Science.gov

Sample records for complex kohn variational

  1. Complex Kohn calculations on an overset grid

    NASA Astrophysics Data System (ADS)

    Greenman, Loren; Lucchese, Robert; McCurdy, C. William

    2016-05-01

    An implentation of the overset grid method for complex Kohn scattering calculations is presented, along with static exchange calculations of electron-molecule scattering for small molecules including methane. The overset grid method uses multiple numerical grids, for instance Finite Element Method - Discrete Variable Representation (FEM-DVR) grids, expanded radially around multiple centers (corresponding to the individual atoms in each molecule as well as the center-of-mass of the molecule). The use of this flexible grid allows the complex angular dependence of the wavefunctions near the atomic centers to be well-described, but also allows scattering wavefunctions that oscillate rapidly at large distances to be accurately represented. Additionally, due to the use of multiple grids (and also grid shells), the method is easily parallelizable. The method has been implemented in ePolyscat, a multipurpose suite of programs for general molecular scattering calculations. It is interfaced with a number of quantum chemistry programs (including MolPro, Gaussian, GAMESS, and Columbus), from which it can read molecular orbitals and wavefunctions obtained using standard computational chemistry methods. The preliminary static exchange calculations serve as a test of the applicability.

  2. A Variational Framework for Spectral Approximations of Kohn-Sham Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Wang, Xin-Cindy; Blesgen, Thomas; Bhattacharya, Kaushik; Ortiz, Michael

    2016-08-01

    We reformulate the Kohn-Sham density functional theory (KSDFT) as a nested variational problem in the one-particle density operator, the electrostatic potential and a field dual to the electron density. The corresponding functional is linear in the density operator and thus amenable to spectral representation. Based on this reformulation, we introduce a new approximation scheme, termed spectral binning, which does not require smoothing of the occupancy function and thus applies at arbitrarily low temperatures. We prove convergence of the approximate solutions with respect to spectral binning and with respect to an additional spatial discretization of the domain.

  3. Complex-Kohn Approach to Molecular Ionization by High-Energy Electrons: Application to H2, H2O and CH4

    NASA Astrophysics Data System (ADS)

    Lin, Chih-Yuan; McCurdy, C. W.; Rescigno, T. N.

    2014-05-01

    The complex Kohn variational method, which has been extensively applied to low-energy molecule scattering, is extended to treat molecular ionization by fast electrons under the assumption that the incident and scattered electrons can be described by plane-waves. In contrast to other perturbative approches, the interaction between the slow ejected electron and the residual molecular ion is treated by a close-coupling method and for that we employ the complex Kohn variational method. The formulation reduces to the computation of the continuum generalized oscillation strength, which amounts to a generalization of the molecular photoionization problem to which the Kohn method has been successfully applied. The essential point is that the use of a correct electron-ion scattering wave function as the final state for the ejected electron enables us to treat high-energy electron impact ionization of molecules at the same level of sophistication achieved for atomic targets. We will present fully differential cross sections for ionization of water and methane, as well as for excitation/ionization of H2, along with comparisons to available experimental data. Work performed under the auspices of the US DOE by the LBNL and supported by the U.S. DOE Office of Basic Energy Sciences, Division of Chemical Sciences.

  4. 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,

  5. 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.

  6. 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…

  7. Kohn-Sham calculations of NMR shifts for paramagnetic 3d metal complexes: protocols, delocalization error, and the curious amide proton shifts of a high-spin iron(ii) macrocycle complex.

    PubMed

    Martin, Bob; Autschbach, Jochen

    2016-08-01

    A theory for the nuclear chemical shifts of molecules in arbitrary spin states is applied to a set of paramagnetic organometallic complexes of 3d metals. Ligand chemical shifts are calculated and analyzed using Kohn-Sham (KS) density functional theory with and without relativistic corrections. The roles of the KS delocalization error, Gaussian-type versus Slater-type basis sets, relativistic effects (scalar and spin-orbit), and zero field splitting (ZFS) are investigated. A strong functional dependence of the chemical shifts is apparent and correlated with the delocalization error. The functional dependence is between one and two orders of magnitude larger than variations of the NMR shifts due the other influences that are investigated. ZFS effects are negligible in the determination of the NMR chemical shifts of the complexes except at very low temperatures. The DFT calculated shifts agree reasonably well with experiment. A 73 ppm difference in the NMR shifts of the two protons in the amide groups of a high-spin Fe(ii) macrocycle complex arises from selective O → Fe dative bonding that only involves the transfer of β spin density, along with orbital delocalization throughout the ligand bonding framework which electronically couples the coordinating oxygen lone pair orbitals directly to the amide trans proton. PMID:26952694

  8. Defeating the pores of Kohn.

    PubMed

    Ng, Calvin S H; Lau, Rainbow W H; Lau, Kelvin K W; Underwood, Malcolm J; Yim, Anthony P C

    2014-01-01

    In the treatment of emphysema with an endobronchial valve, entire lobar treatment is important in achieving adequate atelectasis. This case illustrates that without treatment of the entire lobe, it can fail to collapse even after several years, leading to treatment failure. Intralobar collateral ventilation through the pores of Kohn is demonstrated in this case, as endobronchial valve blockage of the remaining patent anterior segment resulted in the desired atelectasis and significant improvements in pulmonary function. PMID:24585656

  9. Tucker-tensor algorithm for large-scale Kohn-Sham density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Motamarri, Phani; Gavini, Vikram; Blesgen, Thomas

    2016-03-01

    In this work, we propose a systematic way of computing a low-rank globally adapted localized Tucker-tensor basis for solving the Kohn-Sham density functional theory (DFT) problem. In every iteration of the self-consistent field procedure of the Kohn-Sham DFT problem, we construct an additive separable approximation of the Kohn-Sham Hamiltonian. The Tucker-tensor basis is chosen such as to span the tensor product of the one-dimensional eigenspaces corresponding to each of the spatially separable Hamiltonians, and the localized Tucker-tensor basis is constructed from localized representations of these one-dimensional eigenspaces. This Tucker-tensor basis forms a complete basis, and is naturally adapted to the Kohn-Sham Hamiltonian. Further, the locality of this basis in real-space allows us to exploit reduced-order scaling algorithms for the solution of the discrete Kohn-Sham eigenvalue problem. In particular, we use Chebyshev filtering to compute the eigenspace of the Kohn-Sham Hamiltonian, and evaluate nonorthogonal localized wave functions spanning the Chebyshev filtered space, all represented in the Tucker-tensor basis. We thereby compute the electron-density and other quantities of interest, using a Fermi-operator expansion of the Hamiltonian projected onto the subspace spanned by the nonorthogonal localized wave functions. Numerical results on benchmark examples involving pseudopotential calculations suggest an exponential convergence of the ground-state energy with the Tucker rank. Interestingly, the rank of the Tucker-tensor basis required to obtain chemical accuracy is found to be only weakly dependent on the system size, which results in close to linear-scaling complexity for Kohn-Sham DFT calculations for both insulating and metallic systems. A comparative study has revealed significant computational efficiencies afforded by the proposed Tucker-tensor approach in comparison to a plane-wave basis.

  10. Coherent cyclotron motion beyond Kohn's theorem

    NASA Astrophysics Data System (ADS)

    Maag, T.; Bayer, A.; Baierl, S.; Hohenleutner, M.; Korn, T.; Schüller, C.; Schuh, D.; Bougeard, D.; Lange, C.; Huber, R.; Mootz, M.; Sipe, J. E.; Koch, S. W.; Kira, M.

    2016-02-01

    In solids, the high density of charged particles makes many-body interactions a pervasive principle governing optics and electronics. However, Walter Kohn found in 1961 that the cyclotron resonance of Landau-quantized electrons is independent of the seemingly inescapable Coulomb interaction between electrons. Although this surprising theorem has been exploited in sophisticated quantum phenomena, such as ultrastrong light-matter coupling, superradiance and coherent control, the complete absence of nonlinearities excludes many intriguing possibilities, such as quantum-logic protocols. Here, we use intense terahertz pulses to drive the cyclotron response of a two-dimensional electron gas beyond the protective limits of Kohn's theorem. Anharmonic Landau ladder climbing and distinct terahertz four- and six-wave mixing signatures occur, which our theory links to dynamic Coulomb effects between electrons and the positively charged ion background. This new context for Kohn's theorem unveils previously inaccessible internal degrees of freedom of Landau electrons, opening up new realms of ultrafast quantum control for electrons.

  11. Are Kohn-Sham conductances accurate?

    PubMed

    Mera, H; Niquet, Y M

    2010-11-19

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

  12. On the Kohn-Luttinger conundrum

    NASA Astrophysics Data System (ADS)

    Hirata, So; He, Xiao

    2013-05-01

    Kohn and Luttinger [Phys. Rev. 118, 41 (1960)], 10.1103/PhysRev.118.41 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.

  13. 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.

  14. 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

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

    SciTech Connect

    Pan, Xiao-Yin; Sahni, Viraht

    2015-11-07

    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.

  16. 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.

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

    SciTech Connect

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

    2011-10-15

    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.

  18. Natural Allelic Variations in Highly Polyploidy Saccharum Complex.

    PubMed

    Song, Jian; Yang, Xiping; Resende, Marcio F R; Neves, Leandro G; Todd, James; Zhang, Jisen; Comstock, Jack C; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  19. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    PubMed Central

    Song, Jian; Yang, Xiping; Resende, Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  20. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    DOE PAGESBeta

    Song, Jian; Yang, Xiping; Resende, Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

    2016-06-08

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed basedmore » on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non -redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp, diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

  1. Phenotypic complexity and local variations in neutral degree.

    PubMed

    Lehre, Per Kristian; Haddow, Pauline C

    2007-02-01

    Neutrality is important in natural, molecular and artificial evolution. This work studies how local neutral degree varies over the genospace in a simple class of Lindenmayer-systems, and investigates whether this variation relates to Lempel-Ziv complexity of the phenotype. PMID:17188803

  2. Natural allelic variations in highly polyploidy Saccharum complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane (Saccharum spp.) as important sugar and biofuel crop are highly polypoid with complex genomes. A large amount of natural phenotypic variation exists in sugarcane germplasm. Understanding its allelic variance has been challenging but is a critical foundation for discovery of the genomic seq...

  3. 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.

  4. 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

  5. Kohn-Sham potentials for fullerenes and spherical molecules

    SciTech Connect

    Pavlyukh, Y.; Berakdar, J.

    2010-04-15

    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 C{sub 20}{sup 2+} and C{sub 60} 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.

  6. Decay of the Kohn mode in hydrodynamic regime

    NASA Astrophysics Data System (ADS)

    Iqbal, A.; Levchenko, A.; Khodas, M.

    2015-07-01

    We develop a hydrodynamic description of the collective modes of interacting liquids in a quasi-one-dimensional confining potential. By solving Navier-Stokes equation we determine analytically the excitation spectrum of sloshing oscillations. For parabolic confinement, the lowest frequency eigenmode is not renormalized by interactions and is protected from decay by the Kohn theorem, which states that center of mass motion decouples from internal dynamics. We find that the combined effect of potential anharmonicity and interactions results in a frequency shift and final lifetime of the Kohn mode. All other excited modes of sloshing oscillations thermalize with the parametrically faster rate. Our results are significant for the interpretation of recent experiments with trapped Fermi gases that observed a weak violation of the Kohn theorem.

  7. Second-order kinetic Kohn-Sham lattice model

    NASA Astrophysics Data System (ADS)

    Solórzano, S.; Mendoza, M.; Herrmann, H. J.

    2016-06-01

    In this work, we introduce a semi-implicit second-order correction scheme to the kinetic Kohn-Sham lattice model. This approach is validated by performing realistic exchange-correlation energy calculations of atoms and dimers of the first two rows of the Periodic Table, finding good agreement with the expected values. Additionally, we simulate the ethane molecule, where we recover the bond lengths and compare the results with standard methods. Finally, we discuss the current applicability of pseudopotentials within the lattice kinetic Kohn-Sham approach.

  8. 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.

  9. Schizophrenia risk from complex variation of complement component 4.

    PubMed

    Sekar, Aswin; Bialas, Allison R; de Rivera, Heather; Davis, Avery; Hammond, Timothy R; Kamitaki, Nolan; Tooley, Katherine; Presumey, Jessy; Baum, Matthew; Van Doren, Vanessa; Genovese, Giulio; Rose, Samuel A; Handsaker, Robert E; Daly, Mark J; Carroll, Michael C; Stevens, Beth; McCarroll, Steven A

    2016-02-11

    Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia's strongest genetic association at a population level involves variation in the major histocompatibility complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to identify. Here we show that this association arises in part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles generated widely varying levels of C4A and C4B expression in the brain, with each common C4 allele associating with schizophrenia in proportion to its tendency to generate greater expression of C4A. Human C4 protein localized to neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals with schizophrenia. PMID:26814963

  10. Schizophrenia risk from complex variation of complement component 4

    PubMed Central

    Sekar, Aswin; Bialas, Allison R.; de Rivera, Heather; Davis, Avery; Hammond, Timothy R.; Kamitaki, Nolan; Tooley, Katherine; Presumey, Jessy; Baum, Matthew; Van Doren, Vanessa; Genovese, Giulio; Rose, Samuel A.; Handsaker, Robert E.; Daly, Mark J.; Carroll, Michael C.; Stevens, Beth; McCarroll, Steven A.

    2016-01-01

    Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia’s strongest genetic association at a population level involves variation in the Major Histocompatibility Complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to recognize. We show here that schizophrenia’s association with the MHC locus arises in substantial part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles promoted widely varying levels of C4A and C4B expression and associated with schizophrenia in proportion to their tendency to promote greater expression of C4A in the brain. Human C4 protein localized at neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals affected with schizophrenia. PMID:26814963

  11. 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

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

    PubMed

    Jiang, Hong; Engel, Eberhard

    2005-12-01

    implicit correlation functional: The fundamental variational instability of this functional is recovered for beryllium, for which a breakdown of the self-consistent Kohn-Sham iteration is observed. Moreover, even for those atoms for which the self-consistent iteration is stable, the results indicate that the inclusion of v(c) (MP2) in the total Kohn-Sham potential does not lead to an improvement compared to the complete neglect of the correlation potential. PMID:16375465

  13. Structural genomic variation in childhood epilepsies with complex phenotypes

    PubMed Central

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

    2014-01-01

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

  14. 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.

  15. 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.

  16. A new relativistic scheme in Dirac Kohn Sham theory

    NASA Astrophysics Data System (ADS)

    Nakajima, Takahito; Suzumura, Toshihisa; Hirao, Kimihiko

    1999-04-01

    The relativistic scheme by the elimination of small components (RESC) of the four-component Dirac equation proposed previously has been incorporated into density functional theory (DFT). RESC-DFT results in a computationally efficient and numerically stable two-component Kohn-Sham formalism, suited for molecular applications. Illustrative calculations for AgH, AuH, AgCl, and AuCl have been performed employing various exchange-correlation functionals. A good agreement with experiment is obtained.

  17. 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)].

  18. 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.

  19. 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.

  20. 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)

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

    ERIC Educational Resources Information Center

    Rochester, J. Martin

    1998-01-01

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

  2. 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

  3. Variation in child health care utilization by medical complexity.

    PubMed

    Kuo, Dennis Z; Melguizo-Castro, Maria; Goudie, Anthony; Nick, Todd G; Robbins, James M; Casey, Patrick H

    2015-01-01

    Children with medical complexity (CMC) have multiple specialty need, technology dependence, and high health care utilization. The objective of this study is to profile types of pediatric health care utilization and costs by increasing levels of medical complexity. This is a cross-sectional study of the 2007, 2008 and 2009 Full-Year Data Sets from the Medical Expenditure Panel Survey. Medical complexity was defined by a higher number of positive items from the five question children with special health care needs (CSHCN) Screener. CMC were defined by ≥ 4 positive screener items. Outcomes included the number of inpatient, outpatient, and emergency department visits, associated costs and diagnoses, and reported satisfaction. ICD-9 codes were grouped by Clinical Classifications Software. Of 27,755 total study subjects ≤ 17 years, 4,851 had special needs and 541 were CMC. Older age, male gender, white/non-Hispanic race/ethnicity, and public insurance were all associated with medical complexity (all p < 0.001). CMC had an annual mean of 19 annual outpatient visits ($616) and 0.26 inpatient visits ($3,308), with other significant cost drivers including home health ($2,957) and prescriptions ($2,182). The most common reasons for non-CSHCN and less-complex CSHCN outpatient visits were viral illnesses, while the main reasons for CMC visits were for mental health. Compared to families without CSHCN, those with CMC have, on average, lower satisfaction with health care (8.4 vs. 8.9 out of 10, p < 0.001). Health care models for CMC should account for mental health conditions that may be driving high numbers of outpatient encounters. PMID:24740726

  4. Evaluating Long-Term Complex Professional Development: Using a Variation of the Cohort Control Design

    ERIC Educational Resources Information Center

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

    2010-01-01

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

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

    PubMed

    Ward, Lucas D; Kellis, Manolis

    2012-11-01

    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 mutations. This picture has changed with advances in the systematic annotation of functional noncoding elements. Evolutionary conservation, functional genomics, chromatin state, sequence motifs and molecular quantitative trait loci all provide complementary information about the function of noncoding sequences. These functional maps can help with prioritizing variants on risk haplotypes, filtering mutations encountered in the clinic and performing systems-level analyses to reveal processes underlying disease associations. Advances in predictive modeling can enable data-set 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

  6. Velocity form of the Kohn-Sham frequency-dependent polarizability equations

    SciTech Connect

    Bartolotti, L.J.

    1987-11-01

    A single equation is derived for the determination of the first-order correction to the frequency-dependent density, due to the perturbation of a time-varying electric field. This new expression for the first-order correction to the frequency-dependent Kohn-Sham amplitudes depends explicitly upon the velocity form of the dipole-moment operator and the square of the Kohn-Sham Hamiltonian.

  7. Tight-binding density functional theory: an approximate Kohn-Sham DFT scheme.

    PubMed

    Seifert, G

    2007-07-01

    The DFTB method is an approximate KS-DFT scheme with an LCAO representation of the KS orbitals, which can be derived within a variational treatment of an approximate KS energy functional. But it may also be related to cellular Wigner-Seitz methods and to the Harris functional. It is an approximate method, but it avoids any empirical parametrization by calculating the Hamiltonian and overlap matrices out of DFT-derived local orbitals (atomic orbitals, AO's). The method includes ab initio concepts in relating the Kohn-Sham orbitals of the atomic configuration to a minimal basis of the localized atomic valence orbitals of the atoms. Consistent with this approximation, the Hamiltonian matrix elements can strictly be restricted to a two-center representation. Taking advantage of the compensation of the so-called "double counting terms" and the nuclear repulsion energy in the DFT total energy expression, the energy may be approximated as a sum of the occupied KS single-particle energies and a repulsive energy, which can be obtained from DFT calculations in properly chosen reference systems. This relates the method to common standard "tight-binding" (TB) schemes, as they are well-known in solid-state physics. This approach defines the density-functional tight-binding (DFTB) method in its original (non-self-consistent) version. PMID:17439198

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

    PubMed

    Billeter, Salomon R; Egli, Daniel

    2006-12-14

    This paper generalizes the recently proposed approaches for calculating the derivative couplings between adiabatic states in density-functional theory (DFT) based on a Slater transition-state density to transitions such as singlet-singlet excitations, where a single-determinant ansatz is insufficient. The proposed approach is based on restricted open-shell Frank et al. [J. Chem. Phys. 108, 4060 (1998)] theory used to describe a spin-adapted Slater transition state. To treat the dependence of electron-electron interactions on the nuclear positions, variational linear-response density-functional perturbation theory is generalized to reference states with an orbital-dependent Kohn-Sham Hamiltonian and nontrivial occupation patterns. The methods proposed in this paper are not limited to the calculation of derivative coupling vectors, but can also be used for the calculation of other transition matrix elements. Moreover, they can be used to calculate the linear response of open-shell systems to arbitrary external perturbations in DFT. PMID:17176130

  9. On the Nature of Syntactic Variation: Evidence from Complex Predicates and Complex Word-Formation.

    ERIC Educational Resources Information Center

    Snyder, William

    2001-01-01

    Provides evidence from child language acquisition and comparative syntax for existence of a syntactic parameter in the classical sense of Chomsky (1981), with simultaneous effects on syntactic argument structure. Implications are that syntax is subject to points of substantive parametric variation as envisioned in Chomsky, and the time course of…

  10. A new view of transcriptome complexity and regulation through the lens of local splicing variations

    PubMed Central

    Vaquero-Garcia, Jorge; Barrera, Alejandro; Gazzara, Matthew R; González-Vallinas, Juan; Lahens, Nicholas F; Hogenesch, John B; Lynch, Kristen W; Barash, Yoseph

    2016-01-01

    Alternative splicing (AS) can critically affect gene function and disease, yet mapping splicing variations remains a challenge. Here, we propose a new approach to define and quantify mRNA splicing in units of local splicing variations (LSVs). LSVs capture previously defined types of alternative splicing as well as more complex transcript variations. Building the first genome wide map of LSVs from twelve mouse tissues, we find complex LSVs constitute over 30% of tissue dependent transcript variations and affect specific protein families. We show the prevalence of complex LSVs is conserved in humans and identify hundreds of LSVs that are specific to brain subregions or altered in Alzheimer's patients. Amongst those are novel isoforms in the Camk2 family and a novel poison exon in Ptbp1, a key splice factor in neurogenesis. We anticipate the approach presented here will advance the ability to relate tissue-specific splice variation to genetic variation, phenotype, and disease. DOI: http://dx.doi.org/10.7554/eLife.11752.001 PMID:26829591

  11. Resolution of identity Dirac-Kohn-Sham method using the large component only: Calculations of g-tensor and hyperfine tensor

    NASA Astrophysics Data System (ADS)

    Komorovský, Stanislav; Repiský, Michal; Malkina, Olga L.; Malkin, Vladimir G.; Malkin, Irina; Kaupp, Martin

    2006-02-01

    A new relativistic two-component density functional approach, based on the Dirac-Kohn-Sham method and an extensive use of the technique of resolution of identity (RI), has been developed and is termed the DKS2-RI method. It has been applied to relativistic calculations of g and hyperfine tensors of coinage-metal atoms and some mercury complexes. The DKS2-RI method solves the Dirac-Kohn-Sham equations in a two-component framework using explicitly a basis for the large component only, but it retains all contributions coming from the small component. The DKS2-RI results converge to those of the four-component Dirac-Kohn-Sham with an increasing basis set since the error associated with the use of RI will approach zero. The RI approximation provides a basis for a very efficient implementation by avoiding problems associated with complicated integrals otherwise arising from the elimination of the small component. The approach has been implemented in an unrestricted noncollinear two-component density functional framework. DKS2-RI is related to Dyall's [J. Chem. Phys. 106, 9618 (1997)] unnormalized elimination of the small component method (which was formulated at the Hartree-Fock level and applied to one-electron systems only), but it takes advantage of the local Kohn-Sham exchange-correlation operators (as, e.g., arising from local or gradient-corrected functionals). The DKS2-RI method provides an attractive alternative to existing approximate two-component methods with transformed Hamiltonians (such as Douglas-Kroll-Hess [Ann. Phys. 82, 89 (1974); Phys. Rev. A 33, 3742 (1986)] method, zero-order regular approximation, or related approaches) for relativistic calculations of the structure and properties of heavy-atom systems. In particular, no picture-change effects arise in the property calculations.

  12. 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

  13. Projection potentials and angular momentum convergence of total energies in the full-potential Korringa-Kohn-Rostoker method.

    PubMed

    Zeller, Rudolf

    2013-03-13

    Although the full-potential Korringa-Kohn-Rostoker Green function method yields accurate results for many physical properties, the convergence of calculated total energies with respect to the angular momentum cutoff is usually considered to be less satisfactory. This is surprising because accurate single-particle energies are expected if they are calculated by Lloyd's formula and because accurate densities and hence accurate double-counting energies should result from the total energy variational principle. It is shown how the concept of projection potentials can be used as a tool to analyse the convergence behaviour. The key factor blocking fast convergence is identified and it is illustrated how total energies can be improved with only a modest increase of computing time. PMID:23396831

  14. 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

  15. Genetic Variation of Major Histocompatibility Complex and Microsatellite Loci: A Comparison in Bighorn Sheep

    PubMed Central

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

    1997-01-01

    Examining and comparing genetic variation for major histocompatibility complex (MHC) and microsatellite (MS) loci in the same individuals provides an opportunity to understand the forces influencing genetic variation. We examined five MHC and three MS loci in 235 bighorn sheep (Ovis canadensis) from 14 populations and found that both types of loci were highly variable and were in Hardy-Weinberg proportions. Mean F(ST) values for both markers were very similar and MHC and MS genetic variability was predominantly distributed within rather than among populations. However, analyses of genetic distances and tree topologies revealed different spatial patterns of variation for the two types of loci. Collectively, these results indicated that neutral forces substantially influenced MS and MHC variation, and they provided limited evidence for selection acting on the MHC. PMID:9071595

  16. Functional and architectural complexity within and between muscles: regional variation and intermuscular force transmission

    PubMed Central

    Higham, Timothy E.; Biewener, Andrew A.

    2011-01-01

    Over the past 30 years, studies of single muscles have revealed complex patterns of regional variation in muscle architecture, activation, strain and force. In addition, muscles are often functionally integrated with other muscles in parallel or in series. Understanding the extent of this complexity and the interactions between muscles will profoundly influence how we think of muscles in relation to organismal function, and will allow us to address questions regarding the functional benefits (or lack thereof) and dynamics of this complexity under in vivo conditions. This paper has two main objectives. First, we present a cohesive and integrative review of regional variation in function within muscles, and discuss the functional ramifications that can stem from this variation. This involves splitting regional variation into passive and active components. Second, we assess the functional integration of muscles between different limb segments by presenting new data involving in vivo measurements of activation and strain from the medial gastrocnemius, iliotibialis cranialis and iliotibialis lateralis pars preacetabularis of the helmeted guinea fowl (Numida meleagris) during level running on a motorized treadmill. Future research directions for both of these objectives are presented. PMID:21502119

  17. Cytogeography and genome size variation in the Claytonia perfoliata (Portulacaceae) polyploid complex

    PubMed Central

    McIntyre, Patrick J.

    2012-01-01

    Background and Aims Genome duplication is a central process in plant evolution and contributes to patterns of variation in genome size within and among lineages. Studies that combine cytogeography with genome size measurements contribute to our basic knowledge of cytotype distributions and their associations with variation in genome size. Methods Ploidy and genome size were assessed with direct chromosome counts and flow cytometry for 78 populations within the Claytonia perfoliata complex, comprised of three diploid taxa with numerous polyploids that range to the decaploid level. The relationship between genome size and temperature and precipitation was investigated within and across cytotypes to test for associations between environmental factors and nuclear DNA content. Key Results A euploid series (n = 6) of diploids to octoploids was documented through chromosome counts, and decaploids were suggested by flow cytometry. Increased variation in genome size among populations was found at higher ploidy levels, potentially associated with differential contributions of diploid parental genomes, variation in rates of genomic loss or gain, or undetected hybridization. Several accessions were detected with atypical genome sizes, including a diploid population of C. parviflora ssp. grandiflora with an 18 % smaller genome than typical, and hexaploids of C. perfoliata and C. parviflora with genomes 30 % larger than typical. There was a slight but significant association of larger genome sizes with colder winter temperature across the C. perfoliata complex as a whole, and a strong association between lower winter temperatures and large genome size for tetraploid C. parviflora. Conclusions The C. perfoliata complex is characterized by polyploids ranging from tetraploid to decaploid, with large magnitude variation in genome size at higher ploidy levels, associated in part with environmental variation in temperature. PMID:22962302

  18. Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus).

    PubMed

    Jaeger, Collin P; Duvall, Melvin R; Swanson, Bradley J; Phillips, Christopher A; Dreslik, Michael J; Baker, Sarah J; King, Richard B

    2016-06-01

    Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations. PMID:27516858

  19. 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.

  20. SANS with contrast variation study of the bacteriorhodopsin-octyl glucoside complex

    NASA Astrophysics Data System (ADS)

    Mo, Yiming; Heller, William T.

    2010-11-01

    Membrane proteins (MPs), which play vital roles in trans-membrane trafficking and signalling 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.

  1. 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.

  2. 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

  3. Corrections to the Kohn-Luttinger wave function for donors in silicon

    NASA Astrophysics Data System (ADS)

    Castner, T. G., Jr.

    2008-05-01

    Corrections to the Kohn-Luttinger ground state wave function from subsidiary minima are calculated using first order perturbation theory and a variational approach. The very precise Fermi contact constants ahpf(Rnmm) of the Hale-Mieher data determine a set of linear equations based on donor-dependent ratios such as ∣ψd(333&barbelow;)∣/∣ψd(115)∣=Kd=[ahpf(333&barbelow;)/ahpf(115)]1/2 . The minima considered [ L1(cb1) , Γ2'(cb4) , Σ(cb5) , ΓW(cb2) , Δ2'(cb5) , and XU(cb2) ] are each characterized by an A(k-kj) , a phase eikjṡr and envelope functions Fαj (α=x,y,z) . The ψd employed contains four terms not included in the comprehensive Ivey-Mieher (IM) calculation with pseudopotential Bloch functions for eight bands. Two terms arise from the crucial tetrahedral potential Ut∝xyzf(r) ignored in most earlier work. The admixture coefficients are varied subject to the three constraint equations to minimize the mean-squared deviations of the calculated and experimental ahpf(nnm) of the 11 odd sites identified by IM. The results are not only vastly improved (compared to IM) for site (111) but also reverse the IM assignments for (331) and (551). Some of the inverted donor anomalies are explained. The average root-mean-squared deviation ⟨rmsd⟩ for the 11 sites is better than the IM results for these odd sites. The results suggest that additional changes in the zeroth order ψKL may be required to improve the overall agreement. The uniaxial stress parameters id and 2f/a(0) are also reconsidered with some of the new corrections and compared with experimental values.

  4. Alternative to the Kohn-Sham equations: The Pauli potential differential equation

    NASA Astrophysics Data System (ADS)

    Levämäki, H.; Nagy, Á.; Kokko, K.; Vitos, L.

    2015-12-01

    A recently developed theoretical framework of performing self-consistent orbital-free (OF) density functional theory (DFT) calculations at Kohn-Sham DFT level accuracy is tested in practice. The framework is valid for spherically symmetric systems. Numerical results for the Beryllium atom are presented and compared to accurate Kohn-Sham data. These calculations make use of a differential equation that we have developed for the so called Pauli potential, a key quantity in OF-DFT. The Pauli potential differential equation and the OF Euler equation form a system of two coupled differential equations, which have to be solved simultaneously within the DFT self-consistent loop.

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

    PubMed Central

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

    2010-01-01

    Objective This study was intended to examine variations in electroencephalographic (EEG) complexity in response to photic stimulation (PS) during aging to test the hypothesis that the aging process reduces physiologic complexity and functional responsiveness. Methods Multiscale entropy (MSE), an estimate of time-series signal complexity associated with long-range temporal correlation, is used as a recently proposed method for quantifying EEG complexity with multiple coarse-grained sequences. We recorded EEG in 13 healthy elderly subjects and 12 healthy young subjects during pre-PS and post-PS conditions and estimated their respective MSE values. Results For the pre-PS condition, no significant complexity difference was found between the groups. However, a significant MSE change (complexity increase) was found post-PS only in young subjects, thereby revealing a power-law scaling property, which means long-range temporal correlation. Conclusions Enhancement of long-range temporal correlation in young subjects after PS might reflect a cortical response to stimuli, which was absent in elderly subjects. These results are consistent with the general “loss of complexity/diminished functional response to stimuli” theory of aging. Significance Our findings demonstrate that application of MSE analysis to EEG is a powerful approach for studying age-related changes in brain function. PMID:19231279

  6. 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…

  7. Time-dependent density functional theory beyond Kohn-Sham Slater determinants.

    PubMed

    Fuks, Johanna I; Nielsen, Søren E B; Ruggenthaler, Michael; Maitra, Neepa T

    2016-08-01

    When running time-dependent density functional theory (TDDFT) calculations for real-time simulations of non-equilibrium dynamics, the user has a choice of initial Kohn-Sham state, and typically a Slater determinant is used. We explore the impact of this choice on the exchange-correlation potential when the physical system begins in a 50 : 50 superposition of the ground and first-excited state of the system. We investigate the possibility of judiciously choosing a Kohn-Sham initial state that minimizes errors when adiabatic functionals are used. We find that if the Kohn-Sham state is chosen to have a configuration matching the one that dominates the interacting state, this can be achieved for a finite time duration for some but not all such choices. When the Kohn-Sham system does not begin in a Slater determinant, we further argue that the conventional splitting of the exchange-correlation potential into exchange and correlation parts has limited value, and instead propose a decomposition into a "single-particle" contribution that we denote v, and a remainder. The single-particle contribution can be readily computed as an explicit orbital-functional, reduces to exchange in the Slater determinant case, and offers an alternative to the adiabatic approximation as a starting point for TDDFT approximations. PMID:27010732

  8. The Effects of Occupational Conditions upon the Division of Household Labor: An Application of Kohn's Theory.

    ERIC Educational Resources Information Center

    Seccombe, Karen

    1986-01-01

    Tested Kohn's theory that people who work in highly supervised, routinized occupations are likely to value obedience and conformity in marital and parental relationships. Findings from 244 couples revealed that working conditions were not strong predictors of division of household labor. Concludes that nontraditional gender role values,…

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

    SciTech Connect

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

    2004-04-23

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

  10. 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

  11. 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.

  12. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

    PubMed Central

    Jin, Minliang; Liu, Haijun; He, Cheng; Fu, Junjie; Xiao, Yingjie; Wang, Yuebin; Xie, Weibo; Wang, Guoying; Yan, Jianbing

    2016-01-01

    Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding. PMID:26729541

  13. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation.

    PubMed

    Jin, Minliang; Liu, Haijun; He, Cheng; Fu, Junjie; Xiao, Yingjie; Wang, Yuebin; Xie, Weibo; Wang, Guoying; Yan, Jianbing

    2016-01-01

    Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as "genotype" to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding. PMID:26729541

  14. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations.

    PubMed

    Trotter, Meredith V; Weissman, Daniel B; Peterson, Grant I; Peck, Kayla M; Masel, Joanna

    2014-12-01

    The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations. PMID:25178652

  15. Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome.

    PubMed

    McCall, Matthew N; Illei, Peter B; Halushka, Marc K

    2016-09-01

    The sources of gene expression variability in human tissues are thought to be a complex interplay of technical, compositional, and disease-related factors. To better understand these contributions, we investigated expression variability in a relatively homogeneous tissue expression dataset from the Genotype-Tissue Expression (GTEx) resource. In addition to identifying technical sources, such as sequencing date and post-mortem interval, we also identified several biological sources of variation. An in-depth analysis of the 175 genes with the greatest variation among 133 lung tissue samples identified five distinct clusters of highly correlated genes. One large cluster included surfactant genes (SFTPA1, SFTPA2, and SFTPC), which are expressed exclusively in type II pneumocytes, cells that proliferate in ventilator associated lung injury. High surfactant expression was strongly associated with death on a ventilator and type II pneumocyte hyperplasia. A second large cluster included dynein (DNAH9 and DNAH12) and mucin (MUC5B and MUC16) genes, which are exclusive to the respiratory epithelium and goblet cells of bronchial structures. This indicates heterogeneous bronchiole sampling due to the harvesting location in the lung. A small cluster included acute-phase reactant genes (SAA1, SAA2, and SAA2-SAA4). The final two small clusters were technical and gender related. To summarize, in a collection of normal lung samples, we found that tissue heterogeneity caused by harvesting location (medial or lateral lung) and late therapeutic intervention (mechanical ventilation) were major contributors to expression variation. These unexpected sources of variation were the result of altered cell ratios in the tissue samples, an underappreciated source of expression variation. PMID:27588449

  16. Variation in complex olfactory stimuli and its influence on odour recognition.

    PubMed Central

    Wrigh, Geraldine A.; Smith, Brian H.

    2004-01-01

    Natural olfactory stimuli are often complex and highly variable. The olfactory systems of animals are likely to have evolved to use specific features of olfactory stimuli for identification and discrimination. Here, we train honeybees to learn chemically defined odorant mixtures that systematically vary from trial to trial and then examine how they generalize to each odorant present in the mixture. An odorant that was present at a constant concentration in a mixture becomes more representative of the mixture than other variable odorants. We also show that both variation and intensity of a complex olfactory stimulus affect the rate of generalization by honeybees to subsequent olfactory stimuli. These results have implications for the way that all animals perceive and attend to features of olfactory stimuli. PMID:15058390

  17. An Algorithm for Inferring Complex Haplotypes in a Region of Copy-Number Variation

    PubMed Central

    Kato, Mamoru; Nakamura, Yusuke; Tsunoda, Tatsuhiko

    2008-01-01

    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

  18. Variational regularization of complex deautoconvolution and phase retrieval in ultrashort laser pulse characterization

    NASA Astrophysics Data System (ADS)

    Anzengruber, Stephan W.; Bürger, Steven; Hofmann, Bernd; Steinmeyer, Günter

    2016-03-01

    The SD-SPIDER method for the characterization of ultrashort laser pulses requires the solution of a nonlinear integral equation of autoconvolution type with a device-based kernel function. Taking into account the analytical background of a variational regularization approach for solving the corresponding ill-posed operator equation formulated in complex-valued L 2-spaces over finite real intervals, we suggest and evaluate numerical procedures using NURBS and the TIGRA method for calculating the regularized solutions in a stable manner. In this context, besides the complex deautoconvolution problem with noisy but full data, a phase retrieval problem is introduced which adapts to the experimental state of the art in laser optics. For the treatment of this problem facet, which is formulated as a tensor product operator equation, we derive the well-posedness of variational regularization methods. Case studies with synthetic and real optical data show the capability of the implemented approach as well as its limitations due to measurement deficits.

  19. Model Organisms Retain an “Ecological Memory” of Complex Ecologically Relevant Environmental Variation

    PubMed Central

    Beer, Karlyn D.; Wurtmann, Elisabeth J.; Pinel, Nicolás

    2014-01-01

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

  20. 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

  1. Phase diagram of the Kohn-Luttinger superconducting state for bilayer graphene

    NASA Astrophysics Data System (ADS)

    Kagan, Maxim Yu.; Mitskan, Vitaly A.; Korovushkin, Maxim M.

    2015-06-01

    The effect of Coulomb interaction between Dirac fermions on the formation of the Kohn-Luttinger superconducting state in bilayer doped graphene is studied disregarding of the effect of the van der Waals potential of the substrate and impurities. The phase diagram determining the boundaries of superconductive domains with different types of symmetry of the order parameter is built using the extended Hubbard model in the Born weak-coupling approximation with allowance for the intratomic, interatomic, and interlayer Coulomb interactions between electrons. It is shown that the Kohn-Luttinger polarization contributions up to the second order of perturbation theory in the Coulomb interaction inclusively and an account for the long-range intraplane Coulomb interactions significantly affect the competition between the superconducting phases with the f-, p + ip-, and d + id-wave symmetries of the order parameter. It is demonstrated that the account for the interlayer Coulomb interaction enhances the critical temperature of the transition to the superconducting phase.

  2. Collective mode formulation of the response algorithm for solving Kohn-Sham equations

    NASA Astrophysics Data System (ADS)

    Auer, J.; Krotscheck, E.

    2003-04-01

    We have developed a "collective mode" version of the response-iteration algorithm for solving the nonlinear Kohn-Sham equations. The algorithm utilizes approximation methods for the density-density response function that are known from microscopic many-body theories of strongly interacting Fermi systems. The major advantage over our previously proposed algorithm (J. Auer and E. Krotscheck, Comput. Phys. Comm. 118 (1999) 139-144) is that the new method needs the computation of occupied states only. Using spherical jellium clusters with up to 2000 electrons as an example, we show that the approximations implicit to our new algorithms do not deteriorate the convergence rate. An even simpler version approximates the density-density response function by that of a charged bose gas with the same density. This algorithm converges somewhat more slowly, but still provides a viable method for solving Kohn-Sham equations for small clusters.

  3. 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

  4. Development of Core Complex Domes Due to Along-Axis Variation in Diking

    NASA Astrophysics Data System (ADS)

    Buck, W. R.; Choi, E.; Tian, X.

    2014-12-01

    Continental and oceanic core complexes are characterized by fairly smooth, unfaulted, but corrugated surfaces of high grade rocks often domed both along and orthogonal to the transport direction. The corrugations, or mega-mullions, are remarkably continuous in the transport direction and may be tens of kilometers long. Spencer [1999] suggests that corrugations with across-transport wavelengths of millimeter to ~25 km scales are formed when the lower plate of a large-offset normal fault is "continuously cast," as warm, ductile mantle and gabbro is pulled up against the cooler upper plate. Continuous casting is widely accepted as a mechanism to form the shorter wavelength corrugations as a result of irregularities of the brittle upper plate surface. However, doming is generally ascribed to upflow of buoyant diapirs or transtensional deformation of the lithosphere. We suggest that doming of core complexes can be a product of continuous casting when a large-offset fault evolves to be curved in plan-view. For oceanic core complexes along-axis variation in magmatism can lead to lateral offset of a detachment fault relative to the spreading axis. We assume that near-ridge normal faults form relatively straight and consider that horizontal offsets in the along-axis position of a large-offset fault (or detachment) result from variations in the rate of magmatic diking. Assuming a sinusoidal variation in the rate of dike opening with distance along the axis the evolution of fault offset and the plan-view shape of the active fault is easy to describe. Because the fault length increases as it is offset, the work to slip on the fault increases with time. Eventually, it should be easier to slip in a new straight fault and the conditions for this can be described with an approximate analytic model. We are developing 3D numerical models to test the predictions of this analytic model and show how the topographic amplitude of the domes depends the fault dip, the amplitude of the

  5. 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.

  6. Emergence of an Out-of-Plane Optical Phonon (ZO) Kohn Anomaly in Quasifreestanding Epitaxial Graphene.

    PubMed

    Politano, Antonio; de Juan, Fernando; Chiarello, Gennaro; Fertig, Herbert A

    2015-08-14

    In neutral graphene, two prominent cusps known as Kohn anomalies are found in the phonon dispersion of the highest optical phonon at q=Γ (LO branch) and q=K (TO branch), reflecting a significant electron-phonon coupling (EPC) to undoped Dirac electrons. In this work, high-resolution electron energy loss spectroscopy is used to measure the phonon dispersion around the Γ point in quasifreestanding graphene epitaxially grown on Pt(111). The Kohn anomaly for the LO phonon is observed at finite momentum q~2k_{F} from Γ, with a shape in excellent agreement with the theory and consistent with known values of the EPC and the Fermi level. More strikingly, we also observe a Kohn anomaly at the same momentum for the out-of-plane optical phonon (ZO) branch. This observation is the first direct evidence of the coupling of the ZO mode with Dirac electrons, which is forbidden for freestanding graphene but becomes allowed in the presence of a substrate. Moreover, we estimate the EPC to be even greater than that of the LO mode, making graphene on Pt(111) an optimal system to explore the effects of this new coupling in the electronic properties. PMID:26317732

  7. ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order

    NASA Astrophysics Data System (ADS)

    Verstraelen, T.; Ayers, P. W.; Van Speybroeck, V.; Waroquier, M.

    2013-02-01

    A new polarizable force field (PFF), namely atom-condensed Kohn-Sham density functional theory approximated to second order (ACKS2), is proposed for the efficient computation of atomic charges and linear response properties of extended molecular systems. It is derived from Kohn-Sham density functional theory (KS-DFT), making use of two novel ingredients in the context of PFFs: (i) constrained atomic populations and (ii) the Legendre transform of the Kohn-Sham kinetic energy. ACKS2 is essentially an extension of the Electronegativity Equalization Method (EEM) [W. J. Mortier, S. K. Ghosh, and S. Shankar, J. Am. Chem. Soc. 108, 4315 (1986)], 10.1021/ja00275a013 in which two major EEM shortcomings are fixed: ACKS2 predicts a linear size-dependence of the dipole polarizability in the macroscopic limit and correctly describes the charge distribution when a molecule dissociates. All ACKS2 parameters are defined as atoms-in-molecules expectation values. The implementation of ACKS2 is very similar to that of EEM, with only a small increase in computational cost.

  8. Uniaxial strain-induced Kohn anomaly and electron-phonon coupling in acoustic phonons of graphene

    NASA Astrophysics Data System (ADS)

    Cifuentes-Quintal, M. E.; de la Peña-Seaman, O.; Heid, R.; de Coss, R.; Bohnen, K.-P.

    2016-08-01

    Recent advances in strain engineering at the nanoscale have shown the feasibility to modulate the properties of graphene. Although the electron-phonon (e-ph) coupling and Kohn anomalies in graphene define the phonon branches contributing to the resonance Raman scattering and are relevant to the electronic and thermal transport as a scattering source, the evolution of the e-ph coupling as a function of strain has been less studied. In this work, the Kohn anomalies and the e-ph coupling in uniaxially strained graphene along armchair and zigzag directions were studied by means of density functional perturbation theory calculations. In addition to the phonon anomaly at the transversal optical (TO) phonon branch in the K point for pristine graphene, we found that uniaxial strain induces a discontinuity in the frequency derivative of the longitudinal acoustic phonon branch. This behavior corresponds to the emergence of a Kohn anomaly, as a consequence of a strain-enhanced e-ph coupling. Thus, the present results for uniaxially strained graphene contrast with the commonly assumed view that the e-ph coupling around the K point is only present in the TO phonon branch.

  9. Genetic specificity of a plant-insect food web: Implications for linking genetic variation to network complexity.

    PubMed

    Barbour, Matthew A; Fortuna, Miguel A; Bascompte, Jordi; Nicholson, Joshua R; Julkunen-Tiitto, Riitta; Jules, Erik S; Crutsinger, Gregory M

    2016-02-23

    Theory predicts that intraspecific genetic variation can increase the complexity of an ecological network. To date, however, we are lacking empirical knowledge of the extent to which genetic variation determines the assembly of ecological networks, as well as how the gain or loss of genetic variation will affect network structure. To address this knowledge gap, we used a common garden experiment to quantify the extent to which heritable trait variation in a host plant determines the assembly of its associated insect food web (network of trophic interactions). We then used a resampling procedure to simulate the additive effects of genetic variation on overall food-web complexity. We found that trait variation among host-plant genotypes was associated with resistance to insect herbivores, which indirectly affected interactions between herbivores and their insect parasitoids. Direct and indirect genetic effects resulted in distinct compositions of trophic interactions associated with each host-plant genotype. Moreover, our simulations suggest that food-web complexity would increase by 20% over the range of genetic variation in the experimental population of host plants. Taken together, our results indicate that intraspecific genetic variation can play a key role in structuring ecological networks, which may in turn affect network persistence. PMID:26858398

  10. Excitation Energies from Real-Time Propagation of the Four-Component Dirac-Kohn-Sham Equation.

    PubMed

    Repisky, Michal; Konecny, Lukas; Kadek, Marius; Komorovsky, Stanislav; Malkin, Olga L; Malkin, Vladimir G; Ruud, Kenneth

    2015-03-10

    We report the first implementation of real-time time-dependent density functional theory (RT-TDDFT) at the relativistic four-component level of theory. In contrast to the perturbative linear-response TDDFT approach (LR-TDDFT), the RT-TDDFT approach performs an explicit time propagation of the Dirac-Kohn-Sham density matrix, offering the possibility to simulate molecular spectroscopies involving strong electromagnetic fields while, at the same time, treating relativistic scalar and spin-orbit corrections variationally. The implementation is based on the matrix representation of the Dirac-Coulomb Hamiltonian in the basis of restricted kinetically balanced Gaussian-type functions, exploiting the noncollinear Kramers unrestricted formalism implemented in the program ReSpect. We also present an analytic form for the delta-type impulse commonly used in RT-TDDFT calculations, as well as a dipole-weighted transition matrix analysis, facilitating the interpretation of spectral transitions in terms of ground-state molecular orbitals. The possibilities offered by the methodology are illustrated by investigating vertical excitation energies and oscillator strengths for ground-state to excited-state transitions in the Group 12 atoms and in heavy-element hydrides. The accuracy of the method is assessed by comparing the excitation energies obtained with earlier relativistic linear response TDDFT results and available experimental data. PMID:26579752

  11. Sequence variation at the major histocompatibility complex locus DQ beta in beluga whales (Delphinapterus leucas)

    PubMed

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

    1995-07-01

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

  12. 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

  13. Variations in duodenal cross-sectional area during the interdigestive migrating motility complex.

    PubMed

    Gregersen, H; Kraglund, K; Djurhuus, J C

    1990-07-01

    A probe for measurement of intestinal cross-sectional area (CA) was used to elucidate variations of human gut CA during the interdigestive migrating motility complex (MMC). A balloon was inflated by saline at a pressure of 1 kPa, and variations of balloon CA (BCSA) were measured by means of the field-gradient principle. Duodenal phasic activity was measured by perfused side holes proximal to, distal to, and inside the balloon. In vitro characterization of probe performance showed that static measurement of BCSA was very accurate regardless of the configuration of the balloon. However, during dynamic measurements, BCSA was valid only for slow variations in BCSA due to resistance in the evacuation and inflation system. Eight duodenal MMCs were recorded. BCSA increased consistently from the start of phase I to the end of phase II from 72 (45-100) to 136 (87-154) mm2. During late phase II, a large BCSA increase was recorded. A positive correlation between the phasic activity level in phases I and II of MMC and maximal BCSA in duodenum was demonstrated (proximal P less than 0.01; distal P less than 0.05). BCSA during phase III was small but could not be estimated accurately because steady-state conditions were not obtained. The large BCSA in late phase II suggests a relaxation of the duodenal wall secondary to a decrease in smooth muscle tone. The results add evidence to previous findings of a low-resistance or large-capacitance situation in late phase II, observed as a large pancreaticobiliary excretion into the duodenum and an increased flow of duodenal contents. PMID:2372063

  14. 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

  15. Genetic variation of major histocompatibility complex (MHC) in wild Red Junglefowl (Gallus gallus).

    PubMed

    Nguyen-Phuc, Hoa; Fulton, Janet E; Berres, Mark E

    2016-02-01

    The major histocompatibility complex (MHC) is a multi-family gene cluster that encodes proteins with immuno-responsive function. While studies of MHC in domesticated poultry are relatively common, very little is known about this highly polymorphic locus in wild Red Junglefowl (Gallus gallus), the natural progenitor of domestic chickens. We investigated the diversity of MHC within and among four wild Red Junglefowl populations across diversified natural habitats in South Central Vietnam. Based on a SNP panel of 84 sites spanning 210 Kb of the MHC-B locus, we identified 310 unique haplotypes in 398 chromosomes. None of these haplotypes have been described before and we did not observe any of the wild Red Junglefowl haplotypes in domesticated chickens. Analysis of molecular variance (AMOVA) revealed that 94.51% of observed haplotype variation was accounted for at the within individual level. Little genetic variance was apportioned within and among populations, the latter accounting only for 0.83%. We also found evidence of increased recombination, including numerous hotspots, and limited linkage disequilibrium among the 84 SNP sites. Compared to an average haplotype diversity of 3.55% among seventeen lines of domestic chickens, our results suggest extraordinarily high haplotype diversity remains in wild Red Junglefowl and is consistent with a pattern of balancing selection. Wild Red Junglefowl in Vietnam, therefore, represent a rich resource of natural genomic variation independent from artificial selection. PMID:26839415

  16. The Fine-Scale and Complex Architecture of Human Copy-Number Variation

    PubMed Central

    Perry, George H.; Ben-Dor, Amir; Tsalenko, Anya; Sampas, Nick; Rodriguez-Revenga, Laia; Tran, Charles W.; Scheffer, Alicia; Steinfeld, Israel; Tsang, Peter; Yamada, N. Alice; Park, Han Soo; Kim, Jong-Il; Seo, Jeong-Sun; Yakhini, Zohar; Laderman, Stephen; Bruhn, Laurakay; Lee, Charles

    2008-01-01

    Despite considerable excitement over the potential functional significance of copy-number variants (CNVs), we still lack knowledge of the fine-scale architecture of the large majority of CNV regions in the human genome. In this study, we used a high-resolution array-based comparative genomic hybridization (aCGH) platform that targeted known CNV regions of the human genome at approximately 1 kb resolution to interrogate the genomic DNAs of 30 individuals from four HapMap populations. Our results revealed that 1020 of 1153 CNV loci (88%) were actually smaller in size than what is recorded in the Database of Genomic Variants based on previously published studies. A reduction in size of more than 50% was observed for 876 CNV regions (76%). We conclude that the total genomic content of currently known common human CNVs is likely smaller than previously thought. In addition, approximately 8% of the CNV regions observed in multiple individuals exhibited genomic architectural complexity in the form of smaller CNVs within larger ones and CNVs with interindividual variation in breakpoints. Future association studies that aim to capture the potential influences of CNVs on disease phenotypes will need to consider how to best ascertain this previously uncharacterized complexity. PMID:18304495

  17. Diploptene δ13C values from contemporary thermokarst lake sediments show complex spatial variation

    NASA Astrophysics Data System (ADS)

    Davies, Kimberley L.; Pancost, Richard D.; Edwards, Mary E.; Anthony, Katey M. Walter; Langdon, Peter G.; Chaves Torres, Lidia

    2016-05-01

    Cryospheric changes in northern high latitudes are linked to significant greenhouse gas flux to the atmosphere, for example, methane that originates from organic matter decomposition in thermokarst lakes. The set of pathways that link methane production in sediments, via oxidation in the lake system, to the flux of residual methane to the atmosphere is complex and exhibits temporal and spatial variation. The isotopic signal of bacterial biomarkers (hopanoids, e.g. diploptene) in sediments has been used to identify contemporary ocean-floor methane seeps and, in the geological record, periods of enhanced methane production (e.g. the PETM). The biomarker approach could potentially be used to assess temporal changes in lake emissions through the Holocene via the sedimentary biomarker record. However, there are no data on the consistency of the signal of isotopic depletion in relation to source or on the amount of noise (unexplained variation) in biomarker values from modern lake sediments. We assessed methane oxidation as represented by the isotopic signal of biomarkers from methane oxidising bacteria (MOB) in multiple surface sediment samples in three distinct areas known to emit varying levels of methane in two shallow Alaskan thermokarst lakes. Diploptene was present and had δ13C values lower than -38 ‰ in all sediments analysed, suggesting methane oxidation was widespread. However, there was considerable variation in δ13C values within each area. The most 13C-depleted diploptene was found in an area of high methane ebullition in Ace Lake (diploptene δ13C values between -68.2 and -50.1 ‰). In contrast, significantly higher diploptene δ13C values (between -42.9 and -38.8 ‰) were found in an area of methane ebullition in Smith Lake. δ13C values of diploptene between -56.8 and -46.9 ‰ were found in the centre of Smith Lake, where ebullition rates are low but diffusive methane efflux occurs. The small-scale heterogeneity of the samples may reflect patchy

  18. Uncinate Process Variations and Their Relationship with Ostiomeatal Complex: A Pictorial Essay of Multidedector Computed Tomography (MDCT) Findings.

    PubMed

    Güngör, Gülay; Okur, Nazan; Okur, Erdoğan

    2016-01-01

    The ostiomeatal complex (OMC) is a key area for the drainage and ventilation of the paranasal sinuses. Stenosis created by inflammation and anatomic variations in this region causes an ideal ground for parasanal sinus infections, by preventing the drainage and ventilation of the sinuses. In today's diagnostics of paranasal sinus infections, the role of evaluation of OMC anatomical variations and soft tissue pathology has increased.. Knowing the anatomical details is important in terms of directing both medical and surgical treatment. The uncinate process (UP) constitutes the most important structure of the ostiomeatal complex, playing a role in mucociliary activity. UP variations can cause mucociliary drainage and ventilation problems, causing complications during surgery. Therefore, knowing and identifying their appearances in multidetector computed tomography (MDCT), the most frequently used radiological imaging method for these variations, becomes a very important consideration. PMID:27158282

  19. Uncinate Process Variations and Their Relationship with Ostiomeatal Complex: A Pictorial Essay of Multidedector Computed Tomography (MDCT) Findings

    PubMed Central

    Güngör, Gülay; Okur, Nazan; Okur, Erdoğan

    2016-01-01

    Summary The ostiomeatal complex (OMC) is a key area for the drainage and ventilation of the paranasal sinuses. Stenosis created by inflammation and anatomic variations in this region causes an ideal ground for parasanal sinus infections, by preventing the drainage and ventilation of the sinuses. In today’s diagnostics of paranasal sinus infections, the role of evaluation of OMC anatomical variations and soft tissue pathology has increased.. Knowing the anatomical details is important in terms of directing both medical and surgical treatment. The uncinate process (UP) constitutes the most important structure of the ostiomeatal complex, playing a role in mucociliary activity. UP variations can cause mucociliary drainage and ventilation problems, causing complications during surgery. Therefore, knowing and identifying their appearances in multidetector computed tomography (MDCT), the most frequently used radiological imaging method for these variations, becomes a very important consideration. PMID:27158282

  20. 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.

  1. O the Topological Complexity of the Cost Function in Variational Data Assimilation

    NASA Astrophysics Data System (ADS)

    Li, Yong

    We investigate here the causes and implications of topological complexity in the cost function in the context of the variational data assimilation. This complexity, which can take many forms from multiple minima to very flat regions with almost no curvature, causes severe problems for minimization algorithms and can lead to a retrieved state that is strongly related to the initial guess, i.e., non-uniqueness. To determine the origin of multiple minima, we first utilize guess, simple dynamical systems: the chaotic logistic equation, Duffing's equation, and Burgers equation. We demonstrate that multiple minima are associated with nonlinear dynamics, and that the length of the assimilation window and data availability also exert a strong influence over the topology of the cost function. This finding is validated for the somewhat more complicated resonant Rossby wave model. Having established the principal causes of topological complexity in the cost function, we extend our work to the convective regime by performing retrievals using simulated data from a 3-D Boussinesq model and its adjoint. We find that the complexity of the cost function is not as serious a problem as shown in the simple nonlinear systems. Only in an extreme case, where the first guess is chosen to differ substantially from the true solution, does the retrieved state depart from the control, and even then it does so only superficially. This result could be due to the high dimensionality (i.e., greater degrees of freedom) of the Boussinesq flow. By including a penalty term, consisting of second-order temporal derivatives of the model state variables, the cost function is regularized and an improved retrieval is obtained. Such a penalty term can also improve the conditioning of the Hessian and thus the efficiency of the minimization process. The role of diffusion in data retrieval is also examined, and a linear analysis based on the one-dimensional diffusion equation shows that the retrieved initial

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    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

  3. Natural Variation for Carbohydrate Content in Arabidopsis. Interaction with Complex Traits Dissected by Quantitative Genetics1

    PubMed Central

    Calenge, Fanny; Saliba-Colombani, Véra; Mahieu, Stéphanie; Loudet, Olivier; Daniel-Vedele, Françoise; Krapp, Anne

    2006-01-01

    Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 × Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci. A major QTL for fructose content (FR3.4) and a QTL for starch content (ST3.4) were confirmed in heterogeneous inbred families. Several genes associated with carbon (C) metabolism colocalize with the identified QTL. QTLs for senescence-related traits, and for flowering time, water status, and nitrogen-related traits, previously detected with the same genetic material, colocalize with C-related QTLs. These colocalizations reflect the complex interactions of C metabolism with other physiological processes. QTL fine-mapping and cloning could thus lead soon to the identification of genes potentially involved in the control of different connected physiological processes. PMID:16798941

  4. Genetic variation of the mitochondrial Complex I subunit NDUFV2 and Parkinson disease

    PubMed Central

    Nishioka, Kenya; Vilariño-Güell, Carles; Cobb, Stephanie A.; Kachergus, Jennifer M.; Ross, Owen A.; Hentati, Emna; Hentati, Faycal; Farrer, Matthew J.

    2010-01-01

    NADH dehydrogenase ubiquinone flavoprotein 2 (NDUFV2), encoding a subunit of mitochondrial complex I, is a candidate gene for several neuronal diseases; schizophrenia, bipolar disorder and Parkinson disease (PD). We screened the entire coding region of NDUFV2 in 33 familial PD patients of North African Arab-Berber ethnicity in which all known genetic forms of PD had been excluded. We detected one novel substitution p.K209R (c.626A>G) in one PD. Segregation analysis within the family is inconclusive due to small sample size, but consistent with autosomal dominant mode of inheritance. Subsequent screening of this mutation in ethnically-matched sporadic PD patients (n=238) and controls (n=371) identified p.K209R in one additional patient. The clinical features of the mutation carriers revealed a mild form of parkinsonism with a prognosis similar to idiopathic PD. Our findings suggest further studies addressing the role of NDUFV2 variation in PD may be warranted. PMID:20971673

  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. Variation in complex mating signals in an "island" hybrid zone between Stenobothrus grasshopper species.

    PubMed

    Sradnick, Jan; Klöpfel, Anja; Elsner, Norbert; Vedenina, Varvara

    2016-07-01

    Two grasshopper species Stenobothrus rubicundus and S. clavatus were previously shown to meet in a narrow hybrid zone on Mount Tomaros in northern Greece. The species are remarkable for their complex courtship songs accompanied by conspicuous movements of antennae and wings. We analyzed variations in forewing morphology, antenna shape, and courtship song across the hybrid zone using a geographic information system, and we documented three contact zones on Mount Tomaros. All male traits and female wings show abrupt transitions across the contact zones, suggesting that these traits are driven by selection rather than by drift. Male clines in antennae are displaced toward S. clavatus, whereas all clines in wings are displaced toward S. rubicundus. We explain cline discordance as depending on sexual selection via female choice. The high covariance between wings and antennae found in the centers of all contact zones results from high levels of linkage disequilibria among the underlying loci, which in turn more likely results from assortative mating than from selection against hybrids. The covariance is found to be higher in clavatus-like than rubicundus-like populations, which implies asymmetric assortative mating in parental-like sites of the hybrid zone and a movement of the hybrid zone in favor of S. clavatus. PMID:27547333

  7. Locally Refined Multigrid Solution of the All-Electron Kohn-Sham Equation.

    PubMed

    Cohen, Or; Kronik, Leeor; Brandt, Achi

    2013-11-12

    We present a fully numerical multigrid approach for solving the all-electron Kohn-Sham equation in molecules. The equation is represented on a hierarchy of Cartesian grids, from coarse ones that span the entire molecule to very fine ones that describe only a small volume around each atom. This approach is adaptable to any type of geometry. We demonstrate it for a variety of small molecules and obtain high accuracy agreement with results obtained previously for diatomic molecules using a prolate-spheroidal grid. We provide a detailed presentation of the numerical methodology and discuss possible extensions of this approach. PMID:26583393

  8. Numerical Methods for a Kohn-Sham Density Functional Model Based on Optimal Transport.

    PubMed

    Chen, Huajie; Friesecke, Gero; Mendl, Christian B

    2014-10-14

    In this paper, we study numerical discretizations to solve density functional models in the "strictly correlated electrons" (SCE) framework. Unlike previous studies, our work is not restricted to radially symmetric densities. In the SCE framework, the exchange-correlation functional encodes the effects of the strong correlation regime by minimizing the pairwise Coulomb repulsion, resulting in an optimal transport problem. We give a mathematical derivation of the self-consistent Kohn-Sham-SCE equations, construct an efficient numerical discretization for this type of problem for N = 2 electrons, and apply it to the H2 molecule in its dissociating limit. PMID:26588133

  9. Existence of minimizers for Kohn-Sham within the local spin density approximation

    NASA Astrophysics Data System (ADS)

    Gontier, David

    2015-01-01

    The purpose of this article is to extend the work by Anantharaman and Cancès (2009 Ann. Inst. Henri Poincaré (C) 26 2425-55) and prove the existence of minimizers for the spin-polarized Kohn-Sham model in the presence of a magnetic field within the local spin density approximation. We show that for any magnetic field that vanishes at infinity, the existence of minimizers is ensured for neutral or positively charged systems. The proof relies on classical concentration-compactness techniques.

  10. The Korringa-Kohn-Rostoker method with projection potentials: exact result for the density.

    PubMed

    Zeller, Rudolf

    2015-08-01

    A well known problem in the Korringa-Kohn-Rostoker (KKR) multiple-scattering method concerns the error in density normalization arising from finite angular momentum expansions used in numerical treatments. It is shown that this problem can be solved if the potential around each atom is understood as a non-local projection potential in angular momentum space and that the density can be calculated exactly without infinite angular momentum sums if the projection acts on a finite subspace of spherical harmonics. This restriction implicates no loss of generality because an arbitrary potential can be approximated by increasing the subspace as closely as desired. PMID:26171615

  11. 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.

  12. 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

  13. Pure-state noninteracting v-representability of electron densities from Kohn-Sham calculations with finite basis sets

    NASA Astrophysics Data System (ADS)

    de Silva, Piotr; Wesolowski, Tomasz A.

    2012-03-01

    Within the linear combination of atomic orbitals (LCAO) approximation, one can distinguish two different Kohn-Sham potentials. One is the potential available numerically in calculations, and the other is the exact potential corresponding to the LCAO density. The latter is usually not available, but can be obtained from the total density by a numerical inversion procedure or, as is done here, analytically using only one LCAO Kohn-Sham orbital. In the complete basis-set limit, the lowest-lying Kohn-Sham orbital suffices to perform the analytical inversion, and the two potentials differ by no more than a constant. The relation between these two potentials is investigated here for diatomic molecules and several atomic basis sets of increasing size and quality. The differences between the two potentials are usually qualitative (wrong behavior at nuclear cusps and far from the molecule even if Slater-type orbitals are used) and δ-like features at nodal planes of the lowest-lying LCAO Kohn-Sham orbital. Such nodes occur frequently in LCAO calculations and are not physical. Whereas the behavior of the potential can be systematically improved locally by the increase of the basis sets, the occurrence of nodes is not correlated with the size of the basis set. The presence of nodes in the lowest-lying LCAO orbital can be used to monitor whether the effective potential in LCAO Kohn-Sham equations can be interpreted as the potential needed for pure-state noninteracting v-representability of the LCAO density. Squares of such node-containing lowest-lying LCAO Kohn-Sham orbitals are nontrivial examples of two-electron densities which are not pure-state noninteracting v-representable.

  14. Molecular Variation in the Paragonimus heterotremus Complex in Thailand and Myanmar

    PubMed Central

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

    2013-01-01

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

  15. 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

  16. 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

  17. 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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Lin, Lin; Shao, Sihong; E, Weinan

    2013-07-01

    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 Pt2, Au2, TlF, and Bi2Se3 indicate that the LOBPCG-F method is a robust and efficient method for investigating the relativistic effect in systems containing heavy elements.

  20. Stationary state Kohn-Sham Theory: Modern algorithms breathe new life into an old theory

    NASA Astrophysics Data System (ADS)

    Gunceler, Deniz; Sundararaman, Ravishankar; Arias, T. A.

    2014-03-01

    In this talk, we will discuss stationary-state Kohn-Sham theory, an old (Phys. Rev. B 31, 6264-6272) but largely ignored idea that is recently undergoing revival. It is based on an in-principle exact scheme in which excited states are computed as the stationary states of the Hohenberg-Kohn functional. We will discuss the objections of Gaudoin and Burke (Phys. Rev. Lett. 93, 17), and also describe the computational difficulties which prevented this theory from becoming popular in the past, and present new algorithms for computing the predictions of this theory. The resulting technique has inherent computational advantages over TDDFT and GW, and results using semilocal functionals show great promise for molecules. However, the method as implemented exhibits large errors for solids. In this talk, we shall show that the origin of this behaviour is related to the fact that different errors dominate the solid and molecular cases, and we shall discuss prospects for improvement of the theory in the future.

  1. Generalization of the Kohn-Sham system that can represent arbitrary one-electron density matrices

    NASA Astrophysics Data System (ADS)

    van Dam, Hubertus J. J.

    2016-05-01

    Density functional theory is currently the most widely applied method in electronic structure theory. The Kohn-Sham method, based on a fictitious system of noninteracting particles, is the workhorse of the theory. The particular form of the Kohn-Sham wave function admits only idempotent one-electron density matrices whereas wave functions 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 noninteracting 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. This produces energy levels that are akin to Hartree-Fock orbital energies such that conventional analyses based on Koopmans' theorem are available. Finally, this system is convenient in formalisms that depend on creation and annihilation operators as they are trivially applied to single-determinant wave functions.

  2. Kohn's theorem, Larmor's equivalence principle and the Newton-Hooke group

    SciTech Connect

    Gibbons, G.W.; Pope, C.N.

    2011-07-15

    Highlights: > We show that non-relativistic electrons moving in a magnetic field with trapping potential admits as relativity group the Newton-Hooke group. > We use this fact to give a group theoretic interpretation of Kohn's theorem and to obtain the spectrum. > We obtain the lightlike lift of the system exhibiting showing it coincides with the Nappi-Witten spacetime. - Abstract: We consider non-relativistic electrons, each of the same charge to mass ratio, moving in an external magnetic field with an interaction potential depending only on the mutual separations, possibly confined by a harmonic trapping potential. We show that the system admits a 'relativity group' which is a one-parameter family of deformations of the standard Galilei group to the Newton-Hooke group which is a Wigner-Inoenue contraction of the de Sitter group. This allows a group-theoretic interpretation of Kohn's theorem and related results. Larmor's theorem is used to show that the one-parameter family of deformations are all isomorphic. We study the 'Eisenhart' or 'lightlike' lift of the system, exhibiting it as a pp-wave. In the planar case, the Eisenhart lift is the Brdicka-Eardley-Nappi-Witten pp-wave solution of Einstein-Maxwell theory, which may also be regarded as a bi-invariant metric on the Cangemi-Jackiw group.

  3. Generalization of the Kohn-Sham system that can represent arbitrary one-electron density matrices

    DOE PAGESBeta

    Hubertus J. J. van Dam

    2016-05-23

    Density functional theory is currently the most widely applied method in electronic structure theory. The Kohn-Sham method, based on a fictitious system of noninteracting particles, is the workhorse of the theory. The particular form of the Kohn-Sham wave function admits only idempotent one-electron density matrices whereas wave functions 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 noninteracting system can be chosen that can represent the one-electron density matrix of any system, even one with fractionalmore » 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. This produces energy levels that are akin to Hartree-Fock orbital energies such that conventional analyses based on Koopmans' theorem are available. Lastly, this system is convenient in formalisms that depend on creation and annihilation operators as they are trivially applied to single-determinant wave functions.« less

  4. 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.

  5. DFT study of metal-complex structural variation on tensile force profiles

    NASA Astrophysics Data System (ADS)

    Rinderspacher, B. Christopher; Andzelm, Jan W.; Lambeth, Robert H.

    2012-12-01

    We present calculations on metal-ligand complexes for the evaluation of mechanical properties as they pertain to the inclusion in polymer-linked supramolecular complexes. To this end, we investigate the energy profiles of stretching various complexes according to external forces exerted on each complex via the attached polymer strands. Zn2+ and Fe2+ complexated by 2,6-bisbenzimidazolyl-pyridine (BP) were considered in the presence of tetrafluoro borate. We find that the yield characteristics are subject to a complex interplay of steric and electronic effects of the ligands and metal center.

  6. Visual Complexity in Orthographic Learning: Modeling Learning across Writing System Variations

    ERIC Educational Resources Information Center

    Chang, Li-Yun; Plaut, David C.; Perfetti, Charles A.

    2016-01-01

    The visual complexity of orthographies varies across writing systems. Prior research has shown that complexity strongly influences the initial stage of reading development: the perceptual learning of grapheme forms. This study presents a computational simulation that examines the degree to which visual complexity leads to grapheme learning…

  7. The QTP family of consistent functionals and potentials in Kohn-Sham density functional theory.

    PubMed

    Jin, Yifan; Bartlett, Rodney J

    2016-07-21

    This manuscript presents the second, consistent density functional in the QTP (Quantum Theory Project) family, that is, the CAM-QTP(01). It is a new range-separated exchange-correlation functional in which the non-local exchange contribution is 100% at large separation. It follows the same basic principles of this family that the Kohn-Sham eigenvalues of the occupied orbitals approximately equal the vertical ionization energies, which is not fulfilled by most of the traditional density functional methods. This new CAM-QTP(01) functional significantly improves the accuracy of the vertical excitation energies especially for the Rydberg states in the test set. It also reproduces many other properties such as geometries, reaction barrier heights, and atomization energies. PMID:27448874

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1983-12-01

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

  10. Effects of edge magnetism on the Kohn anomalies of zigzag graphene nanoribbons.

    PubMed

    Culchac, F J; Capaz, Rodrigo B

    2016-02-12

    The effects of edge magnetism on the Kohn anomaly (KA) of the G-band phonons of zigzag graphene nanoribbons (ZGNRs) are studied using a combination of the tight-binding and mean-field Hubbard models. We show that the opening of an energy gap, induced by magnetic ordering, significantly changes the KA effects, particularly for narrow ribbons in which the gap is larger than the phonon energy. Therefore, the G-band phonon frequency and lifetime are altered for a magnetically-ordered edge state with respect to an unpolarized edge state. The effects of temperature, ZGNR width, doping and transverse electric fields are systematically investigated. We propose using this effect to probe the magnetic order of edge states in graphene nanoribbons using Raman spectroscopy. PMID:26762781

  11. The Use of Trust Regions in Kohn-Sham Total EnergyMinimization

    SciTech Connect

    Yang, Chao; Meza, Juan C.; Wang, Lin-wang

    2006-05-30

    The Self Consistent Field (SCF) iteration, widely used forcomputing the ground state energy and the corresponding single particlewave functions associated with a many-electronatomistic system, is viewedin this paper as an optimization procedure that minimizes the Kohn-Shamtotal energy indirectly by minimizing a sequence of quadratic surrogatefunctions. We point out the similarity and difference between the totalenergy and the surrogate, and show how the SCF iteration can fail whenthe minimizer of the surrogate produces an increase in the KS totalenergy. A trust region technique is introduced as a way to restrict theupdate of the wave functions within a small neighborhood of anapproximate solution at which the gradient of the total energy agreeswith that of the surrogate. The use of trust region in SCF is not new.However, it has been observed that directly applying a trust region basedSCF(TRSCF) to the Kohn-Sham total energy often leads to slowconvergence.We propose to use TRSCF within a direct constrainedminimization(DCM) algorithm we developed in \\cite dcm. The keyingredients of theDCM algorithm involve projecting the total energyfunction into a sequence of subspaces of small dimensions and seeking theminimizerof the total energy function within each subspace. Theminimizer of a subspace energy function, which is computed by TRSCF, notonly provides a search direction along which the KS total energy functiondecreases but also gives an optimal "step-length" that yields asufficient decrease in total energy. A numerical example is provided todemonstrate that the combination of TRSCF and DCM is more efficient thanSCF.

  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. Complex spatial and temporal variation of subtropical benthic macrofauna under sewage impact.

    PubMed

    Souza, F M; Brauko, K M; Gilbert, E R; Martins, C C; Lana, P C; Camargo, M G

    2016-05-01

    To better understand variation in sewage-impacted benthic macrofauna from subtropical tidal flats over time and space, we applied a five-factor linear model at a hierarchy of spatial (Condition - Contaminated or Non-Contaminated, Tidal Flat and Plot) and temporal scales (Season and Fortnight). The Contaminated site showed high levels of coprostanol and the presence of Paranais cf frici as markers or indicators of organic enrichment. Differences between Seasons were more pronounced for the faunal variation patterns than for the other parameters, with lower species richness and abundance in summer. There were significant interactions between Fortnight and Tidal Flat for most variables, reflecting marked heterogeneity within Tidal Flats. Benthic community has significantly changed over short periods of time. These rapid changes may lead to erroneous interpretations and mask the true sources of variation. Our results clearly demonstrate the need to better understand benthic temporal variability even at small scales. PMID:26994465

  14. 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

  15. 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…

  16. Converged variational quantum scattering results for the three-dimensional F+HD reaction

    NASA Astrophysics Data System (ADS)

    Manolopoulos, David E.; D'Mello, Michael; Wyatt, Robert E.; Walker, Robert B.

    1990-06-01

    The log derivative version of the Kohn variational principle is used to calculate J=0 reaction probabilities and state-to-state time delays for the F+HD reaction, on the T5A potential energy surface, in the total energy range Etot=0.236 to 0.350 eV. While the computed reaction probabilities to H+DF are comparatively bland, those to D+HF show considerable resonant structure as a function of the scattering energy. For example, the computed state-to-state time delays for the predominant HF( v'=2) resonance et Etot=0.2575 eV imply the existence of a metastable collision complex with a half-life of about 0.1 ps. These results are discussed in the light of the high-resolution molecular beam experiments of Lee and coworkers and the bending corrected rotating linear model calculations of Hayes and Walker.

  17. Variations in the structures and binding energies of binary complexes with HBO

    NASA Astrophysics Data System (ADS)

    Del Bene, Janet E.; Alkorta, Ibon; Sanchez-Sanz, Goar; Elguero, José

    2012-06-01

    Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures and binding energies of binary complexes formed by HBO with a series of small molecules A. Three different types of structures have been identified, which depend on the nature of A. In one structure A:HBO, HBO acts as a weak proton donor. In the second HBO:A, HBO is a relatively strong base. The third type of complex A||HBO has HBO and A in an approximately parallel arrangement. The dipole moment of A influences both the type of complex formed and its binding energy.

  18. 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...

  19. Complexity Variations in the Interplanetary Magnetic Field between 0.4 and 5.3 AU

    NASA Astrophysics Data System (ADS)

    Weygand, J. M.; Kivelson, M.; Velli, M.; Gekelman, W. N.; Khurana, K. K.; Angelopoulos, V.; Walker, R. J.

    2015-12-01

    We have investigated how the character of magnetic fluctuations of solar wind plasma depends on radial distance from the Sun. We use measurements of the magnetic field taken at different distances from the Sun by different spacecraft: Helios between 0.4 and 1 AU, ACE and Wind at about 1 AU, and Ulysses at about 5.3 AU. Data intervals are selected to contain only what appear to be random fluctuations and to exclude solar wind structures such as coronal mass ejections, co-rotating interaction regions, heliospheric current sheets, shocks, etc. With these data we calculate the Jensen-Shannon complexity as a function of permutation entropy. Jensen-Shannon complexity maps indicate if the fluctuations in the magnetic fields are stochastic (low complexity and high entropy), or if they exhibit minimal or maximal complexity and lower entropy. The Jensen-Shannon complexity values determined from the spacecraft measurements evolve from moderate complexity and high entropy at 0.4 AU to lower complexity and higher entropy farther from the Sun. We interpret these data to mean that as the solar wind plasma expands outward, the magnetic field fluctuations evolve from chaotic (i.e., low dimensionality, deterministic fluctuations) to turbulent (i.e., low dimensionality, non-deterministic fluctuations). By separating the magnetic fluctuations into slow solar wind (<450 km/s) and fast solar wind (>550 km/s), we find that the younger solar wind (transported outward rapidly) has higher complexity than the older solar wind (transported outward slowly). These results can be tested by Solar Probe Plus to be launched in 2018.

  20. 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

  1. Between-year variation in population sex ratio increases with complexity of the breeding system in Hymenoptera.

    PubMed

    Kümmerli, Rolf; Keller, Laurent

    2011-06-01

    While adaptive adjustment of sex ratio in the function of colony kin structure and food availability commonly occurs in social Hymenoptera, long-term studies have revealed substantial unexplained between-year variation in sex ratio at the population level. In order to identify factors that contribute to increased between-year variation in population sex ratio, we conducted a comparative analysis across 47 Hymenoptera species differing in their breeding system. We found that between-year variation in population sex ratio steadily increased as one moved from solitary species, to primitively eusocial species, to single-queen eusocial species, to multiple-queen eusocial species. Specifically, between-year variation in population sex ratio was low (6.6% of total possible variation) in solitary species, which is consistent with the view that in solitary species, sex ratio can vary only in response to fluctuations in ecological factors such as food availability. In contrast, we found significantly higher (19.5%) between-year variation in population sex ratio in multiple-queen eusocial species, which supports the view that in these species, sex ratio can also fluctuate in response to temporal changes in social factors such as queen number and queen-worker control over sex ratio, as well as factors influencing caste determination. The simultaneous adjustment of sex ratio in response to temporal fluctuations in ecological and social factors seems to preclude the existence of a single sex ratio optimum. The absence of such an optimum may reflect an additional cost associated with the evolution of complex breeding systems in Hymenoptera societies. PMID:21597259

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  3. 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

  4. Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola.

    PubMed

    Raman, H; Raman, R; Coombes, N; Song, J; Prangnell, R; Bandaranayake, C; Tahira, R; Sundaramoorthi, V; Killian, A; Meng, J; Dennis, E S; Balasubramanian, S

    2016-06-01

    Optimum flowering time is the key to maximize canola production in order to meet global demand of vegetable oil, biodiesel and canola-meal. We reveal extensive variation in flowering time across diverse genotypes of canola under field, glasshouse and controlled environmental conditions. We conduct a genome-wide association study and identify 69 single nucleotide polymorphism (SNP) markers associated with flowering time, which are repeatedly detected across experiments. Several associated SNPs occur in clusters across the canola genome; seven of them were detected within 20 Kb regions of a priori candidate genes; FLOWERING LOCUS T, FRUITFUL, FLOWERING LOCUS C, CONSTANS, FRIGIDA, PHYTOCHROME B and an additional five SNPs were localized within 14 Kb of a previously identified quantitative trait loci for flowering time. Expression analyses showed that among FLC paralogs, BnFLC.A2 accounts for ~23% of natural variation in diverse accessions. Genome-wide association analysis for FLC expression levels mapped not only BnFLC.C2 but also other loci that contribute to variation in FLC expression. In addition to revealing the complex genetic architecture of flowering time variation, we demonstrate that the identified SNPs can be modelled to predict flowering time in diverse canola germplasm accurately and hence are suitable for genomic selection of adaptative traits in canola improvement programmes. PMID:26428711

  5. Sources of variation in the mutagenic potency of complex chemical mixtures based on the salmonella/microsome assay

    SciTech Connect

    Krewski, D.; Leroux, B.G.; Creason, J.; Claxton, L.

    1992-01-01

    Twenty laboratories worldwide participated in a collaborative trial sponsored by the International Program on Chemical Safety on the mutagenicity of complex mixtures as expressed in the Salmonella/microsome assay. The U.S. National Institute of Standards and Technology provided homogeneous reference samples of urban air and diesel particles and a coal tar solution to each participating laboratory, along with samples of benzo(a)pyrene and 1-nitropyrene which served as positive controls. Mutagenic potency was characterized by the slope of the initial linear component of the dose response curve. Analysis of variance revealed significant interlaboratory variation in mutagenic potency, which accounted for 57-96% of the total variance on a logarithmic scale, depending on the sample, strain and activation conditions. No significant differences were noted in the average potency reported for air and diesel particles between laboratories using soxhlet extracts and those using sonication, although there was larger interlaboratory variation for the soxhlet method.

  6. Variation of stability constants of thorium and uranium oxalate complexes with ionic strength

    SciTech Connect

    Erten, H.N; Mohammed, A.K.; Choppin, G.R.

    1993-12-31

    Extraction of Th(IV) and UO{sub 2}{sup 2+} by a solution of TTA and HDEHP, respectively, in toluene was used to obtain stability constants of their oxalate complexes in 1, 3, 5, 7 and 9 M ionic strength (NaClO{sub 2}) solutions. The complexes formed were the MOx, MHOx, MOx{sub 2} and M(HOx){sub 2} (M = Th, UO{sub 2}) species. The values were analyzed by the Specific Interaction Theory and agreed to I {le} 3 M but required an additional term for fitting at I > 3 M.

  7. Variations in task constraints shape emergent performance outcomes and complexity levels in balancing.

    PubMed

    Caballero Sánchez, Carla; Barbado Murillo, David; Davids, Keith; Moreno Hernández, Francisco J

    2016-06-01

    This study investigated the extent to which specific interacting constraints of performance might increase or decrease the emergent complexity in a movement system, and whether this could affect the relationship between observed movement variability and the central nervous system's capacity to adapt to perturbations during balancing. Fifty-two healthy volunteers performed eight trials where different performance constraints were manipulated: task difficulty (three levels) and visual biofeedback conditions (with and without the center of pressure (COP) displacement and a target displayed). Balance performance was assessed using COP-based measures: mean velocity magnitude (MVM) and bivariate variable error (BVE). To assess the complexity of COP, fuzzy entropy (FE) and detrended fluctuation analysis (DFA) were computed. ANOVAs showed that MVM and BVE increased when task difficulty increased. During biofeedback conditions, individuals showed higher MVM but lower BVE at the easiest level of task difficulty. Overall, higher FE and lower DFA values were observed when biofeedback was available. On the other hand, FE reduced and DFA increased as difficulty level increased, in the presence of biofeedback. However, when biofeedback was not available, the opposite trend in FE and DFA values was observed. Regardless of changes to task constraints and the variable investigated, balance performance was positively related to complexity in every condition. Data revealed how specificity of task constraints can result in an increase or decrease in complexity emerging in a neurobiological system during balance performance. PMID:26838357

  8. Species Identification and Variation in the North American Cranberry Fruit Rot Complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complex mixtures of pathogenic fungi cause cranberry fruit rot, with the contribution by any given fungus to the disease varying from bed to bed, cultivar to cultivar, season to season, and across regions. Furthermore, population variability within the individual fungal species across growing region...

  9. Direct calculation of the reactive transition matrix by L-squared quantum mechanical variational methods with complex boundary conditions

    NASA Technical Reports Server (NTRS)

    Sun, Yan; Yu, Chin-Hui; Kouri, Donald J.; Schwenke, David W.; Halvick, Philippe

    1989-01-01

    A new formalism of the generalized Newton variational principle for the calculation of quantum mechanical state-to-state reaction probabilities is presented. The reformulation involves solving directly for the transition matrix rather than the reactance mtrix so that calculations may be carried out for individual columns of the transition matrix without obtaining solutions for all possible initial channels. The convergence of calculations with real and complex boundary conditions are compared for H + H2 - H2 + H, O + H2 - OH + H, and O + HD - OH + D and OD + H.

  10. 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. PMID:26227536

  11. Ribosomal DNA locus variation and REMAP analysis of the diploid and triploid complexes of Lilium lancifolium.

    PubMed

    Nguyen, Truong Xuan; Lee, Sung-Il; Rai, Rameshwar; Kim, Nam-Soo; Kim, Jong Hwa

    2016-08-01

    Lilium lancifolium Thunb. (2n = 2x = 24) is a cytologically conspicuous species with both diploids and triploids in nature. Cytological and molecular genetic analyses were carried out in both diploids and triploids that were collected from 55 geographical locations in Korea, Japan, and China. While the 5S rRNA gene loci were located at duplicated loci on the long arm of chromosome 2, the 45S rRNA gene loci were present in chromosomes 1, 2, 4, 6, 7, and 11. While the loci on chromosomes 1 and 7 were constant, the loci on chromosomes 2, 4, 6, 7, and 11 were variable in some plants so that the L. lancifolium accessions were grouped into 7 cytotypes in diploids and 12 cytotypes in triploids. REMAP marker analysis revealed that the diploids were classified into seven clusters, and the triploids were classified into a large cluster. Geographic, cytological, and genetic differentiations were not related in both the diploid and triploid accessions of L. lancifolium. Thus, current genetic variations occurred prior to the geographic differentiation in both diploids and triploids, and the 45S rDNA cytotype variations occurred after geographic differentiation in the current habitats of L. lancifolium. PMID:27458741

  12. 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.

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

    SciTech Connect

    Sjostrom, Travis; Crockett, Scott

    2015-09-02

    The liquid regime equation of state of silicon dioxide SiO2 is calculated via quantum molecular dynamics in the density range of 5 to 15 g/cc and with temperatures from 0.5 to 100 eV, including the α-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.

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

    DOE PAGESBeta

    Sjostrom, Travis; Crockett, Scott

    2015-09-02

    The liquid regime equation of state of silicon dioxide SiO2 is calculated via quantum molecular dynamics in the density range of 5 to 15 g/cc and with temperatures from 0.5 to 100 eV, including the α-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 newmore » liquid regime equation of state table for SiO2.« less

  15. Alkali Metal Variation and Twisting of the FeNNFe Core in Bridging Diiron Dinitrogen Complexes.

    PubMed

    McWilliams, Sean F; Rodgers, Kenton R; Lukat-Rodgers, Gudrun; Mercado, Brandon Q; Grubel, Katarzyna; Holland, Patrick L

    2016-03-21

    Alkali metal cations can interact with Fe-N2 complexes, potentially enhancing back-bonding or influencing the geometry of the iron atom. These influences are relevant to large-scale N2 reduction by iron, such as in the FeMoco of nitrogenase and the alkali-promoted Haber-Bosch process. However, to our knowledge there have been no systematic studies of a large range of alkali metals regarding their influence on transition metal-dinitrogen complexes. In this work, we varied the alkali metal in [alkali cation]2[LFeNNFeL] complexes (L = bulky β-diketiminate ligand) through the size range from Na(+) to K(+), Rb(+), and Cs(+). The FeNNFe cores have similar Fe-N and N-N distances and N-N stretching frequencies despite the drastic change in alkali metal cation size. The two diketiminates twist relative to one another, with larger dihedral angles accommodating the larger cations. In order to explain why the twisting has so little influence on the core, we performed density functional theory calculations on a simplified LFeNNFeL model, which show that the two metals surprisingly do not compete for back-bonding to the same π* orbital of N2, even when the ligand planes are parallel. This diiron system can tolerate distortion of the ligand planes through compensating orbital energy changes, and thus, a range of ligand orientations can give very similar energies. PMID:26925968

  16. Variation in the biomolecular interactions of nickel(II) hydrazone complexes upon tuning the hydrazide fragment.

    PubMed

    Krishnamoorthy, Paramasivam; Sathyadevi, Palanisamy; Butorac, Rachel R; Cowley, Alan H; Bhuvanesh, Nattamai S P; Dharmaraj, Nallasamy

    2012-06-14

    Three new bivalent nickel hydrazone complexes have been synthesised from the reactions of [NiCl(2)(PPh(3))(2)] with H(2)L {L = dianion of the hydrazones derived from the condensation of o-hydroxynaphthaldehyde with furoic acid hydrazide (H(2)L(1)) (1)/thiophene-2-acid hydrazide (H(2)L(2)) (2)/isonicotinic acid hydrazide (H(2)L(3)) (3)} and formulated as [Ni(L(1))(PPh(3))] (4), [Ni(L(2))(PPh(3))] (5) and [Ni(L(3))(PPh(3))] (6). Structural characterization of these compounds 4-6 were accomplished by using various physico-chemical techniques. Single crystal X-ray diffraction data of complexes 4 and 5 proved their distorted square planar geometry. In order to ascertain the potential of the above synthesised compounds towards biomolecular interactions, additional experiments involving interaction with calf thymus DNA (CT DNA) and bovine serum albumin (BSA) were carried out. All the ligands and corresponding nickel(ii) chelates have been screened for their scavenging effect towards O(2)(-), OH and NO radicals. The efficiency of complexes 4-6 to arrest the growth of HeLa, HepG-2 and A431 tumour cell lines has been studied along with the cell viability test against the non-cancerous NIH 3T3 cells under in vitro conditions. PMID:22506273

  17. Lattice constant variation and complex formation in zincblende gallium manganese arsenide

    NASA Astrophysics Data System (ADS)

    Schott, G. M.; Faschinger, W.; Molenkamp, L. W.

    2001-09-01

    We perform high resolution x-ray diffraction on GaMnAs mixed crystals as well as on GaMnAs/GaAs and GaAs/MnAs superlattices for samples grown by low-temperature molecular-beam epitaxy under different growth conditions. Although all samples are of high crystalline quality and show narrow rocking curve widths and pronounced finite thickness fringes, the lattice constant variation with increasing manganese concentration depends strongly on the growth conditions: For samples grown at substrate temperatures of 220 and 270 °C, the extrapolated relaxed lattice constant of Zincblende MnAs is 0.590 nm and 0.598 nm, respectively. This is in contrast to low-temperature GaAs, for which the lattice constant decreases with increasing substrate temperature.

  18. 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

  19. Complex Copy Number Variation of AMY1 does not Associate with Obesity in two East Asian Cohorts.

    PubMed

    Yong, Rita Y Y; Mustaffa, Su'Aidah B; Wasan, Pavandip S; Sheng, Liang; Marshall, Christian R; Scherer, Stephen W; Teo, Yik-Ying; Yap, Eric P H

    2016-07-01

    The human amylase gene locus at chromosome 1p21.1 is structurally complex. This region contains two pancreatic amylase genes, AMY2B, AMY2A, and a salivary gene AMY1. The AMY1 gene harbors extensive copy number variation (CNV), and recent studies have implicated this variation in adaptation to starch-rich diets and in association to obesity for European and Asian populations. In this study, we showed that by combining quantitative PCR and digital PCR, coupled with careful experimental design and calibration, we can improve the resolution of genotyping CNV with high copy numbers (CNs). In two East Asian populations of Chinese and Malay ethnicity studied, we observed a unique non-normal distribution of AMY1 diploid CN genotypes with even:odd CNs ratio of 4.5 (3.3-4.7), and an association between the common AMY2A CN = 2 genotype and odd CNs of AMY1, that could be explained by the underlying haplotypic structure. In two further case-control cohorts (n = 932 and 145, for Chinese and Malays, respectively), we did not observe the previously reported association between AMY1 and obesity or body mass index. Improved methods for accurately genotyping multiallelic CNV loci and understanding the haplotype complexity at the AMY1 locus are necessary for population genetics and association studies. PMID:27068483

  20. 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

  1. Kohn's theory of the insulating state: a quantum-chemistry viewpoint.

    PubMed

    Resta, Raffaele

    2006-03-14

    The qualitative difference between insulators and conductors not only manifests itself in the excitation spectra but also--according to Kohn's theory [Phys. Rev. 133, A171 (1964)]--in a different organization of the electrons in their ground state: the wave function is localized in insulators and delocalized in conductors. Such localization, however, is hidden in a rather subtle way in the many-body wave function. The theory has been substantially revisited and extended in modern times, invariably within a periodic-boundary-condition framework, i.e., ideally addressing an infinite condensed system. Here we show how the localization/delocalization of the many-body wave function shows up when considering either three-dimensional clusters of increasing size or quasi-one-dimensional systems (linear polymers, nanotubes, and nanowires) of increasing length, within the ordinary "open" boundary conditions adopted for finite systems. We also show that the theory, when specialized to uncorrelated wave functions, has a very close relationship with Boy's theory of localization [Rev. Mod. Phys. 32, 296 (1960)]: the Boys orbitals in the bulk of the sample behave in a qualitatively different way in insulating versus conducting cases. PMID:16542065

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

    SciTech Connect

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

    2015-09-14

    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.

  3. Self-Averaging Stochastic Kohn-Sham Density-Functional Theory

    NASA Astrophysics Data System (ADS)

    Baer, Roi; Neuhauser, Daniel; Rabani, Eran

    2013-09-01

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

  4. Kohn-Sham approach to Fermi gas superfluidity: The bilayer of fermionic polar molecules

    NASA Astrophysics Data System (ADS)

    Ancilotto, Francesco

    2016-05-01

    By using a well-established "ab initio" theoretical approach developed in the past to quantitatively study the superconductivity of condensed matter systems, based on the Kohn-Sham density functional theory, I study the superfluid properties and the BCS-BEC crossover of two parallel bi-dimensional layers of fermionic dipolar molecules, where the pairing mechanism leading to superfluidity is provided by the interlayer coupling between dipoles. The finite temperature superfluid properties of both the homogeneous system and one where the fermions in each layer are confined by a square optical lattice are studied at half filling conditions, and for different values of the strength of the confining optical potential. The T = 0 results for the homogeneous system are found to be in excellent agreement with diffusion Monte Carlo results. The superfluid transition temperature in the BCS region is found to increase, for a given interlayer coupling, with the strength of the confining optical potential. A transition occurs at sufficiently small interlayer distances, where the fermions becomes localized within the optical lattice sites in a square geometry with an increased effective lattice constant, forming a system of localized composite bosons. This transition should be signaled by a sudden drop in the superfluid fraction of the system.

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

    NASA Astrophysics Data System (ADS)

    Holas, A.

    2008-02-01

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

  6. The Kohn-Sham kinetic energy density as indicator of the electron localization: atomic shell structure.

    PubMed

    Navarrete-López, Alejandra M; Garza, Jorge; Vargas, Rubicelia

    2008-03-14

    In this report, it is shown that the Kohn-Sham (KS) kinetic energy density (KED) contains the average local electrostatic potential (ALEP) and the average local ionization energy (ALIE); the shell structure in atomic systems is presented as one application of the KS-KED. By writing the KS-KED from the KS equations, this quantity was divided in three contributions: orbital, Coulomb, and exchange correlation. By studying several closed and open shell atoms, the shell structure was established by the maxima presented by the Coulomb contribution and the minima in the orbital contribution of the KS-KED. The exchange-correlation contribution to the KS-KED does not show maxima or minima, but this quantity shows bumps where the division between shells is expected. The results obtained in this work were compared with other shell structure indicators such as the electron localization function, the ALEP, the ALIE, and the radial distribution function. The most important result in this work is related to the fact that even when the ALEP and the ALIE functions were built with different arguments to each other, they are contained in the KS-KED. In this way, the KS-KED shows its importance to reveal the electron localization in atomic systems. PMID:18345880

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

    SciTech Connect

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

    2015-08-07

    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.

  8. 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).

  9. Kohn-Sham density functional theory prediction of fracture in silicon carbide under mixed mode loading

    NASA Astrophysics Data System (ADS)

    Leung, K. W. K.; Pan, Z. L.; Warner, D. H.

    2016-03-01

    The utility of silicon carbide (SiC) for high temperature structural application has been limited by its brittleness. To improve its ductility, it is paramount to develop a sound understanding of the mechanisms controlling crack propagation. In this manuscript, we present direct ab initio predictions of fracture in SiC under pure mode I and mixed mode loading, utilizing a Kohn-Sham Density Functional Theory (KSDFT) framework. Our results show that in both loading cases, cleavage occurs at a stress intensity factor (SIF) only slightly higher than the Griffith toughness, focusing on a (1 1 1) [1 \\bar{1} 0] crack in the 3C-SiC crystal structure. This lattice trapping effect is shown to decrease with mode mixity, due to the formation of a temporary surface bond that forms during decohesion under shear. Comparing the critical mode I SIF to the value obtained in experiments suggests that some plasticity may occur near a crack tip in SiC even at low temperatures. Ultimately, these findings provide a solid foundation upon which to study the influence of impurities on brittleness, and upon which to develop empirical potentials capable of realistically simulating fracture in SiC.

  10. Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex.

    PubMed

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

    2011-07-01

    The human major histocompatibility complex (MHC) on chromosome 6p21 is a paradigm for genomics, showing remarkable polymorphism and striking association with immune and non-immune diseases. The complex genomic landscape of the MHC, notably strong linkage disequilibrium, has made resolving causal variants very challenging. A promising approach is to investigate gene expression levels considered as tractable intermediate phenotypes in mapping complex diseases. However, how transcription varies across the MHC, notably relative to specific haplotypes, remains unknown. Here, using an original hybrid tiling and splice junction microarray that includes alternate allele probes, we draw the first high-resolution strand-specific transcription map for three common MHC haplotypes (HLA-A1-B8-Cw7-DR3, HLA-A3-B7-Cw7-DR15, and HLA-A26-B18-Cw5-DR3-DQ2) strongly associated with autoimmune diseases including type 1 diabetes, systemic lupus erythematosus, and multiple sclerosis. We find that haplotype-specific differences in gene expression are common across the MHC, affecting 96 genes (46.4%), most significantly the zing finger protein gene ZFP57. Differentially expressed probes are correlated with polymorphisms between haplotypes, consistent with cis effects that we directly demonstrate for ZFP57 in a cohort of healthy volunteers (P = 1.2 × 10(-14)). We establish that alternative splicing is significantly more frequent in the MHC than genome-wide (72.5% vs. 62.1% of genes, P ≤ 1 × 10(-4)) and shows marked haplotypic differences. We also unmask novel and abundant intergenic transcription involving 31% of transcribed blocks identified. Our study reveals that the renowned MHC polymorphism also manifests as transcript diversity, and our novel haplotype-based approach marks a new step toward identification of regulatory variants involved in the control of MHC-associated phenotypes and diseases. PMID:21628452

  11. Effects of parametric variations of complex targets on damage from projectile impact

    SciTech Connect

    Meier, R.W.

    1989-01-01

    The effects of a hypervelocity projectile striking complex targets have been investigated. The targets consisted of metallic and low-density shock attenuating layers and void regions. The major features of the targets were systematically varied to correlate changes in the targets with the projectile's effectiveness in damaging the targets. Two-dimensional numerical simulations were done with the Eulerian computational fluid dynamics program PINON. Projectile effectiveness against the various targets was measured by determining the maximum pressure, pressure integral, P{sup 2}{tau} value, and hole size at several locations in the targets. 9 refs., 13 figs., 6 tabs.

  12. Variational calculations of positronium scattering with hydrogen

    NASA Astrophysics Data System (ADS)

    Woods, Denton

    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 will also be discussed. With these methods, we have computed phase shifts for the first six partial waves for both the singlet and triplet states. The 1S and 1P phase shifts are highly accurate results and could potentially be viewed as benchmark results. Resonance positions and widths for the 1S-, 1P-, 1D-, and 1F-waves have been calculated. We present elastic integrated, elastic differential, and momentum transfer cross sections using all six partial waves and note interesting features of each. We use multiple effective range theories, including several that explicitly take into account the long-range van der Waals interaction, to investigate scattering lengths for the 1,3S and 1,3P partial waves and effective ranges for the 1,3S-wave.

  13. Small-Angle Scattering and Neutron Contrast Variation for Studying Bio-Molecular Complexes

    NASA Astrophysics Data System (ADS)

    Whitten, Andrew E.; Trewhella, Jill

    Structural molecular biology over the past several decades has progressed from studies of the individual proteins, subunits, and domains that accomplish specific biochemistry to seeking to understand the dynamic bio-molecular complexes and assemblies that are responsible for biological function. This progress has led to an expansion of the structural analysis “tool box” to include methods that complement the mainstay techniques of the field: X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-electron microscopy. Small-angle scattering of X-rays or neutrons is one such complementary technique that provides information on the size and shape of scattering particles in solution. This low-resolution structural information can be a powerful complement to high-resolution structural data, especially for the study of bio-molecular interactions with ligands or each other. Further, exploitation of the different neutron-scattering properties of the stable isotopes of hydrogen (1H and 2H) can be used to enrich the information available from the small-angle scattering data, especially for bio-molecular complexes.

  14. Transcontinental latitudinal variation in song performance and complexity in house wrens (Troglodytes aedon).

    PubMed

    Kaluthota, Chinthaka; Brinkman, Benjamin E; Dos Santos, Ednei B; Rendall, Drew

    2016-02-10

    There is growing interest in latitudinal effects on animal behaviour and life history. One recent focus is on birdsong, which is hypothesized to be more elaborated or complex in the north temperate zone compared with the tropics. Current evidence is mixed and based on cross-species comparisons, or single species with restricted distributions. We circumvent these limitations using a transcontinental sample of 358 songs from house wrens (Troglodytes aedon) at 281 locations spanning more than 100° of latitude (52° N-55° S) across the Americas. We found a significant latitudinal gradient in several basic elements of song performance and complexity between north temperate and tropical populations. Furthermore, we document convergence in song patterns between populations at higher latitudes in the Northern and Southern Hemispheres. Effects were strongest for the number of elements in a song, and the rate of element production, both increasing towards the poles, with similar but weaker effects for other song dimensions (e.g. number of unique elements, trills and trill rate). We consider possible causes related to variable habitats and morphology, concluding that the shorter breeding seasons at higher latitudes in both hemispheres may favour greater song elaboration to mediate territory competition and mate choice. PMID:26865297

  15. 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

  16. Variation in predicted internal concentrations in relation to PBPK model complexity for rainbow trout.

    PubMed

    Salmina, E S; Wondrousch, D; Kühne, R; Potemkin, V A; Schüürmann, G

    2016-04-15

    The present study is motivated by the increasing demand to consider internal partitioning into tissues instead of exposure concentrations for the environmental toxicity assessment. To this end, physiologically based pharmacokinetic (PBPK) models can be applied. We evaluated the variation in accuracy of PBPK model outcomes depending on tissue constituents modeled as sorptive phases and chemical distribution tendencies addressed by molecular descriptors. The model performance was examined using data from 150 experiments for 28 chemicals collected from US EPA databases. The simplest PBPK model is based on the "Kow-lipid content" approach as being traditional for environmental toxicology. The most elaborated one considers five biological sorptive phases (polar and non-polar lipids, water, albumin and the remaining proteins) and makes use of LSER (linear solvation energy relationship) parameters to describe the compound partitioning behavior. The "Kow-lipid content"-based PBPK model shows more than one order of magnitude difference in predicted and measured values for 37% of the studied exposure experiments while for the most elaborated model this happens only for 7%. It is shown that further improvements could be achieved by introducing corrections for metabolic biotransformation and compound transmission hindrance through a cellular membrane. The analysis of the interface distribution tendencies shows that polar tissue constituents, namely water, polar lipids and proteins, play an important role in the accumulation behavior of polar compounds with H-bond donating functional groups. For compounds without H-bond donating fragments preferable accumulation phases are storage lipids and water depending on compound polarity. PMID:26849323

  17. Variation in number of hits for complex searches in Google Scholar

    PubMed Central

    Bramer, Wichor Matthijs

    2016-01-01

    Objective Google Scholar is often used to search for medical literature. Numbers of results reported by Google Scholar outperform the numbers reported by traditional databases. How reliable are these numbers? Why are often not all available 1,000 references shown? Methods For several complex search strategies used in systematic review projects, the number of citations and the total number of versions were calculated. Several search strategies were followed over a two-year period, registering fluctuations in reported search results. Results Changes in numbers of reported search results varied enormously between search strategies and dates. Theories for calculations of the reported and shown number of hits were not proved. Conclusions The number of hits reported in Google Scholar is an unreliable measure. Therefore, its repeatability is problematic, at least when equal results are needed. PMID:27076802

  18. 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

  19. A comparative overview of the sperm centriolar complex in mammals and birds: Variations on a theme.

    PubMed

    Soley, John T

    2016-06-01

    This paper presents an overview of the structure, function and anomalies of the sperm centriolar complex (CC) on a comparative basis between mammals and birds. The information is based on selected references from the literature supplemented by original observations on spermiogenesis and sperm structure in disparate mammalian (cheetah and cane rat) and avian (ostrich, rhea and emu) species. Whereas the basic structure of the CC (a diplosome surrounded by pericentriolar material) is similar in Aves and Mammalia, certain differences are apparent. Centriole reduction does not generally occur in birds, but when present as in oscines, involves the loss of the proximal centriole. In ratites, the distal centriole forms the core of the entire midpiece and incorporates the outer dense fibres in addition to initiating axoneme formation. The elements of the connecting piece are not segmented in birds and less complex in basic design than in mammals. The functions of the various components of the CC appear to be similar in birds and mammals. Despite obvious differences in sperm head shape, the centrosomal anomalies afflicting both vertebrate groups demonstrate structural uniformity across species and display a similar range of defects. Most abnormalities result from defective migration and alignment of the CC relative to the nucleus. The most severe manifestation is that of acephalic sperm, while angled tail attachment, abaxial and multiflagellate sperm reflect additional defective forms. The stump-tail defect is not observed in birds. A comparison of defective sperm formation and centrosomal dysfunction at the molecular level is currently difficult owing to the paucity of relevant information on avian sperm. PMID:26907939

  20. An immunohistochemical study of the triangular fibrocartilage complex of the wrist: regional variations in cartilage phenotype

    PubMed Central

    Milz, S; Sicking, B; Sprecher, C M; Putz, R; Benjamin, M

    2007-01-01

    The triangular fibrocartilage complex (TFCC) transmits load from the wrist to the ulna and stabilizes the distal radioulnar joint. Damage to it is a major cause of wrist pain. Although its basic structure is well established, little is known of its molecular composition. We have analysed the immunohistochemical labelling pattern of the extracellular matrix of the articular disc and the meniscal homologue of the TFCC in nine elderly individuals (age range 69–96 years), using a panel of monoclonal antibodies directed against collagens, glycosaminoglycans, proteoglycans and cartilage oligomeric matrix protein (COMP). Although many of the molecules (types I, III and VI collagen, chondroitin 4 sulphate, dermatan sulphate and keratan sulphate, the oversulphated epitope of chondroitin 6 sulphate, versican and COMP) were found in all parts of the TFCC, aggrecan, link protein and type II collagen were restricted to the articular disc and to entheses. They were thus not a feature of the meniscal homologue. The shift in tissue phenotype within the TFCC, from a fibrocartilaginous articular disc to a more fibrous meniscal homologue, correlates with biomechanical data suggesting that the radial region is stiff and subject to considerable stress concentration. The presence of aggrecan, link protein and type II collagen in the articular disc could explain why the TFCC is destroyed in rheumatoid arthritis, given that it has been suggested that autoimmunity to these antigens results in the destruction of articular cartilage. The differential distribution of aggrecan within the TFCC is likely to be reflected by regional differences in water content and mobility on the radial and ulnar side. This needs to be taken into account in the design of improved MRI protocols for visualizing this ulnocarpal complex of the wrist. PMID:17532798

  1. A Survey of Genetic Variation and Genome Evolution within the Invasive Fallopia Complex

    PubMed Central

    Bzdega, Katarzyna; Janiak, Agnieszka; Książczyk, Tomasz; Lewandowska, Agata; Gancarek, Małgorzata; Sliwinska, Elwira; Tokarska-Guzik, Barbara

    2016-01-01

    The knotweed taxa Fallopia japonica, F. sachalinensis and their interspecific hybrid F. × bohemica are some of the most aggressive invaders in Europe and North America and they are serious threats to native biodiversity. At the same time, they constitute a unique model system for the creation of hybrids and studies of the initiation of evolutionary processes. In the presented study, we focused on (i) examining genetic diversity in selected populations of three Fallopia taxa in the invaded (Poland) and native ranges (Japan), (ii) establishing genome size and ploidy levels and (iii) identifying ribosomal DNA (rDNA)-bearing chromosomes in all of the taxa from the invaded range. We found that the genetic diversity within particular taxa was generally low regardless of their geographical origin. A higher level of clonality was observed for the Polish populations compared to the Japanese populations. Our study suggests that the co-occurrence of F. sachalinensis together with the other two taxa in the same stand may be the source of the higher genetic variation within the F. × bohemica hybrid. Some shift towards the contribution of F. japonica alleles was also observed for selected F. × bohemica individuals, which indicates the possibility of producing more advanced generations of F. × bohemica hybrids. All of the F. sachalinensis individuals were hexaploid (2n = 6x = 66; 2C = 6.01 pg), while those of F. japonica were mostly octoploid (2n = 8x = 88; 2C = 8.87 pg) and all of the F. × bohemica plants except one were hexaploid (2n = 6x = 66; 2C = 6.46 pg). Within the chromosome complement of F. japonica, F. sachalinensis and F. × bohemica, the physical mapping of the rDNA loci provided markers for 16, 13 and 10 chromosomes, respectively. In F. × bohemica, a loss of some of rDNA loci was observed, which indicates the occurrence of genome changes in the hybrid. PMID:27575805

  2. A Survey of Genetic Variation and Genome Evolution within the Invasive Fallopia Complex.

    PubMed

    Bzdega, Katarzyna; Janiak, Agnieszka; Książczyk, Tomasz; Lewandowska, Agata; Gancarek, Małgorzata; Sliwinska, Elwira; Tokarska-Guzik, Barbara

    2016-01-01

    The knotweed taxa Fallopia japonica, F. sachalinensis and their interspecific hybrid F. × bohemica are some of the most aggressive invaders in Europe and North America and they are serious threats to native biodiversity. At the same time, they constitute a unique model system for the creation of hybrids and studies of the initiation of evolutionary processes. In the presented study, we focused on (i) examining genetic diversity in selected populations of three Fallopia taxa in the invaded (Poland) and native ranges (Japan), (ii) establishing genome size and ploidy levels and (iii) identifying ribosomal DNA (rDNA)-bearing chromosomes in all of the taxa from the invaded range. We found that the genetic diversity within particular taxa was generally low regardless of their geographical origin. A higher level of clonality was observed for the Polish populations compared to the Japanese populations. Our study suggests that the co-occurrence of F. sachalinensis together with the other two taxa in the same stand may be the source of the higher genetic variation within the F. × bohemica hybrid. Some shift towards the contribution of F. japonica alleles was also observed for selected F. × bohemica individuals, which indicates the possibility of producing more advanced generations of F. × bohemica hybrids. All of the F. sachalinensis individuals were hexaploid (2n = 6x = 66; 2C = 6.01 pg), while those of F. japonica were mostly octoploid (2n = 8x = 88; 2C = 8.87 pg) and all of the F. × bohemica plants except one were hexaploid (2n = 6x = 66; 2C = 6.46 pg). Within the chromosome complement of F. japonica, F. sachalinensis and F. × bohemica, the physical mapping of the rDNA loci provided markers for 16, 13 and 10 chromosomes, respectively. In F. × bohemica, a loss of some of rDNA loci was observed, which indicates the occurrence of genome changes in the hybrid. PMID:27575805

  3. Major histocompatibility complex variation and mate choice in a lekking bird, the great snipe (Gallinago media).

    PubMed

    Ekblom, R; Saether, S A; Grahn, M; Fiske, P; Kålås, J A; Höglund, J

    2004-12-01

    Genes of the major histocompatibility complex (MHC) play a major part in the activation of the vertebrate immune system. In addition, they also appear to function as cues for mate choice. In mammals especially, several kinds of MHC-dependent mate choice have been hypothesized and observed. These include choice of mates that share no or few alleles with the choosing individual, choice of mates with alleles that differ as much as possible from the choosing individual, choice of heterozygous mates, choice of certain genotypes and choice of rare alleles. We investigated these different aspects of mate choice in relation to MHC in a lekking bird species, the great snipe (Gallinago media). We found no evidence for MHC disassortative mating, no preference for males with many MHC alleles and no preference for rare alleles. However, we did find that some allelic lineages were more often found in males with mating success than in males without mating success. Females do not seem to use themselves as references for the MHC-dependent mate choice, rather they seem to prefer males with certain allele types. We speculate that these alleles may be linked to resistance to common parasites. PMID:15548294

  4. Systems-Based Approaches to Probing Metabolic Variation within the Mycobacterium tuberculosis Complex

    PubMed Central

    Lofthouse, Emma K.; Wheeler, Paul R.; Beste, Dany J. V.; Khatri, Bhagwati L.; Wu, Huihai; Mendum, Tom A.; Kierzek, Andrzej M.; McFadden, Johnjoe

    2013-01-01

    The Mycobacterium tuberculosis complex includes bovine and human strains of the tuberculosis bacillus, including Mycobacterium tuberculosis, Mycobacterium bovis and the Mycobacterium bovis BCG vaccine strain. M. bovis has evolved from a M. tuberculosis-like ancestor and is the ancestor of the BCG vaccine. The pathogens demonstrate distinct differences in virulence, host range and metabolism, but the role of metabolic differences in pathogenicity is poorly understood. Systems biology approaches have been used to investigate the metabolism of M. tuberculosis, but not to probe differences between tuberculosis strains. In this study genome scale metabolic networks of M. bovis and M. bovis BCG were constructed and interrogated, along with a M. tuberculosis network, to predict substrate utilisation, gene essentiality and growth rates. The models correctly predicted 87-88% of high-throughput phenotype data, 75-76% of gene essentiality data and in silico-predicted growth rates matched measured rates. However, analysis of the metabolic networks identified discrepancies between in silico predictions and in vitro data, highlighting areas of incomplete metabolic knowledge. Additional experimental studies carried out to probe these inconsistencies revealed novel insights into the metabolism of these strains. For instance, that the reduction in metabolic capability observed in bovine tuberculosis strains, as compared to M. tuberculosis, is not reflected by current genetic or enzymatic knowledge. Hence, the in silico networks not only successfully simulate many aspects of the growth and physiology of these mycobacteria, but also provide an invaluable tool for future metabolic studies. PMID:24098743

  5. 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.

  6. Variation of geometries and electron properties along proton transfer in strong hydrogen-bond complexes

    NASA Astrophysics Data System (ADS)

    Pacios, L. F.; Gálvez, O.; Gómez, P. C.

    2005-06-01

    Proton transfer in hydrogen-bond systems formed by 4-methylimidazole in both neutral and protonated cationic forms and by acetate anion are studied by means of MP2/6-311++G(d,p) ab initio calculations. These two complexes model the histidine (neutral and protonated)-aspartate diad present in the active sites of enzymes the catalytic mechanism of which involves the formation of strong hydrogen bonds. We investigate the evolution of geometries, natural bond orbital populations of bonds and electron lone pairs, topological descriptors of the electron density, and spatial distributions of the electron localization function along the process N-H ⋯O→N⋯H⋯O→N⋯H-O, which represents the stages of the H-transfer. Except for a sudden change in the population of electron lone pairs in N and O at the middle N...H...O stage, all the properties analyzed show a smooth continuous behavior along the covalent → hydrogen bond transit inherent to the transfer, without any discontinuity that could identify a formation or breaking of the hydrogen bond. This way, the distinction between covalent or hydrogen-bonding features is associated to subtle electron rearrangement at the intermolecular space.

  7. Inter- versus Intramolecular Structural Manipulation of a Dichromium(II) Pacman Complex through Pressure Variation.

    PubMed

    Stevens, Charlotte J; Prescimone, Alessandro; Tuna, Floriana; McInnes, Eric J L; Parsons, Simon; Morrison, Carole A; Arnold, Polly L; Love, Jason B

    2016-01-01

    The effect of pressure on the intranuclear M···M separation and intermolecular secondary interactions in the dinuclear chromium Pacman complex [Cr2(L)](C6H6) was evaluated because this compound contains both a short Cr···Cr separation and an exogenously bound molecule of benzene in the solid state. The electronic structure of [Cr2(L)] was determined by electron paramagnetic resonance spectroscopy, SQUID magnetometry, and density functional theory calculations and shows a diamagnetic ground state through antiferromagnetic exchange, with no evidence for a Cr-Cr bond. Analysis of the solid-state structures of [Cr2(L)](C6H6) at pressures varying from ambient to 3.0 GPa shows little deformation in the Cr···Cr separation, i.e., no Cr-Cr bond formation, but instead a significantly increased interaction between the exogenous arene and the chromium iminopyrrolide environment. It is therefore apparent from this analysis that [Cr2(L)] would be best exploited as a rigid chemical synthon, with pressure regulation being used to mediate the approach and secondary interactions of possible substrates. PMID:26683991

  8. Embracing the complexity of matricellular proteins: the functional and clinical significance of splice variation.

    PubMed

    Viloria, Katrina; Hill, Natasha J

    2016-05-01

    Matricellular proteins influence wide-ranging fundamental cellular processes including cell adhesion, migration, growth and differentiation. They achieve this both through interactions with cell surface receptors and regulation of the matrix environment. Many matricellular proteins are also associated with diverse clinical disorders including cancer and diabetes. Alternative splicing is a precisely regulated process that can produce multiple isoforms with variable functions from a single gene. To date, the expression of alternate transcripts for the matricellular family has been reported for only a handful of genes. Here we analyse the evidence for alternative splicing across the matricellular family including the secreted protein acidic and rich in cysteine (SPARC), thrombospondin, tenascin and CCN families. We find that matricellular proteins have double the average number of splice variants per gene, and discuss the types of domain affected by splicing in matricellular proteins. We also review the clinical significance of alternative splicing for three specific matricellular proteins that have been relatively well characterised: osteopontin (OPN), tenascin-C (TNC) and periostin. Embracing the complexity of matricellular splice variants will be important for understanding the sometimes contradictory function of these powerful regulatory proteins, and for their effective clinical application as biomarkers and therapeutic targets. PMID:27135623

  9. Complexity and diversity of F8 genetic variations in the 1000 genomes

    PubMed Central

    Li, J. N.; Carrero, I. G.; Dong, J. F.; Yu, F. L.

    2016-01-01

    Summary Background Hemophilia A (HA) is an X-linked bleeding disorder caused by deleterious mutations in the coagulation factor VIII gene (F8). To date, F8 mutations have been documented predominantly in European subjects and in American subjects of European descent. Information on F8 variants in individuals of more diverse ethnic backgrounds is limited. Objectives To discover novel and rare F8 variants, and to characterize F8 variants in diverse population backgrounds. Patients/methods We analyzed 2535 subjects, including 26 different ethnicities, whose data were available from the 1000 Genomes Project (1000G) phase 3 dataset, for F8 variants and their potential functional impact. Results We identified 3030 single nucleotide variants, 31 short deletions and insertions (Indels) and a large, 497 kb, deletion. Among all variants, 86.4% were rare variants and 55.6% were novel. Eighteen variants previously associated with HA were found in our study. Most of these ‘HA variants’ were ethnic-specific with low allele frequency; however, one variant (p.M2257V) was present in 27% of African subjects. The p.E132D, p.T281A, p.A303V and p.D422H ‘HA variants’ were identified only in males. Twelve novel missense variants were predicted to be deleterious. The large deletion was discovered in eight female subjects without affecting F8 transcription and the transcription of genes on the X chromosome. Conclusion Characterizing F8 in the 1000G project highlighted the complexity of F8 variants and the importance of interrogating genetic variants on multiple ethnic backgrounds for associations with bleeding and thrombosis. The haplotype analysis and the orientation of duplicons that flank the large deletion suggested that the deletion was recurrent and originated by homologous recombination. PMID:26383047

  10. 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

  11. Variation in the Complex Carbohydrate Biosynthesis Loci of Acinetobacter baumannii Genomes

    PubMed Central

    Kenyon, Johanna J.; Hall, Ruth M.

    2013-01-01

    Extracellular polysaccharides are major immunogenic components of the bacterial cell envelope. However, little is known about their biosynthesis in the genus Acinetobacter, which includes A. baumannii, an important nosocomial pathogen. Whether Acinetobacter sp. produce a capsule or a lipopolysaccharide carrying an O antigen or both is not resolved. To explore these issues, genes involved in the synthesis of complex polysaccharides were located in 10 complete A. baumannii genome sequences, and the function of each of their products was predicted via comparison to enzymes with a known function. The absence of a gene encoding a WaaL ligase, required to link the carbohydrate polymer to the lipid A-core oligosaccharide (lipooligosaccharide) forming lipopolysaccharide, suggests that only a capsule is produced. Nine distinct arrangements of a large capsule biosynthesis locus, designated KL1 to KL9, were found in the genomes. Three forms of a second, smaller variable locus, likely to be required for synthesis of the outer core of the lipid A-core moiety, were designated OCL1 to OCL3 and also annotated. Each K locus includes genes for capsule export as well as genes for synthesis of activated sugar precursors, and for glycosyltransfer, glycan modification and oligosaccharide repeat-unit processing. The K loci all include the export genes at one end and genes for synthesis of common sugar precursors at the other, with a highly variable region that includes the remaining genes in between. Five different capsule loci, KL2, KL6, KL7, KL8 and KL9 were detected in multiply antibiotic resistant isolates belonging to global clone 2, and two other loci, KL1 and KL4, in global clone 1. This indicates that this region is being substituted repeatedly in multiply antibiotic resistant isolates from these clones. PMID:23614028

  12. 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

  13. 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

  14. A quasi-optimal coarse problem and an augmented Krylov solver for the variational theory of complex rays

    NASA Astrophysics Data System (ADS)

    Kovalevsky, Louis; Gosselet, Pierre

    2016-09-01

    The Variational Theory of Complex Rays (VTCR) is an indirect Trefftz method designed to study systems governed by Helmholtz-like equations. It uses wave functions to represent the solution inside elements, which reduces the dispersion error compared to classical polynomial approaches but the resulting system is prone to be ill conditioned. This paper gives a simple and original presentation of the VTCR using the discontinuous Galerkin framework and it traces back the ill-conditioning to the accumulation of eigenvalues near zero for the formulation written in terms of wave amplitude. The core of this paper presents an efficient solving strategy that overcomes this issue. The key element is the construction of a search subspace where the condition number is controlled at the cost of a limited decrease of attainable precision. An augmented LSQR solver is then proposed to solve efficiently and accurately the complete system. The approach is successfully applied to different examples.

  15. 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

  16. Complex control of GABA(A) receptor subunit mRNA expression: variation, covariation, and genetic regulation.

    PubMed

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

    2012-01-01

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

  17. Dominant Genetic Variation and Missing Heritability for Human Complex Traits: Insights from Twin versus Genome-wide Common SNP Models

    PubMed Central

    Chen, Xu; Kuja-Halkola, Ralf; Rahman, Iffat; Arpegård, Johannes; Viktorin, Alexander; Karlsson, Robert; Hägg, Sara; Svensson, Per; Pedersen, Nancy L.; Magnusson, Patrik K.E.

    2015-01-01

    In order to further illuminate the potential role of dominant genetic variation in the “missing heritability” debate, we investigated the additive (narrow-sense heritability, h2) and dominant (δ2) genetic variance for 18 human complex traits. Within the same study base (10,682 Swedish twins), we calculated and compared the estimates from classic twin-based structural equation model with SNP-based genomic-relatedness-matrix restricted maximum likelihood [GREML(d)] method. Contributions of δ2 were evident for 14 traits in twin models (average δ2twin = 0.25, range 0.14–0.49), two of which also displayed significant δ2 in the GREMLd analyses (triglycerides δ2SNP = 0.28 and waist circumference δ2SNP = 0.19). On average, the proportion of h2SNP/h2twin was 70% for ADE-fitted traits (for which the best-fitting model included additive and dominant genetic and unique environmental components) and 31% for AE-fitted traits (for which the best-fitting model included additive genetic and unique environmental components). Independent evidence for contribution from shared environment, also in ADE-fitted traits, was obtained from self-reported within-pair contact frequency and age at separation. We conclude that despite the fact that additive genetics appear to constitute the bulk of genetic influences for most complex traits, dominant genetic variation might often be masked by shared environment in twin and family studies and might therefore have a more prominent role than what family-based estimates often suggest. The risk of erroneously attributing all inherited genetic influences (additive and dominant) to the h2 in too-small twin studies might also lead to exaggerated “missing heritability” (the proportion of h2 that remains unexplained by SNPs). PMID:26544805

  18. Unexpected Actinyl Cation-Directed Structural Variation in Neptunyl(VI) A-Type Tri-lacunary Heteropolyoxotungstate Complexes.

    PubMed

    Berg, John M; Gaunt, Andrew J; May, Iain; Pugmire, Alison L; Reilly, Sean D; Scott, Brian L; Wilkerson, Marianne P

    2015-05-01

    A-type tri-lacunary heteropolyoxotungstate anions (e.g., [PW9O34](9-), [AsW9O34](9-), [SiW9O34](10-), and [GeW9O34](10-)) are multidentate oxygen donor ligands that readily form sandwich complexes with actinyl cations ({UO2}(2+), {NpO2}(+), {NpO2}(2+), and {PuO2}(2+)) in near-neutral/slightly alkaline aqueous solutions. Two or three actinyl cations are sandwiched between two tri-lacunary anions, with additional cations (Na(+), K(+), or NH4(+)) also often held within the cluster. Studies thus far have indicated that it is these additional +1 cations, rather than the specific actinyl cation, that direct the structural variation in the complexes formed. We now report the structural characterization of the neptunyl(VI) cluster complex (NH4)13[Na(NpO2)2(A-α-PW9O34)2]·12H2O. The anion in this complex, [Na(NpO2)2(PW9O34)2](13-), contains one Na(+) cation and two {NpO2}(2+) cations held between two [PW9O34](9-) anions, with an additional partial occupancy NH4(+) or {NpO2}(2+) cation also present. In the analogous uranium(VI) system, under similar reaction conditions that include an excess of NH4Cl in the parent solution, it was previously shown that [(NH4)2(U(VI)O2)2(A-PW9O34)2](12-) is the dominant species in both solution and the crystallized salt. Spectroscopic studies provide further proof of differences in the observed chemistry for the {NpO2}(2+)/[PW9O34](9-) and {UO2}(2+)/[PW9O34](9-) systems, both in solution and in solid state complexes crystallized from comparable salt solutions. This work reveals that varying the actinide element (Np vs U) can indeed measurably impact structure and complex stability in the cluster chemistry of actinyl(VI) cations with A-type tri-lacunary heteropolyoxotungstate anions. PMID:25901900

  19. Unexpected Actinyl Cation-Directed Structural Variation in Neptunyl(VI) A-Type Tri-lacunary Heteropolyoxotungstate Complexes

    DOE PAGESBeta

    Berg, John M.; Gaunt, Andrew J.; May, Iain; Pugmire, Alison L.; Reilly, Sean D.; Scott, Brian L.; Wilkerson, Marianne P.

    2015-04-22

    A-type tri-lacunary heteropolyoxotungstate anions (e.g., [PW9O34]9-, [AsW9O34]9-, [SiW9O34]10- and [GeW9O34]10-) are multi-dentate oxygen donor ligands that readily form sandwich complexes with actinyl cations ({UO2}2+, {NpO2}+, {NpO2}2+ & {PuO2}2+) in near neutral/slightly alkaline aqueous solutions. Two or three actinyl cations are sandwiched between two trilacunary anions, with additional cations (Na+, K+ or NH4 +) also often held within the cluster. Studies thus far have indicated that it is these additional +I cations, rather than the specific actinyl cation, that direct the structural variation in the complexes formed. We now report the structural characterization of the neptunyl (VI) cluster complex (NH4)13 [Na(NpO2)2(A-α-more » PW9O34)2]·12H2O. The anion in this complex, [Na(NpO2)2(PW9O34)2]13-, contains one Na+ cation and two {NpO2}2+ cations held between two [PW9O34]9- anions – with an additional partial occupancy NH4 + or {NpO2}2+ cation also present. In the analogous uranium (VI) system, under similar reaction conditions that includes an excess of NH4Cl in the parent solution, it was previously shown that [(NH4)2(UVIO2)2(A-PW9O34)2]12- is the dominant species in both solution and the crystallized salt. Spectroscopic studies provide further proof of differences in the observed chemistry for the {NpO2}2+/[PW9O34]9- and {UO2}2+/[PW9O34]9- systems, both in solution and in solid state complexes crystallized from comparable salt solutions. The work revealed that varying the actinide element (Np vs. U) can indeed measurably impact structure and complex stability in the cluster chemistry of actinyl (VI) cations with A-type tri-lacunary heteropolyoxotungstate anions.« less

  20. Complex mountain terrain and disturbance history drive variation in forest aboveground live carbon density in the western Oregon Cascades, USA

    PubMed Central

    Zald, Harold S.J.; Spies, Thomas A.; Seidl, Rupert; Pabst, Robert J.; Olsen, Keith A.; Steel, E. Ashley

    2016-01-01

    Forest carbon (C) density varies tremendously across space due to the inherent heterogeneity of forest ecosystems. Variation of forest C density is especially pronounced in mountainous terrain, where environmental gradients are compressed and vary at multiple spatial scales. Additionally, the influence of environmental gradients may vary with forest age and developmental stage, an important consideration as forest landscapes often have a diversity of stand ages from past management and other disturbance agents. Quantifying forest C density and its underlying environmental determinants in mountain terrain has remained challenging because many available data sources lack the spatial grain and ecological resolution needed at both stand and landscape scales. The objective of this study was to determine if environmental factors influencing aboveground live carbon (ALC) density differed between young versus old forests. We integrated aerial light detection and ranging (lidar) data with 702 field plots to map forest ALC density at a grain of 25 m across the H.J. Andrews Experimental Forest, a 6369 ha watershed in the Cascade Mountains of Oregon, USA. We used linear regressions, random forest ensemble learning (RF) and sequential autoregressive modeling (SAR) to reveal how mapped forest ALC density was related to climate, topography, soils, and past disturbance history (timber harvesting and wildfires). ALC increased with stand age in young managed forests, with much greater variation of ALC in relation to years since wildfire in old unmanaged forests. Timber harvesting was the most important driver of ALC across the entire watershed, despite occurring on only 23% of the landscape. More variation in forest ALC density was explained in models of young managed forests than in models of old unmanaged forests. Besides stand age, ALC density in young managed forests was driven by factors influencing site productivity, whereas variation in ALC density in old unmanaged forests

  1. 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.

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

    SciTech Connect

    Rampino, Sergio 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), Au{sub 7}– and Au{sub 20}–E (E = Hg, Cn, Pb, Fl, Rn) complexes, where Au{sub 7} (planar) and Au{sub 20} (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 Au{sub 20}-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.

  3. 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

  4. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus

    PubMed Central

    Sylvester, Kayla; Charron, Guillaume; Leducq, Jean-Baptiste; Landry, Christian R.; Libkind, Diego; Hittinger, Chris Todd

    2016-01-01

    Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes. PMID:27385107

  5. Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents

    PubMed Central

    Winternitz, Jamie C; Wares, John P

    2013-01-01

    Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high-amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model-averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC. PMID:23789067

  6. Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents.

    PubMed

    Winternitz, Jamie C; Wares, John P

    2013-06-01

    Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high-amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model-averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC. PMID:23789067

  7. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus.

    PubMed

    Peris, David; Langdon, Quinn K; Moriarty, Ryan V; Sylvester, Kayla; Bontrager, Martin; Charron, Guillaume; Leducq, Jean-Baptiste; Landry, Christian R; Libkind, Diego; Hittinger, Chris Todd

    2016-07-01

    Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes. PMID:27385107

  8. Delocalization error and "functional tuning" in Kohn-Sham calculations of molecular properties.

    PubMed

    Autschbach, Jochen; Srebro, Monika

    2014-08-19

    Kohn-Sham theory (KST) is the "workhorse" of numerical quantum chemistry. This is particularly true for first-principles calculations of ground- and excited-state properties for larger systems, including electronic spectra, electronic dynamic and static linear and higher order response properties (including nonlinear optical (NLO) properties), conformational or dynamic averaging of spectra and response properties, or properties that are affected by the coupling of electron and nuclear motion. This Account explores the sometimes dramatic impact of the delocalization error (DE) and possible benefits from the use of long-range corrections (LC) and "tuning" of functionals in KST calculations of molecular ground-state and response properties. Tuning refers to a nonempirical molecule-specific determination of adjustable parameters in functionals to satisfy known exact conditions, for instance, that the energy of the highest occupied molecular orbital (HOMO) should be equal to the negative vertical ionization potential (IP) or that the energy as a function of fractional electron numbers should afford straight-line segments. The presentation is given from the viewpoint of a chemist interested in computations of a variety of molecular optical and spectroscopic properties and of a theoretician developing methods for computing such properties with KST. In recent years, the use of LC functionals, functional tuning, and quantifying the DE explicitly have provided valuable insight regarding the performance of KST for molecular properties. We discuss a number of different molecular properties, with examples from recent studies from our laboratory and related literature. The selected properties probe different aspects of molecular electronic structure. Electric field gradients and hyperfine coupling constants can be exquisitely sensitive to the DE because it affects the ground-state electron density and spin density distributions. For π-conjugated molecules, it is shown how the

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

    PubMed

    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

  10. Unexpected Actinyl Cation-Directed Structural Variation in Neptunyl(VI) A-Type Tri-lacunary Heteropolyoxotungstate Complexes

    SciTech Connect

    Berg, John M.; Gaunt, Andrew J.; May, Iain; Pugmire, Alison L.; Reilly, Sean D.; Scott, Brian L.; Wilkerson, Marianne P.

    2015-04-22

    A-type tri-lacunary heteropolyoxotungstate anions (e.g., [PW9O34]9-, [AsW9O34]9-, [SiW9O34]10- and [GeW9O34]10-) are multi-dentate oxygen donor ligands that readily form sandwich complexes with actinyl cations ({UO2}2+, {NpO2}+, {NpO2}2+ & {PuO2}2+) in near neutral/slightly alkaline aqueous solutions. Two or three actinyl cations are sandwiched between two trilacunary anions, with additional cations (Na+, K+ or NH4 +) also often held within the cluster. Studies thus far have indicated that it is these additional +I cations, rather than the specific actinyl cation, that direct the structural variation in the complexes formed. We now report the structural characterization of the neptunyl (VI) cluster complex (NH4)13 [Na(NpO2)2(A-α- PW9O34)2]·12H2O. The anion in this complex, [Na(NpO2)2(PW9O34)2]13-, contains one Na+ cation and two {NpO2}2+ cations held between two [PW9O34]9- anions – with an additional partial occupancy NH4 + or {NpO2}2+ cation also present. In the analogous uranium (VI) system, under similar reaction conditions that includes an excess of NH4Cl in the parent solution, it was previously shown that [(NH4)2(UVIO2)2(A-PW9O34)2]12- is the dominant species in both solution and the crystallized salt. Spectroscopic studies provide further proof of differences in the observed chemistry for the {NpO2}2+

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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

    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

  17. 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.

  18. 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.

  19. 2D and 3D endoanal and translabial ultrasound measurement variation in normal postpartum measurements of the anal sphincter complex

    PubMed Central

    MERIWETHER, Kate V.; HALL, Rebecca J.; LEEMAN, Lawrence M.; MIGLIACCIO, Laura; QUALLS, Clifford; ROGERS, Rebecca G.

    2015-01-01

    Introduction Women may experience anal sphincter anatomy changes after vaginal or Cesarean delivery. Therefore, accurate and acceptable imaging options to evaluate the anal sphincter complex (ASC) are needed. ASC measurements may differ between translabial (TL-US) and endoanal ultrasound (EA-US) imaging and between 2D and 3D ultrasound. The objective of this analysis was to describe measurement variation between these modalities. Methods Primiparous women underwent 2D and 3D TL-US imaging of the ASC six months after a vaginal birth (VB) or Cesarean delivery (CD). A subset of women also underwent EA-US measurements. Measurements included the internal anal sphincter (IAS) thickness at proximal, mid, and distal levels and the external anal sphincter (EAS) at 3, 6, 9, and 12 o’clock positions as well as bilateral thickness of the pubovisceralis muscle (PVM). Results 433 women presented for US: 423 had TL-US and 64 had both TL-US and EA-US of the ASC. All IAS measurements were significantly thicker on TL-US than EA-US (all p<0.01), while EAS measurements were significantly thicker on EA-US (p<0.01). PVM measurements with 3D or 2D imaging were similar (p>0.20). On both TL-US and EA-US, there were multiple sites where significant asymmetry existed in left versus right measurements. Conclusion The ultrasound modality used to image the ASC introduces small but significant changes in measurements, and the direction of the bias depends on the muscle and location being imaged. PMID:25344221

  20. Major histocompatibility complex class II A genes in cichlid fishes: identification, expression, linkage relationships, and haplotype variation.

    PubMed

    Murray, B W; Shintani, S; Sültmann, H; Klein, J

    2000-06-01

    Two cichlid species, the haplochromine Aulonocara hansbaenschi and the tilapiine Oreochromis niloticus, were used to study the major histocompatibility complex (Mhc) class II A variation within this group. Multiple class II A sequences were recovered from A. hansbaenschi and O. niloticus cDNA libraries and three sequence families, DAA, DBA, and DCA, were identified. Sets of O. niloticus haploid embryo families were used to determine the linkage relationships of these genes. Two independently assorting linkage groups were detected, DAA and DBA/DCA, neither of which is linked to the previously described Mhc class I gene cluster. Three DCA genes and up to four DBA genes were found to segregate in different haplotypes, whereas DAA occurred as a single locus. Four DBA haplotypes, DBA*H1-H4, were identified and shown to co-segregate with the previously described class II B haplotypes. Four DCA haplotypes, DCA*H1-H4, were found at a distance of 37 cM from the DBA/class II B cluster; in one DCA haplotype, DCA*H5, the genes were tightly linked to the DBA/class II B clusters. Transcripts of DAA and DBA genes were found in O. niloticus hepatopancreas and spleen; transcripts of DCA genes were detected in the A. hansbaenschi cDNA library, but not in O. niloticus. These findings provide a basis for using class II haplotypes as markers in the study of adaptive radiation in the cichlid species flocks of the East African Great Lakes. PMID:10912508

  1. MN15-L: A New Local Exchange-Correlation Functional for Kohn-Sham Density Functional Theory with Broad Accuracy for Atoms, Molecules, and Solids.

    PubMed

    Yu, Haoyu S; He, Xiao; Truhlar, Donald G

    2016-03-01

    Kohn-Sham density functional theory is widely used for applications of electronic structure theory in chemistry, materials science, and condensed-matter physics, but the accuracy depends on the quality of the exchange-correlation functional. Here, we present a new local exchange-correlation functional called MN15-L that predicts accurate results for a broad range of molecular and solid-state properties including main-group bond energies, transition metal bond energies, reaction barrier heights, noncovalent interactions, atomic excitation energies, ionization potentials, electron affinities, total atomic energies, hydrocarbon thermochemistry, and lattice constants of solids. The MN15-L functional has the same mathematical form as a previous meta-nonseparable gradient approximation exchange-correlation functional, MN12-L, but it is improved because we optimized it against a larger database, designated 2015A, and included smoothness restraints; the optimization has a much better representation of transition metals. The mean unsigned error on 422 chemical energies is 2.32 kcal/mol, which is the best among all tested functionals, with or without nonlocal exchange. The MN15-L functional also provides good results for test sets that are outside the training set. A key issue is that the functional is local (no nonlocal exchange or nonlocal correlation), which makes it relatively economical for treating large and complex systems and solids. Another key advantage is that medium-range correlation energy is built in so that one does not need to add damped dispersion by molecular mechanics in order to predict accurate noncovalent binding energies. We believe that the MN15-L functional should be useful for a wide variety of applications in chemistry, physics, materials science, and molecular biology. PMID:26722866

  2. Human cognitive ability is influenced by genetic variation in components of postsynaptic signalling complexes assembled by NMDA receptors and MAGUK proteins.

    PubMed

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

    2014-01-01

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

  3. Accurate Kohn-Sham ionization potentials from scaled-opposite-spin second-order optimized effective potential methods.

    PubMed

    Śmiga, Szymon; Della Sala, Fabio; Buksztel, Adam; Grabowski, Ireneusz; Fabiano, Eduardo

    2016-08-15

    One important property of Kohn-Sham (KS) density functional theory is the exact equality of the energy of the highest occupied KS orbital (HOMO) with the negative ionization potential of the system. This exact feature is out of reach for standard density-dependent semilocal functionals. Conversely, accurate results can be obtained using orbital-dependent functionals in the optimized effective potential (OEP) approach. In this article, we investigate the performance, in this context, of some advanced OEP methods, with special emphasis on the recently proposed scaled-opposite-spin OEP functional. Moreover, we analyze the impact of the so-called HOMO condition on the final quality of the HOMO energy. Results are compared to reference data obtained at the CCSD(T) level of theory. © 2016 Wiley Periodicals, Inc. PMID:27357413

  4. Elliptic Preconditioner for Accelerating the Self-Consistent Field Iteration in Kohn--Sham Density Functional Theory

    SciTech Connect

    Lin, Lin; Yang, Chao

    2013-10-28

    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.

  5. A perturbation-method-based post-processing for the planewave discretization of Kohn-Sham models

    NASA Astrophysics Data System (ADS)

    Cancès, Eric; Dusson, Geneviève; Maday, Yvon; Stamm, Benjamin; Vohralík, Martin

    2016-02-01

    In this article, we propose a post-processing of the planewave solution of the Kohn-Sham LDA model with pseudopotentials. This post-processing is based upon the fact that the exact solution can be interpreted as a perturbation of the approximate solution, allowing us to compute corrections for both the eigenfunctions and the eigenvalues of the problem in order to increase the accuracy. Indeed, this post-processing only requires the computation of the residual of the solution on a finer grid so that the additional computational cost is negligible compared to the initial cost of the planewave-based method needed to compute the approximate solution. Theoretical estimates certify an increased convergence rate in the asymptotic convergence range. Numerical results confirm the low computational cost of the post-processing and show that this procedure improves the energy accuracy of the solution even in the pre-asymptotic regime which comprises the target accuracy of practitioners.

  6. 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.

  7. Patterns of Molecular Variation. II. Associations of Electrophoretic Mobility and Larval Substrate within Species of the DROSOPHILA MULLERI Complex

    PubMed Central

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

    1977-01-01

    Electromorphic variation among populations of Drosophila mojavensis, D. arizonensis and D. longicornis was examined for seven genetic loci. The average electrophoretic mobility for a population was used as the metric. D. mojavensis and D. arizonensis use larval substrates in different parts of their geographic ranges, while D. longicornis is more narrowly restricted to different species of the cactus Opuntia in different localities. There is marked electromorphic variation among populations of either D. mojavensis or D. arizonensis, and the bulk of this variation is accounted for by differences in laval substrate. There is somewhat less variation among populations of D. longicornis, and only a moderate portion of this is accounted for by larval substrate differences. There appears to be an association between the taxonomic diversity of the larval substrates and the electromorphic diversity of the Drosophila populations utilizing those substrates. Evidence is reviewed that suggests physiological mechanisms for these possibly adaptive associations. PMID:838268

  8. 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

  9. 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

  10. 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...

  11. Validation and application of auxiliary density perturbation theory and non-iterative approximation to coupled-perturbed Kohn-Sham approach for calculation of dipole-quadrupole polarizability

    NASA Astrophysics Data System (ADS)

    Shedge, Sapana V.; Pal, Sourav; Köster, Andreas M.

    2011-07-01

    Recently, two non-iterative approaches have been proposed to calculate response properties within density functional theory (DFT). These approaches are auxiliary density perturbation theory (ADPT) and the non-iterative approach to the coupled-perturbed Kohn-Sham (NIA-CPKS) method. Though both methods are non-iterative, they use different techniques to obtain the perturbed Kohn-Sham matrix. In this Letter, for the first time, both of these two independent methods have been used for the calculation of dipole-quadrupole polarizabilities. To validate these methods, three tetrahedral molecules viz., P4,CH4 and adamantane (C10H16) have been used as examples. The comparison with MP2 and CCSD proves the reliability of the methodology.

  12. Extended application of Kohn-Sham first-principles molecular dynamics method with plane wave approximation at high energy—From cold materials to hot dense plasmas

    NASA Astrophysics Data System (ADS)

    Zhang, Shen; Wang, Hongwei; Kang, Wei; Zhang, Ping; He, X. T.

    2016-04-01

    An extended first-principles molecular dynamics (FPMD) method based on Kohn-Sham scheme is proposed to elevate the temperature limit of the FPMD method in the calculation of dense plasmas. The extended method treats the wave functions of high energy electrons as plane waves analytically and thus expands the application of the FPMD method to the region of hot dense plasmas without suffering from the formidable computational costs. In addition, the extended method inherits the high accuracy of the Kohn-Sham scheme and keeps the information of electronic structures. This gives an edge to the extended method in the calculation of mixtures of plasmas composed of heterogeneous ions, high-Z dense plasmas, lowering of ionization potentials, X-ray absorption/emission spectra, and opacities, which are of particular interest to astrophysics, inertial confinement fusion engineering, and laboratory astrophysics.

  13. 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

  14. The static response function in Kohn-Sham theory: An appropriate basis for its matrix representation in case of finite AO basis sets

    SciTech Connect

    Kollmar, Christian Neese, Frank

    2014-10-07

    The role of the static Kohn-Sham (KS) response function describing the response of the electron density to a change of the local KS potential is discussed in both the theory of the optimized effective potential (OEP) and the so-called inverse Kohn-Sham problem involving the task to find the local KS potential for a given electron density. In a general discussion of the integral equation to be solved in both cases, it is argued that a unique solution of this equation can be found even in case of finite atomic orbital basis sets. It is shown how a matrix representation of the response function can be obtained if the exchange-correlation potential is expanded in terms of a Schmidt-orthogonalized basis comprising orbitals products of occupied and virtual orbitals. The viability of this approach in both OEP theory and the inverse KS problem is illustrated by numerical examples.

  15. Stability conditions for exact-exchange Kohn-Sham methods and their relation to correlation energies from the adiabatic-connection fluctuation-dissipation theorem

    SciTech Connect

    Bleiziffer, Patrick Schmidtel, Daniel; Görling, Andreas

    2014-11-28

    The occurrence of instabilities, in particular singlet-triplet and singlet-singlet instabilities, in the exact-exchange (EXX) Kohn-Sham method is investigated. Hessian matrices of the EXX electronic energy with respect to the expansion coefficients of the EXX effective Kohn-Sham potential in an auxiliary basis set are derived. The eigenvalues of these Hessian matrices determine whether or not instabilities are present. Similar as in the corresponding Hartree-Fock case instabilities in the EXX method are related to symmetry breaking of the Hamiltonian operator for the EXX orbitals. In the EXX methods symmetry breaking can easily be visualized by displaying the local multiplicative exchange potential. Examples (N{sub 2}, O{sub 2}, and the polyyne C{sub 10}H{sub 2}) for instabilities and symmetry breaking are discussed. The relation of the stability conditions for EXX methods to approaches calculating the Kohn-Sham correlation energy via the adiabatic-connection fluctuation-dissipation (ACFD) theorem is discussed. The existence or nonexistence of singlet-singlet instabilities in an EXX calculation is shown to indicate whether or not the frequency-integration in the evaluation of the correlation energy is singular in the EXX-ACFD method. This method calculates the Kohn-Sham correlation energy through the ACFD theorem theorem employing besides the Coulomb kernel also the full frequency-dependent exchange kernel and yields highly accurate electronic energies. For the case of singular frequency-integrands in the EXX-ACFD method a regularization is suggested. Finally, we present examples of molecular systems for which the self-consistent field procedure of the EXX as well as the Hartree-Fock method can converge to more than one local minimum depending on the initial conditions.

  16. Bioassays for TSH Receptor Autoantibodies, from FRTL-5 Cells to TSH Receptor–LH/CG Receptor Chimeras: The Contribution of Leonard D. Kohn

    PubMed Central

    Giuliani, Cesidio; Saji, Motoyasu; Bucci, Ines; Napolitano, Giorgio

    2016-01-01

    Since the discovery 60 years ago of the “long-acting thyroid stimulator” by Adams and Purves, great progress has been made in the detection of thyroid-stimulating hormone (TSH) receptor (TSHR) autoantibodies (TRAbs) in Graves’ disease. Today, commercial assays are available that can detect TRAbs with high accuracy and provide diagnostic and prognostic evaluation of patients with Graves’ disease. The present review focuses on the development of TRAbs bioassays, and particularly on the role that Leonard D. Kohn had in this. Indeed, 30 years ago, the Kohn group developed a bioassay based on the use of FRTL-5 cells that was characterized by high reproducibility, feasibility, and diagnostic accuracy. Using this FRTL-5 bioassay, Kohn and his colleagues were the first to develop monoclonal antibodies (moAbs) against the TSHR. Furthermore, they demonstrated the multifaceted functional nature of TRAbs in patients with Graves’ disease, with the identification of stimulating and blocking TRAbs, and even antibodies that activated pathways other than cAMP. After the cloning of the TSHR, the Kohn laboratory constructed human TSHR–rat luteinizing hormone/chorionic gonadotropin receptor chimeras. This paved the way to a new bioassay based on the use of non-thyroid cells transfected with the Mc4 chimera. The new Mc4 bioassay is characterized by high diagnostic and prognostic accuracy, greater than for other assays. The availability of a commercial kit based on the Mc4 chimera is spreading the use of this assay worldwide, indicating its benefits for these patients with Graves’ disease. This review also describes the main contributions made by other researchers in TSHR molecular biology and TRAbs assay, especially with the development of highly potent moAbs. A comparison of the diagnostic accuracies of the main TRAbs assays, as both immunoassays and bioassays, is also provided. PMID:27504107

  17. Bioassays for TSH Receptor Autoantibodies, from FRTL-5 Cells to TSH Receptor-LH/CG Receptor Chimeras: The Contribution of Leonard D. Kohn.

    PubMed

    Giuliani, Cesidio; Saji, Motoyasu; Bucci, Ines; Napolitano, Giorgio

    2016-01-01

    Since the discovery 60 years ago of the "long-acting thyroid stimulator" by Adams and Purves, great progress has been made in the detection of thyroid-stimulating hormone (TSH) receptor (TSHR) autoantibodies (TRAbs) in Graves' disease. Today, commercial assays are available that can detect TRAbs with high accuracy and provide diagnostic and prognostic evaluation of patients with Graves' disease. The present review focuses on the development of TRAbs bioassays, and particularly on the role that Leonard D. Kohn had in this. Indeed, 30 years ago, the Kohn group developed a bioassay based on the use of FRTL-5 cells that was characterized by high reproducibility, feasibility, and diagnostic accuracy. Using this FRTL-5 bioassay, Kohn and his colleagues were the first to develop monoclonal antibodies (moAbs) against the TSHR. Furthermore, they demonstrated the multifaceted functional nature of TRAbs in patients with Graves' disease, with the identification of stimulating and blocking TRAbs, and even antibodies that activated pathways other than cAMP. After the cloning of the TSHR, the Kohn laboratory constructed human TSHR-rat luteinizing hormone/chorionic gonadotropin receptor chimeras. This paved the way to a new bioassay based on the use of non-thyroid cells transfected with the Mc4 chimera. The new Mc4 bioassay is characterized by high diagnostic and prognostic accuracy, greater than for other assays. The availability of a commercial kit based on the Mc4 chimera is spreading the use of this assay worldwide, indicating its benefits for these patients with Graves' disease. This review also describes the main contributions made by other researchers in TSHR molecular biology and TRAbs assay, especially with the development of highly potent moAbs. A comparison of the diagnostic accuracies of the main TRAbs assays, as both immunoassays and bioassays, is also provided. PMID:27504107

  18. Efficient Parallel All-Electron Four-Component Dirac-Kohn-Sham Program Using a Distributed Matrix Approach II.

    PubMed

    Storchi, Loriano; Rampino, Sergio; Belpassi, Leonardo; Tarantelli, Francesco; Quiney, Harry M

    2013-12-10

    We propose a new complete memory-distributed algorithm, which significantly improves the parallel implementation of the all-electron four-component Dirac-Kohn-Sham (DKS) module of BERTHA (J. Chem. Theory Comput. 2010, 6, 384). We devised an original procedure for mapping the DKS matrix between an efficient integral-driven distribution, guided by the structure of specific G-spinor basis sets and by density fitting algorithms, and the two-dimensional block-cyclic distribution scheme required by the ScaLAPACK library employed for the linear algebra operations. This implementation, because of the efficiency in the memory distribution, represents a leap forward in the applicability of the DKS procedure to arbitrarily large molecular systems and its porting on last-generation massively parallel systems. The performance of the code is illustrated by some test calculations on several gold clusters of increasing size. The DKS self-consistent procedure has been explicitly converged for two representative clusters, namely Au20 and Au34, for which the density of electronic states is reported and discussed. The largest gold cluster uses more than 39k basis functions and DKS matrices of the order of 23 GB. PMID:26592273

  19. More realistic band gaps from meta-generalized gradient approximations: Only in a generalized Kohn-Sham scheme

    NASA Astrophysics Data System (ADS)

    Yang, Zeng-hui; Peng, Haowei; Sun, Jianwei; Perdew, John P.

    2016-05-01

    Unlike the local density approximation (LDA) and the generalized gradient approximation (GGA), calculations with meta-generalized gradient approximations (meta-GGA) are usually done according to the generalized Kohn-Sham (gKS) formalism. The exchange-correlation potential of the gKS equation is nonmultiplicative, which prevents systematic comparison of meta-GGA band structures to those of the LDA and the GGA. We implement the optimized effective potential (OEP) of the meta-GGA for periodic systems, which allows us to carry out meta-GGA calculations in the same KS manner as for the LDA and the GGA. We apply the OEP to several meta-GGAs, including the new SCAN functional [Phys. Rev. Lett. 115, 036402 (2015), 10.1103/PhysRevLett.115.036402]. We find that the KS gaps and KS band structures of meta-GGAs are close to those of GGAs. They are smaller than the more realistic gKS gaps of meta-GGAs, but probably close to the less-realistic gaps in the band structure of the exact KS potential, as can be seen by comparing with the gaps of the EXX+RPA OEP potential. The well-known grid sensitivity of meta-GGAs is much more severe in OEP calculations.

  20. 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.

  1. Inelastic light and electron scattering in parabolic quantum dots in magnetic field: Implications of generalized Kohn's theorem

    NASA Astrophysics Data System (ADS)

    Kushwaha, Manvir S.

    2016-03-01

    We investigate a one-component, quasi-zero-dimensional, quantum plasma exposed to a parabolic potential and an applied magnetic field in the symmetric gauge. If the size of such a system as can be realized in the semiconducting quantum dots is on the order of the de Broglie wavelength, the electronic and optical properties become highly tunable. Then the quantum size effects challenge the observation of many-particle phenomena such as the magneto-optical absorption, Raman intensity, and electron energy loss spectrum. An exact analytical solution of the problem leads us to infer that these many-particle phenomena are, in fact, dictated by the generalized Kohn's theorem in the long-wavelength limit. Maneuvering the confinement and/or the magnetic field furnishes the resonance energy capable of being explored with the FIR, Raman, or electron energy loss spectroscopy. This implies that either of these probes should be competent in observing the localized magnetoplasmons in the system. A deeper insight into the physics of quantum dots is paving the way for their implementation in diverse fields such as quantum computing and medical imaging.

  2. Fermi energy dependence of first- and second-order Raman spectra in graphene: Kohn anomaly and quantum interference effect

    NASA Astrophysics Data System (ADS)

    Hasdeo, Eddwi H.; Nugraha, Ahmad R. T.; Dresselhaus, Mildred S.; Saito, Riichiro

    2016-08-01

    Intensities of the first- and the second-order Raman spectra are calculated as a function of the Fermi energy. We show that the Kohn anomaly effect, i.e., phonon frequency renormalization, in the first-order Raman spectra originates from the phonon renormalization by the interband electron-hole excitation, whereas in the second-order Raman spectra, a competition between the interband and intraband electron-hole excitations takes place. By this calculation, we confirm the presence of different dispersive behaviors of the Raman peak frequency as a function of the Fermi energy for the first- and the second-order Raman spectra, as observed in some previous experiments. Moreover, the calculated results of the Raman intensity sensitively depend on the Fermi energy for both the first- and the second-order Raman spectra, indicating the presence of the quantum interference effect. The electron-phonon matrix element plays an important role in the intensity increase (decrease) of the combination (overtone) phonon modes as a function of the Fermi energy.

  3. 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

  4. Challenges and complexities in estimating both the functional impact and the disease risk associated with the extensive genetic variation in human DNA repair genes.

    PubMed

    Mohrenweiser, Harvey W; Wilson, David M; Jones, Irene M

    2003-05-15

    Individual risk and the population incidence of disease result from the interaction of genetic susceptibility and exposure. DNA repair is an example of a cellular process where genetic variation in families with extreme predisposition is documented to be associated with high disease likelihood, including syndromes of premature aging and cancer. Although the identification and characterization of new genes or variants in cancer families continues to be important, the focus of this paper is the current status of efforts to define the impact of polymorphic amino acid substitutions in DNA repair genes on individual and population cancer risk. There is increasing evidence that mild reductions in DNA repair capacity, assumed to be the consequence of common genetic variation, affect cancer predisposition. The extensive variation being found in the coding regions of DNA repair genes and the large number of genes in each of the major repair pathways results in complex genotypes with potential to impact cancer risk in the general population. The implications of this complexity for molecular epidemiology studies, as well as concepts that may make these challenges more manageable, are discussed. The concepts include both experimental and computational approaches that could be employed to develop predictors of disease susceptibility based on DNA repair genotype, focusing initially on studies to assess functional impact on individual proteins and pathways and then on molecular epidemiology studies to assess exposure-dependent health risk. In closing, we raise some of the non-technical challenges to the utilization of the full richness of the genetic variation to reduce disease occurrence and ultimately improve health care. PMID:12714187

  5. 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...

  6. 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.

  7. 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

  8. The electronic structure of alkali aurides. A four-component Dirac-Kohn-Sham study.

    PubMed

    Belpassi, Leonardo; Tarantelli, Francesco; Sgamellotti, Antonio; Quiney, Harry M

    2006-04-01

    Spectroscopic constants, including dissociation energies, harmonic and anharmonic vibrational frequencies, and dipole moments, are calculated for the complete alkali auride series (LiAu, NaAu, KAu, RbAu, CsAu). The four-component formulation of relativistic density functional theory has been employed in this study, using the G-spinor basis sets implemented recently in the program BERTHA. The performance of four standard nonrelativistic density functionals employed is investigated by comparing the results with the best available theoretical and experimental data. The present work provides the first theoretical predictions on the molecular properties of RbAu. The intermetallic bond that occurs in the alkali auride series is highly polar and is characterized by a large charge transfer from the alkali metals to gold. The extent of this electron transfer has been investigated using several different charge analysis methods, enabling us to reach some general conclusions on their relative performance. We further report a detailed analysis of the topological properties of relativistic electron density in the bonding region, discussing the features of this approach which characterize the nature of the chemical bond. We have also computed the fully relativistic density for the alkali halides MBr and MI (M = Li, Na, K, Rb, and Cs). The comparative study shows that, on the basis of several topological properties and the variation in bond lengths, the gold atom behaves similarly to a halogen intermediate between Br and I. PMID:16571062

  9. Role of adaptive and non-adaptive mechanisms forming complex patterns of genome size variation in six cytotypes of polyploid Allium oleraceum (Amaryllidaceae) on a continental scale

    PubMed Central

    Duchoslav, Martin; Šafářová, Lenka; Jandová, Michaela

    2013-01-01

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

  10. Use of natural tracers to identify spatial and temporal variation in runoff sources in a complex, mountainous mesoscale catchment

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

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