaches the Feshbach resonance, so the Kohn theorem is violated.

Al-Jibbouri, Hamid; Pelster, Axel

2013-09-01

37

Comparative Analysis of Hartree-Fock and Kohn-Sham Orbital Energies.

National Technical Information Service (NTIS)

Hartree-Fock and Kohn-Sham orbital energies, the latter computed with several different exchange correlation functionals are compared and analyzed for twelve molecules. The Kohn-Sham energies differ significantly from experimental ionization energies, but...

P. Politzer F. Abu-Awwad

1998-01-01

38

Some Approximate Kohn-Sham Molecular Energy Formulas.

National Technical Information Service (NTIS)

Density functional calculations have been carried out for twelve molecules by several different Kohn-Sham procedures in order to test the effectiveness of two approximate molecular energy formulas that have been applied earlier in the context of Hartree-F...

P. Politzer F. Abu-Awwad

1998-01-01

39

Energy density analysis with Kohn–Sham orbitals

We have proposed a new technique analyzing the results of the density functional theory calculations in the Kohn–Sham (KS) approach. It is named the energy density analysis (EDA), which partitions the total energy of the molecular system into atomic energies. The EDA involves two partition schemes. One is for the exchange-correlation energy computed by the numerical quadrature method with the

Hiromi Nakai

2002-01-01

40

Kinetic energy from a single Kohn-Sham orbital

We observe that the noninteracting kinetic energy, as a functional of the electron density rho , may be obtained from a formula that contains only a single Kohn-Sham orbital, phii(r) , where i is arbitrary. Specifically, Ts[rho]=(-1\\/4)?{?2varphii[rho;r]\\/varphii[rho;r]}[3rho(r)+rs?rho(r)]dr .

Mel Levy; Paul W. Ayers

2009-01-01

41

The Compassion Our Children Deserve: An Interview with Alfie Kohn.

ERIC Educational Resources Information Center

Alfie Kohn, former teacher and current educational theorist and writer, discusses his views on teaching, learning, and parenting. He addresses the problems of reward-based education, the negative effects of competition on learning, and capitalizing on the naturalness of altruistic behavior in humans. He stresses the importance of treating children…

Miller, Ron; Kohn, Alfie

2000-01-01

42

Global Properties and Functional Complexity of Human Gene Regulatory Variation

Identification and functional interpretation of gene regulatory variants is a major focus of modern genomics. The application of genetic mapping to molecular and cellular traits has enabled the detection of regulatory variation on genome-wide scales and revealed an enormous diversity of regulatory architecture in humans and other species. In this review I summarise the insights gained and questions raised by a decade of genetic mapping of gene expression variation. I discuss recent extensions of this approach using alternative molecular phenotypes that have revealed some of the biological mechanisms that drive gene expression variation between individuals. Finally, I highlight outstanding problems and future directions for development.

Gaffney, Daniel J.

2013-01-01

43

Second-order Kohn-Sham perturbation theory: correlation potential for atoms in a cavity.

Second-order perturbation theory based on the Kohn-Sham Hamiltonian leads to an implicit density functional for the correlation energy E(c) (MP2), which is explicitly dependent on both occupied and unoccupied Kohn-Sham single-particle orbitals and energies. The corresponding correlation potential v(c) (MP2), which has to be evaluated by the optimized potential method, was found to be divergent in the asymptotic region of atoms, if positive-energy continuum states are included in the calculation [Facco Bonetti et al., Phys. Rev. Lett. 86, 2241 (2001)]. On the other hand, Niquet et al., [J. Chem. Phys. 118, 9504 (2003)] showed that v(c) (MP2) has the same asymptotic -alpha(2r(4)) behavior as the exact correlation potential, if the system under study has a discrete spectrum only. In this work we study v(c) (MP2) for atoms in a spherical cavity within a basis-set-free finite differences approach, ensuring a completely discrete spectrum by requiring hard-wall boundary conditions at the cavity radius. Choosing this radius sufficiently large, one can devise a numerical continuation procedure which allows to normalize v(c) (MP2) consistent with the standard choice v(c)(r-->infinity)=0 for free atoms, without modifying the potential in the chemically relevant region. An important prerequisite for the success of this scheme is the inclusion of very high-energy virtual states. Using this technique, we have calculated v(c) (MP2) for all closed-shell and spherical open-shell atoms up to argon. One finds that v(c) (MP2) reproduces the shell structure of the exact correlation potential very well but consistently overestimates the corresponding shell oscillations. In the case of spin-polarized atoms one observes a strong interrelation between the correlation potentials of the two spin channels, which is completely absent for standard density functionals. However, our results also demonstrate that E(c) (MP2) can only serve as a first step towards the construction of a suitable implicit correlation functional: The fundamental variational instability of this functional is recovered for beryllium, for which a breakdown of the self-consistent Kohn-Sham iteration is observed. Moreover, even for those atoms for which the self-consistent iteration is stable, the results indicate that the inclusion of v(c) (MP2) in the total Kohn-Sham potential does not lead to an improvement compared to the complete neglect of the correlation potential. PMID:16375465

Jiang, Hong; Engel, Eberhard

2005-12-01

44

Role of variation, error, and complexity in manufacturing defects.

National Technical Information Service (NTIS)

Variation in component properties and dimensions is a widely recognized factor in product defects which can be quantified and controlled by Statistical Process Control methodologies. Our studies have shown, however, that traditional statistical methods ar...

C. M. Hinckley P. Barkan

1994-01-01

45

Upper Bounds for Variational Stochastic Complexities of Bayesian Networks

\\u000a In recent years, variational Bayesian learning has been used as an approximation of Bayesian learning. In spite of the computational\\u000a tractability and good generalization performance in many applications, its statistical properties have yet to be clarified.\\u000a In this paper, we analyze the statistical property in variational Bayesian learning of Bayesian networks which are widely\\u000a used in information processing and uncertain

Kazuho Watanabe; Motoki Shiga; Sumio Watanabe

2006-01-01

46

Luminescence modulations of rhenium tricarbonyl complexes induced by structural variations.

Octahedral d(6) low-spin Re(I) tricarbonyl complexes are of considerable interest as noninvasive imaging probes and have been deeply studied owing to their biological stability, low toxicity, large Stokes shifts, and long luminescence lifetimes. We reported recently the bimodal IR and luminescence imaging of a Re(I) tricarbonyl complex with a Pyta ligand (4-(2-pyridyl)-1,2,3-triazole) in cells and labeled such metal-carbonyl complexes SCoMPIs for single-core multimodal probes for imaging. Re(I) tricarbonyl complexes have unique photophysical properties allowing for their unequivocal detection in cells but also present some weaknesses such as a very low luminescence quantum yield in aqueous medium. Further optimizations would thus be desirable. We therefore developed new Re(I) tricarbonyl complexes prepared from different ancillary ligands. Complexes with benzothiadiazole-triazole ligands show interesting luminescent quantum yields in acetonitrile and may constitute valuable luminescent metal complexes in organic media. A series of complexes with bidentate 1-(2-quinolinyl)-1,2,3-triazole (Taquin) and 1-(2-pyridyl)-1,2,3-triazole (Tapy) ligands bearing various 4-substituted alkyl side chains has been designed and synthesized with efficient procedures. Their photophysical properties have been characterized in acetonitrile and in a H2O/DMSO (98/2) mixture and compared with those of the parent Quinta- and Pyta-based complexes. Tapy complexes bearing long alkyl chains show impressive enhancement of their luminescent properties relative to the parent Pyta complex. Theoretical calculations have been performed to further characterize this new class of rhenium tricarbonyl complexes. Preliminary cellular imaging studies in MDA-MB231 breast cancer cells reveal a strong increase in the luminescence signal in cells incubated with the Tapy complex substituted with a C12 alkyl chain. This study points out the interesting potential of the Tapy ligand in coordination chemistry, which has been so far underexploited. PMID:24905983

Bertrand, Hélène C; Clède, Sylvain; Guillot, Régis; Lambert, François; Policar, Clotilde

2014-06-16

47

Kohn-Sham orbitals and potentials from quantum Monte Carlo molecular densities.

In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H2, Be2, H2O, and C2H4). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory. PMID:24511917

Varsano, Daniele; Barborini, Matteo; Guidoni, Leonardo

2014-02-01

48

Kohn-Sham orbitals and potentials from quantum Monte Carlo molecular densities

NASA Astrophysics Data System (ADS)

In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H2, Be2, H2O, and C2H4). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory.

Varsano, Daniele; Barborini, Matteo; Guidoni, Leonardo

2014-02-01

49

Complex Variation in Measures of General Intelligence and Cognitive Change

Combining information from multiple SNPs may capture a greater amount of genetic variation than from the sum of individual SNP effects and help identifying missing heritability. Regions may capture variation from multiple common variants of small effect, multiple rare variants or a combination of both. We describe regional heritability mapping of human cognition. Measures of crystallised (gc) and fluid intelligence (gf) in late adulthood (64–79 years) were available for 1806 individuals genotyped for 549,692 autosomal single nucleotide polymorphisms (SNPs). The same individuals were tested at age 11, enabling us the rare opportunity to measure cognitive change across most of their lifespan. 547,750 SNPs ranked by position are divided into 10, 908 overlapping regions of 101 SNPs to estimate the genetic variance each region explains, an approach that resembles classical linkage methods. We also estimate the genetic variation explained by individual autosomes and by SNPs within genes. Empirical significance thresholds are estimated separately for each trait from whole genome scans of 500 permutated data sets. The 5% significance threshold for the likelihood ratio test of a single region ranged from 17–17.5 for the three traits. This is the equivalent to nominal significance under the expectation of a chi-squared distribution (between 1df and 0) of P<1.44×10?5. These thresholds indicate that the distribution of the likelihood ratio test from this type of variance component analysis should be estimated empirically. Furthermore, we show that estimates of variation explained by these regions can be grossly overestimated. After applying permutation thresholds, a region for gf on chromosome 5 spanning the PRRC1 gene is significant at a genome-wide 10% empirical threshold. Analysis of gene methylation on the temporal cortex provides support for the association of PRRC1 and fluid intelligence (P?=?0.004), and provides a prime candidate gene for high throughput sequencing of these uniquely informative cohorts.

Rowe, Suzanne J.; Rowlatt, Amy; Davies, Gail; Harris, Sarah E.; Porteous, David J.; Liewald, David C.; McNeill, Geraldine; Starr, John M.

2013-01-01

50

Some approximate Kohn-Sham molecular energy formulas

Density functional calculations have been carried out for 12 molecules by several different Kohn-Sham procedures in order to test the effectiveness of two approximate molecular energy formulas that have been applied earlier in the context of Hartree-Fock theory. The equation Epsilonmolecular = 3\\/7(nune + 2nunn), in which nu ne and nu nn are the nuclear-electronic attraction and the nuclear repulsion,

Peter Politzer Fakher Abu-Awwad; FAKHER ABU-AWWAD

1998-01-01

51

Variations in recollection: The effects of complexity on source recognition

Whether recollection is a threshold or signal detection process is highly controversial. U-shaped zROCs observed in tests thought to rely heavily on recollection, such as source memory tests, have provided evidence in favor of the threshold assumption, but zROCs are not always as U-shaped as threshold theory predicts. Source zROCs have been shown to become more linear when the contribution of familiarity to source discriminations is increased, and this may account for the existing results. However, another way in which source zROCs may become more linear is if recollection can become more graded under certain conditions. We tested the ‘graded recollection’ account in the current study. We found that increasing stimulus complexity (i.e., changing from single words to sentences), or increasing source complexity (i.e., changing the sources from audio to videos of speakers), resulted in flatter source zROCs. In addition, conditions expected to reduce recollection (i.e., divided attention and amnesia) had comparable effects on source memory in simple and complex conditions, suggesting that differences between simple and complex conditions were due to differences in the nature of recollection, rather than differences in the utility of familiarity. The results suggest that under conditions of high complexity recollection can appear more graded and it can produce curved ROCs. The results have implications for measurement models and for current theories of recognition memory.

Parks, Colleen M.; Murray, Linda J.; Elfman, Kane; Yonelinas, Andrew P.

2011-01-01

52

The Kohn-Luttinger superconductivity in idealized doped graphene

NASA Astrophysics Data System (ADS)

Idealized graphene monolayer is considered neglecting the van der Waals potential of the substrate and the role of the nonmagnetic impurities. The effect of the long-range Coulomb repulsion in an ensemble of Dirac fermions on the formation of the superconducting pairing in a monolayer is studied in the framework of the Kohn-Luttinger mechanism. The electronic structure of graphene is described in the strong coupling Wannier representation on the hexagonal lattice. We use the Shubin-Vonsowsky model which takes into account the intra- and intersite Coulomb repulsions of electrons. The Cooper instability is established by solving the Bethe-Salpeter integral equation, in which the role of the effective interaction is played by the renormalized scattering amplitude. The renormalized amplitude contains the Kohn-Luttinger polarization contributions up to and including the second-order terms in the Coulomb repulsion. We construct the superconductive phase diagram for the idealized graphene monolayer and show that the Kohn-Luttinger renormalizations and the intersite Coulomb repulsion significantly affect the interplay between the superconducting phases with f-, d+id-, and p+ip-wave symmetries of the order parameter.

Kagan, M. Yu.; Val?kov, V. V.; Mitskan, V. A.; Korovushkin, M. M.

2014-06-01

53

Functional evaluation of genetic variation in complex human traits

Genome-wide association studies and, more recently, next-generation sequencing studies have accelerated the investigation of complex human traits by providing a wealth of association data linking genetic variants to diseases and other phenotypic traits. These data promise to transform our understanding of the molecular pathways underlying complex human traits, but only if functional evaluation of the novel genetic variants is undertaken. Here, we review recent examples in which such functional evaluation has been attempted, with varying degrees of success, and we highlight new technological advances that should greatly enhance our ability to identify and dissect causal genotype–phenotype relationships.

Peters, Derek T.; Musunuru, Kiran

2012-01-01

54

ERIC Educational Resources Information Center

This paper introduces a variation on the post-test only cohort control design and addresses questions concerning both the methodological credibility and the practical utility of employing this design variation in evaluations of large-scale complex professional development programmes in mathematics education. The original design and design…

Sample Mcmeeking, Laura B.; Cobb, R. Brian; Basile, Carole

2010-01-01

55

Flow-field dependent variation method for complex relativistic fluids

NASA Astrophysics Data System (ADS)

Many current high-energy astrophysics problems, particularly those containing shock waves and high-speed flow, do not take advantage of new computational fluid dynamics (CFD) techniques available in such fields as aerospace engineering. We will present the flow-field dependent variation (FDV) method to accurately solve very high-speed flow problems, as well as capture relativistic shocks, all while allowing the user to apply their familiar finite difference method (FDM) or finite element method (FEM). This method is also versatile enough to apply the non-relativistic Naiver-Stokes equations to solve low speed flows. In the FDV method, numerical schemes are automatically adjusted from the current flow field information reflecting shock discontinuities and/or effects of viscosity in boundary layers. To demonstrate the validity of this theory, the shock tube using the relativistic hydrodynamic equations has been applied. .

Richardson, G. A.; Chung, T. J.; Karr, G. R.; Pendleton, G. N.

2000-09-01

56

Kohn–Sham orbitals and orbital energies: fictitious constructs but good approximations all the same

Kohn and Sham introduced orbitals into density–functional theory (DFT) as a set of physically meaningless auxiliary quantities useful only for calculating the total energy and charge density. While the traditional view is that Kohn–Sham orbitals do not approximate anything, Duffy et al. [Phys. Rev. A 50 (1994) 4707] showed that Kohn–Sham orbitals calculated using approximate exchange-correlation (xc) potentials could provide

Sebastien Hamel; Patrick Duffy; Mark E. Casida; Dennis R. Salahub

2002-01-01

57

Core ionization potentials from self-interaction corrected Kohn-Sham orbital energies

We propose a simple self-interaction correction to Kohn-Sham orbital energies in order to apply ground state Kohn-Sham density functional theory to accurate predictions of core electron binding energies and chemical shifts. The proposition is explored through a series of calculations of organic compounds of different sizes and types. Comparison is made versus experiment and the ``DeltaKohn-Sham'' method employing separate state

Guangde Tu; Vincenzo Carravetta; Olav Vahtras; Hans Gren

2007-01-01

58

Is the Kohn-Sham Oscillator Strength Exact at the Ionization Threshold?

It is well-established that the highest occupied orbital of the exact Kohn-Sham potential of any system is at -I, where I is the ionization energy. Therefore, in optical response, the non-interacting Kohn-Sham electrons in the ground-state potential have a first ionization threshold that exactly matches that of the real system[1]. We show that corresponding the Kohn-Sham oscillator strength is not

Zenghui Yang; Meta van Faassen; Kieron Burke

2009-01-01

59

Low allozymic variation in the Bidens pilosa L. complex (Asteraceae).

Bidens alba, B. subalternans, and B. pilosa form a complex group based on their morphological similarities. Bidens pilosa L. and B. subalternans DC. are herbs with a wide distribution in agricultural and disturbed areas. Bidens alba (L.) DC. varies in size from herb to subshrub and has a coastal distribution. Enzyme electrophoresis was used to evaluate genetic diversity in 12 populations of Bidens. All but three loci (Lap-1, Est, and Got) were monomorphic. Est-1 and Got were polymorphic only in B. alba. Lap-1 was polymorphic only in B. pilosa and B. subalternans. The estimates of genetic variability were low for all three taxa and all of the populations studied. Genetic diversity varied from 0.01 to 0.03. Mean genetic identities were high among populations of each species (0.99 for B. alba and 1.00 for B. pilosa and B. subalternans) and among the three species (1.00). Bidens pilosa and B. subalternans could be considered a single species if the taxonomy of the group were based solely on isozyme data. PMID:16187159

Grombone-Guaratini, Maria Tereza; Semir, João; Solferini, Vera Nisaka

2005-08-01

60

Interpreting non-coding variation in complex disease genetics

Association studies provide genome-wide information about the genetic basis of complex disease, but medical research has primarily focused on protein-coding variants, due to the difficulty of interpreting non-coding mutations. This picture has changed with advances in the systematic annotation of functional non-coding elements. Evolutionary conservation, functional genomics, chromatin state, sequence motifs, and molecular quantitative trait loci all provide complementary information about non-coding function. These functional maps can help prioritize variants on risk haplotypes, filter mutations encountered in the clinic, and perform systems-level analyses to reveal processes underlying disease associations. Advances in predictive modeling can enable dataset integration to reveal pathways shared across loci and alleles, and richer regulatory models can guide the search for epistatic interactions. Lastly, new massively parallel reporter experiments can systematically validate regulatory predictions. Ultimately, advances in regulatory and systems genomics can help unleash the value of whole-genome sequencing for personalized genomic risk assessment, diagnosis, and treatment.

Ward, Lucas D.; Kellis, Manolis

2012-01-01

61

Asymptotic form of the Kohn-Sham correlation potential

The density-functional correlation potential of a finite system is shown to asymptotically approach a nonzero constant along a nodal surface of the energetically highest occupied orbital and zero everywhere else. This nonuniform asymptotic form of the correlation potential exactly cancels the nonuniform asymptotic behavior of the exact exchange potential discussed by Della Sala and Goerling [Phys. Rev. Lett. 89, 33003 (2002)]. The sum of the exchange and correlation potentials therefore asymptotically tends to -1/r everywhere, consistent with the asymptotic form of the Kohn-Sham potential as analyzed by Almbladh and von Barth [Phys. Rev. B 31, 3231 (1985)].

Joubert, D. P. [School of Physics, University of the Witwatersrand, P.O. Wits 2050, Johannesburg (South Africa)

2007-07-15

62

Asymptotic behavior of the Kohn-Sham exchange potential.

The Kohn-Sham exchange potential of finite systems is shown to approach different asymptotic limits on nodal surfaces of the energetically highest-occupied orbital than in other regions. This leads to barrier-well structures in the near asymptotic region, which have a strong influence on virtual orbitals and thus on excitation energies. Common approximations for the exchange potential do not exhibit these features. These asymptotic structures, however, can be correctly described by effective exact-exchange methods. Conditions for the presence of an asymptotic barrier well in the full exchange-correlation potential are discussed. PMID:12144389

Della Sala, Fabio; Görling, Andreas

2002-07-15

63

Element orbitals for Kohn-Sham density functional theory

NASA Astrophysics Data System (ADS)

We present a method to discretize the Kohn-Sham Hamiltonian matrix in the pseudopotential framework by a small set of basis functions automatically contracted from a uniform basis set such as plane waves. Each basis function is localized around an element, which is a small part of the global domain containing multiple atoms. We demonstrate that the resulting basis set achieves meV accuracy for three-dimensional densely packed systems with a small number of basis functions per atom. The procedure is applicable to both insulating and metallic systems.

Lin, Lin; Ying, Lexing

2012-06-01

64

Nonadiabatic Kohn anomaly in a doped graphene monolayer.

We compute, from first principles, the frequency of the E(2g), Gamma phonon (Raman G band) of graphene, as a function of the charge doping. Calculations are done using (i) the adiabatic Born-Oppenheimer approximation and (ii) time-dependent perturbation theory to explore dynamic effects beyond this approximation. The two approaches provide very different results. While the adiabatic phonon frequency weakly depends on the doping, the dynamic one rapidly varies because of a Kohn anomaly. The adiabatic approximation is considered valid in most materials. Here, we show that doped graphene is a spectacular example where this approximation miserably fails. PMID:17280442

Lazzeri, Michele; Mauri, Francesco

2006-12-31

65

Nonadiabatic Kohn Anomaly in a Doped Graphene Monolayer

NASA Astrophysics Data System (ADS)

We compute, from first principles, the frequency of the E2g, ? phonon (Raman G band) of graphene, as a function of the charge doping. Calculations are done using (i) the adiabatic Born-Oppenheimer approximation and (ii) time-dependent perturbation theory to explore dynamic effects beyond this approximation. The two approaches provide very different results. While the adiabatic phonon frequency weakly depends on the doping, the dynamic one rapidly varies because of a Kohn anomaly. The adiabatic approximation is considered valid in most materials. Here, we show that doped graphene is a spectacular example where this approximation miserably fails.

Lazzeri, Michele; Mauri, Francesco

2006-12-01

66

Improved Polarizabilities and Dissociation in DFT: Vignale-Kohn Revisited

NASA Astrophysics Data System (ADS)

We develop a novel approach to the problem of polarizabilities and dissociation in electric fields from the static limit of the Vignale-Kohn (VK) functional. The VK response potential, extracted from the longitudinal component of the VK vector potential has ground-state properties that notably improve over VK response and over usual (semi-)local functionals. The VK density response is not the ground-state response in the corresponding field. Cases where VK density response yields poor polarizabilities, eg the H2 chain, work well in our approach. This is the first density functional method that correctly dissociates open-shell fragments in a field.

Maitra, Neepa; van Faassen, Meta

2007-03-01

67

Asymptotic form of the Kohn-Sham correlation potential

NASA Astrophysics Data System (ADS)

The density-functional correlation potential of a finite system is shown to asymptotically approach a nonzero constant along a nodal surface of the energetically highest occupied orbital and zero everywhere else. This nonuniform asymptotic form of the correlation potential exactly cancels the nonuniform asymptotic behavior of the exact exchange potential discussed by Della Sala and Görling [Phys. Rev. Lett. 89, 33003 (2002)]. The sum of the exchange and correlation potentials therefore asymptotically tends to -1/r everywhere, consistent with the asymptotic form of the Kohn-Sham potential as analyzed by Almbladh and von Barth [Phys. Rev. B 31, 3231 (1985)].

Joubert, D. P.

2007-07-01

68

Relationship between the highest occupied Kohn-Sham orbital eigenvalue and ionization energy

Recent arguments for and against the equivalence of the highest occupied orbital eigenvalue of the Kohn-Sham theory and ionization energy are discussed. It is shown that for physically realistic systems with a nonintegral number of electrons, which are described by the thermal average of two systems, each with an integer number of electrons, an equivalent Kohn-Sham system exists. This is

Manoj K. Harbola

1999-01-01

69

What's It All About, Alfie? A Parent/Educator's Response to Alfie Kohn.

ERIC Educational Resources Information Center

Rebuts Alfie Kohn's article "Only for My Kid: How Privileged Parents are Undermining School Reform" in the April 1998 "Kappan." Kohn expects the author to pay a fortune for a home in an affluent community so his kids can get violence-prevention training and sing "Kumbaya" in a mainstreamed classroom. Earning the right to take an honors class…

Rochester, J. Martin

1998-01-01

70

Theoretical and numerical insight is gained into the ?-I relations between the Kohn-Sham orbital energies ?i and relaxed vertical ionization potentials (VIPs) Ij, which provide an analog of Koopmans' theorem for density functional theory. The Kohn-Sham orbital energy ?i has as leading term -niIi-?j?Omegas(i)njIj, where Ii is the primary VIP for ionization (phii)-1 with spectroscopic factor (proportional to the intensity

O. V. Gritsenko; B. Braïda; E. J. Baerends

2003-01-01

71

Phospholipid transfer protein (PLTP) facilitates the transfer of phospholipids among lipoproteins. Over half of the PLTP in human plasma has been found to have little phospholipid transfer activity (inactive PLTP). We recently observed that plasma PLTP specific activity is inversely correlated with high-density lipoprotein (HDL) level and particle size in healthy adults. The purpose of this study was to evaluate the factors that contribute to the variation in plasma PLTP specific activity. Analysis of the specific activity of PLTP complexes in nine plasma samples from healthy adults revealed two clusters of inactive PLTP complexes with mean molecular weights (MW) of 342kDa and 146kDa. The large and small inactive PLTP complexes represented 52±8% (range 39–63%) and 8±8% (range 1–28%) of the plasma PLTP, respectively. Active PLTP complexes had a mean MW of 207kDa and constituted 40±6% (range 33–50%) of the plasma PLTP. The specific activity of active PLTP varied from 16 to 32 ?mol/?g/h. These data demonstrate for the first time the existence of small inactive plasma PLTP complexes. Variation in the amount of the two clusters of inactive PLTP complexes and the specific activity of the active PLTP contribute to the variation in plasma PLTP specific activity.

Cheung, Marian C.; Wolfbauer, Gertrud; Albers, John J.

2011-01-01

72

Morphological variation in the horse: defining complex traits of body size and shape.

Horses, like many domesticated species, have been selected for broad variation in skeletal size. This variation is not only an interesting model of rapid evolutionary change during domestication, but is also directly applicable to the horse industry. Breeders select for complex traits like body size and skeletal conformation to improve marketability, function, soundness and performance in the show ring. Using a well-defined set of 35 measurements, we have identified and quantified skeletal variation in the horse species. We collected measurements from 1215 horses representing 65 breeds of diverse conformation such as the American Miniature, Shetland Pony, Arabian Horse, Thoroughbred, Shire and Clydesdale. Principal components analysis has identified two key dimensions of skeletal variation in the horse. Principal component 1 is positively correlated with every measurement and quantifies overall body size. Principal component 2 captures a pattern of bone widths vs. lengths and thus quantifies variation in overall bone thickness. By defining these complex skeletal traits, we have created a framework for whole genome association studies to identify quantitative trait loci that contribute to this variation. PMID:21070291

Brooks, S A; Makvandi-Nejad, S; Chu, E; Allen, J J; Streeter, C; Gu, E; McCleery, B; Murphy, B A; Bellone, R; Sutter, N B

2010-12-01

73

Examining and comparing genetic variation for major histocompatibility complex (MHC) and microsatellite (MS) loci in the same individuals provides an opportunity to understand the forces influencing genetic variation. We examined five MHC and three MS loci in 235 bighorn sheep (Ovis canadensis) from 14 populations and found that both types of loci were highly variable and were in Hardy-Weinberg proportions. Mean F(ST) values for both markers were very similar and MHC and MS genetic variability was predominantly distributed within rather than among populations. However, analyses of genetic distances and tree topologies revealed different spatial patterns of variation for the two types of loci. Collectively, these results indicated that neutral forces substantially influenced MS and MHC variation, and they provided limited evidence for selection acting on the MHC.

Boyce, W. M.; Hedrick, P. W.; Muggli-Cockett, N. E.; Kalinowski, S.; Penedo, MCT.; Ramey-II, R. R.

1997-01-01

74

Kohn anomalies and non-adiabaticity in doped carbon nanotubes

NASA Astrophysics Data System (ADS)

The tangential vibrational modes of metallic single-walled carbon nanotubes (SWNTs) are thought to be characterized by Kohn anomalies resulting from the combination of their intrinsic one-dimensional nature and a significant electron- phonon coupling. These properties are modified by the doping- induced tuning of the Fermi energy level ?F, obtained through the intercalation of SWNTs with alkali atoms or the application of a gate potential. We present a Density- Functional Theory (DFT) study of the vibrational properties of a (n,n) metallic SWNT as a function of electronic doping. For such study, we use, as in standard DFT calculations of vibrational properties, the Born-Oppenheimer (BO) approximation, but we also use time-dependent perturbation theory to explore non-adiabatic effects beyond this approximation. We compare our results with existing measurements and suggest features to be explored in future experiments.

Saitta, A. Marco; Caudal, Nicolas; Lazzeri, Michele; Mauri, Francesco

2007-03-01

75

Time-dependent Kohn-Sham theory with memory

NASA Astrophysics Data System (ADS)

In time-dependent density-functional theory, exchange and correlation (xc) beyond the adiabatic local density approximation can be described in terms of viscoelastic stresses in the electron liquid. In the time domain, this leads to a velocity-dependent xc vector potential with a memory containing short- and long-range components. The resulting time-dependent Kohn-Sham formalism describes the dynamics of electronic systems including decoherence and relaxation. For the example of collective charge-density oscillations in a quantum well, we illustrate the xc memory effects, clarify the dissipation mechanism, extract intersubband relaxation rates for weak and strong excitations, and demonstrate the generation of plasmon sidebands. This work was supported by the ACS Petroleum Research Fund and Research Corporation.

Wijewardane, Harshani O.

2005-03-01

76

National Technical Information Service (NTIS)

The Leptodactylus bolivianus complex has been considered to consist of one or two species, L. bolivianus alone or L. bolivianus and L. insularum. Detailed morphological analyses were undertaken to evaluate variation in the complex, which ranges from Costa...

R. O. DeSa W. R. Heyer

2011-01-01

77

Over the past 30 years, studies of single muscles have revealed complex patterns of regional variation in muscle architecture, activation, strain and force. In addition, muscles are often functionally integrated with other muscles in parallel or in series. Understanding the extent of this complexity and the interactions between muscles will profoundly influence how we think of muscles in relation to organismal function, and will allow us to address questions regarding the functional benefits (or lack thereof) and dynamics of this complexity under in vivo conditions. This paper has two main objectives. First, we present a cohesive and integrative review of regional variation in function within muscles, and discuss the functional ramifications that can stem from this variation. This involves splitting regional variation into passive and active components. Second, we assess the functional integration of muscles between different limb segments by presenting new data involving in vivo measurements of activation and strain from the medial gastrocnemius, iliotibialis cranialis and iliotibialis lateralis pars preacetabularis of the helmeted guinea fowl (Numida meleagris) during level running on a motorized treadmill. Future research directions for both of these objectives are presented.

Higham, Timothy E.; Biewener, Andrew A.

2011-01-01

78

Reply to "Comment on `Electron removal energies in Kohn-Sham density-functional theory' "

NASA Astrophysics Data System (ADS)

A local Kohn-Sham potential can be constructed explicitly either in the "exchange-only" density-functional theory of Talman, which does not constrain the density to its Hartree-Fock value, or in the "Hartree-Fock" density-functional theory of von Barth, which does. The Kohn-Sham orbital energies are essentially the same by either choice, as shown here for the beryllium atom. Our conclusion still stands that the exact Kohn-Sham orbital energies for tightly bound electrons are not physical removal energies.

Perdew, John P.; Norman, Michael R.

1984-09-01

79

Puillandre, N. et al. (2010) Genetic divergence and geographic variation in a deep-water cone lineage: molecular and morphological analyses of the Conus orbignyi complex (Mollusca: Conoidea). The cone snails (family Conidae) are a hyperdiverse lineage of venomous gastropods. Two standard markers, COI and ITS2, were used to define six genetically-divergent groups within a subclade of Conidae that includes Conus orbignyi; each of these was then evaluated based on their shell morphology. We conclude that three forms, previously regarded as subspecies of Conus orbignyi are distinct species, now recognized as Conus orbignyi, Conus elokismenos and Conus coriolisi. In addition, three additional species (Conus pseudorbignyi, Conus joliveti and Conus comatosa) belong to this clade. Some of the proposed species (e.g., Conus elokismenos) are possibly in turn complexes comprising multiple species. Groups such as Conidae illustrate the challenges generally faced in species delimitation in biodiverse lineages. In the case of the Conus orbignyi complex, not only are there definable, genetically divergent lineages, but also considerable geographic variation within each group. Our study suggests that an intensive analysis of multiple specimens within a single locality helps to minimize the confounding effects of geographic variation and can be a useful starting point for circumscribing different species within such a confusing complex.

Puillandre, Nicolas; Meyer, Christopher P.; Bouchet, Philippe; Olivera, Baldomero M.

2011-01-01

80

Genotypic and phenotypic variation in transmission traits of a complex life cycle parasite

Characterizing genetic variation in parasite transmission traits and its contribution to parasite vigor is essential for understanding the evolution of parasite life-history traits. We measured genetic variation in output, activity, survival, and infection success of clonal transmission stages (cercaria larvae) of a complex life cycle parasite (Diplostomum pseudospathaceum). We further tested if variation in host nutritional stage had an effect on these traits by keeping hosts on limited or ad libitum diet. The traits we measured were highly variable among parasite genotypes indicating significant genetic variation in these life-history traits. Traits were also phenotypically variable, for example, there was significant variation in the measured traits over time within each genotype. However, host nutritional stage had no effect on the parasite traits suggesting that a short-term reduction in host resources was not limiting the cercarial output or performance. Overall, these results suggest significant interclonal and phenotypic variation in parasite transmission traits that are not affected by host nutritional status.

Louhi, Katja-Riikka; Karvonen, Anssi; Rellstab, Christian; Jokela, Jukka

2013-01-01

81

Genotypic and phenotypic variation in transmission traits of a complex life cycle parasite.

Characterizing genetic variation in parasite transmission traits and its contribution to parasite vigor is essential for understanding the evolution of parasite life-history traits. We measured genetic variation in output, activity, survival, and infection success of clonal transmission stages (cercaria larvae) of a complex life cycle parasite (Diplostomum pseudospathaceum). We further tested if variation in host nutritional stage had an effect on these traits by keeping hosts on limited or ad libitum diet. The traits we measured were highly variable among parasite genotypes indicating significant genetic variation in these life-history traits. Traits were also phenotypically variable, for example, there was significant variation in the measured traits over time within each genotype. However, host nutritional stage had no effect on the parasite traits suggesting that a short-term reduction in host resources was not limiting the cercarial output or performance. Overall, these results suggest significant interclonal and phenotypic variation in parasite transmission traits that are not affected by host nutritional status. PMID:23919156

Louhi, Katja-Riikka; Karvonen, Anssi; Rellstab, Christian; Jokela, Jukka

2013-07-01

82

Mitochondrial DNA sequence variation in a sea star (Leptasterias spp.) species complex.

A 551-bp region of a PCR product containing the putative mitochondrial control region and flanking sequences was analyzed for sequence variation among 19 sea stars representing 10 previously described PCR-RFLP haplotypes within a cryptic species complex (Leptasterias spp.). Most (97%) of the sequence variation was interhaplotypic rather than intrahaplotypic, which greatly reduced the utility of sequence polymorphisms in this mtDNA region as markers of intrahaplotypic population structure and gene flow. The estimated number of transition and transversion substitutions per nucleotide site, corrected for multiple hits, was 0.0364 and 0.0158, respectively. Most of the sequence variation occurred in the first half of the putative control region. Phylogenetic analysis (both maximum parsimony and maximum likelihood) revealed three well-supported clades, but the position of two PCR-RFLP haplotypes was not completely resolved. Low intraspecific mtDNA sequence divergence over large geographic distances may be a general pattern for echinoderm species. PMID:8975695

Hrincevich, A W; Foltz, D W

1996-12-01

83

The Kohn–Sham treatment of anions via the localized Hartree–Fock method

Kohn–Sham calculations of small anions with the localized Hartree–Fock (LHF) method, a recently developed effective exact exchange Kohn–Sham (KS) method, are presented. In contrast to conventional KS methods employing density-functionals from the local density or from generalized gradient approximations, the LHF approach yields bound anions, and thus, is found to be suitable for the treatment of anions. The superiority of

Martin Weimer; Fabio Della Sala; Andreas Görling

2003-01-01

84

Electron removal energies in Kohn-Sham density-functional theory

Talman and co-workers have presented a realization of the exact Kohn-Sham density-functional theory, neglecting correlation. From their numerical results we conclude that the occupied orbital energy eigenvalues of the local-spin-density (LSD) approximation for exchange and correlation are close to the exact Kohn-Sham orbital energies (apart from a constant shift), but that the latter do not accurately predict the removal energies

John P. Perdew; Michael R. Norman

1982-01-01

85

Comment on ``Significance of the highest occupied Kohn-Sham eigenvalue''

With more explanation than usual and without appeal to Janak's theorem, we review the statement and proof of the ionization potential theorems for the exact Kohn-Sham density-functional theory of a many-electron system: (1) For any average electron number N between the integers Z-1 and Z, and thus for N-->Z from below, the highest occupied or partly occupied Kohn-Sham orbital energy

John P. Perdew; Mel Levy

1997-01-01

86

Polarizabilities and excitation energies from the multiplicative Kohn-Sham (MKS) approach

The conventional Kohn-Sham expressions for the static isotropic polarizability and vertical excitation energy are evaluated using Kohn-Sham orbitals and eigenvalues determined directly from theoretical electron densities. For a series of small molecules, polarizabilities determined from wavefunction-based BD(T) electron densities differ, on average, by about 2% from conventional BD(T) polarizabilities when the LDA exchange-correlation integrand is used in the electric Hessian

MARK J. ALLEN; DAVID J. TOZER

2003-01-01

87

Second-order Kohn-Sham perturbation theory: Correlation potential for atoms in a cavity

Second-order perturbation theory based on the Kohn-Sham Hamiltonian leads to an implicit density functional for the correlation energy EcMP2, which is explicitly dependent on both occupied and unoccupied Kohn-Sham single-particle orbitals and energies. The corresponding correlation potential vcMP2, which has to be evaluated by the optimized potential method, was found to be divergent in the asymptotic region of atoms, if

Hong Jiang; Eberhard Engel

2005-01-01

88

Generalized Kohn-Sham Density-Functional Theory via Effective Action Formalism

We present a rigorous formulation of generalized Kohn-Sham density-functional theory. This provides a straightforward Kohn-Sham description of many-body systems based not only on particle-density but also on any other observable. We illustrate the formalism for the case of a particle-density based description of a nonrelativistic many-electron system. We obtain a simple diagrammatic expansion of the exchange-correlation functional in terms of

M. Valiev; G. W. Fernando

1997-01-01

89

A comparative analysis of Hartree-Fock and Kohn-Sham orbital energies

. Hartree-Fock and Kohn-Sham orbital energies, the latter computed with several different exchange\\/correlation functionals,\\u000a are compared and analyzed for 12 molecules. The Kohn-Sham energies differ significantly from experimental ionization energies,\\u000a but by amounts that are, for a given molecule and exchange\\/correlation functional, roughly the same for all of the valence\\u000a orbitals. With the exchange\\/correlation functionals used, the energy of the

Peter Politzer; Fakher Abu-Awwad

1998-01-01

90

Constructing the exact Kohn-Sham potential for orbital dependent functionals

For energy functionals explicitly depending on the Kohn-Sham orbitals, e.g. the exact exchange energy, the corresponding exact Kohn-Sham potential cannot be calculated directly as a functional derivative with respect to the density but must be constructed as the optimized effective potential (OEP). This requires solving an integral equation and, if done straightforwardly, is numerically very involved. We discuss possibilities of

Kuemmel Stephan; John Perdew

2002-01-01

91

Orbital shifts: An easy way to calculate the exact Kohn-Sham exchange potential

The optimized effective potential (OEP) is the exact Kohn-Sham potential for explicitly orbital-dependent energy functionals, e.g.,the exact exchange energy. For such functionals, the Kohn-Sham potential cannot be calculated directly as a functional derivative with respect to the density. Instead, it must be obtained from the solution of the OEP integral equation, which is extremely hard to solve. Here, we show

Stephan Kummel; John Perdew

2003-01-01

92

Lithium local-orbital energy bands using Kohn-Sham and near-Hartree-Fock exchange

The local-orbitals procedure is found to work well with simple metals. Energy bands have been calculated from bcc lithium local orbitals using both Kohn-Sham and near-Hartree-Fock exchange. A free-electron correlation model due to Overhauser was adapted to approximately correct the Hartree-Fock bands for correlation effects. These corrected bands agree well with the Kohn-Sham bands, and both results agree well with

Dwight R. Jennison

1977-01-01

93

Kohn-Sham effective potentials for spin-polarized atomic systems

The Kohn-Sham effective potentials for selected lithium iso-electronic series (Z=3-10) and for the nitrogen atom have been obtained. Configuration interaction and the spin-unrestricted Hartree-Fock (SUHF) densities are used as input and the Kohn-Sham effective potentials for spin-majority and -minority channel are deduced, from which the exchange and correlation contributions are obtained. Accurate values are obtained for such quantities as exchange

Jiqiang Chen; J. B. Krieger; R. O. Esquivel; M. J. Stott; G. J. Iafrate

1996-01-01

94

Exact-exchange Kohn-Sham potential, surface energy, and work function of jellium slabs

Exact-exchange self-consistent calculations of the Kohn-Sham potential, surface energy, and work function of jellium slabs are reported in the framework of the optimized effective potential (OEP) scheme of density functional theory. In the vacuum side of the jellium surface and at a distance z that is larger than the slab thickness, the exchange-only Kohn-Sham potential is found to be imagelike

C. M. Horowitz; C. R. Proetto; J. M. Pitarke

2008-01-01

95

Age-related variation in EEG complexity to photic stimulation: A multiscale entropy analysis

Objective This study was intended to examine variations in electroencephalographic (EEG) complexity in response to photic stimulation (PS) during aging to test the hypothesis that the aging process reduces physiologic complexity and functional responsiveness. Methods Multiscale entropy (MSE), an estimate of time-series signal complexity associated with long-range temporal correlation, is used as a recently proposed method for quantifying EEG complexity with multiple coarse-grained sequences. We recorded EEG in 13 healthy elderly subjects and 12 healthy young subjects during pre-PS and post-PS conditions and estimated their respective MSE values. Results For the pre-PS condition, no significant complexity difference was found between the groups. However, a significant MSE change (complexity increase) was found post-PS only in young subjects, thereby revealing a power-law scaling property, which means long-range temporal correlation. Conclusions Enhancement of long-range temporal correlation in young subjects after PS might reflect a cortical response to stimuli, which was absent in elderly subjects. These results are consistent with the general “loss of complexity/diminished functional response to stimuli” theory of aging. Significance Our findings demonstrate that application of MSE analysis to EEG is a powerful approach for studying age-related changes in brain function.

Takahashi, Tetsuya; Cho, Raymond Y.; Murata, Tetsuhito; Mizuno, Tomoyuki; Kikuchi, Mitsuru; Mizukami, Kimiko; Kosaka, Hirotaka; Takahashi, Koichi; Wada, Yuji

2010-01-01

96

ERIC Educational Resources Information Center

The research project reported in this chapter consists of three studies in which syntactic complexity, lexical variation and fluency appear as dependent variables. The independent variables are task complexity and proficiency level, as the three studies investigate the effect of task complexity on the written and oral performance of L2 learners of…

Kuiken, Folkert; Vedder, Ineke

2012-01-01

97

Calculation of nonadiabatic couplings with restricted open-shell Kohn-Sham density-functional theory

NASA Astrophysics Data System (ADS)

This paper generalizes the recently proposed approaches for calculating the derivative couplings between adiabatic states in density-functional theory (DFT) based on a Slater transition-state density to transitions such as singlet-singlet excitations, where a single-determinant ansatz is insufficient. The proposed approach is based on restricted open-shell Frank et al. [J. Chem. Phys. 108, 4060 (1998)] theory used to describe a spin-adapted Slater transition state. To treat the dependence of electron-electron interactions on the nuclear positions, variational linear-response density-functional perturbation theory is generalized to reference states with an orbital-dependent Kohn-Sham Hamiltonian and nontrivial occupation patterns. The methods proposed in this paper are not limited to the calculation of derivative coupling vectors, but can also be used for the calculation of other transition matrix elements. Moreover, they can be used to calculate the linear response of open-shell systems to arbitrary external perturbations in DFT.

Billeter, Salomon R.; Egli, Daniel

2006-12-01

98

Concern exists about accepting live kidney donation from “medically complex donors” -those with risk factors for future kidney disease. This study’s aim was to examine variation in complex kidney donor use across United States (US) transplant centers. We conducted a retrospective cohort study of live kidney donors using Organ Procurement and Transplantation Network data. Donors with hypertension, obesity, or estimated glomerular filtration rate (eGFR) <60 ml/minute/1.73m2 were considered medically complex. Among 9319 donors, 2254 (24.2%) were complex: 1194 (12.8%) were obese, 956 (10.3%) hypertensive, and 392 (4.2%) had low eGFR. The mean proportion of medically complex donors at a center was 24% (range 0 – 65%.) In multivariate analysis, donor characteristics associated with medical complexity included spousal relationship to the recipient (OR 1.29, CI 1.06-1.56, p<0.01), low education (OR 1.19, CI 1.04-1.37, p=0.01), older age (OR 1.01 per year, CI 1.01-1.02, p<0.01), and non-US citizenship (OR 0.70, CI 0.51-0.97, p=0.01). Renal transplant centers with the highest transplant volume (OR 1.26, CI 1.02-1.57, p=0.03), and with a higher proportion of (living donation)/(all kidney transplants) (OR 1.97, CI 1.23-3.16, p<0.01) were more likely to use medically complex donors. Though controversial, the use of medically complex donors is widespread and varies widely across centers.

Reese, PP; Feldman, HI; McBride, MA; Anderson, K; Asch, DA; Bloom, RD

2008-01-01

99

Kohn-Sham density functional theory is one of the most widely used electronic structure theories. In the pseudopotential framework, uniform discretization of the Kohn-Sham Hamiltonian generally results in a large number of basis functions per atom in order to resolve the rapid oscillations of the Kohn-Sham orbitals around the nuclei. Previous attempts to reduce the number of basis functions per atom

Lin Lin; Jianfeng Lu; Lexing Ying; E. Weinan

2011-01-01

100

Genic heterozygosity and variation were studied in the permanent translocation heterozygotes Oenothera biennis I, Oe. biennis II, Oe. biennis III, Oe. strigosa, Oe. parviflora I, Oe. parviflora II, and in the related bivalent formers Oe. argillicola and Oe. hookeri. From variation at 20 enzyme loci, we find that translocation heterozygosity for the entire chromosome complex is accompanied by only moderate levels of genic heterozygosity: 2.8% in Oe. strigosa, 9.5% in Oe. biennis and 14.9% in Oe. parviflora. Inbred garden strains of Oe. argillicola exhibited 8% heterozygosity; neither garden nor wild strains of Oe. hookeri displayed heterozygosity and only a single allozyme genotype was found. The mean number of alleles per locus is only 1.30 in Oe. strigosa, 1.40 in Oe. biennis, and 1.55 in Oe. parviflora, compared to 1.40 in Oe. argillicola. Clearly, the ability to accumulate and/or retain heterozygosity and variability has not been accompanied by extraordinary levels of either. Clinal variation is evident at some loci in each ring-former. A given translocation complex may vary geographically in its allozymic constitution. From gene frequencies, Oe. biennis I, II, and III, Oe. strigosa and Oe. hookeri are judged to be very closely related, whereas Oe. argillicola seems quite remote; Oe. parviflora is intermediate to the two phylads. Gene frequencies also suggest that Oe. argillicola diverged from the Euoenothera progenitor about 1,000,000 years ago, whereas most of the remaining evolution in the complex has occurred within the last 150,000 years.

Levy, Morris; Levin, Donald A.

1975-01-01

101

Complex potential surface for the {sup 2}B{sub 1} metastable state of the water anion

The potential energy surface corresponding the complex resonance energy of the 2B1 Feshbach resonance state of the water anion is constructed in its full dimensionality. Complex Kohn variational scattering calculations are used to compute the resonance width, while large-scale Configuration Interaction calculations are used to compute the resonance energy. Near the equilibrium geometry, an accompanying ground state potential surface is constructed from Configuration Interaction calculations that treat correlation at a level similar to that used in the calculations on the anion.

Haxton, Daniel J.; Zhang, Zhiyong; McCurdy, C. William; Rescigno, Thomas N.

2004-04-23

102

Measuring method for contour of object in complex high temperature variation environment

NASA Astrophysics Data System (ADS)

The real-time measurement for contour of object would be influenced by many environmental factors when it is taken in complex temperature variation environment. The influence must be eliminated to get effective and accurate measuring results. A new measuring method based on binocular stereo vision is presented. The spectral property of high temperature object is analyzed and adaptive optical band pass filter is designed according to the spectrum. Then the gray value of image is adjusted to get clear images for satisfying the measuring requirement under special conditions.

Liang, Yajun; Miao, Yinxiao; Chen, Xiaohui; Sun, Zengyu

2013-01-01

103

Major histocompatibility complex (MHC) variation in the endangered Mexican wolf and related canids.

We have examined in Mexican wolves and related canids the amount of genetic variation for a class II gene in the major histocompatibility complex (MHC), thought to be part of the most important genetic basis for pathogen resistance in vertebrates. In Mexican wolves, descended from only seven founders over three lineages, there were five different alleles. These were in three phylogenetic groups, only one of which was shared between lineages. Using single stand conformation polymorphism (SSCP), we found that in samples of animals from the two polymorphic lineages, the observed heterozygosity was 0.74 and the genotypes were not different statistically from Hardy-Weinberg proportions. The Ghost Ranch lineage of Mexican wolves was monomorphic for the locus, consistent with the lower level of variation found previously for microsatellite loci and predicted from pedigree analysis. Samples of grey wolves, red wolves, and coyotes had 16 additional alleles. One Mexican wolf allele was also found in grey wolves and another allele was shared between grey and red wolves. Most of the nucleotide variation resulted in amino acid variation and there were five different amino acids found at two different positions. Only two of the 21 variable amino acid positions had solely synonymous nucleotide variation. The average heterozygosity for eight individual amino acid positions in the Mexican wolves was greater than 0.4. The estimated rate of nonsynonymous substitution was 2.5 times higher than that for synonymous substitution for the putative antigen binding site positions, indicative of positive selection acting on these positions. Examination of the known dog sequences for this locus showed that one of the Mexican wolf alleles was found in dogs and that the allele found in both grey and red wolves is also found in dogs. PMID:11240629

Hedrick, P W; Lee, R N; Parker, K M

2000-12-01

104

Efficient construction of exchange and correlation potentials by inverting the Kohn-Sham equations.

Given a set of canonical Kohn-Sham orbitals, orbital energies, and an external potential for a many-electron system, one can invert the Kohn-Sham equations in a single step to obtain the corresponding exchange-correlation potential, vXC(r). For orbitals and orbital energies that are solutions of the Kohn-Sham equations with a multiplicative vXC(r) this procedure recovers vXC(r) (in the basis set limit), but for eigenfunctions of a non-multiplicative one-electron operator it produces an orbital-averaged potential. In particular, substitution of Hartree-Fock orbitals and eigenvalues into the Kohn-Sham inversion formula is a fast way to compute the Slater potential. In the same way, we efficiently construct orbital-averaged exchange and correlation potentials for hybrid and kinetic-energy-density-dependent functionals. We also show how the Kohn-Sham inversion approach can be used to compute functional derivatives of explicit density functionals and to approximate functional derivatives of orbital-dependent functionals. PMID:23968077

Kananenka, Alexei A; Kohut, Sviataslau V; Gaiduk, Alex P; Ryabinkin, Ilya G; Staroverov, Viktor N

2013-08-21

105

Core ionization potentials from self-interaction corrected Kohn-Sham orbital energies.

We propose a simple self-interaction correction to Kohn-Sham orbital energies in order to apply ground state Kohn-Sham density functional theory to accurate predictions of core electron binding energies and chemical shifts. The proposition is explored through a series of calculations of organic compounds of different sizes and types. Comparison is made versus experiment and the "DeltaKohn-Sham" method employing separate state optimizations of the ground and core hole states, with the use of the B3LYP functional and different basis sets. A parameter alpha is introduced for a best fitting of computed and experimental ionization potentials. It is found that internal parametrizations in terms of basis set expansions can be well controlled. With a unique alpha=0.72 and basis set larger than 6-31G, the core ionization energies (IPs) of the self-interaction corrected Kohn-Sham calculations fit quite well to the experimental values. Hence, self-interaction corrected Kohn-Sham calculations seem to provide a promising tool for core IPs that combines accuracy and efficiency. PMID:17994810

Tu, Guangde; Carravetta, Vincenzo; Vahtras, Olav; Agren, Hans

2007-11-01

106

Although tractable model organisms are essential to characterize the molecular mechanisms of evolution and adaptation, the ecological relevance of their behavior is not always clear because certain traits are easily lost during long-term laboratory culturing. Here, we demonstrate that despite their long tenure in the laboratory, model organisms retain "ecological memory" of complex environmental changes. We have discovered that Halobacterium salinarum NRC-1, a halophilic archaeon that dominates microbial communities in a dynamically changing hypersaline environment, simultaneously optimizes fitness to total salinity, NaCl concentration, and the [K]/[Mg] ratio. Despite being maintained under controlled conditions over the last 50 years, peaks in the three-dimensional fitness landscape occur in salinity and ionic compositions that are not replicated in laboratory culturing but are routinely observed in the natural hypersaline environment of this organism. Intriguingly, adaptation to variations in ion composition was associated with differential regulation of anaerobic metabolism genes, suggesting an intertwined relationship between responses to oxygen and salinity. Our results suggest that the ecological memory of complex environmental variations is imprinted in the networks for coordinating multiple cellular processes. These coordination networks are also essential for dealing with changes in other physicochemically linked factors present during routine laboratory culturing and, hence, retained in model organisms. PMID:24413600

Beer, Karlyn D; Wurtmann, Elisabeth J; Pinel, Nicolás; Baliga, Nitin S

2014-03-01

107

Abstract In order to reveal quantitative trait loci (QTL) interactions and the relationship between various interactions in complex traits, we have developed a new QTL mapping approach, named genotype matrix mapping (GMM), which searches for QTL interactions in genetic variation. The central approach in GMM is the following. (1) Each tested marker is given a virtual matrix, named a genotype matrix (GM), containing intersecting lines and rows equal to the total allele number for that marker in the population analyzed. (2) QTL interactions are then estimated and compared through virtual networks among the GMs. To evaluate the contribution of marker combinations to a quantitative phenotype, the GMM method divides the samples into two non-overlapping subclasses, S0 and S1; the former contains the samples that have a specific genotype pattern to be evaluated, and the latter contains samples that do not. Based on this division, the F-measure is calculated as an index of significance. With the GMM method, we extracted significant marker combinations consisting of one to three interacting markers. The results indicated there were multiple QTL interactions affecting the phenotype (flowering date). GMM will be a valuable approach to identify QTL interactions in genetic variation of a complex trait within a variety of organisms.

Isobe, Sachiko; Nakaya, Akihiro; Tabata, Satoshi

2007-01-01

108

Genetic variation in the five taxonomic groups of the Stylosanthes guianensis (Aubl.) Sw. complex was investigated using random amplified polymorphic DNA markers (RAPDs). DNA samples from four plants of each of 45 accessions within the S. guianensis species complex were analyzed using 20 oligonucleotides of random sequence. Little variation was found within each of the 18 accessions (1-7% of total RAPD bands in pairwise comparisons) and none within each of the other 27 accessions. However, higher levels of polymorphisms were observed both within (index of genetic distance = 1 - F = 0.16-0.248) and between (1 - F = 0.254-0.408) the five taxa. This level of differentiation at the DNA level supported an earlier classification of the taxa as distinct species. A phenogram based on band sharing was constructed to show genetic relationships among the taxa studied. This phenogram corroborated the description of relationships based on morphological-agronomic characteristics, seed protein patterns, rhizobial affinities, crossability, and pollen stainability of the hybrids. In this phenogram, the most similar species were S. grandiflora and S. hippocampoides (1 - F = 0.264), with S. acuminata also showing closest similarity to these two species (1 - F = 0.277 and 0.283, respectively). Stylosanthes gracilis accessions showed the closest similarity (1 - F = 0.296) to S. guianensis ssp. guianensis accessions. Lowest similarity values (1 - F = 0.335-0.411) were found between these two species and S. grandiflora, S. acuminata, and S. hippocampoides. PMID:8458571

Kazan, K; Manners, J M; Cameron, D F

1993-02-01

109

Seasonal variations of latent and sensible heat fluxes in complex terrain

NASA Astrophysics Data System (ADS)

Flight altitudes of gliders in early spring indicate that the sensible heat flux into the operationally predicted convective boundary layer has to be increased at the expense of the latent heat flux when vegetation is inactive. In late autumn, winter, and early spring transpiration does not contribute to the latent heat flux and allows for increased sensible heat flux in the surface energy budget. The seasonal variation of the latent heat flux has been parameterized with the climatological daily average temperature: a threshold for the daily average temperature is required for the vegetation to be active. In the complex terrain of the Alps the temperature range from 10 deg C (threshold for active vegetation) down to 2 deg C (threshold for the snow line) for the daily mean temperature covers a significant fraction of the surface. The elevation range corresponding to this temperature range shows a marked seasonal variation. A harmonic seasonal modulation of the daily average temperature was adjusted to climatological station data. Additionally, the vertical decrease of both the annual mean temperature and the seasonal amplitude of the daily mean temperature is relevant in the Alps. Both vertical gradients were again obtained from climatological station data. The threshold parameterization of the transpiration with the climatological daily mean temperature greatly affects the seasonal variation of the predicted depth of the convective boundary layer, as reduced latent heat flux allows for increased sensible heat flux. The effect on the depth of the predicted convection is most pronounced in elevated complex terrain like the Alps. Glider flight trajectories published daily in online soaring contests are used routinely for the verification of operational convection forecasts. With such GPS based flight data regional predictions of the convective updrafts and of the depth of the convective boundary layer can both be verified with great temporal and spatial resolution, throughout the seasons, and almost in real-time. Such glider flight data have been used to develop and verify the described climatological parameterization of transpiration which significantly affects the seasonal variation of the latent and sensible heat fluxes and thus the depth of convection.

Liechti, O.; Thehos, R.

2010-09-01

110

Exact-exchange Kohn-Sham potential, surface energy, and work function of jellium slabs

Exact-exchange self-consistent calculations of the Kohn-Sham potential,\\u000asurface energy, and work function of jellium slabs are reported in the\\u000aframework of the Optimized Effective Potential (OEP) scheme of Density\\u000aFunctional Theory. In the vacuum side of the jellium surface and at a distance\\u000a$z$ that is larger than the slab thickness, the exchange-only Kohn-Sham\\u000apotential is found to be image-like

C. M. Horowitz; C. R. Proetto; J. M. Pitarke

2008-01-01

111

Statistical electron angular correlation coefficients tau = 2 < summation/sup /, have been obtained for the atomic systems /sub 2/He through /sub 14/Si, within the Hohenberg-Kohn-Sham density-functional formalism. These are computed with use of the spectral sum rules obtained from the pseudoexcitation spectrum employing the recent formulation of the time-dependent Kohn-Sham theory due to Bartolotti. Various approximations to the exchange-correlation energy functional are used and for first-row atoms, a comparison is made with the highly accurate correlation coefficients recently obtained by Thakkar. The present tau values show closer agreement with those of Thakkar with increasing number of electrons.

Pathak, R.K.

1985-05-01

112

Genetic variation at the Major Histocompatibility Complex locus DQ beta was analyzed in 233 beluga whales (Delphinapterus leucas) from seven populations: St. Lawrence Estuary, eastern Beaufort Sea, eastern Chukchi Sea, western Hudson Bay, eastern Hudson Bay, southeastern Baffin Island, and High Arctic and in 12 narwhals (Monodon monoceros) sympatric with the High Arctic beluga population. Variation was assessed by amplification of the exon coding for the peptide binding region via the polymerase chain reaction, followed by either cloning and DNA sequencing or single-stranded conformation polymorphism analysis. Five alleles were found across the beluga populations and one in the narwhal. Pairwise comparisons of these alleles showed a 5:1 ratio of nonsynonymous to synonymous substitutions per site leading to eight amino acid differences, five of which were nonconservative substitutions, centered around positions previously shown to be important for peptide binding. Although the amount of allelic variation is low when compared with terrestrial mammals, the nature of the substitutions in the peptide binding sites indicates an important role for the DQ beta locus in the cellular immune response of beluga whales. Comparisons of allele frequencies among populations show the High Arctic population to be different (P < or = .005) from the other beluga populations surveyed. In these other populations an allele, Dele-DQ beta*0101-2, was found in 98% of the animals, while in the High Arctic it was found in only 52% of the animals. Two other alleles were found at high frequencies in the High Arctic population, one being very similar to the single allele found in narwhal. PMID:7659014

Murray, B W; Malik, S; White, B N

1995-07-01

113

Background Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB. Results We sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA. Conclusions Although lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive.

2011-01-01

114

Variations in the identity and complexity of endosymbiont combinations in whitefly hosts

The target of natural selection is suggested to be the holobiont - the organism together with its associated symbiotic microorganisms. The well-defined endosymbiotic communities of insects make them a useful model for exploring the role of symbiotic interactions in shaping the functional repertoire of plants and animals. Here, we studied the variations in the symbiotic communities of the sweet potato whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) by compiling a dataset of over 2000 individuals derived from several independent screenings. The secondary endosymbionts harbored by each individual were clustered into entities termed Facultative Endosymbiont Combinations (FECs), each representing a natural assemblage of co-occurring bacterial genera. The association of FECs with whitefly individuals stratified the otherwise homogeneous population into holobiont units. We both identified bacterial assemblages that are specific to whitefly groups sharing unique genetic backgrounds, and characterized the FEC variations within these groups. The analysis revealed that FEC complexity is positively correlated with both distance from the equator and specificity of the genetic clade of the host insect. These findings highlight the importance of symbiotic combinations in shaping the distribution patterns of B. tabaci and possibly other insect species.

Zchori-Fein, Einat; Lahav, Tamar; Freilich, Shiri

2014-01-01

115

NASA Astrophysics Data System (ADS)

A platinum group element (PGE) investigation of a 5.3 km-thick stratigraphic section of the Stillwater Complex, Montana was undertaken to refine and test a geochemical technique to explore for platiniferous horizons in layered mafic/ultramafic complexes. PGE, Au, major, and trace elements were determined in 92 samples from outcrops along traverses in the Chrome Mountain and Contact Mountain areas in the western part of the Stillwater Complex where the J-M reef occurs ˜1,460 m above the floor of the intrusion. A further 29 samples from a drill hole cored in the immediate vicinity of the J-M reef were analyzed to detail compositional variations directly above and below the J-M reef. Below the J-M reef, background concentrations of Pt (10 ppb) and Pd (7 ppb) are features of peridotites with intermediate S concentrations (mostly 100-200 ppm) and rocks from the Bronzitite, Norite I, and Gabbronorite I zones (mostly <100 ppm S). A sustained increase in S abundance commences at the J-M reef and continues to increase and peaks in the center of the 600 m-thick middle banded series. Over this same interval, Pt, Pd, and Au are initially elevated and then decrease in the order Pd > Pt > Au. Within the middle and upper banded series, S abundances fluctuate considerably, but exhibit an overall upward increase. The behavior of these elements records periodic sulfide saturation during deposition of the Peridotite zone, followed by crystallization under sulfide-undersaturated conditions until saturation is achieved at the base of the J-M reef. Following formation of the reef, sulfide-saturated conditions persisted throughout the deposition of most of the remaining Lower Layered Series. This resulted in a pronounced impoverishment in PGE abundance in the remaining magma, a condition that continued throughout deposition of the remainder of a succession, which is characterized by very low Pt (1.5 ppb) and Pd (0.7 ppb) abundances. Because only unmineralized rock was selected for study in the 5.3 km-thick section, the results provide an unbiased picture of the variation in background PGE levels during crystallization of the Stillwater Complex. In contrast, the variations in the drill core samples through the reef provide a detailed record of ore formation. Plots of Pt, Pd, Pd/S, and Pt + Pd as a function of stratigraphic height in the intrusion show that the location of the J-M reef is defined by an abrupt change in these concentrations and ratios. Although this is the most abrupt change, three other anomalies in PGE abundance and ratios are apparent in the profiles and coincide with known laterally extensive sub-economic sulfide concentrations above the J-M reef. The uppermost of these is the PGE-bearing Picket Pin sulfide horizon. The relative ease with which mineralized horizons can be pinpointed in these diagrams indicates that a similar approach could be used in exploration programs in other ultramafic/mafic intrusions. Our observations exclude the possibilities of either magma mixing within the Stillwater chamber or the fluxing of a volatile-rich fluid as the mechanisms responsible for the genesis of the J-M reef. Rather, our data indicate that the J-M reef formed from a parental magma that was strongly enriched in PGE; this magma likely formed at depth below the Stillwater magma chamber by the interaction of the parental magma with S-rich meta-sedimentary rocks, followed by the re-dissolution of these sulfides in the Stillwater magma.

Keays, Reid R.; Lightfoot, Peter C.; Hamlyn, Paul R.

2012-01-01

116

The Relation between Parental Values and Parenting Behavior: A Test of the Kohn Hypothesis.

ERIC Educational Resources Information Center

To investigate how values influence parenting beliefs and practices, a test was made of Kohn's hypothesis that parents valuing self-direction emphasize the supportive function of parenting, while parents valuing conformity emphasize control of unsanctioned behaviors. Participating in the study were 65 mother-infant dyads. Infants ranged in age…

Luster, Tom; Rhoades, Kelly

117

Interpretation of the Kohn-Sham orbital energies as approximate vertical ionization potentials

Theoretical analysis and results of calculations are put forward to interpret the energies -?k of the occupied Kohn-Sham (KS) orbitals as approximate but rather accurate relaxed vertical ionization potentials (VIPs) Ik. Exact relations between ?k and Ik are established with a set of linear equations for the ?k, which are expressed through Ik and the matrix elements ?kresp of a

D. P. Chong; O. V. Gritsenko; E. J. Baerends

2002-01-01

118

Molecular excitation energies computed with Kohn-Sham orbitals and exact exchange potentials

Exact local exchange potentials are computed for the diatomic molecules N2, O2, and CO, based on expansions in terms of molecular orbitals. Kohn-Sham orbitals and orbital energies are obtained for the exact exchange potentials, with correlation effects neglected. The ionization potential is in all cases found to be accurately predicted by the orbital energy of the highest occupied orbital. Limited

L. Veseth

2001-01-01

119

Comment on "Electron removal energies in Kohn-Sham density-functional theory"

NASA Astrophysics Data System (ADS)

The argument by Perdew and Norman

Trickey, S. B.

1984-09-01

120

"Fighting the Toxic Status Quo": Alfie Kohn on Standardized Tests and Teacher Education.

ERIC Educational Resources Information Center

Considers how many teacher educators feel caught between the need to comply with state and federal laws governing the approval of their teacher education programs and the desire to resist what many feel to be another example of "testing gone wild." Presents a conversation with Alfie Kohn on high stakes tests for teachers and for students. (SG)

Appleman, Deborah; Thompson, Micheal J.

2002-01-01

121

Why Students Lose When "Tougher Standards" Win: A Conversation with Alfie Kohn.

ERIC Educational Resources Information Center

Kohn believes the "tougher standards" movement is incompatible with personalized learning, excellence, and marginalized kids' interests. Horizontal standards that shift how teaching and learning happen in classrooms are terrific, but vertical standards using traditional pedagogy are macho and mindless. Kids need freedom to design their own…

O'Neil, John; Tell, Carol

1999-01-01

122

Density functional theory and Kohn-Sham scheme for self-bound systems

We demonstrate how the separation of the total energy of a self-bound system into a functional of the internal one-body Fermionic density and a function of an arbitrary wave vector describing the center-of-mass kinetic energy can be used to set up an 'internal' Kohn-Sham scheme.

Messud, Jeremie; Suraud, Eric [Universite de Toulouse, UPS, Laboratoire de Physique Theorique (IRSAMC), F-31062 Toulouse (France); CNRS, LPT (IRSAMC), F-31062 Toulouse (France); Bender, Michael [Universite Bordeaux, Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France); CNRS/IN2P3, Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France)

2009-11-15

123

. In order to manage and conserve coral reefs it is essential to understand the factors that structure reef communities. In\\u000a Indonesia’s Jakarta Bay – Pulau Seribu reef complex, pronounced on-to-offshore variation in a number of variables was observed.\\u000a Live coral cover, and echinoderm and fish species richness were higher in midshore sites than either in- or offshore sites.\\u000a Variation in

Daniel F. R. Cleary; Lyndon De Vantier; Giyanto; Lyle Vail; Philip Manto; Nicole J. de Voogd; Paola G. Rachello-Dolmen; Yosephine Tuti; Agus Budiyanto; Jackie Wolstenholme; Bert W. Hoeksema; Suharsono

2008-01-01

124

Localising Loci underlying Complex Trait Variation Using Regional Genomic Relationship Mapping

The limited proportion of complex trait variance identified in genome-wide association studies may reflect the limited power of single SNP analyses to detect either rare causative alleles or those of small effect. Motivated by studies that demonstrate that loci contributing to trait variation may contain a number of different alleles, we have developed an analytical approach termed Regional Genomic Relationship Mapping that, like linkage-based family methods, integrates variance contributed by founder gametes within a pedigree. This approach takes advantage of very distant (and unrecorded) relationships, and this greatly increases the power of the method, compared with traditional pedigree-based linkage analyses. By integrating variance contributed by founder gametes in the population, our approach provides an estimate of the Regional Heritability attributable to a small genomic region (e.g. 100 SNP window covering ca. 1 Mb of DNA in a 300000 SNP GWAS) and has the power to detect regions containing multiple alleles that individually contribute too little variance to be detectable by GWAS as well as regions with single common GWAS-detectable SNPs. We use genome-wide SNP array data to obtain both a genome-wide relationship matrix and regional relationship (“identity by state" or IBS) matrices for sequential regions across the genome. We then estimate a heritability for each region sequentially in our genome-wide scan. We demonstrate by simulation and with real data that, when compared to traditional (“individual SNP") GWAS, our method uncovers new loci that explain additional trait variation. We analysed data from three Southern European populations and from Orkney for exemplar traits – serum uric acid concentration and height. We show that regional heritability estimates are correlated with results from genome-wide association analysis but can capture more of the genetic variance segregating in the population and identify additional trait loci.

Nagamine, Yoshitaka; Pong-Wong, Ricardo; Navarro, Pau; Vitart, Veronique; Hayward, Caroline; Rudan, Igor; Campbell, Harry; Wilson, James; Wild, Sarah; Hicks, Andrew A.; Pramstaller, Peter P.; Hastie, Nicholas; Wright, Alan F.; Haley, Chris S.

2012-01-01

125

We have tested the performance of the Kohn-Sham orbital approach to obtain the electronic coupling and the energetics for hole transfer (HT) in the guanine-indole pair, using a three-state model. The parameters are derived from the simple DFT calculations with 10 different functionals, and compared with benchmark MS-CASPT2 calculations. The guanine-indole pair is a simple model for HT in DNA-protein complexes, which has been postulated as a protection mechanism for DNA against oxidative damage. In this pair, the first excited state of the indole radical cation has low energy (less than 0.3 eV relative to the ground state of the cation), which requires the application of very accurate quantum chemical methods and the invocation of a 3-state model. The Kohn-Sham orbital approach has been tested on six ? stacked and three T-shaped conformers. It has been shown to provide quite accurate results for all ten tested functionals, compared to the reference MS-CASPT2 values. The best performance has been found for the long-range corrected CAM-B3LYP functional. Our results suggest that the Kohn-Sham orbital method can be used to estimate the excited state properties of radical cation systems studied using transient spectroscopy. Because of its accuracy and its low computational cost, the approach allows one to calculate relatively large models and to account for the effects of conformational dynamics on HT between DNA and a protein environment. PMID:25010229

Butchosa, C; Simon, S; Blancafort, L; Voityuk, A A

2014-08-28

126

Impact of complex genetic variation in COMT on human brain function.

Catechol-O-methyltransferase (COMT) has been shown to be critical for prefrontal dopamine flux, prefrontal cortex-dependent cognition and activation. Several potentially functional variants in the gene have been identified, but considerable controversy exists regarding the contribution of individual alleles and haplotypes to risk for schizophrenia, partly because clinical phenotypes are ill-defined and preclinical studies are limited by lack of adequate models. Here, we propose a neuroimaging approach to overcome these limitations by characterizing the functional impact of ambiguous haplotypes on a neural system-level intermediate phenotype in humans. Studying 126 healthy control subjects during a working-memory paradigm, we find that a previously described risk variant in a functional Val158Met (rs4680) polymorphism interacts with a P2 promoter region SNP (rs2097603) and an SNP in the 3' region (rs165599) in predicting inefficient prefrontal working memory response. We report evidence that the nonlinear response of prefrontal neurons to dopaminergic stimulation is a neural mechanism underlying these nonadditive genetic effects. This work provides an in vivo approach to functional validation in brain of the biological impact of complex genetic variations within a gene that may be critical for its clinical association. PMID:16786032

Meyer-Lindenberg, A; Nichols, T; Callicott, J H; Ding, J; Kolachana, B; Buckholtz, J; Mattay, V S; Egan, M; Weinberger, D R

2006-09-01

127

The mechanisms of strong glacial-interglacial variations in the atmospheric CO2 concentration and the role of CO2 in driving glacial cycles still remain debatable. Here using the model of intermediate complexity CLIMBER-2 which includes all major components of the Earth system - atmosphere, ocean, land surface, ice sheets, terrestrial biota and weathering, aeolian dust and marine biogeochemistry - we performed simulation

Victor Brovkin; Andrei Ganopolski; Reinhard Calov; Guy Munhoven; David Archer

2010-01-01

128

Little is currently known about the genetic complexity of quantitative behavioral variation, the types of genes involved, or their effects on intermediate phenotypes. Here, we conduct a genome-wide association study of Drosophila melanogaster courtship song variation using 168 sequenced inbred lines, and fail to find highly significant associations. However, by combining these data with results from a well-powered Evolve and Resequence (E&R) study on the same trait, we provide statistical evidence that some power to associate genotype and phenotype is available. Genes that are significant in both analyses are enriched for expression in the nervous system, and affect neural development and synaptic growth when perturbed. Quantitative complementation at one of these loci, Syntrophin-like 1, supports a hypothesis that variation at this locus affects variation in the inter-pulse interval of courtship song. These results suggest that experimental evolution may provide an approach for genome-scale replication in Drosophila. PMID:23777628

Turner, Thomas L; Miller, Paige M; Cochrane, Veronica A

2013-09-01

129

Theoretical and numerical insight is gained into the &egr;–I relations between the Kohn–Sham orbital energies &egr;i and relaxed vertical ionization potentials (VIPs) Ij, which provide an analog of Koopmans’ theorem for density functional theory. The Kohn–Sham orbital energy &egr;i has as leading term ?niIi??j??s(i)njIj, where Ii is the primary VIP for ionization (?i)?1 with spectroscopic factor (proportional to the intensity

O. V. Gritsenko; E. J. Baerends

2003-01-01

130

The Amsterdam Density Functional (ADF) package has been used to constrain Kohn-Sham DFT in such a fashion that a transition from KS-DFT to ligand-field theory in the form of the parametrical d(q)() model is completely well-defined. A relationship is established between the strong-field approximation of the parametrical d(2) model for the tetrahedral complexes VCl(4)(-) and VBr(4)(-) and certain fixed-orbital ADF-computed energies. In this way values for all the parameters of the d(2)() model may be computed, thus allowing the ADF results to be expressed in terms of a KS-DFT energy matrix that can be diagonalized. This means that the KS-DFT deficiency with regard to computation of nondiagonal elements has been overcome and the KS-DFT eigenenergies have become available through the KS-DFT mimicking of the ligand-field plus repulsion model. By using mutually orthogonal strong-field energy matrices, the mimicking has been further elucidated. The computed values for the empirical parameters of VCl(4)(-) and VBr(4)(-) are in good agreement with experimental data. The spectrochemical and the nephelauxetic series have been computed by including the remaining halide complexes and the quantitatively special position of F(-)() among the halides corroborated for both series. PMID:12817966

Anthon, Christian; Bendix, Jesper; Schäffer, Claus E

2003-06-30

131

The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection.

Grossen, Christine; Keller, Lukas; Biebach, Iris; Croll, Daniel

2014-01-01

132

Molecular variation in the Paragonimus heterotremus complex in Thailand and Myanmar.

Paragonimiasis is an important food-borne parasitic zoonosis caused by infection with lung flukes of the genus Paragonimus. Of the 7 members of the genus known in Thailand until recently, only P. heterotremus has been confirmed as causing human disease. An 8th species, P. pseudoheterotremus, has recently been proposed from Thailand, and has been found in humans. Molecular data place this species as a sister species to P. heterotremus, and it is likely that P. pseudoheterotremus is not specifically distinct from P. heterotremus. In this study, we collected metacercariae of both nominal species (identification based on metacercarial morphology) from freshwater crabs from Phetchabun Province in northern Thailand, Saraburi Province in central Thailand, and Surat Thani Province in southern Thailand. In addition, we purchased freshwater crabs imported from Myanmar at Myawaddy Province, western Thailand, close to the Myanmar-Thailand border. The DNAs extracted from excysted metacercariae were PCR-amplified and sequenced for ITS2 and cox1 genes. The ITS2 sequences were nearly identical among all samples (99-100%). Phylogenies inferred from all available partial cox1 sequences contained several clusters. Sequences from Indian P. heterotremus formed a sister group to sequences from P. pseudoheterotremus-type metacercariae. Sequences of P. heterotremus from Thailand, Vietnam, and China formed a separate distinct clade. One metacercaria from Phitsanulok Province was distinct from all others. There is clearly considerable genetic variation in the P. heterotremus complex in Thailand and the form referred to as P. pseudoheterotremus is widely distributed in Thailand and the Thai-Myanmar border region. PMID:24516273

Sanpool, Oranuch; Intapan, Pewpan M; Thanchomnang, Tongjit; Janwan, Penchom; Nawa, Yukifumi; Blair, David; Maleewong, Wanchai

2013-12-01

133

The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection. PMID:24945814

Grossen, Christine; Keller, Lukas; Biebach, Iris; Croll, Daniel

2014-06-01

134

We examined variation at a class II major histocompatibility complex (MHC) gene (DRB1) in the captive red wolf population and samples of coyotes from Texas and North Carolina. We found 4 alleles in the 48 red wolves, 8 alleles in the 10 coyotes from Texas and 15 alleles in the 29 coyotes from North Carolina. Two of the four alleles found in red wolves, Caru-2 and Caru-4, were found in both the Texas and North Carolina coyote samples. Allele Caru-1, previously found in gray wolves, was also found in the North Carolina sample. The most frequent red wolf allele, Caru-3, was not found in any of the coyote samples. However, an allele found in both the Texas and North Carolina coyote samples is only one nucleotide (one amino acid) different from this red wolf allele. Overall, it appears from examination of this MHC gene that red wolves are more closely related to coyotes than to gray wolves. There were a number of different types of evidence supporting the action of balancing selection in red wolves. Namely, there was: (i) an excess of heterozygotes compared with expectations; (ii) a higher rate of nonsynonymous than synonymous substitution for the functionally important antigen-binding site positions; (iii) an eight times higher average heterozygosity of individual amino acids at the positions identified as part of the antigen-binding site than those not associated with it; (iv) the amino acid divergence of four red wolf alleles was greater than that expected from a simulation of genetic drift; and (v) the distribution of alleles, and the distributions of amino acids at many positions were more even than expected from neutrality. Examination of the level and pattern of linkage disequilibria between pairs of sites suggest that the heterozygosity, substitution and frequencies at individual amino acids are not highly dependent upon each other. PMID:12296935

Hedrick, P W; Lee, R N; Garrigan, D

2002-10-01

135

NASA Astrophysics Data System (ADS)

We assess the accuracy of the LHFX Time-Dependent Density-Functional Theory (TD-DFT) approach, which uses Kohn-Sham orbitals and eigenvalues from the Localized Hartree-Fock (LHF) method and the exchange-only adiabatic local density approximation kernel. We compute 172 singlet and triplet excitation energies of ? ? ??, n ? ??, ? ? ?? and Rydberg character, for organic molecules of different size. We find that the LHFX method, which is free from the Self-Interaction-Error (SIE) and from empirical parameters, outperforms the state-of-the-art hybrid TD-DFT approaches, and provides the same accuracy for all different classes of excitations. The SIE-free Kohn-Sham orbitals can be thus considered as starting point for TD-DFT developments.

Della Sala, F.; Fabiano, E.

2011-11-01

136

Improved Electronic Excitation Energies from Shape-Corrected Semilocal Kohn-Sham Potentials

NASA Astrophysics Data System (ADS)

We propose a general method for obtaining accurate valence and Rydberg excitation energies from standard density-functional approximations in adiabatic linear-response time-dependent density-functional theory. The method consists in modeling the sum of Hartree (Coulomb) and exchange-correlation potentials, vHXC(r), by the Hartree-exchange-correlation potential of the corresponding partially ionized system in which a fraction of electron charge (?=0.15 to 0.30, depending on the functional) is removed from the highest occupied Kohn-Sham orbital level. The model potential is less repulsive and closer to exact in valence and near asymptotic regions, so it yields more accurate Kohn-Sham orbitals and orbital eigenvalues. By applying this scheme to conventional local, semilocal, and hybrid density-functional approximations, we improve their accuracy for Rydberg excitations by almost an order of magnitude without sacrificing the already good performance for valence transitions.

Gaiduk, Alex P.; Firaha, Dzmitry S.; Staroverov, Viktor N.

2012-06-01

137

Improved electronic excitation energies from shape-corrected semilocal Kohn-Sham potentials.

We propose a general method for obtaining accurate valence and Rydberg excitation energies from standard density-functional approximations in adiabatic linear-response time-dependent density-functional theory. The method consists in modeling the sum of Hartree (Coulomb) and exchange-correlation potentials, v(HXC)(r), by the Hartree-exchange-correlation potential of the corresponding partially ionized system in which a fraction of electron charge (? = 0.15 to 0.30, depending on the functional) is removed from the highest occupied Kohn-Sham orbital level. The model potential is less repulsive and closer to exact in valence and near asymptotic regions, so it yields more accurate Kohn-Sham orbitals and orbital eigenvalues. By applying this scheme to conventional local, semilocal, and hybrid density-functional approximations, we improve their accuracy for Rydberg excitations by almost an order of magnitude without sacrificing the already good performance for valence transitions. PMID:23004596

Gaiduk, Alex P; Firaha, Dzmitry S; Staroverov, Viktor N

2012-06-22

138

Electron removal energies in Kohn-Sham density-functional theory

NASA Astrophysics Data System (ADS)

Talman and co-workers have presented a realization of the exact Kohn-Sham density-functional theory, neglecting correlation. From their numerical results we conclude that the occupied orbital energy eigenvalues of the local-spin-density (LSD) approximation for exchange and correlation are close to the exact Kohn-Sham orbital energies (apart from a constant shift), but that the latter do not accurately predict the removal energies of tightly-bound electrons in atoms, molecules, and solids. For the calculation of these removal energies, we propose an add-on, single-shot self-interaction correction (SIC) to the LSD orbital energies, based on a simplification and representation-invariant transformation of the original SIC method. This correction's relationship to the Dyson mass operator is briefly discussed.

Perdew, John P.; Norman, Michael R.

1982-11-01

139

NASA Astrophysics Data System (ADS)

We present an accurate method for constructing the Kohn-Sham effective potential corresponding to a given electron density in one-dimensional and spherically symmetric systems. The method is based on the differential virial theorem--an exact relation between the effective potential, the electron density, and the kinetic energy density. A distinctive feature of the proposed technique is that it employs a size-consistent bosonic reference potential to ensure the correct asymptotic behavior of the resulting Kohn-Sham potential. We describe a practical implementation of our method and use it to obtain high-quality exchange-correlation and correlation potentials of the neon and argon atoms from ab initio densities generated in large Slater- and Gaussian-type basis sets.

Ryabinkin, Ilya G.; Staroverov, Viktor N.

2012-10-01

140

We present an accurate method for constructing the Kohn-Sham effective potential corresponding to a given electron density in one-dimensional and spherically symmetric systems. The method is based on the differential virial theorem--an exact relation between the effective potential, the electron density, and the kinetic energy density. A distinctive feature of the proposed technique is that it employs a size-consistent bosonic reference potential to ensure the correct asymptotic behavior of the resulting Kohn-Sham potential. We describe a practical implementation of our method and use it to obtain high-quality exchange-correlation and correlation potentials of the neon and argon atoms from ab initio densities generated in large Slater- and Gaussian-type basis sets. PMID:23126701

Ryabinkin, Ilya G; Staroverov, Viktor N

2012-10-28

141

We assess the accuracy of the LHFX Time-Dependent Density-Functional Theory (TD-DFT) approach, which uses Kohn–Sham orbitals and eigenvalues from the Localized Hartree–Fock (LHF) method and the exchange-only adiabatic local density approximation kernel. We compute 172 singlet and triplet excitation energies of ????, n???, ???? and Rydberg character, for organic molecules of different size. We find that the LHFX method, which

F. Della Sala; E. Fabiano

142

Conventional continuum exchange-correlation functionals (e.g., local density approximation, generalized gradient approximation) offer a poor description of many response properties, such as static polarizabilities and single photon vertical excitation energies to Rydberg states. These deficiencies are related to errors in the virtual Kohn–Sham orbitals and eigenvalues, which arise due to a fundamental deficiency in the potentials of conventional continuum functionals. Namely,

David J. Tozer; Nicholas C. Handy

1998-01-01

143

Exact Exchange Treatment for Molecules in Finite-Basis-Set Kohn-Sham Theory

The exact orbital-dependent exchange (EXX) energy formalism within the linear-combination-of-atomic-orbital Kohn-Sham density functional theory for polyatomic molecules is presented and implemented. The exchange energies and occupied orbital energies obtained from EXX are very close to the corresponding Hartree-Fock (HF) values, whereas the EXX unoccupied orbital energies are significantly lower than the HF values. We demonstrate that the current approximate correlation

Stanislav Ivanov; So Hirata; Rodney J. Bartlett

1999-01-01

144

On the Presumptive Similarity of Kohn–Sham and Brueckner Orbitals

For states of many-electron systems disclosing various degrees of quasidegeneracy, we have carried out comparative studies of Kohn–Sham orbitals (KSO) generated for several xc-potentials, Brueckner orbitals (BO) represented by the Brueckner-coupled cluster orbitals, and Hartree–Fock (HF) orbitals by means of criteria directly related to the orbital structure which are based on relative distance indices for various pairs of equidimensional subspaces

J. Wasilewski; K. Nowakowski; K. Jankowski

2004-01-01

145

Electron correlation effects on the shape of the Kohn–Sham molecular orbital

. Even systems in which strong electron correlation effects are present, such as the large near-degeneracy correlation in a\\u000a dissociating electron pair bond exemplified by stretched H2, are represented in the Kohn–Sham (KS) model of non-interacting electrons by a determinantal wavefunction built from the\\u000a KS molecular orbitals. As a contribution to the discussion on the status and meaning of the

Oleg V. Gritsenko; Evert Jan Baerends

1997-01-01

146

Physical Content of the Exact Kohn-Sham Orbital Energies: Band Gaps and Derivative Discontinuities

The local-density approximation for the exchange-correlation potential understimates the fundamental band gaps of semiconductors and insulators by about 40%. It is argued here that underestimation of the gap width is also to be expected from the unknown exact potential of Kohn-Sham density-functional theory, because of derivative discontinuities of the exchange-correlation energy. The need for an energy-dependent potential in band theory

John P. Perdew; Mel Levy

1983-01-01

147

Correlated intermolecular interaction components from asymptotically corrected Kohn-Sham orbitals

The symmetry-adapted perturbation theory (SAPT) that has the ability in decomposition of the total interaction energy into\\u000a physically meaningful components is used to provide a more fundamental understanding of intermolecular forces. This work was\\u000a motivated by the difficulty of standard SAPT in computing the intermolecular interactions for large energetic dimer systems.\\u000a SAPT based on Kohn-Sham orbitals (SAPT(DFT)) proves computationally efficient

Huajie Song; Heming Xiao; Haishan Dong

2004-01-01

148

Interpretation of the Kohn–Sham orbital energies as approximate vertical ionization potentials

Theoretical analysis and results of calculations are put forward to interpret the energies ?&egr;k of the occupied Kohn–Sham (KS) orbitals as approximate but rather accurate relaxed vertical ionization potentials (VIPs) Ik. Exact relations between &egr;k and Ik are established with a set of linear equations for the &egr;k, which are expressed through Ik and the matrix elements &egr;kresp of a

D. P. Chong; O. V. Gritsenko; E. J. Baerends

2002-01-01

149

Using Kohn-Sham density functional theory to describe charged excitations in finite systems

We use projector operators to correct the Kohn-Sham Hamiltonian of density functional theory (KS-DFT) so that, in finite systems, the resulting mean-field scheme yields virtual orbitals and energy gaps in better agreement with those predicted by quasiparticle theory. The proposed correction term is a scissorslike operator of the form (Î-rhoˆ)deltaH(Î-rhoˆ) , where Î is the identity operator, rhoˆ is the

Héctor Mera; Kurt Stokbro

2009-01-01

150

Asymptotic behavior of the electron density and the Kohn-Sham potential

It is known that the asymptotic decay $(r \\\\to \\\\infty)$ of the electron density $n(r)$ outside a molecule is informative about its first ionization potential I_0$. Contrary to conventional wisdom, we demonstrate that this asymptotic decay may not be the same in every direction. When the highest occupied Kohn-Sham molecular orbital has a nodal plane, the decay $n(r_p \\\\to\\\\infty)$ on

E. J. Baerends; P. Gori-Giorgi; T. Gál

2011-01-01

151

Continuous corrections to the molecular Kohn-Sham gap and virtual orbitals

We use projector operators to correct the Kohn-Sham Hamiltonian of density functional theory (KS-DFT) so that the resulting mean-field scheme yields, in finite systems, virtual orbitals and energy gaps in better agreement with those predicted by quasiparticle theory. The proposed correction term is a scissors-like operator of the form $(\\\\hat{I}-\\\\hat{\\\\rho})\\\\delta \\\\hat{H}(\\\\hat{I}-\\\\hat{\\\\rho})$, where $\\\\hat{I}$ is the identity operator, $\\\\hat{\\\\rho}$ the density

Hector Mera

2008-01-01

152

A non-orthogonal Kohn-Sham method using partially fixed molecular orbitals

A density functional theory method using partially fixed molecular orbitals (PFMOs) is presented. The PFMOs, which have some fixed molecular orbital coefficients and are non-orthogonal, are a generalization of the extreme localized orbitals (ELMOs) of Couty, Bayse, and Hall (1997) Theor Chem Acc 97:96. A non-orthogonal Kohn-Sham method with these PFMOs is derived, and is applied to molecular calculations on

Kazushi Sorakubo; Takeshi Yanai; Kenichi Nakayama; Muneaki Kamiya; Haruyuki Nakano; Kimihiko Hirao

2003-01-01

153

Conventional continuum exchange-correlation functionals (e.g., local density approximation, generalized gradient approximation) offer a poor description of many response properties, such as static polarizabilities and single photon vertical excitation energies to Rydberg states. These deficiencies are related to errors in the virtual Kohn-Sham orbitals and eigenvalues, which arise due to a fundamental deficiency in the potentials of conventional continuum functionals. Namely,

David J. Tozer; Nicholas C. Handy

1998-01-01

154

First-order intermolecular interaction energies from Kohn–Sham orbitals

It is investigated whether similar to Brueckner orbitals also Kohn–Sham monomer orbitals from current density functional approaches reliably reproduce electron correlation effects on first-order Coulomb and exchange dimer interaction energies. While the Coulomb energy is potentially exact, i.e., exact, if the monomers exact exchange-correlation potential were known, this is not true for the exchange interaction energy. Considering He2,Ne2,Ar2, NeAr, NeHF,

Andreas Heßelmann; Georg Jansen

2002-01-01

155

Configuration interaction with Kohn–Sham orbitals and their relation to excited electronic states

Kohn–Sham (KS) orbitals in CH2, formaldehyde and acetone molecules were used as reference states for configuration interaction (CI) instead of the usual Hartree–Fock (HF) orbitals. A little difference in overall accuracy of electronic excitation energies was found between these schemes. However, analysis of the wave functions indicated that Slater determinant with the KS orbitals is more suitable for construction of

Petr Bou?

2001-01-01

156

Third-order energy derivative corrections to the Kohn-Sham orbital hardness tensor

The third term in the Taylor expansion of the total energy functional around the number of electronsN is evaluated as the second-order derivative of orbital Kohn-Sham energies with respect to orbital occupancy. Present approach\\u000a is an extension of an efficient algorithm to compute densityfunctional based orbital reactivity indices. Various energy derivatives\\u000a used to approximate orbital reactivity indices are defined within

Tzonka Mineva

2005-01-01

157

The theory is presented for asymptotically correcting the potentials of hybrid exchange-correlation functionals, i.e., those that include a fraction of orbital exchange. The Kohn–Sham equations involve a multiplicative potential due to the continuum part of the hybrid functional and a nonmultiplicative term due to the orbital exchange. In asymptotic regions the multiplicative ?-spin potential is corrected to take the form

Mark J. Allen; David J. Tozer

2000-01-01

158

The theory is presented for asymptotically correcting the potentials of hybrid exchange-correlation functionals, i.e., those that include a fraction of orbital exchange. The Kohn-Sham equations involve a multiplicative potential due to the continuum part of the hybrid functional and a nonmultiplicative term due to the orbital exchange. In asymptotic regions the multiplicative sigma-spin potential is corrected to take the form

Mark J. Allen; David J. Tozer

2000-01-01

159

Using Kohn-Sham (KS) density functional theory, the adsorption of Ar on graphite has been computed with various conventional exchange-correlation functionals. While the local density approximation yields a reasonable estimate of equilibrium distance and energy, three generalized gradient approximated functionals fail. Extending the KS Hamiltonian by an empirical nonlocal and atom-centered potential enables quantitative predictions. The adsorption on the on-top, hollow,

Alexandre Tkatchenko; O. Anatole von Lilienfeld

2006-01-01

160

Energy surface, chemical potentials, Kohn-Sham energies in spin-polarized density functional theory.

On the basis of the zero-temperature grand canonical ensemble generalization of the energy E[N,N(s),v,B] for fractional particle N and spin N(s) numbers, the energy surface over the (N,N(s)) plane is displayed and analyzed in the case of homogeneous external magnetic fields B(r). The (negative of the) left-/right-side derivatives of the energy with respect to N, N(?), and N(?) give the fixed-N(s), spin-up, and spin-down ionization potentials/electron affinities, respectively, while the derivative of E[N,N(s),v,B] with respect to N(s) gives the (signed) half excitation energy to the lowest-lying state with N(s) increased (or decreased) by 2. The highest occupied and lowest unoccupied Kohn-Sham spin-orbital energies are identified as the corresponding spin-up and spin-down ionization potentials and electron affinities. The excitation energies to the lowest-lying states with N(s)±2 can be obtained as the differences between the lowest unoccupied and the opposite-spin highest occupied spin-orbital energies, if the (N,N(s)) representation of the Kohn-Sham spin-potentials is used. The cases where the convexity condition on the energy does not hold are also discussed. Finally, the discontinuities of the energy derivatives and the Kohn-Sham potential are analyzed and related. PMID:20949985

Gál, T; Geerlings, P

2010-10-14

161

Stability of minor histocompatibility antigen-MHC molecule complexes is a major requirement for the successful presentation of the antigen to T cell receptors. In this letter we show thermodynamic features of the complexes made of a peptide antigen and its three variants to explain molecular basis of variable stability of the complexes. Our analysis suggests that enthalpy is a major factor in determining the stability of the complexes. We also found that the dissociation of the peptides from the complexes exhibits enthalpy-entropy compensation. Two structural features of the complexes, noncovalent chemical bondings and flexibility of the peptides in the complexes, are in a good agreement with our thermodynamic analysis. We expect thermodynamic investigation of peptide antigen-MHC protein complexes will provide valuable information on the stability. PMID:19564042

Kang, Jonghoon; Auerbach, Jeremy D

2009-09-01

162

The purpose of this investigation was to determine the effects of an increased vitamin B complex diet upon the mental test performances of young children who, prior to the testing period, had been fed a diet inadequate in vitamin B complex. Analysis of the findings reveals an increased efficiency of performance with increased feeding of vitamin B complex. The suggestion

E. R. Balken; S. Maurer

1934-01-01

163

Heritability of variation in glycaemic response to metformin: a genome-wide complex trait analysis

Summary Background Metformin is a first-line oral agent used in the treatment of type 2 diabetes, but glycaemic response to this drug is highly variable. Understanding the genetic contribution to metformin response might increase the possibility of personalising metformin treatment. We aimed to establish the heritability of glycaemic response to metformin using the genome-wide complex trait analysis (GCTA) method. Methods In this GCTA study, we obtained data about HbA1c concentrations before and during metformin treatment from patients in the Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS) study, which includes a cohort of patients with type 2 diabetes and is linked to comprehensive clinical databases and genome-wide association study data. We applied the GCTA method to estimate heritability for four definitions of glycaemic response to metformin: absolute reduction in HbA1c; proportional reduction in HbA1c; adjusted reduction in HbA1c; and whether or not the target on-treatment HbA1c of less than 7% (53 mmol/mol) was achieved, with adjustment for baseline HbA1c and known clinical covariates. Chromosome-wise heritability estimation was used to obtain further information about the genetic architecture. Findings 5386 individuals were included in the final dataset, of whom 2085 had enough clinical data to define glycaemic response to metformin. The heritability of glycaemic response to metformin varied by response phenotype, with a heritability of 34% (95% CI 1–68; p=0·022) for the absolute reduction in HbA1c, adjusted for pretreatment HbA1c. Chromosome-wise heritability estimates suggest that the genetic contribution is probably from individual variants scattered across the genome, which each have a small to moderate effect, rather than from a few loci that each have a large effect. Interpretation Glycaemic response to metformin is heritable, thus glycaemic response to metformin is, in part, intrinsic to individual biological variation. Further genetic analysis might enable us to make better predictions for stratified medicine and to unravel new mechanisms of metformin action. Funding Wellcome Trust.

Zhou, Kaixin; Donnelly, Louise; Yang, Jian; Li, Miaoxin; Deshmukh, Harshal; Van Zuydam, Natalie; Ahlqvist, Emma; Spencer, Chris C; Groop, Leif; Morris, Andrew D; Colhoun, Helen M; Sham, Pak C; McCarthy, Mark I; Palmer, Colin N A; Pearson, Ewan R

2014-01-01

164

Mitochondrial (mt) DNA variation in the cultigens leek, kurrat and prei-anak is limited compared to that of their wild relatives\\u000a in the Allium ampeloprasum complex. The phylogenetic relationships among these cultigens and their wild relatives is quite close, with the majority\\u000a of the species clustering within one mitochondrial clade. The presence in leek of an extra-mitochondrial genetic element was\\u000a noted.

C. Kik; A. M. Samoylov; W. H. J. Verbeek; L. W. D. van Raamsdonk

1997-01-01

165

Greenstone, blueschist and eclogite metabasaltic blocks from the Franciscan complex of California preserve extensive petrographic and chemical evidence for interaction with hydrous fluids at high-P, low-T metamorphic conditions. The Nd and Sr isotope variations within and among the blocks constrain the origin of the basaltic protoliths, the nature of the fluid metasomatism that occurred within the upper levels (15–45 km)

Bruce K. Nelson

1995-01-01

166

In this paper, we present a novel constrained variational principle for simultaneous smoothing and estimation of the diffusion tensor field from complex valued diffusion-weighted images (DWI). The constrained variational principle involves the minimization of a regularization term of L(P) norms, subject to a nonlinear inequality constraint on the data. The data term we employ is the original Stejskal-Tanner equation instead of the linearized version usually employed in literature. The complex valued nonlinear form leads to a more accurate (when compared to the linearized version) estimate of the tensor field. The inequality constraint requires that the nonlinear least squares data term be bounded from above by a known tolerance factor. Finally, in order to accommodate the positive definite constraint on the diffusion tensor, it is expressed in terms of Cholesky factors and estimated. The constrained variational principle is solved using the augmented Lagrangian technique in conjunction with the limited memory quasi-Newton method. Experiments with complex-valued synthetic and real data are shown to depict the performance of our tensor field estimation and smoothing algorithm. PMID:15338727

Wang, Zhizhou; Vemuri, Baba C; Chen, Yunmei; Mareci, Thomas H

2004-08-01

167

NASA Astrophysics Data System (ADS)

The role of the functional form of trial functions used in the Schwinger (SVP) and the Newton (NVP) variational principles are examined. The minimum number of variational parameters required for convergence in each case is compared to the results from a recently developed #S# matrix version of the Kohn variational principle (KVP).

Ramachandran, B.; Wei, Tai-Guang; Wyatt, Robert E.

1988-10-01

168

Complex hybridity in Isotoma petraea V. Allozyme variation and the pursuit of hybridity

Isoenzyme analysis of 12 structurally homozygous and 24 complex hybrid population samples of Isotoma petraea for ten enzyme systems revealed 9 polymorphic and 4 monomorphic loci. The structurally homozygous populations were relatively depauperate in allozyme heterozygotes so that rare alleles occurred more frequently as homozygous rather than heterozygous genotypes. The complex hybrid populations exhibited high levels of fixed allozymic hybridity

S H James; A P Wylie; M S Johnson; S A Carstairs; G A Simpson

1983-01-01

169

Cyclotella meneghiniana Kützing is one of the most commonly found and intensively studied freshwater diatom species. However, it is considered taxonomically problematic because of its unusually wide ecological range and large frustule ultrastructural variation. As part of a study of morphological and genetic variation in this morphospecies, we surveyed nucleotide variation in the hypervariable D1/D2 regions of the 28S rDNA, in the ribosomal internal transcribed spacer region (containing ITS1, the 5.8S rDNA and ITS2) and in the 18S rDNA in a collection of 20 sympatric strains. High genetic variability and strong indications of genetic structure among the Cyclotella meneghiniana strains were found. Representatives of four genetically distinct--apparently reproductively isolated--groups were revealed among them. The random distribution of ITS variation within these four groups indicated that the genetic structure in Cyclotella meneghiniana can probably be explained by the presence of cryptic sexual species rather than by the lack of allogamous sexual reproduction. The morphological features traditionally used for species identification in this group cannot distinguish these putative cryptic species. PMID:16325544

Beszteri, Bánk; Acs, Eva; Medlin, Linda K

2005-11-01

170

The principle of environmental policy integration (EPI) has been adopted by the European Community and gained priority status in its fifth Environmental Action Programme. This article investigates the reasons for considerable variation in applying this principle by comparing the experience of environmental policy integration in two 'most similar' although differently evolving cases: the European Regional Development Fund and the Cohesion

Andrea Lenschow

1997-01-01

171

An important but challenging task is to understand microdevelopmental varia- tions in learning and developmental processes—how patterns of performance change over short time periods with growing skill and knowledge or with failure to learn. This study analyzed microdevelopmental variations in learning a basic computing skill. Based on 119 microdevelopmental episodes of 30 students learning a computer program in four sessions

Zheng Yan; Kurt Fischer

172

Brain functional and cytoarchitectural maturation continue until adulthood, but little is known about the evolution of the regional pattern of cortical thickness (CT), complexity (CC), and intensity or gradient (CG) in young adults. We attempted to detect global and regional age- and gender-related variations of brain CT, CC, and CG, in 28 healthy young adults (19-33 years) using a three-dimensional T1 -weighted magnetic resonance imaging sequence and surface-based methods. Whole brain interindividual variations of CT and CG were similar to that in the literature. As a new finding, age- and gender-related variations significantly affected brain complexity (P?

Creze, Maud; Versheure, Leslie; Besson, Pierre; Sauvage, Chloe; Leclerc, Xavier; Jissendi-Tchofo, Patrice

2014-06-01

173

NASA Astrophysics Data System (ADS)

Kohn-Sham density functional theory is one of the most widely used electronic structure theories. In the pseudopotential framework, uniform discretization of the Kohn-Sham Hamiltonian generally results in a large number of basis functions per atom in order to resolve the rapid oscillations of the Kohn-Sham orbitals around the nuclei. Previous attempts to reduce the number of basis functions per atom include the usage of atomic orbitals and similar objects, but the atomic orbitals generally require fine tuning in order to reach high accuracy. We present a novel discretization scheme that adaptively and systematically builds the rapid oscillations of the Kohn-Sham orbitals around the nuclei as well as environmental effects into the basis functions. The resulting basis functions are localized in the real space, and are discontinuous in the global domain. The continuous Kohn-Sham orbitals and the electron density are evaluated from the discontinuous basis functions using the discontinuous Galerkin (DG) framework. Our method is implemented in parallel and the current implementation is able to handle systems with at least thousands of atoms. Numerical examples indicate that our method can reach very high accuracy (less than 1 meV) with a very small number (4-40) of basis functions per atom.

Lin, Lin; Lu, Jianfeng; Ying, Lexing; E, Weinan

2012-02-01

174

Higher-order adaptive finite-element methods for Kohn–Sham density functional theory

We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn–Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss–Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100–200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn–Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn–Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688 atoms using modest computational resources, and good scalability of the present implementation up to 192 processors.

Motamarri, P. [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)] [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Nowak, M.R. [Department of Electrical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)] [Department of Electrical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Leiter, K.; Knap, J. [U.S. Army Research Labs, Aberdeen Proving Ground, Aberdeen, MD 21001 (United States)] [U.S. Army Research Labs, Aberdeen Proving Ground, Aberdeen, MD 21001 (United States); Gavini, V., E-mail: vikramg@umich.edu [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)

2013-11-15

175

Higher-order adaptive finite-element methods for Kohn–Sham density functional theory

NASA Astrophysics Data System (ADS)

We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn–Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss–Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100–200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn–Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn–Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688 atoms using modest computational resources, and good scalability of the present implementation up to 192 processors.

Motamarri, P.; Nowak, M. R.; Leiter, K.; Knap, J.; Gavini, V.

2013-11-01

176

This research addressed the temporal and spatial variation of soil moisture (SM) in a heterogeneous landscape. The research objective was to investigate soil moisture variation in eight homogeneous 30 by 30 m plots, similar to the pixel size of a Landsat Thematic Mapper (TM) or Enhanced Thematic Mapper plus (ETM+) image. The plots were adjacent to eight stations of an in situ soil moisture network operated by the United States Department of Agriculture-Agriculture Research Service USDA-ARS in Tifton, GA. We also studied five adjacent agricultural fields to examine the effect of different landuses/land covers (LULC) (grass, orchard, peanuts, cotton and bare soil) on the temporal and spatial variation of soil moisture. Soil moisture field data were collected on eight occasions throughout 2005 and January 2006 to establish comparisons within and among eight homogeneous plots. Consistently throughout time, analysis of variance (ANOVA) showed high variation in the soil moisture behavior among the plots and high homogeneity in the soil moisture behavior within them. A precipitation analysis for the eight sampling dates throughout the year 2005 showed similar rainfall conditions for the eight study plots. Therefore, soil moisture variation among locations was explained by in situ local conditions. Temporal stability geostatistical analysis showed that soil moisture has high temporal stability within the small plots and that a single point reading can be used to monitor soil moisture status for the plot within a maximum 3% volume/volume (v/v) soil moisture variation. Similarly, t-statistic analysis showed that soil moisture status in the upper soil layer changes within 24 h. We found statistical differences in the soil moisture between the different LULC in the agricultural fields as well as statistical differences between these fields and the adjacent 30 by 30 m plots. From this analysis, it was demonstrated that spatial proximity is not enough to produce similar soil moisture, since t-test's among adjacent plots with different LULCs showed significant differences. These results confirm that a remote sensing approach that considers homogeneous LULC landscape fragments can be used to identify landscape units of similar soil moisture behavior under heterogeneous landscapes. In addition, the in situ USDA-ARS network will serve better in remote sensing studies in which sensors with fine spatial resolution are evaluated. This study is a first step towards identifying landscape units that can be monitored using the single point reading of the USDA-ARS stations network. ?? 2008 Elsevier B.V.

Giraldo, M. A.; Bosch, D.; Madden, M.; Usery, L.; Kvien, C.

2008-01-01

177

NASA Astrophysics Data System (ADS)

SummaryThis research addressed the temporal and spatial variation of soil moisture (SM) in a heterogeneous landscape. The research objective was to investigate soil moisture variation in eight homogeneous 30 by 30 m plots, similar to the pixel size of a Landsat Thematic Mapper (TM) or Enhanced Thematic Mapper plus (ETM+) image. The plots were adjacent to eight stations of an in situ soil moisture network operated by the United States Department of Agriculture-Agriculture Research Service USDA-ARS in Tifton, GA. We also studied five adjacent agricultural fields to examine the effect of different landuses/land covers (LULC) (grass, orchard, peanuts, cotton and bare soil) on the temporal and spatial variation of soil moisture. Soil moisture field data were collected on eight occasions throughout 2005 and January 2006 to establish comparisons within and among eight homogeneous plots. Consistently throughout time, analysis of variance (ANOVA) showed high variation in the soil moisture behavior among the plots and high homogeneity in the soil moisture behavior within them. A precipitation analysis for the eight sampling dates throughout the year 2005 showed similar rainfall conditions for the eight study plots. Therefore, soil moisture variation among locations was explained by in situ local conditions. Temporal stability geostatistical analysis showed that soil moisture has high temporal stability within the small plots and that a single point reading can be used to monitor soil moisture status for the plot within a maximum 3% volume/volume (v/v) soil moisture variation. Similarly, t-statistic analysis showed that soil moisture status in the upper soil layer changes within 24 h. We found statistical differences in the soil moisture between the different LULC in the agricultural fields as well as statistical differences between these fields and the adjacent 30 by 30 m plots. From this analysis, it was demonstrated that spatial proximity is not enough to produce similar soil moisture, since t-test's among adjacent plots with different LULCs showed significant differences. These results confirm that a remote sensing approach that considers homogeneous LULC landscape fragments can be used to identify landscape units of similar soil moisture behavior under heterogeneous landscapes. In addition, the in situ USDA-ARS network will serve better in remote sensing studies in which sensors with fine spatial resolution are evaluated. This study is a first step towards identifying landscape units that can be monitored using the single point reading of the USDA-ARS stations network.

Giraldo, Mario A.; Bosch, David; Madden, Marguerite; Usery, Lynn; Kvien, Craig

2008-08-01

178

Lcao-Gáspár-Kohn-Sham energy bands of trans-polyacetylene-chain

NASA Astrophysics Data System (ADS)

The band structure of the dimerised trans-polyacetylene-chain ( d C?C = 1.35 Å, d C?C = 1.46 Å, ? CCC = 120° , d C?H = 1.09 Å) is calculated with the (parameter-free, non-self-consistent) linear-combination-of-atomic-orbitals method using the Gáspár-Kohn-Sham (GKS) potential for the exchange and correlation. The calculated dimerisation gap of 1.6 eV agrees closely with experiment and also with other GKS calculations when the degree of dimerisation is taken into account. The calculated density of states agrees closely with the X-ray photoemission spectrum of Brundle.

von Boehm, J.; Kuivalainen, P.; Calais, J.-L.

1983-12-01

179

NASA Astrophysics Data System (ADS)

Using Kohn-Sham (KS) density functional theory, the adsorption of Ar on graphite has been computed with various conventional exchange-correlation functionals. While the local density approximation yields a reasonable estimate of equilibrium distance and energy, three generalized gradient approximated functionals fail. Extending the KS Hamiltonian by an empirical nonlocal and atom-centered potential enables quantitative predictions. The adsorption on the on-top, hollow, and bridge sites has been investigated, and it is found that the London dispersion corrected calculations prefer the hollow site which is in agreement with other studies. Furthermore, the adsorption effect of several submonolayer coverages and of the graphitic bulk has been studied.

Tkatchenko, Alexandre; von Lilienfeld, O. Anatole

2006-04-01

180

Giant Kohn anomaly and the phase transition in charge density wave ZrTe3.

A strong Kohn anomaly in ZrTe3 is identified in the mostly transverse acoustic phonon branch along the modulation vector q_{P} with polarization along the a;{*} direction. This soft mode freezes to zero frequency at the transition temperature T_{P}, and the temperature dependence of the frequency is strongly affected by fluctuation effects. Diffuse x-ray scattering of the incommensurate superstructure shows a power-law scaling of the intensity and the correlation length that is compatible with an order parameter of dimension n=2. PMID:19257759

Hoesch, Moritz; Bosak, Alexey; Chernyshov, Dmitry; Berger, Helmuth; Krisch, Michael

2009-02-27

181

VlpE is characterized as a new member in a family of variable surface lipoproteins (Vlps) of Mycoplasma hyorhinis. VlpE shows phenotypic variation in expression and size within isogenic lineages of some strains but is absent from lineages of other strains that express only three previously known Vlps. Expression of four Vlps in some cells further indicates the presence and usage of an expanded reservoir of Vlp coding sequences, which greatly increases the capacity for surface diversification. Images

Rosengarten, R; Theiss, P M; Yogev, D; Wise, K S

1993-01-01

182

Genome partitioning of genetic variation for complex traits using common SNPs

We estimate and partition genetic variation for height, body mass index (BMI), von Willebrand factor and QT interval (QTi) using 586,898 SNPs genotyped on 11,586 unrelated individuals. We estimate that ?45%, ?17%, ?25% and ?21% of the variance in height, BMI, von Willebrand factor and QTi, respectively, can be explained by all autosomal SNPs and a further ?0.5–1% can be

Jian Yang; Teri A Manolio; Louis R Pasquale; Eric Boerwinkle; Neil Caporaso; Julie M Cunningham; Mariza de Andrade; Bjarke Feenstra; Eleanor Feingold; M Geoffrey Hayes; William G Hill; Maria Teresa Landi; Alvaro Alonso; Guillaume Lettre; Peng Lin; Hua Ling; William Lowe; Rasika A Mathias; Mads Melbye; Elizabeth Pugh; Marilyn C Cornelis; Bruce S Weir; Michael E Goddard; Peter M Visscher

2011-01-01

183

The rate of recombination is a key genomic parameter that displays considerable variation among taxa. Species comparisons have demonstrated that the rate of evolution in recombination rate is strongly dependent on the physical scale of measurement. Individual recombination hotspots are poorly conserved among closely related taxa, whereas genomic-scale recombination rate variation bears a strong signature of phylogenetic history. In contrast, the mode and tempo of evolution in recombination rates measured on intermediate physical scales is poorly understood. Here, we conduct a detailed statistical comparison between two whole-genome F2 genetic linkage maps constructed from experimental intercrosses between closely related house mouse subspecies (Mus musculus). Our two maps profile a common wild-derived inbred strain of M. m. domesticus crossed to distinct wild-derived inbred strains representative of two other house mouse subspecies, M. m. castaneus and M. m. musculus. We identify numerous orthologous genomic regions with significant map length differences between these two crosses. Because the genomes of these recently diverged house mice are highly collinear, observed differences in map length (centimorgans) are suggestive of variation in broadscale recombination rate (centimorgans per megabase) within M. musculus. Collectively, these divergent intervals span 19% of the house mouse genome, disproportionately aggregating on the X chromosome. In addition, we uncover strong statistical evidence for a large effect, sex-linked, site-specific modifier of recombination rate segregating within M. musculus. Our findings reveal considerable variation in the megabase-scale recombination landscape among recently diverged taxa and underscore the continued importance of genetic linkage maps in the post-genome era.

Dumont, Beth L.; White, Michael A.; Steffy, Brian; Wiltshire, Tim; Payseur, Bret A.

2011-01-01

184

Toward Failure Modeling In Complex Dynamic Systems: Impact of Design and Manufacturing Variations

NASA Technical Reports Server (NTRS)

When designing vehicle vibration monitoring systems for aerospace devices, it is common to use well-established models of vibration features to determine whether failures or defects exist. Most of the algorithms used for failure detection rely on these models to detect significant changes during a flight environment. In actual practice, however, most vehicle vibration monitoring systems are corrupted by high rates of false alarms and missed detections. Research conducted at the NASA Ames Research Center has determined that a major reason for the high rates of false alarms and missed detections is the numerous sources of statistical variations that are not taken into account in the. modeling assumptions. In this paper, we address one such source of variations, namely, those caused during the design and manufacturing of rotating machinery components that make up aerospace systems. We present a novel way of modeling the vibration response by including design variations via probabilistic methods. The results demonstrate initial feasibility of the method, showing great promise in developing a general methodology for designing more accurate aerospace vehicle vibration monitoring systems.

Tumer, Irem Y.; McAdams, Daniel A.; Clancy, Daniel (Technical Monitor)

2001-01-01

185

Introduction The genetic region coding for D-amino acid oxidase activator (DAOA) is considered an intriguing susceptibility locus for schizophrenia. However, association studies have often resulted in conflicting findings, and the risk conferring variants and their biological impact remain elusive. Our aim in this study was to investigate the relationship between DAOA variation and schizophrenia, and the influence of DAOA on cognitive performance. Methods We analyzed block structure and association patterns of a ~173 kb region on chromosome 13q33, applying genotype data of 55 SNPs derived from Caucasian North American sample (178 cases, 144 healthy controls). Haplotypes were assigned using the program PHASE and frequencies compared between cases and controls. We applied MANOVA to investigate the relationship between the identified risk haplotype on cognitive performance. Results We identified multiple haplotypes within the region containing the DAOA gene. Of these, one was significantly associated with schizophrenia, being over-represented in schizophrenia versus healthy controls. This haplotype was also associated with one aspect of cognitive performance, semantic fluency. Carriers of the risk haplotype showed better semantic fluency than non-carriers. Conclusions We report a significant effect of DAOA variation on risk for schizophrenia. Moreover, we identified a relationship between DAOA genetic variation and specific aspects of neurocognitive function. As the identified DAOA risk haplotype was associated with better performance on a semantic fluency measure, further work is required to identify the mechanism of DAOA action on CNS function, including the possibility of a role for balanced selection at this locus.

Opgen-Rhein, Carolin; Lencz, Todd; Burdick, Katherine E.; Neuhaus, Andres H; DeRosse, Pamela; Goldberg, Terry E.; Malhotra, Anil K.

2008-01-01

186

Structural variation in cobalt halide complexes supported by m-terphenyl isocyanides

Detailed herein are synthetic, spectroscopic and structural studies on trisisocyanide cobalt halide complexes featuring the encumbering m-terphenyl isocyanide CNArMes2 (Mes=2,4,6-Me3C6H3). Addition of CNArMes2 to CoI2 in a 3:1 molar ratio provides the mononuclear complex, CoI2(CNArMes2)3, which can be oxidized to six-coordinate CoI3(CNArMes2)3 upon treatment with 0.5 equivalents of I2. Contrastingly, addition of CNArMes2 to CoBr2 provided the dinuclear complex Br2Co(?2-Br)2Co(CNArMes2)3

Nils Weidemann; Grant W. Margulieux; Curtis E. Moore; Arnold L. Rheingold; Joshua S. Figueroa

2010-01-01

187

Physiological mechanisms that pleiotropically affect condition, life-history decisions, and fitness may covary with the expression of sexually selected ornaments. The adrenocortical stress response regulates energy balance, controls vertebrate responses to survival threats, and may divert energy expenditure away from investment in costly sexual displays. Further, developmental stress may induce correlations between the stress response during adulthood and sexual signals that develop early in life, such as song in oscine birds. We examined the relationship between the adrenocortical stress response (measured by plasma corticosterone concentrations) and the sexually selected traits of song complexity and song rate in song sparrows (Melospiza melodia). Additionally, we explored whether the stress response, song complexity, or song rate predict other male quality and fitness metrics. In contrast to prior research, which reports negative relationships between song complexity and the stress response in this species, males with larger song repertoires had larger stress responses. Song rate was unrelated to the stress response, but positively correlated with male body mass and nestling mass. In addition, males with higher syllable diversity had longer wingchords and lower hematocrit, males with larger song repertoires had heavier nestlings and higher hematocrit, and males with larger stress responses and baseline corticosterone had higher hematocrit. Results suggest that the relationship between the stress response and song complexity is context-dependent, and that song repertoire size, syllable diversity, and song rate serve distinct signaling functions. PMID:24650781

Grunst, Melissa L; Grunst, Andrea S

2014-05-01

188

The Hartree product is analyzed in the context of Kohn–Sham theory. The differential equations that emerge from this theory are solved with the optimized effective potential using the Krieger, Li, and Iafrate approximation, in order to get a local potential as required by the ordinary Kohn–Sham procedure. Because the diagonal terms of the exact exchange energy are included in Hartree

Jorge Garza; Jeffrey A. Nichols; David A. Dixon

2000-01-01

189

The Hartree product is analyzed in the context of Kohn-Sham theory. The differential equations that emerge from this theory are solved with the optimized effective potential using the Krieger, Li, and Iafrate approximation, in order to get a local potential as required by the ordinary Kohn-Sham procedure. Because the diagonal terms of the exact exchange energy are included in Hartree

Jorge Garza; Jeffrey A. Nichols; David A. Dixon

2000-01-01

190

The Fukui function, hardness, and other reactivity indices defined in\\u000a the context of the Kohn-Sham scheme have been further examined following\\u000a up previous developments. An equation analogue to the Berkowitz-Parr\\u000a relationship among the noninteracting linear response function and a new\\u000a Kohn-Sham softness hierarchy can be derived as defined in the present\\u000a study. The thermodynamic-like structure of the mathematical equations is

P. Fuentealba; E. Chamorro; C. Cardenas

2007-01-01

191

Self-interaction correction scheme for approximate Kohn-Sham potentials

NASA Astrophysics Data System (ADS)

Recently [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.108.253005 108, 253005 (2012)], we observed that approximate Hartree-exchange-correlation potentials constructed from electron densities depleted at the highest-occupied molecular orbital (HOMO) level mimic the exact potential at intermediate distances from the nuclei; we then used this fact to obtain accurate Rydberg excitation energies of atoms and molecules within time-dependent density-functional linear-response theory employing standard semilocal approximations. Here we reinterpret this method as a form of self-interaction correction for Kohn-Sham potentials. We show that the greatest improvement in HOMO eigenvalues occurs when the charge removed from the HOMO level is about (1)/(2) electron, which explains why the Slater transition-state method works well for predicting ionization energies. The greatest improvement in Kohn-Sham orbital gaps, however, is achieved when about (1)/(4) electron is removed, which is why smaller HOMO depopulations are required for obtaining accurate excitation energies. The relationship between our self-interaction correction scheme, Slater's transition-state technique, and the X? method is also clarified.

Gaiduk, Alex P.; Mizzi, Dan; Staroverov, Viktor N.

2012-11-01

192

Kohn's localization in the insulating state: One-dimensional lattices, crystalline versus disordered

NASA Astrophysics Data System (ADS)

The qualitative difference between insulators and metals stems from the nature of the low-lying excitations, but also-according to Kohn's theory [W. Kohn, Phys. Rev. 133, A171 (1964)]-from a different organization of the electrons in their ground state: electrons are localized in insulators and delocalized in metals. We adopt a quantitative measure of such localization, by means of a ``localization length'' ?, finite in insulators and divergent in metals. We perform simulations over a one-dimensional binary alloy model, in a tight-binding scheme. In the ordered case the model is either a band insulator or a band metal, whereas in the disordered case it is an Anderson insulator. The results show indeed a localized/delocalized ground state in the insulating/metallic cases, as expected. More interestingly, we find a significant difference between the two insulating cases: band versus Anderson. The insulating behavior is due to two very different scattering mechanisms; we show that the corresponding values of ? differ by a large factor for the same alloy composition. We also investigate the organization of the electrons in the many body ground state from the viewpoint of the density matrices and of Boys' theory of localization.

Bendazzoli, Gian Luigi; Evangelisti, Stefano; Monari, Antonio; Resta, Raffaele

2010-08-01

193

The polychromatic and trophically polymorphic Midas cichlid fish species complex (Amphilophus cf. citrinellus) is an excellent model system for studying the mechanisms of speciation and patterns of phenotypic diversification in allopatry and in sympatry. Here, we first review research to date on the species complex and the geological history of its habitat. We analyse body shape variation from all currently described species in the complex, sampled from six crater lakes (maximally 1.2–23.9 kyr old) and both great lakes in Nicaragua. We find that Midas cichlid populations in each lake have their own characteristic body shape. In lakes with multiple sympatric species of Midas cichlid, each species has a distinct body shape. Across the species complex, most body shape change relates to body depth, head, snout and mouth shape and caudal peduncle length. There is independent parallel evolution of an elongate limnetic species in at least two crater lakes. Mitochondrial genetic diversity is higher in crater lakes with multiple species. Midas cichlid species richness increases with the size and age of the crater lakes, though no such relationship exists for the other syntopic fishes. We suggest that crater lake Midas cichlids follow the predicted pattern of an adaptive radiation, with early divergence of each crater lake colonization, followed by intralacustrine diversification and speciation by ecological adaptation and sexual selection.

Elmer, Kathryn R.; Kusche, Henrik; Lehtonen, Topi K.; Meyer, Axel

2010-01-01

194

CO Isotopologues in the Perseus Molecular Cloud Complex: the X-factor and Regional Variations

We use data gathered by the COMPLETE survey of star-forming regions to find new calibrations of the ``X-factor'' and 13CO abundance within the Perseus molecular cloud. We divide Perseus into six subregions, using groupings in a dust temperature vs. LSR velocity plot. The standard X-factor, X?N(H2)\\/W(12CO), is derived both for the whole Perseus complex and for each of the six

Jaime E. Pineda; Paola Caselli; Alyssa A. Goodman

2008-01-01

195

Phase effects on the masking of speech by harmonic complexes: Variations with level

Speech reception thresholds were obtained in normally hearing listeners for sentence targets masked by harmonic complexes constructed with different phase relationships. Maskers had either a constant fundamental frequency (F0), or had F0 changing over time, following a pitch contour extracted from natural speech. The median F0 of the target speech was very similar to that of the maskers. In experiment 1 differences in the masking produced by Schroeder positive and Schroeder negative phase complexes were small (around 1.5 dB) for moderate levels [60 dB sound pressure level (SPL)], but increased to around 6 dB for maskers at 80 dB SPL. Phase effects were typically around 1.5 dB larger for maskers that had naturally varying F0 contours than for maskers with constant F0. Experiment 2 showed that shaping the long-term spectrum of the maskers to match the target speech had no effect. Experiment 3 included additional phase relationships at moderate levels and found no effect of phase. Therefore, the phase relationship within harmonic complexes appears to have only minor effects on masking effectiveness, at least at moderate levels, and when targets and maskers are in the same F0 range.

Green, Tim; Rosen, Stuart

2013-01-01

196

Lrp-DNA complex stability determines the level of ON cells in type P fimbriae phase variation.

F165(1) and the pyelonephritis-associated pili (Pap) are two members of the type P family of adhesive factors that play a key role in the establishment of disease caused by extraintestinal Escherichia coli (ExPEC) strains. They are both under the control of an epigenetic and reversible switch that defines the number of fimbriated (ON) and afimbriated (OFF) cells within a clonal population. Our present study demonstrates that the high level of ON cells found during F165(1) phase variation is due to altered stability of the DNA complex formed by the leucine-responsive regulatory protein (Lrp) at its repressor binding sites 1-3; after each cell cycle, complex formation is also modulated by the local regulator FooI (homologue to PapI) which promotes the transit of Lrp towards its activator binding sites 4-6. Furthermore, we identified two nucleotides (T490, G508) surrounding the Lrp binding site 1 that are critical to maintaining a high OFF to ON switch rate during F165(1) phase variation, as well as switching Pap fimbriae towards the OFF state. PMID:21752106

Graveline, Richard; Mourez, Michaël; Hancock, Mark A; Martin, Christine; Boisclair, Stéphanie; Harel, Josée

2011-09-01

197

Genetic differences among tree species, their hybrids and within tree species are known to influence associated ecological communities and ecosystem processes in areas of limited species diversity. The extent to which this same phenomenon occurs based on genetic variation within a single tree species, in a diverse complex ecosystem such as a tropical forest, is unknown. The level of biodiversity and complexity of the ecosystem may reduce the impact of a single tree species on associated communities. We assessed the influence of within-species genetic variation in the tree Brosimum alicastrum (Moraceae) on associated epiphytic and invertebrate communities in a neotropical rainforest. We found a significant positive association between genetic distance of trees and community difference of the epiphytic plants growing on the tree, the invertebrates living among the leaf litter around the base of the tree, and the invertebrates found on the tree trunk. This means that the more genetically similar trees are host to more similar epiphyte and invertebrate communities. Our work has implications for whole ecosystem conservation management, since maintaining sufficient genetic diversity at the primary producer level will enhance species diversity of other plants and animals.

Zytynska, Sharon E.; Fay, Michael F.; Penney, David; Preziosi, Richard F.

2011-01-01

198

Genetic differences among tree species, their hybrids and within tree species are known to influence associated ecological communities and ecosystem processes in areas of limited species diversity. The extent to which this same phenomenon occurs based on genetic variation within a single tree species, in a diverse complex ecosystem such as a tropical forest, is unknown. The level of biodiversity and complexity of the ecosystem may reduce the impact of a single tree species on associated communities. We assessed the influence of within-species genetic variation in the tree Brosimum alicastrum (Moraceae) on associated epiphytic and invertebrate communities in a neotropical rainforest. We found a significant positive association between genetic distance of trees and community difference of the epiphytic plants growing on the tree, the invertebrates living among the leaf litter around the base of the tree, and the invertebrates found on the tree trunk. This means that the more genetically similar trees are host to more similar epiphyte and invertebrate communities. Our work has implications for whole ecosystem conservation management, since maintaining sufficient genetic diversity at the primary producer level will enhance species diversity of other plants and animals. PMID:21444307

Zytynska, Sharon E; Fay, Michael F; Penney, David; Preziosi, Richard F

2011-05-12

199

NASA Astrophysics Data System (ADS)

Complicated patterns and trench-parallel components of seismic anisotropy in the central portion of the subduction zones have not been link to three-dimensional flow in general, as toroidal circulations may mostly occur in the vicinity of a plate edge. Nevertheless, recent dynamical models demonstrate that complex flow forms when lateral heterogeneities in the subduction zone are considered. Seismic studies often show gradual variations in slab length along strike. The southern Chilean subduction zone is a notable example. The Peru-Chile Trench roughly extending 5900 km is the longest trench worldwide. Most of the regions are distant from the subduction zone edges. In this study the effects of slab-length variations are examined with numerical experiments. The results are used to characterize the regional mantle circulations and the potential heat sources for the recent Patagonian plateau basalts in the southern South America. The model results show that rollback subduction induces both significant poloidal components and trench-parallel flow, extending over 1500 kilometers along the strike of the subduction zone. The trajectories of a set of passive tracers show intricate patterns such as helical streamlines, revealing complex mantle circulations in systems with the along-arc slab-length variations. The upwelling may lead to decompression melting of the heterogeneous asthenosphere to cause extensive lavas in the back arc. Mantle upwelling of the sub-slab mantle moving towards supra-slab regions is observed in the southernmost portion of the subduction system, but only for models with slab segments roughly deeper than 100 km depth. The results indicate that certain segments of the Antarctic slab may reach at least 100 km depth.

Lin, S.; Chung, S.

2013-12-01

200

The human major histocompatibility complex (MHC) on chromosome 6p21 is a paradigm for genomics, showing remarkable polymorphism and striking association with immune and non-immune diseases. The complex genomic landscape of the MHC, notably strong linkage disequilibrium, has made resolving causal variants very challenging. A promising approach is to investigate gene expression levels considered as tractable intermediate phenotypes in mapping complex diseases. However, how transcription varies across the MHC, notably relative to specific haplotypes, remains unknown. Here, using an original hybrid tiling and splice junction microarray that includes alternate allele probes, we draw the first high-resolution strand-specific transcription map for three common MHC haplotypes (HLA-A1-B8-Cw7-DR3, HLA-A3-B7-Cw7-DR15, and HLA-A26-B18-Cw5-DR3-DQ2) strongly associated with autoimmune diseases including type 1 diabetes, systemic lupus erythematosus, and multiple sclerosis. We find that haplotype-specific differences in gene expression are common across the MHC, affecting 96 genes (46.4%), most significantly the zing finger protein gene ZFP57. Differentially expressed probes are correlated with polymorphisms between haplotypes, consistent with cis effects that we directly demonstrate for ZFP57 in a cohort of healthy volunteers (P = 1.2 × 10?14). We establish that alternative splicing is significantly more frequent in the MHC than genome-wide (72.5% vs. 62.1% of genes, P ? 1 × 10?4) and shows marked haplotypic differences. We also unmask novel and abundant intergenic transcription involving 31% of transcribed blocks identified. Our study reveals that the renowned MHC polymorphism also manifests as transcript diversity, and our novel haplotype-based approach marks a new step toward identification of regulatory variants involved in the control of MHC-associated phenotypes and diseases.

Vandiedonck, Claire; Taylor, Martin S.; Lockstone, Helen E.; Plant, Katharine; Taylor, Jennifer M.; Durrant, Caroline; Broxholme, John; Fairfax, Benjamin P.; Knight, Julian C.

2011-01-01

201

Energy crops can provide a sustainable source of power and fuels, and mitigate the negative effects of CO2 emissions associated with fossil fuel use. Miscanthus is a perennial C4 energy crop capable of producing large biomass yields whilst requiring low levels of input. Miscanthus is largely unimproved and therefore there could be significant opportunities to increase yield. Further increases in yield will improve the economics, energy balance, and carbon mitigation of the crop, as well as reducing land-take. One strategy to increase yield in Miscanthus is to maximize the light captured through an extension of canopy duration. In this study, canopy duration was compared among a diverse collection of 244 Miscanthus genotypes. Canopy duration was determined by calculating the number of days between canopy establishment and senescence. Yield was positively correlated with canopy duration. Earlier establishment and later senescence were also both separately correlated with higher yield. However, although genotypes with short canopy durations were low yielding, not all genotypes with long canopy durations were high yielding. Differences of yield between genotypes with long canopy durations were associated with variation in stem and leaf traits. Different methodologies to assess canopy duration traits were investigated, including visual assessment, image analysis, light interception, and different trait thresholds. The highest correlation coefficients were associated with later assessments of traits and the use of quantum sensors for canopy establishment. A model for trait optimization to enable yield improvement in Miscanthus and other bioenergy crops is discussed. PMID:23599277

Robson, Paul R H; Farrar, Kerrie; Gay, Alan P; Jensen, Elaine F; Clifton-Brown, John C; Donnison, Iain S

2013-05-01

202

Statistical analyses were applied at the Hanford Site, USA, to assess groundwater contamination problems that included (1) determining local backgrounds to ascertain whether a facility is affecting the groundwater quality and (2) determining a 'pre-Hanford' groundwater background to allow formulation of background-based cleanup standards. The primary purpose of this paper is to extend the random effects models for (1) assessing the spatial, temporal, and analytical variability of groundwater background measurements; (2) demonstrating that the usual variance estimate s2, which ignores the variance components, is a biased estimator; (3) providing formulas for calculating the amount of bias; and (4) recommending monitoring strategies to reduce the uncertainty in estimating the average background concentrations. A case study is provided. Results indicate that (1) without considering spatial and temporal variability, there is a high probability of false positives, resulting in unnecessary remediation and/or monitoring expenses; (2) the most effective way to reduce the uncertainty in estimating the average background, and enhance the power of the statistical tests in general, is to increase the number of background wells; and (3) background for a specific constituent should be considered as a statistical distribution, not as a single value or threshold. The methods and the related analysis of variance tables discussed in this paper can be used as diagnostic tools in documenting the extent of inherent spatial and/or temporal variation and to help select an appropriate statistical method for testing purposes. PMID:16758293

Chou, Charissa J

2006-08-01

203

Statistical analyses were applied at the Hanford Site, USA to assess groundwater contamination problems that included (1) determining local backgrounds to ascertain whether a facility is affecting the groundwater quality; and (2) determining a ‘pre-Hanford’ groundwater background to allow formulation of background-based cleanup standards. The primary purpose of this paper is to extend the random effects models for (1) assessing the spatial, temporal, and analytical variability of groundwater background measurements; (2) demonstrating that the usual variance estimate s-squared, which ignores the variance components, is a biased estimator; (3) providing formulas for calculating the amount of bias; and (4) recommending monitoring strategies to reduce the uncertainty in estimating the average background concentrations. A case study is provided. Results indicate that (1) without considering spatial and temporal variability, there is a high probability of false positives, resulting in unnecessary remediation and/or monitoring expenses; (2) the most effective way to reduce the uncertainty in estimating the average background, and enhance the power of the statistical tests in general, is to increase the number of background wells; and (3) background for a specific constituent should be considered as a statistical distribution, not as a single value or threshold. The methods and the related analysis of variance tables discussed in this paper can be used as diagnostic tools in documenting the extent of inherent spatial and/or temporal variation and to help select an appropriate statistical method for testing purposes.

Chou, Charissa J.

2006-08-01

204

Energy crops can provide a sustainable source of power and fuels, and mitigate the negative effects of CO2 emissions associated with fossil fuel use. Miscanthus is a perennial C4 energy crop capable of producing large biomass yields whilst requiring low levels of input. Miscanthus is largely unimproved and therefore there could be significant opportunities to increase yield. Further increases in yield will improve the economics, energy balance, and carbon mitigation of the crop, as well as reducing land-take. One strategy to increase yield in Miscanthus is to maximize the light captured through an extension of canopy duration. In this study, canopy duration was compared among a diverse collection of 244 Miscanthus genotypes. Canopy duration was determined by calculating the number of days between canopy establishment and senescence. Yield was positively correlated with canopy duration. Earlier establishment and later senescence were also both separately correlated with higher yield. However, although genotypes with short canopy durations were low yielding, not all genotypes with long canopy durations were high yielding. Differences of yield between genotypes with long canopy durations were associated with variation in stem and leaf traits. Different methodologies to assess canopy duration traits were investigated, including visual assessment, image analysis, light interception, and different trait thresholds. The highest correlation coefficients were associated with later assessments of traits and the use of quantum sensors for canopy establishment. A model for trait optimization to enable yield improvement in Miscanthus and other bioenergy crops is discussed.

Robson, Paul R.H.

2013-01-01

205

Genetic variation for total fitness in Drosophila melanogaster: complex yet replicable patterns.

The extent of genetic variation in fitness is a crucial issue in evolutionary biology and yet remains largely unresolved. In Drosophila melanogaster, we have devised a method that allows the net effects on fitness of heterozygous wild-type chromosomes to be measured, by competing them against two different "balancer" chromosomes. We have applied the method to a large sample of 40 wild-type third chromosomes and have measured fitnesses of nonlethal chromosomes as well as chromosomes bearing recessive lethals. The measurements were made in the environment to which the population was adapted and did not involve inbreeding. The results show an extraordinary similarity in the behavior of replicates of the same chromosome, indicating consistent genetic effects on total fitness. Some invading chromosomes increased rapidly and some slowly, and some rose to appreciable frequency after several months, but then declined again: in every case, the same pattern was seen in each replicate. We estimated relative fitnesses, rates of change of fitness, and relative viabilities, for each chromosome. There were significant fluctuations around the fitted model, which were also highly replicable. Wild-type chromosomes varied substantially in their effects on heterozygous fitness, and these effects vary through time, most likely as a result of genotype x environment interactions. PMID:15545656

Gardner, Michael P; Fowler, Kevin; Barton, Nicholas H; Partridge, Linda

2005-03-01

206

Complex Period Variations of the Neglected W UMa-type Binary System NY Lyrae

NASA Astrophysics Data System (ADS)

Orbital-period variations of the neglected W UMa-type binary star, NY Lyr, were analyzed based on two newly determined eclipse times together with the others compiled from the literature. A cyclic oscillation with a period of 82.1 yr and an amplitude of 0.0247 d was discovered to be superimposed on a continuous period increase (dP/dt = +1.33 × 10-7 d yr-1). After the long-term period increase and the large-amplitude cyclic oscillation were removed from the O-C diagram, the residuals suggest that there is another small-amplitude period oscillation (A4 = 0.0053 d, P4 = 19.4 years) in the orbital period changes. As in the cases of AH Cnc and AD Cnc, both the continuous period increase and the two cyclic period oscillations make NY Lyr an interesting system to study in the future. In order to understand the evolutionary state of the binary system, new photometric and spectroscopic observations and a careful investigation on those data are needed.

Qian, S.-B.; Liu, L.; Zhu, L.-Y.

2009-04-01

207

Dairy protein composition is known to influence the structure and the texture characteristics of yogurt. The objective of the present work was therefore to investigate the impact of protein composition, at a constant protein level, on the physicochemical properties of 4% fat flavored stirred yogurt and, more specifically, on the rheological properties, the microstructure, and the aroma release. The results showed that caseinate-enriched yogurt generally presented changes in their microstructure network and had a higher complex viscosity than whey protein-enriched yogurt. To a lesser extent, the release of the majority of aroma compounds was lower in caseinate-enriched yogurt. It was therefore possible to quantify physicochemical interactions between aroma compounds and proteins. The influence of gel structure on the flavor release was observed and was in agreement with sensory characteristics previously studied for these products. PMID:16719526

Saint-Eve, Anne; Juteau, Alexandre; Atlan, Samuel; Martin, Nathalie; Souchon, Isabelle

2006-05-31

208

Variation of complex permittivity of soils with moisture content using VNA

NASA Astrophysics Data System (ADS)

The complex dielectric permittivity (?', ?'') of sand (Kukas region field, Jaipur District, Rajasthan) and sandy loam soil (Sayla, Surendranagar District field, Gujarat) was measured in the frequency range from 100 MHz to 1.5 GHz, for various moisture contents in the soils, using a Vector Network Analyzer (VNA). It has been observed that, the dielectric constant and dielectric loss of the dry soils remain almost constant over this frequency range. The dielectric constant and dielectric loss increase with increase in moisture content in the soil, at any fixed frequency in this frequency region. At given moisture content in the soil, the dielectric constant of the soils decreases slowly with increase in frequency up to 1.5 GHz, whereas the dielectric loss of the soils decreases rapidly with increase in frequency up to 0.5 GHz, after which it decreases slowly with increase in frequency up to 1.5 GHz.

Gadani, D. H.; Rana, V. A.; Bhatnagar, S. P.; Prajapati, A. N.; Vyas, A. D.

2013-06-01

209

We describe a methodology for assigning individual estimates of long-term average air pollution concentrations that accounts for a complex spatio-temporal correlation structure and can accommodate spatio-temporally misaligned observations. This methodology has been developed as part of the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air), a prospective cohort study funded by the U.S. EPA to investigate the relationship between chronic exposure to air pollution and cardiovascular disease. Our hierarchical model decomposes the space-time field into a “mean” that includes dependence on covariates and spatially varying seasonal and long-term trends and a “residual” that accounts for spatially correlated deviations from the mean model. The model accommodates complex spatio-temporal patterns by characterizing the temporal trend at each location as a linear combination of empirically derived temporal basis functions, and embedding the spatial fields of coefficients for the basis functions in separate linear regression models with spatially correlated residuals (universal kriging). This approach allows us to implement a scalable single-stage estimation procedure that easily accommodates a significant number of missing observations at some monitoring locations. We apply the model to predict long-term average concentrations of oxides of nitrogen (NOx) from 2005–2007 in the Los Angeles area, based on data from 18 EPA Air Quality System regulatory monitors. The cross-validated R2 is 0.67. The MESA Air study is also collecting additional concentration data as part of a supplementary monitoring campaign. We describe the sampling plan and demonstrate in a simulation study that the additional data will contribute to improved predictions of long-term average concentrations.

Szpiro, Adam A.; Sampson, Paul D.; Sheppard, Lianne; Lumley, Thomas; Adar, Sara D.; Kaufman, Joel

2014-01-01

210

Condition on the Kohn-Sham kinetic energy and modern parametrization of the Thomas-Fermi density

We study the asymptotic expansion of the neutral-atom energy as the atomic number Z-->?, presenting a new method to extract the coefficients from oscillating numerical data. Recovery of the correct expansion yields a condition on the Kohn-Sham kinetic energy that is important for the accuracy of approximate kinetic energy functionals for atoms, molecules, and solids. For example, this determines the

Donghyung Lee; Lucian A. Constantin; John P. Perdew; Kieron Burke

2009-01-01

211

Condition on the Kohn–Sham kinetic energy and modern parametrization of the Thomas–Fermi density

We study the asymptotic expansion of the neutral-atom energy as the atomic number Z??, presenting a new method to extract the coefficients from oscillating numerical data. Recovery of the correct expansion yields a condition on the Kohn–Sham kinetic energy that is important for the accuracy of approximate kinetic energy functionals for atoms, molecules, and solids. For example, this determines the

Donghyung Lee; Lucian A. Constantin; John P. Perdew; Kieron Burke

2009-01-01

212

Isozyme phenotypes were determined for 101 strains of Gibberella fujikuroi and 2 strains of Gibberella nygamai that represent seven biological species (mating populations) isolated from a variety of plant hosts in dispersed geographic locations. Fourteen enzymes were resolved in one or more of three buffer systems. Two of the enzymes, arylesterase and acid phosphatase, were polymorphic within two or more biological species and are suitable for intraspecific studies of population variation. Six enzymes, alcohol dehydrogenase, aspartate aminotransferase, glucose-6-phosphate dehydrogenase, mannitol dehydrogenase, phosphoglucomutase, and phosphogluconate dehydrogenase, were monomorphic in all of the isolates examined. The remaining six enzymes, fumarase, glucose phosphate isomerase, glutamate dehydrogenase (NADP), isocitrate dehydrogenase (NADP), malate dehydrogenase, and triose-phosphate isomerase, could potentially be used to distinguish the different biological species. Mating populations C and D are the most similar, since the mating population C isolates examined had the same isozyme phenotype as did a subset of the isolates in mating population D. Mating population E is the least similar to the other taxa examined. Unique isozyme phenotypes are present but are composed of banding patterns shared among the biological species. This finding supports the hypothesis that these biological species, with the possible exception of mating populations C and D, are reproductively isolated from one another and that no significant gene flow is occurring between them. Isozyme analysis is a useful method to distinguish these closely related biological species. Examination of isozyme phenotypes is more rapid than the present technique, which is based on sexual crosses; can be applied to strains that are not sexually fertile; and is more sensitive than traditional morphological characters, which cannot distinguish more than three or four morphological groups among the seven biological species. While emphasizing the discreteness of the mating populations as biological entities, our isozyme data also reaffirm the close genetic relationship among these groups.

Huss, M. J.; Campbell, C. L.; Jennings, D. B.; Leslie, J. F.

1996-01-01

213

Molecular variation and distribution of Anopheles fluviatilis (Diptera: Culicidae) complex in Iran.

Anopheles fluviatilis James (Diptera: Culicidae) is one of the known malaria vectors in south and southeastern Iran. Earlier ITS2 sequences analysis of specimens from Iran demonstrated only a single genotype that was identical to species Y in India, which is also the same as species T. We identified 2 haplotypes in the An. fluviatilis populations of Iran based on differences in nucleotide sequences of D3 domain of the 28S locus of ribosomal DNA (rDNA). Comparison of sequence data from 44 Iranian specimens with those publicly available in the Genbank database showed that all of the 28S-D3 sequences from Kazeroun and Khesht regions in Fars Province were identical to the database entry representing species U in India. In other regions, all the individuals showed heterozygosity at the single nucleotide position, which identifies species U and T. It is argued that the 2 species may co-occur in some regions and hybridize; however, the heterozygosity in the 28S-D3 locus was not reflected in ITS2 sequences and this locus for all individuals was identical to species T. This study shows that in a newly diverged species, like members of An. fluviatilis complex, a single molecular marker may not be sufficiently discriminatory to identify all the taxa over a vast geographical area. In addition, other molecular markers may provide more reliable information for species discrimination. PMID:20877502

Naddaf, Saied Reza; Razavi, Mohammad Reza; Bahramali, Golnaz

2010-09-01

214

Molecular Variation and Distribution of Anopheles fluviatilis (Diptera: Culicidae) Complex in Iran

Anopheles fluviatilis James (Diptera: Culicidae) is one of the known malaria vectors in south and southeastern Iran. Earlier ITS2 sequences analysis of specimens from Iran demonstrated only a single genotype that was identical to species Y in India, which is also the same as species T. We identified 2 haplotypes in the An. fluviatilis populations of Iran based on differences in nucleotide sequences of D3 domain of the 28S locus of ribosomal DNA (rDNA). Comparison of sequence data from 44 Iranian specimens with those publicly available in the Genbank database showed that all of the 28S-D3 sequences from Kazeroun and Khesht regions in Fars Province were identical to the database entry representing species U in India. In other regions, all the individuals showed heterozygosity at the single nucleotide position, which identifies species U and T. It is argued that the 2 species may co-occur in some regions and hybridize; however, the heterozygosity in the 28S-D3 locus was not reflected in ITS2 sequences and this locus for all individuals was identical to species T. This study shows that in a newly diverged species, like members of An. fluviatilis complex, a single molecular marker may not be sufficiently discriminatory to identify all the taxa over a vast geographical area. In addition, other molecular markers may provide more reliable information for species discrimination.

Razavi, Mohammad Reza; Bahramali, Golnaz

2010-01-01

215

NASA Astrophysics Data System (ADS)

Ionic solutions are mixtures of interacting anions and cations. They hardly resemble dilute gases of uncharged noninteracting point particles described in elementary textbooks. Biological and electrochemical solutions have many components that interact strongly as they flow in concentrated environments near electrodes, ion channels, or active sites of enzymes. Interactions in concentrated environments help determine the characteristic properties of electrodes, enzymes, and ion channels. Flows are driven by a combination of electrical and chemical potentials that depend on the charges, concentrations, and sizes of all ions, not just the same type of ion. We use a variational method EnVarA (energy variational analysis) that combines Hamilton's least action and Rayleigh's dissipation principles to create a variational field theory that includes flow, friction, and complex structure with physical boundary conditions. EnVarA optimizes both the action integral functional of classical mechanics and the dissipation functional. These functionals can include entropy and dissipation as well as potential energy. The stationary point of the action is determined with respect to the trajectory of particles. The stationary point of the dissipation is determined with respect to rate functions (such as velocity). Both variations are written in one Eulerian (laboratory) framework. In variational analysis, an ``extra layer'' of mathematics is used to derive partial differential equations. Energies and dissipations of different components are combined in EnVarA and Euler-Lagrange equations are then derived. These partial differential equations are the unique consequence of the contributions of individual components. The form and parameters of the partial differential equations are determined by algebra without additional physical content or assumptions. The partial differential equations of mixtures automatically combine physical properties of individual (unmixed) components. If a new component is added to the energy or dissipation, the Euler-Lagrange equations change form and interaction terms appear without additional adjustable parameters. EnVarA has previously been used to compute properties of liquid crystals, polymer fluids, and electrorheological fluids containing solid balls and charged oil droplets that fission and fuse. Here we apply EnVarA to the primitive model of electrolytes in which ions are spheres in a frictional dielectric. The resulting Euler-Lagrange equations include electrostatics and diffusion and friction. They are a time dependent generalization of the Poisson-Nernst-Planck equations of semiconductors, electrochemistry, and molecular biophysics. They include the finite diameter of ions. The EnVarA treatment is applied to ions next to a charged wall, where layering is observed. Applied to an ion channel, EnVarA calculates a quick transient pile-up of electric charge, transient and steady flow through the channel, stationary ``binding'' in the channel, and the eventual accumulation of salts in ``unstirred layers'' near channels. EnVarA treats electrolytes in a unified way as complex rather than simple fluids. Ad hoc descriptions of interactions and flow have been used in many areas of science to deal with the nonideal properties of electrolytes. It seems likely that the variational treatment can simplify, unify, and perhaps derive and improve those descriptions.

Eisenberg, Bob; Hyon, Yunkyong; Liu, Chun

2010-09-01

216

Ionic solutions are mixtures of interacting anions and cations. They hardly resemble dilute gases of uncharged noninteracting point particles described in elementary textbooks. Biological and electrochemical solutions have many components that interact strongly as they flow in concentrated environments near electrodes, ion channels, or active sites of enzymes. Interactions in concentrated environments help determine the characteristic properties of electrodes, enzymes, and ion channels. Flows are driven by a combination of electrical and chemical potentials that depend on the charges, concentrations, and sizes of all ions, not just the same type of ion. We use a variational method EnVarA (energy variational analysis) that combines Hamilton's least action and Rayleigh's dissipation principles to create a variational field theory that includes flow, friction, and complex structure with physical boundary conditions. EnVarA optimizes both the action integral functional of classical mechanics and the dissipation functional. These functionals can include entropy and dissipation as well as potential energy. The stationary point of the action is determined with respect to the trajectory of particles. The stationary point of the dissipation is determined with respect to rate functions (such as velocity). Both variations are written in one Eulerian (laboratory) framework. In variational analysis, an "extra layer" of mathematics is used to derive partial differential equations. Energies and dissipations of different components are combined in EnVarA and Euler-Lagrange equations are then derived. These partial differential equations are the unique consequence of the contributions of individual components. The form and parameters of the partial differential equations are determined by algebra without additional physical content or assumptions. The partial differential equations of mixtures automatically combine physical properties of individual (unmixed) components. If a new component is added to the energy or dissipation, the Euler-Lagrange equations change form and interaction terms appear without additional adjustable parameters. EnVarA has previously been used to compute properties of liquid crystals, polymer fluids, and electrorheological fluids containing solid balls and charged oil droplets that fission and fuse. Here we apply EnVarA to the primitive model of electrolytes in which ions are spheres in a frictional dielectric. The resulting Euler-Lagrange equations include electrostatics and diffusion and friction. They are a time dependent generalization of the Poisson-Nernst-Planck equations of semiconductors, electrochemistry, and molecular biophysics. They include the finite diameter of ions. The EnVarA treatment is applied to ions next to a charged wall, where layering is observed. Applied to an ion channel, EnVarA calculates a quick transient pile-up of electric charge, transient and steady flow through the channel, stationary "binding" in the channel, and the eventual accumulation of salts in "unstirred layers" near channels. EnVarA treats electrolytes in a unified way as complex rather than simple fluids. Ad hoc descriptions of interactions and flow have been used in many areas of science to deal with the nonideal properties of electrolytes. It seems likely that the variational treatment can simplify, unify, and perhaps derive and improve those descriptions. PMID:20849161

Eisenberg, Bob; Hyon, Yunkyong; Liu, Chun

2010-09-14

217

Excitation energies and Stokes shifts from a restricted open-shell Kohn-Sham approach

NASA Astrophysics Data System (ADS)

Restricted open-shell Kohn-Sham (ROKS) theory provides a powerful computational tool for calculating singlet excited state energies and dynamics. However, the possibility of multiple solutions to the ROKS equations -- with the associated difficulty of automatically selecting the physically meaningful solution -- limits its usefulness for intensive applications such as long-time Born-Oppenheimer molecular dynamics. We present an implementation of ROKS for excited states which prescribes the physically correct solution from an overlap criterion and guarantees that this solution is stationary, allowing for straightforward evaluation of nuclear gradients. The method is used to benchmark ROKS for vertical excitation energies of small and large organic dyes and for the calculation of Stokes shifts. With common density functional approximations, ROKS vertical excitation energies, and Stokes shifts show similar accuracy to those from time-dependent density functional theory and ?-self-consistent-field approaches. Advantages of the ROKS approach for excited state structure and molecular dynamics are discussed.

Kowalczyk, Tim; Tsuchimochi, Takashi; Chen, Po-Ta; Top, Laken; Van Voorhis, Troy

2013-04-01

218

Quadratic response functions in the relativistic four-component Kohn-Sham approximation

NASA Astrophysics Data System (ADS)

A formulation and implementation of the quadratic response function in the adiabatic four-component Kohn-Sham approximation is presented. The noninteracting reference state is time-reversal symmetric and formed from Kramers pair spinors, and the energy density is gradient corrected. Example calculations are presented for the optical properties of disubstituted halobenzenes in their meta and ortho conformations. It is demonstrated that correlation and relativistic effects are not additive, and it is shown that relativity alone reduces the ??-response signal by 62% and 75% for meta- and ortho-bromobenzene, respectively, and enhances the same response by 17% and 21% for meta- and ortho-iodobenzene, respectively. Of the employed functionals, CAM-B3LYP shows the best performance and gives hyperpolarizabilities ? distinctly different from B3LYP.

Henriksson, Johan; Saue, Trond; Norman, Patrick

2008-01-01

219

A directly approximated exchange-correlation potential should, by construction, be a functional derivative of some density functional in order to avoid unphysical results. Using generalized gradient approximations (GGAs) as an example, we show that functional derivatives of explicit density functionals have a very rigid inner structure, the knowledge of which allows one to build the entire functional derivative from a small part. Based on this analysis, we develop a method for direct construction of integrable Kohn-Sham potentials. As an illustration, we transform the model potential of van Leeuwen and Baerends (which is not a functional derivative) into a semilocal exchange potential that has a parent GGA, yields accurate energies, and is free from the artifacts inherent in existing semilocal potential approximations.

Gaiduk, Alex P.; Staroverov, Viktor N. [Department of Chemistry, University of Western Ontario, London, Ontario N6A 5B7 (Canada)

2011-01-15

220

Fundamental gaps in finite systems from eigenvalues of a generalized Kohn-Sham method.

We present a broadly applicable, physically motivated, first-principles approach to determining the fundamental gap of finite systems from single-electron orbital energies. The approach is based on using a range-separated hybrid functional within the generalized Kohn-Sham approach to density functional theory. Its key element is the choice of a range-separation parameter such that Koopmans' theorem for both neutral and anion is obeyed as closely as possible. We demonstrate the validity, accuracy, and advantages of this approach on first, second and third row atoms, the oligoacene family of molecules, and a set of hydrogen-passivated silicon nanocrystals. This extends the quantitative usage of density functional theory to an area long believed to be outside its reach. PMID:21231698

Stein, Tamar; Eisenberg, Helen; Kronik, Leeor; Baer, Roi

2010-12-31

221

The Korringa-Kohn-Rostoker Method Applied to Warm Dense Matter

NASA Astrophysics Data System (ADS)

The electronic structure, EOS and transport properties of warm electrons in an amorphous or disordered configuration of ions is not well described by either solid-state or plasma models. Such warm, dense systems share the characteristic of the solid state that multi-center scattering effects are of paramount importance in forming bands of valence states. Theoretical treatment of the EOS of warm, dense matter therefore requires a way to include significant occupation of higher energy and angular momentum channel continuum states. We are extending the Green's function Kohn-Korringa-Rostoker code MECCA as an all-electron (non-pseudo potential) method that treats arbitrary mixtures of atoms on an ab-initio basis over a broad range of conditions, from cold, solid matter up to hot plasmas at extreme (ICF) compression. Specific examples of Aluminum and Boron-Nitride will be discussed.

Finkenstadt, Daniel; Newnam, Charles E.; Wilson, Brian G.

2012-02-01

222

Adiabatic and local approximations for the Kohn-Sham potential in time-dependent Hubbard chains

NASA Astrophysics Data System (ADS)

We obtain the exact Kohn-Sham potentials VKS of time-dependent density-functional theory for one-dimensional Hubbard chains, driven by a dc external field, using the time-dependent electron density and current density obtained from exact many-body time evolution. The exact Vxc is compared to the adiabatically exact Vxcad and the "instantaneous ground state" Vxcigs. The latter is shown to work effectively in some cases when the former fails. Approximations for the exchange-correlation potential Vxc and its gradient, based on the local density and on the local current density, are also considered and both physical quantities are observed to be far outside the reach of any possible local approximation. Insight into the respective roles of ground-state and excited-state correlation in the time-dependent system, as reflected in the potentials, is provided by the pair correlation function.

Mancini, L.; Ramsden, J. D.; Hodgson, M. J. P.; Godby, R. W.

2014-05-01

223

Background Characterizing intra-urban variation in air quality is important for epidemiological investigation of health outcomes and disparities. To date, however, few studies have been designed to capture spatial variation during select hours of the day, or to examine the roles of meteorology and complex terrain in shaping intra-urban exposure gradients. Methods We designed a spatial saturation monitoring study to target local air pollution sources, and to understand the role of topography and temperature inversions on fine-scale pollution variation by systematically allocating sampling locations across gradients in key local emissions sources (vehicle traffic, industrial facilities) and topography (elevation) in the Pittsburgh area. Street-level integrated samples of fine particulate matter (PM2.5), black carbon (BC), nitrogen dioxide (NO2), sulfur dioxide (SO2), and ozone (O3) were collected during morning rush and probable inversion hours (6-11 AM), during summer and winter. We hypothesized that pollution concentrations would be: 1) higher under inversion conditions, 2) exacerbated in lower-elevation areas, and 3) vary by season. Results During July - August 2011 and January - March 2012, we observed wide spatial and seasonal variability in pollution concentrations, exceeding the range measured at regulatory monitors. We identified elevated concentrations of multiple pollutants at lower-elevation sites, and a positive association between inversion frequency and NO2 concentration. We examined temporal adjustment methods for deriving seasonal concentration estimates, and found that the appropriate reference temporal trend differs between pollutants. Conclusions Our time-stratified spatial saturation approach found some evidence for modification of inversion-concentration relationships by topography, and provided useful insights for refining and interpreting GIS-based pollution source indicators for Land Use Regression modeling.

2014-01-01

224

GABA type-A receptors are essential for fast inhibitory neurotransmission and are critical in brain function. Surprisingly, expression of receptor subunits is highly variable among individuals, but the cause and impact of this fluctuation remains unknown. We have studied sources of variation for all 19 receptor subunits using massive expression data sets collected across multiple brain regions and platforms in mice and humans. Expression of Gabra1, Gabra2, Gabrb2, Gabrb3, and Gabrg2 is highly variable and heritable among the large cohort of BXD strains derived from crosses of fully sequenced parents—C57BL/6J and DBA/2J. Genetic control of these subunits is complex and highly dependent on tissue and mRNA region. Remarkably, this high variation is generally not linked to phenotypic differences. The single exception is Gabrb3, a locus that is linked to anxiety. We identified upstream genetic loci that influence subunit expression, including three unlinked regions of chromosome 5 that modulate the expression of nine subunits in hippocampus, and that are also associated with multiple phenotypes. Candidate genes within these loci include, Naaa, Nos1, and Zkscan1. We confirmed a high level of coexpression for subunits comprising the major channel—Gabra1, Gabrb2, and Gabrg2—and identified conserved members of this expression network in mice and humans. Gucy1a3, Gucy1b3, and Lis1 are novel and conserved associates of multiple subunits that are involved in inhibitory signaling. Finally, proximal and distal regions of the 3? UTRs of single subunits have remarkably independent expression patterns in both species. However, corresponding regions of different subunits often show congruent genetic control and coexpression (proximal-to-proximal or distal-to-distal), even in the absence of sequence homology. Our findings identify novel sources of variation that modulate subunit expression and highlight the extraordinary capacity of biological networks to buffer 4–100 fold differences in mRNA levels.

Mulligan, Megan K.; Wang, Xusheng; Adler, Adrienne L.; Mozhui, Khyobeni; Lu, Lu; Williams, Robert W.

2012-01-01

225

NASA Astrophysics Data System (ADS)

Measurements of erodibility, porosity and sediment size were made three times over the course of a year at sites within a muddy, mesotidal flat-channel complex in southern Willapa Bay, WA, to examine spatial and seasonal variations in sediment properties and transport potential. Average critical shear stress profiles, the metric we used for erodibility, were quantified using a power-law fit to cumulative eroded mass vs. shear stress for the flats and channel. Laboratory erosion measurements of deposits made from slurries of flat and channel sediment were used to quantify erodibility over consolidation time scales ranging from 6 to 96h. Erodibility of the tidal flats was consistently low, with spatial variability comparable to seasonal variability despite seasonal changes in biological activity. In contrast, channel-bed erodibility underwent large seasonal variations, with mobile sediment present in the channel thalweg during winter that was absent in the spring and summer, when channel-bed erodibility was low and comparable to that of the tidal flats. Sediment on the northern (left) channel flank was mobile in summer and winter, whereas sediment on the southern flank was not. Seasonal changes in channel-bed erodibility are sufficient to produce order-of-magnitude changes in suspended sediment concentrations during peak tidal flows. Porosity just below the sediment surface was the best predictor of erodibility in our study area.

Wiberg, Patricia L.; Law, Brent A.; Wheatcroft, Robert A.; Milligan, Timothy G.; Hill, Paul S.

2013-06-01

226

NASA Astrophysics Data System (ADS)

Measurements of erodibility, porosity and sediment size were made three times over the course of a year at sites within a muddy, mesotidal flat-channel complex in southern Willapa Bay, WA, to examine spatial and seasonal variations in sediment properties and transport potential. Average critical shear stress profiles, the metric we used for erodibility, were quantified using a power-law fit to cumulative eroded mass vs. shear stress for the flats and channel. Laboratory erosion measurements of deposits made from slurries of flat and channel sediment were used to quantify erodibility over consolidation time scales ranging from 6 to 96 h. Erodibility of the tidal flats was consistently low, with spatial variability comparable to seasonal variability despite seasonal changes in biological activity. In contrast, channel-bed erodibility underwent large seasonal variations, with mobile sediment present in the channel thalweg during winter that was absent in the spring and summer, when channel-bed erodibility was low and comparable to that of the tidal flats. Sediment on the northern (left) channel flank was mobile in summer and winter, whereas sediment on the southern flank was not. Seasonal changes in channel-bed erodibility are sufficient to produce order-of-magnitude changes in suspended sediment concentrations during peak tidal flows. Porosity just below the sediment surface was the best predictor of erodibility in our study area.

Wiberg, Patricia L.; Law, Brent A.; Wheatcroft, Robert A.; Milligan, Timothy G.; Hill, Paul S.

227

A number of consequences of the presence of the exchange-correlation hole potential in the Kohn-Sham potential are elucidated. One consequence is that the HOMO-LUMO orbital energy difference in the KS-DFT model (the KS gap) is not "underestimated" or even "wrong", but that it is physically expected to be an approximation to the excitation energy if electrons and holes are close, and numerically proves to be so rather accurately. It is physically not an approximation to the difference between ionization energy and electron affinity I-A (fundamental gap or chemical hardness) and also numerically differs considerably from this quantity. The KS virtual orbitals do not possess the notorious diffuseness of the Hartree-Fock virtual orbitals, they often describe excited states much more closely as simple orbital transitions. The Hartree-Fock model does yield an approximation to I-A as the HOMO-LUMO orbital energy difference (in Koopmans' frozen orbital approximation), if the anion is bound, which is often not the case. We stress the spurious nature of HF LUMOs if the orbital energy is positive. One may prefer Hartree-Fock, or mix Hartree-Fock and (approximate) KS operators to obtain a HOMO-LUMO gap as a Koopmans' approximation to I-A (in cases where A exists). That is a different one-electron model, which exists in its own right. But it is not an "improvement" of the KS model, it necessarily deteriorates the (approximate) excitation energy property of the KS gap in molecules, and deteriorates the good shape of the KS virtual orbitals. PMID:24002107

Baerends, E J; Gritsenko, O V; van Meer, R

2013-10-21

228

Helium Isotope Variations in Peridotite, Gabbro and Basalt from the Kane Oceanic Core Complex

NASA Astrophysics Data System (ADS)

A fundamental assumption in mapping geochemical variability of the upper mantle is that the isotope composition of mid-ocean ridge basalt is representative of its mantle source region, being largely unmodified during its transport through the crust and eruption on the seafloor. We have begun to test this assumption through measurement of He isotopes in a suite of rocks from the Kane oceanic core complex (OCC) along the Mid-Atlantic Ridge (23oN). The Kane OCC provides a valuable window into crustal architecture and chemical composition of a slow-spreading ridge (Dick et. al. 2008, 2010). A suite of > 30 samples (comprised of whole rocks, mineral separates and basalt glasses) has been analyzed for 3He/4He and He concentrations. Gas extraction experiments included crushing in vacuum, step heating, and fusion in a high-vacuum furnace. We found 3He/4He in the two freshest peridotites (harzburgite and olivine websterite) to be identical to that measured in the most depleted MORB glasses collected from the ridge axis (8.4-8.7 RA). Notably, the freshest and least deformed peridotite (a porphyroclastic harzburgite) has the highest helium content of any of the OCC rocks (~200 ncc/g), and the majority of its helium (>2/3) is only released by melting. In contrast to the results of Kurz et al. (2009), which clearly show increasing helium concentration levels with increasing deformation in abyssal peridotites from other localities, at the Kane OCC we found lower helium contents in three mylonitized peridotites compared to the less deformed peridotites. Troctolites from the Kane OCC experienced very late-stage melt impregnation fed through a conduit represented by a large dunite body near the MOHO. 3He/4He ratios in the troctolites (8.6-9.0 RA) also overlap with values in the fresh peridotites and in the most depleted basalts from the area. Collectively, fresh Kane OCC peridotites and troctolites, having [He] above 10 ncc/g, show a narrow range of 3He/4He ratio (8.4-9.0 RA). This value is elevated compared to the median value for MORBs (8 RA). Our observations suggest that domains of highly depleted MORB mantle tend to have higher 3He/4He ratios, approaching 9 RA, consistent with what is observed in depleted MORB glasses globally. Kane gabbroic rocks are more variable, and typically show lower 3He/4He ratios, often accompanied by lower He concentrations. This likely reflects an increased importance of atmospheric and radiogenic components. Lower initial 3He/4He ratios (<8 RA) may also be present in some of the gabbros, perhaps from partial meting of a lithologically heterogeneous mantle source.

Konrad, K.; Graham, D. W.; Dick, H. J.

2012-12-01

229

NASA Astrophysics Data System (ADS)

Slip-rates along individual faults may differ as a function of measurement time scale. Short-term slip-rates may be higher than the long term rate and vice versa. For example, vertical slip-rates along the Wasatch Fault, Utah are 1.7+/-0.5 mm/yr since 6ka, <0.6 mm/yr since 130ka, and 0.5-0.7 mm/yr since 10Ma (Friedrich et al., 2003). Following conventional earthquake recurrence models like the characteristic earthquake model, this observation implies that the driving strain accumulation rates may have changed over the respective time scales as well. While potential explanations for such slip-rate variations may be found for example in the reorganization of plate tectonic motion or mantle flow dynamics, causing changes in the crustal velocity field over long spatial wavelengths, no single geophysical explanation exists. Temporal changes in earthquake rate (i.e., event clustering) due to elastic interactions within a complex fault system may present an alternative explanation that requires neither variations in strain accumulation rate or nor changes in fault constitutive behavior for frictional sliding. In the presented study, we explore this scenario and investigate how fault geometric complexity, fault segmentation and fault (segment) interaction affect the seismic behavior and slip-rate along individual faults while keeping tectonic stressing-rate and frictional behavior constant in time. For that, we used FIMozFric--a physics-based numerical earthquake simulator, based on Okada's (1992) formulations for internal displacements and strains due to shear and tensile faults in a half-space. Faults are divided into a large number of equal-sized fault patches which communicate via elastic interaction, allowing implementation of geometrically complex, non-planar faults. Each patch has assigned a static and dynamic friction coefficient. The difference between those values is a function of depth--corresponding to the temperature-dependence of velocity-weakening that is observed in laboratory friction experiments and expressed in an [a-b] term in Rate-State-Friction (RSF) theory. Patches in the seismic zone are incrementally loaded during the interseismic phase. An earthquake initiates if shear stress along at least one (seismic) patch exceeds its static frictional strength and may grow in size due to elastic interaction with other fault patches (static stress transfer). Aside from investigating slip-rate variations due to the elastic interactions within a fault system with this tool, we want to show how such modeling results can be very useful in exploring the physics underlying the patterns that the paleoseismology sees and that those methods (simulation and observations) can be merged, with both making important contributions. Using FIMozFric, we generated synthetic seismic records for a large number of fault geometries and structural scenarios to investigate along-fault slip accumulation patterns and the variability of slip at a point. Our simulations show that fault geometric complexity and the accompanied fault interactions and multi-fault ruptures may cause temporal deviations from the average fault slip-rate, in other words phases of earthquake clustering or relative quiescence. Slip-rates along faults within an interacting fault system may change even when the loading function (stressing rate) remains constant and the magnitude of slip rate change is suggested to be proportional to the magnitude of fault interaction. Thus, spatially isolated and structurally mature faults are expected to experience less slip-rate changes than strongly interacting and less mature faults. The magnitude of slip-rate change may serve as a proxy for the magnitude of fault interaction and vice versa.

Zielke, Olaf; Arrowsmith, Ramon

2010-05-01

230

NASA Astrophysics Data System (ADS)

The 466Ma Hortavær complex is a layered intrusion in north-central Norway; it evolved by assimilation of carbonate and silicate rocks. Carbonate assimilation involved expulsion of Ca-rich melt from calc-silicates into host magmas and reactive assimilation to produce clinopyroxene, titanite, Ca-amphibole, grossular- andradite garnet, and calcite. The complex was constructed by batch-wise intrusion and subsequent assimilation, leading to compositional and isotopic heterogeneity. Original evidence for carbonate assimilation came from delta 13C in interstital calcite (1). Isotopic variation of mafic compositions are epsilon Nd +4 to -7 over a range of 87Sr/86Sr(466Ma) from 0.707 to 0.708, which overlap those of calcite marble host rocks. Evolved rocks have higher 87Sr/86Sr (> 0.7080) and lower epsilon Nd (< -7); values similar to metapelitic host rocks. Some garnet, amphibole and cpx grains are zoned in 87Sr/86Sr, epsilon Nd, or both. Trends and ranges of variation within minerals are similar to the whole rocks; an indication carbonate and silicate rocks were assimilated, generally within individual magma batches. From gabbro to syenite, cpx ranges from diopside to hedenbergite and amphibole from pargasite to hastingsite. Cpx and amphibole from syenite have high calculated Fe3+ and anomalously high HREE. We infer that oxidation of the magma was in the presence of a mixed CO2 + H2O fluid that formed during carbonate assimilation (2). Increased Fe3+ in cpx allowed for enrichment of the HREE by exchange on the M1 site. The calcite from host-rock screens has REE abundances <5x, and generally <2x chondrites. In contrast, calcite grains in dioritic rocks have REE abundances up to 100x chondritic values. Calcite from two syenitic samples is variable, with abundances of heavy and middle REE from 1 to 10x chondrites. A clue to this variability comes from calcite in melasyenitic endoskarn, where calcite inclusions in garnet show higher REE contents (20-50x chondritic La and 10x chondritic Lu), but interstitial calcite has positive slopes and a wide range of LREE contents. Calcite with high LREE contents is interpreted as of igneous origin; interstitial calcite with positive slopes and low LREE contents is taken to be hydrothermal. Grossular-andradite garnet in endoskarn has Lu from 100 to 1000x chondritic values, and this variation may be observed within a single sample. All garnets have steep positive slopes from La to Sm but variable M- and HREE patterns: negative, flat, or cup-shaped. Si and Ti contents indicate a mixed igneous and hydrothermal origin. The Horta complex was constructed by a complex process involving assimilation of calcareous and silicate rocks in many magma batches. Evolution of a mixed CO2 + H2O fluid increased the oxidation state of the system, permitting growth of Fe3+ rich cpx and grossular-andradite garnet. 1. Barnes et al., 2005, Lithos, 80, 179-199. 2. Iacono Marziano et al., 2007, J volc and geothermal res., 66, 91-105.

Li, Y.; Barnes, C. G.; Frost, C. D.; Prestvik, T.; Allen, C. M.

2008-12-01

231

Objective: To study the genetic variation and haplotype structure of Vitamin K epoxide reductase complex, subunit 1 (VKORC1) gene in the Tamilian population. Materials And Methods: The study was performed on 210 unrelated, healthy volunteers of the Tamilian population, of either sex between the age group of 18-60 years. Five ml of venous blood sample was collected using sodium ethylene diamine tetra acetic acid (EDTA) as anticoagulant. DNA was extracted using phenol-chloroform extraction method. Eight single nucleotide polymorphisms (SNPs) VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), rs23596121 (C), and rs7294 (A) were studied using real-time quantitative Polymerase Chain Reaction (qPCR) method and they were included for constructing five-major haplotype blocks of VKORC1 gene. Results: The major alleles of VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), and rs23596121 (C), were found to be at frequencies of 90.0%, 89.2%, 90.9%, 94.1%, 90.7%, 89.5% and 91.2%, respectively. The variant allele of VKORC1 rs7294 (A) was more frequent (83.6%) in the Tamilian population. The frequencies of haplotypes HAP1 (GTTCCGCA), HAP2 (ACGCTCTG), HAP3 (GTTTCGCG), HAP4 (GTTCCGCG) and HAP5 (GCTCCCCG) were found to be 80.0%, 7.4%, 4.7%, 1.5% and 1.1%, respectively. Conclusion: In the present study the allele- frequency distributions, genotype and haplotype frequencies of the VKORC1 gene was considered. The findings of this study provide the genetic information required for learning the association of VKORC1 genetic variation and oral anticoagulant dose variability among patients receiving oral anticoagulants in the Tamilian population.

Kumar, Dhakchinamoorthi Krishna; Shewade, Deepak Gopal; Surendiran, Adithan; Adithan, Chandrasekaran

2013-01-01

232

The species of the Leishmania donovani species complex cause visceral leishmaniasis, a debilitating infectious disease transmitted by sandflies. Understanding molecular changes associated with population structure in these parasites can help unravel their epidemiology and spread in humans. In this study, we used a panel of standard microsatellite loci and genome-wide SNPs to investigate population-level diversity in L. donovani strains recently isolated from a small geographic area spanning India, Bihar and Nepal, and compared their variation to that found in diverse strains of the L. donovani complex isolates from Europe, Africa and Asia. Microsatellites and SNPs could clearly resolve the phylogenetic relationships of the strains between continents, and microsatellite phylogenies indicated that certain older Indian strains were closely related to African strains. In the context of the anti-malaria spraying campaigns in the 1960s, this was consistent with a pattern of episodic population size contractions and clonal expansions in these parasites that was supported by population history simulations. In sharp contrast to the low resolution provided by microsatellites, SNPs retained a much more fine-scale resolution of population-level variability to the extent that they identified four different lineages from the same region one of which was more closely related to African and European strains than to Indian or Nepalese ones. Joining results of in vitro testing the antimonial drug sensitivity with the phylogenetic signals from the SNP data highlighted protein-level mutations revealing a distinct drug-resistant group of Nepalese and Indian L. donovani. This study demonstrates the power of genomic data for exploring parasite population structure. Furthermore, markers defining different genetic groups have been discovered that could potentially be applied to investigate drug resistance in clinical Leishmania strains.

Downing, Tim; Stark, Olivia; Vanaerschot, Manu; Imamura, Hideo; Sanders, Mandy; Decuypere, Saskia; de Doncker, Simonne; Maes, Ilse; Rijal, Suman; Sundar, Shyam; Dujardin, Jean-Claude; Berriman, Matthew; Schonian, Gabriele

2012-01-01

233

The local Kohn-Sham potential is constructed for the 1s2s S-3 state of the helium atom, using the procedure proposed by van Leeuwen and Baerends (Phys. Rev. A, 49, 2138 (1994)) and the many-body electron density, obtained from the pair-correlation program of Salomonson and Oster (Phys. Rev. A, 40, 5559 (1989)). The Kohn-Sham orbitals reproduce the many-body density very accurately, demonstrating

Sten Salomonson; F. Moller; Ingvar Lindgren

2005-01-01

234

Accurate local Kohn-Sham potentials have been constructed for the ground 1s21S state and, in particular, for the lowest triplet 1s2s3S state of the helium atom, using electron densities from many-body calculations and the procedure of van Leeuwen and Baerends. The resulting Kohn-Sham orbitals reproduce the many-body densities very accurately; furthermore, we have demonstrated that the negative of the energy eigenvalue

I. Lindgren; S. Salomonson; F. Möller

2005-01-01

235

Interaction of phonons and dirac fermions on the surface of Bi2Se3: a strong Kohn anomaly.

We report the first measurements of phonon dispersion curves on the (001) surface of the strong three-dimensional topological insulator Bi2Se3. The surface phonon measurements were carried out with the aid of coherent helium beam surface scattering techniques. The results reveal a prominent signature of the exotic metallic Dirac fermion quasiparticles, including a strong Kohn anomaly. The signature is manifest in a low energy isotropic convex dispersive surface phonon branch with a frequency maximum of 1.8 THz and having a V-shaped minimum at approximately 2kF that defines the Kohn anomaly. Theoretical analysis attributes this dispersive profile to the renormalization of the surface phonon excitations by the surface Dirac fermions. The contribution of the Dirac fermions to this renormalization is derived in terms of a Coulomb-type perturbation model. PMID:22107648

Zhu, Xuetao; Santos, L; Sankar, R; Chikara, S; Howard, C; Chou, F C; Chamon, C; El-Batanouny, M

2011-10-28

236

NASA Technical Reports Server (NTRS)

The shock-capturing capability of total variation diminishing (TVD) schemes is demonstrated for a more realistic complex shock-diffraction problem for which the experimental data are available. Second-order explicit upwind and symmetric TVD schemes are used to solve the time-dependent Euler equations of gas dynamics for the interaction of a blast wave with an airfoil at high angle-of-attack. The test cases considered are a time-dependent moving curved-shock wave and a contant moving planar-shock wave impinging at an angle-of-attack 30 deg on a NACA 0018 airfoil. Good agreement is obtained between isopycnic contours computed by the TVD schemes and those from experimental interferograms. No drastic difference in flow-field structure is found between the curved- and planar-shock wave cases, except for a difference in density level near the lower surface of the airfoil. Computation for cases with higher shock Mach numbers is also possible. Numerical experiments show that the symmetric TVD scheme is less sensitive to the boundary conditions treatment than the upwind scheme.

Moon, Young J.; Yee, H. C.

1987-01-01

237

A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability. PMID:19063545

Thorvaldsen, Andreas J; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia

2008-12-01

238

NASA Astrophysics Data System (ADS)

A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.

Thorvaldsen, Andreas J.; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia

2008-12-01

239

It is found that for closed-l-shell atoms, the exact local exchange potential vx(r) calculated in the exchange-only Kohn-Sham (KS) scheme of the density functional theory (DFT) is very well represented within the region of every atomic shell by each of the suitably shifted potentials obtained with the nonlocal Fock exchange operator for the individual Hartree-Fock (HF) orbitals belonging to this

M. Cinal

2010-01-01

240

A time-independent density functional approach to the calculation of excitation energies from the ground states of molecules typified by the strong nondynamic electron correlation is suggested. The new method is based on the use of the spin-restricted ensemble-referenced Kohn-Sham formalism (Filatov, M.; Shaik, S. Chem. Phys. Lett. 1999, 304, 429) for the calculation of the ground state. In the new

Andranik Kazaryan; Jeroen Heuver; Michael Filatov

2008-01-01

241

The optimized effective potential (OEP) is the exact Kohn-Sham potential for explicitly orbital-dependent energy functionals, e.g., the exact exchange energy. We give a proof for the OEP equation which does not depend on the chain rule for functional derivatives and directly yields the equation in its simplest form: a certain first-order density shift must vanish. This condition explains why the

Stephan Kümmel; John P. Perdew

2003-01-01

242

By developing our previous method [Phys. Rev. A 46, 2337 (1992); J. Chem. Phys. 98, 543 (1993)], we show how to calculate Kohn-Sham kinetic energies, orbitals, orbital energies, and exchange-correlation potentials, starting from accurate ground-state electron densities. In addition, given correct total energies, we also show how to obtain exchange-correlation energies. The scheme used is based on the Levy constrained-search

Qingsheng Zhao; Robert C. Morrison; Robert G. Parr

1994-01-01

243

For functionals that depend on the Kohn–Sham orbitals, the optimized effective potential method (OEP) of density functional theory (DFT) seeks a lowest energy solution by finding that particular local potential vs for which a stationary value of the energy is obtained, ?E\\/?vs=0. We assess the performance of a particular method of solution, namely the expansion of vs, or the rest

Daniel R. Rohr; Oleg V. Gritsenko; Evert Jan Baerends

2006-01-01

244

Comment on ``Asymptotic form of the Kohn-Sham correlation potential''

NASA Astrophysics Data System (ADS)

For finite systems that have the energetically highest-occupied molecular orbital (HOMO) with an asymptotic nodal surface, Joubert demonstrated recently [Phys. Rev. A 76, 012501 (2007)] strongly anisotropic behavior (in the asymptotic large- r region) of the exact correlation potential of density-functional theory. As is shown by us, this result is a direct and simple consequence of the strong anisotropy of the exact exchange potential obtained by Della Sala and Görling [Phys. Rev. Lett. 89, 033003 (2002); Della Sala and GörlingJ. Chem. Phys. 116, 5374 (2002)] and the assumption about the asymptotic isotropy of the Kohn-Sham (KS) potential (based on the investigation of Almbladh and von Barth [Phys. Rev. B 31, 3231 (1985)] for atoms). Joubert’s result remains a hypothesis only, because the last assumption is in contradiction with the asymptotic strong anisotropy of the KS potential for systems with asymptotic nodal surface of the HOMO, demonstrated by Wu, Ayers, and Yang [J. Chem. Phys. 119, 2978 (2003)]. The correlation potential in the asymptotic region, stemming from their results, is given.

Holas, A.

2008-02-01

245

Applications of electrostatic interpretation of components of effective Kohn-Sham potential in atoms

NASA Astrophysics Data System (ADS)

The fundamental significance of the components of the electronic Kohn-Sham potential evaluated at the nucleus is highlighted via the numerical studies on atoms He-Lu which suggest their formally similar power-law relationship in expressing the associated components of total electronic energy. Similar studies on the isoelectronic series of closed shell atoms lead to the linear correlations. The proposed static exchange-correlation charge density concept [S. Liu, P. A. Ayers, and R. G. Parr, J. Chem. Phys. 111, 6197 (1999)] is used to interpret these relationships. The maxima in the static integrated radial exchange-correlation charge density function, Qxc)(r, in atoms are shown to reflect the shell boundaries. The quantum Monte Carlo density derived exchange-correlation potentials for Be and Ne are used to obtain Qxc)(r that can be used as standards to directly assess the quality of approximate exchange-correlation potentials. For the negative ions, Qxc)(r displays a characterstic outer minimum as a consequence of the Sen-Politzer theorem [K. D. Sen and P. Politzer, J. Chem. Phys. 90, 4370 (1989)]. This minimum is found to be related with the stability of negative ions.

Sen, K. D.; De Proft, Frank; Geerlings, Paul

2002-09-01

246

All-electron Kohn-Sham density functional theory on hierarchic finite element spaces

NASA Astrophysics Data System (ADS)

In this work, a real space formulation of the Kohn-Sham equations is developed, making use of the hierarchy of finite element spaces from different polynomial order. The focus is laid on all-electron calculations, having the highest requirement onto the basis set, which must be able to represent the orthogonal eigenfunctions as well as the electrostatic potential. A careful numerical analysis is performed, which points out the numerical intricacies originating from the singularity of the nuclei and the necessity for approximations in the numerical setting, with the ambition to enable solutions within a predefined accuracy. In this context the influence of counter-charges in the Poisson equation, the requirement of a finite domain size, numerical quadratures and the mesh refinement are examined as well as the representation of the electrostatic potential in a high order finite element space. The performance and accuracy of the method is demonstrated in computations on noble gases. In addition the finite element basis proves its flexibility in the calculation of the bond-length as well as the dipole moment of the carbon monoxide molecule.

Schauer, Volker; Linder, Christian

2013-10-01

247

Potential-energy surfaces of local excited states from subsystem- and selective Kohn-Sham-TDDFT

NASA Astrophysics Data System (ADS)

Calculating excited-state potential-energy surfaces for systems with a large number of close-lying excited states requires the identification of the relevant electronic transitions for several geometric structures. Time-dependent density functional theory (TDDFT) is very efficient in such calculations, but the assignment of local excited states of the active molecule can be difficult. We compare the results of the frozen-density embedding (FDE) method with those of standard Kohn-Sham density-functional theory (KS-DFT) and simpler QM/MM-type methods. The FDE results are found to be more accurate for the geometry dependence of excitation energies than classical models. We also discuss how selective iterative diagonalization schemes can be exploited to directly target specific excitations for different structures. Problems due to strongly interacting orbital transitions and possible solutions are discussed. Finally, we apply FDE and the selective KS-TDDFT to investigate the potential energy surface of a high-lying ? ? ?? excitation in a pyridine molecule approaching a silver cluster.

Kovyrshin, Arseny; Neugebauer, Johannes

2011-11-01

248

Comment on 'Asymptotic form of the Kohn-Sham correlation potential'

For finite systems that have the energetically highest-occupied molecular orbital (HOMO) with an asymptotic nodal surface, Joubert demonstrated recently [Phys. Rev. A 76, 012501 (2007)] strongly anisotropic behavior (in the asymptotic large-r region) of the exact correlation potential of density-functional theory. As is shown by us, this result is a direct and simple consequence of the strong anisotropy of the exact exchange potential obtained by Della Sala and Goerling [Phys. Rev. Lett. 89, 033003 (2002); Della Sala and GoerlingJ. Chem. Phys. 116, 5374 (2002)] and the assumption about the asymptotic isotropy of the Kohn-Sham (KS) potential (based on the investigation of Almbladh and von Barth [Phys. Rev. B 31, 3231 (1985)] for atoms). Joubert's result remains a hypothesis only, because the last assumption is in contradiction with the asymptotic strong anisotropy of the KS potential for systems with asymptotic nodal surface of the HOMO, demonstrated by Wu, Ayers, and Yang [J. Chem. Phys. 119, 2978 (2003)]. The correlation potential in the asymptotic region, stemming from their results, is given.

Holas, A. [Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warszawa (Poland)

2008-02-15

249

Self-Averaging Stochastic Kohn-Sham Density-Functional Theory

NASA Astrophysics Data System (ADS)

We formulate the Kohn-Sham density functional theory (KS-DFT) as a statistical theory in which the electron density is determined from an average of correlated stochastic densities in a trace formula. The key idea is that it is sufficient to converge the total energy per electron to within a predefined statistical error in order to obtain reliable estimates of the electronic band structure, the forces on nuclei, the density and its moments, etc. The fluctuations in the total energy per electron are guaranteed to decay to zero as the system size increases. This facilitates “self-averaging” which leads to the first ever report of sublinear scaling KS-DFT electronic structure. The approach sidesteps calculation of the density matrix and thus, is insensitive to its evasive sparseness, as demonstrated here for silicon nanocrystals. The formalism is not only appealing in terms of its promise to far push the limits of application of KS-DFT, but also represents a cognitive change in the way we think of electronic structure calculations as this stochastic theory seamlessly converges to the thermodynamic limit.

Baer, Roi; Neuhauser, Daniel; Rabani, Eran

2013-09-01

250

The development of the cyclic cluster model (CCM) formalism for Kohn-Sham auxiliary density functional theory (KS-ADFT) methods is presented. The CCM is a direct space approach for the calculation of perfect and defective systems under periodic boundary conditions. Translational symmetry is introduced in the CCM by integral weighting. A consistent weighting scheme for all two-center and three-center interactions appearing in the KS-ADFT method is presented. For the first time, an approach for the numerical integration of the exchange-correlation potential within the cyclic cluster formalism is derived. The presented KS-ADFT CCM implementation was applied to covalent periodic systems. The results of cyclic and molecular cluster model (MCM) calculations for trans-polyacetylene, graphene, and diamond are discussed as examples for systems periodic in one, two, and three dimensions, respectively. All structures were optimized. It is shown that the CCM results represent the results of MCM calculations in the limit of infinite molecular clusters. By analyzing the electronic structure, we demonstrate that the symmetry of the corresponding periodic systems is retained in CCM calculations. The obtained geometric and electronic structures are compared with available data from the literature. PMID:18205438

Janetzko, Florian; Köster, Andreas M; Salahub, Dennis R

2008-01-14

251

All-electron Kohn–Sham density functional theory on hierarchic finite element spaces

In this work, a real space formulation of the Kohn–Sham equations is developed, making use of the hierarchy of finite element spaces from different polynomial order. The focus is laid on all-electron calculations, having the highest requirement onto the basis set, which must be able to represent the orthogonal eigenfunctions as well as the electrostatic potential. A careful numerical analysis is performed, which points out the numerical intricacies originating from the singularity of the nuclei and the necessity for approximations in the numerical setting, with the ambition to enable solutions within a predefined accuracy. In this context the influence of counter-charges in the Poisson equation, the requirement of a finite domain size, numerical quadratures and the mesh refinement are examined as well as the representation of the electrostatic potential in a high order finite element space. The performance and accuracy of the method is demonstrated in computations on noble gases. In addition the finite element basis proves its flexibility in the calculation of the bond-length as well as the dipole moment of the carbon monoxide molecule.

Schauer, Volker [Institute of Applied Mechanics (CE) Chair I, University of Stuttgart, 70550 Stuttgart, Pfaffenwaldring 7 (Germany)] [Institute of Applied Mechanics (CE) Chair I, University of Stuttgart, 70550 Stuttgart, Pfaffenwaldring 7 (Germany); Linder, Christian, E-mail: linder@stanford.edu [Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305 (United States)] [Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305 (United States)

2013-10-01

252

Background Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have great potential for improving the efficiency of hop breeding. The success of MAS is reliant on the identification of reliable marker-trait associations. This study used quantitative trait loci (QTL) analysis to identify marker-trait associations for hop, focusing on traits related to expediting plant sex identification, increasing yield capacity and improving bittering, flavour and aroma chemistry. Results QTL analysis was performed on two new linkage maps incorporating transferable Diversity Arrays Technology (DArT) markers. Sixty-three QTL were identified, influencing 36 of the 50 traits examined. A putative sex-linked marker was validated in a different pedigree, confirming the potential of this marker as a screening tool in hop breeding programs. An ontogenetically stable QTL was identified for the yield trait dry cone weight; and a QTL was identified for essential oil content, which verified the genetic basis for variation in secondary metabolite accumulation in hop cones. A total of 60 QTL were identified for 33 secondary metabolite traits. Of these, 51 were pleiotropic/linked, affecting a substantial number of secondary metabolites; nine were specific to individual secondary metabolites. Conclusions Pleiotropy and linkage, found for the first time to influence multiple hop secondary metabolites, have important implications for molecular selection methods. The selection of particular secondary metabolite profiles using pleiotropic/linked QTL will be challenging because of the difficulty of selecting for specific traits without adversely changing others. QTL specific to individual secondary metabolites, however, offer unequalled value to selection programs. In addition to their potential for selection, the QTL identified in this study advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS.

2013-01-01

253

A restriction enzyme survey of a 110-kb region including the achaete scute complex (ASC) examined 14 polymorphic molecular markers in a sample of 56 naturally occurring chromosomes. Large insertions as a class were associated with a reduction in both sternopleural and abdominal bristle number, supporting deleterious mutation-selection equilibrium models for the maintenance of quantitative genetic variation. Two polymorphic sites were independently associated with variation in bristle number measured in two genetic backgrounds as assessed by a permutation test. A 6-bp deletion near sc alpha is associated with sternopleural bristle number variation in both sexes and a 3.4-kb insertion between sc beta and sc gamma is associated with abdominal bristle number variation in females. Under an additive genetic model, the small deletion polymorphism near sc alpha accounts for 25% of the total X chromosome genetic variation in sternopleural bristle number, and the 3.4 kb insertion accounts for 22% of the total X chromosome variation in female abdominal bristle number. The observation of common polymorphisms associated with variation in bristle number is more parsimoniously explained by models that incorporate balancing selection or assume variants affecting bristle number are neutral, than mutation-selection equilibrium models. PMID:10757767

Long, A D; Lyman, R F; Morgan, A H; Langley, C H; Mackay, T F

2000-03-01

254

Differences in general cognitive ability (intelligence) account for approximately half of the variation in any large battery of cognitive tests and are predictive of important life events including health. Genome-wide analyses of common single-nucleotide polymorphisms indicate that they jointly tag between a quarter and a half of the variance in intelligence. However, no single polymorphism has been reliably associated with variation in intelligence. It remains possible that these many small effects might be aggregated in networks of functionally linked genes. Here, we tested a network of 1461 genes in the postsynaptic density and associated complexes for an enriched association with intelligence. These were ascertained in 3511 individuals (the Cognitive Ageing Genetics in England and Scotland (CAGES) consortium) phenotyped for general cognitive ability, fluid cognitive ability, crystallised cognitive ability, memory and speed of processing. By analysing the results of a genome wide association study (GWAS) using Gene Set Enrichment Analysis, a significant enrichment was found for fluid cognitive ability for the proteins found in the complexes of N-methyl-D-aspartate receptor complex; P=0.002. Replication was sought in two additional cohorts (N=670 and 2062). A meta-analytic P-value of 0.003 was found when these were combined with the CAGES consortium. The results suggest that genetic variation in the macromolecular machines formed by membrane-associated guanylate kinase (MAGUK) scaffold proteins and their interaction partners contributes to variation in intelligence. PMID:24399044

Hill, W D; Davies, G; van de Lagemaat, L N; Christoforou, A; Marioni, R E; Fernandes, C P D; Liewald, D C; Croning, M D R; Payton, A; Craig, L C A; Whalley, L J; Horan, M; Ollier, W; Hansell, N K; Wright, M J; Martin, N G; Montgomery, G W; Steen, V M; Le Hellard, S; Espeseth, T; Lundervold, A J; Reinvang, I; Starr, J M; Pendleton, N; Grant, S G N; Bates, T C; Deary, I J

2014-01-01

255

Exact exchange potential evaluated from occupied Kohn-Sham and Hartree-Fock solutions

The reported algorithm determines the exact exchange potential v{sub x} in an iterative way using energy shifts (ESs) and orbital shifts (OSs) obtained with finite-difference formulas from the solutions (occupied orbitals and their energies) of the Hartree-Fock-like equation and the Kohn-Sham-like equation, the former used for the initial approximation to v{sub x} and the latter for increments of ES and OS due to subsequent changes of v{sub x}. Thus, the need for solution of the differential equations for OSs, used by Kuemmel and Perdew [Phys. Rev. Lett. 90, 043004 (2003)], is bypassed. The iterated exchange potential, expressed in terms of ESs and OSs, is improved by modifying ESs at odd iteration steps and OSs at even steps. The modification formulas are related to the optimized-effective-potential equation (satisfied at convergence) written as the condition of vanishing density shift (DS). They are obtained, respectively, by enforcing its satisfaction through corrections to approximate OSs and by determining the optimal ESs that minimize the DS norm. The proposed method, successfully tested for several closed-(sub)shell atoms, from Be to Kr, within the density functional theory exchange-only approximation, proves highly efficient. The calculations using the pseudospectral method for representing orbitals give iterative sequences of approximate exchange potentials (starting with the Krieger-Li-Iafrate approximation) that rapidly approach the exact v{sub x} so that, for Ne, Ar, and Zn, the corresponding DS norm becomes less than 10{sup -6} after 13, 13, and 9 iteration steps for a given electron density. In self-consistent density calculations, orbital energies of 10{sup -4} hartree accuracy are obtained for these atoms after, respectively, 9, 12, and 12 density iteration steps, each involving just two steps of v{sub x} iteration, while the accuracy limit of 10{sup -6} to 10{sup -7} hartree is reached after 20 density iterations.

Cinal, M.; Holas, A. [Institute of Physical Chemistry of the Polish Academy of Sciences, 44/52 Kasprzaka, 01-224 Warsaw (Poland)

2011-06-15

256

Electromorphic variation among populations of Drosophila mojavensis, D. arizonensis and D. longicornis was examined for seven genetic loci. The average electrophoretic mobility for a population was used as the metric. D. mojavensis and D. arizonensis use larval substrates in different parts of their geographic ranges, while D. longicornis is more narrowly restricted to different species of the cactus Opuntia in different localities. There is marked electromorphic variation among populations of either D. mojavensis or D. arizonensis, and the bulk of this variation is accounted for by differences in laval substrate. There is somewhat less variation among populations of D. longicornis, and only a moderate portion of this is accounted for by larval substrate differences. There appears to be an association between the taxonomic diversity of the larval substrates and the electromorphic diversity of the Drosophila populations utilizing those substrates. Evidence is reviewed that suggests physiological mechanisms for these possibly adaptive associations.

Richardson, R. H.; Smouse, Peter E.; Richardson, Martha E.

1977-01-01

257

NASA Astrophysics Data System (ADS)

The density functional approach in the Kohn-Sham approximation is widely used to study properties of many-electron systems. Due to the nonlinearity of the Kohn-Sham equations, the general self-consistence searching method involves iterations with alternate solving of the Poisson and Schrödinger equations. One of problems of such an approach is that the charge distribution renewed by means of the solution of the Schrödinger equation does not conform to boundary conditions of the Poisson equation for the Coulomb potential. The resulting instability or even divergence of iterations manifests itself most appreciably in the case of infinitely extended systems. The known attempts to deal with this problem are reduced in fact to abandoning the original iterative method and replacing it with some approximate calculation scheme, which is usually semi-empirical and does not permit to evaluate the extent of deviation from the exact solution. In this work, we realize the iterative scheme of solving the Kohn-Sham equations for extended systems with inhomogeneous electron gas, which is based on eliminating the long-range character of Coulomb interaction as the cause of tight coupling between charge distribution and boundary conditions. The suggested algorithm is employed to calculate energy the spectrum, self-consistent potential, and electrostatic capacitance of the semi-infinite degenerate electron gas bounded by an infinitely high barrier, as well as the work function and surface energy of simple metals in the model with homogeneous distribution of positive background. The difference between self-consistent Hartree solutions and those taking into account the exchange-correlation interaction is analyzed. The comparison with the results previously published in the literature is carried out. The case study of the metal-semiconductor tunnel contact shows this method as applied to an infinitely extended system where the steady-state current can flow.

Posvyanskii, D. V.; Shul'Man, A. Ya.

2009-07-01

258

The density functional approach in the Kohn-Sham approximation is widely used to study properties of many-electron systems. Due to the nonlinearity of the Kohn-Sham equations, the general self-consistence searching method involves iterations with alternate solving of the Poisson and Schroedinger equations. One of problems of such an approach is that the charge distribution renewed by means of the solution of the Schroedinger equation does not conform to boundary conditions of the Poisson equation for the Coulomb potential. The resulting instability or even divergence of iterations manifests itself most appreciably in the case of infinitely extended systems. The known attempts to deal with this problem are reduced in fact to abandoning the original iterative method and replacing it with some approximate calculation scheme, which is usually semi-empirical and does not permit to evaluate the extent of deviation from the exact solution. In this work, we realize the iterative scheme of solving the Kohn-Sham equations for extended systems with inhomogeneous electron gas, which is based on eliminating the long-range character of Coulomb interaction as the cause of tight coupling between charge distribution and boundary conditions. The suggested algorithm is employed to calculate energy the spectrum, self-consistent potential, and electrostatic capacitance of the semi-infinite degenerate electron gas bounded by an infinitely high barrier, as well as the work function and surface energy of simple metals in the model with homogeneous distribution of positive background. The difference between self-consistent Hartree solutions and those taking into account the exchange-correlation interaction is analyzed. The comparison with the results previously published in the literature is carried out. The case study of the metal-semiconductor tunnel contact shows this method as applied to an infinitely extended system where the steady-state current can flow.

Posvyanskii, D. V., E-mail: posvyanskii@cplire.ru; Shul'man, A. Ya., E-mail: ash@cplire.r [Russian Academy of Sciences, Kotel'nikov Institute of Radio Engineering and Electronics (Russian Federation)

2009-07-15

259

NASA Astrophysics Data System (ADS)

The density functional approach in the Kohn-Sham approximation is widely used to study properties of many-electron systems. Due to the nonlinearity of the Kohn-Sham equations, the general self-consistent solution method for infinite systems involves iterations with alternate solutions of the Poisson and Schrödinger equations. One of problems with such an approach is that the charge distribution, updated by solving the Schrodinger equation, may be incompatible with the boundary conditions of the Poisson equation for Coulomb potential. The resulting instability or divergence manifests itself most appreciably in the case of infinitely extended systems because the corresponding boundary-value problem becomes singular. In this work the stable iterative scheme for solving the Kohn-Sham equations for infinite systems with inhomogeneous electron gas is described based on eliminating the long-range character of the Coulomb interaction, which causes the tight coupling of the charge distribution with the boundary conditions. This algorithm has been previously successfully implemented in the calculation of work function and surface energy of simple metals in the jellium model. Here it is used to calculate the energy spectrum of quasi-two-dimensional electron gas in the accumulation layer at the semiconductor surface n-InAs. The electrons in such a structure occupy states that belong to both discrete and continuous parts of the energy spectrum. This causes the problems of convergence in the usually used approaches, which do not exist in our case. Because of the narrow bandgap of InAs, it is necessary to take the nonparabolicity of the conduction band into account; this is done by means of a new effective mass method. The calculated quasi-two-dimensional energy bands correspond well to experimental data measured by the angle resolved photoelectron spectroscopy technique.

Shul'man, A. Ya; Posvyanskii, D. V.

2014-05-01

260

NASA Astrophysics Data System (ADS)

We discuss two basic problems in the Hohenberg-Kohn-Sham version of density functional theory, HKS-DFT: the first, the N-representability of the functional F[?] and, the second, the universality of F[?]. In relation to the first, we show that F[?] must satisfy N-representability conditions that follow from those on the 2-matrix D2(r1, r2; r', r'2). In the case of the second, we provide arguments based on the equivalence between ab initio DFT and HKS-DFT to show that the functional F[?] is not universal.

Ludeña, Eduardo V.; Illas, Francesc; Ramirez-Solis, Alejandro

2009-12-01

261

NASA Astrophysics Data System (ADS)

We discuss two basic problems in the Hohenberg-Kohn-Sham version of density functional theory, HKS-DFT: the first, the N-representability of the functional F[?] and, the second, the universality of F[?]. In relation to the first, we show that F[?] must satisfy N-representability conditions that follow from those on the 2-matrix D2(r1, r2; r?, r?2). In the case of the second, we provide arguments based on the equivalence between ab initio DFT and HKS-DFT to show that the functional F[?] is not universal.

Ludeña, Eduardo V.; Illas, Francesc; Ramirez-Solis, Alejandro

262

NASA Astrophysics Data System (ADS)

We have extended the recently formulated Korringa-Kohn-Rostoker coherent-potential approximation (KKR-CPA) for the treatment of substitutionally disordered alloys within the KKR atomic-spheres approximation (ASA) to include charge self-consistency. To test the accuracy of the present approach we have carried out self-consistent-field (SCF) KKR-ASA-CPA calculations of Cu-Pd alloys. Our results are in good agreement with experimental results and previous SCF-KKR-CPA calculations. We also present a comparison of the electronic structures of the ordered with the disordered Cu-Pd alloys.

Singh, Prabhakar P.; de Fontaine, Didier; Gonis, A.

1991-10-01

263

The measurement of the copper complexing capacity of natural waters by anodic stripping voltammeting (ASV) has been shown to be dependent on the plating potential used to measure the concentration of electroactive copper in solution. Results are presented for the complexing capacities and conditional stability constants of 3 Papua New Guinean lake waters at pH 6.0 measured at the plating

J. H. Kyle

1987-01-01

264

Two major inconsistencies exist in the current neo-Darwinian evolutionary theory that random chromosomal mutations acted on by natural selection generate new species. First, natural selection does not require the evolution of ever increasing complexity, yet this is the hallmark of biology. Second, human chromosomal DNA sequence variation is predominantly either neutral or deleterious and is insufficient to provide the variation required for speciation or for predilection to common diseases. Complexity is explained by the continuous flow of energy through the biosphere that drives the accumulation of nucleic acids and information. Information then encodes complex forms. In animals, energy flow is primarily mediated by mitochondria whose maternally inherited mitochondrial DNA (mtDNA) codes for key genes for energy metabolism. In mammals, the mtDNA has a very high mutation rate, but the deleterious mutations are removed by an ovarian selection system. Hence, new mutations that subtly alter energy metabolism are continuously introduced into the species, permitting adaptation to regional differences in energy environments. Therefore, the most phenotypically significant gene variants arise in the mtDNA, are regional, and permit animals to occupy peripheral energy environments where rarer nuclear DNA (nDNA) variants can accumulate, leading to speciation. The neutralist–selectionist debate is then a consequence of mammals having two different evolutionary strategies: a fast mtDNA strategy for intra-specific radiation and a slow nDNA strategy for speciation. Furthermore, the missing genetic variation for common human diseases is primarily mtDNA variation plus regional nDNA variants, both of which have been missed by large, inter-population association studies.

Wallace, Douglas C.

2013-01-01

265

NASA Astrophysics Data System (ADS)

The standard diagonalization based method for solving Kohn-Sham density functional theory (KSDFT) requires N eigenvectors for an O(N) * O(N) Kohn-Sham Hamiltonian matrix, with N being the number of electrons in the system. The computational cost for such procedure is expensive and scales as O(N^3). We have developed a novel pole expansion plus selected inversion (PEXSI) method, in which KSDFT is solved by evaluating the selected elements of the inverse of a series of sparse symmetric matrices, and the overall algorithm scales at most O(N^2) for all materials including metallic and insulating systems without any truncation. The PEXSI method can be used with orthogonal or nonorthogonal basis set, and the electron density, total energy, Helmholtz free energy and atomic force are calculated simultaneously and accurately without using the eigenvalues and eigenvectors. Combined with atomic orbital basis functions, the PEXSI method can be applied to study the electronic structure of boron nitride nanotube and carbon nanotube with more than 10,000 atoms on a single processor.

Lin, Lin; Chen, Mohan; E, Weinan; He, Lixin; Lu, Jianfeng; Yang, Chao; Ying, Lexing

2013-03-01

266

NASA Astrophysics Data System (ADS)

The electronic and optical properties of extended functionalized carbyne chains, polyynes and cumulenes, are investigated with the localized Hartree-Fock method, with conventional Kohn-Sham methods, and with the Hartree-Fock method. It is found that even for very long polyynes the carbon-carbon bond lengths within a polyyne alternate while for long cumulenes no carbon-carbon bond length alternation occurs. Polyynes exhibit a finite HOMO-LUMO gap even if they become very long while cumulenes are found to become metallic in the limit of long chain lengths. The geometry and the electro-optical properties of polyynes cannot be influenced significantly by simple sp-?-bonded end groups. The optically active 1? u+?X 1? g+ electronic transition in polyynes is investigated by time-dependent density-functional theory (TDDFT). The known systematic underestimation of excitation energies in large chain-like systems by TDDFT methods is also found for the systems considered here. Deficiencies in the commonly used exchange-correlation kernels are identified as the main source of this shortcoming of TDDFT methods. Unphysical Coulomb self-interactions present in conventional Kohn-Sham potentials seem to not contribute significantly to the problem.

Weimer, Martin; Hieringer, Wolfgang; Sala, Fabio Della; Görling, Andreas

2005-02-01

267

Using the Shubin-Vonsovsky model in the weak-coupling regime W > U > V (W is the bandwidth, U is the Hubbard onsite repulsion, and V is the Coulomb interaction at neighboring sites) based on the Kohn-Luttinger mechanism, we determined the regions of the existence of the superconducting phases with the d{sub xy}, p, s, and d{sub x{sup 2}-y{sup 2}} symmetry types of the order parameter. It is shown that the effective interaction in the Cooper channel considerably depends not only on single-site but also on intersite Coulomb correlations. This is demonstrated by the example of the qualitative change and complication of the phase diagram of the superconducting state. The superconducting (SC) phase induction mechanism is determined taking into account polarization contributions in the second-order perturbation theory in the Coulomb interaction. The results obtained for the angular dependence of the superconducting gap in different channels are compared with angule-resolved photoemission spectroscopy (ARPES) results. The influence of long-range hops in the phase diagram and critical superconducting transition temperature in different channels is analyzed. The conditions for the appearance of the Kohn-Luttinger superconductivity with the d{sub x{sup 2}-y{sup 2}} symmetry and high critical temperatures T{sub c} {approx} 100 K near the half-filling are determined.

Kagan, M. Yu., E-mail: kagan@kapitza.ras.ru [Russian Academy of Sciences, Kapitza Institute for Physical Problems (Russian Federation); Val'kov, V. V.; Mitskan, V. A.; Korovuskin, M. M. [Russian Academy of Sciences, Kirenskii Physics Institute, Siberian Branch (Russian Federation)] [Russian Academy of Sciences, Kirenskii Physics Institute, Siberian Branch (Russian Federation)

2013-10-15

268

NASA Astrophysics Data System (ADS)

The effective cohesion of the cratered region during crater collapse is determined via the widths of slump terraces of complex craters. Terrace widths are measured for complex craters on Mercury; these generally increase outward toward the rim for a given crater, and the width of the outermost major terrace is generally an increasing function of crater diameter. The terrace widths on Mercury and a gravity-driven slump model are used to estimate the strength of the cratered region immediately after impact (about 1-2 MPa). A comparison with the previous study of lunar complex craters by Pearce and Melosh (1986) indicates that the transient strength of cratered Mercurian crust is no greater than that of the moon. The strength estimates vary only slightly with the geometric model used to restore the outermost major terrace to its precollapse configuration and are consistent with independent strength estimates from the simple-to-complex crater depth/diameter transition.

Leith, Andrew C.; McKinnon, William B.

1991-11-01

269

NASA Astrophysics Data System (ADS)

Mafic enclaves in silicic volcanic rocks provide vital information regarding the role of mafic replenishment in the long-term evolution and triggering of eruptions in silicic magma systems. In this study, we are investigating textural and compositional variations in a single large (~25 x 10 cm) mafic enclave from the Cerro Chascon lava dome in the Purico-Chascon Volcanic Complex of Northern Chile. The Cerro Chascon lava dome is predominantly high-K crystal-rich dacite, similar to other major volcanic units in the region, but is rare in that it contains significant basaltic-andesite mafic enclaves. The mafic enclave analyzed in this study is porphyritic containing plagioclase + amphibole + clinopyroxene + olivine + Fe-Ti oxides in a groundmass of high-silica (~69-73 wt.% SiO2) glass with plagioclase and amphibole micro-phenocrysts, and acicular plagioclase microlites. There is also strong evidence for the incorporation of crystalline material from the dacite host. In particular, the mafic enclave contains large embayed quartz crystals that are rimmed with clinopyroxene, and large plagioclase crystals with heavily sieved high anorthite (An70-85) rims and clear cores that are compositionally indistinguishable from plagioclase crystals in the host (An45-50). There do not appear to be significant variations in the distribution of the xenocrysts within the enclave, but there are significant variations in the texture, composition, and microlite content of the groundmass glass. More specifically, there is a systematic increase in the amount of vesicularity (~3-5 vol.%) and decrease in vesicle size from the enclave interior to the enclave-host contact. These textural variations are accompanied by small but significant variations in the major element chemistry, (SiO2 and K2O increase from rim-ward, and CaO, Na2O, and Cl decrease) and a rim-ward increase in the proportion of plagioclase microlites. The random distribution of xenocrysts and systematic textural, chemical, and modal (microlites) variations within the mafic enclave indicate the transfer of crystalline material into the enclave occurred prior to the formation of the textural, chemical, and microlite gradients. We believe that the xenocrysts were incorporated prior to the emplacement of the enclave into the dacite host, and that the variations in vesicularity, major element chemistry, and microlite content formed post emplacement. Furthermore, there is strong evidence that the observed major element variations resulted from the increase in microlite crystallization near the enclave-host contact. The rim-ward increase in vesicularity is consistent with this model, assuming the amount of crystallization is sufficient to cause vapor oversaturation in the residual melt.

Burns, D. H.; Tepley, F. J.; de Silva, S. L.; Carter, Z. G.

2011-12-01

270

Genome copy number changes (copy number variations: CNVs) include inherited, de novo and somatically acquired deviations from a diploid state within a particular chromosomal segment. CNVs are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. CNVs are distributed widely in the genomes of apparently healthy individuals and thus constitute significant amounts of population-based genomic variation. Human CNV loci are enriched for immune genes and one of the most striking examples of CNV in humans involves a genomic region containing the chemokine genes CCL3L and CCL4L. The CCL3L-CCL4L copy number variable region (CNVR) shows extensive architectural complexity, with smaller CNVs within the larger ones and with interindividual variation in breakpoints. Furthermore, the individual genes embedded in this CNVR account for an additional level of genetic and mRNA complexity: CCL4L1 and CCL4L2 have identical exonic sequences but produce a different pattern of mRNAs. CCL3L2 was considered previously as a CCL3L1 pseudogene, but is actually transcribed. Since 2005, CCL3L-CCL4L CNV has been associated extensively with various human immunodeficiency virus-related outcomes, but some recent studies called these associations into question. This controversy may be due in part to the differences in alternative methods for quantifying gene copy number and differentiating the individual genes. This review summarizes and discusses the current knowledge about CCL3L-CCL4L CNV and points out that elucidating their complete phenotypic impact requires dissecting the combinatorial genomic complexity posed by various proportions of distinct CCL3L and CCL4L genes among individuals. PMID:20659124

Colobran, R; Pedrosa, E; Carretero-Iglesia, L; Juan, M

2010-10-01

271

Genome copy number changes (copy number variations: CNVs) include inherited, de novo and somatically acquired deviations from a diploid state within a particular chromosomal segment. CNVs are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. CNVs are distributed widely in the genomes of apparently healthy individuals and thus constitute significant amounts of population-based genomic variation. Human CNV loci are enriched for immune genes and one of the most striking examples of CNV in humans involves a genomic region containing the chemokine genes CCL3L and CCL4L. The CCL3L–CCL4L copy number variable region (CNVR) shows extensive architectural complexity, with smaller CNVs within the larger ones and with interindividual variation in breakpoints. Furthermore, the individual genes embedded in this CNVR account for an additional level of genetic and mRNA complexity: CCL4L1 and CCL4L2 have identical exonic sequences but produce a different pattern of mRNAs. CCL3L2 was considered previously as a CCL3L1 pseudogene, but is actually transcribed. Since 2005, CCL3L-CCL4L CNV has been associated extensively with various human immunodeficiency virus-related outcomes, but some recent studies called these associations into question. This controversy may be due in part to the differences in alternative methods for quantifying gene copy number and differentiating the individual genes. This review summarizes and discusses the current knowledge about CCL3L–CCL4L CNV and points out that elucidating their complete phenotypic impact requires dissecting the combinatorial genomic complexity posed by various proportions of distinct CCL3L and CCL4L genes among individuals.

Colobran, R; Pedrosa, E; Carretero-Iglesia, L; Juan, M

2010-01-01

272

We present a novel tunable dispersion compensator that can provide pure slope compensation. The approach uses two specially designed complex fiber Bragg gratings (FBGs) with reversely varied third-order group delay curves to generate the dispersion slope. The slope can be changed by adjusting the relative wavelength positions of the two FBGs. Several design examples of such complex gratings are presented and discussed. Experimentally, we achieve a dispersion slope tuning range of +/- 650 ps/nm(2) with > 0.9 nm usable bandwidth. PMID:18679483

Shu, Xuewen; Turitsyna, Elena; Sugden, Kate; Bennion, Ian

2008-08-01

273

Spin-unrestricted Kohn-Sham (KS) solutions are constructed from accurate ab initio spin densities for the prototype doublet molecules NO(2), ClO(2), and NF(2) with the iterative local updating procedure of van Leeuwen and Baerends (LB). A qualitative justification of the LB procedure is given with a "strong" form of the Hohenberg-Kohn theorem. The calculated energies epsilon(isigma) of the occupied KS spin orbitals provide numerical support to the analogue of Koopmans' theorem in spin-density functional theory. In particular, the energies -epsilon(ibeta) of the minor spin (beta) valence orbitals of the considered doublet molecules correspond fairly well to the experimental vertical ionization potentials (VIPs) I(i) (1) to the triplet cationic states. The energy -epsilon(Halpha) of the highest occupied (spin-unpaired) alpha orbital is equal to the first VIP I(H) (0) to the singlet cationic state. In turn, the energies -epsilon(ialpha) of the major spin (alpha) valence orbitals of the closed subshells correspond to a fifty-fifty average of the experimental VIPs I(i) (1) and I(i) (0) to the triplet and singlet states. For the Li atom we find that the exact spin densities are represented by a spin-polarized Kohn-Sham system which is not in its ground state, i.e., the orbital energy of the lowest unoccupied beta spin orbital is lower than that of the highest occupied alpha spin orbital ("a hole below the Fermi level"). The addition of a magnetic field in the -z direction will shift the beta levels up so as to restore the Aufbau principle. This is an example of the nonuniqueness of the mapping of the spin density on the KS spin-dependent potentials discussed recently in the literature. The KS potentials may no longer go to zero at infinity, and it is in general the differences nu(ssigma)( infinity )-epsilon(isigma) that can be interpreted as (averages of) ionization energies. In total, the present results suggest the spin-unrestricted KS theory as a natural one-electron independent-particle model for interpretation and assignment of the experimental photoelectron spectra of open-shell molecules. PMID:15267759

Gritsenko, O V; Baerends, E J

2004-05-01

274

To analyze candidate genes and establish complex genotype-phenotype relationships against a back- ground of high natural genome sequence variability, we have developed approaches to (i) compare candidate gene sequence information in multiple individuals; (ii) predict haplotypes from numerous variants; and (iii) classify haplotypes and identify specific sequence variants, or combinations of variants (pattern), asso- ciated with the phenotype. Using the

Margret R. Hoehe; Birgit Wendel; Klaus Rohde; Christina Flachmeier; Kenneth K. Kidd; W ade H. Berrettini; George M. Church

2000-01-01

275

Sediment cores were obtained from several locations in the Calcasieu River\\/Lake Complex (Lousiana), including Calcasieu Lake, Calcasieu River, two bayou tributaries, and Lake Charles, during the period from November 1983 to November 1985. The cores were analyzed for Cu, Zn, Cr, and Pb. The approximate sedimentation rate and a core chronology were determined by the use of 137Cs and 210Pb.

C. S. Mueller; G. J. Ramelow; J. N. Beck

1989-01-01

276

Widely distributed species often display intraspecific morphological variation due to the abiotic and biotic gradients experienced across their ranges. Historically, in many vertebrate taxa, such as birds and reptiles, these morphological differences within a species were used to delimit subspecies. Graptemys nigrinoda is an aquatic turtle species endemic to the Mobile Bay Basin. Colour pattern and morphological variability were used to describe a subspecies (G.?n. delticola) from the lower reaches of the system, although it and the nominate subspecies also reportedly intergrade over a large portion of the range. Other researchers have suggested that these morphological differences merely reflect clinal variation. Our molecular data (mtDNA) did not support the existence of the subspecies, as the haplotypes were differentiated by only a few base pairs and one haplotype was shared between the putative subspecies. While there were significant morphological and pattern differences among putative specimens of G.?n. nigrinoda, G.?n. delticola and G.?n.?nigrinoda × delticola, these differences probably represent clinal variation as they were also related to environmental variables [i.e. cumulative drainage area and drainage (categorical)]. Specimens occupying slow-current, high-turbidity river reaches (e.g. the Tensaw River) exhibited greater relative carapace heights and more dark pigmentation, while specimens occupying fast-current, clearer rivers (e.g. the upper Alabama, Cahaba and Tallapoosa rivers) exhibited lower carapace heights and more yellow pigmentation. Given the absence of clear molecular and morphological differences that are related to drainage characteristics, we suggest that there is not sufficient evidence for the recognition of G.?n. delticola as a distinct subspecies.

Ennen, Joshua R.; Kalis, Marley E.; Patterson, Adam L.; Kreiser, Brian R.; Lovich, Jeffrey E.; Godwin, James; Qualls, Carl P.

2014-01-01

277

Background and Aims Although the large variation in genome size among different species is widely acknowledged, the occurrence and extent of variation below the species level are still controversial and have not yet been satisfactorily analysed. The aim of this study was to assess genome size variation in six ploidy levels (2n = 3x–8x) of the polyploid Allium oleraceum over a large geographical gradient and to search for potential interpretations of the size variation. Methods The genome sizes of 407 individuals of A. oleraceum collected from 114 populations across Europe were determined by flow cytometry using propidium iodide staining. The genome size variation was correlated with spatial, climatic and habitat variables. Key Results The mean holoploid genome size (2C DNA) was 42·49, 52·14, 63·34, 71·94, 85·51 and 92·12 pg at the tri-, tetra-, penta-, hexa-, hepta- and octoploid levels, respectively. Genome size varied from a minimum of 2·3 % in the octoploids to a maximum of 18·3 % in the tetraploids. Spatial structuring of genome size was observed within the tetra- and pentaploids, where 2C DNA significantly increased with both latitude and longitude, and correlated with several climatic variables, suggesting a gradient of continentality. Genome size in hexaploids showed low variation, weak correlation with climatic variables and no spatial structuring. Downsizing in monoploid genome size was observed between all cytotypes except for heptaploids. Splitting populations into western and eastern European groups resulted in strong differences in monoploid genome size between groups in tetra- and pentaploids but not in hexaploids. The monoploid genome sizes of the cytotypes were similar in the western group but diverged in the eastern group. Conclusions Complex patterns of holoploid and monoploid genome size variation found both within and between A. oleraceum cytotypes are most likely the result of several interacting factors, including different evolutionary origins of cytotypes via hybridization of parental combinations with different genome sizes in the south-western and south-eastern part of Europe, introgression between cytotypes, and antropic dispersal. The role of broad-scale and fine-scale environmental variables in shaping genome size is probably of minor importance in A. oleraceum.

Duchoslav, Martin; Safarova, Lenka; Jandova, Michaela

2013-01-01

278

NASA Astrophysics Data System (ADS)

The parameters characterizing shifting ionospheric disturbances were determined in a complex SUNDIAL experiment conducted during the time period September 11-October 6, 1989, which included vertical sounding of the ionosphere and satellite radioscopy. Results are also presented on quantitive verifications of the dispersion ratios of the acoustic-gravitational waves and on the correlation between the statistical parameters of ionospheric disturbances during the September-October period with magnitudes of the magnetic disturbance for that period.

Biriukov, O. V.; Saenko, Iu. S.; Shagimuratov, I. I.

1993-02-01

279

Red list species densities of birds (maximally 22 km?2), and angiosperms (maximally 39 km?2) were used as biodiversity indicators in 21 larger complexes of wetlands across the Netherlands. Their covariability with\\u000a a range of indicators of human land use was assessed, including population, road and visitor density, area covered by agriculture,\\u000a open water, forest and residential housing. Data were collected on the

Jan E. Vermaat; Hasse Goosen; Nancy Omtzigt

2007-01-01

280

Red list species densities of birds (maximally 22 km?2), and angiosperms (maximally 39 km?2) were used as biodiversity indicators in 21 larger complexes of wetlands across the Netherlands. Their covariability with\\u000a a range of indicators of human land use was assessed, including population, road and visitor density, area covered by agriculture,\\u000a open water, forest and residential housing. Data were collected on the

Jan E. Vermaat; Hasse Goosen; Nancy Omtzigt

281

Genes of the vertebrate major histocompatibility complex (MHC) are crucial to defense against infectious disease, provide\\u000a an important measure of functional genetic diversity, and have been implicated in mate choice and kin recognition. As a result,\\u000a MHC loci have been characterized for a number of vertebrate species, especially mammals; however, elephants are a notable\\u000a exception. Our study is the first

Elizabeth A. Archie; Tammy Henry; Jesus E. Maldonado; Cynthia J. Moss; Joyce H. Poole; Virginia R. Pearson; Suzan Murray; Susan C. Alberts; Robert C. Fleischer

2010-01-01

282

Onshore aeolian sand transport beyond the beach and foredune is often overlooked in the morphodynamics and sediment budgets of sandy coastal systems. This study provides detailed measurements of airflow, sand transport (via saltation and modified suspension), vegetation density, and surface elevation changes over an extensive (325×30 m) “swath” of a backshore foredune–parabolic dune plain complex. Near-surface (30 cm) wind speeds

Jeffrey L. Anderson; Ian J. Walker

2006-01-01

283

The climate model of intermediate complexity developed at the Oboukhov Institute of Atmospheric Physics, Russian Academy of\\u000a Sciences (IAP RAS CM), has been supplemented by a zero-dimensional carbon cycle model. With the carbon dioxide emissions prescribed\\u000a for the second half of the 19th century and for the 20th century, the model satisfactorily reproduces characteristics of the\\u000a carbon cycle over this

A. V. Eliseev; I. I. Mokhov; A. A. Karpenko

2007-01-01

284

West Nile virus (family Flaviviridae, genus Flavivirus, WNV) is now endemic in California across a variety of ecological regions that support a wide diversity of potential avian and mammalian host species. Because different avian hosts have varying competence for WNV, determining the blood-feeding patterns of Culex (Diptera: Culicidae) vectors is a key component in understanding the maintenance and amplification of the virus as well as tangential transmission to humans and horses. We investigated the blood-feeding patterns of Culex tarsalis Coquillett and members of the Culex pipiens L. complex from southern to northern California. Nearly 100 different host species were identified from 1,487 bloodmeals, by using the mitochondrial gene cytochrome c oxidase I (COI). Cx. tarsalis fed on a higher diversity of hosts and more frequently on nonhuman mammals than did the Cx. pipiens complex. Several WNV-competent host species, including house finch and house sparrow, were common bloodmeal sources for both vector species across several biomes and could account for WNV maintenance and amplification in these areas. Highly competent American crow, western scrub-jay and yellow-billed magpie also were fed upon often when available and are likely important as amplifying hosts for WNV in some areas. Neither species fed frequently on humans (Cx. pipiens complex [0.4%], Cx. tarsalis [0.2%]), but with high abundance, both species could serve as both enzootic and bridge vectors for WNV.

THIEMANN, T. C.; LEMENAGER, D. A.; KLUH, S.; CARROLL, B. D.; LOTHROP, H. D.; REISEN, W. K.

2012-01-01

285

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats. PMID:24671976

Pearse, Devon E; Miller, Michael R; Abadía-Cardoso, Alicia; Garza, John Carlos

2014-05-22

286

NASA Astrophysics Data System (ADS)

From the perspective of perturbation theory, we propose a systematic procedure for the evaluation of the derivative discontinuity (DD) of the exchange-correlation energy functional in Kohn-Sham (KS) density functional theory, wherein the exact DD can in principle be obtained by summing up all the perturbation corrections to infinite order. Truncation of the perturbation series at low order yields an efficient scheme for obtaining the approximate DD. While the zeroth-order theory yields a vanishing DD, the first-order correction to the DD can be expressed as an explicit universal functional of the ground-state density and the KS lowest unoccupied molecular orbital density, allowing the direct evaluation of the DD in the standard KS method without extra computational cost. The fundamental gap can be predicted by adding the estimated DD to the KS gap. This scheme is shown to be accurate in the prediction of the fundamental gaps for a wide variety of atoms and molecules.

Chai, Jeng-Da; Chen, Po-Ta

2013-01-01

287

An important chemical property emerging from density-functional theory is the hardness, which can be evaluated as half of the difference between the vertical ionisation energy and electron affinity of the system. For many gas phase molecules, however, the electron affinity is negative and standard ways of evaluating this property are troublesome. In this contribution, we investigate an unconventional approximation for the electron affinity, based on the Kohn-Sham orbital energies of the frontier orbitals and the ionisation potential. It is shown that, for a large series of molecules possessing negative electron affinities, this methodology yields reasonable values for this quantity and that the correlation of the computed values with the experimental affinities from electron transmission spectroscopy is superior to other theoretical approaches. In a second part of this contribution, the hardness of a series of stable negative ions is evaluated in aqueous solution. PMID:17328427

De Proft, Frank; Sablon, Nick; Tozer, David J; Geerlings, Paul

2007-01-01

288

NASA Astrophysics Data System (ADS)

Natural tracers (18O, Si and alkalinity) were used to assess the spatial and temporal variation in runoff sources within the 230 km^2 Feshie catchment in the Cairngorm Mountains of Scotland as part of the UK Catchment Hydrology And Sustainable Management (CHASM) initiative. The elevation of the mesoscale catchment ranges between 230--1110 m and snowfall comprises, on average, ca. 30% of annual precipitation. Tracer behavior was monitored by routine sampling in gauged, nested subcatchments ranging from 3--90 km^2 over a hydrological year. In addition, extensive surveys sampled the spatial variation in tracer concentrations throughout the catchment river network at low, moderate and high flows at sampling intensities of 1 per 1 km^2. Use of tracer data and GIS-based assessment indicated that catchment characteristics, rather than scale, accounted for the major differences in contributions from contrasting hydrological sources in nested subcatchments. Most notably, geology and the distribution of soil types exerted a strong control on the partitioning of runoff sources and groundwater contributions to flow (which mixing analysis showed range between 25 and 52% of annual flow in different subcatchments). Coverage of organic peat soils and thin montane podzols strongly influenced the storm runoff response of different subcatchments (with average runoff coefficients ranging from 0.75 to 0.4 for different sub-catchments) and dominated stream hydrochemistry at high flows. Despite the dominant influence of catchment characteristics at the sub-catchment scale, as spatial scale increased beyond 100 km^2 within the mesoscale catchment, the influence of significant alluvial aquifers on hydrological response became apparent. Neverthless, at scales >3 km^2, preliminary analysis of weekly 18O data indicated that mean residence times are similar, though it is reasonable to expect that residence time distributions would vary if high resolution tracer samples (ie daily or sub-daily) were available. Tracer studies such as this provide valuable insight into catchment flow path partitioning that can inform rainfall-runoff modelling in larger mesoscale catchments. However, spatial variation in sub-catchment runoff responses indicates that knowledge of the spatial variability in precipitation and snowmelt are likely to be the main constraints on modelling in such mountainous environments as the Feshie catchment.

Soulsby, C.; Rodgers, P.; Petry, J.; Dunn, S.

2003-04-01

289

NASA Astrophysics Data System (ADS)

Questionable chronologies have limited detailed reconstructions of past vegetation and climate trends for the Karginskii/Middle Wisconsinan interstade (abbreviated here as MW). However, recent results from continuous lake records, while not resolving all the dating issues, do provide a new framework within which to examine this intriguing period. Paleobotanical data suggest significant regional variations in the interstadial vegetation of Beringia. Larix forests were relatively common in central and western areas of western Beringia through much of the middle and late MW, whereas tundra dominated most eastern Beringian landscapes. During relatively warm intervals within the interstade, western Beringia was more extensively forested (at times achieving modern forest distribution) than was eastern Beringia, where Picea forests were limited to lowlands of interior Alaska and the Yukon Territory. A period of maximum tree-cover occurred between ca. 35 and 33 ka BP, but forests were also present in western Beringia and the Yukon Territory between ca. 39 and 33 ka BP. Although a period of maximum warmth probably occurred throughout Beringia between ca. 35 and 33 ka BP, significant regional variability characterized other intervals, with differences not only in the timing of climatic changes but also in their trends (e.g., warming in the upper Kolyma region, cooling in interior Alaska). The paleovegetational data suggest that the greatest interstadial warming occurred in far eastern and far western regions of Beringia, with areas that are now closest to Bering Strait showing more moderate climatic fluctuations. The causes for either the long-term or the rapid climatic variations within interstadial Beringia do not seem to relate simply to either Milankovitch or sub-Milankovitch scale forcings.

Anderson, Patricia M.; V. Lozhkin, Anatoly

2001-01-01

290

Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG-1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical. PMID:19625623

Leaché, Adam D; Koo, Michelle S; Spencer, Carol L; Papenfuss, Theodore J; Fisher, Robert N; McGuire, Jimmy A

2009-07-28

291

NASA Astrophysics Data System (ADS)

Foodborne illness outbreaks and product recalls are occasionally associated with ready-to-eat (RTE) sandwiches and other "heat and eat" multi-component RTE products. Ionizing radiation can inactivate foodborne pathogens on meat and poultry, fruits and vegetables, seafood, and RTE meat products. However, less data are available on the ability of low-dose ionizing radiation, doses under 5 kGy typically used for pasteurization purposes, to inactivate pathogenic bacteria on complex multi-component food products. In this study, the efficacy of ionizing radiation to inactivate Salmonella spp., Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, and Yersinia enterocolitica on RTE foods including a "frankfurter on a roll", a "beef cheeseburger on a bun" and a "vegetarian cheeseburger on a bun" was investigated. The average D-10 values, the radiation dose needed to inactivate 1 log 10 of pathogen, by bacterium species, were 0.61, 0.54, 0.47, 0.36 and 0.15 kGy for Salmonella spp., S. aureus, L. monocytogenes, E. coli O157:H7, and Y. enterocolitica, respectively when inoculated onto the three product types. These results indicate that irradiation may be an effective means for inactivating common foodborne pathogens including Salmonella spp, S. aureus, L. monocytogenes, E. coli O157:H7 and Y. enterocolitica in complex RTE food products such as 'heat and eat" sandwich products.

Sommers, Christopher H.; Boyd, Glenn

2006-07-01

292

Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation.We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG-1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.

Leache, A. D.; Koo, M. S.; Spencer, C. L.; Papenfuss, T. J.; Fisher, R. N.; McGuire, J. A.

2009-01-01

293

Five new trinuclear heterometallic Cu(II)-Mn(II) complexes [(CuL)2Mn(O2CPh)2] (1), [(CuL)2Mn(N3)2] (2), [(CuL)2Mn(NCO)2] (3), [(CuL)2Mn(NO3)2] (4) and [(CuL)2Mn(Sal)2]·CH2Cl2 (5) have been synthesized with the di-Schiff base ligand H2L (where H2L = N,N'-bis(salicylidene)-1,3-propanediamine and Sal = salicylate). These complexes with different anionic co-ligands have been synthesized to attain a large variation in phenoxido bridging angles and to investigate its consequence on magnetic properties. Single crystal X-ray diffraction analyses reveal that complexes 1, 2, 4 and 5 are linear, whereas 3 has an angular geometry. Variable temperature magnetic susceptibility measurements suggest that all five complexes possess an overall antiferromagnetic interaction between Cu(II) and Mn(II) ions, which results in a final ferrimagnetic ground state with spin 3/2 in the Cu(II)-Mn(II)-Cu(II) trinuclear structure. The weakest antiferromagnetic interaction (J(Cu-Mn) = -7.0 cm(-1)) is observed for 2 having the lowest value of the Cu-O-Mn angle (92.0°), while the strongest antiferromagnetic interaction (J(Cu-Mn) = -26.5 cm(-1)) is observed for 3 having the largest Cu-O-Mn angle (101.4°). Complexes 1, 4 and 5 show average Cu-O-Mn angles of 98.2°, 97.6° and 97.7°, respectively, that lead to intermediate antiferromagnetic interactions (J(Cu-Mn) = -9.6, -9.7, -9.3 cm(-1) respectively). PMID:24162065

Seth, Piya; Ghosh, Soumavo; Figuerola, Albert; Ghosh, Asutosh

2014-01-21

294

This study investigated the tempospatial variation of atmospheric mercury and its gas-particulate partition in the vicinity of a semiconductor manufacturing complex, where a plenty of flat-monitor manufacturing plants using elemental mercury as a light-initiating medium to produce backlight fluorescence tubes and may fugitively emit mercury-containing air pollutants to the atmosphere. Atmospheric mercury speciation, concentration, and the partition of total gaseous mercury (TGM) and particulate mercury (Hgp) were measured at four sites surrounding the semiconductor manufacturing intensive district/complex. One-year field measurement showed that the seasonal averaged concentrations of TGM and Hgp were in the range of 3.30-6.89 and 0.06-0.14 ng/m(3), respectively, whereas the highest 24-h TGM and Hgp concentrations were 10.33 and 0.26 ng/m(3), respectively. Atmospheric mercury apportioned as 92.59-99.01 % TGM and 0.99-7.41 % Hgp. As a whole, the highest and lowest concentrations of TGM were observed in the winter and summer sampling periods, respectively, whereas the concentration of Hgp did not vary much seasonally. The highest TGM concentrations were always observed at the downwind sites, indicating that the semiconductor manufacturing complex was a hot spot of mercury emission source, which caused severe atmospheric mercury contamination over the investigation region. PMID:24407780

Jen, Yi-Hsiu; Chen, Wei-Hsiang; Yuan, Chung-Shin; Ie, Iau-Ren; Hung, Chung-Hsuang

2014-04-01

295

Glial hypertrophy is associated with synaptogenesis in visual cortex and with stress-induced damage in the hippocampus. This study examined astrocytes in the dentate gyrus of male weanling rats exposed to complex or standard laboratory environments. No group differences in astrocytic surface density were observed, as expected in this brain region where group differences in synaptogenesis in male rats are reportedly minimal. Similarly, no group differences in adrenal weight were observed. Across all treatment groups, however, a significant positive correlation (r = 0.57) between adrenal weight and surface density of astrocytic processes was found. Considerable variation in responses of individual rats to their environments occurs in both the complex and the laboratory cage environments, and animals responding poorly may have had heavier adrenals and greater astrocyte reactivity in the dentate gyrus. Thus astrocyte hypertrophy in the dentate gyrus reflects the stress history of the individual rat and not any differential effects of rearing in a complex or a laboratory cage environment. PMID:1984435

Sirevaag, A M; Black, J E; Greenough, W T

1991-01-01

296

NASA Astrophysics Data System (ADS)

The levels of uranium and radon concentration in groundwater samples collected from some regions along the track from Amritsar city (Punjab) to Tusham ring complex (Haryana) has been analysed using SSTNDs from the health aspects point of view and also to observe its variation with the geological formations of the respective regions. In the high heat producing (HHP) granitic region of Tusham ring complex, Bhiwani District, Haryana, known to be composed of acid volcanics & associated HHP granites, uranium concentration in the groundwater water samples varies from 7.6±0.03 - 59.6±0.20 ?gl-1 with the average of 27.9 ?g l-1, which is comparatively higher than the average value of 17.4 ?g l-1 observed in non-HHP/non-granitic region of Amritsar, Punjab. Uranium concentration values in these samples show a wide range of variation depending upon different factors like source, location, depth and local geology etc. Except at certain specific locations in the HHP Tusham region, the levels of uranium concentration in the samples of ground water are lower than the international recommended safe limits. The radon concentration in the ground water samples along this track has also been studied using the Alpha-Scintillometer (GmBH 2002). Although the radon concentration varied from 3.4±0.6 to 15.7±0.5 Bq l-1 for the non-HHP Punjab region , but it has been to have a wide variation from 4.7±0.7 to 49.7±1.7 Bq l-1 on approaching the HHP Tusham region. Although both uranium and radon distribution in groundwater was found to be related with the acid volcanics and HHP zones in the respective regions, but no general trend was observed for any relation with the source depth and surface radionuclide content. On the other hand, a slightly positive correlation (R2 = 0.5) between radon content and uranium concentration in water samples of the studied region explicitly depicts that 222Rn concentration strongly depends on its progenitor content in water. The slightly higher values were observed from the ground water samples particularly of the areas falling in this belt of pre-Malani igneous rocks famous for lithological units, including felsite, granite and schist exposed in the area near Haryana-Rajasthan border. The values observed at certain locations are found to be higher than the international recommendations. The high uranium concentration observed particularly in some locations around Tusham Ring Complex can be attributed due to interaction of ground water with the soils as well as rock formations of this region and the local subsurface geology of the region.

Bikram Jit Singh, Bajwa; Harman, Singh; Vishal, Arora; Surinder, Singh

2010-05-01

297

A realistic description of how temperatures vary with elevation is crucial for ecosystem studies and for models of basin-scale snowmelt and spring streamflow. This paper explores surface temperature variability using temperature data from an array of 37 sensors, called the Yosemite network, which traverses both slopes of the Sierra Nevada in the vicinity of Yosemite National Park, California. These data indicate that a simple lapse rate is often a poor description of the spatial temperature structure. Rather, the spatial pattern of temperature over the Yosemite network varies considerably with synoptic conditions. Empirical orthogonal functions (EOFs) were used to identify the dominant spatial temperature patterns and how they vary in time. Temporal variations of these surface temperature patterns were correlated with large-scale weather conditions, as described by National Centers for Environmental Prediction-National Center for Atmospheric Research Reanalysis data. Regression equations were used to downscale larger-scale weather parameters, such as Reanalysis winds and pressure, to the surface temperature structure over the Yosemite network. These relationships demonstrate that strong westerly winds are associated with relatively warmer temperatures on the east slope and cooler temperatures on the west slope of the Sierra, and weaker westerly winds are associated with the opposite pattern. Reanalysis data from 1948 to 2005 indicate weakening westerlies over this time period, a trend leading to relatively cooler temperatures on the east slope over decadal timescale's. This trend also appears in long-term observations and demonstrates the need to consider topographic effects when examining long-term changes in mountain regions. Copyright 2007 by the American Geophysical Union.

Lundquist, J. D.; Cayan, D. R.

2007-01-01

298

The major histocompatibility complex is one of the best studied systems in vertebrates providing evidence for the long-term action of selection. Here, we examined the intra- and inter-population genetic diversity of the MHC class II DRB locus in European brown hare (Lepus europaeus) and correlated the results with genetic variability already estimated from the MHC DQA locus and from maternally (mitochondrial DNA (mtDNA)) and biparentally (allozymes, microsatellites) inherited loci. L. europaeus showed remarkable genetic polymorphism in both DQA and DRB1 loci. The Anatolian populations exhibited the highest genetic polymorphism for both loci. Balancing selection has established increased variability in the European populations despite the founder effects after the last glaciation. Different evolutionary rates were traced for DRB1 and DQA loci, as evidenced by the higher number of common DRB1 than DQA alleles and the greater differences between DRB1 alleles with common origin in comparison with DQA alleles. The high number of rare alleles with low frequencies detected implies that frequency-dependent selection drives MHC evolution in the brown hare through the advantage of rare alleles. Both loci were under the influence of positive selection within the peptide-binding region. The functional polymorphism, recorded as amino acid substitutions within the binding pockets, fell also within distinct geographic patterns, yet it was much narrower than the genetic polymorphism. We hypothesize that certain structural and functional characteristics of the binding pockets set limitations to the actual shape of genetic polymorphism in MHC. PMID:24743946

Koutsogiannouli, Evagelia A; Moutou, Katerina A; Stamatis, Costas; Walter, Lutz; Mamuris, Zissis

2014-06-01

299

Following administration to rats of various doses of N-nitrosodimethylamine (NDMA), O(6)-methylguanine (O(6)-meG) was lost from the DNA of four tissues (liver, white blood cells, lymph nodes, bone marrow) over two, sharply demarcated phases with substantially differing repair rates. Repair during each phase followed approximately first-order kinetics in O(6)-meG, even after a high dose of NDMA which caused substantial depletion of O(6)-alkylguanine-DNA alkyltransferase (AGT), a suicide repair protein. This is compatible with rate-determining adduct repair being brought about by a distinct, minor pool of AGT molecules which is rapidly replenished by de novo AGT synthesis. Similar biphasic repair kinetics were also observed in HepG2 cells treated in vitro with NDMA. In this case, the first phase of repair was inhibited by alpha-amanitin, an inhibitor of RNA polymerase II-mediated transcription. However, no dependence on transcriptional activity was found when O(6)-meG repair in specific gene sequences with different transcriptional status in rat liver was examined, suggesting that the effects of alpha-amanitin in HepG2 cells did not reflect inhibition of preferential repair of transcribed sequences. Repair was also examined in rat liver hepatocytes and non-parenchymal cells separately after administration of NDMA at non-AGT depleting doses. Within each cell-population, the repair followed single phase, first-order kinetics, with adduct loss from AGT-rich hepatocytes being significantly faster than from the relatively AGT-deficient non-parenchymal cells. In conclusion, differences in the AGT content of different cell subpopulations in the liver (and probably in other tissues), as well as additional cellular factors affecting repair efficiency, appear to determine the observed variation in the kinetics of repair of O(6)-meG. The additional cellular factors involved appear not to be related to the transcriptional state of the sequences being repaired, but may reflect different states of chromatin condensation. PMID:15542103

Souliotis, Vassilis L; Sfikakis, Petros P; Anderson, Lucy M; Kyrtopoulos, Soterios A

2004-12-21

300

BACKGROUND: Genetic variation in the vitamin K epoxide reductase complex (VKORC1) and cytochrome P450 4F2 (CYP4F2) genes were found to be strongly associated with the oral anticoagulant (OA) dose requirement. The distribution of genetic variation in these two genes was found to show large inter- and intra-ethnic difference. MATERIALS AND METHODS: A total of 470 unrelated, healthy volunteers of South Indians of either sex (age: 18-60 years) were enrolled for the study. A 5 ml of venous blood was collected and the genomic deoxyribonucleic acid (DNA) was extracted by using phenol-chloroform extraction method. Real-time quantitative polymerase chain reaction (RT-PCR) method was used for genotyping. RESULTS: The variant allele frequencies of VKORC1 rs2359612 (T), rs8050894 (C), rs9934438 (T) and rs9923231 (A) were found to be 11.0%, 11.8%, 11.7% and 12.0%, respectively. The variant allele VKORC1 rs7294 was (80.1%) more frequent and the variant allele CYP4F2 * 3 was found to be 41.8% in South Indians. The allele, genotype and haplotype frequencies of VKORC1 and CYP4F2 gene were distinct from other compared HapMap populations (P < 0.0001). CONCLUSION: The findings of our study provide the basic genetic information for further pharmacogenetic based investigation of OA therapy in the population.

Kumar, Dhakchinamoorthi Krishna; Shewade, Deepak Gopal; Manjunath, Sajjanavar; Ushakiran, Prayaga; Reneega, Gangadharan; Adithan, Chandrasekaran

2013-01-01

301

Periodontitis is a chronic inflammatory disease with a multifactorial etiology. We investigated whether human major histocompatibility complex (MHC) polymorphisms (6p21.3) are associated with periodontal parameters. Parogene 1 population samples (n = 169) were analyzed with 13,245 single nucleotide polymorphisms (SNPs) of the MHC region. Eighteen selected SNPs (P ? 0.001) were replicated in Parogene 2 population samples (n = 339) and the Health 2000 Survey (n = 1,420). All subjects had a detailed clinical and radiographic oral health examination. Serum lymphotoxin-? (LTA) concentrations were measured in the Parogene populations, and the protein was detected in inflamed periodontal tissue. In the Parogene 1 population, 10 SNPs were associated with periodontal parameters. The strongest associations emerged from the parameters bleeding on probing (BOP) and a probing pocket depth (PPD) of ?6 mm with the genes BAT1, NFKBIL1, and LTA. Six SNPs, rs11796, rs3130059, rs2239527, rs2071591, rs909253, and rs1041981 (r(2), ?0.92), constituted a risk haplotype. In the Parogene 1 population, the haplotype had the strongest association with the parameter BOP, a PPD of ?6 mm, and severe periodontitis with odds ratios (95% confidence intervals) of 2.63 (2.21 to 3.20), 2.90 (2.37 to 3.52), and 3.10 (1.63 to 5.98), respectively. These results were replicated in the other two populations. High serum LTA concentrations in the Parogene population were associated with the periodontitis risk alleles of the LTA SNPs (rs909253 and rs1041981) of the haplotype. In addition, the protein was expressed in inflamed gingival connective tissue. We identified a novel BAT1-NFKBIL1-LTA haplotype as a significant contributor to the risk of periodontitis. The genetic polymorphisms in the MHC class III region may be functionally important in periodontitis susceptibility. PMID:24566624

Kallio, K A Elisa; Marchesani, Marja; Vlachopoulou, Efthymia; Mäntylä, Päivi; Paju, Susanna; Buhlin, Kåre; Suominen, Anna L; Contreras, Johanna; Knuuttila, Matti; Hernandez, Marcela; Huumonen, Sisko; Nieminen, Markku S; Perola, Markus; Sinisalo, Juha; Lokki, Marja-Liisa; Pussinen, Pirkko J

2014-05-01

302

Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C?N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy beaches as functional ecosystems in their own right. PMID:21858213

Ortega Cisneros, Kelly; Smit, Albertus J; Laudien, Jürgen; Schoeman, David S

2011-01-01

303

The planar NNN-pincer complexes [M(II)(pyN(2)(Me2))(OH)](1-) (M(II) = Ni, Cu) fix CO(2) in ?(1)-OCO(2)H complexes; results for the copper system are described. Mn(II), Fe(II), Co(II), and Zn(II) behave differently, forming [M(II)(pyN(2)(Me2))(2)](2-) with N(4)O(2) coordination. Incorporation of the Ni(II) pincer into binucleating macrocycle 2 containing a triamino M(II) locus connected by two 1,3-biphenylene groups affords proximal Ni(II) and M(II) sites for investigation of the synthesis, structure, and reactivity of Ni-X-M bridge units. This ligand structure is taken as a reference for variations in M(II) atoms and binding sites and bridges X = OH(-) and CN(-) to produce additional members of the macrocyclic family with improved properties. Macrocycle 2 with a 22-membered ring is shown to bind M(II) = Mn, Fe, and Cu with hydroxo bridges. Introduction of the 4-Bu(i)O group (macrocycle 3) improves the solubility of neutral complexes such as those with Ni(II)-OH-Cu(II) and Ni(II)-CN-Fe(II) bridges. Syntheses of macrocycle 5 with a 7-Me-[12]aneSN(3) and macrocycle 6 with a 1,8-Me(2)-[14]aneN(4) M(II) binding site are described together with hydoxo-bridged Ni/Cu and cyano-bridged Ni/Fe complexes. This work was motivated by the presence of a Ni···(HO)-Fe bridge grouping in a reactive state of carbon monoxide dehydrogenase. Attempted decrease in Ni-(OH)-M distances (3.70-3.87 Å) to smaller values observed in the enzyme by use of macrocycle 4 having 1,2-biphenylene connectors led to a mononuclear octahedral Ni(II) complex. Bridge structural units are summarized, and the structures of 14 macrocyclic complexes including 8 with bridges are described. PMID:23030366

Zhang, Xiaofeng; Huang, Deguang; Chen, Yu-Sheng; Holm, R H

2012-10-15

304

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide and results from a complex interaction between carcinogen exposure and inherent susceptibility. Despite its prevalence genetic factors that predispose to the development of lung cancer remain elusive. Inbred mouse models offer a unique and clinically relevant tool to study genetic factors that contribute to lung carcinogenesis due to the development of tumors that resemble human adenocarcinoma and broad strain-specific variation in cancer incidence after carcinogen administration. Here we set out to investigate whether strain-specific variability in tumor immunosurveillance contributes to differences in lung cancer. Using bone marrow transplantation we determined that hematopoietic cells from lung cancer-resistant mice could significantly impede the development of cancer in a susceptible strain. Furthermore, we show that this is not due to differences in tumor-promoting inflammatory changes or variability in immunosurveillance by the adaptive immune system, but results from strain-specific differences in natural killer cell (NK) cytotoxicity. Using a newly discovered congenic strain of mice we demonstrate a previously unrecognized role for strain-specific polymorphisms in the natural killer gene complex (NKC) in immunosurveillance for carcinogen-induced lung cancer. Since polymorphisms in the NKC are highly prevalent in man, our data may explain why certain individuals without obvious risk factors develop lung cancer while others remain resistant to the disease despite heavy environmental carcinogen exposure.

Kreisel, Daniel; Gelman, Andrew E.; Higashikubo, Ryuji; Lin, Xue; Vikis, Haris G.; White, J. Michael; Toth, Kelsey A.; Deshpande, Charuhas; Carreno, Beatriz M.; You, Ming; Taffner, Samantha M.; Yokoyama, Wayne M.; Bui, Jack D.; Schreiber, Robert D.; Krupnick, Alexander S.

2012-01-01

305

Developing the random phase approximation into a practical post-Kohn-Sham correlation model

The random phase approximation (RPA) to the density functional correlation energy systematically improves upon many limitations of present semilocal functionals, but was considered too computationally expensive for widespread use in the past. Here a physically appealing reformulation of the RPA correlation model is developed that substantially reduces its computational complexity. The density functional RPA correlation energy is shown to equal

Filipp Furche

2008-01-01

306

We present a second-quantization based atomic-orbital method for the computation of time-dependent response functions within Hartree-Fock and Kohn-Sham density-functional theories. The method is suited for linear scaling. Illustrative results are presented for excitation energies, one- and two-photon transition moments, polarizabilities, and hyperpolarizabilities for hexagonal BN sheets with up to 180 atoms. PMID:18698887

Kjaergaard, Thomas; Jørgensen, Poul; Olsen, Jeppe; Coriani, Sonia; Helgaker, Trygve

2008-08-01

307

We have investigated the accuracy of the local-spin-density approximation with orbital-density-dependent self-interaction correction (LSDSIC) as proposed by Perdew and Zunger within a Kohn-Sham approach in which electrons with a given spin projection all move in a single optimized effective potential (OEP). We have also studied the accuracy of the Krieger-Li-Iafrate (KLI) approximation to the OEP for the same energy functional

Jiqiang Chen; J. B. Krieger; Yan Li; G. J. Iafrate

1996-01-01

308

A linear relationship was found between the singlet–triplet excitation energy and the energy difference presented by the Kohn–Sham frontier molecular orbitals, independently of the used exchange-correlation functional and of the basis set functions quality. The relationship was explored in three different situations: (a) when the number of carbons is increased in an all-trans acetylene family; (b) rotation of the trans-butadiene

Álvaro Vázquez-Mayagoitia; Rubicelia Vargas; Jeffrey A. Nichols; Patricio Fuentealba; Jorge Garza

2006-01-01

309

We have employed the local-spin-density approximation with orbital self-interaction-correction (LSDSIC) for the exchange-correlation energy functional in the calculation of the ground state properties of first row heteropolar diatomic molecules. The Kohn-Sham molecular orbitals are obtained by fully numerical solution of a Schrodinger equation including the Optimized Effective Potential in the KLIfootnote J. B. Krieger, Y. Li and G. J Iafrate

J. B. Krieger; Jiqiang Chen; G. J. Iafrate

1996-01-01

310

The standard local density approximation and generalized gradient approximations fail to properly describe the dissociation of an electron pair bond, yielding large errors (on the order of 50 kcal\\/mol) at long bond distances. To remedy this failure, a self-consistent Kohn-Sham (KS) method is proposed with the exchange-correlation (xc) energy and potential depending on both occupied and virtual KS orbitals. The

M. Grüning; O. V. Gritsenko; E. J. Baerends

2003-01-01

311

Density functional theory with fractionally occupied frontier orbitals was combined with an analysis of the instability of the Kohn-Sham solutions and applied to the study of the ring-opening reactions of 1,2-dioxetene, 1,2-dithiete, 1,2-diselenete, and 1,2-ditellurete. These molecules possess transition structures and reactive intermediates for the ring-opening reactions which exhibit strong nondynamical electron correlation. All restricted density functional theory (DFT) solutions

John D. Goddard; Galina Orlova

1999-01-01

312

The standard local density approximation and generalized gradient approximations fail to properly describe the dissociation of an electron pair bond, yielding large errors (on the order of 50 kcal\\/mol) at long bond distances. To remedy this failure, a self-consistent Kohn–Sham (KS) method is proposed with the exchange-correlation (xc) energy and potential depending on both occupied and virtual KS orbitals. The

O. V. Gritsenko; E. J. Baerends

2003-01-01

313

We discuss two basic problems in the Hohenberg-Kohn-Sham version of density functional theory, HKS-DFT: the first, the N-representability of the functional F[rho] and, the second, the universality of F[rho]. In relation to the first, we show that F[rho] must satisfy N-representability conditions that follow from those on the 2-matrix D2(r1, r2; r', r'2). In the case of the second, we

Eduardo V. Ludeña; Francesc Illas; Alejandro Ramirez-Solis

2009-01-01

314

We discuss two basic problems in the Hohenberg-Kohn-Sham version of density functional theory, HKS-DFT: the first, the N-representability of the functional F[rho] and, the second, the universality of F[rho]. In relation to the first, we show that F[rho] must satisfy N-representability conditions that follow from those on the 2-matrix D2(r1, r2; r', r'2). In the case of the second, we

Eduardo V. Ludeña; Francesc Illas; Alejandro Ramirez-Solis

2008-01-01

315

NASA Astrophysics Data System (ADS)

Two facets of paleomagnetism are discussed as part of this study; the use of paleomagnetic records to improve our understanding of magnetic field reversals, and the use of paleosecular variation in volcanology studies. A detailed volcanic record of the Matuyama-Brunhes (MBR) reversal (780 ka) suggests that the reversing magnetic field remains dipolar throughout the transition. This record, taken from the Tatara-San Pedro Volcanic Complex located in the Andean region (36sp°S, 71sp°W) of central Chile, is recorded in 29 andesite flows. The record is exceptionally well constrained temporally and geochemically as well as paleomagnetically. The lavas record a quick change from reversed polarity to a period of transitional stability, with virtual geomagnetic poles (VGP) forming a cluster centered in Australia, followed by a quick swing to normal polarity. The Chilean data demonstrate that the dipole assumes an intermediate subequatorial position before completing the transition. VGP data from the four other available MBR lava records are largely coincident with the Chilean grouping and further strengthen the suggestion of a dipolar Matuyama-Brunhes reversal field geometry. The integration of paleomagnetism with geochemistry offers volcanologists an efficient and independent correlation tool for studying geochemical trends and growth morphology in volcanic centers. The Tatara-San Pedro Volcanic Complex, a Quaternary arc volcanic center in the Chilean Andes (Singer et al., in press), serves as an excellent model of complex stratocone evolution and lends itself well to a demonstration of this technique. Three fundamental relationships between paleomagnetic and geochemical data are demonstrated within the TSPVC: an absolute correlation, a paleomagnetic dependent correlation, and a geochemical dependent correlation. These correlations provide a degree of temporal insight into the rates of magma productivity that would be difficult to gain through conventional radiometric dating techniques.

Pickens, James Cecil

316

NASA Astrophysics Data System (ADS)

We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potentials is not yet satisfactory, and if we choose to optimize their prediction, a rather different value of the functional's parameter is obtained. We put this finding in a larger context by discussing similar observations for other functionals and possible directions for further functional development that our findings suggest.

Schmidt, Tobias; Kraisler, Eli; Makmal, Adi; Kronik, Leeor; Kümmel, Stephan

2014-05-01

317

We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potentials is not yet satisfactory, and if we choose to optimize their prediction, a rather different value of the functional's parameter is obtained. We put this finding in a larger context by discussing similar observations for other functionals and possible directions for further functional development that our findings suggest. PMID:24832318

Schmidt, Tobias; Kraisler, Eli; Makmal, Adi; Kronik, Leeor; Kümmel, Stephan

2014-05-14

318

NASA Astrophysics Data System (ADS)

The use of the relativistic and spin-polarized real-space Korringa-Kohn-Rostoker (KKR) method is limited to small systems (less than 100 atoms). This is due to the prohibitively large CPU times needed for the inversion of the KKR matrix. To study systems of more than a thousand atoms, we have implemented the concept of a screened reference medium, within the fully relativistic spin-polarized version of the real-space locally self-consistent multiple-scattering method (LSMS). The LSMS method makes use of a local interaction zone (LIZ) for solving the quantum mechanical problem, while the Poisson equation is solved in the whole space. The screened reference medium gives rise to sparse KKR matrices and using state-of-the-art sparse matrix technology a substantial reduction in the CPU times is obtained, enabling applications of the method to systems whose LIZ consists of more than a thousand atoms. The method is benchmarked by application to the elemental transition metals, the fcc (face-centred-cubic) Co and Ni, and the bcc (body-centred cubic) Fe, and compared to the results of the conventional k-space methods. The convergence in real space of the magnetic moments, the magnetocrystalline anisotropy energy and the orbital moment anisotropy is discussed in detail.

Petit, L.; Beiden, S. V.; Temmerman, W. M.; Szotek, Z.; Stocks, G. M.; Gehring, G. A.

2000-10-01

319

Dissociation of diatomic molecules and the exact-exchange Kohn-Sham potential: The case of LiF

We examine the role of the exact-exchange (EXX) Kohn-Sham potential in curing the problem of fractional molecular dissociation. This is achieved by performing EXX calculations for the illustrative case of the LiF molecule. We show that by choosing the lowest-energy electronic configuration for each interatomic distance, a qualitatively correct binding energy curve, reflecting integer dissociation, is obtained. Surprisingly, for LiF this comes at the cost of violating the Aufbau principle, a phenomenon we discuss at length. Furthermore, we numerically confirm that in the EXX potential of the diatomic molecule, one of the atomic potentials is shifted by a constant while the other one is not, depending on where the highest occupied molecular orbital is localized. This changes the relative positions of the energies of each atom and enforces the integer configuration by preventing spurious charge transfer. The size of the constant shift becomes increasingly unstable numerically the larger the interatomic separation is, reflecting the increasing absence of coupling between the atoms.

Makmal, Adi; Kronik, Leeor [Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100 (Israel); Kuemmel, Stephan [Physikalisches Institut, Universitaet Bayreuth, D-95440 Bayreuth (Germany)

2011-06-15

320

It is found that for closed-l-shell atoms, the exact local exchange potential v(x)(r) calculated in the exchange-only Kohn-Sham (KS) scheme of the density functional theory (DFT) is very well represented within the region of every atomic shell by each of the suitably shifted potentials obtained with the nonlocal Fock exchange operator for the individual Hartree-Fock (HF) orbitals belonging to this shell. This newly revealed property is not related to the well-known steplike shell structure in the response part of v(x)(r), but it results from specific relations satisfied by the HF orbital exchange potentials. These relations explain the outstanding proximity of the occupied HF and exchange-only KS orbitals as well as the high quality of the Krieger-Li-Iafrate and localized HF (or, equivalently, common-energy-denominator) approximations to the DFT exchange potential v(x)(r). Another highly accurate representation of v(x)(r) is given by the continuous piecewise function built of shell-specific exchange potentials, each defined as the weighted average of the shifted orbital exchange potentials corresponding to a given shell. The constant shifts added to the HF orbital exchange potentials, to map them onto v(x)(r), are nearly equal to the differences between the energies of the corresponding KS and HF orbitals. It is discussed why these differences are positive and grow when the respective orbital energies become lower for inner orbitals. PMID:20078143

Cinal, M

2010-01-01

321

NASA Astrophysics Data System (ADS)

The concept of a ``consistent,'' Kohn-Sham (KS) density functional theory (DFT) is discussed, where the functional is able to provide good total energies and its self-consistent potential is such that the KS eigenvalues correspond to accurate approximations to the principal ionization potentials for the molecule. Today, none of the vast number of DFT approximations show this property. The one exception is the ab initio dft method built upon the optimized effective potential strategy for exchange and correlation. This qualifies as a DFT method because it represents the correlated density as a single determinant and by imposing that condition, generates local exchange and correlation operators which are used in self-consistent solutions of the orbitals and eigenvalues. Such a ``consistent'' DFT shares many of the properties of the Dyson equation, but without its frequency dependence and associated complications. The relationship between ab initio dft based on MBPT2 functional and GW method is discussed. Ab initio dft provides a self-consistent, frequency independent, effective independent particle alternative with a local correlation potential.

Verma, Prakash; Bartlett, Rodney J.

2012-10-01

322

From the perspective of perturbation theory, we propose a systematic procedure for the evaluation of the derivative discontinuity (DD) of the exchange-correlation energy functional in Kohn-Sham (KS) density functional theory, wherein the exact DD can in principle be obtained by summing up all the perturbation corrections to infinite order. Truncation of the perturbation series at low order yields an efficient scheme for obtaining the approximate DD. While the zeroth-order theory yields a vanishing DD, the first-order correction to the DD can be expressed as an explicit universal functional of the ground-state density and the KS lowest unoccupied molecular orbital density, allowing the direct evaluation of the DD in the standard KS method without extra computational cost. The fundamental gap can be predicted by adding the estimated DD to the KS gap. This scheme is shown to be accurate in the prediction of the fundamental gaps for a wide variety of atoms and molecules. PMID:23373919

Chai, Jeng-Da; Chen, Po-Ta

2013-01-18

323

Variational definitions of orbital energies

NASA Astrophysics Data System (ADS)

A formulation of Koopmans' theorem is derived for high-spin half-filled open shells in the restricted openshell Hartree-Fock (ROHF) method based on a variational treatment of both the initial (non-ionized) open-shell system X with spin S and the corresponding ions having a hole or an extra electron in the closed, open and virtual shells respectively. The six processes for forming ions with spin S+/-1/2 require two different definitions for canonical orbitals within each shell. These processes may be treated equivalently within a restricted CI using arbitrary non-canonical linear transforms of the ROHF orbitals optimal for the initial system. Canonical UHF orbitals also obey a variational principle for the ion energies, but they provide less appropriate estimates for actual states of the ion. Canonical spin-unrestricted Kohn-Sham orbitals with common exchange-correlation functionals suffer from all of the UHF problems and from selfinteraction error. They generally are not useful estimates for ion energies.

Davidson, Ernest R.

2012-12-01

324

B-G antigens are cell-surface molecules encoded by a highly polymorphic multigene family located in the chicken major histocompatibility complex (MHC). Rabbit antisera to B-G molecules immunoprecipitate 3-6 bands from iodinated erythrocytes by sodium dodecyl sulfate (SDS) gels under reducing conditions. These are all B-G molecules because they all map to the B-G region of the chicken MHC in congenic and recombinant chickens, most are directly recognized by the antisera, most form disulfide-linked dimers, and none bear N-linked carbohydrate. Both apparent homodimers and heterodimers are found, which bear intrachain disulfide bonds. All 3-6 bands have different mobilities in SDS gels between different haplotypes, ranging from 30 to 55 kDa. This size polymorphism is not affected by glycosidase treatment or addition of protease inhibitors. Partial proteolysis of cell surface-iodinated B-G molecules generates extremely similar patterns of spots, both within and between haplotypes. These surface-iodinated peptides bear either interchain or intrachain disulfide bonds. Additional peptides are generated by proteolysis of B-G molecules iodinated after isolation. Thus, it appears that the extracellular regions of these molecules are very similar and that the length polymorphism is due to variations in the cytoplasmic regions. Inspection of the cDNA-derived protein sequence in this region shows many heptad repeats, which may allow variation in length by step deletion and alternative splicing. The repeats indicate an alpha-helical coiled-coil structure, which could form an interaction between subunits of the dimer or with the cytoskeleton or both. Images

Kaufman, J; Salomonsen, J; Skj?dt, K; Thorpe, D

1990-01-01

325

Background Pattern-oriented chemical profiling is increasingly being used to characterize the phytochemical composition of herbal medicines for quality control purposes. Ideally, a fingerprint of the biological effects should complement the chemical fingerprint. For ethical and practical reasons it is not possible to test each herbal extract in laboratory animals or humans. What is needed is a test system consisting of an organism with relevant biology and complexity that can serve as a surrogate in vitro system. The purpose of this study was to test the hypothesis that the Saccharomyces cerevisiae transcriptome might be used as an indicator of phytochemical variation of closely-related yet distinctly different extracts prepared from a single species of a phytogeographically widely distributed medicinal plant. We combined phytochemical profiling using chromatographic methods (HPTLC, HPLC-PDA-MS/MS) and gene expression studies using Affymetrix Yeast 2.0 gene chip with principal component analysis and k-nearest neighbor clustering analysis to test this hypothesis using extracts prepared from the phytogeographically widely distributed medicinal plant Equisetum arvense as a test case. Results We found that the Equisetum arvense extracts exhibited qualitative and quantitative differences in their phytochemical composition grouped along their phytogeographical origin. Exposure of yeast to the extracts led to changes in gene expression that reflected both the similarities and differences in the phytochemical composition of the extracts. The Equisetum arvense extracts elicited changes in the expression of genes involved in mRNA translation, drug transport, metabolism of energy reserves, phospholipid metabolism, and the cellular stress response. Conclusions Our data show that functional genomics in S. cerevisiae may be developed as a sensitive bioassay for the scientific investigation of the interplay between phytochemical composition and transcriptional effects of complex mixtures of chemical compounds. S. cerevisiae transcriptomics may also be developed for testing of mixtures of conventional drugs (“polypills”) to discover novel antagonistic or synergistic effects of those drug combinations.

2013-01-01

326

Ultrastructural observations of spermatogenesis and sperm development of Saccocoelioides godoyi, an intestinal parasite of Leporinus friderici (Bloch, 1794) are described. The irregular-shaped spermatogonia form a peripheral layer, and show a prominent nucleus. Spermatocytes are larger than spermatogonia, and in the early stage present synaptonemal complex. Spermatids show nuclei smaller than the spermatocytes. Spermiogenesis is characterized by outgrowth of the zone of differentiation, presenting basal bodies, separated by an intercentriolar body. At the end of this process, the spermatozoa are released into the residual cytoplasmic mass. The spermatozoa of S. godoyi are elongate, similar to the pattern described for other Digenea, showing nuclei, mitochondria and two axonemes with the 9+1 configuration. The peripheral cortical microtubules on the dorsal and ventral faces are laterally interrupted. PMID:11285476

Baptista-Farias, M F; Kohn, A; Cohen, S C

2001-01-01

327

Abstract Echinorhynchus truttae and the Echinorhynchus bothniensis species complex are common parasites of salmoniform and other fishes in northern Europe. Echinorhynchus bothniensis and its sibling species Echinorhynchus 'bothniensis' are thought to be closely related to the Nearctic Echinorhynchus leidyi Van Cleave, 1924 based on morphological similarity and common usage of a mysid intermediate host. This study provides the first analysis of morphological and meristic variation in Echinorhynchus truttae and expands our knowledge of anatomical variability in the Echinorhynchus bothniensis group. Morphological variability in Echinorhynchus truttae was found to be far greater than previously reported, with part of the variance attributable to sexual dimorphism. Echinorhynchus truttae, the two species of the Echinorhynchus bothniensis group and Echinorhynchus leidyi displayed considerable interspecific overlap in the ranges of all conventional morphological characters. However, Proboscis profiler, a tool for detecting acanthocephalan morphotypes using multivariate analysis of hook morphometrics, successfully separated Echinorhynchus truttae from the other taxa. The Echinorhynchus bothniensis species group could not be reliably distinguished from Echinorhynchus leidyi (or each other), providing further evidence of the affinity of these taxa. Observations on the distribution of Echinorhynchus truttae in its definitive host population are also reported.

2013-01-01

328

Repeat sequences of approximately 100 base pairs in length were found in the rDNA ITS2 region of Anopheles barbirostris van der Wulp (Diptera: Culicidae) species A1, A2, A3, A4, and An. campestris-like in the An. barbirostris complex. Variation in the number of repeats was observed among the five sibling species. Specifically, 10 repeats were observed in A1, eight in A2, A4, and campestris-like, and three in A3. Based on similarities in the sequences of the repeats, related repeats were classified into nine groups. Although A2, A4, and the campestris-like species had the same number of repeats, the ITS2 region of the three species contained different groups of repeats. Excluding the repeat sequences facilitated good alignment of the ITS2 region in the five sibling species. Phylogenetic analyses of the 95 isolines were compared with results obtained from mitochondrial genes (COI and COII). The results revealed marked differences among the five sibling species, particularly regarding the ITS2 region of A3, which was more distinct from the other four species than COI and COIL Repeat sequences in the ITS2 region of other Anopheles species retrieved from GenBank also were analyzed. New repeat sequences were found in An. beklemishevi Stegnii and Kabanova, An. crucians Wiedemann and An. funestus Giles, suggesting that the occurrence of repeat sequences in the ITS2 region are not rare in anopheline mosquitoes.

Otsuka, Yasushi

2011-01-01

329

Maximizing the quality and benefits of newly established chiropractic services represents an important policy and practice goal for the US Department of Veterans Affairs' healthcare system. Understanding the implementation process and characteristics of new chiropractic clinics and the determinants and consequences of these processes and characteristics is a critical first step in guiding quality improvement. This paper reports insights and lessons learned regarding the successful application of mixed methods research approaches-insights derived from a study of chiropractic clinic implementation and characteristics, Variations in the Implementation and Characteristics of Chiropractic Services in VA (VICCS). Challenges and solutions are presented in areas ranging from selection and recruitment of sites and participants to the collection and analysis of varied data sources. The VICCS study illustrates the importance of several factors in successful mixed-methods approaches, including (1) the importance of a formal, fully developed logic model to identify and link data sources, variables, and outcomes of interest to the study's analysis plan and its data collection instruments and codebook and (2) ensuring that data collection methods, including mixed-methods, match study aims. Overall, successful application of a mixed-methods approach requires careful planning, frequent trade-offs, and complex coding and analysis. PMID:24489589

Khorsan, Raheleh; Cohen, Angela B; Lisi, Anthony J; Smith, Monica M; Delevan, Deborah; Armstrong, Courtney; Mittman, Brian S

2013-01-01

330

Did you mean: Tuning photochemical photophysical properties ruin(2 2'-bipyridine)2Lx complexes nonchromophoric ligand variations Ingle Simon D Lima Francisco C A Camilo Mariana R Daniel Julian F S Santos Evan D A Lima-Nett bandit S Carlos Rose M ?

331

NASA Astrophysics Data System (ADS)

Two related methods to calculate the Kohn-Sham correlation energy within the framework of the adiabatic-connection fluctuation-dissipation theorem are presented. The required coupling-strength-dependent density-density response functions are calculated within exact-exchange time-dependent density-functional theory, i.e., within time-dependent density-functional response theory using the full frequency-dependent exchange kernel in addition to the Coulomb kernel. The resulting resolution-of-identity exact-exchange random-phase approximation (RI-EXXRPA) methods in contrast to previous EXXRPA methods employ an auxiliary basis set (RI basis set) to improve the computational efficiency, in particular, to reduce the formal scaling of the computational effort with respect to the system size N from N6 to N5. Moreover, the presented RI-EXXRPA methods, in contrast to previous ones, do not treat products of occupied times unoccupied orbitals as if they were linearly independent. Finally, terms neglected in previous EXXRPA methods can be included, which leads to a method designated RI-EXXRPA+, while the method without these extra terms is simply referred to as RI-EXXRPA. Both EXXRPA methods are shown to yield total energies, reaction energies of small molecules, and binding energies of noncovalently bonded dimers of a quality that is similar and in some cases even better than that obtained with quantum chemistry methods such as Møller-Plesset perturbation theory of second order (MP2) or with the coupled cluster singles doubles method. In contrast to MP2 and to conventional density-functional methods, the presented RI-EXXRPA methods are able to treat static correlation.

Bleiziffer, Patrick; Heßelmann, Andreas; Görling, Andreas

2012-04-01

332

NASA Astrophysics Data System (ADS)

Aspects of density functional resonance theory (DFRT) [D. L. Whitenack and A. Wasserman, Phys. Rev. Lett. 107, 163002 (2011)], a recently developed complex-scaled version of ground-state density functional theory (DFT), are studied in detail. The asymptotic behavior of the complex density function is related to the complex resonance energy and system's threshold energy, and the function's local oscillatory behavior is connected with preferential directions of electron decay. Practical considerations for implementation of the theory are addressed including sensitivity to the complex-scaling parameter, ?. In Kohn-Sham DFRT, it is shown that almost all ?-dependence in the calculated energies and lifetimes can be extinguished via use of a proper basis set or fine grid. The highest occupied Kohn-Sham orbital energy and lifetime are related to physical affinity and width, and the threshold energy of the Kohn-Sham system is shown to be equal to the threshold energy of the interacting system shifted by a well-defined functional. Finally, various complex-scaling conditions are derived which relate the functionals of ground-state DFT to those of DFRT via proper scaling factors and a non-Hermitian coupling-constant system.

Whitenack, Daniel L.; Wasserman, Adam

2012-04-01

333

Aspects of density functional resonance theory (DFRT) [D. L. Whitenack and A. Wasserman, Phys. Rev. Lett. 107, 163002 (2011)], a recently developed complex-scaled version of ground-state density functional theory (DFT), are studied in detail. The asymptotic behavior of the complex density function is related to the complex resonance energy and system's threshold energy, and the function's local oscillatory behavior is connected with preferential directions of electron decay. Practical considerations for implementation of the theory are addressed including sensitivity to the complex-scaling parameter, ?. In Kohn-Sham DFRT, it is shown that almost all ?-dependence in the calculated energies and lifetimes can be extinguished via use of a proper basis set or fine grid. The highest occupied Kohn-Sham orbital energy and lifetime are related to physical affinity and width, and the threshold energy of the Kohn-Sham system is shown to be equal to the threshold energy of the interacting system shifted by a well-defined functional. Finally, various complex-scaling conditions are derived which relate the functionals of ground-state DFT to those of DFRT via proper scaling factors and a non-Hermitian coupling-constant system. PMID:22559469

Whitenack, Daniel L; Wasserman, Adam

2012-04-28

334

NASA Astrophysics Data System (ADS)

We present a fully analytical formulation for calculating Raman intensities of crystalline periodic systems using a local basis set. Numerical differentiation with respect to atomic coordinates and with respect to wavevectors is entirely avoided as is the determination of crystal orbital coefficient derivatives with respect to nuclear displacements. Instead, our method utilizes the orbital energy-weighted density matrix and is based on the self-consistent solution of first- and second-order Coupled Perturbed Hartree-Fock/Kohn-Sham equations for the electronic response to external electric fields at the equilibrium geometry. This method has also been implemented in the Crystal program, which uses a Gaussian type basis set.

Maschio, Lorenzo; Kirtman, Bernard; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

2013-10-01

335

A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol. PMID:19603962

Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L

2009-07-14

336

The Gordian knot of density-functional theories for classical molecular liquids remains finding an accurate free-energy functional in terms of the densities of the atomic sites of the molecules. Following Kohn and Sham, we show how to solve this problem by considering noninteracting molecules in a set of effective potentials. This shift in perspective leads to an accurate and computationally tractable description in terms of simple three-dimensional functions. We also treat both the linear- and saturation- dielectric responses of polar systems, presenting liquid hydrogen chloride as a case study. PMID:19113431

Lischner, Johannes; Arias, T A

2008-11-21

337

The now classic optimized-effective-potential (OEP) approach of Sharp and Horton [Phys Rev. 90, 317 (1953)] and Talman and Shadwick [Phys. Rev. A 14, 36 (1976)] seeks the local potential that is variationally optimized to best approximate the Hartree-Fock exchange operator. The resulting OEP can be identified as the exchange potential of Kohn-Sham density-functional theory. The present work generalizes this OEP approach to treat the correlated case, and shows that the Kohn-Sham exchange-correlation potential is the variationally best local approximation to the exchange-correlation self-energy. This provides a variational derivation of the equation for the exact exchange-correlation potential that was derived by Sham and Schlueter using a density condition. Implications for an approximate physical interpretation of the Kohn-Sham orbitals are discussesd. A correlated generalization of the Sharp-Horton--Krieger-Li-Iafrate [Phys Lett. A 146, 256 (1990)] approximation of the exchange potential is introduced in the quasiparticle limit.

Casida, M.E. (Departement de Chimie, Universite de Montreal, Case Postale 6128, Succursale Centre-ville, Montreal, Quebec, H3C 3J7 (Canada))

1995-03-01

338

The objective of this study is to assess the variation of pollution in the Thai-Laos Mekong associated with seasonal dynamics concomitant with the natural geological features and human activities that impact on the adverse quality of the river. The complex ecology of the 1500 km stretch of the Thai-Laos Mekong River has been studied in this paper to understand the relationship with the geomorphology, with the sub-tropical monsoonal climate and the impact of human activity. Sub-surface geology controls the nature and extent of the drainage basin and of the river channel. The volume flow of the river varies naturally and dynamically in phase with the rainfall; traditional models based on steady state hydraulics are inappropriate. Continuous erosion of the river banks and bed generates a sediment load of impure silt, mica, quartz and clay minerals that inhibits light penetration and limits the primary productivity of the river. The river separates two countries at different stages of development; it flows through or close to eight non-industrial conurbations (Populations 350,000-2,000,000) but is otherwise sparsely populated. The river is used for subsistence agriculture, village transport, fishing including aquaculture and as a source of domestic water. Hydroelectricity is generated from the Laos tributaries. The river is a depository for partially treated urban waste and untreated village waste, hence populations of E.coli bacteria sometimes render the water unsuitable for drinking unless treated with the highest value of 240/100 ml found at station 7 during the summer season of 2003. Furthermore the river is polluted by trace metals, notably cadmium and mercury, and by Polycyclic Aromatic Hydrocarbons (PAHs), which are particularly concentrated in the sediments. Previous work has shown that cadmium and mercury exceed the Probable Effect Level (PEL) values of Canadian Environmental Quality Guidelines and that the PAH concentrations were also greater than the Interim Sediment Quality Guidelines (ISQG). Consequently the fish stock, a vital source of protein for the local human population maybe seriously affected. As conflict between the demands of human activities will be exacerbated by the continuing development of the basin; monitoring must be continued and a better model of the river's ecology is needed to predict the impact of development. PMID:20859820

Udomchoke, Veerasak; Sunthornranun, Patcharee; Songsasen, Apisit; Phanwichien, Kantimanee; Jiwapornkupt, Pongsakorn; Homchan, Unop; Lauhachinda, Nitaya; Sakultantimetha, Arthit; Bangkedphol, Sornnarin; Torrance, Keith; Gibson, Mark D; Gaines, Alec F; Booth, Peter H; Keenan, Helen E

2010-11-01

339

NASA Astrophysics Data System (ADS)

We describe a method for constructing a hierarchy of model potentials approximating the functional derivative of a given orbital-dependent exchange-correlation functional with respect to electron density. Each model is derived by assuming a particular relationship between the self-consistent solutions of Kohn-Sham (KS) and generalized Kohn-Sham (GKS) equations for the same functional. In the KS scheme, the functional is differentiated with respect to density, in the GKS scheme—with respect to orbitals. The lowest-level approximation is the orbital-averaged effective potential (OAEP) built with the GKS orbitals. The second-level approximation, termed the orbital-consistent effective potential (OCEP), is based on the assumption that the KS and GKS orbitals are the same. It has the form of the OAEP plus a correction term. The highest-level approximation is the density-consistent effective potential (DCEP), derived under the assumption that the KS and GKS electron densities are equal. The analytic expression for a DCEP is the OCEP formula augmented with kinetic-energy-density-dependent terms. In the case of exact-exchange functional, the OAEP is the Slater potential, the OCEP is roughly equivalent to the localized Hartree-Fock approximation and related models, and the DCEP is practically indistinguishable from the true optimized effective potential for exact exchange. All three levels of the proposed hierarchy require solutions of the GKS equations as input and have the same affordable computational cost.

Kohut, Sviataslau V.; Ryabinkin, Ilya G.; Staroverov, Viktor N.

2014-05-01

340

We describe a method for constructing a hierarchy of model potentials approximating the functional derivative of a given orbital-dependent exchange-correlation functional with respect to electron density. Each model is derived by assuming a particular relationship between the self-consistent solutions of Kohn-Sham (KS) and generalized Kohn-Sham (GKS) equations for the same functional. In the KS scheme, the functional is differentiated with respect to density, in the GKS scheme--with respect to orbitals. The lowest-level approximation is the orbital-averaged effective potential (OAEP) built with the GKS orbitals. The second-level approximation, termed the orbital-consistent effective potential (OCEP), is based on the assumption that the KS and GKS orbitals are the same. It has the form of the OAEP plus a correction term. The highest-level approximation is the density-consistent effective potential (DCEP), derived under the assumption that the KS and GKS electron densities are equal. The analytic expression for a DCEP is the OCEP formula augmented with kinetic-energy-density-dependent terms. In the case of exact-exchange functional, the OAEP is the Slater potential, the OCEP is roughly equivalent to the localized Hartree-Fock approximation and related models, and the DCEP is practically indistinguishable from the true optimized effective potential for exact exchange. All three levels of the proposed hierarchy require solutions of the GKS equations as input and have the same affordable computational cost. PMID:24832343

Kohut, Sviataslau V; Ryabinkin, Ilya G; Staroverov, Viktor N

2014-05-14

341

Landscape-driven microclimates in mountainous terrain pose significant obstacles to predicting the re- sponse of organisms to atmospheric warming, but few if any studies have documented the extent of such finescale variation over large regions. This paper demonstrates that ground-level temperature regimes in Great Smoky Mountains National Park (Tennessee and North Carolina) vary considerably over fine spatial scales and are only

Jason D. Fridley

2009-01-01

342

A previously detected copy number polymorphism (Ep CNP) in patients affected with neuroectodermal tumors led us to investigate its frequency and length in the normal population. For this purpose, a program called Sequence Allocator was developed and applied for the construction of an array that consisted of unique and duplicated fragments, allowing the assessment of copy number variation within regions

Cecilia de Bustos; Teresita Díaz de Ståhl; Arkadiusz Piotrowski; Kiran K. Mantripragada; Patrick G. Buckley; Eva Darai; Caisa M. Hansson; Gintautas Grigelionis; Uwe Menzel; Jan P. Dumanski

2006-01-01

343

NSDL National Science Digital Library

This learning unit from Regents Prep Exam Center introduces the topic of direct variation equations. The material includes a lesson plan, practice problems and a teacher's guide. Students will learn the basics of what a direct variation equation is and the formula for direct variation.

2012-01-01

344

NASA Astrophysics Data System (ADS)

We quantified the increase in the sediment-water interface created by the burrowing activities of the resident macrofaunal community and its variation with respect to the physical conditions of the habitat on a tidal fat. We investigated environmental factors and dimensions of macrofaunal burrows with respect to tidal height and vegetation during spring and summer at three sites. A resin-casting method was used to quantify the dimensions of all burrows at each site. The dimensions of macrofaunal burrows varied both temporally and spatially and the increase in the sediment-water interface reached a maximum of 311%, ranging from 20 to 255% under different habitat conditions. The sediment-water interface depended on the duration of exposure resulting from tidal height, increased temperatures resulting from seasonality, and marsh plant density. Burrows were deeper and more expansive at both higher tidal levels and higher temperatures in summer. Burrow dimensions were sharply reduced with the disappearance of adult macrofauna in areas where the roots of the marsh plant Suaeda japonica were dense. The significance of this study lies in quantifying the burrow dimensions of the entire macrofaunal community, rather than just a single population, and confirming their spatial and temporal variation with respect to physical conditions of the habitat. Environmental factors responsible for variation in burrow dimensions are discussed.

Koo, Bon Joo; Kwon, Kae Kyoung; Hyun, Jung-Ho

2007-11-01

345

Variational description of continuum states in terms of integral relations

Two integral relations derived from the Kohn variational principle (KVP) are used for describing scattering states. In usual applications the KVP requires the explicit form of the asymptotic behavior of the scattering wave function. This is not the case when the integral relations are applied since, due to their short-range nature, the only condition for the scattering wave function PSI is that it be the solution of (H-E)PSI=0 in the internal region. Several examples are analyzed for the computation of phase shifts from bound-state-type wave functions or, in the case of the scattering of charged particles, it is possible to obtain phase shifts using free asymptotic conditions. As a final example we discuss the use of the integral relations in the case of the hyperspherical adiabatic method.

Kievsky, A.; Viviani, M.; Barletta, Paolo; Romero-Redondo, C.; Garrido, E. [Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa (Italy); Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Instituto de Estructura de la Materia, CSIC, Serrano 123, E-28006 Madrid (Spain)

2010-03-15

346

Pleistocene, or younger, mud diapirism is recorded along the arcuated crest of the Mediterranean Ridge Accretionary Complex over a distance of more than 450 km. The extruded mud-supported breccia, named mud breccia, is poorly fossiliferous, but the matrix may be dated as Late Aptian to Albian and Late Burdigalian to Langhian in age based on the calcareous plankton content.Calcareous nannofossils

Isabella Premoli Silva; Elisabetta Erba; Silvia Spezzaferri; Maria Bianca Cita

1996-01-01

347

NASA Astrophysics Data System (ADS)

The variations in the electron density measured with the incoherent scatter radar, DPS-4 digisonde, and FMCW ionosonde are compared in this work. The main regularities in differences are explained by the effect of different-scale ionospheric irregularities. Considerable morning gradients of electron density result in that ionosondes give increased values as compared to the incoherent scatter radar data. Electron density disturbances measured with different instruments can be of correlated and uncorrelated character. Uncorrelated disturbances are explained by intense medium-scale ionospheric irregularities. Correlated disturbances are caused by large-scale irregularities. Observation of such disturbances can be used to determine the velocity and direction of a disturbance.

Ratovsky, K. G.; Shpynev, B. G.; Kim, A. G.; Medvedev, A. V.; Potekhin, A. P.; Petko, P. V.; Kushnarev, D. S.

2007-06-01

348

The vector competence and bionomics of Culex pipiens form pipiens L. and Cx. pipiens f. molestus Forskäl were evaluated for populations from the Sacramento Valley. Both f. pipiens and f. molestus females became infected, produced disseminated infections, and were able to transmit West Nile virus. Form molestus females also transmitted West Nile virus vertically to egg rafts and F1 progeny, whereas f. pipiens females only transmitted to egg rafts. Culex pipiens complex from urban Sacramento blood-fed on seven different avian species and two mammalian species. Structure analysis of blood-fed mosquitoes identified K = 4 genetic clusters: f. molestus, f. pipiens, a group of genetically similar hybrids (Cluster X), and admixed individuals. When females were exposed as larvae to midwinter conditions in bioenvironmental chambers, 85% (N = 79) of aboveground Cx. pipiens complex females and 100% (N = 34) of underground f. molestus females did not enter reproductive diapause. PMID:24043690

Nelms, Brittany M; Kothera, Linda; Thiemann, Tara; Macedo, Paula A; Savage, Harry M; Reisen, William K

2013-12-01

349

A phenylthiophenyl-bearing Ru(II) complex of [Ru(bpy)2(Hbptip)](PF6)2 {bpy?=?2,2?-bipyridine, Hbptip?=?2-(4-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} was synthesized and characterized by elemental analysis, H NMR spectroscopy, and electrospray ionization mass spectrometry. The ground- and excited-state acid–base properties of the complex were studied by UV–visible absorption and photoluminescence spectrophotometric pH titrations and the negative logarithm values of the ground-state acid ionization constants were derived to be pKa1?=?1.31?±?0.09 and pKa2?=?5.71?±?0.11

Cui-Li Yuan; An-Guo Zhang; Ze-Bo Zheng; Ke-Zhi Wang

2012-01-01

350

Harzburgite and lherzolite tectonites from the Horoman peridotite complex, Hokkaido, northern Japan, contain variable amounts\\u000a of secondary phlogopite and amphibole. Phlogopite-rich veinlets parallel to the foliation planes usually cut olivine-rich\\u000a parts of the rocks; single-grained interstitial phlogopites are usually associated with orthopyroxene grains. Amphiboles are\\u000a disseminated in rocks or sometimes occur in the phlogopite-rich veinlets. Within individual veinlets, phlogopites show

Shoji Arai; Natsuko Takahashi

1989-01-01

351

NASA Astrophysics Data System (ADS)

Using 1,9-salicylamide bissubstituted oxadecane ligand, 1,9-bis [2-(2'-picolylaminoformyl)-1,4,7,9-tetraoxadecane (L), two novel lanthanide complexes have been prepared and well characterized by means of elemental analysis, IR spectroscopy, UV-vis spectroscopy, TGA analysis and single-crystal X-ray diffraction. {[PrL(NO 3) 3(H 2O) 2]·CH 3OH} n is a 1D zigzag polymer with three-dimensional supramolecular structure formed by hydrogen bonds, while [EuL(NO 3) 3(H 2O)] n is a linear coordination polymer and present an interesting supramolecular double chain, which are very different from the structure of terbium complex reported before. The result reported herein demonstrated that steric crowding associated with the decreasing lanthanide ion radius causes changes of the conformation of the ligand as well as structures. Luminescence studies for the Eu(III) complexes demonstrated that the salicylamide ligand also exhibits a good antennae effect for the Eu(III) ion due to efficient intersystem crossing and ligand-to-metal energy transfer and the Eu(III) ion is well shielded from the surrounding environment.

Song, Xue-Qin; Zang, Zhi-Peng; Liu, Wei-Sheng; Zhang, Yu-Jie

2009-04-01

352

Detailed studies are presented on the structure and aggregation of an experimental high surface area carbon black (HSA) using small-angle neutron scattering and the method of contrast variation. We find that the approximately 27 mn HSA particle form small, linear aggregates of average aggregation number 5 when suspended in cyclohexane. There is considerable density fluctuation in the interior of these particles, with the denser regions being toward the outer part of the spherically-averaged structure. This information would not have been obtained from studies of carbon black without solvent. The results will be applied to similar scattering studies on solvent-swollen bound rubber gels made from HSA-polyisoprene. These result show, however, that the strong internal fluctuations of the carbon black will limit the information that can be obtained on the structure and conformation of the elastomer in the gel. There are additional limitation from compositional heterogeneity of the sample.

Hjelm, R.P. Jr.; Seeger, P.A. [Los Alamos National Lab., NM (United States); Wampler, W.A. [Sid Richardson Carbon Co., Fort Worth, TX (United States)

1993-05-01

353

Detailed studies are presented on the structure and aggregation of an experimental high surface area carbon black (HSA) using small-angle neutron scattering and the method of contrast variation. We find that the approximately 27 mn HSA particle form small, linear aggregates of average aggregation number 5 when suspended in cyclohexane. There is considerable density fluctuation in the interior of these particles, with the denser regions being toward the outer part of the spherically-averaged structure. This information would not have been obtained from studies of carbon black without solvent. The results will be applied to similar scattering studies on solvent-swollen bound rubber gels made from HSA-polyisoprene. These result show, however, that the strong internal fluctuations of the carbon black will limit the information that can be obtained on the structure and conformation of the elastomer in the gel. There are additional limitation from compositional heterogeneity of the sample.

Hjelm, R.P. Jr.; Seeger, P.A. (Los Alamos National Lab., NM (United States)); Wampler, W.A. (Sid Richardson Carbon Co., Fort Worth, TX (United States))

1993-01-01

354

Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and genetically complex. Using a recombinant inbred line population of Solanum lycopersicum?×?Solanum pimpinellifolium, we identified quantitative trait loci (QTLs) influencing seed quality phenotypes under non-stress, as well as salt, osmotic, cold, high-temperature and oxidative stress conditions. In total, 42 seed quality traits were analysed and 120 QTLs were identified for germination traits under different conditions. Significant phenotypic correlations were observed between germination traits under optimal conditions, as well as under different stress conditions. In conclusion, one or more QTLs were identified for each trait with some of these QTLs co-locating. Co-location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. However, several QTLs also dissected seed quality in its separate components, suggesting different physiological mechanisms and signalling pathways for different seed quality attributes. PMID:22074055

Kazmi, Rashid H; Khan, Noorullah; Willems, Leo A J; VAN Heusden, Adriaan W; Ligterink, Wilco; Hilhorst, Henk W M

2012-05-01

355

The metabolic control analysis was applied to digitonin-permeabilized HepG2 cell line to assess the flux control exerted by cytochrome c oxidase on the mitochondrial respiration. Experimental conditions eliciting different energy/respiratory states in mitochondria were settled. The results obtained show that the mitochondrial electrochemical potential accompanies a depressing effect on the control coefficient exhibited by the cytochrome c oxidase. Both the components of the protonmotive force, i.e. the voltage (??(m)) and the proton (?pH(m)) gradient, displayed a similar effect. Quantitative estimation of the ??(m) unveiled that the voltage-dependent effect on the control coefficient of cytochrome c oxidase takes place sharply in a narrow range of membrane potential from 170-180 to 200-210mV consistent with the physiologic transition from state 3 to state 4 of respiration. Extension of the metabolic flux control analysis to the NADH dehydrogenase and bc(1) complexes of the mitochondrial respiratory chain resulted in a similar effect. A mechanistic model is put forward whereby the respiratory chain complexes are proposed to exist in a voltage-mediated threshold-controlled dynamic equilibrium between supercomplexed and isolated states. PMID:21565165

Quarato, Giovanni; Piccoli, Claudia; Scrima, Rosella; Capitanio, Nazzareno

2011-09-01

356

In the major independent particle models of electronic structure theory—Hartree–Fock, Kohn–Sham (KS), and natural orbital (NO) theories—occupations are constrained to 0 and 1 or to the interval [0,1]. We carry out a constrained optimization of the orbitals and occupation numbers with application of the usual equality constraints ?i? ni=N and ??i|?j?=?ij. The occupation number optimization is carried out, allowing for

K. J. H. Giesbertz; E. J. Baerends

2010-01-01

357

The Kohn-Sham (KS) solution is constructed from an accurate CI density and the KS exchange and correlation energies Ex and Ec, as well as the corresponding exchange and exchange-correlation energy densities ?x(r) and ?xc(r), which are obtained for the hydrogen abstraction reaction H+H2 and the symmetrical four-center exchange reaction H2+H2. The KS quantities are compared with those of the standard

P. R. T. Schipper; O. V. Gritsenko; E. J. Baerends

1999-01-01

358

In the major independent particle models of electronic structure theory-Hartree-Fock, Kohn-Sham (KS), and natural orbital (NO) theories-occupations are constrained to 0 and 1 or to the interval [0,1]. We carry out a constrained optimization of the orbitals and occupation numbers with application of the usual equality constraints ?i? ni=N and

K. J. H. Giesbertz; E. J. Baerends

2010-01-01

359

The plastid genomes of some nonphotosynthetic parasitic plants have experienced an extreme reduction in gene content and an increase in evolutionary rate of remaining genes. Nothing is known of the dynamics of these events or whether either is a direct outcome of the loss of photosynthesis. The parasitic Scrophulariaceae and Orobanchaceae, representing a continuum of heterotrophic ability ranging from photosynthetic hemiparasites to nonphotosynthetic holoparasites, are used to investigate these issues. We present a phylogenetic hypothesis for parasitic Scrophulariaceae and Orobanchaceae based on sequences of the plastid gene rps2, encoding the S2 subunit of the plastid ribosome. Parasitic Scrophulariaceae and Orobanchaceae form a monophyletic group in which parasitism can be inferred to have evolved once. Holoparasitism has evolved independently at least five times, with certain holoparasitic lineages representing single species, genera, and collections of nonphotosynthetic genera. Evolutionary loss of the photosynthetic gene rbcL is limited to a subset of holoparasitic lineages, with several holoparasites retaining a full length rbcL sequence. In contrast, the translational gene rps2 is retained in all plants investigated but has experienced rate accelerations in several hemi- as well as holoparasitic lineages, suggesting that there may be substantial molecular evolutionary changes to the plastid genome of parasites before the loss of photosynthesis. Independent patterns of synonymous and nonsynonymous rate acceleration in rps2 point to distinct mechanisms underlying rate variation in different lineages. Parasitic Scrophulariaceae (including the traditional Orobanchaceae) provide a rich platform for the investigation of molecular evolutionary process, gene function, and the evolution of parasitism.

dePamphilis, Claude W.; Young, Nelson D.; Wolfe, Andrea D.

1997-01-01

360

Accumulating evidence suggests that breast cancer metastatic progression is modified by germline polymorphism, although specific modifier genes have remained largely undefined. In the current study, we employ the MMTV-PyMT transgenic mouse model and the AKXD panel of recombinant inbred mice to identify AT–rich interactive domain 4B (Arid4b; NM_194262) as a breast cancer progression modifier gene. Ectopic expression of Arid4b promoted primary tumor growth in vivo as well as increased migration and invasion in vitro, and the phenotype was associated with polymorphisms identified between the AKR/J and DBA/2J alleles as predicted by our genetic analyses. Stable shRNA–mediated knockdown of Arid4b caused a significant reduction in pulmonary metastases, validating a role for Arid4b as a metastasis modifier gene. ARID4B physically interacts with the breast cancer metastasis suppressor BRMS1, and we detected differential binding of the Arid4b alleles to histone deacetylase complex members mSIN3A and mSDS3, suggesting that the mechanism of Arid4b action likely involves interactions with chromatin modifying complexes. Downregulation of the conserved Tpx2 gene network, which is comprised of many factors regulating cell cycle and mitotic spindle biology, was observed concomitant with loss of metastatic efficiency in Arid4b knockdown cells. Consistent with our genetic analysis and in vivo experiments in our mouse model system, ARID4B expression was also an independent predictor of distant metastasis-free survival in breast cancer patients with ER+ tumors. These studies support a causative role of ARID4B in metastatic progression of breast cancer.

Winter, Scott F.; Lukes, Luanne; Walker, Renard C.; Welch, Danny R.; Hunter, Kent W.

2012-01-01

361

Background Copy number variation (CNV) is a major source of structural variants and has been commonly identified in mammalian genome. It is associated with gene expression and may present a major genetic component of phenotypic diversity. Unlike many other mammalian genomes where CNVs have been well annotated, studies of porcine CNV in diverse breeds are still limited. Result Here we used Porcine SNP60 BeadChip and PennCNV algorithm to identify 1,315 putative CNVs belonging to 565 CNV regions (CNVRs) in 1,693 pigs from 18 diverse populations. Total 538 out of 683 CNVs identified in a White Duroc?×?Erhualian F2 population fit Mendelian transmission and 6 out of 7 randomly selected CNVRs were confirmed by quantitative real time PCR. CNVRs were non-randomly distributed in the pig genome. Several CNV hotspots were found on pig chromosomes 6, 11, 13, 14 and 17. CNV numbers differ greatly among different pig populations. The Duroc pigs were identified to have the most number of CNVs per individual. Among 1,765 transcripts located within the CNVRs, 634 genes have been reported to be copy number variable genes in the human genome. By integrating analysis of QTL mapping, CNVRs and the description of phenotypes in knockout mice, we identified 7 copy number variable genes as candidate genes for phenotypes related to carcass length, backfat thickness, abdominal fat weight, length of scapular, intermuscle fat content of logissimus muscle, body weight at 240 day, glycolytic potential of logissimus muscle, mean corpuscular hemoglobin, mean corpuscular volume and humerus diameter. Conclusion We revealed the distribution of the unprecedented number of 565 CNVRs in pig genome and investigated copy number variable genes as the possible candidate genes for phenotypic traits. These findings give novel insights into porcine CNVs and provide resources to facilitate the identification of trait-related CNVs.

2012-01-01

362

The MHC genes have a profound effect on animal abilities to respond to specific antigens because they play a role in presenting foreign antigens to T cells during the course of the humoral or cellular immune response. In the current study, polymorphism in the MHC class I alpha2 domain was compared in 2 lines divergently selected for high (HH) or low (LL) antibody response to Escherichia coli vaccine. These lines also differ markedly in their antibody response to natural E. coli exposure and to vaccination with Newcastle disease virus, infectious bronchitis virus, and infectious bursa disease virus. Recent trials have shown that the LL chicks exhibit a significantly higher percentage of CD8+ T lymphocytes in their peripheral blood lymphocytes and spleen than HH chicks. Despite symmetrical selection intensity in both lines, polymorphism of the alpha2-domain gene was higher in the LL line than in the HH line. Among 29 single-nucleotide polymorphism positions found, 3 were unique to the HH line, 15 were unique to the LL line, and 11 were polymorphic in both lines. These single nucleotide polymorphism positions were not 100% line specific and were in agreement with the genetic variation in antibody level or cellular response still found within the selection lines. Five amino acid positions showed significant differences in polymorphism between the selection lines. These were located within the antigen-binding cleft, suggesting that these positions might influence the ability of MHC class I to bind foreign antigens and leading to differences in immunocompetence between the lines. PMID:16156203

Lavi, Y; Cahaner, A; Pleban, T; Pitcovski, J

2005-08-01

363

The coupled perturbed Kohn-Sham (CPKS) computational scheme for the evaluation of electric susceptibility tensors in periodic systems, recently implemented in the CRYSTAL code, has been extended to third-order. It is, then, used to obtain static electronic hyperpolarizabilities of zigzag BN nanotubes for the first time. This procedure, which is fully analytic in all key steps, requires a double self-consistent treatment for taking into account the first- and second-order response of the system to the applied field. The performance of different functionals is compared and the B3LYP hybrid is ultimately chosen for calculations on nanotubes having radii as large as R = 20 Å (6-200 atoms in the unit cell). Such large radii are sufficient to give the pure longitudinal component of the (hyper)polarizability tensors to within 1% of the "exact" hexagonal BN monolayer limit. Other tensor components involving the transverse direction converge more slowly. They can, however, be extrapolated to the monolayer limit to within 4% accuracy except for the pure transverse second hyperpolarizability, which has an error of 13% in that limit. PMID:21699207

Orlando, Roberto; Bast, Radovan; Ruud, Kenneth; Ekström, Ulf; Ferrabone, Matteo; Kirtman, Bernard; Dovesi, Roberto

2011-11-17

364

The optimized-effective-potential (OEP) method and a method developed recently by Krieger, Li, and Iafrate (KLI) are applied to the band-structure calculations of noble-gas and alkali halide solids employing the self-interaction-corrected (SIC) local-spin-density (LSD) approximation for the exchange-correlation energy functional. The resulting band gaps from both calculations are found to be in fair agreement with the experimental values. The discrepancies are typically within a few percent with results that are nearly the same as those of previously published orbital-dependent multipotential SIC calculations, whereas the LSD results underestimate the band gaps by as much as 40%. As in the LSD---and it is believed to be the case even for the exact Kohn-Sham potential---both the OEP and KLI predict valence-band widths which are narrower than those of experiment. In all cases, the KLI method yields essentially the same results as the OEP.

Li, Y.; Krieger, J.B. (Department of Physics, Brooklyn College, City University of New York, Brooklyn, New York 11210 (United States)); Norman, M.R. (Material Sciences Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)); Iafrate, G.J. (U.S. Army Research Office, Research Triangle Park, North Carolina 27709-2211 (United States))

1991-11-15

365

In view of further application to the study of molecular and atomic sticking on dust particles, we investigated the capability of the ``freeze-and-thaw'' cycle of the Kohn-Sham equations with constrained electron density (KSCED) to describe potential energy surfaces of weak van der Waals complexes. We report the results obtained for C6H6...X (X=O2, N2, and CO) as test cases. In the

T. A. Wesolowski; Y. Ellinger; J. Weber

1998-01-01

366

The frequent variations of human complement component C4 gene size and gene numbers, plus the extensive polymorphism of the proteins, render C4 an excellent marker for major histocompatibility complex disease associations. As shown by definitive RFLPs, the tandemly arranged genes RP, C4, CYP21, and TNX are duplicated together as a discrete genetic unit termed the RCCX module. Duplications of the RCCX modules occurred by the addition of genomic fragments containing a long (L) or a short (S) C4 gene, a CYP21A or a CYP21B gene, and the gene fragments TNXA and RP2. Four major RCCX structures with bimodular L-L, bimodular L-S, monomodular L, and monomodular S are present in the Caucasian population. These modules are readily detectable by TaqI RFLPs. The RCCX modular variations appear to be a root cause for the acquisition of deleterious mutations from pseudogenes or gene segments in the RCCX to their corresponding functional genes. In a patient with congenital adrenal hyperplasia, we discovered a TNXB-TNXA recombinant with the deletion of RP2-C4B-CYP21B. Elucidation of the DNA sequence for the recombination breakpoint region and sequence analyses yielded definitive proof for an unequal crossover between TNXA from a bimodular chromosome and TNXB from a monomodular chromosome. PMID:10207042

Yang, Z; Mendoza, A R; Welch, T R; Zipf, W B; Yu, C Y

1999-04-23

367

Growing evidence has shown that proNGF-p75NTR-sortilin signaling might be a crucial factor in neurodegeneration, but it remains unclear if it may function in nigral neurons under aging and disease. The purpose of this study is to examine and quantify proNGF and sortilin expression in the substantia nigra and dynamic changes of aging in lactacystin and 6-hydroxydopamine (6-OHDA) rat models of Parkinson’s disease using immunofluorescence, electronic microscopy, western blot and FLIVO staining methods. The expression of proNGF and sortilin was abundantly and selectively identified in tyrosine hydroxylase (TH)-containing dopamine neurons in the substantia nigra. These proNGF/TH, sortilin/TH-positive neurons were densely distributed in the ventral tier, while they were less distributed in the dorsal tier, where calbindin-D28K-containing neurons were numerously located. A correlated decrease of proNGF, sortilin and TH was also detected during animal aging process. While increase of proNGF, sortilin and cleaved (active) caspase-3 expression was found in the lactacystin model, dynamic proNGF and sortilin changes along with dopamine neuronal loss were demonstrated in the substantia nigra of both the lactacystin and 6-OHDA models. This study has thus revealed the presence of the proNGF-sortilin signaling complex in nigral dopamine neurons and its response to aging, lactacystin and 6-OHDA insults, suggesting that it might contribute to neuronal apoptosis or neurodegeneration during pathogenesis and disease progression of Parkinson’s disease; the underlying mechanism and key signaling pathways involved warrant further investigation.

Xia, Yi; Chen, Bei-Yu; Sun, Xiao-Long; Duan, Li; Gao, Guo-Dong; Wang, Jing-Jie; Yung, Ken Kam-Lin; Chen, Liang-Wei

2013-01-01

368

Modelling excited states of weakly bound complexes with density functional theory.

The binding within the ethene-argon and formaldehyde-methane complexes in the ground and electronically excited states is studied with equation of motion coupled cluster theory (EOM-CCSD), second-order Møller-Plesset perturbation theory (MP2) and density functional theory with dispersion corrections (DFT-D). Electronically excited states are studied within MP2 and Kohn-Sham DFT formalisms by exploiting a procedure called the maximum overlap method that allows convergence of the relevant self-consistent field equations to higher energy (or excited state) solutions. Potential energy curves computed using MP2 are in good agreement with the EOM-CCSD calculations for both the valence and Rydberg excited states studied. For the DFT-D approach, B3LYP-D3/aug-cc-pVTZ calculations are found to be in agreement with EOM-CCSD for the ground and valence excited states. However, for the ?3s Rydberg state of ethene-argon and the n3s Rydberg state of formaldehyde-methane significant deviation is observed, and this disagreement with EOM-CCSD is present for a variety of DFT-D based approaches. Variation of the parameters within the D2 dispersion correction results in closer agreement with EOM-CCSD for the Rydberg states but demonstrates that a different parameterisation from the ground state is required for these states. This indicates that time-dependent density functional theory calculations based upon a DFT-D reference may be satisfactory for excitations to valence states, but will potentially be inaccurate for excitations to Rydberg states, or more generally states where the nature of the electron density is significantly different from the ground state. PMID:24531883

Briggs, Edward A; Besley, Nicholas A

2014-06-25

369

NSDL National Science Digital Library

In this set of outdoor games, learners play the role of monkeys that are trying to get enough resources (food, shelter, and space) to survive. They play several simple games which involve strength, quickness, coordination, intuition, and luck in order to acquire these resources. The games focus attention on the participantsâ individual variations in these areas. There are three âroundsâ which represent three different changing environments, each of which requires different skills for survival. After the games, learners compare who got enough resources and what variations among the players may have affected how the game went.

Science, Lawrence H.

1980-01-01

370

Variation in environmental complexity and brain measures

Rats maintained in isolation for 81 days, rats maintained in an enriched environment for 81 days, and rats kept in isolation for 33 days followed by 48 days of enrichment were compared on measures of brain weight and cholinesterase activity. Significant differences were obtained, the isolation-enrichment group in general showing values intermediate between those of the other groups.

Mark R. Rosenzweig; David Krech; Edward L. Bennett; James F. Zolman

1962-01-01

371

Exterior complex scaling method in TDDFT: HHG of Ar atoms in intense laser fields

NASA Astrophysics Data System (ADS)

Exterior complex scaling (ECS) method is applied in the framework of the time-dependent density functional theory to study high-order harmonic generation (HHG) of multielectron atoms in intense laser fields. ECS allows to impose correct (outgoing-wave) boundary conditions on the wave functions at large distances. In the present work, ECS is combined with the time-dependent generalized pseudospectral method for accurate and efficient solution of the time-dependent Kohn-Sham equations. Results for HHG of Ar atoms are presented.

Sosnova, Ksenia E.; Telnov, Dmitry A.; Rozenbaum, Efim; Chu, Shih-I.

2014-04-01

372

NASA Astrophysics Data System (ADS)

The implementation of fewest-switches surface-hopping (FSSH) within time-dependent Kohn-Sham (TDKS) theory [Phys. Rev. Lett. 95, 163001 (2005)] has allowed us to study successfully excited state dynamics involving many electronic states in a variety of molecular and nanoscale systems, including chromophore-semiconductor interfaces, semiconductor and metallic quantum dots, carbon nanotubes and graphene nanoribbons, etc. At the same time, a concern has been raised that the KS orbital basis used in the calculation provides only approximate potential energy surfaces [J. Chem. Phys. 125, 014110 (2006)]. While this approximation does exist in our method, we show here that FSSH-TDKS is a viable option for computationally efficient calculations in large systems with straightforward excited state dynamics. We demonstrate that the potential energy surfaces and nonadiabatic transition probabilities obtained within the TDKS and linear response (LR) time-dependent density functional theories (TDDFT) agree semiquantitatively for three different systems, including an organic chromophore ligating a transition metal, a quantum dot, and a small molecule. Further, in the latter case the FSSH-TDKS procedure generates results that are in line with FSSH implemented within LR-TDDFT. The FSSH-TDKS approach is successful for several reasons. First, single-particle KS excitations often give a good representation of LR excitations. In this regard, DFT compares favorably with the Hartree-Fock theory, for which LR excitations are typically combinations of multiple single-particle excitations. Second, the majority of the FSSH-TDKS applications have been performed with large systems involving simple excitations types. Excitation of a single electron in such systems creates a relatively small perturbation to the total electron density summed over all electrons, and it has a small effect on the nuclear dynamics compared, for instance, with thermal nuclear fluctuations. In such cases an additional, classical-path approximation can be made. Third, typical observables measured in time-resolved experiments involve averaging over many initial conditions. Such averaging tends to cancel out random errors that may be encountered in individual simulated trajectories. Finally, if the flow of energy between electronic and nuclear subsystems is insignificant, the ad hoc FSSH procedure is not required, and a straightforward mean-field, Ehrenfest approach is sufficient. Then, the KS representation provides rigorously a convenient and efficient basis for numerically solving the TDDFT equations of motion.

Fischer, Sean A.; Habenicht, Bradley F.; Madrid, Angeline B.; Duncan, Walter R.; Prezhdo, Oleg V.

2011-01-01

373

NASA Astrophysics Data System (ADS)

It is shown that the non-terminating expansions of the wave function within the variational coupled cluster singles (VCCS) can be exactly treated by summing up the one-particle density matrix elements in the occupied block using simple recurrence relation. At the same time, this leads to an extremely simple 'a priori' diagonalization free algorithm for the solution of the Hartree-Fock equations. This treatment corresponds to a non-unitary transformation of orbitals, however, preserving the norm and idempotency of the density matrix. The resulting algorithm enables a Hartree-Fock solution with 'a priori' localized orbitals. Similar approach can be applied within the Kohn-Sham theory. Analysis of the VCCS expansion in terms of the generalized perturbation theory is also presented. Numerical results are presented for model systems N2, F2, H2O, NH3 but also for a larger Uracile molecule and an interaction of four Guanine molecules.

Šimunek, Ján; Noga, Jozef

2012-12-01

374

Kohn's theorem and Galilean symmetry

NASA Astrophysics Data System (ADS)

The relation between the separability of a system of charged particles in a uniform magnetic field and Galilean symmetry is revisited using Duval's “Bargmann framework”. If the charge-to-mass ratios of the particles are identical, e/m=? for all particles, then the Bargmann space of the magnetic system is isometric to that of an anisotropic harmonic oscillator. Assuming that the particles interact through a potential which only depends on their relative distances, the system splits into one representing the center of mass plus a decoupled internal part, and can be mapped further into an isolated system using Niederer's transformation. Conversely, the manifest Galilean boost symmetry of the isolated system can be “imported” to the oscillator and to the magnetic systems, respectively, to yield the symmetry used by Gibbons and Pope to prove the separability. For vanishing interaction potential the isolated system is free and our procedure endows all our systems with a hidden Schrödinger symmetry, augmented with independent internal rotations. All these properties follow from the cohomological structure of the Galilei group, as explained by Souriau's “décomposition barycentrique”.

Zhang, P.-M.; Horvathy, P. A.

2011-08-01

375

In a chemical genetics screen we identified the small-molecule [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione (DFPM) that triggers rapid inhibition of early abscisic acid signal transduction via PHYTOALEXIN DEFICIENT4 (PAD4)- and ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1)-dependent immune signaling mechanisms. However, mechanisms upstream of EDS1 and PAD4 in DFPM-mediated signaling remain unknown. Here, we report that DFPM generates an Arabidopsis thaliana accession-specific root growth arrest in Columbia-0 (Col-0) plants. The genetic locus responsible for this natural variant, VICTR (VARIATION IN COMPOUND TRIGGERED ROOT growth response), encodes a TIR-NB-LRR (for Toll-Interleukin1 Receptor–nucleotide binding–Leucine-rich repeat) protein. Analyses of T-DNA insertion victr alleles showed that VICTR is necessary for DFPM-induced root growth arrest and inhibition of abscisic acid–induced stomatal closing. Transgenic expression of the Col-0 VICTR allele in DFPM-insensitive Arabidopsis accessions recapitulated the DFPM-induced root growth arrest. EDS1 and PAD4, both central regulators of basal resistance and effector-triggered immunity, as well as HSP90 chaperones and their cochaperones RAR1 and SGT1B, are required for the DFPM-induced root growth arrest. Salicylic acid and jasmonic acid signaling pathway components are dispensable. We further demonstrate that VICTR associates with EDS1 and PAD4 in a nuclear protein complex. These findings show a previously unexplored association between a TIR-NB-LRR protein and PAD4 and identify functions of plant immune signaling components in the regulation of root meristematic zone-targeted growth arrest.

Kim, Tae-Houn; Kunz, Hans-Henning; Bhattacharjee, Saikat; Hauser, Felix; Park, Jiyoung; Engineer, Cawas; Liu, Amy; Ha, Tracy; Parker, Jane E.; Gassmann, Walter; Schroeder, Julian I.

2012-01-01

376

NASA Astrophysics Data System (ADS)

Mineral dust and other constituents of Devonian atmospheric aerosols together with certain amounts of aquatic suspensions of riverine detrital origin, colloidal particle dispersions and seawater solutes were embedded in ~95-98% (or purer) limestones on a consistently subsiding isolated carbonate platform where they formed very complex impurity systems. Very low Th/U values, relative abundance of Fe but a slight excess of K typically characterize these ultrafine impurities which are mineralogically dominated by smectite-illite and mica (sericite) together with goethite. In vertical section, these impurities are arranged like incremental series of light and dense bands. The combined method of natural gamma-ray spectrometric and magnetic susceptibility measurements (GRS-MS) together with background of major and trace element analyses provided first systematic insights into fine-scale variability of these impurities in a pile of pure carbonate platform beds, mostly in inner platform Amphipora limestone facies. These carbonates were deposited close to sea level but far from river mouths, and they represented a certain sort of a relatively “independent” medium that was primarily sensitive to climatically (and by rare events) controlled input of atmospheric dust. A remarkable similarity of MS stratigraphic patterns that reflect the quantity and quality of embedded impurities in very distant and paleogeographically separated Devonian basins might be seen as supporting this viewpoint. A long composite stratigraphic section of the Moravian Karst ranges from mid-Eifelian to end-Frasnian levels and yields a number of time characterizing GRS-MS variations that can potentially serve as templates for high-resolution stratigraphic correlations over long distances.

Hladil, J.; Gersl, M.; Strnad, L.; Frana, J.; Langrova, A.; Spisiak, J.

2006-07-01

377

This paper discusses three forms of complex holograms, described by means of complex Fourier, Fresnel, and Hartley transformations. Digital models of these holograms and algorithms for modelling them digitally are presented. It is shown that the reflectance and the phase variation upon reflection from the surface of an object can be determined not only from the reconstructed image but also

T. V. Bogdanova; V. P. Titar

2004-01-01

378

NASA Astrophysics Data System (ADS)

The Green function Korringa-Kohn-Rostoker methodology with the coherent potential approximation was used to calculate complex energy band structure. In the framework of Boltzmann approach life time and velocity of electron were determined on complex energy Fermi surface. Then electron transport properties as temperature dependent Seebeck coefficient, residual resistivity were investigated. Calculations were performed with several approximations, compared and demonstrated for the TiFe1-xNixSb half-Heusler compound that experimentally revealed tunable electron transport properties, i.e. a metal-semiconductor-metal crossover and change in sign of thermopower.

Kutorasinski, K.; Tobola, J.; Kaprzyk, S.

2012-06-01

379

NASA Astrophysics Data System (ADS)

This paper discusses three forms of complex holograms, described by means of complex Fourier, Fresnel, and Hartley transformations. Digital models of these holograms and algorithms for modelling them digitally are presented. It is shown that the reflectance and the phase variation upon reflection from the surface of an object can be determined not only from the reconstructed image but also by analyzing the structure of the recorded pair of quadrature components of a complex hologram.Â© 2004

Bogdanova, T. V.; Titar, V. P.

2004-05-01

380

Anatomic Variations in Head and Neck Reconstruction

Head and neck reconstruction is a technically challenging procedure. Variations encountered in the recipient vessels and commonly used flaps add to the complexity of surgery. This article reviews the commonly encountered variations in the recipient vessels in the neck with emphasis on alternatives and techniques to circumvent these variations. Flaps commonly used in head and neck reconstruction are also reviewed in detail. Furthermore, safety, potential pitfalls, and technical pearls are highlighted.

Tan, Bien-Keem; Wong, Chin-Ho; Chen, Hung-Chi

2010-01-01

381

A Koopmans-like approximation is introduced in the spin-polarized version of the Kohn-Sham (KS) density functional theory to obtain a relation between KS orbital energies and vertical ionization potential and electron affinity. Expressions for reactivity indexes (like electronegativity, hardness, electrophilicity, and excitation energies) include KS frontier orbital energies and additional contributions associated with the self-interaction correction. Those reactivity parameters were computed with different exchange-correlation functionals to test the approach for a set of small molecules. The results show that the present approximation provides a better way to estimate hardness, electronegativity, and electrophilicity than just the use of frontier orbital energy values. However KS HOMO and LUMO energy gap gives a better agreement with excitation energies. PMID:16834292

Vargas, Rubicelia; Garza, Jorge; Cedillo, Andrés

2005-10-01

382

NASA Astrophysics Data System (ADS)

The high-frequency dielectric ? and the first nonlinear electric susceptibility ?(2) tensors of crystalline potassium dihydrogen phosphate (KH2PO4) are calculated by using the coupled perturbed Hartree-Fock and Kohn-Sham methods as implemented in the CRYSTAL code. The effect of basis sets of increasing size on ? and ?(2) is explored. Five different levels of theory, namely, local-density approximation, generalized gradient approximation (PBE), hybrids (B3LYP and PBE0), and HF are compared using the experimental and theoretical structures corresponding not only to the tetragonal geometry I4d2 at room temperature but also to the orthorhombic phase Fdd2 at low temperature. Comparison between the two phases and their optical behavior is made. The calculated results for the tetragonal phase are in good agreement with the experimental data.

Lacivita, Valentina; Rérat, Michel; Kirtman, Bernard; Ferrero, Mauro; Orlando, Roberto; Dovesi, Roberto

2009-11-01

383

Heritable Epigenetic Variation among Maize Inbreds

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation was profiled using immunoprecipitation of methylated DNA followed by hybridization to a high-density tiling microarray. The comparison of the DNA methylation levels in the two genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions (DMRs). Several of these DMRs occur in genomic regions that are apparently identical by descent in B73 and Mo17 suggesting that they may be examples of pure epigenetic variation. The methylation levels of the DMRs were further studied in a panel of near-isogenic lines to evaluate the stable inheritance of the methylation levels and to assess the contribution of cis- and trans- acting information to natural epigenetic variation. The majority of DMRs that occur in genomic regions without genetic variation are controlled by cis-acting differences and exhibit relatively stable inheritance. This study provides evidence for naturally occurring epigenetic variation in maize, including examples of pure epigenetic variation that is not conditioned by genetic differences. The epigenetic differences are variable within maize populations and exhibit relatively stable trans-generational inheritance. The detected examples of epigenetic variation, including some without tightly linked genetic variation, may contribute to complex trait variation.

Schnable, James C.; Waters, Amanda J.; Hermanson, Peter J.; Liu, Sanzhen; Yeh, Cheng-Ting; Jia, Yi; Gendler, Karla; Freeling, Michael; Schnable, Patrick S.; Vaughn, Matthew W.; Springer, Nathan M.

2011-01-01

384

Nonlinear d10-ML2 Transition-Metal Complexes

We have investigated the molecular geometries of a series of dicoordinated d10-transition-metal complexes ML2 (M=Co?, Rh?, Ir?, Ni, Pd, Pt, Cu+, Ag+, Au+; L=NH3, PH3, CO) using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Not all complexes have the expected linear ligand–metal–ligand (L–M–L) angle: this angle varies from 180° to 128.6° as a function of the metal as well as the ligands. Our main objective is to present a detailed explanation why ML2 complexes can become bent. To this end, we have analyzed the bonding mechanism in ML2 as a function of the L–M–L angle using quantitative Kohn–Sham molecular orbital (MO) theory in combination with an energy decomposition analysis (EDA) scheme. The origin of bent L–M–L structures is ? backdonation. In situations of strong ? backdonation, smaller angles increase the overlap of the ligand’s acceptor orbital with a higher-energy donor orbital on the metal-ligand fragment, and therefore favor ? backdonation, resulting in additional stabilization. The angle of the complexes thus depends on the balance between this additional stabilization and increased steric repulsion that occurs as the complexes are bent.

Wolters, Lando P; Bickelhaupt, F Matthias

2013-01-01

385

Nonlinear d(10)-ML2 Transition-Metal Complexes.

We have investigated the molecular geometries of a series of dicoordinated d(10)-transition-metal complexes ML2 (M=Co(-), Rh(-), Ir(-), Ni, Pd, Pt, Cu(+), Ag(+), Au(+); L=NH3, PH3, CO) using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Not all complexes have the expected linear ligand-metal-ligand (L-M-L) angle: this angle varies from 180° to 128.6° as a function of the metal as well as the ligands. Our main objective is to present a detailed explanation why ML2 complexes can become bent. To this end, we have analyzed the bonding mechanism in ML2 as a function of the L-M-L angle using quantitative Kohn-Sham molecular orbital (MO) theory in combination with an energy decomposition analysis (EDA) scheme. The origin of bent L-M-L structures is ? backdonation. In situations of strong ? backdonation, smaller angles increase the overlap of the ligand's acceptor orbital with a higher-energy donor orbital on the metal-ligand fragment, and therefore favor ? backdonation, resulting in additional stabilization. The angle of the complexes thus depends on the balance between this additional stabilization and increased steric repulsion that occurs as the complexes are bent. PMID:24551547

Wolters, Lando P; Bickelhaupt, F Matthias

2013-06-01

386

The complexity of 3D shapes that are represented in digital form and processed in CAD\\/CAM\\/CAE, entertainment, biomedical, and other applications has increased considerably. Much research was focused on coping with or on reducing shape complexity. But, what exactly is shape complexity? We discuss several complexity measures and the corresponding complexity reduction techniques. Algebraic complexity measures the degree of polynomials needed

Jarek Rossignac

2005-01-01

387

Five heterobimetallic copper(II)-uranium(VI) complexes [(CuL(1))UO2(NO3)2] (1), [{CuL(1)(CH3CN)}UO2(NO3)2] (2), [{CuL(1)(CH3COCH3)}UO2(NO3)2] (3), [{CuL(2)(CH3CN)}UO2(NO3)2](4), and [{CuL(2)(CH3COCH3)}UO2(NO3)2][{CuL(2)}UO2(NO3)2] (5) have been synthesized by reacting the Cu(II)-derived metalloligands [CuL(1)] and [CuL(2)] (where, H2L(1) = N,N'-bis(?-methylsalicylidene)-1,3-propanediamine and H2L(2) = N,N'-bis(salicylidene)-1,3-propanediamine) with UO2(NO3)2·6H2O in 1:1 ratio by varying the reaction temperature and solvents. Absorption and fluorescence quenching experiments (steady-state and time-resolved) indicate the formation of 1:1 ground-state charge transfer copper(II)-uranium(VI) complexes in solution. X-ray single-crystal structure reveals that each complex contains diphenoxido bridged Cu(II)-U(VI) dinuclear core with two chelated nitrato coligands. The complexes are solvated (acetonitrile or acetone) in the axial position of the Cu(II) in different manner or desolvated. The supramolecular interactions that depend upon the co-ordinating metalloligands seem to control the solvation. In complexes 2 and 3 a rare NO3(-)···NO3(-) weak interaction plays an important role in forming supramolecular network whereas an uncommon U?O···NO3(-) weak interaction helps to self-assemble heterobinuclear units in complex 5. The significance of the noncovalent interactions in terms of energies and geometries has been analyzed using theoretical calculations. PMID:23786416

Ghosh, Soumavo; Biswas, Saptarshi; Bauzá, Antonio; Barceló-Oliver, Miquel; Frontera, Antonio; Ghosh, Ashutosh

2013-07-01

388

The interaction of the aluminum ion [Al(III)] with the major constituent of soil organic matter, fulvic acids (FA), was investigated in the acid pH range. The complexation of a FA extracted from a humic cambisol soil (at a concentration of 80 mg/L) when titrated with Al(III) were monitored directly by synchronous fluorescence (SyF) spectroscopy at five pH values (3.0, 3.5, 4.0, 4.5, and 5.0), at 25 C and with 0.1 N KNO{sub 3}. Inverted second derivative SyF data were preprocessed by a self-modeling mixture analysis method to obtain fluorescence enhancement profiles as a function of the increasing Al(III) concentration. Assuming that the concentration of complexes formed between Al(III) and FA is proportional to the fluorescence intensity, these profiles were adjusted to a 1:1 complexation model and the following conditional stability constants (log K{sub c}) were calculated (standard deviation in parenthesis), pH = 3.0, 4.3 (1); pH = 3.5, 4.3 (1); pH = 4.0, 5.0 (1); pH = 4.5, 5.1 (3); and pH = 5.0, 5.3 (2). These constants show that the stability of the complexes decreases markedly at pH < 4. The environmental implication of this result is that an increase in the extent of the dissociation of the Al(III) + FA complexes is expected at pH < 4, increasing the free Al(III) concentration and probably its ecotoxicity.

Esteves da Silva, J.C.G.; Machado, A.A.S.C. [LAQUIPAI, Porto (Portugal). Faculdade de Ciencias; Ramos, M.A.; Arce, F. [Univ. de Santiago de Compostela (Spain). Dept. de Quimica Fisica; Rey, F. [Univ. de Vigo (Spain). Dept. de Quimica Fisica

1997-09-01

389

Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology to profile complex microbial communities\\u000a over time and in response to different stimuli. However, inherent gel-to-gel variability has always been a barrier toward\\u000a meaningful interpretation of DGGE profiles obtained from multiple gels. To address this problem, we developed a two-step methodology\\u000a to align DGGE profiles across a large dataset.

Panagiotis Tourlomousis; E. Katherine Kemsley; Karyn P. Ridgway; Michael J. Toscano; Thomas J. Humphrey; Arjan Narbad

2010-01-01

390

Oceanic, non-hydrothermal ferromanganese crusts and nodules are variably enriched in Mn, Fe, Co, Cu, Ni and Zn. Comparison of the content of these elements in crusts and nodules with the level of primary productivity in the South Pacific Ocean suggests that primary-producer-mediated complexation of several of these elements by organic ligands in solution may contribute to explaining a pattern of

Philomene A. Verlaan

2008-01-01

391

A series of [Ni(PR2NPh2)2(CH3CN)](BF4)2 complexes containing the cyclic diphosphine ligands (PR2NPh2 = 1,5-diaza-3,7-diphosphacyclooctane; R = benzyl (Bn), n-butyl (n-Bu), 2-phenylethyl (PE), 2,4,4-trimethylpentyl (TP), and cyclohexyl (Cy)) have been synthesized and characterized. X-ray diffraction studies reveal that the cations of [Ni(PBn2NPh2)2(CH3CN)](BF4)2 and [Ni(Pn-Bu2NPh2)2(CH3CN)](BF4)2 have distorted trigonal bipyramidal geometries. The Ni(0) complex [Ni(PBn2NPh2)2 (CH3CN)] was also synthesized and characterized by X-ray diffraction studies and shown to have a distorted tetrahedral structure. These complexes, with the exception of [Ni(PCy2NPh2)2(CH3CN)](BF4)2, all exhibit reversible electron transfer processes for both the Ni(II/I) and Ni(I/0) couples and are electrocatalysts for the production of H2 in acidic acetonitrile solutions. The heterolytic cleavage of H2 by [Ni(PR2NPh2)2(CH3CN)](BF4)2 complexes in the presence of p-anisidine or p-bromoaniline was used to determine the hydride donor abilities of the corresponding [HNi(PR2NPh2)2](BF4) complexes. However, the failure to observe a strong correlation between the turnover frequencies for H2 production and the hydride donor abilities, along with structural features of [Ni(PBn2NPh2)2(CH3CN)], suggest that steric interactions between the alkyl substituents on phosphorus and the nitrogen atom of the pendant amines play an important role in determining the overall catalytic rate. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

Kilgore, Uriah J.; Stewart, Michael P.; Helm, Monte L.; Dougherty, William G.; Kassel, W. S.; Rakowski DuBois, Mary; DuBois, Daniel L.; Bullock, R. Morris

2011-11-07

392

Many of the radioactive waste storage tanks at USDOE facilities contain organic compounds that have been degraded by radiolysis and chemical reactions during decades of storage. Objective of this study was to measure effects of soluble organic complexants and their degradation products on sorption of Sr, Cs, Tc, Pu and Am onto 33 absorbers that in the absence of these organic compounds offer high sorption of these elements. The elements were in a generic simulant for Hanford complexant concentrate supernate that initially contained six organic complexants: EDTA, HEDTA, NTA, citrate, gluconate, and iminodiacetate. This simulant was tested as prepared and after gamma-irradiation to approximately 34 Mrads. Two other variations consisted of the unirradiated and irradiated simulants after treatment at 450C and 15,000 psi in a hydrothermal organic-destruction process. These experiments were conducted with a 3:1 water-to-simulant dilution of each of the four simulant variations. To determine effects of varying dilution ratios on the sorption of these five elements from the unirradiated and gamma-irradiated simulants that were not treated with the hydrothermal process, we measured their distribution from a 1:1 dilution, using 1 M NaOH as the diluent, onto the 12 best-performing absorbers. We then measured the sorption of these five elements from solutions having diluent-simulant ratios of 0, 0.5, 2.0, and 3.0 onto the three absorbers that performed best for sorbing Sr, Pu and Am from the 1:1 dilution. For each of 900 element/absorber/solution combinations, we measured distribution coefficients (Kd values) twice for each period for dynamic contact periods of 30 min, 2 h, and 6 h to obtain information about absorber stability and sorption kinetics. The 5400 measured Kd values indicate that the sorption of Sr, Pu, and Am is significantly decreased by the organic complexants in these simulant solutions, whereas the sorption of Cs and Tc is much less affected.

Marsh, S.F. [Sandia National Labs., Albuquerque, NM (United States); Svitra, Z.V.; Bowen, S.M. [Los Alamos National Lab., NM (United States)

1995-09-01

393

An age-dependent association between variation at the FTO locus and BMI in children has been suggested. We meta-analyzed associations between the FTO locus (rs9939609) and BMI in samples, aged from early infancy to 13 years, from 8 cohorts of European ancestry. We found a positive association between additional minor (A) alleles and BMI from 5.5 years onwards, but an inverse association below age 2.5 years. Modelling median BMI curves for each genotype using the LMS method, we found that carriers of minor alleles showed lower BMI in infancy, earlier adiposity rebound (AR), and higher BMI later in childhood. Differences by allele were consistent with two independent processes: earlier AR equivalent to accelerating developmental age by 2.37% (95% CI 1.87, 2.87, p?=?10?20) per A allele and a positive age by genotype interaction such that BMI increased faster with age (p?=?10?23). We also fitted a linear mixed effects model to relate genotype to the BMI curve inflection points adiposity peak (AP) in infancy and AR. Carriage of two minor alleles at rs9939609 was associated with lower BMI at AP (?0.40% (95% CI: ?0.74, ?0.06), p?=?0.02), higher BMI at AR (0.93% (95% CI: 0.22, 1.64), p?=?0.01), and earlier AR (?4.72% (?5.81, ?3.63), p?=?10?17), supporting cross-sectional results. Overall, we confirm the expected association between variation at rs9939609 and BMI in childhood, but only after an inverse association between the same variant and BMI in infancy. Patterns are consistent with a shift on the developmental scale, which is reflected in association with the timing of AR rather than just a global increase in BMI. Results provide important information about longitudinal gene effects and about the role of FTO in adiposity. The associated shifts in developmental timing have clinical importance with respect to known relationships between AR and both later-life BMI and metabolic disease risk.

Briollais, Laurent; Palmer, Colin N. A.; Cecil, Joanne; Sandling, Johanna K.; Syvanen, Ann-Christine; Kaakinen, Marika; Beilin, Lawrie J.; Millwood, Iona Y.; Bennett, Amanda J.; Laitinen, Jaana; Pouta, Anneli; Molitor, John; Davey Smith, George; Ben-Shlomo, Yoav; Jaddoe, Vincent W. V.; Palmer, Lyle J.; Pennell, Craig E.; Cole, Tim J.; McCarthy, Mark I.; Jarvelin, Marjo-Riitta; Timpson, Nicholas J.

2011-01-01

394

An age-dependent association between variation at the FTO locus and BMI in children has been suggested. We meta-analyzed associations between the FTO locus (rs9939609) and BMI in samples, aged from early infancy to 13 years, from 8 cohorts of European ancestry. We found a positive association between additional minor (A) alleles and BMI from 5.5 years onwards, but an inverse association below age 2.5 years. Modelling median BMI curves for each genotype using the LMS method, we found that carriers of minor alleles showed lower BMI in infancy, earlier adiposity rebound (AR), and higher BMI later in childhood. Differences by allele were consistent with two independent processes: earlier AR equivalent to accelerating developmental age by 2.37% (95% CI 1.87, 2.87, p?=?10(-20)) per A allele and a positive age by genotype interaction such that BMI increased faster with age (p?=?10(-23)). We also fitted a linear mixed effects model to relate genotype to the BMI curve inflection points adiposity peak (AP) in infancy and AR. Carriage of two minor alleles at rs9939609 was associated with lower BMI at AP (-0.40% (95% CI: -0.74, -0.06), p?=?0.02), higher BMI at AR (0.93% (95% CI: 0.22, 1.64), p?=?0.01), and earlier AR (-4.72% (-5.81, -3.63), p?=?10(-17)), supporting cross-sectional results. Overall, we confirm the expected association between variation at rs9939609 and BMI in childhood, but only after an inverse association between the same variant and BMI in infancy. Patterns are consistent with a shift on the developmental scale, which is reflected in association with the timing of AR rather than just a global increase in BMI. Results provide important information about longitudinal gene effects and about the role of FTO in adiposity. The associated shifts in developmental timing have clinical importance with respect to known relationships between AR and both later-life BMI and metabolic disease risk. PMID:21379325

Sovio, Ulla; Mook-Kanamori, Dennis O; Warrington, Nicole M; Lawrence, Robert; Briollais, Laurent; Palmer, Colin N A; Cecil, Joanne; Sandling, Johanna K; Syvänen, Ann-Christine; Kaakinen, Marika; Beilin, Lawrie J; Millwood, Iona Y; Bennett, Amanda J; Laitinen, Jaana; Pouta, Anneli; Molitor, John; Davey Smith, George; Ben-Shlomo, Yoav; Jaddoe, Vincent W V; Palmer, Lyle J; Pennell, Craig E; Cole, Tim J; McCarthy, Mark I; Järvelin, Marjo-Riitta; Timpson, Nicholas J

2011-02-01

395

Non-uniform random variate generation

Abstract. This chapter provides a survey of the main methods in non-uniform random variate generation, and highlights recent research on the subject. Classical paradigms such as inversion, rejection, guide tables, and transformations are reviewed. We provide information on the expected time complexity of various algorithms, before addressing modern topics such as indirectly specied distributions, random processes, and Markov chain methods.

L. Devroye

1986-01-01

396

We investigated the genetic structure and population frequency of an Alu repeat dimorphism (absence or presence) located near the OR12D2 gene within the olfactory receptor gene region telomeric of the alpha HLA class I region (HLA-J, -A, -G, -F). The structurally polymorphic Alu insertion (POALIN) locus rs33972478 that we designated as AluOR and its allele and haplotype frequencies and association with HLA-A and six other structurally polymorphic retroelements (3 Alu, 2 SVA and an HERVK9) were determined in 100 Japanese, 174 Caucasians and 100 African American DNA samples. The AluOR insertion varied in population frequency between 14.4% and 31.5% with significant differences between the Japanese and Caucasians, but not between the Caucasian and African Americans. Although AluOR is located 600 kb from the HLA-A gene, there was a significant linkage disequilibrium between the two loci and a high percentage association of the AluOR insertion with HLA-A29 (79%) in Caucasians and HLA-A31 (69.4%) in Japanese. Inferred haplotypes among three-locus to eight-locus haplotype structures showed maximum differences between the populations with the eight-locus haplotypes. The most frequent multilocus haplotype shared between the populations was the HLA-A2 allele in combination with the AluHG insertion. The AluOR whether investigated alone or together with the HLA class I alleles and other dimorphic retroelements is an informative ancestral marker for the identification of lineages and variations within the same and/or different populations and for examining the linkage and crossing-over between the HLA and OR genomic regions in the extended MHC. PMID:24305111

Kulski, J K; Shigenari, A; Inoko, H

2014-06-01

397

Genetic Variation and its Role in Malignancy

Genetic variation has long been thought associated with common complex disease and has therefore been widely studied. Genetic variation in the human genome is present in many forms and have been summarised in this review. The potential role of DNA damage, DNA repair and environmental influence on genetic variation in the development of cancer will be discussed, before significant genome projects are reviewed. All the various forms of genetic variation have been associated with malignancies and have been extensively studied and this is a review of the state of the field. We also discuss the road ahead in fulfilling the ultimate goal in all cancer genetic studies, which is decreasing deaths caused by cancer.

Talseth-Palmer, Bente A.; Scott, Rodney J.

2011-01-01

398

Eukaryotic initiation factor (eIF) 4B is known to interact with multiple initiation factors, mRNA, rRNA, and poly(A) binding protein (PABP). To gain a better understanding of the function of eIF4B, the two isoforms from Arabidopsis (Arabidopsis thaliana) were expressed and analyzed using biophysical and biochemical methods. Plant eIF4B was found by ultracentrifugation and light scattering analysis to most likely be a monomer with an extended structure. An extended structure would facilitate the multiple interactions of eIF4B with mRNA as well as other initiation factors (eIF4A, eIF4G, PABP, and eIF3). Eight mRNAs, barley (Hordeum vulgare) ?-amylase mRNA, rabbit ?-hemoglobin mRNA, Arabidopsis heat shock protein 21 (HSP21) mRNA, oat (Avena sativa) globulin, wheat (Triticum aestivum) germin, maize (Zea mays) alcohol dehydrogenase, satellite tobacco necrosis virus RNA, and alfalfa mosaic virus (AMV) 4, were used in wheat germ in vitro translation assays to measure their dependence on eIF4B and eIF4F isoforms. The two Arabidopsis eIF4B isoforms, as well as native and recombinant wheat eIF4B, showed similar responses in the translation assay. AMV RNA 4 and Arabidopsis HSP21 showed only a slight dependence on the presence of eIF4B isoforms, whereas rabbit ?-hemoglobin mRNA and wheat germin mRNA showed modest dependence. Barley ?-amylase, oat globulin, and satellite tobacco necrosis virus RNA displayed the strongest dependence on eIF4B. These results suggest that eIF4B has some effects on mRNA discrimination during initiation of translation. Barley ?-amylase, oat globulin, and rabbit ?-hemoglobin mRNA showed the highest activity with eIF4F, whereas Arabidopsis HSP21 and AMV RNA 4 used both eIF4F and eIF(iso)4F equally well. These results suggest that differential or optimal translation of mRNAs may require initiation complexes composed of specific isoforms of initiation factor gene products. Thus, individual mRNAs or classes of mRNAs may respond to the relative abundance of a particular initiation factor(s), which in turn may affect the amount of protein translated. It is likely that optimal multifactor initiation complexes exist that allow for optimal translation of mRNAs under a variety of cellular conditions.

Mayberry, Laura K.; Allen, M. Leah; Dennis, Michael D.; Browning, Karen S.

2009-01-01

399

NASA Astrophysics Data System (ADS)

In Upper Normandy, where drinking water supply comes from karst aquifers, rainfall events may involve turbid runoffs. These events induce sanitary crises and shutdowns of the water supply. The springs of Fontaine-Sous-Préaux provide 60% of Rouen's population (400,000) (France). These springs are highly vulnerable and their exploitation is confronted with the recurrence of turbid events, which can reach up to 150 NTU during highly rain events. The turbidity observed at karst springs is a complex signal composed by two parts of different origins: a first part coming from the direct transfer of particles from the surface following runoff events, and a second part involving the resuspension of materials previously deposited within karst conduits. The disctinction between those two part has always been very challenging. In this study, taking the example of a karst spring in Upper Normandy (Fontaine Sous Préaux spring), we attempted to refine a turbidigraph decomposition method based on the comparison between electrical conductivity (EC) and turbidity (T) using separated modelled hysteresis curves. In a first step, the EC and T breakthrough curves are modelled using an appropriate number of sub-peaks. Second, local EC-T hysteresis curves are builded up in order to characterize the time-varying changes of the dissolved/particulate transports relationships and to assess the respective contribution of the direct transfer and resuspended parts of turbidity throughout complex floods. Associated to cross-correlation analyses of the EC and T sub-peaks separated, the method allowed identification of the (potentially changing) lag time between EC and T. The results obtained highlighted the pre-eminence of resuspension phenomena at the spring for all floods studied. Nevertheless, four different types of hysteresis curves could be distinguished: i) wide clockwise hysteresis expressing the pre-eminence of resuspension accompanied by pressure pulse transfer phenomena; ii) wide clockwise hysteresis expressing the pre-eminence of resuspension of sediments arriving simultaneously with surface waters; iii) a thin hystérésis equivalent to an almost linear relationship between EC and T, corresponding to a simultaneous transfer of surface water and particles, iv) a thin and curved counter-clockwise hysteresis representing a direct transfer of particles and water from the surface characterizing a deficit of available sedimentary stock. Keywords : transport processes, hysteresis, resuspension, direct transfer, deposition.

Mouhri, A.; Motelay, A.; Hanin, G.; Massei, N.; Fournier, M.; Dupont, J. P.; Laignel, B.

2009-04-01

400

Multi-objective optimization shapes ecological variation.

Ecological systems contain a huge amount of quantitative variation between and within species and locations, which makes it difficult to obtain unambiguous verification of theoretical predictions. Ordinary experiments consider just a few explanatory factors and are prone to providing oversimplified answers because they ignore the complexity of the factors that underlie variation. We used multi-objective optimization (MO) for a mechanistic analysis of the potential ecological and evolutionary causes and consequences of variation in the life-history traits of a species of moth. Optimal life-history solutions were sought for environmental conditions where different life stages of the moth were subject to predation and other known fitness-reducing factors in a manner that was dependent on the duration of these life stages and on variable mortality rates. We found that multi-objective optimal solutions to these conditions that the moths regularly experience explained most of the life-history variation within this species. Our results demonstrate that variation can have a causal interpretation even for organisms under steady conditions. The results suggest that weather and species interactions can act as underlying causes of variation, and MO acts as a corresponding adaptive mechanism that maintains variation in the traits of organisms. PMID:21849318

Kaitaniemi, Pekka; Scheiner, Annette; Klemola, Tero; Ruohomäki, Kai

2012-02-22

401

Homo- and heterometallic octanuclear complexes of formula Na?{[Cu?(mpba)?][Cu(Me?dien)]?}-(ClO?)?·12H?O (1), Na?{[Cu?(Mempba)?][Cu(Me?dien)]?}(ClO?)?·12H?O (2), Na?{[Ni?(mpba)?]-[Cu(Me?dien)]?}(ClO?)?·12H?O (3), Na?{[Ni?(Mempba)?][Cu(Me?dien)]?}(ClO?)?·9H?O (4), {[Ni?(mpba)?][Ni(dipn)(H?O)]?}(ClO?)?·12.5H?O (5), and {[Ni?(Mempba)?][Ni(dipn)-(H?O)]?}(ClO?)?·12H?O (6) [mpba = 1,3-phenylenebis(oxamate), Mempba = 4-methyl-1,3-phenylenebis(oxamate), Me?dien = N,N,N',N'',N''-pentamethyldiethylenetriamine, and dipn = dipropylenetriamine] have been synthesized through the "complex-as-ligand/complex-as-metal" strategy. Single-crystal X-ray diffraction analyses of 1, 3, and 5 show cationic M(II)?M'(II)? entities (M, M' = Cu and Ni) with an overall double-star architecture, which is made up of two oxamato-bridged M(II)M'(II)? star units connected through three meta-phenylenediamidate bridges between the two central metal atoms leading to a binuclear metallacryptand core of the meso-helicate-type. Dc magnetic susceptibility data for 1-6 in the temperature range 2-300 K have been analyzed through a "dimer-of-tetramers" model [H = - J(S(1A)·S(3A) + S(1A)·S(4A) + S(1A)·S(5A) + S(2B)·S(6B) + S(2B)·S(7B) + S(2B)·S(8B)) - J'S(1A)·S(2B), with S(1A) = S(2B) = S(M) and S(3A) = S(4A) = S(5A) = S(6B) = S(7B) = S(8B) = S(M')]. The moderate to strong antiferromagnetic coupling between the M(II) and M'(II) ions through the oxamate bridge in 1-6 (-J(Cu-Cu) = 52.0-57.0 cm?¹, -J(Ni-Cu) = 39.1-44.7 cm?¹, and -J(Ni-Ni) = 26.3-26.6 cm?¹) leads to a non-compensation of the ground spin state for the tetranuclear M(II)M'(II)? star units [S(A) = S(B) = 3S(M') - S(M) = 1 (1 and 2), 1/2 (3 and 4), and 2 (5 and 6)]. Within the binuclear M(II)? meso-helicate cores of 1-4, a moderate to weak antiferromagnetic coupling between the M(II) ions (-J'(Cu-Cu) = 28.0-48.0 cm?¹ and -J'(Ni-Ni) = 0.16-0.97 cm?¹) is mediated by the triple m-phenylenediamidate bridge to give a ground spin singlet (S = S(A) - S(B) = 0) state for the octanuclear M(II)?Cu(II)? molecule. Instead, a weak ferromagnetic coupling between the Ni(II) ions (J'(Ni-Ni) = 2.07-3.06 cm?¹) operates in the binuclear Ni(II)? meso-helicate core of 5 and 6 leading thus to a ground spin nonet (S = S(A) + S(B) = 4) state for the octanuclear Ni(II)? molecule. Dc magnetization data for 5 reveal a small but non-negligible axial magnetic anisotropy (D = -0.23 cm?¹) of the S = 4 Ni(II)? ground state with an estimated value of the energy barrier for magnetization reversal of 3.7 cm?¹ (U = -DS²). Ac magnetic susceptibility data for 5 show an unusual slow magnetic relaxation behaviour at low temperatures which is typical of "cluster glasses". The temperature dependence of the relaxation time for 5 has been interpreted on the basis of the Vogel-Fulcher law for weakly interacting clusters, with values of 2.5 K, 1.4 × 10?? s, and 4.0 cm?¹ for the intermolecular interaction parameter (T?), the pre-exponential factor (??), and the effective energy barrier (U(eff)), respectively. PMID:21491690

Pardo, Emilio; Dul, Marie-Claire; Lescouëzec, Rodrigue; Chamoreau, Lise-Marie; Journaux, Yves; Pasán, Jorge; Ruiz-Pérez, Catalina; Julve, Miguel; Lloret, Francesc; Ruiz-García, Rafael; Cano, Joan

2010-05-28

402

Nd, Sr and O isotopic data were obtained from silicic ash-flow tuffs and lavas at the Tertiary age (16-9 Ma) Timber (Mountain/Oasis Valley volcanic center (TMOV) in southern Nevada, to assess models for the origin and evolution of the large-volume silicic magma bodies generated in this region. The large-volume (>900 km3), chemically-zoned, Topopah Spring (TS) and Tiva Canyon (TC) members of the Paintbrush Tuff, and the Rainier Mesa (RM) and Ammonia Tanks (AT) members of the younger Timber Mountain Tuff all have internal Nd and Sr isotopic zonations. In each tuff, high-silica rhyolites have lower initial e{open}Nd values (???1 e{open}Nd unit), higher87Sr/86Sr, and lower Nd and Sr contents, than cocrupted trachytes. The TS, TC, and RM members have similar e{open}Nd values for high-silica rhyolites (-11.7 to -11.2) and trachytes (-10.5 to -10.7), but the younger AT member has a higher e{open}Nd for both compositional types (-10.3 and -9.4). Oxygen isotope data confirm that the TC and AT members were derived from low e{open}Nd magmas. The internal Sr and Nd isotopic variations in each tuff are interpreted to be the result of the incorporation of 20-40% (by mass) wall-rock into magmas that were injected into the upper crust. The low e{open}Nd magmas most likely formed via the incorporation of low ??18O, hydrothermally-altered, wall-rock. Small-volume rhyolite lavas and ash-flow tuffs have similar isotopic characteristics to the large-volume ash-flow tuffs, but lavas erupted from extracaldera vents may have interacted with higher ??18O crustal rocks peripheral to the main magma chamber(s). Andesitic lavas from the 13-14 Ma Wahmonie/Salyer volcanic center southeast of the TMOV have low e{open}Nd (-13.2 to -13.8) and are considered on the basis of textural evidence to be mixtures of basaltic composition magmas and large proportions (70-80%) of anatectic crustal melts. A similar process may have occurred early in the magmatic history of the TMOV. The large-volume rhyolites may represent a mature stage of magmatism after repeated injection of basaltic magmas, crustal melting, and volcanism cleared sufficient space in the upper crust for large magma bodies to accumulate and differentiate. The TMOV rhyolites and 0-10 Ma old basalts that erupted in southern Nevada all have similar Nd and Sr isotopic compositions, which suggests that silicic and mafic magmatism at the TMOV were genetically related. The distinctive isotopic compositions of the AT member may reflect temporal changes in the isotopic compositions of basaltic magmas entering the upper crust, possibly as a result of increasing "basification" of a lower crustal magma source by repeated injection of mantle-derived mafic magmas. ?? 1991 Springer-Verlag.

Farmer, G. L.; Broxton, D. E.; Warren, R. G.; Pickthorn, W.

1991-01-01

403

NASA Astrophysics Data System (ADS)

Nd, Sr and O isotopic data were obtained from silicic ash-flow tuffs and lavas at the Tertiary age (16 9 Ma) Timber (Mountain/Oasis Valley volcanic center (TMOV) in southern Nevada, to assess models for the origin and evolution of the large-volume silicic magma bodies generated in this region. The large-volume (>900 km3), chemically-zoned, Topopah Spring (TS) and Tiva Canyon (TC) members of the Paintbrush Tuff, and the Rainier Mesa (RM) and Ammonia Tanks (AT) members of the younger Timber Mountain Tuff all have internal Nd and Sr isotopic zonations. In each tuff, high-silica rhyolites have lower initial ? Nd values (˜1 ? Nd unit), higher87Sr/86Sr, and lower Nd and Sr contents, than cocrupted trachytes. The TS, TC, and RM members have similar ? Nd values for high-silica rhyolites (-11.7 to -11.2) and trachytes (-10.5 to -10.7), but the younger AT member has a higher ? Nd for both compositional types (-10.3 and -9.4). Oxygen isotope data confirm that the TC and AT members were derived from low ? Nd magmas. The internal Sr and Nd isotopic variations in each tuff are interpreted to be the result of the incorporation of 20 40% (by mass) wall-rock into magmas that were injected into the upper crust. The low ? Nd magmas most likely formed via the incorporation of low ? 18O, hydrothermally-altered, wall-rock. Small-volume rhyolite lavas and ash-flow tuffs have similar isotopic characteristics to the large-volume ash-flow tuffs, but lavas erupted from extracaldera vents may have interacted with higher ? 18O crustal rocks peripheral to the main magma chamber(s). Andesitic lavas from the 13 14 Ma Wahmonie/Salyer volcanic center southeast of the TMOV have low ? Nd (-13.2 to -13.8) and are considered on the basis of textural evidence to be mixtures of basaltic composition magmas and large proportions (70 80%) of anatectic crustal melts. A similar process may have occurred early in the magmatic history of the TMOV. The large-volume rhyolites may represent a mature stage of magmatism after repeated injection of basaltic magmas, crustal melting, and volcanism cleared sufficient space in the upper crust for large magma bodies to accumulate and differentiate. The TMOV rhyolites and 0 10 Ma old basalts that erupted in southern Nevada all have similar Nd and Sr isotopic compositions, which suggests that silicic and mafic magmatism at the TMOV were genetically related. The distinctive isotopic compositions of the AT member may reflect temporal changes in the isotopic compositions of basaltic magmas entering the upper crust, possibly as a result of increasing “basification” of a lower crustal magma source by repeated injection of mantle-derived mafic magmas.

Farmer, G. Lang; Broxton, David E.; Warren, Richard G.; Pickthorn, William

1991-03-01

404

More than 100 000 human genetic variations have been described in various genes that are associated with a wide variety of diseases. Such data provides invaluable information for both clinical medicine and basic science. A number of locus-specific databases have been developed to exploit this huge amount of data. However, the scope, format and content of these databases differ strongly and as no standard for variation databases has yet been adopted, the way data is presented varies enormously. This review aims to give an overview of current resources for human variation data in public and commercial resources.

Kuntzer, Jan; Eggle, Daniela; Klostermann, Stefan; Burtscher, Helmut

2010-01-01

405

Modeling Investigation of Volume Variation Kinetics of Fast Response Hydrogels

Fast response hydrogels have attracted great attention recently. Three kinds of models with different complexity are available in the literature to investigate their volume variation kinetics. A phenomenal model based on second?order reaction kinetics provides a simple method to correlate the experimental kinetic data. A power law model can be employed to evaluate different volume variation mechanisms according to the

Shunnian Wu; Hua Li; J. Paul Chen

2004-01-01

406

This chapter presents selected ideas concerning complexes that are formed either by oppositely charged polyelectrolytes or by polyelectrolytes and surfactants of opposite charge. The polyelectrolyte complexes polyelectrolyte complexe (PECs PEC ), which are surfactant-free, form typical structures of a low degree of order such as the ladder ladder-egg structure - and scrambled-egg structures scrambled-egg structure . In contrast, polyelectrolyte-surfactant complexes

Andreas F. Thünemann; Martin Müller; Herbert Dautzenberg; Jean-François Joanny; Hartmut Löwen

407

Efficient implementation of the Gutzwiller variational method

NASA Astrophysics Data System (ADS)

We present a self-consistent numerical approach to solve the Gutzwiller variational problem for general multiband models with arbitrary on-site interaction. The proposed method generalizes and improves the procedure derived by Deng [Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.79.075114 79, 075114 (2009)], overcoming the restriction to density-density interaction without increasing the complexity of the computational algorithm. Our approach drastically reduces the problem of the high-dimensional Gutzwiller minimization by mapping it to a minimization only in the variational density matrix, in the spirit of the Levy and Lieb formulation of density functional theory (DFT). For fixed density the Gutzwiller renormalization matrix is determined as a fixpoint of a proper functional, whose evaluation requires only ground-state calculations of matrices defined in the Gutzwiller variational space. Furthermore, the proposed method is able to account for the symmetries of the variational function in a controlled way, reducing the number of variational parameters. After a detailed description of the method we present calculations for multiband Hubbard models with full (rotationally invariant) Hund’s rule on-site interaction. Our analysis shows that the numerical algorithm is very efficient, stable, and easy to implement. For these reasons this method is particularly suitable for first-principles studies (e.g., in combination with DFT) of many complex real materials, where the full intra-atomic interaction is important to obtain correct results.

Lanatà, Nicola; Strand, Hugo U. R.; Dai, Xi; Hellsing, Bo

2012-01-01

408

ERIC Educational Resources Information Center

To determine whether consensus existed among teachers about