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Sample records for complex kohn variational

  1. Complex Correlation Kohn-T Method of Calculating Total and Elastic Cross Sections. Part 1; Electron-Hydrogen Elastic Scattering

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

    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,

  2. The calculation of the contributions to low energy e+H2 scattering from sigma u+ and Pion u symmetries using the Kohn variational method

    NASA Technical Reports Server (NTRS)

    Armour, E. A. G.; Baker, D. J.; Plummer, M.

    1990-01-01

    Above incident energies of about 2 eV, the contribution to the total cross section in positron+H2 scattering from the sigma g+ symmetry is insufficient to account for the experimental value. Calculations carried out of the lowest partial waves of sigma u+ symmetry and Pion u symmetry using the Kohn variational method are described. The contributions to the total cross section from the two equivalent partial waves of Pion u symmetry significantly reduce the discrepancy with experiment up to incident energies of 4 to 5 eV. Comparisons are made with recent R-matrix calculations performed by Danby and Tennyson.

  3. The Mathematics of Wrinkles and Folds Robert V. Kohn

    E-print Network

    The Mathematics of Wrinkles and Folds Robert V. Kohn Courant Institute, NYU NYU Mathematics Society, 2/2/2012 Robert V. Kohn Wrinkles and Folds #12;Wrinkles and folds We'll be talking about a little geometry and mechanics a lot of calculus of variations Robert V. Kohn Wrinkles and Folds #12;Paper

  4. Competition: Was Kohn Right?

    ERIC Educational Resources Information Center

    Shields, David Light; Bredemeier, Brenda Light

    2010-01-01

    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…

  5. On complexes related with calculus of variations

    E-print Network

    Hovhannes Khudaverdian; Theodore Voronov

    2001-05-27

    We consider the variational complex on infinite jet space and the complex of variational derivatives for Lagrangians of multidimensional paths and study relations between them. The discussion of the variational (bi)complex is set up in terms of a flat connection in the jet bundle. We extend it to supercase using a particular new class of forms. We establish relation of the complex of variational derivatives and the variational complex. Certain calculus of Lagrangians of multidimensional paths is developed. It is shown how covariant Lagrangians of higher order can be used to represent characteristic classes.

  6. Hohenberg-Kohn redux

    E-print Network

    Paul E. Lammert

    2015-02-08

    The Hohenberg-Kohn theorem is a cornerstone of electronic density functional theory, yet completing its proof in the traditional way requires the {\\em assumption} that ground state wavefunctions never vanish on sets of nonzero Lebesgue measure. This is an unsatisfactory situation, since DFT is supposed to obviate knowledge of many-body wavefunctions. We approach the issue from a more density-centric direction, allowing mild hypotheses on the density which can be regarded as checkable in a DFT context. By ordinary Hilbert space analysis, the following is proved: If the density $\\rho$ is continuous and everywhere nonzero, then there can be at most one potential (modulo constants) expressible as a sum of a square-integrable and a bounded function (i.e., Kato-Rellich) with $\\rho$ as a ground state density. In case $\\rho$ is not nonzero everywhere, the theorem allows an independent constant on each connected component of the set where the density is positive, a weakening which can be reversed by requiring locally weak-$L^3$ potentials and calling on a unique continuation result of Schechter and Simon.

  7. J. Phys. Chem. 1990, 94, 7785-7789 7785 Quasi-Adiabatic Basis Functions for the S-Matrix Kohn Variational Approach to Quantum

    E-print Network

    Miller, William H.

    published. (c) Buntin, S.A,; Giese, C. F.; Gentry, W. R. J. Chem. Phys. 1987, 87, 1443. (d) Phillips, D. L Variational Approach to Quantum Reactive Scattering John Z. H. Zhang and William H. Miller* Department^.^ More recently, the first converged integral and differential cross sections for the D + H2-HD + H

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

    E-print Network

    De Sole, Alberto

    Calculus structure on the Lie conformal algebra complex and the variational complex Alberto De Sole, and the Cartan calculus turns into the variational calculus. Our aim in this paper is to extend the structure OF MATHEMATICAL PHYSICS 52, 053510 (2011) Calculus structure on the Lie conformal algebra complex

  9. Explaining additional genetic variation in complex traits

    PubMed Central

    Robinson, Matthew R.; Wray, Naomi R.; Visscher, Peter M.

    2015-01-01

    Genome-wide association studies (GWAS) have provided valuable insights into the genetic basis of complex traits, discovering >6000 variants associated with >500 quantitative traits and common complex diseases in humans. The associations identified so far represent only a fraction of those which influence phenotype, as there are likely to be very many variants across the entire frequency spectrum, each of which influences multiple traits, with only a small average contribution to the phenotypic variance. This presents a considerable challenge to further dissection of the remaining unexplained genetic variance within populations, which limits our ability to predict disease risk, identify new drug targets, improve and maintain food sources, and understand natural diversity. This challenge will be met within the current framework through larger sample size, better phenotyping including recording of non-genetic risk factors, focused study designs, and an integration of multiple sources of phenotypic and genetic information. The current evidence supports the application of quantitative genetic approaches, and we argue that one should retain simpler theories until simplicity can be traded for greater explanatory power. PMID:24629526

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

    SciTech Connect

    Hinckley, C.M.; Barkan, P.

    1994-03-01

    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.

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

    E-print Network

    Alberto De Sole; Pedram Hekmati; Victor Kac

    2010-07-21

    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 [DSK]. A special case of this construction is the variational calculus, for which we provide explicit formulas.

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

    SciTech Connect

    De Sole, Alberto; Hekmati, Pedram; Kac, Victor G.

    2011-05-15

    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.

  13. Cloaking by Change of Variables Robert V. Kohn

    E-print Network

    Eilbeck, Chris

    Cloaking by Change of Variables Robert V. Kohn Courant Institute, NYU Edinburgh, June 2008 Robert V getting it right. Robert V. Kohn Courant Institute, NYU Cloaking by Change of Variables #12;What to analyze: scattering at fixed frequency Easier still: frequency zero (impedance tomography). Robert V. Kohn

  14. Structural Optimization and 3D Printing Robert V. Kohn

    E-print Network

    Structural Optimization and 3D Printing Robert V. Kohn Courant Institute, NYU SIAM CS&E Meeting, March 2015 Robert V. Kohn Structural Optimization and 3D Printing #12;Outline Mandate: identify areas, J. Ricci, and Y. Zhang co-PI's) Robert V. Kohn Structural Optimization and 3D Printing #12;Outline

  15. A complex Noether approach for variational partial differential equations

    NASA Astrophysics Data System (ADS)

    Naz, R.; Mahomed, F. M.

    2015-10-01

    Scalar complex partial differential equations which admit variational formulations are studied. Such a complex partial differential equation, via a complex dependent variable, splits into a system of two real partial differential equations. The decomposition of the Lagrangian of the complex partial differential equation in the real domain is shown to yield two real Lagrangians for the split system. The complex Maxwellian distribution, transonic gas flow, Maxwellian tails, dissipative wave and Klein-Gordon equations are considered. The Noether symmetries and gauge terms of the split system that correspond to both the Lagrangians are constructed by the Noether approach. In the case of coupled split systems, the same Noether symmetries are obtained. The Noether symmetries for the uncoupled split systems are different. The conserved vectors of the split system which correspond to both the Lagrangians are compared to the split conserved vectors of the complex partial differential equation for the examples. The split conserved vectors of the complex partial differential equation are the same as the conserved vectors of the split system of real partial differential equations in the case of coupled systems. Moreover a Noether-like theorem for the split system is proved which provides the Noether-like conserved quantities of the split system from knowledge of the Noether-like operators. An interesting result on the split characteristics and the conservation laws is shown as well. The Noether symmetries and gauge terms of the Lagrangian of the split system with the split Noether-like operators and gauge terms of the Lagrangian of the given complex partial differential equation are compared. Folklore suggests that the split Noether-like operators of a Lagrangian of a complex Euler-Lagrange partial differential equation are symmetries of the Lagrangian of the split system of real partial differential equations. This is not the case. They are proved to be the same if the Noether symmetries of the Lagrangian of the complex partial differential equation have either pure real or pure imaginary form.

  16. Morphological Variation in Leaf Dissection of Rheum palmatum Complex (Polygonaceae)

    PubMed Central

    Wang, Xu-Mei; Hou, Xiao-Qi; Zhang, Yu-Qu; Li, Yan

    2014-01-01

    Aims Rheum palmatum complex comprises all taxa within section Palmata in the genus Rheum, including R. officinale, R. palmatum, R. tanguticum, R. tanguticum var. liupanshanense and R. laciniatum. The identification of the taxa in section Palmata is based primarily on the degree of leaf blade dissection and the shape of the lobes; however, difficulties in species identification may arise from their significant variation. The aim of this study is to analyze the patterns of variation in leaf blade characteristics within and among populations through population-based sampling covering the entire distribution range of R. palmatum complex. Methods Samples were taken from 2340 leaves from 780 individuals and 44 populations representing the four species, and the degree of leaf blade dissection and the shape of the lobe were measured to yield a set of quantitative data. Furthermore, those data were statistically analyzed. Important Findings The statistical analysis showed that the degree of leaf blade dissection is continuous from lobed to parted, and the shape of the lobe is also continuous from broadly triangular to lanceolate both within and between populations. We suggested that taxa in section Palmata should be considered as one species. Based on the research on the R. palmatum complex, we considered that the quantitative characteristics were greatly influenced by the environment. Therefore, it is not reliable to delimitate the species according to the continuously quantitative vegetative characteristics. PMID:25349989

  17. Climatic variation and the distribution of an amphibian polyploid complex.

    PubMed

    Otto, Clint R V; Snodgrass, Joel W; Forester, Don C; Mitchell, Joseph C; Miller, Robert W

    2007-11-01

    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. 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. 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. Clusters of syntopic sites were associated with areas of high variation in annual temperature and precipitation during the breeding season. 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 possess a tolerance of severe environmental conditions that is not possessed by the diploid progenitor. Our findings support the hypothesis that increased tolerance to severe environmental conditions is a plausible mechanism of polyploid establishment. PMID:17922702

  18. Climatic variation and the distribution of an amphibian polyploid complex

    USGS Publications Warehouse

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

    2007-01-01

    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.

  19. Parabolic PDEs and Deterministic Games Robert V. Kohn

    E-print Network

    Parabolic PDEs and Deterministic Games Robert V. Kohn Courant Institute, NYU Joint work with Sylvia Serfaty ICIAM07, Zurich, July 2007 Robert V. Kohn Courant Institute, NYU Parabolic PDEs and Deterministic-Lax solution formula; and finance, for example through Merton's analysis of portfolio optimization. Robert V

  20. 60 : DVD (9.1) 1998, Walter Kohn

    E-print Network

    Zexian, Cao

    ...... , , , : 50% , Crest Union #12;3/30 -- John Cleese, ? , , ...... : 1-1 Newton;8/30 , : , : " " " ", , 2-2 2-3 #12;9/30 (Shockley)(Bardeen) ......(Kohn) 20 , 1947 Shockley,Bardeen , , 50)Fuller 1954 4 25 " " Kohn John Perlin / 3-1 #12;13/30 Americus , , ? , , (Perlin

  1. Energy-Driven Pattern Formation Robert V. Kohn

    E-print Network

    Energy-Driven Pattern Formation Robert V. Kohn Grad Student and Postdoc Seminar April 22, 2011 Robert V. Kohn Energy-Driven Pattern Formation #12;Overview What is energy-driven pattern formation? Hard by singular perturbation Statics: minimum energy scaling laws Dynamics: patterns induced by steepest

  2. On the Kohn-Luttinger conundrum

    SciTech Connect

    Hirata, So; He Xiao

    2013-05-28

    Kohn and Luttinger [Phys. Rev. 118, 41 (1960)] showed that the conventional finite-temperature extension of the second-order many-body perturbation theory had the incorrect zero-temperature limit in metals and, on this basis, argued that the theory was incorrect. We show that this inconsistency arises from the noninclusion of the temperature effect in the energies of the zeroth-order eigenstates of the perturbation theory, which causes not only the Kohn-Luttinger conundrum but also another inconsistency with the zero-temperature many-body perturbation theory, namely, the different rates of divergence of the correlation energy in a homogeneous electron gas (HEG). We propose a renormalized many-body perturbation theory derivable from the finite-temperature extension of the normal-ordered second quantization applied to the denominators of the energy expression, which involves the energies of the zeroth-order states, as well as to the numerators. The renormalized theory is shown to have the correct zero-temperature limit and the same rate of divergence in a HEG as the zero-temperature counterpart, and is, therefore, the correct finite-temperature many-body perturbation theory.

  3. Hohenberg-Kohn theorems in electrostatic and uniform magnetostatic fields.

    PubMed

    Pan, Xiao-Yin; Sahni, Viraht

    2015-11-01

    The Hohenberg-Kohn (HK) theorems of bijectivity between the external scalar potential and the gauge invariant nondegenerate ground state density, and the consequent Euler variational principle for the density, are proved for arbitrary electrostatic field and the constraint of fixed electron number. The HK theorems are generalized for spinless electrons to the added presence of an external uniform magnetostatic field by introducing the new constraint of fixed canonical orbital angular momentum. Thereby, a bijective relationship between the external scalar and vector potentials, and the gauge invariant nondegenerate ground state density and physical current density, is proved. A corresponding Euler variational principle in terms of these densities is also developed. These theorems are further generalized to electrons with spin by imposing the added constraint of fixed canonical orbital and spin angular momenta. The proofs differ from the original HK proof and explicitly account for the many-to-one relationship between the potentials and the nondegenerate ground state wave function. A Percus-Levy-Lieb constrained-search proof expanding the domain of validity to N-representable functions, and to degenerate states, again for fixed electron number and angular momentum, is also provided. PMID:26547156

  4. Hohenberg-Kohn theorems in electrostatic and uniform magnetostatic fields

    NASA Astrophysics Data System (ADS)

    Pan, Xiao-Yin; Sahni, Viraht

    2015-11-01

    The Hohenberg-Kohn (HK) theorems of bijectivity between the external scalar potential and the gauge invariant nondegenerate ground state density, and the consequent Euler variational principle for the density, are proved for arbitrary electrostatic field and the constraint of fixed electron number. The HK theorems are generalized for spinless electrons to the added presence of an external uniform magnetostatic field by introducing the new constraint of fixed canonical orbital angular momentum. Thereby, a bijective relationship between the external scalar and vector potentials, and the gauge invariant nondegenerate ground state density and physical current density, is proved. A corresponding Euler variational principle in terms of these densities is also developed. These theorems are further generalized to electrons with spin by imposing the added constraint of fixed canonical orbital and spin angular momenta. The proofs differ from the original HK proof and explicitly account for the many-to-one relationship between the potentials and the nondegenerate ground state wave function. A Percus-Levy-Lieb constrained-search proof expanding the domain of validity to N-representable functions, and to degenerate states, again for fixed electron number and angular momentum, is also provided.

  5. Time-dependent Kohn-Sham approach to quantum electrodynamics

    NASA Astrophysics Data System (ADS)

    Ruggenthaler, M.; Mackenroth, F.; Bauer, D.

    2011-10-01

    We prove a generalization of the van Leeuwen theorem toward quantum electrodynamics, providing the formal foundations of a time-dependent Kohn-Sham construction for coupled quantized matter and electromagnetic fields. We circumvent the symmetry-causality problems associated with the action-functional approach to Kohn-Sham systems. We show that the effective external four-potential and four-current of the Kohn-Sham system are uniquely defined and that the effective four-current takes a very simple form. Further we rederive the Runge-Gross theorem for quantum electrodynamics.

  6. Interpreting noncoding genetic variation in complex traits and human disease

    E-print Network

    Kellis, Manolis

    Association studies provide genome-wide information about the genetic basis of complex disease, but medical research has focused primarily on protein-coding variants, owing to the difficulty of interpreting noncoding ...

  7. Complex Variation in Measures of General Intelligence and Cognitive Change

    PubMed Central

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

    2013-01-01

    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. PMID:24349040

  8. Syntheses of Variations of Stereogenic-at-Metal Imido Alkylidene Complexes of Molybdenum

    E-print Network

    Müller, Peter

    Syntheses of Variations of Stereogenic-at-Metal Imido Alkylidene Complexes of Molybdenum Smaranda C of several new stereogenic-at-metal imido alkylidene complexes of molybdenum, Mo(NR)(CHR)(X)(Y), many to the alkylidene and imido ligands. INTRODUCTION Recent advances in olefin metathesis by molybdenum,1 tungsten,2

  9. Kohn-Sham potentials for fullerenes and spherical molecules

    NASA Astrophysics Data System (ADS)

    Pavlyukh, Y.; Berakdar, J.

    2010-04-01

    We present a procedure for the construction of accurate Kohn-Sham potentials of quasispherical molecules starting from the first-principles valence densities. The method is demonstrated for the case of icosahedral C202+ and C60 molecules. Provided the density is N representable the Hohenberg-Kohn theorem guarantees the uniqueness of the obtained potentials. The potential is iteratively built following the suggestion of R. van Leeuwen and E. J. Baerends [Phys. Rev. A 49, 2421 (1994)]. The high symmetry of the molecules allows a parametrization of the angular dependence of the densities and the potentials using a small number of symmetry-adapted spherical harmonics. The radial behavior of these quantities is represented on a grid and the density is reconstructed from the approximate potential by numerically solving the coupled-channel Kohn-Sham equations. Subsequently, the potential is updated and the procedure is continued until convergence is achieved.

  10. Four-Component Relativistic KohnSham Theory TROND SAUE,1

    E-print Network

    Helgaker, Trygve

    /Universite´ Louis Pasteur, Laboratoire de Chimie Quantique et Mode´lisation Mole´culaire, 4 rue Blaise Pascal, F of the Ho- henberg­Kohn theorem.6 Subsequently, relativistic versions of the Kohn­Sham equations have been

  11. The importance of an accurate target wave function in variational calculations for (e^{+}-H_{2}) scattering

    E-print Network

    J. N. Cooper; E. A. G. Armour; M. Plummer

    2008-11-03

    Using the complex Kohn method, we have calculated variational values of phase shifts and the annihilation parameter, Z_{eff}, for the elastic scattering of positrons by molecular hydrogen. Our results are sensitive to small changes in the accuracy of the wave function representing the target hydrogen molecule. We have developed a systematic approach to demonstrate that, at low positron energies, there are particular forms of the Kohn trial wave function for which the results of variational calculations are not reliable, even when the target wave function accounts for as much as 96.8% of the correlation energy of H_{2}. We find that reliable results can be recovered if our calculations are extended to admit more sophisticated target wave functions accounting for 99.7% of the correlation energy. Remaining discrepancies between theory and experiment are briefly discussed.

  12. A Kohn-Sham system at zero temperature

    E-print Network

    Horia Cornean; Kurt Hoke; Hagen Neidhardt; Paul N. Racec; Joachim Rehberg

    2008-01-17

    An one-dimensional Kohn-Sham system for spin particles is considered which effectively describes semiconductor {nano}structures and which is investigated at zero temperature. We prove the existence of solutions and derive a priori estimates. For this purpose we find estimates for eigenvalues of the Schr\\"odinger operator with effective Kohn-Sham potential and obtain $W^{1,2}$-bounds of the associated particle density operator. Afterwards, compactness and continuity results allow to apply Schauder's fixed point theorem. In case of vanishing exchange-correlation potential uniqueness is shown by monotonicity arguments. Finally, we investigate the behavior of the system if the temperature approaches zero.

  13. Must Kohn-Sham oscillator strengths be accurate at threshold?

    SciTech Connect

    Yang Zenghui; Burke, Kieron; Faassen, Meta van

    2009-09-21

    The exact ground-state Kohn-Sham (KS) potential for the helium atom is known from accurate wave function calculations of the ground-state density. The threshold for photoabsorption from this potential matches the physical system exactly. By carefully studying its absorption spectrum, we show the answer to the title question is no. To address this problem in detail, we generate a highly accurate simple fit of a two-electron spectrum near the threshold, and apply the method to both the experimental spectrum and that of the exact ground-state Kohn-Sham potential.

  14. Kohn's theorem and Newton-Hooke symmetry for Hill's equations

    NASA Astrophysics Data System (ADS)

    Zhang, P. M.; Gibbons, G. W.; Horvathy, P. A.

    2012-02-01

    Hill’s equations, which first arose in the study of the Earth-Moon-Sun system, admit the two-parameter centrally extended Newton-Hooke symmetry without rotations. This symmetry allows us to extend Kohn’s theorem about the center-of-mass decomposition. Particular light is shed on the problem using Duval’s “Bargmann” framework. The separation of the center-of-mass motion into that of a guiding center and relative motion is derived by a generalized chiral decomposition.

  15. Interpreting non-coding variation in complex disease genetics

    PubMed Central

    Ward, Lucas D.; Kellis, Manolis

    2012-01-01

    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. PMID:23138309

  16. Between-Year Variation in Population Sex Ratio Increases with Complexity of the Breeding System in Hymenoptera.

    E-print Network

    Keller, Laurent

    between-year variation in population sex ratio, we conducted a comparative anal- ysis across 47Between-Year Variation in Population Sex Ratio Increases with Complexity of the Breeding System naturalist june 2011 Between-Year Variation in Population Sex Ratio Increases with Complexity of the Breeding

  17. Korringa-Kohn-Rostoker electronic structure method for space-filling cell potentials

    SciTech Connect

    Gonis, A.; Butler, W.H.; Zhang, X.-G.

    1991-12-31

    The multiple scattering theory (MST) method of Korringa, and of Kohn and Rostoker for determining the electronic structure of solids, originally developed in connection with potentials bounded by non-overlapping spheres (muffin-tin (MT) potentials), is generalized to the case of space-filling potential cells of arbitrary shape through the use of a variational formalism. This generalized version of MST retains the separability of structure and potential characteristic of the application of MST to MT potentials. However, in contrast to the MT case, different forms of MST exhibit different convergence rates for the energy and the wave function. Numerical results are presented which illustrate the differing convergence rates of the variational and nonvariational forms of MST for space-filling potentials.

  18. Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation

    PubMed Central

    Brand, Harrison; Collins, Ryan L.; Hanscom, Carrie; Rosenfeld, Jill A.; Pillalamarri, Vamsee; Stone, Matthew R.; Kelley, Fontina; Mason, Tamara; Margolin, Lauren; Eggert, Stacey; Mitchell, Elyse; Hodge, Jennelle C.; Gusella, James F.; Sanders, Stephan J.; Talkowski, Michael E.

    2015-01-01

    Copy-number variants (CNVs) have been the predominant focus of genetic studies of structural variation, and chromosomal microarray (CMA) for genome-wide CNV detection is the recommended first-tier genetic diagnostic screen in neurodevelopmental disorders. We compared CNVs observed by CMA to the structural variation detected by whole-genome large-insert sequencing in 259 individuals diagnosed with autism spectrum disorder (ASD) from the Simons Simplex Collection. These analyses revealed a diverse landscape of complex duplications in the human genome. One remarkably common class of complex rearrangement, which we term dupINVdup, involves two closely located duplications (“paired duplications”) that flank the breakpoints of an inversion. This complex variant class is cryptic to CMA, but we observed it in 8.1% of all subjects. We also detected other paired-duplication signatures and duplication-mediated complex rearrangements in 15.8% of all ASD subjects. Breakpoint analysis showed that the predominant mechanism of formation of these complex duplication-associated variants was microhomology-mediated repair. On the basis of the striking prevalence of dupINVdups in this cohort, we explored the landscape of all inversion variation among the 235 highest-quality libraries and found abundant complexity among these variants: only 39.3% of inversions were canonical, or simple, inversions without additional rearrangement. Collectively, these findings indicate that dupINVdups, as well as other complex duplication-associated rearrangements, represent relatively common sources of genomic variation that is cryptic to population-based microarray and low-depth whole-genome sequencing. They also suggest that paired-duplication signatures detected by CMA warrant further scrutiny in genetic diagnostic testing given that they might mark complex rearrangements of potential clinical relevance. PMID:26094575

  19. Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation.

    PubMed

    Brand, Harrison; Collins, Ryan L; Hanscom, Carrie; Rosenfeld, Jill A; Pillalamarri, Vamsee; Stone, Matthew R; Kelley, Fontina; Mason, Tamara; Margolin, Lauren; Eggert, Stacey; Mitchell, Elyse; Hodge, Jennelle C; Gusella, James F; Sanders, Stephan J; Talkowski, Michael E

    2015-07-01

    Copy-number variants (CNVs) have been the predominant focus of genetic studies of structural variation, and chromosomal microarray (CMA) for genome-wide CNV detection is the recommended first-tier genetic diagnostic screen in neurodevelopmental disorders. We compared CNVs observed by CMA to the structural variation detected by whole-genome large-insert sequencing in 259 individuals diagnosed with autism spectrum disorder (ASD) from the Simons Simplex Collection. These analyses revealed a diverse landscape of complex duplications in the human genome. One remarkably common class of complex rearrangement, which we term dupINVdup, involves two closely located duplications ("paired duplications") that flank the breakpoints of an inversion. This complex variant class is cryptic to CMA, but we observed it in 8.1% of all subjects. We also detected other paired-duplication signatures and duplication-mediated complex rearrangements in 15.8% of all ASD subjects. Breakpoint analysis showed that the predominant mechanism of formation of these complex duplication-associated variants was microhomology-mediated repair. On the basis of the striking prevalence of dupINVdups in this cohort, we explored the landscape of all inversion variation among the 235 highest-quality libraries and found abundant complexity among these variants: only 39.3% of inversions were canonical, or simple, inversions without additional rearrangement. Collectively, these findings indicate that dupINVdups, as well as other complex duplication-associated rearrangements, represent relatively common sources of genomic variation that is cryptic to population-based microarray and low-depth whole-genome sequencing. They also suggest that paired-duplication signatures detected by CMA warrant further scrutiny in genetic diagnostic testing given that they might mark complex rearrangements of potential clinical relevance. PMID:26094575

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

    PubMed

    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

    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

  1. Dominance Genetic Variation Contributes Little to the Missing Heritability for Human Complex Traits

    PubMed Central

    Zhu, Zhihong; Bakshi, Andrew; Vinkhuyzen, Anna A.E.; Hemani, Gibran; Lee, Sang Hong; Nolte, Ilja M.; van Vliet-Ostaptchouk, Jana V.; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Hill, William G.; Weir, Bruce S.; Goddard, Michael E.; Visscher, Peter M.; Yang, Jian

    2015-01-01

    For human complex traits, non-additive genetic variation has been invoked to explain “missing heritability,” but its discovery is often neglected in genome-wide association studies. Here we propose a method of using SNP data to partition and estimate the proportion of phenotypic variance attributed to additive and dominance genetic variation at all SNPs (hSNP2 and ?SNP2) in unrelated individuals based on an orthogonal model where the estimate of hSNP2 is independent of that of ?SNP2. With this method, we analyzed 79 quantitative traits in 6,715 unrelated European Americans. The estimate of ?SNP2 averaged across all the 79 quantitative traits was 0.03, approximately a fifth of that for additive variation (average hSNP2 = 0.15). There were a few traits that showed substantial estimates of ?SNP2, none of which were replicated in a larger sample of 11,965 individuals. We further performed genome-wide association analyses of the 79 quantitative traits and detected SNPs with genome-wide significant dominance effects only at the ABO locus for factor VIII and von Willebrand factor. All these results suggest that dominance variation at common SNPs explains only a small fraction of phenotypic variation for human complex traits and contributes little to the missing narrow-sense heritability problem. PMID:25683123

  2. Exact Kohn-Sham potential of strongly correlated finite systems

    SciTech Connect

    Helbig, N.; Rubio, A.

    2009-12-14

    The dissociation of molecules, even the most simple hydrogen molecule, cannot be described accurately within density functional theory because none of the currently available functionals accounts for strong on-site correlation. This problem led to a discussion of properties that the local Kohn-Sham potential has to satisfy in order to correctly describe strongly correlated systems. We derive an analytic expression for the nontrivial form of the Kohn-Sham potential in between the two fragments for the dissociation of a single bond. We show that the numerical calculations for a one-dimensional two-electron model system indeed approach and reach this limit. It is shown that the functional form of the potential is universal, i.e., independent of the details of the two fragments.

  3. SANS with Contrast Variation Study of the Bacteriorhodopsin-octyl Glucoside Complex

    SciTech Connect

    Heller, William T; Mo, Yiming

    2010-01-01

    Membrane proteins (MPs), which play vital roles in trans-membrane trafficking and signaling between cells and their external environment, comprise a major fraction of the expressed proteomes of many organisms. MP production for biophysical characterization requires detergents for extracting MPs from their native membrane and to solubilize the MP in solution for purification and study. In a proper detergent solution, the detergent-associated MPs retain their native fold and oligomerization state, key requirements for biophysical characterization and crystallization. SANS with contrast variation was performed to characterize BR in complex with OG to better understand the MP-detergent complex. Contrast variation makes it possible to not only probe the conformation of the entire structure but also investigate the conformation of the polypeptide chain within the BR-OG complex. The BR-OG SANS contrast variation series is not consistent with a compact structure, such as a trimeric BR complex surrounded by a belt of detergent. The data strongly suggest that the protein is partially unfolded through its association with the detergent micelles.

  4. Stochastic variational method as quantization scheme: Field quantization of the complex Klein-Gordon equation

    NASA Astrophysics Data System (ADS)

    Koide, T.; Kodama, T.

    2015-09-01

    The stochastic variational method (SVM) is the generalization of the variational approach to systems described by stochastic variables. In this paper, we investigate the applicability of SVM as an alternative field-quantization scheme, by considering the complex Klein-Gordon equation. There, the Euler-Lagrangian equation for the stochastic field variables leads to the functional Schrödinger equation, which can be interpreted as the Euler (ideal fluid) equation in the functional space. The present formulation is a quantization scheme based on commutable variables, so that there appears no ambiguity associated with the ordering of operators, e.g., in the definition of Noether charges.

  5. A Study of Anatomical Variations of Osteomeatal Complex in Chronic Rhinosinusitis Patients-CT Findings

    PubMed Central

    Karadi, R.N.; Kumar, Saurabh

    2014-01-01

    Background: Chronic rhino sinusitis (CRS) is the most common disease for which consultation of otorhinolaryngologist is sought. The approach to patients with chronic rhino sinusitis is endoscopic surgery which aims at removing the obstruction of the main drainage pathway. The osteomeatal complex based essentially on the concept that such obstruction perpetuates the sinus disease. This in turn requires the surgeons to have detailed knowledge of the anatomy of the lateral nasal wall, paranasal sinuses and surrounding vital structures and of the large number of anatomical variants in the region. Aim: To study anatomical variations of osteomeatal complex in chronic sinusitis patients. Materials and Methods: Descriptive cross-sectional study design in which 54 consecutive cases of chronic rhino sinusitis patients attending the ENT outpatient department, who had chronic sinusitis for more than three months duration not responding to the medical line of treatment and who were willing to undergo Functional Endoscopic Sinus Surgery satisfying the inclusion criteria were studied. The results were expressed in percentage and proportions. Results: In our study it was observed that 53.7% of the chronic sinusitis cases had two or more anatomical variations and 33.3% of the cases had single anatomical variation. Deviated nasal septum was found to be the most common amongst the anatomical variations in chronic sinusitis cases in the present study which was followed by unilateral concha bullosa and paradoxically bent middle turbinate. Agger nasi cell and Haller cell were seen in one case each. Conclusion: Prevalence of multiple anatomical variations was more in our study in comparison to single anatomical variation. Deviated nasal septum was the most common anatomical variation encountered in our study followed by concha bullosa. PMID:25478374

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

    PubMed Central

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

    2013-01-01

    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

  7. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history.

    PubMed Central

    Yuhki, N; O'Brien, S J

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. We present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations. Images PMID:1967831

  8. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history

    SciTech Connect

    Yuhki, Naoya; O'Brien, S.J. )

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. The authors present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations.

  9. Substantial variation in the acceptance of medically complex live kidney donors across US renal transplant centers

    PubMed Central

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

    2008-01-01

    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. PMID:18727695

  10. Kohn-Sham Theory for Ground-State Ensembles

    SciTech Connect

    Ullrich, C. A.; Kohn, W.

    2001-08-27

    An electron density distribution n(r) which can be represented by that of a single-determinant ground state of noninteracting electrons in an external potential v(r) is called pure-state v -representable (P-VR). Most physical electronic systems are P-VR. Systems which require a weighted sum of several such determinants to represent their density are called ensemble v -representable (E-VR). This paper develops formal Kohn-Sham equations for E-VR physical systems, using the appropriate coupling constant integration. It also derives local density- and generalized gradient approximations, and conditions and corrections specific to ensembles.

  11. Asymptotic form of the Kohn-Sham correlation potential

    SciTech Connect

    Joubert, D. P.

    2007-07-15

    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)].

  12. Element orbitals for Kohn-Sham density functional theory

    SciTech Connect

    Lin, Lin; Ying, Lexing

    2012-05-08

    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 planewaves. 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 3D densely packed systems with a small number of basis functions per atom. The procedure is applicable to insulating and metallic systems.

  13. a new approach to Hohenberg-Kohn theorem

    NASA Astrophysics Data System (ADS)

    Lammert, Paul

    2015-03-01

    The Hohenberg-Kohn theorem is a cornerstone of electronic density functional theory, and yet in order to carry through its proof one must assume that ground state wavefunctions never vanish on a set of nonzero Lebesgue measure. This is a particularly unsatisfactory situation since DFT is supposed to avoid needing knowledge of the many-body wavefunction. I propose a new approach which puts conditions only on the density and potentials. This approach allows a proof that if the density is continuous and nowhere vanishing, then a representing potential in L2 +L? is unique up to an overall constant.

  14. [Tempo-spatial variation of non-point source pollutants in a complex landscape].

    PubMed

    Chen, Liding; Qiu, Jun; Zhang, Shurong; Fu, Bojie

    2003-05-01

    The occurrence of non-point source pollution, is not only related to its sources, landscape pattern, but also dependents on the factors such as soil erosion, rainfall, irrigation, surface and underground run-off. Thus non-point source pollution is characterized by in nature tempo-spatial variation. In this paper, the tempo-spatial variation of non-point source pollution due to nutrient salts in a complex landscape was studied by field water sampling and analysis. The results were as follow: 1. Spatial variability of all nutrient concentration in rainfall-deficit year was generally smaller than that in normal rainfall year with different level for different pollutants in a single period. 2. Spatial variability of solid particles in surface water was much marked than the other pollutants studied both in the rainfall-deficit year and in the normal rainfall year, while the smaller variation in different water periods of a year in the normal rainfall year. 3. Apparently, those areas with stable run-off had a small seasonal variation of non-point source pollution. However, large seasonal change occurred mainly in the upper reach of river where run-off changed seasonally, and/or where farmland dominated, as well as where point-source pollution occurred. PMID:12916209

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

    ERIC Educational Resources Information Center

    Luster, Tom; And Others

    1989-01-01

    Used data on 65 mother-infant dyads to test Kohn's hypothesis concerning the relation between values and parenting behavior. Findings support Kohn's hypothesis that parents who value self-direction would emphasize supportive function of parenting and parents who value conformity would emphasize their obligations to impose restraints. (Author/NB)

  16. An algorithm for inferring complex haplotypes in a region of copy-number variation.

    PubMed

    Kato, Mamoru; Nakamura, Yusuke; Tsunoda, Tatsuhiko

    2008-08-01

    Recent studies have extensively examined the large-scale genetic variants in the human genome known as copy-number variations (CNVs), and the universality of CNVs in normal individuals, along with their functional importance, has been increasingly recognized. However, the absence of a method to accurately infer alleles or haplotypes within a CNV region from high-throughput experimental data hampers the finer analyses of CNV properties and applications to disease-association studies. Here we developed an algorithm to infer complex haplotypes within a CNV region by using data obtained from high-throughput experimental platforms. We applied this algorithm to experimental data and estimated the population frequencies of haplotypes that can yield information on both sequences and numbers of DNA copies. These results suggested that the analysis of such complex haplotypes is essential for accurately detecting genetic differences within a CNV region between population groups. PMID:18639202

  17. Melanoma susceptibility as a complex trait: genetic variation controls all stages of tumor progression.

    PubMed

    Ferguson, B; Ram, R; Handoko, H Y; Mukhopadhyay, P; Muller, H K; Soyer, H P; Morahan, G; Walker, G J

    2015-05-28

    Susceptibility to most common cancers is likely to involve interaction between multiple low risk genetic variants. Although there has been great progress in identifying such variants, their effect on phenotype and the mechanisms by which they contribute to disease remain largely unknown. We have developed a mouse melanoma model harboring two mutant oncogenes implicated in human melanoma, CDK4(R24C) and NRAS(Q61K). In these mice, tumors arise from benign precursor lesions that are a recognized strong risk factor for this neoplasm in humans. To define molecular events involved in the pathway to melanoma, we have for the first time applied the Collaborative Cross (CC) to cancer research. The CC is a powerful resource designed to expedite discovery of genes for complex traits. We characterized melanoma genesis in more than 50 CC strains and observed tremendous variation in all traits, including nevus and melanoma age of onset and multiplicity, anatomical site predilection, time for conversion of nevi to melanoma and metastases. Intriguingly, neonatal ultraviolet radiation exposure exacerbated nevus and melanoma formation in most, but not all CC strain backgrounds, suggesting that genetic variation within the CC will help explain individual sensitivity to sun exposure, the major environmental skin carcinogen. As genetic variation brings about dramatic phenotypic diversity in a single mouse model, melanoma-related endophenotype comparisons provide us with information about mechanisms of carcinogenesis, such as whether melanoma incidence is dependent upon the density of pre-existing nevus cells. Mouse models have been used to examine the functional role of gene mutations in tumorigenesis. This work represents their next phase of development to study how biological variation greatly influences lesion onset and aggressiveness even in the setting of known somatic driver mutations. PMID:25088201

  18. Time-dependent Internal DFT formalism and Kohn-Sham scheme

    E-print Network

    J. Messud

    2009-11-05

    We generalize to the time-dependent case the stationary Internal DFT / Kohn-Sham formalism presented in Ref. [14]. We prove that, in the time-dependent case, the internal properties of a self-bound system (as an atomic nuclei) are all defined by the internal one-body density and the initial state. We set-up a time-dependent Internal Kohn-Sham scheme as a practical way to compute the internal density. The main difference with the traditional DFT / Kohn-Sham formalism is the inclusion of the center-of-mass correlations in the functional.

  19. Major histocompatibility complex class II genetic variation in forest musk deer (Moschus berezovskii) in China.

    PubMed

    Yao, Gang; Zhu, Ying; Wan, Qiu-Hong; Fang, Sheng-Guo

    2015-10-01

    The major histocompatibility complex (MHC) plays an important role in the immune system of vertebrates. We used the second exon of four MHC class II genes (DRA, DQA1, DQA2 and DRB3) to assess the overall MHC variation in forest musk deer (Moschus berezovskii). We also compared the MHC variation in captive and wild populations. We observed 22 alleles at four loci (four at DRA, four at DQA1, four at DQA2 and 10 at DRB3), 15 of which were newly identified alleles. Results suggest that forest musk deer maintain relatively high MHC variation, which may result from balancing selection. Moreover, considerable diversity was observed at the DRA locus. We found a high frequency of Mobe-DRA*02, Mobe-DQA1*01 and Mobe-DQA2*05 alleles, which may be important for pathogen resistance. A Ewens-Watterson test showed that the DRB3 locus in the wild population had experienced recent balancing selection. We detected a small divergence at the DRA locus, suggesting the effect of weak positive selection on the DRA gene. Alternatively, this locus may be young and not yet adapted a wide spectrum of alleles for pathogen resistance. The significant heterozygosity deficit observed at the DQA1 and DRB3 loci in the captive population and at all four loci in the wild population may be the result of a population bottleneck. Additionally, MHC genetic diversity was higher in the wild population than in the captive, suggesting that the wild population may have the ability to respond to a wider range of pathogens. PMID:26370614

  20. The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses.

    PubMed

    Caballero, Armando; Tenesa, Albert; Keightley, Peter D

    2015-12-01

    We use computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. We model a large population subject to mutation, recombination, selection, and drift, assuming a pleiotropic model of mutations sampled from a bivariate distribution of effects of mutations on a quantitative trait and fitness. The pleiotropic model investigated, in contrast to previous models, implies that common mutations of large effect are responsible for most of the genetic variation for quantitative traits, except when the trait is fitness itself. We show that GWAS applied to the full sequence increases the number of QTL detected by as much as 50% compared to the number found with SNP chips but only modestly increases the amount of additive genetic variance explained. Even with full sequence data, the total amount of additive variance explained is generally below 50%. Using RHM on the full sequence data, a slightly larger number of QTL are detected than by GWAS if the same probability threshold is assumed, but these QTL explain a slightly smaller amount of genetic variance. Our results also suggest that most of the missing heritability is due to the inability to detect variants of moderate effect (?0.03-0.3 phenotypic SDs) segregating at substantial frequencies. Very rare variants, which are more difficult to detect by GWAS, are expected to contribute little genetic variation, so their eventual detection is less relevant for resolving the missing heritability problem. PMID:26482794

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

    PubMed Central

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

    2014-01-01

    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. PMID:25071729

  2. VES: VIRTUAL ECHOCARDIOGRAPHY SYSTEM Sascha Kohn, Rolf H. van Lengen, Gerd Reis, Martin Bertram, Hans Hagen

    E-print Network

    Hering-Bertram, Martin

    VES: VIRTUAL ECHOCARDIOGRAPHY SYSTEM Sascha K¨ohn, Rolf H. van Lengen, Gerd Reis, Martin Bertram Kaiserslautern, Germany Sascha.Koehn, Rolf-Hendrik.van Lengen, Gerd.Reis, Martin.Hering-Bertram, Hans.Hagen @dfki

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

    E-print Network

    Kowalczyk, Timothy Daniel

    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 ...

  4. Localising Loci underlying Complex Trait Variation Using Regional Genomic Relationship Mapping

    PubMed Central

    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

    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. PMID:23077511

  5. Sexual selection explains more functional variation in the mammalian major histocompatibility complex than parasitism

    PubMed Central

    Winternitz, J. C.; Minchey, S. G.; Garamszegi, L. Z.; Huang, S.; Stephens, P. R.; Altizer, S.

    2013-01-01

    Understanding drivers of genetic diversity at the major histocompatibility complex (MHC) is vitally important for predicting how vertebrate immune defence might respond to future selection pressures and for preserving immunogenetic diversity in declining populations. Parasite-mediated selection is believed to be the major selective force generating MHC polymorphism, and while MHC-based mating preferences also exist for multiple species including humans, the general importance of mate choice is debated. To investigate the contributions of parasitism and sexual selection in explaining among-species variation in MHC diversity, we applied comparative methods and meta-analysis across 112 mammal species, including carnivores, bats, primates, rodents and ungulates. We tested whether MHC diversity increased with parasite richness and relative testes size (as an indicator of the potential for mate choice), while controlling for phylogenetic autocorrelation, neutral mutation rate and confounding ecological variables. We found that MHC nucleotide diversity increased with parasite richness for bats and ungulates but decreased with parasite richness for carnivores. By contrast, nucleotide diversity increased with relative testes size for all taxa. This study provides support for both parasite-mediated and sexual selection in shaping functional MHC polymorphism across mammals, and importantly, suggests that sexual selection could have a more general role than previously thought. PMID:23966643

  6. The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

    PubMed

    Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

    2015-01-01

    Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches. PMID:25658107

  7. Capturing variations in inundation with satellite remote sensing in a morphologically complex, large lake

    NASA Astrophysics Data System (ADS)

    Wu, Guiping; Liu, Yuanbo

    2015-04-01

    Poyang Lake is the largest freshwater lake in China, with high morphological complexity from south to north. In recent years, the lake has experienced expansion and shrinkage processes over both short- and long-term scales, resulting in significant hydrological, ecological and economic problems. Exactly how and how rapidly the processes of spatial change have occurred in the lake during the expansion and shrinkage periods is unknown. Such knowledge is of great importance for policymakers as it may help with flood/drought prevention, land use planning and lake ecological conservation. In this study, we investigated the spatial-temporal distribution and changing processes of inundation in Poyang Lake based on Moderate Resolution Imaging Spectroradiometer (MODIS) Level-1B data from 2000 to 2011. A defined water variation rate (WVR) and inundation frequency (IF) indicator revealed the water surface submersion and exposure processes of lake expansion and shrinkage in different zones which were divided according to the lake's hydrological and topographic features. Regional differences and significant seasonality variability were found in the annual and monthly mean IF. The monthly mean IF increased slowly from north to south during January-August but decreased quickly from south to north during September-December. During the lake expansion period, the lake-type water body zone (Zone II) had the fastest expansion rate, with a mean monthly WVR value of 34.47% in February-March, and was followed by the channel-type water body zone (Zone I) in March-May (22.47%). However, during the lake shrinkage period, rapid shrinkage first appeared around the alluvial delta zones in August-October. The sequence of lake surface shrinkage from August to December is exactly opposite to that of lake expansion from February to July. These complex inundation characteristics and changing process were driven by the high temporal variability of the river flows, the morphological diversity of the benthic landforms and the patterns of water movement. These results provide a foundation for basic hydrological and ecological studies and are valuable for the conservation and management of water resources in Poyang Lake.

  8. Latitudinal Variation of a Defensive Symbiosis in the Bugula neritina (Bryozoa) Sibling Species Complex

    PubMed Central

    Linneman, Jonathan; Paulus, Darcy; Lim-Fong, Grace; Lopanik, Nicole B.

    2014-01-01

    Mutualistic relationships are beneficial for both partners and are often studied within a single environment. However, when the range of the partners is large, geographical differences in selective pressure may shift the relationship outcome from positive to negative. The marine bryozoan Bugula neritina is a colonial invertebrate common in temperate waters worldwide. It is the source of bioactive polyketide metabolites, the bryostatins. Evidence suggests that an uncultured vertically transmitted symbiont, “Candidatus Endobugula sertula”, hosted by B. neritina produces the bryostatins, which protect the vulnerable larvae from predation. Studies of B. neritina along the North American Atlantic coast revealed a complex of two morphologically similar sibling species separated by an apparent biogeographic barrier: the Type S sibling species was found below Cape Hatteras, North Carolina, while Type N was found above. Interestingly, the Type N colonies lack “Ca. Endobugula sertula” and, subsequently, defensive bryostatins; their documented northern distribution was consistent with traditional biogeographical paradigms of latitudinal variation in predation pressure. Upon further sampling of B. neritina populations, we found that both host types occur in wider distribution, with Type N colonies living south of Cape Hatteras, and Type S to the north. Distribution of the symbiont, however, was not restricted to Type S hosts. Genetic and microscopic evidence demonstrates the presence of the symbiont in some Type N colonies, and larvae from these colonies are endowed with defensive bryostatins and contain “Ca. Endobugula sertula”. Molecular analysis of the symbiont from Type N colonies suggests an evolutionarily recent acquisition, which is remarkable for a symbiont thought to be transmitted only vertically. Furthermore, most Type S colonies found at higher latitudes lack the symbiont, suggesting that this host-symbiont relationship is more flexible than previously thought. Our data suggest that the symbiont, but not the host, is restricted by biogeographical boundaries. PMID:25275632

  9. Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

    PubMed Central

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

    2014-01-01

    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

  10. Latitudinal variation of a defensive symbiosis in the Bugula neritina (Bryozoa) sibling species complex.

    PubMed

    Linneman, Jonathan; Paulus, Darcy; Lim-Fong, Grace; Lopanik, Nicole B

    2014-01-01

    Mutualistic relationships are beneficial for both partners and are often studied within a single environment. However, when the range of the partners is large, geographical differences in selective pressure may shift the relationship outcome from positive to negative. The marine bryozoan Bugula neritina is a colonial invertebrate common in temperate waters worldwide. It is the source of bioactive polyketide metabolites, the bryostatins. Evidence suggests that an uncultured vertically transmitted symbiont, "Candidatus Endobugula sertula", hosted by B. neritina produces the bryostatins, which protect the vulnerable larvae from predation. Studies of B. neritina along the North American Atlantic coast revealed a complex of two morphologically similar sibling species separated by an apparent biogeographic barrier: the Type S sibling species was found below Cape Hatteras, North Carolina, while Type N was found above. Interestingly, the Type N colonies lack "Ca. Endobugula sertula" and, subsequently, defensive bryostatins; their documented northern distribution was consistent with traditional biogeographical paradigms of latitudinal variation in predation pressure. Upon further sampling of B. neritina populations, we found that both host types occur in wider distribution, with Type N colonies living south of Cape Hatteras, and Type S to the north. Distribution of the symbiont, however, was not restricted to Type S hosts. Genetic and microscopic evidence demonstrates the presence of the symbiont in some Type N colonies, and larvae from these colonies are endowed with defensive bryostatins and contain "Ca. Endobugula sertula". Molecular analysis of the symbiont from Type N colonies suggests an evolutionarily recent acquisition, which is remarkable for a symbiont thought to be transmitted only vertically. Furthermore, most Type S colonies found at higher latitudes lack the symbiont, suggesting that this host-symbiont relationship is more flexible than previously thought. Our data suggest that the symbiont, but not the host, is restricted by biogeographical boundaries. PMID:25275632

  11. Vesicularity variation to pyroclasts from silicic eruptions at Laguna del Maule volcanic complex, Chile

    NASA Astrophysics Data System (ADS)

    Wright, H. M. N.; Fierstein, J.; Amigo, A.; Miranda, J.

    2014-12-01

    Crystal-poor rhyodacitic to rhyolitic volcanic eruptions at Laguna del Maule volcanic complex, Chile have produced an astonishing range of textural variation to pyroclasts. Here, we focus on eruptive deposits from two Quaternary eruptions from vents on the northwestern side of the Laguna del Maule basin: the rhyolite of Loma de Los Espejos and the rhyodacite of Laguna Sin Puerto. Clasts in the pyroclastic fall and pyroclastic flow deposits from the rhyolite of Loma de Los Espejos range from dense, non-vesicular (obsidian) to highly vesicular, frothy (coarsely vesicular reticulite); where vesicularity varies from <1% to >90%. Bulk compositions range from 75.6-76.7 wt.% SiO2. The highest vesicularity clasts are found in early fall deposits and widely dispersed pyroclastic flow deposits; the frothy carapace to lava flows is similarly highly vesicular. Pyroclastic deposits also contain tube pumice, and macroscopically folded, finely vesicular, breadcrusted, and heterogeneously vesiculated textures. We speculate that preservation of the highest vesicularities requires relatively low decompression rates or open system degassing such that relaxation times were sufficient to allow extensive vesiculation. Such an inference is in apparent contradiction to documentation of Plinian dispersal to the eruption. Clasts in the pyroclastic fall deposit of the rhyodacite (68-72 wt.% SiO2) of Laguna Sin Puerto are finely vesicular, with vesicularity modes at ~50% and ~68% corresponding to gray and white pumice colors, respectively. Some clasts are banded in color (and vesicularity). All clasts were fragmented into highly angular particles, with subplanar to slightly concave exterior surfaces (average Wadell Roundness of clast margins between 0.32 and 0.39), indicating brittle fragmentation. In contrast to Loma de Los Espejos, high bubble number densities to Laguna Sin Puerto rhyodacite imply high decompression rates.

  12. A global conformance quality model. A new strategic tool for minimizing defects caused by variation, error, and complexity

    SciTech Connect

    Hinckley, C.M.

    1994-01-01

    The performance of Japanese products in the marketplace points to the dominant role of quality in product competition. Our focus is motivated by the tremendous pressure to improve conformance quality by reducing defects to previously unimaginable limits in the range of 1 to 10 parts per million. Toward this end, we have developed a new model of conformance quality that addresses each of the three principle defect sources: (1) Variation, (2) Human Error, and (3) Complexity. Although the role of variation in conformance quality is well documented, errors occur so infrequently that their significance is not well known. We have shown that statistical methods are not useful in characterizing and controlling errors, the most common source of defects. Excessive complexity is also a root source of defects, since it increases errors and variation defects. A missing link in the defining a global model has been the lack of a sound correlation between complexity and defects. We have used Design for Assembly (DFA) methods to quantify assembly complexity and have shown that assembly times can be described in terms of the Pareto distribution in a clear exception to the Central Limit Theorem. Within individual companies we have found defects to be highly correlated with DFA measures of complexity in broad studies covering tens of millions of assembly operations. Applying the global concepts, we predicted that Motorola`s Six Sigma method would only reduce defects by roughly a factor of two rather than orders of magnitude, a prediction confirmed by Motorola`s data. We have also shown that the potential defects rates of product concepts can be compared in the earliest stages of development. The global Conformance Quality Model has demonstrated that the best strategy for improvement depends upon the quality control strengths and weaknesses.

  13. The transient variation in the complexes of the low-latitude ionosphere within the equatorial ionization anomaly region of Nigeria

    NASA Astrophysics Data System (ADS)

    Rabiu, A. B.; Ogunsua, B. O.; Fuwape, I. A.; Laoye, J. A.

    2015-09-01

    The quest to find an index for proper characterization and description of the dynamical response of the ionosphere to external influences and its various internal irregularities has led to the study of the day-to-day variations of the chaoticity and dynamical complexity of the ionosphere. This study was conducted using Global Positioning System (GPS) total electron content (TEC) time series, measured in the year 2011, from five GPS receiver stations in Nigeria, which lies within the equatorial ionization anomaly region. The non-linear aspects of the TEC time series were obtained by detrending the data. The detrended TEC time series were subjected to various analyses to obtain the phase space reconstruction and to compute the chaotic quantifiers, which are Lyapunov exponents LE, correlation dimension, and Tsallis entropy, for the study of dynamical complexity. Considering all the days of the year, the daily/transient variations show no definite pattern for each month, but day-to-day values of Lyapunov exponents for the entire year show a wavelike semiannual variation pattern with lower values around March, April, September and October. This can be seen from the correlation dimension with values between 2.7 and 3.2, with lower values occurring mostly during storm periods, demonstrating a phase transition from higher dimension during the quiet periods to lower dimension during storms for most of the stations. The values of Tsallis entropy show a similar variation pattern to that of the Lyapunov exponent, with both quantifiers correlating within the range of 0.79 to 0.82. These results show that both quantifiers can be further used together as indices in the study of the variations of the dynamical complexity of the ionosphere. The presence of chaos and high variations in the dynamical complexity, even in quiet periods in the ionosphere, may be due to the internal dynamics and inherent irregularities of the ionosphere which exhibit non-linear properties. However, this inherent dynamics may be complicated by external factors like geomagnetic storms. This may be the main reason for the drop in the values of the Lyapunov exponent and Tsallis entropy during storms. The dynamical behaviour of the ionosphere throughout the year, as described by these quantifiers, was discussed in this work.

  14. The filial piety complex: variations on the Oedipus theme in Chinese literature and culture.

    PubMed

    Gu, Ming Dong

    2006-01-01

    The Oedipus complex is central to Western tradition, but not to Chinese culture. Occurrence of oedipal themes in Chinese literature is almost negligible. This phenomenon seems to support a contra-Freud claim: that a theory of European origin, the Oedipus complex, is not universal to human experience in non-Western cultures. However, this article suggests that powerful moral repression may cause the Oedipus complex to undergo structural transformations in some cultures. Through studying a sample of Chinese literary and film representations, the author argues that the Oedipus complex in Chinese culture has been transformed into a filial piety complex. Some conceptual issues are considered from a cross-cultural perspective. PMID:16482964

  15. Paradoxical Pathways: An Ethnographic Extension of Kohn's Findings on Class and Childrearing

    ERIC Educational Resources Information Center

    Weininger, Elliot B.; Lareau, Annette

    2009-01-01

    Stratification is a central issue in family research, yet relatively few studies highlight its impact on family processes. Drawing on in-depth interviews (N = 137) and observational data (N = 12), we extend Melvin Kohn's research on childrearing values by examining how parental commitments to self-direction and conformity are enacted in daily…

  16. Cloaking via change of variables for the Helmholtz ROBERT V. KOHN

    E-print Network

    Onofrei, Daniel

    Cloaking via change of variables for the Helmholtz equation ROBERT V. KOHN Courant Institute, NYU approach to cloaking uses a singular change of coordi- nates, which blows up a point to the region being cloaked. This paper examines a natural regularization, obtained by (i) blowing up a ball of radius rather

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

    ERIC Educational Resources Information Center

    Luster, Tom; Rhoades, Kelly

    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…

  18. 31 Kohn-Sham Master Equation Approach to Transport Through Single Molecules

    E-print Network

    Burke, Kieron

    31 Kohn-Sham Master Equation Approach to Transport Through Single Molecules R. Gebauer, K. Burke. Such junctions are expected to be at the basis of future molecular-based electronic devices. But apart from in general. The theoretical modeling of molecular transport, however, is a very chal- lenging task: On one

  19. Variation of large elastodynamic earthquakes on complex fault systems Bruce E. Shaw

    E-print Network

    Shaw, Bruce E.

    of segments and a decrease in variation for the longest segments. INDEX TERMS: 7209 Seismology: Earthquake dynamics and mechanics; 7221 Seismology: Paleoseismology; 7223 Seismology: Seismic hazard assessment and prediction; 7260 Seismology: Theory and modeling; 8010 Structural Geology: Fractures and faults. Citation

  20. A Longitudinal Study of Complexity, Accuracy and Fluency Variation in Second Language Development

    ERIC Educational Resources Information Center

    Ferraris, Stefania

    2012-01-01

    This chapter presents the results of a study on interlanguage variation. The production of four L2 learners of Italian, tested four times at yearly intervals while engaged in four oral tasks, is compared to that of two native speakers, and analysed with quantitative CAF measures. Thus, time, task type, nativeness, as well as group vs. individual…

  1. Genetic variation in isolates of the Fusarium incarnatum-equiseti species complex recovered from cereals

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Fusarium incarnatum-equiseti species complex (FIESC) includes mycotoxigenic species associated with several diseases of cereals and other crops. These species are considered moderately aggressive and are reported to produce multiple mycotoxins, including beauvericin, zearalenone, equisetin, fusa...

  2. Syntheses of Variations of Stereogenic-at-Metal Imido Alkylidene Complexes of Molybdenum

    E-print Network

    Marinescu, Smaranda C.

    In this paper we describe the syntheses of several new stereogenic-at-metal imido alkylidene complexes of molybdenum, Mo(NR)(CHR?)(X)(Y), many of which had to be prepared through selective nucleophilic displacement reactions ...

  3. Landscape complexity and soil moisture variation in south Georgia, USA, for remote sensing applications

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

    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.

  4. Landscape complexity and soil moisture variation in south Georgia, USA, for remote sensing applications

    USGS Publications Warehouse

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

    2008-01-01

    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.

  5. Chromatic variation of the abundance of PSII complexes observed with the red alga Prophyridium cruentum.

    PubMed

    Fujita, Y

    2001-11-01

    Chromatic regulation of photosystem stoichiometry in cyanophytes, green algae and probably vascular plants is achieved by regulation of the abundance of PSI in response to thylakoid electron transport state at least under our experimental conditions [cf. Fujita (1997) Photosyn. Res. 53: 83]. However, variation of not only PSI but also PSII, in reverse of each other, is characteristic of the stoichiometry regulation in red algae and some of marine cyanophytes. Our previous study with the red alga Porphyridium cruentum has revealed that PSII is inactivated by 50% upon a light shift from the light absorbed by Chl a, PSI light, to that mainly absorbed by phycobilisomes (PBS), PSII light [Fujita (1999) Plant Cell Physiol. 40: 924]. To evaluate the contribution of the photoinactivation to the chromatic variation of PSII, variation of the abundance of PSI, PSII and PBS, together with the fluorescence parameter and the activity of PSII, was followed after a light shift from PSI light to PSII light. Upon a light shift to PSII light, PSII, determined as Cyt b(559) per PBS, decreased rapidly, following the photoinactivation, down to the level a half of that before the light shift, and remained constant. Since the increase in PBS was not significant during this period, a rapid decrease of PSII/PBS led us to tentatively conclude that the degradation of PSII is a main cause for variation of the abundance of PSII. Photoinactivation of PSII, and also decrease in Cyt b(559), was accelerated, but only slightly, by the addition of chloramphenicol (CAP) at a moderate concentration while CAP at the same concentration significantly suppressed the increment of PSI determined as P700. A selective effect of CAP supports the above conclusion. PMID:11726709

  6. Read clouds uncover variation in complex regions of the human genome.

    PubMed

    Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E; West, Robert; Sidow, Arend; Batzoglou, Serafim

    2015-10-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies. PMID:26286554

  7. Read clouds uncover variation in complex regions of the human genome

    PubMed Central

    Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E.; West, Robert; Sidow, Arend; Batzoglou, Serafim

    2015-01-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies. PMID:26286554

  8. Chemical data and variation diagrams of igneous rocks from the Timber Mountain-Oasis Valley Caldera Complex, southern Nevada

    USGS Publications Warehouse

    Quinlivan, W.D.; Byers, F.M.

    1977-01-01

    Silica variation diagrams presented here are based on 162 chemical analyses of tuffs, lavas, and intrusives, representative of volcanic centers of the Timber Mountain-Oasis Valley caldera complex and cogenetic rocks of the Silent Canyon ca1dera. Most of the volcanic units sampled are shown on the U.S. Geological Survey geologic map of the Timber Mountain caldera area (I-891) and are described in U.S. Geological Survey Professional Paper 919. Early effusives of the complex, although slightly altered, are probably chemically, and petrographically, more like the calc-alkalic Fraction Tuff (Miocene) of the northern Nellis Air Force Base Bombing and Gunnery Range to the north, whereas effusives of later Miocene age, such as the Paintbrush and Timber Mountain Tuffs, are alkali-calcic.

  9. Variations of trends of indicators describing complex systems: change of scaling precursory to extreme events.

    PubMed

    Keilis-Borok, V I; Soloviev, A A

    2010-09-01

    Socioeconomic and natural complex systems persistently generate extreme events also known as disasters, crises, or critical transitions. Here we analyze patterns of background activity preceding extreme events in four complex systems: economic recessions, surges in homicides in a megacity, magnetic storms, and strong earthquakes. We use as a starting point the indicators describing the system's behavior and identify changes in an indicator's trend. Those changes constitute our background events (BEs). We demonstrate a premonitory pattern common to all four systems considered: relatively large magnitude BEs become more frequent before extreme event. A premonitory change of scaling has been found in various models and observations. Here we demonstrate this change in scaling of uniformly defined BEs in four real complex systems, their enormous differences notwithstanding. PMID:20887044

  10. Fractal based complexity measure and variation in force during sustained isometric muscle contraction: effect of aging.

    PubMed

    Arjunan, Sridhar P; Kumar, Dinesh K; Bastos, Teodiano

    2012-01-01

    This study has investigated the effect of age on the fractal based complexity measure of muscle activity and variance in the force of isometric muscle contraction. Surface electromyogram (sEMG) and force of muscle contraction were recorded from 40 healthy subjects categorized into: Group 1: Young - age range 20-30; 10 Males and 10 Females, Group 2: Old - age range 55-70; 10 Males and 10 Females during isometric exercise at Maximum Voluntary contraction (MVC). The results show that there is a reduction in the complexity of surface electromyogram (sEMG) associated with aging. The results demonstrate that there is an increase in the coefficient of variance (CoV) of the force of muscle contraction and a decrease in complexity of sEMG for the Old age group when compared with the Young age group. PMID:23366677

  11. Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes.

    PubMed

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

    2010-06-12

    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. PMID:20439280

  12. Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes

    PubMed Central

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

    2010-01-01

    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. PMID:20439280

  13. Genetic variation in a tropical tree species influences the associated epiphytic plant and invertebrate communities in a complex forest ecosystem

    PubMed Central

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

    2011-01-01

    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

  14. The transient variation of the complexes of the low latitude ionosphere within the equatorial ionization anomaly region of Nigeria

    NASA Astrophysics Data System (ADS)

    Rabiu, A. B.; Ogunsua, B. O.; Fuwape, I. A.; Laoye, J. A.

    2014-12-01

    The quest to find an index for proper characterization and description of the dynamical response of the ionosphere to external influences and its various internal irregularities has led to the study of the day to day variations of the chaoticity and dynamical complexity of the ionosphere. This study was conducted using Global Positioning System (GPS) Total Electron Content (TEC) time series, measured in the year 2011, from 5 GPS receiver stations in Nigeria which lies within the Equatorial Ionization Anomaly region. The nonlinear aspect of the TEC time series were obtained by detrending the data. The detrended TEC time series were subjected to various analyses for phase space reconstruction and to obtain the values of chaotic quantifiers which are Lyapunov exponents LE, correlation dimension, and Tsallis entropy for the study of dynamical complexity. The results show positive Lyapunov exponents for all days which indicate chaoticity of the ionosphere with no definite pattern for both quiet and disturbed days. However values of LE were lower for the storm period compared to its nearest relative quiet periods for all the stations. Considering all the days of the year the daily/transient variations show no definite pattern for each month but day to day values of Lyapunov exponent for the entire year show a wavelike semiannual variation pattern with lower values around March, April, September and October, a change in pattern which demonstrates the self-organized critical phenomenon of the system. This can be seen from the correlation dimension with values between 2.7 and 3.2 with lower values occurring mostly during storm periods demonstrating a phase transition from higher dimension during the quiet periods to lower dimension during storms for most of the stations. The values of Tsallis entropy show similar variation pattern with that of Lyapunov exponent with a lot of agreement in their comparison, with all computed values of Lyapunov exponent correlating with values of Tsallis entropy within the range of 0.79 to 0.82. These results show that Lyapunov quantifiers can be used together as indices in the study of the variations of the dynamical complexity of the ionosphere. The presence of chaos and high variations in the dynamical complexity, even at quiet periods in the ionosphere may be due to the internal dynamics and inherent irregularities of the ionosphere which exhibit non-linear properties. However, this inherent dynamics may be complicated by external factors like geomagnetic storms. This may be the main reason for the drop in the values of Lyapunov exponent and Tsallis entropy during storms. The results also show a strong interplay between determinism and stochasticity, as the ionosphere shows its response to changes in solar activities and in its internal dynamics. The dynamical behavior of the ionosphere throughout the year as described by these quantifiers, were discussed in this work.

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

    PubMed Central

    Green, Tim; Rosen, Stuart

    2013-01-01

    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. PMID:24116424

  16. Building blocks of a fish head: Developmental and variational modularity in a complex system.

    PubMed

    Lehoux, Caroline; Cloutier, Richard

    2015-11-01

    Evolution of the vertebrate skull is developmentally constrained by the interactions among its anatomical systems, such as the dermatocranium and the sensory system. The interaction between the dermal bones and lateral line canals has been debated for decades but their morphological integration has never been tested. An ontogenetic series of 97 juvenile and adult Amia calva (Actinopterygii) was used to describe the patterning and modularity of sensory lateral line canals and their integration with supporting cranial bones. Developmental modules were tested for the otic canal and supratemporal commissure by computing correlations in the branching sequence of groups of pores. Landmarks were digitized on 25 specimens to test a priori hypotheses of variational and developmental modularity at the level of canals and dermal bones. Branching sequence suggests a specific patterning supported by significant positive correlations in the sequence of appearance of branches between bilateral sides. Differences in patterning between the otic canal and the supratemporal commissure and tests of modularity with geometric morphometrics suggest that both canals form distinct modules. The integration between bones and canals was insufficient to detect a module. However, both components were not independent. Groups of pores tended to disappear without affecting other groups of pores suggesting that they are quasi-independent units acting as modules. This study provides evidence of a hierarchical organization for the modular sensory system that could explain variation of pattern of canals among species and their association with dermal bones. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 614-628, 2015. © 2015 Wiley Periodicals, Inc. PMID:26227536

  17. How to tell when a model Kohn-Sham potential is not a functional derivative

    NASA Astrophysics Data System (ADS)

    Gaiduk, Alex P.; Staroverov, Viktor N.

    2009-07-01

    A model exchange-correlation potential constructed with Kohn-Sham orbitals should be a functional derivative of some density functional. Several necessary conditions for a functional derivative are discussed including: (i) minimization of the total-energy expression by the ground-state solution of the Kohn-Sham equations, (ii) path independence of the van Leeuwen-Baerends line integral, and (iii) net zero force and zero torque on the density. A number of existing model potentials are checked for these properties and it is found that most of the potentials tested are not functional derivatives. Physical properties obtained from potentials that have no parent functionals are ambiguous and, therefore, should be interpreted with caution.

  18. Determination of Kohn-Sham effective potentials from electron densities using the differential virial theorem.

    PubMed

    Ryabinkin, Ilya G; Staroverov, Viktor N

    2012-10-28

    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

  19. Observation of a Kohn anomaly in the surface-phonon dispersion curves of Pt(111)

    NASA Astrophysics Data System (ADS)

    Harten, U.; Toennies, J. Peter; Wöll, Christof; Zhang, G.

    1985-11-01

    Surface-phonon dispersion curves have been measured by He-atom inelastic scattering for Pt(111) along the <11¯0> and <112¯> azimuths with greatly reduced scatter compared to earlier work. Along the <11¯0> direction the results reveal a number of anomalous kinks in the Rayleigh-mode dispersion curve. Comparison with the corresponding anomaly in the bulk suggests that the effect is due to a two-dimensional surface Kohn anomaly.

  20. Assessing spatial, temporal, and analytical variation of groundwater chemistry in a large nuclear complex, USA.

    PubMed

    Chou, Charissa J

    2006-08-01

    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

  1. Variation of complex permittivity of soils with moisture content using VNA

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    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.

  2. Complex offspring size effects: variations across life stages and between species

    PubMed Central

    Sun, Zhao; Hamel, Jean-François; Parrish, Christopher C; Mercier, Annie

    2015-01-01

    Classical optimality models of offspring size and number assume a monotonically increasing relationship between offspring size and performance. In aquatic organisms with complex life cycles, the size–performance function is particularly hard to grasp because measures of performance are varied and their relationships with size may not be consistent throughout early ontogeny. Here, we examine size effects in premetamorphic (larval) and postmetamorphic (juvenile) stages of brooding marine animals and show that they vary contextually in strength and direction during ontogeny and among species. Larger offspring of the sea anemone Urticina felina generally outperformed small siblings at the larval stage (i.e., greater settlement and survival rates under suboptimal conditions). However, results differed when analyses were conducted at the intrabrood versus across-brood levels, suggesting that the relationship between larval size and performance is mediated by parentage. At the juvenile stage (15 months), small offspring were less susceptible than large ones to predation by subadult nudibranchs and both sizes performed similarly when facing adult nudibranchs. In a sympatric species with a different life history (Aulactinia stella), all juveniles suffered similar predation rates by subadult nudibranchs, but smaller juveniles performed better (lower mortalities) when facing adult nudibranchs. Size differences in premetamorphic performance of U. felina were linked to total lipid contents of larvae, whereas size-specific predation of juvenile stages followed the general predictions of the optimal foraging strategy. These findings emphasize the challenge in gathering empirical support for a positive monotonic size–performance function in taxa that exhibit complex life cycles, which are dominant in the sea. PMID:25798228

  3. Complex offspring size effects: variations across life stages and between species.

    PubMed

    Sun, Zhao; Hamel, Jean-François; Parrish, Christopher C; Mercier, Annie

    2015-03-01

    Classical optimality models of offspring size and number assume a monotonically increasing relationship between offspring size and performance. In aquatic organisms with complex life cycles, the size-performance function is particularly hard to grasp because measures of performance are varied and their relationships with size may not be consistent throughout early ontogeny. Here, we examine size effects in premetamorphic (larval) and postmetamorphic (juvenile) stages of brooding marine animals and show that they vary contextually in strength and direction during ontogeny and among species. Larger offspring of the sea anemone Urticina felina generally outperformed small siblings at the larval stage (i.e., greater settlement and survival rates under suboptimal conditions). However, results differed when analyses were conducted at the intrabrood versus across-brood levels, suggesting that the relationship between larval size and performance is mediated by parentage. At the juvenile stage (15 months), small offspring were less susceptible than large ones to predation by subadult nudibranchs and both sizes performed similarly when facing adult nudibranchs. In a sympatric species with a different life history (Aulactinia stella), all juveniles suffered similar predation rates by subadult nudibranchs, but smaller juveniles performed better (lower mortalities) when facing adult nudibranchs. Size differences in premetamorphic performance of U. felina were linked to total lipid contents of larvae, whereas size-specific predation of juvenile stages followed the general predictions of the optimal foraging strategy. These findings emphasize the challenge in gathering empirical support for a positive monotonic size-performance function in taxa that exhibit complex life cycles, which are dominant in the sea. PMID:25798228

  4. A spectral scheme for Kohn-Sham density functional theory of clusters

    NASA Astrophysics Data System (ADS)

    Banerjee, Amartya S.; Elliott, Ryan S.; James, Richard D.

    2015-04-01

    Starting from the observation that one of the most successful methods for solving the Kohn-Sham equations for periodic systems - the plane-wave method - is a spectral method based on eigenfunction expansion, we formulate a spectral method designed towards solving the Kohn-Sham equations for clusters. This allows for efficient calculation of the electronic structure of clusters (and molecules) with high accuracy and systematic convergence properties without the need for any artificial periodicity. The basis functions in this method form a complete orthonormal set and are expressible in terms of spherical harmonics and spherical Bessel functions. Computation of the occupied eigenstates of the discretized Kohn-Sham Hamiltonian is carried out using a combination of preconditioned block eigensolvers and Chebyshev polynomial filter accelerated subspace iterations. Several algorithmic and computational aspects of the method, including computation of the electrostatics terms and parallelization are discussed. We have implemented these methods and algorithms into an efficient and reliable package called ClusterES (Cluster Electronic Structure). A variety of benchmark calculations employing local and non-local pseudopotentials are carried out using our package and the results are compared to the literature. Convergence properties of the basis set are discussed through numerical examples. Computations involving large systems that contain thousands of electrons are demonstrated to highlight the efficacy of our methodology. The use of our method to study clusters with arbitrary point group symmetries is briefly discussed.

  5. Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids.

    PubMed

    Eisenberg, Bob; Hyon, Yunkyong; Liu, Chun

    2010-09-14

    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

  6. Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids

    PubMed Central

    Eisenberg, Bob; Hyon, YunKyong; Liu, Chun

    2010-01-01

    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

  7. Isozyme Variation among Biological Species in the Gibberella fujikuroi Species Complex (Fusarium Section Liseola)

    PubMed Central

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

    1996-01-01

    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. PMID:16535423

  8. Saturation sampling for spatial variation in multiple air pollutants across an inversion-prone metropolitan area of complex terrain

    PubMed Central

    2014-01-01

    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. PMID:24735818

  9. Spatial variation and low diversity in the major histocompatibility complex in walrus (Odobenus rosmarus)

    USGS Publications Warehouse

    Sonsthagen, Sarah A.; Fales, Krystal; Jay, Chadwick V.; Sage, George K.; Talbot, Sandra L.

    2014-01-01

    Increased global temperature and associated changes to Arctic habitats will likely result in the northward advance of species, including an influx of pathogens novel to the Arctic. How species respond to these immunological challenges will depend in part on the adaptive potential of their immune response system. We compared levels of genetic diversity at a gene associated with adaptive immune response [Class II major histocompatibility complex (MHC), DQB exon 2] between populations of walrus (Odobenus rosmarus), a sea ice-dependent Arctic species. Walrus was represented by only five MHC DQB alleles, with frequency differences observed between Pacific and Atlantic populations. MHC DQB alleles appear to be under balancing selection, and most (80 %; n = 4/5) of the alleles were observed in walruses from both oceans, suggesting broad scale differences in the frequency of exposure and diversity of pathogens may be influencing levels of heterozygosity at DQB in walruses. Limited genetic diversity at MHC, however, suggests that walrus may have a reduced capacity to respond to novel immunological challenges associated with shifts in ecological communities and environmental stressors predicted for changing climates. This is particularly pertinent for walrus, since reductions in summer sea ice may facilitate both northward expansion of marine species and associated pathogens from more temperate regions, and exchange of marine mammals and associated pathogens through the recently opened Northwest Passage between the Atlantic and Pacific Oceans in the Canadian high Arctic.

  10. Genetic variation and origin of parthenogenesis in the Aspidoscelis cozumela complex: evidence from mitochondrial genes.

    PubMed

    Manríquez-Morán, Norma L; Cruz, Fausto R Méndez-de la; Murphy, Robert W

    2014-01-01

    Parthenogenesis is a form of clonal reproduction. Eggs develop in the absence of sperm and offspring are genetically identical to their mother. Although common in invertebrates, it occurs in only a few species of squamate reptiles. Parthenogenetic reptiles have their origin in interspecific hybridization, and their populations are exclusively female. Because of its high mutation rate and maternal inheritance, mitochondrial DNA sequence data can evaluate the origin and evolution of all-female vertebrates. Partial sequences from two mitochondrial genes, Cytb and ND4, were analyzed to investigate questions about the origin of parthenogenesis in the Aspidoscelis cozumela complex, which includes A. cozumela, A. maslini and A. rodecki. Low levels of divergence were detected among parthenogenetic species, and between them and A. angusticeps, confirming it as the maternal species of the parthenoforms. A gene tree was constructed using sequences from three populations of A. angusticeps and nine of its unisexual daughter species. The phylogeny suggests that two independent hybridization events between A. angusticeps and A. deppii formed three unisexual species. One hybridization resulted in A. rodecki and the other formed A. maslini and A. cozumela. Although A. cozumela has the haplotype characteristic of A. maslini from Puerto Morelos, it is considered to be a different species based on karyological and morphological characteristics and its geographical isolation. PMID:24410491

  11. Complex and multi-allelic copy number variation in human disease

    PubMed Central

    McCarroll, Steven A.

    2015-01-01

    Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who contributed chromosomes to current humans. Not only are the relationships of these multi-allelic CNVs (mCNVs) to phenotypes generally unknown, but many mCNVs have not yet been described at the basic levels—alleles, allele frequencies, structural features—that support genetic investigation. To date, most reported disease associations to these variants have been ascertained through candidate gene studies. However, only a few associations have reached the level of acceptance defined by durable replications in many cohorts. This likely stems from longstanding challenges in making precise molecular measurements of the alleles individuals have at these loci. However, approaches for mCNV analysis are improving quickly, and some of the unique characteristics of mCNVs may assist future association studies. Their various structural alleles are likely to have different magnitudes of effect, creating a natural allelic series of growing phenotypic impact and giving investigators a set of natural predictions and testable hypotheses about the extent to which each allele of an mCNV predisposes to a phenotype. Also, mCNVs’ low-to-modest correlation to individual single-nucleotide polymorphisms (SNPs) may make it easier to distinguish between mCNVs and nearby SNPs as the drivers of an association signal, and perhaps, make it possible to preliminarily screen candidate loci, or the entire genome, for the many mCNV–disease relationships that remain to be discovered. PMID:26163405

  12. Complex and multi-allelic copy number variation in human disease.

    PubMed

    Usher, Christina L; McCarroll, Steven A

    2015-09-01

    Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who contributed chromosomes to current humans. Not only are the relationships of these multi-allelic CNVs (mCNVs) to phenotypes generally unknown, but many mCNVs have not yet been described at the basic levels-alleles, allele frequencies, structural features-that support genetic investigation. To date, most reported disease associations to these variants have been ascertained through candidate gene studies. However, only a few associations have reached the level of acceptance defined by durable replications in many cohorts. This likely stems from longstanding challenges in making precise molecular measurements of the alleles individuals have at these loci. However, approaches for mCNV analysis are improving quickly, and some of the unique characteristics of mCNVs may assist future association studies. Their various structural alleles are likely to have different magnitudes of effect, creating a natural allelic series of growing phenotypic impact and giving investigators a set of natural predictions and testable hypotheses about the extent to which each allele of an mCNV predisposes to a phenotype. Also, mCNVs' low-to-modest correlation to individual single-nucleotide polymorphisms (SNPs) may make it easier to distinguish between mCNVs and nearby SNPs as the drivers of an association signal, and perhaps, make it possible to preliminarily screen candidate loci, or the entire genome, for the many mCNV-disease relationships that remain to be discovered. PMID:26163405

  13. Human radiation studies: Remembering the early years: Oral history of radiologist Henry I. Kohn, M.D., Ph.D., conducted September 13, 1994

    SciTech Connect

    1995-06-01

    This report is a transcript of an interview of Dr. Henry I. Kohn by representatives of the US DOE Office of Human Radiation Experiments. Dr. Kohn was selected for this interview because of the positions he held at Oak Ridge National Laboratory, University of California at San Francisco, and Harvard Medical School. Dr. Kohn discussed his remembrances of his experiences in blood chemistry of animals and patients exposed to radiation, and his remembrances of several radiobiologists.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    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.

  15. Variational Calculations of Positronium Scattering with Hydrogen

    E-print Network

    Woods, Denton

    2015-01-01

    Positronium-hydrogen (Ps-H) scattering is of interest, as it is a fundamental four-body Coulomb problem. We have investigated low-energy Ps-H scattering below the Ps(n=2) excitation threshold using the Kohn variational method and variants of the method with a trial wavefunction that includes highly correlated Hylleraas-type short-range terms. We give an elegant formalism that combines all Kohn-type variational methods into a single form. Along with this, we have also developed a general formalism for Kohn-type matrix elements that allows us to evaluate arbitrary partial waves with a single codebase. Computational strategies we have developed and use in this work are also discussed. With these methods, we have computed phase shifts for the first six partial waves for both the singlet and triplet states. The $^{1,3}$S and $^{1,3}$P phase shifts are highly accurate results and could potentially be viewed as benchmark results. Resonance positions and widths for the $^1$S-, $^1$P-, $^1$D-, and $^1$F-waves have bee...

  16. Variation of atomic charges on proton transfer in strong hydrogen bonds: the case of anionic and neutral imidazole-acetate complexes.

    PubMed

    Pacios, Luis F; Gómez, Pedro C; Gálvez, Oscar

    2006-11-15

    The variation of atomic charges upon proton transfer in hydrogen bonding complexes of 4-methylimidazole, in both neutral and protonated cationic forms, and acetate anion, is investigated. These complexes model the histidine (neutral and protonated)-aspartate pair present in active sites of proteases where strong N--H...O hydrogen bonds are formed. Three procedures (Merz-Kollman scheme, Natural Population Analysis, and Atoms in Molecules Method) are used to compute atomic charges and explore their variation upon H-transfer in the gas phase and in the presence of two continuum media with dielectric constants 5 (protein interiors) and 78.39 (water). The effect of electron correlation was also studied by comparing Hartree-Fock and MP2 results for both complexes in the gas phase. Greater net charge interchanged upon H-transfer is observed in the anionic complex with respect to the neutral complex. Raising the polarity of the medium increases the amount of net charge transfer in both complexes, although the neutral system exhibits a larger sensitivity to the presence of solvent. Charge transfer associated to N--H...O and N...H--O bonds reveal the ionic contribution to the interaction depending on the number of charged subunits but the presence of solvent affects little this quantity. The lack of electron correlation overestimates all the charges as well as their variations and so uncorrelated calculations should be avoided. PMID:16900495

  17. Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex

    PubMed Central

    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; Schönian, Gabriele

    2012-01-01

    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. PMID:22119748

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

    SciTech Connect

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

    2013-11-15

    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.

  19. Variation of the ultraviolet extinction law across the Taurus-Auriga star-forming complex. A GALEX based study

    NASA Astrophysics Data System (ADS)

    Gómez de Castro, Ana I.; López-Santiago, Javier; López-Martínez, Fátima; Sánchez, Néstor; de Castro, Elisa; Cornide, Manuel

    2015-06-01

    The Taurus-Auriga molecular complex (TMC) is the main laboratory for the study of low-mass star formation. The density and properties of interstellar dust are expected to vary across the TMC. These variations trace important processes such as dust nucleation or the magnetic field coupling with the cloud. In this paper, we show how the combination of near ultraviolet (NUV) and infrared (IR) photometry can be used to derive the strength of the 2175 Å bump and thus any enhancement in the abundance of small dust grains and polycyclic aromatic hydrocarbons in the dust grains size distribution. This technique is applied to the envelope of the TMC, mapped by the GALEXAll Sky Survey (AIS). Ultraviolet and IR photometric data have been retrieved from the GALEX-AIS and the 2MASS catalogues. NUV and K-band star counts have been used to identify the areas in the cloud envelope where the 2175 Å bump is weaker than in the diffuse interstellar medium namely, the low column density extensions of L1495, L1498 and L1524 in Taurus, L1545, L1548, L1519, L1513 in Auriga and L1482-83 in the California region. This finding agrees with previous results on dust evolution derived from Spitzer data and suggests that dust grains begin to decouple from the environmental Galactic magnetic field already in the envelope.

  20. Numerical simulation by TVD schemes of complex shock reflections from airfoils at high angle of attack. [Total Variation Diminishing

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

    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.

  1. Genetic variation of the major histocompatibility complex (MHC class II B gene) in the threatened Hume's pheasant, Syrmaticus humiae.

    PubMed

    Chen, Weicai; Bei, Yongjian; Li, Hanhua

    2015-01-01

    Major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates and encode molecules that play a crucial role in pathogen resistance. As a result of their diversity, they have received much attention in the fields of evolutionary and conservation biology. Here, we described the genetic variation of MHC class II B (MHCIIB) exon 2 in a wild population of Hume's pheasant (Syrmaticus humiae), which has suffered a dramatic decline in population over the last three decades across its ranges in the face of heavy exploitation and habitat loss. Twenty-four distinct alleles were found in 73 S. humiae specimens. We found seven shared alleles among four geographical groups as well as six rare MHCIIB alleles. Most individuals displayed between one to five alleles, suggesting that there are at least three MHCIIB loci of the Hume's pheasant. The dN ? dS ratio at putative antigen-binding sites (ABS) was significantly greater than one, indicating balancing selection is acting on MHCIIB exon 2. Additionally, recombination and gene conversion contributed to generating MHCIIB diversity in the Hume's pheasant. One to three recombination events and seventy-five significant gene conversion events were observed within the Hume's pheasant MHCIIB loci. The phylogenetic tree and network analysis revealed that the Hume's pheasant alleles do not cluster together, but are scattered through the tree or network indicating a trans-species evolutionary mode. These findings revealed the evolution of the Hume's pheasant MHC after suffering extreme habitat fragmentation. PMID:25629763

  2. Quantifying lithic microwear with load variation on experimental basalt flakes using LSCM and area-scale fractal complexity (Asfc)

    NASA Astrophysics Data System (ADS)

    Stemp, W. James; Morozov, Mikhail; Key, Alastair J. M.

    2015-09-01

    Working load is one factor that affects wear on stone tools. Despite the recognition of the importance of the relationship between working load and the development of microwear on stone tools, there have been few attempts to quantify differences in wear due to changes in load. In a controlled experiment, we used 30 basalt flakes knapped from raw material collected in Olduvai Gorge, Tanzania, Africa, to cut oak branches for the same number of strokes. For each flake, a different loading level was applied starting at 150 g and increasing by increments of 150 g to a maximum load of 4.5 kg. A laser scanning confocal microscope was used to mathematically document the surface texture of the flakes. The worn surface data were compared using area-scale fractal complexity (Asfc), calculated from relative areas, to determine the degree to which variation in loading significantly affected the amount of wear on the flake surfaces. Our results indicate that working load does play a role in the development of lithic microwear on these flakes and that discrimination of two worn flake surfaces, using mean square ratios of Asfc, based on variable load is consistently possible with load differences between ?100 g and 4.5 kg. However, discrimination of microwear on flake surfaces was not consistent for all load level differences and discrimination became less consistent when working load differences were below ?100 g.

  3. A Century of Chemical Dynamics Traced through the Nobel Prizes. 1998: Walter Kohn and John Pople

    NASA Astrophysics Data System (ADS)

    van Houten, Josh

    2002-11-01

    The 1998 Nobel Prize was awarded to Walter Kohn "for his development of the density-functional theory" and to John Pople "for his development of computational methods in quantum chemistry." They enabled improved energy calculations on molecules and other multi-atom systems. Chemists have taken advantage of those developments to perform calculations on systems during reactive encounters, thereby obtaining a better understanding of chemical dynamics and allowing for predictions regarding the course of chemical reactions based on the energies of various possible transition states.

  4. Evolution of reproductive mode variation and host associations in a sexual-asexual complex of aphid parasitoids

    PubMed Central

    2011-01-01

    Background The Lysiphlebus fabarum group is a taxonomically poorly resolved complex of aphid parasitoids, presently split into three described species that comprise sexual (arrhenotokous) and asexual (thelytokous) lineages of unknown relationship. Specifically, it is unclear how asexuals evolved from sexuals in this system, to what extent reproductive modes are still connected by genetic exchange, how much the complex is structured by geography or by host-associated differentiation, and whether species designations are valid. Using a combination of population genetic and phylogenetic approaches, we addressed these issues in a comprehensive sample of parasitoid wasps from across Europe. Results Asexual reproduction predominated in parasitoids of the L. fabarum group, with asexual populations exhibiting high genotypic diversity. Sexual populations were only common in southern France; elsewhere sexual reproduction was restricted to specific aphid hosts. Although reproductive modes were aggregated on the mitochondrial genealogy and significantly differentiated at nuclear microsatellite loci, there was clear evidence for genetic exchange, especially on hosts attacked by sexual and asexual parasitoids. The microsatellite data further revealed that parasitoids collected from certain host aphids were significantly differentiated, yet the mitochondrial sequence variation across the entire L. fabarum group did not exceed 1.32% and exhibited a very shallow topology. Morphological characters used for delineation of described species were found to be phylogenetically non-conservative. Conclusions Our results suggest that the sexual-asexual L. fabarum group represents a young complex of lineages with incomplete isolation between reproductive modes. We propose three mechanisms of genetic exchange that may jointly explain the high genotypic diversity observed in asexual parasitoids: (i) the formation of new asexual lineages via 'contagious parthenogenesis', (ii) introgression from sexual lineages through matings between sexual males and thelytokous females, and (iii) 'cryptic sex' within asexuals, mediated by rare males that thelytokous lines are known to produce spontaneously. The partially strong differentiation among wasps collected from different aphids suggests that host specialization can evolve readily in these parasitoids. Finally, we conclude that in the light of our data, the current taxonomic division of the L. fabarum group into three species cannot be upheld. PMID:22132834

  5. Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals.

    PubMed

    Li, Chen; Lu, Jianfeng; Yang, Weitao

    2015-12-14

    We develop the gentlest ascent dynamics for Kohn-Sham density functional theory to search for the index-1 saddle points on the energy landscape of the Kohn-Sham density functionals. These stationary solutions correspond to excited states in the ground state functionals. As shown by various examples, the first excited states of many chemical systems are given by these index-1 saddle points. Our novel approach provides an alternative, more robust way to obtain these excited states, compared with the widely used ?SCF approach. The method can be easily generalized to target higher index saddle points. Our results also reveal the physical interest and relevance of studying the Kohn-Sham energy landscape. PMID:26671361

  6. Response of a hydrothermal system to magmatic heat inferred from temporal variations in the complex frequencies of long-period events at Kusatsu-Shirane Volcano, Japan

    USGS Publications Warehouse

    Nakano, M.; Kumagai, H.

    2005-01-01

    We investigate temporal variations in the complex frequencies (frequency and quality factor Q) of long-period (LP) events that occurred at Kusatsu-Shirane Volcano, central Japan. We analyze LP waveforms observed at this volcano in the period between 1988 and 1995, which covers a seismically active period between 1989 and 1993. Systematic temporal variations in the complex frequencies are observed in October-November 1989, July-October 1991, and September 1992-January 1993. We use acoustic properties of a crack filled with hydrothermal fluids to interpret the observed temporal variations in the complex frequencies. The temporal variations in October-November 1989 can be divided into two periods, which are explained by a gradual decrease and increase of a gas-volume fraction in a water-steam mixture in a crack, respectively. The temporal variations in July-October 1991 can be also divided into two periods. These variations in the first and second periods are similar to those observed in November 1989 and in September-November 1992, respectively, and are interpreted as drying of a water-steam mixture and misty gas in a crack, respectively. The repeated nature of the temporal variations observed in similar seasons between July and November suggests the existence of seasonality in the occurrence of LP events. This may be caused by a seasonally variable meteoritic water supply to a hydrothermal system, which may have been heated by the flux of volcanic gases from magma beneath this volcano. ?? 2005 Elsevier B.V. All rights reserved.

  7. Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry

    PubMed Central

    2013-01-01

    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. PMID:23718194

  8. Complex L[sup 2] calculation of the variation of resonance widths of HOCl with total angular momentum

    SciTech Connect

    Skokov, S.; Bowman, J.M. )

    1999-09-01

    Complex L[sup 2] calculations of the variation of the resonance width of HOCl(6[nu][sub OH])[r arrow]Cl+OH with total angular momentum, [ital J], are reported, using a recently developed, accurate [ital ab initio] potential energy surface [S. Skokov, J. M. Bowman, and K. A. Peterson, J. Chem. Phys. [bold 109], 2662 (1998)]. The calculations are carried out using the adiabatic rotation approximation for the overall rotation and a truncation/recoupling method for the vibrational states. An [ital ab initio] calculation of the [ital J] and [ital K] dependence of the intensity of the absorption spectrum of the [ital Q] branch in the neighborhood of the 2[nu][sub OH][r arrow]6[nu][sub OH] transition is presented, and compared to results of recent experiments of Rizzo and co-workers. The variation of the resonance width of the 6,0,0 and the 3,8,0 states with [ital J] and [ital K] is presented, and comparisons with recent double-resonance experiments of the Rizzo and Sinha groups for the 6,0,0 state show encouraging qualitative agreement. The fluctuations of the dissociation rate with [ital J] is shown to be due to rotation-induced coupling of the 6[nu][sub OH] state to a dense set of highly excited OCl stretch states. A simple model describing the coupling of 6[nu][sub OH] with background states, using a coupling constant of 0.05 cm[sup [minus]1] is shown to give a qualitatively correct picture of the fluctuation of the resonance width with [ital J]. Finally, the energies of many nonoverlapping resonances, some of which are assigned, for J=18 and K=0 are presented and compared to Rice[endash]Ramsperger[endash]Kassel[endash]Marcus (RRKM) theory. It is found that due to slow, rate limiting, intramolecular vibrational relaxation the RRKM overestimates the average dissociation rate by an order of magnitude. [copyright] [ital 1999 American Institute of Physics.

  9. Generalization of the Kohn-Sham system enabling representing arbitary one electron density matrices

    E-print Network

    van Dam, Hubertus J J

    2015-01-01

    Density functional theory is currently the most widely applied method in electronic structure theory. The Kohn-Sham method, based on a fictitious system of non-interacting particles, is the work horse of the theory. The particular form of the Kohn-Sham wavefunction admits only idem-potent one electron density matrices whereas wavefunctions of correlated electrons in post-Hartree-Fock methods invariably have fractional occupation numbers. Here we show that by generalizing the orbital concept, and introducing a suitable dot-product as well as a probability density a non-interacting system can be chosen that can represent the one-electron density matrix of any system, even one with fractional occupation numbers. This fictitious system ensures that the exact electron density is accessible within density functional theory. It can also serve as the basis for reduced density matrix functional theory. Moreover, to aid the analysis of the results the orbitals may be assigned energies from a mean-field Hamiltonian. Thi...

  10. Efficient iterative method for solving the Dirac-Kohn-Sham density functional theory

    SciTech Connect

    Lin, Lin; Shao, Sihong; E, Weinan

    2012-11-06

    We present for the first time an efficient iterative method to directly solve the four-component Dirac-Kohn-Sham (DKS) density functional theory. Due to the existence of the negative energy continuum in the DKS operator, the existing iterative techniques for solving the Kohn-Sham systems cannot be efficiently applied to solve the DKS systems. The key component of our method is a novel filtering step (F) which acts as a preconditioner in the framework of the locally optimal block preconditioned conjugate gradient (LOBPCG) method. The resulting method, dubbed the LOBPCG-F method, is able to compute the desired eigenvalues and eigenvectors in the positive energy band without computing any state in the negative energy band. The LOBPCG-F method introduces mild extra cost compared to the standard LOBPCG method and can be easily implemented. We demonstrate our method in the pseudopotential framework with a planewave basis set which naturally satisfies the kinetic balance prescription. Numerical results for Pt$_{2}$, Au$_{2}$, TlF, and Bi$_{2}$Se$_{3}$ indicate that the LOBPCG-F method is a robust and efficient method for investigating the relativistic effect in systems containing heavy elements.

  11. More than the sum of its parts: a complex epistatic network underlies natural variation in thermal preference behavior in Caenorhabditis elegans.

    PubMed

    Gaertner, Bryn E; Parmenter, Michelle D; Rockman, Matthew V; Kruglyak, Leonid; Phillips, Patrick C

    2012-12-01

    Behavior is a complex trait that results from interactions among multiple genes and the environment. Both additive and nonadditive effects are expected to contribute to broad-sense heritability of complex phenotypes, although the relative contribution of each of these mechanisms is unknown. Here, we mapped genetic variation in the correlated phenotypes of thermal preference and isothermal dispersion in the nematode Caenorhabditis elegans. Genetic variation underlying these traits is characterized by a set of linked quantitative trait loci (QTL) that interact in a complex epistatic network. In particular, two loci located on the X chromosome interact with one another to generate extreme thermophilic behavior and are responsible for ?50% of the total variation observed in a cross between two parental lines, even though these loci individually explain very little of the among-line variation. Our results demonstrate that simultaneously considering the influence of a quantitative trait locus (QTL) on multiple scales of behavior can inform the physiological mechanism of the QTL and show that epistasis can explain significant proportions of otherwise unattributed variance within populations. PMID:23086219

  12. More Than the Sum of Its Parts: A Complex Epistatic Network Underlies Natural Variation in Thermal Preference Behavior in Caenorhabditis elegans

    PubMed Central

    Gaertner, Bryn E.; Parmenter, Michelle D.; Rockman, Matthew V.; Kruglyak, Leonid; Phillips, Patrick C.

    2012-01-01

    Behavior is a complex trait that results from interactions among multiple genes and the environment. Both additive and nonadditive effects are expected to contribute to broad-sense heritability of complex phenotypes, although the relative contribution of each of these mechanisms is unknown. Here, we mapped genetic variation in the correlated phenotypes of thermal preference and isothermal dispersion in the nematode Caenorhabditis elegans. Genetic variation underlying these traits is characterized by a set of linked quantitative trait loci (QTL) that interact in a complex epistatic network. In particular, two loci located on the X chromosome interact with one another to generate extreme thermophilic behavior and are responsible for ?50% of the total variation observed in a cross between two parental lines, even though these loci individually explain very little of the among-line variation. Our results demonstrate that simultaneously considering the influence of a quantitative trait locus (QTL) on multiple scales of behavior can inform the physiological mechanism of the QTL and show that epistasis can explain significant proportions of otherwise unattributed variance within populations. PMID:23086219

  13. Parity-time-symmetric solitons in trapped Bose-Einstein condensates and the influence of varying complex potentials: A variational approach.

    PubMed

    Devassy, Lini; Jisha, Chandroth P; Alberucci, Alessandro; Kuriakose, V C

    2015-08-01

    Dynamics and properties of nonlinear matter waves in a trapped BEC subject to a PT-symmetric linear potential, with the trap in the form of a super-Gaussian potential, are investigated via a variational approach accounting for the complex nature of the soliton. In the process, we address how the shape of the imaginary part of the potential, that is, a gain-loss mechanism, affects the self-localization and the stability of the condensate. Variational results are found to be in good agreement with full numerical simulations for predicting the shape, width, and chemical potential of the condensate until the PT breaking point. Variational computation also predicts the existence of solitary solution only above a threshold in the particle number as the gain-loss is increased, in agreement with numerical simulations. PMID:26382483

  14. Ground-state densities from the Rayleigh-Ritz variation principle and from density-functional theory

    NASA Astrophysics Data System (ADS)

    Kvaal, Simen; Helgaker, Trygve

    2015-11-01

    The relationship between the densities of ground-state wave functions (i.e., the minimizers of the Rayleigh-Ritz variation principle) and the ground-state densities in density-functional theory (i.e., the minimizers of the Hohenberg-Kohn variation principle) is studied within the framework of convex conjugation, in a generic setting covering molecular systems, solid-state systems, and more. Having introduced admissible density functionals as functionals that produce the exact ground-state energy for a given external potential by minimizing over densities in the Hohenberg-Kohn variation principle, necessary and sufficient conditions on such functionals are established to ensure that the Rayleigh-Ritz ground-state densities and the Hohenberg-Kohn ground-state densities are identical. We apply the results to molecular systems in the Born-Oppenheimer approximation. For any given potential v ? L3/2(?3) + L?(?3), we establish a one-to-one correspondence between the mixed ground-state densities of the Rayleigh-Ritz variation principle and the mixed ground-state densities of the Hohenberg-Kohn variation principle when the Lieb density-matrix constrained-search universal density functional is taken as the admissible functional. A similar one-to-one correspondence is established between the pure ground-state densities of the Rayleigh-Ritz variation principle and the pure ground-state densities obtained using the Hohenberg-Kohn variation principle with the Levy-Lieb pure-state constrained-search functional. In other words, all physical ground-state densities (pure or mixed) are recovered with these functionals and no false densities (i.e., minimizing densities that are not physical) exist. The importance of topology (i.e., choice of Banach space of densities and potentials) is emphasized and illustrated. The relevance of these results for current-density-functional theory is examined.

  15. Construction of integrable model Kohn-Sham potentials by analysis of the structure of functional derivatives

    NASA Astrophysics Data System (ADS)

    Gaiduk, Alex P.; Staroverov, Viktor N.

    2011-01-01

    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.

  16. Reduction of Electronic Wave Functions to Kohn-Sham Effective Potentials

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    A method for calculating the Kohn-Sham exchange-correlation potential vXC(r ) from a given electronic wave function is devised and implemented. It requires on input one- and two-electron reduced density matrices and involves construction of the generalized Fock matrix. The method is free from numerical limitations and basis-set artifacts of conventional schemes for constructing vXC(r ) in which the potential is recovered from a given electron density, and is simpler than various many-body techniques. The chief significance of this development is that it allows one to directly probe the functional derivative of the true exchange-correlation energy functional and to rigorously test and improve various density-functional approximations.

  17. Communication: Kohn-Sham theory for excited states of Coulomb systems

    NASA Astrophysics Data System (ADS)

    Ayers, P. W.; Levy, M.; Nagy, Á.

    2015-11-01

    For obtaining individual excited-state energies and densities of Coulomb electronic systems, by means of an energy stationary principle, it was shown previously that there exists a universal functional of the density, FCoul[?], for the kinetic plus electron-electron repulsion part of the total energy. Here, we make knowledge of the existence of FCoul[?] practical for calculation by identifying Ts Coul [ ? ] , the non-interacting kinetic energy component of FCoul[?], and by showing that Ts Coul [ ? ] may be computed exactly by means of orbitals that are obtained through a set of single-particle Kohn-Sham equations. Constraints for obtaining accurate approximations to the remaining unknown component of FCoul[?] are presented.

  18. Construction of integrable model Kohn-Sham potentials by analysis of the structure of functional derivatives

    SciTech Connect

    Gaiduk, Alex P.; Staroverov, Viktor N.

    2011-01-15

    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.

  19. Elliptic preconditioner for accelerating the self consistent field iteration in Kohn-Sham density functional theory

    SciTech Connect

    Lin, Lin; Yang, Chao

    2012-06-11

    We discuss techniques for accelerating the self consistent field (SCF) iteration for solving the Kohn-Sham equations. These techniques are all based on constructing approximations to the inverse of the Jacobian associated with a fixed point map satisfied by the total potential. They can be viewed as preconditioners for a fixed point iteration. We point out different requirements for constructing preconditioners for insulating and metallic systems respectively, and discuss how to construct preconditioners to keep the convergence rate of the fixed point iteration independent of the size of the atomistic system. We propose a new preconditioner that can treat insulating and metallic system in a unified way. The new preconditioner, which we call an elliptic preconditioner, is constructed by solving an elliptic partial differential equation. The elliptic preconditioner is shown to be more effective in accelerating the convergence of a fixed point iteration than the existing approaches for large inhomogeneous systems at low temperature.

  20. Implementation of Kohn's theorem for the ellipsoidal quantum dot in the presence of external magnetic field

    NASA Astrophysics Data System (ADS)

    Hayrapetyan, D. B.; Kazaryan, E. M.; Sarkisyan, H. A.

    2016-01-01

    An electron gas in a strongly oblated ellipsoidal quantum dot with impenetrable walls in the presence of external magnetic field is considered. Influence of the walls of the quantum dot is assumed to be so strong in the direction of the minor axis (the OZ axis) that the Coulomb interaction between electrons in this direction can be neglected and considered as two-dimensional. On the basis of geometric adiabaticity we show that in the case of a few-particle gas a powerful repulsive potential of the quantum dot walls has a parabolic form and localizes the gas in the geometric center of the structure. Due to this fact, conditions occur to implement the generalized Kohn theorem for this system. The parabolic confinement potential depends on the geometry of the ellipsoid, which allows, together with the magnetic field to control resonance frequencies of transitions by changing the geometric dimensions of the QD.

  1. Solving the self-interaction problem in Kohn-Sham density functional theory: Application to atoms

    NASA Astrophysics Data System (ADS)

    Däne, M.; Gonis, A.; Nicholson, D. M.; Stocks, G. M.

    2015-04-01

    In previous work, we proposed a computational methodology that addresses the elimination of the self-interaction error from the Kohn-Sham formulation of the density functional theory. We demonstrated how the exchange potential can be obtained, and presented results of calculations for atomic systems up to Kr carried out within a Cartesian coordinate system. In this paper, we provide complete details of this self-interaction free method formulated in spherical coordinates based on the explicit equidensity basis ansatz. We prove analytically that derivatives obtained using this method satisfy the Virial theorem for spherical orbitals, where the problem can be reduced to one dimension. We present the results of calculations of ground-state energies of atomic systems throughout the periodic table carried out within the exchange-only mode.

  2. Communication: Kohn-Sham theory for excited states of Coulomb systems.

    PubMed

    Ayers, P W; Levy, M; Nagy, Á

    2015-11-21

    For obtaining individual excited-state energies and densities of Coulomb electronic systems, by means of an energy stationary principle, it was shown previously that there exists a universal functional of the density, F(Coul)[?], for the kinetic plus electron-electron repulsion part of the total energy. Here, we make knowledge of the existence of F(Coul)[?] practical for calculation by identifying Ts (Coul)[?], the non-interacting kinetic energy component of F(Coul)[?], and by showing that Ts (Coul)[?] may be computed exactly by means of orbitals that are obtained through a set of single-particle Kohn-Sham equations. Constraints for obtaining accurate approximations to the remaining unknown component of F(Coul)[?] are presented. PMID:26590518

  3. High order forces and nonlocal operators in a Kohn-Sham Hamiltonian.

    PubMed

    Scott Bobbitt, N; Schofield, Grady; Lena, Charles; Chelikowsky, James R

    2015-11-25

    Real space pseudopotentials have a number of advantages in solving for the electronic structure of materials. These advantages include ease of implementation, implementation on highly parallel systems, and great flexibility for describing partially periodic systems. One limitation of this approach, shared by other electronic structure methods, is the slow convergence of interatomic forces when compared to total energies. For real space methods, this requires a fine grid to converge a solution of the Kohn-Sham problem, which is accompanied by concurrent increase in memory and additional matrix-vector multiplications. Here we introduce a method to expedite the computation of interatomic forces by employing a high order integration technique. We demonstrate the usefulness of this technique by calculating accurate bond lengths and vibrational frequencies for molecules and nanocrystals without using fine real space grids. PMID:26106967

  4. Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases

    PubMed Central

    Wallace, Douglas C.

    2013-01-01

    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. PMID:23754818

  5. Measurement of Complex Relative Permittivity of Pure Water and its Variation with Respect to Water Amount using Open-Ended Coaxial Probe

    NASA Astrophysics Data System (ADS)

    Takeda, Akira; Takata, Kazuyuki; Sato, Yusuke; Taka, Yoshinori; Fujiwara, Osamu

    A commercially available open-ended coaxial probe has often been used to measure dielectric properties in combination with a network-analyzer, while it can be applied to semi-infinite homogeneous materials. For thickness and size of the materials to be measured, however, their influences have not well been examined. In this study, using such an open-ended coaxial probe, we measured complex relative permittivity of pure water in the frequency range from 200MHz to 6GHz with respect to its measurement amount, and investigated the variation in comparison with the calculated values from an empirical formula for water permittivity. As a result, we found that the amount of water in a beaker with a diameter of over 35mm and a depth of 50mm provides the measurement variation within ±0.3% and -5.5% for real and imaginary parts of complex relative permittivity, respectively. It was also found that a water amount of 1.9ml in a beaker with a diameter of 35mm and a depth of over 2mm gives the variation within ±0.5% for real part and ±7% for imaginary part.

  6. Mitochondrial-DNA variation and the evolutionary affinities of the Peromyscus maniculatus complex from western North America 

    E-print Network

    Walker, Mindy Lynn

    2006-04-12

    . Mitochondrial DNA (mtDNA) fits these criteria and was thereby ideal for analyzing genetic variation within and among the youngest taxonomic members of the Peromyscus maniculatus species group, P. sejugis (restricted to two islands in the Sea of Cort���©s), P...

  7. SOURCES OF VARIATION IN THE MUTAGENIC POTENCY OF COMPLEX CHEMICAL MIXTURES BASED ON THE SALMONELLA/MICROSOME ASSAY

    EPA Science Inventory

    Twenty laboratories worldwide participated in a collaborative trial sponsored by the International Programme on Chemical Safety on the mutagenicity of complex mixtures as expressed in the Salmonella/ microsome assay. he U.S. National Institute of Standards and Technology provided...

  8. Terrace width variations in complex Mercurian craters and the transient strength of cratered Mercurian and lunar crust

    NASA Technical Reports Server (NTRS)

    Leith, Andrew C.; Mckinnon, William B.

    1991-01-01

    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.

  9. Elimination of the asymptotic fractional dissociation problem in Kohn-Sham density functional theory using the ensemble-generalization approach

    E-print Network

    Kraisler, Eli

    2015-01-01

    Many approximations within density-functional theory spuriously predict that a many-electron system can dissociate into fractionally charged fragments. Here, we revisit the case of dissociated diatomic molecules, known to exhibit this problem when studied within standard approaches, including the local spin-density approximation (LSDA). By employing our recently proposed [E. Kraisler and L. Kronik, Phys. Rev. Lett. 110, 126403 (2013)] ensemble-generalization we find that asymptotic fractional dissociation is eliminated in all systems examined, even if the underlying exchange-correlation (xc) is still the LSDA. Furthermore, as a result of the ensemble generalization procedure, the Kohn-Sham potential develops a spatial step between the dissociated atoms, reflecting the emergence of the derivative discontinuity in the xc energy functional. This step, predicted in the past for the exact Kohn-Sham potential and observed in some of its more advanced approximate forms, is a desired feature that prevents any fractio...

  10. Orbital-free extension to Kohn-Sham density functional theory equation of state calculations: Application to silicon dioxide

    NASA Astrophysics Data System (ADS)

    Sjostrom, Travis; Crockett, Scott

    2015-09-01

    The liquid regime equation of state of silicon dioxide SiO2 is calculated via quantum molecular dynamics in the density range of 5 -15 g/cm 3 and with temperatures from 0.5 to 100 eV, including the ? -quartz and stishovite phase Hugoniot curves. Below 8 eV calculations are based on Kohn-Sham density functional theory (DFT), and above 8 eV a new orbital-free DFT formulation, presented here, based on matching Kohn-Sham DFT calculations is employed. Recent experimental shock data are found to be in very good agreement with the current results. Finally both experimental and simulation data are used in constructing a new liquid regime equation of state table for SiO2.

  11. Structure variation and luminescence properties of lanthanide complexes with 1,9-bis [2-(2'-picolylaminoformyl)-1,4,7,9-tetraoxadecane

    SciTech Connect

    Song Xueqin; Zang Zhipeng; Liu Weisheng; Zhang Yujie

    2009-04-15

    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. {l_brace}[PrL(NO{sub 3}){sub 3}(H{sub 2}O){sub 2}].CH{sub 3}OH{r_brace}{sub n} is a 1D zigzag polymer with three-dimensional supramolecular structure formed by hydrogen bonds, while [EuL(NO{sub 3}){sub 3}(H{sub 2}O)]{sub 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. - Graphical abstract: Structure variation and luminescence properties of lanthanide complexes with 1,9-bis [2-(2'-picolylaminoformyl)-1,4,7,9-tetraoxadecane.

  12. Comparative patterns of genetic variation among populations of the Zamia pumila L. complex across three islands of the Greater Antilles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Zamia pumila L. complex (Cycadales: Zamiaceae) is a distinctive, monophyletic, diploid (2n =16) assemblage of populations restricted to the West Indies and southeastern U. S. (Florida) that is currently considered to encompass either a single polymorphic, or nine distinct species. We are extensi...

  13. Synthesis of Binucleating Macrocycles and their Nickel(II) Hydroxo- and Cyano-Bridged Complexes with Divalent Ions: Anatomical Variation of Ligand Features

    PubMed Central

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

    2012-01-01

    The planar NNN-pincer complexes [MII(pyN Me2)(OH)]1? (MII = Ni, Cu) fix CO2 in ?1-OCO2H complexes; results for the copper system are described. MnII, FeII, CoII, and ZnII behave differently, forming [MII(pyN2Me)2]2? with N4O2 coordination. Incorporation of the NiII pincer into binucleating macrocycle 2 containing a triamino MII locus connected by two 1,3-biphenylene groups affords proximal NiII and MII 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 MII 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 MII = Mn, Fe, and Cu with hydroxo bridges. Introduction of the 4-BuiO group (macrocycle 3) improves the solubility of neutral complexes such as those with NiII-OH-CuII and NiII-CN-FeII bridges. The syntheses of macrocycle 5 with a 7-Me-[12]aneSN3 and macrocycle 6 with a 1,8-Me2-[14]aneN4 MII binding site are described to 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 NiII complex. Bridge structural units are summarized and the structures of fourteen macrocyclic complexes including eight with bridges are described. PMID:23030366

  14. Orbitals from local RDMFT: Are they Kohn-Sham or natural orbitals?

    PubMed

    Theophilou, Iris; Lathiotakis, Nektarios N; Gidopoulos, Nikitas I; Rubio, Angel; Helbig, Nicole

    2015-08-01

    Recently, an approximate theoretical framework was introduced, called local reduced density matrix functional theory (local-RDMFT), where functionals of the one-body reduced density matrix (1-RDM) are minimized under the additional condition that the optimal orbitals satisfy a single electron Schrödinger equation with a local potential. In the present work, we focus on the character of these optimal orbitals. In particular, we compare orbitals obtained by local-RDMFT with those obtained with the full minimization (without the extra condition) by contrasting them against the exact NOs and orbitals from a density functional calculation using the local density approximation (LDA). We find that the orbitals from local-RMDFT are very close to LDA orbitals, contrary to those of the full minimization that resemble the exact NOs. Since local RDMFT preserves the good quality of the description of strong static correlation, this finding opens the way to a mixed density/density matrix scheme, where Kohn-Sham orbitals obtain fractional occupations from a minimization of the occupation numbers using 1-RDM functionals. This will allow for a description of strong correlation at a cost only minimally higher than a density functional calculation. PMID:26254641

  15. Orbitals from local RDMFT: Are they Kohn-Sham or natural orbitals?

    NASA Astrophysics Data System (ADS)

    Theophilou, Iris; Lathiotakis, Nektarios N.; Gidopoulos, Nikitas I.; Rubio, Angel; Helbig, Nicole

    2015-08-01

    Recently, an approximate theoretical framework was introduced, called local reduced density matrix functional theory (local-RDMFT), where functionals of the one-body reduced density matrix (1-RDM) are minimized under the additional condition that the optimal orbitals satisfy a single electron Schrödinger equation with a local potential. In the present work, we focus on the character of these optimal orbitals. In particular, we compare orbitals obtained by local-RDMFT with those obtained with the full minimization (without the extra condition) by contrasting them against the exact NOs and orbitals from a density functional calculation using the local density approximation (LDA). We find that the orbitals from local-RMDFT are very close to LDA orbitals, contrary to those of the full minimization that resemble the exact NOs. Since local RDMFT preserves the good quality of the description of strong static correlation, this finding opens the way to a mixed density/density matrix scheme, where Kohn-Sham orbitals obtain fractional occupations from a minimization of the occupation numbers using 1-RDM functionals. This will allow for a description of strong correlation at a cost only minimally higher than a density functional calculation.

  16. Local reduced-density-matrix-functional theory: Incorporating static correlation effects in Kohn-Sham equations

    NASA Astrophysics Data System (ADS)

    Lathiotakis, Nektarios N.; Helbig, Nicole; Rubio, Angel; Gidopoulos, Nikitas I.

    2014-09-01

    We propose a scheme to bring reduced-density-matrix-functional theory into the realm of density functional theory (DFT) that preserves the accurate density functional description at equilibrium, while incorporating accurately static and left-right correlation effects in molecules and keeping the good computational performance of DFT-based schemes. The key ingredient is to relax the requirement that the local potential is the functional derivative of the energy with respect to the density. Instead, we propose to restrict the search for the approximate natural orbitals within a domain where these orbitals are eigenfunctions of a single-particle Hamiltonian with a local effective potential. In this way, fractional natural occupation numbers are accommodated into Kohn-Sham equations allowing for the description of molecular dissociation without breaking spin symmetry. Additionally, our scheme provides a natural way to connect an energy eigenvalue spectrum to the approximate natural orbitals and this spectrum is found to represent accurately the ionization potentials of atoms and small molecules.

  17. Full Parallel Implementation of an All-Electron Four-Component Dirac-Kohn-Sham Program.

    PubMed

    Rampino, Sergio; Belpassi, Leonardo; Tarantelli, Francesco; Storchi, Loriano

    2014-09-01

    A full distributed-memory implementation of the Dirac-Kohn-Sham (DKS) module of the program BERTHA (Belpassi et al., Phys. Chem. Chem. Phys. 2011, 13, 12368-12394) is presented, where the self-consistent field (SCF) procedure is replicated on all the parallel processes, each process working on subsets of the global matrices. The key feature of the implementation is an efficient procedure for switching between two matrix distribution schemes, one (integral-driven) optimal for the parallel computation of the matrix elements and another (block-cyclic) optimal for the parallel linear algebra operations. This approach, making both CPU-time and memory scalable with the number of processors used, virtually overcomes at once both time and memory barriers associated with DKS calculations. Performance, portability, and numerical stability of the code are illustrated on the basis of test calculations on three gold clusters of increasing size, an organometallic compound, and a perovskite model. The calculations are performed on a Beowulf and a BlueGene/Q system. PMID:26588521

  18. Noncollinear Korringa-Kohn-Rostoker Green function method: Application to 3d nanostructures on Ni(001)

    NASA Astrophysics Data System (ADS)

    Lounis, S.; Mavropoulos, Ph.; Dederichs, P. H.; Blügel, S.

    2005-12-01

    Magnetic nanostructures on nonmagnetic or magnetic substrates have attracted strong attention due to the development of interesting experimental methods with atomic resolution. Motivated by this progress we have extended the full-potential Korringa-Kohn-Rostoker Green-function method to treat noncollinear magnetic nanostructures on surfaces. We focus on magnetic 3d impurity nanoclusters, sitting as adatoms on or in the first surface layer on Ni(001) , and investigate the size and orientation of the local moments and, moreover, the stabilization of noncollinear magnetic solutions. While clusters of Fe, Co, Ni atoms are magnetically collinear, noncollinear magnetic coupling is expected for Cr and Mn clusters on surfaces of elemental ferromagnets. The origin of frustration is the competition of the antiferromagnetic exchange coupling among the Cr or Mn atoms with the antiferromagnetic (for Cr) or ferromagnetic (for Mn) exchange coupling between the impurities and the substrate. We find that Cr and Mn first-neighboring dimers and a Mn trimer on Ni(001) show noncollinear behavior nearly degenerate with the most stable collinear configuration. Increasing the distance between the dimer atoms leads to a collinear behavior, similar to the one of the single impurities. Finally, we compare some of the noncollinear ab initio results to those obtained within a classical Heisenberg model, where the exchange constants are fitted to total energies of the collinear states; the agreement is surprisingly good.

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

    SciTech Connect

    Schauer, Volker; Linder, Christian

    2013-10-01

    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.

  20. Effect of ensemble generalization on the highest-occupied Kohn-Sham eigenvalue

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    There are several approximations to the exchange-correlation functional in density-functional theory, which accurately predict total energy-related properties of many-electron systems, such as binding energies, bond lengths, and crystal structures. Other approximations are designed to describe potential-related processes, such as charge transfer and photoemission. However, the development of a functional which can serve the two purposes simultaneously is a long-standing challenge. Trying to address it, we employ in the current work the ensemble generalization procedure proposed by Kraisler and Kronik [Phys. Rev. Lett. 110, 126403 (2013)]. Focusing on the prediction of the ionization potential via the highest occupied Kohn-Sham eigenvalue, we examine a variety of exchange-correlation approximations: the local spin-density approximation, semi-local generalized gradient approximations, and global and local hybrid functionals. Results for a test set of 26 diatomic molecules and single atoms are presented. We find that the aforementioned ensemble generalization systematically improves the prediction of the ionization potential, for various systems and exchange-correlation functionals, without compromising the accuracy of total energy-related properties. We specifically examine hybrid functionals. These depend on a parameter controlling the ratio of semi-local to non-local functional components. The ionization potential obtained with ensemble-generalized functionals is found to depend only weakly on the parameter value, contrary to common experience with non-generalized hybrids, thus eliminating one aspect of the so-called "parameter dilemma" of hybrid functionals.

  1. Accurate Energies and Orbital Description in Semi-Local Kohn-Sham DFT

    NASA Astrophysics Data System (ADS)

    Lindmaa, Alexander; Kuemmel, Stephan; Armiento, Rickard

    2015-03-01

    We present our progress on a scheme in semi-local Kohn-Sham density-functional theory (KS-DFT) for improving the orbital description while still retaining the level of accuracy of the usual semi-local exchange-correlation (xc) functionals. DFT is a widely used tool for first-principles calculations of properties of materials. A given task normally requires a balance of accuracy and computational cost, which is well achieved with semi-local DFT. However, commonly used semi-local xc functionals have important shortcomings which often can be attributed to features of the corresponding xc potential. One shortcoming is an overly delocalized representation of localized orbitals. Recently a semi-local GGA-type xc functional was constructed to address these issues, however, it has the trade-off of lower accuracy of the total energy. We discuss the source of this error in terms of a surplus energy contribution in the functional that needs to be accounted for, and offer a remedy for this issue which formally stays within KS-DFT, and, which does not harshly increase the computational effort. The end result is a scheme that combines accurate total energies (e.g., relaxed geometries) with an improved orbital description (e.g., improved band structure).

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

    SciTech Connect

    Holas, A.

    2008-02-15

    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.

  3. Clinal variation or validation of a subspecies? A case study of the Graptemys nigrinoda complex (Testudines: Emydidae)

    USGS Publications Warehouse

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

    2014-01-01

    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.

  4. Geographic variation in size and coloration in the Turdus poliocephalus complex: A first review of species limits

    E-print Network

    Peterson, A. Townsend

    2007-09-12

    on Mann-Whitney U-tests when pairs of populations are compared, and a z value (standard normal variate) is reported; H statistics are provided where >2 populations were available, based on a Kruskal-Wallis Test. Sc i e n t i f i c Pa P e r S , na t u r a... most dramatic exploration during the famous Whitney South Sea expeditions, and exploration of the region ornithologically largely ceased with the initiation of conflicts in the Pacific theater of World War II. More - over, the ornithological leader...

  5. Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

    PubMed Central

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

    2014-01-01

    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

  6. Variational theory of complex rays applied to shell structures: in-plane inertia, quasi-symmetric ray distribution, and orthotropic materials

    NASA Astrophysics Data System (ADS)

    Cattabiani, Alessandro; Barbarulo, Andrea; Riou, Hervé; Ladevèze, Pierre

    2015-10-01

    Recently, interest of aerospace and automotive industries on medium-frequency vibrational behavior of composite shell structures has grown due to their high specific stiffness and fatigue resistance. Conventional methods such as the finite element method and the statistical energy analysis are not suitable for the medium-frequency bandwidth. Conversely, the variational theory of complex rays (VTCR) is taking place as an ad-hoc technique to tackle such frequency band. It is a Trefftz method based on a weak variational formulation. Equilibrium equations are met using exact solutions as shape functions. The variational problem imposes boundary conditions in weak form. The present paper extends VTCR to orthotropic shell structures. Moreover, several new enhancements are introduced. Now, we use a quasi-symmetric ray distribution which can greatly reduce computational costs, and addresses in-plane inertia which was neglected in previous works. Some relevant numerical examples are presented to show the strategy and results are compared with a FEM reference to study performances.

  7. An assessment indicator for air ventilation and pollutant dispersion potential in an urban canopy with complex natural terrain and significant wind variations

    NASA Astrophysics Data System (ADS)

    Yim, S. H. L.; Fung, J. C. H.; Ng, E. Y. Y.

    2014-09-01

    In an urban planning context, an assessment indicator for evaluating a city's dispersion potential is beneficial, especially if the city has a complex natural terrain and significant wind variations. A study was conducted to implement an urban canopy drag indicator, taking site wind variation into account by involving both wind speed and direction in the calculations. Hong Kong (HK) was taken as an example due to its complicated natural topography and wind characteristics. A spatial distribution of an urban canopy drag over HK was determined based on wind data from 2004. The urban canopy drag values in three highly urbanized areas in HK, including Kowloon West, Kowloon East and Hong Kong Island North, were obtained and are discussed in detail. A fluid particle tracking program was developed and applied to identify the major wind paths in Kowloon West, with an area of approximately 5.5 × 6 km as an example. We analyzed the diurnal variation in the dispersion times and the major wind paths in the region during both summer and winter. Our results estimated that the horizontal dispersion times of Kowloon West during both winter and summer were approximately 20 min. By combining the wind paths from both seasons, we identified several major wind paths and critical ventilation areas in Kowloon West. This paper demonstrates the potential use of an urban canopy drag indicator for assessing air ventilation and pollutant dispersion in a city planning context.

  8. Gold-superheavy-element interaction in diatomics and cluster adducts: A combined four-component Dirac-Kohn-Sham/charge-displacement study

    NASA Astrophysics Data System (ADS)

    Rampino, Sergio; Storchi, Loriano; Belpassi, Leonardo

    2015-07-01

    The chemistry of superheavy elements (Z ? 104) is actively investigated in atom-at-a-time experiments of volatility through adsorption on gold surfaces. In this context, common guidelines for interpretation based on group trends in the periodic table should be used cautiously, because relativistic effects play a central role and may cause predictions to fall short. In this paper, we present an all-electron four-component Dirac-Kohn-Sham comparative study of the interaction of gold with Cn (Z = 112), Fl (Z = 114), and Uuo (Z = 118) versus their lighter homologues of the 6th period, Hg, Pb, and Rn plus the noble gas Xe. Calculations were carried out for Au-E (E = Hg, Cn, Pb, Fl, Xe, Rn, Uuo), Au7- and Au20-E (E = Hg, Cn, Pb, Fl, Rn) complexes, where Au7 (planar) and Au20 (pyramidal) are experimentally determined clusters having structures of increasing complexity. Results are analysed both in terms of the energetics of the complexes and of the electron charge rearrangement accompanying their formation. In line with the available experimental data, Cn and more markedly Fl are found to be less reactive than their lighter homologues. On the contrary, Uuo is found to be more reactive than Rn and Xe. Cn forms the weakest bond with the gold atom, compared to Fl and Uuo. The reactivity of Fl decreases with increasing gold-fragment size more rapidly than that of Cn and, as a consequence, the order of the reactivity of these two elements is inverted upon reaching the Au20-cluster adduct. Density difference maps between adducts and fragments reveal similarities in the behaviour of Cn and Xe, and in that of Uuo and the more reactive species Hg and Pb. These findings are given a quantitative ground via charge-displacement analysis.

  9. Gold-superheavy-element interaction in diatomics and cluster adducts: A combined four-component Dirac-Kohn-Sham/charge-displacement study.

    PubMed

    Rampino, Sergio; Storchi, Loriano; Belpassi, Leonardo

    2015-07-14

    The chemistry of superheavy elements (Z ? 104) is actively investigated in atom-at-a-time experiments of volatility through adsorption on gold surfaces. In this context, common guidelines for interpretation based on group trends in the periodic table should be used cautiously, because relativistic effects play a central role and may cause predictions to fall short. In this paper, we present an all-electron four-component Dirac-Kohn-Sham comparative study of the interaction of gold with Cn (Z = 112), Fl (Z = 114), and Uuo (Z = 118) versus their lighter homologues of the 6th period, Hg, Pb, and Rn plus the noble gas Xe. Calculations were carried out for Au-E (E = Hg, Cn, Pb, Fl, Xe, Rn, Uuo), Au7- and Au20-E (E = Hg, Cn, Pb, Fl, Rn) complexes, where Au7 (planar) and Au20 (pyramidal) are experimentally determined clusters having structures of increasing complexity. Results are analysed both in terms of the energetics of the complexes and of the electron charge rearrangement accompanying their formation. In line with the available experimental data, Cn and more markedly Fl are found to be less reactive than their lighter homologues. On the contrary, Uuo is found to be more reactive than Rn and Xe. Cn forms the weakest bond with the gold atom, compared to Fl and Uuo. The reactivity of Fl decreases with increasing gold-fragment size more rapidly than that of Cn and, as a consequence, the order of the reactivity of these two elements is inverted upon reaching the Au20-cluster adduct. Density difference maps between adducts and fragments reveal similarities in the behaviour of Cn and Xe, and in that of Uuo and the more reactive species Hg and Pb. These findings are given a quantitative ground via charge-displacement analysis. PMID:26178105

  10. Structural variations in terbium(III) complexes with 1,3-adamantanedicarboxylate and diverse co-ligands

    NASA Astrophysics Data System (ADS)

    Thuéry, Pierre

    2015-07-01

    Terbium nitrate was reacted with 1,3-adamantanedicarboxylic acid (LH2) under solvo-hydrothermal conditions with either N,N-dimethylformamide (DMF) or N,N-dimethylacetamide (DMA) as organic solvents. Hydrolysation of the latter co-solvents resulted in the formation of formate or acetate ions, which are present as co-ligands in the 1D coordination polymer [Tb(L)(HCOO)(H2O)2] (1) and the 2D assembly [Tb(L)(CH3COO)(H2O)] (2). The increase in dimensionality in the latter arises from the higher connectivity provided by acetate versus formate, the L2- ligand being bis-chelating in both cases. The complex [Tb2(L)3(H2O)5][Tb2(L)3(H2O)4]·3H2O (3), another 1D species, crystallizes alongside crystals of 2. Further addition of cucurbit[6]uril (CB6), with DMF as co-solvent, gave the two complexes [Tb2(L)2(CB6)(H2O)6](NO3)2·6H2O (4) and [H2NMe2]2[Tb(L)(HCOO)2]2·CB6·3H2O (5). Complex 4 crystallizes as a 3D framework in which Tb(L)+ chains are connected by tetradentate CB6 molecules, while 5 unites a carboxylate-bridged anionic 2D planar assembly and layers of CB6 molecules with counter-cations held at both portals.

  11. Spatial Variation in Host Feeding Patterns of Culex tarsalis and the Culex pipiens complex (Diptera: Culicidae) in California

    PubMed Central

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

    2012-01-01

    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. PMID:22897051

  12. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma)

    USGS Publications Warehouse

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

    2009-01-01

    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.

  13. Variations in the radiation sensitivity of foodborne pathogens associated with complex ready-to-eat food products

    NASA Astrophysics Data System (ADS)

    Sommers, Christopher H.; Boyd, Glenn

    2006-07-01

    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.

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

    SciTech Connect

    Cinal, M.; Holas, A.

    2011-06-15

    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.

  15. Magma Mixing in Uralian-Alaskan Type Complexes in the Ural Mountains, Russia: Implications from the Trace Element Variation in Clinopyroxene

    NASA Astrophysics Data System (ADS)

    Krause, J.; Bruegmann, G. E.; Pushkarev, E.

    2006-12-01

    The distinctive geologic and petrographic feature of classical Uralian-Alaskan-type zoned mafic-ultramafic complexes is a zonal distribution of mafic and ultramafic rocks, with a central dunite body that grades outward into clinopyroxenite and gabbroic lithologies. This rock association is considered to represent cumulates of a single parental melt feeding a magma chamber system. In this study we discuss in-situ trace element variations (LA-ICPMS analyses) in clinopyroxene from gabbros of the Nizhnii Tagil and Kytlym complexes in the Ural Mountains in Russia. The gabbros have porphyric textures with clinopyroxene phenocrysts in a matrix of olivine, clinopyroxene and spinel. Two gabbro types can be distinguished based on additional matrix minerals. One type of gabbro is silica saturated, contains plagioclase (An57-88) and in places orthopyroxene as matrix phases. This type occurs in all complexes. The second gabbro type is silica undersaturated and contains in the matrix plagioclase (An29-56) and pseudoleucite, a fine grained intergrowth of nepheline and K- feldspar (Or30-81). It is only observed in Nizhnii Tagil and the western part of the Kytlym Complex, however, it is interbedded on a scale of decimeter to tens of meters with the silica-saturated gabbro. Clinopyroxene of gabbros from Nizhnii Tagil and the western part of the Kytlym Complex is enriched in LREEN (4.4-33.6; normalized to the primitive mantle values of Hofmann (1988)) relative to HREEN (1.4-8.4) and have high Sr concentrations (130-470 ppm). Phenocryst cores from pseudoleucite-bearing gabbros tend to have higher La/Lu (30-35) than those of silicate-saturated gabbros (La/Lu: 17-30). Towards the phenocryst rims the La/Lu increases up to 45 in the pseudolucite bearing gabbros monitoring the trend of fractional crystallization. However, the continuous increase of La/Lu from silica-saturated to silica-undersaturated gabbro traces the mixing of two different parental magmas. Clinopyroxene from gabbros of the Tilay Mountain area in the eastern part of the Kytlym Complex are consistently less enriched in LREEN (0.9-13.1) relative to the HREEN (0.7-9.1) and have lower Sr concentrations (27-76ppm) than those from the other localities. On the scale of a thin section cores of phenocrysts with different LREE/HREE can be observed. Cores, rich in inclusions of olivine, plagioclase, spinel and phlogopite have La/Lu of 13-16, whereas other clinopyroxene cores are poor in inclusions and have lower La/Lu of 5-8 at similar Lu concentrations (0.15-0.2 ppm). Just outside of the core both phenocryst types have similar La/Lu of 9-11 and Lu 0.2-0.3 ppm. The rims of the phenocrysts and the interstitial clinopyroxene have similar trace element compositions with lower La/Lu (9-7) and higher Lu concentrations (0.3-0.5ppm). This reflects the crystallization of a common interstitial pore liquid. However, the core compositions indicate the presence of two different parental magmas. After mixing of these magmas the clinopyroxene cores were overgrown by clinopyroxene crystallizing from the hybrid magma. The observed variations in the trace element content of clinopyroxene monitor the evolution of the parental melts of Uralian-Alaskan-type Complexes and emphasize the importance of magma mixing processes. The contemporaneous occurrence of silica-saturated and -undersaturated melts appears to be a common feature of the Uralian complexes.

  16. Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia

    PubMed Central

    Getachew, Sisay; To, Sheren; Trimarsanto, Hidayat; Thriemer, Kamala; Clark, Taane G.; Petros, Beyene; Aseffa, Abraham; Price, Ric N.; Auburn, Sarah

    2015-01-01

    Background P. vivax is an important public health burden in Ethiopia, accounting for almost half of all malaria cases. Owing to heterogeneous transmission across the country, a stronger evidence base on local transmission dynamics is needed to optimise allocation of resources and improve malaria interventions. Methodology and Principal Findings In a pilot evaluation of local level P. vivax molecular surveillance in southern Ethiopia, the diversity and population structure of isolates collected between May and November 2013 were investigated. Blood samples were collected from microscopy positive P. vivax patients recruited to clinical and cross-sectional surveys from four sites: Arbaminch, Halaba, Badawacho and Hawassa. Parasite genotyping was undertaken at nine tandem repeat markers. Eight loci were successfully genotyped in 197 samples (between 36 and 59 per site). Heterogeneity was observed in parasite diversity and structure amongst the sites. Badawacho displayed evidence of unstable transmission, with clusters of identical clonal infections. Linkage disequilibrium in Badawacho was higher (IAS = 0.32, P = 0.010) than in the other populations (IAS range = 0.01–0.02) and declined markedly after adjusting for identical infections (IAS = 0.06, P = 0.010). Other than Badawacho (HE = 0.70), population diversity was equivalently high across the sites (HE = 0.83). Polyclonal infections were more frequent in Hawassa (67%) than the other populations (range: 8–44%). Despite the variable diversity, differentiation between the sites was low (FST range: 5 x 10?3–0.03). Conclusions Marked variation in parasite population structure likely reflects differing local transmission dynamics. Parasite genotyping in these heterogeneous settings has potential to provide important complementary information with which to optimise malaria control interventions. PMID:26468643

  17. Variations in atmospheric PM trace metal content in Spanish towns: Illustrating the chemical complexity of the inorganic urban aerosol cocktail

    NASA Astrophysics Data System (ADS)

    Moreno, Teresa; Querol, Xavier; Alastuey, Andrés; Viana, Mar; Salvador, Pedro; Sánchez de la Campa, Ana; Artiñano, Begoña; de la Rosa, Jesús; Gibbons, Wes

    The majority of the Spanish urban population breathe air containing inhalable ambient airborne particles at average concentrations of 30-46 ?g m -3 (PM 10) and 20-30 ?g m -3 (PM 2.5). Even though the average weight of inhaled urban aerosol is commonly similar, however, there can be large chemical differences between the ambient dusts from different towns, including the more bioreactive elements such as some metals. In this context, we compare the source-apportioned trace metal content of airborne PM 10 and PM 2.5 collected daily over a 1-year period from six population centres in Spain: Barcelona, Alcobendas, Llodio, Huelva, Tarragona and Las Palmas de Gran Canaria. Total average trace metal (?TM) PM 10 and PM 2.5 contents vary by up to a factor of around 3, reaching a maximum of ?TM 10 811 ng m -3 and ?TM 2.5 503 ng m -3 at Llodio, an industrial but humid site with the lowest PM 10 mass levels but high contamination by Zn, Pb, Mn, Sn, Ni and Cr. In contrast, pollution at Huelva, although another industrially influenced site, instead emphasises Cu and As, whereas Barcelona, where traffic emissions and resuspension contribute to some of the highest average PM 10 levels in Spain, has unusually raised levels of Ti, V and Ba. Such variations in both daily and annual average PM bulk chemistry, particularly in potentially toxic trace metals concentrated in the finer aerosols (such as Cd, As, Pb, Hg and Ni), predict that PM health effects on resident populations from different towns are unlikely to be the same.

  18. The Power of Gene-Based Rare Variant Methods to Detect Disease-Associated Variation and Test Hypotheses About Complex Disease

    PubMed Central

    Fuchsberger, Christian; Flannick, Jason; Rivas, Manuel A.; Gaulton, Kyle J.; Albers, Patrick K.; McVean, Gil; Boehnke, Michael; Altshuler, David; McCarthy, Mark I.

    2015-01-01

    Genome and exome sequencing in large cohorts enables characterization of the role of rare variation in complex diseases. Success in this endeavor, however, requires investigators to test a diverse array of genetic hypotheses which differ in the number, frequency and effect sizes of underlying causal variants. In this study, we evaluated the power of gene-based association methods to interrogate such hypotheses, and examined the implications for study design. We developed a flexible simulation approach, using 1000 Genomes data, to (a) generate sequence variation at human genes in up to 10K case-control samples, and (b) quantify the statistical power of a panel of widely used gene-based association tests under a variety of allelic architectures, locus effect sizes, and significance thresholds. For loci explaining ~1% of phenotypic variance underlying a common dichotomous trait, we find that all methods have low absolute power to achieve exome-wide significance (~5-20% power at ?=2.5×10-6) in 3K individuals; even in 10K samples, power is modest (~60%). The combined application of multiple methods increases sensitivity, but does so at the expense of a higher false positive rate. MiST, SKAT-O, and KBAC have the highest individual mean power across simulated datasets, but we observe wide architecture-dependent variability in the individual loci detected by each test, suggesting that inferences about disease architecture from analysis of sequencing studies can differ depending on which methods are used. Our results imply that tens of thousands of individuals, extensive functional annotation, or highly targeted hypothesis testing will be required to confidently detect or exclude rare variant signals at complex disease loci. PMID:25906071

  19. Variation of bulk Lorentz factor in AGN jets due to Compton rocket in a complex photon field

    NASA Astrophysics Data System (ADS)

    Vuillaume, T.; Henri, G.; Petrucci, P.-O.

    2015-09-01

    Radio-loud active galactic nuclei are among the most powerful objects in the universe. In these objects, most of the emission comes from relativistic jets getting their power from the accretion of matter ontosupermassive black holes. However, despite the number of studies, a jet's acceleration to relativistic speeds is still poorly understood. It is widely known that jets contain relativistic particles that emit radiation through several physical processes, one of them being the inverse Compton scattering of photons coming from external sources. In the case of a plasma composed of electrons and positrons continuously heated by the turbulence, inverse Compton scattering can lead to relativistic bulk motions through the Compton rocket effect. We investigate this process and compute the resulting bulk Lorentz factor in the complex photon field of an AGN composed of several external photon sources. We consider various sources:the accretion disk, the dusty torus, and the broad line region. We take their geometry and anisotropy carefully into account in order to numerically compute the bulk Lorentz factor of the jet at every altitude. The study, made for a broad range of parameters, shows interesting and unexpected behaviors of the bulk Lorentz factor, exhibiting acceleration and deceleration zones in the jet. We investigate the patterns of the bulk Lorentz factor along the jet depending on the source sizes and on the observation angle and we finally show that these patterns can induce variability in the AGN emission with timescales going from hours to months.

  20. Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas.

    PubMed

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

    2014-06-01

    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

  1. Genetic Variation on the BAT1-NFKBIL1-LTA Region of Major Histocompatibility Complex Class III Associates with Periodontitis

    PubMed Central

    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.

    2014-01-01

    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 (r2, ?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

  2. Alkaloid polymorphism and ITS sequence variation in the Spiraea japonica complex (Rosaceae) in China: traces of the biological effects of the Himalaya-Tibet Plateau uplift.

    PubMed

    Zhang, Zhaoyang; Fan, Liming; Yang, Junbo; Hao, Xiaojiang; Gu, Zhijian

    2006-05-01

    Spiraea japonica, a diverse, perennial shrubby species complex widespread across E Asia, was a useful model in a first attempt to link specific phylogeny, floristic evolution, and historical environmental changes in E Asia. DNA-based phylogenetic reconstruction served as a framework to investigate whether the patterns of variation in alkaloids and nrITS from varieties of S. japonica reflect the geological history of China and the uplifting of the Himalaya-Tibet plateau, the most significant geological event in E Asia since the late Paleocene. The high geographical structure found in the phylogenetic trees was corroborated by the distribution of alkaloids. All populations from E China, with mainly hetisine-type alkaloids, formed a single clade, sister to a clade of all populations from SW China, with mainly atisine-type alkaloids. The distribution boundary between the two clades roughly matched the floristic division between the Sino-Japanese Forest and the Sino-Himalayan Forest subkingdoms, as well as the environmental division between SW and E China, suggesting a close link between specific phylogeny, floristic evolution, and geographical changes in E Asia. The divergence between lineages at variety and population level within the eastern clade was slightly older than those within the southwestern clade, supporting the hypothesis of a northeast-southwest migration of Spiraea since the Eocene. The uplift of the Himalaya-Tibet plateau and subsequent increase in geographical complexity in SW China, could facilitate divergence maintenance, thus accelerating the evolutionary rate. PMID:21642139

  3. One-electron self-interaction and the asymptotics of the Kohn-Sham potential: an impaired relation

    E-print Network

    Schmidt, Tobias; Kronik, Leeor; Kümmel, Stephan

    2015-01-01

    One-electron self-interaction and an incorrect asymptotic behavior of the Kohn-Sham exchange-correlation potential are among the most prominent limitations of many present-day density functionals. However, a one-electron self-interaction-free energy does not necessarily lead to the correct long-range potential. This is here shown explicitly for local hybrid functionals. Furthermore, carefully studying the ratio of the von Weizs\\"acker kinetic energy density to the (positive) Kohn-Sham kinetic energy density, $\\tau_\\mathrm{W}/\\tau$, reveals that this ratio, which frequently serves as an iso-orbital indicator and is used to eliminate one-electron self-interaction effects in meta-generalized-gradient approximations and local hybrid functionals, can fail to approach its expected value in the vicinity of orbital nodal planes. This perspective article suggests that the nature and consequences of one-electron self-interaction and some of the strategies for its correction need to be reconsidered.

  4. Kohn–Sham approach to quantum electrodynamical density-functional theory: Exact time-dependent effective potentials in real space

    PubMed Central

    Flick, Johannes; Ruggenthaler, Michael; Appel, Heiko; Rubio, Angel

    2015-01-01

    The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron–photon interactions in terms of effective Kohn–Sham potentials. In this work, we numerically construct the exact electron–photon Kohn–Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light–matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account. PMID:26627715

  5. The Kohn-Luttinger mechanism and phase diagram of the superconducting state in the Shubin-Vonsovsky model

    SciTech Connect

    Kagan, M. Yu.; Val'kov, V. V.; Mitskan, V. A.; Korovuskin, M. M.

    2013-10-15

    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.

  6. Kohn-Sham approach to quantum electrodynamical density-functional theory: Exact time-dependent effective potentials in real space.

    PubMed

    Flick, Johannes; Ruggenthaler, Michael; Appel, Heiko; Rubio, Angel

    2015-12-15

    The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron-photon interactions in terms of effective Kohn-Sham potentials. In this work, we numerically construct the exact electron-photon Kohn-Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light-matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account. PMID:26627715

  7. Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory

    NASA Technical Reports Server (NTRS)

    Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.

    1990-01-01

    New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.

  8. Of mice and the 'Age of Discovery': the complex history of colonization of the Azorean archipelago by the house mouse (Mus musculus) as revealed by mitochondrial DNA variation.

    PubMed

    Gabriel, S I; Mathias, M L; Searle, J B

    2015-01-01

    Humans have introduced many species onto remote oceanic islands. The house mouse (Mus musculus) is a human commensal and has consequently been transported to oceanic islands around the globe as an accidental stowaway. The history of these introductions can tell us not only about the mice themselves but also about the people that transported them. Following a phylogeographic approach, we used mitochondrial D-loop sequence variation (within an 849- to 864-bp fragment) to study house mouse colonization of the Azores. A total of 239 sequences were obtained from all nine islands, and interpretation was helped by previously published Iberian sequences and 66 newly generated Spanish sequences. A Bayesian analysis revealed presence in the Azores of most of the D-loop clades previously described in the domesticus subspecies of the house mouse, suggesting a complex colonization history of the archipelago as a whole from multiple geographical origins, but much less heterogeneity (often single colonization?) within islands. The expected historical link with mainland Portugal was reflected in the pattern of D-loop variation of some of the islands but not all. A more unexpected association with a distant North European source area was also detected in three islands, possibly reflecting human contact with the Azores prior to the 15th century discovery by Portuguese mariners. Widening the scope to colonization of the Macaronesian islands as a whole, human linkages between the Azores, Madeira, the Canaries, Portugal and Spain were revealed through the sharing of mouse sequences between these areas. From these and other data, we suggest mouse studies may help resolve historical uncertainties relating to the 'Age of Discovery'. PMID:25394749

  9. A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations.

    PubMed

    Rai, Rajani; Kim, Jong Joo; Misra, Sanjeev; Kumar, Ashok; Mittal, Balraj

    2015-01-01

    Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR) and Classification and Regression Tree Analysis (CRT) to investigate the gene-gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634); FAS (rs2234767); FASL (rs763110); DCC (rs2229080, rs4078288, rs7504990, rs714); PSCA (rs2294008, rs2978974); ADRA2A (rs1801253); ADRB1 (rs1800544); ADRB3 (rs4994); CYP17 (rs2486758)) involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634), DCC (rs714, rs2229080, rs4078288) and ADRB3 (rs4994) polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994) to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10) or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10). Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility. PMID:26602921

  10. Spin densities and covalency in transition-metal complexes: A comparison of discrete variational X? calculations with polarised neutron diffraction data

    NASA Astrophysics Data System (ADS)

    Deeth, Robert J.; Figgis, Brian N.; Ogden, Mark I.

    1988-03-01

    Spin-unrestricted discrete variational X? self-consistent charge (DVX? SCC) calculations for the cubic transition-metal complexes [CoCl 4] 2-, [CoBr 4] 2-, [FeCl 4] -, [CrF 6] 3- and [Cr(CN) 6] 3- are reported. The calculated covalencies exhibit the same trends predicted by empirical nephelauxetic parameters. However, agreement between the experimental ligand-field splittings and theoretical values determined via Koopman's theorem is poorer, particularly for the tetrahedral species. The computed spin densities are compared in detail with experimental results derived from polarised neutron diffraction (PND) studies and with unrestricted Hartree-Fock (UHF) calculations. The qualitative agreement with the PND data is good and for [CoCl 4] 2- and [CrF 6] 3- the DVX? SCC and UHF models give almost identical spin densities. However, quantitative agreement with experiment is not obtained because the calculations ignore the real molecular site symmetry, the crystalline environment and configuration interaction (CI). These features appear to influence significantly the experimental spin and charge densities and, except for CI, can be readily included in DVX? SCC calculations. The present work suggests that the DVX? SCC scheme gives a sufficiently accurate description of electron distributions to provide a useful tool for further examination of these effects.

  11. Morphological variation in Echinorhynchus truttae Schrank, 1788 and the Echinorhynchus bothniensis Zdzitowiecki & Valtonen, 1987 species complex from freshwater fishes of northern Europe

    PubMed Central

    2013-01-01

    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. PMID:24723769

  12. Mixed-Methods Research in a Complex Multisite VA Health Services Study: Variations in the Implementation and Characteristics of Chiropractic Services in VA

    PubMed Central

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

    2013-01-01

    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

  13. Variations on Instant Insanity

    E-print Network

    Demaine, Erik D.

    2013-01-01

    In one of the first papers about the complexity of puzzles, Robertson and Munro [14] proved that a generalized form of the then-popular Instant Insanity puzzle is NP-complete. Here we study several variations of this puzzle, ...

  14. Linear interpolation method in ensemble Kohn-Sham and range-separated density-functional approximations for excited states

    NASA Astrophysics Data System (ADS)

    Senjean, Bruno; Knecht, Stefan; Jensen, Hans Jørgen Aa.; Fromager, Emmanuel

    2015-07-01

    Gross-Oliveira-Kohn density-functional theory (GOK-DFT) for ensembles is, in principle, very attractive but has been hard to use in practice. A practical model based on GOK-DFT for the calculation of electronic excitation energies is discussed. The model relies on two modifications of GOK-DFT: use of range separation and use of the slope of the linearly interpolated ensemble energy, rather than orbital energies. The range-separated approach is appealing, as it enables the rigorous formulation of a multideterminant state-averaged DFT method. In the exact theory, the short-range density functional, which complements the long-range wave-function-based ensemble energy contribution, should vary with the ensemble weights even when the density is held fixed. This weight dependence ensures that the range-separated ensemble energy varies linearly with the ensemble weights. When the (weight-independent) ground-state short-range exchange-correlation functional is used in this context, curvature appears, thus leading to an approximate weight-dependent excitation energy. In order to obtain unambiguous approximate excitation energies, we propose to interpolate linearly the ensemble energy between equiensembles. It is shown that such a linear interpolation method (LIM) can be rationalized and that it effectively introduces weight dependence effects. As proof of principle, the LIM has been applied to He, Be, and H2 in both equilibrium and stretched geometries as well as the stretched HeH+ molecule. Very promising results have been obtained for both single (including charge transfer) and double excitations with spin-independent short-range local and semilocal functionals. Even at the Kohn-Sham ensemble DFT level, which is recovered when the range-separation parameter is set to 0, LIM performs better than standard time-dependent DFT.

  15. Genetic Variation of the Major Histocompatibility Complex (MHC Class II B Gene) in the Threatened Hume’s Pheasant, Syrmaticus humiae

    PubMed Central

    Chen, Weicai; Bei, Yongjian; Li, Hanhua

    2015-01-01

    Major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates and encode molecules that play a crucial role in pathogen resistance. As a result of their diversity, they have received much attention in the fields of evolutionary and conservation biology. Here, we described the genetic variation of MHC class II B (MHCIIB) exon 2 in a wild population of Hume’s pheasant (Syrmaticus humiae), which has suffered a dramatic decline in population over the last three decades across its ranges in the face of heavy exploitation and habitat loss. Twenty-four distinct alleles were found in 73 S. humiae specimens. We found seven shared alleles among four geographical groups as well as six rare MHCIIB alleles. Most individuals displayed between one to five alleles, suggesting that there are at least three MHCIIB loci of the Hume’s pheasant. The dN ? dS ratio at putative antigen-binding sites (ABS) was significantly greater than one, indicating balancing selection is acting on MHCIIB exon 2. Additionally, recombination and gene conversion contributed to generating MHCIIB diversity in the Hume’s pheasant. One to three recombination events and seventy-five significant gene conversion events were observed within the Hume’s pheasant MHCIIB loci. The phylogenetic tree and network analysis revealed that the Hume’s pheasant alleles do not cluster together, but are scattered through the tree or network indicating a trans-species evolutionary mode. These findings revealed the evolution of the Hume’s pheasant MHC after suffering extreme habitat fragmentation. PMID:25629763

  16. Calculations of Al dopant in ?-quartz using a variational implementation of the Perdew-Zunger self-interaction correction

    NASA Astrophysics Data System (ADS)

    Gudmundsdóttir, Hildur; Jónsson, Elvar Ö.; Jónsson, Hannes

    2015-08-01

    The energetics and atomic structure associated with the localized hole formed near an Al-atom dopant in ?-quartz are calculated using a variational, self-consistent implementation of the Perdew-Zunger self-interaction correction with complex optimal orbitals. This system has become an important test problem for theoretical methodology since generalized gradient approximation energy functionals, as well as commonly used hybrid functionals, fail to produce a sufficiently localized hole due to the self-interaction error inherent in practical implementations of Kohn-Sham density functional theory. The self-interaction corrected calculations are found to give accurate results for the energy of the defect state with respect to both valence and conduction band edges as well as the experimentally determined atomic structure where only a single Al-O bond is lengthened by 11%. The HSE hybrid functional, as well as the PW91 generalized gradient approximation functional, however, gives too small an energy gap between the defect state and the valence band edge, overly delocalized spin density and lengthening of more than one Al-O bond.

  17. A low-complexity 2-point step size gradient projection method with selective function evaluations for smoothed total variation based CBCT reconstructions

    NASA Astrophysics Data System (ADS)

    Song, Bongyong; Park, Justin C.; Song, William Y.

    2014-11-01

    The Barzilai-Borwein (BB) 2-point step size gradient method is receiving attention for accelerating Total Variation (TV) based CBCT reconstructions. In order to become truly viable for clinical applications, however, its convergence property needs to be properly addressed. We propose a novel fast converging gradient projection BB method that requires ‘at most one function evaluation’ in each iterative step. This Selective Function Evaluation method, referred to as GPBB-SFE in this paper, exhibits the desired convergence property when it is combined with a ‘smoothed TV’ or any other differentiable prior. This way, the proposed GPBB-SFE algorithm offers fast and guaranteed convergence to the desired 3DCBCT image with minimal computational complexity. We first applied this algorithm to a Shepp-Logan numerical phantom. We then applied to a CatPhan 600 physical phantom (The Phantom Laboratory, Salem, NY) and a clinically-treated head-and-neck patient, both acquired from the TrueBeam™ system (Varian Medical Systems, Palo Alto, CA). Furthermore, we accelerated the reconstruction by implementing the algorithm on NVIDIA GTX 480 GPU card. We first compared GPBB-SFE with three recently proposed BB-based CBCT reconstruction methods available in the literature using Shepp-Logan numerical phantom with 40 projections. It is found that GPBB-SFE shows either faster convergence speed/time or superior convergence property compared to existing BB-based algorithms. With the CatPhan 600 physical phantom, the GPBB-SFE algorithm requires only 3 function evaluations in 30 iterations and reconstructs the standard, 364-projection FDK reconstruction quality image using only 60 projections. We then applied the algorithm to a clinically-treated head-and-neck patient. It was observed that the GPBB-SFE algorithm requires only 18 function evaluations in 30 iterations. Compared with the FDK algorithm with 364 projections, the GPBB-SFE algorithm produces visibly equivalent quality CBCT image for the head-and-neck patient with only 180 projections, in 131.7?s, further supporting its clinical applicability.

  18. The ecological complexity of the Thai-Laos Mekong River: I. Geology, seasonal variation and human impact assessment on river quality.

    PubMed

    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

    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

  19. Plane-wave pseudopotential implementation of explicit integrators for time-dependent Kohn-Sham equations in large-scale simulations.

    PubMed

    Schleife, André; Draeger, Erik W; Kanai, Yosuke; Correa, Alfredo A

    2012-12-14

    Explicit integrators for real-time propagation of time-dependent Kohn-Sham equations are compared regarding their suitability for performing large-scale simulations. Four algorithms are implemented and assessed for both stability and accuracy within a plane-wave pseudopotential framework, employing the adiabatic approximation to the exchange-correlation functional. Simulation results for a single sodium atom and a sodium atom embedded in bulk magnesium oxide are discussed. While the first-order Euler scheme and the second-order finite-difference scheme are unstable, the fourth-order Runge-Kutta scheme is found to be conditionally stable and accurate within this framework. Excellent parallel scalability of the algorithm up to more than a thousand processors is demonstrated for a system containing hundreds of electrons, evidencing the suitability for large-scale simulations based on real-time propagation of time-dependent Kohn-Sham equations. PMID:23249083

  20. A self-interaction-free local hybrid functional: Accurate binding energies vis-à-vis accurate ionization potentials from Kohn-Sham eigenvalues

    SciTech Connect

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

    2014-05-14

    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.

  1. Variation in DNA binding constants with a change in geometry of ternary copper(II) complexes with N2O donor Schiff base and cyanate or dicyanamide

    NASA Astrophysics Data System (ADS)

    Jana, Subrata; Santra, Ramesh Chandra; Das, Saurabh; Chattopadhyay, Shouvik

    2014-09-01

    Two new copper(II) complexes, [Cu(L)(OCN)] (1) and [CuL(dca)]n (2), where HL = 2-(-(2-(diethylamino)ethylimino)methyl)naphthalen-1-ol, dca = N(CN)2-, have been synthesized and characterized by elemental analysis, IR, UV-VIS spectroscopy and single crystal X-ray diffraction studies. Complex 1 has square planar and complex 2 square pyramidal geometries in solid state around metal centre. Interactions of the complexes with calf thymus DNA (CT DNA) were studied by UV-VIS spectroscopy. Binding constant and site size of interaction were determined. Binding site size and intrinsic binding constant K revealed complex 1 interacted with calf thymus DNA better than complex 2.

  2. Combining Kohn-Sham and orbital-free density-functional theory for Hugoniot calculations to extreme pressures

    NASA Astrophysics Data System (ADS)

    Sheppard, Daniel; Kress, Joel D.; Crockett, Scott; Collins, Lee A.; Desjarlais, Michael P.

    2014-12-01

    The shock Hugoniot for lithium 6 deuteride (6LiD) was calculated via first principles using Kohn-Sham density-functional theory molecular dynamics (KSMD) for temperatures of 0.5-25 eV. The upper limit of 25 eV represents a practical limit where KSMD is no longer computationally feasible due to the number of electronic bands which are required to be populated. To push the Hugoniot calculations to higher temperatures we make use of orbital-free density-functional theory molecular dynamics (OFMD). Thomas-Fermi-Dirac-based OFMD gives a poor description of the electronic structure at low temperatures so the initial state is not well defined. We propose a method of bootstrapping the Hugoniot from OFMD to the Hugoniot from KSMD between 10 and 20 eV, where the two methods are in agreement. The combination of KSMD and OFMD allows construction of a first-principles Hugoniot from the initial state to 1000 eV. Theoretical shock-compression results are in good agreement with available experimental data and exhibit the appropriate high-temperature limits. We show that a unified KSMD-OFMD Hugoniot can be used to assess the quality of the existing equation-of-state (EOS) models and inform better EOS models based on justifiable physics.

  3. Direct mapping between exchange potentials of Hartree-Fock and Kohn-Sham schemes as origin of orbital proximity.

    PubMed

    Cinal, M

    2010-01-01

    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

  4. Kohn-Sham Band Structure Benchmark Including Spin-Orbit Coupling for 2D and 3D Solids

    NASA Astrophysics Data System (ADS)

    Huhn, William; Blum, Volker

    2015-03-01

    Accurate electronic band structures serve as a primary indicator of the suitability of a material for a given application, e.g., as electronic or catalytic materials. Computed band structures, however, are subject to a host of approximations, some of which are more obvious (e.g., the treatment of the exchange-correlation of self-energy) and others less obvious (e.g., the treatment of core, semicore, or valence electrons, handling of relativistic effects, or the accuracy of the underlying basis set used). We here provide a set of accurate Kohn-Sham band structure benchmarks, using the numeric atom-centered all-electron electronic structure code FHI-aims combined with the ``traditional'' PBE functional and the hybrid HSE functional, to calculate core, valence, and low-lying conduction bands of a set of 2D and 3D materials. Benchmarks are provided with and without effects of spin-orbit coupling, using quasi-degenerate perturbation theory to predict spin-orbit splittings. This work is funded by Fritz-Haber-Institut der Max-Planck-Gesellschaft.

  5. Combining Kohn-Sham and orbital-free density-functional theory for Hugoniot calculations to extreme pressures.

    PubMed

    Sheppard, Daniel; Kress, Joel D; Crockett, Scott; Collins, Lee A; Desjarlais, Michael P

    2014-12-01

    The shock Hugoniot for lithium 6 deuteride ((6)LiD) was calculated via first principles using Kohn-Sham density-functional theory molecular dynamics (KSMD) for temperatures of 0.5-25 eV. The upper limit of 25 eV represents a practical limit where KSMD is no longer computationally feasible due to the number of electronic bands which are required to be populated. To push the Hugoniot calculations to higher temperatures we make use of orbital-free density-functional theory molecular dynamics (OFMD). Thomas-Fermi-Dirac-based OFMD gives a poor description of the electronic structure at low temperatures so the initial state is not well defined. We propose a method of bootstrapping the Hugoniot from OFMD to the Hugoniot from KSMD between 10 and 20 eV, where the two methods are in agreement. The combination of KSMD and OFMD allows construction of a first-principles Hugoniot from the initial state to 1000 eV. Theoretical shock-compression results are in good agreement with available experimental data and exhibit the appropriate high-temperature limits. We show that a unified KSMD-OFMD Hugoniot can be used to assess the quality of the existing equation-of-state (EOS) models and inform better EOS models based on justifiable physics. PMID:25615229

  6. Estimation of formamide harmonic and anharmonic modes in the Kohn-Sham limit using the polarization consistent basis sets.

    PubMed

    Buczek, Aneta; Kupka, Teobald; Broda, Ma?gorzata A

    2011-09-01

    Formamide harmonic and anharmonic frequencies of fundamental vibrations in the gas phase and in several solvents were successfully estimated in the B3LYP Kohn-Sham complete basis set limit (KS CBS). CBS results were obtained by extrapolating a power function (two-parameter formula) to the results calculated with polarization-consistent basis sets. Anharmonic corrections using the second order perturbation treatment (PT2) and hybrid B3LYP functional combined with polarization consistent pc-n (n=0, 1, 2, 3, 4) and several Pople's basis sets were analyzed for all fundamental formamide vibrational modes in the gas phase and solution. Solvent effects were modeled within a PCM method. The anharmonic frequency of diagnostic amide vibration C=O in the gas phase and the CCl(4) solution calculated with the VPT2 method was significantly closer to experimental data than the corresponding harmonic frequency. Both harmonic and anharmonic frequencies of C=O stretching mode decreased linearly with solvent polarity, expressed by relative environment permittivity (?) ratio (?-1)/(2?+1). However, an unphysical behavior of solvent dependence of some low frequency anharmonic amide modes of formamide (e.g., CN stretch, NH(2) scissoring, and NH(2) in plane bend) was observed, probably due to the presence of severe anharmonicity and Fermi resonance. PMID:21267754

  7. Chebyshev-filtered subspace iteration method free of sparse diagonalization for solving the Kohn–Sham equation

    SciTech Connect

    Zhou, Yunkai; Chelikowsky, James R.; Saad, Yousef

    2014-10-01

    First-principles density functional theory (DFT) calculations for the electronic structure problem require a solution of the Kohn–Sham equation, which requires one to solve a nonlinear eigenvalue problem. Solving the eigenvalue problem is usually the most expensive part in DFT calculations. Sparse iterative diagonalization methods that compute explicit eigenvectors can quickly become prohibitive for large scale problems. The Chebyshev-filtered subspace iteration (CheFSI) method avoids most of the explicit computation of eigenvectors and results in a significant speedup over iterative diagonalization methods for the DFT self-consistent field (SCF) calculations. However, the original formulation of the CheFSI method utilizes a sparse iterative diagonalization at the first SCF step to provide initial vectors for subspace filtering at latter SCF steps. This diagonalization is expensive for large scale problems. We develop a new initial filtering step to avoid completely this diagonalization, thus making the CheFSI method free of sparse iterative diagonalizations at all SCF steps. Our new approach saves memory usage and can be two to three times faster than the original CheFSI method.

  8. Photoluminescent mixed ligand complexes of CuX (X = Cl, Br, I) with PPh3 and a polydentate imino-pyridyl ligand - Syntheses, structural variations and catalytic property

    NASA Astrophysics Data System (ADS)

    Ghorai, Anupam; Mondal, Jahangir; Patra, Goutam K.

    2015-10-01

    Three ternary copper(I) complexes [CuI2Cl2(L1)(PPh3)4] (1), [CuI2Br2(L1) (PPh3)4] (2) and [CuI2(?-I)2 (?-L1) (PPh3)2]n (3) have been prepared by reactions of CuX (X = Cl, Br and I) with PPh3 and the polydentate imino-pyridyl ligand L1. These complexes have been characterized by elemental analysis, IR, UV-Vis, NMR and X-ray crystallography. From single crystal structural analysis it has been found that complexes 1 and 2 are homo-dinuclear having non-bridging halide ions whereas complex 3 is a 1-D zig-zag co-ordination polymer containing bridged iodide ions. Complexes 1, 2 and 3 are photoluminescent at room temperature in chloroform whereas ligand L1 is non-emissive. The E½ values of the CuIsbnd CuII couple of 1, 2 and 3 are 0.98 V, 0.92 V and 0.42 V respectively (vs Ag/AgCl in 1 M KCl, scan rate 100 mV s-1). All three complexes function as effective catalysts for the synthesis of 2-substituted benzoxazoles.

  9. X-ray absorption resonances near L2,3-edges from real-time propagation of the Dirac-Kohn-Sham density matrix.

    PubMed

    Kadek, Marius; Konecny, Lukas; Gao, Bin; Repisky, Michal; Ruud, Kenneth

    2015-09-21

    The solution of the Liouville-von Neumann equation in the relativistic Dirac-Kohn-Sham density matrix formalism is presented and used to calculate X-ray absorption cross sections. Both dynamical relaxation effects and spin-orbit corrections are included, as demonstrated by calculations of the X-ray absorption of SF6 near the sulfur L2,3-edges. We also propose an analysis facilitating the interpretation of spectral transitions from real-time simulations, and a selective perturbation that eliminates nonphysical excitations that are artifacts of the finite basis representation. PMID:26268195

  10. "Kohn-Shamification" of the classical density-functional theory of inhomogeneous polar molecular liquids with application to liquid hydrogen chloride

    E-print Network

    Johannes Lischner; T. A. Arias

    2008-06-27

    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.

  11. Generalization of internal density-functional theory and Kohn-Sham scheme to multicomponent self-bound systems, and link with traditional density-functional theory

    SciTech Connect

    Messud, Jeremie

    2011-11-15

    We generalize the recently developed ''internal'' density-functional theory (DFT) and Kohn-Sham scheme to multicomponent systems. We obtain a general formalism, applicable for the description of multicomponent self-bound systems (such as molecular systems where the nuclei are treated explicitly, atomic nuclei and mixtures of {sup 3}He and {sup 4}He droplets), where the fundamental translational symmetry has been treated correctly. The main difference with traditional DFT is the explicit inclusion of center-of-mass correlations in the functional. A large part of the paper is dedicated to the application to molecular systems, which permits us to clarify the approximations that underly traditional DFT.

  12. Virial theorem in the Kohn-Sham density-functional theory formalism: accurate calculation of the atomic quantum theory of atoms in molecules energies.

    PubMed

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

    2009-07-14

    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

  13. Phenotypic Variation among Culex pipiens Complex (Diptera: Culicidae) Populations from the Sacramento Valley, California: Horizontal and Vertical Transmission of West Nile Virus, Diapause Potential, Autogeny, and Host Selection

    PubMed Central

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

    2013-01-01

    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

  14. Phenotypic variation among Culex pipiens complex (Diptera: Culicidae) populations from the Sacramento Valley, California: horizontal and vertical transmission of West Nile virus, diapause potential, autogeny, and host selection.

    PubMed

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

    2013-12-01

    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

  15. Small-angle scattering, contrast variation and the study of complex composite materials: A study of the structure of carbon black

    SciTech Connect

    Hjelm, R.P. Jr.; Seeger, P.A. ); Wampler, W.A. )

    1993-01-01

    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.

  16. Small-angle scattering, contrast variation and the study of complex composite materials: A study of the structure of carbon black

    SciTech Connect

    Hjelm, R.P. Jr.; Seeger, P.A.; Wampler, W.A.

    1993-05-01

    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.

  17. Regularity underlying complexity: a redshift-independent description of the continuous variation of galaxy-scale molecular gas properties in the mass-star formation rate plane

    SciTech Connect

    Sargent, M. T.; Daddi, E.; Béthermin, M.; Aussel, H.; Juneau, S.; Elbaz, D.; Hwang, H. S.; Da Cunha, E.

    2014-09-20

    Star-forming galaxies (SFGs) display a continuous specific star formation rate (sSFR) distribution, which can be approximated by two log-normal functions: one encompassing the galaxy main sequence (MS), and the other a rarer, starbursting population. Starburst (SB) sSFRs can be regarded as the outcome of a physical process (plausibly merging) taking the mathematical form of a log-normal boosting kernel that enhances star formation activity. We explore the utility of splitting the star-forming population into MS and SB galaxies—an approach we term the '2-Star Formation Mode' framework—for understanding their molecular gas properties. Star formation efficiency (SFE) and gas fraction variations among SFGs take a simple redshift-independent form, once these quantities are normalized to the corresponding values for average MS galaxies. SFE enhancements during SB episodes scale supra-linearly with the SFR increase, as expected for mergers. Consequently, galaxies separate more clearly into loci for SBs and normal galaxies in the Schmidt-Kennicutt plane than in (s)SFR versus M {sub *} space. SBs with large deviations (>10 fold) from the MS, e.g., local ULIRGs, are not average SBs, but are much rarer events whose progenitors had larger gas fractions than typical MS galaxies. Statistically, gas fractions in SBs are reduced two- to threefold compared to their direct MS progenitors, as expected for short-lived SFR boosts where internal gas reservoirs are depleted more quickly than gas is re-accreted from the cosmic web. We predict variations of the conversion factor ?{sub CO} in the SFR-M {sub *} plane and we show that the higher sSFR of distant galaxies is directly related to their larger gas fractions.

  18. Ecological Variation in Response to Mass-Flowering Oilseed Rape and Surrounding Landscape Composition by Members of a Cryptic Bumblebee Complex

    PubMed Central

    Stanley, Dara A.; Knight, Mairi E.; Stout, Jane C.

    2013-01-01

    The Bombus sensu stricto species complex is a widespread group of cryptic bumblebee species which are important pollinators of many crops and wild plants. These cryptic species have, until now, largely been grouped together in ecological studies, and so little is known about their individual colony densities, foraging ranges or habitat requirements, which can be influenced by land use at a landscape scale. We used mass-flowering oilseed rape fields as locations to sample bees of this complex, as well as the second most common visitor to oilseed rape B. lapidarius, and molecular RFLP methods to distinguish between the cryptic species. We then used microsatellite genotyping to identify sisters and estimate colony densities, and related both proportions of cryptic species and their colony densities to the composition of the landscape surrounding the fields. We found B. lucorum was the most common member of the complex present in oilseed rape followed by B. terrestris. B. cryptarum was also present in all but one site, with higher proportions found in the east of the study area. High numbers of bumblebee colonies were estimated to be using oilseed rape fields as a forage resource, with B. terrestris colony numbers higher than previous estimates from non-mass-flowering fields. We also found that the cryptic species responded differently to surrounding landscape composition: both relative proportions of B. cryptarum in samples and colony densities of B. lucorum were negatively associated with the amount of arable land in the landscape, while proportions and colony densities of other species did not respond to landscape variables at the scale measured. This suggests that the cryptic species have different ecological requirements (which may be scale-dependent) and that oilseed rape can be an important forage resource for many colonies of bumblebees. Given this, we recommend sustainable management of this crop to benefit bumblebees. PMID:23840338

  19. Protein Folding as a Complex Reaction: A Two-Component Potential for the Driving Force of Folding and Its Variation with Folding Scenario

    PubMed Central

    Chekmarev, Sergei F.

    2015-01-01

    The Helmholtz decomposition of the vector field of probability fluxes in a two-dimensional space of collective variables makes it possible to introduce a potential for the driving force of protein folding [Chekmarev, J. Chem. Phys. 139 (2013) 145103]. The potential has two components: one component (?) is responsible for the source and sink of the folding flow, which represent, respectively, the unfolded and native state of the protein, and the other (?) accounts for the flow vorticity inherently generated at the periphery of the flow field and provides the canalization of the flow between the source and sink. Both components obey Poisson’s equations with the corresponding source/sink terms. In the present paper, we consider how the shape of the potential changes depending on the scenario of protein folding. To mimic protein folding dynamics projected onto a two-dimensional space of collective variables, the two-dimensional Müller and Brown potential is employed. Three characteristic scenarios are considered: a single pathway from the unfolded to the native state without intermediates, two parallel pathways without intermediates, and a single pathway with an off-pathway intermediate. To determine the probability fluxes, the hydrodynamic description of the folding reaction is used, in which the first-passage folding is viewed as a steady flow of the representative points of the protein from the unfolded to the native state. We show that despite the possible complexity of the folding process, the ?-component is simple and universal in shape. The ?-component is more complex and reveals characteristic features of the process of folding. The present approach is potentially applicable to other complex reactions, for which the transition from the reactant to the product can be described in a space of two (collective) variables. PMID:25848943

  20. Protein folding as a complex reaction: a two-component potential for the driving force of folding and its variation with folding scenario.

    PubMed

    Chekmarev, Sergei F

    2015-01-01

    The Helmholtz decomposition of the vector field of probability fluxes in a two-dimensional space of collective variables makes it possible to introduce a potential for the driving force of protein folding [Chekmarev, J. Chem. Phys. 139 (2013) 145103]. The potential has two components: one component (?) is responsible for the source and sink of the folding flow, which represent, respectively, the unfolded and native state of the protein, and the other (?) accounts for the flow vorticity inherently generated at the periphery of the flow field and provides the canalization of the flow between the source and sink. Both components obey Poisson's equations with the corresponding source/sink terms. In the present paper, we consider how the shape of the potential changes depending on the scenario of protein folding. To mimic protein folding dynamics projected onto a two-dimensional space of collective variables, the two-dimensional Müller and Brown potential is employed. Three characteristic scenarios are considered: a single pathway from the unfolded to the native state without intermediates, two parallel pathways without intermediates, and a single pathway with an off-pathway intermediate. To determine the probability fluxes, the hydrodynamic description of the folding reaction is used, in which the first-passage folding is viewed as a steady flow of the representative points of the protein from the unfolded to the native state. We show that despite the possible complexity of the folding process, the ?-component is simple and universal in shape. The ?-component is more complex and reveals characteristic features of the process of folding. The present approach is potentially applicable to other complex reactions, for which the transition from the reactant to the product can be described in a space of two (collective) variables. PMID:25848943

  1. Regulation of genes encoding subunits of the trehalose synthase complex in Saccharomyces cerevisiae: novel variations of STRE-mediated transcription control?

    PubMed

    Winderickx, J; de Winde, J H; Crauwels, M; Hino, A; Hohmann, S; Van Dijck, P; Thevelein, J M

    1996-09-25

    Saccharomyces cerevisiae cells show under suboptimal growth conditions a complex response that leads to the acquisition of tolerance to different types of environmental stress. This response is characterised by enhanced expression of a number of genes which contain so-called stress-responsive elements (STREs) in their promoters. In addition, the cells accumulate under suboptimal conditions the putative stress protectant trehalose. In this work, we have examined the expression of four genes encoding subunits of the trehalose synthase complex, GGS1/TPS1, TPS2, TPS3 and TSL1. We show that expression of these genes is coregulated under stress conditions. Like for many other genes containing STREs, expression of the trehalose synthase genes is also induced by heat and osmotic stress and by nutrient starvation, and negatively regulated by the Ras-cAMP pathway. However, during fermentative growth only TSL1 shows an expression pattern like that of the STRE-controlled genes CTT1 and SSA3, while expression of the three other trehalose synthase genes is only transiently down-regulated. This difference in expression might be related to the known requirement of trehalose biosynthesis for the control of yeast glycolysis and hence for fermentative growth. We conclude that the mere presence in the promoter of (an) active STRE(s) does not necessarily imply complete coregulation of expression. Additional mechanisms appear to fine tune the activity of STREs in order to adapt the expression of the downstream genes to specific requirements. PMID:8879249

  2. Evaluation of the behavior of clouds in a region of severe acid rain pollution in southern China: species, complexes, and variations.

    PubMed

    Sun, Lei; Wang, Yan; Yue, Taixing; Yang, Xueqiao; Xue, Likun; Wang, Wenxing

    2015-09-01

    Cloud samples were collected during the summer of 2011 and the spring of 2012 at a high-elevation site in southern China in an effort to examine the chemical characteristics of acid clouds. In total, 141 cloud samples were collected during 44 cloud events over the observation period. The dominant ionic species were SO4(2-), NH4(+), and NO3(-), contributing approximately 75% of the total inorganic ion concentration. The primary acidifying factors were sulfate and nitrate, and the primary neutralizing factors were ammonium and calcium. The volume-weighted mean (VWM) pH of the cloud water was 3.79, indicating an acidic nature. In these cloud samples, Zn and Al exhibited the highest trace metal concentrations, contributing approximately 60% of the total trace element concentration. Toxic metals, such as Pb, Ba, As, and Cr, were detected at high concentrations, indicating potential hazards for human health, vegetation, and waters in this region. Visual MINTEQ 3.0 results revealed that the majority of Zn(II) and Pb(II) existed in the form of free ions. The behavior of Al, however, differed from the behaviors of zinc and lead. The temporal variation in cloud chemistry indicated that temperature, sandstorms, and long-range transport could affect the concentrations of species. During the lifetime of a cloud event, the concentrations of the chemical species were controlled by the transfer of gases or particles to liquid droplets. PMID:25976330

  3. Unprecedented structural variations in trinuclear mixed valence Co(II/III) complexes: theoretical studies, pnicogen bonding interactions and catecholase-like activities.

    PubMed

    Hazari, Alokesh; Kanta Das, Lakshmi; Kadam, Ramakant M; Bauzá, Antonio; Frontera, Antonio; Ghosh, Ashutosh

    2015-02-28

    Three new mixed valence trinuclear Co(II/III) compounds cis-[Co3L2(MeOH)2(N3)2(?1,1-N3)2] (1), trans-[Co3L2(H2O)2(N3)2(?1,1-N3)2]·(H2O)2 (2) and [Co3L(R)2(N3)3(?1,3-N3)] (3) have been synthesized by reacting a di-Schiff base ligand (H2L) or its reduced form [H2LR] (where H2L= N,N'-bis(salicylidene)-1,3-propanediamine and H2LR= N,N'-bis(2-hydroxybenzyl)-1,3-propanediamine) with cobalt perchlorate hexahydrate and sodium azide. All three products have been characterized by IR, UV-Vis and EPR spectroscopies, ESI-MS, elemental, powder and single crystal X-ray diffraction analyses. Complex 2 is an angular trinuclear species in which two terminal octahedral Co(III)N2O4 centers coordinate to the central octahedral cobalt(II) ion through ?2-phenoxido oxygen and ?1,1-azido nitrogen atoms along with two mutually cis-oxygen atoms of methanol molecules. On the other hand, in linear trinuclear complex , in addition to the ?2-phenoxido and ?1,1-azido bridges with terminal octahedral Co(III) centres, the central Co(II) is bonded with two mutually trans-oxygen atoms of water molecules. Thus the cis-trans configuration of the central Co(II) is solvent dependent. In complex 3, the two terminal octahedral Co(III)N2O4 centers coordinate to the central penta-coordinated Co(II) ion through double phenoxido bridges along with the nitrogen atom of a terminal azido ligand. In addition, the two terminal Co(III) are connected through a ?1,3-azido bridge that participates in pnicogen bonding interactions (intermolecular N-N interaction) as an acceptor. Both the cis and trans isomeric forms of 1 and 2 have been optimized using density functional theory (DFT) calculations and it is found that the cis configuration is energetically more favorable than the trans one. However, the trans configuration of 2 is stabilized by the hydrogen bonding network involving a water dimer. The pnicogen bonding interactions have been demonstrated using MEP surfaces and CSD search which support the counter intuitive electron acceptor ability of the ?1,3-azido ligand. Complexes 1-3 exhibit catecholase-like activities in the aerial oxidation of 3,5-di-tert-butylcatechol to the corresponding o-quinone. Kinetic data analyses of this oxidation reaction in acetonitrile reveal that the catecholase-like activity follows the order: 1 (kcat = 142 h(-1)) > 3 (kcat = 99 h(-1)) > 2 (kcat = 85 h(-1)). Mechanistic investigations of the catalytic behaviors by X-band EPR spectroscopy and estimation of hydrogen peroxide formation indicate that the oxidation reaction proceeds through the reduction of Co(III) to Co(II). PMID:25611163

  4. Variation of exciton-vibrational coupling in photosystem II core complexes from Thermosynechococcus elongatus as revealed by single-molecule spectroscopy.

    PubMed

    Skandary, Sepideh; Hussels, Martin; Konrad, Alexander; Renger, Thomas; Müh, Frank; Bommer, Martin; Zouni, Athina; Meixner, Alfred J; Brecht, Marc

    2015-03-19

    The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang-Rhys factor) with high precision. The Huang-Rhys factors vary between 0.03 and 0.8. The values of the Huang-Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system. PMID:25708355

  5. Variation of Exciton-Vibrational Coupling in Photosystem II Core Complexes from Thermosynechococcus elongatus As Revealed by Single-Molecule Spectroscopy

    PubMed Central

    2015-01-01

    The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang–Rhys factor) with high precision. The Huang–Rhys factors vary between 0.03 and 0.8. The values of the Huang–Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system. PMID:25708355

  6. Variation in parental magmas of Mt Rouse, a complex polymagmatic monogenetic volcano in the basaltic intraplate Newer Volcanics Province, southeast Australia

    NASA Astrophysics Data System (ADS)

    Boyce, Julie A.; Nicholls, Ian A.; Keays, Reid R.; Hayman, Patrick C.

    2015-02-01

    Monogenetic volcanoes have long been regarded as simple in nature, involving single magma batches and uncomplicated evolutions; however, recent detailed research into individual centres is challenging that assumption. Mt Rouse (Kolor) is the volumetrically largest volcano in the monogenetic Newer Volcanics Province of southeast Australia. This study presents new major, trace and Sr-Nd-Pb isotope data for samples selected on the basis of a detailed stratigraphic framework analysis of the volcanic products from Mt Rouse. The volcano is the product of three magma batches geochemically similar to Ocean-Island basalts, featuring increasing LREE enrichment with each magma batch (batches A, B and C) but no evidence of crustal contamination; the Sr-Nd-Pb isotopes define two groupings. Modelling suggests that the magmas were sourced from a zone of partial melting crossing the lithosphere-asthenosphere boundary, with batch A forming a large-volume partial melt in the deep lithosphere (1.7 GPa/55.5 km); and batches B and C from similar areas within the shallow asthenosphere (1.88 GPa/61 km and 1.94 GPa/63 km, respectively). The formation and extraction of these magmas may have been due to high deformation rates in the mantle caused by edge-driven convection and asthenospheric upwelling. The lithosphere-asthenosphere boundary is important with respect to NVP volcanism. An eruption chronology involves sequential eruption of magma batches A, C and B, followed by simultaneous eruption of batches A and B. Mt Rouse is a complex polymagmatic monogenetic volcano that illustrates the complexity of monogenetic volcanism and demonstrates the importance of combining detailed stratigraphic analysis alongside systematic geochemical sampling.

  7. Supramolecular structural variations with changes in anion and solvent in silver(I) complexes of a semirigid, bitopic tris(pyrazolyl)methane ligand.

    PubMed

    Reger, Daniel L; Semeniuc, Radu F; Rassolov, Vitaly; Smith, Mark D

    2004-01-26

    The bitopic ligand p-C(6)H(4)[CH(2)OCH(2)C(pz)(3)](2) (pz = pyrazolyl ring) that contains two tris(pyrazolyl)methane units connected by a semirigid organic spacer reacts with silver(I) salts to yield [p-C(6)H(4)[CH(2)OCH(2)C(pz)(3)](2)(AgX)(2)]( infinity ), where X = CF(3)SO(3)(-) (1), SbF(6)(-) (2), PF(6)(-) (3), BF(4)(-) (4), and NO(3)(-) (5). Crystallization of the first three compounds from acetone yields [p-C(6)H(4)[CH(2)OCH(2)C(pz)(3)](2)(AgCF(3)SO(3))(2)]( infinity ) (1a), [p-C(6)H(4)[CH(2)OCH(2)C(pz)(3)](2)(AgSbF(6))(2)[(CH(3))(2)CO](2)]( infinity ) (2b), and [p-C(6)H(4)[CH(2)OCH(2)C(pz)(3)](2)AgPF(6)]( infinity ) (3a), where the stoichiometry for the latter compound has changed from a metal:ligand ratio of 2:1 to 1:1. The structure of 1a is based on helical argentachains constructed by a kappa(2)-kappa(1) coordination to silver of the tris(pyrazolyl)methane units. These chains are organized into a tubular 3D structure by cylindrical [(CF(3)SO(3))(6)](6)(-) clusters that form weak C-H...O hydrogen bonds with the bitopic ligand. The same kappa(2)-kappa(1) coordination is present in the structure of 2a, but the structure is organized by six different tris(pyrazolyl)methane units from six ligands bonding with six silvers to form a 36-member argentamacrocycle core. The cores are organized in a tubular array by the organic spacers where each pair of macrocycles sandwich six acetone molecules and one SbF(6)(-) counterion. The structure of 3a is based on a kappa(2)-kappa(0) coordination mode of each tris(pyrazolyl)methane unit forming a helical coordination polymer, with two strands organized in a double stranded helical structure by a series of C-H...pi interactions between the central arene rings. Crystallization of 2-4 from acetonitrile yields complexes of the formula [p-C(6)H(4)[CH(2)OCH(2)C(pz)(3)](2)[(AgX)(2)(CH(3)CN)(n)

  8. Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems

    NASA Astrophysics Data System (ADS)

    Hodak, Miroslav; Lu, Wenchang; Bernholc, J.

    2008-01-01

    A hybrid computational method intended for simulations of biomolecules in solution is described. The ab initio Kohn-Sham (KS) density functional theory (DFT) method is used to describe the chemically active part of the system and its first solvation shells, while a frozen-density orbital-free (FDOF) DFT method is used to treat the rest of the solvent. The molecules in the FDOF method have fixed internal structures and frozen electron densities. The hybrid method provides a seamless description of the boundary between the subsystems and allows for the flow of molecules across the boundary. Tests on a liquid water system show that the total energy is conserved well during molecular dynamics and that the effect of the solvent environment on the KS subsystem is well described. An initial application to copper ion binding to the prion protein is also presented.

  9. The one-electron description of excited states: Natural excitation orbitals of density matrix theory and Kohn-Sham orbitals of density functional theory as ideal orbitals

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    Linear response density matrix functional theory has been shown to solve the main problems of time-dependent density functional theory (deficient in case of double, charge transfer and bond breaking excitations). However, the natural orbitals preclude the description of excitations as (approximately) simple orbital-to-orbital transitions: many weakly occupied 'virtual' natural orbitals are required to describe the excitations. Kohn-Sham orbitals on the other hand afford for many excitations such a simple orbital description. In this communication we show that a transformation of the set of weakly occupied NOs can be defined such that the resulting natural excitation orbitals (NEOs) restore the single orbital transition structure for excitations generated by the linear response DMFT formalism.

  10. FROG - Fingerprinting Genomic Variation Ontology.

    PubMed

    Abinaya, E; Narang, Pankaj; Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog. PMID:26244889

  11. FROG - Fingerprinting Genomic Variation Ontology

    PubMed Central

    Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: “FingeRprinting Ontology of Genomic variations” is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog. PMID:26244889

  12. Velocity resolved [CII], [CI], and CO observations of the N159 star-forming region in the Large Magellanic Cloud: a complex velocity structure and variation of the column densities

    E-print Network

    Okada, Yoko; Güsten, Rolf; Stutzki, Jürgen; Wiesemeyer, Helmut; Pütz, Patrick; Ricken, Oliver

    2015-01-01

    The [CII]158um line is one of the dominant cooling lines in star-forming active regions. The commonly assumed clumpy UV-penetrated cloud models predict a [CII] line profile similar to that of CO. However, recent spectral-resolved observations show that they are often very different, indicating a more complex origin of the line emission including the dynamics of the source region. The aim of our study is to investigate the physical properties of the star-forming ISM in the Large Magellanic Cloud (LMC) by separating the origin of the emission lines spatially and spectrally. In this paper, we focus on the spectral characteristics and the origin of the emission lines, and the phases of carbon-bearing species in the N159 star-forming region in the LMC. We mapped a 4'x(3-4)' region in N159 in [CII]158um and [NII]205um with the GREAT on board SOFIA, and in CO(3-2), (4-3), (6-5), 13CO(3-2), and [CI]3P1-3P0 and 3P2-3P1 with APEX. The emission of all transitions observed shows a large variation in the line profiles acr...

  13. Natural Variation in Small Molecule–Induced TIR-NB-LRR Signaling Induces Root Growth Arrest via EDS1- and PAD4-Complexed R Protein VICTR in Arabidopsis[C][W

    PubMed Central

    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

    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. PMID:23275581

  14. Symmetry-adapted perturbation theory with Kohn-Sham orbitals using non-empirically tuned, long-range-corrected density functionals

    SciTech Connect

    Lao, Ka Un; Herbert, John M.

    2014-01-28

    The performance of second-order symmetry-adapted perturbation theory (SAPT) calculations using Kohn-Sham (KS) orbitals is evaluated against benchmark results for intermolecular interactions. Unlike previous studies of this “SAPT(KS)” methodology, the present study uses non-empirically tuned long-range corrected (LRC) functionals for the monomers. The proper v{sub xc} (r)?0 asymptotic limit is achieved by tuning the range separation parameter in order to satisfy the condition that the highest occupied KS energy level equals minus the molecule's ionization energy, for each monomer unit. Tests for He{sub 2}, Ne{sub 2}, and the S22 and S66 data sets reveal that this condition is important for accurate prediction of the non-dispersion components of the energy, although errors in SAPT(KS) dispersion energies remain unacceptably large. In conjunction with an empirical dispersion potential, however, the SAPT(KS) method affords good results for S22 and S66, and also accurately predicts the whole potential energy curve for the sandwich isomer of the benzene dimer. Tuned LRC functionals represent an attractive alternative to other asymptotic corrections that have been employed in density-functional-based SAPT calculations, and we recommend the use of tuned LRC functionals in both coupled-perturbed SAPT(DFT) calculations and dispersion-corrected SAPT(KS) calculations.

  15. Band-structure calculations of noble-gas and alkali halide solids using accurate Kohn-Sham potentials with self-interaction correction

    SciTech Connect

    Li, Y.; Krieger, J.B. ); Norman, M.R. ); Iafrate, G.J. )

    1991-11-15

    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.

  16. Worm variation made accessible

    PubMed Central

    Snoek, L Basten; Joeri van der Velde, K; Li, Yang; Jansen, Ritsert C; Swertz, Morris A; Kammenga, Jan E

    2014-01-01

    In Caenorhabditis elegans, the recent advances in high-throughput quantitative analyses of natural genetic and phenotypic variation have led to a wealth of data on genotype phenotype relations. This data has resulted in the discovery of genes with major allelic effects and insights in the effect of natural genetic variation on a whole range of complex traits as well as how this variation is distributed across the genome. Regardless of the advances presented in specific studies, the majority of the data generated in these studies had yet to be made easily accessible, allowing for meta-analysis. Not only data in figures or tables but meta-data should be accessible for further investigation and comparison between studies. A platform was created where all the data, phenotypic measurements, genotypes, and mappings can be stored, compared, and new linkages within and between published studies can be discovered. WormQTL focuses on quantitative genetics in Caenorhabditis and other nematode species, whereas WormQTLHD quantitatively links gene expression quantitative trait loci (eQTL) in C. elegans to gene–disease associations in humans. PMID:24843834

  17. Explaining Variational Approximations J. T. ORMEROD and M. P. WAND

    E-print Network

    Wand, Matt

    approximations is a body of deterministic tech- niques for making approximate inference for parameters in complex0877055. approximate inference, as well as Laplace approximation meth- ods. Variational approximations

  18. Proteins and Complexity

    NASA Astrophysics Data System (ADS)

    Murray, Joelle; Gibbon, Dana; Runyon, Alissa; Bajracharya, Arun

    2015-03-01

    A protein's tertiary structure determines its function in living organisms. The different functions proteins serve necessitate variety in native structures. How is variation in tertiary structure created from a common set of amino acids and molecular forces? In other words, what generates complexity in structures across all types of native proteins? To explore this question, a simple HP model of protein folding was explored for evidence of self-organized criticality, a potential generator of complexity.

  19. Architecting complex systems for robustness

    E-print Network

    Slagle, Jason C

    2007-01-01

    Robust design methodologies are frequently utilized by organizations to develop robust and reliable complex systems. The intent of robust design is to create systems that are insensitive to variations from production, the ...

  20. Patterned variation in prehistoric chiefdoms

    PubMed Central

    Drennan, Robert D.; Peterson, Christian E.

    2006-01-01

    Comparative study of early complex societies (chiefdoms) conjures visions of a cultural evolutionary emphasis on similarities and societal typology. Variation within the group has not been as systematically examined but offers an even more productive avenue of approach to fundamental principles of organization and change. Three widely separated trajectories of early chiefdom development are compared here: the Valley of Oaxaca (Mexico), the Alto Magdalena (Colombia), and Northeast China. Archaeological data from all three regions are analyzed with the same tools to reveal variation in human activities, relationships, and interactions as these change in the emergence of chiefly communities. Patterning in this variation suggests the operation of underlying general principles, which are offered as hypotheses that merit further investigation and evaluation in comparative study of a much larger number of cases. PMID:16473941

  1. Velocity resolved [C ii], [C i], and CO observations of the N159 star-forming region in the Large Magellanic Cloud: a complex velocity structure and variation of the column densities

    NASA Astrophysics Data System (ADS)

    Okada, Yoko; Requena-Torres, Miguel Angel; Güsten, Rolf; Stutzki, Jürgen; Wiesemeyer, Helmut; Pütz, Patrick; Ricken, Oliver

    2015-08-01

    Context. The [C ii] 158 ?m fine structure line is one of the dominant cooling lines in star-forming active regions. Together with models of photon-dominated regions, the data is used to constrain the physical properties of the emitting regions, such as the density and the radiation field strength. According to the modeling, the [C ii] 158 ?m line integrated intensity compared to the CO emission is expected to be stronger in lower metallicity environments owing to lower dust shielding of the UV radiation, a trend that is also shown by spectral-unresolved observations. In the commonly assumed clumpy UV-penetrated cloud scenario, the models predict a [C ii] line profile similar to that of CO. However, recent spectral-resolved observations by Herschel/HIFI and SOFIA/GREAT (as well as the observations presented here) show that the velocity resolved line profile of the [C ii] emission is often very different from that of CO lines, indicating a more complex origin of the line emission including the dynamics of the source region. Aims: The Large Magellanic Cloud (LMC) provides an excellent opportunity to study in great detail the physics of the interstellar medium (ISM) in a low-metallicity environment by spatially resolving individual star-forming regions. The aim of our study is to investigate the physical properties of the star-forming ISM in the LMC by separating the origin of the emission lines spatially and spectrally. In this paper, we focus on the spectral characteristics and the origin of the emission lines, and the phases of carbon-bearing species in the N159 star-forming region in the LMC. Methods: We mapped a 4' × (3'-4') region in N159 in [C ii] 158 ?m and [N ii] 205 ?m with the GREAT instrument on board SOFIA. We also observed CO(3-2), (4-3), (6-5), 13CO(3-2), and [C i] 3P1-3P0 and 3P2-3P1 with APEX. All spectra are velocity resolved. Results: The emission of all transitions observed shows a large variation in the line profiles across the map and in particular between the different species. At most positions the [C ii] emission line profile is substantially wider than that of CO and [C i]. We estimated the fraction of the [C ii] integrated line emission that cannot be fitted by the CO line profile to be 20% around the CO cores, and up to 50% at the area between the cores, indicating a gas component that has a much larger velocity dispersion than the ones probed by the CO and [C i] emission. We derived the relative contribution from C+, C, and CO to the column density in each velocity bin. The result clearly shows that the contribution from C+ dominates the velocity range far from the velocities traced by the dense molecular gas. Spatially, the region located between the CO cores of N159 W and E has a higher fraction of C+ over the whole velocity range. We estimate the contribution of the ionized gas to the [C ii] emission using the ratio to the [N ii] emission, and find that the ionized gas contributes ?19% to the [C ii] emission at its peak position, and ?15% over the whole observed region. Using the integrated line intensities, we present the spatial distribution of I[CII]/IFIR. Conclusions: This study demonstrates that the [C ii] emission in the LMC N159 region shows significantly different velocity profiles from that of CO and [C i] emissions, emphasizing the importance of velocity resolved observations in order to distinguish different cloud components.

  2. Self-consistent Kohn-Sham method based on the adiabatic-connection fluctuation-dissipation theorem and the exact-exchange kernel

    NASA Astrophysics Data System (ADS)

    Bleiziffer, Patrick; Krug, Marcel; Görling, Andreas

    2015-06-01

    A self-consistent Kohn-Sham method based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem, employing the frequency-dependent exact exchange kernel fx is presented. The resulting SC-exact-exchange-only (EXX)-ACFD method leads to even more accurate correlation potentials than those obtained within the direct random phase approximation (dRPA). In contrast to dRPA methods, not only the Coulomb kernel but also the exact exchange kernel fx is taken into account in the EXX-ACFD correlation which results in a method that, unlike dRPA methods, is free of self-correlations, i.e., a method that treats exactly all one-electron systems, like, e.g., the hydrogen atom. The self-consistent evaluation of EXX-ACFD total energies improves the accuracy compared to EXX-ACFD total energies evaluated non-self-consistently with EXX or dRPA orbitals and eigenvalues. Reaction energies of a set of small molecules, for which highly accurate experimental reference data are available, are calculated and compared to quantum chemistry methods like Møller-Plesset perturbation theory of second order (MP2) or coupled cluster methods [CCSD, coupled cluster singles, doubles, and perturbative triples (CCSD(T))]. Moreover, we compare our methods to other ACFD variants like dRPA combined with perturbative corrections such as the second order screened exchange corrections or a renormalized singles correction. Similarly, the performance of our EXX-ACFD methods is investigated for the non-covalently bonded dimers of the S22 reference set and for potential energy curves of noble gas, water, and benzene dimers. The computational effort of the SC-EXX-ACFD method exhibits the same scaling of N5 with respect to the system size N as the non-self-consistent evaluation of only the EXX-ACFD correlation energy; however, the prefactor increases significantly. Reaction energies from the SC-EXX-ACFD method deviate quite little from EXX-ACFD energies obtained non-self-consistently with dRPA orbitals and eigenvalues, and the deviation reduces even further if the Coulomb kernel is scaled by a factor of 0.75 in the dRPA to reduce self-correlations in the dRPA correlation potential. For larger systems, such a non-self-consistent EXX-ACFD method is a competitive alternative to high-level wave-function-based methods, yielding higher accuracy than MP2 and CCSD methods while exhibiting a better scaling of the computational effort than CCSD or CCSD(T) methods. Moreover, EXX-ACFD methods were shown to be applicable in situation characterized by static correlation.

  3. Merging Kohn-Sham and Orbital-Free DFT Calculations to Extend the LiH Hugoniot to Very High Pressures

    NASA Astrophysics Data System (ADS)

    Kress, Joel

    2013-06-01

    Large-scale hydrodynamic simulations of fluids and plasmas under extreme conditions require knowledge of various properties such as the equation of state (EOS), mass diffusion, and shear viscosity. While many approaches exist for the determination of these properties, one of the most accurate employs quantum molecular dynamics (QMD) simulations on large samples of atoms of the various species. Examples include the shock compression of metal hydrides and the mixing of deuterium/tritium (DT) fuel with ablator materials (such as C/H plastics and Be) in inertial confinement fusion capsules. The quantum nature of the electrons is described with two flavors of finite-temperature density functional theory (DFT), namely orbital-based Kohn-Sham (KS) and Orbital Free (OF). EOSs for Lithium Hydride and Lithium 6 Deuteride (Li6D) have been calculated with both KSMD and with OFMD. The shock Hugoniot for Li6D has been determined for temperatures up to 25 eV (5000 GPa) using a KSMD based EOS, and for T = 5 eV and above (up to 10,000 GPa) using an OFMD based EOS. KSMD simulations here have a practical upper limit of T = 25 eV due to the scaling of the computational work. The OFMD simulations have a lower limit of T = 5 eV since the OF DFT yields a poor description at low temperatures. The KSMD and OFMD Hugoniots agree well in the region of overlap (T = 5 to 25 eV). Comparisons will be presented with experimental data and with shock Hugoniots constructed from both existing EOS tables and from a new, improved SESAME table. By utilizing the KSMD and OFMD results to guide the parameter choices, the new EOS overall is a better match to melt and shock experimental data. This work was performed in collaboration with L. A. Collins, S. Crockett, M. P. Desjarlais, and F. Lambert and under the auspices of an agreement between CEA/DAM and NNSA/DP on cooperation on fundamental science. LANL is operated by LANS, LLC for the NNSA of the USDoE under contract no. DE-AC52-06NA25396.

  4. Tooth Size Variation in Pinniped Dentitions

    PubMed Central

    Wolsan, Mieczyslaw; Suzuki, Satoshi; Asahara, Masakazu; Motokawa, Masaharu

    2015-01-01

    It is contentious whether size variation among mammalian teeth is heterogeneous or homogeneous, whether the coefficient of variation is reliable, and whether the standard deviation of log-transformed data and the residual of standard deviation on mean variable size are useful replacements for the coefficient of variation. Most studies of tooth size variation have been on mammals with complex-crowned teeth, with relatively little attention paid to taxa with simple-crowned teeth, such as Pinnipedia. To fill this gap in knowledge and to resolve the existing controversies, we explored the variation of linear size variables (length and width) for all teeth from complete permanent dentitions of four pinniped species, two phocids (Histriophoca fasciata, Phoca largha) and two otariids (Callorhinus ursinus, Eumetopias jubatus). Size variation among these teeth was mostly heterogeneous both along the toothrow and among species. The incisors, canines, and mesial and distal postcanines were often relatively highly variable. The levels of overall dental size variation ranged from relatively low as in land carnivorans (Phoca largha and both otariids) to high (Histriophoca fasciata). Sexual size dimorphism varied among teeth and among species, with teeth being, on average, larger in males than in females. This dimorphism was more pronounced, and the canines were larger and more dimorphic relative to other teeth in the otariids than in the phocids. The coefficient of variation quantified variation reliably in most cases. The standard deviation of log-transformed data was redundant with the coefficient of variation. The residual of standard deviation on mean variable size was inaccurate when size variation was considerably heterogeneous among the compared variables, and was incomparable between species and between sexes. The existing hypotheses invoking developmental fields, occlusal complexity, and the relative timing of tooth formation and sexually dimorphic hormonal activity do not adequately explain the differential size variation along the pinniped toothrow. PMID:26317362

  5. A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels.

    PubMed

    Kussmann, Jörg; Ochsenfeld, Christian

    2007-11-28

    A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions. PMID:18052415

  6. Innovation et variation en didactique des langues etrangeres (Innovation and Variation in Foreign Language Instruction).

    ERIC Educational Resources Information Center

    Puren, Christian

    1991-01-01

    A model of foreign language education is presented that takes into account the complexity of instruction itself and the dimensions added by interaction of teacher, learner, institution, materials, and environment. Uncertainty is seen as a by-product of complexity, and innovation and variation in instructional practice are ways of dealing with…

  7. Orbital variations, climate and paleoecology.

    PubMed

    Bartlein, P J; Prentice, I C

    1989-07-01

    One of the most exciting discoveries in the earth sciences in recent decades has been the proof that ice ages are governed by deterministic variations in the earth's orbit. These variations modify the latitudinal and seasonal distribution of solar radiation at periods ranging from 103 to 10(5) years, and alternately produce conditions for building and melting continental ice. The same solar radiation variations also govern other aspects of world climate, including the temperatures of the midlatitude continental interiors, the intensity of upwelling in the tropical oceans, and the strength and extent of the monsoons. The interplay of solar radiation, seasonality and ice-sheet changes is responsible for the complex ecological history documented in the fossil record of the past 20 000 years. But the orbital variations have occurred throughout earth's history, and have caused periodic environmental changes in both terrestrial and marine environments even during times when there was no ice. Species have responded to these changes by range migration, an evolved ability that may maintain their genetic coherence in the face of a continually changing environment. PMID:21227349

  8. Self-consistent Kohn-Sham method based on the adiabatic-connection fluctuation-dissipation theorem and the exact-exchange kernel.

    PubMed

    Bleiziffer, Patrick; Krug, Marcel; Görling, Andreas

    2015-06-28

    A self-consistent Kohn-Sham method based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem, employing the frequency-dependent exact exchange kernel fx is presented. The resulting SC-exact-exchange-only (EXX)-ACFD method leads to even more accurate correlation potentials than those obtained within the direct random phase approximation (dRPA). In contrast to dRPA methods, not only the Coulomb kernel but also the exact exchange kernel fx is taken into account in the EXX-ACFD correlation which results in a method that, unlike dRPA methods, is free of self-correlations, i.e., a method that treats exactly all one-electron systems, like, e.g., the hydrogen atom. The self-consistent evaluation of EXX-ACFD total energies improves the accuracy compared to EXX-ACFD total energies evaluated non-self-consistently with EXX or dRPA orbitals and eigenvalues. Reaction energies of a set of small molecules, for which highly accurate experimental reference data are available, are calculated and compared to quantum chemistry methods like Møller-Plesset perturbation theory of second order (MP2) or coupled cluster methods [CCSD, coupled cluster singles, doubles, and perturbative triples (CCSD(T))]. Moreover, we compare our methods to other ACFD variants like dRPA combined with perturbative corrections such as the second order screened exchange corrections or a renormalized singles correction. Similarly, the performance of our EXX-ACFD methods is investigated for the non-covalently bonded dimers of the S22 reference set and for potential energy curves of noble gas, water, and benzene dimers. The computational effort of the SC-EXX-ACFD method exhibits the same scaling of N(5) with respect to the system size N as the non-self-consistent evaluation of only the EXX-ACFD correlation energy; however, the prefactor increases significantly. Reaction energies from the SC-EXX-ACFD method deviate quite little from EXX-ACFD energies obtained non-self-consistently with dRPA orbitals and eigenvalues, and the deviation reduces even further if the Coulomb kernel is scaled by a factor of 0.75 in the dRPA to reduce self-correlations in the dRPA correlation potential. For larger systems, such a non-self-consistent EXX-ACFD method is a competitive alternative to high-level wave-function-based methods, yielding higher accuracy than MP2 and CCSD methods while exhibiting a better scaling of the computational effort than CCSD or CCSD(T) methods. Moreover, EXX-ACFD methods were shown to be applicable in situation characterized by static correlation. PMID:26133411

  9. Variational Information Theory

    E-print Network

    Penny, Will

    Variational Inference Will Penny Information Theory Information Entropy Kullback-Liebler Divergence;Variational Inference Will Penny Information Theory Information Entropy Kullback-Liebler Divergence Gaussians(xi) This is the self-information or surprise. #12;Variational Inference Will Penny Information Theory Information

  10. Variation of fundamental constants

    E-print Network

    V. V. Flambaum

    2006-08-25

    We present a review of recent works devoted to the variation of the fine structure constant alpha, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feschbach resonance.

  11. Variation of fundamental constants

    E-print Network

    Flambaum, V V

    2006-01-01

    We present a review of recent works devoted to the variation of the fine structure constant alpha, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feschbach resonance.

  12. Non-differentiable variational principles

    NASA Astrophysics Data System (ADS)

    Cresson, Jacky

    2005-07-01

    We develop a calculus of variations for functionals which are defined on a set of non-differentiable curves. We first extend the classical differential calculus in a quantum calculus, which allows us to define a complex operator, called the scale derivative, which is the non-differentiable analogue of the classical derivative. We then define the notion of extremals for our functionals and obtain a characterization in term of a generalized Euler-Lagrange equation. We finally prove that solutions of the Schrödinger equation can be obtained as extremals of a non-differentiable variational principle, leading to an extended Hamilton's principle of least action for quantum mechanics. We compare this approach with the scale relativity theory of Nottale, which assumes a fractal structure of space-time.Résumé (Principes variationnels non différentiable). Nous développons un calcul des variations pour des fonctionnelles définies sur un ensemble de courbes non différentiables. Pour cela, nous étendons le calcul différentiel classique, en calcul appelé calcul quantique, qui nous permet de définir un opérateur à valeur complexes, appelé dérivée d'échelle, qui est l'analogue non différentiable de la dérivée usuelle. On définit alors la notion d'extremale pour ces fonctionnelles pour lesquelles nous obtenons une caractérisation via une équation d'Euler-Lagrange généralisée. On prouve enfin que les solutions de l'équation de Schrödinger peuvent s'obtenir comme solution d'un problème variationnel non différentiable, étendant ainsi le principe de moindre action de Hamilton au cadre de la mécanique quantique. On discute enfin la connexion entre ce travail et la théorie de la relativité d'échelle développée par Nottale, et qui suppose une structure fractale de l'espace-temps.

  13. Carney Complex

    MedlinePLUS

    ... Ephelides (freckles) LAMB syndrome – Lentigines, Atrial Myxoma, and Blue nevi What causes Carney complex? Carney complex is ... melanotic schwannoma, meaning tumors that grow on nerves Blue nevi, which are blue-black moles Osteochondromyxoma (bone ...

  14. Complexity Survey.

    ERIC Educational Resources Information Center

    Gordon, Sandra L.; Anderson, Beth C.

    To determine whether consensus existed among teachers about the complexity of common classroom materials, a survey was administered to 66 pre-service and in-service kindergarten and prekindergarten teachers. Participants were asked to rate 14 common classroom materials as simple, complex, or super-complex. Simple materials have one obvious part,…

  15. Technical Note Variational free energy and the Laplace approximation

    E-print Network

    Penny, Will

    Technical Note Variational free energy and the Laplace approximation Karl Friston,a, Jérémie the variational free energy under the Laplace approximation, with a focus on accounting for additional model complexity induced by increasing the number of model parameters. This is relevant when using the free energy

  16. Communication complexity and information complexity

    NASA Astrophysics Data System (ADS)

    Pankratov, Denis

    Information complexity enables the use of information-theoretic tools in communication complexity theory. Prior to the results presented in this thesis, information complexity was mainly used for proving lower bounds and direct-sum theorems in the setting of communication complexity. We present three results that demonstrate new connections between information complexity and communication complexity. In the first contribution we thoroughly study the information complexity of the smallest nontrivial two-party function: the AND function. While computing the communication complexity of AND is trivial, computing its exact information complexity presents a major technical challenge. In overcoming this challenge, we reveal that information complexity gives rise to rich geometrical structures. Our analysis of information complexity relies on new analytic techniques and new characterizations of communication protocols. We also uncover a connection of information complexity to the theory of elliptic partial differential equations. Once we compute the exact information complexity of AND, we can compute exact communication complexity of several related functions on n-bit inputs with some additional technical work. Previous combinatorial and algebraic techniques could only prove bounds of the form theta( n). Interestingly, this level of precision is typical in the area of information theory, so our result demonstrates that this meta-property of precise bounds carries over to information complexity and in certain cases even to communication complexity. Our result does not only strengthen the lower bound on communication complexity of disjointness by making it more exact, but it also shows that information complexity provides the exact upper bound on communication complexity. In fact, this result is more general and applies to a whole class of communication problems. In the second contribution, we use self-reduction methods to prove strong lower bounds on the information complexity of two of the most studied functions in the communication complexity literature: Gap Hamming Distance (GHD) and Inner Product mod 2 (IP). In our first result we affirm the conjecture that the information complexity of GHD is linear even under the uniform distribution. This strengthens the O(n) bound shown by Kerenidis et al. (2012) and answers an open problem by Chakrabarti et al. (2012). We also prove that the information complexity of IP is arbitrarily close to the trivial upper bound n as the permitted error tends to zero, again strengthening the O(n) lower bound proved by Braverman and Weinstein (2011). More importantly, our proofs demonstrate that self-reducibility makes the connection between information complexity and communication complexity lower bounds a two-way connection. Whereas numerous results in the past used information complexity techniques to derive new communication complexity lower bounds, we explore a generic way, in which communication complexity lower bounds imply information complexity lower bounds in a black-box manner. In the third contribution we consider the roles that private and public randomness play in the definition of information complexity. In communication complexity, private randomness can be trivially simulated by public randomness. Moreover, the communication cost of simulating public randomness with private randomness is well understood due to Newman's theorem (1991). In information complexity, the roles of public and private randomness are reversed: public randomness can be trivially simulated by private randomness. However, the information cost of simulating private randomness with public randomness is not understood. We show that protocols that use only public randomness admit a rather strong compression. In particular, efficient simulation of private randomness by public randomness would imply a version of a direct sum theorem in the setting of communication complexity. This establishes a yet another connection between the two areas. (Abstract shortened by UMI.).

  17. Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli

    E-print Network

    Gat-Viks, Irit

    Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to ...

  18. Discrete Calculus of Variations

    NASA Astrophysics Data System (ADS)

    Guseinov, Gusein Sh.

    2004-10-01

    The continuous calculus of variations is concerned mainly with the determination of minima or maxima of certain definite integrals involving unknown functions. In this paper, a discrete calculus of variations for sums is treated, including the discrete Euler-Lagrange equation.

  19. Efficient implementation of the Gutzwiller variational method

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

    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.

  20. Analysis of biomarkers for complex human diseases 

    E-print Network

    Ansari, Morad

    2009-01-01

    The aims of this study were to analyse known and potential biomarkers of common and genetically complex human disorders and to identify genetic and environmental variation associated with plasma biomarker concentrations. ...

  1. Dissecting genetic interactions in complex traits 

    E-print Network

    Hemani, Gibran

    2012-06-30

    Of central importance in the dissection of the components that govern complex traits is understanding the architecture of natural genetic variation. Genetic interaction, or epistasis, constitutes one aspect of this, but ...

  2. Nd, Sr, and O isotopic variations in metaluminous ash-flow tuffs and related volcanic rocks at the Timber Mountain/Oasis Valley Caldera, Complex, SW Nevada: implications for the origin and evolution of large-volume silicic magma bodies

    USGS Publications Warehouse

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

    1991-01-01

    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.

  3. Medically Complex Home Care and Caregiver Strain

    ERIC Educational Resources Information Center

    Moorman, Sara M.; Macdonald, Cameron

    2013-01-01

    Purpose of the study: To examine (a) whether the content of caregiving tasks (i.e., nursing vs. personal care) contributes to variation in caregivers' strain and (b) whether the level of complexity of nursing tasks contributes to variation in strain among caregivers providing help with such tasks. Design and methods: The data came from the Cash…

  4. Complex polarization propagator calculations of magnetic circular dichroism spectra

    NASA Astrophysics Data System (ADS)

    Solheim, Harald; Ruud, Kenneth; Coriani, Sonia; Norman, Patrick

    2008-03-01

    It is demonstrated that the employment of the nonlinear complex polarization propagator enables the calculation of the complete magnetic circular dichroism spectra of closed-shell molecules, including at the same time both the so-called Faraday A and B terms. In this approach, the differential absorption of right and left circularly polarized light in the presence of a static magnetic field is determined from the real part of the magnetic field-perturbed electric dipole polarizability. The introduction of the finite lifetimes of the electronically excited states into the theory results in response functions that are well behaved in the entire spectral region, i.e., the divergencies that are found in conventional response theory approaches at the transition energies of the system are not present. The applicability of the approach is demonstrated by calculations of the ultraviolet magnetic circular dichroism spectra of para-benzoquinone, tetrachloro-para-benzoquinone, and cyclopropane. The present results are obtained with the complex polarization propagator approach in conjunction with Kohn-Sham density functional theory and the standard adiabatic density functionals B3LYP, CAM-B3LYP, and BHLYP.

  5. Variation tolerant SoC design

    NASA Astrophysics Data System (ADS)

    Kozhikkottu, Vivek J.

    The scaling of integrated circuits into the nanometer regime has led to variations emerging as a primary concern for designers of integrated circuits. Variations are an inevitable consequence of the semiconductor manufacturing process, and also arise due to the side-effects of operation of integrated circuits (voltage, temperature, and aging). Conventional design approaches, which are based on design corners or worst-case scenarios, leave designers with an undesirable choice between the considerable overheads associated with over-design and significantly reduced manufacturing yield. Techniques for variation-tolerant design at the logic, circuit and layout levels of the design process have been developed and are in commercial use. However, with the incessant increase in variations due to technology scaling and design trends such as near-threshold computing, these techniques are no longer sufficient to contain the effects of variations, and there is a need to address variations at all stages of design. This thesis addresses the problem of variation-tolerant design at the earliest stages of the design process, where the system-level design decisions that are made can have a very significant impact. There are two key aspects to making system-level design variation-aware. First, analysis techniques must be developed to project the impact of variations on system-level metrics such as application performance and energy. Second, variation-tolerant design techniques need to be developed to absorb the residual impact of variations (that cannot be contained through lower-level techniques). In this thesis, we address both these facets by developing robust and scalable variation-aware analysis and variation mitigation techniques at the system level. The first contribution of this thesis is a variation-aware system-level performance analysis framework. We address the key challenge of translating the per-component clock frequency distributions into a system-level application performance distribution. This task is particularly complex and challenging due to the inter-dependencies between components' execution, indirect effects of shared resources, and interactions between multiple system-level "execution paths". We argue that accurate variation-aware performance analysis requires Monte-Carlo based repeated system execution. Our proposed analysis framework leverages emulation to significantly speedup performance analysis without sacrificing the generality and accuracy achieved by Monte-Carlo based simulations. Our experiments show performance improvements of around 60x compared to state-of-the-art hardware-software co-simulation tools and also underscore the framework's potential to enable variation-aware design and exploration at the system level. Our second contribution addresses the problem of designing variation-tolerant SoCs using recovery based design, a popular circuit design paradigm that addresses variations by eliminating guard-bands and operating circuits at close to "zero margins" while detecting and recovering from timing errors. While previous efforts have demonstrated the potential benefits of recovery based design, we identify several challenges that need to be addressed in order to apply this technique to SoCs. We present a systematic design framework to apply recovery based design at the system level. We propose to partition SoCs into "recovery islands", wherein each recovery island consists of one or more SoC components that can recover independent of the rest of the SoC. We present a variation-aware design methodology that partitions a given SoC into recovery islands and computes the optimal operating points for each island, taking into account the various trade-offs involved. Our experiments demonstrate that the proposed design framework achieves an average of 32% energy savings over conventional worst-case designs, with negligible losses in performance. The third contribution of this thesis introduces disproportionate allocation of shared system resources as a means to combat the advers

  6. Variations of solar irradiance

    SciTech Connect

    Willson, R.C.; Hudson, H.S.

    1981-03-15

    The Active Cavity Radiometer experiment on the Solar Maximum Mission is providing sensitive measurements of time variations of the total solar irradiance with greater accuracy and precision than previously achieved. The mean 1 AU irradiance for the first 45 days' operation is 1368.64 W m/sup -2/ with an abolute uncertainty of less than +- 0.5%. Variations about this mean have been observed on time scales of hours to days with amplitudes up to +- 0.04%, resolved with a statistical uncertainty as low as 0.001%. Variations with a single orbit with amplitudes as large as +- 0.05% have been resolved with 0.005% or smaller statistical uncertainty. Although these variations do not display a systematic relationship to conventional solar activity indices over the period, correlative behavior cannot be ruled out on the basis of the present limited data set.

  7. The Schwinger Variational Method

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    1995-01-01

    Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. For collisional problems they can be grouped into two types: those based on the Schroedinger equation and those based on the Lippmann-Schwinger equation. The application of the Schwinger variational (SV) method to e-molecule collisions and photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions.

  8. Variations in the rotation of the earth

    NASA Astrophysics Data System (ADS)

    Carter, W. E.; Robertson, D. S.; Pettey, J. E.; Tapley, B. D.; Schutz, B. E.; Eanes, R. J.; Miao, L.

    Variations in the earth's rotation (UTI) and length of day have been tracked at the submillisecond level by astronomical radio interferometry and laser ranging to the LAGEOS satellite. Three years of regular measurements reveal complex patterns of variations including UTI fluctuations as large as 5 milliseconds in a few weeks. Comparison of the observed changes in length of day with variations in the global atmospheric angular momentum indicates that the dominant cause of changes in the earth's spin rate, on time scales from a week to several years, is the exchange of angular momentum between the atmosphere and the mantle. The unusually intense El Nino of 1982-1983 was marked by a strong peak in the length of day.

  9. Ab initio calculations on collisions of low energy electrons with polyatomic molecules

    SciTech Connect

    Rescigno, T.N.

    1991-08-01

    The Kohn variational method is one of simplest, and oldest, techniques for performing scattering calculations. Nevertheless, a number of formal problems, as well as practical difficulties associated with the computation of certain required matrix elements, delayed its application to electron--molecule scattering problems for many years. This paper will describe the recent theoretical and computational developments that have made the complex'' Kohn variational method a practical tool for carrying out calculations of low energy electron--molecule scattering. Recent calculations on a number of target molecules will also be summarized. 41 refs., 7 figs.

  10. Softball Complex

    ERIC Educational Resources Information Center

    Ellis, Jim

    1977-01-01

    The Parks and Recreation Department of Montgomery, Alabama, has developed a five-field softball complex as part of a growing community park with facilities for camping, golf, aquatics, tennis, and picnicking. (MJB)

  11. Variations in Recollection: The Effects of Complexity on Source Recognition

    ERIC Educational Resources Information Center

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

    2011-01-01

    Whether recollection is a threshold or signal detection process is highly controversial, and the controversy has centered in part on the shape of receiver operating characteristics (ROCs) and z-transformed ROCs (zROCs). U-shaped zROCs observed in tests thought to rely heavily on recollection, such as source memory tests, have provided evidence in…

  12. Complex Ploidy Level Variation in Guayule Breeding Programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Guayule (Parthenium argentatum Gray) is a potential source of natural rubber, but attempts to domesticate and cultivate this perennial crop for large-scale commercial production in the southwestern United States have been intermittent over the past century. Genetic improvement through modern plant b...

  13. Variations in cell morphology in the canine cruciate ligament complex.

    PubMed

    Smith, K D; Vaughan-Thomas, A; Spiller, D G; Clegg, P D; Innes, J F; Comerford, E J

    2012-08-01

    Cell morphology may reflect the mechanical environment of tissues and influence tissue physiology and response to injury. Normal cruciate ligaments (CLs) from disease-free stifle joints were harvested from dog breeds with a high (Labrador retriever) and low (Greyhound) risk of cranial cruciate ligament (CCL) rupture. Antibodies against the cytoskeletal components vimentin and alpha tubulin were used to analyse cell morphology; nuclei were stained with 4',6-diamidino-2-phenylindole, and images were collected using conventional and confocal microscopy. Both cranial and caudal CLs contained cells of heterogenous morphologies. Cells were arranged between collagen bundles and frequently had cytoplasmic processes. Some of these processes were long (type A cells), others were shorter, thicker and more branched (type B cells), and some had no processes (type C cells). Processes were frequently shown to contact other cells, extending longitudinally and transversely through the CLs. Cells with longer processes had fusiform nuclei, and those with no processes had rounded nuclei and were more frequent in the mid-substance of both CLs. Cells with long processes were more commonly noted in the CLs of the Greyhound. As contact between cells may facilitate direct communication, variances in cell morphology between breeds at a differing risk of CCL rupture may reflect differences in CL physiology. PMID:22465617

  14. Variational transition state theory

    SciTech Connect

    Truhlar, D.G.

    1993-12-01

    This research program involves the development of variational transition state theory (VTST) and semiclassical tunneling methods for the calculation of gas-phase reaction rates and selected applications. The applications are selected for their fundamental interest and/or their relevance to combustion.

  15. Seasonal Variation in Epidemiology

    ERIC Educational Resources Information Center

    Marrero, Osvaldo

    2013-01-01

    Seasonality analyses are important in medical research. If the incidence of a disease shows a seasonal pattern, then an environmental factor must be considered in its etiology. We discuss a method for the simultaneous analysis of seasonal variation in multiple groups. The nuts and bolts are explained using simple trigonometry, an elementary…

  16. Language Variation and Literacy.

    ERIC Educational Resources Information Center

    Shuy, Roger W.

    Characteristics of language variety are identified, and language systems are viewed as having their own sympathetic patterns which are not deviant from but which are different from each other. The relationship of language variation to literacy is discussed, and matching beginning reading materials to the child's oral language is seen to facilitate…

  17. Variational Methods Zoubin Ghahramani

    E-print Network

    Mitchell, Tom

    Machines Factorial HMM HMM Mixture of HMMs Switching State-space Models ICA Linear Dynamical Systems (SSMsVariational Methods Zoubin Ghahramani zoubin@cs.cmu.edu http://www.gatsby.ucl.ac.uk Statistical : switching #12;Example: Dynamic Bayesian Networks Factorial Hidden Markov Models, Switching State Space

  18. Low Pacific secular variation

    NASA Astrophysics Data System (ADS)

    Gubbins, David; Gibbons, Steven J.

    The historical record shows that secular variation at Hawaii is limited to a few degrees in the last 400 years, whereas in the Atlantic hemisphere it often exceeds 30°. Paleomagnetic measurements from Hawaii show virtually no change in declination during the last 5 kyr and only a slow, millenium-scale inclination change of less than 20°. The usual directional scatter analysis of paleomagnetic data cannot discriminate between the two time scales. The disparity of time scales and difference in activity suggest different physical mechanisms for secular variation in the two hemispheres. This could arise from thermal core-mantle interaction. Seismic models of the lower mantle give a pattern of lateral variations that is nearly symmetric about the Pacific rim: two slow regions centered beneath the Pacific and Atlantic separated by a fast ring below the Pacific rim. These seismic anomalies are thought to be caused mostly by temperature variations in the bottom 200 km of the mantle. It is difficult to see how such a symmetric pattern could lead to long-term hemispheric differences. We show here a convection solution in a rapidly rotating sphere with heat flux on the outer boundary determined from a seismic model. The convection is suppressed beneath the Pacific but the usual drifting convection (Busse) rolls remain beneath the Atlantic. This mode of periodic convection arises because the Pacific hot region extends east-west and is much larger than a single convection roll, whereas the Atlantic hot region is elongated north-south and is about the same east-west size as a convection roll. This could explain the absence of normal, century-long secular variation in the Pacific: hot mantle suppresses short wavelength phenomena at the century time scale but not the longer wavelengths at the millenium time scale.

  19. Grasping Complexity

    E-print Network

    A. N. Gorban; G. S. Yablonsky

    2013-03-15

    The century of complexity has come. The face of science has changed. Surprisingly, when we start asking about the essence of these changes and then critically analyse the answers, the result are mostly discouraging. Most of the answers are related to the properties that have been in the focus of scientific research already for more than a century (like non-linearity). This paper is Preface to the special issue "Grasping Complexity" of the journal "Computers and Mathematics with Applications". We analyse the change of era in science, its reasons and main changes in scientific activity and give a brief review of the papers in the issue.

  20. The Schwinger Variational Method

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    1995-01-01

    Variational methods have proven invaluable in theoretical physics and chemistry, both for bound state problems and for the study of collision phenomena. The application of the Schwinger variational (SV) method to e-molecule collisions and molecular photoionization has been reviewed previously. The present chapter discusses the implementation of the SV method as applied to e-molecule collisions. Since this is not a review of cross section data, cross sections are presented only to server as illustrative examples. In the SV method, the correct boundary condition is automatically incorporated through the use of Green's function. Thus SV calculations can employ basis functions with arbitrary boundary conditions. The iterative Schwinger method has been used extensively to study molecular photoionization. For e-molecule collisions, it is used at the static exchange level to study elastic scattering and coupled with the distorted wave approximation to study electronically inelastic scattering.

  1. Seasonal Variation in Human Gut Microbiome Composition

    PubMed Central

    Davenport, Emily R.; Mizrahi-Man, Orna; Michelini, Katelyn; Barreiro, Luis B.; Ober, Carole; Gilad, Yoav

    2014-01-01

    The composition of the human gut microbiome is influenced by many environmental factors. Diet is thought to be one of the most important determinants, though we have limited understanding of the extent to which dietary fluctuations alter variation in the gut microbiome between individuals. In this study, we examined variation in gut microbiome composition between winter and summer over the course of one year in 60 members of a founder population, the Hutterites. Because of their communal lifestyle, Hutterite diets are similar across individuals and remarkably stable throughout the year, with the exception that fresh produce is primarily served during the summer and autumn months. Our data indicate that despite overall gut microbiome stability within individuals over time, there are consistent and significant population-wide shifts in microbiome composition across seasons. We found seasonal differences in both (i) the abundance of particular taxa (false discovery rate <0.05), including highly abundant phyla Bacteroidetes and Firmicutes, and (ii) overall gut microbiome diversity (by Shannon diversity; P?=?0.001). It is likely that the dietary fluctuations between seasons with respect to produce availability explain, at least in part, these differences in microbiome composition. For example, high levels of produce containing complex carbohydrates consumed during the summer months might explain increased abundance of Bacteroidetes, which contain complex carbohydrate digesters, and decreased levels of Actinobacteria, which have been negatively correlated to fiber content in food questionnaires. Our observations demonstrate the plastic nature of the human gut microbiome in response to variation in diet. PMID:24618913

  2. An index of floodplain surface complexity

    NASA Astrophysics Data System (ADS)

    Scown, M. W.; Thoms, M. C.; De Jager, N. R.

    2015-04-01

    Floodplain surface topography is an important component of floodplain ecosystems. It is the primary physical template upon which ecosystem processes are acted out. There has been a limited appreciation of floodplain surface complexity because of the traditional focus on temporal variability in floodplains as well as limitations to quantifying spatial complexity. An index of floodplain surface complexity (FSC) is developed in this paper and applied to eight floodplains from different geographic settings. The index is based on the two key indicators of complexity; variability in surface geometry (VSG) and the spatial organization of surface conditions (SOC) and was determined at three sampling scales. Relationships between these measures of spatial complexity and environmental drivers, namely; flow variability (mean daily discharge [Q], the coefficient of variation of daily discharge [QCV], the coefficient of variation of mean annual discharge [QCVAnn], the coefficient of variation of maximum annual discharge [QCVMax]), sediment yield (SY), valley slope (Vs), and floodplain width (Fpw) were examined. FSC, VSG, and SOC varied between the eight floodplains and this was dependent upon sampling scale. All complexity values declined with increasing Fpw in either a power, logarithmic, or exponential function. There was little change in surface complexity with floodplain widths greater than 10 km. VSG was significantly related to SY and no significant relationships were determined between any of the hydrological variables and floodplain surface complexity.

  3. Complex Adaptations and the Structure of Recombination Spaces

    E-print Network

    Stadler, Peter F.

    , as well as the theory of complex adaptive systems. In addition the availability of large amountsComplex Adaptations and the Structure of Recombination Spaces G¨ unter P. Wagner a by the processes which generate genetic variation (mutation and/or recombination). The theory of complex adaptive

  4. Managing Complexity

    SciTech Connect

    Chassin, David P.; Posse, Christian; Malard, Joel M.

    2004-08-01

    Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today’s most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically-based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This paper explores the state of the art in the use physical analogs for understanding the behavior of some econophysical systems and to deriving stable and robust control strategies for them. In particular we review and discussion applications of some analytic methods based on the thermodynamic metaphor according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood.

  5. A Variational Formulation of Dissipative Quasicontinuum Methods

    E-print Network

    Rokoš, Ond?ej; Zeman, Jan; Peerlings, Ron H J

    2016-01-01

    Lattice systems and discrete networks with dissipative interactions are successfully employed as meso-scale models of heterogeneous solids. As the application scale generally is much larger than that of the discrete links, physically relevant simulations are computationally expensive. The QuasiContinuum (QC) method is a multiscale approach that reduces the computational cost of direct numerical simulations by fully resolving complex phenomena only in regions of interest while coarsening elsewhere. In previous work (Beex et al., J. Mech. Phys. Solids 64, 154-169, 2014), the originally conservative QC methodology was generalized to a virtual-power-based QC approach that includes local dissipative mechanisms. In this contribution, the virtual-power-based QC method is reformulated from a variational point of view, by employing the energy-based variational framework for rate-independent processes (Mielke and Roub\\'{i}\\v{c}ek, Rate-Independent Systems: Theory and Application, Springer-Verlag, 2015). By construction...

  6. Comprehensive variation discovery in single human genomes

    PubMed Central

    Weisenfeld, Neil I.; Yin, Shuangye; Sharpe, Ted; Lau, Bayo; Hegarty, Ryan; Holmes, Laurie; Sogoloff, Brian; Tabbaa, Diana; Williams, Louise; Russ, Carsten; Nusbaum, Chad; Lander, Eric S.; MacCallum, Iain; Jaffe, David B.

    2014-01-01

    Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing individual genomes and comparing reads to a reference. Existing methods do an excellent job of detecting variants in approximately 90% of the human genome, however calling variants in the remaining 10% of the genome (largely low-complexity sequence and segmental duplications) is challenging. To improve variant calling, we developed a new algorithm, DISCOVAR, and examined its performance on improved, low-cost sequence data. Using a newly created reference set of variants from finished sequence of 103 randomly chosen Fosmids, we find that some standard variant call sets miss up to 25% of variants. We show that the combination of new methods and improved data increases sensitivity several-fold, with the greatest impact in challenging regions of the human genome. PMID:25326702

  7. Comprehensive variation discovery in single human genomes.

    PubMed

    Weisenfeld, Neil I; Yin, Shuangye; Sharpe, Ted; Lau, Bayo; Hegarty, Ryan; Holmes, Laurie; Sogoloff, Brian; Tabbaa, Diana; Williams, Louise; Russ, Carsten; Nusbaum, Chad; Lander, Eric S; MacCallum, Iain; Jaffe, David B

    2014-12-01

    Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing individual genomes and comparing reads to a reference. Existing methods do an excellent job of detecting variants in approximately 90% of the human genome; however, calling variants in the remaining 10% of the genome (largely low-complexity sequence and segmental duplications) is challenging. To improve variant calling, we developed a new algorithm, DISCOVAR, and examined its performance on improved, low-cost sequence data. Using a newly created reference set of variants from the finished sequence of 103 randomly chosen fosmids, we find that some standard variant call sets miss up to 25% of variants. We show that the combination of new methods and improved data increases sensitivity by several fold, with the greatest impact in challenging regions of the human genome. PMID:25326702

  8. Structure of complexes between aluminum chloride and other chlorides, 2: Alkali-(chloroaluminates). Gaseous complexes

    NASA Technical Reports Server (NTRS)

    Hargittai, M.

    1980-01-01

    The structural chemistry of complexes between aluminum chloride and other metal chlorides is important both for practice and theory. Condensed-phase as well as vapor-phase complexes are of interest. Structural information on such complexes is reviewed. The first emphasis is given to the molten state because of its practical importance. Aluminum chloride forms volatile complexes with other metal chlorides and these vapor-phase complexes are dealt with in the second part. Finally, the variations in molecular shape and geometrical parameters are summarized.

  9. Contour Stencils and Variational Image Processing

    NASA Astrophysics Data System (ADS)

    Getreuer, Pascal Tom

    The first part of this thesis is on contour stencils, a new method for edge adaptive image processing. We focus particularly on image zooming, which is the problem of increasing the resolution of a given image. An important aspect of zooming is accurate estimation of edge orientations. Contour stencils is a new method for estimating the image contours based on total variation along curves. Contour stencils are applied in designing several edge-adaptive color zooming methods. These zooming methods fall at different points in the balance between speed and quality. One of these zooming methods, contour stencil windowed zooming, is particular successful. Although most zooming methods require either solving a large linear system or running many iterations, this method has linear complexity in the number of pixels and can be computed in a single pass through the image. The zoomed image is constructed as a function that may be sampled anywhere, enabling arbitrary resampling operations. Comparisons show that contour stencil zooming methods are competitive with existing methods. Applications of contour stencils to corner detection and image enhancement are also illustrated. The second part of this thesis is on topics in variational image processing. First, we apply variational techniques to formulate a total variation optimal prediction in Harten multiresolution schemes. We show that this prediction is well-defined, construct a Harten multiresolution using this prediction, and show that a modified encoding strategy is possible for approximation using the scheme. We also investigate the efficient numerical solution of the prediction and compare several different algorithms. Examples show that image approximation with this scheme is competitive with the CDF 9/7 wavelet. Next, we investigate nonconvex potentials in variational image problems. For the approximate solution of these nonconvex problems, we develop a particle swarm optimization like algorithm that avoids becoming trapped in shallow local minima. Examples in denoising and image zooming show that the method can outperform gradient descent. Finally, the last topic is on image restoration with Rician noise. Total variation regularization is usually applied with L² data fidelity assuming an additive white Gaussian noise model. However, better results are possible when the noise model accurately describes the noise in the given image. Total variation denoising has already been developed with the Laplace noise model (L¹ data fidelity) and the Poisson noise model. A challenge with Rician noise is that the resulting objective function is nonconvex. We develop a convex variational problem that closely approximates the Rician noise model. The problem is efficiently solved using the split Bregman method.

  10. Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation.

    PubMed

    Hedrick, Philip W

    2013-09-01

    Adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. Another potential source of adaptive variation is adaptive variants from other (donor) species that are introgressed into the (recipient) species, termed adaptive introgression. Here, the various attributes of these three potential sources of adaptive variation are compared. For example, the rate of adaptive change is generally thought to be faster from standing variation, slower from mutation and potentially intermediate from adaptive introgression. Additionally, the higher initial frequency of adaptive variation from standing variation and lower initial frequency from mutation might result in a higher probability of fixation of the adaptive variants for standing variation. Adaptive variation from introgression might have higher initial frequency than new adaptive mutations but lower than that from standing variation, again making the impact of adaptive introgression variation potentially intermediate. Adaptive introgressive variants might have multiple changes within a gene and affect multiple loci, an advantage also potentially found for adaptive standing variation but not for new adaptive mutants. The processes that might produce a common variant in two taxa, convergence, trans-species polymorphism from incomplete lineage sorting or from balancing selection and adaptive introgression, are also compared. Finally, potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin's finches, yellow skin in chickens and non-native ancestry in an endangered native salamander, are examined. PMID:23906376

  11. Variations in brain DNA

    PubMed Central

    Avila, Jesús; Gómez-Ramos, Alberto; Soriano, Eduardo

    2014-01-01

    It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain) of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain. PMID:25505410

  12. Harmonically excited orbital variations

    SciTech Connect

    Morgan, T.

    1985-08-06

    Rephrasing the equations of motion for orbital maneuvers in terms of Lagrangian generalized coordinates instead of Newtonian rectangular cartesian coordinates can make certain harmonic terms in the orbital angular momentum vector more readily apparent. In this formulation the equations of motion adopt the form of a damped harmonic oscillator when torques are applied to the orbit in a variationally prescribed manner. The frequencies of the oscillator equation are in some ways unexpected but can nonetheless be exploited through resonant forcing functions to achieve large secular variations in the orbital elements. Two cases are discussed using a circular orbit as the control case: (1) large changes in orbital inclination achieved by harmonic excitation rather than one impulsive velocity change, and (2) periodic and secular changes to the longitude of the ascending node using both stable and unstable excitation strategies. The implications of these equations are also discussed for both artificial satellites and natural satellites. For the former, two utilitarian orbits are suggested, each exploiting a form of harmonic excitation. 5 refs.

  13. Anisotropic Total Variation Filtering

    SciTech Connect

    Grasmair, Markus; Lenzen, Frank

    2010-12-15

    Total variation regularization and anisotropic filtering have been established as standard methods for image denoising because of their ability to detect and keep prominent edges in the data. Both methods, however, introduce artifacts: In the case of anisotropic filtering, the preservation of edges comes at the cost of the creation of additional structures out of noise; total variation regularization, on the other hand, suffers from the stair-casing effect, which leads to gradual contrast changes in homogeneous objects, especially near curved edges and corners. In order to circumvent these drawbacks, we propose to combine the two regularization techniques. To that end we replace the isotropic TV semi-norm by an anisotropic term that mirrors the directional structure of either the noisy original data or the smoothed image. We provide a detailed existence theory for our regularization method by using the concept of relaxation. The numerical examples concluding the paper show that the proposed introduction of an anisotropy to TV regularization indeed leads to improved denoising: the stair-casing effect is reduced while at the same time the creation of artifacts is suppressed.

  14. Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants

    ERIC Educational Resources Information Center

    Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

  15. Redox site confinement in highly unsymmetric dimanganese complexes.

    PubMed

    Sheng, Tianlu; Dechert, Sebastian; Hyla-Kryspin, Isabella; Winter, Rainer F; Meyer, Franc

    2005-05-30

    A set of highly preorganized pyrazolate-bridged dimanganese complexes L(Mn)MnX have been prepared and structurally characterized. They can be described as hybrid organometallic/Werner-type systems that consist of a low-spin CpMn(I)(CO)2 subunit (Mn1) and a proximate tripodal tetradentate {N4} binding pocket accommodating a high-spin Mn(II) ion (Mn2), with Mn...Mn distances of approximately 4.3 A and different coligands bound to Mn2. Density functional theory (DFT) calculations (both the hybrid B3LYP and the pure BP86 functionals and the all-electron basis sets 6-311G and 6-311G*) confirm that the valence alpha and beta Kohn-Sham molecular orbitals (MOs) of these mixed-valent Mn(I)Mn(II) compounds have predominant Mn(3d) character and an almost perfectly localized nature: all five unpaired electrons are essentially localized at the Werner-type Mn2, whereas Mn1 possesses an effective closed-shell structure with the MOs of highest energy centered there. One-electron oxidation occurs in a clean process at approximately E(1/2) = -0.6 V (versus ferrocene/ferrocinium), giving the low-spin/high-spin Mn(II)Mn(II) species. UV/vis and IR spectroelectrochemistry as well as a detailed theoretical analysis reveal that the redox process takes place with strict site control at the organometallic subunit, while it does not significantly influence the spin and charge distribution on the Werner-type site. Positions and shifts of the nu(C[triple bond]O) absorptions are largely reproduced by the DFT calculations. These systems thus represent an exceptional example of the effect the unsymmetry of a dinucleating ligand scaffold has on the spin and charge distribution in homobimetallic complexes and might offer interesting prospects for the study of the cooperative effects of bimetallic arrays. PMID:15907112

  16. The complexity of anatomical systems

    PubMed Central

    Grizzi, Fabio; Chiriva-Internati, Maurizio

    2005-01-01

    Background The conception of anatomical entities as a hierarchy of infinitely graduated forms and the increase in the number of observed anatomical sub-entities and structural variables has generated a growing complexity, thus highlighting new properties of organised biological matter. Results (1) Complexity is so pervasive in the anatomical world that it has come to be considered as a primary characteristic of anatomical systems. (2) Anatomical entities, when viewed at microscopic as well as macroscopic level of observation, show a different degree of complexity. (3) Complexity can reside in the structure of the anatomical system (having many diverse parts with varying interactions or an intricate architecture) or in its behaviour. Often complexity in structure and behaviour go together. (4) Complex systems admit many descriptions (ways of looking at the system) each of which is only partially true. Each way of looking at a complex system requires its own description, its own mode of analysis and its own breaking down of the system in different parts; (5) Almost all the anatomical entities display hierarchical forms: their component structures at different spatial scales or their process at different time scales are related to each other. Conclusion The need to find a new way of observing and measuring anatomical entities, and objectively quantifying their different structural changes, prompted us to investigate the non-Euclidean geometries and the theories of complexity, and to apply their concepts to human anatomy. This attempt has led us to reflect upon the complex significance of the shape of an observed anatomical entity. Its changes have been defined in relation to variations in its status: from a normal (i.e. natural) to a pathological or altered state introducing the concepts of kinematics and dynamics of anatomical forms, speed of their changes, and that of scale of their observation. PMID:16029490

  17. Cosmic Complexity

    NASA Technical Reports Server (NTRS)

    Mather, John C.

    2012-01-01

    What explains the extraordinary complexity of the observed universe, on all scales from quarks to the accelerating universe? My favorite explanation (which I certainty did not invent) ls that the fundamental laws of physics produce natural instability, energy flows, and chaos. Some call the result the Life Force, some note that the Earth is a living system itself (Gaia, a "tough bitch" according to Margulis), and some conclude that the observed complexity requires a supernatural explanation (of which we have many). But my dad was a statistician (of dairy cows) and he told me about cells and genes and evolution and chance when I was very small. So a scientist must look for me explanation of how nature's laws and statistics brought us into conscious existence. And how is that seemll"!gly Improbable events are actually happening a!1 the time? Well, the physicists have countless examples of natural instability, in which energy is released to power change from simplicity to complexity. One of the most common to see is that cooling water vapor below the freezing point produces snowflakes, no two alike, and all complex and beautiful. We see it often so we are not amazed. But physlc!sts have observed so many kinds of these changes from one structure to another (we call them phase transitions) that the Nobel Prize in 1992 could be awarded for understanding the mathematics of their common features. Now for a few examples of how the laws of nature produce the instabilities that lead to our own existence. First, the Big Bang (what an insufficient name!) apparently came from an instability, in which the "false vacuum" eventually decayed into the ordinary vacuum we have today, plus the most fundamental particles we know, the quarks and leptons. So the universe as a whole started with an instability. Then, a great expansion and cooling happened, and the loose quarks, finding themselves unstable too, bound themselves together into today's less elementary particles like protons and neutrons, liberating a little energy and creating complexity. Then, the expanding universe cooled some more, and neutrons and protons, no longer kept apart by immense temperatures, found themselves unstable and formed helium nuclei. Then, a little more cooling, and atomic nuclei and electrons were no longer kept apart, and the universe became transparent. Then a little more cooling, and the next instability began: gravitation pulled matter together across cosmic distances to form stars and galaxies. This instability is described as a "negative heat capadty" in which extracting energy from a gravitating system makes it hotter -- clearly the 2nd law of thermodynamics does not apply here! (This is the physicist's part of the answer to e e cummings' question: what is the wonder that's keeping the stars apart?) Then, the next instability is that hydrogen and helium nuclei can fuse together to release energy and make stars burn for billions of years. And then at the end of the fuel source, stars become unstable and explode and liberate the chemical elements back into space. And because of that, on planets like Earth, sustained energy flows support the development of additional instabilities and all kinds of complex patterns. Gravitational instability pulls the densest materials into the core of the Earth, leaving a thin skin of water and air, and makes the interior churn incessantly as heat flows outwards. And the heat from the sun, received mostly near the equator and flowing towards the poles, supports the complex atmospheric and oceanic circulations. And because or that, the physical Earth is full of natural chemical laboratories, concentrating elements here, mixing them there, raising and lowering temperatures, ceaselessly experimenting with uncountable events where new instabilities can arise. At least one of them was the new experiment called life. Now that we know that there are at least as many planets as there are stars, it is hard to imagine that nature's ceasess experimentation would not be able to produce life elsewhere

  18. Variational Structure of Inverse Problems in Wave Propagation and Vibration

    E-print Network

    Variational Structure of Inverse Problems in Wave Propagation and Vibration James G. Berryman in wave propagation (traveltime tomography) and two examples in vibration (the plucked string and free.'' For vibrating systems, the apparently very complex behavior of an excited string, drumhead, or the Earth can

  19. Higher Education Earnings Premium: Value, Variation, and Trends

    ERIC Educational Resources Information Center

    Baum, Sandy

    2014-01-01

    Much of the current skepticism about the financial payoff of higher education emerges from recent media focus on young college graduates struggling to enter a weak labor market. This brief highlights some of the complexities underlying discussions of the return to the investment in postsecondary education and describes some of the variation in…

  20. Lunar Global Petrologic Variations

    NASA Astrophysics Data System (ADS)

    Bussey, D. B. J.; Spudis, P. D.; Gillis, J. J.

    1999-01-01

    An initial attempt at producing petrologic province maps of the lunar highlands combined orbital and sample geochemical data in variation diagrams.Three different variation diagrams were produced: Mg* (= 100 Mg/Mg+Fe) vs. [(Th/Ti)c, Al vs. Mg*/(Th/Ti)c, and Fe vs. (Th/Ti)c. ([Th/Ti]c is the ratio of Th to Ti, normalized to the chrondritic ratio for these elements.] Later work applied a ternary diagram approach to look at global lunar petrologic variations. This work used the Fe-(Th/Ti)c technique as this had the most spatial coverage with the available data and also appeared to be adequate at distinguishing between different rock types. In the ternary diagram, the apexes were assigned the average Fe and (Th/Ti), values of ferroan anorthosite, mare basalt, and KREEP rocks. Each apex was assigned a primary color while the center of the triangle was represented by gray. Each point on the lunar surface, covered by the Apollo geochemical instruments, was then assigned a color depending on where in the ternary their composition placed them. The resultant petrologic classification map shows how the petrologic units vary spatially. The main results from this work were as follows: (1) The highlands contain large areas of relatively pure ferroan anorthosite; (2) KREEP/Mg suite rocks represent a small percentage of the upper lunar crust; (3) farside outcrops of KREEP/ Mg suite rocks are associated with areas of crustal thinning, particularly on the floor of South Pole Aitken Basin; (4) the average composition of the highlands is richer in Fe than ferroan anorthosite, which supports the magma ocean hypothesis of crystal formation; and (5) regions of the eastern limb and farside highlands are relatively more mafic than average highlands. These areas have a high density of dark halo craters, supporting the idea that mare volcanism occurred in this region before the end of the heavy bombardment. This earlier work utilized the Apollo gamma and X-ray orbital datasets. These data provided limited coverage of the lunar surface (mostly confined to the equatorial latitudes). The gamma ray instrument covered approximately 19% of the lunar surface while the X-ray only covered 9%. With the Clementine and Lunar Prospector datasets, we now have global maps of Fe, Ti, and Th. Apart from global coverage, another important advantage of the new datasets is higher spatial resolution. The resolution of the Apollo instruments was 15 km for the X-ray and 100 km for the gamma ray. The Fe and Ti maps are derived from the full-resolution Clementine UV-VIS data, i.e., about 250 m/pixel. The resolution of the Th data, obtained by Lunar Prospector's neutron spectrometer, is currently about 150 km, but will be available in the future with a spatial resolution of 60 km. The other improvement provided by the recent lunar missions is the error associated with the data. The errors associated with the Fe, Ti, and Th values obtained by Apollo were 10-25 wt%. The error of the Clementine-derived Fe and Ti values is about 1% while the Th data have an error of about 1 ppm. We intend to investigate the petrologic variations on the Moon at a global scale using the new Clementine and Lunar Prospector elemental maps for Fe, Ti, and Th. We shall use the technique described in Davis and Spudis. An initial study has been undertaken that looks at some regions that were covered by the Apollo geochemistry data. Two mare regions, one in Imbrium and the other in Procellarum, match well with the results using the Apollo data. The highland terrain appears problematic. The calibration of the Th data is based on the assumption of a constant background. This is a valid assumption where Th counts are well above background limits, but as count rates decrease variations in Th concentration are more sensitive to background fluctuations. Eventually we will circumvent this problem by using the lower-altitude (i.e., higher resolution) Prospector data and a calibration derived from deconvolution of the gamma ray spectra with proper attention to background variations. The Th/Ti vs. Fe technique p

  1. Conservation genetics of the species complex Cochlearia officinalis L. s.l. in Britain 

    E-print Network

    Gill, Estelle

    2008-01-01

    The genus Cochlearia is a taxonomically complex genus with a circumpolar distribution. In common with many other post-glacial colonisers it exhibits complex patterns of morphological and ecological variation. The genus ...

  2. RESULTS OF IPCS COLLABORATIVE STUDY ON COMPLEX MIXTURES

    EPA Science Inventory

    The International Programme on Chemical Safety (IPCS) sponsored a collaborative study to examine the intra- and interlaboratory variation associated with the preparation and bioassay of complex chemical mixtures. The mixtures selected were National Institute of Standards and Tech...

  3. Speciation in the Emerald Toucanet (*Aulacorhynchus prasinus*) complex

    E-print Network

    Puebla-Olivares, Fernando; Bonaccorso, Elisa; Monteros, Alejandro Espinosa de los; Omland, Kevin E.; Llorente-Bousquets, Jeorge E.; Peterson, A. Townsend; Navarro-Sigü enza, Adolfo G.

    2008-01-01

    We analyzed genetic variation in the Emerald Toucanet (Aulacorhynchus prasinus), a species complex that ranges primarily along the montane forests of southern and eastern Mexico south to Bolivia. Segments of three mitochondrial DNA genes (cytochrome...

  4. Stability of asynchronous variational integrators

    NASA Astrophysics Data System (ADS)

    Fong, William; Darve, Eric; Lew, Adrian

    2008-09-01

    The adoption of multiple time step integrators can provide substantial computational savings for mechanical systems with multiple time scales. However, the scope of these savings may be limited by the range of allowable time step choices. In this paper we analyze the linear stability of the fully asynchronous methods termed AVI, for asynchronous variational integrators. We perform a detailed analysis for the case of a one-dimensional particle moving under the action of a soft and a stiff quadratic potential, integrated with two time steps in rational ratios. In this case, we provide sufficient conditions for the stability of the method. These generalize to the fully asynchronous AVI case the results obtained for synchronous multiple time stepping schemes, such as r-RESPA, which show resonances when the larger time step is a multiple of the effective half-period of the stiff potential. Additionally, we numerically investigate the appearance of instabilities. Based on the experimental observations, we conjecture the existence of a dense set of unstable time steps when arbitrary rational ratios of time steps are considered. In this way, unstable schemes for arbitrarily small time steps can be obtained. However, the vast majority of these instabilities are extremely weak and do not present an obstacle to the use of these integrators. We then applied these results to analyze the stability of multiple time step integrators in the more complex mechanical systems arising in molecular dynamics and solid dynamics. We explained why strong resonances are ubiquitously found in the former, while rarely encountered in the latter. Finally, in this paper we introduce a formulation of AVI that highlights the symplectic nature of the algorithm, complementing those introduced earlier by other authors.

  5. Variational methods for cellular models

    NASA Astrophysics Data System (ADS)

    Nesbet, R. K.

    1988-11-01

    Two complementary variational principles are derived for the one-electron Schrödinger or local-density-functional equation in a closed cell of arbitrary shape, for external Neumann and Dirichlet boundary conditions, respectively. The surface operators scrR and scrR-1, respectively, are stationary in these two variational principles. Subject to a condition of compatibility of the boundary conditions, these results are combined to give variational equations that are valid for an arbitrary cluster of atomic cells, assumed to fill space within an outer boundary. Cell interface terms agree with prior variational derivations for discontinuous functions. It is shown that structure constants of multiple scattering theory can be used within the variational formalism, giving contracted Hermitian matrix equations linearized in energy. New variational prescriptions are given for two broad classes of applications: (i) electron scattering by a cluster, or bound states using scattering theory; (ii) embedding a cluster in a substrate.

  6. Variational multiscale models for charge transport

    PubMed Central

    Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin

    2012-01-01

    This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle for chemo-electro-fluid systems. A number of computational algorithms is developed to implement the proposed new variational multiscale models in an efficient manner. A set of ten protein molecules and a realistic ion channel, Gramicidin A, are employed to confirm the consistency and verify the capability. Extensive numerical experiment is designed to validate the proposed variational multiscale models. A good quantitative agreement between our model prediction and the experimental measurement of current-voltage curves is observed for the Gramicidin A channel transport. This paper also provides a brief review of the field. PMID:23172978

  7. FUNCTIONAL IMPLICATION OF MAJOR HISTOCOMPATIBILITY (MH) VARIATION USING AN ESTUARINE FISH POPULATION

    EPA Science Inventory

    Recently, there has been a dramatic expansion of studies of major histocompatibility complex (MHC) variation aimed at discovering functional differences in immunity across wild populations of diverse vertebrate species. Some species with relatively low genetic diversity or under ...

  8. Holding the Words in Our Mouths: Responses to Dialect Variations in Oral Reading

    ERIC Educational Resources Information Center

    Van Duinen, Deborah Vriend; Wilson, Marilyn J.

    2008-01-01

    Deborah Vriend Van Duinen and Marilyn J. Wilson confront normalized notions of "correct" English. They offer suggestions for teaching about marginalized voices and introducing students to the complexities of English dialect variations. (Contains 1 figure.)

  9. Quantifying Cell-to-Cell Variation in Power-Law Rheology

    E-print Network

    Cai, PingGen

    Among individual cells of the same source and type, the complex shear modulus G[subscript ?] exhibits a large log-normal distribution that is the result of spatial, temporal, and intrinsic variations. Such large distributions ...

  10. Strong correlation in Kohn-Sham DFT

    NASA Astrophysics Data System (ADS)

    Malet Giralt, Francesc; Mirtschink, André; Cremon, Jonas; Mendl, Christian; Giesbertz, Klaas; Reimann, Stephanie; Gori-Giorgi, Paola; Mathematical Physics, Lund University Collaboration; Mathematics Department, Technische Universität München Collaboration

    2014-03-01

    The knowledge on the strong-interacting limit of density functional theory can be used to construct exchange- correlation functionals able to address strongly-correlated systems without introducing any symmetry breaking. We report calculations on semiconductor nanostructures and one-dimensional models for chemical systems, showing that this approach yields quantitatively good results in both the weakly- and the strongly-correlated regimes, with a numerical cost much lower than the traditional wavefunction methods. This work has been supported by a VIDI grant of the NWO and a Marie Curie grant within the FP7 programme.

  11. Seasonal Variations in Soudan 2

    NASA Astrophysics Data System (ADS)

    Goodman, Maury

    1999-08-01

    Seasonal Variations in an underground detector may be a signature for Dark Matter. 1 The Soudan 2 detector searches for nucleon decay and atmospheric neutrinos. The trigger rate is about 0.5 Hertz. It is dominated by approximately equal numbers of atmospheric muons and low level radioactivity. The muon rate has a seasonal variation of +-2°, which is consistent with a similar e ect at MACRO. The MACRO e ect has been correlated with temperature in the upper atmosphere. Our trigger rate has a seasonal variation of +-15° which we believe is due to radon in the mine, and variations in air ow with outside temperature.

  12. Explorations in Regional Variation: A Variational Pragmatic Perspective

    ERIC Educational Resources Information Center

    Barron, Anne

    2015-01-01

    The present article introduces the Special Issue entitled "A Variational Pragmatic Approach to Regional Variation in Language," a collection of papers which celebrates the work of Klaus P. Schneider (Rheinische Friedrich-Wilhelms-Universität Bonn, Germany) on the occasion of his 60th birthday.

  13. Algorithms, complexity, and the sciences

    PubMed Central

    Papadimitriou, Christos

    2014-01-01

    Algorithms, perhaps together with Moore’s law, compose the engine of the information technology revolution, whereas complexity—the antithesis of algorithms—is one of the deepest realms of mathematical investigation. After introducing the basic concepts of algorithms and complexity, and the fundamental complexity classes P (polynomial time) and NP (nondeterministic polynomial time, or search problems), we discuss briefly the P vs. NP problem. We then focus on certain classes between P and NP which capture important phenomena in the social and life sciences, namely the Nash equlibrium and other equilibria in economics and game theory, and certain processes in population genetics and evolution. Finally, an algorithm known as multiplicative weights update (MWU) provides an algorithmic interpretation of the evolution of allele frequencies in a population under sex and weak selection. All three of these equivalences are rife with domain-specific implications: The concept of Nash equilibrium may be less universal—and therefore less compelling—than has been presumed; selection on gene interactions may entail the maintenance of genetic variation for longer periods than selection on single alleles predicts; whereas MWU can be shown to maximize, for each gene, a convex combination of the gene’s cumulative fitness in the population and the entropy of the allele distribution, an insight that may be pertinent to the maintenance of variation in evolution. PMID:25349382

  14. Algorithms, complexity, and the sciences.

    PubMed

    Papadimitriou, Christos

    2014-11-11

    Algorithms, perhaps together with Moore's law, compose the engine of the information technology revolution, whereas complexity--the antithesis of algorithms--is one of the deepest realms of mathematical investigation. After introducing the basic concepts of algorithms and complexity, and the fundamental complexity classes P (polynomial time) and NP (nondeterministic polynomial time, or search problems), we discuss briefly the P vs. NP problem. We then focus on certain classes between P and NP which capture important phenomena in the social and life sciences, namely the Nash equlibrium and other equilibria in economics and game theory, and certain processes in population genetics and evolution. Finally, an algorithm known as multiplicative weights update (MWU) provides an algorithmic interpretation of the evolution of allele frequencies in a population under sex and weak selection. All three of these equivalences are rife with domain-specific implications: The concept of Nash equilibrium may be less universal--and therefore less compelling--than has been presumed; selection on gene interactions may entail the maintenance of genetic variation for longer periods than selection on single alleles predicts; whereas MWU can be shown to maximize, for each gene, a convex combination of the gene's cumulative fitness in the population and the entropy of the allele distribution, an insight that may be pertinent to the maintenance of variation in evolution. PMID:25349382

  15. M-Theory on Complex Spacetime

    E-print Network

    Abdul Rouf Samurah

    2012-09-26

    In this paper we will analyse ABJM theory in N=1 superspace formalism on complex spacetime. We will then analyse the BRST and anti-BRST symmetries for this theory. We will show that the sum of gauge fixing and ghost terms for this theory can be expressed as a combination of the total BRST or the total anti-BRST variations.

  16. Statistical Analysis of Variation in the Human Plasma Proteome

    DOE PAGESBeta

    Corzett, Todd H.; Fodor, Imola K.; Choi, Megan W.; Walsworth, Vicki L.; Turteltaub, Kenneth W.; McCutchen-Maloney, Sandra L.; Chromy, Brett A.

    2010-01-01

    Quantifying the variation in the human plasma proteome is an essential prerequisite for disease-specific biomarker detection. We report here on the longitudinal and individual variation in human plasma characterized by two-dimensional difference gel electrophoresis (2-D DIGE) using plasma samples from eleven healthy subjects collected three times over a two week period. Fixed-effects modeling was used to remove dye and gel variability. Mixed-effects modeling was then used to quantitate the sources of proteomic variation. The subject-to-subject variation represented the largest variance component, while the time-within-subject variation was comparable to the experimental variation found in a previous technical variability study where onemore »human plasma sample was processed eight times in parallel and each was then analyzed by 2-D DIGE in triplicate. Here, 21 protein spots had larger than 50% CV, suggesting that these proteins may not be appropriate as biomarkers and should be carefully scrutinized in future studies. Seventy-eight protein spots showing differential protein levels between different individuals or individual collections were identified by mass spectrometry and further characterized using hierarchical clustering. The results present a first step toward understanding the complexity of longitudinal and individual variation in the human plasma proteome, and provide a baseline for improved biomarker discovery.« less

  17. Population genetic variation in gene expression is associated withphenotypic variation in Saccharomyces cerevisiae

    SciTech Connect

    Fay, Justin C.; McCullough, Heather L.; Sniegowski, Paul D.; Eisen, Michael B.

    2004-02-25

    The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits. Results: We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes,20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2. Conclusions: Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.

  18. A variational principle for compressible fluid mechanics: Discussion of the multi-dimensional theory

    NASA Technical Reports Server (NTRS)

    Prozan, R. J.

    1982-01-01

    The variational principle for compressible fluid mechanics previously introduced is extended to two dimensional flow. The analysis is stable, exactly conservative, adaptable to coarse or fine grids, and very fast. Solutions for two dimensional problems are included. The excellent behavior and results lend further credence to the variational concept and its applicability to the numerical analysis of complex flow fields.

  19. Computational Complexity and Knowledge Complexity \\Lambda

    E-print Network

    Goldreich, Oded

    Computational Complexity and Knowledge Complexity \\Lambda Oded Goldreich y Rafail Ostrovsky z Erez Petrank x March 20, 1995 Abstract We study the computational complexity of languages which have interactive proofs of logarithmic knowledge complexity. We show that all such languages can be recog­ nized

  20. Transmissivity variations in mudstones.

    PubMed

    MacDonald, Alan M; Kemp, Simon J; Davies, Jeff

    2005-01-01

    Many people in sub-Saharan Africa have to rely on meager water resources within mudstones for their only water supply. Although mudstones have been extensively researched for their low permeability behavior, little research has been undertaken to examine their ability to provide sustainable water supplies. To investigate the factors controlling the occurrence of usable ground water in mudstone environments, an area of Cretaceous mudstones in southeastern Nigeria was studied over a 3 yr period. Transmissivity (T) variations in a range of mudstone environments were studied. The investigations demonstrate that within the top 40 m of mudstones, transmissivity can be sufficient to develop village water supplies (T > 1 m2/d). Transmissivity is controlled by two factors: low-grade metamorphism and the presence of other, subordinate, lithologies within the mudstones. Largely unaltered mudstones (early diagenetic zone), comprising mainly smectite clays, are mostly unfractured and have a low T of < 0.1 m2/d. Mudstones that have undergone limited metamorphism (late diagenetic zone) comprise mixed layered illite/smectite clays, and ground water is found in widely spaced fracture zones (T > 1 m2/d in large fracture zones; T < 0.1 m2/d away from fracture zones). Mudstones that have been further altered and approach the anchizone comprise illite clays, are pervasively fractured, and have the highest transmissivity values (T > 4 m2/d). Dolerite intrusions in unaltered, smectitic mudstones are highly fractured with transmissivity in the range of 1 < T < 60 m2/d. Thin limestone and sandstone layers can also enhance transmissivity sufficiently to provide community water supplies. PMID:15819947

  1. variational method for rel ativistic

    E-print Network

    on a rigourous variational meth od. Th is provides a numerical meth od wh ich is free of th e numerical drawbacks anics -- relativistic models for atoms and molecules -- computational meth ods -- ab­initio meth ods -- basis sets -- B­splines -- Dirac operators-- e#ective Hamiltonians -- variational meth ­ ods -- min

  2. Sea level variation

    NASA Technical Reports Server (NTRS)

    Douglas, Bruce C.

    1992-01-01

    Published values for the long-term, global mean sea level rise determined from tide gauge records range from about one to three mm per year. The scatter of the estimates appears to arise largely from the use of data from gauges located at convergent tectonic plate boundaries where changes of land elevation give fictitious sea level trends, and the effects of large interdecadal and longer sea level variations on short (less than 50+ years) or sappy records. In addition, virtually all gauges undergo subsidence or uplift due to isostatic rebound from the last deglaciation at a rate comparable to or greater than the secular rise of sea level. Modeling rebound by the ICE-3G model of Tushingham and Peltier (1990) and avoiding tide gauge records in areas of converging tectonic plates produces a highly consistent set of long sea level records. A global set of 21 such stations in nine oceanic regions with an average record length of 76 years during the period 1880-1980 yields the global sea level rise value 1.8 mm/year +/- 0.1. Greenhouse warming scenarios commonly forecast an additional acceleration of global sea level in the next 5 or 6+ decades in the range 0.1-0.2 mm/yr2. Because of the large power at low frequencies in the sea level spectrum, very long tide gauge records (75 years minimum) have been examined for past apparent sea level acceleration. For the 80-year period 1905-1985, 23 essentially complete tide gauge records in 10 geographic groups are available for analysis. These yielded the apparent global acceleration -0.011 (+/- 0.012) mm/yr2. A larger, less uniform set of 37 records in the same 10 groups with 92 years average length covering the 141 years from 1850-1991 gave 0.001 (+/- 0.008) mm/yr2. Thus there is no evidence for an apparent acceleration in the past 100+ years that is significant either statistically, or in comparison to values associated with global warming. Unfortunately, the large interdecadal fluctuations of sea level severely affect estimates of global sea level acceleration for time spans of less than about 50 years. This means that tide gauges alone cannot serve as a reliable leading indicator of climate change in less than many decades. This time required can be significantly reduced if the interdecadal fluctuations of sea level can be understood in terms of their forcing mechanisms, and then removed from the tide gauge records.

  3. Circadian variation in disease activity in rheumatoid arthritis.

    PubMed Central

    Harkness, J A; Richter, M B; Panayi, G S; Van de Pette, K; Unger, A; Pownall, R; Geddawi, M

    1982-01-01

    Disease activity in rheumatoid arthritis as measured by repeated estimation of joint pain, stiffness, articular index, and grip strength was shown to have a circadian rythm, maximal activity being seen between 0200 and 0400 and minimal activity in the early afternoon. This variation in disease activity may be related to circadian alterations in immune and inflammatory responses (such as immune complexes and neutrophil function) dependent on alterations in circulating concentrations of steroids. The circadian variation in disease activity has important implications in assessment of patients, prescription of drugs, and performance of drug trials. PMID:6800538

  4. Spatial Variation as a Tool for Inferring Temporal Variation and Diagnosing Types of Mechanisms in Ecosystems

    PubMed Central

    Hammond, Matthew P.; Kolasa, Jurek

    2014-01-01

    Ecological processes, like the rise and fall of populations, leave an imprint of their dynamics as a pattern in space. Mining this spatial record for insight into temporal change underlies many applications, including using spatial snapshots to infer trends in communities, rates of species spread across boundaries, likelihood of chaotic dynamics, and proximity to regime shifts. However, these approaches rely on an inherent but undefined link between spatial and temporal variation. We present a quantitative link between a variable’s spatial and temporal variation based on established variance-partitioning techniques, and test it for predictive and diagnostic applications. A strong link existed between spatial and regional temporal variation (estimated as Coefficients of Variation or CV’s) in 136 variables from three aquatic ecosystems. This association suggests a basis for substituting one for the other, either quantitatively or qualitatively, when long time series are lacking. We further show that weak substitution of temporal for spatial CV results from distortion by specific spatiotemporal patterns (e.g., inter-patch synchrony). Where spatial and temporal CV’s do not match, we pinpoint the spatiotemporal causes of deviation in the dynamics of variables and suggest ways that may control for them. In turn, we demonstrate the use of this framework for describing spatiotemporal patterns in multiple ecosystem variables and attributing them to types of mechanisms. Linking spatial and temporal variability makes quantitative the hitherto inexact practice of space-for-time substitution and may thus point to new opportunities for navigating the complex variation of ecosystems. PMID:24586627

  5. Pronunciation Variation in ASR: Which Variation to Model? 

    E-print Network

    Wester, Mirjam; Kessens, Judith M; Strik, Helmer

    This paper describes how the performance of a continuous speech recognizer for Dutch has been improved by modeling within-word and cross-word pronunciation variation. A relative improvement of 8.8% in WER was found compared ...

  6. Constrained variational calculus: the second variation (part I)

    E-print Network

    Enrico Massa; Danilo Bruno; Gianvittorio Luria; Enrico Pagani

    2012-10-16

    Within the geometrical framework developed in arXiv:0705.2362, the problem of minimality for constrained calculus of variations is analysed among the class of differentiable curves. A fully covariant representation of the second variation of the action functional, based on a suitable gauge transformation of the Lagrangian, is explicitly worked out. Both necessary and sufficient conditions for minimality are proved, and are then reinterpreted in terms of Jacobi fields.

  7. Variational formulation of high performance finite elements: Parametrized variational principles

    NASA Technical Reports Server (NTRS)

    Felippa, Carlos A.; Militello, Carmello

    1991-01-01

    High performance elements are simple finite elements constructed to deliver engineering accuracy with coarse arbitrary grids. This is part of a series on the variational basis of high-performance elements, with emphasis on those constructed with the free formulation (FF) and assumed natural strain (ANS) methods. Parametrized variational principles that provide a foundation for the FF and ANS methods, as well as for a combination of both are presented.

  8. Statistics, Uncertainty, and Transmitted Variation

    SciTech Connect

    Wendelberger, Joanne Roth

    2014-11-05

    The field of Statistics provides methods for modeling and understanding data and making decisions in the presence of uncertainty. When examining response functions, variation present in the input variables will be transmitted via the response function to the output variables. This phenomenon can potentially have significant impacts on the uncertainty associated with results from subsequent analysis. This presentation will examine the concept of transmitted variation, its impact on designed experiments, and a method for identifying and estimating sources of transmitted variation in certain settings.

  9. 3D VIDEO QUALITY EVALUATION WITH DEPTH QUALITY VARIATIONS Gustavo Leon, Hari Kalva, and Borko Furht

    E-print Network

    Kalva, Hari

    the perception of depth, depth complexity and motion. Motion and complexity of the depth image have a strongD perception, additional work is necessary for developing objective metrics based on depth quality3D VIDEO QUALITY EVALUATION WITH DEPTH QUALITY VARIATIONS Gustavo Leon, Hari Kalva, and Borko Furht

  10. VARIATION OF AEROSOL OPTICAL PROPERTIES

    E-print Network

    Schwartz, Stephen E.

    VARIATION OF AEROSOL OPTICAL PROPERTIES AND RADIATIVE IMPLICATIONS Stephen E. Schwartz Upton, Long of the geographical region under consideration, m2 Charlson, Schwartz, Hales, Cess, Coakley, Hansen & Hofmann, Science

  11. Variational MCMC Nando de Freitas

    E-print Network

    Jordan, Michael I.

    -1776 USA fjfgf,jordan,russellg@cs.berkeley.edu Pedro H#28;jen-S#28;rensen y Michael I. Jordan Stuart (Jaakkola and Jordan 1999, Jordan, Ghahramani, Jaakkola and Saul 1999). However, variational approx

  12. Fc? receptors: genetic variation, function, and disease.

    PubMed

    Hargreaves, Chantal E; Rose-Zerilli, Matthew J J; Machado, Lee R; Iriyama, Chisako; Hollox, Edward J; Cragg, Mark S; Strefford, Jonathan C

    2015-11-01

    Fc? receptors (Fc?Rs) are key immune receptors responsible for the effective control of both humoral and innate immunity and are central to maintaining the balance between generating appropriate responses to infection and preventing autoimmunity. When this balance is lost, pathology results in increased susceptibility to cancer, autoimmunity, and infection. In contrast, optimal Fc?R engagement facilitates effective disease resolution and response to monoclonal antibody immunotherapy. The underlying genetics of the Fc?R gene family are a central component of this careful balance. Complex in humans and generated through ancestral duplication events, here we review the evolution of the gene family in mammals, the potential importance of copy number, and functionally relevant single nucleotide polymorphisms, as well as discussing current approaches and limitations when exploring genetic variation in this region. PMID:26497510

  13. Variation of fundamental constants: theory

    NASA Astrophysics Data System (ADS)

    Flambaum, Victor

    2008-05-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. There are some hints for the variation of different fundamental constants in quasar absorption spectra and Big Bang nucleosynthesis data. A large number of publications (including atomic clocks) report limits on the variations. We want to study the variation of the main dimensionless parameters of the Standard Model: 1. Fine structure constant alpha (combination of speed of light, electron charge and Plank constant). 2. Ratio of the strong interaction scale (LambdaQCD) to a fundamental mass like electron mass or quark mass which are proportional to Higgs vacuum expectation value. The proton mass is propotional to LambdaQCD, therefore, the proton-to-electron mass ratio comes into this second category. We performed necessary atomic, nuclear and QCD calculations needed to study variation of the fundamental constants using the Big Bang Nucleosynthsis, quasar spectra, Oklo natural nuclear reactor and atomic clock data. The relative effects of the variation may be enhanced in transitions between narrow close levels in atoms, molecules and nuclei. If one will study an enhanced effect, the relative value of systematic effects (which are not enhanced) may be much smaller. Note also that the absolute magnitude of the variation effects in nuclei (e.g. in very narrow 7 eV transition in 229Th) may be 5 orders of magnitude larger than in atoms. A different possibility of enhancement comes from the inversion transitions in molecules where splitting between the levels is due to the quantum tunneling amplitude which has strong, exponential dependence on the electron to proton mass ratio. Our study of NH3 quasar spectra has already given the best limit on the variation of electron to proton mass ratio.

  14. Coupled dark energy field variation

    NASA Astrophysics Data System (ADS)

    García-Zúñiga, Roberto Carlos; Izquierdo, Germán

    2014-10-01

    The variation of the dark energy field is found under the assumption that the dark energy is parametric and interacts with the cold dark matter. Considering that the variation of the field could not exceed the Planck mass, we obtain bounds on the coupling and adiabatic coefficients. Three parametrizations of the adiabatic coefficients are considered and two coupling terms where the energy flows from dark energy to dark matter, or the other way around.

  15. Variational calculus on Banach spaces

    SciTech Connect

    Uglanov, A V

    2000-10-31

    The problem of variational calculus is considered in a (variable) subdomain of a Banach space. Analogues of the basic principles of the finite-dimensional theory are derived: the main formula for variations of a functional, necessary conditions of an extremum, Noether's theorem. All the results obtained are dimension-invariant and become the classical ones in the finite-dimensional setting. The main tool of the analysis is the theory of surface integration in Banach spaces.

  16. On State Complexes and Special Cube Complexes

    ERIC Educational Resources Information Center

    Peterson, Valerie J.

    2009-01-01

    This thesis presents the first steps toward a classification of non-positively curved cube complexes called state complexes. A "state complex" is a configuration space for a "reconfigurable system," i.e., an abstract system in which local movements occur in some discrete manner. Reconfigurable systems can be used to describe, for example,…

  17. Variational integrators for electric circuits

    SciTech Connect

    Ober-Blöbaum, Sina; Tao, Molei; Cheng, Mulin; Owhadi, Houman; Marsden, Jerrold E.; Applied and Computational Mathematics, California Institute of Technology

    2013-06-01

    In this contribution, we develop a variational integrator for the simulation of (stochastic and multiscale) electric circuits. When considering the dynamics of an electric circuit, one is faced with three special situations: 1. The system involves external (control) forcing through external (controlled) voltage sources and resistors. 2. The system is constrained via the Kirchhoff current (KCL) and voltage laws (KVL). 3. The Lagrangian is degenerate. Based on a geometric setting, an appropriate variational formulation is presented to model the circuit from which the equations of motion are derived. A time-discrete variational formulation provides an iteration scheme for the simulation of the electric circuit. Dependent on the discretization, the intrinsic degeneracy of the system can be canceled for the discrete variational scheme. In this way, a variational integrator is constructed that gains several advantages compared to standard integration tools for circuits; in particular, a comparison to BDF methods (which are usually the method of choice for the simulation of electric circuits) shows that even for simple LCR circuits, a better energy behavior and frequency spectrum preservation can be observed using the developed variational integrator.

  18. Diffusion and thermodynamic equilibrium under pressure variations

    NASA Astrophysics Data System (ADS)

    Moulas, Evangelos; Taj?manová, Lucie; Vrijmoed, Johannes; Podladchikov, Yuri

    2015-04-01

    Pressure is one of the most fundamental variables in mineral thermodynamics. In that respect, pressure-sensitive mineral reactions provide an important constraint on pressure under which the rock was developed. One implicit assumption when interpreting such pressure estimates is that the state-of-stress is close to hydrostatic, homogeneous and that the differential stress is negligible. Recent spectroscopic data from the mineral scale documenting pressure variations do not support this assumption. In addition to observations, mechanical models (numerical and analytical) suggest that rocks can develop and maintain heterogeneous pressure distributions at geological time scales. The recently developed unconventional barometry explains chemical zoning in minerals as a result of a pressure variation. We focus to apply the unconventional barometry in cases where chemical zoning in minerals cannot be explained by sluggish kinetics. In that respect, the unconventional barometry offers an alternative view of the chemical zoning which is consistent with thermodynamic equilibrium. However, to distinguish between a pressure-controlled chemical zoning and a zoning reflecting an incomplete chemical reaction is still challenging, especially for multicomponent systems. In this contribution, different types of chemical zoning are discussed. We investigate plagioclase rims around kyanite from an amphibolitized eclogite from Rhodope Metamorphic Complex (Greece-Bulgaria) as a case study and compare them with similar published textures from the Bohemian Massif. Mineral microstructures and phase equilibrium suggest that both rocks experienced near-isothermal decompression at high (>700C) temperatures. However, several distinct microstructural features suggest the development and/or the decay of mechanically maintained heterogeneous pressure distributions. We discuss our results and interpretations based on phase-equilibrium modeling, unconventional barometry and diffusion modeling under pressure variations.

  19. Genetic Architecture of Natural Variation in Thermal Responses of Arabidopsis.

    PubMed

    Sanchez-Bermejo, Eduardo; Zhu, Wangsheng; Tasset, Celine; Eimer, Hannes; Sureshkumar, Sridevi; Singh, Rupali; Sundaramoorthi, Vignesh; Colling, Luana; Balasubramanian, Sureshkumar

    2015-09-01

    Wild strains of Arabidopsis (Arabidopsis thaliana) exhibit extensive natural variation in a wide variety of traits, including response to environmental changes. Ambient temperature is one of the major external factors that modulates plant growth and development. Here, we analyze the genetic architecture of natural variation in thermal responses of Arabidopsis. Exploiting wild accessions and recombinant inbred lines, we reveal extensive phenotypic variation in response to ambient temperature in distinct developmental traits such as hypocotyl elongation, root elongation, and flowering time. We show that variation in thermal response differs between traits, suggesting that the individual phenotypes do not capture all the variation associated with thermal response. Genome-wide association studies and quantitative trait locus analyses reveal that multiple rare alleles contribute to the genetic architecture of variation in thermal response. We identify at least 20 genomic regions that are associated with variation in thermal response. Further characterizations of temperature sensitivity quantitative trait loci that are shared between traits reveal a role for the blue-light receptor CRYPTOCHROME2 (CRY2) in thermosensory growth responses. We show the accession Cape Verde Islands is less sensitive to changes in ambient temperature, and through transgenic analysis, we demonstrate that allelic variation at CRY2 underlies this temperature insensitivity across several traits. Transgenic analyses suggest that the allelic effects of CRY2 on thermal response are dependent on genetic background suggestive of the presence of modifiers. In addition, our results indicate that complex light and temperature interactions, in a background-dependent manner, govern growth responses in Arabidopsis. PMID:26195568

  20. Variation Ontology for annotation of variation effects and mechanisms.

    PubMed

    Vihinen, Mauno

    2014-02-01

    Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological annotations facilitate systematic description and data organization, data integration and mining, and pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology (VariO) was developed to allow the annotation of effects, consequences, and mechanisms of DNA, RNA, and protein variations. Variation types are systematically organized, and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal-state features or properties, and requires a reference (e.g., reference sequence, reference-state property, activity, etc.) compared to which the changes are indicated. VariO is versatile and can be used for variations ranging from genomic multiplications to single nucleotide or amino acid changes, whether of genetic or nongenetic origin. VariO annotations are position-specific and can be used for variations in any organism. PMID:24162187

  1. The impact of human copy number variation on gene expression.

    PubMed

    Gamazon, Eric R; Stranger, Barbara E

    2015-09-01

    Recent years have witnessed a flurry of important technological and methodological developments in the discovery and analysis of copy number variations (CNVs), which are increasingly enabling the systematic evaluation of their impact on a broad range of phenotypes from molecular-level (intermediate) traits to higher-order clinical phenotypes. Like single nucleotide variants in the human genome, CNVs have been linked to complex traits in humans, including disease and drug response. These recent developments underscore the importance of incorporating complex forms of genetic variation into disease mapping studies and promise to transform our understanding of genome function and the genetic basis of disease. Here we review some of the findings that have emerged from transcriptome studies of CNVs facilitated by the rapid advances in -omics technologies and corresponding methodologies. PMID:25922366

  2. 45 CFR 156.420 - Plan variations.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...420 Plan variations. (a) Submission of silver plan variations. For each of its silver health plans that an issuer offers, or intends...certification prior to each benefit year the standard silver plan and three variations of the standard...

  3. 45 CFR 156.420 - Plan variations.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...420 Plan variations. (a) Submission of silver plan variations. For each of its silver health plans that an issuer offers, or intends...certification prior to each benefit year the standard silver plan and three variations of the standard...

  4. Nobel Lecture: Electronic structure of matter--wave functions and density functionals*

    E-print Network

    Wu, Zhigang

    Nobel Lecture: Electronic structure of matter--wave functions and density functionals* W. Kohn-physical-chemical considerations 1257 III. Density-Functional Theory--Background 1258 IV. The Hohenberg-Kohn Formulation of Density- Functional Theory 1259 A. The density n(r) as the basic variable 1259 B. The Hohenberg-Kohn variational

  5. Variational approach to enhanced sampling and free energy calculations.

    PubMed

    Valsson, Omar; Parrinello, Michele

    2014-08-29

    The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem. PMID:25215968

  6. An experimental trip to the Calculus of Variations

    NASA Astrophysics Data System (ADS)

    Arroyo, Josu

    2008-04-01

    This paper presents a collection of experiments in the Calculus of Variations. The implementation of the Gradient Descent algorithm built on cubic-splines acting as "numerically friendly" elementary functions, give us ways to solve variational problems by constructing the solution. It wins a pragmatic point of view: one gets solutions sometimes as fast as possible, sometimes as close as possible to the true solutions. The balance speed/precision is not always easy to achieve. Starting from the most well-known, classic or historical formulation of a variational problem, section 2 describes briefly the bridge between theoretical and computational formulations. The next sections show the results of several kind of experiments; from the most basics, as those about geodesics, to the most complex, as those about vesicles.

  7. [Geographic variations in freshwater molluscs].

    PubMed

    Vinarski?, M V

    2012-01-01

    The phenomenon of geographic variation is known in practically all taxa of living beings. However, the reality of this phenomenon in freshwater molluscs (snails and bivalves) has many times been questioned in the past. It was accepted that these animals do not demonstrate spatially-oriented variation, where specific "local race" is arisen in each specific habitat. Till the beginning of 1970s, there was no statistical evidence that geographic clines in freshwater molluscs really exist. However, a few species of freshwater molluscs has been studied in this respect so far, therefore it is almost impossible to draw any general patterns of geographical variation in this group of animals. Most species of freshwater molluscs studied to the date exhibit statistically significant decrease of their body size in the south-north direction. Perhaps, it may be explained by decrease of the duration of the growth season in high latitudes. Some species of freshwater snails demonstrate clinal changes in shell proportions. This allows to reject subspecies separation within these species since diagnostic characters of such "subspecies" may blur when geographic variation is taken into consideration. The data on geographic variation in anatomical traits in freshwater molluscs is much more scarce. At least one species of pond snails (Lymnaea terebra) demonstrates clinal variation in proportions of the copulative apparatus in the south-north direction. Further studies of geographic variation in freshwater molluscs should reveal whether it is truly adaptive, i.e. whether geographical clines have underlying genetic basis. Otherwise, the clines may arise as a result of direct modifying effect of a habitat. PMID:22590907

  8. CONSERTING: integrating copy number analysis with structural variation detection

    PubMed Central

    Chen, Xiang; Gupta, Pankaj; Wang, Jianmin; Nakitandwe, Joy; Roberts, Kathryn; Dalton, James D.; Parker, Matthew; Patel, Samir; Holmfeldt, Linda; Payne, Debbie; Easton, John; Ma, Jing; Rusch, Michael; Wu, Gang; Patel, Aman; J. Baker, Suzanne; Dyer, Michael A.; Shurtleff, Sheila; Espy, Stephen; Pounds, Stanley; Downing, James R.; Ellison, David W.; Mullighan, Charles G.; Zhang, Jinghui

    2015-01-01

    We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), a novel algorithm for detecting somatic copy number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation by read depth change and localized structural variation detection, achieving high accuracy and sensitivity. Analysis of 43 pediatric and adult cancer genomes revealed novel oncogenic CNAs, complex re-arrangements and subclonal CNAs missed by alternative approaches. PMID:25938371

  9. Existence of evolutionary variational solutions via the calculus of variations

    NASA Astrophysics Data System (ADS)

    Bögelein, Verena; Duzaar, Frank; Marcellini, Paolo

    In this paper we introduce a purely variational approach to time dependent problems, yielding the existence of global parabolic minimizers, that is ?0T ?? [u??t?+f(x,Du)] dx dt??0T ?? f(x,Du+D?) dx dt, whenever T>0 and ??C0?(?×(0,T),RN). For the integrand f:?×R?[0,?] we merely assume convexity with respect to the gradient variable and coercivity. These evolutionary variational solutions are obtained as limits of maps depending on space and time minimizing certain convex variational functionals. In the simplest situation, with some growth conditions on f, the method provides the existence of global weak solutions to Cauchy-Dirichlet problems of parabolic systems of the type ?tu-divD?f(x,Du)=0 in ?×(0,?).

  10. Magma rheology variation in sheet intrusions (Invited)

    NASA Astrophysics Data System (ADS)

    Magee, C.; O'Driscoll, B.; Petronis, M. S.; Stevenson, C.

    2013-12-01

    The rheology of magma fundamentally controls igneous intrusion style as well as the explosivity and type of volcanic eruptions. Importantly, the dynamic interplay between the viscosity of magma and other processes active during intrusion (e.g., crystallisation, magma mixing, assimilation of crystal mushes and/or xenolith entrainment) will likely bear an influence on the temporal variation of magma rheology. Constraining the timing of rheological changes during magma transit therefore plays an important role in understanding the nuances of volcanic systems. However, the rheological evolution of actively emplacing igneous intrusions cannot be directly studied. While significant advances have been made via experimental modelling and analysis of lava flows, how these findings relate to intruding magma remains unclear. This has led to an increasing number of studies that analyse various characteristics of fully crystallised intrusions in an attempt to ';back-out' the rheological conditions governing emplacement. For example, it has long been known that crystallinity affects the rheology and, consequently, the velocity of intruding magma. This means that quantitative textural analysis of crystal populations (e.g., crystal size distribution; CSD) used to elucidate crystallinity at different stages of emplacement can provide insights into magma rheology. Similarly, methods that measure flow-related fabrics (e.g., anisotropy of magnetic susceptibility; AMS) can be used to discern velocity profiles, a potential proxy for the magma rheology. To illustrate these ideas, we present an integrated AMS and petrological study of several sheet intrusions located within the Ardnamurchan Central Complex, NW Scotland. We focus on the entrainment and transport dynamics of gabbroic inclusions that were infiltrated by the host magma upon entrainment. Importantly, groundmass magnetic fabrics within and external to these inclusions are coaxial. This implies that a deviatoric stress was transmitted into the inclusions during magma flow. We suggest that this represents a modification of the magma dynamics from Newtonian-like to Bingham-like behaviour. Furthermore, the spatial restriction of inclusions within the sheet intrusions suggest that subtle variations in magma rheology may partition apparently continuous intrusions, perhaps affecting lateral mixing and the longevity of discrete sheet segments. Detailed fabric analysis of other inclusion-free intrusions in the Ardnamurchan Central Complex supports this interpretation. Our results highlight that the crystalline cargo of a magma can result in temporal and spatial variations in magma rheology. This can partition coalesced magma bodies into ';zones' characterised by different magma properties, potentially affecting the location of magma flow pathways or even eruption sites.

  11. Computational Complexity and the Existence of Complexity Gaps

    E-print Network

    Borodin, Allan

    Computational Complexity and the Existence of Complexity Gaps A. BORODIN University of Toronto are inves- tigated. Complexity classes of recursive functions are introduced analogous to the Hartmanis complexity hierarchy. KEY WORDS AND PHRASES: computational complexity, measures of complexity, recursive func

  12. Variation in Medicaid Coverage for Hematopoietic Cell Transplantation

    PubMed Central

    Preussler, Jaime M.; Farnia, Stephanie H.; Denzen, Ellen M.; Majhail, Navneet S.

    2014-01-01

    Purpose: Variation in Medicaid policies among states may lead to differences in coverage for complex treatments. This article uses hematopoietic cell transplantation (HCT), an established treatment for patients with hematologic cancers, as a case study to highlight state variation in Medicaid coverage of complex oncology treatments. Methods: Information on HCT coverage benefits for 2012 was collected from state Medicaid Web sites and was compared with recommended HCT benefits developed by multiple stakeholders. Coverage was reviewed for five categories: one, transplantation procedure; two, donor search; three, prescriptions; four, clinical trials; and five, patient food, lodging, and transportation. Coverage was coded on a three-point scale for each category for each state. States were ranked by the number of variables for which they met recommended benefits criteria (maximum rank score, 5). Results: Detailed information on Medicaid coverage was available for 47 states. No state provided the recommended coverage benefits in all five categories. Prescription coverage most often met the recommended criteria, whereas only a small number of states provided clinical trial coverage for HCT. There was substantial variation in Medicaid coverage for HCT by state. Conclusion: Findings highlight substantial variation in Medicaid coverage for HCT by state, which may increase disparities in access for already medically underserved populations. PMID:24715266

  13. Implementing variation risk management during product development

    E-print Network

    Padgalskas, Nicholas (Nicholas Keith)

    2007-01-01

    All manufactured systems exhibit some degree of variation. Manufacturing organizations should be aware of those parameters whose variation will impact product performance and customer satisfaction. Such parameters are ...

  14. Complexation of Sr in aqueous fluids equilibrated with silicate melts: effect of melt and fluid composition

    NASA Astrophysics Data System (ADS)

    Borchert, Manuela; Wilke, Max; Schmidt, Christian; Kvashnina, Kristina

    2010-05-01

    At crustal conditions, the fluid-melt partitioning of Sr is mainly controlled by the salinity of the fluid and the composition of the melt (Borchert et al., 2010). The data show a sharp increase in the Sr partition coefficient with the alumina saturation index (ASI) to a maximum of 0.3 at an ASI of 1.05. Because fluid-melt partitioning of a given element depends on its complexation in the fluid and its incorporation in the melt, these data imply a change in the Sr speciation at least one of the two phases. For silicate melts, Kohn et al. (1990) found only small changes in the first coordination shell of Sr in a suite of melts with various degrees of polymerization, and argued that incorporation of Sr in the melt should not play a major role in controlling Sr partitioning. For the aqueous fluid, Bai and Koster van Groos (1999) and Webster et al. (1989) suggested a control of the Sr partition coefficient by SrCl2 complexes based on the correlation between partition coefficient and Cl concentration in the fluid after quenching. Both hypotheses cannot explain our partitioning data. Thus, new information on Sr complexation is required. Here, we studied the complexation of Sr in peraluminous or peralkaline melt dissolved in aqueous fluids in-situ at elevated PT conditions using hydrothermal diamond-anvil cells (HDAC) and X-ray absorption near edge structure (XANES) spectroscopy. The starting materials were peraluminous or peralkaline glass and H2O or a chloridic solution. The glass was doped with high concentrations of 5000 or 10000 ppm Sr. We used bulk compositions with 10 to 15 wt.% glass to ensure that the melt was completely dissolved in the fluid at high PT conditions. For qualitative evaluation, we analyzed the starting glasses and various crystalline compounds and standard solutions. The experiments were performed at beamline ID26 at ESRF (Grenoble, France) using a high resolution emission spectrometer and Si(311) monochromator crystals for high resolution and Si(111) for low resolution measurements. An overall resolution of 1.98 eV (Si(311)) and 3 eV (Si(111)) was achieved using a beamsize of 120x400 ?m, Si(777) analyzer crystals and a Rowland circle diameter of 1 m. Strontium XANES spectra of peraluminous and peralkaline starting glasses show distinct differences in pre-edge, main edge and position of the first EXAFS maximum which is directly correlated to the distance of Sr and its nearest neighbor. Therefore, the spectra indicate an effect of the ASI on the local structure around Sr. Spectra of standard solution at various PT conditions indicate detectable temperature-dependent changes in the intensity and peak width of the white line. The XANES spectra of chloridic solutions with peraluminous or peralkaline melt dissolved differ significantly from each other. The latter are similar to the one of the peralkaline starting glass, while this is not the case for solutions with peraluminous melt. The spectra of water with dissolved peralkaline melt distinctly differ from those using chloridic fluids. In conclusion, the first spectroscopic evidence on Sr complexation at elevated PT condition indicates significant speciation changes in both fluid and melt, and suggest ASI-dependent formation of Sr-Si complexes in the fluids. Literature Bai and Koster van Groos (1999), GCA 63, 1117-1131. Borchert et al. (2010), GCA 74, 1057-1076. Kohn et al. (1990), CMP 105, 359-368. Webster et al. (1989), Econ. Geol. 84, 116-134.

  15. Towards the blackbox computation of magnetic exchange coupling parameters in polynuclear transition-metal complexes: theory, implementation, and application.

    PubMed

    Phillips, Jordan J; Peralta, Juan E

    2013-05-01

    We present a method for calculating magnetic coupling parameters from a single spin-configuration via analytic derivatives of the electronic energy with respect to the local spin direction. This method does not introduce new approximations beyond those found in the Heisenberg-Dirac Hamiltonian and a standard Kohn-Sham Density Functional Theory calculation, and in the limit of an ideal Heisenberg system it reproduces the coupling as determined from spin-projected energy-differences. Our method employs a generalized perturbative approach to constrained density functional theory, where exact expressions for the energy to second order in the constraints are obtained by analytic derivatives from coupled-perturbed theory. When the relative angle between magnetization vectors of metal atoms enters as a constraint, this allows us to calculate all the magnetic exchange couplings of a system from derivatives with respect to local spin directions from the high-spin configuration. Because of the favorable computational scaling of our method with respect to the number of spin-centers, as compared to the broken-symmetry energy-differences approach, this opens the possibility for the blackbox exploration of magnetic properties in large polynuclear transition-metal complexes. In this work we outline the motivation, theory, and implementation of this method, and present results for several model systems and transition-metal complexes with a variety of density functional approximations and Hartree-Fock. PMID:23656122

  16. a Variational Derivation of P

    NASA Astrophysics Data System (ADS)

    Rulko, Robert Pawel

    Multigroup P_{N} theory is a widely-used approximation to multigroup transport theory. However, there are aspects of multigroup P _{N} theory that are not satisfactory, particularly regarding boundary conditions at a boundary having a prescribed incident flux. Historically, P _{N} boundary conditions at such a boundary have been assumed to be in the form given by Marshak or Mark, although Federighi and Pomraning have considered other possibilities for the case of one energy group. In this work we introduce two new variational principles. The first principle, unambiguously leads from a steady-state, first order, slab geometry multigroup transport problem to a multigroup P_{N} problem. The variationally-derived P_{N } problem consists of the conventional multigroup P_{N} equations and variational boundary conditions. At a boundary with a prescribed incident flux, these conditions are new and consistitute a generalization of Pomraning's boundary conditions applied to each energy group. For a vacuum boundary, these conditions reduce the Federighi's boundary condition applied to each energy group. Therefore, we refer to these newly developed P _{N} boundary conditions as the Generalized Federighi-Pomraning (GFP) boundary conditions. The second variational principle introduced in this work leads from a steady-state, even-parity slab geometry, multigroup transport problem to a multigroup, second-order P _{N} problem. This problem consists of the multigroup second-order P_{N } equations and Marshak boundary conditions. We generalize the second-order variational procedure to the three-dimensional geometry and obtain the general geometry multigroup second-order P_{N} equations and the three-dimensional Marshak-like boundary conditions. We also show how the first-order variational principle can be used to derive rigorous boundary conditions for the even-order P_{N}~imations and that these P_{N} approximations can provide accurate numerical results. Finally, a numerical comparison of the Generalized Federighi-Pomraning, Mark, Marshak and (newly developed by Larsen and Pomraning) variational-asymptotic boundary conditions shows that outside the asymptotic limit in which the variational-asymptotic and GFP boundary conditions are always superior, different boundary conditions perform best in different physical situations.

  17. Variational Gaussian Process Dynamical Systems

    E-print Network

    Damianou, Andreas C; Lawrence, Neil D

    2011-01-01

    High dimensional time series are endemic in applications of machine learning such as robotics (sensor data), computational biology (gene expression data), vision (video sequences) and graphics (motion capture data). Practical nonlinear probabilistic approaches to this data are required. In this paper we introduce the variational Gaussian process dynamical system. Our work builds on recent variational approximations for Gaussian process latent variable models to allow for nonlinear dimensionality reduction simultaneously with learning a dynamical prior in the latent space. The approach also allows for the appropriate dimensionality of the latent space to be automatically determined. We demonstrate the model on a human motion capture data set and a series of high resolution video sequences.

  18. A model for monitoring of Hsp90-buffered genetic variations

    NASA Astrophysics Data System (ADS)

    Kozeko, Liudmyla

    Genetic material of terrestrial organisms can be considerably injured by cosmic rays and UV-radiation in the space environment. Organisms onboard are also exposed to the entire complex of negative physical factors which can generate genetic variations and affect morphogenesis. However, species phenotypes must be robust to genetic variation, requiring "buffering" systems to ensure normal development. The molecular chaperone Hsp90 can serve as such "a buffer". It is important in the maturation and conformational regulation of a diverse set of signal transducers. The requirement of many principal regulatory proteins for Hsp90 renders entire metabolic pathways sensitive to impairment of its function. So inhibition of Hsp90 function can open cryptic genetic variations and produce morphological changes. In this paper, we present a model for monitoring of cryptic Hsp90-buffered genetic variations arising during exposure to space and spaceflight factors. This model has been developed with Arabidopsis thaliana seeds gathered in natural habitats with high anthropogenic pressure and wild type (Col-0) seeds subjected to negative influences (UV, heavy metals) experimentally. The phenotypic traits of early seedlings grown under reduction of Hsp90 activity were characterized to estimate Hsp90-buffered genetic variations. Geldanamycin was used as an inhibitor of Hsp90 function.

  19. Basic Complexity Eric Allender

    E-print Network

    Allender, Eric

    we would like complexity theory to do, it may be best to start by considering a "dream result Zealand. Lecture 1 presents the goals of computational complexity theory. We discuss (a) what complexity. In Lecture 3 we present a few of the most beautiful results in computational complexity theory. In particular

  20. Spatiotemporal imaging of complexity

    PubMed Central

    Robinson, Stephen E.; Mandell, Arnold J.; Coppola, Richard

    2013-01-01

    What are the functional neuroimaging measurements required for more fully characterizing the events and locations of neocortical activity? A prime assumption has been that modulation of cortical activity will inevitably be reflected in changes in energy utilization (for the most part) changes of glucose and oxygen consumption. Are such a measures complete and sufficient? More direct measures of cortical electrophysiological activity show event or task-related modulation of amplitude or band-limited oscillatory power. Using magnetoencephalography (MEG), these measures have been shown to correlate well with energy utilization sensitive BOLD fMRI. In this paper, we explore the existence of state changes in electrophysiological cortical activity that can occur independently of changes in averaged amplitude, source power or indices of metabolic rates. In addition, we demonstrate that such state changes can be described by applying a new measure of complexity, rank vector entropy (RVE), to source waveform estimates from beamformer-processed MEG. RVE is a non-parametric symbolic dynamic informational entropy measure that accommodates the wide dynamic range of measured brain signals while resolving its temporal variations. By representing the measurements by their rank values, RVE overcomes the problem of defining embedding space partitions without resorting to signal compression. This renders RVE-independent of absolute signal amplitude. In addition, this approach is robust, being relatively free of tunable parameters. We present examples of task-free and task-dependent MEG demonstrating that RVE provides new information by uncovering hidden dynamical structure in the apparent turbulent (or chaotic) dynamics of spontaneous cortical activity. PMID:23355820

  1. Complexes of clusters and complexes of stars

    E-print Network

    Yu. N. Efremov

    2005-12-12

    Most star complexes are in fact complexes of stars, clusters and gas clouds; term "star complexes" was introduced as general one disregarding the preferential content of a complex. Generally the high rate of star formation in a complex is accompanied by the high number of bound clusters, including massive ones, what was explained by the high gas pressure in such regions. However, there are also complexes, where clusters seems to be more numerous in relation to stars than in a common complex. The high rate of clusters - but not isolated stars - formation seems to be typical for many isolated bursts of star formation, but deficit of stars might be still explained by the observational selection. The latter cannot, however, explain the complexes or the dwarf galaxies, where the high formation rate of only stars is observed. The possibility of the very fast dissolution of parental clusters just in such regions should itself be explained. Some difference in the physical conditions (turbulence parameters ?) within the initial gas supercloud might be a reason for the high or low stars/clusters number ratio in a complex.

  2. Complex Multiplicative Calculus

    E-print Network

    Bashirov, Agamirza

    2011-01-01

    In the present paper we extend the concepts of multiplicative de- rivative and integral to complex-valued functions of complex variable. Some drawbacks, arising with these concepts in the real case, are explained satis- factorily. Properties of complex multiplicative derivatives and integrals are studied. In particular, the fundamental theorem of complex multiplicative calculus, relating these concepts, is proved. It is shown that complex multi- plicative calculus is not just another realization of the ordinary calculus. In particular, the Cauchy formula of complex calculus disappears in multiplicative complex calculus.

  3. Hyper Space Complex Number

    E-print Network

    Shanguang Tan

    2007-04-23

    A new kind of numbers called Hyper Space Complex Numbers and its algebras are defined and proved. It is with good properties as the classic Complex Numbers, such as expressed in coordinates, triangular and exponent forms and following the associative and commutative laws of addition and multiplication. So the classic Complex Number is developed from in complex plane with two dimensions to in complex space with N dimensions and the number system is enlarged also.

  4. MATHEMATICS 648 -CALCULUS OF VARIATIONS SPRING 2010

    E-print Network

    Stanislavova, Milena

    MATHEMATICS 648 - CALCULUS OF VARIATIONS SPRING 2010 · Instructor: Professor Milena Stanislavova: To expose students to the techniques of the modern theory of calculus of variations with mainly physical: ­ Basic concepts of calculus of variations, formulating variational problems. ­ Geodesics, catenary

  5. Variational q-calculus. Gaspard Bangerezako 1

    E-print Network

    Magnus, Alphonse P.

    Variational q-calculus. Gaspard Bangerezako 1 Universite du Burundi, Faculte des Sciences@yahoo.fr. Abstract. We propose q-versions of some basic concepts of continuous variational calculus such as of the continuous (differential) variational calculus, to the calculus of variation on lattices more general than

  6. Calculus of Variations Wintersemester 2009/10

    E-print Network

    Mielke, Alexander

    Calculus of Variations Wintersemester 2009/10 Prof. Alexander Mielke 15th of October 2009 Calculus in the Calculus of Variations. Springer-Verlag, Berlin, 1989. [Dac04] B. Dacorogna. Introduction to the calculus and Variational Problems. North Holland, 1976. [GiH96a] M. Giaquinta and S. Hildebrandt. Calculus of Variations I

  7. Protein Complexes in Bacteria

    PubMed Central

    Caufield, J. Harry; Abreu, Marco; Wimble, Christopher; Uetz, Peter

    2015-01-01

    Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies. PMID:25723151

  8. Modeling Natural Variation through Distribution

    ERIC Educational Resources Information Center

    Lehrer, Richard; Schauble, Leona

    2004-01-01

    This design study tracks the development of student thinking about natural variation as late elementary grade students learned about distribution in the context of modeling plant growth at the population level. The data-modeling approach assisted children in coordinating their understanding of particular cases with an evolving notion of data as an…

  9. Variation in Swedish Address Practices

    ERIC Educational Resources Information Center

    Norrby, Catrin

    2006-01-01

    This article explores variation in address in contemporary Swedish in Sweden-Swedish and Finland-Swedish. The research is part of a large-scale Australian project on changes in the address systems of French, German and Swedish. The present article focuses on results from 72 social network interviews conducted in Sweden (Gothenburg) and Finland…

  10. Variational Principles for Water Waves

    E-print Network

    Boris Kolev; David H. Sattinger

    2007-12-01

    We describe the Hamiltonian structures, including the Poisson brackets and Hamiltonians, for free boundary problems for incompressible fluid flows with vorticity. The Hamiltonian structure is used to obtain variational principles for stationary gravity waves both for irrotational flows as well as flows with vorticity.

  11. Head Start Planned Variation Program.

    ERIC Educational Resources Information Center

    Klein, Jenny

    There is little agreement concerning which methods of preschool intervention are most effective. In order to evaluate several approaches to early childhood education, Project Head Start, in conjunction with Project Follow Through, has initiated the Planned Variation program. This year only a pilot project is underway with eight schools…

  12. Seasonal Variation of Substorm Recovery

    E-print Network

    Fillingim, Matthew

    Seasonal Variation of Substorm Recovery Time Scales M. O. Fillingim1, D. Chua2, G. A. Germany3 substorm characteristics; 350 substorms from Polar UVI [see Chua et al., 2004] · IMF orientation · Season May 2007 IMFOrientation Season #12;median 29.1x1013 J median 17.7x1013 J median 23.9x1013 J median 32

  13. Genetic variation and its maintenance

    SciTech Connect

    Roberts, D.F.; De Stefano, G.F.

    1986-01-01

    This book contains several papers divided among three sections. The section titles are: Genetic Diversity--Its Dimensions; Genetic Diversity--Its Origin and Maintenance; and Genetic Diversity--Applications and Problems of Complex Characters.

  14. Variation in Congenital Heart Surgery Costs Across Hospitals

    PubMed Central

    Jacobs, Marshall L.; He, Xia; Shah, Samir S.; Peterson, Eric D.; Hall, Matthew; Gaynor, J. William; Hill, Kevin D.; Mayer, John E.; Jacobs, Jeffrey P.; Li, Jennifer S.

    2014-01-01

    BACKGROUND: A better understanding of costs associated with common and resource-intense conditions such as congenital heart disease has become increasingly important as children’s hospitals face growing pressure to both improve quality and reduce costs. We linked clinical information from a large registry with resource utilization data from an administrative data set to describe costs for common congenital cardiac operations and assess variation across hospitals. METHODS: Using linked data from The Society of Thoracic Surgeons and Pediatric Health Information Systems Databases (2006–2010), estimated costs/case for 9 operations of varying complexity were calculated. Between-hospital variation in cost and associated factors were assessed by using Bayesian methods, adjusting for important patient characteristics. RESULTS: Of 12?718 operations (27 hospitals) included, median cost/case increased with operation complexity (atrial septal defect repair, [$25?499] to Norwood operation, [$165?168]). Significant between-hospital variation (up to ninefold) in adjusted cost was observed across operations. Differences in length of stay (LOS) and complication rates explained an average of 28% of between-hospital cost variation. For the Norwood operation, high versus low cost hospitals had an average LOS of 50.8 vs 31.8 days and a major complication rate of 50% vs 25.3%. High volume hospitals had lower costs for the most complex operations. CONCLUSIONS: This study establishes benchmarks for hospital costs for common congenital heart operations and demonstrates wide variability across hospitals related in part to differences in LOS and complication rates. These data may be useful in designing initiatives aimed at both improving quality of care and reducing cost. PMID:24567024

  15. Relating Human Genetic Variation to Variation in Drug Responses

    PubMed Central

    Madian, Ashraf G.; Wheeler, Heather E.; Jones, Richard Baker; Dolan, M. Eileen

    2012-01-01

    Although sequencing a single human genome was a monumental effort a decade ago, more than one thousand genomes have now been sequenced. The task ahead lies in transforming this information into personalized treatment strategies that are tailored to the unique genetics of each individual. One important aspect of personalized medicine is patient-to-patient variation in drug response. Pharmacogenomics addresses this issue by seeking to identify genetic contributors to human variation in drug efficacy and toxicity. Here, we present a summary of the current status of this field, which has evolved from studies of single candidate genes to comprehensive genome-wide analyses. Additionally, we discuss the major challenges in translating this knowledge into a systems-level understanding of drug physiology with the ultimate goal of developing more effective personalized clinical treatment strategies. PMID:22840197

  16. Variation of Parameters in Differential Equations (A Variation in Making Sense of Variation of Parameters)

    ERIC Educational Resources Information Center

    Quinn, Terry; Rai, Sanjay

    2012-01-01

    The method of variation of parameters can be found in most undergraduate textbooks on differential equations. The method leads to solutions of the non-homogeneous equation of the form y = u[subscript 1]y[subscript 1] + u[subscript 2]y[subscript 2], a sum of function products using solutions to the homogeneous equation y[subscript 1] and…

  17. Cyanobacterial NADPH dehydrogenase complexes

    SciTech Connect

    Ogawa, Teruo; Mi, Hualing

    2007-07-01

    Cyanobacteria possess functionally distinct multiple NADPH dehydrogenase (NDH-1) complexes that are essential to CO2 uptake, photosystem-1 cyclic electron transport and respiration. The unique nature of cyanobacterial NDH-1 complexes is the presence of subunits involved in CO2 uptake. Other than CO2 uptake, chloroplastic NDH-1 complex has similar role as cyanobacterial NDH-1 complexes in photosystem-1 cyclic electron transport and respiration (chlororespiration). In this mini-review we focus on the structure and function of cyanobacterial NDH-1 complexes and their phylogeny. The function of chloroplastic NDH-1 complex and characteristics of plants defective in NDH-1 are also described forcomparison.

  18. Synthesis, Physicochemical Properties, and Antimicrobial Studies of Iron (III) Complexes of Ciprofloxacin, Cloxacillin, and Amoxicillin

    PubMed Central

    Ajali, Uzoechi; Ukoha, Pius O.

    2014-01-01

    Iron (III) complexes of ciprofloxacin, amoxicillin, and cloxacillin were synthesized and their aqueous solubility profiles, relative stabilities, and antimicrobial properties were evaluated. The complexes showed improved aqueous solubility when compared to the corresponding ligands. Relative thermal and acid stabilities were determined spectrophotometrically and the results showed that the complexes have enhanced thermal and acid stabilities when compared to the pure ligands. Antimicrobial studies showed that the complexes have decreased activities against most of the tested microorganisms. Ciprofloxacin complex, however, showed almost the same activity as the corresponding ligand. Job's method of continuous variation suggested 1?:?2 metals to ligand stoichiometry for ciprofloxacin complex but 1?:?1 for cloxacillin complex. PMID:25505991

  19. An alternative form of the Helmholtz criterion in the inverse problem of calculus of variations

    E-print Network

    Theodore Voronov

    2003-10-21

    We give a necessary and sufficient condition for the existence of a local solution of the inverse problem of calculus of variations in terms of the identical vanishing of the variation of a functional on an extended space (with the number of independent variables increased by one), and explain its relation with the classical Helmholtz criterion using the de Rham complex on an infinite-dimensional space of fields.

  20. Polytopal complexes: maps, chain complexes and... necklaces

    E-print Network

    Meunier, Frédéric

    2008-01-01

    The notion of polytopal map between two polytopal complexes is defined. Surprisingly, this definition is quite simple and extends naturally those of simplicial and cubical maps. It is then possible to define an induced chain map between the associated chain complexes. Finally, we use this new tool to give the first combinatorial proof of the splitting necklace theorem of Alon. The paper ends with open questions, such as the existence of Sperner's lemma for a polytopal complex or the existence of a cubical approximation theorem.

  1. Detailed investigation of low-energy positronium-hydrogen scattering

    NASA Astrophysics Data System (ADS)

    Woods, Denton; Ward, S. J.; Van Reeth, P.

    2015-08-01

    We investigate the four-body Coulomb process of low-energy elastic positronium-hydrogen (Ps-H) scattering below the Ps(n =2 ) excitation threshold using scattering wave functions that include Hylleraas-type correlation terms. Using the complex Kohn variational method, we compute phase shifts through the H,31 wave and obtain highly accurate S,31 - and P,31 -wave phase shifts. The complex Kohn variational results compare well to a number of other calculations for this system. We present elastic differential, elastic integrated, and momentum transfer cross sections, and for the singlet, resonances through the 1F wave. The differential cross section exhibits interesting features, including a change from slightly backward peaked to forward peaked scattering as the energy of the incident positronium increases and rich structure due to multiple resonances near the Ps(n =2 ) threshold. We also give a detailed analysis of the scattering lengths and effective ranges using multiple effective range theories.

  2. Variational Integrators for Reduced Magnetohydrodynamics

    E-print Network

    Kraus, Michael; Grasso, Daniela

    2015-01-01

    Reduced magnetohydrodynamics is a simplified set of magnetohydrodynamics equations with applications to both fusion and astrophysical plasmas, possessing a noncanonical Hamiltonian structure and consequently a number of conserved functionals. We propose a new discretisation strategy for these equations based on a discrete variational principle applied to a formal Lagrangian. The resulting integrator preserves important quantities like the total energy, magnetic helicity and cross helicity exactly (up to machine precision). As the integrator is free of numerical resistivity, spurious reconnection along current sheets is absent in the ideal case. If effects of electron inertia are added, reconnection of magnetic field lines is allowed, although the resulting model still possesses a noncanonical Hamiltonian structure. After reviewing the conservation laws of the model equations, the adopted variational principle with the related conservation laws are described both at the continuous and discrete level. We verify...

  3. Variational method with staggered fermions

    NASA Astrophysics Data System (ADS)

    DeTar, Carleton; Lee, Song-Haeng

    2015-02-01

    The variational method is used widely for determining the hadronic spectrum for Wilson and improved Wilson fermions. The method has not been applied to staggered fermions because the hadronic correlation functions in that formalism include terms that oscillate with Euclidean time, and they often include states of both parities. We show that with a simple modification, the variational method can also be applied to staggered fermions. In some cases the method also provides a mechanism for separating the commonly paired parity-partner states. We discuss the extension to staggered fermions and illustrate it by applying it to the calculation of the spectrum of charmed-antistrange mesons consisting of a clover charm quark and a staggered strange antiquark.

  4. Coastal eutrophication and temperature variation

    SciTech Connect

    Ganoulis, J.; Rafailidis, S.; Bogardi, I.; Duckstein, L.; Matyasovszky, I.

    1994-12-31

    A 3-D hydroecological model has been developed to simulate the impact of climate-change-induced daily temperature variation on coastal water quality and eutrophication. Historical daily temperature time series over a thirty-year period have been used to link local meteorological variables to large-scale atmospheric circulation patterns (CPs). Then, CPs generated under a 2{times}CO{sub 2} scenario have been used to simulate climate-change-induced local daily temperature variations. Both historical and climate-change-induced temperature time series have been introduced as inputs into the hydroecological model to simulate coastal water quality and eutrophication. Subject to model validation with available data, a case study in the bay of Thessaloniki (N. Greece) indicates a risk of increasing eutrophication and oxygen depletion in coastal areas due to possible climate change.

  5. Heritability of the Human Craniofacial Complex.

    PubMed

    Šešelj, Maja; Duren, Dana L; Sherwood, Richard J

    2015-09-01

    Quantifying normal variation and the genetic underpinnings of anatomical structures is one of the main goals of modern morphological studies. However, the extent of genetic contributions to normal variation in craniofacial morphology in humans is still unclear. The current study addresses this gap by investigating the genetic underpinnings of normal craniofacial morphology. The sample under investigation consists of 75 linear and angular measurements spanning the entire craniofacial complex, recorded from lateral cephalographs of 1,379 participants in the Fels Longitudinal Study. Heritabilities for each trait were estimated using SOLAR, a maximum-likelihood variance components approach utilizing all pedigree information for parameter estimation. Trait means and mean effects of the covariates age, sex, age(2) , sex × age, and sex × age(2) were simultaneously estimated in the analytic models. All traits of the craniofacial complex were significantly heritable. Heritability estimates ranged from 0.10 to 0.60, with the majority being moderate. It is important to note that we found similar ranges of heritability occurring across the different functional/developmental components of the craniofacial complex, the splanchnocranium, the basicranium, and the neurocranium. This suggests that traits from different regions of the craniofacial complex are of comparable utility for the purposes of population history and phylogeny reconstruction. At the same time, this genetic influence on craniofacial morphology signals a caution to researchers of nongenetic studies to consider the implications of this finding when selecting samples for study given their project design and goals. PMID:26097051

  6. Compositional variations in lunar spinels.

    NASA Technical Reports Server (NTRS)

    Haggerty, S. E.

    1971-01-01

    Electron probe data for spinels from Apollo 11, 12, and 14 are presented and analyzed. A modified Johnstone spinel prism showing the data distribution is given. Three projections of this prism are then presented which illustrate the variations of simple ratios that are present in the prism and permit three different perspectives of the data. The results are summarized as fO2 isobars on the spinel prism.

  7. Oligocyclopentadienyl transition metal complexes

    SciTech Connect

    de Azevedo, Cristina G.; Vollhardt, K. Peter C.

    2002-01-18

    Synthesis, characterization, and reactivity studies of oligocyclopentadienyl transition metal complexes, namely those of fulvalene, tercyclopentadienyl, quatercyclopentadienyl, and pentacyclopentadienyl(cyclopentadienyl) are the subject of this account. Thermal-, photo-, and redox chemistries of homo- and heteropolynuclear complexes are described.

  8. Complex Regional Pain Syndrome

    MedlinePLUS

    ... NINDS Complex Regional Pain Syndrome Information Page Synonym(s): Reflex Sympathetic Dystrophy Syndrome, Causalgia Condensed from Complex Regional ... Tel: 813-907-2312 Fax: 813-830-7446 Reflex Sympathetic Dystrophy Syndrome Association (RSDSA) P.O. Box ...

  9. Complex Elliptic Pendulum

    E-print Network

    Carl M. Bender; Daniel W. Hook; Karta Kooner

    2009-12-31

    This paper briefly summarizes previous work on complex classical mechanics and its relation to quantum mechanics. It then introduces a previously unstudied area of research involving the complex particle trajectories associated with elliptic potentials.

  10. Daunorubicin Lipid Complex Injection

    MedlinePLUS

    Daunorubicin lipid complex is used to treat advanced Kaposi's sarcoma (a type of cancer that causes abnormal tissue to ... body) related to acquired immunodeficiency syndrome (AIDS). Daunorubicin lipid complex is in a class of medications called ...

  11. Vincristine Lipid Complex Injection

    MedlinePLUS

    Vincristine lipid complex is used to treat a certain type of acute lymphoblastic leukemia (ALL; a type of cancer ... least two different treatments with other medications. Vincristine lipid complex is in a class of medications called ...

  12. Doxorubicin Lipid Complex Injection

    MedlinePLUS

    Doxorubicin lipid complex is used to treat ovarian cancer that has not improved or that has worsened after treatment with other medications. Doxorubicin lipid complex is also used to treat Kaposi's sarcoma ( ...

  13. Copy number variations among silkworms

    PubMed Central

    2014-01-01

    Background Copy number variations (CNVs), which are important source for genetic and phenotypic variation, have been shown to be associated with disease as well as important QTLs, especially in domesticated animals. However, little is known about the CNVs in silkworm. Results In this study, we have constructed the first CNVs map based on genome-wide analysis of CNVs in domesticated silkworm. Using next-generation sequencing as well as quantitative PCR (qPCR), we identified ~319 CNVs in total and almost half of them (~ 49%) were distributed on uncharacterized chromosome. The CNVs covered 10.8 Mb, which is about 2.3% of the entire silkworm genome. Furthermore, approximately 61% of CNVs directly overlapped with SDs in silkworm. The genes in CNVs are mainly related to reproduction, immunity, detoxification and signal recognition, which is consistent with the observations in mammals. Conclusions An initial CNVs map for silkworm has been described in this study. And this map provides new information for genetic variations in silkworm. Furthermore, the silkworm CNVs may play important roles in reproduction, immunity, detoxification and signal recognition. This study provided insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research. PMID:24684762

  14. Longitudinal Variations in Jupiter's Winds

    NASA Technical Reports Server (NTRS)

    Simon-Miller, Amy A.; Gierasch, P. J.; Tierney, G.

    2010-01-01

    Long-term studies of Jupiter's zonal wind field revealed temporal variations on the order of 20 to 40 m/s at many latitudes, greater than the typical data uncertainties of 1 to 10 m/s. No definitive periodicities were evident, however, though some latitudinally-confined signals did appear at periods relevant to the Quasi- Quadrennial Oscillation (Simon-Miller & Gierasch, Icarus, in press). As the QQO appears, from vertical temperature profiles, to propagate downward, it is unclear why a signal is not more obvious, unless other processes dominate over possibly weaker forcing from the QQO. An additional complication is that zonal wind profiles represent an average over some particular set of longitudes for an image pair and most data sets do not offer global wind coverage. Lien avoiding known features, such as the large anticyclonic vortices especially prevalent in the south, there can be distinct variations in longitude. We present results on the full wind field from Voyager and Cassini data, showing apparent longitudinal variations of up to 60 m/s or more. These are particularly obvious near disruptions such as the South Equatorial Disturbance, even when the feature itself is not clearly visible. These two dates represent very different states of the planet for comparison: Voyagers 1 & 2 flew by Jupiter shortly after a global upheaval, while many regions were in a disturbed state, while the Cassini view is typical of a more quiescent period present during much of the 1990s and early 2000s.

  15. Phase Variation of Hadronic Amplitudes

    E-print Network

    J. P. Dedonder; W. R. Gibbs; Mutazz Nuseirat

    2007-12-03

    The phase variation with angle of hadronic amplitudes is studied with a view to understanding the underlying physical quantities which control it and how well it can be determined in free space. We find that unitarity forces a moderately accurate determination of the phase in standard amplitude analyses but that the nucleon-nucleon analyses done to date do not give the phase variation needed to achieve a good representation of the data in multiple scattering calculations. Models are examined which suggest its behavior near forward angles is related to the radii of the real and absorptive parts of the interaction. The dependence of this phase on model parameters is such that if these radii are modified in the nuclear medium (in combination with the change due to the shift in energy of the effective amplitude in the medium) then the larger magnitudes of the phase needed to fit the data might be attainable, but only for negative values of the phase variation parameter.

  16. Thermal variation, thermal extremes and the physiological performance of individuals.

    PubMed

    Dowd, W Wesley; King, Felicia A; Denny, Mark W

    2015-06-01

    In this review we consider how small-scale temporal and spatial variation in body temperature, and biochemical/physiological variation among individuals, affect the prediction of organisms' performance in nature. For 'normal' body temperatures - benign temperatures near the species' mean - thermal biology traditionally uses performance curves to describe how physiological capabilities vary with temperature. However, these curves, which are typically measured under static laboratory conditions, can yield incomplete or inaccurate predictions of how organisms respond to natural patterns of temperature variation. For example, scale transition theory predicts that, in a variable environment, peak average performance is lower and occurs at a lower mean temperature than the peak of statically measured performance. We also demonstrate that temporal variation in performance is minimized near this new 'optimal' temperature. These factors add complexity to predictions of the consequences of climate change. We then move beyond the performance curve approach to consider the effects of rare, extreme temperatures. A statistical procedure (the environmental bootstrap) allows for long-term simulations that capture the temporal pattern of extremes (a Poisson interval distribution), which is characterized by clusters of events interspersed with long intervals of benign conditions. The bootstrap can be combined with biophysical models to incorporate temporal, spatial and physiological variation into evolutionary models of thermal tolerance. We conclude with several challenges that must be overcome to more fully develop our understanding of thermal performance in the context of a changing climate by explicitly considering different forms of small-scale variation. These challenges highlight the need to empirically and rigorously test existing theories. PMID:26085672

  17. Tending a complex microbiota requires major immune complexity

    PubMed Central

    STAGAMAN, KEATON; GUILLEMIN, KAREN; MILLIGAN-MYHRE, KATHRYN

    2015-01-01

    Animals maintain complex microbial communities within their guts that fill important roles in the health and development of the host. To what degree a host’s genetic background influences the establishment and maintenance of its gut microbial communities is still an open question. We know from studies in mice and humans that external factors, such as diet and environmental sources of microbes, and host immune factors play an important role in shaping the microbial communities (Costello et al. 2012). In this issue of Molecular Ecology, Bolnick et al. (2014a) sample the gut microbial community from 150 genetically diverse stickleback isolated from a single lake to provide evidence that another part of the adaptive immune response, the major histocompatibility complex class II (MHCII) receptors of antigen-presenting cells, may play a role in shaping the gut microbiota of the threespine stickleback, Gasterosteus aculeatus (Bolnick et al. 2014a). Bolnick et al. (2014a) provide insight into natural, interindividual variation in the diversity of both stickleback MHCII alleles and their gut microbial communities and correlate changes in the diversity of MHCII receptor alleles with changes in the microbiota. PMID:25263404

  18. Tending a complex microbiota requires major immune complexity.

    PubMed

    Stagaman, Keaton; Guillemin, Karen; Milligan-Myhre, Kathryn

    2014-10-01

    Animals maintain complex microbial communities within their guts that fill important roles in the health and development of the host. To what degree a host's genetic background influences the establishment and maintenance of its gut microbial communities is still an open question. We know from studies in mice and humans that external factors, such as diet and environmental sources of microbes, and host immune factors play an important role in shaping the microbial communities (Costello et al. ). In this issue of Molecular Ecology, Bolnick et al. (2014a) sample the gut microbial community from 150 genetically diverse stickleback isolated from a single lake to provide evidence that another part of the adaptive immune response, the major histocompatibility complex class II (MHCII) receptors of antigen-presenting cells, may play a role in shaping the gut microbiota of the threespine stickleback, Gasterosteus aculeatus (Bolnick et al. 2014a). Bolnick et al. (2014a) provide insight into natural, interindividual variation in the diversity of both stickleback MHCII alleles and their gut microbial communities and correlate changes in the diversity of MHCII receptor alleles with changes in the microbiota. PMID:25263404

  19. Variations in the abundance of transiently heated particles within nearby molecular clouds

    NASA Technical Reports Server (NTRS)

    Boulanger, F.; Falgarone, E.; Puget, J. L.; Helou, G.

    1990-01-01

    IRAS images of molecular clouds in the Chamaeleon, Taurus, and Ursa Major complexes show that the mid-IR emission from transiently heated particles is distributed very differently from the 100 micron emission from large dust grains. The ratio between 12 and 100 micron emission varies by more than one order of magnitude in each complex from about 5 times to about one-quarter of the average value in the solar neighborhood. Within a complex, color variations are seen on all scales. No significant variations of the I(v)(100 micron)/A(v) ratio are observed between clouds of widely different mid- to far-IR color. It is shown that neither the large amplitude of the color variations nor their morphology can be explained by changes of the excitation by the UV radiation field and it is concluded that the color variations trace variations in the abundance of transiently heated particles. A scenario is proposed which relates the abundance variations to the cycling of interstellar matter between the gas-phase and grain surfaces.

  20. ENGI 9420 Lecture Notes 6 Calculus of Variations Page 6.01 6. Calculus of Variations

    E-print Network

    George, Glyn

    ENGI 9420 Lecture Notes 6 ­ Calculus of Variations Page 6.01 6. Calculus of Variations The method of calculus of variations involves finding the path between two points that provides the minimum (or maximum

  1. 133238 171114 Isambard Complex

    E-print Network

    Martin, Ralph R.

    Security 133238 171114 Isambard Complex A. North B. Meadow C. Michael Bevis D. Concourse E. Stephen Hall Bishop Complex 8 Bishop Hall 9 Kilmorey Hall 10 Lacy Hall 11 St Margarets Hall 12 Faraday Complex Michael Sterling Wilfred Brown Zone D Antonin Artaud Howell Joseph Lowe Medical Centre Tower A Tower B

  2. Simply Complex by Design

    ERIC Educational Resources Information Center

    Nelson, Harold G.

    2007-01-01

    Reality--real life--is complex, more complex than can be imagined. The majority of our most pressing issues confronted in the management of organizations are overwhelmingly complex. I make the case for a systems design approach as a remedy. Examples introduced in this paper illuminate conceptual tools that advance how people transform their…

  3. 133238 171114 Isambard Complex

    E-print Network

    Martin, Ralph R.

    Security 133238 171114 Isambard Complex A. North B. Meadow C. Michael Bevis D. Concourse E. Stephen Bragg F. West G. Maurice Kogan H. David Neave I. Central J. East K. Runnymede L. George Shipp M. Trevor Hall Bishop Complex 8 Bishop Hall 9 Kilmorey Hall 10 Lacy Hall 11 St Margarets Hall 12 Faraday Complex

  4. Bioenergetic origins of complexity and disease.

    PubMed

    Wallace, D C

    2011-01-01

    The organizing power of energy flow is hypothesized to be the origin of biological complexity and its decline the basis of "complex" diseases and aging. Energy flow through organic systems creates nucleic acids, which store information, and the annual accumulation of information generates today's complexity. Energy flow through our bodies is mediated by the mitochondria, symbiotic bacteria whose genomes encompass the mitochondrial DNA (mtDNA) and more than 1000 nuclear genes. Inherited and/or epigenomic variation of the mitochondrial genome determines our initial energetic capacity, but the age-related accumulation of somatic cell mtDNA mutations further erodes energy flow, leading to disease. This bioenergetic perspective on disease provides a unifying pathophysiological and genetic mechanism for neuropsychiatric diseases such as Alzheimer and Parkinson Disease, metabolic diseases such as diabetes and obesity, autoimmune diseases, aging, and cancer. PMID:22194359

  5. Geochemistry and petrogenesis of the Laramie anorthosite complex, Wyoming

    USGS Publications Warehouse

    Fountain, J.C.; Hodge, D.S.; Allan, Hills F.

    1981-01-01

    A geochemical investigation of the Laramie anorthosite complex determined that monsonite associated with the complex are characterized by positive Eu anomalies and display a regular variation in composition with distance from the monzonite/county rock contact. Anorthositic rocks have major and trace element abundance typical of similar complexes. The internal variations in the monzonite were produced by in situ fractionation and contamination. The data indicate that anorthosite and monzonite cannot be comagmatic. It is proposed that the anorthosite and monzonite of the complex evolved from two distinct magmas, and that two stages of anatectic melting contributed to the evolution of the monzonite. An initial stage of partial melting was induced by intrusion of a gabbroic anorthosite magma into the lower crust; a second partial melting event occurred after emplacement where heat from the intrusions melted country rocks resulting in extensive contamination ofthe monzonite. ?? 1981.

  6. The genetic basis of natural variation in mushroom body size in Drosophila melanogaster

    PubMed Central

    Zwarts, Liesbeth; Vanden Broeck, Lies; Cappuyns, Elisa; Ayroles, Julien F.; Magwire, Michael M.; Vulsteke, Veerle; Clements, Jason; Mackay, Trudy F. C.; Callaerts, Patrick

    2015-01-01

    Genetic variation in brain size may provide the basis for the evolution of the brain and complex behaviours. The genetic substrate and the selective pressures acting on brain size are poorly understood. Here we use the Drosophila Genetic Reference Panel to map polymorphic variants affecting natural variation in mushroom body morphology. We identify 139 genes and 39 transcription factors and confirm effects on development and adult plasticity. We show correlations between morphology and aggression, sleep and lifespan. We propose that natural variation in adult brain size is controlled by interaction of the environment with gene networks controlling development and plasticity. PMID:26656654

  7. The genetic basis of natural variation in mushroom body size in Drosophila melanogaster.

    PubMed

    Zwarts, Liesbeth; Vanden Broeck, Lies; Cappuyns, Elisa; Ayroles, Julien F; Magwire, Michael M; Vulsteke, Veerle; Clements, Jason; Mackay, Trudy F C; Callaerts, Patrick

    2015-01-01

    Genetic variation in brain size may provide the basis for the evolution of the brain and complex behaviours. The genetic substrate and the selective pressures acting on brain size are poorly understood. Here we use the Drosophila Genetic Reference Panel to map polymorphic variants affecting natural variation in mushroom body morphology. We identify 139 genes and 39 transcription factors and confirm effects on development and adult plasticity. We show correlations between morphology and aggression, sleep and lifespan. We propose that natural variation in adult brain size is controlled by interaction of the environment with gene networks controlling development and plasticity. PMID:26656654

  8. Exploiting Gene Expression Variation to Capture Gene-Environment Interactions for Disease

    PubMed Central

    Idaghdour, Youssef; Awadalla, Philip

    2013-01-01

    Gene-environment interactions have long been recognized as a fundamental concept in evolutionary, quantitative, and medical genetics. In the genomics era, study of how environment and genome interact to shape gene expression variation is relevant to understanding the genetic architecture of complex phenotypes. While genetic analysis of gene expression variation focused on main effects, little is known about the extent of interaction effects implicating regulatory variants and their consequences on transcriptional variation. Here we survey the current state of the concept of transcriptional gene-environment interactions and discuss its utility for mapping disease phenotypes in light of the insights gained from genome-wide association studies of gene expression. PMID:23755064

  9. Spatial Variation of the Pre-reversal Enhancement - Model Results

    NASA Astrophysics Data System (ADS)

    Fang, T.; Richmond, A.; Liu, J.; Maute, A.

    2008-12-01

    The pre-reversal enhancement (PRE) is one of the most important phenomena controlling the nighttime ionosphere and the generation of equatorial spread F (ESF), but its causal mechanism is still not fully understood. Radar and satellite observations provide us important but incomplete information about it: radars can only observe local time variations at a specific location, while satellites provide data mainly at a single altitude. The NCAR Thermosphere Ionosphere Mesosphere Electrodynamics General Circulation Model (TIME-GCM) is capable of simulating ionospheric phenomena and the pre-reversal enhancement. In this research, we run the model under moderate solar activity (F10.7=150) and geomagnetic quiet conditions to monitor the variation of ionospheric parameters when the maximum upward drift of the PRE is occurring in the Peruvian longitude (75°W). Since it is a three dimensional model, it can provide us current flows, electric field changes and conductivity variations in Peruvian longitude and also longitudes to the east (after PRE) and west (before PRE). From the results, we are able to picture the spatial variations of the ionosphere surrounding the PRE and to evaluate effects due to wind driven current, the equatorial electrojet, and conductivity gradients. In addition, we evaluate the effects of winds and conductivities separately in the ionospheric E and F regions on the PRE, to understand and diagnose the complex electrodynamic processes.

  10. A Simple Genetic Architecture Underlies Morphological Variation in Dogs

    PubMed Central

    Schoenebeck, Jeffrey J.; Degenhardt, Jeremiah D.; Lohmueller, Kirk E.; Zhao, Keyan; Brisbin, Abra; Parker, Heidi G.; vonHoldt, Bridgett M.; Cargill, Michele; Auton, Adam; Reynolds, Andy; Elkahloun, Abdel G.; Castelhano, Marta; Mosher, Dana S.; Sutter, Nathan B.; Johnson, Gary S.; Novembre, John; Hubisz, Melissa J.; Siepel, Adam; Wayne, Robert K.; Bustamante, Carlos D.; Ostrander, Elaine A.

    2010-01-01

    Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (?3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species. PMID:20711490

  11. Heterochrony underpins natural variation in Cardamine hirsuta leaf form

    PubMed Central

    Cartolano, Maria; Pieper, Bjorn; Lempe, Janne; Tattersall, Alex; Huijser, Peter; Tresch, Achim; Darrah, Peter R.; Hay, Angela; Tsiantis, Miltos

    2015-01-01

    A key problem in biology is whether the same processes underlie morphological variation between and within species. Here, by using plant leaves as an example, we show that the causes of diversity at these two evolutionary scales can be divergent. Some species like the model plant Arabidopsis thaliana have simple leaves, whereas others like the A. thaliana relative Cardamine hirsuta bear complex leaves comprising leaflets. Previous work has shown that these interspecific differences result mostly from variation in local tissue growth and patterning. Now, by cloning and characterizing a quantitative trait locus (QTL) for C. hirsuta leaf shape, we find that a different process, age-dependent progression of leaf form, underlies variation in this trait within species. This QTL effect is caused by cis-regulatory variation in the floral repressor ChFLC, such that genotypes with low-expressing ChFLC alleles show both early flowering and accelerated age-dependent changes in leaf form, including faster leaflet production. We provide evidence that this mechanism coordinates leaf development with reproductive timing and may help to optimize resource allocation to the next generation. PMID:26243877

  12. GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

    PubMed Central

    Paila, Umadevi; Chapman, Brad A.; Kirchner, Rory; Quinlan, Aaron R.

    2013-01-01

    Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics. PMID:23874191

  13. Variation in trajectories of women's marital quality.

    PubMed

    James, Spencer L

    2015-01-01

    I examine variation in trajectories of women's marital quality across the life course. The analysis improves upon earlier research in three ways: (1) the analysis uses a sequential cohort design and data from the first 35years of marriage; (2) I analyze rich data from a national sample; (3) I examine multiple dimensions of marital quality. Latent class growth analyses estimated on data from women in the National Longitudinal Survey of Youth-1979 (N=2604) suggest multiple trajectories for each of three dimensions of marital quality, including two trajectories of marital happiness, two trajectories of marital communication, and three trajectories of marital conflict. Socioeconomic and demographic covariates are then used to illustrate how factors such as income, cohabitation, and race-ethnicity set individuals at risk of poor marital quality throughout the life course by differentiating between high and low trajectories of marital quality. Women on low marital quality trajectories are, as expected, at much greater risk of divorce. Taken together, these findings show how fundamental socioeconomic and demographic characteristics contribute to subsequent marital outcomes via their influence on trajectories of marital quality as well as providing a better picture of the complexity in contemporary patterns of marital quality. PMID:25432600

  14. Spatiotemporal Floral Scent Variation of Penstemon digitalis.

    PubMed

    Burdon, Rosalie C F; Raguso, Robert A; Kessler, André; Parachnowitsch, Amy L

    2015-07-01

    Variability in floral volatile emissions can occur temporally through floral development, during diel cycles, as well as spatially within a flower. These spatiotemporal patterns are hypothesized to provide additional information to floral visitors, but they are rarely measured, and their attendant hypotheses are even more rarely tested. In Penstemon digitalis, a plant whose floral scent has been shown to be under strong phenotypic selection for seed fitness, we investigated spatiotemporal variation in floral scent by using dynamic headspace collection, respectively solid-phase microextraction, and analyzed the volatile samples by combined gas chromatography-mass spectrometry. Total volatile emission was greatest during flowering and peak pollinator activity hours, suggesting its importance in mediating ecological interactions. We also detected tissue and reward-specific compounds, consistent with the hypothesis that complexity in floral scent composition reflects several ecological functions. In particular, we found tissue-specific scents for the stigma, stamens, and staminode (a modified sterile stamen common to all Penstemons). Our findings emphasize the dynamic nature of floral scents and highlight a need for greater understanding of ecological and physiological mechanisms driving spatiotemporal patterns in scent production. PMID:26133675

  15. Effects of soluble organic complexants and their degradation products on the removal of selected radionuclides from high-level waste. Part II: Distributions of Sr, Cs, Tc, and Am onto 32 absorbers from four variations of Hanford tank 101-SY simulant solution

    SciTech Connect

    Marsh, S.F.; Svitra, Z.V.; Bowen, S.M.

    1995-04-01

    Many of the radioactive waste storage tanks at U.S. Department of Energy facilities contain organic compounds that have been degraded by radiolysis and chemical reactions during decades of storage. In this second part of our three-part investigation of the effects of soluble organic complexants and their degradation products, we measured the sorption of strontium, cesium, technetium, and americium onto 32 absorbers that offer high sorption of these elements in the absence of organic complexants. The four solutions tested were (1) a simulant for a 3:1 dilution of Hanford Tank 101-SY contents that initially contained ethylenediaminetetraacetic acid (EDTA), (2) this simulant after gamma-irradiation to 34 Mrads, (3) the unirradiated simulant after treatment with a hydrothermal organic-destruction process, and (4) the irradiated simulant after hydrothermal processing. For each of 512 element/absorber/solution combinations, we measured distribution coefficients (Kds) twice for each period for dynamic contact periods of 30 min, 2 h, and 6 h to obtain information about sorption kinetics. On the basis of our 3,072 measured Kd values, the sorption of strontium and americium is significantly decreased by the organic components of the simulant solutions, whereas the sorption of cesium and technetium appears unaffected by the organic components of the simulant solutions.

  16. APPROACHES TO NONCONVEX VARIATIONAL PROBLEMS OF MECHANICS

    E-print Network

    Cherkaev, Andrej

    , variations, extensions, bounds, and duality A. CHERKAEV Department of mathematics, University of Utah Salt- timal microstructured media. We discuss variational formulations of these problems, properties of properties. Several examples are presented. Particularly, the bound for the tensor of thermal expansion

  17. Identification of structural variation in mouse genomes

    PubMed Central

    Keane, Thomas M.; Wong, Kim; Adams, David J.; Flint, Jonathan; Reymond, Alexandre; Yalcin, Binnaz

    2014-01-01

    Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation. PMID:25071822

  18. Liss M. Andreassen Glacier variations in

    E-print Network

    Andreassen, Liss Marie

    Liss M. Andreassen Glacier variations in Norway - Measurements and modelling Faculty of Mathematics and Natural Sciences University of Oslo 2008 #12;#12;Glacier variations in Norway - Measurements and modelling.................................................................................................................... 15 1.2 Glaciers in Norway

  19. Comprehensive variation discovery in single human genomes

    E-print Network

    Weisenfeld, Neil I

    Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing individual genomes and ...

  20. Lunar ferroan anorthosites: mineralogy, compositional variations, and petrogenesis

    USGS Publications Warehouse

    McGee, J.J.

    1993-01-01

    Details petrologic study of a suite of lunar ferroan anorthosites indicates that their mineral compositional variations are generally consistent with derivation of these anorthosites from a common parent magma. Relict textures, zoning, and possible primary trends of mineral compositional variations are preserved in many of the anorthosites. The presence of heterogeneous, bimodal, and/or trimodal pyroxene compositions suggests that some of the anorthosites are polymict rocks. Some aspects of the mineral composition data suggest that complex processes operated during formation of the ferroan anorthosites. Processes operative during anorthosite formation may have included some mixing of different melts, trapping of variable amounts of intercumulus liquid, postcrystallization redistribution of elements, or perturbations both during adcumulus growth and subsequent to crystallization by impact events. -from Author

  1. Nuthatches eavesdrop on variations in heterospecific chickadee mobbing alarm calls

    PubMed Central

    Templeton, Christopher N.; Greene, Erick

    2007-01-01

    Many animals recognize the alarm calls produced by other species, but the amount of information they glean from these eavesdropped signals is unknown. We previously showed that black-capped chickadees (Poecile atricapillus) have a sophisticated alarm call system in which they encode complex information about the size and risk of potential predators in variations of a single type of mobbing alarm call. Here we show experimentally that red-breasted nuthatches (Sitta canadensis) respond appropriately to subtle variations of these heterospecific “chick-a-dee” alarm calls, thereby evidencing that they have gained important information about potential predators in their environment. This study demonstrates a previously unsuspected level of discrimination in intertaxon eavesdropping. PMID:17372225

  2. Spindle Speed Variation for the Suppression of Regenerative Chatter

    NASA Astrophysics Data System (ADS)

    Sri Namachchivaya, G.; Beddini, J. A.

    2003-06-01

    A phenomenon commonly encountered during machining operations is chatter. It manifests itself as a vibration between workpiece and cutting tool, leading to poor dimensional accuracy and surface finish of the workpiece and to premature failure of the cutting tool. A chatter suppression method that has received attention in recent years is the spindle speed variation method, whereby greater widths of cut are achieved by modulating the spindle speed continuously. By adapting existing mathematical techniques, a perturbative method is developed in this paper to obtain finite-dimensional equations in order to systematically study the mechanism of spindle speed variation for chatter suppression. The results indicate both modest increase of stability and complex nonlinear dynamics close to the new stability boundary. The method developed in this paper can readily be applied to any other system with time-delay characteristics.

  3. Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

    E-print Network

    King, Elizabeth G.; Merkes, Chris M.; McNeil, Casey Lee; Hoofer, Steven R.; Sen, Saunak; Long, Anthony D.; Macdonald, Stuart J.

    2012-08-22

    , and an inability to identify variants that cumulatively explain the bulk of standing genetic variation in genome-wide association studies (GWAS). Thus, much of the heritability remains unexplained for most complex traits. Here we describe a novel, freely available...

  4. Correlation of ISS Electric Potential Variations with Mission Operations

    NASA Technical Reports Server (NTRS)

    Willis, Emily M.; Minow, Joseph I.; Parker, Linda Neergaard

    2014-01-01

    Spacecraft charging on the International Space Station (ISS) is caused by a complex mix of the low Earth orbit plasma environment, space weather events, operations of the high voltage solar arrays, and changes in the ISS configuration and orbit parameters. Measurements of the ionospheric electron density and temperature along the ISS orbit and variations in the ISS electric potential are obtained from the Floating Potential Measurement Unit (FPMU) suite of four plasma instruments (two Langmuir probes, a Floating Potential Probe, and a Plasma Impedance Probe) on the ISS. These instruments provide a unique capability for monitoring the response of the ISS electric potential to variations in the space environment, changes in vehicle configuration, and operational solar array power manipulation. In particular, rapid variations in ISS potential during solar array operations on time scales of tens of milliseconds can be monitored due to the 128 Hz sample rate of the Floating Potential Probe providing an interesting insight into high voltage solar array interaction with the space plasma environment. Comparing the FPMU data with the ISS operations timeline and solar array data provides a means for correlating some of the more complex and interesting ISS electric potential variations with mission operations. In addition, recent extensions and improvements to the ISS data downlink capabilities have allowed more operating time for the FPMU than ever before. The FPMU was operated for over 200 days in 2013 resulting in the largest data set ever recorded in a single year for the ISS. This presentation will provide examples of a number of the more interesting ISS charging events observed during the 2013 operations including examples of rapid charging events due to solar array power operations, auroral charging events, and other charging behavior related to ISS mission operations.

  5. Correlation of ISS Electric Potential Variations with Mission Operations

    NASA Technical Reports Server (NTRS)

    Willis, Emily M.; Minow, Joseph I.; Parker, Linda Neergaard

    2014-01-01

    Spacecraft charging on the International Space Station (ISS) is caused by a complex combination of the low Earth orbit plasma environment, space weather events, operations of the high voltage solar arrays, and changes in the ISS configuration and orbit parameters. Measurements of the ionospheric electron density and temperature along the ISS orbit and variations in the ISS electric potential are obtained from the Floating Potential Measurement Unit (FPMU) suite of four plasma instruments (two Langmuir probes, a Floating Potential Probe, and a Plasma Impedance Probe) on the ISS. These instruments provide a unique capability for monitoring the response of the ISS electric potential to variations in the space environment, changes in vehicle configuration, and operational solar array power manipulation. In particular, rapid variations in ISS potential during solar array operations on time scales of tens of milliseconds can be monitored due to the 128 Hz sample rate of the Floating Potential Probe providing an interesting insight into high voltage solar array interaction with the space plasma environment. Comparing the FPMU data with the ISS operations timeline and solar array data provides a means for correlating some of the more complex and interesting ISS electric potential variations with mission operations. In addition, recent extensions and improvements to the ISS data downlink capabilities have allowed more operating time for the FPMU than ever before. The FPMU was operated for over 200 days in 2013 resulting in the largest data set ever recorded in a single year for the ISS. In this paper we provide examples of a number of the more interesting ISS charging events observed during the 2013 operations including examples of rapid charging events due to solar array power operations, auroral charging events, and other charging behavior related to ISS mission operations.

  6. Calculus of Variations and Partial Differential Equations

    E-print Network

    Gomes, Diogo

    Calculus of Variations and Partial Differential Equations Diogo Aguiar Gomes #12;#12;Contents 37 6. Bibliographical notes 48 2. Calculus of variations in one independent variable 49 1. Euler. Perturbation theory 122 12. Bibliographical notes 126 3. Calculus of variations and elliptic equations 127 1

  7. Aristotle on Species Variation James Franklin

    E-print Network

    Franklin, James

    Aristotle on Species Variation James Franklin Philosophy, Vol. 61, No. 236. (Apr., 1986), pp. 245@jstor.org. http://www.jstor.org Wed Aug 8 21:54:23 2007 #12;Aristotle on Species Variation JAMES FRANKLIN. This article will consider whether Aristotle admitted or denied the possibility of continuous variation

  8. Local Regulatory Variation in Saccharomyces cerevisiae

    E-print Network

    Kruglyak, Leonid

    Local Regulatory Variation in Saccharomyces cerevisiae James Ronald1,2 , Rachel B. Brem2 individuals within a species. We and others have previously shown that such regulatory variation can occur both at the same locus as the gene whose expression it affects (local regulatory variation

  9. Variation in Atmospheric Helium Isotopes

    NASA Astrophysics Data System (ADS)

    Mabry, J. C.; Marty, B.; Burnard, P.; Blard, P.

    2010-12-01

    Anthropogenic activity such as oil and gas exploitation releases crustal helium, which has excess 4He compared to atmospheric helium. This may give rise to both spatial and temporal variations in the atmospheric 3He/4He. Helium is present in trace quantities in the air (5 ppm) and has a very low ratio (3He/4Heair = 1.38 x 10-6), consequently high precision measurements of atmospheric He presents a significant analytical challenge. Recent work by Sano et al. [1] has endeavored to experimentally quantify these potential variations in the atmospheric 3He/4He by measuring the helium isotopes from air samples collected around the globe and from samples of ancient trapped atmosphere. Their results indicate an increase in the atmospheric 3He/4He from northern to southern latitudes of the order 2 - 4 ‰, which they attribute to greater use of fossil fuels in the northern hemisphere. However, since most of their data points overlap at the 2-3 ‰ (2?) level, additional measurements (with increased precision if possible) are needed. We have constructed an automated extraction line dedicated to measuring He in samples of air which can rapidly switch between measuring aliquots of sample with standards. It additionally features an adjustable bellows on the sample aliquot volume that enables us to adjust the size of a sample aliquot to precisely match the standard, eliminating biases arising from nonlinear pressure effects in the mass spectrometer. The measurements are made using a Helix SFT multi-collector mass spectrometer. At present, repeat measurements of 3He/4He from our standard (purified air) have a reproducibility of 2‰ (2?), while measurements of local (Nancy, France) air samples have a reproducibility of 3He/4He of 3‰ (2?), which are at a similar level to the uncertainties reported by Sano. Modifications are underway to improve 3He measurements which are the principal source of error. We have collected atmospheric samples from around the globe over a wide range of latitudes to search for spatial variations. In addition to samples from France and Iceland, we have samples collected over a two week period in January 2010 from north to south of the South American continent with a sampling interval of 500km. We also have samples collected from ships sailing between Hobart, Tasmania and Antarctica and then further samples collected into the interior of Antarctica to the Dome C station. [1] Sano, Y., Furukawa, Y. & Takahata, N. Atmospheric helium isotope ratio: Possible temporal and spatial variations. Geochimica et Cosmochimica Acta 74, 4893-4901 (2010).

  10. Neodymium isotopic variations in seawater

    NASA Technical Reports Server (NTRS)

    Piepgras, D. J.; Wasserburg, G. J.

    1980-01-01

    Direct measurement of the isotopic composition of Nd in the Atlantic agree with the Nd content in ferromanganese sediments and differ from the observed amounts in the Pacific samples. These data indicate the existence of distinctive differences in the isotopic composition of Nd in the waters of major oceans; the average values determined from seawater and ferromanganese sediments are considerably lower than in sources with oceanic mantle affinities showing that the REE in the oceans is dominated by continental sources. The Nd isotopic variations in seawater are applied to relate the residence time of Nd and mixing rates between the oceans.

  11. Variational Depth From Focus Reconstruction

    NASA Astrophysics Data System (ADS)

    Moeller, Michael; Benning, Martin; Schonlieb, Carola; Cremers, Daniel

    2015-12-01

    This paper deals with the problem of reconstructing a depth map from a sequence of differently focused images, also known as depth from focus or shape from focus. We propose to state the depth from focus problem as a variational problem including a smooth but nonconvex data fidelity term, and a convex nonsmooth regularization, which makes the method robust to noise and leads to more realistic depth maps. Additionally, we propose to solve the nonconvex minimization problem with a linearized alternating directions method of multipliers (ADMM), allowing to minimize the energy very efficiently. A numerical comparison to classical methods on simulated as well as on real data is presented.

  12. NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the complex between pseudohevein and N,N',N"-triacetylchitotriose.

    PubMed

    Asensio, J L; Siebert, H C; von Der Lieth, C W; Laynez, J; Bruix, M; Soedjanaamadja, U M; Beintema, J J; Cañada, F J; Gabius, H J; Jiménez-Barbero, J

    2000-08-01

    Model studies on lectins and their interactions with carbohydrate ligands in solution are essential to gain insights into the driving forces for complex formation and to optimize programs for computer simulations. The specific interaction of pseudohevein with N,N', N"-triacetylchitotriose has been analyzed by (1)H-NMR spectroscopy. Because of its small size, with a chain length of 45 amino acids, this lectin is a prime target to solution-structure determination by NOESY NMR experiments in water. The NMR-analysis was extended to assessment of the topology of the complex between pseudohevein and N, N',N"-triacetylchitotriose. NOESY experiments in water solution provided 342 protein proton-proton distance constraints. Binding of the ligand did not affect the pattern of the protein nuclear Overhauser effect signal noticeably, what would otherwise be indicative of a ligand-induced conformational change. The average backbone (residues 3-41) RMSD of the 20 refined structures was 1.14 A, whereas the heavy atom RMSD was 2.18 A. Two different orientations of the trisaccharide within the pseudohevein binding site are suggested, furnishing an explanation in structural terms for the lectin's capacity to target chitin. In both cases, hydrogen bonds and van der Waals contacts confer stability to the complexes. This conclusion is corroborated by the thermodynamic parameters of binding determined by NMR and isothermal titration calorimetry. The association process was enthalpically driven. In relation to hevein, the Trp/Tyr-substitution in the binding pocket has only a small effect on the free energy of binding in contrast to engineered galectin-1 and a mammalian C-type lectin. A comparison of the three-dimensional structure of pseudohevein in solution to those reported for wheat germ agglutinin (WGA) in the solid state and for hevein and WGA-B in solution has been performed, providing a data source about structural variability of the hevein domains. The experimentally derived structures and the values of the solvent accessibilities for several key residues have also been compared with conformations obtained by molecular dynamics simulations, pointing to the necessity to further refine the programs to enhance their predictive reliability and, thus, underscoring the importance of this kind of combined analysis in model systems. PMID:10842338

  13. Assessing physiological complexity.

    PubMed

    Burggren, W W; Monticino, M G

    2005-09-01

    Physiologists both admire and fear complexity, but we have made relatively few attempts to understand it. Inherently complex systems are more difficult to study and less predictable. However, a deeper understanding of physiological systems can be achieved by modifying experimental design and analysis to account for complexity. We begin this essay with a tour of some mathematical views of complexity. After briefly exploring chaotic systems, information theory and emergent behavior, we reluctantly conclude that, while a mathematical view of complexity provides useful perspectives and some narrowly focused tools, there are too few generally practical take-home messages for physiologists studying complex systems. Consequently, we attempt to provide guidelines as to how complex systems might be best approached by physiologists. After describing complexity based on the sum of a physiological system's structures and processes, we highlight increasingly refined approaches based on the pattern of interactions between structures and processes. We then provide a series of examples illustrating how appreciating physiological complexity can improve physiological research, including choosing experimental models, guiding data collection, improving data interpretations and constructing more rigorous system models. Finally, we conclude with an invitation for physiologists, applied mathematicians and physicists to collaborate on describing, studying and learning from studies of physiological complexity. PMID:16109885

  14. Variation in the Management of Thyroid Cancer

    PubMed Central

    Banerjee, Mousumi; Yang, Di; Stewart, Andrew K.; Sisson, James C.; Koenig, Ronald J.; Doherty, Gerard M.; Griggs, Jennifer J.

    2013-01-01

    Context: Little is known about practice patterns in thyroid cancer, a cancer that is increasing in incidence. Objective: We sought to identify aspects of thyroid cancer management that have the greatest variation. Design/Setting/Participants: We surveyed 944 physicians involved in thyroid cancer care from 251 hospitals affiliated with the US National Cancer Database. Physicians were asked questions in the following four domains: thyroid surgery, radioactive iodine use, thyroid hormone replacement postsurgery, and long-term thyroid cancer management. We calculated the ratio of observed variation to hypothetical maximum variation under the assumed distribution of the response. Ratios closer to 1 indicate greater variation. Results: We had a 66% response rate. We found variation in multiple aspects of thyroid cancer management, including the role of central lymph node dissections (variation, 0.99; 95% confidence interval [CI], 0.98–1.00), the role of pretreatment scans before radioactive iodine treatment (variation, 1.00; 95% CI, 0.98–1.00), and all aspects of long-term thyroid cancer management, including applications of ultrasound (variation, 0.97; 95% CI, 0.93–0.99) and radioactive iodine scans (variation, 0.99; 95% CI, 0.97–1.00). For the management of small thyroid cancers, variation exists in all domains, including optimal extent of surgery (variation, 0.91; 95% CI, 0.88–0.94) and the role of both radioactive iodine treatment (variation, 0.91; 95% CI, 0.89–0.93) and suppressive doses of thyroid hormone replacement (variation, 1.00; 95% CI, 0.99–1.00). Conclusion: We identified areas of variation in thyroid cancer management. To reduce the variation and improve the management of thyroid cancer, there is a need for more research and more research dissemination. PMID:23539722

  15. Environmental and biomedical applications of natural metal stable isotope variations

    USGS Publications Warehouse

    Bullen, T.D.; Walczyk, T.

    2009-01-01

    etal stable isotopes are now being used to trace metal contaminants in the environment and as indicators of human systemic function where metals play a role. Stable isotope abundance variations provide information about metal sources and the processes affecting metals in complex natural systems, complementing information gained from surrogate tracers, such as metal abundance ratios or biochemical markers of metal metabolism. The science is still in its infancy, but the results of initial studies confirm that metal stable isotopes can provide a powerful tool for forensic and biomedical investigations.

  16. Local Variation of Hashtag Spike Trains and Popularity in Twitter

    PubMed Central

    Sanl?, Ceyda; Lambiotte, Renaud

    2015-01-01

    We draw a parallel between hashtag time series and neuron spike trains. In each case, the process presents complex dynamic patterns including temporal correlations, burstiness, and all other types of nonstationarity. We propose the adoption of the so-called local variation in order to uncover salient dynamical properties, while properly detrending for the time-dependent features of a signal. The methodology is tested on both real and randomized hashtag spike trains, and identifies that popular hashtags present regular and so less bursty behavior, suggesting its potential use for predicting online popularity in social media. PMID:26161650

  17. Towards Practical Quantum Variational Algorithms

    E-print Network

    D. Wecker; M. B. Hastings; M. Troyer

    2015-09-08

    The preparation of quantum states using short quantum circuits is one of the most promising near-term applications of small quantum computers, especially if the circuit is short enough and the fidelity of gates high enough that it can be executed without quantum error correction. Such quantum state preparation can be used in variational approaches, optimizing parameters in the circuit to minimize the energy of the constructed quantum state for a given problem Hamiltonian. For this purpose we propose a simple-to-implement class of quantum states motivated by adiabatic state preparation. We test its accuracy and determine the required circuit depth for a Hubbard model on ladders with up to 12 sites (24 spin-orbitals), and for small molecules. We find that this ansatz converges faster than previously proposed schemes based on unitary coupled clusters. While the required number of measurements is astronomically large for quantum chemistry applications to molecules, applying the variational approach to the Hubbard model (and related models) is found to be far less demanding and potentially practical on small quantum computers. We also discuss another application of quantum state preparation using short quantum circuits, to prepare trial ground states of models faster than using adiabatic state preparation.

  18. Antigenic variation in African trypanosomes

    PubMed Central

    Horn, David

    2014-01-01

    Studies on Variant Surface Glycoproteins (VSGs) and antigenic variation in the African trypanosome, Trypanosoma brucei, have yielded a remarkable range of novel and important insights. The features first identified in T. brucei extend from unique to conserved-among-trypanosomatids to conserved-among-eukaryotes. Consequently, much of what we now know about trypanosomatid biology and much of the technology available has its origin in studies related to VSGs. T. brucei is now probably the most advanced early branched eukaryote in terms of experimental tractability and can be approached as a pathogen, as a model for studies on fundamental processes, as a model for studies on eukaryotic evolution or often all of the above. In terms of antigenic variation itself, substantial progress has been made in understanding the expression and switching of the VSG coat, while outstanding questions continue to stimulate innovative new approaches. There are large numbers of VSG genes in the genome but only one is expressed at a time, always immediately adjacent to a telomere. DNA repair processes allow a new VSG to be copied into the single transcribed locus. A coordinated transcriptional switch can also allow a new VSG gene to be activated without any detectable change in the DNA sequence, thereby maintaining singular expression, also known as allelic exclusion. I review the story behind VSGs; the genes, their expression and switching, their central role in T. brucei virulence, the discoveries that emerged along the way and the persistent questions relating to allelic exclusion in particular. PMID:24859277

  19. COMPLEX EVOLUTION OF BILE SALTS IN BIRDS

    PubMed Central

    Hagey, Lee R.; Vidal, Nicolas; Hofmann, Alan F.; Krasowski, Matthew D.

    2010-01-01

    Bile salts are the major end-metabolites of cholesterol and are important in lipid digestion and shaping of the gut microflora. There have been limited studies of bile-salt variation in birds. The purpose of our study was to determine bile-salt variation among birds and relate this variation to current avian phylogenies and hypotheses on the evolution of bile salt pathways. We determined the biliary bile-salt composition of 405 phylogenetically diverse bird species, including 7 paleognath species. Bile salt profiles were generally stable within bird families. Complex bile-salt profiles were more common in omnivores and herbivores than in carnivores. The structural variation of bile salts in birds is extensive and comparable to that seen in surveys of bile salts in reptiles and mammals. Birds produce many of the bile salts found throughout nonavian vertebrates and some previously uncharacterized bile salts. One difference between birds and other vertebrates is extensive hydroxylation of carbon-16 of bile salts in bird species. Comparison of our data set of bird bile salts with that of other vertebrates, especially reptiles, allowed us to infer evolutionary changes in the bile salt synthetic pathway. PMID:21113274

  20. Between and within-site variation in qualitative implementation research

    PubMed Central

    2013-01-01

    Background Multisite qualitative studies are challenging in part because decisions regarding within-site and between-site sampling must be made to reduce the complexity of data collection, but these decisions may have serious implications for analyses. There is not yet consensus on how to account for within-site and between-site variations in qualitative perceptions of the organizational context of interventions. The purpose of this study was to analyze variation in perceptions among key informants in order to demonstrate the importance of broad sampling for identifying both within-site and between-site implementation themes. Methods Case studies of four sites were compared to identify differences in how Department of Veterans Affairs (VA) medical centers implemented a Primary Care/Mental Health Integration (PC/MHI) intervention. Qualitative analyses focused on between-profession variation in reported referral and implementation processes within and between sites. Results Key informants identified co-location, the consultation-liaison service, space, access, and referral processes as important topics. Within-site themes revealed the importance of coordination, communication, and collaboration for implementing PC/MHI. The between-site theme indicated that the preexisting structure of mental healthcare influenced how PC/MHI was implemented at each site and that collaboration among both leaders and providers was critical to overcoming structural barriers. Conclusions Within- and between-site variation in perceptions among key informants within different professions revealed barriers and facilitators to the implementation not available from a single source. Examples provide insight into implementation barriers for PC/MHI. Multisite implementation studies may benefit from intentionally eliciting and analyzing variation within and between sites. Suggestions for implementation research design are presented. PMID:23286552

  1. Quantum Computational Complexity

    E-print Network

    John Watrous

    2008-04-21

    This article surveys quantum computational complexity, with a focus on three fundamental notions: polynomial-time quantum computations, the efficient verification of quantum proofs, and quantum interactive proof systems. Properties of quantum complexity classes based on these notions, such as BQP, QMA, and QIP, are presented. Other topics in quantum complexity, including quantum advice, space-bounded quantum computation, and bounded-depth quantum circuits, are also discussed.

  2. Accommodating Variation: Dialects, Idiolects, and Speech Processing

    PubMed Central

    Kraljic, Tanya; Brennan, Susan E.; Samuel, Arthur G.

    2008-01-01

    Listeners are faced with enormous variation in pronunciation, yet they rarely have difficulty understanding speech. Although much research has been devoted to figuring out how listeners deal with variability, virtually none (outside of sociolinguistics) has focused on the source of the variation itself. The current experiments explore whether different kinds of variation lead to different cognitive and behavioral adjustments. Specifically, we compare adjustments to the same acoustic consequence when it is due to context-independent variation (resulting from articulatory properties unique to a speaker) versus context-conditioned variation (resulting from common articulatory properties of speakers who share a dialect). The contrasting results for these two cases show that the source of a particular acoustic-phonetic variation affects how that variation is handled by the perceptual system. We also show that changes in perceptual representations do not necessarily lead to changes in production. PMID:17803986

  3. Understanding bistability in complex enzyme-driven reaction networks

    E-print Network

    Craciun, Gheorghe

    to variations in enzyme transcription activity (or even to enzyme malformation) when, in fact, those changesUnderstanding bistability in complex enzyme-driven reaction networks Gheorghe Craciun* , Yangzhong for enzyme catalysis of a single overall reaction. We present a theorem that distinguishes between those mass

  4. On a family of Hill's equations in the complex field

    NASA Astrophysics Data System (ADS)

    Makhlouf, Amar; Nahon, Fernand

    1991-09-01

    The variational equation of the periodic solution in an homogeneous potential of degree 2m leads to a family of Hill's equations. Yoshida (1986, 1987) solves these equations by a transformation to the Gauss equation of hypergeometric functions. This family is studied directly for complex t, and in the case m = 2, a detailed description of critical solutions is given.

  5. Representational Complexity and Memory Retrieval in Language Comprehension

    ERIC Educational Resources Information Center

    Hofmeister, Philip

    2011-01-01

    Mental representations formed from words or phrases may vary considerably in their feature-based complexity. Modern theories of retrieval in sentence comprehension do not indicate how this variation and the role of encoding processes should influence memory performance. Here, memory retrieval in language comprehension is shown to be influenced by…

  6. Phase Shifting and the Beating of Complex Waves

    ERIC Educational Resources Information Center

    Keeports, David

    2011-01-01

    At the introductory level, the demonstration and analysis of sound beating is usually limited to the superposition of two purely sinusoidal waves with equal amplitudes and very similar frequencies. Under such conditions, an observer hears the periodic variation of the loudness of a sound with an unchanging timbre. On the other hand, when complex

  7. Does complex learning require complex connectivity?

    E-print Network

    Guerra Hernández, Alejandro

    - proach different issues in behavior based Artificial Intelligence (AI) that usually have been ill defined when performing complex learning. 1 Introduction Behavior based AI [6, 21, 23] claims the necessity [27], autonomy [7], or even the epigenetic [13, 14], are ill defined or even are used with different

  8. Complexity and Stability in Biological Systems

    NASA Astrophysics Data System (ADS)

    Demongeot, Jacques; Demetrius, Lloyd A.

    2015-06-01

    The hypothesis that a positive correlation exists between the complexity of a biological system, as described by its connectance, and its stability, as measured by its ability to recover from disturbance, derives from the investigations of the physiologists, Bernard and Cannon, and the ecologist Elton. Studies based on the ergodic theory of dynamical systems and the theory of large deviations have furnished an analytic support for this hypothesis. Complexity in this context is described by the mathematical object evolutionary entropy, stability is characterized by the rate at which the system returns to its stable conditions (steady state or periodic attractor) after a random perturbation of its robustness. This article reviews the analytical basis of the entropy — robustness theorem — and invokes studies of genetic regulatory networks to provide empirical support for the correlation between complexity and stability. Earlier investigations based on numerical studies of random matrix models and the notion of local stability have led to the claim that complex ecosystems tend to be more dynamically fragile. This article elucidates the basis for this claim which is largely inconsistent with the empirical observations of Bernard, Cannon and Elton. Our analysis thus resolves a long standing controversy regarding the relation between complex biological systems and their capacity to recover from perturbations. The entropy-robustness principle is a mathematical proposition with implications for understanding the basis for the large variations in stability observed in biological systems having evolved under different environmental conditions.

  9. Diagnosing Source Geometrical Complexity of Large Earthquakes

    NASA Astrophysics Data System (ADS)

    Rivera, L.; Kanamori, H.

    2014-10-01

    We investigated the possible frequency dependence of the moment tensor of large earthquakes by performing W phase inversions using teleseismic data and equally-spaced narrow, overlapping frequency bands. We investigated frequencies from 0.6 to 3.8 mHz. Our focus was on the variation with frequency of the scalar moment, the amount of non-double-couple, and the focal mechanism. We applied this technique to 30 major events in the period 1994-2013 and used the results to detect source complexity. Based on the results, we classed them into three groups according to the variability of the source parameters with frequency: simple, complex and intermediate. Twelve of these events fell into the simple category: Bolivia-1994, Kuril-1994, Sanriku-1994, Antofagasta-1995, Andreanoff-1996, Peru-2001, Sumatra-2004, Sumatra-2005, Tonga-2006, Sumatra-2007, Japan-2011, and the recent Sea of Okhotsk-2013. Seven exhibited significant complexity: Balleny-1998, Sumatra-2000, Indian Ocean-2000, Macquarie Island-2004, Sichuan-2008, and Samoa-2009. The remaining 11 events showed a moderate degree of complexity. Here, we discuss the results of this study in light of independent observations of source complexity, made by various investigators.

  10. Hamiltonian maps in the complex plane

    SciTech Connect

    Greene, J.M.; Percival, I.C.

    1981-01-01

    Following Arnol'd's proof of the KAM theorem, an analogy with the vertical pendulum, and some general arguments concerning maps in the complex plane, detailed calculations are presented and illustrated graphically for the standard map at the golden mean frequency. The functional dependence of the coordinate q on the canonical angle variable theta is analytically continued into the complex theta-plane, where natural boundaries are found at constant absolute values of Im theta. The boundaries represent the appearance of chaotic motion in the complex plane. Two independent numerical methods based on Fourier analysis in the angle variable were used, one based on a variation-annihilation method and the other on a double expansion. The results were further checked by direct solution of the complex equations of motion. The numerically simpler, but intrinsically complex, semipendulum and semistandard map are also studied. We conjecture that natural boundaries appear in the analogous analytic continuation of the invariant tori or KAM surfaces of general nonintegrable systems.

  11. A discrete time method to the first variation of fractional order variational functionals

    NASA Astrophysics Data System (ADS)

    Pooseh, Shakoor; Almeida, Ricardo; Torres, Delfim F. M.

    2013-10-01

    The fact that the first variation of a variational functional must vanish along an extremizer is the base of most effective solution schemes to solve problems of the calculus of variations. We generalize the method to variational problems involving fractional order derivatives. First order splines are used as variations, for which fractional derivatives are known. The Grünwald-Letnikov definition of fractional derivative is used, because of its intrinsic discrete nature that leads to straightforward approximations.

  12. Seasonal variation in human births.

    PubMed

    James, W H

    1990-01-01

    During the first half of this century, the seasonal pattern of births in European countries showed a major peak in the spring and a minor peak in the autumn. In contrast, the pattern in the US was of a minor peak in spring and a major peak in autumn. Over the last 20 years, the pattern in England and Wales has changed to resemble the US pattern, and the same seems to be true of several other European countries. A hypothesis is offered to account for the difference between the European and the US patterns and for the change from one to the other in some countries. The magnitude of seasonality correlates positively with latitude: it is suggested that this is partially consequent on variation in luminosity. PMID:2298756

  13. Variational Approach and Deformed Derivatives

    E-print Network

    José Weberszpil; José Abdalla Helayël-Neto

    2015-11-09

    Recently, we have demonstrated that there exists a possible relationship between q-deformed algebras in two different contexts of Statistical Mechanics, namely, the Tsallis' framework and the Kaniadakis' scenario, with a local form of fractional-derivative operators for fractal media, the so-called Hausdorff derivatives, mapped into a continuous medium with a fractal measure. Here, in this paper, we present an extension of the traditional calculus of variations for systems containing deformed-derivatives embedded into the Lagrangian and the Lagrangian densities for classical and field systems. The results extend the classical Euler-Lagrange equations and the Hamiltonian formalism. The resulting dynamical equations seem to be compatible with those found in the literature, specially with mass-dependent and with nonlinear equations for systems in classical and quantum mechanics. Examples are presented to illustrate applications of the formulation. Also, the conserved Nether current, are worked out.

  14. Variational Approach and Deformed Derivatives

    E-print Network

    Weberszpil, José

    2015-01-01

    Recently, we have demonstrated that there exists a possible relationship between q-deformed algebras in two different contexts of Statistical Mechanics, namely, the Tsallis' framework and the Kaniadakis' scenario, with a local form of fractional-derivative operators for fractal media, the so-called Hausdorff derivatives, mapped into a continuous medium with a fractal measure. Here, in this paper, we present an extension of the traditional calculus of variations for systems containing deformed-derivatives embedded into the Lagrangian and the Lagrangian densities for classical and field systems. The results extend the classical Euler-Lagrange equations and the Hamiltonian formalism. The resulting dynamical equations seem to be compatible with those found in the literature, specially with mass-dependent and with nonlinear equations for systems in classical and quantum mechanics. Examples are presented to illustrate applications of the formulation. Also, the conserved Nether current, are worked out.

  15. Communication variations and aircrew performance

    NASA Technical Reports Server (NTRS)

    Kanki, Barbara G.; Folk, Valerie G.; Irwin, Cheryl M.

    1991-01-01

    The relationship between communication variations and aircrew performance (high-error vs low-error performances) was investigated by analyzing the coded verbal transcripts derived from the videotape records of 18 two-person air transport crews who participated in a high-fidelity, full-mission flight simulation. The flight scenario included a task which involved abnormal operations and required the coordinated efforts of all crew members. It was found that the best-performing crews were characterized by nearly identical patterns of communication, whereas the midrange and poorer performing crews showed a great deal of heterogeneity in their speech patterns. Although some specific speech sequences can be interpreted as being more or less facilitative to the crew-coordination process, predictability appears to be the key ingredient for enhancing crew performance. Crews communicating in highly standard (hence predictable) ways were better able to coordinate their task, whereas crews characterized by multiple, nonstandard communication profiles were less effective in their performance.

  16. Variational identities and Hamiltonian structures

    NASA Astrophysics Data System (ADS)

    Ma, Wen-Xiu

    2010-03-01

    This report is concerned with Hamiltonian structures of classical and super soliton hierarchies. In the classical case, basic tools are variational identities associated with continuous and discrete matrix spectral problems, targeted to soliton equations derived from zero curvature equations over general Lie algebras, both semisimple and non-semisimple. In the super case, a supertrace identity is presented for constructing Hamiltonian structures of super soliton equations associated with Lie superalgebras. We illustrate the general theories by the KdV hierarchy, the Volterra lattice hierarchy, the super AKNS hierarchy, and two hierarchies of dark KdV equations and dark Volterra lattices. The resulting Hamiltonian structures show the commutativity of each hierarchy discussed and thus the existence of infinitely many commuting symmetries and conservation laws.

  17. Variational identities and Hamiltonian structures

    SciTech Connect

    Ma Wenxiu

    2010-03-08

    This report is concerned with Hamiltonian structures of classical and super soliton hierarchies. In the classical case, basic tools are variational identities associated with continuous and discrete matrix spectral problems, targeted to soliton equations derived from zero curvature equations over general Lie algebras, both semisimple and non-semisimple. In the super case, a supertrace identity is presented for constructing Hamiltonian structures of super soliton equations associated with Lie superalgebras. We illustrate the general theories by the KdV hierarchy, the Volterra lattice hierarchy, the super AKNS hierarchy, and two hierarchies of dark KdV equations and dark Volterra lattices. The resulting Hamiltonian structures show the commutativity of each hierarchy discussed and thus the existence of infinitely many commuting symmetries and conservation laws.

  18. Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes

    E-print Network

    Jamieson, Ian

    forces, selection and genetic drift, acting on MHC genes during population bottlenecks. Here, we take-bottlenecked populations. Keywords: adaptive variation, balancing selection, major histocompatibility complex, meta as the main mechanism driving MHC polymorphism (Spurgin & Richardson 2010). There are three main, non

  19. Study of Genomic Copy Number Variation in Equine Health and Disease 

    E-print Network

    Ghosh, Sharmila

    2014-07-30

    This is a study of copy number variations (CNVs) in the horse genome to gain knowledge about the role of CNVs in equine biology, and their contribution to complex diseases and disorders. We constructed a 400K whole-genome tiling array and applied...

  20. Topic Familiarity and Interlanguage Variation: A Study of the Impact of Interactional Feedback

    ERIC Educational Resources Information Center

    Rahimpour, Massoud; Hazar, Fatemeh

    2009-01-01

    This paper presents the results of a study investigating the impact of interactional feedback on interlanguage variation in terms of accuracy, complexity, and fluency of learners' discourse in performing tasks with familiar vs. unfamiliar topics. The participant of the study who were randomly assigned into an experimental and a control group were…

  1. Correlates of interspecific synchrony and interannual variation in seed production by deciduous trees

    E-print Network

    Goheen, Jacob R.

    Correlates of interspecific synchrony and interannual variation in seed production by deciduous 2006; received in revised form 31 January 2007; accepted 31 January 2007 Abstract Eastern deciduous by a complex interplay of temperature, moisture, and disturbance. An understanding of seed production

  2. Making Sense of Stochastic Variation and Causality in a Virtual Environment

    ERIC Educational Resources Information Center

    Prodromou, Theodosia; Pratt, Dave

    2013-01-01

    This paper presents a case study of students (age 14-15) as they attempt to make sense of distribution, adopting a range of causal meanings for the variation observed in the animated computer display and in the graphs generated by a "BasketBall" simulation. The student activity is analysed through dimensions of complex causality. The…

  3. Genotypic variation in physiological strategies for attaining cotton lint yield production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The quality and quantity of cotton (Gossypium hirsutum L.) lint produced are complex traits controlled by multiple processes. The physiology behind yield and quality variations is not completely understood. Objectives for this research were to document the physiological strategies diverse cotton g...

  4. Variations in solar luminosity and their effect on the Earth's climate

    E-print Network

    Cambridge, University of

    complex to evaluate meaningfully at present. T he possible effect on climate of variations in the Sun it allows us to use the relatively short time series of space-borne measurements, along with other kinds avoided completely freezing over, most probably because of much higher concentrations of greenhouse gases

  5. Stress-induced variation in evolution: from behavioural plasticity to genetic assimilation

    E-print Network

    Badyaev, Alex

    Review Stress-induced variation in evolution: from behavioural plasticity to genetic assimilation, morphological and behavioural regulatory systems. Second, such reduced integration and subsequent accommodation as well as phenotypic and genetic assimilation of the response to a stressor. Third, in complex functional

  6. Maize HapMap2 identifies extant variation from a genome in flux

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The maize genome is the largest, most diverse and complex plant genome sequenced to date. Using high-throughput sequencing to access genetic variation and a population genetics model to score the polymorphisms, we characterize and unite the diversity of the world’s key breeding germplasm, wild rela...

  7. Genetic variation and human longevity.

    PubMed

    Soerensen, Mette

    2012-05-01

    The overall aim of the PhD project was to elucidate the association of human longevity with genetic variation in major candidate genes and pathways of longevity. Based on a thorough literature and database search we chose to apply a pathway approach; to explore variation in genes composing the DNA damage signaling, DNA repair, GH/IGF-1/insulin signaling and pro-/antioxidant pathways. In addition, 16 genes which did not belong to the core of either pathway, however recurrently regarded as candidate genes of longevity (e.g. APOE), were included. In this way a total of 168 genes were selected for investigation. We decided to explore the genetic variation in the form of single nucleotide polymorphisms (SNPs), a highly investigated type of genetic variation. SNPs having potential functional impact (e.g. affecting binding of transcription factors) were identified, so were specific SNPs in the candidate genes previously published to be associated with human longevity. To cover the majority of the common genetic variation in the 168 gene regions (encoding regions plus 5,000 bp upstream and 1,000 downstream) we applied the tagging SNP approach via the HapMap Consortium. Consequently 1,536 SNPs were selected. The majority of the previous publications on genetic variation and human longevity had employed a case-control study design, e.g. comparing centenarians to middle-aged controls. This type of study design is somehow prone to bias introduced by for instance cohort effects, i.e. differences in characteristics of cases and controls, a kind of bias which is avoided when a prospective cohort is under study. Therefore, we chose to investigate 1,200 individuals of the Danish 1905 birth cohort, which have been followed since 1998 when the members were 92-93 years old. The genetic contribution to human longevity has been estimated to be most profound during the late part of life, thus these oldest-old individuals are excellent for investigating such effect. The follow-up survival data enabled performance of longitudinal analysis, which is quite unique in the field of genetic epidemiology of human longevity. Since the cohort was nearly extinct when initiating the PhD study we were able to conduct the longitudinal analyses as regression analyses enabling the estimation of the quantitative effects of the associated SNPs. However, this study explores the genetic contribution to survival during the ninth decade of life, hence, in order to investigate the genetic contribution to survival in younger elderly we also included 800 individuals of the Study of Middle-aged Danish twins (MADT). MADT was initiated in 1998 by random selection of 2,640 intact twin pairs from 22 consecutive birth years (1931-1952) via the Danish Central Person Registry. Only one twin from each twin pair was included in the PhD study. The inclusion of these 800 middle-aged individuals enabled the performance of case-control analysis. Consequently DNA was purified from 2,000 blood samples, genotyping was carried out via the GoldenGate genotyping platform (Illumina Inc.), quality control and data cleaning were conducted, leading to genotype data on 1,394 SNPs in 1,089 oldest-old and 736 middle-aged individuals. The genotype data were analysed at the single-SNP and haplotype levels, and for the 16 candidate genes also at the gene level. The analyses of the data set verified the association of a few of the 16 candidate genes not being part of the candidate pathways under study: SNPs in the APOE, CETP and IL6 genes, while the analyses of the 152 pathway-related genes pointed to new candidate genes of human longevity: especially SNPs in the INS, RAD52 and NTHL1 genes appeared promising. As part of these investigations, replication studies of the single-SNP level findings were conducted in German case-control samples of 1,613 oldest-old (ages 95-110) and 1,104 middle-aged individuals and in a Dutch prospective cohort of 563 oldest-old (age 85+). The Dutch oldest-old have been followed for approximately the same number of years as the Danish oldest-old. Interesting aspects of th

  8. A variational model for PolSAR data speckle reduction based on the Wishart distribution.

    PubMed

    Nie, Xiangli; Qiao, Hong; Zhang, Bo

    2015-04-01

    In this paper, we propose a variational model for polarimetric synthetic aperture radar (PolSAR) data speckle reduction, which is based on the complex Wishart distribution of the covariance or coherency matrix and multichannel total variation (TV) regularization defined for complex-valued matrices. By assuming the TV regularization to be a prior and taking the statistical distribution of the covariance matrix in each resolution element into account, the variational model for PolSAR covariance data speckle suppression, named WisTV-C, is derived from the maximum a posteriori estimate. A similar variational model for PolSAR coherency data speckle reduction, named WisTV-T, is also obtained. As far as we know, this is the first variational model for the whole PolSAR covariance or coherency matrix data despeckling. Since the model is nonconvex, a convex relaxation iterative algorithm is designed to solve the variational problem, based on the variable splitting and alternating minimization techniques. Experimental results on both simulated and real PolSAR data demonstrate that the proposed approach notably removes speckles in the extended uniform areas and, meanwhile, better preserves the spatial resolution, the details such as edges and point scatterers, and the polarimetric scattering characteristics, compared with other methods. PMID:25622321

  9. South Campus Recreation Complex

    E-print Network

    McLaughlin, Richard M.

    Basketball Court Navy Field Tennis Court E. Tennis Court W. COEC Play Field Branson Basketball Court Navy Field Volleyball Court South Campus Recreation Complex Basketball Half Court Sand Court Kenan Stadium Field North Campus Recreation Complex Belk Track Hooker Fields Basketball Half Court Basketball

  10. Complexity and Relations

    ERIC Educational Resources Information Center

    Lancaster, Jeanette Elizabeth

    2013-01-01

    A central feature of complexity is that it is based on non-linear, recursive relations. However, in most current accounts of complexity such relations, while non-linear, are based on the reductive relations of a Newtonian onto-epistemological framework. This means that the systems that are emergent from the workings of such relations are a…

  11. Complex Materials Research Profile

    E-print Network

    Giger, Christine

    , and the co-assembly of particles, droplets and bubbles in complex suspensions for 3D printing and other ­ Composites with complex reinforcement architectures ­ Bioinspired composites ­ 3D Printing ­ Fracture inno- vative ways to integrate the organic and inorganic worlds into bioinspired hybrid systems

  12. Schools and Complexity

    ERIC Educational Resources Information Center

    Trombly, Christopher E.

    2014-01-01

    As schools, districts, and the overall education system are complex entities, both the approaches taken to improve them and the methods used to study them must be similarly complex. Simple solutions imposed with no regard for schools' or districts' unique contexts hold little promise, while seemingly insignificant differences between those…

  13. Complex Organic Interstellar Molecules

    E-print Network

    van Dishoeck, Ewine F.

    Complex Organic Interstellar Molecules Eric Herbst1 and Ewine F. van Dishoeck2 1 Departments complex by astronomers if not by chemists, all contain the element carbon and so can be called organic and a solid phase of tiny dust particles. The dense interstellar matter can be found in small individual

  14. Complexity in Picture Books

    ERIC Educational Resources Information Center

    Sierschynski, Jarek; Louie, Belinda; Pughe, Bronwyn

    2015-01-01

    One of the key requirements of Common Core State Standards (CCSS) in English Language Arts is that students are able to read and access complex texts across all grade levels. The CCSS authors emphasize both the limitations and lack of accuracy in the current CCSS model of text complexity, calling for the development of new frameworks. In response…

  15. Gold trifluoromethyl complexes.

    PubMed

    Gil-Rubio, Juan; Vicente, José

    2015-12-01

    This article reviews the synthesis, reactivity and applications of gold trifluoromethyl complexes, which are the only isolated perfluoroalkyl complexes of gold. The most reported examples are neutral Au(i) complexes of the type [Au(CF3)L], whereas only two Au(ii) trifluoromethyl complexes have been reported, both being diamagnetic and containing a strong Au-Au bond. A number of Au(iii) trifluoromethyl complexes have been prepared by oxidative addition of halogens or iodotrifluoromethane to Au(i) complexes or, in a few cases, by transmetallation reactions. Owing to the limitations of the available synthetic methods, a lower number of examples is known, particularly for the oxidation states (ii) and (iii). Gold trifluoromethyl complexes present singular characteristics, such as thermal stability, strong Au-C bonds and, in some cases, reactive ?-C-F bonds. Some of the Au(iii) complexes reported, show unusually easy reductive elimination reactions of trifluoromethylated products which could be applied in the development of gold-catalyzed processes for the trifluoromethylation of organic compounds. PMID:26169553

  16. U1A Complex

    SciTech Connect

    2014-10-28

    Some of the most sophisticated experiments in the stockpile stewardship program are conducted in an environmentally safe manner, nearly 1000 feet below the ground at the site. The U1a complex a sprawling underground laboratory and tunnel complex is home to a number of unique capabilities.

  17. U1A Complex

    ScienceCinema

    None

    2015-01-09

    Some of the most sophisticated experiments in the stockpile stewardship program are conducted in an environmentally safe manner, nearly 1000 feet below the ground at the site. The U1a complex a sprawling underground laboratory and tunnel complex is home to a number of unique capabilities.

  18. UNCORRECTEDPROOF Springer Complexity

    E-print Network

    Breakspear, Michael

    the best research and academic-level teaching on both fundamental and applied aspects of complex systems, medicine, neuroscience, social and computer science. Complex Systems are systems that comprise many automata, adaptive systems, genetic al- gorithms and computational intelligence. The two major book

  19. Performance Improvement Assuming Complexity

    ERIC Educational Resources Information Center

    Rowland, Gordon

    2007-01-01

    Individual performers, work teams, and organizations may be considered complex adaptive systems, while most current human performance technologies appear to assume simple determinism. This article explores the apparent mismatch and speculates on future efforts to enhance performance if complexity rather than simplicity is assumed. Included are…

  20. Freestanding Complex Optical Scanners.

    ERIC Educational Resources Information Center

    Frisbie, David A.

    A complex freestanding optical mark recognition (OMR) scanner is one which is not on-line to an external processor; it has intelligence stemming from an internal processor located within the unit or system. The advantages and disadvantages of a complex OMR can best be assessed after identifying the scanning needs and constraints of the potential…

  1. Bacterial formate hydrogenlyase complex

    PubMed Central

    McDowall, Jennifer S.; Murphy, Bonnie J.; Haumann, Michael; Palmer, Tracy; Armstrong, Fraser A.; Sargent, Frank

    2014-01-01

    Under anaerobic conditions, Escherichia coli can carry out a mixed-acid fermentation that ultimately produces molecular hydrogen. The enzyme directly responsible for hydrogen production is the membrane-bound formate hydrogenlyase (FHL) complex, which links formate oxidation to proton reduction and has evolutionary links to Complex I, the NADH:quinone oxidoreductase. Although the genetics, maturation, and some biochemistry of FHL are understood, the protein complex has never been isolated in an intact form to allow biochemical analysis. In this work, genetic tools are reported that allow the facile isolation of FHL in a single chromatographic step. The core complex is shown to comprise HycE (a [NiFe] hydrogenase component termed Hyd-3), FdhF (the molybdenum-dependent formate dehydrogenase-H), and three iron-sulfur proteins: HycB, HycF, and HycG. A proportion of this core complex remains associated with HycC and HycD, which are polytopic integral membrane proteins believed to anchor the core complex to the cytoplasmic side of the membrane. As isolated, the FHL complex retains formate hydrogenlyase activity in vitro. Protein film electrochemistry experiments on Hyd-3 demonstrate that it has a unique ability among [NiFe] hydrogenases to catalyze production of H2 even at high partial pressures of H2. Understanding and harnessing the activity of the FHL complex is critical to advancing future biohydrogen research efforts. PMID:25157147

  2. COMPLEXITY IN ECOLOGICAL SYSTEMS

    EPA Science Inventory

    The enormous complexity of ecosystems is generally obvious under even the most cursory examination. In the modern world, this complexity is further augmented by the linkage of ecosystems to economic and social systems through the human use of the environment for technological pu...

  3. [Complexity: an introduction].

    PubMed

    Gómez, Carlos Alberto Palacio; Jaramillo, Francisco Luis Ochoa

    2011-01-01

    Complexity appears in the twentieth century as a way to understand many phenomena that are perceived as chaotic and complex from classical thought, which still persist in our way of explaining the world. Its purpose is to study the complex and adaptive systems that are sensitive to initial conditions. Some of the characteristics of complex thought are systemic perspective, autopoiesis, self-organization, emergent properties, unpredictability of the systems, analogic thought, and the complementarity of the phenomena, among others. Living systems respond to a complex logic, and in that sense, our vision of human populations and patients, and how we try to solve problems and human diseases, should be open to the possibilities that arise from this form of understand the world. PMID:21503430

  4. Leading healthcare in complexity.

    PubMed

    Cohn, Jeffrey

    2014-12-01

    Healthcare institutions and providers are in complexity. Networks of interconnections from relationships and technology create conditions in which interdependencies and non-linear dynamics lead to surprising, unpredictable outcomes. Previous effective approaches to leadership, focusing on top-down bureaucratic methods, are no longer effective. Leading in complexity requires leaders to accept the complexity, create an adaptive space in which innovation and creativity can flourish and then integrate the successful practices that emerge into the formal organizational structure. Several methods for doing adaptive space work will be discussed. Readers will be able to contrast traditional leadership approaches with leading in complexity. They will learn new behaviours that are required of complexity leaders, along with challenges they will face, often from other leaders within the organization. PMID:25815410

  5. A variational technique for spacecraft trajectory planning

    NASA Astrophysics Data System (ADS)

    Henshaw, Carl Glen

    A successful autonomous spacecraft must be able to navigate "intelligently". Intelligent navigation entails finding and following collision-free paths through space which can be traversed in a reasonable time and which use a reasonable amount of fuel. Several spacecraft have been recently proposed for which intelligent navigation abilities are either desirable or necessary. Among these are NASA's AERCam, PSA, and ISS Inspector, ESA's Automated Transfer Vehicle (ATV), and DARPA's Orbital Express. These mission scenarios present challenging guidance problems, as the vehicles may in general start in different orbits from their targets. Trajectory planners for these vehicles must therefore combine "long range" orbital maneuvering, with its attendant nonlinear dynamics and fuel use constraints, and "short range" proximity operations where collision avoidance is paramount. We describe a spacecraft trajectory planning algorithm based on the calculus of variations which can solve 6-DOF spacecraft docking and proximity operations problems. The design of a cost functional which trades off fuel use, obstacle clearance distance, and arrival time is discussed. The nonlinear orbital dynamic equations are treated as dynamic constraints. The Euler-Lagrange equations for this functional are derived, as are the Pontryagin criteria for the optimal control input given realistic saturating on-off thrusters. The collocation method is chosen to solve the attendant boundary-value problem, and a number of features added to further improve the algorithm's robustness. The manipulation of the Euler-Lagrange equations and the transversality condition into a form suitable for use with collocation methods is also discussed. The algorithm is shown to be capable of solving "traditional" free-space path planning problems with complex-shaped, moving obstacles. Trajectories are also shown for a variety of orbital maneuvers, culminating in an end-to-end docking maneuver with a tumbling satellite. The computation effort needed to solve these problems is discussed, as are the tradeoffs between fuel use, obstacle clearance distance, and arrival time.

  6. Mitochondrial complex 1 gene analysis in keratoconus

    PubMed Central

    Pathak, Dhananjay; Nayak, Bhagabat; Singh, Manvendra; Sharma, Namrata; Tandon, Radhika; Sinha, Rajesh; Titiyal, Jeewan S.

    2011-01-01

    Purpose Keratoconus is characterized by the thinning of corneal stroma, resulting in reduced vision. The exact etiology of keratoconus (KC) is still unknown. The involvement of oxidative stress (OS) in this disease has been reported. However, the exact mechanism of OS in keratoconus is still unknown. Thus we planned this study to screen mitochondrial complex I genes for sequence changes in keratoconus patients and controls, as mitochondrial complex I is the chief source of reactive oxygen species (ROS) production. Methods A total of 20 keratoconus cases and 20 healthy controls without any ocular disorder were enrolled in this study. Mitochondrial complex I genes (ND1, 2, 3, 4, 4L, 5, and 6) were amplified in all patients and controls using 12 pairs of primers by PCR. After sequencing, DNA sequences were analyzed against the mitochondrial reference sequence NC_012920. Haplogroup frequency based Principle Component Analysis (PCA) was constructed to determine whether the gene pool of keratoconus patients is closer to major populations in India. Results DNA sequencing revealed a total 84 nucleotide variations in patients and 29 in controls. Of 84 nucleotide changes, 18 variations were non-synonymous and two novel frame-shift mutations were detected in cases. Non-synonymous mtDNA sequence variations may account for increased ROS and decreased ATP production. This ultimately leads to OS; which is a known cause for variety of corneal abnormalities. Haplotype analysis showed that most of the patients were clustered under the haplogroups: T, C4a2a, R2’TJ, M21’Q1a, M12’G2a2a, M8’CZ and M7a2a, which are present as negligible frequency in normal Indian population, whereas only few patients were found to be a part of the other haplogroups like U7 (Indo-European), R2 and R31, whose origin is contentious. Conclusions Mt complex I sequence variations are the main cause of elevated ROS production which leads oxidative stress. This oxidative stress then starts a cascade of events which ultimately can lead to keratoconus. Prompt antioxidant therapy should be initiated in keratoconus patients to minimize ROS related damage. PMID:21691575

  7. Optimization strategies for complex engineering applications

    SciTech Connect

    Eldred, M.S.

    1998-02-01

    LDRD research activities have focused on increasing the robustness and efficiency of optimization studies for computationally complex engineering problems. Engineering applications can be characterized by extreme computational expense, lack of gradient information, discrete parameters, non-converging simulations, and nonsmooth, multimodal, and discontinuous response variations. Guided by these challenges, the LDRD research activities have developed application-specific techniques, fundamental optimization algorithms, multilevel hybrid and sequential approximate optimization strategies, parallel processing approaches, and automatic differentiation and adjoint augmentation methods. This report surveys these activities and summarizes the key findings and recommendations.

  8. Atmospheric Flux Computations in Complex Terrain

    NASA Technical Reports Server (NTRS)

    Smith, Paul L.; Kopp, Fred J.; Orville, Harold D.

    2000-01-01

    The greatest challenges in applying atmospheric water budget expressions are in determining the divergence and evapotranspiration terms. The evapotranspiration problem is ubiquitous, and critical issues of spatial and temporal resolution commonly arise in establishing the divergence term. In complex terrain, further difficulties crop up in using typical data on atmospheric profiles of water vapor and wind to estimate the divergence term. Those difficulties are the subject of this paper; considerations related to topographic variations both along and normal to the flow direction are treated.

  9. Complex earthquake rupture and local tsunamis

    USGS Publications Warehouse

    Geist, E.L.

    2002-01-01

    In contrast to far-field tsunami amplitudes that are fairly well predicted by the seismic moment of subduction zone earthquakes, there exists significant variation in the scaling of local tsunami amplitude with respect to seismic moment. From a global catalog of tsunami runup observations this variability is greatest for the most frequently occuring tsunamigenic subduction zone earthquakes in the magnitude range of 7 < Mw < 8.5. Variability in local tsunami runup scaling can be ascribed to tsunami source parameters that are independent of seismic moment: variations in the water depth in the source region, the combination of higher slip and lower shear modulus at shallow depth, and rupture complexity in the form of heterogeneous slip distribution patterns. The focus of this study is on the effect that rupture complexity has on the local tsunami wave field. A wide range of slip distribution patterns are generated using a stochastic, self-affine source model that is consistent with the falloff of far-field seismic displacement spectra at high frequencies. The synthetic slip distributions generated by the stochastic source model are discretized and the vertical displacement fields from point source elastic dislocation expressions are superimposed to compute the coseismic vertical displacement field. For shallow subduction zone earthquakes it is demonstrated that self-affine irregularities of the slip distribution result in significant variations in local tsunami amplitude. The effects of rupture complexity are less pronounced for earthquakes at greater depth or along faults with steep dip angles. For a test region along the Pacific coast of central Mexico, peak nearshore tsunami amplitude is calculated for a large number (N = 100) of synthetic slip distribution patterns, all with identical seismic moment (Mw = 8.1). Analysis of the results indicates that for earthquakes of a fixed location, geometry, and seismic moment, peak nearshore tsunami amplitude can vary by a factor of 3 or more. These results indicate that there is substantially more variation in the local tsunami wave field derived from the inherent complexity subduction zone earthquakes than predicted by a simple elastic dislocation model. Probabilistic methods that take into account variability in earthquake rupture processes are likely to yield more accurate assessments of tsunami hazards.

  10. Complexation of buffer constituents with neutral complexation agents: part I. Impact on common buffer properties.

    PubMed

    Riesová, Martina; Svobodová, Jana; Tošner, Zden?k; Beneš, Martin; Tesa?ová, Eva; Gaš, Bohuslav

    2013-09-17

    The complexation of buffer constituents with the complexation agent present in the solution can very significantly influence the buffer properties, such as pH, ionic strength, or conductivity. These parameters are often crucial for selection of the separation conditions in capillary electrophoresis or high-pressure liquid chromatography (HPLC) and can significantly affect results of separation, particularly for capillary electrophoresis as shown in Part II of this paper series (Beneš, M.; Riesová, M.; Svobodová, J.; Tesa?ová, E.; Dubský, P.; Gaš, B. Anal. Chem. 2013, DOI: 10.1021/ac401381d). In this paper, the impact of complexation of buffer constituents with a neutral complexation agent is demonstrated theoretically as well as experimentally for the model buffer system composed of benzoic acid/LiOH or common buffers (e.g., CHES/LiOH, TAPS/LiOH, Tricine/LiOH, MOPS/LiOH, MES/LiOH, and acetic acid/LiOH). Cyclodextrins as common chiral selectors were used as model complexation agents. We were not only able to demonstrate substantial changes of pH but also to predict the general complexation characteristics of selected compounds. Because of the zwitterion character of the common buffer constituents, their charged forms complex stronger with cyclodextrins than the neutral ones do. This was fully proven by NMR measurements. Additionally complexation constants of both forms of selected compounds were determined by NMR and affinity capillary electrophoresis with a very good agreement of obtained values. These data were advantageously used for the theoretical descriptions of variations in pH, depending on the composition and concentration of the buffer. Theoretical predictions were shown to be a useful tool for deriving some general rules and laws for complexing systems. PMID:23889602

  11. The African Genome Variation Project shapes medical genetics in Africa

    NASA Astrophysics Data System (ADS)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

    2015-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  12. Variationally Optimized Free-Energy Flooding for Rate Calculation.

    PubMed

    McCarty, James; Valsson, Omar; Tiwary, Pratyush; Parrinello, Michele

    2015-08-14

    We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free energy surface up to a predefined level. The resulting bias potential effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained. We test the method on a few illustrative systems for which we obtain an order of magnitude improvement in efficiency relative to previous approaches and several orders of magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in more complex systems. This and the ability of the variational approach to deal efficiently with a large number of collective variables will greatly enhance the scope of these calculations. This work is a vindication of the potential that the variational principle has if applied in innovative ways. PMID:26317704

  13. Unified CFD Methods Via Flowfield-Dependent Variation Theory

    NASA Technical Reports Server (NTRS)

    Chung, T. J.; Schunk, Greg; Canabal, Francisco; Heard, Gary

    1999-01-01

    This paper addresses the flowfield-dependent variation (FDV) methods in which complex physical phenomena are taken into account in the final form of partial differential equations to be solved so that finite difference methods (FDM) or finite element methods (FEM) themselves will not dictate the physics, but rather are no more than simply the options how to discretize between adjacent nodal points or within an element. The variation parameters introduced in the formulation are calculated from the current flowfield based on changes of Mach numbers, Reynolds numbers, Peclet numbers, and Damkohler numbers between adjacent nodal points, which play many significant roles such as adjusting the governing equations (hyperbolic, parabolic, and/or e!liptic), resolving various physical phenomena, and controlling the accuracy and stability of the numerical solution. The theory is verified by a number of example problems addressing the physical implications of the variation parameters which resemble the flowfield itself, shock capturing mechanism, transitions and interactions between inviscid/viscous, compressibility/incompressibility, and laminar/turbulent flows.

  14. Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior.

    PubMed

    Shorter, John; Couch, Charlene; Huang, Wen; Carbone, Mary Anna; Peiffer, Jason; Anholt, Robert R H; Mackay, Trudy F C

    2015-07-01

    Aggression is an evolutionarily conserved complex behavior essential for survival and the organization of social hierarchies. With the exception of genetic variants associated with bioamine signaling, which have been implicated in aggression in many species, the genetic basis of natural variation in aggression is largely unknown. Drosophila melanogaster is a favorable model system for exploring the genetic basis of natural variation in aggression. Here, we performed genome-wide association analyses using the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and replicate advanced intercross populations derived from the most and least aggressive DGRP lines. We identified genes that have been previously implicated in aggressive behavior as well as many novel loci, including gustatory receptor 63a (Gr63a), which encodes a subunit of the receptor for CO2, and genes associated with development and function of the nervous system. Although genes from the two association analyses were largely nonoverlapping, they mapped onto a genetic interaction network inferred from an analysis of pairwise epistasis in the DGRP. We used mutations and RNAi knock-down alleles to functionally validate 79% of the candidate genes and 75% of the candidate epistatic interactions tested. Epistasis for aggressive behavior causes cryptic genetic variation in the DGRP that is revealed by changing allele frequencies in the outbred populations derived from extreme DGRP lines. This phenomenon may pertain to other fitness traits and species, with implications for evolution, applied breeding, and human genetics. PMID:26100892

  15. The African Genome Variation Project shapes medical genetics in Africa.

    PubMed

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O; Choudhury, Ananyo; Ritchie, Graham R S; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N; Young, Elizabeth H; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S

    2015-01-15

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa. PMID:25470054

  16. Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior

    PubMed Central

    Shorter, John; Couch, Charlene; Huang, Wen; Carbone, Mary Anna; Peiffer, Jason; Anholt, Robert R. H.; Mackay, Trudy F. C.

    2015-01-01

    Aggression is an evolutionarily conserved complex behavior essential for survival and the organization of social hierarchies. With the exception of genetic variants associated with bioamine signaling, which have been implicated in aggression in many species, the genetic basis of natural variation in aggression is largely unknown. Drosophila melanogaster is a favorable model system for exploring the genetic basis of natural variation in aggression. Here, we performed genome-wide association analyses using the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and replicate advanced intercross populations derived from the most and least aggressive DGRP lines. We identified genes that have been previously implicated in aggressive behavior as well as many novel loci, including gustatory receptor 63a (Gr63a), which encodes a subunit of the receptor for CO2, and genes associated with development and function of the nervous system. Although genes from the two association analyses were largely nonoverlapping, they mapped onto a genetic interaction network inferred from an analysis of pairwise epistasis in the DGRP. We used mutations and RNAi knock-down alleles to functionally validate 79% of the candidate genes and 75% of the candidate epistatic interactions tested. Epistasis for aggressive behavior causes cryptic genetic variation in the DGRP that is revealed by changing allele frequencies in the outbred populations derived from extreme DGRP lines. This phenomenon may pertain to other fitness traits and species, with implications for evolution, applied breeding, and human genetics. PMID:26100892

  17. Molecular Mechanisms of Epigenetic Variation in Plants

    PubMed Central

    Fujimoto, Ryo; Sasaki, Taku; Ishikawa, Ryo; Osabe, Kenji; Kawanabe, Takahiro; Dennis, Elizabeth S.

    2012-01-01

    Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation. PMID:22949838

  18. Representational Complexity and Memory Retrieval in Language Comprehension

    PubMed Central

    Hofmeister, Philip

    2012-01-01

    Mental representations formed from words or phrases may vary considerably in their feature-based complexity. Modern theories of retrieval in sentence comprehension do not indicate how this variation and the role of encoding processes should influence memory performance. Here, memory retrieval in language comprehension is shown to be influenced by a target’s representational complexity in terms of syntactic and semantic features. Three self-paced reading experiments provide evidence that reading times at retrieval sites (but not earlier) decrease when more complex phrases occur as filler-phrases in filler-gap dependencies. The data also show that complexity-based effects are not dependent on string length, syntactic differences, or the amount of processing the stimuli elicit. Activation boosting and reduced similarity-based interference are implicated as likely sources of these complexity-based effects. PMID:22675235

  19. Influence of Design Variations on Systems Performance

    NASA Technical Reports Server (NTRS)

    Tumer, Irem Y.; Stone, Robert B.; Huff, Edward M.; Norvig, Peter (Technical Monitor)

    2000-01-01

    High-risk aerospace components have to meet very stringent quality, performance, and safety requirements. Any source of variation is a concern, as it may result in scrap or rework. poor performance, and potentially unsafe flying conditions. The sources of variation during product development, including design, manufacturing, and assembly, and during operation are shown. Sources of static and dynamic variation during development need to be detected accurately in order to prevent failure when the components are placed in operation. The Systems' Health and Safety (SHAS) research at the NASA Ames Research Center addresses the problem of detecting and evaluating the statistical variation in helicopter transmissions. In this work, we focus on the variations caused by design, manufacturing, and assembly of these components, prior to being placed in operation (DMV). In particular, we aim to understand and represent the failure and variation information, and their correlation to performance and safety and feed this information back into the development cycle at an early stage. The feedback of such critical information will assure the development of more reliable components with less rework and scrap. Variations during design and manufacturing are a common source of concern in the development and production of such components. Accounting for these variations, especially those that have the potential to affect performance, is accomplished in a variety ways, including Taguchi methods, FMEA, quality control, statistical process control, and variation risk management. In this work, we start with the assumption that any of these variations can be represented mathematically, and accounted for by using analytical tools incorporating these mathematical representations. In this paper, we concentrate on variations that are introduced during design. Variations introduced during manufacturing are investigated in parallel work.

  20. Modulating the frequency and bias of stochastic switching to control phenotypic variation.

    PubMed

    Hung, Michelle; Chang, Emily; Hussein, Razika; Frazier, Katya; Shin, Jung-Eun; Sagawa, Shiori; Lim, Han N

    2014-01-01

    Mechanisms that control cell-to-cell variation in gene expression ('phenotypic variation') can determine a population's growth rate, robustness, adaptability and capacity for complex behaviours. Here we describe a general strategy (termed FABMOS) for tuning the phenotypic variation and mean expression of cell populations by modulating the frequency and bias of stochastic transitions between 'OFF' and 'ON' expression states of a genetic switch. We validated the strategy experimentally using a synthetic fim switch in Escherichia coli. Modulating the frequency of switching can generate a bimodal (low frequency) or a unimodal (high frequency) population distribution with the same mean expression. Modulating the bias as well as the frequency of switching can generate a spectrum of bimodal and unimodal distributions with the same mean expression. This remarkable control over phenotypic variation, which cannot be easily achieved with standard gene regulatory mechanisms, has many potential applications for synthetic biology, engineered microbial ecosystems and experimental evolution. PMID:25087841