Equivalence of the generalized and complex Kohn variational methods
J. N. Cooper; M. Plummer; E. A. G. Armour
2010-03-11
For Kohn variational calculations on low energy positron hydrogen molecule elastic scattering, we prove that the phase shift approximation obtained using the complex Kohn method is precisely equal to a value which can be obtained immediately via the real-generalized Kohn method. Our treatment is sufficiently general to be applied directly to arbitrary potential scattering or single open channel scattering problems, with exchange if required. In the course of our analysis, we develop a framework formally to describe the anomalous behaviour of our generalized Kohn calculations in the regions of the well known Schwartz singularities. This framework also explains the mathematical origin of the anomaly-free singularities we reported in a previous article. Moreover, we demonstrate a novelty, that explicit solutions of the Kohn equations are not required in order to calculate optimal phase shift approximations. We relate our rigorous framework to earlier descriptions of the Kohn-type methods.
The complex Kohn variational method applied to N-d scattering
Alejandro Kievsky
1997-06-24
The three-nucleon ground state and the N--d scattering states are obtained using variational principles. The wave function of the system is decomposed into angular-spin-isospin channels and the corresponding two dimensional spatial amplitudes are expanded in a correlated polynomial basis. For the scattering states, the complex form of the Kohn variational principle is used to determine the $S$--matrix. Special attention is given to the convergence pattern of the phase-shift and mixing parameters. The calculations have been performed using realistic local NN potentials and three-nucleon forces. Important features of the method are anomaly-free solutions and the low dimensionality of the matrices involved allowing for the inclusion of a large number of states. Very precise and stable numerical results have been obtained.
Anomaly-free singularities in the generalized Kohn variational method
J. N. Cooper; E. A. G. Armour; M. Plummer
2009-01-09
We have carried out an analysis of singularities in Kohn variational calculations for low energy e^{+}-H_{2} elastic scattering. Provided that a sufficiently accurate trial wavefunction is used, we argue that our implementation of the Kohn variational principle necessarily gives rise to singularities which are not spurious. We propose two approaches for optimizing a free parameter of the trial wavefunction in order to avoid anomalous behaviour in scattering phase shift calculations, the first of which is based on the existence of such singularities. The second approach is a more conventional optimization of the generalized Kohn method. Close agreement is observed between the results of the two optimization schemes; further, they give results which are seen to be effectively equivalent to those obtained with the complex Kohn method. The advantage of the first optimization scheme is that it does not require an explicit solution of the Kohn equations to be found. We give examples of anomalies which cannot be avoided using either optimization scheme but show that it is possible to avoid these anomalies by considering variations in the nonlinear parameters of the trial function.
Variational method for inverting the Kohn-Sham procedure
Kadantsev, Eugene S.; Stott, M.J. [Department of Physics, Queen's University, Kingston, Ontario, K7L 3N6 (Canada)
2004-01-01
A procedure based on a variational principle is developed for determining the local Kohn-Sham (KS) potential corresponding to a given ground-state electron density. This procedure is applied to calculate the exchange-correlation part of the effective Kohn-Sham (KS) potential for the neon atom and the methane molecule.
A pointwise representation of the s-matrix Kohn variational principle for quantum scattering
Andrew C. Peet; William H. Miller
1988-01-01
A method is proposed for reducing the complexity of scattering calculations carried out using the Kohn variational principle. The technique is based upon the use of a pointwise representation for the L2 part of the basis set and eliminates the need to explicitly evaluate any integrals involving such functions. Application to potential and inelastic scattering test cases show the method
Engel, Eberhard
Kohn-Sham perturbation theory: Simple solution to variational instability of second order resulting from second order Kohn-Sham perturbation theory leads to atomic correlation potentials we examine the simplest resummation of the Kohn-Sham perturbation series which has the potential
Nonexistence of a Hohenberg-Kohn variational principle in total current-density-functional theory
NASA Astrophysics Data System (ADS)
Laestadius, Andre; Benedicks, Michael
2015-03-01
For a many-electron system, whether the particle density ? (r ) and the total current density j (r ) are sufficent to determine the one-body potential V (r ) and vector potential A (r ) is still an open question. For the one-electron case, a Hohenberg-Kohn theorem exists formulated with the total current density. Here we show that the generalized Hohenberg-Kohn energy functional EV0,A0(? ,j ) = can be minimal for densities that are not the ground-state densities of the fixed potentials V0 and A0. Furthermore, for an arbitrary number of electrons and under the assumption that a Hohenberg-Kohn theorem exists formulated with ? and j , we discuss the possibility of a variational principle in total current-density-functional theory such as that of Hohenberg-Kohn.
M. Viviani; A. Kievsky; S. Rosati
2001-02-21
The Kohn variational principle is formulated for calculating elastic proton-deuteron scattering amplitudes at energies above the deuteron breakup threshold. The use of such a principle with an expansion of the wave function on the (correlated) hyperspherical harmonic basis is discussed.
Non-existence of a Hohenberg-Kohn Variational Principle in Total Current Density Functional Theory
Andre Laestadius; Michael Benedicks
2014-04-12
For a many-electron system, whether the particle density $\\rho(\\mathbf{r})$ and the total current density $\\mathbf{j}(\\mathbf{r})$ are sufficient to determine the one-body potential $V(\\mathbf{r})$ and vector potential $\\mathbf{A}(\\mathbf{r})$, is still an open question. For the one-electron case, a Hohenberg-Kohn theorem exists formulated with the total current density. Here we show that the generalized Hohenberg-Kohn energy functional $\\mathord{\\cal E}_{V_0,\\mathbf{A}_0}(\\rho,\\mathbf{j}) = \\langle \\psi(\\rho,\\mathbf{j}),H(V_0,\\mathbf{A}_0)\\psi(\\rho,\\mathbf{j})\\rangle$ can be minimal for densities that are not the ground-state densities of the fixed potentials $V_0$ and $\\mathbf{A}_0$. Furthermore, for an arbitrary number of electrons and under the assumption that a Hohenberg-Kohn theorem exists formulated with $\\rho$ and $\\mathbf{j}$, we show that a variational principle for Total Current Density Functional Theory as that of Hohenberg-Kohn for Density Functional Theory does not exist. The reason is that the assumed map from densities to the vector potential, written $(\\rho,\\mathbf{j})\\mapsto \\mathbf{A}(\\rho,\\mathbf{j};\\mathbf{r})$, enters explicitly in $\\mathord{\\cal E}_{V_0,\\mathbf{A}_0}(\\rho,\\mathbf{j})$.
Non-existence of a Hohenberg-Kohn Variational Principle in Total Current Density Functional Theory
Laestadius, Andre
2014-01-01
For a many-electron system, whether the particle density $\\rho(\\mathbf{r})$ and the total current density $\\mathbf{j}(\\mathbf{r})$ are sufficient to determine the one-body potential $V(\\mathbf{r})$ and vector potential $\\mathbf{A}(\\mathbf{r})$, is still an open question. For the one-electron case, a Hohenberg-Kohn theorem exists formulated with the total current density. Here we show that the generalized Hohenberg-Kohn energy functional $\\mathord{\\cal E}_{V_0,\\mathbf{A}_0}(\\rho,\\mathbf{j}) = \\langle \\psi(\\rho,\\mathbf{j}),H(V_0,\\mathbf{A}_0)\\psi(\\rho,\\mathbf{j})\\rangle$ can be minimal for densities that are not the ground-state densities of the fixed potentials $V_0$ and $\\mathbf{A}_0$. Furthermore, for an arbitrary number of electrons and under the assumption that a Hohenberg-Kohn theorem exists formulated with $\\rho$ and $\\mathbf{j}$, we show that a variational principle for Total Current Density Functional Theory as that of Hohenberg-Kohn for Density Functional Theory does not exist. The reason is that the ...
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,
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.
The Mathematics of Wrinkles and Folds Robert V. Kohn
The Mathematics of Wrinkles and Folds Robert V. Kohn Courant Institute, NYU NYU Mathematics Society, 2/2/2012 Robert V. Kohn Wrinkles and Folds #12;Wrinkles and folds We'll be talking about a little geometry and mechanics a lot of calculus of variations Robert V. Kohn Wrinkles and Folds #12;Paper
Linear complex polarization propagator in a four-component Kohn-Sham framework
Sebastien Villaume; Trond Saue; Patrick Norman
2010-01-01
An algorithm for the solution of the linear response equation in the random phase approximation is presented. All entities including frequency arguments, matrices, and vectors, are assumed to be complex, and it represents the core equation solver needed in complex polarization propagator approaches where nonstimulated relaxation channels are taken into account. Stability and robustness of the algorithm are demonstrated in
Miller, William H.
J. Phys. Chem. 1990, 94, 7785-7789 7785 Quasi-Adiabatic Basis Functions for the S-Matrix Kohn is described for carrying out reactive scattering calculations within the S-matrix version of the Kohn systematicallyby increasing the basis in a determined fashion. 1. Introduction The S-matrix version' of the Kohn
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…
A PARAMETRIX FOR KOHN'S OPERATOR BRIAN STREET
Street, Brian
A PARAMETRIX FOR KOHN'S OPERATOR BRIAN STREET Abstract. Recently, Kohn constructed examples of sums parametricies for Kohn's operators, which lead to the corresponding Lp (1 in Lipschitz and Lp Sobolev spaces (1 Kohn [Koh05] studied the analogous question
Kohn anomalies in graphene nanoribbons
Dresselhaus, Mildred
The quantum corrections to the energies of the ? point optical phonon modes (Kohn anomalies) in graphene nanoribbons (NRs) are investigated. We show theoretically that the longitudinal optical (LO) modes undergo a Kohn ...
Miller, William H.
-matrix Kohn method Daniel T. Colbert and William H. Miller Department of Chemistry, University of California as the L 2basis of the S- matrix version of the Kohn variational method [ Zhang, Chu, and Miller, J. Chem-matrix Kohn calculations. Test calculations for the collinear Cl + HCl-+ CIH + Cl reaction shows
Gross, E.K.U.
, and Their Correction, in the Ensemble-Kohn-Sham Scheme for Excited States N. I. Gidopoulos,1 P. G. Papaconstantinou,2-dependent Kohn-Sham equations [24]. In this Letter, we shall focus on the DFT for ensembles which,28]. On the basis of the ensemble variational principle, Hohenberg-Kohn (HK) and Kohn-Sham (KS) type theo- rems have
60 : DVD (9.1) 1998, Walter Kohn
Zexian, Cao
1/30 60 : DVD (9.1) 1998, Walter Kohn ""1998 Walter Kohn Chadwick "the royal joke". Kohn 80 Kohn 20090513 #12;2/30 (, ). ...... [] []: 100 50 ... 200(Huygens) () --- : Pharoah Akhenaten) , "" 300 " " #12;4/30 (Walter Kohn): , : . , : "" , ...... 1
A NEW CHARACTERIZATION OF THE CR SPHERE AND THE SHARP EIGENVALUE ESTIMATE FOR THE KOHN
Wang, Xiaodong
A NEW CHARACTERIZATION OF THE CR SPHERE AND THE SHARP EIGENVALUE ESTIMATE FOR THE KOHN LAPLACIAN of the Kohn Laplacian by Chanillo, Chiu and Yang [CCY], just as Theorem 1 is 1 #12;2 SONG-YING LI, DUONG NGOC of the sublaplacian b. Recall that the Kohn Laplacian on a (complex-valued) function f is defined by (1.2) bf = b bf
Paul E. Lammert
2015-02-08
The Hohenberg-Kohn theorem is a cornerstone of electronic density functional theory, yet completing its proof in the traditional way requires the {\\em assumption} that ground state wavefunctions never vanish on sets of nonzero Lebesgue measure. This is an unsatisfactory situation, since DFT is supposed to obviate knowledge of many-body wavefunctions. We approach the issue from a more density-centric direction, allowing mild hypotheses on the density which can be regarded as checkable in a DFT context. By ordinary Hilbert space analysis, the following is proved: If the density $\\rho$ is continuous and everywhere nonzero, then there can be at most one potential (modulo constants) expressible as a sum of a square-integrable and a bounded function (i.e., Kato-Rellich) with $\\rho$ as a ground state density. In case $\\rho$ is not nonzero everywhere, the theorem allows an independent constant on each connected component of the set where the density is positive, a weakening which can be reversed by requiring locally weak-$L^3$ potentials and calling on a unique continuation result of Schechter and Simon.
ERIC Educational Resources Information Center
Swan, Deborah
1997-01-01
An interview with educator-author Alfie Kohn discusses student motivation and the need to move away from giving rewards, praise as a form of control, the importance of genuine encouragement that fosters intrinsic motivation and lifelong learning, and the role of mentors in supporting teachers who seek to change or improve traditional teaching…
Human genetic variation and its contribution to complex traits
Sarah S. Murray; Nicholas J. Schork; Eric J. Topol; Kelly A. Frazer
2009-01-01
The last few years have seen extensive efforts to catalogue human genetic variation and correlate it with phenotypic differences. Most common SNPs have now been assessed in genome-wide studies for statistical associations with many complex traits, including many important common diseases. Although these studies have provided new biological insights, only a limited amount of the heritable component of any complex
Axiomatic formulations of the Hohenberg-Kohn functional
Ayers, Paul W. [Department of Chemistry, McMaster University, Hamilton, Ontario, Canada L8S 4M1 (Canada)
2006-01-15
Properties of the Hohenberg-Kohn functional are considered. In particular, the Hohenberg-Kohn functional should (a) give correct results in the variational principle and should be (b) continuous, (c) convex, and (d) size consistent. All of these properties are satisfied by the Legendre-transform functional (equivalently, the density matrix constrained search functional) and, moreover, this is the only functional that possesses all these properties. Not only that, but the Legendre-transform functional is determined uniquely by requiring (a) (b), and either (c) or (d). This shows how an 'axiomatic' approach to constructing the Hohenberg-Kohn functional leads naturally to the Legendre-transform functional. Among all functionals consistent with the variational principle, the Legendre-transform functional is the smallest. One corollary to this approach is a simple proof of the equivalence of the Legendre-transform and density-matrix constrained search functionals. For completeness, the Appendix shows that ensemble-v-representable densities lie dense in the set of N-representable densities.
On the Occasion of the Birthday of Walter Kohn
Geller, Michael R.
#12;#12;On the Occasion of the 80th Birthday of Walter Kohn #12;Walter Kohn receiving his Prize: Hans Mehlin) #12;Preface All of Walter Kohn's personal friends readily agree that it is almost unthink could not be banished VII #12;Preface Walter Kohn, Thanksgiving in Santa Barbara, 2002 (photo: M
Anderson and Kohn, page 1 Dikaryons, diploids, and evolution
Anderson, James B.
Anderson and Kohn, page 1 - Dikaryons, diploids, and evolution James B. Anderson and Linda M Kohn@utm.utoronto.ca #12;Anderson and Kohn, page 2 - The regular association of unfused, haploid, gametic- type nuclei genomes follow different rules, iii) #12;Anderson and Kohn, page 3 - dikaryons produce recombinant
Epistasis and balanced polymorphism influencing complex trait variation
Juergen Kroymann; Thomas Mitchell-Olds
2005-01-01
Complex traits such as human disease, growth rate, or crop yield are polygenic, or determined by the contributions from numerous genes in a quantitative manner. Although progress has been made in identifying major quantitative trait loci (QTL), experimental constraints have limited our knowledge of small-effect QTL, which may be responsible for a large proportion of trait variation. Here, we identified
Kohn-Luttinger effect in gauge theories
Schaefer, T. [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695 (United States)
2006-09-01
Kohn and Luttinger showed that a many body system of fermions interacting via short range forces becomes superfluid even if the interaction is repulsive in all partial waves. In gauge theories such as QCD the interaction between fermions is long range and the assumptions of Kohn and Luttinger are not satisfied. We show that in a U(1) gauge theory the Kohn-Luttinger phenomenon does not take place. In QCD attractive channels always exist, but there are cases in which the primary pairing channel leaves some fermions ungapped. As an example we consider the unpaired fermion in the 2SC phase of QCD with two flavors. We show that it acquires a very small gap via a mechanism analogous to the Kohn-Luttinger effect. The gap is too small to be phenomenologically relevant.
Calculus structure on the Lie conformal algebra complex and the variational complex
De Sole, Alberto [Dipartimento di Matematica, Universita di Roma ''La Sapienza'', 00185 Roma (Italy); Hekmati, Pedram [School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005 (Australia); Kac, Victor G. [Department of Mathematics, MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States)
2011-05-15
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.
Major histocompatibility complex variation in the endangered Przewalski's horse.
Hedrick, P W; Parker, K M; Miller, E L; Miller, P S
1999-01-01
The major histocompatibility complex (MHC) is a fundamental part of the vertebrate immune system, and the high variability in many MHC genes is thought to play an essential role in recognition of parasites. The Przewalski's horse is extinct in the wild and all the living individuals descend from 13 founders, most of whom were captured around the turn of the century. One of the primary genetic concerns in endangered species is whether they have ample adaptive variation to respond to novel selective factors. In examining 14 Przewalski's horses that are broadly representative of the living animals, we found six different class II DRB major histocompatibility sequences. The sequences showed extensive nonsynonymous variation, concentrated in the putative antigen-binding sites, and little synonymous variation. Individuals had from two to four sequences as determined by single-stranded conformation polymorphism (SSCP) analysis. On the basis of the SSCP data, phylogenetic analysis of the nucleotide sequences, and segregation in a family group, we conclude that four of these sequences are from one gene (although one sequence codes for a nonfunctional allele because it contains a stop codon) and two other sequences are from another gene. The position of the stop codon is at the same amino-acid position as in a closely related sequence from the domestic horse. Because other organisms have extensive variation at homologous loci, the Przewalski's horse may have quite low variation in this important adaptive region. PMID:10430594
A mesh-free convex approximation scheme for Kohn-Sham density functional theory
Suryanarayana, Phanish [Division of Engineering and Applied Science, California Institute of Technology, CA 91125 (United States); Bhattacharya, Kaushik, E-mail: bhatta@caltech.ed [Division of Engineering and Applied Science, California Institute of Technology, CA 91125 (United States); Ortiz, Michael [Division of Engineering and Applied Science, California Institute of Technology, CA 91125 (United States)
2011-06-10
Density functional theory developed by Hohenberg, Kohn and Sham is a widely accepted, reliable ab initio method. We present a non-periodic, real space, mesh-free convex approximation scheme for Kohn-Sham density functional theory. We rewrite the original variational problem as a saddle point problem and discretize it using basis functions which form the Pareto optimum between competing objectives of maximizing entropy and minimizing the total width of the approximation scheme. We show the utility of the approximation scheme in performing both all-electron and pseudopotential calculations, the results of which are in good agreement with literature.
LOCAL SAMPLING AND APPROXIMATION OF OPERATORS WITH BANDLIMITED KOHN-NIRENBERG SYMBOLS
Pfander, GÃ¶tz
LOCAL SAMPLING AND APPROXIMATION OF OPERATORS WITH BANDLIMITED KOHN-NIRENBERG SYMBOLS FELIX KRAHMER with bandlimited Kohn-Nirenberg symbols from their response to a single discretely supported identifier signal Kohn-Nirenberg symbol. Keywords. Operator identification, pseudodifferential operators, Kohn
Morphological Variation in Leaf Dissection of Rheum palmatum Complex (Polygonaceae)
Wang, Xu-Mei; Hou, Xiao-Qi; Zhang, Yu-Qu; Li, Yan
2014-01-01
Aims Rheum palmatum complex comprises all taxa within section Palmata in the genus Rheum, including R. officinale, R. palmatum, R. tanguticum, R. tanguticum var. liupanshanense and R. laciniatum. The identification of the taxa in section Palmata is based primarily on the degree of leaf blade dissection and the shape of the lobes; however, difficulties in species identification may arise from their significant variation. The aim of this study is to analyze the patterns of variation in leaf blade characteristics within and among populations through population-based sampling covering the entire distribution range of R. palmatum complex. Methods Samples were taken from 2340 leaves from 780 individuals and 44 populations representing the four species, and the degree of leaf blade dissection and the shape of the lobe were measured to yield a set of quantitative data. Furthermore, those data were statistically analyzed. Important Findings The statistical analysis showed that the degree of leaf blade dissection is continuous from lobed to parted, and the shape of the lobe is also continuous from broadly triangular to lanceolate both within and between populations. We suggested that taxa in section Palmata should be considered as one species. Based on the research on the R. palmatum complex, we considered that the quantitative characteristics were greatly influenced by the environment. Therefore, it is not reliable to delimitate the species according to the continuously quantitative vegetative characteristics. PMID:25349989
Genetic Encoding Strategies for Neural Networks Philipp Kohn
Koehn, Philipp
Genetic Encoding Strategies for Neural Networks Philipp K¨ohn University of Tennessee --- Universit¨at ErlangenN¨urnberg Dreibergstr. 5, 91056 Erlangen, Germany kohn@cs.utk.edu Abstract The application
Parabolic PDEs and Deterministic Games Robert V. Kohn
Parabolic PDEs and Deterministic Games Robert V. Kohn Courant Institute, NYU Joint work with Sylvia Serfaty ICIAM07, Zurich, July 2007 Robert V. Kohn Courant Institute, NYU Parabolic PDEs and Deterministic. Kohn Courant Institute, NYU Parabolic PDEs and Deterministic Games #12;Goals and perspective Part 1
27 January 2012 Extremal functions for Caffarelli-Kohn-Nirenberg
Boyer, Edmond
27 January 2012 Extremal functions for Caffarelli-Kohn-Nirenberg and logarithmic Hardy inequalities Jean Dolbeault & Maria J. Esteban We consider a family of Caffarelli-Kohn-Nirenberg interpolation-Sobolev inequality; Caffarelli-Kohn-Nirenberg inequality; logarithmic Hardy inequality; extremal functions; Kelvin
1 July 2010 Extremal functions for Caffarelli-Kohn-Nirenberg
1 July 2010 Extremal functions for Caffarelli-Kohn-Nirenberg and logarithmic Hardy inequalities Jean Dolbeault & Maria J. Esteban We consider a family of Caffarelli-Kohn-Nirenberg interpolation-Sobolev inequality; Caffarelli-Kohn-Nirenberg inequality; logarithmic Hardy inequality; extremal functions; Kelvin
Cloaking by Change of Variables Robert V. Kohn
Eilbeck, Chris
Cloaking by Change of Variables Robert V. Kohn Courant Institute, NYU Edinburgh, June 2008 Robert V. Kohn Courant Institute, NYU Cloaking by Change of Variables #12;Points of contact with John Some themes getting it right. Robert V. Kohn Courant Institute, NYU Cloaking by Change of Variables #12;What
Robin M. Kohn, MSW, LCSW University of Central Florida
Wu, Shin-Tson
1 Robin M. Kohn, MSW, LCSW University of Central Florida School of Social Work P.O. Box 163358 Orlando, Florida 32816-3358 407-823-2967 robin.kohn@ucf.edu EDUCATION 1979 Master of Social Work, Clinical Education Seminar PUBLICATIONS Manuals Kohn, R.M., Percal, S., Keckley, J., Sofar, S. (2007). Train
Energy-Driven Pattern Formation Robert V. Kohn
Energy-Driven Pattern Formation Robert V. Kohn Courant Institute, NYU ICM2006, Madrid Robert V. Kohn Energy-Driven Pattern Formation #12;Outline What is energy-driven pattern formation? Hard: challenges to nonlinear PDE and calc of varns, coming from physics and materials science. Robert V. Kohn
5 July 2010 Extremal functions for Caffarelli-Kohn-Nirenberg
Dolbeault, Jean
5 July 2010 Extremal functions for Caffarelli-Kohn-Nirenberg and logarithmic Hardy inequalities Jean Dolbeault & Maria J. Esteban We consider a family of Caffarelli-Kohn-Nirenberg interpolation-Sobolev inequality; Caffarelli-Kohn-Nirenberg inequality; logarithmic Hardy inequality; extremal functions; Kelvin
Energy-Driven Pattern Formation Robert V. Kohn
Energy-Driven Pattern Formation Robert V. Kohn Grad Student and Postdoc Seminar April 22, 2011 Robert V. Kohn Energy-Driven Pattern Formation #12;Overview What is energy-driven pattern formation? Hard challenges). Robert V. Kohn Energy-Driven Pattern Formation #12;Statics Pattern formation from energy
A Geometric Formula for the Fundamental Solution of the Kohn
Tie, Jingzhi
A Geometric Formula for the Fundamental Solution of the Kohn Laplacian Der-Chen Chang Peter Greiner. In this article, we shall study geometric and analytical problems related to the Kohn Laplacian b = Â¯b Â¯ b + Â¯ b function. Using this function, one may construct the fundamental solution for the Kohn Laplacian
5 November 2011 Extremal functions for Caffarelli-Kohn-Nirenberg
Dolbeault, Jean
5 November 2011 Extremal functions for Caffarelli-Kohn-Nirenberg and logarithmic Hardy inequalities Jean Dolbeault & Maria J. Esteban We consider a family of Caffarelli-Kohn-Nirenberg interpolation-Sobolev inequality; Caffarelli-Kohn-Nirenberg inequality; logarithmic Hardy inequality; extremal functions; Kelvin
Talks with Teachers: Clyde F. Kohn.
ERIC Educational Resources Information Center
Souza, Anthony R. de
1984-01-01
Kohn--a geographer who has taught at all educational levels and is a former president of the National Council for Geographic Education and the American Association of Geographers--talks about his family and schooling, cooperation between professional organizations, his role in the High School Geography Project, and his interest in enology. (RM)
The Jost-Kohn inversion procedure
NASA Technical Reports Server (NTRS)
Prosser, R. T.
1972-01-01
Conditions are considered that must be imposed on a class of quantum mechanical problems to obtain reasonable results by the Jost-Kohn procedure. The discussion is restricted to problems in three space-dimensions without assuming any radial or other symmetry of the potential.
Variation at the major histocompatibility complex in Savannah sparrows.
Freeman-Gallant, Corey R; Johnson, Elizabeth M; Saponara, Fiorella; Stanger, Matthew
2002-06-01
The class I and class II genes of the major histocompatibility complex (Mhc) encode dimeric glycoproteins responsible for eliciting the adaptive immune response of vertebrates. Recent work with birds suggests that the number, size, and arrangement of these genes can differ markedly across species, although the extent of this variation, and its causes and consequences, are poorly understood. We have used a 157-base-pair (bp) portion of the second exon of a class II B gene to probe the Mhc in a free-living population of Savannah sparrows (Passerculus sandwichensis). Segregation analysis of Mhc bands suggests that class II B genes can be found in two independently assorting clusters, as previously described for domestic chickens (Gallus gallus) and ring-necked pheasants (Phasianus colchicus) but unlike gene organization in mammals. The Mhc in Savannah sparrows appears large (with many class II B genes) and variable; we found 42 unique genotypes among 48 adults breeding on Kent Island, New Brunswick, Canada in 1995. Savannah sparrows are long-distance migrants, and these results support recent predictions that migratory birds should show higher levels of Mhc polymorphism and/or a greater number of genes than sedentary species. Savannah sparrows are also socially polygynous with high levels of extra-pair paternity, suggesting that a history of sexual selection might also influence the size and/or structure of the avian Mhc. PMID:12030987
Are Kohn-Sham conductances accurate?
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
Copy number variation and susceptibility to complex traits
Canales, Cesar P; Walz, Katherina
2011-01-01
Copy number variations (CNV) within the genome are extremely abundant. In this closeup, Canales and Walz discuss how CNV are associated with normal variation, genomic disorders, genome evolution, adaptive traits and how the use of a novel screen described by Ermakova et al in this issue that is designed to identify human disease-relevant phenotypes associated with CNV in the mouse can help elucidating susceptibility or predisposition to diseases loci. PMID:21204264
ERIC Educational Resources Information Center
Kohn, Martin
1977-01-01
The paper focuses on two research instruments, the Kohn Social Competence Scale and the Kohn Symptom Checklist, designed to assess the behavior of children in a preschool setting as well as on two factor-analytically derived dimensions of social-emotional functioning which the instruments measure. (SBH)
On Kohn-Sham models with LDA and GGA exchange-correlation functionals
Paris-Sud XI, UniversitÃ© de
On Kohn-Sham models with LDA and GGA exchange-correlation functionals Arnaud Anantharaman and Eric analysis of the Kohn-Sham and extended Kohn-Sham models, in the local density approximation (LDA) and gener- alized gradient approximation (GGA) frameworks. After recalling the mathematical derivation of the Kohn
ccsd00004344, Fast computation of the Kohn-Sham susceptibility of large systems
ccsdÂ00004344, version 1 Â 1 Mar 2005 Fast computation of the Kohn-Sham susceptibility of large, in #24; N 4 operations, the susceptibility of N non inter- acting Kohn-Sham reference electrons. We on the charge susceptibility of the non interacting Kohn-Sham reference fermions. Here we focus on the Kohn
Reducing the Complexity of VLSI Performance Variation Modeling Via Parameter Dimension Reduction
Zhuo Feng; Guo Yu; Peng Li
2007-01-01
Parameterized circuit models are desired at various VLSI design stages to account for the increasing process-induced performance variations. However, the large number of process variation sources encountered in modern VLSI technologies often lead to overly complex parameterized models whose generation as well as application is computationally expensive. In this paper, we address this challenge by proposing a general VLSI parameter
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…
Hohenberg-Kohn Theorem for Coulomb Type Systems
Aihui Zhou
2011-08-23
Density functional theory (DFT) has become a basic tool for the study of electronic structure of matter, in which the Hohenberg-Kohn theorem plays a fundamental role in the development of DFT. Unfortunately, the existing proofs are incomplete even incorrect; besides, the statement of the Hohenberg-Kohn theorem for many-electron Coulomb systems is not perfect. In this paper, we shall restate the Hohenberg-Kohn theorem for Coulomb type systems and present a rigorous proof by using the Fundamental Theorem of Algebra.
Time-dependent Kohn-Sham approach to quantum electrodynamics
M. Ruggenthaler; F. Mackenroth; D. Bauer
2011-10-10
We prove a generalization of the van Leeuwen theorem towards quantum electrodynamics, providing the formal foundations of a time-dependent Kohn-Sham construction for coupled quantized matter and electromagnetic fields. Thereby 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.
Time-dependent Kohn-Sham approach to quantum electrodynamics
Ruggenthaler, M. [Institut fuer Physik, Universitaet Rostock, DE-18051 Rostock (Germany); Department of Physics, Nanoscience Center, University of Jyvaeskylae, FI-40014 Jyvaeskylae (Finland); Mackenroth, F. [Max-Planck-Institut fuer Kernphysik, Postfach 103980, DE-69029 Heidelberg (Germany); Bauer, D. [Institut fuer Physik, Universitaet Rostock, DE-18051 Rostock (Germany)
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.
Converting Kohn-Sham eigenenergies into electron binding energies.
Jellinek, J.; Acioli, P. H.; Chemistry
2003-05-01
A new accurate scheme for converting the Kohn-Sham eigenenergies into electron binding energies is formulated. The accuracy of the scheme is illustrated in applications to ten atoms and three molecules.
The Kohn-Luttinger Effect in Gauge Theories
Thomas Schaefer
2006-09-07
Kohn and Luttinger showed that a many body system of fermions interacting via short range forces becomes superfluid even if the interaction is repulsive in all partial waves. In gauge theories such as QCD the interaction between fermions is long range and the assumptions of Kohn and Luttinger are not satisfied. We show that in a U(1) gauge theory the Kohn-Luttinger phenomenon does not take place. In QCD attractive channels always exist, but there are cases in which the primary pairing channel leaves some fermions ungapped. As an example we consider the unpaired fermion in the 2SC phase of QCD with two flavors. We show that it acquires a very small gap via a mechanism analogous to the Kohn-Luttinger effect. The gap is too small to be phenomenologically relevant.
Adaptive Finite Element Method for Solving the Exact Kohn-Sham Equation of Density Functional Theory
Bylaska, Eric J.; Holst, Michael; Weare, John H.
2009-04-14
Results of the application of an adaptive finite element (FE) based solution using the FETK library of M. Holst to Density Functional Theory (DFT) approximation to the electronic structure of atoms and molecules are reported. The severe problem associated with the rapid variation of the electronic wave functions in the near singular regions of the atomic centers is treated by implementing completely unstructured simplex meshes that resolve these features around atomic nuclei. This concentrates the computational work in the regions in which the shortest length scales are necessary and provides for low resolution in regions for which there is no electron density. The accuracy of the solutions significantly improved when adaptive mesh refinement was applied, and it was found that the essential difficulties of the Kohn-Sham eigenvalues equation were the result of the singular behavior of the atomic potentials. Even though the matrix representations of the discrete Hamiltonian operator in the adaptive finite element basis are always sparse with a linear complexity in the number of discretization points, the overall memory and computational requirements for the solver implemented were found to be quite high. The number of mesh vertices per atom as a function of the atomic number Z and the required accuracy e (in atomic units) was esitmated to be v (e;Z) = 122:37 * Z2:2346 /1:1173 , and the number of floating point operations per minimization step for a system of NA atoms was found to be 0(N3A*v(e,Z0) (e.g. Z=26, e=0.0015 au, and NA=100, the memory requirement and computational cost would be ~0.2 terabytes and ~25 petaflops). It was found that the high cost of the method could be reduced somewhat by using a geometric based refinement strategy to fix the error near the singularities.
On Kohn-Sham models with LDA and GGA exchange-correlation functionals
Arnaud Anantharaman; Eric Cancès
2008-09-30
This article is concerned with the mathematical analysis of the Kohn-Sham and extended Kohn-Sham models, in the local density approximation (LDA) and generalized gradient approximation (GGA) frameworks. After recalling the mathematical derivation of the Kohn-Sham and extended Kohn-Sham LDA and GGA models from the Schr\\"odinger equation, we prove that the extended Kohn-Sham LDA model has a solution for neutral and positively charged systems. We then prove a similar result for the spin-unpolarized Kohn-Sham GGA model for two-electron systems, by means of a concentration-compactness argument.
Anatomical Variations of Ostiomeatal Complex in CBCT of Patients Seeking Rhinoplasty
Khojastepour, Leila; Mirhadi, Sabah; Mesbahi, Seyed Alireza
2015-01-01
Statement of the Problem Anatomic variation can potentially impact the surgical safety. Purpose The purpose of this cross-sectional study was to assess the prevalence of ostiomeatal complex variations based on cone beam computed tomography (CBCT) images of the patients seeking rhinoplasty. Materials and Method In this cross-sectional study, CBCT images of 281 patients including 153 female and 128 male with Mean±SD age of 26.97±7.38 were retrieved and analyzed for presence of variations of ostiomeatal complex and mucosal thickening. All CBCT images were acquired by NewTom VGi scanner with 15×15 field of view, as a part of preoperative recording of patients seeking rhinoplasty in an otolaryngology clinic. Chi- square test and Odds ratio were used for statistical analysis of the obtained data and p< 0.05 was considered to be statistically significant. Results Agger nasi cells which were seen in 93.2% of the cases were the most common anatomic variation. It was followed by Haller cells (68%), concha bullosa (67.3%), uncinate process variations (54.8%), nasal sepal deviation (49.5%) and paradoxical curvature of middle turbinate (10%). Mucosal thickening were detected in 60.7% of the studied cases. Conclusion Ostiomeatal complex variations and mucosal thickening are considerably prevalent among the patients seeking rhinoplasty. This study also revealed that CBCT evaluation of paranasal sinuses has comparable result in delineation of the sinonasal anatomy. PMID:25759857
Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation.
Brand, Harrison; Collins, Ryan L; Hanscom, Carrie; Rosenfeld, Jill A; Pillalamarri, Vamsee; Stone, Matthew R; Kelley, Fontina; Mason, Tamara; Margolin, Lauren; Eggert, Stacey; Mitchell, Elyse; Hodge, Jennelle C; Gusella, James F; Sanders, Stephan J; Talkowski, Michael E
2015-07-01
Copy-number variants (CNVs) have been the predominant focus of genetic studies of structural variation, and chromosomal microarray (CMA) for genome-wide CNV detection is the recommended first-tier genetic diagnostic screen in neurodevelopmental disorders. We compared CNVs observed by CMA to the structural variation detected by whole-genome large-insert sequencing in 259 individuals diagnosed with autism spectrum disorder (ASD) from the Simons Simplex Collection. These analyses revealed a diverse landscape of complex duplications in the human genome. One remarkably common class of complex rearrangement, which we term dupINVdup, involves two closely located duplications ("paired duplications") that flank the breakpoints of an inversion. This complex variant class is cryptic to CMA, but we observed it in 8.1% of all subjects. We also detected other paired-duplication signatures and duplication-mediated complex rearrangements in 15.8% of all ASD subjects. Breakpoint analysis showed that the predominant mechanism of formation of these complex duplication-associated variants was microhomology-mediated repair. On the basis of the striking prevalence of dupINVdups in this cohort, we explored the landscape of all inversion variation among the 235 highest-quality libraries and found abundant complexity among these variants: only 39.3% of inversions were canonical, or simple, inversions without additional rearrangement. Collectively, these findings indicate that dupINVdups, as well as other complex duplication-associated rearrangements, represent relatively common sources of genomic variation that is cryptic to population-based microarray and low-depth whole-genome sequencing. They also suggest that paired-duplication signatures detected by CMA warrant further scrutiny in genetic diagnostic testing given that they might mark complex rearrangements of potential clinical relevance. PMID:26094575
Duane S. Boning; Karthik Balakrishnan; Hong Cai; Nigel Drego; Ali Farahanchi; Karen M. Gettings; Lim Daihyun; Ajay Somani; Hayden Taylor; Daniel Truque; Xie Xiaolin
2008-01-01
Variation afflicts the design, manufacture, and operation of integrated circuits. Techniques and tools are needed in three areas to address variation: statistical metrology, advanced process control, and design for manufacturability. First, statistical metrology seeks to characterize and model variations and their sources. Advanced metrology helps to understand geometric and material property variations, while variation test structures and test circuits enable
Stimulus-Evoked Modulation of Sensorimotor Pyramidal Neuron ADAM KOHN,1
Kohn, Adam
Stimulus-Evoked Modulation of Sensorimotor Pyramidal Neuron EPSPs ADAM KOHN,1 CAROL METZ,2 MARK A Carolina 27599 Received 11 December 2001; accepted in final form 21 August 2002 Kohn, Adam, Carol Metz
Irregular CoarseGrain Data Parallelism Under LPARX \\Lambda Scott R. Kohn Scott B. Baden
Baden, Scott B.
Irregular CoarseGrain Data Parallelism Under LPARX \\Lambda Scott R. Kohn Scott B. Baden Department was provided by the Cornell Theory Center. Portions of this paper are taken from Kohn's Ph.D. dissertation [24
Variational Approach in Two-Phase Flows of Complex Fluids: Transport and Induced Elastic Stress
Feng, James J.
Variational Approach in Two-Phase Flows of Complex Fluids: Transport and Induced Elastic Stress the transport of the microscopic variables by the flow and the induced elastic stress is elaborated be attributed to the special coupling between the transport of the internal variable and the induced elastic
Full variational molecular orbital method: Application to the positron-molecule complexes
Masanori Tachikawa; Kazuhide Mori; Kazunari Suzuki; Kaoru Iguchi
1998-01-01
Optimal Gaussian-type orbital (GTO) basis sets of positron and electron in positron-molecule complexes are proposed by using the full variational treatment of molecular orbital (FVMO) method. The analytical expression for the energy gradient with respect to parameters of positronic and electronic GTO such as the orbital exponents, the orbital centers, and the linear combination of atomic orbital (LCAO) coefficients, is
Morphological variation in the horse: defining complex traits of body size and shape.
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
Kohn-Sham Theory in the Presence of Magnetic Field
Andre Laestadius
2014-04-11
In the well-known Kohn-Sham theory in Density Functional Theory, a fictitious non-interacting system is introduced that has the same particle density as a system of $N$ electrons subjected to mutual Coulomb repulsion and an external electric field. For a long time, the treatment of the kinetic energy was not correct and the theory was not well-defined for $N$-representable particle densities. In the work of [Hadjisavvas and Theophilou, Phys. Rev. A, 1984, 30, 2183], a rigorous Kohn-Sham theory for $N$-representable particle densities was developed using the Levy-Lieb functional. Since a Levy-Lieb-type functional can be defined for Current Density Functional Theory formulated with the paramagnetic current density, we here develop a rigorous $N$-representable Kohn-Sham approach for interacting electrons in magnetic field. Furthermore, in the one-electron case, criteria for $N$-representable particle densities to be $v$-representable are given.
Kohn-Sham potentials for fullerenes and spherical molecules
Pavlyukh, Y.; Berakdar, J. [Institut fuer Physik, Martin-Luther-Universitaet Halle-Wittenberg, Heinrich-Damerow-Strasse 4, D-06120 Halle (Germany)
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.
Kohn-Sham Theory in the Presence of Magnetic Field
Laestadius, Andre
2014-01-01
In the well-known Kohn-Sham theory in Density Functional Theory, a fictitious non-interacting system is introduced that has the same particle density as a system of $N$ electrons subjected to mutual Coulomb repulsion and an external electric field. For a long time, the treatment of the kinetic energy was not correct and the theory was not well-defined for $N$-representable particle densities. In the work of [Hadjisavvas and Theophilou, Phys. Rev. A, 1984, 30, 2183], a rigorous Kohn-Sham theory for $N$-representable particle densities was developed using the Levy-Lieb functional. Since a Levy-Lieb-type functional can be defined for Current Density Functional Theory formulated with the paramagnetic current density, we here develop a rigorous $N$-representable Kohn-Sham approach for interacting electrons in magnetic field. Furthermore, in the one-electron case, criteria for $N$-representable particle densities to be $v$-representable are given.
Caffarelli-Kohn-Nirenberg inequality on metric measure spaces with applications
Ohta, Shin-ichi
Caffarelli-Kohn-Nirenberg inequality on metric measure spaces with applications Alexandru Krist the volume doubling condition and the Caffarelli-Kohn-Nirenberg inequality with the same exponent n 3 of non-negative n-Ricci curvature satisfies the Caffarelli-Kohn- Nirenberg inequality with the sharp
KSSOLV -A MATLAB Toolbox for Solving the Kohn-Sham Equations
Yang, Chao
KSSOLV - A MATLAB Toolbox for Solving the Kohn-Sham Equations Chao Yang and Juan C. Meza for solving a class of nonlinear eigenvalue problems known as the Kohn-Sham equations. These types of problems for developing new algorithms for solving the Kohn-Sham equations and is designed to enable researchers
Non-periodic finite-element formulation of Kohn-Sham Density Functional Theory
Blesgen, Thomas
Non-periodic finite-element formulation of Kohn-Sham Density Functional Theory Phanish-periodic, finite-element formulation for Kohn- Sham Density Functional Theory (KS-DFT). In doing so, we transform 2008 #12;Suryanarayana, Gavini, Blesgen, Bhattacharya & Ortiz Key words: Finite-elements; Kohn
Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin
Lu, Jianfeng
Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin University, Princeton, NJ 08544. Abstract Kohn-Sham density functional theory is one of the most widely used electronic structure theories. Uniform discretization of the Kohn-Sham Hamiltonian gen- erally results
Accurate Kohn-Sham potential for the S state of the helium atom: Tests
Lindgren, Ingvar
1 Accurate Kohn-Sham potential for the 1s2s 3 S state of the helium atom: Tests of the locality and the ionization-potential theorems Sten Salomonson, Fredrik MÂ¨oller and Ingvar Lindgren Abstract: The local Kohn from the pair-correlation program of Salomonson and Â¨Oster (Phys. Rev. A 40, 5559 (1989)). The Kohn
A Caffarelli-Kohn-Nirenberg type inequality with variable exponent and applications to PDE's
A Caffarelli-Kohn-Nirenberg type inequality with variable exponent and applications to PDE's Mihai.stancu@yahoo.com Abstract. Given RN (N 2) a bounded smooth domain we establish a Caffarelli-Kohn-Nirenberg type words: Caffarelli-Kohn-Nirenberg type inequality, eigenvalue problem, degenerate elliptic equation
A scenario for symmetry breaking in Caffarelli-Kohn-Nirenberg inequalities
Paris-Sud XI, UniversitÃ© de
A scenario for symmetry breaking in Caffarelli-Kohn-Nirenberg inequalities Jean DOLBEAULT, Maria J- Kohn-Nirenberg inequalities this conjecture was not true. In order to understand this new symmetry. The computations have been performed using Freefem++. Keywords: ground state; SchrÂ¨odinger operator; Caffarelli-Kohn
Symmetry breaking in the self-consistent Kohn-Sham equations
Symmetry breaking in the self-consistent Kohn-Sham equations E. Prodan March 2, 2005 Abstract The Kohn-Sham (KS) equations determine, in a self-consistent way, the particle density of an interacting . According to the Kohn-Sham theory [1] (and later extensions), the particle density at thermal equilibrium
ON THE SYMMETRY OF EXTREMALS FOR THE CAFFARELLI-KOHN-NIRENBERG INEQUALITIES
Dolbeault, Jean
ON THE SYMMETRY OF EXTREMALS FOR THE CAFFARELLI-KOHN-NIRENBERG INEQUALITIES JEAN DOLBEAULT, MARIA J for the extremals of the Caffarelli-Kohn-Nirenberg inequalities, in any dimen- sion larger or equal than 2 . 1. Introduction The Caffarelli-Kohn-Nirenberg inequality (see [2]) in space dimension N 2 , can be written
Numerical analysis of the planewave discretization of some orbital-free and Kohn-Sham models
Numerical analysis of the planewave discretization of some orbital-free and Kohn-Sham models Eric-von WeizsÂ¨acker (TFW) model and for the spectral discretization of the Kohn-Sham model, within the local to the electronic density, and allows for a comprehensive analysis. This is not the case for the Kohn-Sham LDA model
THE USE OF TRUST REGIONS IN KOHN-SHAM TOTAL ENERGY MINIMIZATION
Geddes, Cameron Guy Robinson
THE USE OF TRUST REGIONS IN KOHN-SHAM TOTAL ENERGY MINIMIZATION CHAO YANG , JUAN C. MEZA , AND LIN system, is viewed in this paper as an optimization procedure that minimizes the Kohn- Sham total energy based SCF (TRSCF) to the Kohn-Sham total energy often leads to slow convergence. We propose to use TRSCF
What Can You Do With a Math Degree? Robert V. Kohn
What Can You Do With a Math Degree? Robert V. Kohn Courant Institute, NYU NYU Mathematics Society Colloquium, 2/8/2011 Robert V. Kohn What Can You Do With a Math Degree? #12;A math degree provides professional programs PhD study in a math-intensive field PhD study in mathematics Robert V. Kohn What Can You
On the Caffarelli-Kohn-Nirenberg Inequalities: Sharp Constants, Existence (and Nonexistence),
Wang, Zhi-Qiang
On the Caffarelli-Kohn-Nirenberg Inequalities: Sharp Constants, Existence (and Nonexistence to Caffarelli, Kohn, and Nirenberg [6]: RN |x|-bp|u|p dx 2/p Ca,b RN |x|-2a| u|2 dx where, for N 3 general family of inequalities, Caffarelli, Kohn, and Nirenberg established the following inequalities
ON THE SYMMETRY OF EXTREMALS FOR THE CAFFARELLI-KOHN-NIRENBERG INEQUALITIES
Boyer, Edmond
ON THE SYMMETRY OF EXTREMALS FOR THE CAFFARELLI-KOHN-NIRENBERG INEQUALITIES JEAN DOLBEAULT, MARIA J for the extremals of the Caffarelli-Kohn-Nirenberg inequalities, in any dimen- sion larger or equal than 2 . Dedicato a Vieri 1. Introduction The Caffarelli-Kohn-Nirenberg inequality (see [2]) in space dimension N 2
Adiabatic Connection and the Kohn-Sham Variety of Potential-Functional Theory
Gross, E.K.U.
Adiabatic Connection and the Kohn-Sham Variety of Potential-Functional Theory E. K. U. Gross* and C] is evaluated at the Kohn-Sham potential vs, which, in turn, is determined by an iterative procedure. Advantages and disadvantages of the two approaches are discussed. The Kohn-Sham equations of density functional theory (DFT
Real-Space Localization Methods for Minimizing the Kohn-Sham Energy
Mohri, Mehryar
Real-Space Localization Methods for Minimizing the Kohn-Sham Energy by Marc Millstone for minimizing the Kohn-Sham energy, which is used to describe a system of non-interacting electrons through, each algorithm evaluates the Kohn-Sham energy function and gradient at a set of iterates that have
Optimized local basis set for Kohn-Sham density functional theory , Jianfeng Lub
Lu, Jianfeng
Optimized local basis set for Kohn-Sham density functional theory Lin Lina,1 , Jianfeng Lub a technique for generating a set of optimized local basis functions to solve models in the Kohn-Sham density: electronic structure, Kohn-Sham density functional theory, optimized local basis set, discontinuous Galerkin
The Alan J. Kohn Endowed Fellowship at UW Friday Harbor Laboratories
Carrington, Emily
The Alan J. Kohn Endowed Fellowship at UW Friday Harbor Laboratories This endowment provides and colleagues of Alan J. Kohn as a tribute to his many contributions as a scientist, teacher, mentor and friend. Alan Kohn joined the University of Washington Faculty as an assistant professor of zoology in 1961
Real-Time Adaptive Finite Element Solution of Time-Dependent Kohn-Sham Equation
Liu, Di "Richard"
Real-Time Adaptive Finite Element Solution of Time-Dependent Kohn-Sham Equation Gang Baoa], a general framework of using adaptive finite element methods to solve the Kohn-Sham equation has been presented. This work is concerned with solving the time-dependent Kohn-Sham equations. The numerical methods
Wang, Yan Alexander
Transferable local pseudopotentials derived via inversion of the Kohn-Sham equations in a bulk. We exploit the first Hohenberg-Kohn theorem, which states that the external potential is one-to-one mapped to the ground-state electron density. By employing a scheme for inverting the Kohn-Sham KS
Second-order Kohn-Sham perturbation theory: Correlation potential for atoms in a cavity
Engel, Eberhard
Second-order Kohn-Sham perturbation theory: Correlation potential for atoms in a cavity Hong Jiang online 12 December 2005 Second-order perturbation theory based on the Kohn-Sham Hamiltonian leads occupied and unoccupied Kohn-Sham single-particle orbitals and energies. The corresponding correlation
THE KOHN-SHAM EQUATION FOR DEFORMED CRYSTALS WEINAN E AND JIANFENG LU
Lu, Jianfeng
THE KOHN-SHAM EQUATION FOR DEFORMED CRYSTALS WEINAN E AND JIANFENG LU Abstract. The solution to the Kohn-Sham equation in the density functional theory of the quantum many-body problem is studied is rigorously derived. Along the way, we also establish a number of fundamental properties of the Kohn-Sham map
IMPROVED CAFFARELLI-KOHN-NIRENBERG AND TRACE INEQUALITIES FOR RADIAL FUNCTIONS
Duran, Ricardo
IMPROVED CAFFARELLI-KOHN-NIRENBERG AND TRACE INEQUALITIES FOR RADIAL FUNCTIONS PABLO L. DE NÂ´APOLI, IRENE DRELICHMAN, AND RICARDO G. DURÂ´AN Abstract. We show that Caffarelli-Kohn-Nirenberg first order of this paper is to show that inequalities of Caffarelli-Kohn-Nirenberg type hold for a wider class of exponents
Coarsening rates for models of multicomponent phase separation Robert V. Kohn and Xiaodong Yan
Coarsening rates for models of multicomponent phase separation Robert V. Kohn and Xiaodong Yan Courant Institute, 251 Mercer Street, New York, NY 10012 kohn@cims.nyu.edu xiayan@cims.nyu.edu September follows a strategy intro- duced by Kohn and Otto for problems with a scalar-valued order parameter
Locally Refined Multigrid Solution of the All-Electron Kohn-Sham Equation
Locally Refined Multigrid Solution of the All-Electron Kohn-Sham Equation Or Cohen,,, Leeor Kronik present a fully-numerical multigrid approach for solving the all-electron Kohn-Sham equation in molecules 76100, Israel 1 #12;problem is mapped onto the Kohn-Sham equation of noninteracting electrons, given
A Kohn-Vogelius formulation to detect an obstacle immersed in a fluid
Dambrine, Marc
A Kohn-Vogelius formulation to detect an obstacle immersed in a fluid F Caubet1 , M Dambrine2 , D thanks to the tools of shape optimization by minimizing the Kohn-Vogelius cost function. We first from a single #12;A Kohn-Vogelius formulation to detect an obstacle immersed in a fluid 2 boundary
Must Kohn-Sham oscillator strengths be accurate at threshold?
Yang Zenghui; Burke, Kieron [Department of Chemistry, University of California, Irvine, California 92697 (United States); Faassen, Meta van [Department of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, NL-1081 HV Amsterdam (Netherlands)
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.
A Kohn-Sham system at zero temperature
Horia Cornean; Kurt Hoke; Hagen Neidhardt; Paul N. Racec; Joachim Rehberg
2008-01-17
An one-dimensional Kohn-Sham system for spin particles is considered which effectively describes semiconductor {nano}structures and which is investigated at zero temperature. We prove the existence of solutions and derive a priori estimates. For this purpose we find estimates for eigenvalues of the Schr\\"odinger operator with effective Kohn-Sham potential and obtain $W^{1,2}$-bounds of the associated particle density operator. Afterwards, compactness and continuity results allow to apply Schauder's fixed point theorem. In case of vanishing exchange-correlation potential uniqueness is shown by monotonicity arguments. Finally, we investigate the behavior of the system if the temperature approaches zero.
A More Complex Analysis Is Needed.
ERIC Educational Resources Information Center
Lickona, Thomas
1998-01-01
Alfie Kohn's critique of character education in the February 1997 "Kappan" is constructive but not complex enough to provide guidance for the field. Except for briefly describing the Child Development Project, Kohn omits books and articles advocating a comprehensive approach to character education and does not fairly represent some…
Dominance genetic variation contributes little to the missing heritability for human complex traits.
Zhu, Zhihong; Bakshi, Andrew; Vinkhuyzen, Anna A E; Hemani, Gibran; Lee, Sang Hong; Nolte, Ilja M; van Vliet-Ostaptchouk, Jana V; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Hill, William G; Weir, Bruce S; Goddard, Michael E; Visscher, Peter M; Yang, Jian
2015-03-01
For human complex traits, non-additive genetic variation has been invoked to explain "missing heritability," but its discovery is often neglected in genome-wide association studies. Here we propose a method of using SNP data to partition and estimate the proportion of phenotypic variance attributed to additive and dominance genetic variation at all SNPs (hSNP(2) and ?SNP(2)) in unrelated individuals based on an orthogonal model where the estimate of hSNP(2) is independent of that of ?SNP(2). With this method, we analyzed 79 quantitative traits in 6,715 unrelated European Americans. The estimate of ?SNP(2) averaged across all the 79 quantitative traits was 0.03, approximately a fifth of that for additive variation (average hSNP(2) = 0.15). There were a few traits that showed substantial estimates of ?SNP(2), none of which were replicated in a larger sample of 11,965 individuals. We further performed genome-wide association analyses of the 79 quantitative traits and detected SNPs with genome-wide significant dominance effects only at the ABO locus for factor VIII and von Willebrand factor. All these results suggest that dominance variation at common SNPs explains only a small fraction of phenotypic variation for human complex traits and contributes little to the missing narrow-sense heritability problem. PMID:25683123
Puillandre, Nicolas; Meyer, Christopher P.; Bouchet, Philippe; Olivera, Baldomero M.
2011-01-01
Puillandre, N. et al. (2010) Genetic divergence and geographic variation in a deep-water cone lineage: molecular and morphological analyses of the Conus orbignyi complex (Mollusca: Conoidea). The cone snails (family Conidae) are a hyperdiverse lineage of venomous gastropods. Two standard markers, COI and ITS2, were used to define six genetically-divergent groups within a subclade of Conidae that includes Conus orbignyi; each of these was then evaluated based on their shell morphology. We conclude that three forms, previously regarded as subspecies of Conus orbignyi are distinct species, now recognized as Conus orbignyi, Conus elokismenos and Conus coriolisi. In addition, three additional species (Conus pseudorbignyi, Conus joliveti and Conus comatosa) belong to this clade. Some of the proposed species (e.g., Conus elokismenos) are possibly in turn complexes comprising multiple species. Groups such as Conidae illustrate the challenges generally faced in species delimitation in biodiverse lineages. In the case of the Conus orbignyi complex, not only are there definable, genetically divergent lineages, but also considerable geographic variation within each group. Our study suggests that an intensive analysis of multiple specimens within a single locality helps to minimize the confounding effects of geographic variation and can be a useful starting point for circumscribing different species within such a confusing complex. PMID:21712968
Puillandre, Nicolas; Meyer, Christopher P; Bouchet, Philippe; Olivera, Baldomero M
2011-07-01
Puillandre, N. et al. (2010) Genetic divergence and geographic variation in a deep-water cone lineage: molecular and morphological analyses of the Conus orbignyi complex (Mollusca: Conoidea).The cone snails (family Conidae) are a hyperdiverse lineage of venomous gastropods. Two standard markers, COI and ITS2, were used to define six genetically-divergent groups within a subclade of Conidae that includes Conus orbignyi; each of these was then evaluated based on their shell morphology. We conclude that three forms, previously regarded as subspecies of Conus orbignyi are distinct species, now recognized as Conus orbignyi, Conus elokismenos and Conus coriolisi. In addition, three additional species (Conus pseudorbignyi, Conus joliveti and Conus comatosa) belong to this clade. Some of the proposed species (e.g., Conus elokismenos) are possibly in turn complexes comprising multiple species. Groups such as Conidae illustrate the challenges generally faced in species delimitation in biodiverse lineages. In the case of the Conus orbignyi complex, not only are there definable, genetically divergent lineages, but also considerable geographic variation within each group. Our study suggests that an intensive analysis of multiple specimens within a single locality helps to minimize the confounding effects of geographic variation and can be a useful starting point for circumscribing different species within such a confusing complex. PMID:21712968
Karadi, R.N.; Kumar, Saurabh
2014-01-01
Background: Chronic rhino sinusitis (CRS) is the most common disease for which consultation of otorhinolaryngologist is sought. The approach to patients with chronic rhino sinusitis is endoscopic surgery which aims at removing the obstruction of the main drainage pathway. The osteomeatal complex based essentially on the concept that such obstruction perpetuates the sinus disease. This in turn requires the surgeons to have detailed knowledge of the anatomy of the lateral nasal wall, paranasal sinuses and surrounding vital structures and of the large number of anatomical variants in the region. Aim: To study anatomical variations of osteomeatal complex in chronic sinusitis patients. Materials and Methods: Descriptive cross-sectional study design in which 54 consecutive cases of chronic rhino sinusitis patients attending the ENT outpatient department, who had chronic sinusitis for more than three months duration not responding to the medical line of treatment and who were willing to undergo Functional Endoscopic Sinus Surgery satisfying the inclusion criteria were studied. The results were expressed in percentage and proportions. Results: In our study it was observed that 53.7% of the chronic sinusitis cases had two or more anatomical variations and 33.3% of the cases had single anatomical variation. Deviated nasal septum was found to be the most common amongst the anatomical variations in chronic sinusitis cases in the present study which was followed by unilateral concha bullosa and paradoxically bent middle turbinate. Agger nasi cell and Haller cell were seen in one case each. Conclusion: Prevalence of multiple anatomical variations was more in our study in comparison to single anatomical variation. Deviated nasal septum was the most common anatomical variation encountered in our study followed by concha bullosa. PMID:25478374
Second-order Kohn-Sham perturbation theory: correlation potential for atoms in a cavity.
Jiang, Hong; Engel, Eberhard
2005-12-01
Second-order perturbation theory based on the Kohn-Sham Hamiltonian leads to an implicit density functional for the correlation energy E(c) (MP2), which is explicitly dependent on both occupied and unoccupied Kohn-Sham single-particle orbitals and energies. The corresponding correlation potential v(c) (MP2), which has to be evaluated by the optimized potential method, was found to be divergent in the asymptotic region of atoms, if positive-energy continuum states are included in the calculation [Facco Bonetti et al., Phys. Rev. Lett. 86, 2241 (2001)]. On the other hand, Niquet et al., [J. Chem. Phys. 118, 9504 (2003)] showed that v(c) (MP2) has the same asymptotic -alpha(2r(4)) behavior as the exact correlation potential, if the system under study has a discrete spectrum only. In this work we study v(c) (MP2) for atoms in a spherical cavity within a basis-set-free finite differences approach, ensuring a completely discrete spectrum by requiring hard-wall boundary conditions at the cavity radius. Choosing this radius sufficiently large, one can devise a numerical continuation procedure which allows to normalize v(c) (MP2) consistent with the standard choice v(c)(r-->infinity)=0 for free atoms, without modifying the potential in the chemically relevant region. An important prerequisite for the success of this scheme is the inclusion of very high-energy virtual states. Using this technique, we have calculated v(c) (MP2) for all closed-shell and spherical open-shell atoms up to argon. One finds that v(c) (MP2) reproduces the shell structure of the exact correlation potential very well but consistently overestimates the corresponding shell oscillations. In the case of spin-polarized atoms one observes a strong interrelation between the correlation potentials of the two spin channels, which is completely absent for standard density functionals. However, our results also demonstrate that E(c) (MP2) can only serve as a first step towards the construction of a suitable implicit correlation functional: The fundamental variational instability of this functional is recovered for beryllium, for which a breakdown of the self-consistent Kohn-Sham iteration is observed. Moreover, even for those atoms for which the self-consistent iteration is stable, the results indicate that the inclusion of v(c) (MP2) in the total Kohn-Sham potential does not lead to an improvement compared to the complete neglect of the correlation potential. PMID:16375465
The Compassion Our Children Deserve: An Interview with Alfie Kohn.
ERIC Educational Resources Information Center
Miller, Ron; Kohn, Alfie
2000-01-01
Alfie Kohn, former teacher and current educational theorist and writer, discusses his views on teaching, learning, and parenting. He addresses the problems of reward-based education, the negative effects of competition on learning, and capitalizing on the naturalness of altruistic behavior in humans. He stresses the importance of treating children…
Kohn-Sham orbitals and potentials from quantum Monte Carlo molecular densities
Varsano, Daniele, E-mail: daniele.varsano@nano.cnr.it [Dipartimento di Fisica, Sapienza-Università di Roma, P.le Aldo Moro 5, 00185 Roma (Italy)] [Dipartimento di Fisica, Sapienza-Università di Roma, P.le Aldo Moro 5, 00185 Roma (Italy); Barborini, Matteo [Dipartimento di ingegneria e scienze dell'informazione e matematica, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy) [Dipartimento di ingegneria e scienze dell'informazione e matematica, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy)] [Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell'Aquila, Via Vetoio, Coppito, 67100 L'Aquila (Italy)
2014-02-07
In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H{sub 2}, Be{sub 2}, H{sub 2}O, and C{sub 2}H{sub 4}). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory.
Kohn-Sham orbitals and potentials from quantum Monte Carlo molecular densities
NASA Astrophysics Data System (ADS)
Varsano, Daniele; Barborini, Matteo; Guidoni, Leonardo
2014-02-01
In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H2, Be2, H2O, and C2H4). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory.
ERIC Educational Resources Information Center
Kuiken, Folkert; Vedder, Ineke
2012-01-01
The research project reported in this chapter consists of three studies in which syntactic complexity, lexical variation and fluency appear as dependent variables. The independent variables are task complexity and proficiency level, as the three studies investigate the effect of task complexity on the written and oral performance of L2 learners of…
Variation in complex semiochemical signals arising from insects and host plants.
Aukema, Brian H; Powell, Jaimie S; Clayton, Murray K; Raffa, Kenneth F
2010-06-01
Chemical communication by many insect species involves complex signals of both insect and plant origin. Much attention has been focused on the behavioral activities of these components but less on their sources of variation, despite implications for evolutionary theory and pest management. We studied variation in chemical signaling at host, tree-within-host, and beetle-on-tree scales using tunneling male pine engravers [Ips pini (Say)] on jack, Pinus banksiana Lamb, red, P. resinosa Aiton, and white, P. strobus L. pines. Pine engravers are distributed transcontinentally, and stereoisomeric ratios of their principal pheromone component ipsdienol varies regionally. Linear mixed-effects models were used to examine variation in monoterpene and pheromone volatile profiles, determined by gas chromatography. Phloem from white pine had the greatest concentration of monoterpenes, although insects tunneling in white pine produced the smallest ratios of monoterpenes to pheromones (1:2) in their volatile plumes relative to jack and red pine (1:1). Beetle-to-beetle variation in plume composition was approximately 2-9 times greater than the inter-tree variation within a tree species. The stereoisomeric ratio of ipsdienol was highly consistent within the pheromone component of the plume. The little variation present existed almost entirely at the level of the insects. Within the pheromone component of the plume in a given host species, there was up to 13 times more beetle-to-beetle than tree-to-tree variation. This magnitude was almost double the magnitudes of the ratios among components within the entire plumes. Implications to the behavioral ecology of bark beetle communication, such as potential strategies of cheating and predator avoidance, are discussed. PMID:20550801
Real-time adaptive finite element solution of time-dependent Kohn-Sham equation
NASA Astrophysics Data System (ADS)
Bao, Gang; Hu, Guanghui; Liu, Di
2015-01-01
In our previous paper (Bao et al., 2012 [1]), a general framework of using adaptive finite element methods to solve the Kohn-Sham equation has been presented. This work is concerned with solving the time-dependent Kohn-Sham equations. The numerical methods are studied in the time domain, which can be employed to explain both the linear and the nonlinear effects. A Crank-Nicolson scheme and linear finite element space are employed for the temporal and spatial discretizations, respectively. To resolve the trouble regions in the time-dependent simulations, a heuristic error indicator is introduced for the mesh adaptive methods. An algebraic multigrid solver is developed to efficiently solve the complex-valued system derived from the semi-implicit scheme. A mask function is employed to remove or reduce the boundary reflection of the wavefunction. The effectiveness of our method is verified by numerical simulations for both linear and nonlinear phenomena, in which the effectiveness of the mesh adaptive methods is clearly demonstrated.
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
Remarks on the semi-classical Hohenberg-Kohn functional
Brendan Pass
2012-11-12
In this note, we study an optimal transportation problem arising in density functional theory. We derive an upper bound on the semi-classical Hohenberg-Kohn functional derived by Cotar, Friesecke and Kl\\"{u}ppelberg (2012) which can be computed in a straightforward way for a given single particle density. This complements a lower bound derived by the aforementioned authors. We also show that for radially symmetric densities the optimal transportation problem arising in the semi-classical Hohenberg-Kohn functional can be reduced to a 1-dimensional problem. This yields a simple new proof of the explicit solution to the optimal transport problem for two particles found by Cotar, Friesecke and Kl\\"{u}ppelberg (2012). For more particles, we use our result to demonstrate two new qualitative facts: first, that the solution can concentrate on higher dimensional submanifolds and second that the solution can be non-unique, even with an additional symmetry constraint imposed.
Exact Kohn-Sham potential of strongly correlated finite systems
Helbig, N. [Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Dpto. Fisica de Materiales, Universidad del Pais Vasco, Centro de Fisica de Materiales CSIC-UPV/EHU-MPC and DIPC, Av. Tolosa 72, San Sebastian E-20018 (Spain); Tokatly, I. V. [Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Dpto. Fisica de Materiales, Universidad del Pais Vasco, Centro de Fisica de Materiales CSIC-UPV/EHU-MPC and DIPC, Av. Tolosa 72, San Sebastian E-20018 (Spain); IKERBASQUE, Basque Foundation for Science, Bilbao E-48011 (Spain); Rubio, A. [Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Dpto. Fisica de Materiales, Universidad del Pais Vasco, Centro de Fisica de Materiales CSIC-UPV/EHU-MPC and DIPC, Av. Tolosa 72, San Sebastian E-20018 (Spain); Fritz-Haber-Institut, Max-Planck-Gesellschaft, Berlin D-14195 (Germany)
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.
Kohn's theorem and Newton-Hooke symmetry for Hill's equations
P. M. Zhang; G. W. Gibbons; P. A. Horvathy
2012-02-24
Hill's equations, which first arose in the study of the Earth-Moon-Sun system, admit the two-parameter centrally extended Newton-Hooke symmetry without rotations. This symmetry allows for extending Kohn's theorem about the center-of-mass decomposition. Particular light is shed on the problem using Duval's "Bargmann" framework. The separation of the center-of-mass motion into that of a guiding center and relative motion is derived by a generalized chiral decomposition.
P. Ann K. Eastman; Fiona B. Webster; Jack A. Pitel; Dane R. Roberts
1991-01-01
Somaclonal variation during interior spruce (Picea glauca engelmannii complex) somatic embryogenesis was evaluated using culture morphology and isozyme analysis. Genotype-specific abscisic acid-dependent developmental profiles and isozyme patterns were similar for subclone and parent line embryogenic cultures and cotyledonary somatic embryos. Extensive analysis of fifteen hundred subclone embryos of one genotype revealed no isozyme pattern variation. Initiation of embryogenic cultures was
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
Holst, Michael
2010-01-01
A recent paper of Arnold, Falk, and Winther [Bull AMS, 47 (2010)] showed that a large class of mixed finite element methods can be formulated naturally on Hilbert complexes, where using a Galerkin-like approach, one solves a variational problem on a finite-dimensional subcomplex. In a seemingly unrelated research direction, Dziuk [Lect Notes in Math, vol 1357 (1988)] analyzed a class of nodal finite elements for the Laplace-Beltrami equation on smooth 2-surfaces approximated by a piecewise-linear triangulation; Demlow later extended this analysis [SIAM J Numer Anal, 47 (2009)] to 3-surfaces, as well as to higher-order surface approximation. In this article, we bring these lines of research together, first developing a framework for the analysis of variational crimes in abstract Hilbert complexes, and then applying this abstract framework to the setting of finite element exterior calculus on hypersurfaces. Our framework extends the work of Arnold, Falk, and Winther to problems that violate their subcomplex ass...
Babik, Wieslaw; Kawalko, Agata; Wójcik, Jan M; Radwan, Jacek
2012-01-01
Variation in the major histocompatibility complex (MHC) class I of the European bison was characterized in a sample of 99 individuals using both classical cloning/Sanger sequencing and 454 pyrosequencing. Three common (frequencies: 0.348, 0.328, and 0.283) haplotypes contain 1-3 classical class I loci. A variable and difficult to estimate precisely number of nonclassical transcribed loci, pseudogenes, and/or gene fragments were also found. The presence of additional 2 rare haplotypes (frequency of 0.020 each), observed only in heterozygotes, was inferred. The overall organization of MHC I appears similar to the cattle system, but genetic variation is much lower with only 7 classical class I alleles, approximately one-tenth of the number known in cattle and a quarter known in the American bison. An extensive transspecific polymorphism was found. MHC I is in a strong linkage disequilibrium with previously studied MHC II DRB3 gene. The most likely explanation for the low variation is a drastic bottleneck at the beginning of the 20th century. Genotype frequencies conformed to Hardy-Weinberg expectations, and no signatures of selection in contemporary populations but strong signatures of historical positive selection in sequences of classical alleles were found. A quick and reliable method of MHC I genotyping was developed. PMID:22496313
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
Learned Vocal Variation Is Associated with Abrupt Cryptic Genetic Change in a Parrot Species Complex
Ribot, Raoul F. H.; Buchanan, Katherine L.; Endler, John A.; Joseph, Leo; Bennett, Andrew T. D.; Berg, Mathew L.
2012-01-01
Contact zones between subspecies or closely related species offer valuable insights into speciation processes. A typical feature of such zones is the presence of clinal variation in multiple traits. The nature of these traits and the concordance among clines are expected to influence whether and how quickly speciation will proceed. Learned signals, such as vocalizations in species having vocal learning (e.g. humans, many birds, bats and cetaceans), can exhibit rapid change and may accelerate reproductive isolation between populations. Therefore, particularly strong concordance among clines in learned signals and population genetic structure may be expected, even among continuous populations in the early stages of speciation. However, empirical evidence for this pattern is often limited because differences in vocalisations between populations are driven by habitat differences or have evolved in allopatry. We tested for this pattern in a unique system where we may be able to separate effects of habitat and evolutionary history. We studied geographic variation in the vocalizations of the crimson rosella (Platycercus elegans) parrot species complex. Parrots are well known for their life-long vocal learning and cognitive abilities. We analysed contact calls across a ca 1300 km transect encompassing populations that differed in neutral genetic markers and plumage colour. We found steep clinal changes in two acoustic variables (fundamental frequency and peak frequency position). The positions of the two clines in vocal traits were concordant with a steep cline in microsatellite-based genetic variation, but were discordant with the steep clines in mtDNA, plumage and habitat. Our study provides new evidence that vocal variation, in a species with vocal learning, can coincide with areas of restricted gene flow across geographically continuous populations. Our results suggest that traits that evolve culturally can be strongly associated with reduced gene flow between populations, and therefore may promote speciation, even in the absence of other barriers. PMID:23227179
Variations of oxygen and carbon isotopes in carbonatites: A study of Brazilian alkaline complexes
NASA Astrophysics Data System (ADS)
Santos, Roberto V.; clayton, Robert N.
1995-04-01
We have studied the oxygen and carbon isotopic compositions of carbonatite complexes from South America (Jacupiranga, Araxá, Catalão, Tapira, and Mato Preto) and interpreted the results in terms of magmatism, contamination by country rocks, and hydrothermal processes. These complexes range in age from 130 to 65 Ma and were emplaced during the reactivation of the South American Platform during the Mesozoic Era. Except for the samples from Mato Preto ( ?13C = -6.9 to + 0.8%), which have been contaminated by limestone from the country rock, there are no large carbon isotope differences among the samples of Jacupiranga (-7.3 to -6.6%), Araxá (-7.5 to -4.8%), Catalão (-7.1 to -5.3%), and Tapira (-6.8 to -4.8%). In contrast, the carbonatites have a wide range in oxygen isotopic composition, which seems to be related to their degree of hydrothermal alteration and their emplacement level. For instance, while the samples from Jacupiranga have a narrow range of ?18O (6.6 to 7.3%) and have not been extensively affected by fertilization, the carbonatites from the complexes of Araxa (8.7 to 16.3%o), Catalão (7.3 to 19.3%), and Tapira (9.7 to 15.4%) have a wide range in ?18O and are accompanied by pervasive potash-fenitization of their host rock. The potash-fenitization is marked by the replacement of carbonatite host rock (mainly pyroxenite) by carbonate-phlogopite-magnetite-rich rocks. We conclude that fractional crystallization and liquid immiscibility may not significantly affect the oxygen and carbon isotopic composition of carbonatites. Large isotopic variations may be produced when these rocks intrude limestone country rocks (i.e., Mato Preto) and/or have been subjected to postcrystallization alteration processes. Variations of ?18O and ?13C in the carbonatites may be explained by isotopic exchange between these rocks and H 20?CO 2-fluids at different temperatures and with different H 2O/CO 2 ratios. The isotope exchange model implies that the isotopic variations in carbonatites take place under low-temperature conditions (below 300°C) and involve fluids with high H 2O/CO 2 ratios.
Kohn-Sham calculations with the exact functional
Wagner, Lucas O; Stoudenmire, E M; Burke, Kieron; White, Steven R
2014-01-01
As a proof of principle, self-consistent Kohn-Sham calculations are performed with the exact exchange-correlation functional. The systems calculated are one-dimensional real-space interacting fermions with more than two electrons. To find the exact functional for trial densities requires solving the interacting Schroedinger equation multiple times, a much more demanding task than direct solution of the Schr\\"odinger equation. The density matrix renormalization group method makes this possible. We illustrate and explore the convergence properties of the exact KS scheme for both weakly and strongly correlated systems. We also explore the spin-dependent generalization and densities for which the functional is ill defined.
a new approach to Hohenberg-Kohn theorem
NASA Astrophysics Data System (ADS)
Lammert, Paul
2015-03-01
The Hohenberg-Kohn theorem is a cornerstone of electronic density functional theory, and yet in order to carry through its proof one must assume that ground state wavefunctions never vanish on a set of nonzero Lebesgue measure. This is a particularly unsatisfactory situation since DFT is supposed to avoid needing knowledge of the many-body wavefunction. I propose a new approach which puts conditions only on the density and potentials. This approach allows a proof that if the density is continuous and nowhere vanishing, then a representing potential in L2 +L? is unique up to an overall constant.
Asymptotic form of the Kohn-Sham correlation potential
Joubert, D. P. [School of Physics, University of the Witwatersrand, P.O. Wits 2050, Johannesburg (South Africa)
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)].
Element orbitals for Kohn-Sham density functional theory
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.
Bjørnstad, Ottar Nordal
Stability of titanium oxide phases in Kohn-Sham density functional theory A well known problem in practical Kohn-Sham (KS) density functional theory (DFT) calculations is that it yields the wrong order-DFT, but with different levels of corrections to the exchange-correlation functional. Kohn-Sham density functional theory
2011-01-01
Background Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB. Results We sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA. Conclusions Although lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive. PMID:21767386
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)
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…
A new generalized KohnSham method for fundamental band-gaps in solids
Baer, Roi
A new generalized KohnSham method for fundamental band-gaps in solids Helen R. Eisenberg and Roi-state properties and fundamental band-gaps of solids, using a generalized KohnSham approach combining a local dielectric constant of the solid and ~e = 0.84 and A = 0.216 a0 À1 , predictions of the fundamental band
Paris-Sud XI, UniversitÃ© de
L-607 Superconductivityand absence of a Kohn anomaly in the quasi-one-dimensional organic conductor Kohn Ã 2 kF Ã basse tempÃ©rature et Ã pression atmosphÃ©rique. Abstract. 2014 Superconductivity has been to detect any Kohn anomaly at low temperature. J. Physique - LETTRES 41 (1980) L-607 - L-610 Classification
Herbert, John
2014-01-01
THE JOURNAL OF CHEMICAL PHYSICS 140, 044108 (2014) Symmetry-adapted perturbation theory with Kohn of second-order symmetry-adapted perturbation theory (SAPT) calculations using Kohn-Sham (KS) orbitals correlation.4,5 Such a hybrid approach was first tested in 2001,6 simply by substituting Kohn-Sham (KS
Pelster, Axel
2013-01-01
PHYSICAL REVIEW A 88, 033621 (2013) Breakdown of the Kohn theorem near a Feshbach resonance decreases when the bias magnetic field approaches the Feshbach resonance, so the Kohn theorem is violated, by modifying the three-body interaction strength [12,13,18]. In 1961 Kohn [21] showed in a three
Igic, Boris
,y and Joshua R. Kohn1, y *Department of Biological Sciences (M/C 067), University of Illinois at Chicago, 840 and Kohn 2006). Here we are primarily concerned with SI, broadly defined as any postpollination prezygotic and Kohn 2001; Steinbachs and Holsinger 2002; Castric and Vekemans 2004; Igic et al. 2006), and the causes
ccsd-00004344,version1-1Mar2005 Fast computation of the Kohn-Sham susceptibility of large systems
Paris-Sud XI, UniversitÃ© de
ccsd-00004344,version1-1Mar2005 Fast computation of the Kohn-Sham susceptibility of large systems D operations, the susceptibility of N non inter- acting Kohn-Sham reference electrons. We observe and paradoxically, most of the CPU time is actually spent on the charge susceptibility of the non interacting Kohn
Wang, Yan Alexander
Kohn-Sham method as a free-energy minimization at infinite temperature Robert G. Parr and Y that the exact Kohn-Sham equations result from a minimization with respect to , at some very high temperature-Oppenheimer approximation, with the electrons mov- ing in an external potential due to the atomic nuclei, v0 r . The Kohn
Trajectory Surface Hopping in the Time-Dependent Kohn-Sham Approach for Electron-Nuclear Dynamics
Trajectory Surface Hopping in the Time-Dependent Kohn-Sham Approach for Electron-Nuclear Dynamics-field treatment of electron-nuclear interaction results in many qualitative breakdowns in the time-dependent Kohn. Developed as an extension of the Hohenberg-Kohn-Sham theory [3] for arbitrary TD systems by Runge and Gross
Propagators for the time-dependent Kohn-Sham equations
NASA Astrophysics Data System (ADS)
Castro, Alberto; Marques, Miguel A. L.; Rubio, Angel
2004-08-01
In this paper we address the problem of the numerical integration of the time-dependent Schrödinger equation i?t?=??. In particular, we are concerned with the important case where ? is the self-consistent Kohn-Sham Hamiltonian that stems from time-dependent functional theory. As the Kohn-Sham potential depends parametrically on the time-dependent density, ? is in general time dependent, even in the absence of an external time-dependent field. The present analysis also holds for the description of the excited state dynamics of a many-electron system under the influence of arbitrary external time-dependent electromagnetic fields. Our discussion is separated in two parts: (i) First, we look at several algorithms to approximate exp( ), where is a time-independent operator [e.g., =-i?t?(?) for some given time ?]. In particular, polynomial expansions, projection in Krylov subspaces, and split-operator methods are investigated. (ii) We then discuss different approximations for the time-evolution operator, such as the midpoint and implicit rules, and Magnus expansions. Split-operator techniques can also be modified to approximate the full time-dependent propagator. As the Hamiltonian is time dependent, problem (ii) is not equivalent to (i). All these techniques have been implemented and tested in our computer code OCTOPUS, but can be of general use in other frameworks and implementations.
Ryan, Michael J.
Geographic variation in female mate-copying in the species complex of a unisexual fish, Poecilia molly, Poecilia formosa, is a gynogenetic, all-female fish. Its mating system relies on heterospecific by the sexual species P. mexicana and P. latipinna, and the asexual P. formosa. Both sexual and asexual females
Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen
2015-01-01
Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches. PMID:25658107
Variation of slow-wave frequency and locking during the migrating myoelectric complex in dogs.
Caenepeel, P; Janssens, W; Accarino, A; Janssens, J; Vantrappen, G; Eyssen, H
1991-12-01
Slow waves determine rhythm and polarity of spike bursts. We measured the variation of slow-wave frequency (swf) and locking (swl) in the canine jejunum during the various phases of the migrating myoelectric complex (MMC) and during induced phase III (erythromycin 125 micrograms/kg iv bolus or somatostatin 2.5 micrograms.kg-1.h-1 iv infusion), blocked phase III (atropine 20 micrograms/kg iv bolus), and so-called stationary phase III activity (cisapride 150 micrograms/kg iv bolus). The EMG of 4 dogs, implanted with 10 bipolar electrodes, was recorded on a polygraph. Our results indicate that swf and swl change during the MMC from a stepwise swf gradient with slow waves locked in plateaus during phase I to a continuous swf gradient without or with significantly reduced phase locking during phase III. The length of the first swf plateau decreases significantly from 42 +/- 12 cm post Treitz during phase I to 11 +/- 4 cm during spontaneous phase III. Atropine block of phase III activity prevents phase unlocking and development of a continuous swf gradient. Our hypothesis is that phase unlocking may be one of the induction mechanisms of spike-burst activity. PMID:1685071
Time-dependent Internal DFT formalism and Kohn-Sham scheme
J. Messud
2009-11-05
We generalize to the time-dependent case the stationary Internal DFT / Kohn-Sham formalism presented in Ref. [14]. We prove that, in the time-dependent case, the internal properties of a self-bound system (as an atomic nuclei) are all defined by the internal one-body density and the initial state. We set-up a time-dependent Internal Kohn-Sham scheme as a practical way to compute the internal density. The main difference with the traditional DFT / Kohn-Sham formalism is the inclusion of the center-of-mass correlations in the functional.
The Kohn mode for trapped Bose gases within the dielectric formalism
Jürgen Reidl; Gyula Bene; Robert Graham; Péter Szépfalusy
2000-10-17
The presence of undamped harmonic center of mass oscillations of a weakly interacting Bose gas in a harmonic trap is demonstrated within the dielectric formalism for a previously introduced finite temperature approximation including exchange. The consistency of the approximation with the Kohn theorem is thereby demonstrated. The Kohn modes are found explicitly, generalizing an earlier zero-temperature result found in the literature. It is shown how the Kohn mode disappears from the single-particle spectrum, while remaining in the density oscillation spectrum, when the temperature increases from below to above the condensation temperature.
NASA Astrophysics Data System (ADS)
Wu, Guiping; Liu, Yuanbo
2015-04-01
Poyang Lake is the largest freshwater lake in China, with high morphological complexity from south to north. In recent years, the lake has experienced expansion and shrinkage processes over both short- and long-term scales, resulting in significant hydrological, ecological and economic problems. Exactly how and how rapidly the processes of spatial change have occurred in the lake during the expansion and shrinkage periods is unknown. Such knowledge is of great importance for policymakers as it may help with flood/drought prevention, land use planning and lake ecological conservation. In this study, we investigated the spatial-temporal distribution and changing processes of inundation in Poyang Lake based on Moderate Resolution Imaging Spectroradiometer (MODIS) Level-1B data from 2000 to 2011. A defined water variation rate (WVR) and inundation frequency (IF) indicator revealed the water surface submersion and exposure processes of lake expansion and shrinkage in different zones which were divided according to the lake's hydrological and topographic features. Regional differences and significant seasonality variability were found in the annual and monthly mean IF. The monthly mean IF increased slowly from north to south during January-August but decreased quickly from south to north during September-December. During the lake expansion period, the lake-type water body zone (Zone II) had the fastest expansion rate, with a mean monthly WVR value of 34.47% in February-March, and was followed by the channel-type water body zone (Zone I) in March-May (22.47%). However, during the lake shrinkage period, rapid shrinkage first appeared around the alluvial delta zones in August-October. The sequence of lake surface shrinkage from August to December is exactly opposite to that of lake expansion from February to July. These complex inundation characteristics and changing process were driven by the high temporal variability of the river flows, the morphological diversity of the benthic landforms and the patterns of water movement. These results provide a foundation for basic hydrological and ecological studies and are valuable for the conservation and management of water resources in Poyang Lake.
Fractional kohn-sham occupancies from a strong-correlation density functional.
Becke, Axel D
2015-01-01
It is not always possible in Kohn-Sham density-functional theory for the non-interacting reference state to have integer-only occupancies. Cases of "strong" correlation, with very small HOMO-LUMO gaps, involve fractional occupancies. At the transition states of symmetric avoided-crossing reactions, for example, representation of the correct density requires a 50/50 mixing of degenerate HOMOs. In a recent paper (Becke, J Chem Phys 139:021104, 2013) the "B13" strong-correlation density functional of Becke (J Chem Phys 138:074109, 2013 and 138:161101, 2013) was shown to give excellent barrier heights in symmetric avoided-crossing reactions. However, the calculations were performed only at reactant and transition-state geometries, where the fractional HOMO-LUMO occupancies in the latter are 50/50 by symmetry. In the present chapter, we compute full reaction curves for avoided crossings in H2?+?H2, ethylene (twisting around the double bond), and cyclobutadiene (double-bond automerization) by determining fractional occupancies variationally. We adopt a practical strategy for doing so which does not involve self-consistent B13 computations (not yet possible) and involves minimal cost. Single-bond dissociation curves for H2 and LiH are also presented. PMID:25467535
Molecular variation in the Paragonimus heterotremus complex in Thailand and Myanmar.
Sanpool, Oranuch; Intapan, Pewpan M; Thanchomnang, Tongjit; Janwan, Penchom; Nawa, Yukifumi; Blair, David; Maleewong, Wanchai
2013-12-01
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
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
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.
Molecular Variation in the Paragonimus heterotremus Complex in Thailand and Myanmar
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
Excitation energies and Stokes shifts from a restricted open-shell Kohn-Sham approach
Kowalczyk, Tim
Restricted open-shell Kohn-Sham (ROKS) theory provides a powerful computational tool for calculating singlet excited state energies and dynamics. However, the possibility of multiple solutions to the ROKS equations — with ...
Atomic Compton profile of neon calculated from an accurate Kohn-Sham potential
Al-Sharif, A.I. [Department of Physics, Faculty of Science, Yarmouk University, Irbid (Jordan)
2005-07-15
The Compton profile of the neon atom is calculated from an accurate Kohn-Sham potential derived from accurate quantum Monte Carlo wave functions. Compared to the experiment, the results are better than the Hartree-Fock ones in the low-wave-vector region. This suggests that the systematic error in the Kohn-Sham formulation in momentum space is relatively small. The first-order Lam-Plazman correction is also calculated. This correction is less than 1% on the average.
Change." Pp. 50-69 in Aleksandra Jasinska-Kania, Melvin L. Kohn, and Kazimierz Slomczynski (Eds.), Power. Kohn The Johns Hopkins University In this essay, I examine the effects of radical social change of meaning and measurement (see in particular Kohn 1987; Kohn and Slomczynski 1990, chap. 2; #12;Kohn et al
DOUGLAS A. BELLY
Survey of morphometric, calorimetric, and allozymic variation in the Glau- cous-winged Gull (Larus glaucescens), the Western Gull (L. occidentalis) and their hybrids is based on 706 specimens taken from 33 colony areas located throughout the breeding range of both species. Whereas most morphometric characters overlap between taxa, col- orimetric characters exhibited significant intraspecific and interspecific clinal variation. Ca- nonical discriminant
Fundamental Gaps in Finite Systems from Eigenvalues of a Generalized Kohn-Sham Method Tamar Stein,1
Baer, Roi
Fundamental Gaps in Finite Systems from Eigenvalues of a Generalized Kohn-Sham Method Tamar Stein,1-separated hybrid functional within the generalized Kohn-Sham approach to density functional theory. Its key element to be outside its reach. DOI: 10.1103/PhysRevLett.105.266802 PACS numbers: 73.22.Àf, 71.15.Àm The Kohn-Sham (KS
On the Efficient Solution of Variational Inequalities; Complexity and Computational Efficiency
Perakis, Georgia
In this paper we combine ideas from cutting plane and interior point methods in order to solve variational inequality problems efficiently. In particular, we introduce a general framework that incorporates nonlinear as ...
Kohn-Luttinger effect in nested Fermion liquids
Hyok-Jon Kwon
1997-01-29
We study the Kohn-Luttinger effect in a two-dimensional (2D) nested Fermion liquid with a repulsive interaction via the renormalization group method and identify the resulting order parameter symmetry. Using the band structure of the 2D Hubbard model close to half-filling as a prototype, we construct an effective low-energy theory. We use multidimensional bosonization to incorporate the zero-sound channel and find marginal Fermi liquid behavior in the absence of any instability. We show an analog of the Landau theorem in nested Fermion liquids, which serves as the criterion of the BCS instability. Including repulsive or antiferromagnetic exchange interactions in the low-energy theory, we show that the $d_{x^2-y^2}$-wave BCS channel is renormalized to be the most attractive. Below half-filling, when the nesting is not perfect, there is competition between the spin-density-wave (SDW) and the BCS channels; when the SDW coupling is small enough, there occurs a $d_{x^2-y^2}$-wave superconducting instability at sufficiently low temperatures.
NASA Astrophysics Data System (ADS)
Yamamoto, Y.; Kameda, J.; Yamaguchi, H.
2009-12-01
Although deformation and physical/chemical properties variation in aseismic-seismic transition zone were essential to examine critical changes in environmental parameters that result in earthquake, they are poorly understood because the appropriate samples buried 2-4 km have not been collected yet (scientific drilling has never reached there and most of ancient examples experienced the deeper burial depth and suffered thermal and physical overprinting). The lower to middle Miocene Hota accretionary complex is a unique example of on land accretionary complex, representing deformation and its physical/chemical properties of sediments just prior to entering the seismogenic realm. The maximum paleotemperature was estimated approximately 55-70°C (based on vitrinite reflectance) indicative of a maximum burial depth about 2-3 km assuming a paleo-geothermal gradient as 25-35°C/km. Accretionary complex in this temperature/depth range corresponds with an intermediate range between the core samples collected from the modern accretionary prism (e.g. Nankai, Barbados, and so on) and rocks in the ancient accretionary complexes on land. This presentation will treat the detailed structural and chemical analyses of the Hota accretionary complex to construct deformation properties of décollement zone and accretionary complex in its 2-3 km depth range and to discuss the interrelation between the early diagenesis (hydrocarbon/cations generation and sediment dewatering, etc.) and transition of the deformation properties. The deformation in this accretionary complex is characterized by two deformation styles: one is a few centimeter-scale phacoidal deformation representing clay minerals preferred orientation in the outer rim, whereas random fabric in the core, quite similar texture to the rocks in the present-Nankai décollement. The other is S-C style deformation (similar deformation to the mélanges in ancient accretionary complex on land) exhibiting block-in-matrix texture and quite intense clay minerals preferred orientation in the matrix, cutting the phacoidal deformation. The host and faulted (S-C structure) rocks composed of hemipelagic siltstone containing 70-80% of clay minerals. Considerable-smectite reduction and positive anomaly of illite/smectite ratio were clearly identified inside the latter S-C structure, which would cause remarkable increase in friction coefficient. Such strain hardening associated with dynamic clay-mineral variation would be the primary mechanism in décollement -zone and/or mélange-zone thickening and fundamental mechanical transition just prior to entering the seismogenic zone. Positive anomaly of the vitrinite reflectance data (Ro) inside infers frictional heating during the deformation plausibly caused the clay mineral variation.
Yan He; Cheng Wei; He Guang-min; Li Gang; Dong Shi-du
2007-01-01
A new image transform, namely, the quad-tree complex wavelet packets transform (QCWPT) is introduced ,which both has shift invariance and good direction analysis ability and other merits of the dual-tree complex wavelet transform (DCWT), and has the ability of analyzing the high frequency detail signal carefully like the wavelet packet transform (WPT). Furthermore, a novel image denoising scheme based on
Variations of oxygen and carbon isotopes in carbonatites: A study of Brazilian alkaline complexes
Roberto V. Santos; Robert N. clayton
1995-01-01
We have studied the oxygen and carbon isotopic compositions of carbonatite complexes from South America (Jacupiranga, Araxá, Catalão, Tapira, and Mato Preto) and interpreted the results in terms of magmatism, contamination by country rocks, and hydrothermal processes. These complexes range in age from 130 to 65 Ma and were emplaced during the reactivation of the South American Platform during the
Moen, Erika L.; Zhang, Xu; Mu, Wenbo; Delaney, Shannon M.; Wing, Claudia; McQuade, Jennifer; Myers, Jamie; Godley, Lucy A.
2013-01-01
Elucidating cytosine modification differences between human populations can enhance our understanding of ethnic specificity in complex traits. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines derived from individuals of European or African ancestry were profiled using the Illumina HumanMethylation450 BeadChip. Approximately 13% of the analyzed CpG sites showed differential modification between the two populations at a false discovery rate of 1%. The CpG sites with greater modification levels in European descent were enriched in the proximal regulatory regions, while those greater in African descent were biased toward gene bodies. More than half of the detected population-specific cytosine modifications could be explained primarily by local genetic variation. In addition, a substantial proportion of local modification quantitative trait loci exhibited population-specific effects, suggesting that genetic epistasis and/or genotype × environment interactions could be common. Distinct correlations were observed between gene expression levels and cytosine modifications in proximal regions and gene bodies, suggesting epigenetic regulation of interindividual expression variation. Furthermore, quantitative trait loci associated with population-specific modifications can be colocalized with expression quantitative trait loci and single nucleotide polymorphisms previously identified for complex traits with known racial disparities. Our findings revealed abundant population-specific cytosine modifications and the underlying genetic basis, as well as the relatively independent contribution of genetic and epigenetic variations to population differences in gene expression. PMID:23792949
Efficient construction of exchange and correlation potentials by inverting the Kohn-Sham equations
NASA Astrophysics Data System (ADS)
Kananenka, Alexei A.; Kohut, Sviataslau V.; Gaiduk, Alex P.; Ryabinkin, Ilya G.; Staroverov, Viktor N.
2013-08-01
Given a set of canonical Kohn-Sham orbitals, orbital energies, and an external potential for a many-electron system, one can invert the Kohn-Sham equations in a single step to obtain the corresponding exchange-correlation potential, v_XC({r}). For orbitals and orbital energies that are solutions of the Kohn-Sham equations with a multiplicative v_XC({r}) this procedure recovers v_XC({r}) (in the basis set limit), but for eigenfunctions of a non-multiplicative one-electron operator it produces an orbital-averaged potential. In particular, substitution of Hartree-Fock orbitals and eigenvalues into the Kohn-Sham inversion formula is a fast way to compute the Slater potential. In the same way, we efficiently construct orbital-averaged exchange and correlation potentials for hybrid and kinetic-energy-density-dependent functionals. We also show how the Kohn-Sham inversion approach can be used to compute functional derivatives of explicit density functionals and to approximate functional derivatives of orbital-dependent functionals.
Kirkwood, Kathryn J.; Ahmad, Yasmeen; Larance, Mark; Lamond, Angus I.
2013-01-01
Proteins form a diverse array of complexes that mediate cellular function and regulation. A largely unexplored feature of such protein complexes is the selective participation of specific protein isoforms and/or post-translationally modified forms. In this study, we combined native size-exclusion chromatography (SEC) with high-throughput proteomic analysis to characterize soluble protein complexes isolated from human osteosarcoma (U2OS) cells. Using this approach, we have identified over 71,500 peptides and 1,600 phosphosites, corresponding to over 8,000 proteins, distributed across 40 SEC fractions. This represents >50% of the predicted U2OS cell proteome, identified with a mean peptide sequence coverage of 27% per protein. Three biological replicates were performed, allowing statistical evaluation of the data and demonstrating a high degree of reproducibility in the SEC fractionation procedure. Specific proteins were detected interacting with multiple independent complexes, as typified by the separation of distinct complexes for the MRFAP1-MORF4L1-MRGBP interaction network. The data also revealed protein isoforms and post-translational modifications that selectively associated with distinct subsets of protein complexes. Surprisingly, there was clear enrichment for specific Gene Ontology terms associated with differential size classes of protein complexes. This study demonstrates that combined SEC/MS analysis can be used for the system-wide annotation of protein complexes and to predict potential isoform-specific interactions. All of these SEC data on the native separation of protein complexes have been integrated within the Encyclopedia of Proteome Dynamics, an online, multidimensional data-sharing resource available to the community. PMID:24043423
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…
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...
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.
Giraldo, M.A.; Bosch, D.; Madden, M.; Usery, L.; Kvien, C.
2008-01-01
This research addressed the temporal and spatial variation of soil moisture (SM) in a heterogeneous landscape. The research objective was to investigate soil moisture variation in eight homogeneous 30 by 30 m plots, similar to the pixel size of a Landsat Thematic Mapper (TM) or Enhanced Thematic Mapper plus (ETM+) image. The plots were adjacent to eight stations of an in situ soil moisture network operated by the United States Department of Agriculture-Agriculture Research Service USDA-ARS in Tifton, GA. We also studied five adjacent agricultural fields to examine the effect of different landuses/land covers (LULC) (grass, orchard, peanuts, cotton and bare soil) on the temporal and spatial variation of soil moisture. Soil moisture field data were collected on eight occasions throughout 2005 and January 2006 to establish comparisons within and among eight homogeneous plots. Consistently throughout time, analysis of variance (ANOVA) showed high variation in the soil moisture behavior among the plots and high homogeneity in the soil moisture behavior within them. A precipitation analysis for the eight sampling dates throughout the year 2005 showed similar rainfall conditions for the eight study plots. Therefore, soil moisture variation among locations was explained by in situ local conditions. Temporal stability geostatistical analysis showed that soil moisture has high temporal stability within the small plots and that a single point reading can be used to monitor soil moisture status for the plot within a maximum 3% volume/volume (v/v) soil moisture variation. Similarly, t-statistic analysis showed that soil moisture status in the upper soil layer changes within 24 h. We found statistical differences in the soil moisture between the different LULC in the agricultural fields as well as statistical differences between these fields and the adjacent 30 by 30 m plots. From this analysis, it was demonstrated that spatial proximity is not enough to produce similar soil moisture, since t-test's among adjacent plots with different LULCs showed significant differences. These results confirm that a remote sensing approach that considers homogeneous LULC landscape fragments can be used to identify landscape units of similar soil moisture behavior under heterogeneous landscapes. In addition, the in situ USDA-ARS network will serve better in remote sensing studies in which sensors with fine spatial resolution are evaluated. This study is a first step towards identifying landscape units that can be monitored using the single point reading of the USDA-ARS stations network. ?? 2008 Elsevier B.V.
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.
Correlating genetic variation in carbon isotopic composition with complex climatic gradients.
Comstock, J P; Ehleringer, J R
1992-01-01
Genetic variation in both carbon isotope discrimination and the proportions of leaf and photosynthetic twig tissues were observed in ecotypes of Hymenoclea salsola T.G., a common shrub in the deserts of the western United States, when grown under common garden conditions. These variations were correlated with climatic conditions in the habitats of origin through a model that described the leaf-to-air water vapor gradients experienced by plants during the growing season. Both carbon isotope discrimination and the proportion of leaves in the canopy were lower in plants derived from habitats with higher leaf-to-air vapor gradients, despite the fact that some of these sites received relatively high amounts of annual precipitation. These patterns were consistent with the notion that plants are able to maintain substantial control of water-use efficiency over large environmental gradients of temperature and moisture availability. PMID:1502194
Orbital relaxation effects on Kohn-Sham frontier orbital energies in density functional theory.
Zhang, DaDi; Zheng, Xiao; Li, Chen; Yang, Weitao
2015-04-21
We explore effects of orbital relaxation on Kohn-Sham frontier orbital energies in density functional theory by using a nonempirical scaling correction approach developed in Zheng et al. [J. Chem. Phys. 138, 174105 (2013)]. Relaxation of Kohn-Sham orbitals upon addition/removal of a fractional number of electrons to/from a finite system is determined by a systematic perturbative treatment. The information of orbital relaxation is then used to improve the accuracy of predicted Kohn-Sham frontier orbital energies by Hartree-Fock, local density approximation, and generalized gradient approximation methods. The results clearly highlight the significance of capturing the orbital relaxation effects. Moreover, the proposed scaling correction approach provides a useful way of computing derivative gaps and Fukui quantities of N-electron finite systems (N is an integer), without the need to perform self-consistent-field calculations for (N ± 1)-electron systems. PMID:25903872
Orbital relaxation effects on Kohn-Sham frontier orbital energies in density functional theory
NASA Astrophysics Data System (ADS)
Zhang, DaDi; Zheng, Xiao; Li, Chen; Yang, Weitao
2015-04-01
We explore effects of orbital relaxation on Kohn-Sham frontier orbital energies in density functional theory by using a nonempirical scaling correction approach developed in Zheng et al. [J. Chem. Phys. 138, 174105 (2013)]. Relaxation of Kohn-Sham orbitals upon addition/removal of a fractional number of electrons to/from a finite system is determined by a systematic perturbative treatment. The information of orbital relaxation is then used to improve the accuracy of predicted Kohn-Sham frontier orbital energies by Hartree-Fock, local density approximation, and generalized gradient approximation methods. The results clearly highlight the significance of capturing the orbital relaxation effects. Moreover, the proposed scaling correction approach provides a useful way of computing derivative gaps and Fukui quantities of N-electron finite systems (N is an integer), without the need to perform self-consistent-field calculations for (N ± 1)-electron systems.
A spectral scheme for Kohn-Sham density functional theory of clusters
Banerjee, Amartya S; James, Richard D
2014-01-01
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 ha...
Dumont, Beth L.; White, Michael A.; Steffy, Brian; Wiltshire, Tim; Payseur, Bret A.
2011-01-01
The rate of recombination is a key genomic parameter that displays considerable variation among taxa. Species comparisons have demonstrated that the rate of evolution in recombination rate is strongly dependent on the physical scale of measurement. Individual recombination hotspots are poorly conserved among closely related taxa, whereas genomic-scale recombination rate variation bears a strong signature of phylogenetic history. In contrast, the mode and tempo of evolution in recombination rates measured on intermediate physical scales is poorly understood. Here, we conduct a detailed statistical comparison between two whole-genome F2 genetic linkage maps constructed from experimental intercrosses between closely related house mouse subspecies (Mus musculus). Our two maps profile a common wild-derived inbred strain of M. m. domesticus crossed to distinct wild-derived inbred strains representative of two other house mouse subspecies, M. m. castaneus and M. m. musculus. We identify numerous orthologous genomic regions with significant map length differences between these two crosses. Because the genomes of these recently diverged house mice are highly collinear, observed differences in map length (centimorgans) are suggestive of variation in broadscale recombination rate (centimorgans per megabase) within M. musculus. Collectively, these divergent intervals span 19% of the house mouse genome, disproportionately aggregating on the X chromosome. In addition, we uncover strong statistical evidence for a large effect, sex-linked, site-specific modifier of recombination rate segregating within M. musculus. Our findings reveal considerable variation in the megabase-scale recombination landscape among recently diverged taxa and underscore the continued importance of genetic linkage maps in the post-genome era. PMID:20978138
Fujita, Y
2001-11-01
Chromatic regulation of photosystem stoichiometry in cyanophytes, green algae and probably vascular plants is achieved by regulation of the abundance of PSI in response to thylakoid electron transport state at least under our experimental conditions [cf. Fujita (1997) Photosyn. Res. 53: 83]. However, variation of not only PSI but also PSII, in reverse of each other, is characteristic of the stoichiometry regulation in red algae and some of marine cyanophytes. Our previous study with the red alga Porphyridium cruentum has revealed that PSII is inactivated by 50% upon a light shift from the light absorbed by Chl a, PSI light, to that mainly absorbed by phycobilisomes (PBS), PSII light [Fujita (1999) Plant Cell Physiol. 40: 924]. To evaluate the contribution of the photoinactivation to the chromatic variation of PSII, variation of the abundance of PSI, PSII and PBS, together with the fluorescence parameter and the activity of PSII, was followed after a light shift from PSI light to PSII light. Upon a light shift to PSII light, PSII, determined as Cyt b(559) per PBS, decreased rapidly, following the photoinactivation, down to the level a half of that before the light shift, and remained constant. Since the increase in PBS was not significant during this period, a rapid decrease of PSII/PBS led us to tentatively conclude that the degradation of PSII is a main cause for variation of the abundance of PSII. Photoinactivation of PSII, and also decrease in Cyt b(559), was accelerated, but only slightly, by the addition of chloramphenicol (CAP) at a moderate concentration while CAP at the same concentration significantly suppressed the increment of PSI determined as P700. A selective effect of CAP supports the above conclusion. PMID:11726709
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.
Variation of stability constants of thorium and uranium oxalate complexes with ionic strength
Erten, H.N; Mohammed, A.K.; Choppin, G.R. [Florida State Univ., Tallahassee, FL (United States). Dept. of Chemistry
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.
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
Elmer, Kathryn R; Kusche, Henrik; Lehtonen, Topi K; Meyer, Axel
2010-06-12
The polychromatic and trophically polymorphic Midas cichlid fish species complex (Amphilophus cf. citrinellus) is an excellent model system for studying the mechanisms of speciation and patterns of phenotypic diversification in allopatry and in sympatry. Here, we first review research to date on the species complex and the geological history of its habitat. We analyse body shape variation from all currently described species in the complex, sampled from six crater lakes (maximally 1.2-23.9 kyr old) and both great lakes in Nicaragua. We find that Midas cichlid populations in each lake have their own characteristic body shape. In lakes with multiple sympatric species of Midas cichlid, each species has a distinct body shape. Across the species complex, most body shape change relates to body depth, head, snout and mouth shape and caudal peduncle length. There is independent parallel evolution of an elongate limnetic species in at least two crater lakes. Mitochondrial genetic diversity is higher in crater lakes with multiple species. Midas cichlid species richness increases with the size and age of the crater lakes, though no such relationship exists for the other syntopic fishes. We suggest that crater lake Midas cichlids follow the predicted pattern of an adaptive radiation, with early divergence of each crater lake colonization, followed by intralacustrine diversification and speciation by ecological adaptation and sexual selection. PMID:20439280
Kohn, Michael
Program Director/Principal Investigator (Last, First, Middle): Kohn, Michael Hans PHS 398/2590 (Rev. Song Y., Endepols S., Klemann N., Richter D., Matuschka F., Shih C., Nachman M. and Kohn M.H. 2011. Curr Biol 21 (15), 1296-1301. 2. Diaz J.C., Song Y., Moore A., Borchert J.N. and Kohn M.H. 2010
Bonitz, Michael
Invariance of the Kohn center-of-mass mode in a conserving theory M. Bonitz,1 K. Balzer,1 and R by Kohn14 and Brey et al.7 This issue has more recently re- gained interest in the context of trapped Bose condensates. In particular, the invariance of the Kohn mode by certain ap- proximate theories has been
Kohn, Linda M.
5 6 7 Caroline Sirjusingh and Linda M. Kohn, Department of Botany, University of Toronto at8 populations of this haploid fungus,35 DNA fingerprints (Kohn et al 1991; Kohli et al 1995) can be combined scales37 (Carbone et al 1999; Carbone and Kohn 2001). Microsatellite loci, due to their high mutation38
Lindgren, Ingvar
Construction of accurate Kohn-Sham potentials for the lowest states of the helium atom: Accurate Kohn-Sham potentials have been constructed for the ground 1s2 1 S state and, in particular and the procedure of van Leeuwen and Baerends (Phys. Rev. A49, 2138 (1994)). The resulting Kohn-Sham orbitals
Kohn, Michael
Program Director/Principal Investigator (Last, First, Middle): Kohn, Michael, Hans PHS 398, Kohn M. Gene-gene network interactions as predictors of intra- chromosomal linkage disequilibrium in the human haplotype map. (Submitted) 4. Li SW, Shih CH, Kohn M. Functional and evolutionary correlates
Stefanucci, Gianluca
Assessing the accuracy of Kohn-Sham conductances using the Friedel sum rule H. Mera,1 K. Kaasbjerg the Friedel sum rule FSR to discuss the accuracy of exact and approximated Kohn-Sham density- functional prove that if the Kohn-Sham Hamiltonian reproduces the density of the interacting system calculated
Krekelberg, Bart
and Adam Kohn Carlyn A. Patterson, Jacob Duijnhouwer, Stephanie C. Wissig, Bart Krekelberg stimulus conditions Carlyn A. Patterson,1 Jacob Duijnhouwer,3 Stephanie C. Wissig,1 Bart Krekelberg,3 and Adam Kohn1 CA, Duijnhouwer J, Wissig SC, Krekelberg B, Kohn A. Similar adaptation effects in primary visual
On the Necessary Conditions for the Validity of the Hohenberg-Kohn Theorem
V. B. Bobrov; S. A. Trigger; G. J. F. van Heijst
2010-08-14
It is shown that the Hohenberg-Kohn lemma and theorem are direct consequences of the statement that the ground state energy (or free energy) of a system of interacting particles in an external field is a unique functional of the potential of this field. This means that, if the Hohenberg-Kohn theorem is valid, the nonuniform density in the equilibrium system and the external field potential are biunique functionals. In this case, the nonuniform density is intimately related to the inverse response function. On this basis, a regular procedure can be constructed for determining the density functional for the free energy or ground state energy.
N-density representability and the optimal transport limit of the Hohenberg-Kohn functional
Gero Friesecke; Christian B. Mendl; Brendan Pass; Codina Cotar; Claudia Klüppelberg
2013-04-02
We derive and analyze a hierarchy of approximations to the strongly correlated limit of the Hohenberg-Kohn functional. These "density representability approximations" are obtained by first noting that in the strongly correlated limit, N-representability of the pair density reduces to the requirement that the pair density must come from a symmetric N-point density. One then relaxes this requirement to the existence of a representing symmetric k-point density with k Kohn-Sham calculation for small atoms. We find that the low order representability conditions already capture the main part of the correlations.
ANE S. GULDAHL; LIV BORGEN; INGER NORDAL
2001-01-01
Contrasting with former taxonomic treatments, chromosome numbers and isozyme data support the delimitation of the seminiferous representatives of the Festuca brachyphylla complex in Svalbard into four species F. baffinensis, F. brachyphylla, F. hyperborea and F. edlundiae. Unique enzyme markers were found for all species. Festuca brachyphylla proved hexaploid, and the others, tetraploid. The chromosome numbers of F. hyperborea and F.
NASA Astrophysics Data System (ADS)
Rabiu, A. B.; Ogunsua, B. O.; Fuwape, I. A.; Laoye, J. A.
2014-12-01
The quest to find an index for proper characterization and description of the dynamical response of the ionosphere to external influences and its various internal irregularities has led to the study of the day to day variations of the chaoticity and dynamical complexity of the ionosphere. This study was conducted using Global Positioning System (GPS) Total Electron Content (TEC) time series, measured in the year 2011, from 5 GPS receiver stations in Nigeria which lies within the Equatorial Ionization Anomaly region. The nonlinear aspect of the TEC time series were obtained by detrending the data. The detrended TEC time series were subjected to various analyses for phase space reconstruction and to obtain the values of chaotic quantifiers which are Lyapunov exponents LE, correlation dimension, and Tsallis entropy for the study of dynamical complexity. The results show positive Lyapunov exponents for all days which indicate chaoticity of the ionosphere with no definite pattern for both quiet and disturbed days. However values of LE were lower for the storm period compared to its nearest relative quiet periods for all the stations. Considering all the days of the year the daily/transient variations show no definite pattern for each month but day to day values of Lyapunov exponent for the entire year show a wavelike semiannual variation pattern with lower values around March, April, September and October, a change in pattern which demonstrates the self-organized critical phenomenon of the system. This can be seen from the correlation dimension with values between 2.7 and 3.2 with lower values occurring mostly during storm periods demonstrating a phase transition from higher dimension during the quiet periods to lower dimension during storms for most of the stations. The values of Tsallis entropy show similar variation pattern with that of Lyapunov exponent with a lot of agreement in their comparison, with all computed values of Lyapunov exponent correlating with values of Tsallis entropy within the range of 0.79 to 0.82. These results show that Lyapunov quantifiers can be used together as indices in the study of the variations of the dynamical complexity of the ionosphere. The presence of chaos and high variations in the dynamical complexity, even at quiet periods in the ionosphere may be due to the internal dynamics and inherent irregularities of the ionosphere which exhibit non-linear properties. However, this inherent dynamics may be complicated by external factors like geomagnetic storms. This may be the main reason for the drop in the values of Lyapunov exponent and Tsallis entropy during storms. The results also show a strong interplay between determinism and stochasticity, as the ionosphere shows its response to changes in solar activities and in its internal dynamics. The dynamical behavior of the ionosphere throughout the year as described by these quantifiers, were discussed in this work.
Mordaunt, Dylan A; Jolley, Alexandra; Balasubramaniam, Shanti; Thorburn, David R; Mountford, Hayley S; Compton, Alison G; Nicholl, Jillian; Manton, Nicholas; Clark, Damian; Bratkovic, Drago; Friend, Kathryn; Yu, Sui
2015-06-01
Isolated mitochondrial respiratory chain complex III deficiency has been described in a heterogeneous group of clinical presentations in children and adults. It has been associated with mutations in MT-CYB, the only mitochondrial DNA encoded subunit, as well as in nine nuclear genes described thus far: BCS1L, TTC19, UQCRB, UQCRQ, UQCRC2, CYC1, UQCC2, LYRM7, and UQCC3. BCS1L, TTC19, UQCC2, LYRM7, and UQCC3 are complex III assembly factors. We report on an 8-year-old girl born to consanguineous Iraqi parents presenting with slowly progressive encephalomyopathy, severe failure to thrive, significant delays in verbal and communicative skills and bilateral retinal cherry red spots on fundoscopy. SNP array identified multiple regions of homozygosity involving 7.5% of the genome. Mutations in the TTC19 gene are known to cause complex III deficiency and TTC19 was located within the regions of homozygosity. Sequencing of TTC19 revealed a homozygous nonsense mutation at exon 6 (c.937C?>?T; p.Q313X). We reviewed the phenotypes and genotypes of all 11 patients with TTC19 mutations leading to complex III deficiency (including our case). The consistent features noted are progressive neurodegeneration with Leigh-like brain MRI abnormalities. Significant variability was observed however with the age of symptom onset and rate of disease progression. The bilateral retinal cherry red spots and failure to thrive observed in our patient are unique features, which have not been described, in previously reported patients with TTC19 mutations. Interestingly, all reported TTC19 mutations are nonsense mutations. The severity of clinical manifestations however does not specifically correlate with the residual complex III enzyme activities. © 2015 Wiley Periodicals, Inc. PMID:25899669
NASA Astrophysics Data System (ADS)
Lin, S.; Chung, S.
2013-12-01
Complicated patterns and trench-parallel components of seismic anisotropy in the central portion of the subduction zones have not been link to three-dimensional flow in general, as toroidal circulations may mostly occur in the vicinity of a plate edge. Nevertheless, recent dynamical models demonstrate that complex flow forms when lateral heterogeneities in the subduction zone are considered. Seismic studies often show gradual variations in slab length along strike. The southern Chilean subduction zone is a notable example. The Peru-Chile Trench roughly extending 5900 km is the longest trench worldwide. Most of the regions are distant from the subduction zone edges. In this study the effects of slab-length variations are examined with numerical experiments. The results are used to characterize the regional mantle circulations and the potential heat sources for the recent Patagonian plateau basalts in the southern South America. The model results show that rollback subduction induces both significant poloidal components and trench-parallel flow, extending over 1500 kilometers along the strike of the subduction zone. The trajectories of a set of passive tracers show intricate patterns such as helical streamlines, revealing complex mantle circulations in systems with the along-arc slab-length variations. The upwelling may lead to decompression melting of the heterogeneous asthenosphere to cause extensive lavas in the back arc. Mantle upwelling of the sub-slab mantle moving towards supra-slab regions is observed in the southernmost portion of the subduction system, but only for models with slab segments roughly deeper than 100 km depth. The results indicate that certain segments of the Antarctic slab may reach at least 100 km depth.
Effects of parametric variations of complex targets on damage from projectile impact
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.
Density functional theory and Kohn-Sham scheme for self-bound systems
Messud, Jeremie; Suraud, Eric [Universite de Toulouse, UPS, Laboratoire de Physique Theorique (IRSAMC), F-31062 Toulouse (France); CNRS, LPT (IRSAMC), F-31062 Toulouse (France); Bender, Michael [Universite Bordeaux, Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France); CNRS/IN2P3, Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France)
2009-11-15
We demonstrate how the separation of the total energy of a self-bound system into a functional of the internal one-body Fermionic density and a function of an arbitrary wave vector describing the center-of-mass kinetic energy can be used to set up an 'internal' Kohn-Sham scheme.
Density functional theory and Kohn-Sham scheme for self-bound systems
J. Messud; M. Bender; E. Suraud
2009-11-10
We demonstrate how the separation of the total energy of a self-bound system into a functional of the internal one-body Fermionic density and a function of an arbitrary wave vector describing the center-of-mass kinetic energy can be used to set-up an "internal" Kohn-Sham scheme.
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…
"Fighting the Toxic Status Quo": Alfie Kohn on Standardized Tests and Teacher Education.
ERIC Educational Resources Information Center
Appleman, Deborah; Thompson, Micheal J.
2002-01-01
Considers how many teacher educators feel caught between the need to comply with state and federal laws governing the approval of their teacher education programs and the desire to resist what many feel to be another example of "testing gone wild." Presents a conversation with Alfie Kohn on high stakes tests for teachers and for students. (SG)
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,…
Kohn's theorem in a superfluid Fermi gas with a Feshbach resonance
Yoji Ohashi
2004-07-15
We investigate the dipole mode in a superfluid gas of Fermi atoms trapped in a harmonic potential. According to Kohn's theorem, the frequency of this collective mode is not affected by an interaction between the atoms and is always equal to the trap frequency. This remarkable property, however, does not necessarily hold in an approximate theory. We explicitly prove that the Hartree-Fock-Bogoliubov generalized random phase approximation (HFB-GRPA), including a coupling between fluctuations in the density and Cooper channels, is consistent with both Kohn's theorem as well as Goldstone's theorem. This proof can be immediately extended to the strong-coupling superfluid theory developed by Nozi\\'eres and Schmitt-Rink (NSR), where the effect of superfluid fluctuations is included within the Gaussian level. As a result, the NSR-GRPA formalism can be used to study collective modes in the BCS-BEC crossover region in a manner which is consistent with Kohn's theorem. We also include the effect of a Feshbach resonance and a condensate of the associated molecular bound states. A detailed discussion is given of the unusual nature of the Kohn mode eigenfunctions in a Fermi superfluid, in the presence and absence of a Feshbach resonance. When the molecular bosons feel a different trap frequency from the Fermi atoms, the dipole frequency is shown to {\\it depend} on the strength of effective interaction associated with the Feshbach resonance.
Why Students Lose When "Tougher Standards" Win: A Conversation with Alfie Kohn.
ERIC Educational Resources Information Center
O'Neil, John; Tell, Carol
1999-01-01
Kohn believes the "tougher standards" movement is incompatible with personalized learning, excellence, and marginalized kids' interests. Horizontal standards that shift how teaching and learning happen in classrooms are terrific, but vertical standards using traditional pedagogy are macho and mindless. Kids need freedom to design their own…
Sex and Class Differences in Parent-Child Interaction: A Test of Kohn's Hypothesis
ERIC Educational Resources Information Center
Gecas, Viktor; Nye, F. Ivan
1974-01-01
This paper focuses on Melvin Kohn's suggestive hypothesis that white-collar parents stress the development of internal standards of conduct in their children while blue-collar parents are more likely to react on the basis of the consequences of the child's behavior. This hypothesis was supported. (Author)
Paradoxical Pathways: An Ethnographic Extension of Kohn's Findings on Class and Childrearing
ERIC Educational Resources Information Center
Weininger, Elliot B.; Lareau, Annette
2009-01-01
Stratification is a central issue in family research, yet relatively few studies highlight its impact on family processes. Drawing on in-depth interviews (N = 137) and observational data (N = 12), we extend Melvin Kohn's research on childrearing values by examining how parental commitments to self-direction and conformity are enacted in daily…
KSSOLV—a MATLAB toolbox for solving the Kohn-Sham equations
Chao Yang; Juan C. Meza; Byounghak Lee; Lin-wang Wang
2009-01-01
We describe the design and implementation of KSSOLV, a MATLAB toolbox for solving a class of nonlinear eigenvalue problems known as the Kohn-Sham equations. These types of problems arise in electronic structure calculations, which are nowadays essential for studying the microscopic quantum mechanical properties of molecules, solids and other nanoscale materials. KSSOLV is well suited for developing new algorithms for
Robin M. Kohn University of Central Florida School of Social Work
Van Stryland, Eric
Robin M. Kohn University of Central Florida School of Social Work P.O. Box 163358 Orlando, FL 32816-3358 (407) 823-2967 EDUCATION Masters in Clinical Social Work (1979) Florida State University Tallahassee/Facilitator of ALS Support Group August 2002-Present Bachelors in Social Work (BSW) Program Coordinator August 2001
Baer, Roi
of the Density Matrix in Kohn-Sham Density Functional Theory and an Assessment of Linear System-Size Scaling. These findings sup- port "principle of nearsightedness" introduced recently by W. Kohn [Phys. Rev. Lett. 76, 3168 of the system. [S0031-9007(97)04543-2] PACS numbers: 71.15.Mb The Hohenberg-Kohn and Kohn-Sham (KS) density
Robson, Paul R H; Farrar, Kerrie; Gay, Alan P; Jensen, Elaine F; Clifton-Brown, John C; Donnison, Iain S
2013-05-01
Energy crops can provide a sustainable source of power and fuels, and mitigate the negative effects of CO2 emissions associated with fossil fuel use. Miscanthus is a perennial C4 energy crop capable of producing large biomass yields whilst requiring low levels of input. Miscanthus is largely unimproved and therefore there could be significant opportunities to increase yield. Further increases in yield will improve the economics, energy balance, and carbon mitigation of the crop, as well as reducing land-take. One strategy to increase yield in Miscanthus is to maximize the light captured through an extension of canopy duration. In this study, canopy duration was compared among a diverse collection of 244 Miscanthus genotypes. Canopy duration was determined by calculating the number of days between canopy establishment and senescence. Yield was positively correlated with canopy duration. Earlier establishment and later senescence were also both separately correlated with higher yield. However, although genotypes with short canopy durations were low yielding, not all genotypes with long canopy durations were high yielding. Differences of yield between genotypes with long canopy durations were associated with variation in stem and leaf traits. Different methodologies to assess canopy duration traits were investigated, including visual assessment, image analysis, light interception, and different trait thresholds. The highest correlation coefficients were associated with later assessments of traits and the use of quantum sensors for canopy establishment. A model for trait optimization to enable yield improvement in Miscanthus and other bioenergy crops is discussed. PMID:23599277
Variation of complex permittivity of soils with moisture content using VNA
NASA Astrophysics Data System (ADS)
Gadani, D. H.; Rana, V. A.; Bhatnagar, S. P.; Prajapati, A. N.; Vyas, A. D.
2013-06-01
The complex dielectric permittivity (?', ??) of sand (Kukas region field, Jaipur District, Rajasthan) and sandy loam soil (Sayla, Surendranagar District field, Gujarat) was measured in the frequency range from 100 MHz to 1.5 GHz, for various moisture contents in the soils, using a Vector Network Analyzer (VNA). It has been observed that, the dielectric constant and dielectric loss of the dry soils remain almost constant over this frequency range. The dielectric constant and dielectric loss increase with increase in moisture content in the soil, at any fixed frequency in this frequency region. At given moisture content in the soil, the dielectric constant of the soils decreases slowly with increase in frequency up to 1.5 GHz, whereas the dielectric loss of the soils decreases rapidly with increase in frequency up to 0.5 GHz, after which it decreases slowly with increase in frequency up to 1.5 GHz.
Variationally consistent approximation scheme for charge transfer
NASA Technical Reports Server (NTRS)
Halpern, A. M.
1978-01-01
The author has developed a technique for testing various charge-transfer approximation schemes for consistency with the requirements of the Kohn variational principle for the amplitude to guarantee that the amplitude is correct to second order in the scattering wave functions. Applied to Born-type approximations for charge transfer it allows the selection of particular groups of first-, second-, and higher-Born-type terms that obey the consistency requirement, and hence yield more reliable approximation to the amplitude.
Quantum scattering via the S?matrix version of the Kohn variational principle
Zhang, John Z. H.; Chu, Shih-I; Miller, William H.
1988-11-17
ib, Eq. (2.2) may also be viewed as the distorted wave Born approximation, where ib is the distorted wave.] We take the trial function ib(r) in the form N ib(r) = - uo(r) + L u/(r)c/, (2.4) 1=1 where uo(r) is a function that is regular at r = 0... and has asymptotic form (2.5) In applications we have chosen (2.6) wheref(r) is a cutoff function to regularize uo(r) as r .... O, fer) .... 0, r-O, fer) -1, r-... 00; e.g.,f(r) = (l_e- ar). Thefunctionu,(r) is ul(r) = uo(r)*, (2.7) (2...
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
Messud, Jeremie [Universite de Toulouse, UPS, Laboratoire de Physique Theorique (IRSAMC), F-31062 Toulouse, France, and CNRS, LPT (IRSAMC), F-31062 Toulouse (France)
2009-11-15
The stationary internal density functional theory (DFT) formalism and Kohn-Sham scheme are generalized to the time-dependent case. It is proven that, in the time-dependent case, the internal properties of a self-bound system (such as an atomic nuclei or a helium droplet) are all defined by the internal one-body density and the initial state. A time-dependent internal Kohn-Sham scheme is set up as a practical way to compute the internal density. The main difference from the traditional DFT formalism and Kohn-Sham scheme is the inclusion of the center-of-mass correlations in the functional.
Manríquez-Morán, Norma L; Cruz, Fausto R Méndez-de la; Murphy, Robert W
2014-01-01
Parthenogenesis is a form of clonal reproduction. Eggs develop in the absence of sperm and offspring are genetically identical to their mother. Although common in invertebrates, it occurs in only a few species of squamate reptiles. Parthenogenetic reptiles have their origin in interspecific hybridization, and their populations are exclusively female. Because of its high mutation rate and maternal inheritance, mitochondrial DNA sequence data can evaluate the origin and evolution of all-female vertebrates. Partial sequences from two mitochondrial genes, Cytb and ND4, were analyzed to investigate questions about the origin of parthenogenesis in the Aspidoscelis cozumela complex, which includes A. cozumela, A. maslini and A. rodecki. Low levels of divergence were detected among parthenogenetic species, and between them and A. angusticeps, confirming it as the maternal species of the parthenoforms. A gene tree was constructed using sequences from three populations of A. angusticeps and nine of its unisexual daughter species. The phylogeny suggests that two independent hybridization events between A. angusticeps and A. deppii formed three unisexual species. One hybridization resulted in A. rodecki and the other formed A. maslini and A. cozumela. Although A. cozumela has the haplotype characteristic of A. maslini from Puerto Morelos, it is considered to be a different species based on karyological and morphological characteristics and its geographical isolation. PMID:24410491
Kuusemets, V; Mander, U; Lõhmus, K; Ivask, M
2001-01-01
The study of purification efficiency and nutrient assimilation in plants was made in two riparian buffer zones with a complex of wet meadow and grey alder (Alnus incana) stand. In the less polluted Porijõgi test site, the 31 m wide buffer zone removed 40% of total nitrogen (total-N) and 78% of total phosphorus (total-P), while a heavily polluted 51 m wide buffer zone in Viiratsi retained 85% of total-N and 84% of total-P. The input of nutrients and purification efficiency displayed a significant relationship. The total-N removal in buffer zone was negative when the input value was less than 0.3 mg l(-1) and the purification efficiency was always positive when the input value exceeded 5 mg l(-1). The purification efficiency of total-P was positive when the input value exceeded 0.15 mg l(-1). Grass vegetation plays an important role in nutrient retention in riparian buffer strips. The maximum phytomass production was measured in Porijõgi site where production of the Filipendula ulmaria community was up to 2,358 g m(-2), assimilation of N 32.1 and of P 4.9 g m(-2), respectively. This is much higher than the biomass production and N and P uptake of the grey alders (Alnus incana) at the same site--1,730, 20.5 and 1.5 g m(-2), respectively. PMID:11804159
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.
NASA Astrophysics Data System (ADS)
Krone, F.; Muller, P. D.; Silverman, J.; Schaumloffel, J.
2004-05-01
The purpose of this study was to determine if migmatitic gneisses of the New Russia complex (NRC)adjacent to the Marcy Anorthosite massif (MAM) near Elizabethtown, NY display geochemical signatures indicative of partial melting. Alcock and Muller (2000) proposed that intrusion of the easternmost portion of the MAM into the NRC resulted in a thermal aureole in which gabbroic, mangeritic, and charnockitic gneisses of NRC experienced local anatexis. Petrologic and microtextural data indicate dehydration melting involving the following reaction: hbl + ksp+ qz = ga + cpx + Pl(antiperthitic) + melt +/- oxide at T greater than 900 C and P greater than 700 MPa. Fine-grained mangerite close to the anorthosite contacts has significantly greater amounts of garnet and oxides than mangerites further away from the contact. Field relationships indicate melt segregated into lenses and pods near the end of and after regional foliation formation. Eight samples taken along a transect at a high angle the steeply-dipping MAM/NRC contact were collected and locations were determined using a handheld GPS unit. Samples were cleaned, powdered, and dissolved for ICP-AES analysis for the following elements: Ba, Co, Cr, Eu, La, Mn, Nb, Ni, P, Sc, Sr, V, Yb, and Zr. Of these elements, Co, Ba, V, Yb, and Zr display patterns suggestive of partial melting and melt loss in mangeritic gneiss near the MAM/NRC contact. Ba and Zr concentrations in the mangerites are up to several hundred ppm lower than values reported for other Grenville mangerites. Ba depletion is consistent with breakdown of K-bearing phases such as Hbl and perthitic feldspar and removal with the melt. Co, and V show concentrations up to several hundred ppm higher than reported values for other Grenville mangerites. While we have no Yb concentration data to compare our values to, our Yb values are several times higher than those of other Grenville jotunites and which should have higher concentrations than mangerites. Further, Yb has been shown to concentrate in garnet formed during partial melting reactions such as those that occurred in the mangerites. We have no mineral chemistry data to document which mineral phases contain Co, however, we assume it partitions in a similar fashion to Yb and occurs as a trace component of pyroxene, garnet, and oxides, all of which are products of the melting reaction given above. This would explain its enrichment in the melt depleted contact zone gneisses.
Helium Isotope Variations in Peridotite, Gabbro and Basalt from the Kane Oceanic Core Complex
NASA Astrophysics Data System (ADS)
Konrad, K.; Graham, D. W.; Dick, H. J.
2012-12-01
A fundamental assumption in mapping geochemical variability of the upper mantle is that the isotope composition of mid-ocean ridge basalt is representative of its mantle source region, being largely unmodified during its transport through the crust and eruption on the seafloor. We have begun to test this assumption through measurement of He isotopes in a suite of rocks from the Kane oceanic core complex (OCC) along the Mid-Atlantic Ridge (23oN). The Kane OCC provides a valuable window into crustal architecture and chemical composition of a slow-spreading ridge (Dick et. al. 2008, 2010). A suite of > 30 samples (comprised of whole rocks, mineral separates and basalt glasses) has been analyzed for 3He/4He and He concentrations. Gas extraction experiments included crushing in vacuum, step heating, and fusion in a high-vacuum furnace. We found 3He/4He in the two freshest peridotites (harzburgite and olivine websterite) to be identical to that measured in the most depleted MORB glasses collected from the ridge axis (8.4-8.7 RA). Notably, the freshest and least deformed peridotite (a porphyroclastic harzburgite) has the highest helium content of any of the OCC rocks (~200 ncc/g), and the majority of its helium (>2/3) is only released by melting. In contrast to the results of Kurz et al. (2009), which clearly show increasing helium concentration levels with increasing deformation in abyssal peridotites from other localities, at the Kane OCC we found lower helium contents in three mylonitized peridotites compared to the less deformed peridotites. Troctolites from the Kane OCC experienced very late-stage melt impregnation fed through a conduit represented by a large dunite body near the MOHO. 3He/4He ratios in the troctolites (8.6-9.0 RA) also overlap with values in the fresh peridotites and in the most depleted basalts from the area. Collectively, fresh Kane OCC peridotites and troctolites, having [He] above 10 ncc/g, show a narrow range of 3He/4He ratio (8.4-9.0 RA). This value is elevated compared to the median value for MORBs (8 RA). Our observations suggest that domains of highly depleted MORB mantle tend to have higher 3He/4He ratios, approaching 9 RA, consistent with what is observed in depleted MORB glasses globally. Kane gabbroic rocks are more variable, and typically show lower 3He/4He ratios, often accompanied by lower He concentrations. This likely reflects an increased importance of atmospheric and radiogenic components. Lower initial 3He/4He ratios (<8 RA) may also be present in some of the gabbros, perhaps from partial meting of a lithologically heterogeneous mantle source.
Sulfur and halogen gases at Masaya Caldera Complex, Nicaragua: Total flux and variations with time
NASA Astrophysics Data System (ADS)
Stoiber, Richard E.; Williams, Stanley N.; Huebert, Barry J.
1986-11-01
Santiago Crater, of Masaya Caldera Complex near Managua, Nicaragua, entered a phase of intense magmatic degassing in late 1979. The flux of SO2 increased rapidly from a previous average of 380 t d-1 to approximately 1200 t d-1 in February 1980. We report on results of a study of the gas flux and geochemistry conducted as part of a broader interdisciplinary study of the volcano and its impact on the adjacent environment. Masaya is an unusual volcano because of its low shield like form, consistent tholeiitic basaltic composition, frequent activity, and especially because of the approximately 25 year cycle of major non-eruptive degassing crises. We have used a combination of techniques involving remote sensing (using a correlation spectrometer (COSPEC)) of the flux of SO2 and direct filter sampling of the ratios of the sulfur and halogen gases and aerosols to quantify the flux of all of these species. The three-stage filters successively trap aerosols, halogen acid gases, and sulfur dioxide and are analyzed by ion chromatography. We have used the ratios of various species, with the COSPEC measurements of the flux of SO2, to calculate that the average flux of SO2 is 1275 t d-1, HCl is 830 t d-1, HF is about 16 t d-1, and HBr is at most 1 t d-1. H2S and SO4 = are only minor sulfur species. The flux of SO2 and HCl represents the largest reported noneruptive sustained volcanic release of these species in the world. Masaya contributed 7% of the total SO2 estimated to have been released by volcanoes worldwide in 1981. The flux of SO2 has declined by about 9% each year since 1979 and can be modeled as a first-order kinetic rate law with a decay constant of approximately 0.04 yr-1. Approximately 2.2 × 106 tons of SO2 has been released between September 1979 and September 1985. The ratio S/Cl has declined more rapidly than the flux of SO2, reflecting the greater solubility of HCl than SO2 in the magma. The SO2 flux at Santiago varies more widely within a single day than observed at other degassing volcanoes and may be controlled at least in part by effects of the solid earth tide. An area larger than 500 km2 has been severely impacted downwind of the volcano. Downwind ground-level concentrations of SO2 of 0.25 ppm are frequently encountered. Acid rain, unusually chloride rich, has a pH as low as 2.63. S/Cl ratios in the gas plume increase downwind, probably as a result of the high solubility and dry-deposition velocity of HCl. Preliminary analyses of primary concentrations of sulfur and chlorine in the magma of the present lava lake are used to calculate that at least 1.2 km3 has been completely degassed, with respect to sulfur, to provide the observed flux. This implies that 10 km3 have been degassed by previous crises in the past century and further suggests a magma supply rate of approximately 0.1 km3/yr (comparable with Kilauea or Etna volcanoes). During historic time, only two lava flows have been extruded, implying an unusually low ratio of extrusion/intrusion of only 0.0007
Kumar, Dhakchinamoorthi Krishna; Shewade, Deepak Gopal; Surendiran, Adithan; Adithan, Chandrasekaran
2013-01-01
Objective: To study the genetic variation and haplotype structure of Vitamin K epoxide reductase complex, subunit 1 (VKORC1) gene in the Tamilian population. Materials And Methods: The study was performed on 210 unrelated, healthy volunteers of the Tamilian population, of either sex between the age group of 18-60 years. Five ml of venous blood sample was collected using sodium ethylene diamine tetra acetic acid (EDTA) as anticoagulant. DNA was extracted using phenol-chloroform extraction method. Eight single nucleotide polymorphisms (SNPs) VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), rs23596121 (C), and rs7294 (A) were studied using real-time quantitative Polymerase Chain Reaction (qPCR) method and they were included for constructing five-major haplotype blocks of VKORC1 gene. Results: The major alleles of VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), and rs23596121 (C), were found to be at frequencies of 90.0%, 89.2%, 90.9%, 94.1%, 90.7%, 89.5% and 91.2%, respectively. The variant allele of VKORC1 rs7294 (A) was more frequent (83.6%) in the Tamilian population. The frequencies of haplotypes HAP1 (GTTCCGCA), HAP2 (ACGCTCTG), HAP3 (GTTTCGCG), HAP4 (GTTCCGCG) and HAP5 (GCTCCCCG) were found to be 80.0%, 7.4%, 4.7%, 1.5% and 1.1%, respectively. Conclusion: In the present study the allele- frequency distributions, genotype and haplotype frequencies of the VKORC1 gene was considered. The findings of this study provide the genetic information required for learning the association of VKORC1 genetic variation and oral anticoagulant dose variability among patients receiving oral anticoagulants in the Tamilian population. PMID:23662025
O. V. Gritsenko; E. J. Baerends
2004-01-01
Spin-unrestricted Kohn-Sham (KS) solutions are constructed from accurate ab initio spin densities for the prototype doublet molecules NO2, ClO2, and NF2 with the iterative local updating procedure of van Leeuwen and Baerends (LB). A qualitative justification of the LB procedure is given with a ``strong'' form of the Hohenberg-Kohn theorem. The calculated energies ?isigma of the occupied KS spin orbitals
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
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.
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
Existence of minimizers for Kohn-Sham within the Local Spin Density Approximation
David Gontier
2014-04-20
The purpose of this article is to extend the work by Anantharaman and Canc\\`es [1], 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.
Wayland, Matthew T
2013-01-01
Echinorhynchustruttae and the Echinorhynchusbothniensis species complex are common parasites of salmoniform and other fishes in northern Europe. Echinorhynchusbothniensis and its sibling species Echinorhynchus 'bothniensis' are thought to be closely related to the Nearctic Echinorhynchusleidyi Van Cleave, 1924 based on morphological similarity and common usage of a mysid intermediate host. This study provides the first analysis of morphological and meristic variation in Echinorhynchustruttae and expands our knowledge of anatomical variability in the Echinorhynchusbothniensis group. Morphological variability in Echinorhynchustruttae was found to be far greater than previously reported, with part of the variance attributable to sexual dimorphism. Echinorhynchustruttae, the two species of the Echinorhynchusbothniensis group and Echinorhynchusleidyi displayed considerable interspecific overlap in the ranges of all conventional morphological characters. However, Proboscis profiler, a tool for detecting acanthocephalan morphotypes using multivariate analysis of hook morphometrics, successfully separated Echinorhynchustruttae from the other taxa. The Echinorhynchusbothniensis species group could not be reliably distinguished from Echinorhynchusleidyi (or each other), providing further evidence of the affinity of these taxa. Observations on the distribution of Echinorhynchustruttae in its definitive host population are also reported. PMID:24723769
NASA Astrophysics Data System (ADS)
Gómez de Castro, Ana I.; López-Santiago, Javier; López-Martínez, Fátima; Sánchez, Néstor; de Castro, Elisa; Cornide, Manuel
2015-06-01
The Taurus-Auriga molecular complex (TMC) is the main laboratory for the study of low-mass star formation. The density and properties of interstellar dust are expected to vary across the TMC. These variations trace important processes such as dust nucleation or the magnetic field coupling with the cloud. In this paper, we show how the combination of near ultraviolet (NUV) and infrared (IR) photometry can be used to derive the strength of the 2175 Å bump and thus any enhancement in the abundance of small dust grains and polycyclic aromatic hydrocarbons in the dust grains size distribution. This technique is applied to the envelope of the TMC, mapped by the GALEXAll Sky Survey (AIS). Ultraviolet and IR photometric data have been retrieved from the GALEX-AIS and the 2MASS catalogues. NUV and K-band star counts have been used to identify the areas in the cloud envelope where the 2175 Å bump is weaker than in the diffuse interstellar medium namely, the low column density extensions of L1495, L1498 and L1524 in Taurus, L1545, L1548, L1519, L1513 in Auriga and L1482-83 in the California region. This finding agrees with previous results on dust evolution derived from Spitzer data and suggests that dust grains begin to decouple from the environmental Galactic magnetic field already in the envelope.
de Castro, Ana I Gomez; Lopez-Martinez, Fatima; Sanchez, Nestor; de Castro, Elisa; Cornide, Manuel
2015-01-01
The Taurus-Auriga molecular complex (TMC) is the main laboratory for the study of low mass star formation. The density and properties of interstellar dust are expected to vary across the TMC. These variations trace important processes such as dust nucleation or the magnetic field coupling with the cloud. In this article, we show how the combination of near ultraviolet (NUV) and infrared (IR) photometry can be used to derive the strength of the 2175 \\AA\\ bump and thus any enhancement in the abundance of small dust grains and PAHs in the dust grains size distribution. This technique is applied to the envelope of the TMC, mapped by the GALEX All Sky Survey (AIS). UV and IR photometric data have been retrieved from the GALEX-AIS and the 2MASS catalogues. NUV and K-band star counts have been used to identify the areas in the cloud envelope where the 2175 \\AA\\ bump is weaker than in the diffuse ISM namely, the low column density extensions of L1495, L1498 and L1524 in Taurus, L1545, L1548, L1519, L1513 in Auriga an...
Kohn-Luttinger Effect in a Two-dimensional Dense Fermi Liquid with Coulomb Repulsion.
NASA Astrophysics Data System (ADS)
Galitski, Victor
2000-03-01
In 1965 Kohn and Luttinger showed that a Fermi-liquid is unstable against the superconductive transition even in the case of purely repulsive interaction among particles. It has been shown that there is a pairing due to this singularity at least for large orbital momenta l. Recent experiments on 2-D electron gas have renewed interest in Kohn-Luttinger effect. In this work we consider the case of 2-D dense Fermi-liquid with pure Coulomb interaction among electrons. We show that such a system becomes superconductive at very low temperatures. Following Chubukov [2], we calculate the singular part of the scattering amplitude ?(q) up to the third order in the perturbation theory. To calculate diagrams we use screened Coulomb interaction. This allows us to avoid divergencies of the scattering amplitude appearing due to the Coulomb potential being long-range and also makes the problem similar to the one for the dilute Fermi-gas with short-range repulsive forces. The desired singularity ?^sing(q) ~ ?( 2 pF )^2 -q^2 appears in the third order perturbation theory and allows us to find the transition temperature Tc for large l. [1] W. Kohn and J. H. Luttinger, Phys. Rev. Lett. 15, 524 (1965), [2] A. Chubukov, Phys. Rev. B 48, 1097 (1993).
Periodicity of the time-dependent Kohn-Sham equation and the Floquet theorem
V. Kapoor; M. Ruggenthaler; D. Bauer
2013-02-25
The Floquet theorem allows to reformulate periodic time-dependent problems such as the interaction of a many-body system with a laser field in terms of time-independent, field-dressed states, also known as Floquet states. If this was possible for density functional theory as well, one could reduce in such cases time-dependent density functional theory to a time-independent Floquet density functional theory. We analyze under which conditions the Floquet theorem is applicable in a density-functional framework. By employing numerical {\\em ab initio} solutions of the interacting time-dependent Schr\\"odinger equation with time-periodic external potentials we show that the exact effective potential in the corresponding Kohn-Sham equation is {\\em not} unconditionally periodic. Whenever several Floquet states in the interacting system are involved in a physical process the corresponding Hartree-exchange-correlation potential is not periodic with the external frequency only. Using an analytically solvable example we demonstrate that, in general, the periodicity of the time-dependent Kohn-Sham Hamiltonian cannot be restored by choosing a different initial state. Only if the external periodic potential is sufficiently weak such that the initial state of the interacting system evolves adiabatically to a single, field-dressed state, the resulting Kohn-Sham system admits the application of the Floquet theorem.
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.
Skokov, S.; Bowman, J.M. (Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States))
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.
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
Chen, Liang; Chavda, Kalyan D.; Solanki, Mihir; Mediavilla, José R.; Mathema, Barun; Schlievert, Patrick M.
2013-01-01
Clonal complex 30 (CC30), one of the major Staphylococcus aureus lineages, has caused extensive hospital-acquired and community-acquired infections worldwide. Recent comparative genomics studies have demonstrated that three CC30 clones—phage type 80/81, Southwest Pacific (SWP), and contemporary EMRSA-16 associated (Con) strains—shared a recent common ancestor more than 100 years ago. Panton-Valentine leukocidin (PVL), a bacteriophage encoded toxin that has been epidemiologically linked with community-associated methicillin-resistant S. aureus (CA-MRSA), has frequently been identified in CC30 clones, although the pvl gene variation and distribution of PVL-encoding phages are poorly understood. We determined here the distribution of PVL phages, PVL gene sequences, and chromosomal phage insertion sites in 52 S. aureus CC30 PVL-harboring isolates, collected from four continents over a 75-year period. Our results indicate that PVL phages with icosahedral heads, including ?108PVL and ?PVL, were mainly associated with phage 80/81 strains, whereas phages with elongated heads were predominantly found in SWP (?Sa2958 and ?TCH60) and Con (?Sa2USA) strains. Nine single-nucleotide polymorphisms were identified in the lukSF-PV gene, with six isolates harboring the R variant that has been previously associated with CA-MRSA strains. Interestingly, all six R variant strains belonged to the same Con CC30 clone and carried a ?Sa2USA-like phage. Similar chromosomal phage insertion sites were also identified in all 52 PVL-harboring CC30 strains. These analyses provide important insights into the microepidemiology of PVL-harboring CC30 strains, while the discovery of ?Sa2USA-associated R variant strains sheds further light on the evolution of PVL-positive CA-MRSA. PMID:23284024
Donelle M. Robinson; Molly R. Morris
2010-01-01
Investigations into the nature of mate choice suggest that variation in female mate preferences is often context dependent,\\u000a varying in response to genetic and environmental influences on female condition as well as to external environmental stimuli.\\u000a Determining whether variation in female mate preference is adaptive requires understanding the variables involved that produce\\u000a this variation and how they interact. Comparative, multivariate
NASA Astrophysics Data System (ADS)
Schmid, K. W.; Grümmer, F.; Faessler, Amand
1987-11-01
The Hartree-Fock-Bogoliuboy problem with restoration of the broken symmetries before the variation as it has been formulated recently within the VAMPIR and EXCITED VAMPIR approaches is studied in more detail. Special emphasis is put on the implications of various symmetry restrictions imposed on the quasiparticle transformations. It is shown that the use of essentially complex transformations provides a possibility to account for time-odd unnatural parity pairing correlations in the wavefunctions without being forced to give up axial and time-reversal symmetry. It is illustrated that together with parity and neutron-proton mixing the use of such complex mean fields extends the applicability of the VAMPIR and EXCITED VAMPIR approaches to states with arbitrary spin and parity in both doubly even and doubly odd nuclear systems. The corresponding variational equations are explicitly evaluated and the numerical feasibility of their solution is investigated.
L. I. Dorman
1985-01-01
The Samarkand complex setup is aimed at the study of cosmic ray variations in a wide energy range from 7 billion eV (which corresponds to the geomagnetic threshold in the region of Samarkand) up to approx 10 to the 15th power to 10 to the 16th power eV. The setup consists of four 6-counter sections of neutron supermonitor with counters
A. Galvé; M. Sapin; A. Hirn; J. Diaz; J.-C. Lépine; M. Laigle; J. Gallart; M. Jiang
2002-01-01
Teleseismic receiver functions (RF) allow us to image the spatial variation of the crust-mantle boundary (Moho) along a tight array spanning from south of the Himalayas to the centre of the Tibetan Plateau. This approach is cross-tested with wide-angle reflection imaging (WARR). Highlighted by each of the two independent methods, a complex architecture of the Moho with dipping and overlapping
Higher-order adaptive finite-element methods for Kohn–Sham density functional theory
Motamarri, P. [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)] [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Nowak, M.R. [Department of Electrical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)] [Department of Electrical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Leiter, K.; Knap, J. [U.S. Army Research Labs, Aberdeen Proving Ground, Aberdeen, MD 21001 (United States)] [U.S. Army Research Labs, Aberdeen Proving Ground, Aberdeen, MD 21001 (United States); Gavini, V., E-mail: vikramg@umich.edu [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)
2013-11-15
We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn–Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss–Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100–200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn–Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn–Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688 atoms using modest computational resources, and good scalability of the present implementation up to 192 processors.
Kohn condition and exotic Newton-Hooke symmetry in the non-commutative Landau problem
P-M. Zhang; P. A. Horvathy
2011-11-15
$N$ "exotic" [alias non-commutative] particles with masses $m_a$, charges $e_a$ and non-commutative parameters $\\theta_a$, moving in a uniform magnetic field $B$, separate into center-of-mass and internal motions if Kohn's condition $e_a/m_a=\\const$ is supplemented with $e_a\\theta_a=\\const.$ Then the center-of-mass behaves as a single exotic particle carrying the total mass and charge of the system, $M$ and $e$, and a suitably defined non-commutative parameter $\\Theta$. For vanishing electric field off the critical case $e\\Theta B\
Restricted open-shell Kohn-Sham theory: Simulation of the pyrrole photodissociation
Frank, Irmgard; Damianos, Konstantina [Department Chemie und Biochemie, Universitat Muenchen, Butenandtstrasse 11, 81377 Muenchen, Germany and Center for Nanoscience, LMU Muenchen, 80539 Muenchen Germany (Germany)
2007-03-28
The authors study the photodissociation reactions of pyrrole and N-methylpyrrole using first-principles molecular dynamics. The first excited state is described with restricted open-shell Kohn-Sham theory. They find a small barrier in the excited state potential energy surface. The possibility of energy redistribution near the Franck-Condon region leads to two different reaction channels in on-the-fly simulations on a single diabatic potential energy surface. The results are discussed in comparison with previous ab initio calculations and with experiments.
Compressed representation of Kohn-Sham orbitals via selected columns of the density matrix
Damle, Anil; Ying, Lexing
2014-01-01
Given a set of Kohn-Sham orbitals from an insulating system, we present a direct method to construct a localized basis for the associated subspace. We construct the basis via the use of a set of selected columns of the density matrix (SCDM) coupled with an optional orthogonalization procedure. Our method is simple, robust, does not depend on any adjustable parameters, and may be used in any code for electronic structure calculations. We demonstrate the benefits of such a localized basis by using the SCDM to efficiently perform Hartree-Fock exchange energy calculations with near linear scaling.
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.
The Korringa-Kohn-Rostoker method with projection potentials: exact result for the density.
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
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
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.
Efficient iterative method for solving the Dirac-Kohn-Sham density functional theory
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.
The education of Walter Kohn and the creation of density functional theory
Zangwill, Andrew
2014-01-01
The theoretical solid-state physicist Walter Kohn was awarded one-half of the 1998 Nobel Prize in Chemistry for his mid-1960's creation of an approach to the many-particle problem in quantum mechanics called density functional theory (DFT). In its exact form, DFT establishes that the total charge density of any system of electrons and nuclei provides all the information needed for a complete description of that system. This was a breakthrough for the study of atoms, molecules, gases, liquids, and solids. Before DFT, it was thought that only the vastly more complicated many-electron wave function was needed for a complete description of such systems. Today, fifty years after its introduction, DFT (in one of its approximate forms) is the method of choice used by most scientists to calculate the physical properties of materials of all kinds. In this paper, I present a biographical essay of Kohn's educational experiences and professional career up to and including the creation of DFT.
Optimized Unrestricted Kohn-Sham Potentials from Ab Initio Spin Densities
Katharina Boguslawski; Christoph R. Jacob; Markus Reiher
2012-11-21
The reconstruction of the exchange-correlation potential from accurate ab initio electron densities can provide insights into the limitations of the currently available approximate functionals and provide guidance for devising improved approximations for density-functional theory (DFT). For open-shell systems, the spin density is introduced as an additional fundamental variable in Spin-DFT. Here, we consider the reconstruction of the corresponding unrestricted Kohn-Sham potentials from accurate ab initio spin densities. In particular, we investigate whether it is possible to reconstruct the spin exchange-correlation potential, which determines the spin density in spin-unrestricted Kohn-Sham-DFT, despite the numerical difficulties inherent to the optimization of potentials with finite orbital basis sets. We find that the recently developed scheme for unambiguously singling out an optimal optimized potential [J. Chem. Phys. 135, 244102 (2011)] can provide such spin potentials accurately. This is demonstrated for two test cases, the lithium atom and the dioxygen molecule, and target (spin) densities from Full-CI and CASSCF calculations, respectively.
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.
Kohn's theorem, Larmor's equivalence principle and the Newton-Hooke group
Gibbons, G.W., E-mail: gwg1@amtp.cam.ac.uk [DAMTP, Centre for Mathematical Sciences, Cambridge University, Wilberforce Road, Cambridge CB3 OWA (United Kingdom); Pope, C.N. [DAMTP, Centre for Mathematical Sciences, Cambridge University, Wilberforce Road, Cambridge CB3 OWA (United Kingdom); George P. and Cynthia W. Mitchell Institute for Fundamental Physics and Astronomy, Texas A and M University, College Station, TX 77843-4242 (United States)
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.
NASA Astrophysics Data System (ADS)
Nakano, M.; Kumagai, H.
2003-12-01
The waveform of a volcanic long-period (LP) event is characterized by a superposition of decaying sinusoids. It has been recognized that the complex frequencies (frequency, f and the quality factor, Q) of the decaying sinusoids show significant temporal variations. In this paper, we present a detailed description of temporal variations in f and Q of LP events at Kusatsu-Shirane Volcano to investigate the relation between LP events and magmatic activity. Extensive LP seismicity and systematic temporal variations in the complex frequencies of LP events are identified in 1989, 1991, 1992, and 1993. The complex frequencies of the LP events occurred between 1992 and 1993 were investigated by Kumagai et al. [2002, JGR, 10.129/2001JB000653]. In this paper, we determine f and Q of LP events occurred in 1989, when the renewed eruption activity started in Kusatsu-Shirane Volcano and a swarm of 40 LP events within 25 days occured. Our Sompi spectral analysis of the LP events shows that the frequency decreases from about 3.2 Hz to 1.7 Hz at the middle of the period, and then increases up to about 4 Hz. The Q factor increases from about 30 to 100, and then decreases down to about 20 at the middle of the period. After that, the Q factor again increases up to about 100 and then decreases down to about 30 at the end of the period. We find that the observed temporal variations in 1989 can be reasonably interpreted by oscillations of a crack filled with a water-gas mixture. The frequency of the oscillations of such a crack increases with increasing gas-volume fraction (GVF). On the other hand, the Q factor is around few tens at GVF of 0 and 1, and reaches a maximum value of about 100 in the vicinity of GVF of 0.5. Therefore, the temporal variations in f and Q can be explained by a change of GVF in a water-gas mixture: In the first half of this period, GVF changes from 1 to 0, and then changes from 0 to 1 in the second half of this period. This change may be interpreted as a dry crack gets wet by a seepage of hydrothermal water into the crack in the first half of the period. As heat supply from deeper magma become higher or water supply decreases in the hydrothermal system, the crack again gets dry in the second half of the period. We suggest that the LP activity in Kusatsu-Shirane Volcano may be basically controlled by an interaction between magmatic heat and water supply with possible seasonal variations in the hydrothermal system.
N. Pantic; D. Stefanovic
1984-01-01
The authors try to identify the specific role of orbital forcing, geodynamic phenomena and complex interaction of hydrosphere, cryosphere, atmosphere and biosphere through the geological history. This complex interaction can explain why there were no glaciations between Late Paleozoic and Neogene.
Patricia M. Anderson; Anatoly V. Lozhkin
2001-01-01
Questionable chronologies have limited detailed reconstructions of past vegetation and climate trends for the Karginskii\\/Middle Wisconsinan interstade (abbreviated here as MW). However, recent results from continuous lake records, while not resolving all the dating issues, do provide a new framework within which to examine this intriguing period. Paleobotanical data suggest significant regional variations in the interstadial vegetation of Beringia. Larix
ERIC Educational Resources Information Center
Gecas, Viktor; Nye, F. Ivan
This paper examines sex and class differences in the style and circumstances of parental discipline of the child. Specifically, we have focused on Melvin Kohn's suggestive hypothesis that white collar parents stress the development of internal standards of conduct in their children and thus are more likely to discipline the child on the basis of…
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...
Jeon, Jong Yeob; Lee, Jung Jae; Varghese, Jobi Kodiyan; Na, Sung Jae; Sujith, S; Go, Min Jeong; Lee, Junseong; Ok, Myung-Ahn; Lee, Bun Yeoul
2013-07-01
A cobalt(III) complex (1) of a salcy-type ligand tethering 4 quaternary ammonium salts, which is thought to act as a highly active catalyst for CO2/propylene oxide (PO) copolymerization, also shows high activity (TOF, 25,900 h(-1); TON, 518,000; 2.72 kg polymer per g cat) and selectivity (>98%) for CO2/ethylene oxide (EO) copolymerization that results in high-molecular-weight polymers (M(n), 200,000-300,000) that have strictly alternating repeating units. The related cobalt(III) complexes 11-14 were prepared through variations of the ligand framework of 1 by replacing the trans-1,2-diaminocyclohexane unit with 2,2-dimethyl-1,3-propanediamine, trans-1,2-diaminocyclopentane, or 1,1'-binaphthyl-2,2'-diamine or by replacing the aldimine bond with ketimine. These ligand frameworks are thought to favour the formation of the cis-? configuration in complexation, and the formation of the cis-? configuration in 11-14 was confirmed through NMR studies or X-ray crystallographic studies of model complexes not bearing the quaternary ammonium salts. Complexes 11, 13, and 14, which adopt the cis-? configuration even in DMSO did not show any activity for CO2/PO copolymerization. Complex 12, which was constructed with trans-1,2-diaminocyclopentane and fluctuated in DMSO between the coordination and de-coordination of the acetate ligand as observed for 1, showed fairly high activity (TOF, 12,400 h(-1)). This fluctuating behaviour may play a role in polymerization. However, complex 12 did not compete with 1 in terms of activity, selectivity, and the catalyst cost. PMID:23104466
Junie B. Billones; Eva Marie A. Ratilla; Graham A. Heath
2011-01-01
An extensive series of butyronitrile-substituted ruthenium chloride complexes [RuCl6?nLn]z (n=0–6; L?CH3(CH2)2CN or PrCN) has been prepared and characterized spectro-electrochemically. The complete series allowed the examination of the variation in electrode potential of RuIII\\/II couple and the accompanying trends in both Cl?Ru(III) and Ru(II)?PrCN charge-transfer spectra. Systematic analysis of electrochemical and spectroscopic data led to a conceptual representation of the relative
Veerappa, Avinash M.; Nachappa, Somanna Ajjamada; Prashali, Nelchi; Yadav, Sangeetha Nuggehalli; Srikanta, Manjula Arsikere; Manjegowda, Dinesh S.; Seshachalam, Keshava B.; Ramachandra, Nallur B.
2014-01-01
MicroRNAs are involved in post-transcriptional down-regulation of gene expression. Variations in miRNA genes can severely affect downstream-regulated genes and their pathways. However, population-specific burden of CNVs on miRNA genes and the complexities created towards the phenotype is not known. From a total of 44109 CNVs investigated from 1715 individuals across 12 populations using high-throughput arrays, 4007 miRNA-CNVs (?9%) consisting 6542 (?5%) miRNA genes with a total of 333 (?5%) singleton miRNA genes were identified. We found miRNA-CNVs across the genomes of individuals showing multiple hits in many targets, co-regulated under the same pathway. This study proposes four mechanisms unraveling the many complexities in miRNA genes, targets and co-regulated miRNA genes towards establishment of phenotypic diversity. PMID:24587348
Marine Guillaud-Bataille; Alexander Valent; Pascal Soularue; Christine Perot; Maria-del-Mar Inda; Aline Receveur; Sadek Smaili; Hugues Roest Crollius; Jean Benard; Alain Bernheim; Xavier Gidrol; Gisele Danglot
2004-01-01
Comparative genomic hybridization to bacterial artificial chromosome (BAC)-arrays (array-CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci, and the reliable detec- tion of local one-copy-level variations. We report a genome-wide amplification method allowing the same measurement sensitivity, using 1 ng of starting genomic DNA, instead of the classical
Kohn-Luttinger effect and the instability of a repulsive Fermi-liquid at T = 0
Chubukov, A.V. [Univ. of Illinois, Urbana (United States)]|[P.L. Kapitza Inst. for Physical Problems, Moscow (Russian Federation)
1992-11-01
The author considers the possibility for a pairing instability in a 2D repulsive Fermi-liquid due to the singularity in the scattering amplitude {Gamma}(q) at the momentum transfer q {approx} 2p{sub F} (Kohn-Luttinger effect). For arbitrary Fermi-liquid, {Gamma}(q) for the particles at the Fermi surface is found to have a singular part. For large 2D orbital momentum l, this term gives a dominant attractive contribution to the scattering amplitude and leads to a pairing instability in a 2D Fermi-liquid with arbitrary short-range repulsion. In the dilute limit, numerical studies show that the effect survives down to l = 1 and gives rise to a p-wave pairing. 12 refs.
Numerical methods for a Kohn-Sham density functional model based on optimal transport
Huajie Chen; Gero Friesecke; Christian B. Mendl
2014-05-27
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. Moreover, we prove that the SCE density functional model is correct for the H2 molecule in its dissociating limit.
Numerical methods for a Kohn-Sham density functional model based on optimal transport
Chen, Huajie; Mendl, Christian B
2014-01-01
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. Moreover, we prove that the SCE density functional model is correct for the H2 molecule in its dissociating limit.
Lathiotakis, Nektarios N; Rubio, Angel; Gidopoulos, Nikitas I
2014-01-01
We propose a novel scheme to bring reduced density matrix functional theory (RDMFT) into the realm of density functional theory (DFT) that preserves the accurate density functional description at equilibrium, while incorporating accurately static and left-right correlation effects in molecules and keeping the good computational performance of DFT-based schemes. The key ingredient is to relax the requirement that the local potential is the functional derivative of the energy with respect to the density. Instead, we propose to restrict the search for the approximate natural orbitals within a domain where these orbitals are eigenfunctions of a single-particle hamiltonian with a local effective potential. In this way, fractional natural occupation numbers are accommodated into Kohn-Sham equations allowing for the description of molecular dissociation without breaking spin symmetry. Additionally, our scheme provides a natural way to connect an energy eigenvalue spectrum to the approximate natural orbitals and this...
Kohn-Sham potentials in exact density-functional theory at non-integer electron numbers
Gould, Tim
2014-01-01
Within exact electron density-functional theory, we investigate Kohn-Sham (KS) potentials, orbital energies, and non-interacting kinetic energies of the fractional ions of Li, C and F. We use quantum Monte Carlo densities as input, which are then fitted, interpolated at non-integer electron numbers $N$, and inverted to produce accurate KS potentials $v_s^N(r)$. We study the dependence of the KS potential on $N$, and in particular we numerically confirm the existence of the theoretically predicted spatially constant discontinuity of $v_s^N(r)$ as $N$ passes through an integer. We further show that, for all the cases considered, the inner orbital energies and the non-interacting kinetic energy are nearly piecewise linear functions of $N$. This leads us to propose a simple approximation of the KS potential $v_s^N(r)$ at any fractional electron number $N$ which uses only quantities of the systems with the adjacent integer electron numbers.
Multiband Hamiltonians of the Luttinger-Kohn Theory and Ellipticity Requirements
Dmytro Sytnyk; Sunil Patil; Roderick Melnik
2010-04-14
Modern applications require a robust and theoretically strong tool for the realistic modeling of electronic states in low dimensional nanostructures. The $k \\cdot p$ theory has fruitfully served this role for the long time since its creation. During last two decades several problems have been detected in connection with the application of the $k \\cdot p$ approach to such nanostructures. These problems are closely related to the violation of the ellipticity conditions for the underlying system, the fact that until recently has been largely overlooked. We demonstrate that in many cases the models derived by a formal application of the Luttinger-Kohn theory fail to satisfy the ellipticity requirements. The detailed analysis, presented here on an example of the $6 \\times 6$ Hamiltonians, shows that this failure has a strong impact on the physically important properties conventionally studied with these models.
Gaiduk, Alex P.; Staroverov, Viktor N. [Department of Chemistry, University of Western Ontario, London, Ontario N6A 5B7 (Canada)
2011-01-15
A directly approximated exchange-correlation potential should, by construction, be a functional derivative of some density functional in order to avoid unphysical results. Using generalized gradient approximations (GGAs) as an example, we show that functional derivatives of explicit density functionals have a very rigid inner structure, the knowledge of which allows one to build the entire functional derivative from a small part. Based on this analysis, we develop a method for direct construction of integrable Kohn-Sham potentials. As an illustration, we transform the model potential of van Leeuwen and Baerends (which is not a functional derivative) into a semilocal exchange potential that has a parent GGA, yields accurate energies, and is free from the artifacts inherent in existing semilocal potential approximations.
Zhang, Xiaofeng; Huang, Deguang; Chen, Yu-Sheng; Holm, R. H.
2012-01-01
The planar NNN-pincer complexes [MII(pyN Me2)(OH)]1? (MII = Ni, Cu) fix CO2 in ?1-OCO2H complexes; results for the copper system are described. MnII, FeII, CoII, and ZnII behave differently, forming [MII(pyN2Me)2]2? with N4O2 coordination. Incorporation of the NiII pincer into binucleating macrocycle 2 containing a triamino MII locus connected by two 1,3-biphenylene groups affords proximal NiII and MII sites for investigation of the synthesis, structure, and reactivity of Ni-X-M bridge units. This ligand structure is taken as a reference for variations in MII atoms and binding sites and bridges X = OH? and CN? to produce additional members of the macrocyclic family with improved properties. Macrocycle 2 with a 22-membered ring is shown to bind MII = Mn, Fe, and Cu with hydroxo bridges. Introduction of the 4-BuiO group (macrocycle 3) improves the solubility of neutral complexes such as those with NiII-OH-CuII and NiII-CN-FeII bridges. The syntheses of macrocycle 5 with a 7-Me-[12]aneSN3 and macrocycle 6 with a 1,8-Me2-[14]aneN4 MII binding site are described to together with hydoxo-bridged Ni-Cu and cyano-bridged Ni-Fe complexes. This work was motivated by the presence of a Ni?(HO)-Fe bridge grouping in a reactive state of carbon monoxide dehydrogenase. Attempted decrease in Ni-(OH)-M distances (3.70-3.87 Å) to smaller values observed in the enzyme by use of macrocycle 4 having 1,2-biphenylene connectors led to a mononuclear octahedral NiII complex. Bridge structural units are summarized and the structures of fourteen macrocyclic complexes including eight with bridges are described. PMID:23030366
The Use of Trust Regions in Kohn-Sham Total EnergyMinimization
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.
A gentle introduction to algorithm complexity for CS1 with nine variations on a theme by Fibonacci
Óscar Martín-Sánchez; Cristóbal Pareja-Flores
1995-01-01
In this paper, we propose our ideas about didactic methods and a few examples appropriate to motivate in students the comprehension of the basic principles related to algorithm complexity. Emphasis is put on avoiding formalisms and presenting gradually every new concepts. This paper as well provides for both: an organisation of these ideas and a collection of, we hope, useful
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...
Pearse, Devon E.; Miller, Michael R.; Abadía-Cardoso, Alicia; Garza, John Carlos
2014-01-01
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss. Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats. PMID:24671976
Morris, Brian J; Donlon, Timothy A; He, Qimei; Grove, John S; Masaki, Kamal H; Elliott, Ayako; Willcox, D Craig; Allsopp, Richard; Willcox, Bradley J
2015-02-01
The mechanistic target of rapamycin (mTOR) pathway is crucial for life span determination in model organisms. The aim of the present study was to test tagging single-nucleotide polymorphisms that captured most of the genetic variation across key TOR complex 1 (TORC1) and TOR complex 2 (TORC2) genes MTOR, RPTOR, and RICTOR and the important downstream effector gene RPS6KA1 for association with human longevity (defined as attainment of at least 95 years of age) as well as health span phenotypes. Subjects comprised a homogeneous population of American men of Japanese ancestry, well characterized for aging phenotypes and who have been followed for 48 years. The study used a nested case-control design involving 440 subjects aged 95 years and older and 374 controls. It found no association of 6 tagging single-nucleotide polymorphisms for MTOR, 61 for RPTOR, 7 for RICTOR, or 5 for RPS6KA1 with longevity. Of 40 aging-related phenotypes, no significant association with genotype was seen. Thus common genetic variation (minor allele frequency ?10%) in MTOR, RPTOR, RICTOR, and RPS6KA1 is not associated with extreme old age or aging phenotypes in this population. Further research is needed to assess the potential genetic contribution of other mTOR pathway genes to human longevity, gene expression, upstream and downstream targets, and clinically relevant aging phenotypes. PMID:24589862
NASA Astrophysics Data System (ADS)
Yim, S. H. L.; Fung, J. C. H.; Ng, E. Y. Y.
2014-09-01
In an urban planning context, an assessment indicator for evaluating a city's dispersion potential is beneficial, especially if the city has a complex natural terrain and significant wind variations. A study was conducted to implement an urban canopy drag indicator, taking site wind variation into account by involving both wind speed and direction in the calculations. Hong Kong (HK) was taken as an example due to its complicated natural topography and wind characteristics. A spatial distribution of an urban canopy drag over HK was determined based on wind data from 2004. The urban canopy drag values in three highly urbanized areas in HK, including Kowloon West, Kowloon East and Hong Kong Island North, were obtained and are discussed in detail. A fluid particle tracking program was developed and applied to identify the major wind paths in Kowloon West, with an area of approximately 5.5 × 6 km as an example. We analyzed the diurnal variation in the dispersion times and the major wind paths in the region during both summer and winter. Our results estimated that the horizontal dispersion times of Kowloon West during both winter and summer were approximately 20 min. By combining the wind paths from both seasons, we identified several major wind paths and critical ventilation areas in Kowloon West. This paper demonstrates the potential use of an urban canopy drag indicator for assessing air ventilation and pollutant dispersion in a city planning context.
Santoro, Davide; Polidori, Carlo; Asís, Josep D; Tormos, José
2011-11-01
1.?Individual foraging behaviour defines the use of resources by a given population and its variation in different ways such as, for example, unpredictable interactions between taxon-biased and size-biased selection. Here we investigated how the environmental availability of prey and individual specialization, for both prey taxa and prey size, shape niche variation across generations in the grasshopper-hunting digger wasp Stizus continuus. 2.?The population of S. continuus expressed selective predation, females mainly hunting species encountered on large bushes; diet changed across generations, due more to size increase in potential prey than to changes in the orthopteran community. 3.?Individual females of both generations weakly overlapped the size and taxa of prey, and the niche width of the second generation increased for both prey size and taxa. 4.?The greater variance in prey size in the environment accounted for the enlarged prey size niche of the second generation, but the load-lifting constraints of the wasps maintained individual prey size specialization constant. In contrast, the enlarged prey taxon niche paralleled a smaller overlap of diets between wasps in the second generation. 5.?Increased niche width in the S. continuus population was thus achieved in two ways. Regarding prey size, all individuals shifted towards the use of the full set of available resources (parallel release). For prey taxa, according to the classical niche variation hypothesis, individuals diverged to minimize resource use overlap and perhaps intraspecific competition. These two mechanisms were observed for the first time simultaneously in a single predator population. PMID:21644980
A. V. Eliseev; I. I. Mokhov; A. A. Karpenko
2007-01-01
The climate model of intermediate complexity developed at the Oboukhov Institute of Atmospheric Physics, Russian Academy of\\u000a Sciences (IAP RAS CM), has been supplemented by a zero-dimensional carbon cycle model. With the carbon dioxide emissions prescribed\\u000a for the second half of the 19th century and for the 20th century, the model satisfactorily reproduces characteristics of the\\u000a carbon cycle over this
Ashlee S. Henig; Donna K. Blackman; Alistair J. Harding; Graham M. Kent; Juan-Pablo Canales
The Atlantis Massif, an oceanic core complex (OCC) at 30ºN on the Mid-Atlantic Ridge, is hypothesized to have formed via long-lived slip on a detachment fault. Due to unroofing that results from this sustained slip, the domal core of the OCC is predicted to comprise lower crustal and\\/or upper mantle rock. Seafloor mapping and deep drilling confirm that this is
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
Sirevaag, A M; Black, J E; Greenough, W T
1991-01-01
Glial hypertrophy is associated with synaptogenesis in visual cortex and with stress-induced damage in the hippocampus. This study examined astrocytes in the dentate gyrus of male weanling rats exposed to complex or standard laboratory environments. No group differences in astrocytic surface density were observed, as expected in this brain region where group differences in synaptogenesis in male rats are reportedly minimal. Similarly, no group differences in adrenal weight were observed. Across all treatment groups, however, a significant positive correlation (r = 0.57) between adrenal weight and surface density of astrocytic processes was found. Considerable variation in responses of individual rats to their environments occurs in both the complex and the laboratory cage environments, and animals responding poorly may have had heavier adrenals and greater astrocyte reactivity in the dentate gyrus. Thus astrocyte hypertrophy in the dentate gyrus reflects the stress history of the individual rat and not any differential effects of rearing in a complex or a laboratory cage environment. PMID:1984435
Leaché, Adam D.; Koo, Michelle S.; Spencer, Carol L.; Papenfuss, Theodore J.; Fisher, Robert N.; McGuire, Jimmy A.
2009-01-01
Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG?1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical. PMID:19625623
Leache, A.D.; Koo, M.S.; Spencer, C.L.; Papenfuss, T.J.; Fisher, R.N.; McGuire, J.A.
2009-01-01
Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation.We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG-1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.
Leaché, Adam D; Koo, Michelle S; Spencer, Carol L; Papenfuss, Theodore J; Fisher, Robert N; McGuire, Jimmy A
2009-07-28
Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG-1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical. PMID:19625623
Donghyung Lee; Kieron Burke; Lucian A. Constantin; John P. Perdew
2008-10-11
We study the asymptotic expansion of the neutral-atom energy as the atomic number Z goes to infinity, presenting a new method to extract the coefficients from oscillating numerical data. We find that recovery of the correct expansion is an exact condition on the Kohn-Sham kinetic energy that is important for the accuracy of approximate kinetic energy functionals for atoms, molecules and solids, when evaluated on a Kohn-Sham density. For example, this determines the small gradient limit of any generalized gradient approximation, and conflicts somewhat with the standard gradient expansion. Tests are performed on atoms, molecules, and jellium clusters. We also give a modern, highly accurate parametrization of the Thomas-Fermi density of neutral atoms.
NASA Astrophysics Data System (ADS)
Kraisler, Eli; Kronik, Leeor
2015-03-01
Many approximations within density-functional theory (DFT) spuriously predict that a many-electron system can dissociate into fractionally charged fragments. Here, we revisit the case of infinitely separated diatomic molecules, known to exhibit this problem when studied within standard approximations, including the local spin-density approximation (LSDA). We apply the recently suggested ensemble-generalization to LSDA (eLSDA) and find that fractional dissociation is eliminated in all systems examined. The eLSDA Kohn-Sham potential develops a spatial step, associated with the emergence of the derivative discontinuity in the exchange-correlation energy functional. This step, predicted in the past for the exact Kohn-Sham potential and observed in some of its more advanced approximate forms, is a desired feature that prevents any fractional charge transfer between the system's fragments. Our findings show that, if appropriately generalized for fractional electron densities, even the most simple approximate functionals correctly predict integer dissociation.
Hofmann, D.; Koerzdoerfer, T.; Kuemmel, S. [Physikalisches Institut, Universitaet Bayreuth, D-95440 Bayreuth (Germany)
2010-07-15
We present a scheme to investigate energy transfer by real-time propagation of the Kohn-Sham equations. The scheme's purpose is to check and go beyond the dipole coupling approximation underlying a Foerster-type energy transfer, and to obtain information about the coupling on the grounds of the density-functional theory. We observe deviations from the dipole coupling approximation for small molecules.
Fuchsberger, Christian; Flannick, Jason; Rivas, Manuel A.; Gaulton, Kyle J.; Albers, Patrick K.; McVean, Gil; Boehnke, Michael; Altshuler, David; McCarthy, Mark I.
2015-01-01
Genome and exome sequencing in large cohorts enables characterization of the role of rare variation in complex diseases. Success in this endeavor, however, requires investigators to test a diverse array of genetic hypotheses which differ in the number, frequency and effect sizes of underlying causal variants. In this study, we evaluated the power of gene-based association methods to interrogate such hypotheses, and examined the implications for study design. We developed a flexible simulation approach, using 1000 Genomes data, to (a) generate sequence variation at human genes in up to 10K case-control samples, and (b) quantify the statistical power of a panel of widely used gene-based association tests under a variety of allelic architectures, locus effect sizes, and significance thresholds. For loci explaining ~1% of phenotypic variance underlying a common dichotomous trait, we find that all methods have low absolute power to achieve exome-wide significance (~5-20% power at ?=2.5×10-6) in 3K individuals; even in 10K samples, power is modest (~60%). The combined application of multiple methods increases sensitivity, but does so at the expense of a higher false positive rate. MiST, SKAT-O, and KBAC have the highest individual mean power across simulated datasets, but we observe wide architecture-dependent variability in the individual loci detected by each test, suggesting that inferences about disease architecture from analysis of sequencing studies can differ depending on which methods are used. Our results imply that tens of thousands of individuals, extensive functional annotation, or highly targeted hypothesis testing will be required to confidently detect or exclude rare variant signals at complex disease loci. PMID:25906071
NASA Astrophysics Data System (ADS)
Dorman, L. I.
1985-08-01
The Samarkand complex setup is aimed at the study of cosmic ray variations in a wide energy range from 7 billion eV (which corresponds to the geomagnetic threshold in the region of Samarkand) up to approx 10 to the 15th power to 10 to the 16th power eV. The setup consists of four 6-counter sections of neutron supermonitor with counters SNM-15 and 48 scintillator detectors (1 sq m each) placed under and above the supermonitor. The effective area of the setup for recording neutrons and muons is 24 sq m. The setup can register time variations of the following cosmic ray components: (1) the total neutron counting rate, (2) counting rates for neutrons of different multiplicity, (3) soft-muon fluxes, (4) hard-muon fluxes at various zenith and azimuth angles, (5) electron-photon component, (6) extensive air showers (EAS) induced by primary particles in a wide energy range and accompanied or not accompanied by muons and neutrons.
Zhang, Xiaofeng; Huang, Deguang; Chen, Yu-Sheng; Holm, R H
2012-10-15
The planar NNN-pincer complexes [M(II)(pyN(2)(Me2))(OH)](1-) (M(II) = Ni, Cu) fix CO(2) in ?(1)-OCO(2)H complexes; results for the copper system are described. Mn(II), Fe(II), Co(II), and Zn(II) behave differently, forming [M(II)(pyN(2)(Me2))(2)](2-) with N(4)O(2) coordination. Incorporation of the Ni(II) pincer into binucleating macrocycle 2 containing a triamino M(II) locus connected by two 1,3-biphenylene groups affords proximal Ni(II) and M(II) sites for investigation of the synthesis, structure, and reactivity of Ni-X-M bridge units. This ligand structure is taken as a reference for variations in M(II) atoms and binding sites and bridges X = OH(-) and CN(-) to produce additional members of the macrocyclic family with improved properties. Macrocycle 2 with a 22-membered ring is shown to bind M(II) = Mn, Fe, and Cu with hydroxo bridges. Introduction of the 4-Bu(i)O group (macrocycle 3) improves the solubility of neutral complexes such as those with Ni(II)-OH-Cu(II) and Ni(II)-CN-Fe(II) bridges. Syntheses of macrocycle 5 with a 7-Me-[12]aneSN(3) and macrocycle 6 with a 1,8-Me(2)-[14]aneN(4) M(II) binding site are described together with hydoxo-bridged Ni/Cu and cyano-bridged Ni/Fe complexes. This work was motivated by the presence of a Ni···(HO)-Fe bridge grouping in a reactive state of carbon monoxide dehydrogenase. Attempted decrease in Ni-(OH)-M distances (3.70-3.87 Å) to smaller values observed in the enzyme by use of macrocycle 4 having 1,2-biphenylene connectors led to a mononuclear octahedral Ni(II) complex. Bridge structural units are summarized, and the structures of 14 macrocyclic complexes including 8 with bridges are described. PMID:23030366
Chen, Hsin-Yi Tiffany; Di Tommaso, Devis; Hogarth, Graeme; Catlow, C Richard A
2012-02-14
Density functional theory calculations have been used to investigate the hydrogenation of acetophenone (ACP) catalysed by the RuH(2)(diphosphine)(diamine) complexes with emphasis on the effect of the structure of the diphosphine and diamine ligands on the enantioselectivity. The computed reaction coordinate diagrams of RuH(2)(diphosphine)[(S,S)-DPEN] catalysed reactions with different (S)-diphosphine ligands (XylBINAP, TolBINAP, and BINAP) show that the presence of two methyl groups in the meta position is critical to obtaining a high difference in activation energy for the reaction pathways associated with the (R)- and (S)-alcohols, and consequently high enantioselectivity. The effect of the diamine structure while keeping the TolBINAP and XylBINAP fixed has also been analysed. To enhance the enantioselectivity of the TolBINAP system, the addition of two methyl groups and the removal of a phenyl group of the diamine (DMAPEN) offer the necessary steric interactions. We conclude by reporting a correlation between the enantiomeric excess and the difference in the computed activation energies of the two most favourable (S) and (R) reaction pathways, which shows that the computational procedure adopted could be used to predict the enantiomeric excess of ketone hydrogenation reactions catalysed by the Noyori-type catalysts, and assist in the choice of ligand when optimising the enantiomeric excess. PMID:22166917
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
Kohn condition and exotic Newton-Hooke symmetry in the non-commutative Landau problem
NASA Astrophysics Data System (ADS)
Zhang, P.-M.; Horvathy, P. A.
2012-01-01
N “exotic” [alias non-commutative] particles with masses ma, charges ea and non-commutative parameters ?a, moving in a uniform magnetic field B, separate into center-of-mass and internal motions if Kohn's condition ea /ma =const is supplemented with ea?a =const. Then the center-of-mass behaves as a single exotic particle carrying the total mass and charge of the system, M and e, and a suitably defined non-commutative parameter ?. For vanishing electric field off the critical case e?B ? 1, the particles perform the usual cyclotronic motion with modified but equal frequency. The system is symmetric under suitable time-dependent translations which span a (4 + 2)-parameter centrally-extended subgroup of the “exotic” [i.e., two-parameter centrally-extended] Newton-Hooke group. In the critical case B =Bc =(e?) - 1 the system is frozen into a static “crystal” configuration. Adding a constant electric field, all particles perform, collectively, a cyclotronic motion combined with a drift perpendicular to the electric field when e?B ? 1. For B =Bc the cyclotronic motion is eliminated and all particles move, collectively, following the Hall law. Our time-dependent symmetries are reduced to the (2 + 1)-parameter Heisenberg group of centrally-extended translations.
Orbitals from local RDMFT: Are they Kohn-Sham or Natural Orbitals?
Theophilou, Iris; Gidopoulos, Nikitas I; Rubio, Angel; Helbig, Nicole
2015-01-01
Recently, an approximation was introduced in reduced density matrix functional theory (RDMFT), called 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 Schr\\"odinger equation with a local potential. In the present work, we assess the impact of this additional condition on the optimal orbitals. In particular we compare orbitals obtained by local-RDMFT with those obtained with the full minimization (without the extra condition) by comparing them with 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 o...
Kohn's Theorem, Larmor's Equivalence Principle and the Newton-Hooke Group
G. W. Gibbons; C. N. Pope
2010-11-10
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-Inonu 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.
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).
Comment on 'Asymptotic form of the Kohn-Sham correlation potential'
Holas, A. [Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warszawa (Poland)
2008-02-15
For finite systems that have the energetically highest-occupied molecular orbital (HOMO) with an asymptotic nodal surface, Joubert demonstrated recently [Phys. Rev. A 76, 012501 (2007)] strongly anisotropic behavior (in the asymptotic large-r region) of the exact correlation potential of density-functional theory. As is shown by us, this result is a direct and simple consequence of the strong anisotropy of the exact exchange potential obtained by Della Sala and Goerling [Phys. Rev. Lett. 89, 033003 (2002); Della Sala and GoerlingJ. Chem. Phys. 116, 5374 (2002)] and the assumption about the asymptotic isotropy of the Kohn-Sham (KS) potential (based on the investigation of Almbladh and von Barth [Phys. Rev. B 31, 3231 (1985)] for atoms). Joubert's result remains a hypothesis only, because the last assumption is in contradiction with the asymptotic strong anisotropy of the KS potential for systems with asymptotic nodal surface of the HOMO, demonstrated by Wu, Ayers, and Yang [J. Chem. Phys. 119, 2978 (2003)]. The correlation potential in the asymptotic region, stemming from their results, is given.
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.
Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory
NASA Technical Reports Server (NTRS)
Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.
1990-01-01
New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.
Lim, Jeong Hak; You, Young Sin; Yoo, Houng Sik; Yoon, Jung Hee; Kim, Jae Il; Koh, Eui Kwan; Hong, Chang Seop
2007-12-10
Four octacyanometalate-based bimetallic Cu-M (M = Mo, W) assemblies coordinated by tetradentate macrocyclic ligands were prepared via self-assembly process in a stoichiometric ratio of [M(CN)8]3- and Cu(macrocycle)2+ and characterized in terms of structures and magnetic properties. The crystal structures are varied depending on the macrocycles used. The employment of cyclam with no pendant groups produced a one-dimensional chain (1) with a rope-ladder pattern, whereas macrocycles with side groups allowed for the formation of two-dimensional honeycomb-like architectures (2-4). From the crystal structures, the variations in apical Cu-Nax lengths and Cu-Nax-Cax angles on the bridging pathways are observed, which arises from the existence of side groups on macrocyclic ligands. The magnetic results reveal that all of the prepared compounds show ferromagnetic couplings between magnetic centers transimitted through CN bridges under the present structural parameters. Comparing the magnetic strength of the Cu-Mo (3d-4d; 2) and Cu-W (3d-5d; 3) complexes supports that 3d-5d magnetic coupling is stronger than 3d-4d because the 5d orbital is more diffuse than 4d. The magnetic analyses for 1-4 and related complexes tentatively suggest that, when the Cu-Nax distances are long enough, the axial Cu-Nax bond length in the bridging route may be one of the major structural parameters to determine the magnitude of the ferromagnetic exchange coupling. PMID:17985870
Exact exchange potential evaluated from occupied Kohn-Sham and Hartree-Fock solutions
Cinal, M.; Holas, A. [Institute of Physical Chemistry of the Polish Academy of Sciences, 44/52 Kasprzaka, 01-224 Warsaw (Poland)
2011-06-15
The reported algorithm determines the exact exchange potential v{sub x} in an iterative way using energy shifts (ESs) and orbital shifts (OSs) obtained with finite-difference formulas from the solutions (occupied orbitals and their energies) of the Hartree-Fock-like equation and the Kohn-Sham-like equation, the former used for the initial approximation to v{sub x} and the latter for increments of ES and OS due to subsequent changes of v{sub x}. Thus, the need for solution of the differential equations for OSs, used by Kuemmel and Perdew [Phys. Rev. Lett. 90, 043004 (2003)], is bypassed. The iterated exchange potential, expressed in terms of ESs and OSs, is improved by modifying ESs at odd iteration steps and OSs at even steps. The modification formulas are related to the optimized-effective-potential equation (satisfied at convergence) written as the condition of vanishing density shift (DS). They are obtained, respectively, by enforcing its satisfaction through corrections to approximate OSs and by determining the optimal ESs that minimize the DS norm. The proposed method, successfully tested for several closed-(sub)shell atoms, from Be to Kr, within the density functional theory exchange-only approximation, proves highly efficient. The calculations using the pseudospectral method for representing orbitals give iterative sequences of approximate exchange potentials (starting with the Krieger-Li-Iafrate approximation) that rapidly approach the exact v{sub x} so that, for Ne, Ar, and Zn, the corresponding DS norm becomes less than 10{sup -6} after 13, 13, and 9 iteration steps for a given electron density. In self-consistent density calculations, orbital energies of 10{sup -4} hartree accuracy are obtained for these atoms after, respectively, 9, 12, and 12 density iteration steps, each involving just two steps of v{sub x} iteration, while the accuracy limit of 10{sup -6} to 10{sup -7} hartree is reached after 20 density iterations.
Khorsan, Raheleh; Cohen, Angela B; Lisi, Anthony J; Smith, Monica M; Delevan, Deborah; Armstrong, Courtney; Mittman, Brian S
2013-01-01
Maximizing the quality and benefits of newly established chiropractic services represents an important policy and practice goal for the US Department of Veterans Affairs' healthcare system. Understanding the implementation process and characteristics of new chiropractic clinics and the determinants and consequences of these processes and characteristics is a critical first step in guiding quality improvement. This paper reports insights and lessons learned regarding the successful application of mixed methods research approaches-insights derived from a study of chiropractic clinic implementation and characteristics, Variations in the Implementation and Characteristics of Chiropractic Services in VA (VICCS). Challenges and solutions are presented in areas ranging from selection and recruitment of sites and participants to the collection and analysis of varied data sources. The VICCS study illustrates the importance of several factors in successful mixed-methods approaches, including (1) the importance of a formal, fully developed logic model to identify and link data sources, variables, and outcomes of interest to the study's analysis plan and its data collection instruments and codebook and (2) ensuring that data collection methods, including mixed-methods, match study aims. Overall, successful application of a mixed-methods approach requires careful planning, frequent trade-offs, and complex coding and analysis. PMID:24489589
2013-01-01
Abstract Echinorhynchus truttae and the Echinorhynchus bothniensis species complex are common parasites of salmoniform and other fishes in northern Europe. Echinorhynchus bothniensis and its sibling species Echinorhynchus 'bothniensis' are thought to be closely related to the Nearctic Echinorhynchus leidyi Van Cleave, 1924 based on morphological similarity and common usage of a mysid intermediate host. This study provides the first analysis of morphological and meristic variation in Echinorhynchus truttae and expands our knowledge of anatomical variability in the Echinorhynchus bothniensis group. Morphological variability in Echinorhynchus truttae was found to be far greater than previously reported, with part of the variance attributable to sexual dimorphism. Echinorhynchus truttae, the two species of the Echinorhynchus bothniensis group and Echinorhynchus leidyi displayed considerable interspecific overlap in the ranges of all conventional morphological characters. However, Proboscis profiler, a tool for detecting acanthocephalan morphotypes using multivariate analysis of hook morphometrics, successfully separated Echinorhynchus truttae from the other taxa. The Echinorhynchus bothniensis species group could not be reliably distinguished from Echinorhynchus leidyi (or each other), providing further evidence of the affinity of these taxa. Observations on the distribution of Echinorhynchus truttae in its definitive host population are also reported. PMID:24723769
Posvyanskii, D. V., E-mail: posvyanskii@cplire.ru; Shul'man, A. Ya., E-mail: ash@cplire.r [Russian Academy of Sciences, Kotel'nikov Institute of Radio Engineering and Electronics (Russian Federation)
2009-07-15
The density functional approach in the Kohn-Sham approximation is widely used to study properties of many-electron systems. Due to the nonlinearity of the Kohn-Sham equations, the general self-consistence searching method involves iterations with alternate solving of the Poisson and Schroedinger equations. One of problems of such an approach is that the charge distribution renewed by means of the solution of the Schroedinger equation does not conform to boundary conditions of the Poisson equation for the Coulomb potential. The resulting instability or even divergence of iterations manifests itself most appreciably in the case of infinitely extended systems. The known attempts to deal with this problem are reduced in fact to abandoning the original iterative method and replacing it with some approximate calculation scheme, which is usually semi-empirical and does not permit to evaluate the extent of deviation from the exact solution. In this work, we realize the iterative scheme of solving the Kohn-Sham equations for extended systems with inhomogeneous electron gas, which is based on eliminating the long-range character of Coulomb interaction as the cause of tight coupling between charge distribution and boundary conditions. The suggested algorithm is employed to calculate energy the spectrum, self-consistent potential, and electrostatic capacitance of the semi-infinite degenerate electron gas bounded by an infinitely high barrier, as well as the work function and surface energy of simple metals in the model with homogeneous distribution of positive background. The difference between self-consistent Hartree solutions and those taking into account the exchange-correlation interaction is analyzed. The comparison with the results previously published in the literature is carried out. The case study of the metal-semiconductor tunnel contact shows this method as applied to an infinitely extended system where the steady-state current can flow.
Gonis, Antonios [ORNL; Daene, Markus W [ORNL; Nicholson, Don M [ORNL; Stocks, George Malcolm [ORNL
2012-01-01
We have developed and tested in terms of atomic calculations an exact, analytic and computationally simple procedure for determining the functional derivative of the exchange energy with respect to the density in the implementation of the Kohn Sham formulation of density functional theory (KS-DFT), providing an analytic, closed-form solution of the self-interaction problem in KS-DFT. We demonstrate the efficacy of our method through ground-state calculations of the exchange potential and energy for atomic He and Be atoms, and comparisons with experiment and the results obtained within the optimized effective potential (OEP) method.
Jeremie Messud
2011-11-21
We generalize the recently developped "internal" Density Functional Theory (DFT) and Kohn-Sham scheme to multicomponent systems. We obtain a general formalism, applicable for the description of multicomponent self-bound systems (as molecules where the nuclei are treated explicitely, atomic nuclei and mix of 3He and 4He droplets), where the fundamental translational symmetry has been treated correctly. The main difference with traditional DFT is the explicit inclusion of center-of-mass correlations in the functional. A large part of the paper is dedicated to the application to molecules, which permits among other to clarify the approximations that underly traditional DFT.
Schmidt, Tobias; Makmal, Adi; Kronik, Leeor; Kümmel, Stephan
2014-01-01
We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potent...
Delocalization error and "functional tuning" in Kohn-Sham calculations of molecular properties.
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 ?-conjugated molecules, it is shown how the DE manifests itself either in too strong or too weak delocalization of localized molecular orbitals (LMOs). Optical rotation is an electric-magnetic linear response property that is calculated in a similar fashion as the electric polarizability, but it is more sensitive to approximations and can benefit greatly from tuning and small DE. Hyperpolarizabilities of ?-conjugated "push-pull" systems are examples of NLO properties that can be greatly improved by tuning of range-separated exchange (RSE) functionals, in part due to improved charge-transfer excitation energies. On-going work on band gap predictions is also mentioned. The findings may provide clues for future improvements of KST because different molecular properties exhibit varying sensitivity to approximations in the electronic structure model. The utility of analyzing molecular properties and the impact of the DE in terms of LMOs, representing "chemist's orbitals" such as individual lone pairs and bonds, is highlighted. PMID:24968277
Kagan, M. Yu., E-mail: kagan@kapitza.ras.ru [Russian Academy of Sciences, Kapitza Institute for Physical Problems (Russian Federation); Val'kov, V. V.; Mitskan, V. A.; Korovuskin, M. M. [Russian Academy of Sciences, Kirenskii Physics Institute, Siberian Branch (Russian Federation)] [Russian Academy of Sciences, Kirenskii Physics Institute, Siberian Branch (Russian Federation)
2013-10-15
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.
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
NASA Astrophysics Data System (ADS)
Depristo, Andrew E.
1996-11-01
An implicit Poisson equation is derived for the change in density ?n(r) from summed atomic or atomiclike densities within the Hohenberg-Kohn formulation of density-functional theory. Iterative and perturbation solutions are detailed. The first-order perturbation and first iterative solutions are equivalent, yielding ?n(r)=(4?)-1?2[(?G/?n)system-(?G/?n)atoms], where the kinetic-exchange-correlation potential of the full system and the summed isolated atoms are (?G/?n)system and (?G/?n)atoms, respectively. G is the integrand of the kinetic-exchange-correlation energy. The second-order perturbation solution leads to a Fredholm equation relating (1) the second functional derivative, (?2G/?n2)system, with summed atomic densities; (2) the induced electrostatic energy; and, (3) the difference between (?G/?n)system and (?G/?n)atoms. Numerical examples are shown for the Ni, O, and Na atoms embedded in jellium.
NASA Astrophysics Data System (ADS)
Jana, Subrata; Santra, Ramesh Chandra; Das, Saurabh; Chattopadhyay, Shouvik
2014-09-01
Two new copper(II) complexes, [Cu(L)(OCN)] (1) and [CuL(dca)]n (2), where HL = 2-(-(2-(diethylamino)ethylimino)methyl)naphthalen-1-ol, dca = N(CN)2-, have been synthesized and characterized by elemental analysis, IR, UV-VIS spectroscopy and single crystal X-ray diffraction studies. Complex 1 has square planar and complex 2 square pyramidal geometries in solid state around metal centre. Interactions of the complexes with calf thymus DNA (CT DNA) were studied by UV-VIS spectroscopy. Binding constant and site size of interaction were determined. Binding site size and intrinsic binding constant K revealed complex 1 interacted with calf thymus DNA better than complex 2.
Yoo, Jina; Na, Sung Jae; Park, Hyeong Cheol; Cyriac, Anish; Lee, Bun Yeoul
2010-03-14
Anion exchange of BF(4)(-) occurs by stirring a cobalt(III) complex of salen-type ligand tethered by four quaternary ammonium BF(4)(-) salts over a slurry of NaX in CH(2)Cl(2), affording a complex containing four X's per cobalt (X = 2,4,5-trichlorophenolate, 6; X = 4-nitrophenolate, 10; X = 2,4-dichlorophenolate, 12). The (1)H and (13)C NMR spectra are in agreement with an unusual imine uncoordinated structure. The two salen-phenoxys and the two X's persistently coordinate with cobalt(III) to form a square planar cobaltate complex while the other two X's scramble through coordination and decoordination to the axial sites of the square plane. Another form of the complex (X = 2,4,5-trichlorophenolate, 14; X = 4-nitrophenolate, 15; X = 2,4-dichlorophenolate, 16) is also prepared, in which the scrambling two X's in 6, 10, or 12 are replaced with the corresponding [X...H...X](-) homoconjugate. These complexes, which adopt an unusual imine uncoordinated structure, are excellent catalysts for CO(2)/propylene oxide copolymerization (turnover frequency (TOF), 8300-16,000 h(-1)). In all cases, the complex containing the homoconjugate [X...H...X](-) shows higher activity than the corresponding phenol-free complex. Among the prepared complexes, 4-nitrophenol-4-nitrophenolate homoconjugate complex 15 showed the best performance (TOF, 16,000 h(-1); selectivity, 98%; M(n), 273,000), allowing for replacement of the explosive 2,4-dinitrophenolate complex. PMID:20179856
Computational complexity of time-dependent density functional theory
J. D. Whitfield; M. -H. Yung; D. G. Tempel; S. Boixo; A. Aspuru-Guzik
2014-08-21
Time-dependent density functional theory (TDDFT) is rapidly emerging as a premier method for solving dynamical many-body problems in physics and chemistry. The mathematical foundations of TDDFT are established through the formal existence of a fictitious non-interacting system (known as the Kohn-Sham system), which can reproduce the one-electron reduced probability density of the actual system. We build upon these works and show that on the interior of the domain of existence, the Kohn-Sham system can be efficiently obtained given the time-dependent density. Since a quantum computer can efficiently produce such time-dependent densities, we present a polynomial time quantum algorithm to generate the time-dependent Kohn-Sham potential with controllable error bounds. As a consequence, in contrast to the known intractability result for ground state density functional theory (DFT), the computation of the necessary time-dependent potentials given the initial state is in the complexity class described by bounded error quantum computation in polynomial time (BQP).
Adam J de Smith; Anya Tsalenko; Nick Sampas; Alicia Scheffer; N Alice Yamada; Peter Tsang; A. Ben-Dor; Zohar Yakhini; Richard J Ellis; Laurakay Bruhn; Stephen Laderman; Philippe Froguel; Alexandra I. F. Blakemore
2007-01-01
The discovery of copy number variation in healthy individuals is far from complete, and owing to the resolution of detection systems used, the majority of loci reported so far are relatively large (65% > 10 kb). Applying a two-stage high-resolution array comparative genomic hybridization approach to analyse 50 healthy Caucasian males from northern France, we discovered 2208 copy number variants
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 (N2, O2, and the polyyne C10H2) 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. PMID:25429933
J. B. Krieger; Jiqiang Chen; G. J. Iafrate
1996-01-01
We have employed the local-spin-density approximation with orbital self-interaction-correction (LSDSIC) for the exchange-correlation energy functional in the calculation of the ground state properties of first row heteropolar diatomic molecules. The Kohn-Sham molecular orbitals are obtained by fully numerical solution of a Schrodinger equation including the Optimized Effective Potential in the KLIfootnote J. B. Krieger, Y. Li and G. J Iafrate
Jiqiang Chen; J. B. Krieger; Yan Li; G. J. Iafrate
1996-01-01
We have investigated the accuracy of the local-spin-density approximation with orbital-density-dependent self-interaction correction (LSDSIC) as proposed by Perdew and Zunger within a Kohn-Sham approach in which electrons with a given spin projection all move in a single optimized effective potential (OEP). We have also studied the accuracy of the Krieger-Li-Iafrate (KLI) approximation to the OEP for the same energy functional
J. B. Krieger; Yan Li; G. J. Iafrate
1992-01-01
An accurate spin-polarized exchange-only Kohn-Sham (KS) potential is constructed from a consideration of the optimized-effective-potential (OEP) method. A detailed analysis of the OEP integral equation for the exchange-only case results in a set of conditions which are manifestly satisfied by the exact OEP; these conditions are employed to construct an approximate OEP, Vxsigma, and therefore an approximate KS exchange-only potential
NSDL National Science Digital Library
2012-08-29
This learning unit from Regents Prep Exam Center introduces the topic of direct variation equations. The material includes a lesson plan, practice problems and a teacher's guide. Students will learn the basics of what a direct variation equation is and the formula for direct variation.
Samal, Prasanjit; Chauhan, Sourabh S
2014-01-01
The Hohenberg-Kohn theorem and constrained search formalism of density functional theory are in principle sufficient to address the question of mapping from an excited-state density of an interacting many-electron system to the external potential. Which is also equally applicable to the model noninteracting system. Be it the lowest (non)degenerate excited state of a given symmetry or any other many-particle quantum states with differing symmetry and thus corresponding to arbitrary order of excitations, the analogue of Hohenberg-Kohn theorem and constrained search formalism can uniquely establish the one-to-one density-to-potential mapping. We have rigorously investigated and also shown by examples that the existence of multiple effective/external potentials for excited-states and the seemingly contradictory results in connection to the applicability of Gunnarsson-Lundqvist theorem even for the lowest excited-state is not truly a failure or violation of Hohenberg-Kohn/Gunnarsson-Lundqvist theorem. Rather these...
Schmidt, Tobias; Kümmel, Stephan [Theoretical Physics IV, University of Bayreuth, 95440 Bayreuth (Germany)] [Theoretical Physics IV, University of Bayreuth, 95440 Bayreuth (Germany); Kraisler, Eli; Makmal, Adi; Kronik, Leeor [Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100 (Israel)] [Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100 (Israel)
2014-05-14
We present and test a new approximation for the exchange-correlation (xc) energy of Kohn-Sham density functional theory. It combines exact exchange with a compatible non-local correlation functional. The functional is by construction free of one-electron self-interaction, respects constraints derived from uniform coordinate scaling, and has the correct asymptotic behavior of the xc energy density. It contains one parameter that is not determined ab initio. We investigate whether it is possible to construct a functional that yields accurate binding energies and affords other advantages, specifically Kohn-Sham eigenvalues that reliably reflect ionization potentials. Tests for a set of atoms and small molecules show that within our local-hybrid form accurate binding energies can be achieved by proper optimization of the free parameter in our functional, along with an improvement in dissociation energy curves and in Kohn-Sham eigenvalues. However, the correspondence of the latter to experimental ionization potentials is not yet satisfactory, and if we choose to optimize their prediction, a rather different value of the functional's parameter is obtained. We put this finding in a larger context by discussing similar observations for other functionals and possible directions for further functional development that our findings suggest.
Quinzin, Maud C; Mardulyn, Patrick
2014-09-01
While the importance for including multiple independent loci in phylogeographic studies is largely acknowledged, a majority of these still focus on a single species. We combine the study of multilocus DNA sequence variation (one mitochondrial and four unlinked nuclear fragments) at both the inter- and intraspecific levels to explore the evolutionary history of four closely related specialized herbivorous insects (Chrysomelidae, genus Gonioctena). Analyzing the sequences for samples collected across their entire European range allows us to (1) characterize the genetic boundaries among species, i.e. the degree of lineage sorting, (2) infer their phylogenetic relationships and (3) explore reproductive barriers among them in regions where their ranges overlap. For two sister species, we identify multiple independent cases of unidirectional transfer of genetic material (introgression) at both mitochondrial and nuclear loci, demonstrating recent hybridization between both species in the overlapping regions of their range. The highlighted pattern of genetic variation suggests that Gonioctena intermedia expanded its range into that of G. quinquepunctata, and that both species may experience mutual exclusion. Overall, this study illustrates that interpreting intraspecific genetic variation for the purpose of evolutionary inference without the broader context of the other closely related species could lead to erroneous conclusions. PMID:24821620
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.
The augmented Roothaan-Hall method for optimizing Hartree-Fock and Kohn-Sham density matrices
NASA Astrophysics Data System (ADS)
Høst, Stinne; Olsen, Jeppe; Jansík, Branislav; Thøgersen, Lea; Jørgensen, Poul; Helgaker, Trygve
2008-09-01
We present a novel method for the optimization of Hartree-Fock and Kohn-Sham energies that does not suffer from the flaws of the conventionally used two-step Roothaan-Hall (RH) with direct inversion in iterative subspace (DIIS) acceleration scheme, improving the reliability of the optimization while reducing its cost. The key to its success is the replacement of the two separate steps of each RH/DIIS iteration by a single concerted step that fully exploits the Hessian information available from the previous iterations. It is a trust-region based method and therefore by design converges to an energy minimum. Numerical examples are given to illustrate that the algorithm is robust and cost efficient, converging smoothly to a minimum also in cases when the RH/DIIS algorithm fails to converge or when it converges to a saddle point rather than to a minimum. The algorithm is based on matrix multiplications and becomes linearly scaling for sufficiently large systems.
Jeng-Da Chai; Po-Ta Chen
2012-12-20
From the perspective of perturbation theory, we propose a systematic procedure for the evaluation of the derivative discontinuity (DD) of the exchange-correlation energy functional in Kohn-Sham density functional theory (KS-DFT), wherein the exact DD can in principle be obtained by summing up all the perturbation corrections to infinite order. Truncation of the perturbation series at low order yields an efficient scheme for obtaining the approximate DD. While the zeroth-order theory yields a vanishing DD, the first-order correction to the DD can be expressed as an explicit universal functional of the ground-state density and the KS lowest unoccupied molecular orbital density, allowing the direct evaluation of the DD in the standard KS method without extra computational cost. The fundamental gap can be predicted by adding the estimated DD to the KS gap. This scheme is shown to be accurate in the prediction of the fundamental gaps for a wide variety of atoms and molecules.
Dissociation of diatomic molecules and the exact-exchange Kohn-Sham potential: The case of LiF
Makmal, Adi; Kronik, Leeor [Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100 (Israel); Kuemmel, Stephan [Physikalisches Institut, Universitaet Bayreuth, D-95440 Bayreuth (Germany)
2011-06-15
We examine the role of the exact-exchange (EXX) Kohn-Sham potential in curing the problem of fractional molecular dissociation. This is achieved by performing EXX calculations for the illustrative case of the LiF molecule. We show that by choosing the lowest-energy electronic configuration for each interatomic distance, a qualitatively correct binding energy curve, reflecting integer dissociation, is obtained. Surprisingly, for LiF this comes at the cost of violating the Aufbau principle, a phenomenon we discuss at length. Furthermore, we numerically confirm that in the EXX potential of the diatomic molecule, one of the atomic potentials is shifted by a constant while the other one is not, depending on where the highest occupied molecular orbital is localized. This changes the relative positions of the energies of each atom and enforces the integer configuration by preventing spurious charge transfer. The size of the constant shift becomes increasingly unstable numerically the larger the interatomic separation is, reflecting the increasing absence of coupling between the atoms.
NASA Astrophysics Data System (ADS)
Petit, L.; Beiden, S. V.; Temmerman, W. M.; Szotek, Z.; Stocks, G. M.; Gehring, G. A.
2000-10-01
The use of the relativistic and spin-polarized real-space Korringa-Kohn-Rostoker (KKR) method is limited to small systems (less than 100 atoms). This is due to the prohibitively large CPU times needed for the inversion of the KKR matrix. To study systems of more than a thousand atoms, we have implemented the concept of a screened reference medium, within the fully relativistic spin-polarized version of the real-space locally self-consistent multiple-scattering method (LSMS). The LSMS method makes use of a local interaction zone (LIZ) for solving the quantum mechanical problem, while the Poisson equation is solved in the whole space. The screened reference medium gives rise to sparse KKR matrices and using state-of-the-art sparse matrix technology a substantial reduction in the CPU times is obtained, enabling applications of the method to systems whose LIZ consists of more than a thousand atoms. The method is benchmarked by application to the elemental transition metals, the fcc (face-centred-cubic) Co and Ni, and the bcc (body-centred cubic) Fe, and compared to the results of the conventional k-space methods. The convergence in real space of the magnetic moments, the magnetocrystalline anisotropy energy and the orbital moment anisotropy is discussed in detail.
The alkali metal trifluorides M F3: how well can theory predict experiment? +Kohn-Sham
NASA Astrophysics Data System (ADS)
Tozer, David J.; Sosa, Carlos P.
The alkali metal trifluorides M+ F3- (M = Na, K, Rb, and Cs) are studied using density functional theory and traditional ab initio methods. Experimental infrared a +nd- Raman spectroscopic results suggest a pronounced change in the structure o +f-the M F3 species with decreasing cation size. Stationary points are located on the M F3 potential energy surfaces and harmonic vibrational frequencies computed to assess how well the variou-s theoretical methods can describe this alkali metal dependence. As with the isolated F3 anion, the theoretical results are strongly dependent on the method used, with only the B3-LYP density functional calculations reproducing correctly the structural variation inferred from the vibrational spect-ra. Additional calculations also demonstrate that this functional significantly reduces the F3 overbinding observed using B-LYP.
Cui-Li Yuan; An-Guo Zhang; Ze-Bo Zheng; Ke-Zhi Wang
2012-01-01
A phenylthiophenyl-bearing Ru(II) complex of [Ru(bpy)2(Hbptip)](PF6)2 {bpy?=?2,2?-bipyridine, Hbptip?=?2-(4-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} was synthesized and characterized by elemental analysis, H NMR spectroscopy, and electrospray ionization mass spectrometry. The ground- and excited-state acid–base properties of the complex were studied by UV–visible absorption and photoluminescence spectrophotometric pH titrations and the negative logarithm values of the ground-state acid ionization constants were derived to be pKa1?=?1.31?±?0.09 and pKa2?=?5.71?±?0.11
Curtis D. Williams; Edward M. Ripley; Chusi Li
2010-01-01
Os isotope ratios in pyrrhotite-bearing pelitic rocks of the ?1.85Ga Virginia Formation are variable, with perturbations linked to the emplacement of the ?1.1Ga Duluth Complex. Pyrrhotite in footwall rocks of the contact aureole show evidence for a mixing event at 1.1Ga involving a low 187Os\\/188Os fluid. However, because rocks with perturbed pyrrhotite Os isotope ratios occur 1½km or more from
NASA Astrophysics Data System (ADS)
Ramírez-Solís, Alejandro; Castillo A., Sidonio
1993-05-01
The Cd(1S,3,1P)-CH4 interaction is studied for the C3v vertex-on Cd(1S,3,1P)-HCH3 and face-on Cd(1S,3,1P)-H3CH approaches as well as the C2v Cd(1S,3,1P)-H2CH2 edge-on approach of the metal atom to methane using extensive ab initio multireference configuration interaction plus second order multireference Møller-Plesset calculations. The ground state Cd(1S)-CH4 is totally repulsive for the C3v vertex-on and C2v edge-on approaches. Only a stable face-on Cd(1S)-H3CH complex was found. Although vertex-on and edge-on minima were found for the Cd(3P)-CH4 excited complexes, they are less attractive than the corresponding Cd(3P)-H3CH face-on exciplexes. The optimal orientation of the face-on occupied 5p orbital of Cd(5s5p) is that which minimizes the overlap with C-H bonds leading to a ``3?y'' exciplex. For the Cd(1P)-CH4 interaction, two face-on and two edge-on very stable complexes (all with De?1300 cm-1) were found. The Cd(1S)-H3CH (1A1) complex was found to have a 185 cm-1 well at 8.03 a.u. Both excited P states present shorter equilibrium distances—the Cd(3P)-H3CH (3E) exciplex has a 799 cm-1 well at 6.08 a.u., while the Cd(1P)-H3CH exciplex (1E) has a 1337 cm-1 well at 5.57 a.u. These results are in good agreement with the recent experimental values X 1O+(1S)—(De=121 cm-1, Re=7.9 a.u.); A 3O+(3P)—(De=677 cm-1, Re=5.80 a.u.); and 1P—(De?1300 cm-1, Re=5.59 a.u.) obtained by Wallace and Breckenridge [J. Chem. Phys. 97, 2318 (1992)]. The present work confirms the C3v facial nature of the observed (1S) ground and (3P) excited complexes. The present results are inconclusive as to the facial or edge-on nature of the Cd(1P)-CH4 exciplex, but they preclude the C3v vertex-on possibility.
Chekmarev, Sergei F.
2015-01-01
The Helmholtz decomposition of the vector field of probability fluxes in a two-dimensional space of collective variables makes it possible to introduce a potential for the driving force of protein folding [Chekmarev, J. Chem. Phys. 139 (2013) 145103]. The potential has two components: one component (?) is responsible for the source and sink of the folding flow, which represent, respectively, the unfolded and native state of the protein, and the other (?) accounts for the flow vorticity inherently generated at the periphery of the flow field and provides the canalization of the flow between the source and sink. Both components obey Poisson’s equations with the corresponding source/sink terms. In the present paper, we consider how the shape of the potential changes depending on the scenario of protein folding. To mimic protein folding dynamics projected onto a two-dimensional space of collective variables, the two-dimensional Müller and Brown potential is employed. Three characteristic scenarios are considered: a single pathway from the unfolded to the native state without intermediates, two parallel pathways without intermediates, and a single pathway with an off-pathway intermediate. To determine the probability fluxes, the hydrodynamic description of the folding reaction is used, in which the first-passage folding is viewed as a steady flow of the representative points of the protein from the unfolded to the native state. We show that despite the possible complexity of the folding process, the ?-component is simple and universal in shape. The ?-component is more complex and reveals characteristic features of the process of folding. The present approach is potentially applicable to other complex reactions, for which the transition from the reactant to the product can be described in a space of two (collective) variables. PMID:25848943
J. Zambrini
A new class of diffusion processes, the Bernstein processes, is introduced in Theoretical Physics. Their dynamical realization, the Variational processes yields a new probabilistic interpretation of the Heat equation, much closer to quantum mechanics than the other known classical analogies, and also a new constructive variational approach to Stochastic Mechanics.
Electron-impact ionization of atomic hydrogen: dynamical variational treatment
NASA Astrophysics Data System (ADS)
Defrance, P.; Kereselidze, T.; Lecointre, J.; Machavariani, Z. S.
2011-10-01
A simple and straightforward calculating scheme is proposed for electron-impact single and multiple ionization of atoms. The method is based on the application of the Hulthén-Kohn dynamical variational principle. An effective charge seen by the scattered electron is determined for a certain type of trial wave functions mathematically in a rigorous way excluding any empirical assumptions. Validity of the elaborated approach is assessed by calculating triply differential cross section (TDCS) for electron-impact ionization of hydrogen. It is shown that, inclusion of the effective charge into the calculation reduces height of a "binary peak" in comparison with the first Born approximation result. The height of a "recoil peak" depends on the sign of the effective charge. The calculated TDCS are compared with the available experimental data and with the results of sophisticated theories and agreement is found.
NASA Astrophysics Data System (ADS)
Görling, Andreas
2015-06-01
It is shown how to properly construct exchange-correlation (xc) potentials in the Kohn-Sham (KS) formalism of density-functional theory such that physically meaningful KS eigenvalues result. A potential adjustor ?Hx c N - is derived which enables for any approximate functional for the xc energy the construction of a consistent xc potential leading to an eigenvalue of the energetically highest occupied KS orbital equal to the negative of the ionization potential. Together with a second potential adjustor ?Hx c N + KS band structures can be converted in approximate quasiparticle band structures exhibiting the exact physical instead of the KS band gap. This represents an alternative route to the fundamental quasiparticle band gap, completely within the KS formalism without the need to resort to many-body perturbation theory approaches like the G W method. It is shown that, for any finite system, approximate xc potentials including those in the local density and generalized gradient approximations, in contrast to common belief, always exhibit consistent nonzero discontinuities at integer electron numbers, if constructed properly. Thus the discontinuity of xc potentials is identified as a derived quantity which emerges automatically by properly constructing xc potentials without the need to be specifically incorporated in approximate xc functionals. It is demonstrated that all relevant objects of the ensemble KS formalism, in particular functional derivatives and their discontinuities, can be expressed in terms of quantities readily available in the KS formalism of integer electron numbers within an approach named integer electron ensemble approach (IEEA). Attempts to specifically construct ensemble density functionals are shown to be needless. Taking the known asymptotic behavior of the electron density into account an internal consistency condition for xc potentials is presented which justifies tuning procedures of xc functionals and, furthermore, indicates how asymptotic corrections for xc potentials have to be properly employed.
Bleiziffer, Patrick; Hesselmann, Andreas; Görling, Andreas
2012-04-01
Two related methods to calculate the Kohn-Sham correlation energy within the framework of the adiabatic-connection fluctuation-dissipation theorem are presented. The required coupling-strength-dependent density-density response functions are calculated within exact-exchange time-dependent density-functional theory, i.e., within time-dependent density-functional response theory using the full frequency-dependent exchange kernel in addition to the Coulomb kernel. The resulting resolution-of-identity exact-exchange random-phase approximation (RI-EXXRPA) methods in contrast to previous EXXRPA methods employ an auxiliary basis set (RI basis set) to improve the computational efficiency, in particular, to reduce the formal scaling of the computational effort with respect to the system size N from N(6) to N(5). Moreover, the presented RI-EXXRPA methods, in contrast to previous ones, do not treat products of occupied times unoccupied orbitals as if they were linearly independent. Finally, terms neglected in previous EXXRPA methods can be included, which leads to a method designated RI-EXXRPA+, while the method without these extra terms is simply referred to as RI-EXXRPA. Both EXXRPA methods are shown to yield total energies, reaction energies of small molecules, and binding energies of noncovalently bonded dimers of a quality that is similar and in some cases even better than that obtained with quantum chemistry methods such as Mo?ller-Plesset perturbation theory of second order (MP2) or with the coupled cluster singles doubles method. In contrast to MP2 and to conventional density-functional methods, the presented RI-EXXRPA methods are able to treat static correlation. PMID:22482535
Balloch, Liam; Drummond, Allison M; García-Alvarez, Pablo; Graham, David V; Kennedy, Alan R; Klett, Jan; Mulvey, Robert E; O'Hara, Charles T; Rodger, Philip J A; Rushworth, Iain D
2009-07-20
Treatment of 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) with a group 1 metal (Li, Na, K, Rb, or Cs), resulted in the reduction of this important radical to the TEMPO(-) anion--the first examples of elemental-metal single electron reduction of the radical to its anionic form. The synthesis and characterization of seven alkali metal TEMPO(-) complexes are reported. A variety of structural motifs are encountered depending on the choice of metal and/or solvent. (THF)(2) x [Li(+)(TEMPO(-))](4) 1 crystallized from THF as a cyclic (Li(4)O(4)) molecule. Two Li centers are stabilized by coordination to a THF molecule; the others by intramolecular coordination to N(TEMPO) atoms. [(THF) x Na(+)(TEMPO(-))](4) 2 exists as a distorted cubane where each Na center is coordinated to a THF molecule. No appreciable Na-N(TEMPO) coordination is observed. [(THF)(2) x Na(+)(3)(TEMPO(-))(2)(OH)](2) 3 was serendipitously prepared and exists as a distorted bis(cubane). It is envisaged that 3 is formed from 2 by insertion of a (Na-OH)(2) double bridge into its framework. [Na(+)(4)(mu(3)-TEMPO(-))(2)(mu(2)-TEMPO(-))(2)(TMEDA)(2)] 4, adopts a four-runged ladder structure, whereby the two outer Na centers are coordinated to TMEDA, in addition to two mu(2)-O and a N atom. The inner metal atoms are bound to three mu(3)-O atoms and a N atom. [(THF) x K(+)(TEMPO(-))](4) 5 resembles the motif found for 2; however, presumably because of the larger size of the metal, K-N(TEMPO) interactions are present in 5. The asymmetric unit of [(TMEDA) x Rb(+)(2)(TEMPO(-))(2)](2) 6 comprises a Rb(4)O(4) cubane with half a molecule of TMEDA coordinated to each metal. From a supramolecular perspective, 6 exists as a polymeric array of cubane units connected by TMEDA bridges. Completing the series, [Cs(+)(TEMPO)](infinity) 7 crystallizes from hexane to form a donor-free polymeric complex. Complexes 1, 2, and 4-7 are soluble in D(8)-THF solution, and their NMR spectra are reported. The solution structures in donor solvent appear virtually identical. PMID:19459697
Hazari, Alokesh; Kanta Das, Lakshmi; Kadam, Ramakant M; Bauzá, Antonio; Frontera, Antonio; Ghosh, Ashutosh
2015-02-28
Three new mixed valence trinuclear Co(II/III) compounds cis-[Co3L2(MeOH)2(N3)2(?1,1-N3)2] (1), trans-[Co3L2(H2O)2(N3)2(?1,1-N3)2]·(H2O)2 (2) and [Co3L(R)2(N3)3(?1,3-N3)] (3) have been synthesized by reacting a di-Schiff base ligand (H2L) or its reduced form [H2LR] (where H2L= N,N'-bis(salicylidene)-1,3-propanediamine and H2LR= N,N'-bis(2-hydroxybenzyl)-1,3-propanediamine) with cobalt perchlorate hexahydrate and sodium azide. All three products have been characterized by IR, UV-Vis and EPR spectroscopies, ESI-MS, elemental, powder and single crystal X-ray diffraction analyses. Complex 2 is an angular trinuclear species in which two terminal octahedral Co(III)N2O4 centers coordinate to the central octahedral cobalt(II) ion through ?2-phenoxido oxygen and ?1,1-azido nitrogen atoms along with two mutually cis-oxygen atoms of methanol molecules. On the other hand, in linear trinuclear complex , in addition to the ?2-phenoxido and ?1,1-azido bridges with terminal octahedral Co(III) centres, the central Co(II) is bonded with two mutually trans-oxygen atoms of water molecules. Thus the cis-trans configuration of the central Co(II) is solvent dependent. In complex 3, the two terminal octahedral Co(III)N2O4 centers coordinate to the central penta-coordinated Co(II) ion through double phenoxido bridges along with the nitrogen atom of a terminal azido ligand. In addition, the two terminal Co(III) are connected through a ?1,3-azido bridge that participates in pnicogen bonding interactions (intermolecular N-N interaction) as an acceptor. Both the cis and trans isomeric forms of 1 and 2 have been optimized using density functional theory (DFT) calculations and it is found that the cis configuration is energetically more favorable than the trans one. However, the trans configuration of 2 is stabilized by the hydrogen bonding network involving a water dimer. The pnicogen bonding interactions have been demonstrated using MEP surfaces and CSD search which support the counter intuitive electron acceptor ability of the ?1,3-azido ligand. Complexes 1-3 exhibit catecholase-like activities in the aerial oxidation of 3,5-di-tert-butylcatechol to the corresponding o-quinone. Kinetic data analyses of this oxidation reaction in acetonitrile reveal that the catecholase-like activity follows the order: 1 (kcat = 142 h(-1)) > 3 (kcat = 99 h(-1)) > 2 (kcat = 85 h(-1)). Mechanistic investigations of the catalytic behaviors by X-band EPR spectroscopy and estimation of hydrogen peroxide formation indicate that the oxidation reaction proceeds through the reduction of Co(III) to Co(II). PMID:25611163
2015-01-01
The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang–Rhys factor) with high precision. The Huang–Rhys factors vary between 0.03 and 0.8. The values of the Huang–Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system. PMID:25708355
Skandary, Sepideh; Hussels, Martin; Konrad, Alexander; Renger, Thomas; Müh, Frank; Bommer, Martin; Zouni, Athina; Meixner, Alfred J; Brecht, Marc
2015-03-19
The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang-Rhys factor) with high precision. The Huang-Rhys factors vary between 0.03 and 0.8. The values of the Huang-Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system. PMID:25708355
NASA Astrophysics Data System (ADS)
Sample, J. C.; Tripati, A. K.
2010-12-01
The Cascadia subduction zone is a site of significant gas hydrate and carbonate formation. At ODP Sites 891 and 892, which penetrated the deformed sediment of the accretionary prism to depths of 472 and 176 m, respectively, carbonate cements and veins occur throughout the section. Previous isotopic studies of the carbonates indicate that at several horizons the ?18OVPDB values of carbonates are low (commonly < -5 ‰) and are substantially out of equilibrium with modern pore water isotopic compositions and temperature. At Site 892, ?18O values are consistent with precipitation temperatures of 100°C at a depth of 67 meters below seafloor (mbsf). A proposed explanation is that periodic upward migration of warm fluids occurred at short time scales. But the ambiguity of interpreting oxygen isotope variations in carbonates in relation to precipitation temperature or past variations in fluid oxygen isotope composition allows for the possibility of isotopically light fluids causing the low ?18O values. We used the technique of clumped isotope analysis, which relies on the correlation between the prevalence of 13C-18O-16O isotopologues (?47 measurements) in carbonate with temperature during carbonate formation, to determine temperature and oxygen isotopic composition of fluids. The samples are mainly from two horizons at Site 892 - a zone of faulting and coarse sediment at 66.7 mbsf, and the main thrust fault at 106.2 mbsf. A variety of evidence suggests these horizons are active fluid conduits. The resulting temperatures calculated using ?47 measurements of four samples from the 66.7 mbsf horizon range from 80.3°C to 103.6°C (± 3.1° to 4.6°C 1?). This range is very similar to previous estimates from conventional ?18O isotope-ratio mass-spectrometry (IRMS) measurements of 80°C to 101°C. For the main thrust horizon at 106.2 mbsf, calculated temperatures from ?47 measurements of three samples are 38.4 ± 4.4°C, 63.6 ± 4.4°C, and 70.5 ± 4.2°C. These are somewhat higher than temperatures calculated from previous IRMS analyses (24°C to 60°C). The new data presented here corroborate a model of periodic, nonsteady-state fluid migration in the Cascadia accretionary prism, perhaps related to large-magnitude earthquakes that appear to be rare along this margin. Further, ?47 measurements indicate a large range in fluid isotopic compositions during carbonate mineral formation, from ?18OVSMOW = -3.5‰ to +6.5‰. This suggests that during nonsteady-state flow events a variety of fluid reservoirs are tapped. All analyzed samples occurred at depths well below the depth of gas hydrates and thus the process of hydrate formation did not likely influence pore-fluid isotopic compositions. A more thorough understanding of the processes at Cascadia is important for understanding the deformation and seismicity along the margin, and the potential destabilizing impact on gas hydrates and sudden release of greenhouse gases into the atmosphere. Additional results from Sites 891 and 892 will be presented.
dePamphilis, Claude W.; Young, Nelson D.; Wolfe, Andrea D.
1997-01-01
The plastid genomes of some nonphotosynthetic parasitic plants have experienced an extreme reduction in gene content and an increase in evolutionary rate of remaining genes. Nothing is known of the dynamics of these events or whether either is a direct outcome of the loss of photosynthesis. The parasitic Scrophulariaceae and Orobanchaceae, representing a continuum of heterotrophic ability ranging from photosynthetic hemiparasites to nonphotosynthetic holoparasites, are used to investigate these issues. We present a phylogenetic hypothesis for parasitic Scrophulariaceae and Orobanchaceae based on sequences of the plastid gene rps2, encoding the S2 subunit of the plastid ribosome. Parasitic Scrophulariaceae and Orobanchaceae form a monophyletic group in which parasitism can be inferred to have evolved once. Holoparasitism has evolved independently at least five times, with certain holoparasitic lineages representing single species, genera, and collections of nonphotosynthetic genera. Evolutionary loss of the photosynthetic gene rbcL is limited to a subset of holoparasitic lineages, with several holoparasites retaining a full length rbcL sequence. In contrast, the translational gene rps2 is retained in all plants investigated but has experienced rate accelerations in several hemi- as well as holoparasitic lineages, suggesting that there may be substantial molecular evolutionary changes to the plastid genome of parasites before the loss of photosynthesis. Independent patterns of synonymous and nonsynonymous rate acceleration in rps2 point to distinct mechanisms underlying rate variation in different lineages. Parasitic Scrophulariaceae (including the traditional Orobanchaceae) provide a rich platform for the investigation of molecular evolutionary process, gene function, and the evolution of parasitism. PMID:9207097
Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L
2009-07-14
A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol. PMID:19603962
E. S. Kryachko
2006-02-06
It is demonstrated that the original reductio ad absurdum proof of the generalization of the Hohenberg-Kohn theorem for ensembles of fractionally occupied states for isolated many-electron Coulomb systems with Coulomb-type external potentials by Gross et al. [Phys. Rev. A 37, 2809 (1988)] is self-contradictory since the to-be-refuted assumption (negation) regarding the ensemble one-electron densities and the assumption about the external potentials are logically incompatible to each other due to the Kato electron-nuclear cusp theorem. It is however proved that the Kato theorem itself provides a satisfactory proof of this theorem.
Messud, Jeremie [Universite Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France) and Conseil Regional d'Aquitaine, F-33077 Bordeaux (France)
2011-11-15
We generalize the recently developed ''internal'' density-functional theory (DFT) and Kohn-Sham scheme to multicomponent systems. We obtain a general formalism, applicable for the description of multicomponent self-bound systems (such as molecular systems where the nuclei are treated explicitly, atomic nuclei and mixtures of {sup 3}He and {sup 4}He droplets), where the fundamental translational symmetry has been treated correctly. The main difference with traditional DFT is the explicit inclusion of center-of-mass correlations in the functional. A large part of the paper is dedicated to the application to molecular systems, which permits us to clarify the approximations that underly traditional DFT.
Johannes Lischner; T. A. Arias
2008-06-27
The Gordian knot of density-functional theories for classical molecular liquids remains finding an accurate free-energy functional in terms of the densities of the atomic sites of the molecules. Following Kohn and Sham, we show how to solve this problem by considering noninteracting molecules in a set of effective potentials. This shift in perspective leads to an accurate and computationally tractable description in terms of simple three-dimensional functions. We also treat both the linear- and saturation- dielectric responses of polar systems, presenting liquid hydrogen chloride as a case study.
Komeda, Tadahiro; Isshiki, Hironari; Liu, Jie; Katoh, Keiichi; Shirakata, Minoru; Breedlove, Brian K; Yamashita, Masahiro
2013-02-26
By using scanning tunneling microscopy (STM), we studied the heteroleptic double-decker complex TbNPcPc (NPc = naphthalocyaninato and Pc = phthalocyaninato), where two different planar ligands sandwich a Tb(III) ion and an unpaired ? electron causes Kondo resonance upon adsorption on the Au(111) surface. Kondo resonance is a good conductance control mechanism originating from interactions between conduction electrons and a localized spin. Two types of adsorption geometries appear depending on which side contacts the substrate surface, which we call Pc-up and NPc-up molecules. They make intriguing molecular assemblies by segregation. In addition, different adsorption geometries and molecular assemblies provide a variety of spin and electronic configurations. Pc-up and NPc-up molecules both showed the Kondo resonance when they were isolated from other molecules, but their Kondo temperatures were different. A one-dimensional chain composed of only NPc-up molecules was found, in which the dI/dV plot showed a conversion from the Kondo peak to a dip at the Fermi energy. In addition, a two-dimensional lattice with an ordering of Pc-up and NPc-up molecules in an alternative manner was observed, in which no Kondo peak was detected in the molecule. The absence of the Kondo peak was accounted for by the change of azimuthal rotational angle of the two ligands of both molecules. The results imply that a molecule design and adsorption configuration tailoring can be used for the spin-mediated control of the electronic conductance of the molecule. PMID:23363375
ERIC Educational Resources Information Center
Wright, James D.; Wright, Sonia R.
1976-01-01
Argues that their paper is almost entirely programmatic: It attempts to indicate roughly how much we can expect to know about parental values for children once we know all there is to know about their relationship to social class; how much more might be known if similar efforts were expended on other factors; and what lines of inquiry these…
Okada, Yoko; Güsten, Rolf; Stutzki, Jürgen; Wiesemeyer, Helmut; Pütz, Patrick; Ricken, Oliver
2015-01-01
The [CII]158um line is one of the dominant cooling lines in star-forming active regions. The commonly assumed clumpy UV-penetrated cloud models predict a [CII] line profile similar to that of CO. However, recent spectral-resolved observations show that they are often very different, indicating a more complex origin of the line emission including the dynamics of the source region. The aim of our study is to investigate the physical properties of the star-forming ISM in the Large Magellanic Cloud (LMC) by separating the origin of the emission lines spatially and spectrally. In this paper, we focus on the spectral characteristics and the origin of the emission lines, and the phases of carbon-bearing species in the N159 star-forming region in the LMC. We mapped a 4'x(3-4)' region in N159 in [CII]158um and [NII]205um with the GREAT on board SOFIA, and in CO(3-2), (4-3), (6-5), 13CO(3-2), and [CI]3P1-3P0 and 3P2-3P1 with APEX. The emission of all transitions observed shows a large variation in the line profiles acr...
NASA Astrophysics Data System (ADS)
Della Sala, Fabio; Fabiano, Eduardo; Constantin, Lucian A.
2015-01-01
We show that the Kohn-Sham positive-definite kinetic energy (KE) density significantly differs from the von Weizsäcker (VW) one at the nuclear cusp as well as in the asymptotic region. At the nuclear cusp, the VW functional is shown to be linear, and the contribution of p -type orbitals to the KE density is theoretically derived and numerically demonstrated in the limit of infinite nuclear charge as well in the semiclassical limit of neutral large atoms. In the latter case, it reaches 12% of the KE density. In the asymptotic region we find new exact constraints for meta-generalized gradient approximation (meta-GGA) exchange functionals: with an exchange enhancement factor proportional to ?{? }, where ? is the common meta-GGA ingredient, both the exchange energy density and the potential are proportional to the exact ones. In addition, this describes exactly the large-gradient limit of quasi-two-dimensional systems.
Eli Kraisler; Guy Makov; Nathan Argaman; Itzhak Kelson
2010-11-20
In the framework of Kohn-Sham density-functional theory, systems with ground-state densities that are not pure-state v-representable in the non-interacting reference system (PSVR) occur frequently. In the present contribution, a new algorithm, which allows the solution of such systems, is proposed. It is shown that the use of densities which do not correspond to a ground state of their non-interacting reference system is forbidden. As a consequence, the proposed algorithm considers only non-interacting ensemble v-representable densities. The Fe atom, a well-known non-PSVR system, is used as an illustration. Finally, the problem is analyzed within finite temperature density-functional theory, where the physical significance of fractional occupations is exposed and the question of why degenerate states can be unequally occupied is resolved.
Della Sala, F; Constantin, L A
2014-01-01
We show that the Kohn-Sham positive-definite kinetic energy (KE) density significantly differs from the von Weizs\\"acker (VW) one at the nuclear cusp as well as in the asymptotic region. At the nuclear cusp, the VW functional is shown to be linear and the contribution of p-type orbitals to the KE density is theoretically derived and numerically demonstrated in the limit of infinite nuclear charge, as well in the semiclassical limit of neutral large atoms. In the latter case, it reaches 12 of the KE density. In the asymptotic region we find new exact constraints for meta Generalized Gradient Approximation (meta-GGA) exchange functionals: with an exchange enhancement factor proportional to $\\sqrt{\\alpha}$, where $\\alpha$ is the common meta-GGA ingredient, both the exchange energy density and the potential are proportional to the exact ones. In addition, this describes exactly the large-gradient limit of quasi-two dimensional systems.
Motamarri, Phani
2014-01-01
We present a subspace projection technique to conduct large-scale Kohn-Sham density functional theory calculations using spectral finite-element discretization. The proposed method treats both metallic and insulating materials in a single framework, and is applicable to both pseudopotential as well as all-electron calculations. The key ideas involved in the method include: (i) employing a higher-order spectral finite-element basis that is amenable to mesh adaption; (ii) using a Chebyshev filter to construct a subspace which is an approximation to the occupied eigenspace in a given self-consistent field iteration; (iii) using a localization procedure to construct a non-orthogonal localized basis spanning the Chebyshev filtered subspace; (iv) using a Fermi-operator expansion in terms of the subspace-projected Hamiltonian represented in the non-orthogonal localized basis to compute relevant quantities like the density matrix, electron density and band energy. We demonstrate the accuracy and efficiency of the app...
?-Electronic communication through mono and multinuclear gold(I) complexes
NASA Astrophysics Data System (ADS)
Palusiak, Marcin; Fonseca Guerra, Célia; Bickelhaupt, F. Matthias
We have theoretically studied gold(I) complexes of the type L1-AuI-L2 and HCN-[AuI-CN]n (n = 1-8) using relativistic density functional theory at ZORA-BP86/TZ2P. Our purpose, besides determining structure and stability, is to analyze the bonding in our model systems in the conceptual framework of Kohn-Sham molecular orbital theory in combination with a quantitative bond energy decomposition scheme and analysis of the charge distribution. We focus on the ?-bonding interaction for a given ligand-gold coordination bond and how this is affected by the presence of the other ligand. We find pronounced ?-electronic communication through the gold(I) valence shell in complexes that involve a ?-donor as well as a ?-acceptor ligand.
Exterior complex scaling method in TDDFT: HHG of Ar atoms in intense laser fields
NASA Astrophysics Data System (ADS)
Sosnova, Ksenia E.; Telnov, Dmitry A.; Rozenbaum, Efim; Chu, Shih-I.
2014-04-01
Exterior complex scaling (ECS) method is applied in the framework of the time-dependent density functional theory to study high-order harmonic generation (HHG) of multielectron atoms in intense laser fields. ECS allows to impose correct (outgoing-wave) boundary conditions on the wave functions at large distances. In the present work, ECS is combined with the time-dependent generalized pseudospectral method for accurate and efficient solution of the time-dependent Kohn-Sham equations. Results for HHG of Ar atoms are presented.
NASA Astrophysics Data System (ADS)
Pueyo Bellafont, Noèlia; Bagus, Paul S.; Illas, Francesc
2015-06-01
A systematic study of the N(1s) core level binding energies (BE's) in a broad series of molecules is presented employing Hartree-Fock (HF) and the B3LYP, PBE0, and LC-BPBE density functional theory (DFT) based methods with a near HF basis set. The results show that all these methods give reasonably accurate BE's with B3LYP being slightly better than HF but with both PBE0 and LCBPBE being poorer than HF. A rigorous and general decomposition of core level binding energy values into initial and final state contributions to the BE's is proposed that can be used within either HF or DFT methods. The results show that Koopmans' theorem does not hold for the Kohn-Sham eigenvalues. Consequently, Kohn-Sham orbital energies of core orbitals do not provide estimates of the initial state contribution to core level BE's; hence, they cannot be used to decompose initial and final state contributions to BE's. However, when the initial state contribution to DFT BE's is properly defined, the decompositions of initial and final state contributions given by DFT, with several different functionals, are very similar to those obtained with HF. Furthermore, it is shown that the differences of Kohn-Sham orbital energies taken with respect to a common reference do follow the trend of the properly calculated initial state contributions. These conclusions are especially important for condensed phase systems where our results validate the use of band structure calculations to determine initial state contributions to BE shifts.
NASA Astrophysics Data System (ADS)
Murray, Joelle; Gibbon, Dana; Runyon, Alissa; Bajracharya, Arun
2015-03-01
A protein's tertiary structure determines its function in living organisms. The different functions proteins serve necessitate variety in native structures. How is variation in tertiary structure created from a common set of amino acids and molecular forces? In other words, what generates complexity in structures across all types of native proteins? To explore this question, a simple HP model of protein folding was explored for evidence of self-organized criticality, a potential generator of complexity.
M. W. C. Dharma-wardana; Michael S. Murillo
2007-10-15
Two-temperature, two-mass quasi-equilibrium plasmas may occur in electron-ion plasmas,nuclear-matter, as well as in electron-hole condensed-matter systems. Dense two-temperature hydrogen plasmas straddle the difficult partially - degenerate regime of electron densities and temperatures which are important in astrophysics, in inertial-confinement fusion research, and other areas of warm dense matter physics. Results from Kohn-Sham calculations and QMC are used to benchmark the procedures used in classical molecular-dynamics simulations, HNC and CHNC methods to derive electron-electron and electron-proton pair - distribution functions. Then, nonequilibrium molecular dynamics for two -temperature, two-mass plasmas are used to obtain the pair distribution. Using these results, the correct HNC and CHNC procedures for the evaluation of pair-distribution functions in two-temperature two-mass two-component charged fluids are established. Results for a mass ratio of 1:5, typical of electron-hole fluids, as well as for compressed hydrogen are presented. PACS Numbers: 52.25.Kn, 52.25Gj, 71.10.-w, 52.27.Gr, 26.30.+k
NASA Astrophysics Data System (ADS)
Ye, Lin-Hui
2015-02-01
The Kohn-Sham orbital kinetic energy density ??(r ) =?iwi ?|??i ?(r ) | 2 is one fundamental quantity for constructing metageneralized gradient approximations (meta-GGAs) for use by density functional theory. We present a computational scheme of ??(r ) for the full-potential linearized augmented plane-wave (FLAPW) method. Our scheme is highly accurate and efficient and easy to implement with existing computer codes. To illustrate its performance, we construct the Becke-Johnson meta-GGA exchange potentials for Be, Ne, Mg, Ar, Ca, Zn, Kr, and Cd atoms, which are in very good agreement with the original results. For bulk solids, we construct the Tran-Blaha modified Becke-Johnson potential (mBJ) and confirm its capability to calculate band gaps with the reported bad convergence of the mBJ potential being substantially improved. The present computational scheme of ??(r ) should also be valuable for developing other meta-GGAs in the FLAPW as well as in similar methods utilizing atom centered basis functions.
Lao, Ka Un; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 (United States)
2014-01-28
The performance of second-order symmetry-adapted perturbation theory (SAPT) calculations using Kohn-Sham (KS) orbitals is evaluated against benchmark results for intermolecular interactions. Unlike previous studies of this “SAPT(KS)” methodology, the present study uses non-empirically tuned long-range corrected (LRC) functionals for the monomers. The proper v{sub xc} (r)?0 asymptotic limit is achieved by tuning the range separation parameter in order to satisfy the condition that the highest occupied KS energy level equals minus the molecule's ionization energy, for each monomer unit. Tests for He{sub 2}, Ne{sub 2}, and the S22 and S66 data sets reveal that this condition is important for accurate prediction of the non-dispersion components of the energy, although errors in SAPT(KS) dispersion energies remain unacceptably large. In conjunction with an empirical dispersion potential, however, the SAPT(KS) method affords good results for S22 and S66, and also accurately predicts the whole potential energy curve for the sandwich isomer of the benzene dimer. Tuned LRC functionals represent an attractive alternative to other asymptotic corrections that have been employed in density-functional-based SAPT calculations, and we recommend the use of tuned LRC functionals in both coupled-perturbed SAPT(DFT) calculations and dispersion-corrected SAPT(KS) calculations.
NASA Astrophysics Data System (ADS)
Bast, Radovan; Saue, Trond; Henriksson, Johan; Norman, Patrick
2009-01-01
The quadratic response function has been derived and implemented at the adiabatic four-component Kohn-Sham density functional theory level with inclusion of noncollinear spin magnetization and gradient corrections in the exchange-correlation functional—a work that is an extension of our previous report where magnetization dependencies in the exchange-correlation functional were ignored [J. Henriksson, T. Saue, and P. Norman, J. Chem. Phys. 128, 024105 (2008)]. The electric-field induced second-harmonic generation experiments on CF3Cl and CF3Br are addressed by a determination of ?¯(-2?;?,?) for a wavelength of 694.3 nm, and the same property is also determined for CF3I. The relativistic effects on the static hyperpolarizability for the series of molecules amount to 1%, 5%, and 9%, respectively. At the experimental wavelength, the contributions to ? due to the magnetization dependence in the exchange-correlation functional are negligible for CF3Cl and CF3Br and small for CF3I. The noticeable effect of magnetization in the latter case is attributed to a near two-photon resonance with the excited state 1 E3 (nonrelativistic notation). It is emphasized, however, that the effect of magnetization on ? for CF3I is negligible both in comparison to the total relativistic correction as well as to the effects of electron correlation. It is concluded that, in calculations of hyperpolarizabilities under nonresonant conditions, the magnetization dependence in the exchange-correlation functional may be ignored.
NASA Astrophysics Data System (ADS)
Grüning, M.; Gritsenko, O. V.; Baerends, E. J.
2003-04-01
The standard local density approximation and generalized gradient approximations fail to properly describe the dissociation of an electron pair bond, yielding large errors (on the order of 50 kcal/mol) at long bond distances. To remedy this failure, a self-consistent Kohn-Sham (KS) method is proposed with the exchange-correlation (xc) energy and potential depending on both occupied and virtual KS orbitals. The xc energy functional of Buijse and Baerends [Mol. Phys. 100, 401 (2002); Phys. Rev. Lett. 87, 133004 (2001)] is employed, which, based on an ansatz for the xc-hole amplitude, is able to reproduce the important dynamical and nondynamical effects of Coulomb correlation through the efficient use of virtual orbitals. Self-consistent calculations require the corresponding xc potential to be obtained, to which end the optimized effective potential (OEP) method is used within the common energy denominator approximation for the static orbital Green's function. The problem of the asymptotic divergence of the xc potential of the OEP when a finite number of virtual orbitals is used is addressed. The self-consistent calculations reproduce very well the entire H2 potential curve, describing correctly the gradual buildup of strong left-right correlation in stretched H2.
Li, Y.; Krieger, J.B. (Department of Physics, Brooklyn College, City University of New York, Brooklyn, New York 11210 (United States)); Norman, M.R. (Material Sciences Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)); Iafrate, G.J. (U.S. Army Research Office, Research Triangle Park, North Carolina 27709-2211 (United States))
1991-11-15
The optimized-effective-potential (OEP) method and a method developed recently by Krieger, Li, and Iafrate (KLI) are applied to the band-structure calculations of noble-gas and alkali halide solids employing the self-interaction-corrected (SIC) local-spin-density (LSD) approximation for the exchange-correlation energy functional. The resulting band gaps from both calculations are found to be in fair agreement with the experimental values. The discrepancies are typically within a few percent with results that are nearly the same as those of previously published orbital-dependent multipotential SIC calculations, whereas the LSD results underestimate the band gaps by as much as 40%. As in the LSD---and it is believed to be the case even for the exact Kohn-Sham potential---both the OEP and KLI predict valence-band widths which are narrower than those of experiment. In all cases, the KLI method yields essentially the same results as the OEP.
Patterned variation in prehistoric chiefdoms
Drennan, Robert D.; Peterson, Christian E.
2006-01-01
Comparative study of early complex societies (chiefdoms) conjures visions of a cultural evolutionary emphasis on similarities and societal typology. Variation within the group has not been as systematically examined but offers an even more productive avenue of approach to fundamental principles of organization and change. Three widely separated trajectories of early chiefdom development are compared here: the Valley of Oaxaca (Mexico), the Alto Magdalena (Colombia), and Northeast China. Archaeological data from all three regions are analyzed with the same tools to reveal variation in human activities, relationships, and interactions as these change in the emergence of chiefly communities. Patterning in this variation suggests the operation of underlying general principles, which are offered as hypotheses that merit further investigation and evaluation in comparative study of a much larger number of cases. PMID:16473941
Irreducible Complexity Revisited
William A. Dembski
2004-01-01
Michael Behe's concept of irreducible complexity, and in particular his use of this concept to critique Darwinism, continues to come under heavy fire from the biological community. The problem with Behe, so Darwinists inform us, is that he has created a problem where there is no problem. Far from constituting an obstacle to the Darwinian mechanism of random variation and
Complexity, Cognitive Load and HCI
Chrsitian Kapp
Complexity and cognitive load are both well-known aspects in Human Computer Interaction. There is a need for optimizing computer based systems in the aspect of complexity and cognitive load. To achieve this optimization information must be represented in an adequate way and input variations and interactive elements must be chosen carefully. But how to decide which interaction or presentation is
NSDL National Science Digital Library
2011-01-01
The lesson begins with a comparison of data tables and graphs of two functions, one directly proportional (cost of gas) and the other exponential (population), before a definition for direct variation is introduced. Direct variation is then linked to linear function (f(x)= kx)and the scaling property of direct variation is examined (i.e. a multiple of the independent variable will always correspond to that same multiple of the dependent variable). Direct variation with a power of x follows with a test for direct variation before indirect variation and indirect variation with a power of x are introduced.
ERIC Educational Resources Information Center
Puren, Christian
1991-01-01
A model of foreign language education is presented that takes into account the complexity of instruction itself and the dimensions added by interaction of teacher, learner, institution, materials, and environment. Uncertainty is seen as a by-product of complexity, and innovation and variation in instructional practice are ways of dealing with…
Pueyo Bellafont, Noèlia; Bagus, Paul S; Illas, Francesc
2015-06-01
A systematic study of the N(1s) core level binding energies (BE's) in a broad series of molecules is presented employing Hartree-Fock (HF) and the B3LYP, PBE0, and LC-BPBE density functional theory (DFT) based methods with a near HF basis set. The results show that all these methods give reasonably accurate BE's with B3LYP being slightly better than HF but with both PBE0 and LCBPBE being poorer than HF. A rigorous and general decomposition of core level binding energy values into initial and final state contributions to the BE's is proposed that can be used within either HF or DFT methods. The results show that Koopmans' theorem does not hold for the Kohn-Sham eigenvalues. Consequently, Kohn-Sham orbital energies of core orbitals do not provide estimates of the initial state contribution to core level BE's; hence, they cannot be used to decompose initial and final state contributions to BE's. However, when the initial state contribution to DFT BE's is properly defined, the decompositions of initial and final state contributions given by DFT, with several different functionals, are very similar to those obtained with HF. Furthermore, it is shown that the differences of Kohn-Sham orbital energies taken with respect to a common reference do follow the trend of the properly calculated initial state contributions. These conclusions are especially important for condensed phase systems where our results validate the use of band structure calculations to determine initial state contributions to BE shifts. PMID:26049474
Variation in form versus variation in meaning
Helen de Hoop; Marco Haverkort; Maurits van den Noort
2004-01-01
The aim of this introductory article is to provide a background to the articles contained in this special issue of Lingua that centers around variation in form, variation in meaning, and markedness. Theoretical and empirical considerations are brought together in this special issue in which the linguistic disciplines that are covered diverge. The different contributions deal with language processing, first
NASA Astrophysics Data System (ADS)
Kress, Joel
2013-06-01
Large-scale hydrodynamic simulations of fluids and plasmas under extreme conditions require knowledge of various properties such as the equation of state (EOS), mass diffusion, and shear viscosity. While many approaches exist for the determination of these properties, one of the most accurate employs quantum molecular dynamics (QMD) simulations on large samples of atoms of the various species. Examples include the shock compression of metal hydrides and the mixing of deuterium/tritium (DT) fuel with ablator materials (such as C/H plastics and Be) in inertial confinement fusion capsules. The quantum nature of the electrons is described with two flavors of finite-temperature density functional theory (DFT), namely orbital-based Kohn-Sham (KS) and Orbital Free (OF). EOSs for Lithium Hydride and Lithium 6 Deuteride (Li6D) have been calculated with both KSMD and with OFMD. The shock Hugoniot for Li6D has been determined for temperatures up to 25 eV (5000 GPa) using a KSMD based EOS, and for T = 5 eV and above (up to 10,000 GPa) using an OFMD based EOS. KSMD simulations here have a practical upper limit of T = 25 eV due to the scaling of the computational work. The OFMD simulations have a lower limit of T = 5 eV since the OF DFT yields a poor description at low temperatures. The KSMD and OFMD Hugoniots agree well in the region of overlap (T = 5 to 25 eV). Comparisons will be presented with experimental data and with shock Hugoniots constructed from both existing EOS tables and from a new, improved SESAME table. By utilizing the KSMD and OFMD results to guide the parameter choices, the new EOS overall is a better match to melt and shock experimental data. This work was performed in collaboration with L. A. Collins, S. Crockett, M. P. Desjarlais, and F. Lambert and under the auspices of an agreement between CEA/DAM and NNSA/DP on cooperation on fundamental science. LANL is operated by LANS, LLC for the NNSA of the USDoE under contract no. DE-AC52-06NA25396.
NASA Astrophysics Data System (ADS)
Bleiziffer, Patrick; Krug, Marcel; Görling, Andreas
2015-06-01
A self-consistent Kohn-Sham method based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem, employing the frequency-dependent exact exchange kernel fx is presented. The resulting SC-exact-exchange-only (EXX)-ACFD method leads to even more accurate correlation potentials than those obtained within the direct random phase approximation (dRPA). In contrast to dRPA methods, not only the Coulomb kernel but also the exact exchange kernel fx is taken into account in the EXX-ACFD correlation which results in a method that, unlike dRPA methods, is free of self-correlations, i.e., a method that treats exactly all one-electron systems, like, e.g., the hydrogen atom. The self-consistent evaluation of EXX-ACFD total energies improves the accuracy compared to EXX-ACFD total energies evaluated non-self-consistently with EXX or dRPA orbitals and eigenvalues. Reaction energies of a set of small molecules, for which highly accurate experimental reference data are available, are calculated and compared to quantum chemistry methods like Møller-Plesset perturbation theory of second order (MP2) or coupled cluster methods [CCSD, coupled cluster singles, doubles, and perturbative triples (CCSD(T))]. Moreover, we compare our methods to other ACFD variants like dRPA combined with perturbative corrections such as the second order screened exchange corrections or a renormalized singles correction. Similarly, the performance of our EXX-ACFD methods is investigated for the non-covalently bonded dimers of the S22 reference set and for potential energy curves of noble gas, water, and benzene dimers. The computational effort of the SC-EXX-ACFD method exhibits the same scaling of N5 with respect to the system size N as the non-self-consistent evaluation of only the EXX-ACFD correlation energy; however, the prefactor increases significantly. Reaction energies from the SC-EXX-ACFD method deviate quite little from EXX-ACFD energies obtained non-self-consistently with dRPA orbitals and eigenvalues, and the deviation reduces even further if the Coulomb kernel is scaled by a factor of 0.75 in the dRPA to reduce self-correlations in the dRPA correlation potential. For larger systems, such a non-self-consistent EXX-ACFD method is a competitive alternative to high-level wave-function-based methods, yielding higher accuracy than MP2 and CCSD methods while exhibiting a better scaling of the computational effort than CCSD or CCSD(T) methods. Moreover, EXX-ACFD methods were shown to be applicable in situation characterized by static correlation.
NASA Astrophysics Data System (ADS)
Dowker, Mark; Ohkitani, Koji
2012-11-01
We study space-time integrals, which appear in the Caffarelli-Kohn-Nirenberg (CKN) theory for the Navier-Stokes equations analytically and numerically. The key quantity is written in standard notations ? (r)=1/(? r)int _{Q_r}left|nabla {u}right|^2 d{{x}} dt, which can be regarded as a local Reynolds number over a parabolic cylinder Qr. First, by re-examining the CKN integral, we identify a cross-over scale r_* ? Lleft( overline{Vert nabla {u} Vert ^2_{L^2}} /Vert nabla {u Vert ^2_{L^infty }} right)^{1/3}, at which the CKN Reynolds number ?(r) changes its scaling behavior. This reproduces a result on the minimum scale rmin in turbulence: r_min^2 Vert nabla {u}Vert _infty ? ? , consistent with a result of Henshaw et al. ["On the smallest scale for the incompressible Navier-Stokes equations," Theor. Comput. Fluid Dyn. 1, 65 (1989), 10.1007/BF00272138]. For the energy spectrum E(k) ? k-q (1 < q < 3), we show that r* ? ?a with a=4/3(3-q)-1. Parametric representations are then obtained as Vert nabla {u}Vert _infty ? ? ^{-(1+3a)/2} and rmin ? ?3(a+1)/4. By the assumptions of the regularity and finite energy dissipation rate in the inviscid limit, we derive lim _{p rArr infty }? _p/p=1 - ? _2 for any phenomenological models on intermittency, where ?p is the exponent of pth order (longitudinal) velocity structure function. It follows that ?p ? (1 - ?2)(p - 3) + 1 for any p ? 3 without invoking fractal energy cascade. Second, we determine the scaling behavior of ?(r) in direct numerical simulations of the Navier-Stokes equations. In isotropic turbulence around R? ? 100 starting from random initial conditions, we have found that ?(r) ? r4throughout the inertial range. This can be explained by the smallness of a ? 0.26,with a result that r* is in the energy-containing range. If the ?-model is perfectly correct, the intermittency parameter a must be related to the dissipation correlation exponent ? as ? =4a/1+a ? 0.8, which is larger than the observed ? ? 0.20. Furthermore, corresponding integrals are studied using the Burgers vortex and the Burgers equation. In those single-scale phenomena, the cross-over scale lies in the dissipative range. The scale r* offers a practical method of quantifying intermittency. This paper also sorts out a number of existing mathematical bounds and phenomenological models on the basis of the CKN Reynolds number.
Kussmann, Jörg; Ochsenfeld, Christian
2007-11-28
A density matrix-based time-dependent self-consistent field (D-TDSCF) method for the calculation of dynamic polarizabilities and first hyperpolarizabilities using the Hartree-Fock and Kohn-Sham density functional theory approaches is presented. The D-TDSCF method allows us to reduce the asymptotic scaling behavior of the computational effort from cubic to linear for systems with a nonvanishing band gap. The linear scaling is achieved by combining a density matrix-based reformulation of the TDSCF equations with linear-scaling schemes for the formation of Fock- or Kohn-Sham-type matrices. In our reformulation only potentially linear-scaling matrices enter the formulation and efficient sparse algebra routines can be employed. Furthermore, the corresponding formulas for the first hyperpolarizabilities are given in terms of zeroth- and first-order one-particle reduced density matrices according to Wigner's (2n+1) rule. The scaling behavior of our method is illustrated for first exemplary calculations with systems of up to 1011 atoms and 8899 basis functions. PMID:18052415
Genetic variations related to hypertension: a review
M O M Tanira; K A Al Balushi; MOM Tanira
2005-01-01
Hypertension is a complex multifactorial disorder with genetic, environmental and demographic factors contributing to its prevalence. The genetic element contribution to blood pressure variation ranges from 30 to 50%. Therefore, identifying hypertension susceptibility genes will help understanding the pathophysiology of the disease. In addition to the potential impact of genomic information in selecting antihypertensive drug therapy, it may also help
COMPLEX DIFFUSION ON IMAGE GRAPHS
Seo, Dohyung; Vemuri, Baba C
2009-01-01
Complex diffusion was introduced in image processing literature as a means to achieve simultaneous denoising and enhancement of scalar valued images. In this paper, we present a novel geometric framework for achieving complex diffusion on color images expressed as image graphs. In this framework, we develop a new variational formulation for achieving complex diffusion. This formulation involves a modified harmonic map functional and is quite distinct from the Polyakov action described in earlier work by Sochen et al. Our formulation provides a framework for simultaneous (feature preserving) denoising and enhancement. We present results of comparison between the complex diffusion, and Beltrami flow all in the image graph framework. PMID:20490365
Biswas, Apurba; Drew, Michael G B; Diaz, Carmen; Bauzá, Antonio; Frontera, Antonio; Ghosh, Ashutosh
2012-10-21
The trans-[Cu(2)L(2)Cl(2)] (1), and cis-[Cu(2)L(2)Cl(2)]·H(2)O (2) isomers of a diphenoxido bridged Cu(2)O(2) core have been synthesized using a tridentate reduced Schiff base ligand 2-[(2-dimethylamino-ethylamino)-methyl]-phenol. The geometry around Cu(II) is intermediate between square pyramid and trigonal bipyramid (Addison parameter, ? = 0.463) in 1 but nearly square pyramidal (? = 0.049) in 2. The chloride ions are coordinated to Cu(II) and are trans oriented in 1 but cis oriented in 2. Both isomers have been optimized using density functional theory (DFT) calculations and it is found that the trans isomer is 7.2 kcal mol(-1) more favorable than the cis isomer. However, the hydrogen bonding interaction of crystallized water molecule with chloride ions compensates for the energy difference and stabilizes the cis isomer. Both complexes have been converted to a very rare phenoxido-azido bridged trinuclear species, [Cu(3)L(2)(?(1,1)-N(3))(2)(H(2)O)(2)(ClO(4))(2)] (3) which has also been characterized structurally. All the complexes are antiferromagnetically coupled but the magnitude of the coupling constants are significantly different (J = -156.60, -652.31, and -31.54 cm(-1) for 1, 2, 3 and respectively). Density functional theory (DFT) calculations have also been performed to gain further insight into the qualitative theoretical interpretation on the overall magnetic behavior of the complexes. PMID:22930034
Kohn's theorem and Galilean symmetry
P-M. Zhang; P. A. Horvathy
2011-07-08
The relation between the separability of a system of charged particles in a uniform magnetic field and Galilean symmetry is revisited using Duval's "Bargmann framework". If the charge-to-mass ratios of the particles are identical, $e_a/m_a=\\epsilon$ for all particles, then the Bargmann space of the magnetic system is isometric to that of an anisotropic harmonic oscillator. Assuming that the particles interact through a potential which only depends on their relative distances, the system splits into one representing the center of mass plus a decoupled internal part, and can be mapped further into an isolated system using Niederer's transformation. Conversely, the manifest Galilean boost symmetry of the isolated system can be "imported" to the oscillator and to the magnetic systems, respectively, to yield the symmetry used by Gibbons and Pope to prove the separability. For vanishing interaction potential the isolated system is free and our procedure endows all our systems with a hidden Schroedinger symmetry, augmented with independent internal rotations. All these properties follow from the cohomological structure of the Galilei group, as explained by Souriau's "d\\'ecomposition barycentrique"
Non-differentiable variational principles
NASA Astrophysics Data System (ADS)
Cresson, Jacky
2005-07-01
We develop a calculus of variations for functionals which are defined on a set of non-differentiable curves. We first extend the classical differential calculus in a quantum calculus, which allows us to define a complex operator, called the scale derivative, which is the non-differentiable analogue of the classical derivative. We then define the notion of extremals for our functionals and obtain a characterization in term of a generalized Euler-Lagrange equation. We finally prove that solutions of the Schrödinger equation can be obtained as extremals of a non-differentiable variational principle, leading to an extended Hamilton's principle of least action for quantum mechanics. We compare this approach with the scale relativity theory of Nottale, which assumes a fractal structure of space-time.Résumé (Principes variationnels non différentiable). Nous développons un calcul des variations pour des fonctionnelles définies sur un ensemble de courbes non différentiables. Pour cela, nous étendons le calcul différentiel classique, en calcul appelé calcul quantique, qui nous permet de définir un opérateur à valeur complexes, appelé dérivée d'échelle, qui est l'analogue non différentiable de la dérivée usuelle. On définit alors la notion d'extremale pour ces fonctionnelles pour lesquelles nous obtenons une caractérisation via une équation d'Euler-Lagrange généralisée. On prouve enfin que les solutions de l'équation de Schrödinger peuvent s'obtenir comme solution d'un problème variationnel non différentiable, étendant ainsi le principe de moindre action de Hamilton au cadre de la mécanique quantique. On discute enfin la connexion entre ce travail et la théorie de la relativité d'échelle développée par Nottale, et qui suppose une structure fractale de l'espace-temps.
First evidence for heritable variation in cooperative breeding behaviour
Anne Charmantier; Amber J. Keyser; Daniel E. L. Promislow
2007-01-01
Understanding the evolution of complex social behaviours, such as cooperative breeding, is a fundamental problem in evolutionary biology, which has attracted much theoretical and empirical interest. Variation within and between species in the frequency of helping behaviour has been typically associated with variation in direct costs and benefits due to ecological constraints, or with indirect fitness payoffs (i.e. kin selection).
Genetic variation in the cysteine biosynthesis pathway causes sensitivity to
Fay, Justin
into genetic variation underlying sensitivity to pharmacological compounds, we show by chemical complementationGenetic variation in the cysteine biosynthesis pathway causes sensitivity to pharmacological for review August 29, 2007) Complex traits are the product of multiple genes with effects that depend on both
Human olfaction: from genomic variation to phenotypic diversity
Yehudit Hasin-Brumshtein; Doron Lancet; Tsviya Olender
2009-01-01
The sense of smell is a complex molecular device, encompassing several hundred olfactory receptor proteins (ORs). These receptors, encoded by the largest human gene superfamily, integrate odorant signals into an accurate 'odor image' in the brain. Widespread phe- notypic diversity in human olfaction is, in part, attribu- table to prevalent genetic variation in OR genes, owing to copy number variation,
A model for monitoring of Hsp90-buffered genetic variations
Liudmyla Kozeko
2010-01-01
Genetic material of terrestrial organisms can be considerably injured by cosmic rays and UV-radiation in the space environment. Organisms onboard are also exposed to the entire complex of negative physical factors which can generate genetic variations and affect morphogenesis. However, species phenotypes must be robust to genetic variation, requiring \\
... Ephelides (freckles) LAMB syndrome – Lentigines, Atrial Myxoma, and Blue nevi What causes Carney complex? Carney complex is ... melanotic schwannoma, meaning tumors that grow on nerves Blue nevi, which are blue-black moles Osteochondromyxoma (bone ...
Wolfgang Fikentscher
1998-01-01
This paper is divided into four parts. The first section (I.) consists of definitions which center on the concept of complexity. As a minimum, the terms, system, complexity, and adaptation as used in this paper need an explanation. The second section (II.) is a sketch of cultural complexity in the real world. I will use Pueblo tribal laws and other
Bleiziffer, Patrick; Krug, Marcel; Görling, Andreas
2015-06-28
A self-consistent Kohn-Sham method based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem, employing the frequency-dependent exact exchange kernel fx is presented. The resulting SC-exact-exchange-only (EXX)-ACFD method leads to even more accurate correlation potentials than those obtained within the direct random phase approximation (dRPA). In contrast to dRPA methods, not only the Coulomb kernel but also the exact exchange kernel fx is taken into account in the EXX-ACFD correlation which results in a method that, unlike dRPA methods, is free of self-correlations, i.e., a method that treats exactly all one-electron systems, like, e.g., the hydrogen atom. The self-consistent evaluation of EXX-ACFD total energies improves the accuracy compared to EXX-ACFD total energies evaluated non-self-consistently with EXX or dRPA orbitals and eigenvalues. Reaction energies of a set of small molecules, for which highly accurate experimental reference data are available, are calculated and compared to quantum chemistry methods like Møller-Plesset perturbation theory of second order (MP2) or coupled cluster methods [CCSD, coupled cluster singles, doubles, and perturbative triples (CCSD(T))]. Moreover, we compare our methods to other ACFD variants like dRPA combined with perturbative corrections such as the second order screened exchange corrections or a renormalized singles correction. Similarly, the performance of our EXX-ACFD methods is investigated for the non-covalently bonded dimers of the S22 reference set and for potential energy curves of noble gas, water, and benzene dimers. The computational effort of the SC-EXX-ACFD method exhibits the same scaling of N(5) with respect to the system size N as the non-self-consistent evaluation of only the EXX-ACFD correlation energy; however, the prefactor increases significantly. Reaction energies from the SC-EXX-ACFD method deviate quite little from EXX-ACFD energies obtained non-self-consistently with dRPA orbitals and eigenvalues, and the deviation reduces even further if the Coulomb kernel is scaled by a factor of 0.75 in the dRPA to reduce self-correlations in the dRPA correlation potential. For larger systems, such a non-self-consistent EXX-ACFD method is a competitive alternative to high-level wave-function-based methods, yielding higher accuracy than MP2 and CCSD methods while exhibiting a better scaling of the computational effort than CCSD or CCSD(T) methods. Moreover, EXX-ACFD methods were shown to be applicable in situation characterized by static correlation. PMID:26133411
Analysis of biomarkers for complex human diseases
Ansari, Morad
2009-01-01
The aims of this study were to analyse known and potential biomarkers of common and genetically complex human disorders and to identify genetic and environmental variation associated with plasma biomarker concentrations. Two groups of protein...
NASA Astrophysics Data System (ADS)
Mouhri, A.; Motelay, A.; Hanin, G.; Massei, N.; Fournier, M.; Dupont, J. P.; Laignel, B.
2009-04-01
In Upper Normandy, where drinking water supply comes from karst aquifers, rainfall events may involve turbid runoffs. These events induce sanitary crises and shutdowns of the water supply. The springs of Fontaine-Sous-Préaux provide 60% of Rouen's population (400,000) (France). These springs are highly vulnerable and their exploitation is confronted with the recurrence of turbid events, which can reach up to 150 NTU during highly rain events. The turbidity observed at karst springs is a complex signal composed by two parts of different origins: a first part coming from the direct transfer of particles from the surface following runoff events, and a second part involving the resuspension of materials previously deposited within karst conduits. The disctinction between those two part has always been very challenging. In this study, taking the example of a karst spring in Upper Normandy (Fontaine Sous Préaux spring), we attempted to refine a turbidigraph decomposition method based on the comparison between electrical conductivity (EC) and turbidity (T) using separated modelled hysteresis curves. In a first step, the EC and T breakthrough curves are modelled using an appropriate number of sub-peaks. Second, local EC-T hysteresis curves are builded up in order to characterize the time-varying changes of the dissolved/particulate transports relationships and to assess the respective contribution of the direct transfer and resuspended parts of turbidity throughout complex floods. Associated to cross-correlation analyses of the EC and T sub-peaks separated, the method allowed identification of the (potentially changing) lag time between EC and T. The results obtained highlighted the pre-eminence of resuspension phenomena at the spring for all floods studied. Nevertheless, four different types of hysteresis curves could be distinguished: i) wide clockwise hysteresis expressing the pre-eminence of resuspension accompanied by pressure pulse transfer phenomena; ii) wide clockwise hysteresis expressing the pre-eminence of resuspension of sediments arriving simultaneously with surface waters; iii) a thin hystérésis equivalent to an almost linear relationship between EC and T, corresponding to a simultaneous transfer of surface water and particles, iv) a thin and curved counter-clockwise hysteresis representing a direct transfer of particles and water from the surface characterizing a deficit of available sedimentary stock. Keywords : transport processes, hysteresis, resuspension, direct transfer, deposition.
Medically Complex Home Care and Caregiver Strain
ERIC Educational Resources Information Center
Moorman, Sara M.; Macdonald, Cameron
2013-01-01
Purpose of the study: To examine (a) whether the content of caregiving tasks (i.e., nursing vs. personal care) contributes to variation in caregivers' strain and (b) whether the level of complexity of nursing tasks contributes to variation in strain among caregivers providing help with such tasks. Design and methods: The data came from the Cash…
Epistasis correlates to genomic complexity
Rafael Sanjuán; Santiago F. Elena
2006-01-01
Whether systematic genetic interactions (epistasis) occur at the genomic scale remains a challenging topic in evolutionary biology. Epistasis should make a significant contribution to variation in complex traits and influence the evolution of genetic systems as sex, diploidy, dominance, or the contamination of genomes with deleterious mutations. We have collected data from widely different organisms and quantified epistasis in a
Narrowband angle modulations in induction motor complex current vectors
Zhi Gao; R. S. Colby; L. Turner; B. Leprettre
2009-01-01
Periodically time-varying loads such as reciprocating compressors produce torque and speed variations in grid-connected induction motors that are used to drive them. In each compression cycle, the torque and speed variations manifest themselves through periodic pulsations in induction motor's complex current vectors. Based on the concept of narrowband angle modulations, this paper analyzes the complex current vector's behavior in a
Population Structure of the North American Cranberry Fruit Rot Complex
Technology Transfer Automated Retrieval System (TEKTRAN)
Cranberry fruit rot is caused by a complex of pathogenic fungi. Variation in the populations within this complex from region to region could delay identification of the causal agents(s) and complicate management strategies. Our objective was to assess genetic variation within the four major fruit ro...
Structural variations in anorthites
W. F. Mfiller; H. R. Wenk; G. Thomas
1972-01-01
Variations of structure and optical properties in anorthites (An 93–97%) of different origin are analyzed with the petrographic microscope, U-stage methods, X-ray single crystal analysis and high voltage electron microscopy. No significant variation has been found in the orientation of the indicatrix and of the lattice constants. But c-type reflections (h + k even, ? odd) are strong and sharp
Margot Scholte
2010-01-01
Samenvatting Ik ben al enige tijd gefascineerd door ‘complexe oplossingen’. Complexe oplossingen zijn oplossingen die qua complexiteit\\u000a niet in verhouding staan tot het ervaren probleem. Denk aan de paarse krokodil: je ziet je verloren opblaasbeest achter glas,\\u000a maar je mag hem niet meenemen, voordat je aan alle procedures hebt voldaan.
NASA Astrophysics Data System (ADS)
Battiston, Stefano; Caldarelli, Guido; Georg, Co-Pierre; May, Robert; Stiglitz, Joseph
2013-03-01
The intrinsic complexity of the financial derivatives market has emerged as both an incentive to engage in it, and a key source of its inherent instability. Regulators now faced with the challenge of taming this beast may find inspiration in the budding science of complex systems.
ERIC Educational Resources Information Center
Glanville, Ranulph
2007-01-01
This article considers the nature of complexity and design, as well as relationships between the two, and suggests that design may have much potential as an approach to improving human performance in situations seen as complex. It is developed against two backgrounds. The first is a world view that derives from second order cybernetics and radical…
Sensor placement strategy for fixture variation diagnosis of compliant sheet metal assembly process
Sun Jin; Kuigang Yu; Xinmin Lai; Yinhua Liu
2009-01-01
Purpose – The purpose of this paper is to focus on optimal sensor placement for the fixture variation diagnosis of compliant sheet metal assembly process. Fixture variations are the main sources for complex automotive body dimensional failures. An effective measurement strategy can help exactly and timely diagnose these fixture variations. Research on sensor placement strategy of compliant sheet metal assembly
Paris-Sud XI, Université de
The complex permeability variation measurements at microwave frequencies of a magnetostrictiveIEEE TRANSACTIONS ON MAGNETICS, VOL. 43, NO. 6, JUNE 2007 2651 Driven-Voltage Permeability Variation Measurements of Bilayered Magnetostrictive/Piezoelectric Materials &for Tunable Microwave
Variation ontology: annotator guide
2014-01-01
Background Systematic representation of information related to genetic and non-genetic variations is required to allow large scale studies, data mining and data integration, and to make it possible to reveal novel relationships between genotype and phenotype. Although lots of variation data is available it is often difficult to use due to lack of systematics. Results A novel ontology, Variation Ontology (VariO http://variationontology.org), was developed for annotation of effects, consequences and mechanisms of variations. In this article instructions are provided on how VariO annotations are made. The major levels for description are the three molecules, namely DNA, RNA and protein. They are further divided to four major sublevels: variation type, function, structure, and property, and further up to eight sublevels. VariO annotation summarizes existing knowledge about a variation and its effects and formalizes it so that computational analyses are efficient. The annotations should be made on as many levels as possible. VariO annotations are made in reference to normal states, which vary for each data item including e.g. reference sequences, wild type properties, and activities. Conclusions Detailed instructions together with examples are provided to indicate how VariO can be used for annotation of variations and their effects. A dedicated tool has been developed for annotation and will be further developed to cover also evidence for the annotations. VariO is suitable for annotation of data in many types of databases. As several different kinds of databases are in a process of adapting VariO annotations it is important to have guidelines to guarantee consistent annotation. PMID:24533660
Measuring temporal gravitational variations using SLR data
NASA Technical Reports Server (NTRS)
Nerem, Robert S.
1994-01-01
Redistribution of mass within the Earth system changes its gravitational field, and thus changes the orbits of Earth satellites. While these variations are small, Satellite Laser Ranging (SLR) to precise geodetic satellites such as Lageos-1, Lageos-2, Starlette, Ajisai, and Stella can detect these changes at their broadest spatial scales (currently greater than 10,000 km). The satellites sense only the combined variation in the solid Earth-ocean-atmosphere system; however, modeling of these different components has led to detection of long-wavelength variations in the distribution of atmospheric mass, changes in the amplitudes of atmospheric and oceanic tides, and secular variations caused by the post-glacial adjustment of the Earth's crust. The unambiguous detection of ocean mass redistribution by SLR has not been verified due largely to inadequacies in current ocean models. Great progress has been made in recent years in the determination of luni-solar tides and the braking they induce in the Earth-Moon-Sun system (leading to secular changes in the length-to-day and lengthening of the lunar orbit period) using a wide variety of techniques including ocean tide gauges, satellite altimetry, Lunar Laser Ranging, and near-Earth satellite orbit modeling. Recent investigations of the more complex and less predictable non-tidal temporal variations in the gravity field have generally proceeded along two fronts: 1) the determination of long-wavelength variations in the gravity field through the changing perturbations seen in the orbits of near-Earth satellites, and 2) the prediction of temporal variations in gravity using geophysical, atmospheric, and oceanic models. A convergence of these efforts is sought to better understand the source of observed changes in the Earth's gravitational field.
A variational principle of hydromechanics
S. Drobot; A. Rybarski
1958-01-01
1. The purpose of this paper is to reveal the part played in variational principles of hydromechanics by a certain group of infinitesimal transformations of the fields of density and velocity. This group, called here the hydromechanical variation and originating from some elementary requirement concerning variation of matter, seems to be essential in variational principles of hydromechanic,4, iaot only in
Variations in sending Morse code
Charles Windle
1955-01-01
Studied the deviations from the theoretical Morse code sequence (dot: dash: space ratios) in inexperienced and experienced Ss. Found evidence of variations due to different contextual occurrences of the signals (heterotaxic variation). Confirmed the finding that variations due to repetition of a signal decrease with expertness but did not confirm that heterotaxic variation increases with expertness. 16 references.
Reduced complexity Retinex algorithm via the variational approachq
Elad, Michael
- mary goal is to decompose a given image S into two different images, the reflectance image R of the reflectance image, and the fact that this image, being the process output, should be visually plea
Complex chemical variation and the taxonomy of Hymenoxys scaposa (Compositae)
Peter Seeligmann; R. E. Alston
1967-01-01
Over 30 flavonoids, some of which are unusual types of flavonols and flavones, occur in the taxaHymenoxys scaposa, H. acaulis, andH. ivesiana. The patterns of distributions of these compounds are correlated more closely with an east-west geographical range than with\\u000a the formally recognized identity of the plant, as deduced from its morphology. The exact significance of these observations\\u000a is not
Variational Information Theory
Penny, Will
is measured in bits. #12;Variational Inference Will Penny Information Theory Information Entropy Kullback Approaches Summary References Prefix Codes No code-word is a prefix of another. Use number of bits b Relative Entropy Average length of code word B(x) = i p(xi )b(xi ) = i p(xi ) log 1 q(xi ) = 2.65bits
Algebra Lab: Inverse Variation
NSDL National Science Digital Library
2012-01-01
This lesson from Algebra Lab demonstrates "how to write equations of quantities which vary inversely." The lesson includes an example of a graph of this type of equation, and several example problems. This supporting material would be best used following some in-class instruction explaining how to solve inverse variation equations.
Lagrangian mechanics and variational integrators on two-spheres
Taeyoung Lee; Melvin Leok; N. Harris McClamroch
2009-01-01
Euler-Lagrange equations and variational integrators are developed for\\u000aLagrangian mechanical systems evolving on a product of two-spheres. The\\u000ageometric structure of a product of two-spheres is carefully considered in\\u000aorder to obtain global equations of motion. Both continuous equations of motion\\u000aand variational integrators completely avoid the singularities and complexities\\u000aintroduced by local parameterizations or explicit constraints. We derive global
Complex human chromosomal and genomic rearrangements
Zhang, Feng; Carvalho, Claudia M.B.; Lupski, James R.
2015-01-01
Copy number variation (CNV) is a major source of genetic variation among humans. In addition to existing as benign polymorphisms, CNVs can also convey clinical phenotypes, including genomic disorders, sporadic diseases and complex human traits. CNV results from genomic rearrangements that can represent simple deletion or duplication of a genomic segment, or be more complex. Complex chromosomal rearrangements (CCRs) have been known for some time but their mechanisms have remained elusive. Recent technology advances and high-resolution human genome analyses have revealed that complex genomic rearrangements can account for a large fraction of non-recurrent rearrangements at a given locus. Various mechanisms, most of which are DNA-replication-based, for example fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR), have been proposed for generating such complex genomic rearrangements and are probably responsible for CCR. PMID:19560228
Density Functional Theory: Toward Better Understanding of Complex Systems in Chemistry and Physics
NASA Astrophysics Data System (ADS)
Luo, Sijie
Density functional theory (DFT) has become the workhorse of computational chemistry and physics in the past two decades. The continuous developments of high-quality exchange-correlation functionals (xcFs) have enabled chemists and physicists to study complex as well as large systems with high accuracy at low-to-moderate computational expense. Although a wide range of normal systems have been well understood by DFT, there are still complex ones presenting particular challenges where most commonly used xcFs have failed due to the complex nature of the system, lack of or difficulty to obtain reliable reference data, or the practical limitations of the Kohn-Sham DFT (KS-DFT) formulation. This thesis presents studies with various exchange-correlation functionals on a wide selection of complex systems in chemistry and solid-state physics, including large organic molecules, adsorption on metallic surfaces, transition states, as well as transition metal atoms, ions, and compounds, to (i) draw conclusions upon recommendations of xcFs for important practical applications; (ii) understand the root of errors to help design better xcFs or propose new theoretical schemes of DFT; (iii) explore the utility of noncollinear spin orbitals in KS-DFT for better description of multi-reference systems.
Epistasis: too often neglected in complex trait studies?
Chris S. Haley; Örjan Carlborg
2004-01-01
Interactions among loci or between genes and environmental factors make a substantial contribution to variation in complex traits such as disease susceptibility. Nonetheless, many studies that attempt to identify the genetic basis of complex traits ignore the possibility that loci interact. We argue that epistasis should be accounted for in complex trait studies; we critically assess current study designs for
Jason A. Johnson; Thomas C. Harrington; C. J. B. Engelbrecht
Ceratocystis fimbriata is a widely distributed, plant pathogenic fungus that causes wilts and cankers on many woody hosts. Earlier phylogenetic analyses of DNA sequences revealed three geographic clades within the C. fimbriata complex that are centered respectively in North America, Latin America and Asia. This study looked for cryptic species within the North American clade. The internal transcribed spacer regions
ERIC Educational Resources Information Center
Sumara, Dennis J.
2000-01-01
Discusses what Complexity Theory (presented as a rubric that collects theoretical understandings from a number of domains such as ecology, biology, neurology, and education) suggests about mind, selfhood, intelligence, and practices of reading, and the import of these reconceptualizations to reader-response researchers. Concludes that developing…
Jean-paul Allouche; Michael Baake; Julien Cassaigne; David Damanik
2003-01-01
We study the palindrome complexity of infinite sequences on finite alphabets, i.e., the number of palindromic factors (blocks) of given length occurring in a given se- quence. We survey the known results and obtain new results for some sequences, in particular for Rote sequences and for fixed points of primitive morphisms of constant length belonging to \\
Deming's Quality: Our Last but Best Hope.
ERIC Educational Resources Information Center
Schenkat, Randy
1993-01-01
If educators endorse Alfie Kohn's surface message about Total Quality Management, they may miss opportunity to professionalize education. Deming's system of profound knowledge (interaction of theories of systems, knowledge, psychology, and variation) is a model for educated people grappling with life's complexities. Moreover, gaining community…
Genetic Variation and Atherosclerosis
Biros, Erik; Karan, Mirko; Golledge, Jonathan
2008-01-01
A family history of atherosclerosis is independently associated with an increased incidence of cardiovascular events. The genetic factors underlying the importance of inheritance in atherosclerosis are starting to be understood. Genetic variation, such as mutations or common polymorphisms has been shown to be involved in modulation of a range of risk factors, such as plasma lipoprotein levels, inflammation and vascular calcification. This review presents examples of present studies of the role of genetic polymorphism in atherosclerosis. PMID:19424482
NSDL National Science Digital Library
The Concord Consortium
2011-12-11
Students discover that variation in plants allows some varieties to survive in near-drought conditions. Next, students learn that different types of rabbits prefer to eat different varieties of plants. Students make the connection between rainfall amount and the rabbit population?s ability to survive by thinking first about rainfall and plants, then about plants and rabbits. Students discover that when certain plants cannot grow and reproduce, the rabbits that eat those plants will not have enough food to survive.
Variation, Repetition, And Choice
Abreu-Rodrigues, Josele; Lattal, Kennon A; dos Santos, Cristiano V; Matos, Ricardo A
2005-01-01
Experiment 1 investigated the controlling properties of variability contingencies on choice between repeated and variable responding. Pigeons were exposed to concurrent-chains schedules with two alternatives. In the REPEAT alternative, reinforcers in the terminal link depended on a single sequence of four responses. In the VARY alternative, a response sequence in the terminal link was reinforced only if it differed from the n previous sequences (lag criterion). The REPEAT contingency generated low, constant levels of sequence variation whereas the VARY contingency produced levels of sequence variation that increased with the lag criterion. Preference for the REPEAT alternative tended to increase directly with the degree of variation required for reinforcement. Experiment 2 examined the potential confounding effects in Experiment 1 of immediacy of reinforcement by yoking the interreinforcer intervals in the REPEAT alternative to those in the VARY alternative. Again, preference for REPEAT was a function of the lag criterion. Choice between varying and repeating behavior is discussed with respect to obtained behavioral variability, probability of reinforcement, delay of reinforcement, and switching within a sequence. PMID:15828592
Meiosis-Driven Genome Variation in Plants
Cai, Xiwen; Xu, Steven S
2007-01-01
Meiosis includes two successive divisions of the nucleus with one round of DNA replication and leads to the formation of gametes with half of the chromosomes of the mother cell during sexual reproduction. It provides a cytological basis for gametogenesis and nheritance in eukaryotes. Meiotic cell division is a complex and dynamic process that involves a number of molecular and cellular events, such as DNA and chromosome replication, chromosome pairing, synapsis and recombination, chromosome segregation, and cytokinesis. Meiosis maintains genome stability and integrity over sexual life cycles. On the other hand, meiosis generates genome variations in several ways. Variant meiotic recombination resulting from specific genome structures induces deletions, duplications, and other rearrangements within the genic and non-genic genomic regions and has been considered a major driving force for gene and genome evolution in nature. Meiotic abnormalities in chromosome segregation lead to chromosomally imbalanced gametes and aneuploidy. Meiotic restitution due to failure of the first or second meiotic division gives rise to unreduced gametes, which triggers polyploidization and genome expansion. This paper reviews research regarding meiosis-driven genome variation, including deletion and duplication of genomic regions, aneuploidy, and polyploidization, and discusses the effect of related meiotic events on genome variation and evolution in plants. Knowledge of various meiosis-driven genome variations provides insight into genome evolution and genetic variability in plants and facilitates plant genome research. PMID:18645601
COMPLEX NUMBERS 1. Definition of complex numbers
La Rosa, Andres H.
COMPLEX NUMBERS 1. Definition of complex numbers Complex conjugate, Magnitude Operations Addition, multiplication, reciprocal number 2. Representation of complex numbers in polar complex variable #12;2.2.A Complex numbers #12;#12;3 #12;4 #12;In short, Anytime we write Ae j we
Comprehensive variation discovery in single human genomes
Weisenfeld, Neil I.; Yin, Shuangye; Sharpe, Ted; Lau, Bayo; Hegarty, Ryan; Holmes, Laurie; Sogoloff, Brian; Tabbaa, Diana; Williams, Louise; Russ, Carsten; Nusbaum, Chad; Lander, Eric S.; MacCallum, Iain; Jaffe, David B.
2014-01-01
Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing individual genomes and comparing reads to a reference. Existing methods do an excellent job of detecting variants in approximately 90% of the human genome, however calling variants in the remaining 10% of the genome (largely low-complexity sequence and segmental duplications) is challenging. To improve variant calling, we developed a new algorithm, DISCOVAR, and examined its performance on improved, low-cost sequence data. Using a newly created reference set of variants from finished sequence of 103 randomly chosen Fosmids, we find that some standard variant call sets miss up to 25% of variants. We show that the combination of new methods and improved data increases sensitivity several-fold, with the greatest impact in challenging regions of the human genome. PMID:25326702
Comprehensive variation discovery in single human genomes.
Weisenfeld, Neil I; Yin, Shuangye; Sharpe, Ted; Lau, Bayo; Hegarty, Ryan; Holmes, Laurie; Sogoloff, Brian; Tabbaa, Diana; Williams, Louise; Russ, Carsten; Nusbaum, Chad; Lander, Eric S; MacCallum, Iain; Jaffe, David B
2014-12-01
Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing individual genomes and comparing reads to a reference. Existing methods do an excellent job of detecting variants in approximately 90% of the human genome; however, calling variants in the remaining 10% of the genome (largely low-complexity sequence and segmental duplications) is challenging. To improve variant calling, we developed a new algorithm, DISCOVAR, and examined its performance on improved, low-cost sequence data. Using a newly created reference set of variants from the finished sequence of 103 randomly chosen fosmids, we find that some standard variant call sets miss up to 25% of variants. We show that the combination of new methods and improved data increases sensitivity by several fold, with the greatest impact in challenging regions of the human genome. PMID:25326702
Chassin, David P.; Posse, Christian; Malard, Joel M.
2004-08-01
Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today’s most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically-based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This paper explores the state of the art in the use physical analogs for understanding the behavior of some econophysical systems and to deriving stable and robust control strategies for them. In particular we review and discussion applications of some analytic methods based on the thermodynamic metaphor according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood.
NASA Astrophysics Data System (ADS)
Borchert, M.; Wilke, M.; Schmidt, C.; Kvashnina, K.
2009-12-01
Experimental data show that fluid-melt partitioning of Sr is controlled by the bulk chemistry of the system. For chloridic fluids, there is a sharp increase in the Sr partition coefficient with the alumina saturation index (ASI) to a maximum of 0.3 at an ASI of 1.05. Because fluid-melt partitioning of a given element depends on its complexation in the fluid and its incorporation in the melt, these data imply a change in the Sr speciation at least one of the two phases. For silicate melts, Kohn et al. (1990) found only small changes in the first coordination shell of Sr in a suite of melts with various degrees of polymerization, and argued that incorporation of Sr in the melt should not play a major role in controlling Sr partitioning. For the aqueous fluid, Bai and Koster van Groos (1999) suggested formation of SrCl2 complexes based on the correlation between partition coefficient and Cl concentration in the fluid after quenching. Here, we studied the complexation of Sr in peraluminous or peralkaline melt dissolved in aqueous fluids in-situ at elevated PT conditions using hydrothermal diamond-anvil cells (HDAC) and X-ray absorption near edge structure (XANES) spectroscopy. The starting materials were peraluminous or peralkaline glass and H2O or a chloridic solution. The glass was doped with high concentrations of 5000 or 10000 ppm Sr to facilitate in-situ analyses of the aqueous fluids. We used bulk compositions of 10 to 15 wt.% glass to ensure that the melt was completely dissolved in the fluid at high PT conditions. For qualitative evaluation, we analyzed the starting glasses and various crystalline compounds and standard solutions. The experiments were performed at beamline ID26 at ESRF (Grenoble, France) using a high resolution emission spectrometer. We applied different monochromator crystals, Si311 for high resolution and Si111 for low resolution measurements. An overall resolution of 1.98 eV (Si311) and 3 eV (Si111) was achieved using a beamsize of 120x400 ?m, Si(777) analyzer crystals and a Rowland circle diameter of 1 m. In contrast to the study by Kohn et al. (1990), XANES spectra of peraluminous and peralkaline starting glasses show distinct differences in pre-edge, main edge and position of the first EXAFS maximum. The latter is directly correlated to the distance of Sr and its nearest neighbor. The spectra of SrCl2 and Sr(OH)2 standard solutions at various PT conditions indicate very small temperature-dependent changes of the complexation. The XANES spectra of solutions after dissolution of peraluminous or peralkaline melt in chloridic fluids vary significantly from each other. The latter are similar to the one of the peralkaline starting glass, while this is not the case for solutions with peraluminous melt. The spectra of water with dissolved peralkaline melt distinctly differ from those using chloridic fluids. In conclusion, the first direct information on Sr complexation at elevated PT condition indicates significant speciation changes in both fluid and melt. Bai and Koster van Groos (1999), GCA 63, 1117-1131. Kohn et. Al. (1990), CMP 105, 359-368.
5, 92079248, 2005 Interannual variations
Paris-Sud XI, Université de
ACPD 5, 92079248, 2005 Interannual variations of total ozone and temperature W. Steinbrecht et al and Physics Discussions Interannual variation patterns of total ozone and temperature in observations a Creative Commons License. 9207 #12;ACPD 5, 92079248, 2005 Interannual variations of total ozone
ERIC Educational Resources Information Center
Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse
2014-01-01
Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…
Hermann Schulz
1998-11-12
Well known from the sixties, the pressure of e.g. massless phi-four theory may be written as a series of 2PI-diagrams (skeletons) with the lines fully dressed. Varying the self-energy Pi in this expression, it turns into a functional U[Y] having a maximum in function space at Y=Pi. There is also the Feynman-Jensen thermal variational principle V[S], a potentially non-perturbative tool. Here actions S are varied. It is shown, through a few formal but exact steps, that the functional U is covered by V. The corresponding special subset of trial actions is made explicit.
Epigenetic variation in plant responses to defence hormones
Latzel, Vít; Zhang, Yuanye; Karlsson Moritz, Kim; Fischer, Markus; Bossdorf, Oliver
2012-01-01
Background and Aims There is currently much speculation about the role of epigenetic variation as a determinant of heritable variation in ecologically important plant traits. However, we still know very little about the phenotypic consequences of epigenetic variation, in particular with regard to more complex traits related to biotic interactions. Methods Here, a test was carried out to determine whether variation in DNA methylation alone can cause heritable variation in plant growth responses to jasmonic acid and salicylic acid, two key hormones involved in induction of plant defences against herbivores and pathogens. In order to be able to ascribe phenotypic differences to epigenetic variation, the hormone responses were studied of epigenetic recombinant inbred lines (epiRILs) of Arabidopsis thaliana – lines that are highly variable at the level of DNA methylation but nearly identical at the level of DNA sequence. Key Results Significant heritable variation was found among epiRILs both in the means of phenotypic traits, including growth rate, and in the degree to which these responded to treatment with jasmonic acid and salicylic acid. Moreover, there was a positive epigenetic correlation between the responses of different epiRILs to the two hormones, suggesting that plant responses to herbivore and pathogen attack may have a similar molecular epigenetic basis. Conclusions This study demonstrates that epigenetic variation alone can cause heritable variation in, and thus potentially microevolution of, plant responses to defence hormones. This suggests that part of the variation of plant defences observed in natural populations may be due to underlying epigenetic, rather than entirely genetic, variation. PMID:22543179
Wolfdieter A. Schenk; Thomas Gutmann
1998-01-01
The synthesis and reactions of bimetallic Zr(II)–Mo(0) complexes with bridging C5H4PPh2 ligands (henceforth abbreviated as Cp?) are described. Reaction of Cp2?ZrCl2 (1) with n-butyllithium in THF produces a metastable material tentatively formulated as Cp2?Zr·2 LiCl·4 THF (2). Diphenyldisulfide instantaneously converts 2 into the Zr(IV) dithiolate Cp2?Zr(SPh)2 (3). When 2 is treated with [Mo(CO)4(norbornadiene)], an unstable intermediate is formed which can
Harmonically excited orbital variations
Morgan, T.
1985-08-06
Rephrasing the equations of motion for orbital maneuvers in terms of Lagrangian generalized coordinates instead of Newtonian rectangular cartesian coordinates can make certain harmonic terms in the orbital angular momentum vector more readily apparent. In this formulation the equations of motion adopt the form of a damped harmonic oscillator when torques are applied to the orbit in a variationally prescribed manner. The frequencies of the oscillator equation are in some ways unexpected but can nonetheless be exploited through resonant forcing functions to achieve large secular variations in the orbital elements. Two cases are discussed using a circular orbit as the control case: (1) large changes in orbital inclination achieved by harmonic excitation rather than one impulsive velocity change, and (2) periodic and secular changes to the longitude of the ascending node using both stable and unstable excitation strategies. The implications of these equations are also discussed for both artificial satellites and natural satellites. For the former, two utilitarian orbits are suggested, each exploiting a form of harmonic excitation. 5 refs.
Conservation genetics of the species complex Cochlearia officinalis L. s.l. in Britain
Gill, Estelle
2008-01-01
The genus Cochlearia is a taxonomically complex genus with a circumpolar distribution. In common with many other post-glacial colonisers it exhibits complex patterns of morphological and ecological variation. The genus ...
3. Complex Numbers 17 3 Complex Numbers
Givental, Alexander
3. Complex Numbers 17 3 Complex Numbers Law and Order Life is unfair: The quadratic equation x2 - 1 solutions to the equation. This is how complex numbers could have been invented. More formally, complex numbers a and b are called respectively the real part and imagi- nary part of the complex number z
CLIMATE VARIATIONS, CLIMATE CHANGE, AND WATER RESOUCES ENGINEERING
Technology Transfer Automated Retrieval System (TEKTRAN)
Complex water resources systems are developed to ensure a continued safe and reliable water supply for our society. Climate variability, one among several factors, can stress these systems and lead to water shortages and related problems. While many aspects of climate variations and their impact o...
Variational Structure of Inverse Problems in Wave Propagation and Vibration
Variational Structure of Inverse Problems in Wave Propagation and Vibration James G. Berryman in wave propagation (traveltime tomography) and two examples in vibration (the plucked string and free.'' For vibrating systems, the apparently very complex behavior of an excited string, drumhead, or the Earth can
Computing reactive front speeds in random flows by variational principle
NASA Astrophysics Data System (ADS)
Nolen, James; Xin, Jack
2008-12-01
We study reactive front speeds in randomly perturbed cellular flows using a variational representation for the front speed. We develop this representation into a computational tool for computing the front speeds without resorting to closure approximations. We demonstrate that the front speeds depend on flow statistics and topologies in a complex and dramatic manner.
Genome-Wide Associations of Gene Expression Variation in Humans
Barbara E. Stranger; Matthew S. Forrest; Andrew G. Clark; Mark J. Minichiello; Samuel Deutsch; Robert Lyle; Sarah Hunt; Brenda Kahl; Stylianos E. Antonarakis; Simon Tavaré; Panagiotis Deloukas; Emmanouil T. Dermitzakis
2005-01-01
The exploration of quantitative variation in human populations has become one of the major priorities for medical genetics. The successful identification of variants that contribute to complex traits is highly dependent on reliable assays and genetic maps. We have performed a genome-wide quantitative trait analysis of 630 genes in 60 unrelated Utah residents with ancestry from Northern and Western Europe
Analysis of Haplotype Structure in the Bovine Major Histocompatibility Complex
Fritz, Krista L.
2011-02-22
The goal of this project was to identify and characterize polymorphic markers spanning regions of the bovine major histocompatibility complex (BoLA) to analyze patterns of genetic variation and haplotype structure across diverse cattle breeds...
What constrains directional selection on complex traits in the wild?
Mojica, Julius Penalba
2011-08-31
The fact that abundant genetic variation persists within populations despite strong directional selection on complex traits is one of the unresolved conundrums in evolutionary biology. In this dissertation, I employed a ...
Visualizing patterns of craniofacial shape variation in Homo sapiens.
Zollikofer, Christoph P E; Ponce De León, Marcia S
2002-04-22
The geometric morphometric analysis of shape variation in complex biological structures such as the human skull poses a number of specific challenges: the registration of homologous morphologies, the treatment of bilateral symmetry, the graphical representation of form variability in three dimensions and the interpretation of the results in terms of differential growth processes. To visualize complex patterns of shape change, we propose an alternative to classical Cartesian deformation grids in the style of D'Arcy W. Thompson. Reference to the surface structures of the organism under investigation permits a comprehensive visual grasp of shape change and its tentative interpretation in terms of differential growth. The application of this method to the analysis of human craniofacial shape variation reveals distinct modes of growth and development of the neurocranial and viscerocranial regions of the skull. Our data further indicate that variations in the orientation of the viscerocranium relative to the neurocranium impinge on the shapes of the face and the cranial vault. PMID:11958711
The overdue promise of short tandem repeat variation for heritability.
Press, Maximilian O; Carlson, Keisha D; Queitsch, Christine
2014-11-01
Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype-phenotype maps. We review here the promise of STRs in contributing to complex trait heritability and highlight the challenges that STRs pose due to their repetitive nature. We argue that STR variants are more likely than single-nucleotide variants to have epistatic interactions, reiterate the need for targeted assays to genotype STRs accurately, and call for more appropriate statistical methods in detecting STR-phenotype associations. Lastly, we suggest that somatic STR variation within individuals may serve as a read-out of disease susceptibility, and is thus potentially a valuable covariate for future association studies. PMID:25182195
CCMR: New Iridium Complexes for the Dehydrogenation of Alkanes
NSDL National Science Digital Library
Wang, David
2004-08-17
To introduce small variations on the previously investigated iridium P-C-P pincer complexes. The variations include substitution of cyclohexyl groups for the tert-butyl and the iso-propyl groups found on the phosphines.Thus, synthesis of these new iridium P-C-P pincer complexes was performed with the aim of improved catalytic dehydrogenation activity as well as a better understand of the influence that ligand sterics and electronics have on the active species.
Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface
Chen, Duan; Chen, Zhan; Wei, Guo-Wei
2011-01-01
Proton transport plays an important role in biological energy transduction and sensory systems. Therefore it has attracted much attention in biological science and biomedical engineering in the past few decades. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins involving continuum, atomic and quantum descriptions, assisted with the evolution, formation and visualization of membrane channel surfaces. We describe proton dynamics quantum mechanically via a new density functional theory based on the Boltzmann statistics, while implicitly model numerous solvent molecules as a dielectric continuum to reduce the number of degrees of freedom. The density of all other ions in the solvent is assumed to obey the Boltzmann distribution in a dynamic manner. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic scale. A variational solute-solvent interface is designed to separate the explicit molecule and implicit solvent regions. We formulate a total free energy functional to put proton kinetic and potential energies, the free energy of all other ions, the polar and nonpolar energies of the whole system on an equal footing. The variational principle is employed to derive coupled governing equations for the proton transport system. Generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation and generalized Kohn-Sham equation are obtained from the present variational framework. The variational solvent-solute interface is generated and visualized to facilitate the multiscale discrete/continuum/quantum descriptions. Theoretical formulations for the proton density and conductance are constructed based on fundamental laws of physics. A number of mathematical algorithms, including the Dirichlet to Neumann mapping (DNM), matched interface and boundary (MIB) method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to validate the performance of the proposed proton transport model and demonstrate the efficiency of the proposed mathematical algorithms. The proton channel conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and confirms the proposed model. PMID:22328970
Holding the Words in Our Mouths: Responses to Dialect Variations in Oral Reading
ERIC Educational Resources Information Center
Van Duinen, Deborah Vriend; Wilson, Marilyn J.
2008-01-01
Deborah Vriend Van Duinen and Marilyn J. Wilson confront normalized notions of "correct" English. They offer suggestions for teaching about marginalized voices and introducing students to the complexities of English dialect variations. (Contains 1 figure.)
Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned
formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluat- ing a diversity in the coast horned lizard (PhrynosQuantifying ecological, morphological, and genetic variation to delimit species in the coast horned
A Model of Genetic Variation in Human Social Networks
Fowler, James H; Christakis, Nicholas A
2008-01-01
Social networks influence the evolution of cooperation and they exhibit strikingly systematic patterns across a wide range of human contexts. Both of these facts suggest that variation in the topological attributes of human social networks might have a genetic basis. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric social network attributes is unknown. Here we show that three of these attributes (in-degree, transitivity, and centrality) are heritable. We then develop a "mirror network" method to test extant network models and show that none accounts for observed genetic variation in human social networks. We propose an alternative "attract and introduce" model that generates significant heritability as well as other important network features, and we show that this model with two simple forms of heterogeneity is well suited to the modeling of real social networks in humans. These results suggest that natural selection ...
Stability of asynchronous variational integrators
NASA Astrophysics Data System (ADS)
Fong, William; Darve, Eric; Lew, Adrian
2008-09-01
The adoption of multiple time step integrators can provide substantial computational savings for mechanical systems with multiple time scales. However, the scope of these savings may be limited by the range of allowable time step choices. In this paper we analyze the linear stability of the fully asynchronous methods termed AVI, for asynchronous variational integrators. We perform a detailed analysis for the case of a one-dimensional particle moving under the action of a soft and a stiff quadratic potential, integrated with two time steps in rational ratios. In this case, we provide sufficient conditions for the stability of the method. These generalize to the fully asynchronous AVI case the results obtained for synchronous multiple time stepping schemes, such as r-RESPA, which show resonances when the larger time step is a multiple of the effective half-period of the stiff potential. Additionally, we numerically investigate the appearance of instabilities. Based on the experimental observations, we conjecture the existence of a dense set of unstable time steps when arbitrary rational ratios of time steps are considered. In this way, unstable schemes for arbitrarily small time steps can be obtained. However, the vast majority of these instabilities are extremely weak and do not present an obstacle to the use of these integrators. We then applied these results to analyze the stability of multiple time step integrators in the more complex mechanical systems arising in molecular dynamics and solid dynamics. We explained why strong resonances are ubiquitously found in the former, while rarely encountered in the latter. Finally, in this paper we introduce a formulation of AVI that highlights the symplectic nature of the algorithm, complementing those introduced earlier by other authors.
Variational multiscale models for charge transport.
Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin
2012-01-01
This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle for chemo-electro-fluid systems. A number of computational algorithms is developed to implement the proposed new variational multiscale models in an efficient manner. A set of ten protein molecules and a realistic ion channel, Gramicidin A, are employed to confirm the consistency and verify the capability. Extensive numerical experiment is designed to validate the proposed variational multiscale models. A good quantitative agreement between our model prediction and the experimental measurement of current-voltage curves is observed for the Gramicidin A channel transport. This paper also provides a brief review of the field. PMID:23172978
Abdul Rouf Samurah
2012-09-26
In this paper we will analyse ABJM theory in N=1 superspace formalism on complex spacetime. We will then analyse the BRST and anti-BRST symmetries for this theory. We will show that the sum of gauge fixing and ghost terms for this theory can be expressed as a combination of the total BRST or the total anti-BRST variations.
A transcriptional network associated with natural variation in Drosophila aggressive behavior
Alexis C Edwards; Julien F Ayroles; Eric A Stone; Mary Anna Carbone; Richard F Lyman; Trudy FC Mackay
2009-01-01
Background Aggressive behavior is an important component of fitness in most animals. Aggressive behavior is genetically complex, with\\u000a natural variation attributable to multiple segregating loci with allelic effects that are sensitive to the physical and social\\u000a environment. However, we know little about the genes and genetic networks affecting natural variation in aggressive behavior.\\u000a Populations of Drosophila melanogaster harbor quantitative genetic variation
Darwin on Variation and Heredity
Rasmus G. Winther
2000-01-01
Darwin’s ideas on variation, heredity, and development differ significantly from twentieth-century views. First, Darwin held\\u000a that environmental changes, acting either on the reproductive organs or the body, were necessary to generate variation. Second,\\u000a heredity was a developmental, not a transmissional, process; variation was a change in the developmental process of change.An\\u000a analysis of Darwin’s elaboration and modification of these two
Diurnal variation of cytokinin, auxin and abscisic acid levels in tobacco leaves
Marie Novakova ´; V aclav Motyka; Petre I. Dobrev; Alena Gaudinova; Radomira Vankova ´
2005-01-01
As many processes are regulated by both light and plant hormones, evaluation of diurnal variations of their levels may contribute to the elucidation of the complex network of light and hormone signal trans- duction pathways. Diurnal variation of cytokinin, auxin, and abscisic acid levels was tested in tobacco leaves (Nicotiana tabacum L. cv. Wisconsin 38) grown under a 16\\/8 h
Anatomic variations of the paranasal sinuses: CT examination for endoscopic sinus surgery
Halil Arslan; At?f Ayd?nl?o?lu; Mehmet Bozkurt; Erol Egeli
1999-01-01
Chronic rhinosinusitis endoscopic surgery requires an accurate evaluation of diseases and paranasal sinus anatomic variations. This study aims to show the main anatomical variations in the ostiomeatal complex and paranasal sinuses which are usually depicted by computed tomography (CT). CT scans obtained 2 mm thickness in axial and coronal plane from a series of 200 patients with chronic sinusitis were
Assembly Root Cause Analysis: A Way to Reduce Dimensional Variation in Assembled Products
Johan S. Carlson; Rikard Söderberg
2003-01-01
The objective of root cause analysis (RCA) is to make the trouble shooting dimensional error efforts in an assembly plant more efficient and successful by pinpointing the underlying reasons for variation. The result of eliminating or limiting these sources of variation is a real and long term process improvement. Complex products are manufactured in multileveled hierarchical assembly processes using positioning
Structural and functional impacts of copy number variations on the cattle genome
Technology Transfer Automated Retrieval System (TEKTRAN)
Although there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs), similar realizations for larger, more complex forms of genetic variation have just emerged. Several recent publications reveal that copy number variations (CNVs) are common an...
Propagation of genetic variation in gene regulatory networks
NASA Astrophysics Data System (ADS)
Plahte, Erik; Gjuvsland, Arne B.; Omholt, Stig W.
2013-08-01
A future quantitative genetics theory should link genetic variation to phenotypic variation in a causally cohesive way based on how genes actually work and interact. We provide a theoretical framework for predicting and understanding the manifestation of genetic variation in haploid and diploid regulatory networks with arbitrary feedback structures and intra-locus and inter-locus functional dependencies. Using results from network and graph theory, we define propagation functions describing how genetic variation in a locus is propagated through the network, and show how their derivatives are related to the network’s feedback structure. Similarly, feedback functions describe the effect of genotypic variation of a locus on itself, either directly or mediated by the network. A simple sign rule relates the sign of the derivative of the feedback function of any locus to the feedback loops involving that particular locus. We show that the sign of the phenotypically manifested interaction between alleles at a diploid locus is equal to the sign of the dominant feedback loop involving that particular locus, in accordance with recent results for a single locus system. Our results provide tools by which one can use observable equilibrium concentrations of gene products to disclose structural properties of the network architecture. Our work is a step towards a theory capable of explaining the pleiotropy and epistasis features of genetic variation in complex regulatory networks as functions of regulatory anatomy and functional location of the genetic variation.
Statistical Analysis of Variation in the Human Plasma Proteome
Corzett, Todd H.; Fodor, Imola K.; Choi, Megan W.; Walsworth, Vicki L.; Turteltaub, Kenneth W.; McCutchen-Maloney, Sandra L.; Chromy, Brett A.
2010-01-01
Quantifying the variation in the human plasma proteome is an essential prerequisite for disease-specific biomarker detection. We report here on the longitudinal and individual variation in human plasma characterized by two-dimensional difference gel electrophoresis (2-D DIGE) using plasma samples from eleven healthy subjects collected three times over a two week period. Fixed-effects modeling was used to remove dye and gel variability. Mixed-effects modeling was then used to quantitate the sources of proteomic variation. The subject-to-subject variation represented the largest variance component, while the time-within-subject variation was comparable to the experimental variation found in a previous technical variability study where onemore »human plasma sample was processed eight times in parallel and each was then analyzed by 2-D DIGE in triplicate. Here, 21 protein spots had larger than 50% CV, suggesting that these proteins may not be appropriate as biomarkers and should be carefully scrutinized in future studies. Seventy-eight protein spots showing differential protein levels between different individuals or individual collections were identified by mass spectrometry and further characterized using hierarchical clustering. The results present a first step toward understanding the complexity of longitudinal and individual variation in the human plasma proteome, and provide a baseline for improved biomarker discovery.« less
Gendron, Frédéric; Páez-Hernández, Dayán; Notter, François-Paul; Pritchard, Ben; Bolvin, Hélène; Autschbach, Jochen
2014-06-23
The electronic structure and magnetic properties of neptunyl(VI), NpO2(2+), and two neptunyl complexes, [NpO2(NO3)3](-) and [NpO2Cl4](2-), were studied with a combination of theoretical methods: ab initio relativistic wavefunction methods and density functional theory (DFT), as well as crystal-field (CF) models with parameters extracted from the ab initio calculations. Natural orbitals for electron density and spin magnetization from wavefunctions including spin-orbit coupling were employed to analyze the connection between the electronic structure and magnetic properties, and to link the results from CF models to the ab initio data. Free complex ions and systems embedded in a crystal environment were studied. Of prime interest were the electron paramagnetic resonance g-factors and their relation to the complex geometry, ligand coordination, and nature of the nonbonding 5f orbitals. The g-factors were calculated for the ground and excited states. For [NpO2Cl4](2-), a strong influence of the environment of the complex on its magnetic behavior was demonstrated. Kohn-Sham DFT with standard functionals can produce reasonable g-factors as long as the calculation converges to a solution resembling the electronic state of interest. However, this is not always straightforward. PMID:24848696
Fay, Justin C.; McCullough, Heather L.; Sniegowski, Paul D.; Eisen, Michael B.
2004-02-25
The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits. Results: We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes,20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2. Conclusions: Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation.
Explorations in Regional Variation: A Variational Pragmatic Perspective
ERIC Educational Resources Information Center
Barron, Anne
2015-01-01
The present article introduces the Special Issue entitled "A Variational Pragmatic Approach to Regional Variation in Language," a collection of papers which celebrates the work of Klaus P. Schneider (Rheinische Friedrich-Wilhelms-Universität Bonn, Germany) on the occasion of his 60th birthday.
Copy number variation in schizophrenia in Sweden.
Szatkiewicz, J P; O'Dushlaine, C; Chen, G; Chambert, K; Moran, J L; Neale, B M; Fromer, M; Ruderfer, D; Akterin, S; Bergen, S E; Kähler, A; Magnusson, P K E; Kim, Y; Crowley, J J; Rees, E; Kirov, G; O'Donovan, M C; Owen, M J; Walters, J; Scolnick, E; Sklar, P; Purcell, S; Hultman, C M; McCarroll, S A; Sullivan, P F
2014-07-01
Schizophrenia (SCZ) is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare copy number variations (CNVs) in SCZ cases and identified multiple rare recurrent CNVs that increase risk of SCZ although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for SCZ CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with SCZ using a Swedish national sample (4719 cases and 5917 controls). High-confidence CNV calls were generated using genotyping array intensity data, and their effect on risk of SCZ was measured. Our data confirm increased burden of large, rare CNVs in SCZ cases as well as significant associations for recurrent 16p11.2 duplications, 22q11.2 deletions and 3q29 deletions. We report a novel association for 17q12 duplications (odds ratio=4.16, P=0.018), previously associated with autism and mental retardation but not SCZ. Intriguingly, gene set association analyses implicate biological pathways previously associated with SCZ through common variation and exome sequencing (calcium channel signaling and binding partners of the fragile X mental retardation protein). We found significantly increased burden of the largest CNVs (>500?kb) in genes present in the postsynaptic density, in genomic regions implicated via SCZ genome-wide association studies and in gene products localized to mitochondria and cytoplasm. Our findings suggest that multiple lines of genomic inquiry--genome-wide screens for CNVs, common variation and exonic variation--are converging on similar sets of pathways and/or genes. PMID:24776740
Temperature Variations and Habitability
NSDL National Science Digital Library
These are the student pages for a two part lesson plan that will teach students about observing, describing, and adapting to temperature variations and relating factors that influence planetary temperature and habitability. The class will decide upon a plan for describing indoor and outdoor environments and compare them with the data on environmental conditions at other Earth locales and planets in our solar system. These will be used to discuss temperature ranges, their relation to habitability, and ways to adapt to these conditions. In the second activity, students will give three examples of how humans modify the environment to improve livability, identify three factors that may determine the average temperature of a planet, identify a minimum of five factors that may determine the habitability of a planet, state the importance of maintaining habitable temperature on a planet, and briefly describe the links between two sets of factors of their choosing. The site provides a list of materials, objectives, and worksheets. Teachers' notes are also included.
Drosophila bristles and the nature of quantitative genetic variation
Mackay, Trudy F.C; Lyman, Richard F
2005-01-01
Numbers of Drosophila sensory bristles present an ideal model system to elucidate the genetic basis of variation for quantitative traits. Here, we review recent evidence that the genetic architecture of variation for bristle numbers is surprisingly complex. A substantial fraction of the Drosophila genome affects bristle number, indicating pervasive pleiotropy of genes that affect quantitative traits. Further, a large number of loci, often with sex- and environment-specific effects that are also conditional on background genotype, affect natural variation in bristle number. Despite this complexity, an understanding of the molecular basis of natural variation in bristle number is emerging from linkage disequilibrium mapping studies of individual candidate genes that affect the development of sensory bristles. We show that there is naturally segregating genetic variance for environmental plasticity of abdominal and sternopleural bristle number. For abdominal bristle number this variance can be attributed in part to an abnormal abdomen-like phenotype that resembles the phenotype of mutants defective in catecholamine biosynthesis. Dopa decarboxylase (Ddc) encodes the enzyme that catalyses the final step in the synthesis of dopamine, a major Drosophila catecholamine and neurotransmitter. We found that molecular polymorphisms at Ddc are indeed associated with variation in environmental plasticity of abdominal bristle number. PMID:16108138
Interpreting phenotypic variation in plants
NSDL National Science Digital Library
This article by Coleman, McConnaughay, and Ackerly discusses how phenotypic variation (variation in observable traits) in plants is influenced by environment, genetics, and developmental stage. The authors stress that understanding the interplay of these factors is important for investigations that involve plant comparisons.
SEMIANNUAL VARIATION OF GEOMAGNETIC ACTIVITY
C.T. Russell; R. L. McPherron
1973-01-01
The semiannual variation in geomagnetic activity is well established in geomagnetic data Its explanation has remained elusive, however. We propose, simply, that it is caused by a semiannual variation in the effective southward component of the interplanetary field. The southward field arises because the interplanetary field is ordered in the solar equatorial coordinate system, whereas the interaction with the magnetosphere
Dynamical systems and variational inequalities
Paul Dupuis; Anna Nagurney
1993-01-01
The variational inequality problem has been utilized to formulate and study a plethora of competitive equilibrium problems in different disciplines, ranging from oligopolistic market equilibrium problems to traffic network equilibrium problems. In this paper we consider for a given variational inequality a naturally related ordinary differential equation. The ordinary differential equations that arise are nonstandard because of discontinuities that appear
Throughfall Variation under Tree Crowns
Benjamin B. Stout; Richard J. McMahon
1961-01-01
It is suggested that the experimental design for sample measurement of through- fall may be improved. Specifically, distance and direction from trunk may constitute a signifi- cant source of variation that could be separated in analysis of variance from the unexplained variation. Throughfall was measured at three positions and four directions under the crowns of four trees during the summer
The strong Ekeland variational principle
NASA Astrophysics Data System (ADS)
Suzuki, Tomonari
2006-08-01
In this paper, we consider the strong Ekeland variational principle due to Georgiev [P.G. Georgiev, The strong Ekeland variational principle, the strong drop theorem and applications, J. Math. Anal. Appl. 131 (1988) 1-21]. We discuss it for functions defined on Banach spaces and on compact metric spaces. We also prove the [tau]-distance version of it.
Understanding Human DNA Sequence Variation
Kidd, Kenneth
From the Department of Genetics, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520 Over the past century researchers have identified normal genetic variation and studied that variation is being used to develop an understanding of the demographic histories of the different populations
Complex dynamics of text analysis
NASA Astrophysics Data System (ADS)
Ke, Xiaohua; Zeng, Yongqiang; Ma, Qinghua; Zhu, Lin
2014-12-01
This paper presents a novel method for the analysis of nonlinear text quality in Chinese language. Texts produced by university students in China were represented as scale-free networks (word adjacency model), from which typical network features such as the in/outdegree, clustering coefficient and network dynamics were obtained. The method integrates the classical concepts of network feature representation and text quality series variation. The analytical and numerical scheme leads to a parameter space representation that constitutes a valid alternative to represent the network features. The results reveal that complex network features of different text qualities can be clearly revealed and applied to potential applications in other instances of text analysis.
Transmissivity variations in mudstones.
MacDonald, Alan M; Kemp, Simon J; Davies, Jeff
2005-01-01
Many people in sub-Saharan Africa have to rely on meager water resources within mudstones for their only water supply. Although mudstones have been extensively researched for their low permeability behavior, little research has been undertaken to examine their ability to provide sustainable water supplies. To investigate the factors controlling the occurrence of usable ground water in mudstone environments, an area of Cretaceous mudstones in southeastern Nigeria was studied over a 3 yr period. Transmissivity (T) variations in a range of mudstone environments were studied. The investigations demonstrate that within the top 40 m of mudstones, transmissivity can be sufficient to develop village water supplies (T > 1 m2/d). Transmissivity is controlled by two factors: low-grade metamorphism and the presence of other, subordinate, lithologies within the mudstones. Largely unaltered mudstones (early diagenetic zone), comprising mainly smectite clays, are mostly unfractured and have a low T of < 0.1 m2/d. Mudstones that have undergone limited metamorphism (late diagenetic zone) comprise mixed layered illite/smectite clays, and ground water is found in widely spaced fracture zones (T > 1 m2/d in large fracture zones; T < 0.1 m2/d away from fracture zones). Mudstones that have been further altered and approach the anchizone comprise illite clays, are pervasively fractured, and have the highest transmissivity values (T > 4 m2/d). Dolerite intrusions in unaltered, smectitic mudstones are highly fractured with transmissivity in the range of 1 < T < 60 m2/d. Thin limestone and sandstone layers can also enhance transmissivity sufficiently to provide community water supplies. PMID:15819947
Plant structural complexity and host-finding by a parasitoid
D. A. Andow; D. R. Prokrym
1990-01-01
There are three major components to plant structure relevant to searching parasitoids: 1) plant size or surface area, 2) the variation among plant parts (structural heterogeneity), such as seed heads, flowers and nectaries, and heterogeneous surfaces (e.g. glabrous, hirsute), and 3) the connectivity of parts or plant form (structural complexity). We examined the effect of structural complexity, while controlling for
Incipient species formation in salamanders of the Ensatina complex
DAVID B. WAKE
1997-01-01
The Ensatina eschscholtzii complex of pleth- odontid salamanders, a well-known ''ring species,'' is thought to illustrate stages in the speciation process. Early research, based on morphology and coloration, has been extended by the incorporation of studies of protein variation and mitochon- drial DNA sequences. The new data show that the complex includes a number of geographically and genetically distinct components
RESEARCH ARTICLE Open Access Evolution of major histocompatibility complex
Paris-Sud XI, Université de
Background The major histocompatibility complex (MHC) is a key element of the vertebrate immune system histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation
NASA Astrophysics Data System (ADS)
Lacivita, Valentina; Rèrat, Michel; Orlando, Roberto; Ferrero, Mauro; Dovesi, Roberto
2012-03-01
The longitudinal polarizability, ?xx, and second hyperpolarizability, ?xxxx, of polyacetylene are evaluated by using the coupled perturbed Hartree-Fock/Kohn-Sham (HF/KS) scheme as implemented in the periodic CRYSTAL code and a split valence type basis set. Four different density functionals, namely local density approximation (LDA) (pure local), Perdew-Becke-Ernzerhof (PBE) (gradient corrected), PBE0, and B3LYP (hybrid), and the Hartree-Fock Hamiltonian are compared. It is shown that very tight computational conditions must be used to obtain well converged results, especially for ?xxxx, that is, very sensitive to the number of k points in reciprocal space when the band gap is small (as for LDA and PBE), and to the extension of summations of the exact exchange series (HF and hybrids). The band gap in LDA is only 0.01 eV: at least 300 k points are required to obtain well converged total energy and equilibrium geometry, and 1200 for well converged optical properties. Also, the exchange series convergence is related to the band gap. The PBE0 band gap is as small as 1.4 eV and the exchange summation must extend to about 130 Å from the origin cell. Total energy, band gap, equilibrium geometry, polarizability, and second hyperpolarizability of oligomers -(C2H2)m-, with m up to 50 (202 atoms), and of the polymer have been compared. It turns out that oligomers of that length provide an extremely poor representation of the infinite chain polarizability and hyperpolarizability when the gap is smaller than 0.2 eV (that is, for LDA and PBE). Huge differences are observed on ?xx and ?xxxx of the polymer when different functionals are used, that is in connection to the well-known density functional theory (DFT) overshoot, reported in the literature about short oligomers: for the infinite model the ratio between LDA (or PBE) and HF becomes even more dramatic (about 500 for ?xx and 1010 for ?xxxx). On the basis of previous systematic comparisons of results obtained with various approaches including DFT, HF, Moller-Plesset (MP2) and coupled cluster for finite chains, we can argue that, for the infinite chain, the present HF results are the most reliable.
Duboc, Carole; Ganyushin, Dmitry; Sivalingam, Kantharuban; Collomb, Marie-Noëlle; Neese, Frank
2010-10-01
This paper presents a detailed evaluation of the performance of density functional theory (DFT) as well as complete active space self-consistent field (CASSCF)-based methods (CASSCF and second-order N-electron valence state perturbation theory, NEVPT2) to predict the zero-field splitting (zfs) parameters for a series of coordination complexes containing the Mn(III) ion. The physical origin of the experimentally determined zfs's was investigated by studying the different contributions to these parameters. To this end, a series of mononuclear Mn(III) complexes was chosen for which the structures have been resolved by X-ray diffraction and the zfs parameters have been accurately determined by high-field EPR spectroscopy. In a second step, small models have been constructed to allow for a systematic assessment of the factors that dominate the variations in the observed zfs parameters and to establish magnetostructural correlations. Among the tested functionals, the best predictions have been obtained with B3LYP, followed by the nonhybrid BP86 functional, which in turn is more successful than the meta-hybrid GGA functional TPSSh. For the estimation of the spin-orbit coupling (SOC) part of the zfs, it was found that the coupled perturbed SOC approach CP is more successful than the Pederson-Khanna method. Concerning the spin-spin interaction (SS), the restricted open-shell Kohn-Sham (ROKS) approach led to a slightly better agreement with the experiment than the unrestricted KS (UKS) approach. The ab initio state-averaged CASSCF (SA-CASSCF) method with a minimal active space and the most recent implementation that treats the SOC and SS contributions on an equal footing provides the best predictions for the zfs. The analysis demonstrates that the major contribution to the axial zfs parameter (D) originates from the SOC interaction but that the SS part is far from being negligible (between 10 and 20% of D). Importantly, the various excited triplet ligand field states account for roughly half of the value of D, contrary to popular ligand field models. Despite covering dynamic correlation contributions to the transition energies, NEVPT2 does not lead to large improvements in the results as the excitation energies of the Mn(III) d-d transitions are already fairly accurate at the SA-CASSCF level. For a given type of coordination sphere (e.g., elongated or compressed octahedron), the magnetic anisotropy of the Mn(III) ion, D, does not appear to be highly sensitive to the nature of the ligands, while the E/D ratio is notably affected by all octahedral distortions. Furthermore, the introduction of different halides into the coordination sphere of Mn(III) only leads to small effects on D. Nevertheless, it appears that oxygen-based ligands afford larger D values than nitrogen-based ligands. PMID:20828179
Effort variation regularization in sound field reproduction.
Stefanakis, Nick; Jacobsen, Finn; Sarris, John
2010-08-01
In this paper, active control is used in order to reproduce a given sound field in an extended spatial region. A method is proposed which minimizes the reproduction error at a number of control positions with the reproduction sources holding a certain relation within their complex strengths. Specifically, it is suggested that the phase differential of the source driving signals should be in agreement with the phase differential of the desired sound pressure field. The performance of the suggested method is compared with that of conventional effort regularization, wave field synthesis (WFS), and adaptive wave field synthesis (AWFS), both under free-field conditions and in reverberant rooms. It is shown that effort variation regularization overcomes the problems associated with small spaces and with a low ratio of direct to reverberant energy, improving thus the reproduction accuracy in the listening room. PMID:20707444
Engineered tissue scaffolds with variational porous architecture.
Khoda, A K M B; Ozbolat, Ibrahim T; Koc, Bahattin
2011-01-01
This paper presents a novel computer-aided modeling of 3D tissue scaffolds with a controlled internal architecture. The complex internal architecture of scaffolds is biomimetically modeled with controlled micro-architecture to satisfy different and sometimes conflicting functional requirements. A functionally gradient porosity function is used to vary the porosity of the designed scaffolds spatially to mimic the functionality of tissues or organs. The three-dimensional porous structures of the scaffold are geometrically partition into functionally uniform porosity regions with a novel offsetting operation technique described in this paper. After determining the functionally uniform porous regions, an optimized deposition-path planning is presented to generate the variational internal porosity architecture with enhanced control of interconnected channel networks and continuous filament deposition. The presented methods are implemented, and illustrative examples are presented in this paper. Moreover, a sample optimized tool path for each example is fabricated layer-by-layer using a micronozzle biomaterial deposition system. PMID:21186891
Is a Morphologically Complex Language Really that Complex in Full-Text Retrieval?
Kimmo Kettunen; Eija Airio
2006-01-01
In this paper we show that keyword variation of a morphologically complex language, Finnish, can be handled effectively for IR purposes by generating only the textually most frequent forms of the keyword. Theoreti- cally Finnish nouns have about 2,000 different forms, but occurrences of most of the forms are rare. Corpus statistics showed that about 84 - 88 per cent
On State Complexes and Special Cube Complexes
ERIC Educational Resources Information Center
Peterson, Valerie J.
2009-01-01
This thesis presents the first steps toward a classification of non-positively curved cube complexes called state complexes. A "state complex" is a configuration space for a "reconfigurable system," i.e., an abstract system in which local movements occur in some discrete manner. Reconfigurable systems can be used to describe, for example,…
RFLP variation in diploid and tetraploid alfalfa.
Brummer, E C; Kochert, G; Bouton, J H
1991-11-01
Alfalfa (Medicago sativa L.) is a major forage crop throughout the world. Although alfalfa has many desirable traits, continued breeding is required to incorporate pest resistances and other traits. We conducted this study to determine the amount of restriction fragment length polymorphism (RFLP) variability present within and between diploid and tetraploid alfalfa populations, and whether or not this variability is sufficient for construction of an RFLP map. Diploid plants from M. sativa ssp. falcata, ssp. coerulea, and ssp. sativa and tetraploid spp. sativa cultivars 'Apollo,' 'Florida 77,' and 'Spredor 2' were included. A total of 19 cDNA clones was probed onto genomic Southern blots containing DNA digested by EcoRI, HindIII, or BamHI. Phylogenetic trees were produced, based on parsimony analysis of shared restriction fragments. Evidence for extensive gene duplication was found; most probes detected complex patterns of restriction fragments. Large amounts of variation are present within all diploid subspecies. M. sativa ssp. falcata plants formed clusters distinct from ssp. sativa or ssp. coerulea plants, which were not distinctly clustered. Some M. sativa ssp. falcata plants were more similar to the other groups than to other plants within ssp. falcata. Variation among tetraploid cultivars showed that Florida 77 and Apollo had more similarities than either showed with Spredor 2. All three cultivars showed large within-population variation, with Apollo being the most diverse and Spredor 2 the least. Based on these results, development of an RFLP map at the diploid level appears possible. Also, differentiation of cultivars, particularly ones of divergent origin, seems possible based on RFLP patterns. PMID:24202261
Variation in spiralian development: insights from polychaetes.
Seaver, Elaine C
2014-01-01
Spiralian development is characterized by the conservation of spindle orientation and cell geometry during early cleavage stages, as well as features of the ultimate fates of identified cells. This complex set of characters is shared by a number of animal lineages including nemerteans, polyclad platyhelminthes, annelids and mollusks. How a similar, highly stereotypical cleavage program can give rise to such diversity of larval and adult forms has intrigued researchers for many years. This review summarizes recent data from polychaete annelids, and highlights both conservation and variation in the cellular and molecular mechanisms that guide the spiral cleavage developmental program. There is a specific focus on comparisons of fate maps, patterns of cleavage, mechanisms of cell fate specification, organizing activity, and differences in molecular patterning. Some of the differences in early development represent intra-clade variation within annelids, and others hint at differences between annelids and other taxa. Because much of the classic work on spiralians has focused on mollusks, these new data from annelids have expanded our knowledge about the evolutionary flexibility in spiralian development and potentially its role in body plan evolution. PMID:25690962
MHC variation in birds and reptiles.
Wittzell, H; Madsen, T; Westerdahl, H; Shine, R; von Schantz, T
The major histocompatibility complex (MHC) has been studied in a multitude of mammals by now, but much less is known about its organisation and variation in other vertebrate species. The mammalian MHC is organised as a single gene cluster, but recent studies on birds suggest that this paradigm of MHC organisation has to be supplemented. The domestic chicken thus possesses two separate gene clusters which both contain MHC class I and class II B genes, and we have shown that the ring-necked pheasant Phasianus colchicus also has two unlinked clusters of class II B genes. We are studying the effect of the MHC on mate choice, survival and reproductive success in natural populations of birds and reptiles. For this reason, we are developing DNA techniques to determine the animals' MHC genotype. The amplification of the hypervariable exon 3 of the class I gene from songbirds and reptiles has provided us with species specific probes that can be used in Southern blot analysis. The first results indicate very extensive variation in all studied species, that is starlings Sturnus vulgaris, great reed warblers Acrocephalus arundinaceus and water pythons Liasis fuscus. The restriction fragment length polymorphism (RFLP) analysis also suggests that the number of MHC genes is significantly larger in these species than in pheasants and domestic chickens. PMID:10386396
Variational elliptic solver for atmospheric applications
Smolarkiewicz, P.K. [National Center for Atmospheric Research, Boulder, CO (United States); Margolin, L.G. [Los Alamos National Lab., NM (United States)
1994-03-01
We discuss a conjugate gradient type method -- the conjugate residual -- suitable for solving linear elliptic equations that result from discretization of complex atmospheric dynamical problems. Rotation and irregular boundaries typically lead to nonself-adjoint elliptic operators whose matrix representation on the grid is definite but not symmetric. On the other hand, most established methods for solving large sparse matrix equations depend on the symmetry and definiteness of the matrix. Furthermore, the explicit construction of the matrix can be both difficult and computationally expensive. An attractive feature of conjugate gradient methods in general is that they do not require any knowledge of the matrix; and in particular, convergence of conjugate residual algorithms do not rely on symmetry for definite operators. We begin by reviewing some basic concepts of variational algorithms from the perspective of a physical analogy to the damped wave equation, which is a simple alternative to the traditional abstract framework of the Krylov subspace methods. We derive two conjugate residual schemes from variational principles, and prove that either definiteness or symmetry ensures their convergence. We discuss issues related to computational efficiency and illustrate our theoretical considerations with a test problem of the potential flow of a Boussinesq fluid flow past a steep, three-dimensional obstacle.
Heat transfer variations of bicycle helmets.
Brühwiler, P A; Buyan, M; Huber, R; Bogerd, C P; Sznitman, J; Graf, S F; Rösgen, T
2006-09-01
Bicycle helmets exhibit complex structures so as to combine impact protection with ventilation. A quantitative experimental measure of the state of the art and variations therein is a first step towards establishing principles of bicycle helmet ventilation. A thermal headform mounted in a climate-regulated wind tunnel was used to study the ventilation efficiency of 24 bicycle helmets at two wind speeds. Flow visualization in a water tunnel with a second headform demonstrated the flow patterns involved. The influence of design details such as channel length and vent placement was studied, as well as the impact of hair. Differences in heat transfer among the helmets of up to 30% (scalp) and 10% (face) were observed, with the nude headform showing the highest values. On occasion, a negative role of some vents for forced convection was demonstrated. A weak correlation was found between the projected vent cross-section and heat transfer variations when changing the head tilt angle. A simple analytical model is introduced that facilitates the understanding of forced convection phenomena. A weak correlation between exposed scalp area and heat transfer was deduced. Adding a wig reduces the heat transfer by approximately a factor of 8 in the scalp region and up to one-third for the rest of the head for a selection of the best ventilated helmets. The results suggest that there is significant optimization potential within the basic helmet structure represented in modern bicycle helmets. PMID:16882634
Hotspots for copy number variation in chimpanzees and humans
Perry, George H.; Tchinda, Joelle; McGrath, Sean D.; Zhang, Junjun; Picker, Simon R.; Cáceres, Angela M.; Iafrate, A. John; Tyler-Smith, Chris; Scherer, Stephen W.; Eichler, Evan E.; Stone, Anne C.; Lee, Charles
2006-01-01
Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number variation in nonhuman primates. We have used two array-based comparative genomic hybridization platforms to identify a total of 355 copy number variants (CNVs) in the genomes of 20 wild-born chimpanzees (Pan troglodytes) and have compared the identified chimpanzee CNVs to known human CNVs from previous studies. Many CNVs were observed in the corresponding regions in both chimpanzees and humans; especially those CNVs of higher frequency. Strikingly, these loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formation through nonallelic homologous recombination mechanisms. Therefore, some of these regions may be unstable “hotspots” for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species. PMID:16702545
A Variational Approach to Enhanced Sampling and Free Energy Calculations
Omar Valsson; Michele Parrinello
2014-08-07
The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variable. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient and flexible sampling method. A number of numerical examples are presented which include the determination of a three dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient standpoint for looking with novel eyes at the sampling problem.
December, 2012. CURRICULUM VITAE: Melvin L. Kohn
the Transformation of Urban China. In collaboration with Weidong Wang of the Renmin (People's) University of China Foundation, Renmin University of China, and the Chinese Fellowship Council. Also in process: A Memoir
Strong correlation in Kohn-Sham DFT
NASA Astrophysics Data System (ADS)
Malet Giralt, Francesc; Mirtschink, André; Cremon, Jonas; Mendl, Christian; Giesbertz, Klaas; Reimann, Stephanie; Gori-Giorgi, Paola; Mathematical Physics, Lund University Collaboration; Mathematics Department, Technische Universität München Collaboration
2014-03-01
The knowledge on the strong-interacting limit of density functional theory can be used to construct exchange- correlation functionals able to address strongly-correlated systems without introducing any symmetry breaking. We report calculations on semiconductor nanostructures and one-dimensional models for chemical systems, showing that this approach yields quantitatively good results in both the weakly- and the strongly-correlated regimes, with a numerical cost much lower than the traditional wavefunction methods. This work has been supported by a VIDI grant of the NWO and a Marie Curie grant within the FP7 programme.
Implementing variation risk management during product development
Padgalskas, Nicholas (Nicholas Keith)
2007-01-01
All manufactured systems exhibit some degree of variation. Manufacturing organizations should be aware of those parameters whose variation will impact product performance and customer satisfaction. Such parameters are ...
Quasi-Periodic Variations of the Pulsation Frequencies of Three White Dwarfs
NASA Astrophysics Data System (ADS)
Dalessio, James; Provencal, Judith L.; Shipman, Harry L.
2015-06-01
We report on variations of the normal mode frequencies of the pulsating DB white dwarfs EC 20058-5234 and KIC 8626021 and the pulsating DA white dwarf GD 66. We discover periodic and quasi-periodic variations of multiple normal mode frequencies that cannot be due to the presence of planetary companions. We note the possible signature of a planetary companion to EC 20058-5234 and now know that GD 66 cannot have a planet in a several AU orbit down to half a Jupiter mass. We also announce secular variations of the normal mode frequencies of all three stars that are inconsistent with cooling alone. Periodic variations in the amplitudes of many of these modes is also noted. We hypothesize that these frequency variations are caused by complex variations of the magnetic field strength and geometry, analogous to behavior observed in the Sun.
Existence of evolutionary variational solutions via the calculus of variations
NASA Astrophysics Data System (ADS)
Bögelein, Verena; Duzaar, Frank; Marcellini, Paolo
In this paper we introduce a purely variational approach to time dependent problems, yielding the existence of global parabolic minimizers, that is ?0T ?? [u??t?+f(x,Du)] dx dt??0T ?? f(x,Du+D?) dx dt, whenever T>0 and ??C0?(?×(0,T),RN). For the integrand f:?×R?[0,?] we merely assume convexity with respect to the gradient variable and coercivity. These evolutionary variational solutions are obtained as limits of maps depending on space and time minimizing certain convex variational functionals. In the simplest situation, with some growth conditions on f, the method provides the existence of global weak solutions to Cauchy-Dirichlet problems of parabolic systems of the type ?tu-divD?f(x,Du)=0 in ?×(0,?).
Exterior complex scaling method in TDDFT: HHG of Ar atoms in intense laser fields
NASA Astrophysics Data System (ADS)
Sosnova, K. E.; Telnov, D. A.; Rozenbaum, E. B.; Chu, S. I.
2014-04-01
The exterior complex scaling (ECS) method is applied in the framework of time-dependent density-functional theory (TDDFT) to study high-order harmonic generation (HHG) of multielectron atoms in intense laser fields. With the help of ECS, correct outgoing-wave boundary conditions can be imposed on the wave functions at large distances. In our implementation, ECS is combined with the time-dependent generalized pseudospectral method for accurate and efficient solution of the time-dependent Kohn-Sham equations. We make use of LB94 exchange-correlation potential which appears quite accurate in calculations of unperturbed electronic structure of Ar. Calculations of HHG are performed for the laser fields with the wavelength of 800 nm and several peak intensities. The HHG spectrum exhibits an intensity-independent minimum corresponding to the photon energy of about 51 eV which is closely related to the Cooper minimum in the photoionization cross section of Ar. We found that HHG spectra calculated with the frozen-core potential (not including dynamic response of the electron density) differ significantly from those obtained by TDDFT.
Mikael Hedrén
2004-01-01
The Carex flava complex (Cyperaceae) was used as a model system in a study of the effects of variation in species delimitation on genetic diversity estimates. The whole complex constitutes a syngameon within which gene flow may occur between taxa. Several more or less distinct evolutionary lineages in the complex are morphologically similar to each other and are often combined
Structure and dynamics affect the controllability of complex systems: a Preliminary Study
Menczer, Filippo
Structure and dynamics affect the controllability of complex systems: a Preliminary Study Alexander the structure or or- ganization of complex systems. The simplest way to study multi-variate dynamics) are canonical models of complex systems and exhibit a wide range of dynamical behaviors [1]. The structure
Individual variation and population dynamics: lessons from a simple system
Benton, T. G.
2012-01-01
The mapping of environment, through variation in individuals' life histories, to dynamics can be complex and often poorly known. Consequently, it is not clear how important it is dynamically. To explore this, I incorporated lessons from an empirical system, a soil mite, into an individual-based model. Individuals compete for resource and allocate this according to eight ‘genetic’ rules that specify investment in growth or reserves (which influences survival or fecundity), size at maturation and reproductive allocation. Density dependence, therefore, emerges from competition for food, limiting individual's growth and fecundity. We use this model to examine the role that genetic and phenotypically plastic variation plays in dynamics, by fixing phenotypes, by allowing phenotypes to vary plastically and by creating genetic variation between individuals. Variation, and how it arises, influences short- and long-run dynamics in a way comparable in magnitude with halving food supply. In particular, by switching variation on and off, it is possible to identify a range of processes necessary to capture the dynamics of the ‘full model’. Exercises like this can help identify key processes and parameters, but a concerted effort is needed across many different systems to search for shared understanding of both process and modelling. PMID:22144383
Sources of floral scent variation
Raguso, Robert A; Ashman, Tia-Lynn
2009-01-01
Studies of floral scent generally assume that genetic adaptation due to pollinator-mediated natural selection explains a significant amount of phenotypic variance, ignoring the potential for phenotypic plasticity in this trait. In this paper, we assess this latter possibility, looking first at previous studies of floral scent variation in relation to abiotic environmental factors. We then present data from our own research that suggests among-population floral scent variation is determined, in part, by environmental conditions and thus displays phenotypic plasticity. Such an outcome has strong ramifications for the study of floral scent variation; we conclude by presenting some fundamental questions that should lead to greater insight into our understanding of the evolution of this trait, which is important to plant-animal interactions. PMID:19649189
Evaluating Software Complexity Measures
Elaine J. Weyuker
1988-01-01
A set of properties of syntactic software complexity measures is proposed to serve as a basis for the evaluation of such measures. Four known complexity measures are evaluated and compared using these criteria. This formalized evaluation clarifies the strengths and weaknesses of the examined complexity measures, which include the statement count, cyclomatic number, effort measure, and data flow complexity measures.
Studies of complexity in fluid systems
Kadanoff, L.P.; Constantin, P.; Dupont, T.F.; Nagel, S.
1993-02-01
Objective is to bring together researchers from several disciplines (mathematics, numerical computation, theoretical and experimental physics) who share an interest in the development of complexity in fluid systems. Work is in progress on development of singular interfluid interfaces on several fronts. Striking variations in droplet formation can be observed in physical experiments and simulations based on simple models. High-speed photographs are being taken of small liquid drop breaking into droplets. Experimental studies of granular materials are being continued.
NASA Astrophysics Data System (ADS)
Borchert, Manuela; Wilke, Max; Schmidt, Christian; Kvashnina, Kristina
2010-05-01
At crustal conditions, the fluid-melt partitioning of Sr is mainly controlled by the salinity of the fluid and the composition of the melt (Borchert et al., 2010). The data show a sharp increase in the Sr partition coefficient with the alumina saturation index (ASI) to a maximum of 0.3 at an ASI of 1.05. Because fluid-melt partitioning of a given element depends on its complexation in the fluid and its incorporation in the melt, these data imply a change in the Sr speciation at least one of the two phases. For silicate melts, Kohn et al. (1990) found only small changes in the first coordination shell of Sr in a suite of melts with various degrees of polymerization, and argued that incorporation of Sr in the melt should not play a major role in controlling Sr partitioning. For the aqueous fluid, Bai and Koster van Groos (1999) and Webster et al. (1989) suggested a control of the Sr partition coefficient by SrCl2 complexes based on the correlation between partition coefficient and Cl concentration in the fluid after quenching. Both hypotheses cannot explain our partitioning data. Thus, new information on Sr complexation is required. Here, we studied the complexation of Sr in peraluminous or peralkaline melt dissolved in aqueous fluids in-situ at elevated PT conditions using hydrothermal diamond-anvil cells (HDAC) and X-ray absorption near edge structure (XANES) spectroscopy. The starting materials were peraluminous or peralkaline glass and H2O or a chloridic solution. The glass was doped with high concentrations of 5000 or 10000 ppm Sr. We used bulk compositions with 10 to 15 wt.% glass to ensure that the melt was completely dissolved in the fluid at high PT conditions. For qualitative evaluation, we analyzed the starting glasses and various crystalline compounds and standard solutions. The experiments were performed at beamline ID26 at ESRF (Grenoble, France) using a high resolution emission spectrometer and Si(311) monochromator crystals for high resolution and Si(111) for low resolution measurements. An overall resolution of 1.98 eV (Si(311)) and 3 eV (Si(111)) was achieved using a beamsize of 120x400 ?m, Si(777) analyzer crystals and a Rowland circle diameter of 1 m. Strontium XANES spectra of peraluminous and peralkaline starting glasses show distinct differences in pre-edge, main edge and position of the first EXAFS maximum which is directly correlated to the distance of Sr and its nearest neighbor. Therefore, the spectra indicate an effect of the ASI on the local structure around Sr. Spectra of standard solution at various PT conditions indicate detectable temperature-dependent changes in the intensity and peak width of the white line. The XANES spectra of chloridic solutions with peraluminous or peralkaline melt dissolved differ significantly from each other. The latter are similar to the one of the peralkaline starting glass, while this is not the case for solutions with peraluminous melt. The spectra of water with dissolved peralkaline melt distinctly differ from those using chloridic fluids. In conclusion, the first spectroscopic evidence on Sr complexation at elevated PT condition indicates significant speciation changes in both fluid and melt, and suggest ASI-dependent formation of Sr-Si complexes in the fluids. Literature Bai and Koster van Groos (1999), GCA 63, 1117-1131. Borchert et al. (2010), GCA 74, 1057-1076. Kohn et al. (1990), CMP 105, 359-368. Webster et al. (1989), Econ. Geol. 84, 116-134.
Variations in Human Skin Color
NSDL National Science Digital Library
American Association for the Advancement of Science (; )
2006-09-09
In this lesson, the students examine their skin types, similarities, differences, etc. and discuss the social implications of each group. They also examine the factors that influence variations in skin color in greater depth. The class is separated into groups and work on presentations, designed to foster peer-teaching with guidance from the instructor. The presentations to be worked on by the students are: Modern Human Variation: Overview, Skin Color Adaptation, and A new Light on Skin Color. All of the resources needed for the students presentations are included. Following each presentation, tips for review and discussion of the learning objectives are given.
Seasonal variation of the global electrical circuit
Edwin J. Adlerman; Earle R. Williams
1996-01-01
The effects of boundary layer aerosol particles on the electric field measurement of the DC global circuit are considered. Aitken (condensation) nuclei concentrations are found to have systematic local seasonal variations which obscure the global behavior of the DC circuit. These local variations appear to be the result of several seasonal factors, including variations in atmospheric mixed layer heights, variations
Variation in emission metrics due to variation in CO2 and temperature impulse response functions
NASA Astrophysics Data System (ADS)
Olivié, D. J. L.; Peters, G. P.
2013-08-01
Emission metrics are used to compare the climate effect of the emission of different species, such as carbon dioxide (CO2) and methane (CH4). The most common metrics use linear impulse response functions (IRFs) derived from a single more complex model. There is currently little understanding on how IRFs vary across models, and how the model variation propagates into the metric values. In this study, we first derive CO2 and temperature IRFs for a large number of complex models participating in different intercomparison exercises, synthesizing the results in distributions representing the variety in behaviour. The derived IRF distributions differ considerably, which is partially related to differences among the underlying models, and partially to the specificity of the scenarios used (experimental setup). In a second part of the study, we investigate how differences among the IRFs impact the estimates of global warming potential (GWP), global temperature change potential (GTP) and integrated global temperature change potential (iGTP) for time horizons between 20 and 500 yr. Within each derived CO2 IRF distribution, underlying model differences give similar spreads on the metrics in the range of -20 to +40% (5-95% spread), and these spreads are similar among the three metrics. GTP and iGTP metrics are also impacted by variation in the temperature IRF. For GTP, this impact depends strongly on the lifetime of the species and the time horizon. The GTP of black carbon shows spreads of up to -60 to +80% for time horizons to 100 yr, and even larger spreads for longer time horizons. For CH4 the impact from variation in the temperature IRF is still large, but it becomes smaller for longer-lived species. The impact from variation in the temperature IRF on iGTP is small and falls within a range of ±10% for all species and time horizons considered here. We have used the available data to estimate the IRFs, but we suggest the use of tailored intercomparison projects specific for IRFs in emission metrics. Intercomparison projects are an effective means to derive an IRF and its model spread for use in metrics, but more detailed analysis is required to explore a wider range of uncertainties. Further work can reveal which parameters in each IRF lead to the largest uncertainties, and this information may be used to reduce the uncertainty in metric values.